fix test data, freesurfer license

scilus · Apr 9, 2024 · 8148b67 · 8148b67
1 parent a1e4240
commit 8148b67
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Showing 3 changed files with 19 additions and 33 deletions.
diff --git a/modules/nf-scil/registration/synthregistration/main.nf b/modules/nf-scil/registration/synthregistration/main.nf
@@ -2,14 +2,15 @@ process REGISTRATION_SYNTHREGISTRATION {
     tag "$meta.id"
     label 'process_single'
 
-    container "freesurfer/synthmorph:latest"
+    container "freesurfer/freesurfer:7.4.1"
+    containerOptions "--entrypoint ''"
 
     input:
     tuple val(meta), path(moving), path(fixed), path(fs_license) /* optional, value = [] */
 
 
     output:
-    tuple val(meta), path("*__*_output_warped.nii.gz"), emit: warped_image
+    tuple val(meta), path("*__output_warped.nii.gz"), emit: warped_image
     tuple val(meta), path("*__deform_warp.nii.gz"), emit: deform_transform
     tuple val (meta), path("*__init_warp.txt"), emit: init_transform
     path "versions.yml"           , emit: versions
@@ -20,13 +21,12 @@ process REGISTRATION_SYNTHREGISTRATION {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def suffix = task.ext.suffix ?: "${meta.id}"
 
     def init = task.ext.init ? "-m " + task.est.init : "-m affine"
     def warp = task.ext.warp ? "-m " + task.est.warp : "-m deform"
-    def header = task.ext.header ? "-H " + task.ext.header : ""
+    def header = task.ext.header ? "-H" : ""
     def threads = task.ext.threads ? "-j " + task.ext.threads : ""
-    def gpu = task.ext.gpu ? "-g " + task.ext.gpu : ""
+    def gpu = task.ext.gpu ? "-g" : ""
     def smooth = task.ext.smooth ? "-s " + task.ext.smooth : ""
     def extent = task.ext.extent ? "-e " + task.ext.extent : ""
     def weight = task.ext.weight ? "-w " + task.ext.weight : ""
@@ -35,29 +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
 
     mri_synthmorph $init -t ${prefix}__init_warp.txt $moving $fixed
-    mri_synthmorph $warp -i ${prefix}__init_warp.txt  -t temp.mgz -o ${prefix}__${suffix}_output_warped.nii.gz $moving $fixed
+    mri_synthmorph $warp -i ${prefix}__init_warp.txt  -t temp.mgz -o ${prefix}__output_warped.nii.gz $moving $fixed
 
     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
@@ -67,14 +53,13 @@ process REGISTRATION_SYNTHREGISTRATION {
     stub:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def suffix = task.ext.suffix ?: ""
 
     """
     mri_synthmorph -h
 
     mri_warp_convert -h
 
-    touch ${prefix}__${suffix}_output_warped.nii.gz
+    touch ${prefix}__output_warped.nii.gz
     touch ${prefix}__deform_warp.nii.gz
     touch ${prefix}__init_warp.txt
 

diff --git a/tests/config/test_data.config b/tests/config/test_data.config
@@ -80,12 +80,6 @@ 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
@@ -2,16 +2,23 @@
 
 nextflow.enable.dsl = 2
 
+include { LOAD_TEST_DATA } from '../../../../../subworkflows/nf-scil/load_test_data/main'
 include { REGISTRATION_SYNTHREGISTRATION } from '../../../../../modules/nf-scil/registration/synthregistration/main.nf'
 
 workflow test_registration_synthregistration {
 
-    input = [
+    input_fetch = Channel.from( [ "freesurfer.zip" ] )
+
+    LOAD_TEST_DATA ( input_fetch, "test.load-test-data" )
+
+    input = LOAD_TEST_DATA.out.test_data_directory
+        .map{ test_data_directory -> [
         [ 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)
-    ]
+        file("${test_data_directory}/t1.nii.gz"),
+        file("${test_data_directory}/fa.nii.gz"),
+        []
+
+    ]}
 
     REGISTRATION_SYNTHREGISTRATION ( input )
 }