Merge pull request #469 from odlgroup/issue-463__phantoms_folder

API: move phantoms to new odl.phantoms dir
odlgroup · Jun 28, 2016 · b8b4eb4 · b8b4eb4
2 parents dcb57e2 + d4eb486
commit b8b4eb4
Show file tree

Hide file tree

Showing 36 changed files with 1,112 additions and 761 deletions.
diff --git a/doc/source/release_notes.rst b/doc/source/release_notes.rst
@@ -6,6 +6,26 @@
 Release Notes
 #############
 
+ODL 0.2.4 Release Notes (2016-06-28)
+====================================
+
+New features
+------------
+- Add ``uniform_discr_fromdiscr`` (`PR 467`).
+- Add conda build files (`commit 86ff166`).
+
+Bugfixes
+--------
+- Fix bug in submarine phantom with non-centered space (`PR 469`).
+- Fix crash when plotting in 1d (`commit 3255fa3`).
+
+Changes
+-------
+- Move phantoms to new module odl.phantom (`PR 469`).
+- Rename ``RectPartition.is_uniform`` to ``RectPartition.is_uniform``
+  (`PR 468`).
+
+
 ODL 0.2.3 Release Notes (2016-06-12)
 ====================================
 

diff --git a/examples/solvers/chambolle_pock_deconvolve.py b/examples/solvers/chambolle_pock_deconvolve.py
@@ -57,7 +57,7 @@
 # odl.diagnostics.OperatorTest(conv_op).run_tests()
 
 # Create phantom
-phantom = odl.util.shepp_logan(space, modified=True)
+phantom = odl.phantom.shepp_logan(space, modified=True)
 
 # Create vector of convolved phantom
 data = convolution(phantom)

diff --git a/examples/solvers/chambolle_pock_tomography.py b/examples/solvers/chambolle_pock_tomography.py
@@ -64,11 +64,11 @@
 
 
 # Create phantom
-discr_phantom = odl.util.shepp_logan(reco_space, modified=True)
+discr_phantom = odl.phantom.shepp_logan(reco_space, modified=True)
 
 # Create sinogram of forward projected phantom with noise
 data = ray_trafo(discr_phantom)
-data += odl.util.white_noise(ray_trafo.range) * np.mean(data) * 0.1
+data += odl.phantom.white_noise(ray_trafo.range) * np.mean(data) * 0.1
 
 
 # --- Set up the inverse problem --- #

diff --git a/examples/solvers/conjugate_gradient_tomography.py b/examples/solvers/conjugate_gradient_tomography.py
@@ -62,11 +62,11 @@
 
 
 # Create phantom
-discr_phantom = odl.util.shepp_logan(reco_space, modified=True)
+discr_phantom = odl.phantom.shepp_logan(reco_space, modified=True)
 
 # Create sinogram of forward projected phantom with noise
 data = ray_trafo(discr_phantom)
-data += odl.util.white_noise(ray_trafo.range) * np.mean(data) * 0.1
+data += odl.phantom.white_noise(ray_trafo.range) * np.mean(data) * 0.1
 
 # Optionally pass partial to the solver to display intermediate results
 partial = (odl.solvers.PrintIterationPartial() &

diff --git a/examples/tomo/filtered_backprojection_parallel_2d.py b/examples/tomo/filtered_backprojection_parallel_2d.py
@@ -70,7 +70,7 @@
 
 
 # Create a discrete Shepp-Logan phantom (modified version)
-phantom = odl.util.phantom.shepp_logan(reco_space, modified=True)
+phantom = odl.phantom.shepp_logan(reco_space, modified=True)
 
 # Create projection data by calling the ray transform on the phantom
 proj_data = ray_trafo(phantom)

diff --git a/examples/tomo/ray_trafo_circular_cone.py b/examples/tomo/ray_trafo_circular_cone.py
@@ -45,7 +45,7 @@
 ray_trafo = odl.tomo.RayTransform(reco_space, geometry, impl='astra_cuda')
 
 # Create a discrete Shepp-Logan phantom (modified version)
-phantom = odl.util.phantom.shepp_logan(reco_space, True)
+phantom = odl.phantom.shepp_logan(reco_space, True)
 
 # Create projection data by calling the ray transform on the phantom
 proj_data = ray_trafo(phantom)

diff --git a/examples/tomo/ray_trafo_fanflat.py b/examples/tomo/ray_trafo_fanflat.py
@@ -44,7 +44,7 @@
 ray_trafo = odl.tomo.RayTransform(reco_space, geometry, impl='astra_cuda')
 
 # Create a discrete Shepp-Logan phantom (modified version)
-phantom = odl.util.phantom.shepp_logan(reco_space, modified=True)
+phantom = odl.phantom.shepp_logan(reco_space, modified=True)
 
 # Create projection data by calling the ray transform on the phantom
 proj_data = ray_trafo(phantom)

diff --git a/examples/tomo/ray_trafo_helical.py b/examples/tomo/ray_trafo_helical.py
@@ -46,7 +46,7 @@
 ray_trafo = odl.tomo.RayTransform(reco_space, geometry, impl='astra_cuda')
 
 # Create a discrete Shepp-Logan phantom (modified version)
-phantom = odl.util.phantom.shepp_logan(reco_space, modified=True)
+phantom = odl.phantom.shepp_logan(reco_space, modified=True)
 
 # Create projection data by calling the ray transform on the phantom
 proj_data = ray_trafo(phantom)

diff --git a/examples/tomo/ray_trafo_parallel_2d.py b/examples/tomo/ray_trafo_parallel_2d.py
@@ -43,7 +43,7 @@
 ray_trafo = odl.tomo.RayTransform(reco_space, geometry, impl='astra_cuda')
 
 # Create a discrete Shepp-Logan phantom (modified version)
-phantom = odl.util.phantom.shepp_logan(reco_space, modified=True)
+phantom = odl.phantom.shepp_logan(reco_space, modified=True)
 
 # Create projection data by calling the ray transform on the phantom
 proj_data = ray_trafo(phantom)

diff --git a/examples/tomo/ray_trafo_parallel_3d.py b/examples/tomo/ray_trafo_parallel_3d.py
@@ -49,7 +49,7 @@
 ray_trafo = odl.tomo.RayTransform(reco_space, geometry, impl='astra_cuda')
 
 # Create a discrete Shepp-Logan phantom (modified version)
-phantom = odl.util.phantom.shepp_logan(reco_space, modified=True)
+phantom = odl.phantom.shepp_logan(reco_space, modified=True)
 
 # Create projection data by calling the ray transform on the phantom
 proj_data = ray_trafo(phantom)

diff --git a/examples/tomo/scikit_ray_trafo_parallel_2d.py b/examples/tomo/scikit_ray_trafo_parallel_2d.py
@@ -37,7 +37,7 @@
 ray_trafo = odl.tomo.RayTransform(reco_space, geometry, impl='scikit')
 
 # Create a discrete Shepp-Logan phantom (modified version)
-phantom = odl.util.phantom.shepp_logan(reco_space, modified=True)
+phantom = odl.phantom.shepp_logan(reco_space, modified=True)
 
 # Create projection data by calling the ray transform on the phantom
 proj_data = ray_trafo(phantom)

diff --git a/examples/tomo/stir_project.py b/examples/tomo/stir_project.py
@@ -46,7 +46,7 @@
     recon_sp, data_sp, volume, proj_data)
 
 # Create shepp-logan phantom
-vol = odl.util.shepp_logan(proj.domain, modified=True)
+vol = odl.phantom.shepp_logan(proj.domain, modified=True)
 
 # Project and show
 result = proj(vol)

diff --git a/examples/tomo/stir_reconstruct.py b/examples/tomo/stir_reconstruct.py
@@ -35,7 +35,7 @@
     volume_file, projection_file)
 
 # Create shepp-logan phantom
-vol = odl.util.shepp_logan(proj.domain, modified=True)
+vol = odl.phantom.shepp_logan(proj.domain, modified=True)
 
 # Project data
 projections = proj(vol)

diff --git a/examples/trafos/fourier_trafo.py b/examples/trafos/fourier_trafo.py
@@ -35,7 +35,7 @@
 ft_op = odl.trafos.FourierTransform(discr_space)
 
 # Create a phantom and its Fourier transfrom and display them
-phantom = odl.util.phantom.shepp_logan(discr_space, modified=True)
+phantom = odl.phantom.shepp_logan(discr_space, modified=True)
 phantom.show(title='Shepp-Logan phantom', show=True)
 phantom_ft = ft_op(phantom)
 phantom_ft.show(title='Full Fourier Transform', show=True)
@@ -51,7 +51,7 @@
 # its complex conjugate. This is faster and more memory efficient.
 discr_space_real = odl.uniform_discr([-1, -1], [1, 1], (512, 512))
 ft_op_halfc = odl.trafos.FourierTransform(discr_space_real, halfcomplex=True)
-phantom_real = odl.util.phantom.shepp_logan(discr_space_real, modified=True)
+phantom_real = odl.phantom.shepp_logan(discr_space_real, modified=True)
 phantom_real.show(title='Shepp-Logan phantom, real version', show=True)
 phantom_real_ft = ft_op_halfc(phantom_real)
 phantom_real_ft.show(title='Half-complex Fourier Transform', show=True)
diff --git a/examples/visualization/show_2d.py b/examples/visualization/show_2d.py
@@ -26,7 +26,7 @@
 import odl
 
 spc = odl.uniform_discr([0, 0], [1, 1], [100, 100])
-vec = odl.util.shepp_logan(spc, modified=True)
+vec = odl.phantom.shepp_logan(spc, modified=True)
 
 # Show all data
 vec.show(show=True)

diff --git a/examples/visualization/show_2d_complex.py b/examples/visualization/show_2d_complex.py
@@ -26,7 +26,7 @@
 import odl
 
 spc = odl.uniform_discr([0, 0], [1, 1], [100, 100], dtype='complex')
-vec = odl.util.shepp_logan(spc, modified=True) * (1 + 0.5j)
+vec = odl.phantom.shepp_logan(spc, modified=True) * (1 + 0.5j)
 
 # Can also force "instant" plotting
 vec.show(show=True)
diff --git a/examples/visualization/show_productspace.py b/examples/visualization/show_productspace.py
@@ -30,10 +30,10 @@
 pspace = odl.ProductSpace(spc, m)
 
 # Making a product space element where each component consists of a
-# Shepp-Logan phantom multiplied by the constant (i+1), where i is the
+# Shepp-Logan phantom multiplied by the constant i, where i is the
 # index of the product space component.
-vec = pspace.element([odl.util.shepp_logan(spc, modified=True) * i
-                      for i in range(1, m + 1)])
+vec = pspace.element([odl.phantom.shepp_logan(spc, modified=True) * i
+                      for i in range(m)])
 
 # By default 4 uniformly spaced elements are shown. Since there are 7 in
 # total, the shown components are 0, 2, 4 and 6

diff --git a/examples/visualization/show_update_2d.py b/examples/visualization/show_update_2d.py
@@ -28,7 +28,7 @@
 n = 100
 m = 20
 spc = odl.uniform_discr([0, 0], [1, 1], [n, n])
-vec = odl.util.shepp_logan(spc, modified=True)
+vec = odl.phantom.shepp_logan(spc, modified=True)
 
 # Create a figure by saving the result of show
 fig = None

diff --git a/odl/__init__.py b/odl/__init__.py
@@ -25,9 +25,9 @@
 
 from __future__ import absolute_import
 
-__version__ = '0.2.3'
+__version__ = '0.2.4'
 __all__ = ('diagnostics', 'discr', 'operator', 'set', 'space', 'solvers',
-           'tomo', 'trafos', 'util')
+           'tomo', 'trafos', 'util', 'phantom')
 
 # Propagate names defined in __all__ of all submodules into the top-level
 # module
@@ -53,6 +53,7 @@
 from . import trafos
 from . import tomo
 from . import util
+from . import phantom
 
 from .util import test
 __all__ += ('test',)
diff --git a/odl/phantom/__init__.py b/odl/phantom/__init__.py
@@ -0,0 +1,39 @@
+# Copyright 2014-2016 The ODL development group
+#
+# This file is part of ODL.
+#
+# ODL is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# ODL is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with ODL.  If not, see <http://www.gnu.org/licenses/>.
+
+"""Test data for tomography problems."""
+
+from __future__ import absolute_import
+
+__all__ = ()
+
+from . import phantom_utils
+
+from .emission import *
+__all__ += emission.__all__
+
+from .geometric import *
+__all__ += geometric.__all__
+
+from .misc_phantoms import *
+__all__ += misc_phantoms.__all__
+
+from .noise import *
+__all__ += noise.__all__
+
+from .transmission import *
+__all__ += transmission.__all__