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‎radiomics2.py

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#rBatch-run radiomics module inside Slicer using a parameter file
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#Usage: Set variables in slicer console according to local file paths and execute python file. For example:
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#base_directory = r"C:\Users\urs\Desktop\hoedha_radiomics\test"
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#paramfilepath = r"C:\urs\urs\Desktop\hoedha_radiomics\Params_radiomics.yaml"
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#pythonfile = r"C:\Users\urs\Desktop\hoedha_radiomics\radiomics.py"
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#exec(open(pythonfile).read())
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import SlicerRadiomics
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import re
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import pandas as pd
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import openpyxl
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import os
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################################SET PARAMETERS###########################################
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#define regex patterns to find correct volumes in scene
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pattern_T1C = r'^(?=.*(?:T1|t1|T1W))(?=.*CE)' #T1C works
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pattern_ADC = r'^\d+:\s.*ADC.*' #works ADC
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pattern_T1 = r'^\d+:\s(T1|t1|T1W)(?!.*CE)' #works T1
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pattern_T2 = r'^\d+:\s(?!(.*FLAIR.*|.*dark-fluid.*))(T2|t2|T2W)'
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pattern_FLAIR = r'^\d+:\s(FLAIR|.*dark-fluid.*)' #works FLAIR
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################# Get a list of subfolders in the base directory####################
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#'base_directory' path is set in the slicer python console
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subfolders = [os.path.join(base_directory, folder) for folder in os.listdir(base_directory) if os.path.isdir(os.path.join(base_directory, folder))]
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# Print the full paths of the subfolders
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print('Processing the following folders:')
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for folder in subfolders:
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print(folder)
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##############################FUNCTIONS################################
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#function to find first mrb files in each patient folder
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def find_file_with_extension(directory, extension):
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for root, dirs, files in os.walk(directory):
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for file in files:
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if file.endswith(extension):
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return os.path.join(root, file)
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return None # If no file with the given extension is found
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##########################export table to csv##############################
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def savecsvandxlsx(nodename,outname):
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result = getNode(nodename)
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rad_outputFilename = subfolders[Index]+'\\Tables\\'+outname+'.csv' #TAKES i from index of mainloop!
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print(rad_outputFilename)
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delayDisplay("Export results to CSV file: "+rad_outputFilename,3000)
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slicer.util.exportNode(result,rad_outputFilename)
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# Read the csv file into a pandas DataFrame for export to xlsx
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df = pd.read_csv(rad_outputFilename, sep=',')
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excel_file_path =re.sub(r'\.csv$', '.xlsx', rad_outputFilename)# Define the Excel file path where you want to save the data
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# Write the DataFrame to an Excel file
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df.to_excel(excel_file_path, index=False)
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os.remove(rad_outputFilename)#remove original csv file if desired
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#savecsvandxlsx('ADC_radiomics','ADC_radiomics')
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#################PROCESS ADC VOLUME - find volume using regex#################
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def process_ADC():
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volnames_original = []
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#loop through names of volumes in original volume folder and test regex rules:
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children = vtk.vtkIdList()
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shNode.GetItemChildren(originalvols, children) #
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for j in range(children.GetNumberOfIds()):
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child = children.GetId(j)
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#print(child)
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print(shNode.GetItemDataNode(child).GetName())# print items in folder
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volnames_original.append(shNode.GetItemDataNode(child).GetName())
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for k in range(0,len(volnames_original)):
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if re.search(pattern_ADC, volnames_original[k]):
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print(f'matched volume at {volnames_original[k]} ')
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refvol = getNode(volnames_original[k])#if match is found
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else:
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print('not target volume...')
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#################################RUN RADIOMICS for ADC Original######################33
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segmentation = getNode('Segmentation')
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table = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLTableNode',f'{refvol.GetName()}_radiomics')
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print(f'applying radiomics to following volume: {refvol.GetName()}')
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delayDisplay(f"applying radiomics to following volume: {refvol.GetName()}")
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logic = SlicerRadiomics.SlicerRadiomicsLogic()
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logic.__init__()
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logic.runSync = True
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logic.runCLIWithParameterFile(refvol,segmentation,table,paramfilepath,callback=lambda: savecsvandxlsx(f'{refvol.GetName()}_radiomics','ADC_radiomics'))
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##############RADIOMICS - coreg-skullstripped volumes- isolate relevent volume using regex###################
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def process_coregskullstripped():
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volnames_skullstripped = []
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#loop through names of volumes in 'skullstripped' folder and test regex rules:
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children = vtk.vtkIdList()
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shNode.GetItemChildren(subjectItemID, children) # Add a third argument with value True for recursive query
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for L in range(children.GetNumberOfIds()):
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child = children.GetId(L)
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print(child)
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print(shNode.GetItemDataNode(child).GetName())# print items in folder
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volnames_skullstripped.append(shNode.GetItemDataNode(child).GetName())
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patterns_skullstripped = [pattern_FLAIR,pattern_T1,pattern_T2,pattern_T1C]#list of regext patterns to find volumes #,pattern_T2
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#################3MAKE TABLES FOR RADIOMICS
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for pattern in patterns_skullstripped:#go through and match each of the patterns to obtain correct reference volume
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for M in range(0,len(volnames_skullstripped)):
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if re.search(pattern, volnames_skullstripped[M]):
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print(f'matched volume at {volnames_skullstripped[M]} ')
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refvol = getNode(volnames_skullstripped[M])#if match is found
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#skullstripvolnamelist.append(volnames_skullstripped[M])
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global table
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table = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLTableNode',f'{volnames_skullstripped[M]}_radiomics' )
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logic = SlicerRadiomics.SlicerRadiomicsLogic()
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logic.__init__()
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logic.runSync = True
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logic.runCLIWithParameterFile(refvol,segmentation,table,paramfilepath, callback = exportskullstriptable)
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#tablenames.append(table.GetName())
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else:
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print('not target volume...')
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#export tables from the coreg-skullstrip group
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def exportskullstriptable():
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nm = table.GetName()
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if re.search(pattern_T1, nm):############export tables that match the correct
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savecsvandxlsx(nm,'T1_radiomics')
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print(f'exported {nm} as T1_radiomics')
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elif re.search(pattern_T2, nm):
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savecsvandxlsx(nm,'T2_radiomics')
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print(f'exported {nm} as T2_radiomics')
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elif re.search(pattern_FLAIR, nm):
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savecsvandxlsx(nm,'FLAIR_radiomics')
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print(f'exported {nm} as FLAIR_radiomics')
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elif re.search(pattern_T1C, nm):
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savecsvandxlsx(nm,'T1C_radiomics')
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print(f'exported {nm} as T1C_radiomics')
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else:
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print("No match")
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##############################LOOP THROUGH PATIENT FILES#############
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def mainloop():
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for i in range(0,len(subfolders)):
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global Index
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Index = i #used in savecsvandxlsx() function
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# Construct the complete path to the new subfolder
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table_folder = os.path.join(subfolders[i], "Tables")
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# Create the subfolder
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if not os.path.exists(table_folder):
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os.mkdir(table_folder)
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#find_first mrb file
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scenefile = find_file_with_extension(subfolders[i],'mrb')
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print(f'searching for scene file in {subfolders[i]}')
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#print(i)
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print(f'opening scenefile: {scenefile}')
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#load scene file
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slicer.util.loadScene(scenefile)
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print(f'opened {scenefile}')
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###################################################Segment statistics export#####################################################################
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import SegmentStatistics
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segmentationNode = getNode('Segmentation')
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segStatLogic = SegmentStatistics.SegmentStatisticsLogic()
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segStatLogic.getParameterNode().SetParameter("Segmentation", segmentationNode.GetID())
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segStatLogic.computeStatistics()
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#stats = segStatLogic.getStatistics()
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resultsTableNode = slicer.vtkMRMLTableNode()
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slicer.mrmlScene.AddNode(resultsTableNode)
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resultsTableNode.SetName('Segment_statistics')
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segStatLogic.exportToTable(resultsTableNode)
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segStatLogic.showTable(resultsTableNode)
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outputFilename = subfolders[i]+'\\Tables\\'+'CalcVolumes.csv'
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delayDisplay("Export results to CSV file: "+outputFilename)
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segStatLogic.exportToCSVFile(outputFilename)
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# Read the csv file into a pandas DataFrame
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df = pd.read_csv(outputFilename, sep=',')
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excel_file_path =re.sub(r'\.csv$', '.xlsx', outputFilename)# Define the Excel file path where you want to save the data
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# Write the DataFrame to an Excel file
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df.to_excel(excel_file_path, index=False) # Set index=False if you don't want to save the row indices
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os.remove(outputFilename)#remove original csv file if desired
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################RADIOMICS##########################################################################################
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#For Radiomics: We will employ the "Radiomics" module.
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#Input Image Volumes are as follows:
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#a. Original ADC
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#b. Coregistered-skullstripped T1
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#c. Coregistered-skullstripped T2
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#d. Coregistered-skullstripped FLAIR
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#e. Coregistered-skullstripped T1C
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#access segmentation node (should be the only segmentation, named 'Segmentation' across all mrb files)
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global segmentation
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segmentation = getNode('Segmentation')
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##################access folder hierarchy###############################
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global shNode
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shNode = slicer.mrmlScene.GetSubjectHierarchyNode()
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# Get folder named 'skullstripped'
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global sceneItemID
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sceneItemID = shNode.GetSceneItemID()
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global subjectItemID
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subjectItemID = shNode.GetItemChildWithName(sceneItemID, "skullstripped")#################coreg-skullstripped volumes
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#for access to original ADC:
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global levelunderscened
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levelunderscened = shNode.GetItemByPositionUnderParent(sceneItemID,0)
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global originalvols
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originalvols = shNode.GetItemByPositionUnderParent(levelunderscened,0)######################original volumes
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process_ADC()
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process_coregskullstripped()
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sceneSaveFilename = subfolders[i] + "\\saved-scene-AIAA segmentation_Tables" + time.strftime("%Y%m%d-%H%M%S") + ".mrb"
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if slicer.util.saveScene(sceneSaveFilename):
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logging.info("Scene saved to: {0}".format(sceneSaveFilename))
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print(f'scene file exported: {sceneSaveFilename}')
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else:
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logging.error("Scene saving failed")
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os.remove(scenefile)
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slicer.mrmlScene.Clear (0)#clear scene
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del Index
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mainloop()
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