Merge branch 'release-1.5.1' into master

.github/workflows/build.yml

@@ -63,6 +63,10 @@ jobs:
           python-version: ${{ matrix.python-version }}
           auto-activate-base: false
 
+      - name: Update dependencies
+        run: |
+          make update_dep_shasum
+
       - name: Build java dependencies
         run: |
           ./build.sh

Makefile

@@ -4,6 +4,7 @@ clean:
 	rm -rf nighresjava/
 	rm -rf cbstools-public/
 	rm -rf imcn-imaging/
+	rm -rf fbpa-tools/
 	rm -rf nighres.egg-info/
 	rm -rf nighres_examples/
 

build.sh

@@ -14,8 +14,11 @@ function join_by { local IFS="$1"; shift; echo "$*"; }
 source dependencies_sha.sh
 cbstools_repo="https://github.com/piloubazin/cbstools-public.git"
 imcntk_repo="https://github.com/piloubazin/imcn-imaging.git"
+fbpa_repo="https://github.com/piloubazin/fbpa-tools.git"
 
-release="release-1.5.0"
+#release="release-1.5.0"
+# for the latest development version
+release="master"
 
 # Check the system has the necessary commands
 hash wget tar javac jar python3 2>/dev/null || fatal "This script needs the following commands available: wget tar javac jar python3"
@@ -153,6 +156,59 @@ jar cf ../nighresjava/src/imcntk-lib.jar nl/uva/imcn/libraries/*.class nl/uva/im
 cp lib/*.jar ../nighresjava/lib/
 cd ..
 
+#
+## COMPILE FbpA tools
+#
+
+# Get FbpA git clone
+test -d fbpa-tools && (
+    cd fbpa-tools
+	git checkout $release
+	git pull
+	cd ..
+) || (
+	git clone -b $release $fbpa_repo --depth 1
+	cd fbpa-tools
+	git checkout
+	git pull
+	cd ..
+)
+
+# Java dependencies. Order matters
+deps=(
+	"."
+	"lib/commons-math3-3.5.jar"
+)
+deps_list=$(join_by ":" "${deps[@]}")
+
+# List of library files needed to run the core functions
+source fbpa-tools-files.sh
+echo $fbpa_files # result is in $fbpa_files
+
+fbpa_list=$(join_by " " "${fbpa_files[@]}")
+
+# Compilation options
+javac_opts=(
+	# "-d build"        # Output dir
+	"-Xlint:none"     # Disable all warnings
+	# "-server"         # ?
+	"-g"              # Generate all debugging info
+	"-O"              # ?
+	"-deprecation"    # Show information about deprecated Java calls
+	"-encoding UTF-8" # Require UTF-8, rather than platform-specifc
+)
+
+echo "Compiling..."
+cd fbpa-tools
+javac -cp ${deps_list} ${javac_opts[@]} nl/fullbrainpicture/algorithms/*.java ${fbpa_list}
+
+echo "Assembling..."
+jar uf ../nighresjava/src/nighresjava.jar nl/fullbrainpicture/algorithms/*.class
+jar cf ../nighresjava/src/fbpa-lib.jar nl/fullbrainpicture/libraries/*.class nl/fullbrainpicture/structures/*.class nl/fullbrainpicture/utilities/*.class
+
+cp lib/*.jar ../nighresjava/lib/
+cd ..
+
 #
 ## WRAP TO PYTHON
 #
@@ -165,6 +221,7 @@ jcc_args=(
 	# Dependencies
 	"--include src/cbstools-lib.jar"
 	"--include src/imcntk-lib.jar"
+	"--include src/fbpa-lib.jar"
 	"--include lib/commons-math3-3.5.jar"
 	"--include lib/Jama-mipav.jar"
 

build_local_nighresjava.sh

@@ -15,6 +15,7 @@ function join_by { local IFS="$1"; shift; echo "$*"; }
 # define here the local folders for your installation of CBSTools, IMCNtk and Nighres
 cbstools_local="/home/pilou/Code/github/cbstools-public"
 imcntk_local="/home/pilou/Code/github/imcn-imaging"
+fbpa_local="/home/pilou/Code/github/fbpa-tools"
 nighres_local="/home/pilou/Code/github/nighres"
 
 # Check the system has the necessary commands
@@ -116,18 +117,55 @@ javac_opts=(
 )
 
 echo "Compiling..."
-#cd cbstools-public
 cd $imcntk_local
-#mkdir -p build
 $JAVA_HOME/bin/javac -cp ${deps_list} ${javac_opts[@]} nl/uva/imcn/algorithms/*.java $imcntk_list
 
 echo "Assembling..."
-#jar cf imcntk.jar     nl/uva/imcn/algorithms/*.class
 $JAVA_HOME/bin/jar uf $nighres_local/nighresjava/src/nighresjava.jar nl/uva/imcn/algorithms/*.class
 $JAVA_HOME/bin/jar cf $nighres_local/nighresjava/src/imcntk-lib.jar nl/uva/imcn/libraries/*.class nl/uva/imcn/methods/*.class nl/uva/imcn/structures/*.class nl/uva/imcn/utilities/*.class
 
 cp lib/*.jar $nighres_local/nighresjava/lib/
 
+#
+## COMPILE FbpA tools
+#
+
+# Java dependencies. Order matters
+deps=(
+	"."
+	"lib/commons-math3-3.5.jar"
+)
+deps_list=$(join_by ":" "${deps[@]}")
+
+# List of library files needed to run the core functions
+source $nighres_local/fbpa-tools-files.sh
+echo $fbpa_files # result is in $fbpa_files
+
+fbpa_list=$(join_by " " "${fbpa_files[@]}")
+
+# Compilation options
+javac_opts=(
+	# "-d build"        # Output dir
+	"-Xlint:none"     # Disable all warnings
+	"-server"         # ?
+	"-g"              # Generate all debugging info
+	"-O"              # ?
+	"-deprecation"    # Show information about deprecated Java calls
+	"-encoding UTF-8" # Require UTF-8, rather than platform-specifc
+)
+
+echo "Compiling..."
+cd $fbpa_local
+#mkdir -p build
+$JAVA_HOME/bin/javac -cp ${deps_list} ${javac_opts[@]} nl/fullbrainpicture/algorithms/*.java $fbpa_list
+
+echo "Assembling..."
+#jar cf imcntk.jar     nl/uva/imcn/algorithms/*.class
+$JAVA_HOME/bin/jar uf $nighres_local/nighresjava/src/nighresjava.jar nl/fullbrainpicture/algorithms/*.class
+$JAVA_HOME/bin/jar cf $nighres_local/nighresjava/src/fbpa-lib.jar nl/fullbrainpicture/libraries/*.class nl/fullbrainpicture/structures/*.class nl/fullbrainpicture/utilities/*.class
+
+cp lib/*.jar $nighres_local/nighresjava/lib/
+
 #
 ## WRAP TO PYTHON
 #
@@ -140,6 +178,7 @@ jcc_args=(
 	# Dependencies
 	"--include src/cbstools-lib.jar"
 	"--include src/imcntk-lib.jar"
+	"--include src/fbpa-lib.jar"
 	"--include lib/commons-math3-3.5.jar"
 	"--include lib/Jama-mipav.jar"
 

create_container_recipe.sh

@@ -26,27 +26,30 @@ else
 
 fi
 
-docker run --rm repronim/neurodocker:0.7.0 generate "${container_type}" \
-    --base debian:stretch-slim \
+docker run ${expose} \
+    --rm repronim/neurodocker:0.9.5 generate "${container_type}" \
+    --base-image debian:stable \
     --pkg-manager apt \
-    --install "openjdk-8-jdk git wget build-essential software-properties-common libffi-dev" \
+    --install "openjdk-17-jdk git wget build-essential software-properties-common libffi-dev" \
+    --env JAVA_HOME="/docker-java-temurin-home" \
+    --env JCC_JDK="/docker-java-temurin-home" \
+    --run 'ln -svT "/usr/lib/jvm/java-17-openjdk-$(dpkg --print-architecture)" /docker-java-temurin-home' \
     --miniconda \
-        create_env="nighres" \
-        conda_install="python=3.9 pip jcc Nilearn" \
-        activate="true" \
-    --env JAVA_HOME="/docker-java-home" \
-    --env JCC_JDK="/docker-java-home" \
-    --run 'ln -svT "/usr/lib/jvm/java-8-openjdk-$(dpkg --print-architecture)" /docker-java-home' \
+        version="latest" \
+        env_name="nighres" \
+        env_exists="false" \
+        conda_install="python=3.9 pip JCC Nilearn" \
     --copy build.sh cbstools-lib-files.sh imcntk-lib-files.sh dependencies_sha.sh setup.py setup.cfg MANIFEST.in README.rst LICENSE /nighres/ \
     --copy nighres /nighres/nighres \
     --workdir /nighres \
-    --run "conda init && . /root/.bashrc && conda activate nighres && conda info --envs && ./build.sh && rm -rf cbstools-public imcn-imaging nighresjava/build nighresjava/src" \
+    --run "conda init && . /root/.bashrc && activate nighres && conda info --envs && pip install jcc && ./build.sh && rm -rf cbstools-public imcn-imaging nighresjava/build nighresjava/src" \
     --miniconda \
-        use_env="nighres" \
+        version="latest" \
+        installed="true" \
+        env_name="nighres" \
         conda_install="jupyterlab" \
         pip_install="." \
     --copy docker/jupyter_notebook_config.py /etc/jupyter \
-    "${expose}" \
     --user neuro \
     --workdir /home/neuro >"${output_file}"
 

fbpa-tools-files.sh

@@ -0,0 +1,7 @@
+fbpa_files=(
+  "nl/fullbrainpicture/libraries/ObjectTransforms.java"
+
+  "nl/fullbrainpicture/structures/BinaryHeap4D.java"
+
+  "nl/fullbrainpicture/utilities/Numerics.java"
+)

nighres/atlases/brain-segmentation-prior3.0/brain-atlas-experimental.txt

@@ -239,6 +239,38 @@ Cerebellum-WM	60.0	10.0	1.00
 Cerebrum-WML	60.0	10.0	1.00
 Cerebrum-WMR	60.0	10.0	1.00
 
+Intensity Prior:	bflidark07
+Background		0.0	    20.0	1.00
+Dura			20.0	20.0	1.00
+Arteries		150.0	30.0	1.00
+Sulcal-CSF		45.0	20.0	1.00
+VentricleL		150.0	30.0	1.00
+VentricleR		150.0	30.0	1.00
+Ventricle3		150.0	30.0	1.00
+Ventricle4		20.0	20.0	1.00
+ChoroidPlexusL	20.0	20.0	1.00
+ChoroidPlexusR	20.0	20.0	1.00
+Sinuses			20.0	20.0	1.00
+Cerebellum-GM	95.0	20.0	1.00
+Cerebrum-GML	90.0	20.0	1.00
+Cerebrum-GMR	90.0	20.0	1.00
+AmygdalaL		80.0	20.0	1.00
+AmygdalaR		80.0	20.0	1.00
+CaudateL		95.0	20.0	1.00
+CaudateR		95.0	20.0	1.00
+HippocampusL	85.0	20.0	1.00
+HippocampusR	85.0	20.0	1.00
+PutamenL		90.0	20.0	1.00
+PutamenR		90.0	20.0	1.00
+ThalamusL		80.0	20.0	1.00
+ThalamusR		80.0	20.0	1.00
+GlobusPallidusL	80.0	20.0	1.00
+GlobusPallidusR	80.0	20.0	1.00
+Brainstem		85.0	20.0	1.00
+Cerebellum-WM	70.0	20.0	1.00
+Cerebrum-WML	65.0	20.0	1.00
+Cerebrum-WMR	65.0	20.0	1.00
+
 Intensity Prior:	bfiqrlog
 Background		0.0	0.5	1.00
 Dura			0.0	0.5	1.00

nighres/atlases/brain-segmentation-prior3.0/brain-atlas-experimental.txt~

@@ -239,6 +239,38 @@ Cerebellum-WM	60.0	10.0	1.00
 Cerebrum-WML	60.0	10.0	1.00
 Cerebrum-WMR	60.0	10.0	1.00
 
+Intensity Prior:	bflidark07
+Background		0.0	    20.0	1.00
+Dura			20.0	20.0	1.00
+Arteries		20.0	30.0	1.00
+Sulcal-CSF		20.0	30.0	1.00
+VentricleL		150.0	30.0	1.00
+VentricleR		150.0	30.0	1.00
+Ventricle3		150.0	30.0	1.00
+Ventricle4		20.0	20.0	1.00
+ChoroidPlexusL	20.0	20.0	1.00
+ChoroidPlexusR	20.0	20.0	1.00
+Sinuses			20.0	20.0	1.00
+Cerebellum-GM	95.0	10.0	1.00
+Cerebrum-GML	95.0	10.0	1.00
+Cerebrum-GMR	95.0	10.0	1.00
+AmygdalaL		80.0	20.0	1.00
+AmygdalaR		80.0	20.0	1.00
+CaudateL		95.0	20.0	1.00
+CaudateR		95.0	20.0	1.00
+HippocampusL	85.0	20.0	1.00
+HippocampusR	85.0	20.0	1.00
+PutamenL		90.0	20.0	1.00
+PutamenR		90.0	20.0	1.00
+ThalamusL		80.0	20.0	1.00
+ThalamusR		80.0	20.0	1.00
+GlobusPallidusL	80.0	20.0	1.00
+GlobusPallidusR	80.0	20.0	1.00
+Brainstem		85.0	20.0	1.00
+Cerebellum-WM	70.0	20.0	1.00
+Cerebrum-WML	65.0	20.0	1.00
+Cerebrum-WMR	65.0	20.0	1.00
+
 Intensity Prior:	bfiqrlog
 Background		0.0	0.5	1.00
 Dura			0.0	0.5	1.00

nighres/data/__init__.py

@@ -5,3 +5,4 @@
 from nighres.data.download_data import download_MP2RAGEME_sample
 from nighres.data.download_data import download_MP2RAGEME_testdata
 from nighres.data.download_data import download_AHEAD_template
+from nighres.data.download_data import download_AHEADmni2009b_template

nighres/data/download_data.py

@@ -419,3 +419,70 @@ def download_AHEAD_template(data_dir=None, overwrite=False):
     return {'qr1': file_targets[0],
             'qr2s': file_targets[1],
             'qsm': file_targets[2]}
+
+def download_AHEADmni2009b_template(data_dir=None, overwrite=False):
+    """
+    Downloads the AHEAD group template in MNI 2009b space _[1].
+
+    Parameters
+    ----------
+    data_dir: str
+        Writeable directory in which downloaded atlas files should be stored. A
+        subdirectory called 'ahead-template' will be created in this location
+        (default is ATLAS_DIR)
+    overwrite: bool
+        Overwrite existing files in the same exact path (default is False)
+
+    Returns
+    ----------
+    dict
+        Dictionary with keys pointing to the location of the downloaded files
+
+        * qr1 : path to quantitative R1 map image
+        * qr2s : path to quantitative R2* map image
+        * qsm : path to QSM image
+        * qpd : path to semi-quantitative PD image
+
+    References
+    ----------
+    .. [1] Alkemade et al (under review). The Amsterdam Ultra-high field adult
+       lifespan database (AHEAD): A freely available multimodal 7 Tesla
+       submillimeter magnetic resonance imaging database.
+    """
+
+    if (data_dir is None):
+        data_dir = ATLAS_DIR
+
+    data_dir = os.path.join(data_dir, 'ahead-template')
+
+    if not os.path.isdir(data_dir):
+        os.makedirs(data_dir)
+
+    figshare = 'https://uvaauas.figshare.com/ndownloader/files/'
+
+# older version of the template
+#    file_sources = [figshare + x for x in
+#                    ['22679537','22679543','22679546','']]
+    file_sources = [figshare + x for x in
+                    ['34892901','34892907','34892883','41498217']]
+
+    file_targets = [os.path.join(data_dir, filename) for filename in
+                    ['ahead_mni2009b_med_qr1.nii.gz',
+                     'ahead_mni2009b_med_qr2s.nii.gz',
+                     'ahead_mni2009b_med_qsm.nii.gz',
+                     'ahead_mni2009b_med_qpd.nii.gz']]
+
+    for source, target in zip(file_sources, file_targets):
+
+        if os.path.isfile(target) and overwrite is False:
+            print("\nThe file {0} exists and overwrite was set to False "
+                  "-- not downloading.".format(target))
+        else:
+            print("\nDownloading to {0}".format(target))
+            urlretrieve(source, target)
+
+    return {'qr1': file_targets[0],
+            'qr2s': file_targets[1],
+            'qsm': file_targets[2],
+            'qpd': file_targets[3]}
+

nighres/filtering/recursive_ridge_diffusion.py

@@ -181,7 +181,7 @@ def recursive_ridge_diffusion(input_image, ridge_intensities, ridge_filter,
     rrd.setMaxIterations(max_iter)
     rrd.setMaxDifference(max_diff)
     rrd.setDetectionThreshold(threshold)
-    rrd.setUseScale(rescale)
+    if dimensions[2]>1: rrd.setUseScale(rescale)
 
     rrd.setDimensions(dimensions[0], dimensions[1], dimensions[2])
     rrd.setResolutions(resolution[0], resolution[1], resolution[2])

nighres/intensity/__init__.py

@@ -8,3 +8,4 @@
 from nighres.intensity.mp2rage_t1_mapping import mp2rage_t1_from_uni
 from nighres.intensity.phase_unwrapping import phase_unwrapping
 from nighres.intensity.t2s_optimal_combination import t2s_optimal_combination
+from nighres.intensity.boundary_sharpness import boundary_sharpness