Merge pull request #39 from decarlof/master

docs update
data-exchange · Sep 28, 2016 · 373b23f · 373b23f
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diff --git a/doc/demo/rec_aps_26id.py b/doc/demo/rec_aps_26id.py
@@ -0,0 +1,57 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+"""
+TomoPy example script to reconstruct the xrm tomography data from
+the original stack of xrm. To use rename the xrm data as 
+radios/image_00000.xrm and flats/ref_00000.xrm
+"""
+
+from __future__ import print_function
+import tomopy
+import dxchange
+
+if __name__ == '__main__':
+    # Set path to the micro-CT data to reconstruct.
+    fname = 'data_dir/'
+
+    proj_start = 0
+    proj_end = 1800
+    flat_start = 0
+    flat_end = 100
+
+    ind_tomo = range(proj_start, proj_end)
+    ind_flat = range(flat_start, flat_end)
+
+    # Select the sinogram range to reconstruct.
+    start = 0
+    end = 16
+
+    # Read the APS 26-ID raw data.
+    proj, flat, metadata = dxchange.read_aps_26id(fname, ind_tomo, ind_flat,
+                                                 sino=(start, end))
+
+    # make the darks
+    dark = np.zeros((1, proj.shape[1], proj.shape[2]))    
+
+    # Set data collection angles as equally spaced between 0-180 degrees.
+    theta = tomopy.angles(proj.shape[0])
+
+    # Flat-field correction of raw data.
+    proj = tomopy.normalize(proj, flat, dark)
+
+    # Find rotation center.
+    rot_center = tomopy.find_center(proj, theta, init=1024,
+                                    ind=0, tol=0.5)
+    print("Center of rotation: ", rot_center)
+
+    proj = tomopy.minus_log(proj)
+
+    # Reconstruct object using Gridrec algorithm.
+    rec = tomopy.recon(proj, theta, center=rot_center, algorithm='gridrec')
+
+    # Mask each reconstructed slice with a circle.
+    rec = tomopy.circ_mask(rec, axis=0, ratio=0.95)
+
+    # Write data as stack of TIFs.
+    dxchange.write_tiff_stack(rec, fname='recon_dir/recon')
diff --git a/doc/demo/rec_aps_8bm.py b/doc/demo/rec_aps_8bm.py
@@ -0,0 +1,57 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+"""
+TomoPy example script to reconstruct the xrm tomography data from
+the original stack of xrm. To use rename the xrm data as 
+radios/image_00000.xrm and flats/ref_00000.xrm
+"""
+
+from __future__ import print_function
+import tomopy
+import dxchange
+
+if __name__ == '__main__':
+    # Set path to the micro-CT data to reconstruct.
+    fname = 'data_dir/'
+
+    proj_start = 0
+    proj_end = 1800
+    flat_start = 0
+    flat_end = 100
+
+    ind_tomo = range(proj_start, proj_end)
+    ind_flat = range(flat_start, flat_end)
+
+    # Select the sinogram range to reconstruct.
+    start = 0
+    end = 16
+
+    # Read the APS 8-BM raw data.
+    proj, flat, metadata = dxchange.read_aps_8bm(fname, ind_tomo, ind_flat,
+                                                 sino=(start, end))
+
+    # make the darks
+    dark = np.zeros((1, proj.shape[1], proj.shape[2]))    
+
+    # Set data collection angles as equally spaced between 0-180 degrees.
+    theta = tomopy.angles(proj.shape[0])
+
+    # Flat-field correction of raw data.
+    proj = tomopy.normalize(proj, flat, dark)
+
+    # Find rotation center.
+    rot_center = tomopy.find_center(proj, theta, init=1024,
+                                    ind=0, tol=0.5)
+    print("Center of rotation: ", rot_center)
+
+    proj = tomopy.minus_log(proj)
+
+    # Reconstruct object using Gridrec algorithm.
+    rec = tomopy.recon(proj, theta, center=rot_center, algorithm='gridrec')
+
+    # Mask each reconstructed slice with a circle.
+    rec = tomopy.circ_mask(rec, axis=0, ratio=0.95)
+
+    # Write data as stack of TIFs.
+    dxchange.write_tiff_stack(rec, fname='recon_dir/recon')
diff --git a/doc/demo/rec_xradia_xrm.py b/doc/demo/rec_xradia_xrm.py
@@ -4,7 +4,7 @@
 """
 TomoPy example script to reconstruct the xrm tomography data from
 the original stack of xrm. To use rename the xrm data as 
-radios/image00000.xrm and flats/image00000.xrm
+radios/image_00000.xrm and flats/ref_00000.xrm
 """
 
 from __future__ import print_function
@@ -27,8 +27,8 @@
     start = 0
     end = 16
 
-    # Read the Anka tiff raw data.
-    proj, flat = dxchange.read_aps_26id(fname, ind_tomo, ind_flat,
+    # APS 26-ID has an x-radia system collecting raw data as xrm.
+    proj, flat, metadata = dxchange.read_aps_26id(fname, ind_tomo, ind_flat,
                                                  sino=(start, end))
 
     # make the darks

diff --git a/doc/source/demo.rst b/doc/source/demo.rst
@@ -1 +1 @@
-Examples========Code example on how to use DXchange to import tomographic data from different synchrotron facilities and process it with TomoPy :cite:`Gursoy:14b`... toctree::   demo/doc.demo.anka   demo/doc.demo.australian   demo/doc.demo.als   demo/doc.demo.elettra   demo/doc.demo.esrf   demo/doc.demo.aps_1id   demo/doc.demo.aps_13bm   demo/doc.demo.aps_32id   demo/doc.demo.petraIII_p05   demo/doc.demo.tomcat   demo/doc.demo.xradia.. automodule:: dxchange   :members:   :undoc-members:   :show-inheritance: 
+Examples========Code example on how to use DXchange to import tomographic data from different synchrotron facilities and process it with TomoPy :cite:`Gursoy:14b`... toctree::   demo/doc.demo.anka   demo/doc.demo.australian   demo/doc.demo.als   demo/doc.demo.elettra   demo/doc.demo.esrf   demo/doc.demo.aps_1id   demo/doc.demo.aps_8bm   demo/doc.demo.aps_13bm   demo/doc.demo.aps_26id   demo/doc.demo.aps_32id   demo/doc.demo.petraIII_p05   demo/doc.demo.tomcat   demo/doc.demo.xradia.. automodule:: dxchange   :members:   :undoc-members:   :show-inheritance: 

diff --git a/doc/source/demo/doc.demo.aps_26id.rst b/doc/source/demo/doc.demo.aps_26id.rst
@@ -0,0 +1,9 @@
+APS 26-ID 
+=========
+
+This section contains a script to read the X-radia XRM tomography dataset and reconstruct it with tomoPy.
+
+Download file: :download:`rec_aps_26id.py<../../../doc/demo/rec_aps_26id.py>`
+
+.. literalinclude:: ../../../doc/demo/rec_aps_26id.py    :tab-width: 4    :linenos:    :language: guess
+

diff --git a/doc/source/demo/doc.demo.aps_8bm.rst b/doc/source/demo/doc.demo.aps_8bm.rst
@@ -0,0 +1,9 @@
+APS 8-BM 
+========
+
+This section contains a script to read the X-radia XRM tomography dataset and reconstruct it with tomoPy.
+
+Download file: :download:`rec_aps_8bm.py<../../../doc/demo/rec_aps_8bm.py>`
+
+.. literalinclude:: ../../../doc/demo/rec_aps_8bm.py    :tab-width: 4    :linenos:    :language: guess
+

diff --git a/doc/source/demo/doc.demo.xradia.rst b/doc/source/demo/doc.demo.xradia.rst
@@ -1,7 +1,7 @@
-X-radia XRM and TXRM 
-====================
+X-radia XRM
+===========
 
-This section contains a script to read the X-radia XRM and TXRM  tomography dataset and reconstruct it with tomoPy.
+This section contains a script to read the X-radia XRM tomography dataset and reconstruct it with tomoPy.
 
 Download file: :download:`rec_xradia_xrm.py<../../../doc/demo/rec_xradia_xrm.py>`