Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

[ENH] Update image/resample #22

Merged
merged 2 commits into from
Oct 30, 2024
Merged

[ENH] Update image/resample #22

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
39a2703
apply Alex's changes to image/resample + update tests
gagnonanthony Oct 25, 2024
e7b304d
change test data to reduce tests time (1h30 -> ~13min)
gagnonanthony Oct 28, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
16 changes: 9 additions & 7 deletions modules/nf-neuro/image/resample/main.nf
View file
Open in desktop
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
View file
Open in desktop
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
View file
Open in desktop
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
View file
Open in desktop
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"
}
}
Loading