main dev, add test and meta

scilus · Sep 12, 2024 · acda670 · acda670
1 parent 9546061
commit acda670
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Showing 4 changed files with 37 additions and 2 deletions.
diff --git a/subworkflows/nf-scil/registration/main.nf b/subworkflows/nf-scil/registration/main.nf
@@ -34,14 +34,17 @@ workflow REGISTRATION {
 
             // ** Setting outputs ** //
             image_warped = REGISTRATION_ANATTODWI.out.t1_warped
+            ref_warped = Channel.empty()
             transfo_image = REGISTRATION_ANATTODWI.out.transfo_image
             transfo_trk = REGISTRATION_ANATTODWI.out.transfo_trk
+            ref_segmentation = Channel.empty()
+            image_segmentation = Channel.empty()
         }
         else if ( params.run_surgery ) {
             // ** Set up input channel ** //
             ch_register = ch_ref.combine(ch_image, by: 0)
-                                .combine(ch_ref_segmentation)
-                                .combine(ch_flo_segmentation)
+                                .combine(ch_ref_segmentation, by: 0)
+                                .combine(ch_flo_segmentation, by: 0)
 
             // ** Registration using Easyreg ** //
             REGISTRATION_EASYREG ( ch_register )
@@ -50,7 +53,15 @@ workflow REGISTRATION {
             // ** Setting outputs ** //
             image_warped = REGISTRATION_EASYREG.out.flo_reg
             transfo_image = REGISTRATION_EASYREG.out.fwd_field
+                                                    .map{ it + [[]] }
             transfo_trk = REGISTRATION_EASYREG.out.bak_field
+                                                    .map{ [[]] + it }
+            ref_warped - REGISTRATON_EASYREG.out.ref_reg
+
+            // ** Setting optional outputs. If segmentations are not provided as inputs, ** //
+            // ** easyreg will outputs synthseg segmentations ** //
+            ref_segmentation = ch_ref_segmentation ? REGISTRATION_EASYREG.out.ref_seg : Channel.empty()
+            flo_segmentation = ch_ref_segmentation ? REGISTRATION_EASYREG.out.flo_seg : Channel.empty()
 
         }
         else {
@@ -72,14 +83,20 @@ workflow REGISTRATION {
 
             // ** Setting outputs ** //
             image_warped = REGISTRATION_ANTS.out.image
+            ref_warped = Channel.empty()
             transfo_image = REGISTRATION_ANTS.out.transfo_image
             transfo_trk = REGISTRATION_ANTS.out.transfo_trk
+            ref_segmentation = Channel.empty()
+            flo_segmentation = Channel.empty()
         }
 
     emit:
         image_warped  = image_warped           // channel: [ val(meta), [ image ] ]
+        ref_warped = ref_warped                // channel: [ val(meta), [ ref ] ]
         transfo_image = transfo_image          // channel: [ val(meta), [ warp, affine ] ]
         transfo_trk   = transfo_trk            // channel: [ val(meta), [ inverseAffine, inverseWarp ] ]
+        ref_segmentation = ref_segmentation    // channel: [ val(meta), [ ref_seg ] ]
+        flo_segmentation = flo_segmentation    // channel: [ val(meta), [ flo_seg ] ]
 
         versions = ch_versions                 // channel: [ versions.yml ]
 }
diff --git a/subworkflows/nf-scil/registration/meta.yml b/subworkflows/nf-scil/registration/meta.yml
@@ -75,6 +75,12 @@ output:
         Channel containing warped moving images. Typically, this would be the warped T1 in DWI space.
         Structure: [ val(meta), path(image) ]
       pattern: "*.{nii,nii.gz}"
+  - ref_warped:
+      type: file
+      description: |
+        Channel containing warped reference images. Typically, this would be the warped T1 in DWI space.
+        Structure: [ val(meta), path(image) ]
+      pattern: "*.{nii,nii.gz}"
   - transfo_image:
       type: file
       description: |
@@ -91,6 +97,16 @@ output:
         be used to register tractograms or bundle in the subject's anatomical space.
         Structure: [ val(meta), [ path(inverseAffine), path(inverseWarp) ]
       pattern: "*.{nii,nii.gz,mat}"
+  - ref_segmentation:
+      type: file
+      description: |
+        Channel containing the file with the SynthSeg v2 (non-robust) segmentation + parcellation of the reference image.
+      pattern: "*.{nii,nii.gz}"
+  - flo_segmentation:
+      type: file
+      description: |
+        Channel containing the file with the SynthSeg v2 (non-robust) segmentation + parcellation of the floating image.
+      pattern: "*.{nii,nii.gz}"
   - versions:
       type: file
       description: |

diff --git a/subworkflows/nf-scil/registration/tests/main.nf.test b/subworkflows/nf-scil/registration/tests/main.nf.test
@@ -12,6 +12,7 @@ nextflow_workflow {
     tag "registration/anattodwi"
     tag "registration"
     tag "registration/ants"
+    tag "registration/easyreg"
 
     tag "load_test_data"
 

diff --git a/subworkflows/nf-scil/registration/tests/nextflow_surgery.config b/subworkflows/nf-scil/registration/tests/nextflow_surgery.config
@@ -1,6 +1,7 @@
 process {
     withName: "REGISTRATION_EASYREG" {
         publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+        ext.field = true
     }
 }