tomophantom version 3

.github/workflows/tomophantom_conda_upload.yml

@@ -0,0 +1,41 @@
+name: tomohantom_conda_upload
+
+on: [push]
+
+jobs:
+  build-linux:
+    runs-on: ubuntu-20.04
+
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+      - name: Checkout repository code
+        uses: actions/checkout@v3
+        with:
+          ref: "master"
+          fetch-depth: 0
+
+      # setup Python 3.9
+      - name: Setup Python 3.9
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.9
+
+      - name: Install dependencies with Conda
+        run: |
+          $CONDA/bin/conda install -c conda-forge conda-build anaconda-client
+          $CONDA/bin/conda update conda
+          $CONDA/bin/conda update conda-build
+          $CONDA/bin/conda list
+
+      - name: Decrypt a secret
+        run: ./.scripts/decrypt_secret.sh
+        env:
+          LARGE_SECRET_PASSPHRASE: ${{ secrets.LARGE_SECRET_PASSPHRASE }}
+
+      - name: Upload the tested package to conda cloud
+        run: |
+          chmod +x ./.scripts/conda_upload.sh
+          ./.scripts/conda_upload.sh

.scripts/conda_upload.sh

@@ -0,0 +1,20 @@
+#!/bin/bash
+
+PKG_NAME=tomophantom
+USER=httomo-team
+OS=noarch
+CONDA_TOKEN=$(cat $HOME/.secrets/my_secret.json)
+
+mkdir ~/conda-bld
+conda config --set anaconda_upload no
+export CONDA_BLD_PATH=~/conda-bld
+
+export CIL_VERSION=3.0
+$CONDA/bin/conda build conda-recipe . -c httomo
+
+# upload packages to conda
+find $CONDA_BLD_PATH/$OS -name *.tar.bz2 | while read file
+do
+    echo $file
+    $CONDA/bin/anaconda -v --show-traceback --token $CONDA_TOKEN upload $file --force
+done

.scripts/decrypt_secret.sh

@@ -0,0 +1,8 @@
+#!/bin/sh
+
+# Decrypt the file
+mkdir $HOME/.secrets
+# --batch to prevent interactive command
+# --yes to assume "yes" for questions
+gpg --quiet --batch --yes --decrypt --passphrase="$LARGE_SECRET_PASSPHRASE" \
+--output $HOME/.secrets/my_secret.json ./.scripts/my_secret.json.gpg

CHANGES.md

@@ -1,43 +1,11 @@
 # ChangeLog
 
-## v1.4.9
-* Artifacts function syntax has changed. Now the dictionaries with keys can be be provided in a random order. Demos updated to make use of the updated function
-* Partial volume effect generator added to the Artifacts script
-* Fresnel propagator simulator added to the Artifacts script
-
-## v1.4.7
-* Flat field simulator has been modified to be based on a speckle generator of the background
-* Flat fields and the background jitter has been incorporated
-* Model 17 has been added to simulate i23 data
-
-## v1.4.5
-* Flat field simulation for 3D case has been re-written to conform the traditional imaging scenario. One can modify the
-inensity of the X-ray source which leads to more imaging artefacts
-* Demo ReconASTRA3D_realistic shows the incorporated changes
-* normraw function has been deleted and replaced with the conventional normaliser from the ToMoBAR software
-
-## v1.4.3
-* Artifacts simulation module has been modified. It is based now on specifying the dictionaries where artifact types are
-described. Stipes can be simulated to be partial and with variable intensity.
-* 2D Model 15 added - DLS phantom
-
-
-## v1.4.2
-* Jupiter Notebook demo added which uses deep learning algorithms to employ TomoPhantom for data generation
-
-## v1.4.1
-* All demos renamed and placed into categories: 2D/3D/4D, Random
-* Random generation of 2D/3D phantoms is initiated using methods from "generator.py" script
-* Foam phantoms can be built
-* Demo 'RandPhantGen.py' shows how phantoms can be generated
-
-## v1.4
-
-* Artifacts generation have been re-written from the class-based structure to function based structure
-* Each method in Artifacts can be called independently or all artefacts+noise can be simulated using _Artifacts_ method
-* Seeding added for noise module
-* Demos changed to adapt new artefacts functions and ToMoBAR changes
-
-## v1.3
-
-* Objects3D (generation of the customised objects) function is fixed
+## v3.0 (2023.12)
+* Project reorganised into two parts: a library that is build as a shared object using Cmake and Ctypes bindings and pure Python part that can be 
+installed separately. 
+* In general, ver.3.* should be fully compatabile to ver2.*, however, please note that paths for some functions have been changed. For instance,
+```python 
+from tomophantom.artefacts import artefacts_mix
+```
+* Documentation is now available, please check all API for TomoPhantom.
+* Demos were updated

CMakeLists.txt

@@ -12,10 +12,9 @@
 #   See the License for the specific language governing permissions and
 #   limitations under the License.
 
-cmake_minimum_required (VERSION 3.0)
+cmake_minimum_required(VERSION 3.5)
 
-project(TomoPhantom)
-#https://stackoverflow.com/questions/13298504/using-cmake-with-setup-py
+project(tomophantom)
 
 # The version number.
 set (CIL_VERSION_MAJOR 0)
@@ -24,14 +23,11 @@ set (CIL_VERSION_PATCH 0)
 
 set (CIL_VERSION '${CIL_VERSION_MAJOR}.${CIL_VERSION_MINOR}.${CIL_VERSION_PATCH}' CACHE INTERNAL "Core Imaging Library version" FORCE)
 
-# set the Python variables for the Conda environment
-#include(${CMAKE_SOURCE_DIR}/CMake/FindAnacondaEnvironment.cmake)
-
 set(CMAKE_BUILD_TYPE "Release")
 
 option (BUILD_MATLAB_WRAPPER "Build Matlab Wrappers" OFF)
-option (BUILD_PYTHON_WRAPPER "Build Python Wrappers" ON)
+option (BUILD_PYTHON_WRAPPER "Build Python Wrappers" OFF)
 option (CONDA_BUILD "Conda Build" OFF)
 
 add_subdirectory(Core)
-add_subdirectory(Wrappers)
+

Core/CCPiDefines.h

@@ -11,14 +11,6 @@
 #   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.
-
-#   Code is derived from code developed by Prof. Brian Bay
 */
 
 #ifndef CCPIDEFINES_H
@@ -36,12 +28,4 @@
  #define CCPI_EXPORT
 #endif
 
-//	Revised:
-
-#define DAY_REV 25
-#define MONTH_REV "Nov"
-#define YEAR_REV 2017
-
-#define VERSION 1.30
-
 #endif

Core/CMakeLists.txt

@@ -1,17 +1,20 @@
-#   Copyright 2018 Edoardo Pasca
-#cmake_minimum_required (VERSION 3.0)
+#   Copyright 2017 Edoardo Pasca
+#
+#   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.
+
+project(tomophantom)
 
-project(RGL_core)
-#https://stackoverflow.com/questions/13298504/using-cmake-with-setup-py
-
-# The version number.
-
-#set (CIL_VERSION $ENV{CIL_VERSION} CACHE INTERNAL "Core Imaging Library version" FORCE)
-
-# conda orchestrated build
 message("CIL_VERSION ${CIL_VERSION}")
-#include (GenerateExportHeader)
-
 
 find_package(OpenMP REQUIRED)
 if (OPENMP_FOUND)
@@ -23,9 +26,7 @@ if (OPENMP_FOUND)
 
 endif()
 
-## Build the regularisers package as a library
-message("Building TomoPhantom as a shared library")
-
+message("Building TomoPhantom core modules as a shared library")
 message("CMAKE_CXX_FLAGS ${CMAKE_CXX_FLAGS}")
 message("CMAKE_C_FLAGS ${CMAKE_C_FLAGS}")
 message("CMAKE_EXE_LINKER_FLAGS ${CMAKE_EXE_LINKER_FLAGS}")
@@ -35,17 +36,14 @@ message("CMAKE_STATIC_LINKER_FLAGS ${CMAKE_STATIC_LINKER_FLAGS}")
 set(CMAKE_BUILD_TYPE "Release")
 
 if(WIN32)
-  set (FLAGS "/DWIN32 /EHsc /DCCPi_EXPORTS")
+  set (FLAGS "/DWIN32 /EHsc /DCCPi_EXPORTS /openmp:experimental")
   set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${FLAGS}")
   set (CMAKE_C_FLAGS "${CMAKE_CXX_FLAGS} ${FLAGS}")
-  set (CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} /NODEFAULTLIB:MSVCRT.lib")
-
-  set (EXTRA_LIBRARIES)
-
-  message("library lib: ${LIBRARY_LIB}")
-
+  set (CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} /NODEFAULTLIB:MSVCRT.lib")  
+  set (EXTRA_LIBRARIES)		
+  message("library lib: ${LIBRARY_LIB}")  
 elseif(UNIX)
-   set (FLAGS "-O2 -funsigned-char -Wall  -Wl,--no-undefined  -DCCPiReconstructionIterative_EXPORTS ")  
+   set (FLAGS "-O2 -funsigned-char -Wall -Wl,--no-undefined  -DCCPiReconstructionIterative_EXPORTS")  
    set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${FLAGS}")
    set (CMAKE_C_FLAGS "${CMAKE_CXX_FLAGS} ${FLAGS}")
    if (OPENMP_FOUND)
@@ -61,59 +59,41 @@ elseif(UNIX)
 endif()
 message("CMAKE_CXX_FLAGS ${CMAKE_CXX_FLAGS}")
 
-## Build the regularisers package as a library
 message("Building TomoPhantom as a shared library")
-
-#set(CMAKE_C_COMPILER /apps/pgi/linux86-64/17.4/bin/pgcc)
-#set(CMAKE_C_FLAGS "-acc -Minfo -ta=tesla:cc20 -openmp")
-#set(CMAKE_C_FLAGS "-acc -Minfo -ta=multicore -openmp -fPIC")
-add_library(ctomophantom "SHARED"
+add_library(tomophantom "SHARED"
 	    ${CMAKE_CURRENT_SOURCE_DIR}/TomoP2DModel_core.c
 	    ${CMAKE_CURRENT_SOURCE_DIR}/TomoP2DModelSino_core.c
-	    ${CMAKE_CURRENT_SOURCE_DIR}/TomoP3DModel_core.c
-	    ${CMAKE_CURRENT_SOURCE_DIR}/TomoP3DModelSino_core.c
+	    ${CMAKE_CURRENT_SOURCE_DIR}/TomoP3DModel_core.c
+	    ${CMAKE_CURRENT_SOURCE_DIR}/TomoP3DModelSino_core.c
 	    ${CMAKE_CURRENT_SOURCE_DIR}/TomoP2DSinoNum_core.c
 	    ${CMAKE_CURRENT_SOURCE_DIR}/utils.c
 		)
-#add_library(ctomophantom_static "STATIC"
-#	    ${CMAKE_CURRENT_SOURCE_DIR}/TomoP2DModel_core.c
-#	    ${CMAKE_CURRENT_SOURCE_DIR}/TomoP2DModelSino_core.c
-#	    ${CMAKE_CURRENT_SOURCE_DIR}/TomoP3DModel_core.c
-#	    ${CMAKE_CURRENT_SOURCE_DIR}/utils.c
-#	    ${CMAKE_CURRENT_SOURCE_DIR}/TomoP2DSinoNum_core.c
-#	    )
-target_link_libraries(ctomophantom ${EXTRA_LIBRARIES} )
-include_directories(ctomophantom PUBLIC 
+target_link_libraries(tomophantom ${EXTRA_LIBRARIES} )
+include_directories(tomophantom PUBLIC 
                       ${LIBRARY_INC}/include 
-					  ${CMAKE_CURRENT_SOURCE_DIR}
+           	      ${CMAKE_CURRENT_SOURCE_DIR}
 		              )
 
 ## Install
-
-set(INSTALL_BIN_DIR ${CMAKE_INSTALL_PREFIX}/bin)
-set(INSTALL_LIB_DIR ${CMAKE_INSTALL_PREFIX}/lib)
-set(INSTALL_INCLUDE_DIR ${CMAKE_INSTALL_PREFIX}/include)
+set(PYTHON_SITE_DIR ${CMAKE_INSTALL_PREFIX}/source)
+set(CMAKE_POSITION_INDEPENDENT_CODE
+    ON
+    CACHE BOOL "Position independent code" FORCE)
+#set(INSTALL_BIN_DIR ${CMAKE_INSTALL_PREFIX}/bin)
+#set(INSTALL_LIB_DIR ${CMAKE_INSTALL_PREFIX}/lib)
+#set(INSTALL_INCLUDE_DIR ${CMAKE_INSTALL_PREFIX}/include)
 
 if (UNIX)
 message ("I'd install into ${CMAKE_INSTALL_PREFIX}/lib")
-install(TARGETS ctomophantom
+install(TARGETS tomophantom
 	LIBRARY DESTINATION lib
 	CONFIGURATIONS ${CMAKE_BUILD_TYPE} 
 	)
 elseif(WIN32)
 message ("I'd install into ${CMAKE_INSTALL_PREFIX} lib bin")
-  install(TARGETS ctomophantom 
+  install(TARGETS tomophantom 
 	RUNTIME DESTINATION bin
 	ARCHIVE DESTINATION lib
 	CONFIGURATIONS ${CMAKE_BUILD_TYPE} 
 	)
 endif()
-
-
-#install(TARGETS ctomophantom
-#	LIBRARY  DESTINATION "${INSTALL_LIB_DIR}" COMPONENT lib
-#	PUBLIC_HEADER DESTINATION "${INSTALL_INCLUDE_DIR}" COMPONENT dev
-#	RUNTIME  DESTINATION "${INSTALL_BIN_DIR}" COMPONENT bin
-#	ARCHIVE  DESTINATION "${INSTALL_LIB_DIR}" COMPONENT lib
-#   CONFIGURATIONS ${CMAKE_BUILD_TYPE}
-#	)