import dicom import numpy as np import matplotlib.pyplot as plt import peakutils import csv import os import time from nptdms import TdmsFile import SimpleITK as sitk start = time.time() from XMLparser import getAcceptance import xml.etree.ElementTree as ET import lxml.etree as etree import warnings import fileName warnings.simplefilter('ignore', RuntimeWarning) """ This script was written to associate files for the MULTIS in vivo and in vitro experimentation. Force data and ultrasound images are collected simultaneously during indentation. In order to synchronize the force data from the .tdms file (from LABview) and the ultrasound images from the dicom file, an encoded signal in the form of pulses is sent from the data collection program (LABview) to the ECG analog input of the ultrasound. On the ultrasound monitor, the pulse can be seen in place of a typical ECG. The ultrasound software typically uses the ECG data to monitor heart rate. It does so by calculating the time intervals between each beat, specifically, the time between each R-Wave peak. By sending a simulated and simplified ECG signal to the ultrasound, we can extract each of the R-Wave time intervals from the DICOM metadata. Next, the peak of each pulse in the signal is found. The array of peaks should correspond to the RWave time vector from the ultrasound. The signal of pulses sent to the ultrasound consists of 2 start pulses + 10 bit Experimental Run Number + 8 Bit Subject ID + 2 end pulses. The start and end pulses act as a primer to ensure the 10 and 8 bit signals are always calculated by the ultrasound. The 10 and 8 bit signal are a set of binary signals. A pulse represents a 1, and no pulse represents a zero. A TDMS file is associated to a DICOM file by comparing the R Wave time vector to the time vector of the pulses (peak to peak). Because of the limited sampling frequency of the Ultrasound, the peak of each pulse sent to the ultrasound is calculated plus or minus 0 to 95 ms of the actual pulse. Sufficient spacing between pulses allows for this margin of error. When comparing signals, the maximum distance between an RWave and pulse peak cannot exceed max absolute value of error. Original Author: Tyler Schimmoeller Department of Biomedical Engineering Lerner Research Institute Cleveland Clinic Cleveland, OH schimmt@ccf.org Place all dicom and tdms files in same directory, the dicom files will be pre-appended with experimental run number Part 1 - Reading files, only extracting tdms files with pulse and dicom files with rwave """ Plot = True # Directory = "../TEST/MULTIS001-1" # change Directory for each subject # tdmsDirectory = Directory + "/Data/" # SubjectID = "MULTIS015-1" # change Directory for each subject # Directory = "../MULTIS_trials/" + SubjectID # tdmsDirectory = Directory + "/Data/" SubjectID = fileName.setDirectory()[1] Directory = fileName.setDirectory()[0] tdmsDirectory = fileName.setDirectory()[2] dicomDirectory = fileName.setDirectory()[3] print "" # for clarity in output dicomFiles = sorted(os.listdir(dicomDirectory)) # This turns a folder of DICOM files in to a list called DicomFiles if len(dicomFiles) < 3: print "No DICOM files present" exit() lengthOfLongFile = len(dicomFiles[16]) # for renaming purposes for files in dicomFiles: # change single digit trial numbers from '1' to '01' for alphabetical order purposes # print lengthOfLongFile, len(files) if len(files) < lengthOfLongFile: newFilename = files[0:-41] + '0' + files[-41:] os.rename(dicomDirectory + files, dicomDirectory + newFilename) # sorted list of files in directory for purpose of checking file extensions in for loop dicomFiles = sorted(os.listdir(dicomDirectory)) tdmsFiles = sorted(os.listdir(tdmsDirectory)) part1 = time.time() # printing a progress line def inprogress(): print ("."), print "{} TDMS Files".format(len(tdmsFiles)) print "{} DICOM Files".format(len(dicomFiles)) # beginning completion countdown count = len(tdmsFiles) print ". " * count pulseList = [] TdmsFilesNoPulse = [] TdmsFiles_WithPulse = [] RWaveList = [] DicomNoRwave = [] DicomFiles_WithRwave = [] Std = [] # check and store directory for dicom files ending in IMA only for i in dicomFiles: if i.endswith('.IMA'): try: dataset = dicom.read_file(dicomDirectory + i, stop_before_pixels=True) # reading all DICOM files RwaveRead = dataset.RWaveTimeVector try: if len(RwaveRead) > 0: RWaveList.append(RwaveRead) # creating list of rwaves DicomFiles_WithRwave.append(i) else: # print "File {} does not have a pulse train".format(i) DicomNoRwave.append(i) except TypeError: DicomNoRwave.append(i) # print "File {} does not have a pulse train".format(i) except AttributeError: DicomNoRwave.append(i) # print "File {} does not have a pulse train" .format(i) # check and store directory for tdms files ending in tdms only for i in tdmsFiles: if i.endswith('.tdms'): inprogress() tdmsFileName = tdmsDirectory + i # tdmsData = tdsmParserMultisCopy.parseTDMSfile(TdmsDirectory + filename) # reading all TDMS data tdmsFile = TdmsFile(tdmsFileName) try: # check to see if pulse exists, if not, exclue TDMS file from directory # pulse1 = tdmsData[u'Sensor.Run Number Pulse Train'][u'Run Number Pulse Train'] # the old way of parsing group = tdmsFile.groups()[3] pulse1 = tdmsFile.group_channels(group)[0].data pulseList.append(pulse1) TdmsFiles_WithPulse.append(i) except KeyError: TdmsFilesNoPulse.append(i) # must create new list because some files have no Pulse Train # print " File '" + i + "' does not have a pulse train" print "" # print "{} Dicom Files without RWaves".format(len(DicomNoRwave)) for files in DicomNoRwave: print files print "" print "{} TDMS Files without Pulse".format(len(TdmsFilesNoPulse)) for files in TdmsFilesNoPulse: print files part2 = time.time() elapsePart2 = part2 - part1 print "" print "Time Part 2 : {}".format(elapsePart2) """ Part 2 - iterating through files, matching associated files """ Tdsm_and_pulses = zip(TdmsFiles_WithPulse, pulseList) Dicom_and_rwaves = zip(DicomFiles_WithRwave, RWaveList) count = len(DicomFiles_WithRwave) def removeZeros_binary(num): Binary = 0 number = 0 num = num[0:3] if num[0] == '0': if num[1] == '0': number = num[2] Binary = bin(int(number))[2:] else: number = num[1:] Binary = bin(int(number))[2:] return number, Binary MatchTDMS = [] # list of matched tdms files MatchDICOM = [] # list of matched dicom files expRunList = [] # list of trial numbers which have matches timeSynchList = [] # list of delta T's for each matched trial run matches = 0 # Lists of running totals of the iteration in which each trial was matched. Ideally, all would match on iter 0 iter_0 = [] iter_1 = [] iter_2 = [] iter_3 = [] iter_4 = [] iter_5 = [] iter_6 = [] iterList = [] for iteration in range(7): for dicom_files, rwaves in Dicom_and_rwaves: if dicom_files not in MatchDICOM: # once a dicom has found a match, it is no longer checked for tdms_files, pulses in Tdsm_and_pulses: if tdms_files not in MatchTDMS: # once a tdms file has found a match, it is no longer checked # dcm_range_check = int(dicom_files[-42:-40]) # tdms_range_check = int(tdms_files[-30:-27]) # range_check = abs(dcm_range_check - tdms_range_check) # # if range_check > 10: # print dcm_range_check, dicom_files # print tdms_range_check, tdms_files # go = raw_input('presss Enter:') # # break # else: # iterations cycle through RWave and Peak variations. The ultrasound has a tendency to skip the first, # second, or fist and second, or last RWaves try: RWave1 = np.array(rwaves)[:] RWave2 = RWave1[1:] RWave3 = RWave1[2:] RWave4 = RWave1[1:] RWave = [RWave1, RWave1, RWave1, RWave1, RWave4, RWave2, RWave2] RWave = RWave[iteration] except ValueError: donothing = 0 pulse = pulses def findPeaks(): Peaks = peakutils.indexes(pulse, thres=0.5 * max(pulse), min_dist=100) return Peaks peaks0 = findPeaks()[:] peaks1 = findPeaks()[1:] peaks2 = findPeaks()[2:] peaks3 = findPeaks()[3:] peaks4 = findPeaks()[:-1] peakLIST = [peaks0, peaks1, peaks2, peaks4, peaks2, peaks0, peaks4] peaks = peakLIST[iteration] # useful when iteration > 1 when peaks taken away peakBits = peaks0 - peaks[0] # Find the avg difference between R Wave's and pulse Peaks def findDeltaT(rwave, Peaks): Delta_T1 = [] for i in range(len(Peaks)): dt = rwave[i] - Peaks[i] Delta_T1.append(dt) Delta_T = sum(Delta_T1) / len(Peaks) return Delta_T # Find a vector of differences to later find max def findDeltaT_vector(rwave, Peaks): Delta_T_Vector = [] for rw, p in zip(rwave, Peaks): Delta_T_Vector.append(rw - p) return Delta_T_Vector # Ensure number of RWave number of Peaks, else end if len(RWave) != len(peaks): # must be equal to continue donothing = True # necessary for an if loop # print "not equal rwave and peaks" else: # find initial difference, use to adjust rwaves for alignment Delta_T_initial = findDeltaT(RWave, peaks) # used for synchronizing files in later modeling if Delta_T_initial > 0: timeSynch = Delta_T_initial else: # if DAQ started before ultrasound timeSynch = RWave[0] + Delta_T_initial RWave_adjusted = RWave - Delta_T_initial # now that rwaves are optimally aligned, the max diff between any rwave and associated peak from signal # should not exceed 95 else not a match Delta_T_opt = np.array(findDeltaT_vector(RWave_adjusted, peaks)) Std.append(round(np.std(Delta_T_opt), 2)) max_dt = max(abs(Delta_T_opt)) if max_dt > 120: donothing = 0 else: print "Files Match" print "Iteration {} ".format(iteration) # import bit widths to decode pulse, each number represents 1 bit def getBits(filename): f = open(filename) PulseWidthsFile = csv.reader(f) Bits = [] for row in PulseWidthsFile: Bits.append(row[0]) return map(int, Bits) # map converts list of strings to list of int # loading bit markers (each at specified location) Bits = getBits('../PulseWidths300.csv') Bits_Original = Bits # to plot unaltered bits if desired # ensuring bit markers line up with pulse peaks in each iteration Bits = Bits - (peakLIST[iteration][0] - peakLIST[0][0]) # Create the x values for pulse plot def createXvals_msec(pulse): xVals_msec = [] for index in range(len(pulse)): # change peaks to peaks0 to plot original peak set xVals_msec.append(range(len(pulse))[index] - len(pulse[0:peaks0[0]])) return xVals_msec def createBinary(Bits, peakBits): # may need to add margin somehow. right now peaks and bits have to be exactly equal # which works for now # notice always adding new number to beginning, hence in reverse # because binary signal was created in reverse Binary = "" for b in Bits: if b in peakBits: # if a peak is located at bit marker -> binary = 1, else 0 Binary = '1' + Binary else: Binary = '0' + Binary SubjID_bin = Binary[0:8] ExpRunNum_bin = Binary[9:18] SubjID_dec = str(int(SubjID_bin, 2)) ExpRunNum_dec = str(int(ExpRunNum_bin, 2)) return Binary, ExpRunNum_bin, SubjID_bin, ExpRunNum_dec, SubjID_dec SubjID_dec = createBinary(Bits, peakBits)[-1] def make3digits(input): if len(input) == 1: output = '00' + str(input) elif len(input) == 2: output = '0' + str(input) else: output = str(input) return output ExpRunNum_dec = createBinary(Bits, peakBits)[-2] subID = make3digits(SubjID_dec) expRun = make3digits(ExpRunNum_dec) if iteration is 0: iter_0.append(expRun) elif iteration is 1: iter_1.append(expRun) elif iteration is 2: iter_2.append(expRun) elif iteration is 3: iter_3.append(expRun) elif iteration is 4: iter_4.append(expRun) elif iteration is 5: iter_5.append(expRun) elif iteration is 6: iter_6.append(expRun) iterList.append(iteration) timeSynchList.append(timeSynch) expRunList.append(expRun) matches += 1 if Plot: # reading the dicom pixel data reader = sitk.ImageFileReader() reader.SetFileName(dicomDirectory + dicom_files) img = reader.Execute() img = img[0:880, 658:702, -1] # indexed to crop image, and use last image in seq. nda = sitk.GetArrayFromImage(img) # optional filter to create black and white figure # filtered = [] # for rows, columns in enumerate(nda): # rowList = [] # for cols in range(len(columns)): # if any(nda[rows][cols] > 160): # rowList.append([0, 0, 0]) # else: # rowList.append([255, 0, 0]) # filtered.append(rowList) fig, (ax1, ax2) = plt.subplots(nrows=2, ncols=1, figsize=(18, 9), dpi=90) ax1 = plt.subplot2grid((7, 1), (0, 0), rowspan=5) ax2 = plt.subplot2grid((7, 1), (5, 0), rowspan=2) # image data found only in R channel of RGB. hence the '0' in the nda index indicating # use of R channel only ax2.imshow(nda[:, :, 0], interpolation=None, cmap='gray') fig.tight_layout(pad=3, w_pad=.5, h_pad=2) # plotting pulse ax1.plot(pulse, color='black', linewidth=2.5, label='$Pulse$') ax1.set_xlim(0, 8000) ax1.set_ylim(-0.1, 0.6) ax1.annotate('', xy=(RWave[0], 0.52), xytext=(RWave_adjusted[0], 0.52), arrowprops=dict(arrowstyle="<|-|>", color="blue", lw=2, alpha=.6)) Xcord = RWave[0] + (RWave_adjusted[0] - RWave[0]) / 2 ax1.annotate('dTavg: ' + str(round(Delta_T_initial, 2)) + " It: " + str(iteration), xy=(Xcord, 0.52), xycoords='data', xytext=(-120, 60), textcoords='offset points', size=12, bbox=dict(boxstyle="round,pad=.2", fc='white', ec='blue', lw=2, alpha=.6), arrowprops=dict(arrowstyle="-", color='blue', lw=2, alpha=.6, connectionstyle="angle,angleA=0,angleB=90,rad=5")) # plotting adjusted R Wave # RWave_adjusted = RWave1 # comment/uncomment to plot synched RWave with ORIGINAL pulse for wave in RWave_adjusted: if wave == RWave_adjusted[0]: ax1.axvline(x=wave, linewidth=2, color='green', linestyle='--', label='$R Wave Adjusted$') else: ax1.axvline(x=wave, linewidth=2, color='green', linestyle='--') # plotting UN adjusted R Wave for wave in RWave: if wave == RWave[0]: ax1.axvline(x=wave, linewidth=2, color='red', linestyle=':', label='$R Wave Un-Adjusted$') else: ax1.axvline(x=wave, linewidth=2, color='red', linestyle=':') # plotting pulse widths for encoding/decoding Bits = Bits_Original + peaks0[0] # comment/uncomment when want to plot original bits for bits in Bits: if bits == Bits[0]: ax1.axvline(x=Bits[0], linewidth=2, color='gray', linestyle='-', alpha=0.4) elif bits == Bits[2]: ax1.axvline(x=Bits[2], linewidth=2, color='gray', linestyle='-', alpha=0.4) elif bits == Bits[12]: ax1.axvline(x=Bits[12], linewidth=2, color='gray', linestyle='-', alpha=0.4) for bits in range(len(Bits)): ax1.axvline(x=Bits[bits], linewidth=.5, color='gray', linestyle='-') # optionally plotting pulse peaks # for j in range(len(peaks): # if j == 0: # ax1.axvline(x=shiftPeaks(peaks)[j], linewidth=1, color='red',linestyle='-', label ='Peaks') # else: # ax1.axvline(x=shiftPeaks(peaks)[j], linewidth=1, color='red', linestyle='-') # # # plotting un-adjusted/raw r wave intervalsi], l # for i in range(len(RWave)): # # if i == 0: # ax1.axvline(x=RWave[i], linewidth=1, color='orange',linestyle='--', label ='$R Wave$') # else: # ax1.axvline(x=RWave[i], linewidth=1, color='orange',linestyle='--') trial = "MULTIS" + str(subID) + " - Trial # " + str(expRun) ax1.set_xlabel("time(ms)") ax1.set_ylabel("Volts") ax1.set_title("TDMS #:" + trial + " - " + "DICOM #: " + dicom_files[-42:-40]) ax1.legend(loc='upper right', prop={'size': 10}, borderpad=0.1, handlelength=5) ax2.set_title("DICOM pulse extracted from last image in sequence. The pattern " "should match pulse above. Will be offset.", fontsize=14) ax2.set_xlabel( "* if pulse not present, error when recording. However, pulse data still collected ", fontsize=10) frame1 = plt.gca() frame1.axes.get_xaxis().set_ticks([]) frame1.axes.get_yaxis().set_ticks([]) plt.draw() if not os.path.exists(Directory + '/FileAssociationPNG'): os.makedirs(Directory + '/FileAssociationPNG') plt.savefig(Directory + '/FileAssociationPNG/' + tdms_files[:-5] + '.png') else: donothing = 0 # Renaming matched files try: os.rename(dicomDirectory + dicom_files, dicomDirectory + expRun + '_' + dicom_files[-61:]) # MatchDICOM.append(expRun + '_' + dicom_files[-61:]) except OSError: try: os.rename(dicomDirectory + dicom_files, dicomDirectory + expRun + '_' + dicom_files[:]) # MatchDICOM.append(expRun + '_' + dicom_files[:]) except OSError: print "check file length" print dicom_files exit() MatchTDMS.append(tdms_files) MatchDICOM.append(dicom_files) print "Time Synchronization : ", timeSynch print "Delta_T_Opt avg SHOULD BE ZERO : ", findDeltaT(RWave_adjusted, peaks) print "Std : {}".format(Std[-1]) print "SubjectID = ", subID print "Experiment Run Num = ", expRun print ". " * count count -= 1 # plt.show() else: continue else: donothing = 0 iterationList = [iter_0, iter_1, iter_2, iter_3, iter_4, iter_5, iter_6] synchList = sorted(zip(expRunList, iterList, timeSynchList, Std)) TDMS_name_list, Total_Accepted = getAcceptance(Directory) cnt = 0 resultsFileName = [] resultsAcceptance = [] resultsIteration = [] resultsTimeSynch = [] resultsStd = [] for filename, acceptance in TDMS_name_list: RunNumber = filename[0:3] resultsFileName.append(filename) resultsAcceptance.append(acceptance) try: if synchList[cnt][0] != RunNumber: resultsIteration.append('N/A') resultsTimeSynch.append('N/A') resultsStd.append('N/A') else: resultsIteration.append(synchList[cnt][1]) resultsTimeSynch.append(round(synchList[cnt][2], 4)) resultsStd.append(round(synchList[cnt][3], 4)) cnt += 1 except IndexError: resultsIteration.append('N/A') resultsTimeSynch.append('N/A') resultsStd.append('N/A') print "index error" results = zip(resultsFileName, resultsAcceptance, resultsIteration, resultsTimeSynch, resultsStd) # timeFile = open(Directory + '/TimeSynchronization.txt', 'wb') unMatched_but_accepted = [] matched_and_accepted = [] for TDMS_name, acc, iter, time, Std in results: if acc == 1: if iter == 'N/A': unMatched_but_accepted.append(TDMS_name) else: matched_and_accepted.append([TDMS_name, time, Std]) # timeFile.write("%s %s\n" % (TDMS_name, time)) def prettyPrintXml(xmlFilePathToPrettyPrint): """Pretty print the xml file after all frames have been analyzed""" assert xmlFilePathToPrettyPrint is not None parser = etree.XMLParser(resolve_entities=False, strip_cdata=False) document = etree.parse(xmlFilePathToPrettyPrint, parser) document.write(xmlFilePathToPrettyPrint, pretty_print=True, encoding='utf-8') # Check for Analysis directory analysis_path = Directory + '/TimeSynchronization/' if not os.path.exists(analysis_path): os.makedirs(analysis_path) ii = 0 for TDMS_name, time_adj, Std in matched_and_accepted: #Define path for the analysis folder # split_name = os.path.split(TDMS_name) # Name of the xml file xml_name = analysis_path + TDMS_name[0:25] + '_dT.xml' tail = TDMS_name[16:25] subID = TDMS_name[4:15] root = ET.Element(subID) loc = ET.SubElement(root, 'Location') ET.SubElement(loc, "Name").text = tail ET.SubElement(loc, "dT").text = str(round(time_adj,4)) tree = ET.ElementTree(root) tree.write(xml_name, xml_declaration=True) prettyPrintXml(xml_name) ii += 1 diff = 56 - len(unMatched_but_accepted) percentage = round((((diff) / float(56))*100), 2) f = open(Directory + '/' + SubjectID + 'readme.txt', 'wb') line1 = "This file contains a summary of file matching results for" line2 = "the Reference Models for Multi-Layer Tissue Structures project." f.write("%s\n%s\n" % (line1, line2)) f.write("\n") f.write("Subject ID: %s\n" % ("MULTIS" + str(subID))) f.write("\n") f.write("Matched Pairs : %i \n" % (matches)) f.write("\n") f.write("DICOM Files (total) : %i\n" % (len(dicomFiles))) f.write("DICOM Files (with RWave) : %i\n" % (len(DicomFiles_WithRwave))) f.write("DICOM Files (w/o RWave) : %i\n" % (len(DicomNoRwave))) f.write("TDMS Files (total) : %i\n" % (len(tdmsFiles))) f.write("TDMS Files (with Pulse) : %i\n" % (len(TdmsFiles_WithPulse))) f.write("TDMS Files (w/o Pulse) : %i\n" % (len(TdmsFilesNoPulse))) f.write("\n") f.write("Iteration Summary:\n" % ()) f.write("%s : %s\n" % ("#", "Count")) for index in range(7): f.write("%i : %i\n" % (index, len(iterationList[index]))) f.write("\n") f.write("Matching and Accepted: %i files - %s %%\n" % (diff, percentage)) f.write("\n") f.write("Unmatched and Accepted Trials:\n") f.write("%s %s %s\n" % ("Run#", "Conversion", "Binary")) for trials in unMatched_but_accepted: f.write("%s %s %s\n" % (trials, removeZeros_binary(trials)[0], removeZeros_binary(trials)[1])) f.write("\n") f.write('[') for trials in unMatched_but_accepted: f.write("['%s',''],\n" % (trials[0:3])) f.write(']') f.write("\n") f.write("\n") f.write('[') for trials in unMatched_but_accepted: f.write("(),\n") f.write(']') f.write("\n") f.write("%s %s %s %s %s\n" % ("Run#", "Acceptance", "Iteration", "Synch(ms)", "Std")) for i in range(len(resultsFileName)): f.write("%s %s %s %s %s\n" % (results[i][0], str(results[i][1]), results[i][2], str(results[i][3]), results[i][4])) f.write("\n") f.write("Manually Matched :\n") f.write("ExpRun# TimeSynch(ms)\n") print "{} matched trials".format(matches) print "" print "Un-matched DICOM Files : " g = open(Directory + '/' + SubjectID + 'UnMatched.txt', 'wb') # creating figures for unmatched dicoms for files in DicomFiles_WithRwave: if files not in MatchDICOM: g.write("%s\n" % (files)) reader = sitk.ImageFileReader() reader.SetFileName(dicomDirectory + files) img = reader.Execute() img = img[0:880, 658:702, -1] nda = sitk.GetArrayFromImage(img) # filtered = [] # for rows, columns in enumerate(nda): # rowList = [] # for cols in range(len(columns)): # if any(nda[rows][cols] > 160): # rowList.append([0, 0, 0]) # else: # rowList.append([255, 0, 0]) # filtered.append(rowList) fig1, ax3 = plt.subplots(nrows=1, ncols=1, figsize=(18, 9), dpi=90) fig1.tight_layout(pad=4, w_pad=.5, h_pad=2) ax3.imshow(nda[:, :, 0], interpolation=None) ax3.set_title("DICOM pulse extracted from last image in sequence. The pattern should match.", fontsize=14) ax3.set_xlabel( "* if pulse not present, error when recording. However, pulse data still collected ", fontsize=10) frame1 = plt.gca() frame1.axes.get_xaxis().set_ticks([]) frame1.axes.get_yaxis().set_ticks([]) plt.savefig(Directory + '/FileAssociationPNG/NMa_' + files + '.png') os.rename(dicomDirectory + files, dicomDirectory + "NMa_" + files[-61:]) print " ", files else: if len(files) > 65: try: os.rename(dicomDirectory + files, dicomDirectory + (files[0:4] + files[-61:])) except OSError: print "Not in directory: " print " {}".format(files) print "" print "Un-matched TDMS Files : " for files in TdmsFiles_WithPulse: if files not in MatchTDMS: os.rename(tdmsDirectory + files, tdmsDirectory + "NMa_" + files[-30:]) print " ", files else: if len(files) > 30: os.rename(tdmsDirectory + files, tdmsDirectory + files[-30:]) print"" for files in DicomNoRwave: os.rename(dicomDirectory + files, dicomDirectory + "NRW_" + files[-61:]) print "" print "{} Dicom Files without RWaves".format(len(DicomNoRwave)) print "" for files in DicomNoRwave: print files print "" print "{} TDMS Files without Pulse".format(len(TdmsFilesNoPulse)) print "" for files in TdmsFilesNoPulse: print files print "UnMatched but Accepted: ", len(unMatched_but_accepted) print Total_Accepted # A final check print "" print "" print "Final Verification" dicomFiles = sorted(os.listdir(dicomDirectory)) tdmsFiles = sorted(os.listdir(tdmsDirectory)) TDMS_name_list, Total_Accepted = getAcceptance(Directory) tdmsList = [] dicomList = [] for trials, acceptance in TDMS_name_list: if acceptance == 1: for dicom_files in dicomFiles: if dicom_files[0:3] == trials[0:3]: dicomList.append(trials) for tdms_files in tdmsFiles: if tdms_files[0:3] == trials[0:3]: tdmsList.append(trials) cnt = 0 for trials in dicomList: for tdmsTrials in tdmsList: if trials == tdmsTrials: cnt += 1 print "Accepted (XML): ", Total_Accepted print "Dicom: ", len(dicomList) print "Tdms: ", len(tdmsList) print "Matchted TDMS with DICOM (checking directory):", cnt