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[ENH] Update image/resample #22

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[ENH] Update image/resample #22

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16 changes: 9 additions & 7 deletions modules/nf-neuro/image/resample/main.nf
View file
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Original file line number Diff line number Diff line change
@@ -1,10 +1,11 @@
process IMAGE_RESAMPLE {
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(image), path(ref) /* optional, input = [] */
Expand All @@ -18,6 +19,7 @@ process IMAGE_RESAMPLE {

script:
def prefix = task.ext.prefix ?: "${meta.id}"
def suffix = task.ext.suffix ? "${task.ext.first_suffix}_resampled" : "resampled"
def reference = "$ref" ? "--ref $ref" : ""
def voxel_size = task.ext.voxel_size ? "--voxel_size " + task.ext.voxel_size : ""
def volume_size = task.ext.volume_size ? "--volume_size " + task.ext.volume_size : ""
Expand All @@ -31,28 +33,28 @@ process IMAGE_RESAMPLE {
export OMP_NUM_THREADS=1
export OPENBLAS_NUM_THREADS=1

scil_volume_resample.py $image ${prefix}__resampled.nii.gz \
scil_volume_resample.py $image ${prefix}_${suffix}.nii.gz \
$voxel_size $volume_size $reference $iso_min \
$f $enforce_dimensions $interp


cat <<-END_VERSIONS > versions.yml
"${task.process}":
scilpy: 2.0.1
scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
END_VERSIONS
"""

stub:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def suffix = task.ext.suffix ? "${task.ext.first_suffix}_resampled" : "resampled"
"""
scil_volume_resample.py -h

touch ${prefix}__resampled.nii.gz
touch ${prefix}_${suffix}.nii.gz

cat <<-END_VERSIONS > versions.yml
"${task.process}":
scilpy: 2.0.1
scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
END_VERSIONS
"""
}
2 changes: 1 addition & 1 deletion modules/nf-neuro/image/resample/meta.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@ keywords:
- resample
- nifti
- volume
- Scilpy
- scilpy
tools:
- "scilpy":
description: "The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox."
Expand Down
70 changes: 35 additions & 35 deletions modules/nf-neuro/image/resample/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -8,31 +8,31 @@
"id": "test",
"single_end": false
},
"test__resampled.nii.gz:md5,f3164907d16ceabf606a03ea0efd3a2f"
"test_resampled.nii.gz:md5,f3164907d16ceabf606a03ea0efd3a2f"
]
],
"1": [
"versions.yml:md5,f2c9fb731758ad9909571d60a85fa792"
"versions.yml:md5,06181e25531a3ebdefdfd2e641a3d645"
],
"image": [
[
{
"id": "test",
"single_end": false
},
"test__resampled.nii.gz:md5,f3164907d16ceabf606a03ea0efd3a2f"
"test_resampled.nii.gz:md5,f3164907d16ceabf606a03ea0efd3a2f"
]
],
"versions": [
"versions.yml:md5,f2c9fb731758ad9909571d60a85fa792"
"versions.yml:md5,06181e25531a3ebdefdfd2e641a3d645"
]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-05-08T12:39:51.794554"
"timestamp": "2024-10-24T15:30:19.061192"
},
"image - resample - nn": {
"content": [
Expand All @@ -43,31 +43,31 @@
"id": "test",
"single_end": false
},
"test__resampled.nii.gz:md5,8d3e1c9552673b1ce60bc4d090198564"
"test_resampled.nii.gz:md5,8d3e1c9552673b1ce60bc4d090198564"
]
],
"1": [
"versions.yml:md5,f2c9fb731758ad9909571d60a85fa792"
"versions.yml:md5,06181e25531a3ebdefdfd2e641a3d645"
],
"image": [
[
{
"id": "test",
"single_end": false
},
"test__resampled.nii.gz:md5,8d3e1c9552673b1ce60bc4d090198564"
"test_resampled.nii.gz:md5,8d3e1c9552673b1ce60bc4d090198564"
]
],
"versions": [
"versions.yml:md5,f2c9fb731758ad9909571d60a85fa792"
"versions.yml:md5,06181e25531a3ebdefdfd2e641a3d645"
]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-05-08T12:40:24.002411"
"timestamp": "2024-10-24T15:30:42.725713"
},
"image - resample - volsize": {
"content": [
Expand All @@ -78,31 +78,31 @@
"id": "test",
"single_end": false
},
"test__resampled.nii.gz:md5,7c83b666f9fb2d68643a20d1c7ac21d8"
"test_resampled.nii.gz:md5,7c83b666f9fb2d68643a20d1c7ac21d8"
]
],
"1": [
"versions.yml:md5,f2c9fb731758ad9909571d60a85fa792"
"versions.yml:md5,06181e25531a3ebdefdfd2e641a3d645"
],
"image": [
[
{
"id": "test",
"single_end": false
},
"test__resampled.nii.gz:md5,7c83b666f9fb2d68643a20d1c7ac21d8"
"test_resampled.nii.gz:md5,7c83b666f9fb2d68643a20d1c7ac21d8"
]
],
"versions": [
"versions.yml:md5,f2c9fb731758ad9909571d60a85fa792"
"versions.yml:md5,06181e25531a3ebdefdfd2e641a3d645"
]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-05-08T12:39:35.764922"
"timestamp": "2024-10-24T15:30:07.1626"
},
"image - resample - voxsize": {
"content": [
Expand All @@ -113,31 +113,31 @@
"id": "test",
"single_end": false
},
"test__resampled.nii.gz:md5,6ffdabab138186db2dab6f98ea6e9ffb"
"test_resampled.nii.gz:md5,6ffdabab138186db2dab6f98ea6e9ffb"
]
],
"1": [
"versions.yml:md5,f2c9fb731758ad9909571d60a85fa792"
"versions.yml:md5,06181e25531a3ebdefdfd2e641a3d645"
],
"image": [
[
{
"id": "test",
"single_end": false
},
"test__resampled.nii.gz:md5,6ffdabab138186db2dab6f98ea6e9ffb"
"test_resampled.nii.gz:md5,6ffdabab138186db2dab6f98ea6e9ffb"
]
],
"versions": [
"versions.yml:md5,f2c9fb731758ad9909571d60a85fa792"
"versions.yml:md5,06181e25531a3ebdefdfd2e641a3d645"
]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-05-08T12:39:18.016911"
"timestamp": "2024-10-24T15:29:55.01735"
},
"image - resample - ref": {
"content": [
Expand All @@ -148,30 +148,30 @@
"id": "test",
"single_end": false
},
"test__resampled.nii.gz:md5,0a45d21ff294fda2e41c620cf83d0406"
"test_resampled.nii.gz:md5,0a45d21ff294fda2e41c620cf83d0406"
]
],
"1": [
"versions.yml:md5,f2c9fb731758ad9909571d60a85fa792"
"versions.yml:md5,06181e25531a3ebdefdfd2e641a3d645"
],
"image": [
[
{
"id": "test",
"single_end": false
},
"test__resampled.nii.gz:md5,0a45d21ff294fda2e41c620cf83d0406"
"test_resampled.nii.gz:md5,0a45d21ff294fda2e41c620cf83d0406"
]
],
"versions": [
"versions.yml:md5,f2c9fb731758ad9909571d60a85fa792"
"versions.yml:md5,06181e25531a3ebdefdfd2e641a3d645"
]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-05-08T12:40:07.720638"
"timestamp": "2024-10-24T15:30:31.018615"
}
}
36 changes: 18 additions & 18 deletions subworkflows/nf-neuro/preproc_dwi/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -13,29 +13,29 @@
[
"versions.yml:md5,0280006ceecc575513278292734ffb27",
"versions.yml:md5,3340c4b5e56ca52f7342be3c9044eb47",
"versions.yml:md5,4d981a0200b8820dd789f135a9dd320f",
"versions.yml:md5,5dce7a8c0b0d6b91ef7826f88c86370e",
"versions.yml:md5,7ddf2e98f59b19c9b933670550f26ad7",
"versions.yml:md5,962f76092c8795ce5e6d768304e2d230",
"versions.yml:md5,b4c068383da080f871c90828b1de0082",
"versions.yml:md5,c15ba5efd24564dba4710b6da8c4b791",
"versions.yml:md5,d1ae2ca80502bf88c4b1c4a42fba6ced",
"versions.yml:md5,d3010f785c88ee5946806a8a758e7efb",
"versions.yml:md5,d68fe3399120f84f1add62181708780b",
"versions.yml:md5,ea5858879452a59bb355228ae7f38111",
"versions.yml:md5,f041502e22449973d84ac1c618e8ebf9"
],
"test_b0.nii.gz",
"test__resampled.nii.gz",
"test_resampled.nii.gz",
"test__dwi_eddy_corrected.bvec",
"test__image_boundingBox.pkl",
"test__image_n4.nii.gz",
"test__resampled.nii.gz",
"test_resampled.nii.gz",
"test__dwi_corrected.nii.gz"
],
"meta": {
"nf-test": "0.9.0-rc1",
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-08-05T18:15:01.714505"
"timestamp": "2024-10-24T15:39:59.890109"
},
"preproc_dwi_rev_b0": {
"content": [
Expand All @@ -51,28 +51,28 @@
[
"versions.yml:md5,0280006ceecc575513278292734ffb27",
"versions.yml:md5,3340c4b5e56ca52f7342be3c9044eb47",
"versions.yml:md5,4d981a0200b8820dd789f135a9dd320f",
"versions.yml:md5,5dce7a8c0b0d6b91ef7826f88c86370e",
"versions.yml:md5,7ddf2e98f59b19c9b933670550f26ad7",
"versions.yml:md5,962f76092c8795ce5e6d768304e2d230",
"versions.yml:md5,b4c068383da080f871c90828b1de0082",
"versions.yml:md5,c15ba5efd24564dba4710b6da8c4b791",
"versions.yml:md5,d1ae2ca80502bf88c4b1c4a42fba6ced",
"versions.yml:md5,d3010f785c88ee5946806a8a758e7efb",
"versions.yml:md5,ea5858879452a59bb355228ae7f38111",
"versions.yml:md5,f041502e22449973d84ac1c618e8ebf9"
],
"test_b0.nii.gz",
"test__resampled.nii.gz",
"test_resampled.nii.gz",
"test__dwi_eddy_corrected.bvec",
"test__image_boundingBox.pkl",
"test__image_n4.nii.gz",
"test__resampled.nii.gz",
"test_resampled.nii.gz",
"test__dwi_corrected.nii.gz"
],
"meta": {
"nf-test": "0.9.0-rc1",
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-08-05T18:10:40.247701"
"timestamp": "2024-10-24T15:35:59.573081"
},
"preproc_dwi_all_options": {
"content": [
Expand All @@ -88,27 +88,27 @@
[
"versions.yml:md5,0280006ceecc575513278292734ffb27",
"versions.yml:md5,3340c4b5e56ca52f7342be3c9044eb47",
"versions.yml:md5,4d981a0200b8820dd789f135a9dd320f",
"versions.yml:md5,5dce7a8c0b0d6b91ef7826f88c86370e",
"versions.yml:md5,7ddf2e98f59b19c9b933670550f26ad7",
"versions.yml:md5,962f76092c8795ce5e6d768304e2d230",
"versions.yml:md5,b4c068383da080f871c90828b1de0082",
"versions.yml:md5,c15ba5efd24564dba4710b6da8c4b791",
"versions.yml:md5,d1ae2ca80502bf88c4b1c4a42fba6ced",
"versions.yml:md5,d68fe3399120f84f1add62181708780b",
"versions.yml:md5,ea5858879452a59bb355228ae7f38111",
"versions.yml:md5,f041502e22449973d84ac1c618e8ebf9"
],
"test_b0.nii.gz",
"test__resampled.nii.gz",
"test_resampled.nii.gz",
"test__dwi_eddy_corrected.bvec",
"test__image_boundingBox.pkl",
"test__image_n4.nii.gz",
"test__resampled.nii.gz",
"test_resampled.nii.gz",
"test__dwi_corrected.nii.gz"
],
"meta": {
"nf-test": "0.9.0-rc1",
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-08-05T18:20:22.568596"
"timestamp": "2024-10-24T15:44:27.839939"
}
}
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