Standard
--------

.. |rec00001| image:: ../img/phantom_00001_00000.png
    :width: 20pt
    :height: 20pt

.. |gt00001| image:: ../img/phantom_00001_ground_truth.png
    :width: 20pt
    :height: 20pt

.. |phan_00001| replace:: :download:`gen_script.py <../../../docs/demo/phantom_00001.py>`

.. _phan_00001: https://app.globus.org/file-manager?origin_id=9f00a780-4aee-42a7-b7f4-6a2773c8da30&origin_path=%2Fphantom_00001%2F

.. |rec00002| image:: ../img/phantom_00002_00000.png
    :width: 20pt
    :height: 20pt

.. |gt00002| image:: ../img/phantom_00002_ground_truth.png
    :width: 20pt
    :height: 20pt

.. |phan_00002| replace:: :download:`gen_script.py <../../../docs/demo/phantom_00002.py>`

.. _phan_00002: https://app.globus.org/file-manager?origin_id=9f00a780-4aee-42a7-b7f4-6a2773c8da30&origin_path=%2Fphantom_00002%2F

.. |rec00003| image:: ../img/phantom_00003_00000.png
    :width: 20pt
    :height: 20pt

.. |gt00003| image:: ../img/phantom_00003_ground_truth.png
    :width: 20pt
    :height: 20pt

.. |phan_00003| replace:: :download:`gen_script.py <../../../docs/demo/phantom_00003.py>`

.. _phan_00003: https://app.globus.org/file-manager?origin_id=9f00a780-4aee-42a7-b7f4-6a2773c8da30&origin_path=%2Fphantom_00003%2F

.. |rec00004| image:: ../img/phantom_00004_00000.png
    :width: 20pt
    :height: 20pt

.. |gt00004| image:: ../img/phantom_00004_ground_truth.png
    :width: 20pt
    :height: 20pt

.. |phan_00004| replace:: :download:`gen_script.py <../../../docs/demo/phantom_00004.py>`

.. _phan_00004: https://app.globus.org/file-manager?origin_id=9f00a780-4aee-42a7-b7f4-6a2773c8da30&origin_path=%2Fphantom_00004%2F

.. |rec00005| image:: ../img/phantom_00005_00000.png
    :width: 20pt
    :height: 20pt

.. |gt00005| image:: ../img/phantom_00005_ground_truth.png
    :width: 20pt
    :height: 20pt

.. |phan_00005| replace:: :download:`gen_script.py <../../../docs/demo/phantom_00005.py>`

.. _phan_00005: https://app.globus.org/file-manager?origin_id=9f00a780-4aee-42a7-b7f4-6a2773c8da30&origin_path=%2Fphantom_00005%2F

.. |rec00006| image:: ../img/phantom_00006_00000.png
    :width: 20pt
    :height: 20pt

.. |gt00006| image:: ../img/phantom_00006_ground_truth.png
    :width: 20pt
    :height: 20pt

.. |phan_00006| replace:: :download:`gen_script.py <../../../docs/demo/phantom_00006.py>`

.. _phan_00006: https://app.globus.org/file-manager?origin_id=9f00a780-4aee-42a7-b7f4-6a2773c8da30&origin_path=%2Fphantom_00006%2F

These phantom use `XDesign <http://myxdesign.readthedocs.io/>`_ 
version `0.2.0.dev0+1d67599 <https://github.com/tomography/xdesign/tree/1d67599b8f104ebded86bac98100dbf15e251a66>`_
are generated as follows:     


.. code:: python

    ccd_x = 256 
    ccd_y = 1
    n_proj = 512

    phantom_00001 = xdesign.SlantedSquares(count=16, angle=5/360*2*np.pi, gap=0.01)
    phantom_00002 = xdesign.UnitCircle(radius=0.4, mass_atten=1)
    phantom_00003 = xdesign.HyperbolicConcentric()
    phantom_00004 = xdesign.DynamicRange(steps=16, jitter=True, shape='square')
    phantom_00005 = xdesign.DogaCircles(n_sizes=8, size_ratio=0.5, n_shuffles=0)
    phantom_00006 = xdesign.SiemensStar(32)

The ground truth, sinogram and projection are obtained with:

.. code:: python

    ground_truth = discrete_phantom(phantom, ccd_x, prop='mass_atten')
    
    sino, probe = sinogram(n_proj, ccd_x, phantom)
    proj = np.expand_dims(sino, 1)

To load the phantom data sets and perform a basic reconstruction using `tomopy <https://tomopy.readthedocs.io>`_  use the 
:download:`tomopy_rec.py <../../demo/tomopy_rec.py>` python script:

::

    tomopy recon --file-name phantom_00001.h5

+---------------+----------------+------------------------+--------------+------------+--------------------+
|  Phantom ID   |    Facility    |    Sample              | Ground Truth |  Grirec    |       Downloads    |
+---------------+----------------+------------------------+--------------+------------+--------------------+
|  phan_00001_  |    XDesign     |  Slanted Squares       |  |gt00001|   | |rec00001| |      |phan_00001|  |
+---------------+----------------+------------------------+--------------+------------+--------------------+
|  phan_00002_  |    XDesign     |  Unit Circle           |  |gt00002|   | |rec00002| |      |phan_00002|  |
+---------------+----------------+------------------------+--------------+------------+--------------------+
|  phan_00003_  |    XDesign     |  Hyperbolic Concentric |  |gt00003|   | |rec00003| |      |phan_00003|  |
+---------------+----------------+------------------------+--------------+------------+--------------------+
|  phan_00004_  |    XDesign     |  Dynamic Range         |  |gt00004|   | |rec00004| |      |phan_00004|  |
+---------------+----------------+------------------------+--------------+------------+--------------------+
|  phan_00005_  |    XDesign     |  Doga's Circles        |  |gt00005|   | |rec00005| |      |phan_00005|  |
+---------------+----------------+------------------------+--------------+------------+--------------------+
|  phan_00006_  |    XDesign     |  Siemens Star          |  |gt00006|   | |rec00006| |      |phan_00006|  |
+---------------+----------------+------------------------+--------------+------------+--------------------+