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ImageAnalysis4DMRIAngiography.py
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ImageAnalysis4DMRIAngiography.py
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import vtk
import numpy
import argparse
from glob import glob
import os
class ImageAnalysis4DMRIAngiography():
def __init__(self,Arg):
self.Args=Arg
def Main(self):
#Separate all images into individual folders
self.SeparateCycles(self.Args.MagnitudeFolder,"Magnitude")
self.SeparateCycles(self.Args.Phase1Folder,"Phase1")
self.SeparateCycles(self.Args.Phase2Folder,"Phase2")
self.SeparateCycles(self.Args.Phase3Folder,"Phase3")
def SeparateCycles(self,FolderName,Tag):
#Get all of the files in the folder
FileNames_=sorted(glob(FolderName+"/*.IMA"))+sorted(glob(FolderName+"/*.dcm"))
#Separte the files in N folders
os.system("mkdir %s/%s"%(self.Args.OutputFolder,Tag))
for i in range(self.Args.Cycles): os.system("mkdir %s/%s/%s_%d"%(self.Args.OutputFolder,Tag,Tag,i))
#Loop over all of the files and stack them into difference folders
counter=0
for i in range(len(FileNames_)):
<<<<<<< HEAD
os.system("cp %s %s/%s/%s_%d/"%(FileNames_[i],self.Args.OutputFolder,Tag,Tag,counter))
if i%(len(FileNames_)/self.Args.Cycles): counter+=1
=======
os.system("cp %s %s/%s/%s_%d"%(FileNames_[i],self.Args.OutputFolder,Tag,Tag,counter))
if (i+1)%(len(FileNames_)/self.Args.Cycles)==0: counter+=1
>>>>>>> 91f3a806e16878b4cedfed998eb790d07bab7964
if __name__=="__main__":
#Description
parser = argparse.ArgumentParser(description="This script will average the 4D Flow MRI data to convert into angiography data to segmentation easier.")
#Provide a path to the Magnitude Images
parser.add_argument('-MagnitudeFolder', '--MagnitudeFolder', type=str, required=True, dest="MagnitudeFolder",help="The foldername that contains the magnitude images")
#Provide a path for phase images 1 2 and 3
parser.add_argument('-Phase1Folder', '--Phase1Folder', type=str, required=True, dest="Phase1Folder",help="The foldername that contains the phase1 images")
parser.add_argument('-Phase2Folder', '--Phase2Folder', type=str, required=True, dest="Phase2Folder",help="The foldername that contains the phase2 images")
parser.add_argument('-Phase3Folder', '--Phase3Folder', type=str, required=True, dest="Phase3Folder",help="The foldername that contains the phase3 images")
#Provide a velocity encoding
parser.add_argument('-Venc', '--Venc', type=int, required=True, dest="Venc",help="The velocity encoding used for this scan.")
#Number of scan cycles
parser.add_argument('-Cycles', '--Cycles', type=int, required=True, dest="Cycles",help="The number of cycles in the 4D MRI images")
#Name of the output folder
parser.add_argument('-OutputFolder', '--OutputFolder', type=str, required=True, dest="OutputFolder",help="The foldername to put all the results in.")
args=parser.parse_args()
ImageAnalysis4DMRIAngiography(args).Main()