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[ENH] tracking module #21

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[ENH] tracking module #21

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c38fb00
changes done
arnaudbore Oct 24, 2024
e064191
fix snap
arnaudbore Oct 24, 2024
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4 changes: 2 additions & 2 deletions .devcontainer/updateContentCommand.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -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))
Expand Down
28 changes: 16 additions & 12 deletions modules/nf-neuro/tracking/localtracking/main.nf
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Original file line number Diff line number Diff line change
@@ -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)
Expand Down Expand Up @@ -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}",
Expand All @@ -97,7 +101,7 @@ process TRACKING_LOCALTRACKING {

cat <<-END_VERSIONS > versions.yml
"${task.process}":
scilpy: 2.0.1
scilpy: 2.0.2
END_VERSIONS
"""

Expand All @@ -115,7 +119,7 @@ process TRACKING_LOCALTRACKING {

cat <<-END_VERSIONS > versions.yml
"${task.process}":
scilpy: 2.0.1
scilpy: 2.0.2
END_VERSIONS
"""
}
16 changes: 8 additions & 8 deletions modules/nf-neuro/tracking/localtracking/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -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": [
Expand Down Expand Up @@ -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"
}
}
20 changes: 10 additions & 10 deletions modules/nf-neuro/tracking/pfttracking/main.nf
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Original file line number Diff line number Diff line change
@@ -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)
Expand Down Expand Up @@ -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}",
Expand All @@ -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
"""
Expand All @@ -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
"""
Expand Down
24 changes: 12 additions & 12 deletions modules/nf-neuro/tracking/pfttracking/tests/main.nf.test.snap
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -39,14 +39,14 @@
]
],
[
"versions.yml:md5,6fa5c5e21149198626b41120de3947c3"
"versions.yml:md5,2ae3399d07ef00610deae7988357dd55"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-05-08T23:44:48.372791"
"timestamp": "2024-10-24T19:53:53.332859167"
},
"tracking - pfttracking - interface": {
"content": [
Expand Down Expand Up @@ -79,7 +79,7 @@
]
],
[
"versions.yml:md5,6fa5c5e21149198626b41120de3947c3"
"versions.yml:md5,2ae3399d07ef00610deae7988357dd55"
],
[
[
Expand All @@ -92,10 +92,10 @@
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-05-08T23:45:02.333851"
"timestamp": "2024-10-24T19:54:04.257171663"
},
"tracking - pfttracking - wm": {
"content": [
Expand Down Expand Up @@ -137,13 +137,13 @@
]
],
[
"versions.yml:md5,6fa5c5e21149198626b41120de3947c3"
"versions.yml:md5,2ae3399d07ef00610deae7988357dd55"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-05-08T23:44:33.456248"
"timestamp": "2024-10-24T19:53:38.784232647"
}
}