Updated README

Added extension to vessel_segementer
Added unit test for extension .nii.gz

.github/workflows/build.yml

@@ -70,12 +70,16 @@ jobs:
           mkdir samples
           cd samples
           gdown https://drive.google.com/uc?id=1shjSrFjS4PHE5sTku30PZTLPZpGu24o3
-          gdown https://drive.google.com/uc?id=1bNmls5o0Rxw5HvBF1IYnEzmpysYJaywN
+          gdown https://drive.google.com/uc?id=1oID3MyN3hjVWF_cfKJg1oL37p7GrvVUh
 
-      - name: Test inference
+      - name: Test inference .nii
         run: |
           livermask --input samples --output samples --verbose --vessels
 
+      - name: Test inference .nii.gz
+        run: |
+          livermask --input samples --output samples --verbose --vessels --extension .nii.gz
+
   conda:
     needs: build
     runs-on: ${{ matrix.os }}

README.md

@@ -61,7 +61,7 @@ python -m livermask.livermask --input path-to-input --output path-to-output
 ```
 
 ## DICOM/NIfTI format
-Pipeline assumes input is in the NIfTI format, and output a binary volume in the same format (.nii).
+Pipeline assumes input is in the NIfTI format, and output a binary volume in the same format (.nii or .nii.gz).
 DICOM can be converted to NIfTI using the CLI [dcm2niix](https://github.com/rordenlab/dcm2niix), as such:
 ```
 dcm2niix -s y -m y -d 1 "path_to_CT_folder" "output_name"

livermask/utils/process.py

@@ -132,7 +132,7 @@ def liver_segmenter(params):
         raise "Caught KeyboardInterrupt, terminating worker"
 
 
-def vessel_segmenter(curr, output, cpu, verbose, multiple_flag, liver_mask, name_vessel):
+def vessel_segmenter(curr, output, cpu, verbose, multiple_flag, liver_mask, name_vessel, extension):
     # check if cupy is available, if not, set cpu=True
     try:
         import cupy
@@ -226,6 +226,6 @@ def vessel_segmenter(curr, output, cpu, verbose, multiple_flag, liver_mask, name
     img = nib.Nifti1Image(pred, affine=resampled_volume.affine)
     resampled_lab = resample_from_to(img, nib_volume, order=0)
     if multiple_flag:
-        nib.save(resampled_lab, output + "/" + curr.split("/")[-1].split(".")[0] + "-vessels.nii")
+        nib.save(resampled_lab, output + "/" + curr.split("/")[-1].split(".")[0] + "-vessels" + extension)
     else:
-        nib.save(resampled_lab, output + "-vessels.nii")
+        nib.save(resampled_lab, output + "-vessels" + extension)