Changes needed for Total-Body

.gitmodules

@@ -3,4 +3,4 @@
 	url = https://github.com/UCL/STIR
 [submodule "submodules/simset_simpet"]
 	path = submodules/simset_simpet
-	url = https://github.com/txusser/simset_simpet.git
+	url = https://github.com/arnaufme8/simset_simpet.git

README.md

@@ -10,7 +10,7 @@ The SIMPET project is intended to allow to setup and launch MC simulation on a s
 - Apply the BrainViset procedure to obtain realistic Activity and Attenuation maps.
 - Run Analytic simulations using STIR simulation procedure and MC simulation using SimSET.
 
-# Installtion
+# Installation
 
 1. Install [Git LFS](https://git-lfs.com/).
 2. Clone the repository by adding the `--recurse-submodules` flag:
@@ -52,6 +52,7 @@ Sometimes, even activating the virtual environemnt, the shell will use the wide
 ```
 make install
 ```
+_NOTE:_ At the moment, to install SimPET you need to have sudo available in your computer. If you don't (e.g., when installing on a HPC), you can make use of the makefile that does not require sudo: ```makefile-withoutsudo```. To use it, simply remove or change the name of ```makefile```, and rename the file ```makefile-withoutsudo``` to ```makefile```. This will allow the installation without root privileges.
 
 7. Decompress dummy data with:
 ```
@@ -277,8 +278,9 @@ See [SimSET](https://depts.washington.edu/simset/html/simset_main.html) document
 
 #### Attenuation correction
 
-- **analytical_att_correction**: performed by SimSET calcattenuation.
+- **analytical_att_correction**: performed by SimSET calcattenuation. (_NOTE: obsolete at the moment and will be removed in further updates_).
 - **stir_recons_att_corr**:  performed in STIR by entering the att image as a normalization map.
+- **attenuation_mode**: it has three options. 0 (no attenuation), 1 (attenuation by SimSET calcattenuation) or 2 (attenuation by STIR computation of the ACFs).
 
 #### Scatter Correction
 
@@ -316,11 +318,13 @@ See [SimSET](https://depts.washington.edu/simset/html/simset_main.html) document
 
 - Jesús Silva-Rodríguez
 - Pablo Aguiar
-- Aida Ninyerola-Baizan
+- Aida Niñerola-Baizán
 - Jeremiah Poveda
 - Francisco Javier López-González
 - Nikos Efthimiou
-- Arnau Farre
+- Arnau Farré-Melero
+- Claudia Dominguez-Borrero
+
 
 # References
 

configs/params/scanner/discovery_st.yaml

@@ -23,7 +23,7 @@ stir_scatt_corr_smoothing: 0
 stir_scatt_simulation: 0
 analytic_randoms_corr_factor: 0.2
 stir_randoms_corr_smoothing: 0
-recons_type: "OSEM3D"
+recons_type: "OSEM3D" #"FBP3D" #"OSEM3D"
 inter_iteration_filter: 0
 subiteration_interval: 4
 x_dir_filter_FWHM: 1.5
@@ -32,7 +32,9 @@ z_dir_filter_FWHM: 3
 psf_value: 0
 add_noise: 0
 max_segment: 23
-zoomFactor: 1.55
+zoomFactor: 1 #For brain: 1.55
 xyOutputSize: 128
 zOutputSize: 47
 zOutputVoxelSize: 3.27
+
+attenuation_mode: 2 #0: no attenuation, 1: attenuation with SimSET, 2: attenuation with STIR

configs/params/scanner/siemens_quadra.yaml

@@ -0,0 +1,42 @@
+scanner_name: "Siemens Quadra"
+simset_material: 18
+average_doi: 0.7
+scanner_radius: 41.0
+num_rings: 320 #Real: 320, With module gaps: 323
+axial_fov: 106
+z_crystal_size: 0.32 #cm
+transaxial_crystal_size: 0.32 #cm
+crystal_thickness: 2 #cm
+energy_resolution: 9
+num_aa_bins: 399
+num_td_bins: 520
+min_energy_window: 435
+max_energy_window: 585
+coincidence_window: 4.7 #ns
+
+numberOfSubsets: 7
+numberOfIterations: 14
+savingInterval: 7
+analytical_att_correction: 0
+stir_recons_att_corr: 0
+analytic_scatt_corr_factor: 0.15
+stir_scatt_corr_smoothing: 0
+stir_scatt_simulation: 0
+analytic_randoms_corr_factor: 0.2
+stir_randoms_corr_smoothing: 0
+recons_type: "OSEM3D" #Options: "FBP2D", "FBP3D", "OSEM2D", "OSEM3D"
+inter_iteration_filter: 0
+subiteration_interval: 4
+x_dir_filter_FWHM: 1.5
+y_dir_filter_FWHM: 1.5
+z_dir_filter_FWHM: 3
+psf_value: 0
+add_noise: 0
+
+max_segment: 85 #Reduced protocol: 85; Full protocol: 319 or 322
+zoomFactor: 1
+xyOutputSize: 220
+zOutputSize: 645
+zOutputVoxelSize: 1.65
+
+attenuation_mode: 0 #0: no attenuation, 1: attenuation with SimSET, 2: attenuation with STIR

configs/params/test.yaml

@@ -11,12 +11,14 @@ patient_dirname: "test_image"
 act_map: "act.hdr"
 att_map: "att.hdr"
 output_dir: "test_image"
-center_slice: 7
+center_slice: 0
 total_dose: 0.1
 simulation_time: 30
 sampling_photons: 0
 photons: 0
 add_randoms: 1
-phglistmode: 0
-detlistmode: 1
-maximumIteration: 1
+
+listmode: True # TODO: to unify both listmodes to only the necessary.
+phglistmode: 1 #MUST BE ACTIVATED IF listmode. 
+detlistmode: 0 #At the moment unused, but may be used in the future.
+maximumIteration: 1 #Unused at the moment.

makefile-withoutsudo

@@ -0,0 +1,231 @@
+SHELL := /bin/bash
+TMPDIR := /tmp
+ROOT_DIR := $(dir $(abspath $(lastword $(MAKEFILE_LIST))))
+ASSETS_DIR := ${ROOT_DIR}assets
+INCLUDE_DIR := ${ROOT_DIR}include
+SUBMODULES_DIR := ${ROOT_DIR}submodules
+
+.PHONY: install-simset check-simset clean-simset 
+.PHONY: install-stir check-stir clean-stir 
+.PHONY: install-resources check-resources clean-resources 
+.PHONY: config-git clean-git smudge-filer config-paths clean-paths 
+.PHONY: dummy-data install clean help
+
+SIMSET_SUBMODULE_DIR = ${ROOT_DIR}/submodules/simset_simpet
+SIMSET_DEST_DIR =  ${INCLUDE_DIR}/SimSET
+SIMSET_PATH = ${SIMSET_DEST_DIR}/2.9.2
+SIMSET_BIN = ${SIMSET_PATH}/bin
+SIMSET_LIB = ${SIMSET_PATH}/lib
+SIMSET_MKALL = ${SIMSET_PATH}/make_all.sh
+SIMSET_MKFILE = ${SIMSET_PATH}/make.files/simset.make
+
+install-simset:
+	if [ ! -d ${SIMSET_DEST_DIR} ]; then \
+		mkdir -p ${SIMSET_PATH} ;\
+		cp -r ${SIMSET_SUBMODULE_DIR}/* ${SIMSET_PATH} ;\
+		sed -i 's/^\(SIMSET_PATH = \).*$$/\1$(subst /,\/,${SIMSET_PATH})/' ${SIMSET_MKFILE} ;\
+		cd ${SIMSET_PATH} && mkdir -p ${SIMSET_LIB} && bash ${SIMSET_MKALL} ;\
+	else \
+		echo "${SIMSET_DEST_DIR} already exists, run clean-simset if you really want to remove it (you will have to intall SimSET again.)" ;\
+	fi
+
+SIMSET_TAR = ${ASSETS_DIR}/phg.2.9.2.tar.Z
+SIMSET_STIR_PATCH = ${ASSETS_DIR}/simset_for_stir.patch
+
+install-canonic-simset: ${SIMSET_TAR}
+	if [ ! -d ${SIMSET_DEST_DIR} ]; then \
+		mkdir -p ${SIMSET_DEST_DIR} && tar -xvf "${SIMSET_TAR}" --directory=${SIMSET_DEST_DIR} ;\
+		cd ${SIMSET_DEST_DIR} && patch -s -p0 < ${SIMSET_STIR_PATCH} ;\
+		sed -i 's/^\(SIMSET_PATH = \).*$$/\1$(subst /,\/,${SIMSET_PATH})/' ${SIMSET_MKFILE} ;\
+		cd ${SIMSET_PATH} && mkdir -p ${SIMSET_LIB} && bash ${SIMSET_MKALL} ;\
+	else \
+		echo "${SIMSET_DEST_DIR} already exists, run clean-simset if you really want to remove it (you will have to intall SimSET again.)" ;\
+	fi
+
+check-simset:
+	declare -a simset_files=(addrandoms bin calcattenuation combinehist makeindexfile phg timesort) ;\
+	for file in "$${simset_files[@]}"; do \
+		if [ ! -f "${SIMSET_BIN}/$${file}" ]; then \
+			echo "${SIMSET_BIN}/$${file} does not exists, check your installation." ;\
+		else \
+			echo "${SIMSET_BIN}/$${file} exists." ;\
+		fi ;\
+	done
+
+clean-simset:
+	rm -rf ${SIMSET_DEST_DIR}
+
+SIMSET_SRC = ${SIMSET_PATH}/src
+SIMSET_LIBSIMSET = ${SIMSET_LIB}/libsimset.so
+STIR_DIR = ${SUBMODULES_DIR}/STIR/STIR
+STIR_BUILD_DIR = ${SUBMODULES_DIR}/STIR/build
+STIR_INSTALL_DIR = ${SUBMODULES_DIR}/STIR/install
+STIR_INSTALL_BIN = ${STIR_INSTALL_DIR}/bin
+STIR_MKFILE = ${STIR_BUILD_DIR}/CMakeCache.txt
+STIR_FINAL_DEST_DIR = ${INCLUDE_DIR}/STIR
+NPROC = $(shell nproc)
+
+install-stir: install-simset ${STIR_DIR}
+	if [ ! -d ${STIR_FINAL_DEST_DIR} ]; then \
+		mkdir -p ${STIR_BUILD_DIR} ${STIR_INSTALL_DIR} ${STIR_FINAL_DEST_DIR} ;\
+		cd ${STIR_BUILD_DIR} && cmake ${STIR_DIR} ;\
+		sed -i \
+			-e 's/^\(BUILD_SWIG_PYTHON\).*$$/\1:BOOL=OFF/' \
+			-e 's/^\(CMAKE_INSTALL_PREFIX\).*$$/\1:PATH=$(subst /,\/,${STIR_INSTALL_DIR})/' \
+			-e 's/^\(SIMSET_INCLUDE_DIRS\).*$$/\1:PATH=$(subst /,\/,${SIMSET_SRC})/' \
+			-e 's/^\(SIMSET_LIBRARY\).*$$/\1:FILEPATH=$(subst /,\/,${SIMSET_LIBSIMSET})/' \
+			-e 's/^\(STIR_OPENMP\).*$$/\1:BOOL=ON/' \
+			${STIR_MKFILE} ;\
+		cmake ${STIR_DIR} ;\
+		make -s -j${NPROC} ;\
+		make install ;\
+		mv ${STIR_BUILD_DIR} ${STIR_INSTALL_DIR} ${STIR_FINAL_DEST_DIR} ;\
+	else \
+		echo "${STIR_FINAL_DEST_DIR} already exists, run clean-stir if you really want to remove it (you will have to intall STIR again)." ;\
+	fi
+
+check-stir:
+	declare -a stir_files=(FBP2D FBP3DRP forward_project lm_to_projdata OSMAPOSL zoom_image) ;\
+	for file in "$${stir_files[@]}"; do \
+		if [ ! -f "${STIR_FINAL_DEST_DIR}/install/bin/$${file}" ]; then \
+			echo "${STIR_FINAL_DEST_DIR}/install/bin/$${file} does not exists, check your installation." ;\
+		else \
+			echo "${STIR_FINAL_DEST_DIR}/install/bin/$${file} exists." ;\
+		fi ;\
+	done
+
+clean-stir:
+	rm -rf ${STIR_FINAL_DEST_DIR}
+
+RESOURCES_ZIP = ${ASSETS_DIR}/fruitcake.zip
+RESOURCES_TMP = ${TMPDIR}/resources
+
+install-resources: ${RESOURCES_ZIP}
+	mkdir -p ${RESOURCES_TMP} ${INCLUDE_DIR} && unzip -o ${RESOURCES_ZIP} -d ${RESOURCES_TMP} ;\
+	declare -a resources=(fruitcake format_converters) ;\
+	for rce in "$${resources[@]}"; do \
+		include_path="${INCLUDE_DIR}/$${rce}" ;\
+		tmp_path="${RESOURCES_TMP}/$${rce}" ;\
+		if [ ! -d $${include_path} ]; then \
+			mv $${tmp_path} ${INCLUDE_DIR} ;\
+			chmod -R +x $${include_path} ;\
+		else \
+			echo "$${include_path} already exists, run make clean-resources in order to clean resources installation (fruitcake will be removed as well)." ;\
+		fi ;\
+	done ;\
+	rm -rf ${RESOURCES_TMP}
+
+check-resources:
+	declare -a resources_paths=(${FRUITCAKE_PATH} ${FORMAT_CONVERTERS_PATH}) ;\
+	for path in "$${resources_paths[@]}"; do \
+		if [ ! -d "$${path}" ]; then \
+			echo "$${path} does not exists, clean fruitcake and format_converters with clean-resources and run install-resources." ;\
+		else \
+			echo "$${path} exists." ;\
+		fi ;\
+	done
+
+clean-resources:
+	rm -rf ${INCLUDE_DIR}/fruitcake ${INCLUDE_DIR}/format_converters
+
+config-git:
+	git config --local filter.config-test.smudge ${ROOT_DIR}scripts/smudge-config_test.sh
+	git config --local filter.config-test.clean ${ROOT_DIR}scripts/clean-config_test.sh
+	chmod +x -R ${ROOT_DIR}scripts
+
+clean-git:
+	git config --local --unset filter.config-test.smudge
+	git config --local --unset filter.config-test.clean
+
+smudge-filter:
+	rm -f ${ROOT_DIR}configs/config.yaml 2> /dev/null
+	git checkout HEAD -- ${ROOT_DIR}configs/config.yaml
+
+FRUITCAKE_PATH = ${INCLUDE_DIR}/fruitcake
+FRUITCAKE_BIN = ${FRUITCAKE_PATH}/bin
+FRUITCAKE_LIB = ${FRUITCAKE_PATH}/book/lib
+FORMAT_CONVERTERS_PATH = ${INCLUDE_DIR}/format_converters
+
+config-paths:
+	touch "$${HOME}"/.bashrc ;\
+	declare -a simpet_paths=( \
+		'export PATH=${FRUITCAKE_BIN}:$$PATH' \
+		'export LD_LIBRARY_PATH=${FRUITCAKE_LIB}:$$LD_LIBRARY_PATH' \
+		'export PATH=${FORMAT_CONVERTERS_PATH}:$$PATH' \
+	) ;\
+	for path in "$${simpet_paths[@]}"; do \
+		grep -qxF "$${path}" "$${HOME}"/.bashrc || echo "$${path}" >> "$${HOME}"/.bashrc ;\
+	done
+
+clean-paths:
+	touch "$${HOME}/.bashrc"
+	sed -i \
+		-e '/export PATH=$(subst /,\/,${FRUITCAKE_BIN}):$$PATH/d' \
+		-e '/export LD_LIBRARY_PATH=$(subst /,\/,${FRUITCAKE_LIB}):$$LD_LIBRARY_PATH/d' \
+		-e '/export PATH=$(subst /,\/,${FORMAT_CONVERTERS_PATH}):$$PATH/d' \
+		"$${HOME}/.bashrc"
+
+DATA_DIR = ${ROOT_DIR}Data
+DATA_ZIP = ${ASSETS_DIR}/Data.zip
+
+dummy-data: ${DATA_ZIP}
+	if [ ! -d "${DATA_DIR}" ]; then \
+		mkdir -p ${DATA_DIR} && unzip -o ${DATA_ZIP} -d ${ROOT_DIR} ;\
+	else \
+		echo "${DATA_DIR} already exists, remove it manually." ;\
+	fi
+
+install:
+	${MAKE} \
+		install-simset \
+		check-simset \
+		install-stir \
+		check-stir \
+		install-resources \
+		check-resources \
+		config-paths \
+
+clean:
+	${MAKE} \
+		clean-simset \
+		clean-stir \
+		clean-resources
+
+help:
+	@echo "Help:"
+	@echo "	- install-simset: Install tweaked version of SimSET.
+	@echo ""
+	@echo "	- install-canonic-simset: Install non-tweaked version of SimSET with STIR patch at directory ${SIMSET_DEST_DIR}."
+	@echo ""
+	@echo "	- check-simset: Check that SimSET binaries exist."
+	@echo ""
+	@echo "	- clean-simset: Clean SimSET installation (removes ${SIMSET_DEST_DIR} directory)."
+	@echo ""
+	@echo "	- install-stir: Install STIR at directory $(shell dirname ${STIR_DIR}), install-simset is a prerequisite. Set NPROC=n to use n CPU cores in compilation."
+	@echo ""
+	@echo "	- check-stir: Check that STIR binaries exist."
+	@echo ""
+	@echo "	- clean-stir: Clean STIR installation removing ${STIR_INSTALL_DIR} and ${STIR_BUILD_DIR} directories."
+	@echo ""
+	@echo "	- install-resources: Decompress ${RESOURCES_ZIP} and move fruitcake and format_converters to ${INCLUDE_DIR}"
+	@echo ""
+	@echo "	- check-resources: Checks that fruitcake and format_converters are in ${INCLUDE_DIR}."
+	@echo ""
+	@echo "	- clean-resources: Remove fruitcake and format_converters from ${INCLUDE_DIR}."
+	@echo ""
+	@echo "	- config-git: Add project filter drivers to local git configuration and make them executable."
+	@echo ""
+	@echo "	- clean-git: Remove project filter drivers from local git configuration."
+	@echo ""
+	@echo "	- smudge-filer: Apply smudge filter to config file (updates paths)."
+	@echo ""
+	@echo "	- config-paths: Iff not present in .bashrc, the paths of the projects will be appended to the file. If ~/.bashrc does not exists it will be created."
+	@echo ""
+	@echo "	- clean-paths: If the paths of the project are present in .bashrc file, they will be deleted. If ~/.bashrc does not exists it will be created."
+	@echo ""
+	@echo "	- dummy-data: Uncompress ${DATA_ZIP} at ${DATA_DIR} if ${DATA_DIR} does not exists."
+	@echo ""
+	@echo "	- install: Run all install, config and check recipes."
+	@echo ""
+	@echo "	- clean: Run all clean recipes."
+