Merge pull request #55 from GaelleLeroux/main

BUG : wrong interface cbct

ALI/ALI.py

@@ -606,7 +606,7 @@ def onPredictButton(self):
 
     ready = True
     system = platform.system()
-    if system=="Windows":
+    if system=="Windows" :
 
       wsl = self.is_ubuntu_installed()
       if wsl :
@@ -665,7 +665,7 @@ def onProcessStarted(self):
     self.startTime = time.time()
 
     system = platform.system()
-    if system=="Windows":
+    if system=="Windows" and not self.CBCT_as_input:
       self.ui.PredScanLabel.setText(f"Beginning of the process")
       self.RunningUIWindows(True)
 
@@ -795,7 +795,7 @@ def onProcessUpdate(self,caller,event):
 
     # print(progress)
     system = platform.system()
-    if system=="Windows":
+    if system=="Windows" and not self.CBCT_as_input:
           line = self.read_txt()
           self.ui.PredScanLabel.setText(f"{line}") 
 

ALI/tempo.txt

@@ -0,0 +1 @@
+Beginning of the process

AREG_IOS/AREG_IOS.py

@@ -140,6 +140,9 @@ def main(args):
         surf_T1 = Patched(dataset[idx, "T1"], surf_T1)
         # pbar.update(1)
 
+        name = os.path.basename(dataset.getUpperPath(idx, "T1"))
+        WriteSurf(surf_T1, args.output, name, args.suffix)
+
         with open(args.log_path, "r+") as log_f:
             log_f.write(str(1))
 
@@ -158,13 +161,19 @@ def main(args):
 
         name = os.path.basename(dataset.getUpperPath(idx, "T2"))
         WriteSurf(output_icp["source_Or"], args.output, name, args.suffix)
+
 
         if lower:
             surf_lower = dataset.getLowerSurf(idx, "T2")
             surf_lower = TransformSurf(surf_lower, output_icp["matrix"])
             name_lower = os.path.basename(dataset.getLowerPath(idx, "T2"))
             WriteSurf(surf_lower, args.output, name_lower, args.suffix)
 
+            surf_lower = dataset.getLowerSurf(idx, "T1")
+            if surf_lower!=None : 
+                name_lower = os.path.basename(dataset.getLowerPath(idx, "T1"))
+                WriteSurf(surf_lower, args.output, name_lower, args.suffix)
+
         # pbar.update(1)
 
         with open(args.log_path, "r+") as log_f:

AutoMatrix/AutoMatrix.py

@@ -502,67 +502,39 @@ def ProcessVolume(self)-> None:
                             if not os.path.exists(os.path.dirname(outpath)):
                                 os.makedirs(os.path.dirname(outpath))
 
-                            if extension_scan!=".nii.gz":
-                                self.UpdateTime()
-                                model.SetAndObserveTransformNodeID(tform.GetID())
-                                model.HardenTransform()
+                            self.UpdateTime()
+                            model.SetAndObserveTransformNodeID(tform.GetID())
+                            model.HardenTransform()
+                            self.UpdateTime()
+
+                            original_stdin = sys.stdin
+                            sys.stdin = DummyFile()
+
+                            process = multiprocessing.Process(target=self.saveOutput, args=(model,outpath.split(extension_scan)[0]+self.ui.LineEditSuffix.text+matrix_name+extension_scan))
+                            process.start()
+
+                            while process.is_alive():
+                                slicer.app.processEvents()
                                 self.UpdateTime()
-                                slicer.util.saveNode(model,outpath.split(extension_scan)[0]+self.ui.LineEditSuffix.text+matrix_name+extension_scan)
 
-                            else:
-                                self.applyBrainsResample(model,tform,outpath.split(extension_scan)[0]+self.ui.LineEditSuffix.text+matrix_name+extension_scan)
+                            sys.stdin = original_stdin
+                            self.UpdateTime()
+
+
 
-                        except:
-                            print("An issue occured")
+                        except Exception as e:
+                            print("An issue occured : ",e)
                             pass
                     self.UpdateProgressBar(False)
                     self.UpdateTime()
                     slicer.mrmlScene.RemoveNode(model)
                     self.UpdateTime()
 
 
-
-    def applyBrainsResample(self, inputVolumeNode, transformationNode, outputFilePath)->None:
-        '''
-        Uses the BRAINS Resample module to apply a transformation to an input volume node
-        and saves the result in a specified file.
-        '''
-        brainsResampleModule = slicer.modules.brainsresample
-        outputVolumeNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLScalarVolumeNode")
-
-
-
-        parameters = {
-            'inputVolume': inputVolumeNode.GetID(),
-            'warpTransform': transformationNode.GetID(),
-            'outputVolume' : outputVolumeNode.GetID(),
-            'interpolationMode': 'Linear'  
-        }
-        self.UpdateTime()
-        cliNode = slicer.cli.run(brainsResampleModule, None, parameters)
-        while cliNode.IsBusy():
-            slicer.app.processEvents() # to let the user interface available
-            self.UpdateTime()
-
-
-        original_stdin = sys.stdin
-        sys.stdin = DummyFile()
-
-        process = multiprocessing.Process(target=self.saveOutputVolume, args=(outputVolumeNode,outputFilePath))
-        process.start()
-
-        while process.is_alive():
-            slicer.app.processEvents()
-            self.UpdateTime()
-
-        sys.stdin = original_stdin
-
-        slicer.mrmlScene.RemoveNode(outputVolumeNode)
-        self.UpdateTime()
 
 
 
-    def saveOutputVolume(self, outputVolumeNode, outputFilePath)->None:
+    def saveOutput(self, outputVolumeNode, outputFilePath)->None:
         """
         Saves the output volume in the specified file with the .nii.gz extension.
         
@@ -572,7 +544,7 @@ def saveOutputVolume(self, outputVolumeNode, outputFilePath)->None:
         if not os.path.exists(os.path.dirname(outputFilePath)):
             os.makedirs(os.path.dirname(outputFilePath))
 
-        slicer.util.saveNode(outputVolumeNode, outputFilePath)
+        slicer.util.exportNode(outputVolumeNode, outputFilePath,world=True)
 
 
 
@@ -631,7 +603,8 @@ def UpdateProgressBar(self,end:bool)->None:
             self.ui.label_time.setVisible(False)
             self.ui.LineEditOutput.setText("")
             self.ui.LineEditPatient.setText("")
-            self.ui.LineEditMatrix.setText("")
+            if not self.ui.CheckBoxMirror.isChecked():
+                self.ui.LineEditMatrix.setText("")
             self.ui.ComboBoxMatrix.setCurrentIndex(1)
             self.ui.ComboBoxPatient.setCurrentIndex(1)