Merge pull request #149 from ThoumyreStanislas/correction_registratio…

…n_tractogram

[MODULE] Migrate tests registraction tractogram

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

@@ -0,0 +1,7 @@
+---
+name: "registration_tractogram"
+channels:
+  - Docker
+  - Apptainer
+dependencies:
+  - "Scilpy"

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

@@ -3,11 +3,11 @@ process REGISTRATION_TRACTOGRAM {
     label 'process_single'
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'scil.usherbrooke.ca/containers/scilus_1.6.0.sif':
-        'scilus/scilus:1.6.0' }"
+        'https://scil.usherbrooke.ca/containers/scilus_2.0.2.sif':
+        'scilus/scilus:2.0.2' }"
 
     input:
-    tuple val(meta), path(anat), path(transfo), path(tractograms_dir, stageAs: 'tractograms/'), path(ref) /* optional, value = [] */, path(deformation) /* optional, value = [] */
+    tuple val(meta), path(anat), path(transfo), path(tractogram), path(ref) /* optional, value = [] */, path(deformation) /* optional, value = [] */
 
     output:
     tuple val(meta), path("*__*.{trk,tck}"), emit: warped_tractogram
@@ -18,6 +18,7 @@ process REGISTRATION_TRACTOGRAM {
 
     script:
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def suffix = task.ext.suffix ? "_${task.ext.suffix}" : ""
     def reference = "$ref" ? "--reference $ref" : ""
     def in_deformation = "$deformation" ? "--in_deformation $deformation" : ""
 
@@ -32,20 +33,19 @@ process REGISTRATION_TRACTOGRAM {
     def no_empty = task.ext.no_empty ? "--no_empty" : ""
 
     """
-    for tractogram in ${tractograms_dir};
+    for tractogram in ${tractogram};
         do \
-        bname=\${tractogram/${prefix}_/_}
         ext=\${tractogram#*.}
-        bname=\$(basename \${bname} .\${ext})
+        bname=\$(basename \${tractogram} .\${ext})
 
-        scil_apply_transform_to_tractogram.py \$tractogram $anat $transfo tmp.trk\
+        scil_tractogram_apply_transform.py \$tractogram $anat $transfo tmp.trk\
                         $in_deformation\
                         $inverse\
                         $reverse_operation\
                         $force\
                         $reference
 
-        scil_remove_invalid_streamlines.py tmp.trk ${prefix}__\${bname}.\${ext}\
+        scil_tractogram_remove_invalid.py tmp.trk ${prefix}__\${bname}${suffix}.\${ext}\
                         $cut_invalid\
                         $remove_single_point\
                         $remove_overlapping_points\
@@ -54,30 +54,32 @@ process REGISTRATION_TRACTOGRAM {
                         -f
     done
 
+
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        scilpy: 1.6.0
+        scilpy: 2.0.2
     END_VERSIONS
     """
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def suffix = task.ext.suffix ? "_${task.ext.suffix}" : ""
     """
-    for tractogram in ${tractograms_dir};
+    scil_tractogram_apply_transform.py -h
+    scil_tractogram_remove_invalid.py -h
+
+    for tractogram in ${tractogram};
         do \
-        bname=\${tractogram/${prefix}_/_}
         ext=\${tractogram#*.}
-        bname=\$(basename \${bname} .\${ext})
+        bname=\$(basename \${tractogram} .\${ext})
 
-        touch ${prefix}__\${bname}.\${ext}
+        touch ${prefix}__\${bname}${suffix}.\${ext}
     done
 
-    scil_apply_transform_to_tractogram.py -h
-    scil_remove_invalid_streamlines.py -h
-
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        scilpy: 1.6.0
+        scilpy: 2.0.2
     END_VERSIONS
     """
 }

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

@@ -28,11 +28,21 @@ input:
       description: ANTs affine transform
       pattern: "*.mat"
 
-  - tractograms_dir:
-      type: directory
-      description: Path to directory containing tractograms to register
+  - tractogram:
+      type: file
+      description: Tractogram or list of tractograms to register
       pattern: "*.{trk,tck}"
 
+  - ref:
+      type: file
+      description: Reference anatomy for tck/vtk/fib/dpy file support (.nii or .nii.gz) (optional)
+      pattern: "*.{tck,vtk,fib,dpy}"
+
+  - deformation:
+      type: file
+      description: Path to the file containing a deformation field (optional)
+      pattern: "*.{nii,nii.gz}"
+
 output:
   - meta:
       type: map

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

@@ -0,0 +1,88 @@
+
+nextflow_process {
+
+    name "Test Process REGISTRATION_TRACTOGRAM"
+    script "../main.nf"
+    process "REGISTRATION_TRACTOGRAM"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "registration"
+    tag "registration/tractogram"
+
+    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( [ "bundles.zip" ] )
+                input[1] = "test.load-test-data"
+                """
+            }
+        }
+    }
+
+
+    test("registration - tractogram_bundles") {
+
+
+        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}/bundle_all_1mm.nii.gz", checkIfExists: true),
+                        file("\${test_data_directory}/affine.txt", checkIfExists: true),
+                        file("\${test_data_directory}/fibercup_atlas/subj_1/*.trk", checkIfExists: true),
+                        [],
+                        []
+                    ]
+                }
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("registration - tractogram") {
+
+        config "./nextflow_suffix.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}/bundle_all_1mm.nii.gz", checkIfExists: true),
+                        file("\${test_data_directory}/affine.txt", checkIfExists: true),
+                        file("\${test_data_directory}/fibercup_atlas/subj_1/bundle_2.trk", checkIfExists: true),
+                        [],
+                        []
+                    ]
+                }
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+}

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

@@ -0,0 +1,88 @@
+{
+    "registration - tractogram_bundles": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test__bundle_0.trk:md5,6e14cc02b66d12d5dde0a0701918385a",
+                            "test__bundle_1.trk:md5,ef5a759144ab7e8d2f5abf30a463a152",
+                            "test__bundle_2.trk:md5,824bcbf796cbce3e1c93e39d1c98dcf9",
+                            "test__bundle_3.trk:md5,8877161b9aebaa6b12a4d7a8f8410407",
+                            "test__bundle_4.trk:md5,6c8658b946154896952ca89e88fcf29f",
+                            "test__bundle_5.trk:md5,fa058f93d9bfe4bed2ff027e9acd5682",
+                            "test__bundle_6.trk:md5,125e50561b4b0c5fd8ee23867c28bc51"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,609469c08e60062eed7528276deddf5e"
+                ],
+                "versions": [
+                    "versions.yml:md5,609469c08e60062eed7528276deddf5e"
+                ],
+                "warped_tractogram": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test__bundle_0.trk:md5,6e14cc02b66d12d5dde0a0701918385a",
+                            "test__bundle_1.trk:md5,ef5a759144ab7e8d2f5abf30a463a152",
+                            "test__bundle_2.trk:md5,824bcbf796cbce3e1c93e39d1c98dcf9",
+                            "test__bundle_3.trk:md5,8877161b9aebaa6b12a4d7a8f8410407",
+                            "test__bundle_4.trk:md5,6c8658b946154896952ca89e88fcf29f",
+                            "test__bundle_5.trk:md5,fa058f93d9bfe4bed2ff027e9acd5682",
+                            "test__bundle_6.trk:md5,125e50561b4b0c5fd8ee23867c28bc51"
+                        ]
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-15T19:11:42.198039"
+    },
+    "registration - tractogram": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test__bundle_2_mni.trk:md5,824bcbf796cbce3e1c93e39d1c98dcf9"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,609469c08e60062eed7528276deddf5e"
+                ],
+                "versions": [
+                    "versions.yml:md5,609469c08e60062eed7528276deddf5e"
+                ],
+                "warped_tractogram": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test__bundle_2_mni.trk:md5,824bcbf796cbce3e1c93e39d1c98dcf9"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-15T19:11:52.03634"
+    }
+}

modules/nf-scil/registration/tractogram/tests/nextflow_suffix.config

@@ -0,0 +1,14 @@
+process {
+    withName: "REGISTRATION_TRACTOGRAM" {
+        publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+        ext.inverse = true
+        ext.force = true
+        ext.reverse_operation = true
+        ext.cut_invalid = true
+        ext.remove_single_point = true
+        ext.remove_overlapping_points = true
+        ext.threshold = 0.001
+        ext.no_empty = true
+        ext.suffix = 'mni'
+    }
+}

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

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