Merge pull request #102 from GaelleLeroux/MRI2CBCT

MRI2CBCT extension

Author: allemangD

ASO_CBCT/LinearTransform_t.tfm

@@ -0,0 +1,5 @@
+#Insight Transform File V1.0
+#Transform 0
+Transform: AffineTransform_double_3_3
+Parameters: 0.9763290732702393 0.15616745925611628 0.14964379491567228 -0.1421477793365056 0.9847545451025459 -0.10026213008697676 -0.16302008930489087 0.07661729941316797 0.9836433499565058 3.8520097928318386 10.915991569159537 -4.582919224464414
+FixedParameters: 0 0 0

AutoMatrix/AutoMatrix.py

@@ -468,7 +468,7 @@ def ProcessVolume(self)-> None:
                         print("not a .nii.gz")
 
                     self.UpdateTime()
-                    if extension_scan!=".nii.gz":
+                    if extension_scan!=".nii.gz" and extension_scan!=".nrrd":
                         model = slicer.util.loadModel(scan)
                     else :
                         model = slicer.util.loadVolume(scan)
@@ -616,7 +616,7 @@ def onProcessStarted(self)->None:
         Initialize the variables and progress bar.
         """
         if os.path.isdir(self.ui.LineEditPatient.text):
-            self.nbFiles = len(self.dico_patient[".vtk"]) + len(self.dico_patient['.vtp']) + len(self.dico_patient['.stl']) + len(self.dico_patient['.off']) + len(self.dico_patient['.obj']) + len(self.dico_patient['.nii.gz'])
+            self.nbFiles = len(self.dico_patient[".vtk"]) + len(self.dico_patient['.vtp']) + len(self.dico_patient['.stl']) + len(self.dico_patient['.off']) + len(self.dico_patient['.obj']) + len(self.dico_patient['.nii.gz']) + len(self.dico_patient['nrrd'])
         else:
             self.nbFiles = 1
         self.ui.progressBar.setValue(0)
@@ -645,20 +645,20 @@ def CheckGoodEntre(self)->bool:
                 warning_text = warning_text + "Enter file patient" + "\n"
         else :
             if self.ui.ComboBoxPatient.currentIndex==1 : #folder option
-                self.dico_patient=search(self.ui.LineEditPatient.text,'.vtk','.vtp','.stl','.off','.obj','.nii.gz')
-                if len(self.dico_patient['.vtk'])==0 and len(self.dico_patient['.vtp']) and len(self.dico_patient['.stl']) and len(self.dico_patient['.off']) and len(self.dico_patient['.obj']) and len(self.dico_patient['.nii.gz']) :
+                self.dico_patient=search(self.ui.LineEditPatient.text,'.vtk','.vtp','.stl','.off','.obj','.nii.gz','nrrd')
+                if len(self.dico_patient['.vtk'])==0 and len(self.dico_patient['.vtp']) and len(self.dico_patient['.stl']) and len(self.dico_patient['.off']) and len(self.dico_patient['.obj']) and len(self.dico_patient['.nii.gz']) and len(self.dico_patient['.nrrd']) :
                     warning_text = warning_text + "Folder empty or wrong type of file patient" + "\n"
-                    warning_text = warning_text + "File authorized : .vtk / .vtp / .stl / .off / .obj / .nii.gz" + "\n"
+                    warning_text = warning_text + "File authorized : .vtk / .vtp / .stl / .off / .obj / .nii.gz / .nrrd" + "\n"
             elif self.ui.ComboBoxPatient.currentIndex==0 : # file option
                 fname, extension = os.path.splitext(os.path.basename(self.ui.LineEditPatient.text))
                 try :
                     fname, extension2 = os.path.splitext(os.path.basename(fname))
                     extension = extension2+extension
                 except :
                     print("not a .nii.gz")
-                if extension != ".vtk" and extension != ".vtp" and extension != ".stl" and extension != ".off" and extension != ".obj" and extension != ".nii.gz" :
+                if extension != ".vtk" and extension != ".vtp" and extension != ".stl" and extension != ".off" and extension != ".obj" and extension != ".nii.gz" and extension != ".nrrd":
                         warning_text = warning_text + "Wrong type of file patient detected" + "\n"
-                        warning_text = warning_text + "File authorized : .vtk / .vtp / .stl / .off / .obj / .nii.gz" + "\n"
+                        warning_text = warning_text + "File authorized : .vtk / .vtp / .stl / .off / .obj / .nii.gz / .nrrd" + "\n"
 
 
         if self.ui.LineEditMatrix.text=="":

AutoMatrix/Method/General_tools.py

@@ -45,7 +45,7 @@ def GetPatients(file_path:str,matrix_path:str):
         files = []
 
         if Path(file_path).is_dir():
-            files_original = search(file_path,'.vtk','.vtp','.stl','.off','.obj','.nii.gz')
+            files_original = search(file_path,'.vtk','.vtp','.stl','.off','.obj','.nii.gz','.nrrd')
             files = []
             for i in range(len(files_original['.vtk'])):
                 files.append(files_original['.vtk'][i])
@@ -64,6 +64,9 @@ def GetPatients(file_path:str,matrix_path:str):
 
             for i in range(len(files_original['.nii.gz'])):
                 files.append(files_original['.nii.gz'][i])
+                
+            for i in range(len(files_original['.nrrd'])):
+                files.append(files_original['.nrrd'][i])
 
             for i in range(len(files)):
                 file = files[i]
@@ -87,7 +90,7 @@ def GetPatients(file_path:str,matrix_path:str):
             except :
                 print("not a .nii.gz")
 
-            if extension ==".vtk" or extension ==".vtp" or extension ==".stl" or extension ==".off" or extension ==".obj" or extension==".nii.gz" :
+            if extension ==".vtk" or extension ==".vtp" or extension ==".stl" or extension ==".off" or extension ==".obj" or extension==".nii.gz" or extension==".nrrd" :
                 files = [file_path]
                 file_pat = os.path.basename(file_path).split('_Seg')[0].split('_seg')[0].split('_Scan')[0].split('_scan')[0].split('_Or')[0].split('_OR')[0].split('_MAND')[0].split('_MD')[0].split('_MAX')[0].split('_MX')[0].split('_CB')[0].split('_lm')[0].split('_T2')[0].split('_T1')[0].split('_Cl')[0].split('.')[0].replace('.','')
                 for i in range(50):

CMakeLists.txt

@@ -35,6 +35,8 @@ add_subdirectory(AREG)
 add_subdirectory(AutoMatrix)
 add_subdirectory(AutoCrop3D)
 
+add_subdirectory(MRI2CBCT)
+add_subdirectory(MRI2CBCT_CLI)
 ## NEXT_MODULE
 
 #-----------------------------------------------------------------------------

MRI2CBCT/CMakeLists.txt

@@ -0,0 +1,37 @@
+#-----------------------------------------------------------------------------
+set(MODULE_NAME MRI2CBCT)
+
+#-----------------------------------------------------------------------------
+set(MODULE_PYTHON_SCRIPTS
+  ${MODULE_NAME}.py
+  utils/Method.py
+  utils/Preprocess_CBCT_MRI.py
+  utils/Preprocess_CBCT.py
+  utils/Preprocess_MRI.py
+  utils/Reg_MRI2CBCT.py
+  utils/utils_CBCT.py
+  )
+
+set(MODULE_PYTHON_RESOURCES
+  Resources/Icons/${MODULE_NAME}.png
+  Resources/UI/${MODULE_NAME}.ui
+  )
+
+#-----------------------------------------------------------------------------
+slicerMacroBuildScriptedModule(
+  NAME ${MODULE_NAME}
+  SCRIPTS ${MODULE_PYTHON_SCRIPTS}
+  RESOURCES ${MODULE_PYTHON_RESOURCES}
+  WITH_GENERIC_TESTS
+  )
+
+#-----------------------------------------------------------------------------
+if(BUILD_TESTING)
+
+  # Register the unittest subclass in the main script as a ctest.
+  # Note that the test will also be available at runtime.
+  slicer_add_python_unittest(SCRIPT ${MODULE_NAME}.py)
+
+  # Additional build-time testing
+  add_subdirectory(Testing)
+endif()