Update based on testing

.github/workflows/python-app.yml

@@ -26,19 +26,13 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install flake8 pytest
+        pip install pytest
         pip install pytest-cov
         pip install coverage        
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
     - name: install elastix
       run: |
         wget -P ~/ElastixDownload "https://github.com/SuperElastix/elastix/releases/download/5.0.1/elastix-5.0.1-linux.tar.bz2"
-    - name: Lint with flake8
-      run: |
-        # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: Test with pytest
       run: |
         mkdir /home/runner/elastix

CBCTCardiacSegmentation/DicomHelper.py

@@ -124,6 +124,11 @@ def PrepareCTData(CTDir,OutputDir='',StructFile='',PreviousNiftiFiles=[],KeepTem
     elif isfile(CTDir):
         CTNiftiFile = CTDir
         StructNiftiDir = ''
+
+    else:
+        print('File type neither directory or file')
+        CTNiftiFile = ''
+        StructNiftiDir = ''
 
     return CTNiftiFile,StructNiftiDir
 

tests/test_CBCT_Segmentation.py

@@ -9,17 +9,12 @@
 import subprocess
 from pathlib import Path
 import sys
-import numpy as np
 from shutil import rmtree
-import glob
-import json
 from platform import system
 import SimpleITK as sitk
 
 from platipy.imaging.tests.data import get_lung_nifti, get_lung_dicom
 from platipy.imaging.projects.cardiac.run import run_hybrid_segmentation
-from platipy.imaging import ImageVisualiser
-from platipy.imaging.label.utils import get_com
 
 '''
 For testing/ example purposes it's safest to manually append the path variable to ensure our 
@@ -34,10 +29,17 @@
 from CBCTCardiacSegmentation.SegUtil import DoDicomProcessing 
 
 def test_DicomProcessing():
-    CTDicomDir = ''
+    # Download the test data
+    data_path = get_lung_dicom()
+    test_pat_path = data_path.joinpath("LCTSC-Test-S1-101")
+
+    CTDicomDir = test_pat_path.joinpath('1.3.6.1.4.1.14519.5.2.1.7014.4598.106943890850011666503487579262')
     OutputDir='./DicomProcessing'
     DoDicomProcessing(CTDicomDir,OutputDir=OutputDir)
 
+    rmtree(data_path)
+    rmtree(OutputDir)
+
 
 def test_PlatipyCTSegmentation():
     # Download the test data
@@ -125,11 +127,15 @@ def test_DicomCBCTSegmentationGeneration():
 
     # Download the test data
     data_path = get_lung_dicom()
+    test_pat_path = data_path.joinpath("LCTSC-Test-S1-101")
+
+    CBCTDir = test_pat_path.joinpath('1.3.6.1.4.1.14519.5.2.1.7014.4598.106943890850011666503487579262')
+    PlanningCTDir = test_pat_path.joinpath('1.3.6.1.4.1.14519.5.2.1.7014.4598.106943890850011666503487579262')
 
     SegmentationMethods = ['Direct','Synthetic','Transform','Test']
 
-    CBCTDir = '' #Is a dicom directory file
-    PlanningCTDir = ''
+    #CBCTDir = '' #Is a dicom directory file
+    #PlanningCTDir = ''
     ElastixParamDir = ''
     StructFile = ''