Define Run directory for elastix

Ooops. Apparently for linux you need to do things like tell it where the code that it should run is. Maybe learn to think independently?

CBCTCardiacSegmentation/CreateCBCTSegmentations.py

@@ -27,6 +27,7 @@
 
 
 def CreateCBCTSegmentations(CBCTDir,OutputDir='./CBCTSegmentations',SegmentationMethod='Synthetic',PlanningCTDir='',ElastixParamDir='',StructFile='',
+                            ElastixRunDir = '',
                             HeartPadDistance=30,
                             KeepTempFiles=False):
 
@@ -68,7 +69,8 @@ def CreateCBCTSegmentations(CBCTDir,OutputDir='./CBCTSegmentations',Segmentation
     Register Images to prepare for Segmentation
     """
     if not(SegmentationMethod == 'Direct'):        
-        VolReg = VolumeRegistration(RegOutputDir=TempDir,ParamDir=ElastixParamDir)
+        VolReg = VolumeRegistration(RegOutputDir=TempDir,ParamDir=ElastixParamDir,
+                                    ElastixDir=ElastixRunDir)
 
         #Align PlanningCT Volume to CBCT Volume
         print('Initial Alignment of Planning CT File to CBCT File')
@@ -179,6 +181,7 @@ def CreateCBCTSegmentations(CBCTDir,OutputDir='./CBCTSegmentations',Segmentation
     parser.add_argument('--SegmentationMethod',default='Synthetic',type=str,help='The method used to segment the CBCT image {Synthetic|Transform|Direct}. Default is Synthetic')
     parser.add_argument('--PlanningCTDir',type=str, default='',help='Location of the Planning CT that is to be segmented. Can be a Dicom Series or Volume file. Default is None')
     parser.add_argument('--ElastixParamDir',type=str,default='',help='Location of the elastix parameter files used for the registrations. Default is the parameters is the provided ElastixParameterFiles')
+    parser.add_argument('--ElastixRunDir',type=str,default='',help='Location of the bin and lib directories from the installed/downaloded version of elastix to be used. Needed for linux implementations')
     parser.add_argument('--StructFile',type=str,default='',help='Location of the structures contoured from the planning CT File. Default is None')
     parser.add_argument('--KeepTempFiles',action='store_true',help='If true the temporary files and directories created will not be deleted. If False these files will be deleted.')
 

CBCTCardiacSegmentation/Registration.py

@@ -14,7 +14,7 @@
 class VolumeRegistration:
 
     def __init__(self, RegOutputDir='', ParamDir='', RigidParamFile='', NonRigidParamFile='', InverseParamFile='',
-                 RigidNonRigidParamFile='',TranslationParamFile='',GPUEnabled=False):
+                 RigidNonRigidParamFile='',TranslationParamFile='',ElastixDir='',GPUEnabled=False):
 
         if not ParamDir:
             #If no elastix parameter directory defined then get the one
@@ -26,6 +26,11 @@ def __init__(self, RegOutputDir='', ParamDir='', RigidParamFile='', NonRigidPara
 
         self.RegOutputDir = RegOutputDir
 
+        if platform.system() == 'Linux':
+            assert not(not ElastixDir),'Directory to elastix bin/lib files needs to be added for linux'
+
+        self.ElastixDir = ElastixDir
+
         if not ParamDir:
             self.RigidParamFile = RigidParamFile
             self.NonRigidParamFile = NonRigidParamFile
@@ -157,7 +162,7 @@ def TransformVolume(self, ParamFile, OutputFile, FixedVolume):
     def CallFunctionFromCmdLine(self,CmdStr):
         # Run command from terminal
         if platform.system() == 'Linux':
-            run(CmdStr, shell=True, env={"PATH": '/home/mark/elastix/bin', "LD_LIBRARY_PATH": '/home/mark/elastix/lib'})
+            run(CmdStr, shell=True, env={"PATH": os.path.join(self.ElastixDir,'bin'), "LD_LIBRARY_PATH": os.path.join(self.ElastixDir,'lib')})
         else:
             run(CmdStr)
 

tests/test_CBCT_Segmentation.py

@@ -113,7 +113,7 @@ def test_BadSegMethodInput():
 
     rmtree(data_path) 
     rmtree(OutputDir) 
-    
+
 def test_NiftiCBCTSegmentationGeneration():
 
     # Download the test data
@@ -131,6 +131,10 @@ def test_NiftiCBCTSegmentationGeneration():
     ElastixParamDir = ''
     StructFile = ''
 
+    #Define Elastix directories
+    home_dir = Path(os.path.expanduser('~'))  # may have to update for github system
+    elastix_dir = home_dir / 'ElastixDownload' / 'elastix-5.0.1-linux'
+
     for SegMethod in SegmentationMethods:
         print(SegMethod)
         OutputDir = './CBCTSegmentations'    
@@ -139,7 +143,8 @@ def test_NiftiCBCTSegmentationGeneration():
                                 SegmentationMethod=SegMethod,
                                 PlanningCTDir=PlanningCTDir,
                                 ElastixParamDir=ElastixParamDir,
-                                StructFile=StructFile)
+                                StructFile=StructFile,
+                                ElastixRunDir=elastix_dir)
 
         CardiacSegList = ['Heart','A_Aorta','A_Cflx','A_Coronary_L','A_Coronary_R','A_LAD','A_Pulmonary','Atrium_L',
                           'Atrium_R','CN_Atrioventricular','CN_Sinoatrial','V_Venacava_S','Valve_Aortic','Valve_Mitral',
@@ -210,4 +215,4 @@ def test_NiftiToDicomStruct():
     assert Path(OutputStructFile).exists(),'Output Struct {} was not created successfully'.format(OutputStructFile)
 
     rmtree(data_path) 
-    rmtree(OutputDir)
+    rmtree(OutputDir)