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-rw-r--r--CMakeLists.txt5
-rw-r--r--Core/CMakeLists.txt2
-rwxr-xr-xCore/regularisers_GPU/TV_FGP_GPU_core.h9
-rwxr-xr-xCore/regularisers_GPU/TV_SB_GPU_core.h10
-rw-r--r--Core/regularisers_GPU/dTV_FGP_GPU_core.h9
-rw-r--r--Readme.md6
-rw-r--r--Wrappers/Python/CMakeLists.txt2
-rw-r--r--Wrappers/Python/conda-recipe/build.sh1
-rw-r--r--Wrappers/Python/conda-recipe/meta.yaml4
-rwxr-xr-xbuild/jenkins-build.sh44
-rw-r--r--recipes/regularisers/build.sh2
11 files changed, 31 insertions, 63 deletions
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 550b896..b95107a 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -25,7 +25,10 @@ set (CIL_VERSION_MAJOR 0)
set (CIL_VERSION_MINOR 10)
set (CIL_VERSION_PATCH 2)
-set (CIL_VERSION '${CIL_VERSION_MAJOR}.${CIL_VERSION_MINOR}.${CIL_VERSION_PATCH}' CACHE INTERNAL "Core Imaging Library version" FORCE)
+# set (CIL_VERSION '${CIL_VERSION_MAJOR}.${CIL_VERSION_MINOR}.${CIL_VERSION_PATCH}' CACHE INTERNAL "Core Imaging Library version" FORCE)
+# get CIL_VERSION from environment variable and set it in cmake
+set (CIL_VERSION $ENV{CIL_VERSION} CACHE INTERNAL "Core Imaging Library version" FORCE)
+message(STATUS "CIL_VERSION set to " ${CIL_VERSION})
# set the Python variables for the Conda environment
#include(${CMAKE_SOURCE_DIR}/CMake/FindAnacondaEnvironment.cmake)
diff --git a/Core/CMakeLists.txt b/Core/CMakeLists.txt
index d92db82..b3c0dfb 100644
--- a/Core/CMakeLists.txt
+++ b/Core/CMakeLists.txt
@@ -6,7 +6,7 @@ project(RGL_core)
# The version number.
-#set (CIL_VERSION $ENV{CIL_VERSION} CACHE INTERNAL "Core Imaging Library version" FORCE)
+set (CIL_VERSION $ENV{CIL_VERSION} CACHE INTERNAL "Core Imaging Library version" FORCE)
# conda orchestrated build
message("CIL_VERSION ${CIL_VERSION}")
diff --git a/Core/regularisers_GPU/TV_FGP_GPU_core.h b/Core/regularisers_GPU/TV_FGP_GPU_core.h
index b28cdf3..bf13508 100755
--- a/Core/regularisers_GPU/TV_FGP_GPU_core.h
+++ b/Core/regularisers_GPU/TV_FGP_GPU_core.h
@@ -1,10 +1,9 @@
-#include <stdio.h>
-#include <stdlib.h>
-#include <memory.h>
-
#ifndef _TV_FGP_GPU_
#define _TV_FGP_GPU_
-extern "C" int TV_FGP_GPU_main(float *Input, float *Output, float lambdaPar, int iter, float epsil, int methodTV, int nonneg, int printM, int dimX, int dimY, int dimZ);
+#include "CCPiDefines.h"
+#include <memory.h>
+
+extern "C" CCPI_EXPORT int TV_FGP_GPU_main(float *Input, float *Output, float lambdaPar, int iter, float epsil, int methodTV, int nonneg, int printM, int dimX, int dimY, int dimZ);
#endif
diff --git a/Core/regularisers_GPU/TV_SB_GPU_core.h b/Core/regularisers_GPU/TV_SB_GPU_core.h
index d44ab77..901b90f 100755
--- a/Core/regularisers_GPU/TV_SB_GPU_core.h
+++ b/Core/regularisers_GPU/TV_SB_GPU_core.h
@@ -1,10 +1,10 @@
-#include <stdio.h>
-#include <stdlib.h>
-#include <memory.h>
-
#ifndef _SB_TV_GPU_
#define _SB_TV_GPU_
-extern "C" int TV_SB_GPU_main(float *Input, float *Output, float mu, int iter, float epsil, int methodTV, int printM, int dimX, int dimY, int dimZ);
+#include "CCPiDefines.h"
+#include <memory.h>
+
+
+extern "C" CCPI_EXPORT int TV_SB_GPU_main(float *Input, float *Output, float mu, int iter, float epsil, int methodTV, int printM, int dimX, int dimY, int dimZ);
#endif
diff --git a/Core/regularisers_GPU/dTV_FGP_GPU_core.h b/Core/regularisers_GPU/dTV_FGP_GPU_core.h
index 9020b1a..f9281e8 100644
--- a/Core/regularisers_GPU/dTV_FGP_GPU_core.h
+++ b/Core/regularisers_GPU/dTV_FGP_GPU_core.h
@@ -1,10 +1,9 @@
-#include <stdio.h>
-#include <stdlib.h>
-#include <memory.h>
-
#ifndef _dTV_FGP_GPU_
#define _dTV_FGP_GPU_
-extern "C" int dTV_FGP_GPU_main(float *Input, float *InputRef, float *Output, float lambdaPar, int iter, float epsil, float eta, int methodTV, int nonneg, int printM, int dimX, int dimY, int dimZ);
+#include "CCPiDefines.h"
+#include <memory.h>
+
+extern "C" CCPI_EXPORT int dTV_FGP_GPU_main(float *Input, float *InputRef, float *Output, float lambdaPar, int iter, float epsil, float eta, int methodTV, int nonneg, int printM, int dimX, int dimY, int dimZ);
#endif
diff --git a/Readme.md b/Readme.md
index cdf823d..4fc23d4 100644
--- a/Readme.md
+++ b/Readme.md
@@ -1,5 +1,11 @@
# CCPi-Regularisation Toolkit (CCPi-RGL)
+
+
+| Master | Development |
+|--------|-------------|
+| [![Build Status](https://anvil.softeng-support.ac.uk/jenkins/buildStatus/icon?job=CILsingle/CCPi-Regularisation-Toolkit)](https://anvil.softeng-support.ac.uk/jenkins/job/CILsingle/job/CCPi-Regularisation-Toolkit/) | [![Build Status](https://anvil.softeng-support.ac.uk/jenkins/buildStatus/icon?job=CILsingle/CCPi-Regularisation-Toolkit-dev)](https://anvil.softeng-support.ac.uk/jenkins/job/CILsingle/job/CCPi-Regularisation-Toolkit-dev/) |
+
**Iterative image reconstruction (IIR) methods normally require regularisation to stabilise the convergence and make the reconstruction problem (inverse problem) more well-posed. The CCPi-RGL software provides 2D/3D and multi-channel regularisation strategies to ensure better performance of IIR methods. The regularisation modules are well-suited to use with [splitting algorithms](https://en.wikipedia.org/wiki/Augmented_Lagrangian_method#Alternating_direction_method_of_multipliers), such as, [ADMM](https://github.com/dkazanc/ADMM-tomo) and [FISTA](https://github.com/dkazanc/FISTA-tomo). Furthermore, the toolkit can be used for simpler inversion tasks, such as, image denoising, inpaiting, deconvolution etc. The core modules are written in C-OMP and CUDA languages and wrappers for Matlab and Python are provided.**
<div align="center">
diff --git a/Wrappers/Python/CMakeLists.txt b/Wrappers/Python/CMakeLists.txt
index d86d0ea..c2ef855 100644
--- a/Wrappers/Python/CMakeLists.txt
+++ b/Wrappers/Python/CMakeLists.txt
@@ -9,7 +9,7 @@ project(regulariserPython)
#set (CIL_VERSION $ENV{CIL_VERSION} CACHE INTERNAL "Core Imaging Library version" FORCE)
# conda orchestrated build
-message("CIL_VERSION ${CIL_VERSION}")
+message("CIL_VERSION: ${CIL_VERSION}")
#include (GenerateExportHeader)
find_package(PythonInterp REQUIRED)
diff --git a/Wrappers/Python/conda-recipe/build.sh b/Wrappers/Python/conda-recipe/build.sh
index eec7c2f..39c0f2c 100644
--- a/Wrappers/Python/conda-recipe/build.sh
+++ b/Wrappers/Python/conda-recipe/build.sh
@@ -5,6 +5,7 @@ cp -rv "$RECIPE_DIR/../../../Core" "$SRC_DIR/Core"
cd $SRC_DIR
##cuda=off
+
cmake -G "Unix Makefiles" $RECIPE_DIR/../../../ -DBUILD_PYTHON_WRAPPER=ON -DCONDA_BUILD=ON -DBUILD_CUDA=ON -DCMAKE_BUILD_TYPE="Release" -DLIBRARY_LIB=$CONDA_PREFIX/lib -DLIBRARY_INC=$CONDA_PREFIX -DCMAKE_INSTALL_PREFIX=$PREFIX
diff --git a/Wrappers/Python/conda-recipe/meta.yaml b/Wrappers/Python/conda-recipe/meta.yaml
index e3258ff..9dd5544 100644
--- a/Wrappers/Python/conda-recipe/meta.yaml
+++ b/Wrappers/Python/conda-recipe/meta.yaml
@@ -5,12 +5,14 @@ package:
build:
preserve_egg_dir: False
number: 0
+ script_env:
+ - CIL_VERSION
test:
files:
- lena_gray_512.tif
requires:
- - pillow
+ - pillow=4.1.1
requirements:
build:
diff --git a/build/jenkins-build.sh b/build/jenkins-build.sh
index 6da2c56..5b6c9ce 100755
--- a/build/jenkins-build.sh
+++ b/build/jenkins-build.sh
@@ -1,44 +1,2 @@
#!/usr/bin/env bash
-if [[ -n ${CIL_VERSION} ]]
-then
- echo Using defined version: $CIL_VERSION
-else
- export CIL_VERSION=0.10.4
- echo Defining version: $CIL_VERSION
-fi
-# Script to builds source code in Jenkins environment
-# module try-load conda
-
-# install miniconda if the module is not present
-if hash conda 2>/dev/null; then
- echo using conda
-else
- if [ ! -f Miniconda3-latest-Linux-x86_64.sh ]; then
- wget -q https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
- chmod +x Miniconda3-latest-Linux-x86_64.sh
- fi
- ./Miniconda3-latest-Linux-x86_64.sh -u -b -p .
- PATH=$PATH:./bin
-fi
-
-# presume that git clone is done before this script is launched, if not, uncomment
-# git clone https://github.com/vais-ral/CCPi-Regularisation-Toolkit
-conda install -y conda-build
-#cd CCPi-Regularisation-Toolkit # already there by jenkins
-# need to call first build
-conda build Wrappers/Python/conda-recipe
-# then need to call the same with --output
-#- otherwise no build is done :-(, just fake file names are generated
-export REG_FILES=`conda build Wrappers/Python/conda-recipe --output`
-# REG_FILES variable should contain output files
-echo files created: $REG_FILES
-#upload to anaconda
-if [[ -n ${CCPI_CONDA_TOKEN} ]]
-then
- conda install anaconda-client
- while read -r outfile; do
- anaconda -v -t ${CCPI_CONDA_TOKEN} upload $outfile --force --label dev
- done <<< "$REG_FILES"
-else
- echo CCPI_CONDA_TOKEN not defined, will not upload to anaconda.
-fi
+bash <(curl -L https://raw.githubusercontent.com/vais-ral/CCPi-VirtualMachine/master/scripts/jenkins-build.sh)
diff --git a/recipes/regularisers/build.sh b/recipes/regularisers/build.sh
index 0b8bce2..eaa778e 100644
--- a/recipes/regularisers/build.sh
+++ b/recipes/regularisers/build.sh
@@ -1,6 +1,6 @@
#!/usr/bin/env bash
-echo $CIL_VERSION
+echo build.sh CIL_VERSION: $CIL_VERSION
#if [ -z "$CIL_VERSION" ]; then
# echo "Need to set CIL_VERSION"
# exit 1
generated by cgit v1.2.3 (git 2.25.1) at 2025-01-04 03:27:56 +0000