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scilus · Oct 24, 2024 · c38fb00 · c38fb00
1 parent 719cb46
commit c38fb00
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Showing 4 changed files with 36 additions and 32 deletions.
diff --git a/.devcontainer/updateContentCommand.sh b/.devcontainer/updateContentCommand.sh
@@ -18,9 +18,9 @@ cat <<EOF > $XDG_CONFIG_HOME/nf-neuro/.env
 # It is sourced by the shell on startup of every terminals.
 
 export PROFILE=docker
-export NFCORE_MODULES_GIT_REMOTE=$GIT_REMOTE
+export NFCORE_MODULES_GIT_REMOTE="$GIT_REMOTE"
 export NFCORE_MODULES_BRANCH=$CURRENT_BRANCH
-export NFCORE_SUBWORKFLOWS_GIT_REMOTE=$GIT_REMOTE
+export NFCORE_SUBWORKFLOWS_GIT_REMOTE="$GIT_REMOTE"
 export NFCORE_SUBWORKFLOWS_BRANCH=$CURRENT_BRANCH
 
 export DEVCONTAINER_RAM_LIMIT_GB=$((maxmem / 1024 / 1024))

diff --git a/modules/nf-neuro/tracking/localtracking/main.nf b/modules/nf-neuro/tracking/localtracking/main.nf
@@ -1,10 +1,10 @@
 process TRACKING_LOCALTRACKING {
     tag "$meta.id"
-    label 'process_single'
+    label 'process_high_memory'
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://scil.usherbrooke.ca/containers/scilus_2.0.1.sif':
-        'scilus/scilus:2.0.1' }"
+        'https://scil.usherbrooke.ca/containers/scilus_2.0.2.sif':
+        'scilus/scilus:2.0.2' }"
 
     input:
     tuple val(meta), path(wm), path(fodf), path(fa)
@@ -39,42 +39,46 @@ process TRACKING_LOCALTRACKING {
     def compress = task.ext.local_compress_streamlines ? "--compress " + task.ext.local_compress_value : ""
     def basis = task.ext.basis ? "--sh_basis " + task.ext.basis : ""
 
+    def gpu_batch_size = task.ext.gpu_batch_size ? "--batch_size " + task.ext.gpu_batch_size : ""
+    def enable_gpu = task.ext.enable_gpu ? "--use_gpu $gpu_batch_size" : ""
+
     """
     export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1
     export OMP_NUM_THREADS=1
     export OPENBLAS_NUM_THREADS=1
 
     if [ "${local_tracking_mask}" == "wm" ]; then
         scil_volume_math.py convert $wm ${prefix}__local_tracking_mask.nii.gz \
-            --data_type uint8
+            --data_type uint8 -f
 
     elif [ "${local_tracking_mask}" == "fa" ]; then
         scil_volume_math.py lower_threshold $fa \
             $local_fa_tracking_mask_threshold \
             ${prefix}__local_tracking_mask.nii.gz \
-            --data_type uint8
+            --data_type uint8 -f
     fi
 
     if [ "${local_seeding_mask}" == "wm" ]; then
         scil_volume_math.py convert $wm ${prefix}__local_seeding_mask.nii.gz \
-            --data_type uint8
+            --data_type uint8 -f
 
     elif [ "${local_seeding_mask}" == "fa" ]; then
         scil_volume_math.py lower_threshold $fa \
             $local_fa_seeding_mask_threshold \
             ${prefix}__local_seeding_mask.nii.gz \
-            --data_type uint8
+            --data_type uint8 -f
     fi
 
-    scil_tracking_local.py $fodf ${prefix}__local_seeding_mask.nii.gz ${prefix}__local_tracking_mask.nii.gz tmp.trk\
+    scil_tracking_local.py $fodf ${prefix}__local_seeding_mask.nii.gz \
+            ${prefix}__local_tracking_mask.nii.gz tmp.trk $enable_gpu\
             $local_algo $local_seeding $local_nbr_seeds\
             $local_random_seed $local_step $local_theta\
             $local_sfthres $local_min_len\
-            $local_max_len $compress $basis
+            $local_max_len $compress $basis -f
 
     scil_tractogram_remove_invalid.py tmp.trk\
             ${prefix}__local_tracking.trk\
-            --remove_single_point
+            --remove_single_point -f
 
     cat <<-TRACKING_INFO > ${prefix}__local_tracking_config.json
     {"algorithm": "${task.ext.local_algo}",
@@ -97,7 +101,7 @@ process TRACKING_LOCALTRACKING {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        scilpy: 2.0.1
+        scilpy: 2.0.2
     END_VERSIONS
     """
 
@@ -115,7 +119,7 @@ process TRACKING_LOCALTRACKING {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        scilpy: 2.0.1
+        scilpy: 2.0.2
     END_VERSIONS
     """
 }
diff --git a/modules/nf-neuro/tracking/localtracking/tests/main.nf.test.snap b/modules/nf-neuro/tracking/localtracking/tests/main.nf.test.snap
@@ -30,14 +30,14 @@
                 ]
             ],
             [
-                "versions.yml:md5,097efc37ca86414ed8d4836991b634b7"
+                "versions.yml:md5,0088e7190e395324acbb8fce5c474750"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-05-08T23:46:42.749206"
+        "timestamp": "2024-10-24T19:38:16.835402429"
     },
     "tracking - localtracking - fa": {
         "content": [
@@ -70,13 +70,13 @@
                 ]
             ],
             [
-                "versions.yml:md5,097efc37ca86414ed8d4836991b634b7"
+                "versions.yml:md5,0088e7190e395324acbb8fce5c474750"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-05-08T23:46:28.766414"
+        "timestamp": "2024-10-24T19:37:54.047881093"
     }
 }
diff --git a/modules/nf-neuro/tracking/pfttracking/main.nf b/modules/nf-neuro/tracking/pfttracking/main.nf
@@ -1,11 +1,11 @@
 
 process TRACKING_PFTTRACKING {
     tag "$meta.id"
-    label 'process_single'
+    label 'process_high_memory'
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://scil.usherbrooke.ca/containers/scilus_2.0.1.sif':
-        'scilus/scilus:2.0.1' }"
+        'https://scil.usherbrooke.ca/containers/scilus_2.0.2.sif':
+        'scilus/scilus:2.0.2' }"
 
     input:
         tuple val(meta), path(wm), path(gm), path(csf), path(fodf), path(fa)
@@ -56,28 +56,28 @@ process TRACKING_PFTTRACKING {
 
     if [ "${pft_seeding_mask}" == "wm" ]; then
         scil_volume_math.py convert $wm ${prefix}__mask_wm.nii.gz \
-            --data_type uint8
+            --data_type uint8 -f
         scil_volume_math.py union ${prefix}__mask_wm.nii.gz \
             ${prefix}__interface.nii.gz ${prefix}__pft_seeding_mask.nii.gz\
-            --data_type uint8
+            --data_type uint8 -f
 
     elif [ "${pft_seeding_mask}" == "interface" ]; then
         cp ${prefix}__interface.nii.gz ${prefix}__pft_seeding_mask.nii.gz
 
     elif [ "${pft_seeding_mask}" == "fa" ]; then
         mrcalc $fa $pft_fa_threshold -ge ${prefix}__pft_seeding_mask.nii.gz\
-            -datatype uint8
+            -datatype uint8 -force
     fi
 
     scil_tracking_pft.py $fodf ${prefix}__pft_seeding_mask.nii.gz \
         ${prefix}__map_include.nii.gz ${prefix}__map_exclude.nii.gz tmp.trk\
         $pft_algo $pft_seeding_type $pft_nbr_seeds \
         $pft_random_seed $pft_step $pft_theta\
         $pft_sfthres $pft_sfthres_init $pft_min_len $pft_max_len\
-        $pft_particles $pft_back $pft_front $compress $basis
+        $pft_particles $pft_back $pft_front $compress $basis -f
 
     scil_tractogram_remove_invalid.py tmp.trk ${prefix}__pft_tracking.trk\
-        --remove_single_point
+        --remove_single_point -f
 
     cat <<-TRACKING_INFO > ${prefix}__pft_tracking_config.json
     {"algorithm": "${task.ext.pft_algo}",
@@ -101,7 +101,7 @@ process TRACKING_PFTTRACKING {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        scilpy: 2.0.1
+        scilpy: 2.0.2
         mrtrix: \$(mrcalc -version 2>&1 | sed -n 's/== mrcalc \\([0-9.]\\+\\).*/\\1/p')
     END_VERSIONS
     """
@@ -124,7 +124,7 @@ process TRACKING_PFTTRACKING {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        scilpy: 2.0.1
+        scilpy: 2.0.2
         mrtrix: \$(mrcalc -version 2>&1 | sed -n 's/== mrcalc \\([0-9.]\\+\\).*/\\1/p')
     END_VERSIONS
     """