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[ENH] Update reconst modules #33

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[ENH] Update reconst modules #33

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15b72c9
update reconst_fodf module
Manonedde Oct 30, 2024
22d4e10
update reconst_meanfrf module
Manonedde Oct 30, 2024
43d2f89
update test modules fodf
Manonedde Oct 31, 2024
f609d8e
update test modules fodf add version
Manonedde Oct 31, 2024
2746dee
Merge branch 'main' into update_reconst_modules
arnaudbore Nov 2, 2024
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14 changes: 7 additions & 7 deletions modules/nf-neuro/reconst/fodf/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,11 +1,11 @@

process RECONST_FODF {
tag "$meta.id"
label 'process_single'
label 'process_high'

container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://scil.usherbrooke.ca/containers/scilus_2.0.0.sif':
'scilus/scilus:2.0.0' }"
'https://scil.usherbrooke.ca/containers/scilus_2.0.2.sif':
'scilus/scilus:2.0.2' }"

input:
tuple val(meta), path(dwi), path(bval), path(bvec), path(mask), path(fa), path(md), path(wm_frf), path(gm_frf), path(csf_frf)
Expand Down Expand Up @@ -40,7 +40,7 @@ process RECONST_FODF {
def sh_order = task.ext.sh_order ? "--sh_order " + task.ext.sh_order : ""
def sh_basis = task.ext.sh_basis ? "--sh_basis " + task.ext.sh_basis : ""
def set_method = task.ext.method ? task.ext.method : "ssst"
def processes = task.ext.processes ? "--processes " + task.ext.processes : ""
def processes = task.cpus > 1 ? "--processes " + task.cpus : ""
def set_mask = mask ? "--mask $mask" : ""
def relative_threshold = task.ext.relative_threshold ? "--rt " + task.ext.relative_threshold : ""
def fodf_metrics_a_factor = task.ext.fodf_metrics_a_factor ? task.ext.fodf_metrics_a_factor : 2.0
Expand Down Expand Up @@ -122,13 +122,13 @@ process RECONST_FODF {
$set_mask $sh_basis $absolute_peaks \
$peaks $peak_values $peak_indices \
$afd_max $afd_total \
$afd_sum $nufo \
$afd_sum $nufo $processes \
$relative_threshold --not_all --at \${a_threshold}
fi

cat <<-END_VERSIONS > versions.yml
"${task.process}":
scilpy: 2.0.0
scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
END_VERSIONS
"""

Expand Down Expand Up @@ -159,7 +159,7 @@ process RECONST_FODF {

cat <<-END_VERSIONS > versions.yml
"${task.process}":
scilpy: 2.0.0
scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
END_VERSIONS
"""
}
7 changes: 6 additions & 1 deletion modules/nf-neuro/reconst/fodf/meta.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ keywords:
- Local Model
- Reconst
tools:
- "Scilpy":
- "scilpy":
description: "The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox."
homepage: "https://github.com/scilus/scilpy.git"

Expand Down Expand Up @@ -146,6 +146,11 @@ output:
description: Number of Fiber Orientation (NuFO) map.
pattern: "*nufo.nii.gz"

- vent_mask:
type: file
description: Ventricule mask estimated from an MD and FA threshold.
pattern: "*ventricles_mask.nii.gz"

- versions:
type: file
description: File containing software versions
Expand Down
223 changes: 136 additions & 87 deletions modules/nf-neuro/reconst/fodf/tests/main.nf.test
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,16 +13,22 @@ nextflow_process {
tag "subworkflows/load_test_data"

setup {
run("LOAD_TEST_DATA", alias: "LOAD_DATA") {
script "../../../../../subworkflows/nf-neuro/load_test_data/main.nf"
process {
"""
input[0] = Channel.from( [ "processing.zip" , "commit_amico.zip" ] )
input[1] = "test.load-test-data"
"""
}
run("LOAD_TEST_DATA", alias: "LOAD_DATA") {
script "../../../../../subworkflows/nf-neuro/load_test_data/main.nf"
process {
"""
input[0] = Channel.from( [
"DWIss2000-dir60.zip",
"DWIms1000-2000-dir32-60.zip" ,
"segmentation.zip",
"dti.zip",
"responses.zip"
] )
input[1] = "test.load-test-data"
"""
}
}
}

test("reconst - fodf") {

Expand All @@ -33,23 +39,43 @@ nextflow_process {
"""
ch_split_test_data = LOAD_DATA.out.test_data_directory
.branch{
ssst: it.simpleName == "processing"
msmt: it.simpleName == "commit_amico"
ssst: it.simpleName == "DWIss2000-dir60"
segmentation: it.simpleName == "segmentation"
dti: it.simpleName == "dti"
responses: it.simpleName == "responses"
}
input[0] = ch_split_test_data.ssst.map{
ch_dwi = ch_split_test_data.ssst.map{
test_data_directory -> [
[ id:'test', single_end:false ],
[ id:'test' ],
file("\${test_data_directory}/dwi.nii.gz"),
file("\${test_data_directory}/dwi.bval"),
file("\${test_data_directory}/dwi.bvec"),
file("\${test_data_directory}/cc.nii.gz"),
file("\${test_data_directory}/dwi.bvec")
]
}
ch_mask = ch_split_test_data.segmentation.map{
test_data_directory -> [
[ id:'test' ],
file("\${test_data_directory}/brainmask/brainmask.nii.gz")
]
}
ch_metrics = ch_split_test_data.dti.map{
test_data_directory -> [
[ id:'test' ],
file("\${test_data_directory}/fa.nii.gz"),
file("\${test_data_directory}/md.nii.gz"),
file("\${test_data_directory}/frf.txt"),
[],
[]
file("\${test_data_directory}/md.nii.gz")
]
}
ch_response = ch_split_test_data.responses.map{
test_data_directory -> [
[ id:'test' ],
file("\${test_data_directory}/DWIss1000-dir32.txt")
]
}
input[0] = ch_dwi
.join(ch_mask)
.join(ch_metrics)
.join(ch_response)
.map{ it + [[], []] }
"""
}
}
Expand All @@ -72,62 +98,43 @@ nextflow_process {
"""
ch_split_test_data = LOAD_DATA.out.test_data_directory
.branch{
ssst: it.simpleName == "processing"
msmt: it.simpleName == "commit_amico"
msmt: it.simpleName == "DWIms1000-2000-dir32-60"
segmentation: it.simpleName == "segmentation"
dti: it.simpleName == "dti"
responses: it.simpleName == "responses"
}
input[0] = ch_split_test_data.ssst.map{
ch_dwi = ch_split_test_data.msmt.map{
test_data_directory -> [
[ id:'test', single_end:false ],
[ id:'test' ],
file("\${test_data_directory}/dwi.nii.gz"),
file("\${test_data_directory}/dwi.bval"),
file("\${test_data_directory}/dwi.bvec"),
file("\${test_data_directory}/cc.nii.gz"),
file("\${test_data_directory}/fa.nii.gz"),
file("\${test_data_directory}/md.nii.gz"),
file("\${test_data_directory}/frf.txt"),
[],
[]
file("\${test_data_directory}/dwi.bvec")
]
}
"""
}
}

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

}

test("reconst - fodf_no_mask") {

config "./nextflow.config"

when {
process {
"""
ch_split_test_data = LOAD_DATA.out.test_data_directory
.branch{
ssst: it.simpleName == "processing"
msmt: it.simpleName == "commit_amico"
}
input[0] = ch_split_test_data.ssst.map{
ch_mask = ch_split_test_data.segmentation.map{
test_data_directory -> [
[ id:'test', single_end:false ],
file("\${test_data_directory}/dwi.nii.gz"),
file("\${test_data_directory}/dwi.bval"),
file("\${test_data_directory}/dwi.bvec"),
[],
[ id:'test' ],
file("\${test_data_directory}/brainmask/brainmask.nii.gz")
]
}
ch_metrics = ch_split_test_data.dti.map{
test_data_directory -> [
[ id:'test' ],
file("\${test_data_directory}/fa.nii.gz"),
file("\${test_data_directory}/md.nii.gz"),
file("\${test_data_directory}/frf.txt"),
[],
[]
file("\${test_data_directory}/md.nii.gz")
]
}
ch_response = ch_split_test_data.responses.map{
test_data_directory -> [
[ id:'test' ],
file("\${test_data_directory}/DWIss1000-dir32.txt")
]
}
input[0] = ch_dwi
.join(ch_mask)
.join(ch_metrics)
.join(ch_response)
.map{ it + [[], []] }
"""
}
}
Expand All @@ -150,23 +157,43 @@ nextflow_process {
"""
ch_split_test_data = LOAD_DATA.out.test_data_directory
.branch{
ssst: it.simpleName == "processing"
msmt: it.simpleName == "commit_amico"
ssst: it.simpleName == "DWIss2000-dir60"
segmentation: it.simpleName == "segmentation"
dti: it.simpleName == "dti"
responses: it.simpleName == "responses"
}
input[0] = ch_split_test_data.ssst.map{
ch_dwi = ch_split_test_data.ssst.map{
test_data_directory -> [
[ id:'test', single_end:false ],
[ id:'test' ],
file("\${test_data_directory}/dwi.nii.gz"),
file("\${test_data_directory}/dwi.bval"),
file("\${test_data_directory}/dwi.bvec"),
file("\${test_data_directory}/cc.nii.gz"),
file("\${test_data_directory}/dwi.bvec")
]
}
ch_mask = ch_split_test_data.segmentation.map{
test_data_directory -> [
[ id:'test' ],
file("\${test_data_directory}/brainmask/brainmask.nii.gz")
]
}
ch_metrics = ch_split_test_data.dti.map{
test_data_directory -> [
[ id:'test' ],
file("\${test_data_directory}/fa.nii.gz"),
file("\${test_data_directory}/md.nii.gz"),
file("\${test_data_directory}/frf.txt"),
[],
[]
file("\${test_data_directory}/md.nii.gz")
]
}
ch_response = ch_split_test_data.responses.map{
test_data_directory -> [
[ id:'test' ],
file("\${test_data_directory}/DWIss1000-dir32.txt")
]
}
input[0] = ch_dwi
.join(ch_mask)
.join(ch_metrics)
.join(ch_response)
.map{ it + [[], []] }
"""
}
}
Expand All @@ -189,32 +216,52 @@ nextflow_process {
"""
ch_split_test_data = LOAD_DATA.out.test_data_directory
.branch{
ssst: it.simpleName == "processing"
msmt: it.simpleName == "commit_amico"
msmt: it.simpleName == "DWIms1000-2000-dir32-60"
segmentation: it.simpleName == "segmentation"
dti: it.simpleName == "dti"
responses: it.simpleName == "responses"
}
input[0] = ch_split_test_data.msmt.map{
ch_dwi = ch_split_test_data.msmt.map{
test_data_directory -> [
[ id:'test', single_end:false ],
[ id:'test' ],
file("\${test_data_directory}/dwi.nii.gz"),
file("\${test_data_directory}/dwi.bval"),
file("\${test_data_directory}/dwi.bvec"),
file("\${test_data_directory}/mask.nii.gz"),
file("\${test_data_directory}/dwi.bvec")
]
}
ch_mask = ch_split_test_data.segmentation.map{
test_data_directory -> [
[ id:'test' ],
file("\${test_data_directory}/brainmask/brainmask.nii.gz")
]
}
ch_metrics = ch_split_test_data.dti.map{
test_data_directory -> [
[ id:'test' ],
file("\${test_data_directory}/fa.nii.gz"),
file("\${test_data_directory}/md.nii.gz"),
file("\${test_data_directory}/wm_frf.txt"),
file("\${test_data_directory}/gm_frf.txt"),
file("\${test_data_directory}/csf_frf.txt")

file("\${test_data_directory}/md.nii.gz")
]
}
ch_response = ch_split_test_data.responses.map{
test_data_directory -> [
[ id:'test' ],
file("\${test_data_directory}/DWIms1000-2000-dir32-60_wm.txt"),
file("\${test_data_directory}/DWIms1000-2000-dir32-60_gm.txt"),
file("\${test_data_directory}/DWIms1000-2000-dir32-60_csf.txt")
]
}
input[0] = ch_dwi
.join(ch_mask)
.join(ch_metrics)
.join(ch_response)
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(
file(process.out.fodf.get(0).get(1)).name,
file(process.out.wm_fodf.get(0).get(1)).name,
file(process.out.gm_fodf.get(0).get(1)).name,
file(process.out.csf_fodf.get(0).get(1)).name,
Expand All @@ -226,7 +273,9 @@ nextflow_process {
file(process.out.afd_max.get(0).get(1)).name,
file(process.out.afd_total.get(0).get(1)).name,
file(process.out.afd_sum.get(0).get(1)).name,
file(process.out.nufo.get(0).get(1)).name).match() }
file(process.out.nufo.get(0).get(1)).name,
file(process.out.vent_mask.get(0).get(1)).name,
file(process.out.versions.get(0).get(1)).name).match() }
)
}

Expand Down
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