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Split transforms into 2 inputs and update versions in registrations/antsapplytransforms #55

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Nov 29, 2024
Merged

Split transforms into 2 inputs and update versions in registrations/antsapplytransforms #55

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cdf932b
split transforms into 2 inputs + cleanup + stub test
gagnonanthony Nov 28, 2024
89c21b3
update meta
gagnonanthony Nov 29, 2024
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23 changes: 9 additions & 14 deletions modules/nf-neuro/registration/antsapplytransforms/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@ process REGISTRATION_ANTSAPPLYTRANSFORMS {
'scilus/scilus:2.0.2' }"

input:
tuple val(meta), path(image), path(reference), path(transform)
tuple val(meta), path(image), path(reference), path(warp), path(affine)

output:
tuple val(meta), path("*__warped.nii.gz") , emit: warped_image
Expand All @@ -17,9 +17,8 @@ process REGISTRATION_ANTSAPPLYTRANSFORMS {
task.ext.when == null || task.ext.when

script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def suffix = task.ext.first_suffix ? "${task.ext.first_suffix}_warped" : "warped"
def suffix = task.ext.first_suffix ? "${task.ext.first_suffix}__warped" : "warped"

def dimensionality = task.ext.dimensionality ? "-d " + task.ext.dimensionality : ""
def image_type = task.ext.image_type ? "-e " + task.ext.image_type : ""
Expand All @@ -37,24 +36,20 @@ process REGISTRATION_ANTSAPPLYTRANSFORMS {
-r $reference\
-o ${prefix}__${suffix}.nii.gz\
$interpolation\
-t $transform\
-t $warp $affine\
$image_type\
$default_val\
$output_dtype

cat <<-END_VERSIONS > versions.yml
"${task.process}":
ants: antsRegistration --version | grep "Version" | sed -E 's/.*v([0-9]+\\.[0-9]+\\.[0-9]+).*/\\1/'
ants: \$(antsRegistration --version | grep "Version" | sed -E 's/.*v([0-9]+\\.[0-9]+\\.[0-9]+).*/\\1/')
END_VERSIONS
"""

stub:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def suffix = task.ext.first_suffix ? "${task.ext.first_suffix}_warped" : "warped"

def dimensionality = task.ext.dimensionality ? "-d " + task.ext.dimensionality : ""
def image_type = task.ext.image_type ? "-e " + task.ext.image_type : ""
def interpolation = task.ext.interpolation ? "-n " + task.ext.interpolation : ""
def output_dtype = task.ext.output_dtype ? "-u " + task.ext.output_dtype : ""
def default_val = task.ext.default_val ? "-f " + task.ext.default_val : ""
def suffix = task.ext.first_suffix ? "${task.ext.first_suffix}__warped" : "warped"

"""
antsApplyTransforms -h
Expand All @@ -63,7 +58,7 @@ process REGISTRATION_ANTSAPPLYTRANSFORMS {

cat <<-END_VERSIONS > versions.yml
"${task.process}":
ants: antsRegistration --version | grep "Version" | sed -E 's/.*v([0-9]+\\.[0-9]+\\.[0-9]+).*/\\1/'
ants: \$(antsRegistration --version | grep "Version" | sed -E 's/.*v([0-9]+\\.[0-9]+\\.[0-9]+).*/\\1/')
END_VERSIONS
"""
}
11 changes: 8 additions & 3 deletions modules/nf-neuro/registration/antsapplytransforms/meta.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -27,10 +27,15 @@ input:
description: Reference image for registration
pattern: "*.{nii.nii.gz}"

- transform:
- warp:
type: file
description: file or tuple of files, transformation file(s) to warp image or trk (*mat or [nii Warp, mat file]). If a rigid or affine transformation needs to be inverted before being applied, use antsApplyTransforms with the -o Linear[inversedTransform,1], as this module does not handles it.
pattern: "*.{nii,nii.gz,mat}"
description: Warp transformation file to warp image or trk.
pattern: "*.{nii,nii.gz}"

- affine:
type: file
description: Affine or rigig transformation file to warp image or trk (*mat). If a rigid or affine transformation needs to be inverted before being applied, use antsApplyTransforms with the -o Linear[inversedTransform,1], as this module does not handles it.
pattern: "*.mat"

output:
- meta:
Expand Down
40 changes: 36 additions & 4 deletions modules/nf-neuro/registration/antsapplytransforms/tests/main.nf.test
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Expand Up @@ -17,23 +17,27 @@ nextflow_process {
script "../../../../../subworkflows/nf-neuro/load_test_data/main.nf"
process {
"""
input[0] = Channel.from( [ "bst.zip" ] )
input[0] = Channel.from( [ "registration.zip" ] )
input[1] = "test.load-test-data"
"""
}
}
}

test("registration - antsapplytransforms") {

config "./nextflow.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}/fa.nii.gz"),
file("\${test_data_directory}/mask.nii.gz"),
file("\${test_data_directory}/output1InverseWarp.nii.gz")
file("\${test_data_directory}/b0.nii.gz"),
file("\${test_data_directory}/mni_masked_2x2x2.nii.gz"),
file("\${test_data_directory}/output1Warp.nii.gz"),
file("\${test_data_directory}/output0GenericAffine.mat")
]}
"""
}
Expand All @@ -45,4 +49,32 @@ nextflow_process {
)
}
}

test("registration - antsapplytransforms - stub-run") {

options "-stub-run"

config "./nextflow.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}/b0.nii.gz"),
file("\${test_data_directory}/mni_masked_2x2x2.nii.gz"),
file("\${test_data_directory}/output1Warp.nii.gz"),
file("\${test_data_directory}/output0GenericAffine.mat")
]}
"""
}
}
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out.versions).match() }
)
}
}
}
22 changes: 17 additions & 5 deletions modules/nf-neuro/registration/antsapplytransforms/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -8,22 +8,22 @@
"id": "test",
"single_end": false
},
"test__warped.nii.gz:md5,f5df5ab8622bfd2f3ea4c59e3c4f482e"
"test__b0__warped.nii.gz:md5,3ae49aacab66fb2378da92155453b1be"
]
],
"1": [
"versions.yml:md5,f45b96ead53b75f1fc565461836b1475"
"versions.yml:md5,180609e91d7d492cd7db9b09f47f055d"
],
"versions": [
"versions.yml:md5,f45b96ead53b75f1fc565461836b1475"
"versions.yml:md5,180609e91d7d492cd7db9b09f47f055d"
],
"warped_image": [
[
{
"id": "test",
"single_end": false
},
"test__warped.nii.gz:md5,f5df5ab8622bfd2f3ea4c59e3c4f482e"
"test__b0__warped.nii.gz:md5,3ae49aacab66fb2378da92155453b1be"
]
]
}
Expand All @@ -32,6 +32,18 @@
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-10-25T18:07:26.443335534"
"timestamp": "2024-11-28T20:21:53.029255208"
},
"registration - antsapplytransforms - stub-run": {
"content": [
[
"versions.yml:md5,180609e91d7d492cd7db9b09f47f055d"
]
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-11-28T20:21:57.642570655"
}
}
5 changes: 5 additions & 0 deletions modules/nf-neuro/registration/antsapplytransforms/tests/nextflow.config
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Original file line number Diff line number Diff line change
@@ -1,5 +1,10 @@
process {
withName: "REGISTRATION_ANTSAPPLYTRANSFORMS" {
ext.interpolation = "linear"
ext.first_suffix = "b0"
ext.dimensionality = 3
ext.image_type = 0
ext.output_dtype = "float"
ext.default_val = 0
}
}