.. imagedata documentation master file, created by
   sphinx-quickstart on Thu Mar  4 14:58:46 2021.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

Imagedata Documentation
=====================================

Imagedata is a python library to read and write medical image data into numpy arrays.
Imagedata will handle multi-dimensional data.
In particular, imagedata will read and sort DICOM 3D and 4D series based on
defined tags.
Imagedata will handle geometry information between the formats.

Imagedata initially supports the following formats:

* DICOM
* Nifti
* ITK (MetaIO)
* Matlab
* PostScript (input only)

Other formats can be added through a plugin architecture.

A simple example reading a time series from in_dir, displaying it, and writing it to out_dir:

.. code-block:: python

  from imagedata import Series
  a = Series('in_dir', 'time')
  a.show()
  a.write('out_dir')

The :ref:`User Guide <UserGuide>` explains how to install and
use imagedata.

*Loading image data with this imagedata Python package simplify image
processing pipelines both in native Python, and when stitching together
modules that require different image file formats. This is especially
important when setting up pipelines for clinical data where patient
information matters.*


.. toctree::
   :maxdepth: 2
   :caption: Contents:

   UserGuide
   DeveloperDocumentation



Indices and tables
==================

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`
