Merge pull request #173 from ThoumyreStanislas/module_easy_reg

[Module][WIP]Module easyreg

.github/workflows/checks.yml

@@ -139,13 +139,13 @@ jobs:
       fail-fast: false
       matrix:
         path: [ "${{ fromJson(needs.nf-test-changes.outputs.paths) }}" ]
-        profile: [ "docker" ]
-        exclude:
-          - path: subworkflows/nf-scil/load_test_data
         include:
+          - profile: docker
           - runner: scilus-nf-scil-runners
           - runner: scilus-nf-scil-bigmem-runners
             path: modules/nf-scil/registration/easyreg
+        exclude:
+          - path: subworkflows/nf-scil/load_test_data
     uses: ./.github/workflows/nf-test_module.yml
     with:
       profile: ${{ matrix.profile }}

modules/nf-scil/registration/easyreg/environment.yml

@@ -0,0 +1,6 @@
+name: "registration_easyreg"
+channels:
+  - Docker
+  - Apptainer
+dependencies:
+  - "Freesurfer"

modules/nf-scil/registration/easyreg/main.nf

@@ -0,0 +1,82 @@
+
+
+process REGISTRATION_EASYREG {
+    tag "$meta.id"
+    label 'process_single'
+    label 'process_high'
+
+    container "freesurfer/freesurfer:7.4.1"
+
+    input:
+    tuple val(meta), path(reference), path(floating), path(ref_segmentation), path(flo_segmentation)
+
+    output:
+    tuple val(meta), path("*_reference_segmentation.nii.gz") , emit: ref_seg
+    tuple val(meta), path("*_floating_segmentation.nii.gz")  , emit: flo_seg
+    tuple val(meta), path("*_reference_registered.nii.gz")   , emit: ref_reg
+    tuple val(meta), path("*_floating_registered.nii.gz")    , emit: flo_reg
+    tuple val(meta), path("*_forward_field.nii.gz")          , emit: fwd_field, optional: true
+    tuple val(meta), path("*_backward_field.nii.gz")         , emit: bak_field, optional: true
+    path "versions.yml"                                      , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def field = task.ext.field ? "--fwd_field ${prefix}_forward_field.nii.gz --bak_field ${prefix}_backward_field.nii.gz " : ""
+    def threads = task.ext.threads ? "--threads " + task.ext.threads : ""
+    def affine = task.ext.affine ? "--affine_only " : ""
+
+    """
+    export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1
+    export OMP_NUM_THREADS=1
+    export OPENBLAS_NUM_THREADS=1
+
+    if [[ -f "$ref_segmentation" ]];
+    then
+        reference_segmentation=$ref_segmentation
+    else
+        reference_segmentation="${prefix}_reference_segmentation.nii.gz"
+    fi
+
+    if [[ -f "$flo_segmentation" ]];
+    then
+        floating_segmentation=$flo_segmentation
+    else
+        floating_segmentation="${prefix}_floating_segmentation.nii.gz"
+    fi
+
+    mri_easyreg \
+        --ref $reference --flo $floating \
+        --ref_seg \${reference_segmentation} \
+        --flo_seg \${floating_segmentation} \
+        --flo_reg ${prefix}_floating_registered.nii.gz \
+        --ref_reg ${prefix}_reference_registered.nii.gz \
+        $field $threads $affine
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        freesurfer: 7.4.1
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    mri_easyreg -h
+
+    touch ${prefix}_reference_segmentation.nii.gz
+    touch ${prefix}_floating_segmentation.nii.gz
+    touch ${prefix}_reference_registered.nii.gz
+    touch ${prefix}_floating_registered.nii.gz
+    touch ${prefix}_forward_field.nii.gz
+    touch ${prefix}_backward_field.nii.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        freesurfer: 7.4.1
+    END_VERSIONS
+    """
+}

modules/nf-scil/registration/easyreg/meta.yml

@@ -0,0 +1,91 @@
+---
+name: "registration_easyreg"
+description: Image registration and SynthSeg v2 segmentation with easyreg from freesurfer
+keywords:
+  - nifti
+  - registration
+  - segmentation
+  - easyreg
+  - freesurfer
+tools:
+  - "Freesurfer":
+      description: "Software package for the analysis and visualization of structural and functional neuroimaging data."
+      homepage: "https://surfer.nmr.mgh.harvard.edu/fswiki"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1', single_end:false ]`
+
+  - reference:
+      type: file
+      description: the reference image in .nii(.gz) or .mgz format (note that, since the method is symmetric, the choice of reference vs floating is arbitrary).
+      pattern: "*.{nii,nii.gz,mgz}"
+
+  - floating:
+      type: file
+      description: the floating image in .nii(.gz) or .mgz format.
+      pattern: "*.{nii,nii.gz,mgz}"
+
+  - ref_segmentation:
+      type: file
+      description: file with the SynthSeg v2 (non-robust) segmentation + parcellation of the reference image.
+        If it does not exist, EasyReg will create it. If it already exists (e.g., from a previous EasyReg run), then EasyReg will read it from disk (which is faster than segmenting).
+      pattern: "*.{nii,nii.gz}"
+
+  - flo_segmentation:
+      type: file
+      description: file with the SynthSeg v2 (non-robust) segmentation + parcellation of the floating image.
+        If it does not exist, EasyReg will create it. If it already exists (e.g., from a previous EasyReg run), then EasyReg will read it from disk (which is faster than segmenting).
+      pattern: "*.{nii,nii.gz}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1', single_end:false ]`
+
+  - ref_seg:
+      type: file
+      description: file with the SynthSeg v2 (non-robust) segmentation + parcellation of the reference image.
+      pattern: "*_reference_segmentation.nii.gz"
+
+  - flo_seg:
+      type: file
+      description: file with the SynthSeg v2 (non-robust) segmentation + parcellation of the floating image.
+      pattern: "*_floating_segmentation.nii.gz"
+
+  - ref_reg:
+      type: file
+      description: this is the file where the deformed (registered) reference image is written.
+      pattern: "*_reference_registered.nii.gz"
+
+  - flo_reg:
+      type: file
+      description: this is the file where the deformed (registered) floating image is written.
+      pattern: "*_floating_registered.nii.gz"
+
+  - fwd_field:
+      type: file
+      description:
+        this is the file where the forward deformation field is written. The deformation includes both the affine and nonlinear components.
+        Must be a nifti (.nii/.nii.gz) or .mgz file; it is encoded as the real world (RAS) coordinates of the target location for each voxel.
+      pattern: "*_forward_field.nii.gz"
+
+  - bak_field:
+      type: file
+      description: this is the file where the backward deformation field is written. It must also be a nifty or mgz file.
+      pattern: "*_backward_field.nii.gz"
+
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@ThoumyreStanislas"
+maintainers:
+  - "@ThoumyreStanislas"

modules/nf-scil/registration/easyreg/tests/main.nf.test

@@ -0,0 +1,72 @@
+nextflow_process {
+
+    name "Test Process REGISTRATION_EASYREG"
+    script "../main.nf"
+    process "REGISTRATION_EASYREG"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "registration"
+    tag "registration/easyreg"
+
+    tag "subworkflows"
+    tag "subworkflows/load_test_data"
+
+
+    setup {
+            run("LOAD_TEST_DATA", alias: "LOAD_DATA") {
+                script "../../../../../subworkflows/nf-scil/load_test_data/main.nf"
+                process {
+                    """
+                    input[0] = Channel.from( [ "freesurfer.zip", "registration.zip" ] )
+                    input[1] = "test.load-test-data"
+                    """
+                }
+            }
+        }
+
+    test("registration - easyreg") {
+        config "./nextflow.config"
+        when {
+            process {
+                """
+                ch_split_test_data = LOAD_DATA.out.test_data_directory
+                    .branch{
+                        t1: it.simpleName == "freesurfer"
+                        b0: it.simpleName == "registration"
+                    }
+                ch_t1 = ch_split_test_data.t1.map{
+                    test_data_directory -> [
+                        [ id:'test' ],
+                        file("\${test_data_directory}/t1.nii.gz")
+                    ]
+                }
+                ch_b0 = ch_split_test_data.b0.map{
+                    test_data_directory -> [
+                        [ id:'test' ],
+                        file("\${test_data_directory}/b0.nii.gz"),
+                        [],
+                        []
+                    ]
+                }
+                input[0] = ch_t1
+                    .join(ch_b0)
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.ref_seg.get(0).get(1)).name,
+                    file(process.out.flo_seg.get(0).get(1)).name,
+                    niftiMD5SUM(process.out.ref_reg.get(0).get(1), 6),
+                    niftiMD5SUM(process.out.flo_reg.get(0).get(1), 6),
+                    niftiMD5SUM(process.out.fwd_field.get(0).get(1), 6),
+                    niftiMD5SUM(process.out.bak_field.get(0).get(1), 6),
+                    process.out.versions
+                ).match() }
+            )
+        }
+    }
+}

modules/nf-scil/registration/easyreg/tests/main.nf.test.snap

@@ -0,0 +1,20 @@
+{
+    "registration - easyreg": {
+        "content": [
+            "test_reference_segmentation.nii.gz",
+            "test_floating_segmentation.nii.gz",
+            "test_reference_registered.nii.gz:md5:header,c5e41f89848f91c53a9a7be44970d4b1,data,1501221fe23cd62bfdafb33367cadf4d",
+            "test_floating_registered.nii.gz:md5:header,ec5893cd9ea024e630c4444bd914c331,data,d75ae3fc935cd5cc70ea6797a4c70775",
+            "test_forward_field.nii.gz:md5:header,0db0a80786ff39864cc17506ed1a0146,data,e4fa6c626729cbf236c34680e5c76df4",
+            "test_backward_field.nii.gz:md5:header,74c92ee4cd3c4abfecf3da6cdb1d4650,data,8f26afa5c3de21469466213498542486",
+            [
+                "versions.yml:md5,4661210880c42a986923e8257f64c760"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0-rc1",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-12T16:01:24.00559"
+    }
+}

modules/nf-scil/registration/easyreg/tests/nextflow.config

@@ -0,0 +1,9 @@
+process {
+    memory = '10G'
+    withName: "REGISTRATION_EASYREG" {
+        publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+        ext.field = true
+        ext.affine = true
+        ext.threads = 1
+    }
+}

modules/nf-scil/registration/easyreg/tests/tags.yml

@@ -0,0 +1,2 @@
+registration/easyreg:
+  - "modules/nf-scil/registration/easyreg/**"