updates to TomoPhantom plugin to use v3.0

CHANGELOG.md

@@ -14,6 +14,7 @@
     - dxchange minimum version set to 0.2.1 to fix #2256 (#2268)
     - improve `tqdm` notebook support (#2241)
     - cvxpy maximum version set to 1.7.5 to fix #2303 (#2304)
+    - Update to TomoPhantom v3.0 (#2287)
     - Handle regularisation toolkit CPU only package error message (#2302)
   - Documentation:
     - Render the user showcase notebooks in the documentation (#2189)

README.md

@@ -54,7 +54,7 @@ While building the CIL package we test with specific versions of dependencies. T
 | [ASTRA toolbox](http://www.astra-toolbox.com) | 2.1 | CPU: `conda-forge::astra-toolbox=2.1=py*` <br> GPU: `conda-forge::astra-toolbox=2.1=cuda*` | CT projectors, FBP and FDK. | [GPL-3.0](https://github.com/astra-toolbox/astra-toolbox/blob/master/COPYING) |
 | [TIGRE](https://github.com/CERN/TIGRE) | 2.6 | `ccpi::tigre=2.6` | CT projectors, FBP and FDK. | [BSD-3-Clause](https://github.com/CERN/TIGRE/blob/master/LICENSE.txt) |
 | [CCPi Regularisation Toolkit](https://github.com/TomographicImaging/CCPi-Regularisation-Toolkit) | 24.0.1 | `ccpi::ccpi-regulariser=24.0.1` | Toolbox of regularisation methods. | [Apache-2.0](https://github.com/TomographicImaging/CCPi-Regularisation-Toolkit/blob/master/LICENSE) |
-| [TomoPhantom](https://github.com/dkazanc/TomoPhantom) | [2.0.0](https://github.com/dkazanc/TomoPhantom/releases/tag/v2.0.0) | `ccpi::tomophantom=2.0.0` | Generates phantoms to use as test data. | [Apache-2.0](https://github.com/dkazanc/TomoPhantom/blob/master/LICENSE) |
+| [TomoPhantom](https://github.com/dkazanc/TomoPhantom) | [3.0.3](https://github.com/dkazanc/TomoPhantom/releases/tag/v3.0) | `ccpi::tomophantom=3.0.3` | Generates phantoms to use as test data. | [Apache-2.0](https://github.com/dkazanc/TomoPhantom/blob/master/LICENSE) |
 | [ipykernel](https://github.com/ipython/ipykernel) || `ipykernel` | Provides the IPython kernel to run Jupyter notebooks. | [BSD-3-Clause](https://github.com/ipython/ipykernel/blob/main/LICENSE) |
 | [ipywidgets](https://github.com/jupyter-widgets/ipywidgets) || `ipywidgets` | Enables visualisation tools within jupyter noteboooks. | [BSD-3-Clause](https://github.com/jupyter-widgets/ipywidgets/blob/main/LICENSE) |
 |[zenodo_get](https://github.com/dvolgyes/zenodo_get)|>= 1.6|`zenodo_get>=1.6`| Downloads datasets from Zenodo, is used by `dataexample` to get data used in CIL-Demos |[AGPL-3.0](https://github.com/dvolgyes/zenodo_get?tab=AGPL-3.0-1-ov-file)|

Wrappers/Python/cil/plugins/TomoPhantom.py

@@ -23,26 +23,12 @@
 import os
 import numpy as np
 
-import ctypes, platform
-from ctypes import util
-# check for the extension
-if platform.system() == 'Linux':
-    dll = 'libctomophantom.so'
-elif platform.system() == 'Windows':
-    dll_file = 'ctomophantom.dll'
-    dll = util.find_library(dll_file)
-elif platform.system() == 'Darwin':
-    dll = 'libctomophantom.dylib'
-else:
-    raise ValueError('Not supported platform, ', platform.system())
-
-libtomophantom = ctypes.cdll.LoadLibrary(dll)
-
-
+import ctypes
+import tomophantom.ctypes.external as external
 
 path = os.path.dirname(tomophantom.__file__)
-path_library2D = os.path.join(path, "Phantom2DLibrary.dat")
-path_library3D = os.path.join(path, "Phantom3DLibrary.dat")
+path_library2D = os.path.join(path, "phantomlib", "Phantom2DLibrary.dat")
+path_library3D = os.path.join(path, "phantomlib", "Phantom3DLibrary.dat")
 
 def is_model_temporal(num_model, num_dims=2):
     '''Returns whether a model in the TomoPhantom library is temporal
@@ -89,24 +75,20 @@ def check_model_params(num_model, num_dims=2):
     :type num_dims: int, default 2
     '''
     if num_dims == 2:
-        libtomophantom.checkParams2D.argtypes = [ctypes.POINTER(ctypes.c_int),  # pointer to the params array
+        external.c_checkParams2D.argtypes = [ctypes.POINTER(ctypes.c_int),  # pointer to the params array
                                   ctypes.c_int,                                   # model number selector (int)
                                   ctypes.c_char_p]                  # string to the library file
         params = np.zeros([10], dtype=np.int32)
-        params_p = params.ctypes.data_as(ctypes.POINTER(ctypes.c_int))
-        lib2d_p = str(path_library2D).encode('utf-8')
-        libtomophantom.checkParams2D(params_p, num_model, lib2d_p)
+        external.c_checkParams2D(params, num_model, str(path_library2D))
 
         return params
 
     elif num_dims == 3:
-        libtomophantom.checkParams3D.argtypes = [ctypes.POINTER(ctypes.c_int),  # pointer to the params array
+        external.c_checkParams3D.argtypes = [ctypes.POINTER(ctypes.c_int),  # pointer to the params array
                                   ctypes.c_int,                                   # model number selector (int)
                                   ctypes.c_char_p]                  # string to the library file
         params = np.zeros([11], dtype=np.int32)
-        params_p = params.ctypes.data_as(ctypes.POINTER(ctypes.c_int))
-        lib2d_p = str(path_library3D).encode('utf-8')
-        libtomophantom.checkParams3D(params_p, num_model, lib2d_p)
+        external.c_checkParams3D(params, num_model, str(path_library3D))
 
         return params
 

Wrappers/Python/test/test_ring_processor.py

@@ -49,7 +49,7 @@ def test_L1Norm_2D(self):
         model = 12 # select a model number from the library
         N = 400 # set dimension of the phantom
         path = os.path.dirname(tomophantom.__file__)
-        path_library2D = os.path.join(path, "Phantom2DLibrary.dat")
+        path_library2D = os.path.join(path, "phantomlib", "Phantom2DLibrary.dat")
 
         phantom_2D = TomoP2D.Model(model, N, path_library2D)
         # data = ImageData(phantom_2D)

recipe/meta.yaml

@@ -15,7 +15,7 @@ test:
     - python-wget
     - cvxpy <= 1.7.5                  # [linux]
     - scikit-image
-    - tomophantom 2.0.0       # [linux]
+    - tomophantom 3.0.3
     - tigre 2.6
     - packaging
     - ccpi-regulariser 24.0.1 # [not osx]
@@ -65,7 +65,7 @@ requirements:
 
   # version constraints of optional dependencies
   run_constrained:
-    - tomophantom >=2
+    - tomophantom >=3.0.3
     - astra-toolbox >=1.9.9.dev5
     - tigre >=2.4
     - ccpi-regulariser >=24.0.1

scripts/requirements-test-windows.yml

@@ -22,8 +22,8 @@ dependencies:
   - ccpi::cil-data >=22
   - ccpi::tigre 2.6
   - ccpi::ccpi-regulariser 24.0.1
-  - ccpi::tomophantom 2.0.0
   - astra-toolbox 2.1 cuda*
+  - ccpi::tomophantom 3.0.3
   - cvxpy <= 1.7.5
   - python-wget
   - scikit-image

scripts/requirements-test.yml

@@ -19,11 +19,11 @@ channels:
 dependencies:
   - python >=3.10
   - numpy >=1.23,<2
-  - libgomp      # [linux]
+  - llvm-openmp
   - ccpi::cil-data >=22
   - ccpi::tigre 2.6
   - ccpi::ccpi-regulariser 24.0.1
-  - ccpi::tomophantom 2.0.0
+  - ccpi::tomophantom 3.0.3
   - astra-toolbox 2.1 cuda*
   - cvxpy <= 1.7.5
   - python-wget