Mercurial > hg > orthanc-book
changeset 820:fa6d9c7237b4
Downloading decoded images from Python
author | Sebastien Jodogne <s.jodogne@gmail.com> |
---|---|
date | Fri, 25 Feb 2022 09:34:37 +0100 |
parents | a67ceccebf02 |
children | d7c8c8f6cffb |
files | Sphinx/source/users/rest.rst |
diffstat | 1 files changed, 63 insertions(+), 0 deletions(-) [+] |
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--- a/Sphinx/source/users/rest.rst Wed Feb 23 18:46:15 2022 +0100 +++ b/Sphinx/source/users/rest.rst Fri Feb 25 09:34:37 2022 +0100 @@ -428,6 +428,69 @@ Users of Matlab or Octave can find related information :ref:`in the dedicated section <matlab>`. + +.. _download_numpy: + +Downloading decoded images from Python +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. highlight:: python + +Starting with Orthanc 1.10.0, it is possible to immediately download +DICOM instances and DICOM series as numpy arrays (even if they use a +compressed transfer syntax). This is especially useful for the +integration within AI (artificial intelligence) pipelines. Here is a +sample call:: + + import io + import numpy + import requests + + r = requests.get('https://demo.orthanc-server.com/instances/6582b1c0-292ad5ab-ba0f088f-f7a1766f-9a29a54f/numpy') + r.raise_for_status() + + image = numpy.load(io.BytesIO(r.content)) + print(image.shape) # (1, 358, 512, 1) + +The downloaded numpy array for one single DICOM instance contains +floating-point values, and has a shape of ``(1, height, width, 1)`` if +the corresponding instance is grayscale, or ``(1, height, width, 3)`` +if the instance has colors (e.g. in ultrasound images). If applicable, +the ``Rescale Slope (0028,1053)`` and ``Rescale Intercept +(0028,1052)`` DICOM tags are applied to the floating-point values. + +Similarly, this feature is available at the series level:: + + import io + import numpy + import requests + + r = requests.get('https://demo.orthanc-server.com/series/dc0216d2-a406a5ad-31ef7a78-113ae9d9-29939f9e/numpy') + r.raise_for_status() + + image = numpy.load(io.BytesIO(r.content)) + print(image.shape) # (100, 256, 256, 1) + +As can be seen, in the case of a DICOM series, the first dimension of +the resulting numpy array corresponds to the depth of the series +(i.e. to its number of 2D slices). + +Some options are available for these ``/instances/.../numpy`` and +``/series/.../numpy`` routes: + +* ``?compress=1`` will return a ``.npz`` compressed numpy archive + instead of a plain ``.npy`` numpy array. This can be used to reduce + the network bandwidth. In such a case, the array of interest is + named ``arr_0`` in the ``.npz`` archive, e.g.:: + + print(image['arr_0'].shape) + +* ``?rescale=0`` will skip the conversion to floating-point values, + and will not apply the rescale slope/intercept. This can be useful + to reduce the network bandwidth or to receive the original integer + values of the voxels. + + Downloading studies ^^^^^^^^^^^^^^^^^^^