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add optional outputs and more tests
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@anroy1
anroy1 committed Sep 1, 2024
1 parent 6a810c3 commit 303864f
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Showing 5 changed files with 194 additions and 9 deletions.
10 changes: 8 additions & 2 deletions modules/nf-scil/segmentation/synthseg/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +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("*__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 @@ -26,7 +29,10 @@ process SEGMENTATION_SYNTHSEG {
def robust = task.ext.robust ? "--robust" : ""
def fast = task.ext.fast ? "--fast" : ""
def ct = task.ext.ct ? "--ct" : ""
//TODO add all the others parameter with the corresponding optional outputs
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: ""

"""
export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1
Expand All @@ -35,7 +41,7 @@ process SEGMENTATION_SYNTHSEG {
cp $fs_license \$FREESURFER_HOME/license.txt
mri_synthseg --i $image --o t1.nii.gz --threads 1 $gpu $parc $robust $fast $ct
mri_synthseg --i $image --threads $task.cpus --o t1.nii.gz $gpu $parc $robust $fast $ct $output_vol $output_qc $output_resample $crop
# WM Mask
mri_binarize --i t1.nii.gz \
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15 changes: 15 additions & 0 deletions modules/nf-scil/segmentation/synthseg/meta.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -53,6 +53,21 @@ output:
description: Nifti CSF mask volume.
pattern: "*.{nii,nii.gz}"

- vol:
type: file
description: (optional) Output CSV file with volumes for all structures and subjects.
pattern: "*.csv"

- qc:
type: file
description: (optional) Output CSV file with qc scores for all subjects.
pattern: "*.csv"

- resample:
type: file
description: (optional) in order to return segmentations at 1mm resolution, the input images are internally resampled (except if they already are at 1mm). Use this optional flag to save the resampled images. This must be the same type as --i.
pattern: "*.{nii,nii.gz}"

- versions:
type: file
description: File containing software versions
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30 changes: 27 additions & 3 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 @@ -24,7 +24,7 @@ nextflow_process {
}
}

test("segmentation - synthseg") {
test("segmentation - synthseg - basic") {
config "./nextflow_basic.config"
when {
process {
Expand All @@ -35,7 +35,6 @@ nextflow_process {
file("\${test_data_directory}/t1.nii.gz", checkIfExists: true,),
[],
file("\${test_data_directory}/license.txt", checkIfExists: true,)

]
}
"""
Expand All @@ -51,8 +50,33 @@ nextflow_process {
}
}

test("segmentation - synthseg - options") {
config "./nextflow_options.config"
when {
process {
"""
input[0] = LOAD_DATA.out.test_data_directory.map{
test_data_directory -> [
[ id:'test', single_end:false ], // meta map
file("\${test_data_directory}/t1.nii.gz", checkIfExists: true,),
[],
file("\${test_data_directory}/license.txt", checkIfExists: true,)
]
}
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }

)
}
}

// test("segmentation - synthseg") {
// test("segmentation - synthseg - lesion") {
// config "./nextflow_lesion.config"
// when {
// process {
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139 changes: 135 additions & 4 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
@@ -1,5 +1,118 @@
{
"segmentation - synthseg": {
"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"
]
]
}
],
"meta": {
"nf-test": "0.9.0-rc1",
"nextflow": "24.04.4"
},
"timestamp": "2024-08-07T20:11:56.005332"
},
"segmentation - synthseg - basic": {
"content": [
{
"0": [
Expand All @@ -26,10 +139,19 @@
"id": "test",
"single_end": false
},
"test__mask_csf.nii.gz:md5,e60ff1b5847502a1e3f8c4a590d4a73c"
"test__mask_csf.nii.gz:md5,1307c8aeae9064d9a5108a01e918ffba"
]
],
"3": [

],
"4": [

],
"5": [

],
"6": [
"versions.yml:md5,b65418e9ce2ab1cce590b1f659e18c1d"
],
"csf_mask": [
Expand All @@ -38,7 +160,7 @@
"id": "test",
"single_end": false
},
"test__mask_csf.nii.gz:md5,e60ff1b5847502a1e3f8c4a590d4a73c"
"test__mask_csf.nii.gz:md5,1307c8aeae9064d9a5108a01e918ffba"
]
],
"gm_mask": [
Expand All @@ -49,9 +171,18 @@
},
"test__mask_gm.nii.gz:md5,432d6a28a10823c0ca5b2f40d2353e2f"
]
],
"qc": [

],
"resample": [

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

],
"wm_mask": [
[
Expand All @@ -68,6 +199,6 @@
"nf-test": "0.9.0-rc1",
"nextflow": "24.04.4"
},
"timestamp": "2024-08-06T19:27:40.416183"
"timestamp": "2024-08-07T20:11:18.859041"
}
}
9 changes: 9 additions & 0 deletions modules/nf-scil/segmentation/synthseg/tests/nextflow_options.config
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Original file line number Diff line number Diff line change
@@ -0,0 +1,9 @@
process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
ext.robust = true
ext.fast = true
ext.output_vol = true
ext.output_qc = true
ext.resample = true
ext.crop = 64
}

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