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radiomics2.py
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radiomics2.py
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#rBatch-run radiomics module inside Slicer using a parameter file
#Usage: Set variables in slicer console according to local file paths and execute python file. For example:
#base_directory = r"C:\Users\urs\Desktop\hoedha_radiomics\test"
#paramfilepath = r"C:\urs\urs\Desktop\hoedha_radiomics\Params_radiomics.yaml"
#pythonfile = r"C:\Users\urs\Desktop\hoedha_radiomics\radiomics.py"
#exec(open(pythonfile).read())
import SlicerRadiomics
import re
import pandas as pd
import openpyxl
import os
################################SET PARAMETERS###########################################
#define regex patterns to find correct volumes in scene
pattern_T1C = r'^(?=.*(?:T1|t1|T1W))(?=.*CE)' #T1C works
pattern_ADC = r'^\d+:\s.*ADC.*' #works ADC
pattern_T1 = r'^\d+:\s(T1|t1|T1W)(?!.*CE)' #works T1
pattern_T2 = r'^\d+:\s(?!(.*FLAIR.*|.*dark-fluid.*))(T2|t2|T2W)'
pattern_FLAIR = r'^\d+:\s(FLAIR|.*dark-fluid.*)' #works FLAIR
################# Get a list of subfolders in the base directory####################
#'base_directory' path is set in the slicer python console
subfolders = [os.path.join(base_directory, folder) for folder in os.listdir(base_directory) if os.path.isdir(os.path.join(base_directory, folder))]
# Print the full paths of the subfolders
print('Processing the following folders:')
for folder in subfolders:
print(folder)
##############################FUNCTIONS################################
#function to find first mrb files in each patient folder
def find_file_with_extension(directory, extension):
for root, dirs, files in os.walk(directory):
for file in files:
if file.endswith(extension):
return os.path.join(root, file)
return None # If no file with the given extension is found
##########################export table to csv##############################
def savecsvandxlsx(nodename,outname):
result = getNode(nodename)
rad_outputFilename = subfolders[Index]+'\\Tables\\'+outname+'.csv' #TAKES i from index of mainloop!
print(rad_outputFilename)
delayDisplay("Export results to CSV file: "+rad_outputFilename,3000)
slicer.util.exportNode(result,rad_outputFilename)
# Read the csv file into a pandas DataFrame for export to xlsx
df = pd.read_csv(rad_outputFilename, sep=',')
excel_file_path =re.sub(r'\.csv$', '.xlsx', rad_outputFilename)# Define the Excel file path where you want to save the data
# Write the DataFrame to an Excel file
df.to_excel(excel_file_path, index=False)
os.remove(rad_outputFilename)#remove original csv file if desired
#savecsvandxlsx('ADC_radiomics','ADC_radiomics')
#################PROCESS ADC VOLUME - find volume using regex#################
def process_ADC():
volnames_original = []
#loop through names of volumes in original volume folder and test regex rules:
children = vtk.vtkIdList()
shNode.GetItemChildren(originalvols, children) #
for j in range(children.GetNumberOfIds()):
child = children.GetId(j)
#print(child)
print(shNode.GetItemDataNode(child).GetName())# print items in folder
volnames_original.append(shNode.GetItemDataNode(child).GetName())
for k in range(0,len(volnames_original)):
if re.search(pattern_ADC, volnames_original[k]):
print(f'matched volume at {volnames_original[k]} ')
refvol = getNode(volnames_original[k])#if match is found
else:
print('not target volume...')
#################################RUN RADIOMICS for ADC Original######################33
segmentation = getNode('Segmentation')
table = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLTableNode',f'{refvol.GetName()}_radiomics')
print(f'applying radiomics to following volume: {refvol.GetName()}')
delayDisplay(f"applying radiomics to following volume: {refvol.GetName()}")
logic = SlicerRadiomics.SlicerRadiomicsLogic()
logic.__init__()
logic.runSync = True
logic.runCLIWithParameterFile(refvol,segmentation,table,paramfilepath,callback=lambda: savecsvandxlsx(f'{refvol.GetName()}_radiomics','ADC_radiomics'))
##############RADIOMICS - coreg-skullstripped volumes- isolate relevent volume using regex###################
def process_coregskullstripped():
volnames_skullstripped = []
#loop through names of volumes in 'skullstripped' folder and test regex rules:
children = vtk.vtkIdList()
shNode.GetItemChildren(subjectItemID, children) # Add a third argument with value True for recursive query
for L in range(children.GetNumberOfIds()):
child = children.GetId(L)
print(child)
print(shNode.GetItemDataNode(child).GetName())# print items in folder
volnames_skullstripped.append(shNode.GetItemDataNode(child).GetName())
patterns_skullstripped = [pattern_FLAIR,pattern_T1,pattern_T2,pattern_T1C]#list of regext patterns to find volumes #,pattern_T2
#################3MAKE TABLES FOR RADIOMICS
for pattern in patterns_skullstripped:#go through and match each of the patterns to obtain correct reference volume
for M in range(0,len(volnames_skullstripped)):
if re.search(pattern, volnames_skullstripped[M]):
print(f'matched volume at {volnames_skullstripped[M]} ')
refvol = getNode(volnames_skullstripped[M])#if match is found
#skullstripvolnamelist.append(volnames_skullstripped[M])
global table
table = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLTableNode',f'{volnames_skullstripped[M]}_radiomics' )
logic = SlicerRadiomics.SlicerRadiomicsLogic()
logic.__init__()
logic.runSync = True
logic.runCLIWithParameterFile(refvol,segmentation,table,paramfilepath, callback = exportskullstriptable)
#tablenames.append(table.GetName())
else:
print('not target volume...')
#export tables from the coreg-skullstrip group
def exportskullstriptable():
nm = table.GetName()
if re.search(pattern_T1, nm):############export tables that match the correct
savecsvandxlsx(nm,'T1_radiomics')
print(f'exported {nm} as T1_radiomics')
elif re.search(pattern_T2, nm):
savecsvandxlsx(nm,'T2_radiomics')
print(f'exported {nm} as T2_radiomics')
elif re.search(pattern_FLAIR, nm):
savecsvandxlsx(nm,'FLAIR_radiomics')
print(f'exported {nm} as FLAIR_radiomics')
elif re.search(pattern_T1C, nm):
savecsvandxlsx(nm,'T1C_radiomics')
print(f'exported {nm} as T1C_radiomics')
else:
print("No match")
##############################LOOP THROUGH PATIENT FILES#############
def mainloop():
for i in range(0,len(subfolders)):
global Index
Index = i #used in savecsvandxlsx() function
# Construct the complete path to the new subfolder
table_folder = os.path.join(subfolders[i], "Tables")
# Create the subfolder
if not os.path.exists(table_folder):
os.mkdir(table_folder)
#find_first mrb file
scenefile = find_file_with_extension(subfolders[i],'mrb')
print(f'searching for scene file in {subfolders[i]}')
#print(i)
print(f'opening scenefile: {scenefile}')
#load scene file
slicer.util.loadScene(scenefile)
print(f'opened {scenefile}')
###################################################Segment statistics export#####################################################################
import SegmentStatistics
segmentationNode = getNode('Segmentation')
segStatLogic = SegmentStatistics.SegmentStatisticsLogic()
segStatLogic.getParameterNode().SetParameter("Segmentation", segmentationNode.GetID())
segStatLogic.computeStatistics()
#stats = segStatLogic.getStatistics()
resultsTableNode = slicer.vtkMRMLTableNode()
slicer.mrmlScene.AddNode(resultsTableNode)
resultsTableNode.SetName('Segment_statistics')
segStatLogic.exportToTable(resultsTableNode)
segStatLogic.showTable(resultsTableNode)
outputFilename = subfolders[i]+'\\Tables\\'+'CalcVolumes.csv'
delayDisplay("Export results to CSV file: "+outputFilename)
segStatLogic.exportToCSVFile(outputFilename)
# Read the csv file into a pandas DataFrame
df = pd.read_csv(outputFilename, sep=',')
excel_file_path =re.sub(r'\.csv$', '.xlsx', outputFilename)# Define the Excel file path where you want to save the data
# Write the DataFrame to an Excel file
df.to_excel(excel_file_path, index=False) # Set index=False if you don't want to save the row indices
os.remove(outputFilename)#remove original csv file if desired
################RADIOMICS##########################################################################################
#For Radiomics: We will employ the "Radiomics" module.
#Input Image Volumes are as follows:
#a. Original ADC
#b. Coregistered-skullstripped T1
#c. Coregistered-skullstripped T2
#d. Coregistered-skullstripped FLAIR
#e. Coregistered-skullstripped T1C
#access segmentation node (should be the only segmentation, named 'Segmentation' across all mrb files)
global segmentation
segmentation = getNode('Segmentation')
##################access folder hierarchy###############################
global shNode
shNode = slicer.mrmlScene.GetSubjectHierarchyNode()
# Get folder named 'skullstripped'
global sceneItemID
sceneItemID = shNode.GetSceneItemID()
global subjectItemID
subjectItemID = shNode.GetItemChildWithName(sceneItemID, "skullstripped")#################coreg-skullstripped volumes
#for access to original ADC:
global levelunderscened
levelunderscened = shNode.GetItemByPositionUnderParent(sceneItemID,0)
global originalvols
originalvols = shNode.GetItemByPositionUnderParent(levelunderscened,0)######################original volumes
process_ADC()
process_coregskullstripped()
sceneSaveFilename = subfolders[i] + "\\saved-scene-AIAA segmentation_Tables" + time.strftime("%Y%m%d-%H%M%S") + ".mrb"
if slicer.util.saveScene(sceneSaveFilename):
logging.info("Scene saved to: {0}".format(sceneSaveFilename))
print(f'scene file exported: {sceneSaveFilename}')
else:
logging.error("Scene saving failed")
os.remove(scenefile)
slicer.mrmlScene.Clear (0)#clear scene
del Index
mainloop()