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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,87 +1,87 @@ | ||
| #!/usr/bin/env python | ||
| # -*- coding: utf-8 -*- | ||
|
|
||
| # ######################################################################### | ||
| # Copyright (c) 2019, UChicago Argonne, LLC. All rights reserved. # | ||
| # # | ||
| # Copyright 2019. UChicago Argonne, LLC. This software was produced # | ||
| # under U.S. Government contract DE-AC02-06CH11357 for Argonne National # | ||
| # Laboratory (ANL), which is operated by UChicago Argonne, LLC for the # | ||
| # U.S. Department of Energy. The U.S. Government has rights to use, # | ||
| # reproduce, and distribute this software. NEITHER THE GOVERNMENT NOR # | ||
| # UChicago Argonne, LLC MAKES ANY WARRANTY, EXPRESS OR IMPLIED, OR # | ||
| # ASSUMES ANY LIABILITY FOR THE USE OF THIS SOFTWARE. If software is # | ||
| # modified to produce derivative works, such modified software should # | ||
| # be clearly marked, so as not to confuse it with the version available # | ||
| # from ANL. # | ||
| # # | ||
| # Additionally, redistribution and use in source and binary forms, with # | ||
| # or without modification, are permitted provided that the following # | ||
| # conditions are met: # | ||
| # # | ||
| # * Redistributions of source code must retain the above copyright # | ||
| # notice, this list of conditions and the following disclaimer. # | ||
| # # | ||
| # * Redistributions in binary form must reproduce the above copyright # | ||
| # notice, this list of conditions and the following disclaimer in # | ||
| # the documentation and/or other materials provided with the # | ||
| # distribution. # | ||
| # # | ||
| # * Neither the name of UChicago Argonne, LLC, Argonne National # | ||
| # Laboratory, ANL, the U.S. Government, nor the names of its # | ||
| # contributors may be used to endorse or promote products derived # | ||
| # from this software without specific prior written permission. # | ||
| # # | ||
| # THIS SOFTWARE IS PROVIDED BY UChicago Argonne, LLC AND CONTRIBUTORS # | ||
| # "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT # | ||
| # LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS # | ||
| # FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL UChicago # | ||
| # Argonne, LLC OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, # | ||
| # INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, # | ||
| # BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; # | ||
| # LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER # | ||
| # CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT # | ||
| # LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN # | ||
| # ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE # | ||
| # POSSIBILITY OF SUCH DAMAGE. # | ||
| # ######################################################################### | ||
|
|
||
| """ | ||
| TomoPy example script to reconstruct the tomography data as | ||
| with gridrec. | ||
| """ | ||
| from __future__ import print_function | ||
| import tomopy | ||
| import dxchange | ||
|
|
||
| if __name__ == '__main__': | ||
|
|
||
| # Set path to the micro-CT data to reconstruct. | ||
| fname = '../../../tomopy/data/tooth.h5' | ||
|
|
||
| # Select the sinogram range to reconstruct. | ||
| start = 0 | ||
| end = 2 | ||
|
|
||
| # Read the APS 2-BM 0r 32-ID raw data. | ||
| proj, flat, dark, theta = dxchange.read_aps_32id(fname, sino=(start, end)) | ||
|
|
||
| # Set data collection angles as equally spaced between 0-180 degrees. | ||
| theta = tomopy.angles(proj.shape[0]) | ||
|
|
||
| # Set data collection angles as equally spaced between 0-180 degrees. | ||
| proj = tomopy.normalize(proj, flat, dark) | ||
|
|
||
| # Set data collection angles as equally spaced between 0-180 degrees. | ||
| rot_center = tomopy.find_center(proj, theta, init=290, ind=0, tol=0.5) | ||
|
|
||
| proj = tomopy.minus_log(proj) | ||
|
|
||
| # Reconstruct object using Gridrec algorithm. | ||
| recon = tomopy.recon(proj, theta, center=rot_center, algorithm='gridrec') | ||
|
|
||
| # Mask each reconstructed slice with a circle. | ||
| recon = tomopy.circ_mask(recon, axis=0, ratio=0.95) | ||
|
|
||
| # Write data as stack of TIFs. | ||
| dxchange.write_tiff_stack(recon, fname='recon_dir/recon') | ||
| #!/usr/bin/env python | ||
| # -*- coding: utf-8 -*- | ||
|
|
||
| # ######################################################################### | ||
| # Copyright (c) 2019, UChicago Argonne, LLC. All rights reserved. # | ||
| # # | ||
| # Copyright 2019. UChicago Argonne, LLC. This software was produced # | ||
| # under U.S. Government contract DE-AC02-06CH11357 for Argonne National # | ||
| # Laboratory (ANL), which is operated by UChicago Argonne, LLC for the # | ||
| # U.S. Department of Energy. The U.S. Government has rights to use, # | ||
| # reproduce, and distribute this software. NEITHER THE GOVERNMENT NOR # | ||
| # UChicago Argonne, LLC MAKES ANY WARRANTY, EXPRESS OR IMPLIED, OR # | ||
| # ASSUMES ANY LIABILITY FOR THE USE OF THIS SOFTWARE. If software is # | ||
| # modified to produce derivative works, such modified software should # | ||
| # be clearly marked, so as not to confuse it with the version available # | ||
| # from ANL. # | ||
| # # | ||
| # Additionally, redistribution and use in source and binary forms, with # | ||
| # or without modification, are permitted provided that the following # | ||
| # conditions are met: # | ||
| # # | ||
| # * Redistributions of source code must retain the above copyright # | ||
| # notice, this list of conditions and the following disclaimer. # | ||
| # # | ||
| # * Redistributions in binary form must reproduce the above copyright # | ||
| # notice, this list of conditions and the following disclaimer in # | ||
| # the documentation and/or other materials provided with the # | ||
| # distribution. # | ||
| # # | ||
| # * Neither the name of UChicago Argonne, LLC, Argonne National # | ||
| # Laboratory, ANL, the U.S. Government, nor the names of its # | ||
| # contributors may be used to endorse or promote products derived # | ||
| # from this software without specific prior written permission. # | ||
| # # | ||
| # THIS SOFTWARE IS PROVIDED BY UChicago Argonne, LLC AND CONTRIBUTORS # | ||
| # "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT # | ||
| # LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS # | ||
| # FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL UChicago # | ||
| # Argonne, LLC OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, # | ||
| # INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, # | ||
| # BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; # | ||
| # LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER # | ||
| # CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT # | ||
| # LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN # | ||
| # ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE # | ||
| # POSSIBILITY OF SUCH DAMAGE. # | ||
| # ######################################################################### | ||
|
|
||
| """ | ||
| TomoPy example script to reconstruct the tomography data as | ||
| with gridrec. | ||
| """ | ||
| from __future__ import print_function | ||
| import tomopy | ||
| import dxchange | ||
|
|
||
| if __name__ == '__main__': | ||
|
|
||
| # Set path to the micro-CT data to reconstruct. | ||
| fname = '../../../source/tomopy/data/tooth.h5' | ||
|
|
||
| # Select the sinogram range to reconstruct. | ||
| start = 0 | ||
| end = 2 | ||
|
|
||
| # Read the APS 2-BM 0r 32-ID raw data. | ||
| proj, flat, dark, theta = dxchange.read_aps_32id(fname, sino=(start, end)) | ||
|
|
||
| # Set data collection angles as equally spaced between 0-180 degrees. | ||
| theta = tomopy.angles(proj.shape[0]) | ||
|
|
||
| # Set data collection angles as equally spaced between 0-180 degrees. | ||
| proj = tomopy.normalize(proj, flat, dark) | ||
|
|
||
| # Set data collection angles as equally spaced between 0-180 degrees. | ||
| rot_center = tomopy.find_center(proj, theta, init=290, ind=0, tol=0.5) | ||
|
|
||
| proj = tomopy.minus_log(proj) | ||
|
|
||
| # Reconstruct object using Gridrec algorithm. | ||
| recon = tomopy.recon(proj, theta, center=rot_center, algorithm='gridrec') | ||
|
|
||
| # Mask each reconstructed slice with a circle. | ||
| recon = tomopy.circ_mask(recon, axis=0, ratio=0.95) | ||
|
|
||
| # Write data as stack of TIFs. | ||
| dxchange.write_tiff_stack(recon, fname='recon_dir/recon') |
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