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createDICOM.py
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###################################################################################################
# Program: createdcm.py #
# This program was written to read in pinnacle text files and convert them into DICOM files #
# The files required: Patient (text file under patient folder), #
# plan.Points (file under Patient folder->plan label folder), #
# plan.roi (file under Patient folder -> plan label folder), #
# plan.Trial (file under Patient folder -> plan label folder), #
# plan.Trial.Binary.xxx (xxx represents number of file, several needed) #
# ImageSet_%s.ImageInfo (text file under patient folder) #
# ImageSet_%s.header #
# Either folder with images or ImageSet_%s file
# Code Authors are: Colleen Henschel, Andrew Alexander #
###################################################################################################
####################################################################################################################################################
# import libraries below
####################################################################################################################################################
from __future__ import print_function
import time #used for getting current date and time for file
import re #used for isolated values from strings
import sys
import os.path
import dicom
import numpy as np
from dicom.dataset import Dataset, FileDataset
from dicom.sequence import Sequence
from dicom.filebase import DicomFile
import dicom.UID
import os
import struct
from random import randint
from PIL import Image
####################################################################################################################################################
# Global Variables
####################################################################################################################################################
ROI_COUNT = 0 #This value will represent the ROI that I'm currently looking at in file, will be incremented for each roi
SeriesUID = "NA"
StudyInstanceUID = "NA"
FrameUID = "NA"
ClassUID = "NA"
patientname = ""
dob = ""
pid = ""
imageslice = []
imageuid = []
Colors = [['255','0','0'],['255','20','147'],['0','0','255'],['0','255','0'],['125','38','205'],['255','255','0'],['255','140','0'],['0','100','0'],['0','191','255'],['255','192','203'],['72','209','204'],['139','69','19'],['255','193','37'],['221','160','221'],['107','142','35'],['142','35','35'],['245','204','176'],['191','239','255'],['139','28','98'],['255','99','71']] #red, pink, blue, green, purple, yellow, orange, dark green, sky blue, light pink, Turquois, brown, gold,lightpurple, olive, brick, peach?, light blue, maroon, tomato
patient_sex = ""
study_date = ""
study_time = ""
model = ""
physician = ""
sid = ""
isocenter = []
ctcenter = []
descrip = ""
plancount = 0
plannamelist = []
planids = []
randval = randint(0,999)
currentdate = time.strftime("%Y%m%d")
currenttime = time.strftime("%H%M%S")
doserefpt = []
patient_position = ""
xshift = 0
yshift = 0
zshift = 0
lname = ""
fname = ""
patientfolder = ""
structsopinstuid = ''
structseriesinstuid = ''
plansopinstuid = ''
planseriesinstuid = ''
doseseriesuid = ''
doseinstuid = ''
planfilename = ''
dosexdim = 0
doseydim = 0
dosezdim = 0
doseoriginx = ""
doseoriginy = ""
doseoriginz = ""
beamdosefiles = []
pixspacingx = ""
pixspacingy = ""
pixspacingz = ""
posrefind = ""
image_orientation = []
imagesetnumber = ""
point_names = []
point_values = []
numfracs = ""
flag_nobinaryfile = False
flag_noimages = False
GTransferSyntaxUID='1.2.840.10008.1.2'
no_setup_file = False
no_beams = False
gImplementationClassUID='1.2.826.0.1.3680043.8.498.75006884747854523615841001'
Manufacturer="Pinnacle Philips"
Inputf="//Inputfolder/"
outputfolder="//outputfolder/"
PDD6MV = 0.6683
PDD10MV = 0.6683 # Also temporary, need to get actual PDD value
PDD15MV = 0.7658
PDD16MV = 0.7658 ## THis is temporary, this value is not correct just using as place holder for now
softwarev = ""
slicethick = 0
x_dim = 0
y_dim = 0
z_dim = 0
xpixdim = 0
ypixdim = 0
#listofversions = []
####################################################################################################################################################
# Function: main
# This main function is what should be called to run program
# The name of the patient folder should be passed into the function for it to be run. This folder should be stored under Inputf directory (line 102)
####################################################################################################################################################
def main(temppatientfolder):
global ROI_COUNT
global structfilename
global outputfolder
global SeriesUID
global StudyInstanceUID
global FrameUID
global ClassUID
global patientname
global dob
global pid
global imageslice
global imageuid
global Colors
global patient_sex
global study_date
global study_time
global model
global physician
global sid
global isocenter
global ctcenter
global descrip
global plancount
global plannamelist
global planids
global randval
global currentdate
global currenttime
global doserefpt
global patient_position
global xshift
global yshift
global lname
global fname
global patientfolder
global structsopinstuid
global structseriesinstuid
global plansopinstuid
global planseriesinstuid
global doseinstuid
global doseseriesuid
global planfilename
global flag_noimages
global no_setup_file
global no_beams
global softwarev
initglobalvars() # First step of the main function is to call the initglobalvars variable to reset everything in case this function is being used in a loop. (see allpatientloop.py)
#print("Input Patient Folder:")
#patientfolder = raw_input("> ")
#temppatientfolder="Patient_9419"
patientfolder = temppatientfolder
print("Current Patient: " + patientfolder)
if not os.path.exists(outputfolder+"%s"%(patientfolder)):
os.makedirs(outputfolder+"%s"%(patientfolder)) #Create folder for exported DICOM files if it does not already exist
print("Output location: " + outputfolder)
structsopinstuid = dicom.UID.generate_uid()
structds = createstructds() #creating dataset for structure file
for j in range(0, 5000):
morewastingtime = j
structseriesinstuid = dicom.UID.generate_uid()
structds.ReferencedStudySequence = Sequence()
structds = initds(structds)
structds = readpatientinfo(structds)
readImageInfo() #Gets UID information for image files
structds = initds(structds) #initializes values like uids, creation time, manufacturer, values that are not patient dependent
for i in range(0, 5000):
timewaster = i
plansopinstuid = dicom.UID.generate_uid()
convertimages() #This function makes the image files usable (matches patient info that will go into other DICOM files). If image files do not exist this function calls createimagefiles function
if flag_noimages:
return
planseriesinstuid = dicom.UID.generate_uid()
patient_position = getpatientsetup("Plan_%s"%planids[0])
if no_setup_file == True:
return
structds.ReferencedFrameOfReferenceSequence = Sequence()
ReferencedFrameofReference1 = Dataset()
structds.ReferencedFrameOfReferenceSequence.append(ReferencedFrameofReference1)
structds.ReferencedFrameOfReferenceSequence[0].FrameofReferenceUID = FrameUID
structds.ReferencedFrameOfReferenceSequence[0].RTReferencedStudySequence = Sequence()
RTReferencedStudy1 = Dataset()
structds.ReferencedFrameOfReferenceSequence[0].RTReferencedStudySequence.append(RTReferencedStudy1)
structds.ReferencedFrameOfReferenceSequence[0].RTReferencedStudySequence[0].ReferencedSOPClassUID = '1.2.840.10008.3.1.2.3.2'
structds.ReferencedFrameOfReferenceSequence[0].RTReferencedStudySequence[0].ReferencedSOPInstanceUID = StudyInstanceUID
structds.StudyInstanceUID = StudyInstanceUID
structds.ReferencedFrameOfReferenceSequence[0].RTReferencedStudySequence[0].RTReferencedSeriesSequence = Sequence()
RTReferencedSeries1 = Dataset()
structds.ReferencedFrameOfReferenceSequence[0].RTReferencedStudySequence[0].RTReferencedSeriesSequence.append(RTReferencedSeries1)
structds.ReferencedFrameOfReferenceSequence[0].RTReferencedStudySequence[0].RTReferencedSeriesSequence[0].SeriesInstanceUID = SeriesUID
structds.ReferencedFrameOfReferenceSequence[0].RTReferencedStudySequence[0].RTReferencedSeriesSequence[0].ContourImageSequence = Sequence()
for i, value in enumerate(imageuid,1):
exec("ContourImage%d = Dataset()"% i)
exec("structds.ReferencedFrameOfReferenceSequence[0].RTReferencedStudySequence[0].RTReferencedSeriesSequence[0].ContourImageSequence.append(ContourImage%d)"%i)
structds.ReferencedFrameOfReferenceSequence[0].RTReferencedStudySequence[0].RTReferencedSeriesSequence[0].ContourImageSequence[i-1].ReferencedSOPClassUID = '1.2.840.10008.5.1.4.1.1.1'
structds.ReferencedFrameOfReferenceSequence[0].RTReferencedStudySequence[0].RTReferencedSeriesSequence[0].ContourImageSequence[i-1].ReferencedSOPInstanceUID = imageuid[i-1]
doseinstuid = dicom.UID.generate_uid()
structds.ROIContourSequence = Sequence()
structds.StructureSetROISequence = Sequence()
structds.RTROIObservationsSequence = Sequence()
if softwarev != "Pinnacle 9.0": # If pinnacle software is version 9.0 the shifts are not needed so this function can be skipped and the values for the shifts will still be set to zero
getstructshift()
structds = readpoints(structds, "Plan_%s"%planids[0])
structds = readroi(structds, "Plan_%s"%planids[0])
structds.ApprovalStatus = 'UNAPPROVED' #find out where to get if its been approved or not
# Set the transfer syntax
structds.is_little_endian = True
structds.is_implicit_VR = True
#structfilepath=outputfolder + patientfolder + "/" + structfilename
#structds.save_as("structfilepath")
print("Structure file being saved\n")
structds.save_as(outputfolder + "/%s/%s"%(patientfolder, structfilename))
doseseriesuid = dicom.UID.generate_uid()
print("creating plan data structures \n")
#############################################################################################
# loop below creates plan files for each plan in directory (based on what is in the Patient file)
for i in range(0, plancount):
planame = plannamelist[i]
plandirect = "Plan_" + planids[i]
exec("plands_%s = createplands(i)"%planids[i])
exec("plands_%s = planinit(plands_%s, planame, plandirect, i)"%(planids[i], planids[i]))
exec("plands_%s = readtrial(plands_%s, plandirect, i)"%(planids[i], planids[i]))
if no_beams == True:
continue
print("Setting plan file name:")
#exec("tempmetainstuid = plands_%s.file_meta.MediaStorageSOPInstanceUID"%planids[i])
tempmetainstuid = plansopinstuid + "." + str(i)
planfilename = 'RP.' + tempmetainstuid + '.dcm'
print("Plan file name: " + planfilename)
planfilepath=outputfolder + patientfolder + "/" + planfilename
print(planfilepath)
print("\n Saving plan file \n")
exec("plands_%s.save_as(planfilepath)"%(planids[i]))
os.rename(outputfolder+'%s'% patientfolder, outputfolder+'%s,%s,%s'%(lname,fname,pid))
#print("\n \n Current software versions found: \n")
#for ver in softwarev:
#print(ver)
return softwarev
####################################################################################################################################################
####################################################################################################################################################
####################################################################################################################################################
# Function: initglobalvars
# This function simply resets all of the global variables to empty values
####################################################################################################################################################
def initglobalvars():
global ROI_COUNT
global structfilename
global SeriesUID
global StudyInstanceUID
global FrameUID
global ClassUID
global patientname
global dob
global pid
global imageslice
global imageuid
global Colors
global patient_sex
global study_date
global study_time
global model
global physician
global sid
global isocenter
global ctcenter
global descrip
global plancount
global plannamelist
global planids
global randval
global currentdate
global currenttime
global doserefpt
global patient_position
global xshift
global yshift
global zshift
global lname
global fname
global patientfolder
global structsopinstuid
global structseriesinstuid
global plansopinstuid
global planseriesinstuid
global doseseriesuid
global doseinstuid
global planfilename
global dosexdim
global doseydim
global dosezdim
global doseoriginx
global doseoriginy
global doseoriginz
global beamdosefiles
global pixspacingx
global pixspacingy
global pixspacingz
global posrefind
global image_orientation
global imagesetnumber
global point_names
global point_values
global numfracs
global flag_nobinaryfile
global flag_noimages
global no_setup_file
global no_beams
global softwarev
global slicethick
global x_dim
global y_dim
global z_dim
global xpixdim
global ypixdim
ROI_COUNT = 0 #This value will represent the ROI that I'm currently looking at in file, will be incremented for each roi
SeriesUID = "NA"
StudyInstanceUID = "NA"
FrameUID = "NA"
ClassUID = "NA"
patientname = ""
dob = ""
pid = ""
imageslice = []
imageuid = []
Colors = [['255','0','0'],['255','20','147'],['0','0','255'],['0','255','0'],['125','38','205'],['255','255','0'],['255','140','0'],['0','100','0'],['0','191','255'],['255','192','203'],['72','209','204'],['139','69','19'],['255','193','37'],['221','160','221'],['107','142','35'],['142','35','35'],['245','204','176'],['191','239','255'],['139','28','98'],['255','99','71']] #red, pink, blue, green, purple, yellow, orange, dark green, sky blue, light pink, Turquois, brown, gold,lightpurple, olive, brick, peach?, light blue, maroon, tomato
patient_sex = ""
study_date = ""
study_time = ""
model = ""
physician = ""
sid = ""
isocenter = []
ctcenter = []
descrip = ""
plancount = 0
plannamelist = []
planids = []
randval = randint(0,999)
currentdate = time.strftime("%Y%m%d")
currenttime = time.strftime("%H%M%S")
doserefpt = []
patient_position = ""
xshift = 0
yshift = 0
zshift = 0
lname = ""
fname = ""
patientfolder = ""
structsopinstuid = ''
structseriesinstuid = ''
plansopinstuid = ''
planseriesinstuid = ''
doseseriesuid = ''
doseinstuid = ''
planfilename = ''
dosexdim = 0
doseydim = 0
dosezdim = 0
doseoriginx = ""
doseoriginy = ""
doseoriginz = ""
beamdosefiles = []
pixspacingx = ""
pixspacingy = ""
pixspacingz = ""
posrefind = ""
image_orientation = []
imagesetnumber = ""
point_names = []
point_values = []
numfracs = ""
flag_nobinaryfile = False
flag_noimages = False
no_setup_file = False
no_beams = False
softwarev = ""
slicethick = 0
x_dim = 0
y_dim = 0
z_dim = 0
xpixdim = 0
ypixdim = 0
####################################################################################################################################################
####################################################################################################################################################
####################################################################################################################################################
# function: convertimages
# The purpose of this function is to read in the image DICOM files
# and to change the patients name to match the name of the patient
# in the pinnacle files, also fills the list values for slicelocation
# and UID. This function needs to be run, even if image files already converted
####################################################################################################################################################
def convertimages():
print("Converting image patient name, birthdate and id to match pinnacle\n")
global patientname
global pid
global dob
global FrameUID
global imageslice
global SeriesUID
global StudyInstanceUID
global imageuid
global patientfolder
global posrefind
global imagesetnumber
global image_orientation
global flag_noimages
if not os.path.exists("%s%s/ImageSet_%s.DICOM"%(Inputf,patientfolder, imagesetnumber)):
#Image set folder not found, need to ignore patient
#Will want to call a function to be written that will create image set files from the condensed pixel data file
print("Image files do not exist. Creating image files")
createimagefiles()
return
for file in os.listdir("%s%s/ImageSet_%s.DICOM"%(Inputf,patientfolder, imagesetnumber)):
if file == '11026.1.img':
continue
imageds = dicom.read_file("%s%s/ImageSet_%s.DICOM/%s"%(Inputf, patientfolder, imagesetnumber, file), force=True)
imageds.PatientsName = patientname
imageds.PatientID = pid
imageds.PatientsBirthDate = dob
imageslice.append(imageds.SliceLocation)
imageuid.append(imageds.SOPInstanceUID)
image_orientation = imageds.ImageOrientationPatient
tempinstuid = imageds.SOPInstanceUID
posrefind = imageds.PositionReferenceIndicator
imageds.SOPInstanceUID = tempinstuid
imageds.FrameOfReferenceUID = FrameUID
imageds.StudyInstanceUID = StudyInstanceUID
imageds.SeriesInstanceUID = SeriesUID
file_meta = Dataset()
file_meta.TransferSyntaxUID = GTransferSyntaxUID
file_meta.MediaStorageSOPClassUID = '1.2.840.10008.5.1.4.1.1.2'
file_meta.MediaStorageSOPInstanceUID = tempinstuid
file_meta.ImplementationClassUID = gImplementationClassUID
imageds.file_meta = file_meta
preamble = getattr(imageds, "preamble", None)
if not preamble:
preamble = b'\x00'*128
currfile = DicomFile(outputfolder+"%s/CT.%s.dcm"%(patientfolder, tempinstuid), 'wb')
currfile.write(preamble)
currfile.write(b'DICM')
dicom.write_file(outputfolder+"%s/CT.%s.dcm"%(patientfolder,tempinstuid), imageds, False)
print("Current image: ", file)
####################################################################################################################################################
####################################################################################################################################################
####################################################################################################################################################
# Function: createimagefiles()
# This function will create dicom image files for each slice using the condensed pixel data from file ImageSet_%s.img
####################################################################################################################################################
def createimagefiles():
global slicethick
global x_dim
global y_dim
global z_dim
global xpixdim
global ypixdim
global patientname
global pid
global dob
global FrameUID
global imageslice
global SeriesUID
global StudyInstanceUID
global imageuid
global patientfolder
global posrefind
global imagesetnumber
global image_orientation
currentpatientposition = getheaderinfo()
if os.path.isfile("%s%s/ImageSet_%s.img"%(Inputf, patientfolder, imagesetnumber)):
allframeslist = []
pixel_array = np.fromfile("%s%s/ImageSet_%s.img"%(Inputf, patientfolder, imagesetnumber), dtype = np.short)
for i in range(0, int(z_dim)): # will loop over every frame
frame_array = pixel_array[i*int(x_dim)*int(y_dim):(i+1)*int(x_dim)*int(y_dim)]
allframeslist.append(frame_array)
"""frame_array = np.array([])
temp_frame_array = pixel_array[i*int(x_dim)*int(y_dim):(i+1)*int(x_dim)*int(y_dim)]
for j in range(0, int(y_dim)):
temprow = temp_frame_array[j*int(x_dim):(j+1)*int(x_dim)][::-1]
frame_array = np.append(frame_array, temprow)
allframeslist.append(frame_array)
"""
print("Length of frames list: " + str(len(allframeslist)))
with open("%s%s/ImageSet_%s.ImageInfo"%(Inputf, patientfolder, imagesetnumber), 'rt', encoding='latin1') as f:
image_info = f.readlines()
curframe = 0
for i, line in enumerate(image_info, 0):
if "ImageInfo ={" in line:
sliceloc = -float(re.findall(r"[-+]?\d*\.\d+|\d+", image_info[i + 1])[0])*10
instuid = re.findall(r'"([^"]*)"', image_info[i + 8])[0]
seriesuid = re.findall(r'"([^"]*)"', image_info[i + 4])[0]
classuid = re.findall(r'"([^"]*)"', image_info[i + 7])[0]
frameuid = re.findall(r'"([^"]*)"', image_info[i + 6])[0]
studyinstuid = re.findall(r'"([^"]*)"', image_info[i + 5])[0]
slicenum = int(re.findall(r"[-+]?\d*\.\d+|\d+", image_info[i + 3])[0])
dateofscan, timeofscan = getdateandtime()
file_meta = Dataset()
file_meta.MediaStorageSOPClassUID = classuid
file_meta.MediaStorageSOPInstanceUID = instuid
file_meta.ImplementationClassUID = gImplementationClassUID #this value remains static since implementation for creating file is the same
ds = FileDataset(planfilename, {}, file_meta=file_meta, preamble=b'\x00'*128)
ds.SpecificCharacterSet = "ISO_IR 100"
ds.ImageType = ['ORIGINAL', 'PRIMARY', 'AXIAL']
ds.AccessionNumber = ''
ds.SOPClassUID = classuid
ds.SOPInstanceUID = instuid
ds.StudyDate = dateofscan
ds.SeriesDate = dateofscan
ds.AcquisitionDate = dateofscan
ds.ContentDate = dateofscan
ds.AcquisitionTime = timeofscan
ds.Modality = "CT" # Also should come from header file, but not always present
ds.Manufacturer = "GE MEDICAL SYSTEMS" #This should come from Manufacturer in header, but for some patients it isn't set??
ds.StationName = "CT"
ds.PatientsName = patientname
ds.PatientID = pid
ds.PatientsBirthDate = dob
ds.BitsAllocated = 16
ds.BitsStored = 16
ds.HighBit = 15
ds.PixelRepresentation = 1
ds.RescaleIntercept = -1024
#ds.RescaleIntercept = 0.0
ds.RescaleSlope = 1.0
# ds.kvp = ?? This should be peak kilovoltage output of x ray generator used
ds.PatientPosition = currentpatientposition
ds.DataCollectionDiameter = xpixdim*float(x_dim) # this is probably x_pixdim * xdim = y_pixdim * ydim
ds.SpatialResolution = 0.35#???????
#ds.DistanceSourceToDetector = #???
#ds.DistanceSourceToPatient = #????
ds.GantryDetectorTilt = 0.0 #??
ds.TableHeight = -158.0#??
ds.RotationDirection = "CW"#???
ds.ExposureTime = 1000#??
ds.XRayTubeCurrent = 398#??
ds.GeneratorPower = 48#??
ds.FocalSpots = 1.2#??
ds.ConvolutionKernel = "STND" #????
ds.SliceThickness = slicethick
ds.NumberOfSlices = int(z_dim)
#ds.StudyInstanceUID = studyinstuid
#ds.SeriesInstanceUID = seriesuid
ds.FrameOfReferenceUID = FrameUID
ds.StudyInstanceUID = StudyInstanceUID
ds.SeriesInstanceUID = SeriesUID
ds.InstanceNumber = slicenum # problem, some of these are repeated in image file so not sure what to do with that
ds.ImagePositionPatient = [-xpixdim*float(x_dim)/2, -ypixdim*float(y_dim)/2, sliceloc]
if "HFS" in currentpatientposition or "FFS" in currentpatientposition:
ds.ImageOrientationPatient = [1.0, 0.0, 0.0, 0.0, 1.0, -0.0]
elif "HFP" in currentpatientposition or "FFP" in currentpatientposition:
ds.ImageOrientationPatient = [-1.0, 0.0, 0.0, 0.0, -1.0, -0.0]
ds.PositionReferenceIndicator = "LM" #???
ds.SliceLocation = sliceloc
ds.SamplesPerPixel = 1
ds.PhotometricInterpretation = "MONOCHROME2"
ds.Rows = int(x_dim)
ds.Columns = int(y_dim)
ds.PixelSpacing = [xpixdim, ypixdim]
#ds.PixelData = allframeslist[curframe]
#ds.PixelData = allframeslist[slicenum - 1]
ds.PixelData = allframeslist[curframe].tostring()
imageslice.append(sliceloc)
imageuid.append(instuid)
image_orientation = ds.ImageOrientationPatient
posrefind = ds.PositionReferenceIndicator
print("Creating image: " + outputfolder + "%s/CT.%s.dcm"%(patientfolder, instuid))
ds.save_as(outputfolder + "%s/CT.%s.dcm"%(patientfolder, instuid))
curframe = curframe + 1
####################################################################################################################################################
####################################################################################################################################################
####################################################################################################################################################
# Function: getheaderinfo
# This function will only be called in cases where image files do not already exist
####################################################################################################################################################
def getheaderinfo():
global slicethick
global x_dim
global y_dim
global z_dim
global xpixdim
global ypixdim
temp_pos = ""
with open("%s%s/ImageSet_%s.header"%(Inputf, patientfolder, imagesetnumber), "rt", encoding='latin1') as f2:
for line in f2:
#print("line in header: " + line)
if "x_dim =" in line:
x_dim = (line.split(" ")[-1]).replace(';','').replace('\n', '')
if "y_dim =" in line:
y_dim = (line.split(" ")[-1]).replace(';','').replace('\n', '')
if "x_pixdim =" in line:
xpixdim = float((line.split(" ")[-1]).replace(';',''))*10
if "y_pixdim =" in line:
ypixdim = float((line.split(" ")[-1]).replace(';',''))*10
if "x_start =" in line and "index" not in line:
xstart = float((line.split(" ")[-1]).replace(';',''))
print("xstart = ", xstart)
if "y_start =" in line:
ystart = float((line.split(" ")[-1]).replace(';',''))
if "z_dim =" in line:
z_dim = (line.split(" ")[-1]).replace(';','').replace('\n', '')
if "z_pixdim =" in line:
slicethick = float((line.split(" ")[-1]).replace(';',''))*10
if "z_start =" in line and "index" not in line:
zstart = float((line.split(" ")[-1]).replace(';',''))
if "patient_position" in line:
temp_pos = (line.split(" ")[-1]).replace("\n","")
print("Patient_position is: " + temp_pos)
return temp_pos
####################################################################################################################################################
####################################################################################################################################################
####################################################################################################################################################
# Function: getdateandtime
# Will read ImageSet_%s.ImageSet file to get date and time of CT image aquisition, only used in cases where image files have not been created
####################################################################################################################################################
def getdateandtime():
with open("//Testfile", "rt", encoding='latin1') as g:
for line in g:
if "ScanTimeFromScanner" in line:
dateandtimestring = re.findall(r'"([^"]*)"', line)[0]
dateandtimelist = dateandtimestring.split(' ')
date = dateandtimelist[0].replace("-", "")
time = dateandtimelist[1].replace(":","")
return date, time
####################################################################################################################################################
####################################################################################################################################################
####################################################################################################################################################
# function: readImageInfo
# Reads in the file ImageSet_0.ImageInfo to get uid values
# Saves the general UIDs as global variables
####################################################################################################################################################
def readImageInfo():
print("Reading image information for all image files\n")
global SeriesUID
global StudyInstanceUID
global FrameUID
global ClassUID
global patientfolder
global randval
global imagesetnumber
#print("Path to image info file: " + "%s%s/ImageSet_%s.ImageInfo"%(Inputf, patientfolder, imagesetnumber))
if not os.path.exists("%s%s/ImageSet_%s.ImageInfo"%(Inputf, patientfolder, imagesetnumber)):
#print("Leaving readImageInfo before getting info")
return
with open("%s%s/ImageSet_%s.ImageInfo"%(Inputf, patientfolder, imagesetnumber), 'rt', encoding='latin1') as f1:
for line in f1:
#print("For loop in readImageInfo")
if "SeriesUID" in line:
SeriesUID = re.findall(r'"([^"]*)"', line)[0]
#print("setting series uid: " + str(SeriesUID))
#SeriesUID = SeriesUID + "." + "0" + str(randval)
if "StudyInstanceUID" in line:
StudyInstanceUID = re.findall(r'"([^"]*)"', line)[0]
#print("setting study uid: " + str(StudyInstanceUID))
#StudyInstanceUID = StudyInstanceUID + "." + "0" + str(randval)
if "FrameUID" in line:
FrameUID = re.findall(r'"([^"]*)"', line)[0]
#print("setting frame uid: " + str(FrameUID))
# FrameUID = FrameUID[:-4] + "." + "0" + str(randval)
if "ClassUID" in line:
ClassUID = re.findall(r'"([^"]*)"', line)[0]
#print("setting class uid: " + str(ClassUID))
#ClassUID = ClassUID + "." + "0" + str(randval)
####################################################################################################################################################
####################################################################################################################################################
####################################################################################################################################################
# Creating a data structure to write to rt struct dicom file
# Based off example file write_new.py from C:\Python27\Lib\site-packages\dicom\examples\write_new.py
# returns data structure ds
####################################################################################################################################################
def createstructds():
print("Creating Data structure")
global structfilename
global structsopinstuid
# Populate required values for file meta information
file_meta = Dataset()
file_meta.MediaStorageSOPClassUID = '1.2.840.10008.5.1.4.1.1.481.3' #RT Structure Set Storage
file_meta.MediaStorageSOPInstanceUID = structsopinstuid
structfilename="RS."+structsopinstuid+".dcm"
file_meta.ImplementationClassUID = gImplementationClassUID #this value remains static since implementation for creating file is the same
# Create the FileDataset instance (initially no data elements, but file_meta supplied)
ds = FileDataset(structfilename, {}, file_meta=file_meta, preamble=b'\x00'*128)
#print(file_meta.preamble)
return ds
####################################################################################################################################################
####################################################################################################################################################
####################################################################################################################################################
# Function: getstructshift()
# Purpose: reads in values from ImageSet_0.header to get x and y shift
####################################################################################################################################################
def getstructshift():
global xshift
global yshift
global zshift
global patient_position
global imagesetnumber
with open("%s%s/ImageSet_%s.header"%(Inputf, patientfolder, imagesetnumber), "rt", encoding='latin1') as f2:
for line in f2:
if "x_dim =" in line:
x_dim = float((line.split(" ")[-1]).replace(';',''))
if "y_dim =" in line:
y_dim = float((line.split(" ")[-1]).replace(';',''))
if "x_pixdim =" in line:
xpixdim = float((line.split(" ")[-1]).replace(';',''))
if "y_pixdim =" in line:
ypixdim = float((line.split(" ")[-1]).replace(';',''))
if "x_start =" in line and "index" not in line:
xstart = float((line.split(" ")[-1]).replace(';',''))
print("xstart = ", xstart)
if "y_start =" in line:
ystart = float((line.split(" ")[-1]).replace(';',''))
if "z_dim =" in line:
z_dim = float((line.split(" ")[-1]).replace(';',''))
if "z_pixdim =" in line:
zpixdim = float((line.split(" ")[-1]).replace(';',''))
if "z_start =" in line and "index" not in line:
zstart = float((line.split(" ")[-1]).replace(';',''))
if patient_position == 'HFS':
xshift = ((x_dim*xpixdim/2)+xstart)*10
print("X shift = ", xshift)
yshift = -((y_dim*ypixdim/2)+ystart)*10
print("Y shift = ", yshift)
zshift = -((z_dim*zpixdim/2)+zstart)*10
elif patient_position == 'HFP':
xshift = -((x_dim*xpixdim/2)+xstart)*10
print("X shift = ", xshift)
yshift = ((y_dim*ypixdim/2)+ystart)*10
print("Y shift = ", yshift)
zshift = -((z_dim*zpixdim/2)+zstart)*10
elif patient_position == 'FFP':
xshift = ((x_dim*xpixdim/2)+xstart)*10
print("X shift = ", xshift)
yshift = ((y_dim*ypixdim/2)+ystart)*10
print("Y shift = ", yshift)
zshift = ((z_dim*zpixdim/2)+zstart)*10
elif patient_position == 'FFS':
xshift = -((x_dim*xpixdim/2)+xstart)*10
print("X shift = ", xshift)
yshift = -((y_dim*ypixdim/2)+ystart)*10
print("Y shift = ", yshift)
zshift = ((z_dim*zpixdim/2)+zstart)*10
####################################################################################################################################################
####################################################################################################################################################
####################################################################################################################################################
# Function: createplands()
# creates a data structure for the rt plan file
# similar to createstructds but different UIDs
####################################################################################################################################################
def createplands(plannumber):
print("Creating plan Data Structure\n")
global planfilename
global plansopinstuid
file_meta = Dataset()
file_meta.MediaStorageSOPClassUID = '1.2.840.10008.5.1.4.1.1.481.5' #RT Plan Storage
file_meta.MediaStorageSOPInstanceUID = plansopinstuid + "." + str(plannumber)
file_meta.ImplementationClassUID = gImplementationClassUID #this value remains static since implementation for creating file is the same
ds = FileDataset(planfilename, {}, file_meta=file_meta, preamble=b'\x00'*128)
return ds
####################################################################################################################################################
####################################################################################################################################################
####################################################################################################################################################
# Function to initialize data structure, sets Specific Character set,
# instance creation time and date, SOP Class UID, and SOP Instance UID
# also sets modality and data structure
####################################################################################################################################################
def initds(ds):
print("initializing data structure\n")
global imageuids
global SeriesUID
global StudyInstanceUID
global FrameUID
global ClassUID
global structsopinstuid
global structseriesinstuid
ds.SpecificCharacterSet = 'ISO_IR 100' # not sure what I want here, going off of template dicom file
ds.InstanceCreationDate = time.strftime("%Y%m%d")
ds.InstanceCreationTime = time.strftime("%H%M%S")
ds.SOPClassUID = '1.2.840.10008.5.1.4.1.1.481.3'
ds.SOPInstanceUID = structsopinstuid
ds.Modality = 'RTSTRUCT'
ds.AccessionNumber = ""
ds.Manufacturer = Manufacturer #from sample dicom file, maybe should change?
ds.StationName = "adacp3u7" # not sure where to get information for this element can find this and read in from
#ds.ManufacturersModelName = 'Pinnacle3'
ReferencedStudy1 = Dataset()
ds.ReferencedStudySequence.append(ReferencedStudy1)
ds.ReferencedStudySequence[0].ReferencedSOPClassUID = '1.2.840.10008.3.1.2.3.2' #Study Component Management SOP Class (chosen from template)
ds.ReferencedStudySequence[0].ReferencedSOPInstanceUID = StudyInstanceUID
ds.StudyInstanceUID = StudyInstanceUID
print("Setting structure file study instance: " + str(StudyInstanceUID))
ds.SeriesInstanceUID = structseriesinstuid
return ds
####################################################################################################################################################
####################################################################################################################################################
####################################################################################################################################################
# function to read in patient info from Patient text file
####################################################################################################################################################
def readpatientinfo(ds):
print ("Reading patient information\n")
mname = ""
flag_first = True
flag_time = True
flag_stid = True
global imageuids
global SeriesUID
global StudyInstanceUID
global FrameUID
global ClassUID
global patientname
global dob
global pid
global patient_sex
global study_time
global study_date
global model
global physician
global sid
global descrip
global plancount
global plannamelist
global patientfolder
global lname
global fname
global imagesetnumber
global softwarev
#global listofversions
with open("%s%s/Patient"%(Inputf, patientfolder), "rt", encoding='latin1') as g:
for line in g:
if "PatientID =" in line:
pid = re.findall(r"[-+]?\d*\.\d+|\d+", line)[0]
ds.PatientID = pid #may want to change pid to be value of medical record number.
if "LastName = " in line:
lname = re.findall(r'"([^"]*)"', line)[0]
lname = lname.replace(' (restored)', '')
lname = lname.replace('\\', '')
lname = lname.replace('/', '')
if "FirstName =" in line:
fname = re.findall(r'"([^"]*)"', line)[0]
fname = fname.replace(" ", "")
fname = fname.replace("\\", '')
fname = fname.replace("/", '')
if "MiddleName = " in line:
mname = re.findall(r'"([^"]*)"', line)[0]
mname = mname.replace("\\", '')
mname = mname.replace('/', '')
if "MedicalRecordNumber =" in line:
medrecnum = re.findall(r'"([^"]*)"', line)[0]
if "ReferringPhysician = " in line:
refphys = re.findall(r'"([^"]*)"', line)[0]
ds.ReferringPhysiciansName = refphys
if "RadiationOncologist = " in line:
physician = re.findall(r'"([^"]*)"', line)[0]
ds.PhysiciansOfRecord = physician
if "Comment = " in line and flag_first:
descrip = re.findall(r'"([^"]*)"', line)[0]
ds.StudyDescription = descrip
if "Gender = " in line:
gen = re.findall(r'"([^"]*)"', line)[0]
if "Male" in gen:
patient_sex = 'M'
elif "Female" in gen:
patient_sex = 'F'
ds.PatientsSex = patient_sex
if "DateOfBirth =" in line:
dobstr = re.findall(r'"([^"]*)"', line) #gets birthday string with numbers and dashes
if '-' in dobstr[0]:
dob_list = dobstr[0].split('-')
elif '/' in dobstr[0]:
dob_list = dobstr[0].split('/')
else:
dob_list = dobstr[0].split(' ')
dob = ""
for num in dob_list:
if len(num) == 1:
num = '0' + num
if num == dob_list[-1] and len(num) == 2:
num = "19" + num
dob = dob + num
ds.PatientsBirthDate = dob
if "ImageSetList ={" in line:
flag_first = False
if "PlanName = " in line:
plancount = plancount + 1
plannamelist.append(re.findall(r'"([^"]*)"', line)[0])
ds.StructureSetLabel = plannamelist[plancount - 1]
if "PrimaryCTImageSetID =" in line:
imagesetnumber = re.findall(r"[-+]?\d*\.\d+|\d+", line)[0]
print("Image set number: " + imagesetnumber)
if " PlanID =" in line:
planids.append(re.findall(r"[-+]?\d*\.\d+|\d+", line)[0])
if " StudyID = " in line and flag_stid:
sid = re.findall(r'"([^"]*)"', line)[0]
print ("Study id: ", sid)
ds.StudyID = sid
flag_stid = False
if "WriteTimeStamp = " in line and flag_time:
dateandtime = re.findall(r'"([^"]*)"', line)[0]
arr = dateandtime.split()
date = arr[0].replace('-', '')
time = arr[1].replace(':', '')
ds.StructureSetDate = date
ds.StructureSetTime = time
study_date = date
study_time = time
ds.StudyDate = date
ds.StudyTime = time
flag_time = False
if "ToolType =" in line:
model = re.findall(r'"([^"]*)"', line)[0]
ds.ManufacturersModelName = model
if "PinnacleVersionDescription" in line:
softwarev = re.findall(r'"([^"]*)"', line)[0]
ds.SoftwareVersions = softwarev
#if listofversions == []:
# listofversions.append(softwarev)
#flagsame = False
#for ver in listofversions:
#if softwarev == ver:
#flagsame = True
#f flagsame == False:
#listofversions.append(softwarev)
ds.StructureSetName = 'POIandROI'
ds.SeriesNumber = '1'