Merge pull request #357 from CJ-Wright/patch-1

Fixes misspelling in tomopy.rst.

doc/source/ipynb/tomopy.rst

@@ -1,150 +1,150 @@
-Gridrec
--------
-
-Here is an example on how to use the gridrec :cite:`Dowd:99`
-reconstruction algorithm with `TomoPy <http://tomopy.readthedocs.io/en/latest/>`__
-:cite:`Gursoy:14a`.  
-You can download the python scritp :download:`here<../../../doc/demo/gridrec.py>`
+Gridrec
+-------
+
+Here is an example on how to use the gridrec :cite:`Dowd:99`
+reconstruction algorithm with `TomoPy <http://tomopy.readthedocs.io/en/latest/>`__
+:cite:`Gursoy:14a`.  
+You can download the python script :download:`here<../../../doc/demo/gridrec.py>`
 or the Jupyter notebook :download:`here<../../../doc/demo/gridrec.ipynb>`
-
-.. code:: python
-
-    %pylab inline
-
-
-`Install <http://tomopy.readthedocs.io/en/latest/install.html>`__ TomoPy
-then:
-
-.. code:: python
-
-    import tomopy
-
-Tomographic data input in TomoPy is supported by 
-`DXchange <http://dxchange.readthedocs.io>`__.
-
-.. code:: python
-
-    import dxchange
-
-matplotlib provide plotting of the result in this notebook.
-`Paraview <http://www.paraview.org/>`__ or other tools are available for
-more sophisticated 3D rendering.
-
-.. code:: python
-
-    import matplotlib.pyplot as plt
-
-Set the path to the micro-CT data to reconstruct.
-
-.. code:: python
-
-    fname = '../../tomopy/data/tooth.h5'
-
-Select the sinogram range to reconstruct.
-
-.. code:: python
-
-    start = 0
-    end = 2
-
-:download:`tooth.h5<../../../tomopy/data/tooth.h5>` data set file format 
-follows the `APS <http://www.aps.anl.gov>`__ beamline `2-BM and 32-ID 
-<https://www1.aps.anl.gov/Imaging>`__ 
-`data-exchange <http://dxfile.readthedocs.io>`__ file format definition.
-Major synchrotron file format `examples <http://dxchange.readthedocs.io/en/latest/source/demo.html>`__
-are available at `DXchange <http://dxchange.readthedocs.io/en/latest/source/api/dxchange.exchange.html>`__.
-
-.. code:: python
-
-    proj, flat, dark, theta = dxchange.read_aps_32id(fname, sino=(start, end))
-
-Plot the sinogram:
-
-.. code:: python
-
-    plt.imshow(proj[:, 0, :], cmap='Greys_r')
-    plt.show()
-
-
-
-.. image:: tomopy_files/tomopy_15_0.png
-
-
-If the angular information is not avaialable from the raw data you need
-to set the data collection angles. In this case theta is set as equally
-spaced between 0-180 degrees.
-
-.. code:: python
-
-    if (theta is None):
-        theta = tomopy.angles(proj.shape[0])
-    else:
-        pass
-
-Perform the flat-field correction of raw data:
-
-.. math::  \frac{proj - dark} {flat - dark} 
-
-.. code:: python
-
-    proj = tomopy.normalize(proj, flat, dark)
-
-Tomopy provides various methods (:cite:`Donath:06`, :cite:`Vo:14`, :cite:`Guizar:08`)
-to find the `rotation center <http://tomopy.readthedocs.io/en/latest/api/tomopy.recon.rotation.html>`__.
-
-.. code:: python
-
-    rot_center = tomopy.find_center(proj, theta, init=290, ind=0, tol=0.5)
-
-
-.. parsed-literal::
-
-    tomopy.rotation:Trying center: [ 290.]
-    tomopy.rotation:Trying center: [ 304.5]
-    tomopy.rotation:Trying center: [ 275.5]
-    tomopy.rotation:Trying center: [ 282.75]
-    tomopy.rotation:Trying center: [ 297.25]
-    tomopy.rotation:Trying center: [ 304.5]
-    tomopy.rotation:Trying center: [ 304.5]
-    tomopy.rotation:Trying center: [ 293.625]
-    tomopy.rotation:Trying center: [ 290.]
-    tomopy.rotation:Trying center: [ 295.4375]
-    tomopy.rotation:Trying center: [ 291.8125]
-    tomopy.rotation:Trying center: [ 294.53125]
-    tomopy.rotation:Trying center: [ 295.4375]
-    tomopy.rotation:Trying center: [ 294.078125]
-
-
-Calculate
-
-.. math::  -log(proj) 
-
-.. code:: python
-
-    proj = tomopy.minus_log(proj)
-
-Reconstruction using Gridrec algorithm.Tomopy provides various
-`reconstruction <http://tomopy.readthedocs.io/en/latest/api/tomopy.recon.algorithm.html>`__
-methods including the one part of the `ASTRA
-toolbox <https://sourceforge.net/p/astra-toolbox/wiki/Home/>`__.
-
-.. code:: python
-
-    recon = tomopy.recon(proj, theta, center=rot_center, algorithm='gridrec')
-
-Mask each reconstructed slice with a circle.
-
-.. code:: python
-
-    recon = tomopy.circ_mask(recon, axis=0, ratio=0.95)
-
-.. code:: python
-
-    plt.imshow(recon[0, :,:], cmap='Greys_r')
-    plt.show()
-
-
-
-.. image:: tomopy_files/tomopy_28_0.png
-
-
+
+.. code:: python
+
+    %pylab inline
+
+
+`Install <http://tomopy.readthedocs.io/en/latest/install.html>`__ TomoPy
+then:
+
+.. code:: python
+
+    import tomopy
+
+Tomographic data input in TomoPy is supported by 
+`DXchange <http://dxchange.readthedocs.io>`__.
+
+.. code:: python
+
+    import dxchange
+
+matplotlib provide plotting of the result in this notebook.
+`Paraview <http://www.paraview.org/>`__ or other tools are available for
+more sophisticated 3D rendering.
+
+.. code:: python
+
+    import matplotlib.pyplot as plt
+
+Set the path to the micro-CT data to reconstruct.
+
+.. code:: python
+
+    fname = '../../tomopy/data/tooth.h5'
+
+Select the sinogram range to reconstruct.
+
+.. code:: python
+
+    start = 0
+    end = 2
+
+:download:`tooth.h5<../../../tomopy/data/tooth.h5>` data set file format 
+follows the `APS <http://www.aps.anl.gov>`__ beamline `2-BM and 32-ID 
+<https://www1.aps.anl.gov/Imaging>`__ 
+`data-exchange <http://dxfile.readthedocs.io>`__ file format definition.
+Major synchrotron file format `examples <http://dxchange.readthedocs.io/en/latest/source/demo.html>`__
+are available at `DXchange <http://dxchange.readthedocs.io/en/latest/source/api/dxchange.exchange.html>`__.
+
+.. code:: python
+
+    proj, flat, dark, theta = dxchange.read_aps_32id(fname, sino=(start, end))
+
+Plot the sinogram:
+
+.. code:: python
+
+    plt.imshow(proj[:, 0, :], cmap='Greys_r')
+    plt.show()
+
+
+
+.. image:: tomopy_files/tomopy_15_0.png
+
+
+If the angular information is not avaialable from the raw data you need
+to set the data collection angles. In this case theta is set as equally
+spaced between 0-180 degrees.
+
+.. code:: python
+
+    if (theta is None):
+        theta = tomopy.angles(proj.shape[0])
+    else:
+        pass
+
+Perform the flat-field correction of raw data:
+
+.. math::  \frac{proj - dark} {flat - dark} 
+
+.. code:: python
+
+    proj = tomopy.normalize(proj, flat, dark)
+
+Tomopy provides various methods (:cite:`Donath:06`, :cite:`Vo:14`, :cite:`Guizar:08`)
+to find the `rotation center <http://tomopy.readthedocs.io/en/latest/api/tomopy.recon.rotation.html>`__.
+
+.. code:: python
+
+    rot_center = tomopy.find_center(proj, theta, init=290, ind=0, tol=0.5)
+
+
+.. parsed-literal::
+
+    tomopy.rotation:Trying center: [ 290.]
+    tomopy.rotation:Trying center: [ 304.5]
+    tomopy.rotation:Trying center: [ 275.5]
+    tomopy.rotation:Trying center: [ 282.75]
+    tomopy.rotation:Trying center: [ 297.25]
+    tomopy.rotation:Trying center: [ 304.5]
+    tomopy.rotation:Trying center: [ 304.5]
+    tomopy.rotation:Trying center: [ 293.625]
+    tomopy.rotation:Trying center: [ 290.]
+    tomopy.rotation:Trying center: [ 295.4375]
+    tomopy.rotation:Trying center: [ 291.8125]
+    tomopy.rotation:Trying center: [ 294.53125]
+    tomopy.rotation:Trying center: [ 295.4375]
+    tomopy.rotation:Trying center: [ 294.078125]
+
+
+Calculate
+
+.. math::  -log(proj) 
+
+.. code:: python
+
+    proj = tomopy.minus_log(proj)
+
+Reconstruction using Gridrec algorithm.Tomopy provides various
+`reconstruction <http://tomopy.readthedocs.io/en/latest/api/tomopy.recon.algorithm.html>`__
+methods including the one part of the `ASTRA
+toolbox <https://sourceforge.net/p/astra-toolbox/wiki/Home/>`__.
+
+.. code:: python
+
+    recon = tomopy.recon(proj, theta, center=rot_center, algorithm='gridrec')
+
+Mask each reconstructed slice with a circle.
+
+.. code:: python
+
+    recon = tomopy.circ_mask(recon, axis=0, ratio=0.95)
+
+.. code:: python
+
+    plt.imshow(recon[0, :,:], cmap='Greys_r')
+    plt.show()
+
+
+
+.. image:: tomopy_files/tomopy_28_0.png
+
+