medh5	module
medh5.Activity	class	(id, type, agent=None, started=None, ended=None, tool=None, inputs=(), outputs=(), params={}) bases=
medh5.Activity.agent	field
medh5.Activity.ended	field
medh5.Activity.from_json	classmethod	(doc)
medh5.Activity.id	field
medh5.Activity.inputs	field
medh5.Activity.outputs	field
medh5.Activity.params	field
medh5.Activity.started	field
medh5.Activity.to_json	method	()
medh5.Activity.tool	field
medh5.Activity.type	field
medh5.Agent	class	(id, type, name, role=None, version=None, qualification=None, organization=None) bases=
medh5.Agent.from_json	classmethod	(doc)
medh5.Agent.id	field
medh5.Agent.name	field
medh5.Agent.organization	field
medh5.Agent.qualification	field
medh5.Agent.role	field
medh5.Agent.to_json	method	()
medh5.Agent.type	field
medh5.Agent.version	field
medh5.Agreement	class	(metric, value, against=None, per_class={}) bases=
medh5.Agreement.against	field
medh5.Agreement.from_json	classmethod	(doc)
medh5.Agreement.metric	field
medh5.Agreement.per_class	field
medh5.Agreement.to_json	method	()
medh5.Agreement.value	field
medh5.Annotation	class	(handle) bases=
medh5.Annotation.ann_id	property
medh5.Annotation.annotated_class_ids	property
medh5.Annotation.annotated_classes	property
medh5.Annotation.class_ids	property
medh5.Annotation.class_key	method	(class_id)
medh5.Annotation.classes	property
medh5.Annotation.closure	property
medh5.Annotation.grid	property
medh5.Annotation.grid_id	property
medh5.Annotation.group	property
medh5.Annotation.has_ignore_region	property
medh5.Annotation.header	property
medh5.Annotation.ignore_id	property
medh5.Annotation.is_annotated	method	(class_key)
medh5.Annotation.is_fully_covered	property
medh5.Annotation.kind	property
medh5.Annotation.label_set	property
medh5.Annotation.prov	property
medh5.Annotation.quality_key	property
medh5.Annotation.resolve_class	method	(class_key)
medh5.Annotation.resolve_classes	method	(keys)
medh5.Annotation.summary	method	()
medh5.Annotation.task	property
medh5.Annotation.timepoints	property
medh5.CODES	constant	dict
medh5.Cohort	class	(dataset_id=None, site_id=None, scanner_id=None, group_id=None, acquisition_protocol=None, extra={}) bases=
medh5.Cohort.acquisition_protocol	field
medh5.Cohort.dataset_id	field
medh5.Cohort.extra	field
medh5.Cohort.from_json	classmethod	(doc)
medh5.Cohort.group_id	field
medh5.Cohort.grouping_key	method	(subject_id)
medh5.Cohort.scanner_id	field
medh5.Cohort.site_id	field
medh5.Cohort.to_json	method	()
medh5.Collection	class	(handle) bases=
medh5.Collection.__contains__	method	(key)
medh5.Collection.__enter__	method	()
medh5.Collection.__exit__	method	(*exc)
medh5.Collection.__getitem__	method	(key)
medh5.Collection.__iter__	method	()
medh5.Collection.__len__	method	()
medh5.Collection.close	method	()
medh5.Collection.group	property
medh5.Collection.kind	property
medh5.Collection.path	property
medh5.Collection.root	property
medh5.Collection.subject_ids	method	()
medh5.Collection.summary	method	()
medh5.Collection.version	property
medh5.Deidentification	class	(method, profile=None, date_shift_days=None, id_mapping=None, performed_by=None, date=None, burned_in_annotation_checked=None, extra={}) bases=
medh5.Deidentification.burned_in_annotation_checked	field
medh5.Deidentification.date	field
medh5.Deidentification.date_shift_days	field
medh5.Deidentification.extra	field
medh5.Deidentification.from_json	classmethod	(doc)
medh5.Deidentification.id_mapping	field
medh5.Deidentification.method	field
medh5.Deidentification.performed_by	field
medh5.Deidentification.profile	field
medh5.Deidentification.to_json	method	()
medh5.FORMAT_VERSION	constant	str
medh5.FeatureCache	class	(handle) bases=
medh5.FeatureCache.__enter__	method	()
medh5.FeatureCache.__exit__	method	(*exc)
medh5.FeatureCache.__len__	method	()
medh5.FeatureCache.abandon	method	()
medh5.FeatureCache.close	method	()
medh5.FeatureCache.entries	property
medh5.FeatureCache.event_entry	method	(content_id, event_id)
medh5.FeatureCache.event_feature	method	(content_id, event_id)
medh5.FeatureCache.get	method	(entry_id)
medh5.FeatureCache.header	property
medh5.FeatureCache.level	property
medh5.FeatureCache.manifest_digest	property
medh5.FeatureCache.open	classmethod	(path)
medh5.FeatureCache.path	property
medh5.FeatureCache.row_feature	method	(row_id)
medh5.Grid	class	(grid_id, shape, axis_names, axis_kinds, spacing, origin, direction, coord_system='LPS', units='mm', timepoint=None, frame_uid=None, time_values=None, time_units=None, chunk_hint=None, patch_hint=None, extra=None) bases=
medh5.Grid.affine	property
medh5.Grid.attrs	method	()
medh5.Grid.axis_kinds	field
medh5.Grid.axis_names	field
medh5.Grid.channel_axis	property
medh5.Grid.check	method	()
medh5.Grid.chunk_hint	field
medh5.Grid.comparable_with	method	(other)
medh5.Grid.coord_system	field
medh5.Grid.direction	field
medh5.Grid.extent	property
medh5.Grid.extra	field
medh5.Grid.frame_uid	field
medh5.Grid.grid_id	field
medh5.Grid.index_to_world	method	(indices)
medh5.Grid.is_congruent	method	(other, tol=1e-06)
medh5.Grid.n_spatial	property
medh5.Grid.n_voxels	property
medh5.Grid.ndim	property
medh5.Grid.origin	field
medh5.Grid.patch_hint	field
medh5.Grid.physical_size	property
medh5.Grid.shape	field
medh5.Grid.spacing	field
medh5.Grid.spatial_axes	property
medh5.Grid.spatial_names	property
medh5.Grid.spatial_shape	property
medh5.Grid.summary	method	()
medh5.Grid.time_axis	property
medh5.Grid.time_units	field
medh5.Grid.time_values	field
medh5.Grid.timepoint	field
medh5.Grid.units	field
medh5.Grid.world_into	method	(other, points)
medh5.Grid.world_to_index	method	(points)
medh5.Identity	class	(sample_id, subject_id, sex=None, laterality=None, bodypart=None, extra={}) bases=
medh5.Identity.bodypart	field
medh5.Identity.extra	field
medh5.Identity.from_json	classmethod	(doc)
medh5.Identity.laterality	field
medh5.Identity.sample_id	field
medh5.Identity.sex	field
medh5.Identity.subject_id	field
medh5.Identity.to_json	method	()
medh5.Image	class	(handle) bases=
medh5.Image.attrs	property
medh5.Image.channel_names	property
medh5.Image.chunks	property
medh5.Image.dataset	property
medh5.Image.digest	property
medh5.Image.dtype	property
medh5.Image.grid	property
medh5.Image.grid_id	property
medh5.Image.image_id	property
medh5.Image.is_multiscale	property
medh5.Image.is_rescaled	property
medh5.Image.level	method	(index)
medh5.Image.levels	property
medh5.Image.modality	property
medh5.Image.nbytes	property
medh5.Image.prov	property
medh5.Image.pyramid	property
medh5.Image.read	method	(roi=None, *, physical=False, dtype=None)
medh5.Image.rescale	property
medh5.Image.shape	property
medh5.Image.summary	method	()
medh5.Image.timepoint	property
medh5.Image.valid_mask	property
medh5.Image.value_type	property
medh5.Image.value_units	property
medh5.Image.window	property
medh5.Instance	class	(index, instance_id, class_id, box, mask=None, score=None) bases=
medh5.Instance.box	field
medh5.Instance.class_id	field
medh5.Instance.index	field
medh5.Instance.instance_id	field
medh5.Instance.mask	field
medh5.Instance.score	field
medh5.Instance.slices	property
medh5.Instance.voxel_count	property
medh5.Issue	class	(code, severity='info', class_ids=(), note=None) bases=
medh5.Issue.class_ids	field
medh5.Issue.code	field
medh5.Issue.from_json	classmethod	(doc)
medh5.Issue.note	field
medh5.Issue.severity	field
medh5.Issue.to_json	method	()
medh5.LabelClass	class	(id, key, name, parents=None, category=None, color=None, codes=None, laterality=None, properties=None) bases=
medh5.LabelClass.category	field
medh5.LabelClass.codes	field
medh5.LabelClass.color	field
medh5.LabelClass.from_json	classmethod	(doc)
medh5.LabelClass.id	field
medh5.LabelClass.is_lesion	property
medh5.LabelClass.key	field
medh5.LabelClass.laterality	field
medh5.LabelClass.name	field
medh5.LabelClass.parents	field
medh5.LabelClass.properties	field
medh5.LabelClass.to_json	method	()
medh5.LabelSet	class	(id, classes=None, *, version='1.0.0', relations=None, skeletons=None, form='inline', uri=None, sha256=None) bases=
medh5.LabelSet.__contains__	method	(key, /)
medh5.LabelSet.__getitem__	method	(key, /)
medh5.LabelSet.__iter__	method	()
medh5.LabelSet.__len__	method	()
medh5.LabelSet.ancestors	method	(key)
medh5.LabelSet.as_ref	method	(uri)
medh5.LabelSet.check	method	()
medh5.LabelSet.classes	property
medh5.LabelSet.close	method	(ids, closure)
medh5.LabelSet.colors	method	()
medh5.LabelSet.content_doc	method	()
medh5.LabelSet.descendants	method	(key)
medh5.LabelSet.digest	method	(algo='sha256')
medh5.LabelSet.form	property
medh5.LabelSet.from_json	classmethod	(doc)
medh5.LabelSet.get	method	(key)
medh5.LabelSet.id	property
medh5.LabelSet.ids	property
medh5.LabelSet.ids_for	method	(keys)
medh5.LabelSet.keys	property
medh5.LabelSet.missing	method	(ids)
medh5.LabelSet.relations	property
medh5.LabelSet.relations_of	method	(key, predicate=None)
medh5.LabelSet.resolve	method	(keys)
medh5.LabelSet.sha256	property
medh5.LabelSet.skeleton	method	(skeleton_id)
medh5.LabelSet.skeletons	property
medh5.LabelSet.subset	method	(keys, *, id=None)
medh5.LabelSet.to_json	method	(*, form=None)
medh5.LabelSet.uri	property
medh5.LabelSet.version	property
medh5.MEDH5Error	class	(?) bases=Exception
medh5.MEDH5FileError	class	(message, errno=None, filename=None) bases=medh5.errors.MEDH5Error,OSError
medh5.MEDH5FileNotFoundError	class	(message, errno=None, filename=None) bases=medh5.errors.MEDH5FileError,FileNotFoundError
medh5.MEDH5IOError	class	(?) bases=OSError
medh5.MEDH5IntegrityError	class	(?) bases=medh5.errors.MEDH5Error
medh5.MEDH5IsADirectoryError	class	(message, errno=None, filename=None) bases=medh5.errors.MEDH5FileError,IsADirectoryError
medh5.MEDH5PermissionError	class	(message, errno=None, filename=None) bases=medh5.errors.MEDH5FileError,PermissionError
medh5.MEDH5SchemaError	class	(?) bases=medh5.errors.MEDH5Error
medh5.MEDH5ValidationError	class	(message, code=None) bases=medh5.errors.MEDH5Error,ValueError
medh5.MEDH5VersionError	class	(?) bases=medh5.errors.MEDH5Error
medh5.Observation	class	(?) bases=
medh5.Observation.annotation	field
medh5.Observation.box	field
medh5.Observation.centroid	property
medh5.Observation.class_id	field
medh5.Observation.extent	property
medh5.Observation.grid	field
medh5.Observation.index	field
medh5.Observation.instance_id	field
medh5.Observation.kind	property
medh5.Observation.score	field
medh5.Observation.timepoint	field
medh5.Observation.to_json	method	()
medh5.Observation.units	field
medh5.Observation.volume	field
medh5.Observation.volume_mm	property
medh5.Observation.voxel_count	field
medh5.PROFILES	constant	tuple
medh5.Patch	class	(slices, pad=(), center=(), strategy='uniform', class_id=None, used_index=None, grid_id=None) bases=
medh5.Patch.apply_padding	method	(array, value=0.0)
medh5.Patch.center	field
medh5.Patch.class_id	field
medh5.Patch.grid_id	field
medh5.Patch.needs_padding	property
medh5.Patch.pad	field
medh5.Patch.padding	property
medh5.Patch.shape	property
medh5.Patch.slices	field
medh5.Patch.strategy	field
medh5.Patch.to_json	method	()
medh5.Patch.used_index	field
medh5.PatchSampler	class	(patch_size, *, strategy='balanced', foreground_prob=0.5, foreground_classes=None, class_weights='uniform') bases=
medh5.PatchSampler.class_weights	property
medh5.PatchSampler.draw	method	(sample, annotation=None, rng=None, *, grid=None)
medh5.PatchSampler.draws	method	(sample, annotation=None, n=1, rng=None, *, grid=None)
medh5.PatchSampler.foreground_classes	property
medh5.PatchSampler.foreground_prob	property
medh5.PatchSampler.patch_size	property
medh5.PatchSampler.strategy	property
medh5.Provenance	class	(agents=None, activities=None) bases=
medh5.Provenance.__iter__	method	()
medh5.Provenance.__len__	method	()
medh5.Provenance.activities	property
medh5.Provenance.activities_by_type	method	(activity_type)
medh5.Provenance.activity	method	(activity_id)
medh5.Provenance.add_activity	method	(activity, *, replace=False)
medh5.Provenance.add_agent	method	(agent, *, replace=False)
medh5.Provenance.agent	method	(agent_id)
medh5.Provenance.agents	property
medh5.Provenance.dangling_agent_refs	method	()
medh5.Provenance.from_json	classmethod	(doc)
medh5.Provenance.has_activity	method	(activity_id)
medh5.Provenance.has_agent	method	(agent_id)
medh5.Provenance.produced_by	method	(object_path)
medh5.Provenance.to_json	method	()
medh5.QualityRecord	class	(status, confidence=None, reviewed_by=(), agreement=(), issues=(), edit_effort_s=None) bases=
medh5.QualityRecord.agreement	field
medh5.QualityRecord.confidence	field
medh5.QualityRecord.edit_effort_s	field
medh5.QualityRecord.from_json	classmethod	(doc)
medh5.QualityRecord.is_usable	property
medh5.QualityRecord.issues	field
medh5.QualityRecord.reviewed_by	field
medh5.QualityRecord.status	field
medh5.QualityRecord.to_json	method	()
medh5.Sample	class	(handle) bases=
medh5.Sample.__enter__	method	()
medh5.Sample.__exit__	method	(*exc)
medh5.Sample.annotations	property
medh5.Sample.at	method	(timepoint)
medh5.Sample.attr_name_map	method	()
medh5.Sample.clinical	property
medh5.Sample.close	method	()
medh5.Sample.cohort	property
medh5.Sample.compute_content_id	method	()
medh5.Sample.content_id	property
medh5.Sample.document	property
medh5.Sample.document_text	method	(document_id)
medh5.Sample.fresh_indices	property
medh5.Sample.grids	property
medh5.Sample.identity	property
medh5.Sample.ignore_region	method	(ann_id, roi=None)
medh5.Sample.images	property
medh5.Sample.index	property
medh5.Sample.is_longitudinal	property
medh5.Sample.is_open	property
medh5.Sample.kind	property
medh5.Sample.label_set	property
medh5.Sample.path	property
medh5.Sample.profiles	property
medh5.Sample.reference_grid	property
medh5.Sample.resolve_frames	method	(from_frame, to_frame)
medh5.Sample.root	property
medh5.Sample.summary	method	()
medh5.Sample.support	property
medh5.Sample.timepoints	property
medh5.Sample.tracks	method	(class_key=None, *, measure=True)
medh5.Sample.transform_between	method	(source, target, *, by=None)
medh5.Sample.transforms	property
medh5.Sample.valid_region	method	(image_id, roi=None)
medh5.Sample.verify	method	(partial=None)
medh5.Sample.version	property
medh5.SampleDocument	class	(identity, timepoints, cohort=None, label_set=None, provenance=None, quality=None, splits=None, acquisition=None, deidentification=None, extra=None) bases=
medh5.SampleDocument.acquisition	field
medh5.SampleDocument.check_schema	method	()
medh5.SampleDocument.cohort	field
medh5.SampleDocument.deidentification	field
medh5.SampleDocument.dumps	method	(*, indent=None)
medh5.SampleDocument.extra	field
medh5.SampleDocument.from_json	classmethod	(doc)
medh5.SampleDocument.group_id	property
medh5.SampleDocument.identity	field
medh5.SampleDocument.label_set	field
medh5.SampleDocument.loads	classmethod	(payload)
medh5.SampleDocument.provenance	field
medh5.SampleDocument.quality	field
medh5.SampleDocument.quality_of	method	(key)
medh5.SampleDocument.splits	field
medh5.SampleDocument.subject_id	property
medh5.SampleDocument.summary	method	()
medh5.SampleDocument.timepoints	field
medh5.SampleDocument.to_json	method	()
medh5.SampleWriter	class	(path, *, sample_id=None, subject_id=None, codec='balanced', profiles=None) bases=
medh5.SampleWriter.__enter__	method	()
medh5.SampleWriter.__exit__	method	(exc_type=None, _exc=None, _tb=None)
medh5.SampleWriter.abort	method	()
medh5.SampleWriter.acquisition	method	(image_id, **params)
medh5.SampleWriter.activity	method	(activity_type, *, agent=None, activity_id=None, **fields)
medh5.SampleWriter.add_boxes	method	(ann_id, boxes, class_ids, *, grid=None, space='index', frame_uid=None, instance_ids=None, scores=None, attributes=None, slice_index=None, annotated_classes=None, closure='explicit', timepoints=None, prov=None, quality=None, derived_from=None, task='detection', codec=None)
medh5.SampleWriter.add_classification	method	(ann_id, labels, *, scope='sample', multilabel=True, scope_ids=None, schemes=None, scheme_values=None, grid=None, annotated_classes=None, closure='explicit', timepoints=None, prov=None, quality=None, derived_from=None, codec=None)
medh5.SampleWriter.add_contours	method	(ann_id, polygons, *, grid=None, space='index', frame_uid=None, annotated_classes=None, closure='explicit', timepoints=None, prov=None, quality=None, derived_from=None, task='segmentation', codec=None)
medh5.SampleWriter.add_document	method	(document=None, **fields)
medh5.SampleWriter.add_event	method	(event=None, **fields)
medh5.SampleWriter.add_grid	method	(grid_id, *, shape, spacing, origin=None, direction=None, axis_names=None, axis_kinds=None, coord_system='LPS', units='mm', timepoint=None, frame_uid=None, patch_hint=None, chunk_hint=None, time_values=None, time_units=None)
medh5.SampleWriter.add_image	method	(image_id, data, *, grid, modality, value_type='intensity', value_units=None, channel_names=None, rescale_slope=None, rescale_intercept=None, window_center=None, window_width=None, valid_mask=None, prov=None, codec=None)
medh5.SampleWriter.add_keypoints	method	(ann_id, points, keypoint_classes, class_ids, *, grid=None, space='index', frame_uid=None, visibility=None, instance_ids=None, scores=None, skeleton=None, annotated_classes=None, closure='explicit', timepoints=None, prov=None, quality=None, derived_from=None, task='detection', codec=None)
medh5.SampleWriter.add_link	method	(link=None, **fields)
medh5.SampleWriter.add_mask	method	(ann_id, mask, *, grid, task='other', prov=None, codec=None)
medh5.SampleWriter.add_mesh	method	(ann_id, vertices, faces, *, grid=None, space='world', frame_uid=None, normals=None, vertex_class_ids=None, mesh_offsets=None, mesh_class_ids=None, annotated_classes=None, closure='explicit', timepoints=None, prov=None, quality=None, derived_from=None, task='segmentation', codec=None)
medh5.SampleWriter.add_obb	method	(ann_id, centers, sizes, rotations, class_ids, *, grid=None, space='index', frame_uid=None, instance_ids=None, scores=None, attributes=None, annotated_classes=None, closure='explicit', timepoints=None, prov=None, quality=None, derived_from=None, task='detection', codec=None)
medh5.SampleWriter.add_points	method	(ann_id, points, *, grid=None, space='index', frame_uid=None, class_ids=None, instance_ids=None, names=None, weights=None, correspondence=None, annotated_classes=None, closure='explicit', timepoints=None, prov=None, quality=None, derived_from=None, task='detection', codec=None)
medh5.SampleWriter.add_pyramid	method	(image_id, levels, *, grid_levels, modality, value_type='intensity', downsample_method='mean', value_units=None, rescale_slope=None, rescale_intercept=None, prov=None, codec=None)
medh5.SampleWriter.add_records	method	(records)
medh5.SampleWriter.add_segmentation	method	(ann_id, *, grid, masks=None, probabilities=None, instances=None, labelmap=None, label_values=None, ignore_value=None, encoding='auto', threshold=None, annotated_classes=None, closure='explicit', ignore=None, ignore_mask=None, timepoints=None, prov=None, quality=None, derived_from=None, task='segmentation', codec=None)
medh5.SampleWriter.add_timepoint	method	(timepoint_id, **fields)
medh5.SampleWriter.add_transform	method	(transform_id, *, kind, from_frame, to_frame, matrix=None, field=None, control_points=None, components=None, field_grid=None, cp_grid=None, vector_space='world', interpolation='linear', extrapolation='zero', order=3, units=None, from_grid=None, to_grid=None, invertible=None, inverse_id=None, metrics=None, prov=None, codec=None, field_dtype='float32')
medh5.SampleWriter.build_index	method	(ann_ids=None, *, max_coords=<value>, occupancy=<value>, seed=0)
medh5.SampleWriter.clinical	method	()
medh5.SampleWriter.closed	property
medh5.SampleWriter.codec	property
medh5.SampleWriter.cohort	method	(**fields)
medh5.SampleWriter.commit	method	(*, digests=True)
medh5.SampleWriter.deidentification	method	(**fields)
medh5.SampleWriter.document	property
medh5.SampleWriter.drop_clinical	method	()
medh5.SampleWriter.extra	method	(namespace, value)
medh5.SampleWriter.frame_uids	method	()
medh5.SampleWriter.grids	property
medh5.SampleWriter.handle	property
medh5.SampleWriter.has_clinical	property
medh5.SampleWriter.identity	method	(**fields)
medh5.SampleWriter.infer_profiles	method	()
medh5.SampleWriter.label_set	method	(label_set)
medh5.SampleWriter.organization	method	(name, **fields)
medh5.SampleWriter.path	property
medh5.SampleWriter.person	method	(name, agent_id=None, **fields)
medh5.SampleWriter.remap_frame_uids	method	(mapping)
medh5.SampleWriter.remove_annotation	method	(ann_id)
medh5.SampleWriter.remove_grid	method	(grid_id)
medh5.SampleWriter.remove_image	method	(image_id)
medh5.SampleWriter.remove_transform	method	(transform_id)
medh5.SampleWriter.set_clock	method	(clock=None, **fields)
medh5.SampleWriter.set_image_attrs	method	(image_id, **attrs)
medh5.SampleWriter.set_quality	method	(key, **fields)
medh5.SampleWriter.software	method	(name, version=None, **fields)
medh5.SampleWriter.split	method	(**fields)
medh5.SampleWriter.transcode_annotation	method	(ann_id, to_kind, *, codec=None, drop_identity=False)
medh5.SplitAudit	class	(memberships=(), conflicts=(), leaks=(), unclaimed=(), unreadable=()) bases=
medh5.SplitAudit.conflicts	field
medh5.SplitAudit.counts	method	()
medh5.SplitAudit.from_fields	classmethod	(fields)
medh5.SplitAudit.leaks	field
medh5.SplitAudit.memberships	field
medh5.SplitAudit.ok	property
medh5.SplitAudit.partitions	method	(set_id)
medh5.SplitAudit.set_ids	property
medh5.SplitAudit.to_json	method	()
medh5.SplitAudit.unclaimed	field
medh5.SplitAudit.unreadable	field
medh5.SplitClaim	class	(set_id, partition, fold=None, assigned_by=None, assigned_at=None, manifest_sha256=None) bases=
medh5.SplitClaim.assigned_at	field
medh5.SplitClaim.assigned_by	field
medh5.SplitClaim.fold	field
medh5.SplitClaim.from_json	classmethod	(doc)
medh5.SplitClaim.manifest_sha256	field
medh5.SplitClaim.partition	field
medh5.SplitClaim.set_id	field
medh5.SplitClaim.to_json	method	()
medh5.TaskManifest	class	(doc, *, base=None) bases=
medh5.TaskManifest.add_row	method	(row_id, subject_id, cutoff_us)
medh5.TaskManifest.add_subject	method	(subject_id, sources, *, partition=None, clock_id=None)
medh5.TaskManifest.base	property
medh5.TaskManifest.declared_fingerprint	property
medh5.TaskManifest.from_cohort	classmethod	(cohort, split, *, task_id, version, identity_namespace, base=None, fold=None, training_partition='train', policy=None, slots=(), target=None, description=None)
medh5.TaskManifest.identity_namespace	property
medh5.TaskManifest.load	classmethod	(path)
medh5.TaskManifest.manifest_fingerprint	property
medh5.TaskManifest.new	classmethod	(task_id, version, *, identity_namespace, policy=None, slots=(), target=None, split=None, description=None, base=None)
medh5.TaskManifest.notes	property
medh5.TaskManifest.partition_of	method	(subject_id)
medh5.TaskManifest.policy	property
medh5.TaskManifest.preflight	method	(base=None, *, deep=False, confine=None)
medh5.TaskManifest.reconcile	method	(base=None, *, confine=None)
medh5.TaskManifest.repin	method	(base=None, *, sources=None, dry_run=False, confine=None)
medh5.TaskManifest.row_fingerprint	method	(row_id)
medh5.TaskManifest.rows	property
medh5.TaskManifest.save	method	(path)
medh5.TaskManifest.slots	property
medh5.TaskManifest.split	property
medh5.TaskManifest.subjects	property
medh5.TaskManifest.subjects_digest	method	(partition)
medh5.TaskManifest.target	property
medh5.TaskManifest.task_fingerprint	property
medh5.TaskManifest.task_id	property
medh5.TaskManifest.task_version	property
medh5.TaskManifest.to_json	method	()
medh5.TaskManifest.training_partition	property
medh5.TaskManifest.validate	method	()
medh5.Timeline	class	(timepoints) bases=
medh5.Timeline.__contains__	method	(key, /)
medh5.Timeline.__getitem__	method	(key, /)
medh5.Timeline.__iter__	method	()
medh5.Timeline.__len__	method	()
medh5.Timeline.baseline	property
medh5.Timeline.check	method	()
medh5.Timeline.count	method	(value)
medh5.Timeline.from_json	classmethod	(docs)
medh5.Timeline.ids	property
medh5.Timeline.index	method	(value, start=0, stop=None)
medh5.Timeline.interval_days	method	(a, b)
medh5.Timeline.is_longitudinal	property
medh5.Timeline.require	method	(timepoint_id, *, where='')
medh5.Timeline.single	classmethod	(timepoint_id='tp0', **kwargs)
medh5.Timeline.to_json	method	()
medh5.Timepoint	class	(id, index, label=None, date=None, days_from_baseline=None, study_uid=None, series_uids={}, subject_age_years=None, description=None) bases=
medh5.Timepoint.date	field
medh5.Timepoint.days_from_baseline	field
medh5.Timepoint.description	field
medh5.Timepoint.from_json	classmethod	(doc)
medh5.Timepoint.id	field
medh5.Timepoint.index	field
medh5.Timepoint.label	field
medh5.Timepoint.series_uids	field
medh5.Timepoint.study_uid	field
medh5.Timepoint.subject_age_years	field
medh5.Timepoint.to_json	method	()
medh5.TimepointPair	class	(first, second, interval_days=None, label=None) bases=
medh5.TimepointPair.first	field
medh5.TimepointPair.interval_days	field
medh5.TimepointPair.label	field
medh5.TimepointPair.second	field
medh5.TimepointPairSampler	class	(mode='consecutive') bases=
medh5.TimepointPairSampler.__call__	method	(sample)
medh5.TimepointPairSampler.mode	property
medh5.TimepointPairSampler.pairs	method	(sample)
medh5.Track	class	(?) bases=
medh5.Track.__iter__	method	()
medh5.Track.__len__	method	()
medh5.Track.at	method	(timepoint)
medh5.Track.class_id	property
medh5.Track.class_ids	field
medh5.Track.class_key	field
medh5.Track.has_class_conflict	property
medh5.Track.instance_id	field
medh5.Track.measurements_at	method	(timepoint)
medh5.Track.observations	field
medh5.Track.observations_at	method	(timepoint)
medh5.Track.relative_change	method	(first, second)
medh5.Track.timepoints	property
medh5.Track.to_json	method	()
medh5.Track.volume	method	(timepoint)
medh5.Track.volumes	property
medh5.Tracking	class	(?) bases=
medh5.Tracking.__contains__	method	(key, /)
medh5.Tracking.__getitem__	method	(key, /)
medh5.Tracking.__iter__	method	()
medh5.Tracking.__len__	method	()
medh5.Tracking.class_conflicts	method	()
medh5.Tracking.coverage	property
medh5.Tracking.get	method	(instance_id, default=None)
medh5.Tracking.is_new	method	(instance_id, *, located=False)
medh5.Tracking.is_persistent	method	(instance_id)
medh5.Tracking.is_resolved	method	(instance_id, *, located=False)
medh5.Tracking.items	method	()
medh5.Tracking.keys	method	()
medh5.Tracking.reason_at	method	(instance_id, timepoint)
medh5.Tracking.reasons	method	(instance_id)
medh5.Tracking.skipped	property
medh5.Tracking.state_at	method	(instance_id, timepoint)
medh5.Tracking.states	method	(instance_id)
medh5.Tracking.summary	method	()
medh5.Tracking.timepoints	property
medh5.Tracking.to_json	method	()
medh5.Tracking.unexamined	method	()
medh5.Tracking.values	method	()
medh5.VoxelAnnotation	class	(handle) bases=medh5.annotations.base.Annotation
medh5.VoxelAnnotation.ann_id	property
medh5.VoxelAnnotation.annotated_class_ids	property
medh5.VoxelAnnotation.annotated_classes	property
medh5.VoxelAnnotation.class_bboxes	method	(classes=None)
medh5.VoxelAnnotation.class_ids	property
medh5.VoxelAnnotation.class_key	method	(class_id)
medh5.VoxelAnnotation.classes	property
medh5.VoxelAnnotation.closure	property
medh5.VoxelAnnotation.contains	method	(class_key, voxel)
medh5.VoxelAnnotation.dense	method	(classes=None, roi=None)
medh5.VoxelAnnotation.grid	property
medh5.VoxelAnnotation.grid_id	property
medh5.VoxelAnnotation.group	property
medh5.VoxelAnnotation.has_ignore_region	property
medh5.VoxelAnnotation.header	property
medh5.VoxelAnnotation.ignore_id	property
medh5.VoxelAnnotation.instances	method	()
medh5.VoxelAnnotation.is_annotated	method	(class_key)
medh5.VoxelAnnotation.is_fully_covered	property
medh5.VoxelAnnotation.kind	property
medh5.VoxelAnnotation.label_set	property
medh5.VoxelAnnotation.labelmap	method	(roi=None, priority=None, *, dtype=<value>)
medh5.VoxelAnnotation.prov	property
medh5.VoxelAnnotation.quality_key	property
medh5.VoxelAnnotation.resolve_class	method	(class_key)
medh5.VoxelAnnotation.resolve_classes	method	(keys)
medh5.VoxelAnnotation.spatial_shape	property
medh5.VoxelAnnotation.summary	method	()
medh5.VoxelAnnotation.task	property
medh5.VoxelAnnotation.timepoints	property
medh5.VoxelAnnotation.voxel_counts	method	(classes=None)
medh5.__format_version__	constant	str
medh5.__version__	constant	str
medh5.amend	function	(path, *, codec=None)
medh5.annotations	module
medh5.annotations.ANNOTATION_KINDS	constant	tuple
medh5.annotations.Annotation	class	(handle) bases=
medh5.annotations.Annotation.ann_id	property
medh5.annotations.Annotation.annotated_class_ids	property
medh5.annotations.Annotation.annotated_classes	property
medh5.annotations.Annotation.class_ids	property
medh5.annotations.Annotation.class_key	method	(class_id)
medh5.annotations.Annotation.classes	property
medh5.annotations.Annotation.closure	property
medh5.annotations.Annotation.grid	property
medh5.annotations.Annotation.grid_id	property
medh5.annotations.Annotation.group	property
medh5.annotations.Annotation.has_ignore_region	property
medh5.annotations.Annotation.header	property
medh5.annotations.Annotation.ignore_id	property
medh5.annotations.Annotation.is_annotated	method	(class_key)
medh5.annotations.Annotation.is_fully_covered	property
medh5.annotations.Annotation.kind	property
medh5.annotations.Annotation.label_set	property
medh5.annotations.Annotation.prov	property
medh5.annotations.Annotation.quality_key	property
medh5.annotations.Annotation.resolve_class	method	(class_key)
medh5.annotations.Annotation.resolve_classes	method	(keys)
medh5.annotations.Annotation.summary	method	()
medh5.annotations.Annotation.task	property
medh5.annotations.Annotation.timepoints	property
medh5.annotations.AnnotationHeader	class	(kind, task, grid=None, timepoints=None, space=None, frame_uid=None, class_ids=None, annotated_class_ids=None, closure='explicit', ignore_id=65535, ignore_mask=None, prov=None, quality=None, derived_from=None, extra=None) bases=
medh5.annotations.AnnotationHeader.annotated_class_ids	field
medh5.annotations.AnnotationHeader.attrs	method	()
medh5.annotations.AnnotationHeader.class_ids	field
medh5.annotations.AnnotationHeader.closure	field
medh5.annotations.AnnotationHeader.derived_from	field
medh5.annotations.AnnotationHeader.extra	field
medh5.annotations.AnnotationHeader.frame_uid	field
medh5.annotations.AnnotationHeader.grid	field
medh5.annotations.AnnotationHeader.ignore_id	field
medh5.annotations.AnnotationHeader.ignore_mask	field
medh5.annotations.AnnotationHeader.kind	field
medh5.annotations.AnnotationHeader.prov	field
medh5.annotations.AnnotationHeader.quality	field
medh5.annotations.AnnotationHeader.read	classmethod	(group)
medh5.annotations.AnnotationHeader.space	field
medh5.annotations.AnnotationHeader.task	field
medh5.annotations.AnnotationHeader.timepoints	field
medh5.annotations.AnnotationPayload	class	(kind, datasets=None, attrs=None, stacked_axes=0, class_ids=None) bases=
medh5.annotations.AnnotationPayload.attrs	field
medh5.annotations.AnnotationPayload.class_ids	field
medh5.annotations.AnnotationPayload.data	property
medh5.annotations.AnnotationPayload.datasets	field
medh5.annotations.AnnotationPayload.describe	method	()
medh5.annotations.AnnotationPayload.kind	field
medh5.annotations.AnnotationPayload.nbytes	property
medh5.annotations.AnnotationPayload.stacked_axes	field
medh5.annotations.Assertion	class	(class_id, value, scope_id=None, scheme=None, scheme_value=None) bases=
medh5.annotations.Assertion.class_id	field
medh5.annotations.Assertion.is_negative	property
medh5.annotations.Assertion.is_positive	property
medh5.annotations.Assertion.scheme	field
medh5.annotations.Assertion.scheme_value	field
medh5.annotations.Assertion.scope_id	field
medh5.annotations.Assertion.value	field
medh5.annotations.BoxesAnnotation	class	(handle) bases=medh5.annotations.geometric.GeometricAnnotation
medh5.annotations.BoxesAnnotation.__iter__	method	()
medh5.annotations.BoxesAnnotation.__len__	method	()
medh5.annotations.BoxesAnnotation.ann_id	property
medh5.annotations.BoxesAnnotation.annotated_class_ids	property
medh5.annotations.BoxesAnnotation.annotated_classes	property
medh5.annotations.BoxesAnnotation.as_slices	method	(grid=None)
medh5.annotations.BoxesAnnotation.as_world	method	(grid=None)
medh5.annotations.BoxesAnnotation.attributes	property
medh5.annotations.BoxesAnnotation.boxes	property
medh5.annotations.BoxesAnnotation.class_ids	property
medh5.annotations.BoxesAnnotation.class_key	method	(class_id)
medh5.annotations.BoxesAnnotation.classes	property
medh5.annotations.BoxesAnnotation.closure	property
medh5.annotations.BoxesAnnotation.frame_uid	property
medh5.annotations.BoxesAnnotation.grid	property
medh5.annotations.BoxesAnnotation.grid_id	property
medh5.annotations.BoxesAnnotation.group	property
medh5.annotations.BoxesAnnotation.has_ignore_region	property
medh5.annotations.BoxesAnnotation.header	property
medh5.annotations.BoxesAnnotation.ignore_id	property
medh5.annotations.BoxesAnnotation.instance_ids	property
medh5.annotations.BoxesAnnotation.is_annotated	method	(class_key)
medh5.annotations.BoxesAnnotation.is_fully_covered	property
medh5.annotations.BoxesAnnotation.kind	property
medh5.annotations.BoxesAnnotation.label_set	property
medh5.annotations.BoxesAnnotation.n_spatial	property
medh5.annotations.BoxesAnnotation.ndim	property
medh5.annotations.BoxesAnnotation.object_class_ids	property
medh5.annotations.BoxesAnnotation.prov	property
medh5.annotations.BoxesAnnotation.quality_key	property
medh5.annotations.BoxesAnnotation.resolve_class	method	(class_key)
medh5.annotations.BoxesAnnotation.resolve_classes	method	(keys)
medh5.annotations.BoxesAnnotation.scores	property
medh5.annotations.BoxesAnnotation.slice_index	property
medh5.annotations.BoxesAnnotation.space	property
medh5.annotations.BoxesAnnotation.summary	method	()
medh5.annotations.BoxesAnnotation.task	property
medh5.annotations.BoxesAnnotation.timepoints	property
medh5.annotations.BoxesAnnotation.to_index	method	(coords, *, grid=None)
medh5.annotations.BoxesAnnotation.to_world	method	(coords, *, grid=None)
medh5.annotations.BoxesAnnotation.world_corners	method	(grid=None)
medh5.annotations.ClassificationAnnotation	class	(handle) bases=medh5.annotations.base.Annotation
medh5.annotations.ClassificationAnnotation.__len__	method	()
medh5.annotations.ClassificationAnnotation.ann_id	property
medh5.annotations.ClassificationAnnotation.annotated_class_ids	property
medh5.annotations.ClassificationAnnotation.annotated_classes	property
medh5.annotations.ClassificationAnnotation.asserted_class_ids	property
medh5.annotations.ClassificationAnnotation.assertions	method	()
medh5.annotations.ClassificationAnnotation.by_scope_id	method	()
medh5.annotations.ClassificationAnnotation.class_ids	property
medh5.annotations.ClassificationAnnotation.class_key	method	(class_id)
medh5.annotations.ClassificationAnnotation.classes	property
medh5.annotations.ClassificationAnnotation.closure	property
medh5.annotations.ClassificationAnnotation.compared_timepoints	property
medh5.annotations.ClassificationAnnotation.grid	property
medh5.annotations.ClassificationAnnotation.grid_id	property
medh5.annotations.ClassificationAnnotation.group	property
medh5.annotations.ClassificationAnnotation.has_ignore_region	property
medh5.annotations.ClassificationAnnotation.header	property
medh5.annotations.ClassificationAnnotation.ignore_id	property
medh5.annotations.ClassificationAnnotation.is_annotated	method	(class_key)
medh5.annotations.ClassificationAnnotation.is_change_label	property
medh5.annotations.ClassificationAnnotation.is_fully_covered	property
medh5.annotations.ClassificationAnnotation.kind	property
medh5.annotations.ClassificationAnnotation.label_set	property
medh5.annotations.ClassificationAnnotation.labels	property
medh5.annotations.ClassificationAnnotation.multilabel	property
medh5.annotations.ClassificationAnnotation.positives	property
medh5.annotations.ClassificationAnnotation.prov	property
medh5.annotations.ClassificationAnnotation.quality_key	property
medh5.annotations.ClassificationAnnotation.resolve_class	method	(class_key)
medh5.annotations.ClassificationAnnotation.resolve_classes	method	(keys)
medh5.annotations.ClassificationAnnotation.scheme	method	(name)
medh5.annotations.ClassificationAnnotation.scheme_values	property
medh5.annotations.ClassificationAnnotation.schemes	property
medh5.annotations.ClassificationAnnotation.scope	property
medh5.annotations.ClassificationAnnotation.scope_ids	property
medh5.annotations.ClassificationAnnotation.state	method	(class_key, *, scope_id=None)
medh5.annotations.ClassificationAnnotation.summary	method	()
medh5.annotations.ClassificationAnnotation.task	property
medh5.annotations.ClassificationAnnotation.timepoints	property
medh5.annotations.ClassificationAnnotation.value	method	(class_key, *, scope_id=None)
medh5.annotations.ClassificationAnnotation.values	property
medh5.annotations.ContoursAnnotation	class	(handle) bases=medh5.annotations.geometric.GeometricAnnotation
medh5.annotations.ContoursAnnotation.__len__	method	()
medh5.annotations.ContoursAnnotation.ann_id	property
medh5.annotations.ContoursAnnotation.annotated_class_ids	property
medh5.annotations.ContoursAnnotation.annotated_classes	property
medh5.annotations.ContoursAnnotation.attributes	property
medh5.annotations.ContoursAnnotation.by_plane	method	()
medh5.annotations.ContoursAnnotation.class_ids	property
medh5.annotations.ContoursAnnotation.class_key	method	(class_id)
medh5.annotations.ContoursAnnotation.classes	property
medh5.annotations.ContoursAnnotation.closure	property
medh5.annotations.ContoursAnnotation.frame_uid	property
medh5.annotations.ContoursAnnotation.grid	property
medh5.annotations.ContoursAnnotation.grid_id	property
medh5.annotations.ContoursAnnotation.group	property
medh5.annotations.ContoursAnnotation.has_ignore_region	property
medh5.annotations.ContoursAnnotation.header	property
medh5.annotations.ContoursAnnotation.ignore_id	property
medh5.annotations.ContoursAnnotation.instance_ids	property
medh5.annotations.ContoursAnnotation.is_annotated	method	(class_key)
medh5.annotations.ContoursAnnotation.is_fully_covered	property
medh5.annotations.ContoursAnnotation.kind	property
medh5.annotations.ContoursAnnotation.label_set	property
medh5.annotations.ContoursAnnotation.n_spatial	property
medh5.annotations.ContoursAnnotation.object_class_ids	property
medh5.annotations.ContoursAnnotation.offsets	property
medh5.annotations.ContoursAnnotation.planes	property
medh5.annotations.ContoursAnnotation.polygon	method	(index)
medh5.annotations.ContoursAnnotation.polygons	method	()
medh5.annotations.ContoursAnnotation.prov	property
medh5.annotations.ContoursAnnotation.quality_key	property
medh5.annotations.ContoursAnnotation.resolve_class	method	(class_key)
medh5.annotations.ContoursAnnotation.resolve_classes	method	(keys)
medh5.annotations.ContoursAnnotation.roles	property
medh5.annotations.ContoursAnnotation.scores	property
medh5.annotations.ContoursAnnotation.space	property
medh5.annotations.ContoursAnnotation.summary	method	()
medh5.annotations.ContoursAnnotation.task	property
medh5.annotations.ContoursAnnotation.timepoints	property
medh5.annotations.ContoursAnnotation.to_index	method	(coords, *, grid=None)
medh5.annotations.ContoursAnnotation.to_world	method	(coords, *, grid=None)
medh5.annotations.ContoursAnnotation.vertices	property
medh5.annotations.GEOMETRIC_KINDS	constant	tuple
medh5.annotations.GeometricAnnotation	class	(handle) bases=medh5.annotations.base.Annotation
medh5.annotations.GeometricAnnotation.__len__	method	()
medh5.annotations.GeometricAnnotation.ann_id	property
medh5.annotations.GeometricAnnotation.annotated_class_ids	property
medh5.annotations.GeometricAnnotation.annotated_classes	property
medh5.annotations.GeometricAnnotation.attributes	property
medh5.annotations.GeometricAnnotation.class_ids	property
medh5.annotations.GeometricAnnotation.class_key	method	(class_id)
medh5.annotations.GeometricAnnotation.classes	property
medh5.annotations.GeometricAnnotation.closure	property
medh5.annotations.GeometricAnnotation.frame_uid	property
medh5.annotations.GeometricAnnotation.grid	property
medh5.annotations.GeometricAnnotation.grid_id	property
medh5.annotations.GeometricAnnotation.group	property
medh5.annotations.GeometricAnnotation.has_ignore_region	property
medh5.annotations.GeometricAnnotation.header	property
medh5.annotations.GeometricAnnotation.ignore_id	property
medh5.annotations.GeometricAnnotation.instance_ids	property
medh5.annotations.GeometricAnnotation.is_annotated	method	(class_key)
medh5.annotations.GeometricAnnotation.is_fully_covered	property
medh5.annotations.GeometricAnnotation.kind	property
medh5.annotations.GeometricAnnotation.label_set	property
medh5.annotations.GeometricAnnotation.n_spatial	property
medh5.annotations.GeometricAnnotation.object_class_ids	property
medh5.annotations.GeometricAnnotation.prov	property
medh5.annotations.GeometricAnnotation.quality_key	property
medh5.annotations.GeometricAnnotation.resolve_class	method	(class_key)
medh5.annotations.GeometricAnnotation.resolve_classes	method	(keys)
medh5.annotations.GeometricAnnotation.scores	property
medh5.annotations.GeometricAnnotation.space	property
medh5.annotations.GeometricAnnotation.summary	method	()
medh5.annotations.GeometricAnnotation.task	property
medh5.annotations.GeometricAnnotation.timepoints	property
medh5.annotations.GeometricAnnotation.to_index	method	(coords, *, grid=None)
medh5.annotations.GeometricAnnotation.to_world	method	(coords, *, grid=None)
medh5.annotations.Instance	class	(index, instance_id, class_id, box, mask=None, score=None) bases=
medh5.annotations.Instance.box	field
medh5.annotations.Instance.class_id	field
medh5.annotations.Instance.index	field
medh5.annotations.Instance.instance_id	field
medh5.annotations.Instance.mask	field
medh5.annotations.Instance.score	field
medh5.annotations.Instance.slices	property
medh5.annotations.Instance.voxel_count	property
medh5.annotations.KeypointsAnnotation	class	(handle) bases=medh5.annotations.geometric.GeometricAnnotation
medh5.annotations.KeypointsAnnotation.__len__	method	()
medh5.annotations.KeypointsAnnotation.ann_id	property
medh5.annotations.KeypointsAnnotation.annotated_class_ids	property
medh5.annotations.KeypointsAnnotation.annotated_classes	property
medh5.annotations.KeypointsAnnotation.attributes	property
medh5.annotations.KeypointsAnnotation.class_ids	property
medh5.annotations.KeypointsAnnotation.class_key	method	(class_id)
medh5.annotations.KeypointsAnnotation.classes	property
medh5.annotations.KeypointsAnnotation.closure	property
medh5.annotations.KeypointsAnnotation.frame_uid	property
medh5.annotations.KeypointsAnnotation.grid	property
medh5.annotations.KeypointsAnnotation.grid_id	property
medh5.annotations.KeypointsAnnotation.group	property
medh5.annotations.KeypointsAnnotation.has_ignore_region	property
medh5.annotations.KeypointsAnnotation.header	property
medh5.annotations.KeypointsAnnotation.ignore_id	property
medh5.annotations.KeypointsAnnotation.instance_ids	property
medh5.annotations.KeypointsAnnotation.is_annotated	method	(class_key)
medh5.annotations.KeypointsAnnotation.is_fully_covered	property
medh5.annotations.KeypointsAnnotation.keypoint_class_ids	property
medh5.annotations.KeypointsAnnotation.kind	property
medh5.annotations.KeypointsAnnotation.label_set	property
medh5.annotations.KeypointsAnnotation.labelled	method	()
medh5.annotations.KeypointsAnnotation.n_spatial	property
medh5.annotations.KeypointsAnnotation.object_class_ids	property
medh5.annotations.KeypointsAnnotation.points	property
medh5.annotations.KeypointsAnnotation.prov	property
medh5.annotations.KeypointsAnnotation.quality_key	property
medh5.annotations.KeypointsAnnotation.resolve_class	method	(class_key)
medh5.annotations.KeypointsAnnotation.resolve_classes	method	(keys)
medh5.annotations.KeypointsAnnotation.scores	property
medh5.annotations.KeypointsAnnotation.skeleton	method	()
medh5.annotations.KeypointsAnnotation.skeleton_id	property
medh5.annotations.KeypointsAnnotation.space	property
medh5.annotations.KeypointsAnnotation.summary	method	()
medh5.annotations.KeypointsAnnotation.task	property
medh5.annotations.KeypointsAnnotation.timepoints	property
medh5.annotations.KeypointsAnnotation.to_index	method	(coords, *, grid=None)
medh5.annotations.KeypointsAnnotation.to_world	method	(coords, *, grid=None)
medh5.annotations.KeypointsAnnotation.visibility	property
medh5.annotations.MeshAnnotation	class	(handle) bases=medh5.annotations.geometric.GeometricAnnotation
medh5.annotations.MeshAnnotation.__len__	method	()
medh5.annotations.MeshAnnotation.ann_id	property
medh5.annotations.MeshAnnotation.annotated_class_ids	property
medh5.annotations.MeshAnnotation.annotated_classes	property
medh5.annotations.MeshAnnotation.attributes	property
medh5.annotations.MeshAnnotation.bounds	method	()
medh5.annotations.MeshAnnotation.class_ids	property
medh5.annotations.MeshAnnotation.class_key	method	(class_id)
medh5.annotations.MeshAnnotation.classes	property
medh5.annotations.MeshAnnotation.closure	property
medh5.annotations.MeshAnnotation.faces	property
medh5.annotations.MeshAnnotation.frame_uid	property
medh5.annotations.MeshAnnotation.grid	property
medh5.annotations.MeshAnnotation.grid_id	property
medh5.annotations.MeshAnnotation.group	property
medh5.annotations.MeshAnnotation.has_ignore_region	property
medh5.annotations.MeshAnnotation.header	property
medh5.annotations.MeshAnnotation.ignore_id	property
medh5.annotations.MeshAnnotation.instance_ids	property
medh5.annotations.MeshAnnotation.is_annotated	method	(class_key)
medh5.annotations.MeshAnnotation.is_fully_covered	property
medh5.annotations.MeshAnnotation.kind	property
medh5.annotations.MeshAnnotation.label_set	property
medh5.annotations.MeshAnnotation.n_spatial	property
medh5.annotations.MeshAnnotation.n_submeshes	property
medh5.annotations.MeshAnnotation.normals	property
medh5.annotations.MeshAnnotation.object_class_ids	property
medh5.annotations.MeshAnnotation.prov	property
medh5.annotations.MeshAnnotation.quality_key	property
medh5.annotations.MeshAnnotation.resolve_class	method	(class_key)
medh5.annotations.MeshAnnotation.resolve_classes	method	(keys)
medh5.annotations.MeshAnnotation.scores	property
medh5.annotations.MeshAnnotation.space	property
medh5.annotations.MeshAnnotation.summary	method	()
medh5.annotations.MeshAnnotation.task	property
medh5.annotations.MeshAnnotation.timepoints	property
medh5.annotations.MeshAnnotation.to_index	method	(coords, *, grid=None)
medh5.annotations.MeshAnnotation.to_world	method	(coords, *, grid=None)
medh5.annotations.MeshAnnotation.vertex_class_ids	property
medh5.annotations.MeshAnnotation.vertices	property
medh5.annotations.ObbAnnotation	class	(handle) bases=medh5.annotations.geometric.GeometricAnnotation
medh5.annotations.ObbAnnotation.__len__	method	()
medh5.annotations.ObbAnnotation.ann_id	property
medh5.annotations.ObbAnnotation.annotated_class_ids	property
medh5.annotations.ObbAnnotation.annotated_classes	property
medh5.annotations.ObbAnnotation.as_aabb	method	()
medh5.annotations.ObbAnnotation.attributes	property
medh5.annotations.ObbAnnotation.centers	property
medh5.annotations.ObbAnnotation.class_ids	property
medh5.annotations.ObbAnnotation.class_key	method	(class_id)
medh5.annotations.ObbAnnotation.classes	property
medh5.annotations.ObbAnnotation.closure	property
medh5.annotations.ObbAnnotation.corners	method	()
medh5.annotations.ObbAnnotation.frame_uid	property
medh5.annotations.ObbAnnotation.grid	property
medh5.annotations.ObbAnnotation.grid_id	property
medh5.annotations.ObbAnnotation.group	property
medh5.annotations.ObbAnnotation.has_ignore_region	property
medh5.annotations.ObbAnnotation.header	property
medh5.annotations.ObbAnnotation.ignore_id	property
medh5.annotations.ObbAnnotation.instance_ids	property
medh5.annotations.ObbAnnotation.is_annotated	method	(class_key)
medh5.annotations.ObbAnnotation.is_fully_covered	property
medh5.annotations.ObbAnnotation.kind	property
medh5.annotations.ObbAnnotation.label_set	property
medh5.annotations.ObbAnnotation.n_spatial	property
medh5.annotations.ObbAnnotation.object_class_ids	property
medh5.annotations.ObbAnnotation.prov	property
medh5.annotations.ObbAnnotation.quality_key	property
medh5.annotations.ObbAnnotation.resolve_class	method	(class_key)
medh5.annotations.ObbAnnotation.resolve_classes	method	(keys)
medh5.annotations.ObbAnnotation.rotations	property
medh5.annotations.ObbAnnotation.scores	property
medh5.annotations.ObbAnnotation.sizes	property
medh5.annotations.ObbAnnotation.space	property
medh5.annotations.ObbAnnotation.summary	method	()
medh5.annotations.ObbAnnotation.task	property
medh5.annotations.ObbAnnotation.timepoints	property
medh5.annotations.ObbAnnotation.to_index	method	(coords, *, grid=None)
medh5.annotations.ObbAnnotation.to_world	method	(coords, *, grid=None)
medh5.annotations.ObbAnnotation.volumes	property
medh5.annotations.PointsAnnotation	class	(handle) bases=medh5.annotations.geometric.GeometricAnnotation
medh5.annotations.PointsAnnotation.__len__	method	()
medh5.annotations.PointsAnnotation.ann_id	property
medh5.annotations.PointsAnnotation.annotated_class_ids	property
medh5.annotations.PointsAnnotation.annotated_classes	property
medh5.annotations.PointsAnnotation.attributes	property
medh5.annotations.PointsAnnotation.class_ids	property
medh5.annotations.PointsAnnotation.class_key	method	(class_id)
medh5.annotations.PointsAnnotation.classes	property
medh5.annotations.PointsAnnotation.closure	property
medh5.annotations.PointsAnnotation.correspondence	property
medh5.annotations.PointsAnnotation.frame_uid	property
medh5.annotations.PointsAnnotation.grid	property
medh5.annotations.PointsAnnotation.grid_id	property
medh5.annotations.PointsAnnotation.group	property
medh5.annotations.PointsAnnotation.has_ignore_region	property
medh5.annotations.PointsAnnotation.header	property
medh5.annotations.PointsAnnotation.ignore_id	property
medh5.annotations.PointsAnnotation.instance_ids	property
medh5.annotations.PointsAnnotation.is_annotated	method	(class_key)
medh5.annotations.PointsAnnotation.is_fully_covered	property
medh5.annotations.PointsAnnotation.kind	property
medh5.annotations.PointsAnnotation.label_set	property
medh5.annotations.PointsAnnotation.n_spatial	property
medh5.annotations.PointsAnnotation.named	method	()
medh5.annotations.PointsAnnotation.names	property
medh5.annotations.PointsAnnotation.object_class_ids	property
medh5.annotations.PointsAnnotation.points	property
medh5.annotations.PointsAnnotation.prov	property
medh5.annotations.PointsAnnotation.quality_key	property
medh5.annotations.PointsAnnotation.resolve_class	method	(class_key)
medh5.annotations.PointsAnnotation.resolve_classes	method	(keys)
medh5.annotations.PointsAnnotation.scores	property
medh5.annotations.PointsAnnotation.space	property
medh5.annotations.PointsAnnotation.summary	method	()
medh5.annotations.PointsAnnotation.task	property
medh5.annotations.PointsAnnotation.timepoints	property
medh5.annotations.PointsAnnotation.to_index	method	(coords, *, grid=None)
medh5.annotations.PointsAnnotation.to_world	method	(coords, *, grid=None)
medh5.annotations.PointsAnnotation.weights	property
medh5.annotations.PointsAnnotation.world_points	method	(grid=None)
medh5.annotations.Polygon	class	(vertices, class_id, plane=(-1, 0), role='outer') bases=
medh5.annotations.Polygon.class_id	field
medh5.annotations.Polygon.plane	field
medh5.annotations.Polygon.role	field
medh5.annotations.Polygon.vertices	field
medh5.annotations.READERS	constant	dict
medh5.annotations.RESERVED_KINDS	constant	tuple
medh5.annotations.SCOPES	constant	tuple
medh5.annotations.SPACES	constant	tuple
medh5.annotations.TASKS	constant	tuple
medh5.annotations.VOXEL_KINDS	constant	tuple
medh5.annotations.VoxelAnnotation	class	(handle) bases=medh5.annotations.base.Annotation
medh5.annotations.VoxelAnnotation.ann_id	property
medh5.annotations.VoxelAnnotation.annotated_class_ids	property
medh5.annotations.VoxelAnnotation.annotated_classes	property
medh5.annotations.VoxelAnnotation.class_bboxes	method	(classes=None)
medh5.annotations.VoxelAnnotation.class_ids	property
medh5.annotations.VoxelAnnotation.class_key	method	(class_id)
medh5.annotations.VoxelAnnotation.classes	property
medh5.annotations.VoxelAnnotation.closure	property
medh5.annotations.VoxelAnnotation.contains	method	(class_key, voxel)
medh5.annotations.VoxelAnnotation.dense	method	(classes=None, roi=None)
medh5.annotations.VoxelAnnotation.grid	property
medh5.annotations.VoxelAnnotation.grid_id	property
medh5.annotations.VoxelAnnotation.group	property
medh5.annotations.VoxelAnnotation.has_ignore_region	property
medh5.annotations.VoxelAnnotation.header	property
medh5.annotations.VoxelAnnotation.ignore_id	property
medh5.annotations.VoxelAnnotation.instances	method	()
medh5.annotations.VoxelAnnotation.is_annotated	method	(class_key)
medh5.annotations.VoxelAnnotation.is_fully_covered	property
medh5.annotations.VoxelAnnotation.kind	property
medh5.annotations.VoxelAnnotation.label_set	property
medh5.annotations.VoxelAnnotation.labelmap	method	(roi=None, priority=None, *, dtype=<value>)
medh5.annotations.VoxelAnnotation.prov	property
medh5.annotations.VoxelAnnotation.quality_key	property
medh5.annotations.VoxelAnnotation.resolve_class	method	(class_key)
medh5.annotations.VoxelAnnotation.resolve_classes	method	(keys)
medh5.annotations.VoxelAnnotation.spatial_shape	property
medh5.annotations.VoxelAnnotation.summary	method	()
medh5.annotations.VoxelAnnotation.task	property
medh5.annotations.VoxelAnnotation.timepoints	property
medh5.annotations.VoxelAnnotation.voxel_counts	method	(classes=None)
medh5.annotations.base	module
medh5.annotations.base.ANNOTATION_KINDS	constant	tuple
medh5.annotations.base.Annotation	class	(handle) bases=
medh5.annotations.base.Annotation.ann_id	property
medh5.annotations.base.Annotation.annotated_class_ids	property
medh5.annotations.base.Annotation.annotated_classes	property
medh5.annotations.base.Annotation.class_ids	property
medh5.annotations.base.Annotation.class_key	method	(class_id)
medh5.annotations.base.Annotation.classes	property
medh5.annotations.base.Annotation.closure	property
medh5.annotations.base.Annotation.grid	property
medh5.annotations.base.Annotation.grid_id	property
medh5.annotations.base.Annotation.group	property
medh5.annotations.base.Annotation.has_ignore_region	property
medh5.annotations.base.Annotation.header	property
medh5.annotations.base.Annotation.ignore_id	property
medh5.annotations.base.Annotation.is_annotated	method	(class_key)
medh5.annotations.base.Annotation.is_fully_covered	property
medh5.annotations.base.Annotation.kind	property
medh5.annotations.base.Annotation.label_set	property
medh5.annotations.base.Annotation.prov	property
medh5.annotations.base.Annotation.quality_key	property
medh5.annotations.base.Annotation.resolve_class	method	(class_key)
medh5.annotations.base.Annotation.resolve_classes	method	(keys)
medh5.annotations.base.Annotation.summary	method	()
medh5.annotations.base.Annotation.task	property
medh5.annotations.base.Annotation.timepoints	property
medh5.annotations.base.AnnotationHeader	class	(kind, task, grid=None, timepoints=None, space=None, frame_uid=None, class_ids=None, annotated_class_ids=None, closure='explicit', ignore_id=65535, ignore_mask=None, prov=None, quality=None, derived_from=None, extra=None) bases=
medh5.annotations.base.AnnotationHeader.annotated_class_ids	field
medh5.annotations.base.AnnotationHeader.attrs	method	()
medh5.annotations.base.AnnotationHeader.class_ids	field
medh5.annotations.base.AnnotationHeader.closure	field
medh5.annotations.base.AnnotationHeader.derived_from	field
medh5.annotations.base.AnnotationHeader.extra	field
medh5.annotations.base.AnnotationHeader.frame_uid	field
medh5.annotations.base.AnnotationHeader.grid	field
medh5.annotations.base.AnnotationHeader.ignore_id	field
medh5.annotations.base.AnnotationHeader.ignore_mask	field
medh5.annotations.base.AnnotationHeader.kind	field
medh5.annotations.base.AnnotationHeader.prov	field
medh5.annotations.base.AnnotationHeader.quality	field
medh5.annotations.base.AnnotationHeader.read	classmethod	(group)
medh5.annotations.base.AnnotationHeader.space	field
medh5.annotations.base.AnnotationHeader.task	field
medh5.annotations.base.AnnotationHeader.timepoints	field
medh5.annotations.base.AnnotationPayload	class	(kind, datasets=None, attrs=None, stacked_axes=0, class_ids=None) bases=
medh5.annotations.base.AnnotationPayload.attrs	field
medh5.annotations.base.AnnotationPayload.class_ids	field
medh5.annotations.base.AnnotationPayload.data	property
medh5.annotations.base.AnnotationPayload.datasets	field
medh5.annotations.base.AnnotationPayload.describe	method	()
medh5.annotations.base.AnnotationPayload.kind	field
medh5.annotations.base.AnnotationPayload.nbytes	property
medh5.annotations.base.AnnotationPayload.stacked_axes	field
medh5.annotations.base.DEFAULT_TASK_FOR_KIND	constant	dict
medh5.annotations.base.GEOMETRIC_KINDS	constant	tuple
medh5.annotations.base.Instance	class	(index, instance_id, class_id, box, mask=None, score=None) bases=
medh5.annotations.base.Instance.box	field
medh5.annotations.base.Instance.class_id	field
medh5.annotations.base.Instance.index	field
medh5.annotations.base.Instance.instance_id	field
medh5.annotations.base.Instance.mask	field
medh5.annotations.base.Instance.score	field
medh5.annotations.base.Instance.slices	property
medh5.annotations.base.Instance.voxel_count	property
medh5.annotations.base.RESERVED_KINDS	constant	tuple
medh5.annotations.base.SPEC_ANNOTATION_ATTRS	constant	tuple
medh5.annotations.base.TASKS	constant	tuple
medh5.annotations.base.VOXEL_KINDS	constant	tuple
medh5.annotations.base.VoxelAnnotation	class	(handle) bases=medh5.annotations.base.Annotation
medh5.annotations.base.VoxelAnnotation.ann_id	property
medh5.annotations.base.VoxelAnnotation.annotated_class_ids	property
medh5.annotations.base.VoxelAnnotation.annotated_classes	property
medh5.annotations.base.VoxelAnnotation.class_bboxes	method	(classes=None)
medh5.annotations.base.VoxelAnnotation.class_ids	property
medh5.annotations.base.VoxelAnnotation.class_key	method	(class_id)
medh5.annotations.base.VoxelAnnotation.classes	property
medh5.annotations.base.VoxelAnnotation.closure	property
medh5.annotations.base.VoxelAnnotation.contains	method	(class_key, voxel)
medh5.annotations.base.VoxelAnnotation.dense	method	(classes=None, roi=None)
medh5.annotations.base.VoxelAnnotation.grid	property
medh5.annotations.base.VoxelAnnotation.grid_id	property
medh5.annotations.base.VoxelAnnotation.group	property
medh5.annotations.base.VoxelAnnotation.has_ignore_region	property
medh5.annotations.base.VoxelAnnotation.header	property
medh5.annotations.base.VoxelAnnotation.ignore_id	property
medh5.annotations.base.VoxelAnnotation.instances	method	()
medh5.annotations.base.VoxelAnnotation.is_annotated	method	(class_key)
medh5.annotations.base.VoxelAnnotation.is_fully_covered	property
medh5.annotations.base.VoxelAnnotation.kind	property
medh5.annotations.base.VoxelAnnotation.label_set	property
medh5.annotations.base.VoxelAnnotation.labelmap	method	(roi=None, priority=None, *, dtype=<value>)
medh5.annotations.base.VoxelAnnotation.prov	property
medh5.annotations.base.VoxelAnnotation.quality_key	property
medh5.annotations.base.VoxelAnnotation.resolve_class	method	(class_key)
medh5.annotations.base.VoxelAnnotation.resolve_classes	method	(keys)
medh5.annotations.base.VoxelAnnotation.spatial_shape	property
medh5.annotations.base.VoxelAnnotation.summary	method	()
medh5.annotations.base.VoxelAnnotation.task	property
medh5.annotations.base.VoxelAnnotation.timepoints	property
medh5.annotations.base.VoxelAnnotation.voxel_counts	method	(classes=None)
medh5.annotations.base.instance_id_dtype	function	(ids)
medh5.annotations.classification	module
medh5.annotations.classification.Assertion	class	(class_id, value, scope_id=None, scheme=None, scheme_value=None) bases=
medh5.annotations.classification.Assertion.class_id	field
medh5.annotations.classification.Assertion.is_negative	property
medh5.annotations.classification.Assertion.is_positive	property
medh5.annotations.classification.Assertion.scheme	field
medh5.annotations.classification.Assertion.scheme_value	field
medh5.annotations.classification.Assertion.scope_id	field
medh5.annotations.classification.Assertion.value	field
medh5.annotations.classification.ClassificationAnnotation	class	(handle) bases=medh5.annotations.base.Annotation
medh5.annotations.classification.ClassificationAnnotation.__len__	method	()
medh5.annotations.classification.ClassificationAnnotation.ann_id	property
medh5.annotations.classification.ClassificationAnnotation.annotated_class_ids	property
medh5.annotations.classification.ClassificationAnnotation.annotated_classes	property
medh5.annotations.classification.ClassificationAnnotation.asserted_class_ids	property
medh5.annotations.classification.ClassificationAnnotation.assertions	method	()
medh5.annotations.classification.ClassificationAnnotation.by_scope_id	method	()
medh5.annotations.classification.ClassificationAnnotation.class_ids	property
medh5.annotations.classification.ClassificationAnnotation.class_key	method	(class_id)
medh5.annotations.classification.ClassificationAnnotation.classes	property
medh5.annotations.classification.ClassificationAnnotation.closure	property
medh5.annotations.classification.ClassificationAnnotation.compared_timepoints	property
medh5.annotations.classification.ClassificationAnnotation.grid	property
medh5.annotations.classification.ClassificationAnnotation.grid_id	property
medh5.annotations.classification.ClassificationAnnotation.group	property
medh5.annotations.classification.ClassificationAnnotation.has_ignore_region	property
medh5.annotations.classification.ClassificationAnnotation.header	property
medh5.annotations.classification.ClassificationAnnotation.ignore_id	property
medh5.annotations.classification.ClassificationAnnotation.is_annotated	method	(class_key)
medh5.annotations.classification.ClassificationAnnotation.is_change_label	property
medh5.annotations.classification.ClassificationAnnotation.is_fully_covered	property
medh5.annotations.classification.ClassificationAnnotation.kind	property
medh5.annotations.classification.ClassificationAnnotation.label_set	property
medh5.annotations.classification.ClassificationAnnotation.labels	property
medh5.annotations.classification.ClassificationAnnotation.multilabel	property
medh5.annotations.classification.ClassificationAnnotation.positives	property
medh5.annotations.classification.ClassificationAnnotation.prov	property
medh5.annotations.classification.ClassificationAnnotation.quality_key	property
medh5.annotations.classification.ClassificationAnnotation.resolve_class	method	(class_key)
medh5.annotations.classification.ClassificationAnnotation.resolve_classes	method	(keys)
medh5.annotations.classification.ClassificationAnnotation.scheme	method	(name)
medh5.annotations.classification.ClassificationAnnotation.scheme_values	property
medh5.annotations.classification.ClassificationAnnotation.schemes	property
medh5.annotations.classification.ClassificationAnnotation.scope	property
medh5.annotations.classification.ClassificationAnnotation.scope_ids	property
medh5.annotations.classification.ClassificationAnnotation.state	method	(class_key, *, scope_id=None)
medh5.annotations.classification.ClassificationAnnotation.summary	method	()
medh5.annotations.classification.ClassificationAnnotation.task	property
medh5.annotations.classification.ClassificationAnnotation.timepoints	property
medh5.annotations.classification.ClassificationAnnotation.value	method	(class_key, *, scope_id=None)
medh5.annotations.classification.ClassificationAnnotation.values	property
medh5.annotations.classification.Labels	alias
medh5.annotations.classification.SCOPES	constant	tuple
medh5.annotations.classification.assertion_rows	function	(labels)
medh5.annotations.classification.check_scope	function	(scope)
medh5.annotations.classification.encode_classification	function	(labels, *, scope='sample', multilabel=True, scope_ids=None, schemes=None, scheme_values=None)
medh5.annotations.encode_boxes	function	(boxes, class_ids, *, instance_ids=None, scores=None, attributes=None, slice_index=None)
medh5.annotations.encode_classification	function	(labels, *, scope='sample', multilabel=True, scope_ids=None, schemes=None, scheme_values=None)
medh5.annotations.encode_contours	function	(polygons, *, ndim=None)
medh5.annotations.encode_keypoints	function	(points, keypoint_class_ids, class_ids, *, visibility=None, instance_ids=None, scores=None, skeleton=None)
medh5.annotations.encode_mesh	function	(vertices, faces, *, normals=None, vertex_class_ids=None, mesh_offsets=None, mesh_class_ids=None)
medh5.annotations.encode_obb	function	(centers, sizes, rotations, class_ids, *, instance_ids=None, scores=None, attributes=None)
medh5.annotations.encode_points	function	(points, *, class_ids=None, instance_ids=None, names=None, weights=None, correspondence=None)
medh5.annotations.encode_voxels	function	(masks, spatial_shape=None, *, encoding='auto', ignore=None, **kwargs)
medh5.annotations.geometric	module
medh5.annotations.geometric.BoxesAnnotation	class	(handle) bases=medh5.annotations.geometric.GeometricAnnotation
medh5.annotations.geometric.BoxesAnnotation.__iter__	method	()
medh5.annotations.geometric.BoxesAnnotation.__len__	method	()
medh5.annotations.geometric.BoxesAnnotation.ann_id	property
medh5.annotations.geometric.BoxesAnnotation.annotated_class_ids	property
medh5.annotations.geometric.BoxesAnnotation.annotated_classes	property
medh5.annotations.geometric.BoxesAnnotation.as_slices	method	(grid=None)
medh5.annotations.geometric.BoxesAnnotation.as_world	method	(grid=None)
medh5.annotations.geometric.BoxesAnnotation.attributes	property
medh5.annotations.geometric.BoxesAnnotation.boxes	property
medh5.annotations.geometric.BoxesAnnotation.class_ids	property
medh5.annotations.geometric.BoxesAnnotation.class_key	method	(class_id)
medh5.annotations.geometric.BoxesAnnotation.classes	property
medh5.annotations.geometric.BoxesAnnotation.closure	property
medh5.annotations.geometric.BoxesAnnotation.frame_uid	property
medh5.annotations.geometric.BoxesAnnotation.grid	property
medh5.annotations.geometric.BoxesAnnotation.grid_id	property
medh5.annotations.geometric.BoxesAnnotation.group	property
medh5.annotations.geometric.BoxesAnnotation.has_ignore_region	property
medh5.annotations.geometric.BoxesAnnotation.header	property
medh5.annotations.geometric.BoxesAnnotation.ignore_id	property
medh5.annotations.geometric.BoxesAnnotation.instance_ids	property
medh5.annotations.geometric.BoxesAnnotation.is_annotated	method	(class_key)
medh5.annotations.geometric.BoxesAnnotation.is_fully_covered	property
medh5.annotations.geometric.BoxesAnnotation.kind	property
medh5.annotations.geometric.BoxesAnnotation.label_set	property
medh5.annotations.geometric.BoxesAnnotation.n_spatial	property
medh5.annotations.geometric.BoxesAnnotation.ndim	property
medh5.annotations.geometric.BoxesAnnotation.object_class_ids	property
medh5.annotations.geometric.BoxesAnnotation.prov	property
medh5.annotations.geometric.BoxesAnnotation.quality_key	property
medh5.annotations.geometric.BoxesAnnotation.resolve_class	method	(class_key)
medh5.annotations.geometric.BoxesAnnotation.resolve_classes	method	(keys)
medh5.annotations.geometric.BoxesAnnotation.scores	property
medh5.annotations.geometric.BoxesAnnotation.slice_index	property
medh5.annotations.geometric.BoxesAnnotation.space	property
medh5.annotations.geometric.BoxesAnnotation.summary	method	()
medh5.annotations.geometric.BoxesAnnotation.task	property
medh5.annotations.geometric.BoxesAnnotation.timepoints	property
medh5.annotations.geometric.BoxesAnnotation.to_index	method	(coords, *, grid=None)
medh5.annotations.geometric.BoxesAnnotation.to_world	method	(coords, *, grid=None)
medh5.annotations.geometric.BoxesAnnotation.world_corners	method	(grid=None)
medh5.annotations.geometric.CONTOUR_ROLES	constant	tuple
medh5.annotations.geometric.ContoursAnnotation	class	(handle) bases=medh5.annotations.geometric.GeometricAnnotation
medh5.annotations.geometric.ContoursAnnotation.__len__	method	()
medh5.annotations.geometric.ContoursAnnotation.ann_id	property
medh5.annotations.geometric.ContoursAnnotation.annotated_class_ids	property
medh5.annotations.geometric.ContoursAnnotation.annotated_classes	property
medh5.annotations.geometric.ContoursAnnotation.attributes	property
medh5.annotations.geometric.ContoursAnnotation.by_plane	method	()
medh5.annotations.geometric.ContoursAnnotation.class_ids	property
medh5.annotations.geometric.ContoursAnnotation.class_key	method	(class_id)
medh5.annotations.geometric.ContoursAnnotation.classes	property
medh5.annotations.geometric.ContoursAnnotation.closure	property
medh5.annotations.geometric.ContoursAnnotation.frame_uid	property
medh5.annotations.geometric.ContoursAnnotation.grid	property
medh5.annotations.geometric.ContoursAnnotation.grid_id	property
medh5.annotations.geometric.ContoursAnnotation.group	property
medh5.annotations.geometric.ContoursAnnotation.has_ignore_region	property
medh5.annotations.geometric.ContoursAnnotation.header	property
medh5.annotations.geometric.ContoursAnnotation.ignore_id	property
medh5.annotations.geometric.ContoursAnnotation.instance_ids	property
medh5.annotations.geometric.ContoursAnnotation.is_annotated	method	(class_key)
medh5.annotations.geometric.ContoursAnnotation.is_fully_covered	property
medh5.annotations.geometric.ContoursAnnotation.kind	property
medh5.annotations.geometric.ContoursAnnotation.label_set	property
medh5.annotations.geometric.ContoursAnnotation.n_spatial	property
medh5.annotations.geometric.ContoursAnnotation.object_class_ids	property
medh5.annotations.geometric.ContoursAnnotation.offsets	property
medh5.annotations.geometric.ContoursAnnotation.planes	property
medh5.annotations.geometric.ContoursAnnotation.polygon	method	(index)
medh5.annotations.geometric.ContoursAnnotation.polygons	method	()
medh5.annotations.geometric.ContoursAnnotation.prov	property
medh5.annotations.geometric.ContoursAnnotation.quality_key	property
medh5.annotations.geometric.ContoursAnnotation.resolve_class	method	(class_key)
medh5.annotations.geometric.ContoursAnnotation.resolve_classes	method	(keys)
medh5.annotations.geometric.ContoursAnnotation.roles	property
medh5.annotations.geometric.ContoursAnnotation.scores	property
medh5.annotations.geometric.ContoursAnnotation.space	property
medh5.annotations.geometric.ContoursAnnotation.summary	method	()
medh5.annotations.geometric.ContoursAnnotation.task	property
medh5.annotations.geometric.ContoursAnnotation.timepoints	property
medh5.annotations.geometric.ContoursAnnotation.to_index	method	(coords, *, grid=None)
medh5.annotations.geometric.ContoursAnnotation.to_world	method	(coords, *, grid=None)
medh5.annotations.geometric.ContoursAnnotation.vertices	property
medh5.annotations.geometric.GEOMETRIC_READERS	constant	dict
medh5.annotations.geometric.GeometricAnnotation	class	(handle) bases=medh5.annotations.base.Annotation
medh5.annotations.geometric.GeometricAnnotation.__len__	method	()
medh5.annotations.geometric.GeometricAnnotation.ann_id	property
medh5.annotations.geometric.GeometricAnnotation.annotated_class_ids	property
medh5.annotations.geometric.GeometricAnnotation.annotated_classes	property
medh5.annotations.geometric.GeometricAnnotation.attributes	property
medh5.annotations.geometric.GeometricAnnotation.class_ids	property
medh5.annotations.geometric.GeometricAnnotation.class_key	method	(class_id)
medh5.annotations.geometric.GeometricAnnotation.classes	property
medh5.annotations.geometric.GeometricAnnotation.closure	property
medh5.annotations.geometric.GeometricAnnotation.frame_uid	property
medh5.annotations.geometric.GeometricAnnotation.grid	property
medh5.annotations.geometric.GeometricAnnotation.grid_id	property
medh5.annotations.geometric.GeometricAnnotation.group	property
medh5.annotations.geometric.GeometricAnnotation.has_ignore_region	property
medh5.annotations.geometric.GeometricAnnotation.header	property
medh5.annotations.geometric.GeometricAnnotation.ignore_id	property
medh5.annotations.geometric.GeometricAnnotation.instance_ids	property
medh5.annotations.geometric.GeometricAnnotation.is_annotated	method	(class_key)
medh5.annotations.geometric.GeometricAnnotation.is_fully_covered	property
medh5.annotations.geometric.GeometricAnnotation.kind	property
medh5.annotations.geometric.GeometricAnnotation.label_set	property
medh5.annotations.geometric.GeometricAnnotation.n_spatial	property
medh5.annotations.geometric.GeometricAnnotation.object_class_ids	property
medh5.annotations.geometric.GeometricAnnotation.prov	property
medh5.annotations.geometric.GeometricAnnotation.quality_key	property
medh5.annotations.geometric.GeometricAnnotation.resolve_class	method	(class_key)
medh5.annotations.geometric.GeometricAnnotation.resolve_classes	method	(keys)
medh5.annotations.geometric.GeometricAnnotation.scores	property
medh5.annotations.geometric.GeometricAnnotation.space	property
medh5.annotations.geometric.GeometricAnnotation.summary	method	()
medh5.annotations.geometric.GeometricAnnotation.task	property
medh5.annotations.geometric.GeometricAnnotation.timepoints	property
medh5.annotations.geometric.GeometricAnnotation.to_index	method	(coords, *, grid=None)
medh5.annotations.geometric.GeometricAnnotation.to_world	method	(coords, *, grid=None)
medh5.annotations.geometric.KeypointsAnnotation	class	(handle) bases=medh5.annotations.geometric.GeometricAnnotation
medh5.annotations.geometric.KeypointsAnnotation.__len__	method	()
medh5.annotations.geometric.KeypointsAnnotation.ann_id	property
medh5.annotations.geometric.KeypointsAnnotation.annotated_class_ids	property
medh5.annotations.geometric.KeypointsAnnotation.annotated_classes	property
medh5.annotations.geometric.KeypointsAnnotation.attributes	property
medh5.annotations.geometric.KeypointsAnnotation.class_ids	property
medh5.annotations.geometric.KeypointsAnnotation.class_key	method	(class_id)
medh5.annotations.geometric.KeypointsAnnotation.classes	property
medh5.annotations.geometric.KeypointsAnnotation.closure	property
medh5.annotations.geometric.KeypointsAnnotation.frame_uid	property
medh5.annotations.geometric.KeypointsAnnotation.grid	property
medh5.annotations.geometric.KeypointsAnnotation.grid_id	property
medh5.annotations.geometric.KeypointsAnnotation.group	property
medh5.annotations.geometric.KeypointsAnnotation.has_ignore_region	property
medh5.annotations.geometric.KeypointsAnnotation.header	property
medh5.annotations.geometric.KeypointsAnnotation.ignore_id	property
medh5.annotations.geometric.KeypointsAnnotation.instance_ids	property
medh5.annotations.geometric.KeypointsAnnotation.is_annotated	method	(class_key)
medh5.annotations.geometric.KeypointsAnnotation.is_fully_covered	property
medh5.annotations.geometric.KeypointsAnnotation.keypoint_class_ids	property
medh5.annotations.geometric.KeypointsAnnotation.kind	property
medh5.annotations.geometric.KeypointsAnnotation.label_set	property
medh5.annotations.geometric.KeypointsAnnotation.labelled	method	()
medh5.annotations.geometric.KeypointsAnnotation.n_spatial	property
medh5.annotations.geometric.KeypointsAnnotation.object_class_ids	property
medh5.annotations.geometric.KeypointsAnnotation.points	property
medh5.annotations.geometric.KeypointsAnnotation.prov	property
medh5.annotations.geometric.KeypointsAnnotation.quality_key	property
medh5.annotations.geometric.KeypointsAnnotation.resolve_class	method	(class_key)
medh5.annotations.geometric.KeypointsAnnotation.resolve_classes	method	(keys)
medh5.annotations.geometric.KeypointsAnnotation.scores	property
medh5.annotations.geometric.KeypointsAnnotation.skeleton	method	()
medh5.annotations.geometric.KeypointsAnnotation.skeleton_id	property
medh5.annotations.geometric.KeypointsAnnotation.space	property
medh5.annotations.geometric.KeypointsAnnotation.summary	method	()
medh5.annotations.geometric.KeypointsAnnotation.task	property
medh5.annotations.geometric.KeypointsAnnotation.timepoints	property
medh5.annotations.geometric.KeypointsAnnotation.to_index	method	(coords, *, grid=None)
medh5.annotations.geometric.KeypointsAnnotation.to_world	method	(coords, *, grid=None)
medh5.annotations.geometric.KeypointsAnnotation.visibility	property
medh5.annotations.geometric.MeshAnnotation	class	(handle) bases=medh5.annotations.geometric.GeometricAnnotation
medh5.annotations.geometric.MeshAnnotation.__len__	method	()
medh5.annotations.geometric.MeshAnnotation.ann_id	property
medh5.annotations.geometric.MeshAnnotation.annotated_class_ids	property
medh5.annotations.geometric.MeshAnnotation.annotated_classes	property
medh5.annotations.geometric.MeshAnnotation.attributes	property
medh5.annotations.geometric.MeshAnnotation.bounds	method	()
medh5.annotations.geometric.MeshAnnotation.class_ids	property
medh5.annotations.geometric.MeshAnnotation.class_key	method	(class_id)
medh5.annotations.geometric.MeshAnnotation.classes	property
medh5.annotations.geometric.MeshAnnotation.closure	property
medh5.annotations.geometric.MeshAnnotation.faces	property
medh5.annotations.geometric.MeshAnnotation.frame_uid	property
medh5.annotations.geometric.MeshAnnotation.grid	property
medh5.annotations.geometric.MeshAnnotation.grid_id	property
medh5.annotations.geometric.MeshAnnotation.group	property
medh5.annotations.geometric.MeshAnnotation.has_ignore_region	property
medh5.annotations.geometric.MeshAnnotation.header	property
medh5.annotations.geometric.MeshAnnotation.ignore_id	property
medh5.annotations.geometric.MeshAnnotation.instance_ids	property
medh5.annotations.geometric.MeshAnnotation.is_annotated	method	(class_key)
medh5.annotations.geometric.MeshAnnotation.is_fully_covered	property
medh5.annotations.geometric.MeshAnnotation.kind	property
medh5.annotations.geometric.MeshAnnotation.label_set	property
medh5.annotations.geometric.MeshAnnotation.n_spatial	property
medh5.annotations.geometric.MeshAnnotation.n_submeshes	property
medh5.annotations.geometric.MeshAnnotation.normals	property
medh5.annotations.geometric.MeshAnnotation.object_class_ids	property
medh5.annotations.geometric.MeshAnnotation.prov	property
medh5.annotations.geometric.MeshAnnotation.quality_key	property
medh5.annotations.geometric.MeshAnnotation.resolve_class	method	(class_key)
medh5.annotations.geometric.MeshAnnotation.resolve_classes	method	(keys)
medh5.annotations.geometric.MeshAnnotation.scores	property
medh5.annotations.geometric.MeshAnnotation.space	property
medh5.annotations.geometric.MeshAnnotation.summary	method	()
medh5.annotations.geometric.MeshAnnotation.task	property
medh5.annotations.geometric.MeshAnnotation.timepoints	property
medh5.annotations.geometric.MeshAnnotation.to_index	method	(coords, *, grid=None)
medh5.annotations.geometric.MeshAnnotation.to_world	method	(coords, *, grid=None)
medh5.annotations.geometric.MeshAnnotation.vertex_class_ids	property
medh5.annotations.geometric.MeshAnnotation.vertices	property
medh5.annotations.geometric.ObbAnnotation	class	(handle) bases=medh5.annotations.geometric.GeometricAnnotation
medh5.annotations.geometric.ObbAnnotation.__len__	method	()
medh5.annotations.geometric.ObbAnnotation.ann_id	property
medh5.annotations.geometric.ObbAnnotation.annotated_class_ids	property
medh5.annotations.geometric.ObbAnnotation.annotated_classes	property
medh5.annotations.geometric.ObbAnnotation.as_aabb	method	()
medh5.annotations.geometric.ObbAnnotation.attributes	property
medh5.annotations.geometric.ObbAnnotation.centers	property
medh5.annotations.geometric.ObbAnnotation.class_ids	property
medh5.annotations.geometric.ObbAnnotation.class_key	method	(class_id)
medh5.annotations.geometric.ObbAnnotation.classes	property
medh5.annotations.geometric.ObbAnnotation.closure	property
medh5.annotations.geometric.ObbAnnotation.corners	method	()
medh5.annotations.geometric.ObbAnnotation.frame_uid	property
medh5.annotations.geometric.ObbAnnotation.grid	property
medh5.annotations.geometric.ObbAnnotation.grid_id	property
medh5.annotations.geometric.ObbAnnotation.group	property
medh5.annotations.geometric.ObbAnnotation.has_ignore_region	property
medh5.annotations.geometric.ObbAnnotation.header	property
medh5.annotations.geometric.ObbAnnotation.ignore_id	property
medh5.annotations.geometric.ObbAnnotation.instance_ids	property
medh5.annotations.geometric.ObbAnnotation.is_annotated	method	(class_key)
medh5.annotations.geometric.ObbAnnotation.is_fully_covered	property
medh5.annotations.geometric.ObbAnnotation.kind	property
medh5.annotations.geometric.ObbAnnotation.label_set	property
medh5.annotations.geometric.ObbAnnotation.n_spatial	property
medh5.annotations.geometric.ObbAnnotation.object_class_ids	property
medh5.annotations.geometric.ObbAnnotation.prov	property
medh5.annotations.geometric.ObbAnnotation.quality_key	property
medh5.annotations.geometric.ObbAnnotation.resolve_class	method	(class_key)
medh5.annotations.geometric.ObbAnnotation.resolve_classes	method	(keys)
medh5.annotations.geometric.ObbAnnotation.rotations	property
medh5.annotations.geometric.ObbAnnotation.scores	property
medh5.annotations.geometric.ObbAnnotation.sizes	property
medh5.annotations.geometric.ObbAnnotation.space	property
medh5.annotations.geometric.ObbAnnotation.summary	method	()
medh5.annotations.geometric.ObbAnnotation.task	property
medh5.annotations.geometric.ObbAnnotation.timepoints	property
medh5.annotations.geometric.ObbAnnotation.to_index	method	(coords, *, grid=None)
medh5.annotations.geometric.ObbAnnotation.to_world	method	(coords, *, grid=None)
medh5.annotations.geometric.ObbAnnotation.volumes	property
medh5.annotations.geometric.PointsAnnotation	class	(handle) bases=medh5.annotations.geometric.GeometricAnnotation
medh5.annotations.geometric.PointsAnnotation.__len__	method	()
medh5.annotations.geometric.PointsAnnotation.ann_id	property
medh5.annotations.geometric.PointsAnnotation.annotated_class_ids	property
medh5.annotations.geometric.PointsAnnotation.annotated_classes	property
medh5.annotations.geometric.PointsAnnotation.attributes	property
medh5.annotations.geometric.PointsAnnotation.class_ids	property
medh5.annotations.geometric.PointsAnnotation.class_key	method	(class_id)
medh5.annotations.geometric.PointsAnnotation.classes	property
medh5.annotations.geometric.PointsAnnotation.closure	property
medh5.annotations.geometric.PointsAnnotation.correspondence	property
medh5.annotations.geometric.PointsAnnotation.frame_uid	property
medh5.annotations.geometric.PointsAnnotation.grid	property
medh5.annotations.geometric.PointsAnnotation.grid_id	property
medh5.annotations.geometric.PointsAnnotation.group	property
medh5.annotations.geometric.PointsAnnotation.has_ignore_region	property
medh5.annotations.geometric.PointsAnnotation.header	property
medh5.annotations.geometric.PointsAnnotation.ignore_id	property
medh5.annotations.geometric.PointsAnnotation.instance_ids	property
medh5.annotations.geometric.PointsAnnotation.is_annotated	method	(class_key)
medh5.annotations.geometric.PointsAnnotation.is_fully_covered	property
medh5.annotations.geometric.PointsAnnotation.kind	property
medh5.annotations.geometric.PointsAnnotation.label_set	property
medh5.annotations.geometric.PointsAnnotation.n_spatial	property
medh5.annotations.geometric.PointsAnnotation.named	method	()
medh5.annotations.geometric.PointsAnnotation.names	property
medh5.annotations.geometric.PointsAnnotation.object_class_ids	property
medh5.annotations.geometric.PointsAnnotation.points	property
medh5.annotations.geometric.PointsAnnotation.prov	property
medh5.annotations.geometric.PointsAnnotation.quality_key	property
medh5.annotations.geometric.PointsAnnotation.resolve_class	method	(class_key)
medh5.annotations.geometric.PointsAnnotation.resolve_classes	method	(keys)
medh5.annotations.geometric.PointsAnnotation.scores	property
medh5.annotations.geometric.PointsAnnotation.space	property
medh5.annotations.geometric.PointsAnnotation.summary	method	()
medh5.annotations.geometric.PointsAnnotation.task	property
medh5.annotations.geometric.PointsAnnotation.timepoints	property
medh5.annotations.geometric.PointsAnnotation.to_index	method	(coords, *, grid=None)
medh5.annotations.geometric.PointsAnnotation.to_world	method	(coords, *, grid=None)
medh5.annotations.geometric.PointsAnnotation.weights	property
medh5.annotations.geometric.PointsAnnotation.world_points	method	(grid=None)
medh5.annotations.geometric.Polygon	class	(vertices, class_id, plane=(-1, 0), role='outer') bases=
medh5.annotations.geometric.Polygon.class_id	field
medh5.annotations.geometric.Polygon.plane	field
medh5.annotations.geometric.Polygon.role	field
medh5.annotations.geometric.Polygon.vertices	field
medh5.annotations.geometric.ROTATION_TOL	constant	float
medh5.annotations.geometric.SPACES	constant	tuple
medh5.annotations.geometric.VISIBILITY	constant	dict
medh5.annotations.geometric.check_slice_index	function	(planes, n_boxes, *, boxes=None, shape=None)
medh5.annotations.geometric.check_space	function	(space)
medh5.annotations.geometric.encode_boxes	function	(boxes, class_ids, *, instance_ids=None, scores=None, attributes=None, slice_index=None)
medh5.annotations.geometric.encode_contours	function	(polygons, *, ndim=None)
medh5.annotations.geometric.encode_keypoints	function	(points, keypoint_class_ids, class_ids, *, visibility=None, instance_ids=None, scores=None, skeleton=None)
medh5.annotations.geometric.encode_mesh	function	(vertices, faces, *, normals=None, vertex_class_ids=None, mesh_offsets=None, mesh_class_ids=None)
medh5.annotations.geometric.encode_obb	function	(centers, sizes, rotations, class_ids, *, instance_ids=None, scores=None, attributes=None)
medh5.annotations.geometric.encode_points	function	(points, *, class_ids=None, instance_ids=None, names=None, weights=None, correspondence=None)
medh5.annotations.open_annotation	function	(handle)
medh5.annotations.select_encoding	function	(masks=None, spatial_shape=None, *, stats=None, soft=False, prefer=None, ignore=False)
medh5.annotations.transcode	function	(annotation, to_kind, *, drop_identity=False)
medh5.annotations.voxel	module
medh5.annotations.voxel.AnnotationPayload	class	(kind, datasets=None, attrs=None, stacked_axes=0, class_ids=None) bases=
medh5.annotations.voxel.AnnotationPayload.attrs	field
medh5.annotations.voxel.AnnotationPayload.class_ids	field
medh5.annotations.voxel.AnnotationPayload.data	property
medh5.annotations.voxel.AnnotationPayload.datasets	field
medh5.annotations.voxel.AnnotationPayload.describe	method	()
medh5.annotations.voxel.AnnotationPayload.kind	field
medh5.annotations.voxel.AnnotationPayload.nbytes	property
medh5.annotations.voxel.AnnotationPayload.stacked_axes	field
medh5.annotations.voxel.BITS_PER_PLANE	constant	int
medh5.annotations.voxel.BitmaskAnnotation	class	(handle) bases=medh5.annotations.base.VoxelAnnotation
medh5.annotations.voxel.BitmaskAnnotation.ann_id	property
medh5.annotations.voxel.BitmaskAnnotation.annotated_class_ids	property
medh5.annotations.voxel.BitmaskAnnotation.annotated_classes	property
medh5.annotations.voxel.BitmaskAnnotation.bit_class_ids	property
medh5.annotations.voxel.BitmaskAnnotation.class_bboxes	method	(classes=None)
medh5.annotations.voxel.BitmaskAnnotation.class_ids	property
medh5.annotations.voxel.BitmaskAnnotation.class_key	method	(class_id)
medh5.annotations.voxel.BitmaskAnnotation.classes	property
medh5.annotations.voxel.BitmaskAnnotation.classes_at	method	(voxel)
medh5.annotations.voxel.BitmaskAnnotation.closure	property
medh5.annotations.voxel.BitmaskAnnotation.contains	method	(class_key, voxel)
medh5.annotations.voxel.BitmaskAnnotation.data	property
medh5.annotations.voxel.BitmaskAnnotation.dense	method	(classes=None, roi=None)
medh5.annotations.voxel.BitmaskAnnotation.grid	property
medh5.annotations.voxel.BitmaskAnnotation.grid_id	property
medh5.annotations.voxel.BitmaskAnnotation.group	property
medh5.annotations.voxel.BitmaskAnnotation.has_ignore_region	property
medh5.annotations.voxel.BitmaskAnnotation.header	property
medh5.annotations.voxel.BitmaskAnnotation.ignore_id	property
medh5.annotations.voxel.BitmaskAnnotation.instances	method	()
medh5.annotations.voxel.BitmaskAnnotation.is_annotated	method	(class_key)
medh5.annotations.voxel.BitmaskAnnotation.is_fully_covered	property
medh5.annotations.voxel.BitmaskAnnotation.kind	property
medh5.annotations.voxel.BitmaskAnnotation.label_set	property
medh5.annotations.voxel.BitmaskAnnotation.labelmap	method	(roi=None, priority=None, *, dtype=<value>)
medh5.annotations.voxel.BitmaskAnnotation.n_planes	property
medh5.annotations.voxel.BitmaskAnnotation.position_of	property
medh5.annotations.voxel.BitmaskAnnotation.prov	property
medh5.annotations.voxel.BitmaskAnnotation.quality_key	property
medh5.annotations.voxel.BitmaskAnnotation.resolve_class	method	(class_key)
medh5.annotations.voxel.BitmaskAnnotation.resolve_classes	method	(keys)
medh5.annotations.voxel.BitmaskAnnotation.spatial_shape	property
medh5.annotations.voxel.BitmaskAnnotation.summary	method	()
medh5.annotations.voxel.BitmaskAnnotation.task	property
medh5.annotations.voxel.BitmaskAnnotation.timepoints	property
medh5.annotations.voxel.BitmaskAnnotation.voxel_counts	method	(classes=None)
medh5.annotations.voxel.CostModel	class	(?) bases=
medh5.annotations.voxel.CostModel.best	method	()
medh5.annotations.voxel.CostModel.bitmask	field
medh5.annotations.voxel.CostModel.detail	field
medh5.annotations.voxel.CostModel.instances	field
medh5.annotations.voxel.CostModel.labelmap	field
medh5.annotations.voxel.CostModel.layers	field
medh5.annotations.voxel.CostModel.probmap	field
medh5.annotations.voxel.CostModel.to_json	method	()
medh5.annotations.voxel.DEFAULT_THRESHOLD	constant	float
medh5.annotations.voxel.IN_BAND_IGNORE_KINDS	constant	tuple
medh5.annotations.voxel.Instance	class	(index, instance_id, class_id, box, mask=None, score=None) bases=
medh5.annotations.voxel.Instance.box	field
medh5.annotations.voxel.Instance.class_id	field
medh5.annotations.voxel.Instance.index	field
medh5.annotations.voxel.Instance.instance_id	field
medh5.annotations.voxel.Instance.mask	field
medh5.annotations.voxel.Instance.score	field
medh5.annotations.voxel.Instance.slices	property
medh5.annotations.voxel.Instance.voxel_count	property
medh5.annotations.voxel.InstanceInput	class	(class_id, instance_id, mask=None, box=None, crop=None, score=None) bases=
medh5.annotations.voxel.InstanceInput.box	field
medh5.annotations.voxel.InstanceInput.class_id	field
medh5.annotations.voxel.InstanceInput.crop	field
medh5.annotations.voxel.InstanceInput.instance_id	field
medh5.annotations.voxel.InstanceInput.mask	field
medh5.annotations.voxel.InstanceInput.score	field
medh5.annotations.voxel.InstancesAnnotation	class	(handle) bases=medh5.annotations.base.VoxelAnnotation
medh5.annotations.voxel.InstancesAnnotation.ann_id	property
medh5.annotations.voxel.InstancesAnnotation.annotated_class_ids	property
medh5.annotations.voxel.InstancesAnnotation.annotated_classes	property
medh5.annotations.voxel.InstancesAnnotation.boxes	property
medh5.annotations.voxel.InstancesAnnotation.class_bboxes	method	(classes=None)
medh5.annotations.voxel.InstancesAnnotation.class_ids	property
medh5.annotations.voxel.InstancesAnnotation.class_key	method	(class_id)
medh5.annotations.voxel.InstancesAnnotation.classes	property
medh5.annotations.voxel.InstancesAnnotation.closure	property
medh5.annotations.voxel.InstancesAnnotation.contains	method	(class_key, voxel)
medh5.annotations.voxel.InstancesAnnotation.crop	method	(index)
medh5.annotations.voxel.InstancesAnnotation.dense	method	(classes=None, roi=None)
medh5.annotations.voxel.InstancesAnnotation.grid	property
medh5.annotations.voxel.InstancesAnnotation.grid_id	property
medh5.annotations.voxel.InstancesAnnotation.group	property
medh5.annotations.voxel.InstancesAnnotation.has_ignore_region	property
medh5.annotations.voxel.InstancesAnnotation.has_masks	property
medh5.annotations.voxel.InstancesAnnotation.header	property
medh5.annotations.voxel.InstancesAnnotation.ignore_id	property
medh5.annotations.voxel.InstancesAnnotation.instance	method	(instance_id)
medh5.annotations.voxel.InstancesAnnotation.instance_ids	property
medh5.annotations.voxel.InstancesAnnotation.instances	method	()
medh5.annotations.voxel.InstancesAnnotation.is_annotated	method	(class_key)
medh5.annotations.voxel.InstancesAnnotation.is_fully_covered	property
medh5.annotations.voxel.InstancesAnnotation.kind	property
medh5.annotations.voxel.InstancesAnnotation.label_set	property
medh5.annotations.voxel.InstancesAnnotation.labelmap	method	(roi=None, priority=None, *, dtype=<value>)
medh5.annotations.voxel.InstancesAnnotation.n_objects	property
medh5.annotations.voxel.InstancesAnnotation.object_class_ids	property
medh5.annotations.voxel.InstancesAnnotation.prov	property
medh5.annotations.voxel.InstancesAnnotation.quality_key	property
medh5.annotations.voxel.InstancesAnnotation.resolve_class	method	(class_key)
medh5.annotations.voxel.InstancesAnnotation.resolve_classes	method	(keys)
medh5.annotations.voxel.InstancesAnnotation.scores	property
medh5.annotations.voxel.InstancesAnnotation.spatial_shape	property
medh5.annotations.voxel.InstancesAnnotation.summary	method	()
medh5.annotations.voxel.InstancesAnnotation.task	property
medh5.annotations.voxel.InstancesAnnotation.timepoints	property
medh5.annotations.voxel.InstancesAnnotation.tracking	method	()
medh5.annotations.voxel.InstancesAnnotation.voxel_counts	method	(classes=None)
medh5.annotations.voxel.LOCALIZED_BBOX_FRACTION	constant	float
medh5.annotations.voxel.LabelmapAnnotation	class	(handle) bases=medh5.annotations.base.VoxelAnnotation
medh5.annotations.voxel.LabelmapAnnotation.ann_id	property
medh5.annotations.voxel.LabelmapAnnotation.annotated_class_ids	property
medh5.annotations.voxel.LabelmapAnnotation.annotated_classes	property
medh5.annotations.voxel.LabelmapAnnotation.class_bboxes	method	(classes=None)
medh5.annotations.voxel.LabelmapAnnotation.class_ids	property
medh5.annotations.voxel.LabelmapAnnotation.class_key	method	(class_id)
medh5.annotations.voxel.LabelmapAnnotation.classes	property
medh5.annotations.voxel.LabelmapAnnotation.closure	property
medh5.annotations.voxel.LabelmapAnnotation.contains	method	(class_key, voxel)
medh5.annotations.voxel.LabelmapAnnotation.data	property
medh5.annotations.voxel.LabelmapAnnotation.dense	method	(classes=None, roi=None)
medh5.annotations.voxel.LabelmapAnnotation.grid	property
medh5.annotations.voxel.LabelmapAnnotation.grid_id	property
medh5.annotations.voxel.LabelmapAnnotation.group	property
medh5.annotations.voxel.LabelmapAnnotation.has_ignore_region	property
medh5.annotations.voxel.LabelmapAnnotation.header	property
medh5.annotations.voxel.LabelmapAnnotation.ignore_id	property
medh5.annotations.voxel.LabelmapAnnotation.ignore_mask	method	(roi=None)
medh5.annotations.voxel.LabelmapAnnotation.instances	method	()
medh5.annotations.voxel.LabelmapAnnotation.is_annotated	method	(class_key)
medh5.annotations.voxel.LabelmapAnnotation.is_fully_covered	property
medh5.annotations.voxel.LabelmapAnnotation.kind	property
medh5.annotations.voxel.LabelmapAnnotation.label_set	property
medh5.annotations.voxel.LabelmapAnnotation.labelmap	method	(roi=None, priority=None, *, dtype=<value>)
medh5.annotations.voxel.LabelmapAnnotation.prov	property
medh5.annotations.voxel.LabelmapAnnotation.quality_key	property
medh5.annotations.voxel.LabelmapAnnotation.resolve_class	method	(class_key)
medh5.annotations.voxel.LabelmapAnnotation.resolve_classes	method	(keys)
medh5.annotations.voxel.LabelmapAnnotation.spatial_shape	property
medh5.annotations.voxel.LabelmapAnnotation.summary	method	()
medh5.annotations.voxel.LabelmapAnnotation.task	property
medh5.annotations.voxel.LabelmapAnnotation.timepoints	property
medh5.annotations.voxel.LabelmapAnnotation.voxel_counts	method	(classes=None)
medh5.annotations.voxel.LayersAnnotation	class	(handle) bases=medh5.annotations.base.VoxelAnnotation
medh5.annotations.voxel.LayersAnnotation.ann_id	property
medh5.annotations.voxel.LayersAnnotation.annotated_class_ids	property
medh5.annotations.voxel.LayersAnnotation.annotated_classes	property
medh5.annotations.voxel.LayersAnnotation.class_bboxes	method	(classes=None)
medh5.annotations.voxel.LayersAnnotation.class_ids	property
medh5.annotations.voxel.LayersAnnotation.class_key	method	(class_id)
medh5.annotations.voxel.LayersAnnotation.classes	property
medh5.annotations.voxel.LayersAnnotation.closure	property
medh5.annotations.voxel.LayersAnnotation.contains	method	(class_key, voxel)
medh5.annotations.voxel.LayersAnnotation.data	property
medh5.annotations.voxel.LayersAnnotation.dense	method	(classes=None, roi=None)
medh5.annotations.voxel.LayersAnnotation.grid	property
medh5.annotations.voxel.LayersAnnotation.grid_id	property
medh5.annotations.voxel.LayersAnnotation.group	property
medh5.annotations.voxel.LayersAnnotation.has_ignore_region	property
medh5.annotations.voxel.LayersAnnotation.header	property
medh5.annotations.voxel.LayersAnnotation.ignore_id	property
medh5.annotations.voxel.LayersAnnotation.ignore_mask	method	(roi=None)
medh5.annotations.voxel.LayersAnnotation.instances	method	()
medh5.annotations.voxel.LayersAnnotation.is_annotated	method	(class_key)
medh5.annotations.voxel.LayersAnnotation.is_fully_covered	property
medh5.annotations.voxel.LayersAnnotation.kind	property
medh5.annotations.voxel.LayersAnnotation.label_set	property
medh5.annotations.voxel.LayersAnnotation.labelmap	method	(roi=None, priority=None, *, dtype=<value>)
medh5.annotations.voxel.LayersAnnotation.layer_class_ids	property
medh5.annotations.voxel.LayersAnnotation.layer_classes	method	()
medh5.annotations.voxel.LayersAnnotation.layer_of	property
medh5.annotations.voxel.LayersAnnotation.n_layers	property
medh5.annotations.voxel.LayersAnnotation.prov	property
medh5.annotations.voxel.LayersAnnotation.quality_key	property
medh5.annotations.voxel.LayersAnnotation.read_layer	method	(layer, roi=None)
medh5.annotations.voxel.LayersAnnotation.resolve_class	method	(class_key)
medh5.annotations.voxel.LayersAnnotation.resolve_classes	method	(keys)
medh5.annotations.voxel.LayersAnnotation.spatial_shape	property
medh5.annotations.voxel.LayersAnnotation.summary	method	()
medh5.annotations.voxel.LayersAnnotation.task	property
medh5.annotations.voxel.LayersAnnotation.timepoints	property
medh5.annotations.voxel.LayersAnnotation.voxel_counts	method	(classes=None)
medh5.annotations.voxel.MaskAnnotation	class	(handle) bases=medh5.annotations.base.VoxelAnnotation
medh5.annotations.voxel.MaskAnnotation.ann_id	property
medh5.annotations.voxel.MaskAnnotation.annotated_class_ids	property
medh5.annotations.voxel.MaskAnnotation.annotated_classes	property
medh5.annotations.voxel.MaskAnnotation.class_bboxes	method	(classes=None)
medh5.annotations.voxel.MaskAnnotation.class_ids	property
medh5.annotations.voxel.MaskAnnotation.class_key	method	(class_id)
medh5.annotations.voxel.MaskAnnotation.classes	property
medh5.annotations.voxel.MaskAnnotation.closure	property
medh5.annotations.voxel.MaskAnnotation.contains	method	(class_key, voxel)
medh5.annotations.voxel.MaskAnnotation.data	property
medh5.annotations.voxel.MaskAnnotation.dense	method	(classes=None, roi=None)
medh5.annotations.voxel.MaskAnnotation.grid	property
medh5.annotations.voxel.MaskAnnotation.grid_id	property
medh5.annotations.voxel.MaskAnnotation.group	property
medh5.annotations.voxel.MaskAnnotation.has_ignore_region	property
medh5.annotations.voxel.MaskAnnotation.header	property
medh5.annotations.voxel.MaskAnnotation.ignore_id	property
medh5.annotations.voxel.MaskAnnotation.instances	method	()
medh5.annotations.voxel.MaskAnnotation.is_annotated	method	(class_key)
medh5.annotations.voxel.MaskAnnotation.is_fully_covered	property
medh5.annotations.voxel.MaskAnnotation.kind	property
medh5.annotations.voxel.MaskAnnotation.label_set	property
medh5.annotations.voxel.MaskAnnotation.labelmap	method	(roi=None, priority=None, *, dtype=<value>)
medh5.annotations.voxel.MaskAnnotation.prov	property
medh5.annotations.voxel.MaskAnnotation.quality_key	property
medh5.annotations.voxel.MaskAnnotation.read	method	(roi=None)
medh5.annotations.voxel.MaskAnnotation.resolve_class	method	(class_key)
medh5.annotations.voxel.MaskAnnotation.resolve_classes	method	(keys)
medh5.annotations.voxel.MaskAnnotation.spatial_shape	property
medh5.annotations.voxel.MaskAnnotation.summary	method	()
medh5.annotations.voxel.MaskAnnotation.task	property
medh5.annotations.voxel.MaskAnnotation.timepoints	property
medh5.annotations.voxel.MaskAnnotation.voxel_counts	method	(classes=None)
medh5.annotations.voxel.Masks	alias
medh5.annotations.voxel.OverlapStats	class	(?) bases=
medh5.annotations.voxel.OverlapStats.class_ids	field
medh5.annotations.voxel.OverlapStats.colouring	field
medh5.annotations.voxel.OverlapStats.counts	field
medh5.annotations.voxel.OverlapStats.depth	property
medh5.annotations.voxel.OverlapStats.edges	field
medh5.annotations.voxel.OverlapStats.fill	property
medh5.annotations.voxel.OverlapStats.is_edgeless	property
medh5.annotations.voxel.OverlapStats.localized	field
medh5.annotations.voxel.OverlapStats.mean_degree	property
medh5.annotations.voxel.OverlapStats.n_classes	property
medh5.annotations.voxel.OverlapStats.n_labelled_voxels	field
medh5.annotations.voxel.OverlapStats.n_layers	property
medh5.annotations.voxel.OverlapStats.n_planes	property
medh5.annotations.voxel.OverlapStats.n_voxels	property
medh5.annotations.voxel.OverlapStats.spatial_shape	field
medh5.annotations.voxel.OverlapStats.summary	method	()
medh5.annotations.voxel.OverlapStats.total_foreground	property
medh5.annotations.voxel.ProbmapAnnotation	class	(handle) bases=medh5.annotations.base.VoxelAnnotation
medh5.annotations.voxel.ProbmapAnnotation.ann_id	property
medh5.annotations.voxel.ProbmapAnnotation.annotated_class_ids	property
medh5.annotations.voxel.ProbmapAnnotation.annotated_classes	property
medh5.annotations.voxel.ProbmapAnnotation.class_bboxes	method	(classes=None)
medh5.annotations.voxel.ProbmapAnnotation.class_ids	property
medh5.annotations.voxel.ProbmapAnnotation.class_key	method	(class_id)
medh5.annotations.voxel.ProbmapAnnotation.classes	property
medh5.annotations.voxel.ProbmapAnnotation.closure	property
medh5.annotations.voxel.ProbmapAnnotation.contains	method	(class_key, voxel)
medh5.annotations.voxel.ProbmapAnnotation.data	property
medh5.annotations.voxel.ProbmapAnnotation.dense	method	(classes=None, roi=None)
medh5.annotations.voxel.ProbmapAnnotation.grid	property
medh5.annotations.voxel.ProbmapAnnotation.grid_id	property
medh5.annotations.voxel.ProbmapAnnotation.group	property
medh5.annotations.voxel.ProbmapAnnotation.has_ignore_region	property
medh5.annotations.voxel.ProbmapAnnotation.header	property
medh5.annotations.voxel.ProbmapAnnotation.ignore_id	property
medh5.annotations.voxel.ProbmapAnnotation.instances	method	()
medh5.annotations.voxel.ProbmapAnnotation.is_annotated	method	(class_key)
medh5.annotations.voxel.ProbmapAnnotation.is_fully_covered	property
medh5.annotations.voxel.ProbmapAnnotation.kind	property
medh5.annotations.voxel.ProbmapAnnotation.label_set	property
medh5.annotations.voxel.ProbmapAnnotation.labelmap	method	(roi=None, priority=None, *, dtype=<value>)
medh5.annotations.voxel.ProbmapAnnotation.normalized	property
medh5.annotations.voxel.ProbmapAnnotation.probabilities	method	(classes=None, roi=None)
medh5.annotations.voxel.ProbmapAnnotation.prov	property
medh5.annotations.voxel.ProbmapAnnotation.quality_key	property
medh5.annotations.voxel.ProbmapAnnotation.resolve_class	method	(class_key)
medh5.annotations.voxel.ProbmapAnnotation.resolve_classes	method	(keys)
medh5.annotations.voxel.ProbmapAnnotation.spatial_shape	property
medh5.annotations.voxel.ProbmapAnnotation.summary	method	()
medh5.annotations.voxel.ProbmapAnnotation.task	property
medh5.annotations.voxel.ProbmapAnnotation.threshold	property
medh5.annotations.voxel.ProbmapAnnotation.timepoints	property
medh5.annotations.voxel.ProbmapAnnotation.voxel_counts	method	(classes=None)
medh5.annotations.voxel.READERS	constant	dict
medh5.annotations.voxel.SLAB_BYTES	constant	int
medh5.annotations.voxel.SPARSE_FILL	constant	float
medh5.annotations.voxel.STORAGE_DTYPES	constant	tuple
medh5.annotations.voxel.TRANSCODABLE	constant	tuple
medh5.annotations.voxel.analyse	function	(masks, spatial_shape=None)
medh5.annotations.voxel.annotation_to_masks	function	(annotation, classes=None)
medh5.annotations.voxel.check_roundtrip	function	(payload, to_kind, *, spatial_shape=None)
medh5.annotations.voxel.checked_class_id	function	(class_id)
medh5.annotations.voxel.contains_at	function	(values, threshold)
medh5.annotations.voxel.cost_model	function	(stats, *, ignore=False)
medh5.annotations.voxel.encode_bitmask	function	(masks, spatial_shape=None)
medh5.annotations.voxel.encode_instances	function	(objects, spatial_shape=None, *, store_masks=True, class_ids=None)
medh5.annotations.voxel.encode_labelmap	function	(masks, spatial_shape=None, *, ignore=None, ignore_id=<value>)
medh5.annotations.voxel.encode_layers	function	(masks, spatial_shape=None, *, colouring=None, ignore=None, ignore_id=<value>)
medh5.annotations.voxel.encode_mask	function	(mask)
medh5.annotations.voxel.encode_masks	function	(masks, kind, spatial_shape=None, **kwargs)
medh5.annotations.voxel.encode_probmap	function	(probabilities, spatial_shape=None, *, dtype=<value>, normalized=False, threshold=None)
medh5.annotations.voxel.encode_voxels	function	(masks, spatial_shape=None, *, encoding='auto', ignore=None, **kwargs)
medh5.annotations.voxel.greedy_colour	function	(class_ids, edges)
medh5.annotations.voxel.instances_from_masks	function	(masks, *, start_id=1)
medh5.annotations.voxel.label_dtype_size	function	(class_ids, *, ignore=False)
medh5.annotations.voxel.layers_from_colouring	function	(colouring)
medh5.annotations.voxel.masks_equal	function	(a, b)
medh5.annotations.voxel.normalize_masks	function	(masks, spatial_shape=None)
medh5.annotations.voxel.payload_to_masks	function	(payload, *, spatial_shape=None, threshold=None)
medh5.annotations.voxel.select_encoding	function	(masks=None, spatial_shape=None, *, stats=None, soft=False, prefer=None, ignore=False)
medh5.annotations.voxel.storage_dtype	function	(planes, threshold, requested=<value>)
medh5.annotations.voxel.transcode	function	(annotation, to_kind, *, drop_identity=False)
medh5.annotations.voxel.transcode_payload	function	(payload, to_kind, *, spatial_shape=None, threshold=None, drop_identity=False, **kwargs)
medh5.audit_splits	function	(paths)
medh5.bench	module
medh5.bench.MANY_CLASSES	constant	int
medh5.bench.Measurement	class	(name, value, unit='ms', target=None, description='', detail=None) bases=
medh5.bench.Measurement.description	field
medh5.bench.Measurement.detail	field
medh5.bench.Measurement.from_json	classmethod	(doc)
medh5.bench.Measurement.name	field
medh5.bench.Measurement.ok	property
medh5.bench.Measurement.target	field
medh5.bench.Measurement.to_json	method	()
medh5.bench.Measurement.unit	field
medh5.bench.Measurement.value	field
medh5.bench.TARGETS	constant	dict
medh5.bench.benchmark_file	function	(path, *, annotation=None, patch=64, repeats=20)
medh5.bench.many_class_measurement	function	(path, *, patch=64, repeats=20)
medh5.bench.report	function	(measurements)
medh5.bench.synthetic_many_class_sample	function	(directory, *, classes=63)
medh5.bench.synthetic_pair	function	(directory, *, shape=(64, 96, 96), codec='training', seed=20260815)
medh5.bench.synthetic_sample	function	(directory, *, shape=(192, 256, 256), classes=8, codec='training', index=True, seed=20260815, name='bench.medh5')
medh5.bench.throughput	function	(paths, *, patch=96, batches=32, batch_size=2, workers=0, annotation=None)
medh5.bench.timed	function	(fn, *, repeats=20, warmup=3)
medh5.cache	module
medh5.cache.CacheEntry	class	(entry_id, sources, digest, event_id=None, document_id=None, row_id=None, cutoff_us=None, event_versions=None, row_fingerprint=None) bases=
medh5.cache.CacheEntry.cutoff_us	field
medh5.cache.CacheEntry.digest	field
medh5.cache.CacheEntry.document_id	field
medh5.cache.CacheEntry.entry_id	field
medh5.cache.CacheEntry.event_id	field
medh5.cache.CacheEntry.event_versions	field
medh5.cache.CacheEntry.from_json	classmethod	(doc)
medh5.cache.CacheEntry.row_fingerprint	field
medh5.cache.CacheEntry.row_id	field
medh5.cache.CacheEntry.sources	field
medh5.cache.CacheReport	class	(path, entries, findings, manifest_digest=None, level=None) bases=
medh5.cache.CacheReport.corrupt	property
medh5.cache.CacheReport.entries	field
medh5.cache.CacheReport.findings	field
medh5.cache.CacheReport.from_json	classmethod	(doc)
medh5.cache.CacheReport.level	field
medh5.cache.CacheReport.manifest_digest	field
medh5.cache.CacheReport.ok	property
medh5.cache.CacheReport.path	field
medh5.cache.CacheReport.stale	property
medh5.cache.CacheReport.to_json	method	()
medh5.cache.CacheWriter	class	(path, *, level, encoder, output, preprocessing=None, task=None, selection=None, fitted_on=None) bases=
medh5.cache.CacheWriter.__enter__	method	()
medh5.cache.CacheWriter.__exit__	method	(exc_type, exc, tb)
medh5.cache.CacheWriter.abort	method	()
medh5.cache.CacheWriter.add	method	(entry_id, values, *, sources, event_id=None, document_id=None, row_id=None, cutoff_us=None, event_versions=None, row_fingerprint=None)
medh5.cache.CacheWriter.add_event	method	(source, event_id, values, *, document_id=None)
medh5.cache.CacheWriter.add_row	method	(row, values, *, entry_id=None, sources=None)
medh5.cache.CacheWriter.commit	method	()
medh5.cache.CacheWriter.digest	property
medh5.cache.CacheWriter.path	property
medh5.cache.FeatureCache	class	(handle) bases=
medh5.cache.FeatureCache.__enter__	method	()
medh5.cache.FeatureCache.__exit__	method	(*exc)
medh5.cache.FeatureCache.__len__	method	()
medh5.cache.FeatureCache.abandon	method	()
medh5.cache.FeatureCache.close	method	()
medh5.cache.FeatureCache.entries	property
medh5.cache.FeatureCache.event_entry	method	(content_id, event_id)
medh5.cache.FeatureCache.event_feature	method	(content_id, event_id)
medh5.cache.FeatureCache.get	method	(entry_id)
medh5.cache.FeatureCache.header	property
medh5.cache.FeatureCache.level	property
medh5.cache.FeatureCache.manifest_digest	property
medh5.cache.FeatureCache.open	classmethod	(path)
medh5.cache.FeatureCache.path	property
medh5.cache.FeatureCache.row_feature	method	(row_id)
medh5.cache.HashingTextEncoder	class	(dim=64) bases=
medh5.cache.HashingTextEncoder.NAME	attribute	str
medh5.cache.HashingTextEncoder.REVISION	attribute	str
medh5.cache.HashingTextEncoder.dim	property
medh5.cache.HashingTextEncoder.encode	method	(text)
medh5.cache.HashingTextEncoder.header	method	()
medh5.cache.LEVELS	constant	tuple
medh5.cache.SCHEMA	constant	str
medh5.cache.SUFFIX	constant	str
medh5.cache.build_document_cache	function	(task, path, encoder, *, base=None, confine=None)
medh5.cache.event_entry_id	function	(content_id, event_id)
medh5.cache.fitted_on	function	(task, partition=None)
medh5.cache.fitted_on_mismatches	function	(task, fitted)
medh5.cache.open_cache	function	(path)
medh5.cache.schema_text	function	()
medh5.cache.validate_cache	function	(path, *, base=None, task=None, task_base=None, check_rows=True, confine=None)
medh5.cli	module
medh5.cli.EXIT_ERROR	constant	int
medh5.cli.EXIT_OK	constant	int
medh5.cli.EXIT_USAGE	constant	int
medh5.cli.command_tree	function	()
medh5.cli.main	function	(argv=None)
medh5.clinical	module
medh5.clinical.ASSESSMENT_SYSTEM	constant	str
medh5.clinical.Bounds	alias
medh5.clinical.CLOCK_REFERENCES	constant	tuple
medh5.clinical.COMPARATORS	constant	tuple
medh5.clinical.Clinical	class	(handle) bases=
medh5.clinical.Clinical.clock	property
medh5.clinical.Clinical.descriptor	property
medh5.clinical.Clinical.document	method	(document_id)
medh5.clinical.Clinical.documents	property
medh5.clinical.Clinical.event	method	(event_id)
medh5.clinical.Clinical.events	property
medh5.clinical.Clinical.links	property
medh5.clinical.Clinical.projection	property
medh5.clinical.Clinical.records	method	()
medh5.clinical.Clinical.select	method	(cutoff_us, policy=None)
medh5.clinical.Clinical.summary	method	()
medh5.clinical.Clinical.text	method	(document_id)
medh5.clinical.ClinicalRecords	class	(clock, events=(), documents=(), links=()) bases=
medh5.clinical.ClinicalRecords.clock	field
medh5.clinical.ClinicalRecords.documents	field
medh5.clinical.ClinicalRecords.events	field
medh5.clinical.ClinicalRecords.from_json	classmethod	(doc)
medh5.clinical.ClinicalRecords.links	field
medh5.clinical.ClinicalRecords.to_json	method	()
medh5.clinical.Clock	class	(id, reference='relative', origin_description=None, unit='us') bases=
medh5.clinical.Clock.from_json	classmethod	(doc)
medh5.clinical.Clock.id	field
medh5.clinical.Clock.origin_description	field
medh5.clinical.Clock.reference	field
medh5.clinical.Clock.relative	classmethod	(clock_id, origin_description)
medh5.clinical.Clock.shifted_utc	classmethod	(clock_id)
medh5.clinical.Clock.to_json	method	()
medh5.clinical.Clock.unit	field
medh5.clinical.Clock.utc	classmethod	(clock_id)
medh5.clinical.DAY	constant	int
medh5.clinical.Document	class	(document_id, text, media_type='text/plain', language=None, source_type=None) bases=
medh5.clinical.Document.document_id	field
medh5.clinical.Document.from_json	classmethod	(doc)
medh5.clinical.Document.language	field
medh5.clinical.Document.media_type	field
medh5.clinical.Document.source_type	field
medh5.clinical.Document.text	field
medh5.clinical.Document.to_json	method	()
medh5.clinical.DocumentInfo	class	(document_id, media_type, language, source_type, n_bytes) bases=
medh5.clinical.DocumentInfo.document_id	field
medh5.clinical.DocumentInfo.language	field
medh5.clinical.DocumentInfo.media_type	field
medh5.clinical.DocumentInfo.n_bytes	field
medh5.clinical.DocumentInfo.source_type	field
medh5.clinical.ENDPOINT_TYPES	constant	tuple
medh5.clinical.EVENT_KINDS	constant	tuple
medh5.clinical.Event	class	(event_id, record_id, kind, temporal_type, status, effective_start_us=None, effective_end_us=None, available_us=None, timepoint_id=None, encounter_id=None, code_system=None, code=None, code_version=None, value_num=None, value_comparator=None, unit=None, value_text=None, missing_reason=None, prov=None) bases=
medh5.clinical.Event.available_us	field
medh5.clinical.Event.code	field
medh5.clinical.Event.code_system	field
medh5.clinical.Event.code_version	field
medh5.clinical.Event.effective_end_us	field
medh5.clinical.Event.effective_start_us	field
medh5.clinical.Event.encounter_id	field
medh5.clinical.Event.event_id	field
medh5.clinical.Event.from_json	classmethod	(doc)
medh5.clinical.Event.is_lesion_assessment	property
medh5.clinical.Event.kind	field
medh5.clinical.Event.missing_reason	field
medh5.clinical.Event.prov	field
medh5.clinical.Event.record_id	field
medh5.clinical.Event.status	field
medh5.clinical.Event.temporal_type	field
medh5.clinical.Event.timepoint_id	field
medh5.clinical.Event.to_json	method	()
medh5.clinical.Event.unit	field
medh5.clinical.Event.value_comparator	field
medh5.clinical.Event.value_num	field
medh5.clinical.Event.value_text	field
medh5.clinical.HOUR	constant	int
medh5.clinical.LESION_PRESENCE	constant	str
medh5.clinical.LESION_VALUES	constant	tuple
medh5.clinical.Link	class	(source_type, source_id, relation, target_type, target_id, source_span=None, target_annotation_id=None, asserted_by_event_id=None) bases=
medh5.clinical.Link.asserted_by_event_id	field
medh5.clinical.Link.between	classmethod	(source, relation, target, *, asserted_by=None, span=None, target_annotation_id=None)
medh5.clinical.Link.from_json	classmethod	(doc)
medh5.clinical.Link.relation	field
medh5.clinical.Link.source_id	field
medh5.clinical.Link.source_span	field
medh5.clinical.Link.source_type	field
medh5.clinical.Link.target_annotation_id	field
medh5.clinical.Link.target_id	field
medh5.clinical.Link.target_type	field
medh5.clinical.Link.to_json	method	()
medh5.clinical.MICROSECOND	constant	int
medh5.clinical.MINUTE	constant	int
medh5.clinical.PROFILE	constant	str
medh5.clinical.RELATIONS	constant	tuple
medh5.clinical.SCHEMA	constant	str
medh5.clinical.SECOND	constant	int
medh5.clinical.SELECTION_POLICIES	constant	tuple
medh5.clinical.STATUSES	constant	tuple
medh5.clinical.SelectedEvent	class	(event_id, record_id, kind, order_us, tie_group, plan) bases=
medh5.clinical.SelectedEvent.event_id	field
medh5.clinical.SelectedEvent.kind	field
medh5.clinical.SelectedEvent.order_us	field
medh5.clinical.SelectedEvent.plan	field
medh5.clinical.SelectedEvent.record_id	field
medh5.clinical.SelectedEvent.tie_group	field
medh5.clinical.Selection	class	(cutoff_us, policy, status, events, links, payloads, uncertain_records, excluded=<factory>) bases=
medh5.clinical.Selection.admits	method	(kind, object_id, fragment=0)
medh5.clinical.Selection.admits_any	method	(kind, object_id)
medh5.clinical.Selection.certified	property
medh5.clinical.Selection.cutoff_us	field
medh5.clinical.Selection.event_ids	property
medh5.clinical.Selection.events	field
medh5.clinical.Selection.excluded	field
medh5.clinical.Selection.from_json	classmethod	(doc)
medh5.clinical.Selection.links	field
medh5.clinical.Selection.payloads	field
medh5.clinical.Selection.policy	field
medh5.clinical.Selection.status	field
medh5.clinical.Selection.uncertain_records	field
medh5.clinical.SelectionPolicy	class	(selection='strict_prospective', order_by='effective', context_us=None, context_boundary='closed', uncertainty='contained', kinds=None, plans=False, static=True, max_events=None, keep='latest', ties='keep_group') bases=
medh5.clinical.SelectionPolicy.context_boundary	field
medh5.clinical.SelectionPolicy.context_us	field
medh5.clinical.SelectionPolicy.from_json	classmethod	(doc)
medh5.clinical.SelectionPolicy.keep	field
medh5.clinical.SelectionPolicy.kinds	field
medh5.clinical.SelectionPolicy.max_events	field
medh5.clinical.SelectionPolicy.order_by	field
medh5.clinical.SelectionPolicy.plans	field
medh5.clinical.SelectionPolicy.selection	field
medh5.clinical.SelectionPolicy.static	field
medh5.clinical.SelectionPolicy.ties	field
medh5.clinical.SelectionPolicy.to_json	method	()
medh5.clinical.SelectionPolicy.uncertainty	field
medh5.clinical.TEMPORAL_TYPES	constant	tuple
medh5.clinical.augment	function	(path, records, *, out=None)
medh5.clinical.baseline_day_clock	function	(clock_id)
medh5.clinical.clock_day	function	(t_us)
medh5.clinical.day_bounds	function	(day, tz=None)
medh5.clinical.days	function	(value)
medh5.clinical.hours	function	(value)
medh5.clinical.imaging_events_from_timepoints	function	(path)
medh5.clinical.records_from	function	(clock, events=(), documents=(), links=())
medh5.clinical.schema_text	function	()
medh5.clinical.select	function	(events, links, cutoff_us, policy=None)
medh5.clinical.strip	function	(path, out)
medh5.clinical.utc_us	function	(moment)
medh5.collection	module
medh5.collection.Collection	class	(handle) bases=
medh5.collection.Collection.__contains__	method	(key)
medh5.collection.Collection.__enter__	method	()
medh5.collection.Collection.__exit__	method	(*exc)
medh5.collection.Collection.__getitem__	method	(key)
medh5.collection.Collection.__iter__	method	()
medh5.collection.Collection.__len__	method	()
medh5.collection.Collection.close	method	()
medh5.collection.Collection.group	property
medh5.collection.Collection.kind	property
medh5.collection.Collection.path	property
medh5.collection.Collection.root	property
medh5.collection.Collection.subject_ids	method	()
medh5.collection.Collection.summary	method	()
medh5.collection.Collection.version	property
medh5.collection.SAMPLES_GROUP	constant	str
medh5.collection.SUFFIX	constant	str
medh5.collection.default_key	function	(path)
medh5.collection.extract	function	(path, key, out)
medh5.collection.is_collection	function	(root)
medh5.collection.open_any	function	(path, *, key=None)
medh5.collection.open_collection	function	(path)
medh5.collection.pack	function	(sources, out, *, keys=None)
medh5.collection.unpack	function	(path, outdir, *, keys=None, suffix='.medh5')
medh5.compare_annotations	function	(a, b, *, metric=None, threshold=None, classes=None, map_classes='id', match_by='auto')
medh5.conformance	module
medh5.conformance.CASES	constant	tuple
medh5.conformance.CHECKSUMS	constant	str
medh5.conformance.Case	class	(name, description, clause, level='semantic', errors=(), warnings=(), suffix='.medh5', mutated=False, format_version='1.0') bases=
medh5.conformance.Case.build	method	(path)
medh5.conformance.Case.clause	field
medh5.conformance.Case.description	field
medh5.conformance.Case.errors	field
medh5.conformance.Case.format_version	field
medh5.conformance.Case.from_record	classmethod	(record)
medh5.conformance.Case.level	field
medh5.conformance.Case.mutated	field
medh5.conformance.Case.name	field
medh5.conformance.Case.suffix	field
medh5.conformance.Case.to_json	method	()
medh5.conformance.Case.valid	property
medh5.conformance.Case.warnings	field
medh5.conformance.CaseResult	class	(case, path, got_errors=(), got_warnings=(), missing=(), unexpected=(), error=None, details=<factory>) bases=
medh5.conformance.CaseResult.case	field
medh5.conformance.CaseResult.details	field
medh5.conformance.CaseResult.error	field
medh5.conformance.CaseResult.from_json	classmethod	(doc)
medh5.conformance.CaseResult.got_errors	field
medh5.conformance.CaseResult.got_warnings	field
medh5.conformance.CaseResult.missing	field
medh5.conformance.CaseResult.ok	property
medh5.conformance.CaseResult.path	field
medh5.conformance.CaseResult.to_json	method	()
medh5.conformance.CaseResult.unexpected	field
medh5.conformance.SCHEMA	constant	str
medh5.conformance.SEED	constant	int
medh5.conformance.build_corpus	function	(outdir, *, names=None)
medh5.conformance.case_by_name	function	(name)
medh5.conformance.check_checksums	function	(root)
medh5.conformance.load_manifest	function	(root)
medh5.conformance.publish	function	(outdir, *, names=None)
medh5.conformance.run_corpus	function	(outdir, *, names=None)
medh5.conformance.score	function	(root, submitted, *, format_version=None, codes_revision=None)
medh5.conformance.score_companion	function	(root, submitted)
medh5.conformance.summarize	function	(results)
medh5.create	function	(path, *, sample_id=None, subject_id=None, codec='balanced', profiles=None)
medh5.curation	module
medh5.curation.ACTIVITY_FIELDS	constant	frozenset
medh5.curation.ACTIVITY_TYPES	constant	tuple
medh5.curation.AGENT_FIELDS	constant	frozenset
medh5.curation.AGENT_TYPES	constant	tuple
medh5.curation.Activity	class	(id, type, agent=None, started=None, ended=None, tool=None, inputs=(), outputs=(), params={}) bases=
medh5.curation.Activity.agent	field
medh5.curation.Activity.ended	field
medh5.curation.Activity.from_json	classmethod	(doc)
medh5.curation.Activity.id	field
medh5.curation.Activity.inputs	field
medh5.curation.Activity.outputs	field
medh5.curation.Activity.params	field
medh5.curation.Activity.started	field
medh5.curation.Activity.to_json	method	()
medh5.curation.Activity.tool	field
medh5.curation.Activity.type	field
medh5.curation.Agent	class	(id, type, name, role=None, version=None, qualification=None, organization=None) bases=
medh5.curation.Agent.from_json	classmethod	(doc)
medh5.curation.Agent.id	field
medh5.curation.Agent.name	field
medh5.curation.Agent.organization	field
medh5.curation.Agent.qualification	field
medh5.curation.Agent.role	field
medh5.curation.Agent.to_json	method	()
medh5.curation.Agent.type	field
medh5.curation.Agent.version	field
medh5.curation.Agreement	class	(metric, value, against=None, per_class={}) bases=
medh5.curation.Agreement.against	field
medh5.curation.Agreement.from_json	classmethod	(doc)
medh5.curation.Agreement.metric	field
medh5.curation.Agreement.per_class	field
medh5.curation.Agreement.to_json	method	()
medh5.curation.Agreement.value	field
medh5.curation.Cohort	class	(dataset_id=None, site_id=None, scanner_id=None, group_id=None, acquisition_protocol=None, extra={}) bases=
medh5.curation.Cohort.acquisition_protocol	field
medh5.curation.Cohort.dataset_id	field
medh5.curation.Cohort.extra	field
medh5.curation.Cohort.from_json	classmethod	(doc)
medh5.curation.Cohort.group_id	field
medh5.curation.Cohort.grouping_key	method	(subject_id)
medh5.curation.Cohort.scanner_id	field
medh5.curation.Cohort.site_id	field
medh5.curation.Cohort.to_json	method	()
medh5.curation.DATE_PATTERN	constant	<external>
medh5.curation.Deidentification	class	(method, profile=None, date_shift_days=None, id_mapping=None, performed_by=None, date=None, burned_in_annotation_checked=None, extra={}) bases=
medh5.curation.Deidentification.burned_in_annotation_checked	field
medh5.curation.Deidentification.date	field
medh5.curation.Deidentification.date_shift_days	field
medh5.curation.Deidentification.extra	field
medh5.curation.Deidentification.from_json	classmethod	(doc)
medh5.curation.Deidentification.id_mapping	field
medh5.curation.Deidentification.method	field
medh5.curation.Deidentification.performed_by	field
medh5.curation.Deidentification.profile	field
medh5.curation.Deidentification.to_json	method	()
medh5.curation.ID_SOURCE	constant	str
medh5.curation.ISSUE_SEVERITY	constant	tuple
medh5.curation.Identity	class	(sample_id, subject_id, sex=None, laterality=None, bodypart=None, extra={}) bases=
medh5.curation.Identity.bodypart	field
medh5.curation.Identity.extra	field
medh5.curation.Identity.from_json	classmethod	(doc)
medh5.curation.Identity.laterality	field
medh5.curation.Identity.sample_id	field
medh5.curation.Identity.sex	field
medh5.curation.Identity.subject_id	field
medh5.curation.Identity.to_json	method	()
medh5.curation.InstanceAgreement	class	(matched=(), only_in_a=(), only_in_b=(), matched_by='instance_id', threshold=0.5, against=None, class_mismatches=(), skipped=(), b_class_ids=<factory>) bases=
medh5.curation.InstanceAgreement.against	field
medh5.curation.InstanceAgreement.b_class_ids	field
medh5.curation.InstanceAgreement.class_mismatches	field
medh5.curation.InstanceAgreement.matched	field
medh5.curation.InstanceAgreement.matched_by	field
medh5.curation.InstanceAgreement.mean_iou	property
medh5.curation.InstanceAgreement.only_in_a	field
medh5.curation.InstanceAgreement.only_in_b	field
medh5.curation.InstanceAgreement.skipped	field
medh5.curation.InstanceAgreement.threshold	field
medh5.curation.InstanceAgreement.to_json	method	()
medh5.curation.InstanceAgreement.to_record	method	(*, against=None)
medh5.curation.InstanceAgreement.value	property
medh5.curation.Issue	class	(code, severity='info', class_ids=(), note=None) bases=
medh5.curation.Issue.class_ids	field
medh5.curation.Issue.code	field
medh5.curation.Issue.from_json	classmethod	(doc)
medh5.curation.Issue.note	field
medh5.curation.Issue.severity	field
medh5.curation.Issue.to_json	method	()
medh5.curation.LATERALITY_VALUES	constant	tuple
medh5.curation.Observation	class	(?) bases=
medh5.curation.Observation.annotation	field
medh5.curation.Observation.box	field
medh5.curation.Observation.centroid	property
medh5.curation.Observation.class_id	field
medh5.curation.Observation.extent	property
medh5.curation.Observation.grid	field
medh5.curation.Observation.index	field
medh5.curation.Observation.instance_id	field
medh5.curation.Observation.kind	property
medh5.curation.Observation.score	field
medh5.curation.Observation.timepoint	field
medh5.curation.Observation.to_json	method	()
medh5.curation.Observation.units	field
medh5.curation.Observation.volume	field
medh5.curation.Observation.volume_mm	property
medh5.curation.Observation.voxel_count	field
medh5.curation.PARTITIONS	constant	tuple
medh5.curation.PRESENT	constant	str
medh5.curation.PSEUDONYM_SOURCE	constant	str
medh5.curation.Provenance	class	(agents=None, activities=None) bases=
medh5.curation.Provenance.__iter__	method	()
medh5.curation.Provenance.__len__	method	()
medh5.curation.Provenance.activities	property
medh5.curation.Provenance.activities_by_type	method	(activity_type)
medh5.curation.Provenance.activity	method	(activity_id)
medh5.curation.Provenance.add_activity	method	(activity, *, replace=False)
medh5.curation.Provenance.add_agent	method	(agent, *, replace=False)
medh5.curation.Provenance.agent	method	(agent_id)
medh5.curation.Provenance.agents	property
medh5.curation.Provenance.dangling_agent_refs	method	()
medh5.curation.Provenance.from_json	classmethod	(doc)
medh5.curation.Provenance.has_activity	method	(activity_id)
medh5.curation.Provenance.has_agent	method	(agent_id)
medh5.curation.Provenance.produced_by	method	(object_path)
medh5.curation.Provenance.to_json	method	()
medh5.curation.QUALITY_FIELDS	constant	frozenset
medh5.curation.QUALITY_STATUS	constant	tuple
medh5.curation.QualityRecord	class	(status, confidence=None, reviewed_by=(), agreement=(), issues=(), edit_effort_s=None) bases=
medh5.curation.QualityRecord.agreement	field
medh5.curation.QualityRecord.confidence	field
medh5.curation.QualityRecord.edit_effort_s	field
medh5.curation.QualityRecord.from_json	classmethod	(doc)
medh5.curation.QualityRecord.is_usable	property
medh5.curation.QualityRecord.issues	field
medh5.curation.QualityRecord.reviewed_by	field
medh5.curation.QualityRecord.status	field
medh5.curation.QualityRecord.to_json	method	()
medh5.curation.REASONS	constant	tuple
medh5.curation.RESOLVED	constant	str
medh5.curation.RFC3339	constant	<external>
medh5.curation.SEX_VALUES	constant	tuple
medh5.curation.STATES	constant	tuple
medh5.curation.SplitAudit	class	(memberships=(), conflicts=(), leaks=(), unclaimed=(), unreadable=()) bases=
medh5.curation.SplitAudit.conflicts	field
medh5.curation.SplitAudit.counts	method	()
medh5.curation.SplitAudit.from_fields	classmethod	(fields)
medh5.curation.SplitAudit.leaks	field
medh5.curation.SplitAudit.memberships	field
medh5.curation.SplitAudit.ok	property
medh5.curation.SplitAudit.partitions	method	(set_id)
medh5.curation.SplitAudit.set_ids	property
medh5.curation.SplitAudit.to_json	method	()
medh5.curation.SplitAudit.unclaimed	field
medh5.curation.SplitAudit.unreadable	field
medh5.curation.SplitClaim	class	(set_id, partition, fold=None, assigned_by=None, assigned_at=None, manifest_sha256=None) bases=
medh5.curation.SplitClaim.assigned_at	field
medh5.curation.SplitClaim.assigned_by	field
medh5.curation.SplitClaim.fold	field
medh5.curation.SplitClaim.from_json	classmethod	(doc)
medh5.curation.SplitClaim.manifest_sha256	field
medh5.curation.SplitClaim.partition	field
medh5.curation.SplitClaim.set_id	field
medh5.curation.SplitClaim.to_json	method	()
medh5.curation.TIMEPOINT_FIELDS	constant	frozenset
medh5.curation.Timeline	class	(timepoints) bases=
medh5.curation.Timeline.__contains__	method	(key, /)
medh5.curation.Timeline.__getitem__	method	(key, /)
medh5.curation.Timeline.__iter__	method	()
medh5.curation.Timeline.__len__	method	()
medh5.curation.Timeline.baseline	property
medh5.curation.Timeline.check	method	()
medh5.curation.Timeline.count	method	(value)
medh5.curation.Timeline.from_json	classmethod	(docs)
medh5.curation.Timeline.ids	property
medh5.curation.Timeline.index	method	(value, start=0, stop=None)
medh5.curation.Timeline.interval_days	method	(a, b)
medh5.curation.Timeline.is_longitudinal	property
medh5.curation.Timeline.require	method	(timepoint_id, *, where='')
medh5.curation.Timeline.single	classmethod	(timepoint_id='tp0', **kwargs)
medh5.curation.Timeline.to_json	method	()
medh5.curation.Timepoint	class	(id, index, label=None, date=None, days_from_baseline=None, study_uid=None, series_uids={}, subject_age_years=None, description=None) bases=
medh5.curation.Timepoint.date	field
medh5.curation.Timepoint.days_from_baseline	field
medh5.curation.Timepoint.description	field
medh5.curation.Timepoint.from_json	classmethod	(doc)
medh5.curation.Timepoint.id	field
medh5.curation.Timepoint.index	field
medh5.curation.Timepoint.label	field
medh5.curation.Timepoint.series_uids	field
medh5.curation.Timepoint.study_uid	field
medh5.curation.Timepoint.subject_age_years	field
medh5.curation.Timepoint.to_json	method	()
medh5.curation.Track	class	(?) bases=
medh5.curation.Track.__iter__	method	()
medh5.curation.Track.__len__	method	()
medh5.curation.Track.at	method	(timepoint)
medh5.curation.Track.class_id	property
medh5.curation.Track.class_ids	field
medh5.curation.Track.class_key	field
medh5.curation.Track.has_class_conflict	property
medh5.curation.Track.instance_id	field
medh5.curation.Track.measurements_at	method	(timepoint)
medh5.curation.Track.observations	field
medh5.curation.Track.observations_at	method	(timepoint)
medh5.curation.Track.relative_change	method	(first, second)
medh5.curation.Track.timepoints	property
medh5.curation.Track.to_json	method	()
medh5.curation.Track.volume	method	(timepoint)
medh5.curation.Track.volumes	property
medh5.curation.Tracking	class	(?) bases=
medh5.curation.Tracking.__contains__	method	(key, /)
medh5.curation.Tracking.__getitem__	method	(key, /)
medh5.curation.Tracking.__iter__	method	()
medh5.curation.Tracking.__len__	method	()
medh5.curation.Tracking.class_conflicts	method	()
medh5.curation.Tracking.coverage	property
medh5.curation.Tracking.get	method	(instance_id, default=None)
medh5.curation.Tracking.is_new	method	(instance_id, *, located=False)
medh5.curation.Tracking.is_persistent	method	(instance_id)
medh5.curation.Tracking.is_resolved	method	(instance_id, *, located=False)
medh5.curation.Tracking.items	method	()
medh5.curation.Tracking.keys	method	()
medh5.curation.Tracking.reason_at	method	(instance_id, timepoint)
medh5.curation.Tracking.reasons	method	(instance_id)
medh5.curation.Tracking.skipped	property
medh5.curation.Tracking.state_at	method	(instance_id, timepoint)
medh5.curation.Tracking.states	method	(instance_id)
medh5.curation.Tracking.summary	method	()
medh5.curation.Tracking.timepoints	property
medh5.curation.Tracking.to_json	method	()
medh5.curation.Tracking.unexamined	method	()
medh5.curation.Tracking.values	method	()
medh5.curation.UNEXAMINED	constant	str
medh5.curation.VoxelAgreement	class	(metric, per_class, skipped=(), against=None, class_ids=<factory>, b_class_ids=<factory>) bases=
medh5.curation.VoxelAgreement.against	field
medh5.curation.VoxelAgreement.b_class_ids	field
medh5.curation.VoxelAgreement.class_ids	field
medh5.curation.VoxelAgreement.metric	field
medh5.curation.VoxelAgreement.per_class	field
medh5.curation.VoxelAgreement.skipped	field
medh5.curation.VoxelAgreement.to_json	method	()
medh5.curation.VoxelAgreement.to_record	method	(*, against=None)
medh5.curation.VoxelAgreement.value	property
medh5.curation.agreement	module
medh5.curation.agreement.ClassMap	alias
medh5.curation.agreement.DEFAULT_IOU	constant	float
medh5.curation.agreement.InstanceAgreement	class	(matched=(), only_in_a=(), only_in_b=(), matched_by='instance_id', threshold=0.5, against=None, class_mismatches=(), skipped=(), b_class_ids=<factory>) bases=
medh5.curation.agreement.InstanceAgreement.against	field
medh5.curation.agreement.InstanceAgreement.b_class_ids	field
medh5.curation.agreement.InstanceAgreement.class_mismatches	field
medh5.curation.agreement.InstanceAgreement.matched	field
medh5.curation.agreement.InstanceAgreement.matched_by	field
medh5.curation.agreement.InstanceAgreement.mean_iou	property
medh5.curation.agreement.InstanceAgreement.only_in_a	field
medh5.curation.agreement.InstanceAgreement.only_in_b	field
medh5.curation.agreement.InstanceAgreement.skipped	field
medh5.curation.agreement.InstanceAgreement.threshold	field
medh5.curation.agreement.InstanceAgreement.to_json	method	()
medh5.curation.agreement.InstanceAgreement.to_record	method	(*, against=None)
medh5.curation.agreement.InstanceAgreement.value	property
medh5.curation.agreement.MatchBy	alias
medh5.curation.agreement.OBJECT_KINDS	constant	tuple
medh5.curation.agreement.VoxelAgreement	class	(metric, per_class, skipped=(), against=None, class_ids=<factory>, b_class_ids=<factory>) bases=
medh5.curation.agreement.VoxelAgreement.against	field
medh5.curation.agreement.VoxelAgreement.b_class_ids	field
medh5.curation.agreement.VoxelAgreement.class_ids	field
medh5.curation.agreement.VoxelAgreement.metric	field
medh5.curation.agreement.VoxelAgreement.per_class	field
medh5.curation.agreement.VoxelAgreement.skipped	field
medh5.curation.agreement.VoxelAgreement.to_json	method	()
medh5.curation.agreement.VoxelAgreement.to_record	method	(*, against=None)
medh5.curation.agreement.VoxelAgreement.value	property
medh5.curation.agreement.box_iou	function	(a, b)
medh5.curation.agreement.compare	function	(a, b, *, metric=None, threshold=None, classes=None, map_classes='id', match_by='auto')
medh5.curation.agreement.compare_instances	function	(a, b, *, threshold=0.5, classes=None, map_classes='id', match_by='auto')
medh5.curation.agreement.compare_voxel	function	(a, b, *, metric='dice', classes=None, map_classes='id')
medh5.curation.agreement.dice	function	(a, b)
medh5.curation.agreement.iou	function	(a, b)
medh5.curation.audit_splits	function	(paths)
medh5.curation.build_tracks	function	(sample, class_key=None, *, measure=True)
medh5.curation.carries_instance_ids	function	(annotation)
medh5.curation.check_timestamp	function	(value, *, where)
medh5.curation.compare	function	(a, b, *, metric=None, threshold=None, classes=None, map_classes='id', match_by='auto')
medh5.curation.compare_instances	function	(a, b, *, threshold=0.5, classes=None, map_classes='id', match_by='auto')
medh5.curation.compare_voxel	function	(a, b, *, metric='dice', classes=None, map_classes='id')
medh5.curation.dice_agreement	function	(per_class, against=None)
medh5.curation.quality_from_json	function	(doc)
medh5.curation.quality_to_json	function	(records)
medh5.curation.scrub	module
medh5.curation.scrub.DATE_KEYS	constant	frozenset
medh5.curation.scrub.Finding	class	(rule, where, detail, value=None, actionable=False, fixable=True) bases=
medh5.curation.scrub.Finding.actionable	field
medh5.curation.scrub.Finding.detail	field
medh5.curation.scrub.Finding.fixable	field
medh5.curation.scrub.Finding.rule	field
medh5.curation.scrub.Finding.to_json	method	()
medh5.curation.scrub.Finding.value	field
medh5.curation.scrub.Finding.where	field
medh5.curation.scrub.IDENTIFYING_KEYS	constant	frozenset
medh5.curation.scrub.IDENTITY_RULES	constant	tuple
medh5.curation.scrub.MAX_DEPTH	constant	int
medh5.curation.scrub.PROFILES	constant	tuple
medh5.curation.scrub.PSEUDONYM_PREFIX	constant	str
medh5.curation.scrub.QUASI_IDENTIFYING_KEYS	constant	frozenset
medh5.curation.scrub.STRICT_RULES	constant	tuple
medh5.curation.scrub.ScrubReport	class	(path, profile='basic', findings=<factory>, actions=<factory>, applied=False, remaining=<factory>, uid_map=<factory>, not_checked=('pixel data (burned-in text, identifiable anatomy)', 'free text whose meaning this tool cannot judge')) bases=
medh5.curation.scrub.ScrubReport.actionable	property
medh5.curation.scrub.ScrubReport.actions	field
medh5.curation.scrub.ScrubReport.add	method	(rule, where, detail, value=None, *, actionable=False, fixable=True)
medh5.curation.scrub.ScrubReport.applied	field
medh5.curation.scrub.ScrubReport.clean	property
medh5.curation.scrub.ScrubReport.findings	field
medh5.curation.scrub.ScrubReport.format	method	()
medh5.curation.scrub.ScrubReport.needs_review	property
medh5.curation.scrub.ScrubReport.not_checked	field
medh5.curation.scrub.ScrubReport.ok	property
medh5.curation.scrub.ScrubReport.open_identity	property
medh5.curation.scrub.ScrubReport.path	field
medh5.curation.scrub.ScrubReport.profile	field
medh5.curation.scrub.ScrubReport.remaining	field
medh5.curation.scrub.ScrubReport.remaining_actionable	property
medh5.curation.scrub.ScrubReport.to_json	method	()
medh5.curation.scrub.ScrubReport.uid_map	field
medh5.curation.scrub.UID_KEYS	constant	frozenset
medh5.curation.scrub.UNFIXABLE_LOCATIONS	constant	tuple
medh5.curation.scrub.apply	function	(path, *, profile='basic', salt='', date_shift_days=None, performed_by=None, pseudonymise_ids=False, date_shift_range=None, withhold_shift=None, out=None, attest_text=None)
medh5.curation.scrub.pseudonymise	function	(uid, salt='')
medh5.curation.scrub.scan	function	(path, *, profile='basic')
medh5.curation.scrub.scan_document	function	(document, report)
medh5.curation.scrub.scrub_paths	function	(paths, *, apply_changes=False, profile='basic', salt='', date_shift_days=None, performed_by=None, pseudonymise_ids=False, date_shift_range=None, withhold_shift=None, out_dir=None, attest_text=None)
medh5.curation.splits	module
medh5.curation.splits.Conflict	class	(set_id, manifests, paths_by_manifest=<factory>) bases=
medh5.curation.splits.Conflict.manifests	field
medh5.curation.splits.Conflict.paths_by_manifest	field
medh5.curation.splits.Conflict.set_id	field
medh5.curation.splits.Conflict.to_json	method	()
medh5.curation.splits.Leak	class	(set_id, group_id, partitions, paths, groups=(), subjects=()) bases=
medh5.curation.splits.Leak.group_id	field
medh5.curation.splits.Leak.groups	field
medh5.curation.splits.Leak.partitions	field
medh5.curation.splits.Leak.paths	field
medh5.curation.splits.Leak.set_id	field
medh5.curation.splits.Leak.subjects	field
medh5.curation.splits.Leak.to_json	method	()
medh5.curation.splits.Membership	class	(path, sample_id, subject_id, group_id, claim) bases=
medh5.curation.splits.Membership.claim	field
medh5.curation.splits.Membership.group_id	field
medh5.curation.splits.Membership.partition	property
medh5.curation.splits.Membership.path	field
medh5.curation.splits.Membership.sample_id	field
medh5.curation.splits.Membership.set_id	property
medh5.curation.splits.Membership.subject_id	field
medh5.curation.splits.Membership.to_json	method	()
medh5.curation.splits.SplitAudit	class	(memberships=(), conflicts=(), leaks=(), unclaimed=(), unreadable=()) bases=
medh5.curation.splits.SplitAudit.conflicts	field
medh5.curation.splits.SplitAudit.counts	method	()
medh5.curation.splits.SplitAudit.from_fields	classmethod	(fields)
medh5.curation.splits.SplitAudit.leaks	field
medh5.curation.splits.SplitAudit.memberships	field
medh5.curation.splits.SplitAudit.ok	property
medh5.curation.splits.SplitAudit.partitions	method	(set_id)
medh5.curation.splits.SplitAudit.set_ids	property
medh5.curation.splits.SplitAudit.to_json	method	()
medh5.curation.splits.SplitAudit.unclaimed	field
medh5.curation.splits.SplitAudit.unreadable	field
medh5.curation.splits.anatomy_units	function	(pairs)
medh5.curation.splits.audit_splits	function	(paths)
medh5.curation.splits_from_json	function	(docs)
medh5.dataset	module
medh5.dataset.Assignment	class	(group, partition, fold=None, stratum=None, entries=()) bases=
medh5.dataset.Assignment.entries	field
medh5.dataset.Assignment.fold	field
medh5.dataset.Assignment.group	field
medh5.dataset.Assignment.partition	field
medh5.dataset.Assignment.stratum	field
medh5.dataset.Assignment.to_json	method	()
medh5.dataset.CHECK_CODES	constant	dict
medh5.dataset.CHECK_CODE_SEVERITY	constant	dict
medh5.dataset.ClassStats	class	(class_id, voxels=0, present_in=0, examined_in=0, key=None) bases=
medh5.dataset.ClassStats.class_id	field
medh5.dataset.ClassStats.examined_in	field
medh5.dataset.ClassStats.examined_prevalence	property
medh5.dataset.ClassStats.key	field
medh5.dataset.ClassStats.present_in	field
medh5.dataset.ClassStats.prevalence	property
medh5.dataset.ClassStats.to_json	method	()
medh5.dataset.ClassStats.voxels	field
medh5.dataset.CohortReport	class	(manifest_sha256, samples, findings=<factory>, coverage=<factory>) bases=
medh5.dataset.CohortReport.add	method	(code, severity, message, where=())
medh5.dataset.CohortReport.coverage	field
medh5.dataset.CohortReport.errors	property
medh5.dataset.CohortReport.findings	field
medh5.dataset.CohortReport.format	method	()
medh5.dataset.CohortReport.from_json	classmethod	(doc)
medh5.dataset.CohortReport.manifest_sha256	field
medh5.dataset.CohortReport.ok	property
medh5.dataset.CohortReport.samples	field
medh5.dataset.CohortReport.to_json	method	()
medh5.dataset.CohortReport.warnings	property
medh5.dataset.DatasetStats	class	(samples=0, images=<factory>, classes=<factory>, total_voxels=0, failures=(), physical=True) bases=
medh5.dataset.DatasetStats.class_weights	method	(*, scheme='inverse_frequency')
medh5.dataset.DatasetStats.classes	field
medh5.dataset.DatasetStats.failures	field
medh5.dataset.DatasetStats.from_json	classmethod	(doc)
medh5.dataset.DatasetStats.images	field
medh5.dataset.DatasetStats.merge	method	(other)
medh5.dataset.DatasetStats.normalization	method	(image_key)
medh5.dataset.DatasetStats.physical	field
medh5.dataset.DatasetStats.samples	field
medh5.dataset.DatasetStats.to_json	method	()
medh5.dataset.DatasetStats.total_voxels	field
medh5.dataset.Entry	class	(path, sample_id, subject_id, group_id, content_id=None, profiles=(), sex=None, laterality=None, bodypart=None, dataset_id=None, site_id=None, scanner_id=None, acquisition_protocol=None, timepoints=(), days_from_baseline=(), images=(), modalities=(), annotations=<factory>, class_ids=(), annotated_class_ids=(), class_keys=<factory>, label_set_id=None, label_set_version=None, label_set_digest=None, quality=<factory>, splits=(), deidentified=False, key=None, size=0, mtime=0.0) bases=
medh5.dataset.Entry.acquisition_protocol	field
medh5.dataset.Entry.annotated_class_ids	field
medh5.dataset.Entry.annotations	field
medh5.dataset.Entry.bodypart	field
medh5.dataset.Entry.class_ids	field
medh5.dataset.Entry.class_keys	field
medh5.dataset.Entry.content_id	field
medh5.dataset.Entry.dataset_id	field
medh5.dataset.Entry.days_from_baseline	field
medh5.dataset.Entry.deidentified	field
medh5.dataset.Entry.examined	method	(class_id)
medh5.dataset.Entry.field	method	(dotted)
medh5.dataset.Entry.from_json	classmethod	(doc)
medh5.dataset.Entry.group_id	field
medh5.dataset.Entry.has_class	method	(class_id)
medh5.dataset.Entry.images	field
medh5.dataset.Entry.is_longitudinal	property
medh5.dataset.Entry.key	field
medh5.dataset.Entry.label_set_digest	field
medh5.dataset.Entry.label_set_id	field
medh5.dataset.Entry.label_set_version	field
medh5.dataset.Entry.laterality	field
medh5.dataset.Entry.modalities	field
medh5.dataset.Entry.mtime	field
medh5.dataset.Entry.path	field
medh5.dataset.Entry.profiles	field
medh5.dataset.Entry.quality	field
medh5.dataset.Entry.sample_id	field
medh5.dataset.Entry.scanner_id	field
medh5.dataset.Entry.sex	field
medh5.dataset.Entry.site_id	field
medh5.dataset.Entry.size	field
medh5.dataset.Entry.splits	field
medh5.dataset.Entry.subject_id	field
medh5.dataset.Entry.timepoints	field
medh5.dataset.Entry.to_json	method	()
medh5.dataset.Finding	class	(code, severity, message, where=()) bases=
medh5.dataset.Finding.code	field
medh5.dataset.Finding.message	field
medh5.dataset.Finding.severity	field
medh5.dataset.Finding.to_json	method	()
medh5.dataset.Finding.where	field
medh5.dataset.Manifest	class	(entries=<factory>, root=None, generator='medh5 2.1.0', format='1.1') bases=
medh5.dataset.Manifest.__getitem__	method	(index)
medh5.dataset.Manifest.__iter__	method	()
medh5.dataset.Manifest.__len__	method	()
medh5.dataset.Manifest.by_path	method	(path)
medh5.dataset.Manifest.entries	field
medh5.dataset.Manifest.filter	method	(predicate)
medh5.dataset.Manifest.format	field
medh5.dataset.Manifest.from_json	classmethod	(doc)
medh5.dataset.Manifest.generator	field
medh5.dataset.Manifest.groups	method	(by='group_id')
medh5.dataset.Manifest.load	classmethod	(path, *, base=None)
medh5.dataset.Manifest.root	field
medh5.dataset.Manifest.save	method	(path, *, paths='keep')
medh5.dataset.Manifest.sha256	method	()
medh5.dataset.Manifest.stale	method	()
medh5.dataset.Manifest.subjects	property
medh5.dataset.Manifest.to_json	method	()
medh5.dataset.Moments	class	(count=0, mean=0.0, m2=0.0, minimum=inf, maximum=-inf, nonfinite=0) bases=
medh5.dataset.Moments.count	field
medh5.dataset.Moments.from_json	classmethod	(doc)
medh5.dataset.Moments.m2	field
medh5.dataset.Moments.maximum	field
medh5.dataset.Moments.mean	field
medh5.dataset.Moments.merge	method	(other)
medh5.dataset.Moments.minimum	field
medh5.dataset.Moments.nonfinite	field
medh5.dataset.Moments.std	property
medh5.dataset.Moments.to_json	method	()
medh5.dataset.Moments.update	method	(values)
medh5.dataset.Split	class	(set_id, manifest_sha256, assignments=<factory>, group_by='group_id', stratify_by=None, seed=0, k_folds=None, ratios=<factory>, algorithm='medh5.split/1', previous=None) bases=
medh5.dataset.Split.algorithm	field
medh5.dataset.Split.assignments	field
medh5.dataset.Split.balance	method	()
medh5.dataset.Split.counts	property
medh5.dataset.Split.empty_folds	property
medh5.dataset.Split.fold_of	method	(entry)
medh5.dataset.Split.from_json	classmethod	(doc)
medh5.dataset.Split.group_by	field
medh5.dataset.Split.k_folds	field
medh5.dataset.Split.leaks	method	()
medh5.dataset.Split.manifest_sha256	field
medh5.dataset.Split.moved_from	method	(other)
medh5.dataset.Split.partition_of	method	(entry)
medh5.dataset.Split.paths	method	(partition)
medh5.dataset.Split.previous	field
medh5.dataset.Split.ratios	field
medh5.dataset.Split.seed	field
medh5.dataset.Split.set_id	field
medh5.dataset.Split.stratify_by	field
medh5.dataset.Split.to_json	method	()
medh5.dataset.Split.underfilled	property
medh5.dataset.check	function	(manifest, *, set_id=None, deep=False)
medh5.dataset.check	module
medh5.dataset.check.CHECK_CODES	constant	dict
medh5.dataset.check.CHECK_CODE_SEVERITY	constant	dict
medh5.dataset.check.CohortReport	class	(manifest_sha256, samples, findings=<factory>, coverage=<factory>) bases=
medh5.dataset.check.CohortReport.add	method	(code, severity, message, where=())
medh5.dataset.check.CohortReport.coverage	field
medh5.dataset.check.CohortReport.errors	property
medh5.dataset.check.CohortReport.findings	field
medh5.dataset.check.CohortReport.format	method	()
medh5.dataset.check.CohortReport.from_json	classmethod	(doc)
medh5.dataset.check.CohortReport.manifest_sha256	field
medh5.dataset.check.CohortReport.ok	property
medh5.dataset.check.CohortReport.samples	field
medh5.dataset.check.CohortReport.to_json	method	()
medh5.dataset.check.CohortReport.warnings	property
medh5.dataset.check.Finding	class	(code, severity, message, where=()) bases=
medh5.dataset.check.Finding.code	field
medh5.dataset.check.Finding.message	field
medh5.dataset.check.Finding.severity	field
medh5.dataset.check.Finding.to_json	method	()
medh5.dataset.check.Finding.where	field
medh5.dataset.check.SEVERITIES	constant	tuple
medh5.dataset.check.check	function	(manifest, *, set_id=None, deep=False)
medh5.dataset.compute_stats	function	(paths, *, images=None, annotations=None, workers=1, sample_stride=1, physical=True)
medh5.dataset.entries_for	function	(path)
medh5.dataset.find	function	(root, *, suffixes=('.medh5', '.medh5c'))
medh5.dataset.make_splits	function	(manifest, *, set_id='default', group_by='group_id', stratify_by=None, ratios=None, k_folds=None, seed=0, algorithm=None, previous=None)
medh5.dataset.manifest	module
medh5.dataset.manifest.Entry	class	(path, sample_id, subject_id, group_id, content_id=None, profiles=(), sex=None, laterality=None, bodypart=None, dataset_id=None, site_id=None, scanner_id=None, acquisition_protocol=None, timepoints=(), days_from_baseline=(), images=(), modalities=(), annotations=<factory>, class_ids=(), annotated_class_ids=(), class_keys=<factory>, label_set_id=None, label_set_version=None, label_set_digest=None, quality=<factory>, splits=(), deidentified=False, key=None, size=0, mtime=0.0) bases=
medh5.dataset.manifest.Entry.acquisition_protocol	field
medh5.dataset.manifest.Entry.annotated_class_ids	field
medh5.dataset.manifest.Entry.annotations	field
medh5.dataset.manifest.Entry.bodypart	field
medh5.dataset.manifest.Entry.class_ids	field
medh5.dataset.manifest.Entry.class_keys	field
medh5.dataset.manifest.Entry.content_id	field
medh5.dataset.manifest.Entry.dataset_id	field
medh5.dataset.manifest.Entry.days_from_baseline	field
medh5.dataset.manifest.Entry.deidentified	field
medh5.dataset.manifest.Entry.examined	method	(class_id)
medh5.dataset.manifest.Entry.field	method	(dotted)
medh5.dataset.manifest.Entry.from_json	classmethod	(doc)
medh5.dataset.manifest.Entry.group_id	field
medh5.dataset.manifest.Entry.has_class	method	(class_id)
medh5.dataset.manifest.Entry.images	field
medh5.dataset.manifest.Entry.is_longitudinal	property
medh5.dataset.manifest.Entry.key	field
medh5.dataset.manifest.Entry.label_set_digest	field
medh5.dataset.manifest.Entry.label_set_id	field
medh5.dataset.manifest.Entry.label_set_version	field
medh5.dataset.manifest.Entry.laterality	field
medh5.dataset.manifest.Entry.modalities	field
medh5.dataset.manifest.Entry.mtime	field
medh5.dataset.manifest.Entry.path	field
medh5.dataset.manifest.Entry.profiles	field
medh5.dataset.manifest.Entry.quality	field
medh5.dataset.manifest.Entry.sample_id	field
medh5.dataset.manifest.Entry.scanner_id	field
medh5.dataset.manifest.Entry.sex	field
medh5.dataset.manifest.Entry.site_id	field
medh5.dataset.manifest.Entry.size	field
medh5.dataset.manifest.Entry.splits	field
medh5.dataset.manifest.Entry.subject_id	field
medh5.dataset.manifest.Entry.timepoints	field
medh5.dataset.manifest.Entry.to_json	method	()
medh5.dataset.manifest.GROUPABLE	constant	tuple
medh5.dataset.manifest.Manifest	class	(entries=<factory>, root=None, generator='medh5 2.1.0', format='1.1') bases=
medh5.dataset.manifest.Manifest.__getitem__	method	(index)
medh5.dataset.manifest.Manifest.__iter__	method	()
medh5.dataset.manifest.Manifest.__len__	method	()
medh5.dataset.manifest.Manifest.by_path	method	(path)
medh5.dataset.manifest.Manifest.entries	field
medh5.dataset.manifest.Manifest.filter	method	(predicate)
medh5.dataset.manifest.Manifest.format	field
medh5.dataset.manifest.Manifest.from_json	classmethod	(doc)
medh5.dataset.manifest.Manifest.generator	field
medh5.dataset.manifest.Manifest.groups	method	(by='group_id')
medh5.dataset.manifest.Manifest.load	classmethod	(path, *, base=None)
medh5.dataset.manifest.Manifest.root	field
medh5.dataset.manifest.Manifest.save	method	(path, *, paths='keep')
medh5.dataset.manifest.Manifest.sha256	method	()
medh5.dataset.manifest.Manifest.stale	method	()
medh5.dataset.manifest.Manifest.subjects	property
medh5.dataset.manifest.Manifest.to_json	method	()
medh5.dataset.manifest.PathStyle	alias
medh5.dataset.manifest.SCHEMA	constant	str
medh5.dataset.manifest.SUFFIXES	constant	tuple
medh5.dataset.manifest.counts	function	(entries, by)
medh5.dataset.manifest.entries_for	function	(path)
medh5.dataset.manifest.find	function	(root, *, suffixes=('.medh5', '.medh5c'))
medh5.dataset.manifest.load	function	(path, *, base=None)
medh5.dataset.manifest.scan	function	(root, *, suffixes=('.medh5', '.medh5c'), on_error='warn')
medh5.dataset.scan	function	(root, *, suffixes=('.medh5', '.medh5c'), on_error='warn')
medh5.dataset.split	module
medh5.dataset.split.Algorithm	alias
medh5.dataset.split.Assignment	class	(group, partition, fold=None, stratum=None, entries=()) bases=
medh5.dataset.split.Assignment.entries	field
medh5.dataset.split.Assignment.fold	field
medh5.dataset.split.Assignment.group	field
medh5.dataset.split.Assignment.partition	field
medh5.dataset.split.Assignment.stratum	field
medh5.dataset.split.Assignment.to_json	method	()
medh5.dataset.split.DEFAULT_RATIOS	constant	dict
medh5.dataset.split.Split	class	(set_id, manifest_sha256, assignments=<factory>, group_by='group_id', stratify_by=None, seed=0, k_folds=None, ratios=<factory>, algorithm='medh5.split/1', previous=None) bases=
medh5.dataset.split.Split.algorithm	field
medh5.dataset.split.Split.assignments	field
medh5.dataset.split.Split.balance	method	()
medh5.dataset.split.Split.counts	property
medh5.dataset.split.Split.empty_folds	property
medh5.dataset.split.Split.fold_of	method	(entry)
medh5.dataset.split.Split.from_json	classmethod	(doc)
medh5.dataset.split.Split.group_by	field
medh5.dataset.split.Split.k_folds	field
medh5.dataset.split.Split.leaks	method	()
medh5.dataset.split.Split.manifest_sha256	field
medh5.dataset.split.Split.moved_from	method	(other)
medh5.dataset.split.Split.partition_of	method	(entry)
medh5.dataset.split.Split.paths	method	(partition)
medh5.dataset.split.Split.previous	field
medh5.dataset.split.Split.ratios	field
medh5.dataset.split.Split.seed	field
medh5.dataset.split.Split.set_id	field
medh5.dataset.split.Split.stratify_by	field
medh5.dataset.split.Split.to_json	method	()
medh5.dataset.split.Split.underfilled	property
medh5.dataset.split.load	function	(path)
medh5.dataset.split.make_splits	function	(manifest, *, set_id='default', group_by='group_id', stratify_by=None, ratios=None, k_folds=None, seed=0, algorithm=None, previous=None)
medh5.dataset.split.write_claims	function	(split, manifest, *, assigned_by=None, fold=None)
medh5.dataset.stats	module
medh5.dataset.stats.ClassStats	class	(class_id, voxels=0, present_in=0, examined_in=0, key=None) bases=
medh5.dataset.stats.ClassStats.class_id	field
medh5.dataset.stats.ClassStats.examined_in	field
medh5.dataset.stats.ClassStats.examined_prevalence	property
medh5.dataset.stats.ClassStats.key	field
medh5.dataset.stats.ClassStats.present_in	field
medh5.dataset.stats.ClassStats.prevalence	property
medh5.dataset.stats.ClassStats.to_json	method	()
medh5.dataset.stats.ClassStats.voxels	field
medh5.dataset.stats.DatasetStats	class	(samples=0, images=<factory>, classes=<factory>, total_voxels=0, failures=(), physical=True) bases=
medh5.dataset.stats.DatasetStats.class_weights	method	(*, scheme='inverse_frequency')
medh5.dataset.stats.DatasetStats.classes	field
medh5.dataset.stats.DatasetStats.failures	field
medh5.dataset.stats.DatasetStats.from_json	classmethod	(doc)
medh5.dataset.stats.DatasetStats.images	field
medh5.dataset.stats.DatasetStats.merge	method	(other)
medh5.dataset.stats.DatasetStats.normalization	method	(image_key)
medh5.dataset.stats.DatasetStats.physical	field
medh5.dataset.stats.DatasetStats.samples	field
medh5.dataset.stats.DatasetStats.to_json	method	()
medh5.dataset.stats.DatasetStats.total_voxels	field
medh5.dataset.stats.Moments	class	(count=0, mean=0.0, m2=0.0, minimum=inf, maximum=-inf, nonfinite=0) bases=
medh5.dataset.stats.Moments.count	field
medh5.dataset.stats.Moments.from_json	classmethod	(doc)
medh5.dataset.stats.Moments.m2	field
medh5.dataset.stats.Moments.maximum	field
medh5.dataset.stats.Moments.mean	field
medh5.dataset.stats.Moments.merge	method	(other)
medh5.dataset.stats.Moments.minimum	field
medh5.dataset.stats.Moments.nonfinite	field
medh5.dataset.stats.Moments.std	property
medh5.dataset.stats.Moments.to_json	method	()
medh5.dataset.stats.Moments.update	method	(values)
medh5.dataset.stats.compute_stats	function	(paths, *, images=None, annotations=None, workers=1, sample_stride=1, physical=True)
medh5.dataset.stats.stats_for	function	(path, *, images=None, annotations=None, sample_stride=1, physical=True)
medh5.dataset.write_claims	function	(split, manifest, *, assigned_by=None, fold=None)
medh5.document	module
medh5.document.META_DATASET	constant	str
medh5.document.SampleDocument	class	(identity, timepoints, cohort=None, label_set=None, provenance=None, quality=None, splits=None, acquisition=None, deidentification=None, extra=None) bases=
medh5.document.SampleDocument.acquisition	field
medh5.document.SampleDocument.check_schema	method	()
medh5.document.SampleDocument.cohort	field
medh5.document.SampleDocument.deidentification	field
medh5.document.SampleDocument.dumps	method	(*, indent=None)
medh5.document.SampleDocument.extra	field
medh5.document.SampleDocument.from_json	classmethod	(doc)
medh5.document.SampleDocument.group_id	property
medh5.document.SampleDocument.identity	field
medh5.document.SampleDocument.label_set	field
medh5.document.SampleDocument.loads	classmethod	(payload)
medh5.document.SampleDocument.provenance	field
medh5.document.SampleDocument.quality	field
medh5.document.SampleDocument.quality_of	method	(key)
medh5.document.SampleDocument.splits	field
medh5.document.SampleDocument.subject_id	property
medh5.document.SampleDocument.summary	method	()
medh5.document.SampleDocument.timepoints	field
medh5.document.SampleDocument.to_json	method	()
medh5.document.new_document	function	(sample_id, subject_id=None, *, timepoints=None, **identity_fields)
medh5.document.read_document	function	(root)
medh5.document.read_document_text	function	(root)
medh5.document.schema	function	()
medh5.document.schema_text	function	()
medh5.document.validate_against_schema	function	(doc)
medh5.errors	module
medh5.errors.CODES	constant	dict
medh5.errors.CODES_REVISION	constant	int
medh5.errors.Code	class	(code, severity, domain, summary, since='1.0', revision=1) bases=
medh5.errors.Code.code	field
medh5.errors.Code.domain	field
medh5.errors.Code.revision	field
medh5.errors.Code.severity	field
medh5.errors.Code.since	field
medh5.errors.Code.summary	field
medh5.errors.Domain	alias
medh5.errors.MEDH5Error	class	(?) bases=Exception
medh5.errors.MEDH5FileError	class	(message, errno=None, filename=None) bases=medh5.errors.MEDH5Error,OSError
medh5.errors.MEDH5FileNotFoundError	class	(message, errno=None, filename=None) bases=medh5.errors.MEDH5FileError,FileNotFoundError
medh5.errors.MEDH5IOError	class	(?) bases=OSError
medh5.errors.MEDH5IntegrityError	class	(?) bases=medh5.errors.MEDH5Error
medh5.errors.MEDH5IsADirectoryError	class	(message, errno=None, filename=None) bases=medh5.errors.MEDH5FileError,IsADirectoryError
medh5.errors.MEDH5PermissionError	class	(message, errno=None, filename=None) bases=medh5.errors.MEDH5FileError,PermissionError
medh5.errors.MEDH5SchemaError	class	(?) bases=medh5.errors.MEDH5Error
medh5.errors.MEDH5ValidationError	class	(message, code=None) bases=medh5.errors.MEDH5Error,ValueError
medh5.errors.MEDH5VersionError	class	(?) bases=medh5.errors.MEDH5Error
medh5.errors.Severity	alias
medh5.errors.code	function	(name)
medh5.errors.codes_for	function	(domain)
medh5.geometry	module
medh5.geometry.AXIS_KINDS	constant	tuple
medh5.geometry.COORD_SYSTEMS	constant	tuple
medh5.geometry.DOWNSAMPLE_METHODS	constant	tuple
medh5.geometry.GEOMETRY_RTOL	constant	float
medh5.geometry.Grid	class	(grid_id, shape, axis_names, axis_kinds, spacing, origin, direction, coord_system='LPS', units='mm', timepoint=None, frame_uid=None, time_values=None, time_units=None, chunk_hint=None, patch_hint=None, extra=None) bases=
medh5.geometry.Grid.affine	property
medh5.geometry.Grid.attrs	method	()
medh5.geometry.Grid.axis_kinds	field
medh5.geometry.Grid.axis_names	field
medh5.geometry.Grid.channel_axis	property
medh5.geometry.Grid.check	method	()
medh5.geometry.Grid.chunk_hint	field
medh5.geometry.Grid.comparable_with	method	(other)
medh5.geometry.Grid.coord_system	field
medh5.geometry.Grid.direction	field
medh5.geometry.Grid.extent	property
medh5.geometry.Grid.extra	field
medh5.geometry.Grid.frame_uid	field
medh5.geometry.Grid.grid_id	field
medh5.geometry.Grid.index_to_world	method	(indices)
medh5.geometry.Grid.is_congruent	method	(other, tol=1e-06)
medh5.geometry.Grid.n_spatial	property
medh5.geometry.Grid.n_voxels	property
medh5.geometry.Grid.ndim	property
medh5.geometry.Grid.origin	field
medh5.geometry.Grid.patch_hint	field
medh5.geometry.Grid.physical_size	property
medh5.geometry.Grid.shape	field
medh5.geometry.Grid.spacing	field
medh5.geometry.Grid.spatial_axes	property
medh5.geometry.Grid.spatial_names	property
medh5.geometry.Grid.spatial_shape	property
medh5.geometry.Grid.summary	method	()
medh5.geometry.Grid.time_axis	property
medh5.geometry.Grid.time_units	field
medh5.geometry.Grid.time_values	field
medh5.geometry.Grid.timepoint	field
medh5.geometry.Grid.units	field
medh5.geometry.Grid.world_into	method	(other, points)
medh5.geometry.Grid.world_to_index	method	(points)
medh5.geometry.KNOWN_UNITS	constant	tuple
medh5.geometry.LABEL_SAFE_METHODS	constant	tuple
medh5.geometry.MAX_SPATIAL	constant	int
medh5.geometry.MIN_SPATIAL	constant	int
medh5.geometry.MM_PER_UNIT	constant	dict
medh5.geometry.ORTHONORMAL_TOL	constant	float
medh5.geometry.Pyramid	class	(levels, downsample_factors, downsample_method, grid_levels) bases=
medh5.geometry.Pyramid.attrs	method	()
medh5.geometry.Pyramid.downsample_factors	field
medh5.geometry.Pyramid.downsample_method	field
medh5.geometry.Pyramid.grid_levels	field
medh5.geometry.Pyramid.levels	field
medh5.geometry.SPEC_GRID_ATTRS	constant	tuple
medh5.geometry.TIME_UNITS	constant	tuple
medh5.geometry.affine_summary	function	(affine)
medh5.geometry.apply_affine_to_box	function	(affine, box)
medh5.geometry.box_corners	function	(box)
medh5.geometry.box_to_slices	function	(box, shape=None)
medh5.geometry.build_affine	function	(spacing, origin, direction)
medh5.geometry.check_orthonormal	function	(direction, tol=<value>, *, what='direction')
medh5.geometry.check_pyramid	function	(base, levels, factors, *, rtol=<value>)
medh5.geometry.decompose_affine	function	(affine)
medh5.geometry.derive_level_grid	function	(base, factors, grid_id, *, shape=None)
medh5.geometry.index_to_world	function	(affine, indices)
medh5.geometry.is_orthonormal	function	(direction, tol=<value>)
medh5.geometry.is_proper_rotation	function	(matrix, tol=<value>)
medh5.geometry.pyramid_factors	function	(base, levels)
medh5.geometry.read_grid	function	(group, grid_id=None)
medh5.geometry.read_grids	function	(root)
medh5.geometry.slices_to_box	function	(slices)
medh5.geometry.voxel_volume	function	(spacing)
medh5.geometry.world_to_index	function	(affine, points)
medh5.grid_patches	function	(shape, patch_size, *, overlap=0, grid_id=None)
medh5.image	module
medh5.image.Image	class	(handle) bases=
medh5.image.Image.attrs	property
medh5.image.Image.channel_names	property
medh5.image.Image.chunks	property
medh5.image.Image.dataset	property
medh5.image.Image.digest	property
medh5.image.Image.dtype	property
medh5.image.Image.grid	property
medh5.image.Image.grid_id	property
medh5.image.Image.image_id	property
medh5.image.Image.is_multiscale	property
medh5.image.Image.is_rescaled	property
medh5.image.Image.level	method	(index)
medh5.image.Image.levels	property
medh5.image.Image.modality	property
medh5.image.Image.nbytes	property
medh5.image.Image.prov	property
medh5.image.Image.pyramid	property
medh5.image.Image.read	method	(roi=None, *, physical=False, dtype=None)
medh5.image.Image.rescale	property
medh5.image.Image.shape	property
medh5.image.Image.summary	method	()
medh5.image.Image.timepoint	property
medh5.image.Image.valid_mask	property
medh5.image.Image.value_type	property
medh5.image.Image.value_units	property
medh5.image.Image.window	property
medh5.image.SPEC_IMAGE_ATTRS	constant	tuple
medh5.image.VALUE_TYPES	constant	tuple
medh5.image.check_value_type	function	(value_type)
medh5.image.is_probability	function	(array)
medh5.image.lossless_as_int16	function	(array)
medh5.integrity	module
medh5.integrity.ATTESTED_GROUPS	constant	tuple
medh5.integrity.DEFAULT_ALGO	constant	str
medh5.integrity.DIGEST_ALGOS	constant	tuple
medh5.integrity.Diagnosis	class	(path, mismatched=(), undigested=(), unattested=(), stale_index=(), missing_index=(), content_id_ok=None, malformed=()) bases=
medh5.integrity.Diagnosis.clean	property
medh5.integrity.Diagnosis.content_id_ok	field
medh5.integrity.Diagnosis.from_json	classmethod	(doc)
medh5.integrity.Diagnosis.malformed	field
medh5.integrity.Diagnosis.mismatched	field
medh5.integrity.Diagnosis.missing_index	field
medh5.integrity.Diagnosis.needs_digests	property
medh5.integrity.Diagnosis.needs_index	property
medh5.integrity.Diagnosis.path	field
medh5.integrity.Diagnosis.stale_index	field
medh5.integrity.Diagnosis.to_json	method	()
medh5.integrity.Diagnosis.unattested	field
medh5.integrity.Diagnosis.undigested	field
medh5.integrity.Repair	class	(path, diagnosis, rebuilt_index=(), rewrote_digests=False, content_id=None, notes=<factory>) bases=
medh5.integrity.Repair.changed	property
medh5.integrity.Repair.content_id	field
medh5.integrity.Repair.diagnosis	field
medh5.integrity.Repair.from_json	classmethod	(doc)
medh5.integrity.Repair.notes	field
medh5.integrity.Repair.path	field
medh5.integrity.Repair.rebuilt_index	field
medh5.integrity.Repair.rewrote_digests	field
medh5.integrity.Repair.to_json	method	()
medh5.integrity.STREAM_BYTES	constant	int
medh5.integrity.VerifyResult	class	(checked=(), mismatched=(), undigested=(), malformed=(), content_id_declared=None, content_id_computed=None, stale_index=(), unattested=(), unverifiable=()) bases=
medh5.integrity.VerifyResult.checked	field
medh5.integrity.VerifyResult.content_id_computed	field
medh5.integrity.VerifyResult.content_id_declared	field
medh5.integrity.VerifyResult.content_id_ok	property
medh5.integrity.VerifyResult.malformed	field
medh5.integrity.VerifyResult.mismatched	field
medh5.integrity.VerifyResult.ok	property
medh5.integrity.VerifyResult.stale_index	field
medh5.integrity.VerifyResult.summary	method	()
medh5.integrity.VerifyResult.unattested	field
medh5.integrity.VerifyResult.undigested	field
medh5.integrity.VerifyResult.unverifiable	field
medh5.integrity.array_digest	function	(path, array, algo='sha256')
medh5.integrity.attrs_digest	function	(obj, names, algo='sha256')
medh5.integrity.canonical_attrs	function	(obj, names)
medh5.integrity.collect_digests	function	(root, skip=<value>)
medh5.integrity.compute_content_id	function	(root, attr_names=None, *, algo=None)
medh5.integrity.dataset_digest	function	(dataset, path=None, algo='sha256')
medh5.integrity.diagnose	function	(path)
medh5.integrity.digest_bytes	function	(payload, algo='sha256')
medh5.integrity.fix	function	(path, *, rebuild_index=False, rewrite_digests=False, reason=None, performed_by=None, max_coords=None)
medh5.integrity.fix_paths	function	(paths, **options)
medh5.integrity.group_digest	function	(group, algo='sha256', *, root=None)
medh5.integrity.parse_digest	function	(value)
medh5.integrity.raw_chunks	function	(dataset)
medh5.integrity.relative_path	function	(node, root=None)
medh5.integrity.stale_index_entries	function	(root)
medh5.integrity.subtrees_identical	function	(a, b)
medh5.integrity.verify_object	function	(root, path)
medh5.integrity.verify_root	function	(root, attr_names=None, *, partial=None, check_content_id=True)
medh5.io	module
medh5.io.ConversionReport	class	(source='', converter='', outputs=<factory>, notes=<factory>) bases=
medh5.io.ConversionReport.add	method	(kind, message, severity='info', detail=None)
medh5.io.ConversionReport.converter	field
medh5.io.ConversionReport.decision	method	(kind, message, detail=None)
medh5.io.ConversionReport.format	method	(*, verbose=False)
medh5.io.ConversionReport.guess	method	(kind, message, detail=None)
medh5.io.ConversionReport.guesses	property
medh5.io.ConversionReport.notes	field
medh5.io.ConversionReport.of_kind	method	(kind)
medh5.io.ConversionReport.ok	property
medh5.io.ConversionReport.outputs	field
medh5.io.ConversionReport.source	field
medh5.io.ConversionReport.to_json	method	()
medh5.io.ConversionReport.warn	method	(kind, message, detail=None)
medh5.io.ConversionReport.warnings	property
medh5.io.ItkTransform	class	(name, matrix, components=()) bases=
medh5.io.ItkTransform.components	field
medh5.io.ItkTransform.dimension	property
medh5.io.ItkTransform.is_composite	property
medh5.io.ItkTransform.matrix	field
medh5.io.ItkTransform.name	field
medh5.io.Note	class	(kind, message, severity='info', detail=<factory>) bases=
medh5.io.Note.detail	field
medh5.io.Note.kind	field
medh5.io.Note.message	field
medh5.io.Note.severity	field
medh5.io.Note.to_json	method	()
medh5.io.Series	class	(series_uid, study_uid, modality, patient_id, study_date, paths=<factory>, description='', frame_uid=None, birth_date=None, sex=None) bases=
medh5.io.Series.birth_date	field
medh5.io.Series.description	field
medh5.io.Series.frame_uid	field
medh5.io.Series.modality	field
medh5.io.Series.n_slices	property
medh5.io.Series.paths	field
medh5.io.Series.patient_id	field
medh5.io.Series.series_uid	field
medh5.io.Series.sex	field
medh5.io.Series.study_date	field
medh5.io.Series.study_uid	field
medh5.io.Series.to_json	method	()
medh5.io.SubjectGroup	class	(subject_id, occasions=<factory>, ordered_by='date') bases=
medh5.io.SubjectGroup.__len__	method	()
medh5.io.SubjectGroup.days_from_baseline	method	()
medh5.io.SubjectGroup.is_longitudinal	property
medh5.io.SubjectGroup.occasions	field
medh5.io.SubjectGroup.ordered_by	field
medh5.io.SubjectGroup.subject_id	field
medh5.io.SubjectGroup.timepoint_ids	method	()
medh5.io.SubjectGroup.to_json	method	()
medh5.io.augment_from_fhir	function	(path, source, *, out=None, **options)
medh5.io.augment_from_meds	function	(path, source, *, out=None, **options)
medh5.io.build_label_set	function	(paths, *, report=None)
medh5.io.convert_world	function	(affine, *, source, target)
medh5.io.dicom	module
medh5.io.dicom.SPACING_TOLERANCE	constant	float
medh5.io.dicom.STORED_TAGS	constant	tuple
medh5.io.dicom.Series	class	(series_uid, study_uid, modality, patient_id, study_date, paths=<factory>, description='', frame_uid=None, birth_date=None, sex=None) bases=
medh5.io.dicom.Series.birth_date	field
medh5.io.dicom.Series.description	field
medh5.io.dicom.Series.frame_uid	field
medh5.io.dicom.Series.modality	field
medh5.io.dicom.Series.n_slices	property
medh5.io.dicom.Series.paths	field
medh5.io.dicom.Series.patient_id	field
medh5.io.dicom.Series.series_uid	field
medh5.io.dicom.Series.sex	field
medh5.io.dicom.Series.study_date	field
medh5.io.dicom.Series.study_uid	field
medh5.io.dicom.Series.to_json	method	()
medh5.io.dicom.from_dicom	function	(root, out, *, group_by='subject', modalities=None, series_uids=None, codec='balanced', report=None, per_slice_rescale='refuse')
medh5.io.dicom.read_series	function	(series, *, report=None, per_slice_rescale='refuse')
medh5.io.dicom.require_pydicom	function	()
medh5.io.dicom.scan_dicom	function	(root, *, report=None)
medh5.io.dicom.select_series	function	(series, *, thinnest=True)
medh5.io.dicom_seg	module
medh5.io.dicom_seg.BINARY	constant	str
medh5.io.dicom_seg.FRACTIONAL	constant	str
medh5.io.dicom_seg.FRACTIONAL_TYPES	constant	tuple
medh5.io.dicom_seg.MAX_FRACTIONAL_VALUE	constant	int
medh5.io.dicom_seg.SEGMENTATION_TYPES	constant	tuple
medh5.io.dicom_seg.SLICE_TOLERANCE	constant	float
medh5.io.dicom_seg.frames_agree	function	(seg_frame, grid_frame, salt=None)
medh5.io.dicom_seg.from_dicom_seg	function	(path, sample, *, ann_id='seg', grid=None, annotated_classes='all_given', frame_salt=None, report=None)
medh5.io.dicom_seg.place_frames	function	(frames, geometry, grid, *, frame_salt=None)
medh5.io.dicom_seg.read_dicom_seg	function	(path, *, report=None)
medh5.io.dicom_seg.read_dicom_seg_frames	function	(path)
medh5.io.dicom_seg.require_highdicom	function	()
medh5.io.dicom_seg.to_dicom_seg	function	(sample, ann_id, source_images, out, *, classes=None, series_description='medh5 segmentation', frame_salt=None, report=None, segmentation_type='binary', fractional_type='PROBABILITY')
medh5.io.fhir	module
medh5.io.fhir.COMPARATORS	constant	dict
medh5.io.fhir.STATUSES	constant	dict
medh5.io.fhir.UCUM	constant	str
medh5.io.fhir.augment_from_fhir	function	(path, source, *, out=None, **options)
medh5.io.fhir.read_fhir	function	(source, *, subject, clock, timezone=None, origin=None, texts=False, prefer_systems=(), image_studies=None)
medh5.io.from_dicom	function	(root, out, *, group_by='subject', modalities=None, series_uids=None, codec='balanced', report=None, per_slice_rescale='refuse')
medh5.io.from_dicom_seg	function	(path, sample, *, ann_id='seg', grid=None, annotated_classes='all_given', frame_salt=None, report=None)
medh5.io.from_itk_transform	function	(path, sample, *, transform_id, fixed, moving, warp=None, vectors=None, inverse_warp=None, report=None)
medh5.io.from_nifti	function	(images, out, *, masks=None, sample_id=None, subject_id=None, modalities=None, coord_system='LPS', transpose=True, fourth_axis='auto', value_units=None, codec='balanced', annotated_classes='all_given', assume_geometry=False, report=None, plane_as_volume=False, label_set=None)
medh5.io.from_nnunetv2	function	(root, out, *, case_ids=None, coord_system='LPS', codec='balanced', report=None, include_test=False)
medh5.io.from_rtstruct	function	(path, sample, *, ann_id='contours', grid=None, rasterize=False, mask_id=None, annotated_classes='all_given', frame_salt=None, report=None, roi_classes=None, points_id=None, open_curves='omit')
medh5.io.group_by_subject	function	(occasions, *, mode='subject', report=None)
medh5.io.grouping	module
medh5.io.grouping.FALLBACK_PREFIX	constant	str
medh5.io.grouping.Occasion	class	(key, subject_id=None, date=None, order_hint=None, payload=None, demographics=<factory>) bases=
medh5.io.grouping.Occasion.date	field
medh5.io.grouping.Occasion.demographics	field
medh5.io.grouping.Occasion.key	field
medh5.io.grouping.Occasion.order_hint	field
medh5.io.grouping.Occasion.payload	field
medh5.io.grouping.Occasion.subject_id	field
medh5.io.grouping.SubjectGroup	class	(subject_id, occasions=<factory>, ordered_by='date') bases=
medh5.io.grouping.SubjectGroup.__len__	method	()
medh5.io.grouping.SubjectGroup.days_from_baseline	method	()
medh5.io.grouping.SubjectGroup.is_longitudinal	property
medh5.io.grouping.SubjectGroup.occasions	field
medh5.io.grouping.SubjectGroup.ordered_by	field
medh5.io.grouping.SubjectGroup.subject_id	field
medh5.io.grouping.SubjectGroup.timepoint_ids	method	()
medh5.io.grouping.SubjectGroup.to_json	method	()
medh5.io.grouping.build_occasions	function	(items, *, key, subject, date=None, order_hint=None)
medh5.io.grouping.contradictions	function	(occasions)
medh5.io.grouping.group_by_subject	function	(occasions, *, mode='subject', report=None)
medh5.io.grouping.note_instance_ids	function	(group, log)
medh5.io.grouping.output_name	function	(group, used, *, safe=None)
medh5.io.import_seg_nifti	function	(path, masks, *, ann_id='seg', grid=None, coord_system=None, transpose=True, annotated_classes='all_given', assume_aligned=False, assume_geometry=False, report=None, plane_as_volume=False)
medh5.io.itk	module
medh5.io.itk.ItkTransform	class	(name, matrix, components=()) bases=
medh5.io.itk.ItkTransform.components	field
medh5.io.itk.ItkTransform.dimension	property
medh5.io.itk.ItkTransform.is_composite	property
medh5.io.itk.ItkTransform.matrix	field
medh5.io.itk.ItkTransform.name	field
medh5.io.itk.from_itk_transform	function	(path, sample, *, transform_id, fixed, moving, warp=None, vectors=None, inverse_warp=None, report=None)
medh5.io.itk.read_itk_transform	function	(path)
medh5.io.itk.to_itk_transform	function	(sample, out, *, transform_id, warp_out=None, vectors=None)
medh5.io.itk.write_itk_transform	function	(path, transform)
medh5.io.legacy	module
medh5.io.legacy.BOX_SHIFT	constant	float
medh5.io.legacy.LegacyMeta	class	(spatial=<factory>, shape=None, image_names=<factory>, seg_names=<factory>, label=None, label_name=None, patch_size=None, extra=<factory>, schema_version='1') bases=
medh5.io.legacy.LegacyMeta.extra	field
medh5.io.legacy.LegacyMeta.image_names	field
medh5.io.legacy.LegacyMeta.label	field
medh5.io.legacy.LegacyMeta.label_name	field
medh5.io.legacy.LegacyMeta.patch_size	field
medh5.io.legacy.LegacyMeta.schema_version	field
medh5.io.legacy.LegacyMeta.seg_names	field
medh5.io.legacy.LegacyMeta.shape	field
medh5.io.legacy.LegacyMeta.spatial	field
medh5.io.legacy.LegacySample	class	(images, seg, bboxes, bbox_scores, bbox_labels, meta) bases=
medh5.io.legacy.LegacySample.bbox_labels	field
medh5.io.legacy.LegacySample.bbox_scores	field
medh5.io.legacy.LegacySample.bboxes	field
medh5.io.legacy.LegacySample.images	field
medh5.io.legacy.LegacySample.meta	field
medh5.io.legacy.LegacySample.seg	field
medh5.io.legacy.LegacySpatial	class	(spacing=None, origin=None, direction=None, axis_labels=None, coord_system=None) bases=
medh5.io.legacy.LegacySpatial.axis_labels	field
medh5.io.legacy.LegacySpatial.coord_system	field
medh5.io.legacy.LegacySpatial.direction	field
medh5.io.legacy.LegacySpatial.origin	field
medh5.io.legacy.LegacySpatial.spacing	field
medh5.io.legacy.SCHEMA_VERSION	constant	str
medh5.io.legacy.SUFFIX	constant	str
medh5.io.legacy.build_label_set	function	(paths, *, report=None)
medh5.io.legacy.is_legacy	function	(path)
medh5.io.legacy.legacy_meta	function	(path)
medh5.io.legacy.load_sidecar	function	(path)
medh5.io.legacy.migrate	function	(path, out, *, label_set=None, codec='balanced', report=None)
medh5.io.legacy.migrate_paths	function	(paths, outdir, *, group_by='study', subject_key=None, label_set=None, codec='balanced')
medh5.io.legacy.read_legacy	function	(path)
medh5.io.legacy.write_sidecar	function	(label_set, path)
medh5.io.meds	module
medh5.io.meds.BIRTH	constant	str
medh5.io.meds.BOTH_VALUES	constant	tuple
medh5.io.meds.COLUMNS	constant	tuple
medh5.io.meds.augment_from_meds	function	(path, source, *, out=None, **options)
medh5.io.meds.read_meds	function	(source, *, subject_id, clock, timezone=None, origin=None, code_system=None, code_systems=None, kinds=None, status='unknown', day_precision=(), document_codes=(), exclude_codes=('MEDS_BIRTH',), texts=False, both_values='refuse', columns=None)
medh5.io.merge_reports	function	(reports, converter='')
medh5.io.migrate	function	(path, out, *, label_set=None, codec='balanced', report=None)
medh5.io.migrate_paths	function	(paths, outdir, *, group_by='study', subject_key=None, label_set=None, codec='balanced')
medh5.io.nifti	module
medh5.io.nifti.COORD_SYSTEMS	constant	tuple
medh5.io.nifti.RAS_TO_LPS	constant	<external>
medh5.io.nifti.convert_world	function	(affine, *, source, target)
medh5.io.nifti.from_nifti	function	(images, out, *, masks=None, sample_id=None, subject_id=None, modalities=None, coord_system='LPS', transpose=True, fourth_axis='auto', value_units=None, codec='balanced', annotated_classes='all_given', assume_geometry=False, report=None, plane_as_volume=False, label_set=None)
medh5.io.nifti.import_seg_nifti	function	(path, masks, *, ann_id='seg', grid=None, coord_system=None, transpose=True, annotated_classes='all_given', assume_aligned=False, assume_geometry=False, report=None, plane_as_volume=False)
medh5.io.nifti.read_nifti	function	(path, *, coord_system='LPS', transpose=True, fourth_axis='auto', assume_geometry=False, plane_as_volume=False)
medh5.io.nifti.require_nibabel	function	()
medh5.io.nifti.to_nifti	function	(path, image_id, out, *, physical=True, annotation=None, class_key=None, report=None)
medh5.io.nnunetv2	module
medh5.io.nnunetv2.BACKGROUND	constant	int
medh5.io.nnunetv2.REQUIRED_KEYS	constant	tuple
medh5.io.nnunetv2.cases	function	(root, document, *, include_test=False)
medh5.io.nnunetv2.from_nnunetv2	function	(root, out, *, case_ids=None, coord_system='LPS', codec='balanced', report=None, include_test=False)
medh5.io.nnunetv2.read_dataset_json	function	(path)
medh5.io.nnunetv2.to_nnunetv2	function	(paths, out, *, dataset_name='Dataset001_medh5', file_ending='.nii.gz', annotation='seg', classes=None, unlabeled='refuse', report=None, split=None, replace=False)
medh5.io.read_fhir	function	(source, *, subject, clock, timezone=None, origin=None, texts=False, prefer_systems=(), image_studies=None)
medh5.io.read_itk_transform	function	(path)
medh5.io.read_meds	function	(source, *, subject_id, clock, timezone=None, origin=None, code_system=None, code_systems=None, kinds=None, status='unknown', day_precision=(), document_codes=(), exclude_codes=('MEDS_BIRTH',), texts=False, both_values='refuse', columns=None)
medh5.io.read_nifti	function	(path, *, coord_system='LPS', transpose=True, fourth_axis='auto', assume_geometry=False, plane_as_volume=False)
medh5.io.report	module
medh5.io.report.ConversionReport	class	(source='', converter='', outputs=<factory>, notes=<factory>) bases=
medh5.io.report.ConversionReport.add	method	(kind, message, severity='info', detail=None)
medh5.io.report.ConversionReport.converter	field
medh5.io.report.ConversionReport.decision	method	(kind, message, detail=None)
medh5.io.report.ConversionReport.format	method	(*, verbose=False)
medh5.io.report.ConversionReport.guess	method	(kind, message, detail=None)
medh5.io.report.ConversionReport.guesses	property
medh5.io.report.ConversionReport.notes	field
medh5.io.report.ConversionReport.of_kind	method	(kind)
medh5.io.report.ConversionReport.ok	property
medh5.io.report.ConversionReport.outputs	field
medh5.io.report.ConversionReport.source	field
medh5.io.report.ConversionReport.to_json	method	()
medh5.io.report.ConversionReport.warn	method	(kind, message, detail=None)
medh5.io.report.ConversionReport.warnings	property
medh5.io.report.Note	class	(kind, message, severity='info', detail=<factory>) bases=
medh5.io.report.Note.detail	field
medh5.io.report.Note.kind	field
medh5.io.report.Note.message	field
medh5.io.report.Note.severity	field
medh5.io.report.Note.to_json	method	()
medh5.io.report.SEVERITIES	constant	tuple
medh5.io.report.merge_reports	function	(reports, converter='')
medh5.io.rtstruct	module
medh5.io.rtstruct.MIN_POLYGON_VERTICES	constant	int
medh5.io.rtstruct.from_rtstruct	function	(path, sample, *, ann_id='contours', grid=None, rasterize=False, mask_id=None, annotated_classes='all_given', frame_salt=None, report=None, roi_classes=None, points_id=None, open_curves='omit')
medh5.io.rtstruct.read_rtstruct	function	(path)
medh5.io.rtstruct.to_rtstruct	function	(sample, ann_id, source_images, out, *, label='medh5 export', frame_salt=None, report=None, points=None)
medh5.io.scan_dicom	function	(root, *, report=None)
medh5.io.to_dicom_seg	function	(sample, ann_id, source_images, out, *, classes=None, series_description='medh5 segmentation', frame_salt=None, report=None, segmentation_type='binary', fractional_type='PROBABILITY')
medh5.io.to_itk_transform	function	(sample, out, *, transform_id, warp_out=None, vectors=None)
medh5.io.to_nifti	function	(path, image_id, out, *, physical=True, annotation=None, class_key=None, report=None)
medh5.io.to_nnunetv2	function	(paths, out, *, dataset_name='Dataset001_medh5', file_ending='.nii.gz', annotation='seg', classes=None, unlabeled='refuse', report=None, split=None, replace=False)
medh5.io.to_rtstruct	function	(sample, ann_id, source_images, out, *, label='medh5 export', frame_salt=None, report=None, points=None)
medh5.io.write_itk_transform	function	(path, transform)
medh5.labels	module
medh5.labels.BACKGROUND_ID	constant	int
medh5.labels.CLOSURES	constant	tuple
medh5.labels.FORMS	constant	tuple
medh5.labels.IGNORE_ID	constant	int
medh5.labels.INLINE_REQUIRED_BELOW	constant	int
medh5.labels.LabelClass	class	(id, key, name, parents=None, category=None, color=None, codes=None, laterality=None, properties=None) bases=
medh5.labels.LabelClass.category	field
medh5.labels.LabelClass.codes	field
medh5.labels.LabelClass.color	field
medh5.labels.LabelClass.from_json	classmethod	(doc)
medh5.labels.LabelClass.id	field
medh5.labels.LabelClass.is_lesion	property
medh5.labels.LabelClass.key	field
medh5.labels.LabelClass.laterality	field
medh5.labels.LabelClass.name	field
medh5.labels.LabelClass.parents	field
medh5.labels.LabelClass.properties	field
medh5.labels.LabelClass.to_json	method	()
medh5.labels.LabelSet	class	(id, classes=None, *, version='1.0.0', relations=None, skeletons=None, form='inline', uri=None, sha256=None) bases=
medh5.labels.LabelSet.__contains__	method	(key, /)
medh5.labels.LabelSet.__getitem__	method	(key, /)
medh5.labels.LabelSet.__iter__	method	()
medh5.labels.LabelSet.__len__	method	()
medh5.labels.LabelSet.ancestors	method	(key)
medh5.labels.LabelSet.as_ref	method	(uri)
medh5.labels.LabelSet.check	method	()
medh5.labels.LabelSet.classes	property
medh5.labels.LabelSet.close	method	(ids, closure)
medh5.labels.LabelSet.colors	method	()
medh5.labels.LabelSet.content_doc	method	()
medh5.labels.LabelSet.descendants	method	(key)
medh5.labels.LabelSet.digest	method	(algo='sha256')
medh5.labels.LabelSet.form	property
medh5.labels.LabelSet.from_json	classmethod	(doc)
medh5.labels.LabelSet.get	method	(key)
medh5.labels.LabelSet.id	property
medh5.labels.LabelSet.ids	property
medh5.labels.LabelSet.ids_for	method	(keys)
medh5.labels.LabelSet.keys	property
medh5.labels.LabelSet.missing	method	(ids)
medh5.labels.LabelSet.relations	property
medh5.labels.LabelSet.relations_of	method	(key, predicate=None)
medh5.labels.LabelSet.resolve	method	(keys)
medh5.labels.LabelSet.sha256	property
medh5.labels.LabelSet.skeleton	method	(skeleton_id)
medh5.labels.LabelSet.skeletons	property
medh5.labels.LabelSet.subset	method	(keys, *, id=None)
medh5.labels.LabelSet.to_json	method	(*, form=None)
medh5.labels.LabelSet.uri	property
medh5.labels.LabelSet.version	property
medh5.labels.MAX_CLASS_ID	constant	int
medh5.labels.OntologyCode	class	(system, code, name=None) bases=
medh5.labels.OntologyCode.code	field
medh5.labels.OntologyCode.from_json	classmethod	(doc)
medh5.labels.OntologyCode.name	field
medh5.labels.OntologyCode.system	field
medh5.labels.OntologyCode.to_json	method	()
medh5.labels.Relation	class	(subject, predicate, object) bases=
medh5.labels.Relation.from_json	classmethod	(doc)
medh5.labels.Relation.object	field
medh5.labels.Relation.predicate	field
medh5.labels.Relation.subject	field
medh5.labels.Relation.to_json	method	()
medh5.labels.Skeleton	class	(id, keypoints, edges=()) bases=
medh5.labels.Skeleton.edges	field
medh5.labels.Skeleton.from_json	classmethod	(doc)
medh5.labels.Skeleton.id	field
medh5.labels.Skeleton.keypoints	field
medh5.labels.Skeleton.to_json	method	()
medh5.labels.available	function	()
medh5.labels.canonical_json	function	(doc)
medh5.labels.check	function	(paths)
medh5.labels.check_class_id	function	(class_id)
medh5.labels.describe	function	()
medh5.labels.from_keys	function	(keys, *, id, version='1.0.0', start=1)
medh5.labels.load	function	(name)
medh5.labels.load_file	function	(path)
medh5.labels.register	function	(name, label_set)
medh5.labels.unregister	function	(name)
medh5.monai	module
medh5.monai.LoadMedH5d	class	(keys='path', *, images=None, annotations=(), space=None, physical=True, allow_missing_keys=False) bases=
medh5.monai.LoadMedH5d.__call__	method	(data)
medh5.monai.MedH5Reader	class	(image=None, *, annotation=None, sample_key=None, physical=True, space=None, level=0, dtype=<value>) bases=
medh5.monai.MedH5Reader.get_data	method	(img)
medh5.monai.MedH5Reader.read	method	(data, **kwargs)
medh5.monai.MedH5Reader.verify_suffix	method	(filename)
medh5.monai.SPACES	constant	tuple
medh5.monai.affine_for	function	(sample, image_id, *, space=None, level=0)
medh5.monai.available	function	()
medh5.monai.convert_affine	function	(affine, *, source, target)
medh5.monai.from_metatensor	function	(tensor)
medh5.monai.meta_dict	function	(sample, image_id, *, space=None, level=0)
medh5.monai.require_monai	function	()
medh5.monai.to_dict	function	(sample, images=None, annotations=(), *, space=None, physical=True)
medh5.monai.to_metatensor	function	(sample, image_id, *, roi=None, physical=True, space=None, level=0, dtype=<value>)
medh5.nodes	module
medh5.nodes.Attrs	class	(?) bases=
medh5.nodes.Attrs.__contains__	method	(key, /)
medh5.nodes.Attrs.__getitem__	method	(key, /)
medh5.nodes.Attrs.__iter__	method	()
medh5.nodes.Attrs.__len__	method	()
medh5.nodes.Attrs.get	method	(name, default=None)
medh5.nodes.Attrs.items	method	()
medh5.nodes.Attrs.keys	method	()
medh5.nodes.Attrs.to_dict	method	()
medh5.nodes.Attrs.values	method	()
medh5.nodes.Dataset	class	(?) bases=
medh5.nodes.Dataset.__getitem__	method	(key, /)
medh5.nodes.Dataset.__len__	method	()
medh5.nodes.Dataset.attrs	property
medh5.nodes.Dataset.chunks	property
medh5.nodes.Dataset.dtype	property
medh5.nodes.Dataset.filters	property
medh5.nodes.Dataset.name	property
medh5.nodes.Dataset.nbytes	property
medh5.nodes.Dataset.ndim	property
medh5.nodes.Dataset.read	method	()
medh5.nodes.Dataset.shape	property
medh5.nodes.Dataset.size	property
medh5.nodes.Dataset.storage_size	property
medh5.nodes.Group	class	(?) bases=
medh5.nodes.Group.__contains__	method	(key, /)
medh5.nodes.Group.__getitem__	method	(key, /)
medh5.nodes.Group.__iter__	method	()
medh5.nodes.Group.__len__	method	()
medh5.nodes.Group.attrs	property
medh5.nodes.Group.get	method	(path, default=None)
medh5.nodes.Group.items	method	()
medh5.nodes.Group.keys	method	()
medh5.nodes.Group.name	property
medh5.nodes.Group.values	method	()
medh5.open	function	(path, mode='r')
medh5.open_collection	function	(path)
medh5.open_sample	function	(path, mode='r')
medh5.pack	function	(sources, out, *, keys=None)
medh5.sample	module
medh5.sample.AnnotationCollection	class	(what, items, lookup=None) bases=
medh5.sample.AnnotationCollection.__contains__	method	(key)
medh5.sample.AnnotationCollection.__getitem__	method	(key)
medh5.sample.AnnotationCollection.__iter__	method	()
medh5.sample.AnnotationCollection.__len__	method	()
medh5.sample.AnnotationCollection.by_kind	method	(kind)
medh5.sample.AnnotationCollection.by_task	method	(task)
medh5.sample.AnnotationCollection.by_timepoint	method	(timepoint_id)
medh5.sample.AnnotationCollection.get	method	(key, default=None)
medh5.sample.AnnotationCollection.spanning	method	()
medh5.sample.FORMAT_VERSION	constant	str
medh5.sample.FRAME_ATTRS	constant	tuple
medh5.sample.ImageCollection	class	(what, items, lookup=None) bases=
medh5.sample.ImageCollection.__contains__	method	(key)
medh5.sample.ImageCollection.__getitem__	method	(key)
medh5.sample.ImageCollection.__iter__	method	()
medh5.sample.ImageCollection.__len__	method	()
medh5.sample.ImageCollection.by_modality	method	(modality)
medh5.sample.ImageCollection.by_timepoint	method	(timepoint_id)
medh5.sample.ImageCollection.get	method	(key, default=None)
medh5.sample.ImageCollection.on_grid	method	(grid_id)
medh5.sample.MANAGED_ROOT_ATTRS	constant	tuple
medh5.sample.PROFILES	constant	tuple
medh5.sample.ROOT_DIGEST_ATTRS	constant	tuple
medh5.sample.STANDARD_GROUPS	constant	tuple
medh5.sample.Sample	class	(handle) bases=
medh5.sample.Sample.__enter__	method	()
medh5.sample.Sample.__exit__	method	(*exc)
medh5.sample.Sample.annotations	property
medh5.sample.Sample.at	method	(timepoint)
medh5.sample.Sample.attr_name_map	method	()
medh5.sample.Sample.clinical	property
medh5.sample.Sample.close	method	()
medh5.sample.Sample.cohort	property
medh5.sample.Sample.compute_content_id	method	()
medh5.sample.Sample.content_id	property
medh5.sample.Sample.document	property
medh5.sample.Sample.document_text	method	(document_id)
medh5.sample.Sample.fresh_indices	property
medh5.sample.Sample.grids	property
medh5.sample.Sample.identity	property
medh5.sample.Sample.ignore_region	method	(ann_id, roi=None)
medh5.sample.Sample.images	property
medh5.sample.Sample.index	property
medh5.sample.Sample.is_longitudinal	property
medh5.sample.Sample.is_open	property
medh5.sample.Sample.kind	property
medh5.sample.Sample.label_set	property
medh5.sample.Sample.path	property
medh5.sample.Sample.profiles	property
medh5.sample.Sample.reference_grid	property
medh5.sample.Sample.resolve_frames	method	(from_frame, to_frame)
medh5.sample.Sample.root	property
medh5.sample.Sample.summary	method	()
medh5.sample.Sample.support	property
medh5.sample.Sample.timepoints	property
medh5.sample.Sample.tracks	method	(class_key=None, *, measure=True)
medh5.sample.Sample.transform_between	method	(source, target, *, by=None)
medh5.sample.Sample.transforms	property
medh5.sample.Sample.valid_region	method	(image_id, roi=None)
medh5.sample.Sample.verify	method	(partial=None)
medh5.sample.Sample.version	property
medh5.sample.SampleWriter	class	(path, *, sample_id=None, subject_id=None, codec='balanced', profiles=None) bases=
medh5.sample.SampleWriter.__enter__	method	()
medh5.sample.SampleWriter.__exit__	method	(exc_type=None, _exc=None, _tb=None)
medh5.sample.SampleWriter.abort	method	()
medh5.sample.SampleWriter.acquisition	method	(image_id, **params)
medh5.sample.SampleWriter.activity	method	(activity_type, *, agent=None, activity_id=None, **fields)
medh5.sample.SampleWriter.add_boxes	method	(ann_id, boxes, class_ids, *, grid=None, space='index', frame_uid=None, instance_ids=None, scores=None, attributes=None, slice_index=None, annotated_classes=None, closure='explicit', timepoints=None, prov=None, quality=None, derived_from=None, task='detection', codec=None)
medh5.sample.SampleWriter.add_classification	method	(ann_id, labels, *, scope='sample', multilabel=True, scope_ids=None, schemes=None, scheme_values=None, grid=None, annotated_classes=None, closure='explicit', timepoints=None, prov=None, quality=None, derived_from=None, codec=None)
medh5.sample.SampleWriter.add_contours	method	(ann_id, polygons, *, grid=None, space='index', frame_uid=None, annotated_classes=None, closure='explicit', timepoints=None, prov=None, quality=None, derived_from=None, task='segmentation', codec=None)
medh5.sample.SampleWriter.add_document	method	(document=None, **fields)
medh5.sample.SampleWriter.add_event	method	(event=None, **fields)
medh5.sample.SampleWriter.add_grid	method	(grid_id, *, shape, spacing, origin=None, direction=None, axis_names=None, axis_kinds=None, coord_system='LPS', units='mm', timepoint=None, frame_uid=None, patch_hint=None, chunk_hint=None, time_values=None, time_units=None)
medh5.sample.SampleWriter.add_image	method	(image_id, data, *, grid, modality, value_type='intensity', value_units=None, channel_names=None, rescale_slope=None, rescale_intercept=None, window_center=None, window_width=None, valid_mask=None, prov=None, codec=None)
medh5.sample.SampleWriter.add_keypoints	method	(ann_id, points, keypoint_classes, class_ids, *, grid=None, space='index', frame_uid=None, visibility=None, instance_ids=None, scores=None, skeleton=None, annotated_classes=None, closure='explicit', timepoints=None, prov=None, quality=None, derived_from=None, task='detection', codec=None)
medh5.sample.SampleWriter.add_link	method	(link=None, **fields)
medh5.sample.SampleWriter.add_mask	method	(ann_id, mask, *, grid, task='other', prov=None, codec=None)
medh5.sample.SampleWriter.add_mesh	method	(ann_id, vertices, faces, *, grid=None, space='world', frame_uid=None, normals=None, vertex_class_ids=None, mesh_offsets=None, mesh_class_ids=None, annotated_classes=None, closure='explicit', timepoints=None, prov=None, quality=None, derived_from=None, task='segmentation', codec=None)
medh5.sample.SampleWriter.add_obb	method	(ann_id, centers, sizes, rotations, class_ids, *, grid=None, space='index', frame_uid=None, instance_ids=None, scores=None, attributes=None, annotated_classes=None, closure='explicit', timepoints=None, prov=None, quality=None, derived_from=None, task='detection', codec=None)
medh5.sample.SampleWriter.add_points	method	(ann_id, points, *, grid=None, space='index', frame_uid=None, class_ids=None, instance_ids=None, names=None, weights=None, correspondence=None, annotated_classes=None, closure='explicit', timepoints=None, prov=None, quality=None, derived_from=None, task='detection', codec=None)
medh5.sample.SampleWriter.add_pyramid	method	(image_id, levels, *, grid_levels, modality, value_type='intensity', downsample_method='mean', value_units=None, rescale_slope=None, rescale_intercept=None, prov=None, codec=None)
medh5.sample.SampleWriter.add_records	method	(records)
medh5.sample.SampleWriter.add_segmentation	method	(ann_id, *, grid, masks=None, probabilities=None, instances=None, labelmap=None, label_values=None, ignore_value=None, encoding='auto', threshold=None, annotated_classes=None, closure='explicit', ignore=None, ignore_mask=None, timepoints=None, prov=None, quality=None, derived_from=None, task='segmentation', codec=None)
medh5.sample.SampleWriter.add_timepoint	method	(timepoint_id, **fields)
medh5.sample.SampleWriter.add_transform	method	(transform_id, *, kind, from_frame, to_frame, matrix=None, field=None, control_points=None, components=None, field_grid=None, cp_grid=None, vector_space='world', interpolation='linear', extrapolation='zero', order=3, units=None, from_grid=None, to_grid=None, invertible=None, inverse_id=None, metrics=None, prov=None, codec=None, field_dtype='float32')
medh5.sample.SampleWriter.build_index	method	(ann_ids=None, *, max_coords=<value>, occupancy=<value>, seed=0)
medh5.sample.SampleWriter.clinical	method	()
medh5.sample.SampleWriter.closed	property
medh5.sample.SampleWriter.codec	property
medh5.sample.SampleWriter.cohort	method	(**fields)
medh5.sample.SampleWriter.commit	method	(*, digests=True)
medh5.sample.SampleWriter.deidentification	method	(**fields)
medh5.sample.SampleWriter.document	property
medh5.sample.SampleWriter.drop_clinical	method	()
medh5.sample.SampleWriter.extra	method	(namespace, value)
medh5.sample.SampleWriter.frame_uids	method	()
medh5.sample.SampleWriter.grids	property
medh5.sample.SampleWriter.handle	property
medh5.sample.SampleWriter.has_clinical	property
medh5.sample.SampleWriter.identity	method	(**fields)
medh5.sample.SampleWriter.infer_profiles	method	()
medh5.sample.SampleWriter.label_set	method	(label_set)
medh5.sample.SampleWriter.organization	method	(name, **fields)
medh5.sample.SampleWriter.path	property
medh5.sample.SampleWriter.person	method	(name, agent_id=None, **fields)
medh5.sample.SampleWriter.remap_frame_uids	method	(mapping)
medh5.sample.SampleWriter.remove_annotation	method	(ann_id)
medh5.sample.SampleWriter.remove_grid	method	(grid_id)
medh5.sample.SampleWriter.remove_image	method	(image_id)
medh5.sample.SampleWriter.remove_transform	method	(transform_id)
medh5.sample.SampleWriter.set_clock	method	(clock=None, **fields)
medh5.sample.SampleWriter.set_image_attrs	method	(image_id, **attrs)
medh5.sample.SampleWriter.set_quality	method	(key, **fields)
medh5.sample.SampleWriter.software	method	(name, version=None, **fields)
medh5.sample.SampleWriter.split	method	(**fields)
medh5.sample.SampleWriter.transcode_annotation	method	(ann_id, to_kind, *, codec=None, drop_identity=False)
medh5.sample.TimepointView	class	(sample, timepoint) bases=
medh5.sample.TimepointView.annotations	property
medh5.sample.TimepointView.grids	property
medh5.sample.TimepointView.id	property
medh5.sample.TimepointView.images	property
medh5.sample.TimepointView.timepoint	property
medh5.sample.amend	function	(path, *, codec=None)
medh5.sample.annotation_id	function	(reference)
medh5.sample.create	function	(path, *, sample_id=None, subject_id=None, codec='balanced', profiles=None)
medh5.sample.open_sample	function	(path, mode='r')
medh5.sampling	module
medh5.sampling.BLEND_MODES	constant	tuple
medh5.sampling.PAIR_MODES	constant	tuple
medh5.sampling.PairReport	class	(files=0, pairs=0, skipped=<factory>) bases=
medh5.sampling.PairReport.add_skip	method	(path)
medh5.sampling.PairReport.files	field
medh5.sampling.PairReport.pairs	field
medh5.sampling.PairReport.skipped	field
medh5.sampling.PairReport.summary	method	()
medh5.sampling.Patch	class	(slices, pad=(), center=(), strategy='uniform', class_id=None, used_index=None, grid_id=None) bases=
medh5.sampling.Patch.apply_padding	method	(array, value=0.0)
medh5.sampling.Patch.center	field
medh5.sampling.Patch.class_id	field
medh5.sampling.Patch.grid_id	field
medh5.sampling.Patch.needs_padding	property
medh5.sampling.Patch.pad	field
medh5.sampling.Patch.padding	property
medh5.sampling.Patch.shape	property
medh5.sampling.Patch.slices	field
medh5.sampling.Patch.strategy	field
medh5.sampling.Patch.to_json	method	()
medh5.sampling.Patch.used_index	field
medh5.sampling.PatchAggregator	class	(spatial_shape, *, channels=None, mode='gaussian', sigma_scale=0.125, dtype=<value>, grid_id=None) bases=
medh5.sampling.PatchAggregator.add	method	(prediction, patch)
medh5.sampling.PatchAggregator.channels	property
medh5.sampling.PatchAggregator.count	property
medh5.sampling.PatchAggregator.coverage	property
medh5.sampling.PatchAggregator.dtype	property
medh5.sampling.PatchAggregator.grid_id	property
medh5.sampling.PatchAggregator.mode	property
medh5.sampling.PatchAggregator.result	method	(*, uncovered=nan)
medh5.sampling.PatchAggregator.sigma_scale	property
medh5.sampling.PatchAggregator.spatial_shape	property
medh5.sampling.PatchSampler	class	(patch_size, *, strategy='balanced', foreground_prob=0.5, foreground_classes=None, class_weights='uniform') bases=
medh5.sampling.PatchSampler.class_weights	property
medh5.sampling.PatchSampler.draw	method	(sample, annotation=None, rng=None, *, grid=None)
medh5.sampling.PatchSampler.draws	method	(sample, annotation=None, n=1, rng=None, *, grid=None)
medh5.sampling.PatchSampler.foreground_classes	property
medh5.sampling.PatchSampler.foreground_prob	property
medh5.sampling.PatchSampler.patch_size	property
medh5.sampling.PatchSampler.strategy	property
medh5.sampling.STRATEGIES	constant	tuple
medh5.sampling.Seed	alias
medh5.sampling.TimepointPair	class	(first, second, interval_days=None, label=None) bases=
medh5.sampling.TimepointPair.first	field
medh5.sampling.TimepointPair.interval_days	field
medh5.sampling.TimepointPair.label	field
medh5.sampling.TimepointPair.second	field
medh5.sampling.TimepointPairSampler	class	(mode='consecutive') bases=
medh5.sampling.TimepointPairSampler.__call__	method	(sample)
medh5.sampling.TimepointPairSampler.mode	property
medh5.sampling.TimepointPairSampler.pairs	method	(sample)
medh5.sampling.blend_weights	function	(patch_size, *, mode='gaussian', sigma_scale=0.125)
medh5.sampling.coerce_patch_size	function	(patch_size, ndim)
medh5.sampling.grid_patches	function	(shape, patch_size, *, overlap=0, grid_id=None)
medh5.sampling.iter_patches	function	(sample, sampler, *, annotation=None, n=1, rng=None, grid=None)
medh5.sampling.window_around	function	(center, patch, shape)
medh5.storage	module
medh5.storage.BLOSC2_FILTER_ID	constant	int
medh5.storage.BLOSC_FILTER_ID	constant	int
medh5.storage.BUILTIN_FILTER_IDS	constant	frozenset
medh5.storage.BULK_MIN_BYTES	constant	int
medh5.storage.CACHE_SAFETY	constant	float
medh5.storage.COMPRESS_MIN_BYTES	constant	int
medh5.storage.Codec	class	(name, blosc2=None, gzip_level=None, shuffle=True) bases=
medh5.storage.Codec.blosc2	field
medh5.storage.Codec.gzip_level	field
medh5.storage.Codec.kwargs	method	()
medh5.storage.Codec.name	field
medh5.storage.Codec.shuffle	field
medh5.storage.CodecProfile	class	(name, image, label, description) bases=
medh5.storage.CodecProfile.codec	method	(role)
medh5.storage.CodecProfile.description	field
medh5.storage.CodecProfile.image	field
medh5.storage.CodecProfile.label	field
medh5.storage.CodecProfile.name	field
medh5.storage.DEFAULT_L3_BYTES	constant	int
medh5.storage.DEFAULT_MAX_COORDS	constant	int
medh5.storage.DEFAULT_OCCUPANCY_FACTOR	constant	int
medh5.storage.DEFAULT_PATCH	constant	int
medh5.storage.DEFAULT_PROFILE	constant	str
medh5.storage.IndexPayload	class	(?) bases=
medh5.storage.IndexPayload.ann_id	field
medh5.storage.IndexPayload.class_bboxes	field
medh5.storage.IndexPayload.class_ids	field
medh5.storage.IndexPayload.fg_coords	field
medh5.storage.IndexPayload.max_coords	field
medh5.storage.IndexPayload.occupancy	field
medh5.storage.IndexPayload.seed	field
medh5.storage.IndexPayload.source_digest	field
medh5.storage.IndexPayload.stats	field
medh5.storage.IndexPayload.voxel_counts	field
medh5.storage.MAX_CHUNK_BYTES	constant	float
medh5.storage.MIN_CHUNK_BYTES	constant	float
medh5.storage.OVERSHOOT_LIMIT	constant	float
medh5.storage.PROFILES	constant	dict
medh5.storage.RecompressResult	class	(path, profile, datasets=0, bytes_before=0, bytes_after=0, content_id=None, content_id_preserved=True, verified=True, mismatched=<factory>, unattested=<factory>, changed=<factory>, kept=<factory>, unverified=<factory>) bases=
medh5.storage.RecompressResult.bytes_after	field
medh5.storage.RecompressResult.bytes_before	field
medh5.storage.RecompressResult.changed	field
medh5.storage.RecompressResult.content_id	field
medh5.storage.RecompressResult.content_id_preserved	field
medh5.storage.RecompressResult.datasets	field
medh5.storage.RecompressResult.from_json	classmethod	(doc)
medh5.storage.RecompressResult.kept	field
medh5.storage.RecompressResult.mismatched	field
medh5.storage.RecompressResult.ok	property
medh5.storage.RecompressResult.path	field
medh5.storage.RecompressResult.profile	field
medh5.storage.RecompressResult.ratio	property
medh5.storage.RecompressResult.to_json	method	()
medh5.storage.RecompressResult.unattested	field
medh5.storage.RecompressResult.unverified	field
medh5.storage.RecompressResult.verified	field
medh5.storage.Role	alias
medh5.storage.SamplingIndex	class	(?) bases=
medh5.storage.SamplingIndex.ann_id	property
medh5.storage.SamplingIndex.bbox	method	(class_id)
medh5.storage.SamplingIndex.class_ids	property
medh5.storage.SamplingIndex.class_weights	method	(mode='inverse_frequency')
medh5.storage.SamplingIndex.coords	method	(class_id)
medh5.storage.SamplingIndex.group	property
medh5.storage.SamplingIndex.has_class	method	(class_id)
medh5.storage.SamplingIndex.has_occupancy	property
medh5.storage.SamplingIndex.is_current	method	(annotation_digest)
medh5.storage.SamplingIndex.max_coords	property
medh5.storage.SamplingIndex.occupancy_plane	method	(position)
medh5.storage.SamplingIndex.sample_foreground	method	(class_id, n=1, rng=None)
medh5.storage.SamplingIndex.source_digest	property
medh5.storage.SamplingIndex.summary	method	()
medh5.storage.SamplingIndex.voxel_counts	property
medh5.storage.build_index	function	(annotation, *, classes=None, max_coords=<value>, occupancy=<value>, seed=0, source_digest=None)
medh5.storage.chunk_report	function	(shape, chunks, itemsize)
medh5.storage.dataset_kwargs	deprecated
medh5.storage.dataset_layout	function	(shape, dtype, *, profile=None, role='image', chunks=None)
medh5.storage.describe_filters	function	(dataset)
medh5.storage.detect_l3_bytes	function	()
medh5.storage.field_chunks	function	(grid, shape, itemsize)
medh5.storage.fit_chunks	function	(proposed, shape)
medh5.storage.grid_chunks	function	(grid, itemsize, *, leading=0)
medh5.storage.is_bulk	function	(dataset)
medh5.storage.occupancy	function	(mask, factor)
medh5.storage.optimize_chunks	function	(shape, axis_kinds, patch=None, *, itemsize=4, l3_bytes=None, leading=0)
medh5.storage.profile_family	function	(path)
medh5.storage.read_indices	function	(root)
medh5.storage.recompress	function	(path, profile, *, out=None, rechunk=False)
medh5.storage.recompress_paths	function	(paths, profile, *, rechunk=False)
medh5.storage.resolve_profile	function	(profile)
medh5.storage.spatial_chunk_for	function	(spatial_shape, patch=None, *, itemsize=4, l3_bytes=None)
medh5.task	module
medh5.task.CENSORING	constant	tuple
medh5.task.CODES	constant	dict
medh5.task.Confine	alias
medh5.task.EventTable	class	(columns) bases=
medh5.task.EventTable.__getitem__	method	(i)
medh5.task.EventTable.__iter__	method	()
medh5.task.EventTable.__len__	method	()
medh5.task.EventTable.column	method	(name)
medh5.task.EventTable.concepts	method	()
medh5.task.EventTable.index	method	(event_id)
medh5.task.Finding	class	(code, location, message) bases=
medh5.task.Finding.code	field
medh5.task.Finding.from_json	classmethod	(doc)
medh5.task.Finding.location	field
medh5.task.Finding.message	field
medh5.task.Finding.summary	property
medh5.task.LABELS	deprecated
medh5.task.LinkTable	class	(columns) bases=
medh5.task.LinkTable.__getitem__	method	(i)
medh5.task.LinkTable.__iter__	method	()
medh5.task.LinkTable.__len__	method	()
medh5.task.LinkTable.column	method	(name)
medh5.task.LinkTable.fragment	method	(i)
medh5.task.Note	class	(location, message) bases=
medh5.task.Note.from_json	classmethod	(doc)
medh5.task.Note.location	field
medh5.task.Note.message	field
medh5.task.Packed	class	(data, offsets, valid=None) bases=
medh5.task.Packed.__getitem__	method	(i)
medh5.task.Packed.__iter__	method	()
medh5.task.Packed.__len__	method	()
medh5.task.Packed.data	property
medh5.task.Packed.from_core	classmethod	(value)
medh5.task.Packed.offsets	property
medh5.task.Packed.tolist	method	()
medh5.task.Packed.valid	property
medh5.task.Preflight	class	(task_fingerprint, manifest_fingerprint, findings, subjects, rows) bases=
medh5.task.Preflight.counts	property
medh5.task.Preflight.eligible	method	(partition=None)
medh5.task.Preflight.findings	property
medh5.task.Preflight.from_core	classmethod	(doc)
medh5.task.Preflight.manifest_fingerprint	property
medh5.task.Preflight.ok	property
medh5.task.Preflight.row	method	(row_id)
medh5.task.Preflight.rows	property
medh5.task.Preflight.subjects	property
medh5.task.Preflight.task_fingerprint	property
medh5.task.ROI	constant	tuple
medh5.task.ROIS	constant	tuple
medh5.task.ROW_STATUSES	constant	tuple
medh5.task.Reconciled	class	(event_id, digest, sources) bases=
medh5.task.Reconciled.digest	field
medh5.task.Reconciled.event_id	field
medh5.task.Reconciled.sources	field
medh5.task.RepinReport	class	(changed, unchanged, reconciled, rows) bases=
medh5.task.RepinReport.changed	field
medh5.task.RepinReport.from_json	classmethod	(doc)
medh5.task.RepinReport.reconciled	field
medh5.task.RepinReport.rows	field
medh5.task.RepinReport.unchanged	field
medh5.task.Repinned	class	(source_id, before, after) bases=
medh5.task.Repinned.after	field
medh5.task.Repinned.before	field
medh5.task.Repinned.source_id	field
medh5.task.Row	class	(row_id, subject_id, cutoff_us) bases=
medh5.task.Row.cutoff_us	field
medh5.task.Row.row_id	field
medh5.task.Row.subject_id	field
medh5.task.RowView	class	(pre, i) bases=
medh5.task.RowView.cutoff_us	property
medh5.task.RowView.eligible	property
medh5.task.RowView.event_fragments	property
medh5.task.RowView.events	property
medh5.task.RowView.fingerprint	property
medh5.task.RowView.order	property
medh5.task.RowView.order_known	property
medh5.task.RowView.partition	property
medh5.task.RowView.plan	property
medh5.task.RowView.reasons	property
medh5.task.RowView.row_id	property
medh5.task.RowView.selected	property
medh5.task.RowView.selection	property
medh5.task.RowView.slots	property
medh5.task.RowView.sources	property
medh5.task.RowView.status	property
medh5.task.RowView.subject	property
medh5.task.RowView.subject_id	property
medh5.task.RowView.subject_index	property
medh5.task.RowView.target	property
medh5.task.RowView.tie_group	property
medh5.task.SCHEMA	constant	str
medh5.task.SELECTION_STATUSES	constant	tuple
medh5.task.STATUSES	deprecated
medh5.task.Slot	class	(name, modality, required=False, patch=None, roi='center', classes=()) bases=
medh5.task.Slot.classes	field
medh5.task.Slot.from_json	classmethod	(doc)
medh5.task.Slot.modality	field
medh5.task.Slot.name	field
medh5.task.Slot.patch	field
medh5.task.Slot.required	field
medh5.task.Slot.roi	field
medh5.task.Slot.to_json	method	()
medh5.task.SlotFill	class	(slot, available, fragment, image_id, grid_id, event_id, center, roi, annotations, label_annotations=()) bases=
medh5.task.SlotFill.annotations	field
medh5.task.SlotFill.available	field
medh5.task.SlotFill.center	field
medh5.task.SlotFill.event_id	field
medh5.task.SlotFill.fragment	field
medh5.task.SlotFill.grid_id	field
medh5.task.SlotFill.image_id	field
medh5.task.SlotFill.label_annotations	field
medh5.task.SlotFill.roi	field
medh5.task.SlotFill.slot	field
medh5.task.SourceRef	class	(uri, content_id, sample_key=None, source_id='', local_subject_id=None) bases=
medh5.task.SourceRef.check	method	(base=None, *, deep=False, root=None)
medh5.task.SourceRef.content_id	field
medh5.task.SourceRef.from_json	classmethod	(doc)
medh5.task.SourceRef.local_subject_id	field
medh5.task.SourceRef.locator	property
medh5.task.SourceRef.open	method	(base=None, *, root=None)
medh5.task.SourceRef.pin	classmethod	(path, *, sample_key=None, source_id=None, uri=None)
medh5.task.SourceRef.resolve	method	(base=None, *, root=None)
medh5.task.SourceRef.sample_key	field
medh5.task.SourceRef.source_id	field
medh5.task.SourceRef.to_json	method	()
medh5.task.SourceRef.uri	field
medh5.task.Subject	class	(subject_id, sources, partition=None, clock_id=None, reconciled=()) bases=
medh5.task.Subject.clock_id	field
medh5.task.Subject.from_json	classmethod	(doc)
medh5.task.Subject.partition	field
medh5.task.Subject.reconciled	field
medh5.task.Subject.sources	field
medh5.task.Subject.subject_id	field
medh5.task.SubjectHistory	class	(subject_id, partition, sources, events, links, document_events, document_fragments, document_ids, payload_fragments, payload_kinds, payload_ids) bases=
medh5.task.SubjectHistory.document_events	field
medh5.task.SubjectHistory.document_fragments	field
medh5.task.SubjectHistory.document_ids	field
medh5.task.SubjectHistory.events	field
medh5.task.SubjectHistory.from_core	classmethod	(doc)
medh5.task.SubjectHistory.links	field
medh5.task.SubjectHistory.owned_documents	method	(event)
medh5.task.SubjectHistory.partition	field
medh5.task.SubjectHistory.payload	method	(k)
medh5.task.SubjectHistory.payload_fragments	field
medh5.task.SubjectHistory.payload_ids	field
medh5.task.SubjectHistory.payload_kinds	field
medh5.task.SubjectHistory.sources	field
medh5.task.SubjectHistory.subject_id	field
medh5.task.TARGET_STATUSES	constant	tuple
medh5.task.Target	class	(id, version, code_system, code, positive, negative=(), *, horizon_us, min_follow_up_us=None, censoring='censor', exclude_prevalent=True, kind=None) bases=
medh5.task.Target.censoring	field
medh5.task.Target.code	field
medh5.task.Target.code_system	field
medh5.task.Target.exclude_prevalent	field
medh5.task.Target.from_json	classmethod	(doc)
medh5.task.Target.horizon_us	field
medh5.task.Target.id	field
medh5.task.Target.kind	field
medh5.task.Target.min_follow_up_us	field
medh5.task.Target.negative	field
medh5.task.Target.positive	field
medh5.task.Target.to_json	method	()
medh5.task.Target.version	field
medh5.task.TargetLabel	class	(status, value, event_id, reason) bases=
medh5.task.TargetLabel.event_id	field
medh5.task.TargetLabel.observed	property
medh5.task.TargetLabel.reason	field
medh5.task.TargetLabel.status	field
medh5.task.TargetLabel.value	field
medh5.task.TaskManifest	class	(doc, *, base=None) bases=
medh5.task.TaskManifest.add_row	method	(row_id, subject_id, cutoff_us)
medh5.task.TaskManifest.add_subject	method	(subject_id, sources, *, partition=None, clock_id=None)
medh5.task.TaskManifest.base	property
medh5.task.TaskManifest.declared_fingerprint	property
medh5.task.TaskManifest.from_cohort	classmethod	(cohort, split, *, task_id, version, identity_namespace, base=None, fold=None, training_partition='train', policy=None, slots=(), target=None, description=None)
medh5.task.TaskManifest.identity_namespace	property
medh5.task.TaskManifest.load	classmethod	(path)
medh5.task.TaskManifest.manifest_fingerprint	property
medh5.task.TaskManifest.new	classmethod	(task_id, version, *, identity_namespace, policy=None, slots=(), target=None, split=None, description=None, base=None)
medh5.task.TaskManifest.notes	property
medh5.task.TaskManifest.partition_of	method	(subject_id)
medh5.task.TaskManifest.policy	property
medh5.task.TaskManifest.preflight	method	(base=None, *, deep=False, confine=None)
medh5.task.TaskManifest.reconcile	method	(base=None, *, confine=None)
medh5.task.TaskManifest.repin	method	(base=None, *, sources=None, dry_run=False, confine=None)
medh5.task.TaskManifest.row_fingerprint	method	(row_id)
medh5.task.TaskManifest.rows	property
medh5.task.TaskManifest.save	method	(path)
medh5.task.TaskManifest.slots	property
medh5.task.TaskManifest.split	property
medh5.task.TaskManifest.subjects	property
medh5.task.TaskManifest.subjects_digest	method	(partition)
medh5.task.TaskManifest.target	property
medh5.task.TaskManifest.task_fingerprint	property
medh5.task.TaskManifest.task_id	property
medh5.task.TaskManifest.task_version	property
medh5.task.TaskManifest.to_json	method	()
medh5.task.TaskManifest.training_partition	property
medh5.task.TaskManifest.validate	method	()
medh5.task.concept_token	function	(kind, code_system, code)
medh5.task.preflight	function	(task, base=None, *, deep=False, confine=None)
medh5.task.schema_text	function	()
medh5.torch	module
medh5.torch.ALIGNMENTS	constant	tuple
medh5.torch.AVAILABLE	constant	bool
medh5.torch.CACHE	constant	medh5.torch.handles.HandleCache
medh5.torch.ClinicalTaskDataset	class	(task, *, partition=None, statuses=('eligible',), concepts=None, documents=None, row_features=None, base=None, strict=True, preflight=None, confine=None, class_ignore=False) bases=
medh5.torch.ClinicalTaskDataset.__getitem__	method	(index)
medh5.torch.ClinicalTaskDataset.__len__	method	()
medh5.torch.ClinicalTaskDataset.file_groups	method	()
medh5.torch.ConceptVocabulary	class	(concepts, stats=<factory>, fitted_on=None, units=<factory>, categories=<factory>) bases=
medh5.torch.ConceptVocabulary.__len__	method	()
medh5.torch.ConceptVocabulary.categories	field
medh5.torch.ConceptVocabulary.check_fitted_on	method	(task)
medh5.torch.ConceptVocabulary.concepts	field
medh5.torch.ConceptVocabulary.digest	property
medh5.torch.ConceptVocabulary.fit	classmethod	(task, preflight=None, *, partition=None)
medh5.torch.ConceptVocabulary.fits_unit	method	(token, unit)
medh5.torch.ConceptVocabulary.fitted_on	field
medh5.torch.ConceptVocabulary.from_json	classmethod	(doc)
medh5.torch.ConceptVocabulary.index	method	(token)
medh5.torch.ConceptVocabulary.load	classmethod	(path)
medh5.torch.ConceptVocabulary.n_values	property
medh5.torch.ConceptVocabulary.normalise	method	(token, value)
medh5.torch.ConceptVocabulary.save	method	(path)
medh5.torch.ConceptVocabulary.stats	field
medh5.torch.ConceptVocabulary.to_json	method	()
medh5.torch.ConceptVocabulary.units	field
medh5.torch.ConceptVocabulary.value_index	method	(token, text)
medh5.torch.FileGroupedSampler	class	(dataset, *, shuffle=True, seed=0, num_replicas=None, rank=None, drop_last=False) bases=
medh5.torch.FileGroupedSampler.__iter__	method	()
medh5.torch.FileGroupedSampler.__len__	method	()
medh5.torch.FileGroupedSampler.groups	property
medh5.torch.FileGroupedSampler.num_replicas	property
medh5.torch.FileGroupedSampler.rank	property
medh5.torch.FileGroupedSampler.set_epoch	method	(epoch)
medh5.torch.GridPatchDataset	class	(paths, patch_size, *, overlap=0, **kwargs) bases=
medh5.torch.GridPatchDataset.__getitem__	method	(index)
medh5.torch.GridPatchDataset.__len__	method	()
medh5.torch.GridPatchDataset.file_groups	method	()
medh5.torch.GridStitcher	class	(dataset, *, channels=None, mode='gaussian', sigma_scale=0.125, dtype=<value>) bases=
medh5.torch.GridStitcher.add	method	(predictions, meta)
medh5.torch.GridStitcher.finish	method	(*, partial=False)
medh5.torch.GridStitcher.pending	property
medh5.torch.HandleCache	class	(maxsize=32) bases=
medh5.torch.HandleCache.__len__	method	()
medh5.torch.HandleCache.clear	method	()
medh5.torch.HandleCache.close_all	method	()
medh5.torch.HandleCache.get	method	(path, sample_key=None)
medh5.torch.HandleCache.lease	method	(path, sample_key=None, *, content_id=None)
medh5.torch.HandleCache.maxsize	property
medh5.torch.HandleCache.opens	property
medh5.torch.HandleCache.owner_pid	property
medh5.torch.HandleCache.resize	method	(maxsize)
medh5.torch.LABEL_FORMATS	constant	tuple
medh5.torch.PairReport	class	(files=0, pairs=0, skipped=<factory>) bases=
medh5.torch.PairReport.add_skip	method	(path)
medh5.torch.PairReport.files	field
medh5.torch.PairReport.pairs	field
medh5.torch.PairReport.skipped	field
medh5.torch.PairReport.summary	method	()
medh5.torch.PairedPatchDataset	class	(paths, sampler, *, pair_sampler=None, align='transform', samples_per_pair=1, annotation=None, label=None, seed=0, **kwargs) bases=
medh5.torch.PairedPatchDataset.__getitem__	method	(index)
medh5.torch.PairedPatchDataset.__len__	method	()
medh5.torch.PairedPatchDataset.epoch	property
medh5.torch.PairedPatchDataset.file_groups	method	()
medh5.torch.PairedPatchDataset.set_epoch	method	(epoch)
medh5.torch.Patch	class	(slices, pad=(), center=(), strategy='uniform', class_id=None, used_index=None, grid_id=None) bases=
medh5.torch.Patch.apply_padding	method	(array, value=0.0)
medh5.torch.Patch.center	field
medh5.torch.Patch.class_id	field
medh5.torch.Patch.grid_id	field
medh5.torch.Patch.needs_padding	property
medh5.torch.Patch.pad	field
medh5.torch.Patch.padding	property
medh5.torch.Patch.shape	property
medh5.torch.Patch.slices	field
medh5.torch.Patch.strategy	field
medh5.torch.Patch.to_json	method	()
medh5.torch.Patch.used_index	field
medh5.torch.PatchDataset	class	(paths, sampler, *, samples_per_volume=1, annotation=None, seed=0, **kwargs) bases=
medh5.torch.PatchDataset.__getitem__	method	(index)
medh5.torch.PatchDataset.__len__	method	()
medh5.torch.PatchDataset.epoch	property
medh5.torch.PatchDataset.file_groups	method	()
medh5.torch.PatchDataset.set_epoch	method	(epoch)
medh5.torch.PatchSampler	class	(patch_size, *, strategy='balanced', foreground_prob=0.5, foreground_classes=None, class_weights='uniform') bases=
medh5.torch.PatchSampler.class_weights	property
medh5.torch.PatchSampler.draw	method	(sample, annotation=None, rng=None, *, grid=None)
medh5.torch.PatchSampler.draws	method	(sample, annotation=None, n=1, rng=None, *, grid=None)
medh5.torch.PatchSampler.foreground_classes	property
medh5.torch.PatchSampler.foreground_prob	property
medh5.torch.PatchSampler.patch_size	property
medh5.torch.PatchSampler.strategy	property
medh5.torch.TimepointPair	class	(first, second, interval_days=None, label=None) bases=
medh5.torch.TimepointPair.first	field
medh5.torch.TimepointPair.interval_days	field
medh5.torch.TimepointPair.label	field
medh5.torch.TimepointPair.second	field
medh5.torch.TimepointPairSampler	class	(mode='consecutive') bases=
medh5.torch.TimepointPairSampler.__call__	method	(sample)
medh5.torch.TimepointPairSampler.mode	property
medh5.torch.TimepointPairSampler.pairs	method	(sample)
medh5.torch.VolumeDataset	class	(paths, *, images=None, annotations=None, label_format='onehot', physical=True, dtype=<value>, timepoint=None) bases=
medh5.torch.VolumeDataset.__getitem__	method	(index)
medh5.torch.VolumeDataset.__len__	method	()
medh5.torch.VolumeDataset.file_groups	method	()
medh5.torch.clinical	module
medh5.torch.clinical.ClinicalTaskDataset	class	(task, *, partition=None, statuses=('eligible',), concepts=None, documents=None, row_features=None, base=None, strict=True, preflight=None, confine=None, class_ignore=False) bases=
medh5.torch.clinical.ClinicalTaskDataset.__getitem__	method	(index)
medh5.torch.clinical.ClinicalTaskDataset.__len__	method	()
medh5.torch.clinical.ClinicalTaskDataset.file_groups	method	()
medh5.torch.clinical.ConceptVocabulary	class	(concepts, stats=<factory>, fitted_on=None, units=<factory>, categories=<factory>) bases=
medh5.torch.clinical.ConceptVocabulary.__len__	method	()
medh5.torch.clinical.ConceptVocabulary.categories	field
medh5.torch.clinical.ConceptVocabulary.check_fitted_on	method	(task)
medh5.torch.clinical.ConceptVocabulary.concepts	field
medh5.torch.clinical.ConceptVocabulary.digest	property
medh5.torch.clinical.ConceptVocabulary.fit	classmethod	(task, preflight=None, *, partition=None)
medh5.torch.clinical.ConceptVocabulary.fits_unit	method	(token, unit)
medh5.torch.clinical.ConceptVocabulary.fitted_on	field
medh5.torch.clinical.ConceptVocabulary.from_json	classmethod	(doc)
medh5.torch.clinical.ConceptVocabulary.index	method	(token)
medh5.torch.clinical.ConceptVocabulary.load	classmethod	(path)
medh5.torch.clinical.ConceptVocabulary.n_values	property
medh5.torch.clinical.ConceptVocabulary.normalise	method	(token, value)
medh5.torch.clinical.ConceptVocabulary.save	method	(path)
medh5.torch.clinical.ConceptVocabulary.stats	field
medh5.torch.clinical.ConceptVocabulary.to_json	method	()
medh5.torch.clinical.ConceptVocabulary.units	field
medh5.torch.clinical.ConceptVocabulary.value_index	method	(token, text)
medh5.torch.clinical.PAD	constant	int
medh5.torch.clinical.UNKNOWN	constant	int
medh5.torch.clinical.collate_clinical	function	(batch)
medh5.torch.clinical.concept_of	function	(event)
medh5.torch.collate	function	(batch)
medh5.torch.collate	module
medh5.torch.collate.collate	function	(batch)
medh5.torch.collate.stack_images	function	(batch, order)
medh5.torch.collate_clinical	function	(batch)
medh5.torch.datasets	module
medh5.torch.datasets.ALIGNMENTS	constant	tuple
medh5.torch.datasets.GridPatchDataset	class	(paths, patch_size, *, overlap=0, **kwargs) bases=
medh5.torch.datasets.GridPatchDataset.__getitem__	method	(index)
medh5.torch.datasets.GridPatchDataset.__len__	method	()
medh5.torch.datasets.GridPatchDataset.file_groups	method	()
medh5.torch.datasets.LABEL_FORMATS	constant	tuple
medh5.torch.datasets.PairedPatchDataset	class	(paths, sampler, *, pair_sampler=None, align='transform', samples_per_pair=1, annotation=None, label=None, seed=0, **kwargs) bases=
medh5.torch.datasets.PairedPatchDataset.__getitem__	method	(index)
medh5.torch.datasets.PairedPatchDataset.__len__	method	()
medh5.torch.datasets.PairedPatchDataset.epoch	property
medh5.torch.datasets.PairedPatchDataset.file_groups	method	()
medh5.torch.datasets.PairedPatchDataset.set_epoch	method	(epoch)
medh5.torch.datasets.PatchDataset	class	(paths, sampler, *, samples_per_volume=1, annotation=None, seed=0, **kwargs) bases=
medh5.torch.datasets.PatchDataset.__getitem__	method	(index)
medh5.torch.datasets.PatchDataset.__len__	method	()
medh5.torch.datasets.PatchDataset.epoch	property
medh5.torch.datasets.PatchDataset.file_groups	method	()
medh5.torch.datasets.PatchDataset.set_epoch	method	(epoch)
medh5.torch.datasets.VolumeDataset	class	(paths, *, images=None, annotations=None, label_format='onehot', physical=True, dtype=<value>, timepoint=None) bases=
medh5.torch.datasets.VolumeDataset.__getitem__	method	(index)
medh5.torch.datasets.VolumeDataset.__len__	method	()
medh5.torch.datasets.VolumeDataset.file_groups	method	()
medh5.torch.grid_patches	function	(shape, patch_size, *, overlap=0, grid_id=None)
medh5.torch.handles	module
medh5.torch.handles.CACHE	constant	medh5.torch.handles.HandleCache
medh5.torch.handles.DEFAULT_MAXSIZE	constant	int
medh5.torch.handles.HandleCache	class	(maxsize=32) bases=
medh5.torch.handles.HandleCache.__len__	method	()
medh5.torch.handles.HandleCache.clear	method	()
medh5.torch.handles.HandleCache.close_all	method	()
medh5.torch.handles.HandleCache.get	method	(path, sample_key=None)
medh5.torch.handles.HandleCache.lease	method	(path, sample_key=None, *, content_id=None)
medh5.torch.handles.HandleCache.maxsize	property
medh5.torch.handles.HandleCache.opens	property
medh5.torch.handles.HandleCache.owner_pid	property
medh5.torch.handles.HandleCache.resize	method	(maxsize)
medh5.torch.handles.open_cached	function	(path, sample_key=None)
medh5.torch.handles.set_cache_size	function	(maxsize)
medh5.torch.handles.worker_init_fn	function	(worker_id)
medh5.torch.open_cached	function	(path, sample_key=None)
medh5.torch.require_torch	function	()
medh5.torch.samplers	module
medh5.torch.samplers.FileGroupedSampler	class	(dataset, *, shuffle=True, seed=0, num_replicas=None, rank=None, drop_last=False) bases=
medh5.torch.samplers.FileGroupedSampler.__iter__	method	()
medh5.torch.samplers.FileGroupedSampler.__len__	method	()
medh5.torch.samplers.FileGroupedSampler.groups	property
medh5.torch.samplers.FileGroupedSampler.num_replicas	property
medh5.torch.samplers.FileGroupedSampler.rank	property
medh5.torch.samplers.FileGroupedSampler.set_epoch	method	(epoch)
medh5.torch.set_cache_size	function	(maxsize)
medh5.torch.stack_images	function	(batch, order)
medh5.torch.stitch	module
medh5.torch.stitch.GridStitcher	class	(dataset, *, channels=None, mode='gaussian', sigma_scale=0.125, dtype=<value>) bases=
medh5.torch.stitch.GridStitcher.add	method	(predictions, meta)
medh5.torch.stitch.GridStitcher.finish	method	(*, partial=False)
medh5.torch.stitch.GridStitcher.pending	property
medh5.torch.worker_init_fn	function	(worker_id)
medh5.transforms	module
medh5.transforms.AffineTransform	class	(handle) bases=medh5.transforms.Transform
medh5.transforms.AffineTransform.from_frame	property
medh5.transforms.AffineTransform.grid_in	method	(frame)
medh5.transforms.AffineTransform.group	property
medh5.transforms.AffineTransform.header	property
medh5.transforms.AffineTransform.inverse	method	()
medh5.transforms.AffineTransform.inverse_matrix	method	()
medh5.transforms.AffineTransform.inverse_points	method	(points)
medh5.transforms.AffineTransform.is_invertible	property
medh5.transforms.AffineTransform.jacobian_determinant_value	property
medh5.transforms.AffineTransform.kind	property
medh5.transforms.AffineTransform.matrix	property
medh5.transforms.AffineTransform.metrics_key	property
medh5.transforms.AffineTransform.n_spatial	property
medh5.transforms.AffineTransform.prov	property
medh5.transforms.AffineTransform.summary	method	()
medh5.transforms.AffineTransform.timepoints	property
medh5.transforms.AffineTransform.to_frame	property
medh5.transforms.AffineTransform.transform_id	property
medh5.transforms.AffineTransform.transform_points	method	(points)
medh5.transforms.AffineTransform.units	property
medh5.transforms.BSplineTransform	class	(handle) bases=medh5.transforms.Transform
medh5.transforms.BSplineTransform.control_points	property
medh5.transforms.BSplineTransform.cp_grid	property
medh5.transforms.BSplineTransform.cp_grid_id	property
medh5.transforms.BSplineTransform.displacement_at	method	(points)
medh5.transforms.BSplineTransform.from_frame	property
medh5.transforms.BSplineTransform.grid_in	method	(frame)
medh5.transforms.BSplineTransform.group	property
medh5.transforms.BSplineTransform.header	property
medh5.transforms.BSplineTransform.inverse	method	()
medh5.transforms.BSplineTransform.is_invertible	property
medh5.transforms.BSplineTransform.kind	property
medh5.transforms.BSplineTransform.metrics_key	property
medh5.transforms.BSplineTransform.order	property
medh5.transforms.BSplineTransform.prov	property
medh5.transforms.BSplineTransform.summary	method	()
medh5.transforms.BSplineTransform.timepoints	property
medh5.transforms.BSplineTransform.to_displacement_field	method	(grid)
medh5.transforms.BSplineTransform.to_frame	property
medh5.transforms.BSplineTransform.transform_id	property
medh5.transforms.BSplineTransform.transform_points	method	(points)
medh5.transforms.BSplineTransform.units	property
medh5.transforms.BSplineTransform.vector_space	property
medh5.transforms.ChainTransform	class	(chain) bases=medh5.transforms.Transform
medh5.transforms.ChainTransform.from_frame	property
medh5.transforms.ChainTransform.grid_in	method	(frame)
medh5.transforms.ChainTransform.group	property
medh5.transforms.ChainTransform.header	property
medh5.transforms.ChainTransform.inverse	method	()
medh5.transforms.ChainTransform.is_invertible	property
medh5.transforms.ChainTransform.kind	property
medh5.transforms.ChainTransform.metrics_key	property
medh5.transforms.ChainTransform.prov	property
medh5.transforms.ChainTransform.steps	property
medh5.transforms.ChainTransform.summary	method	()
medh5.transforms.ChainTransform.timepoints	property
medh5.transforms.ChainTransform.to_frame	property
medh5.transforms.ChainTransform.transform_id	property
medh5.transforms.ChainTransform.transform_points	method	(points)
medh5.transforms.ChainTransform.units	property
medh5.transforms.CompositeTransform	class	(handle) bases=medh5.transforms.Transform
medh5.transforms.CompositeTransform.check_chain	method	()
medh5.transforms.CompositeTransform.component_ids	property
medh5.transforms.CompositeTransform.components	method	()
medh5.transforms.CompositeTransform.from_frame	property
medh5.transforms.CompositeTransform.grid_in	method	(frame)
medh5.transforms.CompositeTransform.group	property
medh5.transforms.CompositeTransform.header	property
medh5.transforms.CompositeTransform.inverse	method	()
medh5.transforms.CompositeTransform.is_invertible	property
medh5.transforms.CompositeTransform.kind	property
medh5.transforms.CompositeTransform.metrics_key	property
medh5.transforms.CompositeTransform.prov	property
medh5.transforms.CompositeTransform.summary	method	()
medh5.transforms.CompositeTransform.timepoints	property
medh5.transforms.CompositeTransform.to_frame	property
medh5.transforms.CompositeTransform.transform_id	property
medh5.transforms.CompositeTransform.transform_points	method	(points)
medh5.transforms.CompositeTransform.units	property
medh5.transforms.DEFAULT_ORDER	constant	int
medh5.transforms.DisplacementTransform	class	(handle) bases=medh5.transforms.Transform
medh5.transforms.DisplacementTransform.displacement_at	method	(points)
medh5.transforms.DisplacementTransform.extrapolation	property
medh5.transforms.DisplacementTransform.field	property
medh5.transforms.DisplacementTransform.field_grid	property
medh5.transforms.DisplacementTransform.field_grid_id	property
medh5.transforms.DisplacementTransform.folding_fraction	method	(roi=None)
medh5.transforms.DisplacementTransform.from_frame	property
medh5.transforms.DisplacementTransform.grid_in	method	(frame)
medh5.transforms.DisplacementTransform.group	property
medh5.transforms.DisplacementTransform.header	property
medh5.transforms.DisplacementTransform.interpolation	property
medh5.transforms.DisplacementTransform.inverse	method	()
medh5.transforms.DisplacementTransform.is_invertible	property
medh5.transforms.DisplacementTransform.jacobian_determinant	method	(roi=None)
medh5.transforms.DisplacementTransform.kind	property
medh5.transforms.DisplacementTransform.max_magnitude	property
medh5.transforms.DisplacementTransform.metrics_key	property
medh5.transforms.DisplacementTransform.prov	property
medh5.transforms.DisplacementTransform.read_field	method	(roi=None, component=None)
medh5.transforms.DisplacementTransform.sample_indices	method	(indices)
medh5.transforms.DisplacementTransform.summary	method	()
medh5.transforms.DisplacementTransform.timepoints	property
medh5.transforms.DisplacementTransform.to_frame	property
medh5.transforms.DisplacementTransform.transform_id	property
medh5.transforms.DisplacementTransform.transform_points	method	(points)
medh5.transforms.DisplacementTransform.units	property
medh5.transforms.DisplacementTransform.vector_space	property
medh5.transforms.EXTRAPOLATIONS	constant	tuple
medh5.transforms.FLOAT16_SAFE_VOXELS	constant	float
medh5.transforms.INTERPOLATIONS	constant	tuple
medh5.transforms.IdentityTransform	class	(handle) bases=medh5.transforms.Transform
medh5.transforms.IdentityTransform.from_frame	property
medh5.transforms.IdentityTransform.grid_in	method	(frame)
medh5.transforms.IdentityTransform.group	property
medh5.transforms.IdentityTransform.header	property
medh5.transforms.IdentityTransform.inverse	method	()
medh5.transforms.IdentityTransform.is_invertible	property
medh5.transforms.IdentityTransform.kind	property
medh5.transforms.IdentityTransform.metrics_key	property
medh5.transforms.IdentityTransform.prov	property
medh5.transforms.IdentityTransform.summary	method	()
medh5.transforms.IdentityTransform.timepoints	property
medh5.transforms.IdentityTransform.to_frame	property
medh5.transforms.IdentityTransform.transform_id	property
medh5.transforms.IdentityTransform.transform_points	method	(points)
medh5.transforms.IdentityTransform.units	property
medh5.transforms.InverseTransform	class	(inner) bases=medh5.transforms.Transform
medh5.transforms.InverseTransform.can_invert	staticmethod	(inner)
medh5.transforms.InverseTransform.from_frame	property
medh5.transforms.InverseTransform.grid_in	method	(frame)
medh5.transforms.InverseTransform.group	property
medh5.transforms.InverseTransform.header	property
medh5.transforms.InverseTransform.inverse	method	()
medh5.transforms.InverseTransform.is_invertible	property
medh5.transforms.InverseTransform.kind	property
medh5.transforms.InverseTransform.metrics_key	property
medh5.transforms.InverseTransform.prov	property
medh5.transforms.InverseTransform.summary	method	()
medh5.transforms.InverseTransform.timepoints	property
medh5.transforms.InverseTransform.to_frame	property
medh5.transforms.InverseTransform.transform_id	property
medh5.transforms.InverseTransform.transform_points	method	(points)
medh5.transforms.InverseTransform.units	property
medh5.transforms.LAST_ROW_TOL	constant	float
medh5.transforms.SPEC_TRANSFORM_ATTRS	constant	tuple
medh5.transforms.SUPPORTED_ORDERS	constant	tuple
medh5.transforms.TRANSFORM_KINDS	constant	tuple
medh5.transforms.Transform	class	(handle) bases=
medh5.transforms.Transform.from_frame	property
medh5.transforms.Transform.grid_in	method	(frame)
medh5.transforms.Transform.group	property
medh5.transforms.Transform.header	property
medh5.transforms.Transform.inverse	method	()
medh5.transforms.Transform.is_invertible	property
medh5.transforms.Transform.kind	property
medh5.transforms.Transform.metrics_key	property
medh5.transforms.Transform.prov	property
medh5.transforms.Transform.summary	method	()
medh5.transforms.Transform.timepoints	property
medh5.transforms.Transform.to_frame	property
medh5.transforms.Transform.transform_id	property
medh5.transforms.Transform.transform_points	method	(points)
medh5.transforms.Transform.units	property
medh5.transforms.TransformHeader	class	(kind, from_frame, to_frame, units='mm', from_grid=None, to_grid=None, invertible=None, inverse_id=None, prov=None, metrics=None, extra=None) bases=
medh5.transforms.TransformHeader.attrs	method	()
medh5.transforms.TransformHeader.extra	field
medh5.transforms.TransformHeader.from_frame	field
medh5.transforms.TransformHeader.from_grid	field
medh5.transforms.TransformHeader.inverse_id	field
medh5.transforms.TransformHeader.invertible	field
medh5.transforms.TransformHeader.kind	field
medh5.transforms.TransformHeader.metrics	field
medh5.transforms.TransformHeader.prov	field
medh5.transforms.TransformHeader.read	classmethod	(group)
medh5.transforms.TransformHeader.to_frame	field
medh5.transforms.TransformHeader.to_grid	field
medh5.transforms.TransformHeader.units	field
medh5.transforms.VECTOR_SPACES	constant	tuple
medh5.transforms.basis	function	(order, t)
medh5.transforms.check_transform_id	function	(transform_id)
medh5.transforms.cubic_sample	function	(field, coords, *, extrapolation='zero')
medh5.transforms.encode_affine	function	(matrix)
medh5.transforms.encode_bspline	function	(control_points, *, cp_grid, order=<value>, vector_space='world')
medh5.transforms.encode_composite	function	(components)
medh5.transforms.encode_displacement	function	(field, *, field_grid, vector_space='world', interpolation='linear', extrapolation='zero', dtype=<value>)
medh5.transforms.encode_identity	function	()
medh5.transforms.folding_fraction	function	(determinants)
medh5.transforms.frame_graph	function	(transforms)
medh5.transforms.frames_of_timepoint	function	(grids, timepoint)
medh5.transforms.inside_extent	function	(spatial, points)
medh5.transforms.jacobian_determinant	function	(field, grid, *, vector_space='world')
medh5.transforms.linear_part	function	(grid)
medh5.transforms.linear_sample	function	(field, coords, *, extrapolation='zero')
medh5.transforms.refuse_outside	function	(inside)
medh5.transforms.resolve_between	function	(transforms, from_frame, to_frame)
medh5.transforms.sample_field	function	(field, coords, *, interpolation='linear', extrapolation='zero')
medh5.transforms.target_registration_error	function	(transform, fixed_points, moving_points, *, weights=None)
medh5.transforms.to_world_vectors	function	(vectors, grid, vector_space)
medh5.transforms.wrap_transform	function	(handle)
medh5.unpack	function	(path, outdir, *, keys=None, suffix='.medh5')
medh5.validate	module
medh5.validate.Diagnostic	class	(code, location, message, severity='error', level='structural') bases=
medh5.validate.Diagnostic.code	field
medh5.validate.Diagnostic.from_json	classmethod	(doc)
medh5.validate.Diagnostic.level	field
medh5.validate.Diagnostic.location	field
medh5.validate.Diagnostic.message	field
medh5.validate.Diagnostic.severity	field
medh5.validate.Diagnostic.summary	property
medh5.validate.Diagnostic.to_json	method	()
medh5.validate.LEVELS	constant	tuple
medh5.validate.LEVEL_ORDER	constant	dict
medh5.validate.Level	alias
medh5.validate.Report	class	(path, level='structural', profiles=(), diagnostics=<factory>, checked=<factory>) bases=
medh5.validate.Report.add	method	(diagnostic)
medh5.validate.Report.checked	field
medh5.validate.Report.codes	property
medh5.validate.Report.diagnostics	field
medh5.validate.Report.dumps	method	(*, indent=2)
medh5.validate.Report.errors	property
medh5.validate.Report.extend	method	(diagnostics)
medh5.validate.Report.format	method	(*, verbose=False)
medh5.validate.Report.from_json	classmethod	(doc)
medh5.validate.Report.level	field
medh5.validate.Report.ok	property
medh5.validate.Report.path	field
medh5.validate.Report.profiles	field
medh5.validate.Report.promoted	property
medh5.validate.Report.to_json	method	()
medh5.validate.Report.warnings	property
medh5.validate.merge	function	(reports, path='<multiple>')
medh5.validate.rules_for	function	(level)
medh5.validate.validate_file	function	(path, *, level='semantic', profiles=None, codes_revision=None)
medh5.validate.validate_paths	function	(paths, *, level='semantic', profiles=None, codes_revision=None)
medh5.validate.validate_root	function	(sample, *, path=None, level='semantic', profiles=None, errors_only=False)
medh5.validate_cache	function	(path, *, base=None, task=None, task_base=None, check_rows=True, confine=None)
