[WIP] fix testing

scilus · Aug 9, 2024 · 9808e7b · 9808e7b
1 parent d344adb
commit 9808e7b
Show file tree

Hide file tree

Showing 4 changed files with 127 additions and 11 deletions.
diff --git a/subworkflows/nf-scil/preproc_t1/main.nf b/subworkflows/nf-scil/preproc_t1/main.nf
@@ -16,7 +16,7 @@ workflow PREPROC_T1 {
         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)
+        val_synth(false)   // value: (default: false),                    , optional
 
     main:
 
@@ -42,6 +42,10 @@ workflow PREPROC_T1 {
             ch_bet = IMAGE_RESAMPLE.out.image
             BETCROP_SYNTHBET ( ch_bet )
             ch_versions = ch_versions.mix(BETCROP_SYNTHBET.out.versions.first())
+
+            // ** Setting BET output ** //
+            image_bet = BETCROP_SYNTHBET.out.bet_image
+            mask_bet = BETCROP_SYNTHBET.out.brain_mask
         }
 
         else {
@@ -50,24 +54,28 @@ workflow PREPROC_T1 {
             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())
+
+            // ** Setting BET output ** //
+            image_bet = BETCROP_ANTSBET.out.t1
+            mask_bet = BETCROP_ANTSBET.out.mask
         }
 
         // ** crop image ** //
-        ch_crop = BETCROP_ANTSBET.out.t1.map{it + [[]]}
+        ch_crop = image_bet.map{it + [[]]}
         BETCROP_CROPVOLUME_T1 ( ch_crop )
         ch_versions = ch_versions.mix(BETCROP_CROPVOLUME_T1.out.versions.first())
 
         // ** crop mask ** //
-        ch_crop_mask = BETCROP_ANTSBET.out.mask.join(BETCROP_CROPVOLUME_T1.out.bounding_box)
+        ch_crop_mask = mask_bet.join(BETCROP_CROPVOLUME_T1.out.bounding_box)
         BETCROP_CROPVOLUME_MASK ( ch_crop_mask )
         ch_versions = ch_versions.mix(BETCROP_CROPVOLUME_MASK.out.versions.first())
 
     emit:
         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       = ch_bet_out.t1                       // channel: [ val(meta), [ t1 ] ]
-        mask_bet        = ch_bet_out.out.mask                 // channel: [ val(meta), [ mask ] ]
+        image_bet       = image_bet                      // channel: [ val(meta), [ t1 ] ]
+        mask_bet        = mask_bet              // 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 ] ]

diff --git a/subworkflows/nf-scil/preproc_t1/tests/main.nf.test b/subworkflows/nf-scil/preproc_t1/tests/main.nf.test
@@ -70,6 +70,7 @@ nextflow_workflow {
                         [ id:'test', single_end:false ],
                         []
                     ]}
+                input[6] = false
                 """
             }
         }
@@ -124,6 +125,7 @@ nextflow_workflow {
                         [ id:'test', single_end:false ],
                         file("\${test_data_directory}/t1_unaligned.nii.gz")
                     ]}
+                input[6] = false
                 """
             }
         }

diff --git a/subworkflows/nf-scil/preproc_t1/tests/main.nf.test.snap b/subworkflows/nf-scil/preproc_t1/tests/main.nf.test.snap
@@ -165,10 +165,115 @@
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0-rc1",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-05-10T19:57:38.341812"
+        "timestamp": "2024-07-26T18:11:30.464682"
+    },
+    "preproc_t1_synth": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_denoised.nii.gz:md5,b6d25b37b1101fea5c77bbbc711757c3"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test__image_n4.nii.gz:md5,ef0d9af46aa1e330c5d7679ead500596"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test__resampled.nii.gz:md5,88bae6bfeea1734111621b437e09548d"
+                    ]
+                ],
+                "3": [
+
+                ],
+                "4": [
+
+                ],
+                "5": [
+
+                ],
+                "6": [
+
+                ],
+                "7": [
+
+                ],
+                "8": [
+                    "versions.yml:md5,97b6b9457caf964b9f20549672f692f0",
+                    "versions.yml:md5,b979132991d8f72a3585465533bd5730",
+                    "versions.yml:md5,c6563545d67d7ab20ad849adcaafcb71"
+                ],
+                "crop_box": [
+
+                ],
+                "image_N4": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test__image_n4.nii.gz:md5,ef0d9af46aa1e330c5d7679ead500596"
+                    ]
+                ],
+                "image_bet": [
+
+                ],
+                "image_nlmeans": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_denoised.nii.gz:md5,b6d25b37b1101fea5c77bbbc711757c3"
+                    ]
+                ],
+                "image_resample": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test__resampled.nii.gz:md5,88bae6bfeea1734111621b437e09548d"
+                    ]
+                ],
+                "mask_bet": [
+
+                ],
+                "mask_final": [
+
+                ],
+                "t1_final": [
+
+                ],
+                "versions": [
+                    "versions.yml:md5,97b6b9457caf964b9f20549672f692f0",
+                    "versions.yml:md5,b979132991d8f72a3585465533bd5730",
+                    "versions.yml:md5,c6563545d67d7ab20ad849adcaafcb71"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0-rc1",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-26T17:13:02.031243"
     },
     "preproc_t1_classic": {
         "content": [
@@ -336,9 +441,9 @@
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0-rc1",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-05-10T19:36:04.155481"
+        "timestamp": "2024-07-26T17:51:34.909311"
     }
 }
diff --git a/subworkflows/nf-scil/preproc_t1/tests/nextflow_synth.config b/subworkflows/nf-scil/preproc_t1/tests/nextflow_synth.config
@@ -1,6 +1,7 @@
 process {
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
     withName: "IMAGE_RESAMPLE" {
+        ext.voxel_size = 1
         ext.interp = "lin"
     }
     withName: "BETCROP_CROPVOLUME_T1" {