[WIP] modify module and test to manage freesurfer license

scilus · Mar 7, 2024 · fe3ce46 · fe3ce46
1 parent f2ab543
commit fe3ce46
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Showing 6 changed files with 38 additions and 22 deletions.
diff --git a/.test_data/heavy/freesurfer/license.txt b/.test_data/heavy/freesurfer/license.txt
diff --git a/modules/nf-scil/registration/synthregistration/main.nf b/modules/nf-scil/registration/synthregistration/main.nf
@@ -5,7 +5,7 @@ process REGISTRATION_SYNTHREGISTRATION {
     container "freesurfer/synthmorph:latest"
 
     input:
-    tuple val(meta), path(moving), path(fixed)
+    tuple val(meta), path(moving), path(fixed), path(fs_license) /* optional, value = [] */
 
 
     output:
@@ -35,6 +35,15 @@ process REGISTRATION_SYNTHREGISTRATION {
     def out_format = task.ext.out_format ? "--out" + task.ext.out_format : "--outlps"
 
     """
+    # Manage the license. (Save old one if existed.)
+    if [ $fs_license = [] ]; then
+        echo "License not given in input. Using default environment. "
+    else
+        cp $fs_license .license
+        here=`pwd`
+        export FS_LICENSE=\$here/.license
+    fi
+
     export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1
     export OMP_NUM_THREADS=1
     export OPENBLAS_NUM_THREADS=1
@@ -44,6 +53,11 @@ process REGISTRATION_SYNTHREGISTRATION {
 
     mri_warp_convert -g $moving --inras temp.mgz $out_format ${prefix}__deform_warp.nii.gz
 
+    # Remove the license
+    if [ ! $fs_license = [] ]; then
+        rm .license
+    fi
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         Freesurfer: 7.4

diff --git a/modules/nf-scil/registration/synthregistration/meta.yml b/modules/nf-scil/registration/synthregistration/meta.yml
@@ -28,6 +28,11 @@ input:
       description: Nifti volume fixed for registration
       pattern: "*.{nii,nii.gz}"
 
+  - fs_license:
+      type: file
+      description: The path to your FreeSurfer license. To get one, go to https://surfer.nmr.mgh.harvard.edu/registration.html. Optional. If you have already set your license as prescribed by Freesurfer (copied to a .license file in your $FREESURFER_HOME), this is not required.
+      pattern: "*.txt"
+
 output:
   - meta:
       type: map

diff --git a/tests/config/test_data.config b/tests/config/test_data.config
@@ -75,6 +75,12 @@ params {
                 frf = "${params.test_data_base}/reconst/frf.txt"
             }
         }
+        "registration" {
+            "synthregistration"{
+                t1 = "${params.test_data_base}/heavy/anat/anat_image.nii.gz"
+                fa = "${params.test_data_base}/heavy/dwi/dwi.nii.gz"
+                fs_license = "${params.test_data_base}/heavy/freesurfer/license.txt"
+            }
         "segmentation" {
             "freesurferseg" {
                 aparc_aseg = "${params.test_data_base}/heavy/freesurfer/aparc_aseg.nii.gz"

diff --git a/tests/modules/nf-scil/registration/synthregistration/main.nf b/tests/modules/nf-scil/registration/synthregistration/main.nf
@@ -2,23 +2,16 @@
 
 nextflow.enable.dsl = 2
 
-include { LOAD_TEST_DATA } from '../../../../../subworkflows/nf-scil/load_test_data/main.nf'
-include {
-    REGISTRATION_SYNTHREGISTRATION as REGISTRATION_SYNTHREGISTRATION_T1FA; } from '../../../../../modules/nf-scil/registration/synthregistration/main.nf'
+include { REGISTRATION_SYNTHREGISTRATION } from '../../../../../modules/nf-scil/registration/synthregistration/main.nf'
 
 workflow test_registration_synthregistration {
 
-    input_fetch = Channel.from( [ "others.zip" ] )
-
-    LOAD_TEST_DATA ( input_fetch, "test.load-test-data" )
-
-    input_t1fa = LOAD_TEST_DATA.out.test_data_directory
-            .map{ test_data_directory -> [
-            [ id:'test', single_end:false ], // meta map
-            file("${test_data_directory}/t1.nii.gz"),
-            file("${test_data_directory}/fa.nii.gz")
-    ]}
-
-    REGISTRATION_SYNTHREGISTRATION_T1FA ( input_t1fa )
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['registration']['synthregistration']['t1'], checkIfExists: true),
+        file(params.test_data['registration']['synthregistration']['fa'], checkIfExists: true),
+        file(params.test_data['registration']['synthregistration']['fs_license'], checkIfExists: true)
+    ]
 
+    REGISTRATION_SYNTHREGISTRATION ( input )
 }
diff --git a/tests/modules/nf-scil/registration/synthregistration/nextflow.config b/tests/modules/nf-scil/registration/synthregistration/nextflow.config
@@ -1,10 +1,5 @@
 process {
 
-    withName: "REGISTRATION_SYNTHREGISTRATION" {
-        publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-    }
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
 
-    withName: "REGISTRATION_SYNTHREGISTRATION_T1FA" {
-        publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-    }
 }