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[WIP] try to fix resample output capture
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@anroy1
anroy1 committed Sep 1, 2024
1 parent 303864f commit 153d114
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Showing 4 changed files with 43 additions and 194 deletions.
14 changes: 11 additions & 3 deletions modules/nf-scil/segmentation/synthseg/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -12,9 +12,9 @@ process SEGMENTATION_SYNTHSEG {
tuple val(meta), path("*__mask_wm.nii.gz") , emit: wm_mask
tuple val(meta), path("*__mask_gm.nii.gz") , emit: gm_mask
tuple val(meta), path("*__mask_csf.nii.gz") , emit: csf_mask
tuple val(meta), path("*__resampled_image.nii.gz") , emit: resample, optional: true
tuple val(meta), path("*__vol.csv") , emit: vol, optional: true
tuple val(meta), path("*__qc.csv") , emit: qc, optional: true
tuple val(meta), path("*__resampled_image.nii.gz") , emit: resample, optional: true
path "versions.yml" , emit: versions

when:
Expand All @@ -29,9 +29,9 @@ process SEGMENTATION_SYNTHSEG {
def robust = task.ext.robust ? "--robust" : ""
def fast = task.ext.fast ? "--fast" : ""
def ct = task.ext.ct ? "--ct" : ""
def output_resample = task.ext.output_resample ? "--resample ${prefix}__resampled_image.nii.gz": ""
def output_vol = task.ext.output_vol ? "--vol ${prefix}__vol.csv" : ""
def output_qc = task.ext.output_qc ? "--qc ${prefix}__qc.csv" : ""
def output_resample = task.ext.output_resample ? "--resample ${prefix}__resampled_image.nii.gz": ""
def crop = task.ext.crop ? "--crop " + task.ext.crop: ""

"""
Expand All @@ -41,7 +41,11 @@ process SEGMENTATION_SYNTHSEG {
cp $fs_license \$FREESURFER_HOME/license.txt
mri_synthseg --i $image --threads $task.cpus --o t1.nii.gz $gpu $parc $robust $fast $ct $output_vol $output_qc $output_resample $crop
mri_synthseg --i $image --threads $task.cpus --o t1.nii.gz $gpu $parc $robust $fast $ct $output_resample $output_vol $output_qc $crop
if [${prefix}__resampled_image.nii.gz]; then
mv ${prefix}__resampled_image.nii.gz test_resample.nii.gz
fi
# WM Mask
mri_binarize --i t1.nii.gz \
Expand Down Expand Up @@ -87,6 +91,10 @@ process SEGMENTATION_SYNTHSEG {
touch ${prefix}__mask_wm.nii.gz
touch ${prefix}__mask_gm.nii.gz
touch ${prefix}__mask_csf.nii.gz
touch ${prefix}__resampled_image.nii.gz
touch ${prefix}__vol.csv
touch ${prefix}__qc.csv
cat <<-END_VERSIONS > versions.yml
"${task.process}":
Expand Down
19 changes: 15 additions & 4 deletions modules/nf-scil/segmentation/synthseg/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -44,8 +44,12 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }

{ assert snapshot(
Nifti_md5sum(process.out.wm_mask.get(0).get(1)),
Nifti_md5sum(process.out.gm_mask.get(0).get(1)),
Nifti_md5sum(process.out.csf_mask.get(0).get(1)),
process.out.versions
).match() }
)
}
}
Expand All @@ -70,8 +74,15 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }

{ assert snapshot(
Nifti_md5sum(process.out.wm_mask.get(0).get(1)),
Nifti_md5sum(process.out.gm_mask.get(0).get(1)),
Nifti_md5sum(process.out.csf_mask.get(0).get(1)),
file(process.out.vol.get(0).get(1)),
file(process.out.qc.get(0).get(1)),
// Nifti_md5sum(process.out.resample.get(0).get(1)),
process.out.versions
).match() }
)
}
}
Expand Down
202 changes: 16 additions & 186 deletions modules/nf-scil/segmentation/synthseg/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
@@ -1,204 +1,34 @@
{
"segmentation - synthseg - options": {
"content": [
{
"0": [
[
{
"id": "test",
"single_end": false
},
"test__mask_wm.nii.gz:md5,8ca305b46341552159e15e6974274358"
]
],
"1": [
[
{
"id": "test",
"single_end": false
},
"test__mask_gm.nii.gz:md5,c8c4f3027132011d98cf4a351230f519"
]
],
"2": [
[
{
"id": "test",
"single_end": false
},
"test__mask_csf.nii.gz:md5,1deff8b0b3d9f883b75bcd5c9f52f2c5"
]
],
"3": [
[
{
"id": "test",
"single_end": false
},
"test__vol.csv:md5,fe0078439655e81ab5777c73b4bd1edf"
]
],
"4": [
[
{
"id": "test",
"single_end": false
},
"test__qc.csv:md5,ede51ac9221945293200793a46c15afa"
]
],
"5": [

],
"6": [
"versions.yml:md5,b65418e9ce2ab1cce590b1f659e18c1d"
],
"csf_mask": [
[
{
"id": "test",
"single_end": false
},
"test__mask_csf.nii.gz:md5,1deff8b0b3d9f883b75bcd5c9f52f2c5"
]
],
"gm_mask": [
[
{
"id": "test",
"single_end": false
},
"test__mask_gm.nii.gz:md5,c8c4f3027132011d98cf4a351230f519"
]
],
"qc": [
[
{
"id": "test",
"single_end": false
},
"test__qc.csv:md5,ede51ac9221945293200793a46c15afa"
]
],
"resample": [

],
"versions": [
"versions.yml:md5,b65418e9ce2ab1cce590b1f659e18c1d"
],
"vol": [
[
{
"id": "test",
"single_end": false
},
"test__vol.csv:md5,fe0078439655e81ab5777c73b4bd1edf"
]
],
"wm_mask": [
[
{
"id": "test",
"single_end": false
},
"test__mask_wm.nii.gz:md5,8ca305b46341552159e15e6974274358"
]
]
}
"test__mask_wm.nii.gz:md5,42ac2ae7eab32edb16f230211e5e55c5",
"test__mask_gm.nii.gz:md5,7a205f13a6894200f0e1a4ea94447390",
"test__mask_csf.nii.gz:md5,7b6125a133adbaae10e94d95782c6678",
"test__vol.csv:md5,fe0078439655e81ab5777c73b4bd1edf",
"test__qc.csv:md5,ede51ac9221945293200793a46c15afa",
[
"versions.yml:md5,b65418e9ce2ab1cce590b1f659e18c1d"
]
],
"meta": {
"nf-test": "0.9.0-rc1",
"nextflow": "24.04.4"
},
"timestamp": "2024-08-07T20:11:56.005332"
"timestamp": "2024-08-16T19:58:49.946322"
},
"segmentation - synthseg - basic": {
"content": [
{
"0": [
[
{
"id": "test",
"single_end": false
},
"test__mask_wm.nii.gz:md5,5aa95919bfa5b1dd2f8f7a0ae2667bfb"
]
],
"1": [
[
{
"id": "test",
"single_end": false
},
"test__mask_gm.nii.gz:md5,432d6a28a10823c0ca5b2f40d2353e2f"
]
],
"2": [
[
{
"id": "test",
"single_end": false
},
"test__mask_csf.nii.gz:md5,1307c8aeae9064d9a5108a01e918ffba"
]
],
"3": [

],
"4": [

],
"5": [

],
"6": [
"versions.yml:md5,b65418e9ce2ab1cce590b1f659e18c1d"
],
"csf_mask": [
[
{
"id": "test",
"single_end": false
},
"test__mask_csf.nii.gz:md5,1307c8aeae9064d9a5108a01e918ffba"
]
],
"gm_mask": [
[
{
"id": "test",
"single_end": false
},
"test__mask_gm.nii.gz:md5,432d6a28a10823c0ca5b2f40d2353e2f"
]
],
"qc": [

],
"resample": [

],
"versions": [
"versions.yml:md5,b65418e9ce2ab1cce590b1f659e18c1d"
],
"vol": [

],
"wm_mask": [
[
{
"id": "test",
"single_end": false
},
"test__mask_wm.nii.gz:md5,5aa95919bfa5b1dd2f8f7a0ae2667bfb"
]
]
}
"test__mask_wm.nii.gz:md5,f35c2cd0f899d5a290083d09bac01670",
"test__mask_gm.nii.gz:md5,ef1aef14d90f78dcae60f3f73066af53",
"test__mask_csf.nii.gz:md5,fa08d8c09176d72b8f9b3667419c3d3e",
[
"versions.yml:md5,b65418e9ce2ab1cce590b1f659e18c1d"
]
],
"meta": {
"nf-test": "0.9.0-rc1",
"nextflow": "24.04.4"
},
"timestamp": "2024-08-07T20:11:18.859041"
"timestamp": "2024-08-16T19:58:09.501194"
}
}
2 changes: 1 addition & 1 deletion modules/nf-scil/segmentation/synthseg/tests/nextflow_options.config
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Original file line number Diff line number Diff line change
Expand Up @@ -2,8 +2,8 @@ process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
ext.robust = true
ext.fast = true
ext.output_resample = true
ext.output_vol = true
ext.output_qc = true
ext.resample = true
ext.crop = 64
}

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