Fix alex comments

scilus · Sep 13, 2024 · bea6c73 · bea6c73
1 parent acda670
commit bea6c73
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Showing 4 changed files with 110 additions and 174 deletions.
diff --git a/subworkflows/nf-scil/registration/main.nf b/subworkflows/nf-scil/registration/main.nf
@@ -2,25 +2,34 @@ include { REGISTRATION_ANATTODWI  } from '../../../modules/nf-scil/registration/
 include { REGISTRATION_ANTS   } from '../../../modules/nf-scil/registration/ants/main'
 include { REGISTRATION_EASYREG } from '../../../modules/nf-scil/registration/easyreg/main'
 
-params.run_surgery = params.run_surgery?: false
+params.run_surgery = false
 
 workflow REGISTRATION {
 
-    // ** The subworkflow requires at least ch_image and ch_ref as inputs to   ** //
+    // ** The subworkflow requires at least ch_image and ch_ref as inputs to ** //
     // ** properly perform the registration. Supplying a ch_metric will select ** //
-    // ** the REGISTRATION_ANATTODWI module meanwhile NOT supplying a ch_metric    ** //
-    // ** will select the REGISTRATION_ANTS (SyN or SyNQuick) module.          ** //
+    // ** the REGISTRATION_ANATTODWI module meanwhile NOT supplying a ch_metric ** //
+    // ** will select the REGISTRATION_ANTS (SyN or SyNQuick) module. Alternatively, ** //
+    // ** NOT supplying ch_metric and activating run_surgery flag with select REGISTRATION_EASYREG ** //
 
     take:
         ch_image                  // channel: [ val(meta), [ image ] ]
         ch_ref                    // channel: [ val(meta), [ ref ] ]
         ch_metric                 // channel: [ val(meta), [ metric ] ], optional
         ch_mask                   // channel: [ val(meta), [ mask ] ], optional
+        ch_segmentation           // channel: [ val(meta), [ flo_segmentation ] ], optional
         ch_ref_segmentation       // channel: [ val(meta), [ ref_segmentation ] ], optional
-        ch_flo_segmentation       // channel: [ val(meta), [ flo_segmentation ] ], optional
+
 
     main:
 
+        image_warped = Channel.empty()
+        ref_warped = Channel.empty()
+        transfo_image = Channel.empty()
+        transfo_trk = Channel.empty()
+        out_segmentation = Channel.empty()
+        out_ref_segmentation = Channel.empty()
+
         ch_versions = Channel.empty()
 
         if ( ch_metric ) {
@@ -34,17 +43,14 @@ 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, by: 0)
-                                .combine(ch_flo_segmentation, by: 0)
+                                .combine(ch_segmentation, by: 0)
 
             // ** Registration using Easyreg ** //
             REGISTRATION_EASYREG ( ch_register )
@@ -53,15 +59,16 @@ workflow REGISTRATION {
             // ** Setting outputs ** //
             image_warped = REGISTRATION_EASYREG.out.flo_reg
             transfo_image = REGISTRATION_EASYREG.out.fwd_field
-                                                    .map{ it + [[]] }
+                .map{ it + [[]] }
             transfo_trk = REGISTRATION_EASYREG.out.bak_field
-                                                    .map{ [[]] + it }
-            ref_warped - REGISTRATON_EASYREG.out.ref_reg
+                .map{ [[]] + it }
+            ref_warped - REGISTRATION_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()
+            out_segmentation = ch_segmentation ? Channel.empty() : REGISTRATION_EASYREG.out.flo_seg
+            out_ref_segmentation = ch_ref_segmentation ? Channel.empty() : REGISTRATION_EASYREG.out.ref_seg
+
 
         }
         else {
@@ -83,20 +90,18 @@ 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 ] ]
+        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 ] ]
+        segmentation = out_segmentation            // channel: [ val(meta), [ segmentation ] ]
+        ref_segmentation = out_ref_segmentation    // channel: [ val(meta), [ ref_segmentation ] ]
+
 
         versions = ch_versions                 // channel: [ versions.yml ]
 }
diff --git a/subworkflows/nf-scil/registration/meta.yml b/subworkflows/nf-scil/registration/meta.yml
@@ -53,21 +53,22 @@ input:
         REGISTRATION_ANTS, see the description section above for more details.
         Structure: [ val(meta), path(mask) ]
       pattern: "*.{nii,nii.gz}"
-  - ch_ref_segmentation:
+  - ch_segmentation:
       type: file
       description: |
-        The input channel containing the the SynthSeg v2 (non-robust) segmentation + parcellation of the reference image.
+        The input channel containing the the SynthSeg v2 (non-robust) segmentation + parcellation of the moving (floating in Easyreg naming convention) image.
         If it des 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}"
-  - ch_flo_segmentation:
+  - ch_ref_segmentation:
       type: file
       description: |
-        The input channel containing the the SynthSeg v2 (non-robust) segmentation + parcellation of the floating image.
+        The input channel containing the the SynthSeg v2 (non-robust) segmentation + parcellation of the fixed (reference in Easyreg naming convention) image.
         If it des 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:
   - image_warped:
       type: file
@@ -97,15 +98,15 @@ 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:
+  - out_segmentation:
       type: file
       description: |
-        Channel containing the file with the SynthSeg v2 (non-robust) segmentation + parcellation of the reference image.
+        Channel containing the file with the SynthSeg v2 (non-robust) segmentation + parcellation of the moving (floating in Easyreg naming convention) image.
       pattern: "*.{nii,nii.gz}"
-  - flo_segmentation:
+  - out_ref_segmentation:
       type: file
       description: |
-        Channel containing the file with the SynthSeg v2 (non-robust) segmentation + parcellation of the floating image.
+        Channel containing the file with the SynthSeg v2 (non-robust) segmentation + parcellation of the fixed (reference in Easyreg naming convention) image.
       pattern: "*.{nii,nii.gz}"
   - versions:
       type: file

diff --git a/subworkflows/nf-scil/registration/tests/main.nf.test b/subworkflows/nf-scil/registration/tests/main.nf.test
@@ -58,7 +58,12 @@ nextflow_workflow {
         then {
             assertAll(
                 { assert workflow.success},
-                { assert snapshot(workflow.out).match()}
+                { assert snapshot(
+                    niftiMD5SUM(workflow.out.image_warped.get(0).get(1)),
+                    workflow.out.transfo_image,
+                    workflow.out.transfo_trk,
+                    workflow.out.versions
+                ).match()}
             )
         }
     }
@@ -89,7 +94,12 @@ nextflow_workflow {
         then {
             assertAll(
                 { assert workflow.success},
-                { assert snapshot(workflow.out).match()}
+                { assert snapshot(
+                    niftiMD5SUM(workflow.out.image_warped.get(0).get(1)),
+                    workflow.out.transfo_image,
+                    workflow.out.transfo_trk,
+                    workflow.out.versions
+                ).match()}
             )
         }
     }
@@ -120,7 +130,15 @@ nextflow_workflow {
         then {
             assertAll(
                 { assert workflow.success},
-                { assert snapshot(workflow.out).match()}
+                { assert snapshot(
+                    niftiMD5SUM(workflow.out.image_warped.get(0).get(1)),
+                    niftiMD5SUM(workflow.out.ref_warped.get(0).get(1)),
+                    workflow.out.transfo_image,
+                    workflow.out.transfo_trk,
+                    niftiMD5SUM(workflow.out.segmentation.get(0).get(1)),
+                    niftiMD5SUM(workflow.out.ref_segmentation.get(0).get(1)),
+                    workflow.out.versions
+                ).match()}
             )
         }
     }