Merge pull request #45 from dkazanc/adaptring

A better data model to supress ring artifacts

.travis.yml

@@ -3,8 +3,8 @@ language: python
 matrix:
   include:
     - python: 2.7
-      env: NUMPY=1.14 
-
+      env: NUMPY=1.14      
+    
     - python: 2.7
       env: NUMPY=1.15 
 
@@ -28,20 +28,20 @@ install:
   - export PATH="$HOME/miniconda/bin:$PATH"
   - hash -r
   - conda config --set always_yes yes --set changeps1 no
-  #- conda update -q conda
+  - conda update -q conda
   - conda info -a
   - conda create -q -n test-environment python=$TRAVIS_PYTHON_VERSION 
   - source activate test-environment
   - conda install --yes numpy=$NUMPY pytest conda-build anaconda-client 
   - conda install -c conda-forge sparse
   - conda config --set anaconda_upload no
-  - export VERSION=`date +%Y.%m`	
-  - conda build src/Python/conda-recipe --numpy=$NUMPY --python=$TRAVIS_PYTHON_VERSION 
+  - export VERSION=`date +%Y.%m`
+  - conda build conda-recipe --numpy=$NUMPY --python=$TRAVIS_PYTHON_VERSION
   - conda install --channel /home/travis/miniconda/envs/test-environment/conda-bld/ tomobar --offline --override-channels
 
 after_success:
   - chmod +x src/Python/conda-recipe/conda_upload.sh
-  - test $TRAVIS_BRANCH = "master" && bash src/Python/conda-recipe/conda_upload.sh
+  - test $TRAVIS_BRANCH = "master" && bash conda-recipe/conda_upload.sh
 
 script:
   - python tests/test.py

CHANGELOG.md

@@ -1,6 +1,17 @@
 # Changelog
 All notable changes to this project will be documented in this file.
 
+## [2019.11]
+
+### Added
+- RING_WEIGHTS module in C which calculates a better ring model to use in non-quadratic data penalties
+- Cmake and Cython wrappers
+- run.sh to run Cmake based installation of Python wrappers
+
+### Changed
+- Installation process to use Cmake and Cython to wrap Python modules
+- Demos and conda-build files moved to the main directory
+
 ## [2019.08]
 ### Added
 - Autocropper to automatically crop the 3D projection data to reduce its size

CMakeLists.txt

@@ -0,0 +1,32 @@
+#   Licensed under the Apache License, Version 2.0 (the "License");
+#   you may not use this file except in compliance with the License.
+#   You may obtain a copy of the License at
+#
+#       http://www.apache.org/licenses/LICENSE-2.0
+#
+#   Unless required by applicable law or agreed to in writing, software
+#   distributed under the License is distributed on an "AS IS" BASIS,
+#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#   See the License for the specific language governing permissions and
+#   limitations under the License.
+
+cmake_minimum_required (VERSION 3.0)
+
+project(tomobar)
+
+set (tomobar_VERSION $ENV{tomobar_VERSION} CACHE INTERNAL "tomobar modules" FORCE)
+message(STATUS "tomobar_VERSION set to " ${tomobar_VERSION})
+
+# set the Python variables for the Conda environment
+option (BUILD_PYTHON_WRAPPER "Build Python Wrappers" ON)
+option (CONDA_BUILD "Conda Build" OFF)
+
+set(PYTHON_DEST_DIR "" CACHE PATH "Directory of the Python wrappers")
+if (PYTHON_DEST_DIR)
+ set(PYTHON_DEST "${PYTHON_DEST_DIR}")
+else() 
+ set(PYTHON_DEST "${CMAKE_INSTALL_PREFIX}/python")
+endif()
+message(STATUS "Python wrappers will be installed in " ${PYTHON_DEST})
+
+add_subdirectory(src)

src/Matlab/Demos/ADMM_2D_Parallel.m → Demos/Matlab/ADMM_2D_Parallel.m

@@ -8,22 +8,7 @@
 % See ReadMe for more information and references
 
 close all;clc;clear;
-% adding paths
-fsep = '/';
-% TomoPhantom paths (TomoPhantom needs to be compiled first)
-pathtoTomoPhantom = sprintf(['..' fsep 'supplementary' fsep 'TomoPhantom' fsep 'Wrappers' fsep 'MATLAB' fsep 'compiled' fsep], 1i);
-addpath(pathtoTomoPhantom);
-pathtoTomoPhantom2 = sprintf(['..' fsep 'supplementary' fsep 'TomoPhantom' fsep 'Wrappers' fsep 'MATLAB' fsep 'supplem' fsep], 1i);
-addpath(pathtoTomoPhantom2);
-pathtoModels = sprintf(['..' fsep 'supplementary' fsep 'TomoPhantom' fsep 'PhantomLibrary' fsep 'models' fsep 'Phantom2DLibrary.dat'], 1i);
-% Regularisation Toolkit path to compiled library (CCPi-RGTtk needs to be compiled first)
-pathtoRGLtk = sprintf(['..' fsep 'supplementary' fsep 'CCPi-Regularisation-Toolkit' fsep 'Wrappers' fsep 'Matlab' fsep 'mex_compile' fsep 'installed'], 1i);
-addpath(pathtoRGLtk);
-
-pathmainFunc = sprintf(['..' fsep 'main_func'], 1i);
-addpath(pathmainFunc); 
-pathSupp = sprintf(['..' fsep 'supplementary'], 1i);
-addpath(pathSupp);
+adding_paths % ading all required paths (modify if required)
 %%
 fprintf('\n %s\n', 'Generating a phantom and projection data using the TomoPhantom package...');
 ModelNo = 14; % Select a model from Phantom2DLibrary.dat

src/Matlab/Demos/ADMM_2D_RealData.m → Demos/Matlab/ADMM_2D_RealData.m

@@ -7,19 +7,9 @@
 % See ReadMe for more information and references
 
 close all;clc;clear;
-% adding paths
-fsep = '/';
-
-% Regularisation Toolkit path to compiled library (CCPi-RGTtk needs to be compiled first)
-pathtoRGLtk = sprintf(['..' fsep 'supplementary' fsep 'CCPi-Regularisation-Toolkit' fsep 'Wrappers' fsep 'Matlab' fsep 'mex_compile' fsep 'installed'], 1i);
-addpath(pathtoRGLtk);
-
-pathmainFunc = sprintf(['..' fsep 'main_func'], 1i);
-addpath(pathmainFunc); 
-pathSupp = sprintf(['..' fsep 'supplementary'], 1i);
-addpath(pathSupp);
+adding_paths % ading all required paths (modify if required)
 %%
-load ../../../data/RealDataDend.mat
+load ../../data/RealDataDend.mat
 sinoRD = sinoRD';
 figure; imshow(sinoRD, [ ]); colormap hot; title('Sinogram');
 %%

src/Matlab/Demos/FISTA_2D_Parallel.m → Demos/Matlab/FISTA_2D_Parallel.m

@@ -8,22 +8,7 @@
 % See ReadMe for more information and links
 
 close all;clc;clear;
-% adding paths
-fsep = '/';
-% TomoPhantom paths (TomoPhantom needs to be compiled first)
-pathtoTomoPhantom = sprintf(['..' fsep 'supplementary' fsep 'TomoPhantom' fsep 'Wrappers' fsep 'MATLAB' fsep 'compiled' fsep], 1i);
-addpath(pathtoTomoPhantom);
-pathtoTomoPhantom2 = sprintf(['..' fsep 'supplementary' fsep 'TomoPhantom' fsep 'Wrappers' fsep 'MATLAB' fsep 'supplem' fsep], 1i);
-addpath(pathtoTomoPhantom2);
-pathtoModels = sprintf(['..' fsep 'supplementary' fsep 'TomoPhantom' fsep 'PhantomLibrary' fsep 'models' fsep 'Phantom2DLibrary.dat'], 1i);
-% Regularisation Toolkit path to compiled library (CCPi-RGTtk needs to be compiled first)
-pathtoRGLtk = sprintf(['..' fsep 'supplementary' fsep 'CCPi-Regularisation-Toolkit' fsep 'Wrappers' fsep 'Matlab' fsep 'mex_compile' fsep 'installed'], 1i);
-addpath(pathtoRGLtk);
-
-pathmainFunc = sprintf(['..' fsep 'main_func'], 1i);
-addpath(pathmainFunc); 
-pathSupp = sprintf(['..' fsep 'supplementary'], 1i);
-addpath(pathSupp);
+adding_paths % ading all required paths (modify if required)
 %%
 fprintf('\n %s\n', 'Generating a phantom and projection data using the TomoPhantom package...');
 ModelNo = 4; % Select a model from Phantom2DLibrary.dat

src/Matlab/Demos/FISTA_2D_Parallel_Artifacts.m → Demos/Matlab/FISTA_2D_Parallel_Artifacts.m

@@ -9,22 +9,7 @@
 % See ReadMe for more information and links
 
 close all;clc;clear;
-% adding paths
-fsep = '/';
-% TomoPhantom paths (TomoPhantom needs to be compiled first)
-pathtoTomoPhantom = sprintf(['..' fsep 'supplementary' fsep 'TomoPhantom' fsep 'Wrappers' fsep 'MATLAB' fsep 'compiled' fsep], 1i);
-addpath(pathtoTomoPhantom);
-pathtoTomoPhantom2 = sprintf(['..' fsep 'supplementary' fsep 'TomoPhantom' fsep 'Wrappers' fsep 'MATLAB' fsep 'supplem' fsep], 1i);
-addpath(pathtoTomoPhantom2);
-pathtoModels = sprintf(['..' fsep 'supplementary' fsep 'TomoPhantom' fsep 'PhantomLibrary' fsep 'models' fsep 'Phantom2DLibrary.dat'], 1i);
-% Regularisation Toolkit path to compiled library (CCPi-RGTtk needs to be compiled first)
-pathtoRGLtk = sprintf(['..' fsep 'supplementary' fsep 'CCPi-Regularisation-Toolkit' fsep 'Wrappers' fsep 'Matlab' fsep 'mex_compile' fsep 'installed'], 1i);
-addpath(pathtoRGLtk);
-
-pathmainFunc = sprintf(['..' fsep 'main_func'], 1i);
-addpath(pathmainFunc); 
-pathSupp = sprintf(['..' fsep 'supplementary'], 1i);
-addpath(pathSupp);
+adding_paths % ading all required paths (modify if required)
 %%
 fprintf('\n %s\n', 'Generating a phantom and projection data using the TomoPhantom package...');
 ModelNo = 4; % Select a model from Phantom2DLibrary.dat

src/Matlab/Demos/FISTA_2D_Parallel_Artifacts_OS.m → Demos/Matlab/FISTA_2D_Parallel_Artifacts_OS.m

@@ -9,22 +9,7 @@
 % See ReadMe for more information and links
 
 close all;clc;clear;
-% adding paths
-fsep = '/';
-% TomoPhantom paths (TomoPhantom needs to be compiled first)
-pathtoTomoPhantom = sprintf(['..' fsep 'supplementary' fsep 'TomoPhantom' fsep 'Wrappers' fsep 'MATLAB' fsep 'compiled' fsep], 1i);
-addpath(pathtoTomoPhantom);
-pathtoTomoPhantom2 = sprintf(['..' fsep 'supplementary' fsep 'TomoPhantom' fsep 'Wrappers' fsep 'MATLAB' fsep 'supplem' fsep], 1i);
-addpath(pathtoTomoPhantom2);
-pathtoModels = sprintf(['..' fsep 'supplementary' fsep 'TomoPhantom' fsep 'PhantomLibrary' fsep 'models' fsep 'Phantom2DLibrary.dat'], 1i);
-% Regularisation Toolkit path to compiled library (CCPi-RGTtk needs to be compiled first)
-pathtoRGLtk = sprintf(['..' fsep 'supplementary' fsep 'CCPi-Regularisation-Toolkit' fsep 'Wrappers' fsep 'Matlab' fsep 'mex_compile' fsep 'installed'], 1i);
-addpath(pathtoRGLtk);
-
-pathmainFunc = sprintf(['..' fsep 'main_func'], 1i);
-addpath(pathmainFunc); 
-pathSupp = sprintf(['..' fsep 'supplementary'], 1i);
-addpath(pathSupp);
+adding_paths % ading all required paths (modify if required)
 %%
 fprintf('\n %s\n', 'Generating a phantom and projection data using the TomoPhantom package...');
 ModelNo = 4; % Select a model from Phantom2DLibrary.dat

src/Matlab/Demos/FISTA_2D_Parallel_OS.m → Demos/Matlab/FISTA_2D_Parallel_OS.m

@@ -8,22 +8,7 @@
 % See ReadMe for more information and links
 
 close all;clc;clear;
-% adding paths
-fsep = '/';
-% TomoPhantom paths (TomoPhantom needs to be compiled first)
-pathtoTomoPhantom = sprintf(['..' fsep 'supplementary' fsep 'TomoPhantom' fsep 'Wrappers' fsep 'MATLAB' fsep 'compiled' fsep], 1i);
-addpath(pathtoTomoPhantom);
-pathtoTomoPhantom2 = sprintf(['..' fsep 'supplementary' fsep 'TomoPhantom' fsep 'Wrappers' fsep 'MATLAB' fsep 'supplem' fsep], 1i);
-addpath(pathtoTomoPhantom2);
-pathtoModels = sprintf(['..' fsep 'supplementary' fsep 'TomoPhantom' fsep 'PhantomLibrary' fsep 'models' fsep 'Phantom2DLibrary.dat'], 1i);
-% Regularisation Toolkit path to compiled library (CCPi-RGTtk needs to be compiled first)
-pathtoRGLtk = sprintf(['..' fsep 'supplementary' fsep 'CCPi-Regularisation-Toolkit' fsep 'Wrappers' fsep 'Matlab' fsep 'mex_compile' fsep 'installed'], 1i);
-addpath(pathtoRGLtk);
-
-pathmainFunc = sprintf(['..' fsep 'main_func'], 1i);
-addpath(pathmainFunc); 
-pathSupp = sprintf(['..' fsep 'supplementary'], 1i);
-addpath(pathSupp);
+adding_paths % ading all required paths (modify if required)
 %%
 fprintf('\n %s\n', 'Generating a phantom and projection data using the TomoPhantom package...');
 ModelNo = 4; % Select a model from Phantom2DLibrary.dat

src/Matlab/Demos/FISTA_3D_ConeBeam.m → Demos/Matlab/FISTA_3D_ConeBeam.m

@@ -7,23 +7,7 @@
 % See ReadMe for more information and links
 
 close all;clc;clear;
-% adding paths
-fsep = '/';
-% TomoPhantom paths (TomoPhantom needs to be compiled first)
-pathtoTomoPhantom = sprintf(['..' fsep 'supplementary' fsep 'TomoPhantom' fsep 'Wrappers' fsep 'MATLAB' fsep 'compiled' fsep], 1i);
-addpath(pathtoTomoPhantom);
-pathtoTomoPhantom2 = sprintf(['..' fsep 'supplementary' fsep 'TomoPhantom' fsep 'Wrappers' fsep 'MATLAB' fsep 'supplem' fsep], 1i);
-addpath(pathtoTomoPhantom2);
-pathtoModels = sprintf(['..' fsep 'supplementary' fsep 'TomoPhantom' fsep 'PhantomLibrary' fsep 'models' fsep 'Phantom2DLibrary.dat'], 1i);
-% Regularisation Toolkit path to compiled library (CCPi-RGTtk needs to be compiled first)
-pathtoRGLtk = sprintf(['..' fsep 'supplementary' fsep 'CCPi-Regularisation-Toolkit' fsep 'Wrappers' fsep 'Matlab' fsep 'mex_compile' fsep 'installed'], 1i);
-addpath(pathtoRGLtk);
-
-pathmainFunc = sprintf(['..' fsep 'main_func'], 1i);
-addpath(pathmainFunc); 
-pathSupp = sprintf(['..' fsep 'supplementary'], 1i);
-addpath(pathSupp);
-
+adding_paths % ading all required paths (modify if required)
 %%
 % Generate 3D phantom:
 fprintf('\n %s\n', 'Generating a phantom using the TomoPhantom package...');

src/Matlab/Demos/FISTA_3D_Parallel.m → Demos/Matlab/FISTA_3D_Parallel.m

@@ -7,23 +7,7 @@
 % See ReadMe for more information and links
 
 close all;clc;clear;
-% adding paths
-fsep = '/';
-% TomoPhantom paths (TomoPhantom needs to be compiled first)
-pathtoTomoPhantom = sprintf(['..' fsep 'supplementary' fsep 'TomoPhantom' fsep 'Wrappers' fsep 'MATLAB' fsep 'compiled' fsep], 1i);
-addpath(pathtoTomoPhantom);
-pathtoTomoPhantom2 = sprintf(['..' fsep 'supplementary' fsep 'TomoPhantom' fsep 'Wrappers' fsep 'MATLAB' fsep 'supplem' fsep], 1i);
-addpath(pathtoTomoPhantom2);
-pathtoModels = sprintf(['..' fsep 'supplementary' fsep 'TomoPhantom' fsep 'PhantomLibrary' fsep 'models' fsep 'Phantom2DLibrary.dat'], 1i);
-% Regularisation Toolkit path to compiled library (CCPi-RGTtk needs to be compiled first)
-pathtoRGLtk = sprintf(['..' fsep 'supplementary' fsep 'CCPi-Regularisation-Toolkit' fsep 'Wrappers' fsep 'Matlab' fsep 'mex_compile' fsep 'installed'], 1i);
-addpath(pathtoRGLtk);
-
-pathmainFunc = sprintf(['..' fsep 'main_func'], 1i);
-addpath(pathmainFunc); 
-pathSupp = sprintf(['..' fsep 'supplementary'], 1i);
-addpath(pathSupp);
-
+adding_paths % ading all required paths (modify if required)
 %%
 % Generate 3D phantom:
 fprintf('\n %s\n', 'Generating a phantom using the TomoPhantom package...');

src/Matlab/Demos/FISTA_RealData_Parallel.m → Demos/Matlab/FISTA_RealData_Parallel.m

@@ -7,18 +7,7 @@
 % See ReadMe for more information and links
 
 close all;clc;clear;
-% adding paths
-fsep = '/';
-% Regularisation Toolkit path to compiled library (CCPi-RGTtk needs to be compiled first)
-pathtoRGLtk = sprintf(['..' fsep 'supplementary' fsep 'CCPi-Regularisation-Toolkit' fsep 'Wrappers' fsep 'Matlab' fsep 'mex_compile' fsep 'installed'], 1i);
-addpath(pathtoRGLtk);
-
-pathmainFunc = sprintf(['..' fsep 'main_func'], 1i);
-addpath(pathmainFunc); 
-pathSupp = sprintf(['..' fsep 'supplementary'], 1i);
-addpath(pathSupp);
-pathtoData = sprintf(['..' fsep '..' fsep '..' fsep 'data'], 1i);
-addpath(pathtoData);
+adding_paths % ading all required paths (modify if required)
 %%
 fprintf('\n %s\n', 'Loading real data...');
 [Sino3D,  Weights3D, anglesRad, Detectors] = exportDemoRD2Data();

Demos/Matlab/adding_paths.m

@@ -0,0 +1,16 @@
+% adding paths
+fsep = '/';
+% TomoPhantom paths (TomoPhantom needs to be compiled first)
+pathtoTomoPhantom = sprintf(['..' fsep '..' fsep 'src' fsep 'Matlab' fsep 'supplementary' fsep 'TomoPhantom' fsep 'Wrappers' fsep 'MATLAB' fsep 'compiled' fsep], 1i);
+addpath(pathtoTomoPhantom);
+pathtoTomoPhantom2 = sprintf(['..' fsep '..' fsep 'src' fsep 'Matlab' fsep  'supplementary' fsep 'TomoPhantom' fsep 'Wrappers' fsep 'MATLAB' fsep 'supplem' fsep], 1i);
+addpath(pathtoTomoPhantom2);
+pathtoModels = sprintf(['..' fsep '..' fsep 'src' fsep 'Matlab' fsep 'supplementary' fsep 'TomoPhantom' fsep 'PhantomLibrary' fsep 'models' fsep 'Phantom2DLibrary.dat'], 1i);
+% Regularisation Toolkit path to compiled library (CCPi-RGTtk needs to be compiled first)
+pathtoRGLtk = sprintf(['..' fsep '..' fsep 'src' fsep 'Matlab' fsep 'supplementary' fsep 'CCPi-Regularisation-Toolkit' fsep 'Wrappers' fsep 'Matlab' fsep 'mex_compile' fsep 'installed'], 1i);
+addpath(pathtoRGLtk);
+
+pathmainFunc = sprintf(['..' fsep '..' fsep 'src' fsep 'Matlab' fsep 'main_func'], 1i);
+addpath(pathmainFunc); 
+pathSupp = sprintf(['..' fsep '..' fsep 'src' fsep 'Matlab' fsep 'supplementary'], 1i);
+addpath(pathSupp);