.gitignore
.pre-commit-config.yaml
LICENSE
MANIFEST.in
README.md
pyproject.toml
docs/images/helicon-home.jpeg
src/helicon/__init__.py
src/helicon/_version.py
src/helicon/_versioninfo.py
src/helicon/helicon.py
src/helicon.egg-info/PKG-INFO
src/helicon.egg-info/SOURCES.txt
src/helicon.egg-info/dependency_links.txt
src/helicon.egg-info/entry_points.txt
src/helicon.egg-info/requires.txt
src/helicon.egg-info/scm_file_list.json
src/helicon.egg-info/scm_version.json
src/helicon.egg-info/top_level.txt
src/helicon/commands/HOM_containerC.py
src/helicon/commands/cryosparc.py
src/helicon/commands/ctfSimulation.py
src/helicon/commands/display.py
src/helicon/commands/images2star.py
src/helicon/commands/map2seq.py
src/helicon/commands/proc3d.py
src/helicon/commands/procart.py
src/helicon/commands/trueFSC.py
src/helicon/commands/update.py
src/helicon/commands/webApps.py
src/helicon/commands/webCalEM.py
src/helicon/lib/__init__.py
src/helicon/lib/alignment.py
src/helicon/lib/analysis.py
src/helicon/lib/angular.py
src/helicon/lib/average_power_spectra.py
src/helicon/lib/cache.py
src/helicon/lib/clustering.py
src/helicon/lib/collections.py
src/helicon/lib/cryosparc_project.py
src/helicon/lib/curvelet.py
src/helicon/lib/dataset.py
src/helicon/lib/epu.py
src/helicon/lib/euler.py
src/helicon/lib/exceptions.py
src/helicon/lib/exposure_groups.py
src/helicon/lib/filters.py
src/helicon/lib/gauss.py
src/helicon/lib/images2star_engine.py
src/helicon/lib/io.py
src/helicon/lib/io_mrc.py
src/helicon/lib/logging.py
src/helicon/lib/numba_compat.py
src/helicon/lib/path_utils.py
src/helicon/lib/point_group.py
src/helicon/lib/proc3d_engine.py
src/helicon/lib/ptycho.py
src/helicon/lib/relion_launcher.py
src/helicon/lib/shiny.py
src/helicon/lib/shiny_file_picker.py
src/helicon/lib/system.py
src/helicon/lib/terminal.py
src/helicon/lib/transforms.py
src/helicon/lib/util.py
src/helicon/lib/gui/__init__.py
src/helicon/lib/gui/caches.py
src/helicon/lib/gui/file_browser.py
src/helicon/lib/gui/file_openers.py
src/helicon/lib/gui/fsc.py
src/helicon/lib/gui/gallery_backends.py
src/helicon/lib/gui/gallery_widget.py
src/helicon/lib/gui/images2star_widget.py
src/helicon/lib/gui/macos.py
src/helicon/lib/gui/proc3d_widget.py
src/helicon/lib/gui/star_parsers.py
src/helicon/lib/gui/theme.py
src/helicon/lib/gui/trackers.py
src/helicon/lib/gui/viewer.py
src/helicon/lib/gui/webapps.py
src/helicon/lib/gui/workers.py
src/helicon/plugins/__init__.py
src/helicon/plugins/cryosparc/__init__.py
src/helicon/plugins/cryosparc/assignexposuregroupbybeamshiftlabel.py
src/helicon/plugins/cryosparc/assignexposuregroupbybeamshiftxy.py
src/helicon/plugins/cryosparc/assignexposuregroupbytime.py
src/helicon/plugins/cryosparc/assignexposuregrouppermicrograph.py
src/helicon/plugins/cryosparc/changepixelsize.py
src/helicon/plugins/cryosparc/copyexposuregroupassignments.py
src/helicon/plugins/cryosparc/copyexposuregroupparameters.py
src/helicon/plugins/cryosparc/extractparticles.py
src/helicon/plugins/cryosparc/resetexposuregroups.py
src/helicon/plugins/cryosparc/splitbymicrograph.py
src/helicon/plugins/images2star/__init__.py
src/helicon/plugins/images2star/addparm.py
src/helicon/plugins/images2star/apix.py
src/helicon/plugins/images2star/assignopticgroupbybeamshiftlabel.py
src/helicon/plugins/images2star/assignopticgroupbybeamshiftxy.py
src/helicon/plugins/images2star/assignopticgroupbytime.py
src/helicon/plugins/images2star/assignopticgrouppermicrograph.py
src/helicon/plugins/images2star/averagepowerspectra.py
src/helicon/plugins/images2star/break_filaments.py
src/helicon/plugins/images2star/calibratepixelsize.py
src/helicon/plugins/images2star/copyctf.py
src/helicon/plugins/images2star/copyparm.py
src/helicon/plugins/images2star/createstack.py
src/helicon/plugins/images2star/delparm.py
src/helicon/plugins/images2star/denoisecurvelet.py
src/helicon/plugins/images2star/duplicateparm.py
src/helicon/plugins/images2star/estimatehelicalanglevariance.py
src/helicon/plugins/images2star/estimatehelicaltubelength.py
src/helicon/plugins/images2star/exclude_file.py
src/helicon/plugins/images2star/extracthelices.py
src/helicon/plugins/images2star/fullstack.py
src/helicon/plugins/images2star/keeponeparticleperhelicaltube.py
src/helicon/plugins/images2star/keeponeparticlepermicrograph.py
src/helicon/plugins/images2star/keepparm.py
src/helicon/plugins/images2star/maskgold.py
src/helicon/plugins/images2star/minduplicates.py
src/helicon/plugins/images2star/minstack.py
src/helicon/plugins/images2star/multparm.py
src/helicon/plugins/images2star/normeulerdist.py
src/helicon/plugins/images2star/path.py
src/helicon/plugins/images2star/process.py
src/helicon/plugins/images2star/psiprior180.py
src/helicon/plugins/images2star/randomsample.py
src/helicon/plugins/images2star/recoverfullfilaments.py
src/helicon/plugins/images2star/removeduplicates.py
src/helicon/plugins/images2star/renameparm.py
src/helicon/plugins/images2star/replaceimagename.py
src/helicon/plugins/images2star/replacestr.py
src/helicon/plugins/images2star/resetintersegmentdistance.py
src/helicon/plugins/images2star/resetopticgroup.py
src/helicon/plugins/images2star/rsort_by.py
src/helicon/plugins/images2star/select.py
src/helicon/plugins/images2star/select_by_particle_location.py
src/helicon/plugins/images2star/select_file.py
src/helicon/plugins/images2star/selectcommonhelices.py
src/helicon/plugins/images2star/selectratiorange.py
src/helicon/plugins/images2star/selectvaluerange.py
src/helicon/plugins/images2star/setbeamtiltclass.py
src/helicon/plugins/images2star/setctf.py
src/helicon/plugins/images2star/setparm.py
src/helicon/plugins/images2star/sets.py
src/helicon/plugins/images2star/showtime.py
src/helicon/plugins/images2star/sort_by.py
src/helicon/plugins/images2star/splitbymicrograph.py
src/helicon/plugins/images2star/summary2d.py
src/helicon/plugins/proc3d/__init__.py
src/helicon/plugins/proc3d/apix.py
src/helicon/plugins/proc3d/clip.py
src/helicon/plugins/proc3d/denoiseCurvelet.py
src/helicon/plugins/proc3d/fft_resample.py
src/helicon/plugins/proc3d/flip_hand.py
src/helicon/plugins/proc3d/helical_sym.py
src/helicon/plugins/proc3d/z_moving_average.py
src/helicon/resources/icon.png
src/helicon/resources/icon.svg
src/helicon/webApps/__init__.py
src/helicon/webApps/app.py
src/helicon/webApps/bookmark.py
src/helicon/webApps/class2d_files.py
src/helicon/webApps/deployment.py
src/helicon/webApps/requirements.txt
src/helicon/webApps/lib/__init__.py
src/helicon/webApps/lib/denovo3d_align.py
src/helicon/webApps/lib/denovo3d_joint.py
src/helicon/webApps/lib/denovo3d_jointsolve.py
src/helicon/webApps/lib/denovo3d_pipeline.py
src/helicon/webApps/lib/denovo3d_register.py
src/helicon/webApps/lib/denovo3d_solver.py
src/helicon/webApps/lib/gauss_align.py
src/helicon/webApps/lib/gauss_mixture.py
src/helicon/webApps/lib/helical_pitch_compute.py
src/helicon/webApps/lib/helical_pitch_map.py
src/helicon/webApps/lib/helical_pitch_phase.py
src/helicon/webApps/lib/helical_pitch_relion.py
src/helicon/webApps/lib/helical_projection_compute.py
src/helicon/webApps/lib/helical_projection_utils.py
src/helicon/webApps/lib/helix_transform.py
src/helicon/webApps/lib/hi3d_core.py
src/helicon/webApps/lib/hill_compute.py
src/helicon/webApps/lib/image_loader.py
src/helicon/webApps/lib/map_gauss_fit.py
src/helicon/webApps/lib/solver_gauss_analytic.py
src/helicon/webApps/lib/solver_gauss_aniso.py
src/helicon/webApps/lib/whereismyclass_compute.py
src/helicon/webApps/tabs/__init__.py
src/helicon/webApps/tabs/abinitio3d_tab.py
src/helicon/webApps/tabs/denovo3d_tab.py
src/helicon/webApps/tabs/helical_lattice_tab.py
src/helicon/webApps/tabs/helical_pitch_tab.py
src/helicon/webApps/tabs/helical_projection_tab.py
src/helicon/webApps/tabs/hi3d_tab.py
src/helicon/webApps/tabs/hill_tab.py
src/helicon/webApps/tabs/home_tab.py
src/helicon/webApps/tabs/where_is_my_class_tab.py
tests/conftest.py
tests/helical_sim.py
tests/test_HOM_containerC.py
tests/test_abinitio3d_tab.py
tests/test_analysis.py
tests/test_angular_property.py
tests/test_average_power_spectra.py
tests/test_background_task.py
tests/test_bookmark.py
tests/test_cache.py
tests/test_class2d_files.py
tests/test_class2d_summary.py
tests/test_cryosparc.py
tests/test_cryosparc_project.py
tests/test_curvelet.py
tests/test_dataset.py
tests/test_denovo3D_align.py
tests/test_denovo3D_app.py
tests/test_denovo3D_autotransform.py
tests/test_denovo3D_display_redraw.py
tests/test_denovo3D_joint.py
tests/test_denovo3D_jointsolve.py
tests/test_denovo3D_pipeline.py
tests/test_denovo3D_register.py
tests/test_denovo3D_solver.py
tests/test_denovo3D_utils.py
tests/test_denovo3d_download.py
tests/test_denovo3d_ranges.py
tests/test_deployment.py
tests/test_display.py
tests/test_display_webapp_procs.py
tests/test_emdb_mirror.py
tests/test_epu_cistem_readers.py
tests/test_exposure_groups.py
tests/test_file_browser_bookmarks.py
tests/test_filters.py
tests/test_fix_cmd_survey.py
tests/test_fix_followups.py
tests/test_fix_gui_survey.py
tests/test_fix_lib_survey.py
tests/test_fix_numeric_lib.py
tests/test_fix_pkg_cache_and_imports.py
tests/test_fix_pkg_conftest.py
tests/test_fix_webapp_survey.py
tests/test_gallery_contrast.py
tests/test_gallery_widget_ortho.py
tests/test_gauss.py
tests/test_gauss_align.py
tests/test_gauss_analytic.py
tests/test_gauss_aniso.py
tests/test_gauss_joint_parallel.py
tests/test_gauss_mixture.py
tests/test_google_analytics.py
tests/test_helical_pitch_angles.py
tests/test_helical_pitch_cs_loader.py
tests/test_helical_pitch_map.py
tests/test_helical_pitch_phase.py
tests/test_helical_pitch_relion.py
tests/test_helical_projection_failure_handling.py
tests/test_helical_projection_gaussian_mode.py
tests/test_helical_projection_joint.py
tests/test_helical_projection_links.py
tests/test_helical_projection_map_table.py
tests/test_helical_projection_transform_ui.py
tests/test_helical_symmetry_background.py
tests/test_helicon_cli.py
tests/test_helix_transform.py
tests/test_hi3d_inputs_are_wired.py
tests/test_hi3d_lattice_lines.py
tests/test_hi3d_radial_range.py
tests/test_hill_tab.py
tests/test_histogram_interaction.py
tests/test_image_gallery.py
tests/test_images2star.py
tests/test_images2star_engine.py
tests/test_images2star_join_filaments.py
tests/test_integration_relion5.py
tests/test_io.py
tests/test_joint_solver_intercept.py
tests/test_logging_handlers.py
tests/test_map_gauss_fit.py
tests/test_no_torch_at_import.py
tests/test_numba_compat.py
tests/test_packaging_metadata.py
tests/test_point_group.py
tests/test_proc3d.py
tests/test_proc3d_engine.py
tests/test_projection_performance.py
tests/test_relion_launcher.py
tests/test_shiny_file_picker.py
tests/test_shiny_range_slider.py
tests/test_split_distinct_filaments.py
tests/test_tabs_independent.py
tests/test_transforms.py
tests/test_update_command.py
tests/test_util.py
tests/test_versioninfo.py
tests/test_webapp_control.py
tests/test_webapp_nonblocking.py
tests/test_webcalem_command.py
tests/test_whereIsMyClass_app.py
tests/test_whereIsMyClass_compute.py
tests/validation/relion_reconstruction.py