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STYLE: Remove trailing white-spaces and fix indentation in CMakeLists.txt #62

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STYLE: Remove trailing white-spaces and fix indentation in CMakeLists.txt #62

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bfb0312
STYLE: Strip trailing whitespaces
jcfr Dec 20, 2023
60e4d9f
STYLE: Update CMakeLists.txt fix indentation and removing extra lines
jcfr Dec 20, 2023
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80 changes: 40 additions & 40 deletions ALI/ALI.py
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Original file line number Diff line number Diff line change
Expand Up @@ -81,7 +81,7 @@ def PathFromNode(node):


# "Dental" : ['LL7','LL6','LL5','LL4','LL3','LL2','LL1','LR1','LR2','LR3','LR4','LR5','LR6','LR7','UL7','UL6','UL5','UL4','UL3','UL2','UL1','UR1','UR2','UR3','UR4','UR5','UR6','UR7'] ,

# "Landmarks type" : ['CL','CB','O','DB','MB','R','RIP','OIP']


Expand Down Expand Up @@ -192,12 +192,12 @@ def __init__(self, parent=None):
self.model_folder = None

self.available_landmarks = [] # list of available landmarks to predict

self.output_folder = None # If save the output in a folder
self.goup_output_files = False

self.scan_count = 0 # number of scans in the input folder
self.landmark_cout = 0 # number of landmark to identify
self.landmark_cout = 0 # number of landmark to identify



Expand Down Expand Up @@ -312,7 +312,7 @@ def SwitchInputType(self,index):
self.lm_tab.FillTab(SURFACE_LANDMARKS)
self.ui.ExtensionLabel.setVisible(False)
self.ui.ExtensioncomboBox.setVisible(False)

else:
self.CBCT_as_input = True
self.ui.MRMLNodeComboBox.nodeTypes = ['vtkMRMLVolumeNode']
Expand All @@ -327,14 +327,14 @@ def SwitchInputType(self,index):
# print()

def SwitchInputExtension(self,index):

if index == 0: # NIFTI, NRRD, GIPL Files
self.SwitchInput(0)
self.isDCMInput = False

self.ui.label_11.setVisible(True)
self.ui.InputComboBox.setVisible(True)

if index == 1: # DICOM Files
self.SwitchInput(1)
self.ui.label_11.setVisible(False)
Expand Down Expand Up @@ -410,7 +410,7 @@ def UpdateSaveType(self,caller=None, event=None):

# self.ui.SearchSaveFolder.setEnabled(not caller)
# self.ui.SaveFolderLineEdit.setEnabled(not caller)

self.save_scan_folder = caller


Expand Down Expand Up @@ -528,7 +528,7 @@ def onPredictButton(self):
if self.model_folder == None:
qt.QMessageBox.warning(self.parent, 'Warning', 'Please select a model folder')
ready = False

if not ready:
return

Expand Down Expand Up @@ -574,7 +574,7 @@ def onPredictButton(self):
param["temp_fold"] = temp_dir

param["DCMInput"] = self.isDCMInput

else:
selected_lm_lst = self.lm_tab.GetSelected()
selected_tooth_lst = self.tooth_lm.GetSelected()
Expand Down Expand Up @@ -607,7 +607,7 @@ def onPredictButton(self):
ready = True
system = platform.system()
if system=="Windows" :

wsl = self.is_ubuntu_installed()
if wsl :
lib = self.check_lib_wsl()
Expand All @@ -616,24 +616,24 @@ def onPredictButton(self):
text = "Code can't be launch. \nWSL doen't have all the necessary libraries, please download the installer and follow the instructin here : https://github.com/DCBIA-OrthoLab/SlicerAutomatedDentalTools/releases/download/wsl2_windows/installer_wsl2.zip\nDownloading may be blocked by Chrome, this is normal, just authorize it."
ready = False
messageBox.information(None, "Information", text)
else :
else :
messageBox = qt.QMessageBox()
text = "Code can't be launch. \nWSL is not installed, please download the installer and follow the instructin here : https://github.com/DCBIA-OrthoLab/SlicerAutomatedDentalTools/releases/download/wsl2_windows/installer_wsl2.zip\nDownloading may be blocked by Chrome, this is normal, just authorize it."
ready = False
messageBox.information(None, "Information", text)

if ready :
script_path = os.path.dirname(os.path.abspath(__file__))
file_path = os.path.join(script_path,"tempo.txt")
with open(file_path, 'a') as file:
file.write("Beginning of the process" + '\n') # Écrire le message suivi d'une nouvelle ligne

self.logic = ALILogic()
self.logic.process(param, self.CBCT_as_input)

self.processObserver = self.logic.cliNode.AddObserver('ModifiedEvent',self.onProcessUpdate)
self.onProcessStarted()


def is_ubuntu_installed(self)->bool:
'''
Expand All @@ -652,8 +652,8 @@ def check_lib_wsl(self)->bool:
'''
result1 = subprocess.run("wsl -- bash -c \"dpkg -l | grep libxrender1\"", capture_output=True, text=True)
output1 = result1.stdout.encode('utf-16-le').decode('utf-8')
clean_output1 = output1.replace('\x00', '')
clean_output1 = output1.replace('\x00', '')

result2 = subprocess.run("wsl -- bash -c \"dpkg -l | grep libgl1-mesa-glx\"", capture_output=True, text=True)
output2 = result2.stdout.encode('utf-16-le').decode('utf-8')
clean_output2 = output2.replace('\x00', '')
Expand All @@ -668,8 +668,8 @@ def onProcessStarted(self):
if system=="Windows" and not self.CBCT_as_input:
self.ui.PredScanLabel.setText(f"Beginning of the process")
self.RunningUIWindows(True)
else :

else :
self.ui.PredScanProgressBar.setMaximum(self.scan_count)
self.ui.PredScanProgressBar.setValue(0)
self.ui.PredSegProgressBar.setValue(0)
Expand All @@ -680,7 +680,7 @@ def onProcessStarted(self):
self.total_seg_progress = self.scan_count * self.landmark_cout

self.ui.PredSegProgressBar.setMaximum(self.total_seg_progress)
self.ui.PredSegLabel.setText(f"Landmarks found : 0 / {self.total_seg_progress}")
self.ui.PredSegLabel.setText(f"Landmarks found : 0 / {self.total_seg_progress}")

else:
self.ui.PredScanLabel.setText(f"Scan : 0 / {self.scan_count}")
Expand All @@ -696,7 +696,7 @@ def onProcessStarted(self):
self.total_seg_progress = len(self.tooth_lm.GetSelected()) * len(model_used)

self.ui.PredSegProgressBar.setMaximum(self.total_seg_progress)
self.ui.PredSegLabel.setText(f"Identified : 0 / {self.total_seg_progress}")
self.ui.PredSegLabel.setText(f"Identified : 0 / {self.total_seg_progress}")

self.prediction_step = 0
self.progress = 0
Expand All @@ -706,8 +706,8 @@ def onProcessStarted(self):

self.RunningUI(True)





def UpdateALICBCT(self,progress):
Expand Down Expand Up @@ -744,7 +744,7 @@ def UpdateALICBCT(self,progress):
if self.prediction_step == 2:
# self.progressBar.setValue(self.progress)
self.ui.PredSegProgressBar.setValue(self.progress)
self.ui.PredSegLabel.setText(f"Landmarks found : {self.progress} / {self.total_seg_progress}")
self.ui.PredSegLabel.setText(f"Landmarks found : {self.progress} / {self.total_seg_progress}")

self.progress += 1

Expand All @@ -756,14 +756,14 @@ def UpdateALIIOS(self,progress):
self.ui.PredScanProgressBar.setValue(self.prediction_step)
self.ui.PredScanLabel.setText(f"Scan : {self.prediction_step} / {self.scan_count}")
self.ui.PredSegProgressBar.setValue(self.progress)
self.ui.PredSegLabel.setText(f"Identified: {self.progress} / {self.total_seg_progress}")
self.ui.PredSegLabel.setText(f"Identified: {self.progress} / {self.total_seg_progress}")


if progress == 100:

self.progress += 1
self.ui.PredSegProgressBar.setValue(self.progress)
self.ui.PredSegLabel.setText(f"Identified : {self.progress} / {self.total_seg_progress}")
self.ui.PredSegLabel.setText(f"Identified : {self.progress} / {self.total_seg_progress}")



Expand Down Expand Up @@ -797,8 +797,8 @@ def onProcessUpdate(self,caller,event):
system = platform.system()
if system=="Windows" and not self.CBCT_as_input:
line = self.read_txt()
self.ui.PredScanLabel.setText(f"{line}")
self.ui.PredScanLabel.setText(f"{line}")

else:
if progress == 0:
self.updateProgessBar = False
Expand Down Expand Up @@ -832,8 +832,8 @@ def onProcessUpdate(self,caller,event):
# success

self.OnEndProcess()


def OnEndProcess(self):

script_path = os.path.dirname(os.path.abspath(__file__))
Expand All @@ -843,7 +843,7 @@ def OnEndProcess(self):
print("File delete")
else:
print("The file doesn't exist")

print('PROCESS DONE.')
# script_path = os.path.dirname(os.path.abspath(__file__))
# file_path = os.path.join(script_path,"tempo.txt")
Expand All @@ -860,7 +860,7 @@ def OnEndProcess(self):

if not self.folder_as_input:

input_id = os.path.basename(self.input_path).split(".")[0]
input_id = os.path.basename(self.input_path).split(".")[0]

normpath = os.path.normpath("/".join([self.output_folder, '**', '']))
for img_fn in sorted(glob.iglob(normpath, recursive=True)):
Expand All @@ -884,7 +884,7 @@ def onCancel(self):


print("Cancelled")

def RunningUI(self, run = False):

self.ui.PredictionButton.setVisible(not run)
Expand All @@ -895,19 +895,19 @@ def RunningUI(self, run = False):
self.ui.PredSegLabel.setVisible(run)
self.ui.PredSegProgressBar.setVisible(run)
self.ui.TimerLabel.setVisible(run)

def RunningUIWindows(self,run=False):
self.ui.TimerLabel.setVisible(run)
self.ui.PredScanLabel.setVisible(run)


def cleanup(self):
"""
Called when the application closes and the module widget is destroyed.
"""
if self.logic.cliNode is not None:
# if self.logic.cliNode.GetStatus() & self.logic.cliNode.Running:
self.logic.cliNode.Cancel()
self.logic.cliNode.Cancel()

self.removeObservers()

Expand Down Expand Up @@ -1129,10 +1129,10 @@ def CheckBox(self, caller=None, event=None):
state = True
else:
state = False

if self.lm_status_dic[lm] != state:
self.UpdateLmSelect(lm,state)

def ToggleSelection(self):
idx = self.LM_tab_widget.currentIndex
# print(idx)
Expand Down Expand Up @@ -1188,7 +1188,7 @@ def GetSelected(self):

def SelectAll(self):
self.UpdateAll(True)

def ClearAll(self):
self.UpdateAll(False)

Expand Down Expand Up @@ -1296,7 +1296,7 @@ def process(self, parameters, ALI_CBCT = True):

# stopTime = time.time()
# logging.info('Processing completed in {0:.2f} seconds'.format(stopTime-startTime))


#
# ALITest
Expand Down
2 changes: 1 addition & 1 deletion ALI/CMakeLists.txt
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -25,6 +25,6 @@ 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)


endif()
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