[WIP] Initial module commit

scilus · Aug 9, 2024 · ac5b6a5 · ac5b6a5
1 parent 719ea69
commit ac5b6a5
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Showing 3 changed files with 84 additions and 8 deletions.
diff --git a/subworkflows/nf-scil/preproc_t1/main.nf b/subworkflows/nf-scil/preproc_t1/main.nf
@@ -3,18 +3,20 @@ include { DENOISING_NLMEANS } from '../../../modules/nf-scil/denoising/nlmeans/m
 include { PREPROC_N4 } from '../../../modules/nf-scil/preproc/n4/main'
 include { IMAGE_RESAMPLE } from '../../../modules/nf-scil/image/resample/main'
 include { BETCROP_ANTSBET } from '../../../modules/nf-scil/betcrop/antsbet/main'
+include { BETCROP_SYNTHBET} from '../../../modules/nf-scil/betcrop/synthbet/main'
 include { BETCROP_CROPVOLUME as BETCROP_CROPVOLUME_T1 } from '../../../modules/nf-scil/betcrop/cropvolume/main'
 include { BETCROP_CROPVOLUME as BETCROP_CROPVOLUME_MASK } from '../../../modules/nf-scil/betcrop/cropvolume/main'
 
 workflow PREPROC_T1 {
 
     take:
         ch_image           // channel: [ val(meta), [ image ] ]
-        ch_template        // channel: [ val(meta), [ template ] ]
-        ch_probability_map // channel: [ val(meta), [ probability_map ] ]
+        ch_template        // channel: [ val(meta), [ template ] ]        , optional
+        ch_probability_map // channel: [ val(meta), [ probability_map ] ] , optional
         ch_mask_nlmeans    // channel: [ val(meta), [ mask ] ]            , optional
         ch_ref_n4          // channel: [ val(meta), [ ref, ref_mask ] ]   , optional
         ch_ref_resample    // channel: [ val(meta), [ ref ] ]             , optional
+        val_synth(false)   // value: (default: false)
 
     main:
 
@@ -36,9 +38,17 @@ workflow PREPROC_T1 {
         ch_versions = ch_versions.mix(IMAGE_RESAMPLE.out.versions.first())
 
         // ** Brain extraction ** //
-        ch_bet = IMAGE_RESAMPLE.out.image.join(ch_template).join(ch_probability_map)
-        BETCROP_ANTSBET ( ch_bet )
-        ch_versions = ch_versions.mix(BETCROP_ANTSBET.out.versions.first())
+        if ( val_synth ) {
+            ch_bet = IMAGE_RESAMPLE.out.image.join(ch_fs_license)
+            BETCROP_SYNTHBET ( ch_bet )
+            ch_versions = ch_versions.mix(BETCROP_SYNTHBET.out.versions.first())
+        }
+
+        else {
+            ch_bet = IMAGE_RESAMPLE.out.image.join(ch_template).join(ch_probability_map)
+            BETCROP_ANTSBET ( ch_bet )
+            ch_versions = ch_versions.mix(BETCROP_ANTSBET.out.versions.first())
+        }
 
         // ** crop image ** //
         ch_crop = BETCROP_ANTSBET.out.t1.map{it + [[]]}
@@ -54,10 +64,10 @@ workflow PREPROC_T1 {
         image_nlmeans   = DENOISING_NLMEANS.out.image         // channel: [ val(meta), [ image ] ]
         image_N4        = PREPROC_N4.out.image                // channel: [ val(meta), [ image ] ]
         image_resample  = IMAGE_RESAMPLE.out.image            // channel: [ val(meta), [ image ] ]
-        image_bet       = BETCROP_ANTSBET.out.t1              // channel: [ val(meta), [ t1 ] ]
-        mask_bet        = BETCROP_ANTSBET.out.mask            // channel: [ val(meta), [ mask ] ]
+        image_bet       = ch_bet_out.t1                       // channel: [ val(meta), [ t1 ] ]
+        mask_bet        = ch_bet_out.out.mask                 // channel: [ val(meta), [ mask ] ]
         crop_box        = BETCROP_CROPVOLUME_T1.out.bounding_box // channel: [ val(meta), [ bounding_box ] ]
         mask_final      = BETCROP_CROPVOLUME_MASK.out.image   // channel: [ val(meta), [ mask ] ]
-        t1_final        = BETCROP_CROPVOLUME_T1.out.image        // channel: [ val(meta), [ image ] ]
+        t1_final        = BETCROP_CROPVOLUME_T1.out.image     // channel: [ val(meta), [ image ] ]
         versions        = ch_versions                         // channel: [ versions.yml ]
 }
diff --git a/subworkflows/nf-scil/preproc_t1/tests/main.nf.test b/subworkflows/nf-scil/preproc_t1/tests/main.nf.test
@@ -12,6 +12,7 @@ nextflow_workflow {
     tag "preproc/n4"
     tag "image/resample"
     tag "betcrop/antsbet"
+    tag "betcrop/synthbet"
     tag "betcrop/cropvolume"
 
     tag "load_test_data"
@@ -127,6 +128,61 @@ nextflow_workflow {
             }
         }
 
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(workflow.out).match()}
+            )
+        }
+    }
+
+test("preproc_t1_synth") {
+        config "./nextflow_synth.config"
+
+        when {
+            workflow {
+                """
+                ch_split_test_data = LOAD_DATA.out.test_data_directory
+                    .branch{
+                        antsbet: it.simpleName == "antsbet"
+                        others: it.simpleName == "others"
+                    }
+                input[0] = ch_split_test_data.antsbet.map{
+                    test_data_directory -> [
+                        [ id:'test', single_end:false ],
+                        file("\${test_data_directory}/t1_unaligned.nii.gz")
+                    ]}
+                input[1] = ch_split_test_data.antsbet.map{
+                    test_data_directory -> [
+                        [ id:'test', single_end:false ],
+                        []
+                    ]}
+                input[2] = ch_split_test_data.antsbet.map{
+                    test_data_directory -> [
+                        [ id:'test', single_end:false ],
+                        []
+                    ]}
+                input[3] = ch_split_test_data.antsbet.map{
+                    test_data_directory -> [
+                        [ id:'test', single_end:false ],
+                        []
+                    ]}
+                input[4] = ch_split_test_data.others.map{
+                    test_data_directory -> [
+                        [ id:'test', single_end:false ],
+                        [],
+                        []
+                    ]}
+                input[5] = ch_split_test_data.antsbet.map{
+                    test_data_directory -> [
+                        [ id:'test', single_end:false ],
+                        []
+                    ]}
+                input[6] = true
+                """
+            }
+        }
+
         then {
             assertAll(
                 { assert workflow.success},

diff --git a/subworkflows/nf-scil/preproc_t1/tests/nextflow_synth.config b/subworkflows/nf-scil/preproc_t1/tests/nextflow_synth.config
@@ -0,0 +1,10 @@
+process {
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    withName: "IMAGE_RESAMPLE" {
+        ext.interp = "lin"
+    }
+    withName: "BETCROP_CROPVOLUME_T1" {
+        ext.output_bbox = true
+        ext.first_suffix = "t1"
+    }
+}