patID = patientdir.split('/')[-1].replace('.','')
patientID[:63] = patID
print("working on patient: "+patientID)
print("in the directory: "+pathT2)
if os.path.isdir(pathT2):
print("T2 dir found.")
pathROI = analasisysdir + "ROI/"
if os.path.isdir(pathROI):
print("ROI dir found.")
infos = info_file_parser(analasisysdir + "info.txt")
timeflag[0] = timeflagconverter_string2int(infos["time"])
ypT[0] = int(infos["ypT"])
# # data, ROI = read_files(pathT2, pathROI, args.verbose, True)
freader = FileReader(pathT2, pathROI, args.verbose)
try:
data, ROI = freader.read(raw=True)
except NotImplementedError:
data = freader.readUsingGDCM(raw=True)
ROI = freader.readROI()
except ValueError:
continue
roinorm=False
if args.verbose:
print("dicom file read")
if args.norm:
myroifilename = analasisysdir + "roinormmuscle.myroi"
for wordnum, word in enumerate(lines):
print(wordnum, word)
if args.verbose:
print(lines)
if lines[0][0] == '#':
continue
patientID[:63] = lines[0]
print("working on patient: "+patientID)
pathT2 = lines[1]
print("in the directory: "+pathT2)
pathROI = lines[2]
timeflag[0] = int(lines[3])
ypT[0] = int(lines[4])
# data, ROI = read_files(pathT2, pathROI, args.verbose, True)
freader = FileReader(pathT2, pathROI, args.verbose)
data, ROI = freader.read(True)
roinorm=False
if args.verbose:
print("dicom file read")
if args.norm:
myroifilename = lines[5]
roireader = roiFileHandler(args.verbose)
myroisnorm, roisnormSetted = roireader.read(myroifilename)
roinorm = myroi2roi(myroisnorm, data.shape, args.verbose)
for wordnum, word in enumerate(lines):
print(wordnum, word)
if args.verbose:
print(lines)
if lines[0][0] == '#':
continue
patientID[:63] = lines[0]
print("working on patient: " + patientID)
pathT2 = lines[1]
print("in the directory: " + pathT2)
pathROI = lines[2]
timeflag[0] = int(lines[3])
ypT[0] = int(lines[4])
# data, ROI = read_files(pathT2, pathROI, args.verbose, True)
freader = FileReader(pathT2, pathROI, args.verbose)
data, ROI = freader.read(True)
roinorm = False
if args.verbose:
print("dicom file read")
if args.norm:
myroifilename = lines[5]
roireader = roiFileHandler(args.verbose)
myroisnorm, roisnormSetted = roireader.read(myroifilename)
roinorm = myroi2roi(myroisnorm, data.shape, args.verbose)
parser.add_argument("-o", "--outfile", help="define output file name (default ./max-roi.txt)")
args = parser.parse_args()
if args.inputpath:
inpath = args.inputpath
if args.roi:
myroifilename = args.roi
if args.outfile:
outfname = args.outfile
out_file = open(outfname,"w")
out_file.write("#layer \t max \t meaninroi \n")
freader = FileReader(inpath, False, args.verbose)
data, unusedROI = freader.read(True)
roireader = roiFileHandler()
rois, roisSetted = roireader.read(myroifilename)
nFette = len(data)
if nFette != len(rois):
print("error: len rois = ",len(rois)," but len dicom=",nFette)
for layer in xrange(0,nFette):
thisroi = grid_points_in_poly(data[layer].shape, rois[layer]['points'])
masked = data[layer]*thisroi
maximum = data[layer].max()
meaninroi = masked.mean()
def __init__(self):
# QtGui.QWidget.__init__(self)
super(Window_dicom_roi2, self).__init__()
# self.setGeometry(50, 50, 500, 300)
self.setWindowTitle("DICOM roi (v3)")
# self.setWindowIcon(QtGui.QIcon('pythonlogo.png'))
widgetWindow = QtGui.QWidget(self)
self.setCentralWidget(widgetWindow)
outfname = "roi.txt"
self.inpath = "."
parser = argparse.ArgumentParser()
parser.add_argument("-v",
"--verbose",
help="increase output verbosity",
action="store_true")
parser.add_argument("-r",
"--raw",
help="dont read raw data",
action="store_true")
parser.add_argument("-i",
"--inputpath",
help="path of the DICOM directory (default ./)")
parser.add_argument("-o",
"--outfile",
help="define output file name (default roi.txt)")
parser.add_argument("-l", "--layer", help="select layer", type=int)
parser.add_argument(
"-f",
"--filterROI",
help=
"filter the image with a ROI (folder path, nrrd file supported)")
group = parser.add_mutually_exclusive_group()
group.add_argument("-y",
"--yview",
help="swap axes",
action="store_true")
group.add_argument("-x",
"--xview",
help="swap axes",
action="store_true")
args = parser.parse_args()
self.layer = 0
if args.outfile:
outfname = args.outfile
if args.inputpath:
self.inpath = args.inputpath
if args.layer:
self.layer = args.layer
self.raw = not args.raw
openFile = QtGui.QAction("&Open ROI File", self)
openFile.setShortcut("Ctrl+O")
openFile.setStatusTip('Open ROI File')
openFile.triggered.connect(self.file_open)
saveFile = QtGui.QAction("&Save ROI on File", self)
saveFile.setShortcut("Ctrl+S")
saveFile.setStatusTip('Save ROI on File')
saveFile.triggered.connect(self.file_save)
# self.statusBar()
mainMenu = self.menuBar()
fileMenu = mainMenu.addMenu('&ROI')
# fileMenu.addAction(extractAction)
fileMenu.addAction(openFile)
fileMenu.addAction(saveFile)
self.verbose = args.verbose
self.filterROI = args.filterROI
freader = FileReader(self.inpath, args.filterROI, args.verbose)
# dataRGB, unusedROI = read_files(inpath, False, args.verbose, False)
if self.raw:
dataBW, ROI = freader.read(True)
self.dataZ = dataBW #[:,:,::-1]
else:
dataRGB, ROI = freader.read(False)
self.dataZ = dataRGB #[:,:,:,0]
#
# self.data = dataRGB[:,:,::-1,:]
#dataswappedX = np.swapaxes(np.swapaxes(self.data,0,1),1,2)
self.dataswappedX = np.swapaxes(np.swapaxes(self.dataZ, 0, 1), 1,
2)[:, ::-1, ::-1]
self.dataswappedY = np.swapaxes(self.dataZ, 0, 2)[:, :, ::-1]
self.ConstPixelDims = freader.ConstPixelDims
self.ConstPixelSpacing = freader.ConstPixelSpacing
if args.verbose:
print(self.dataZ.shape)
print("layer: ", self.layer)
self.xview = args.xview
self.yview = args.yview
self.img1a = pg.ImageItem()
self.arr = None
self.firsttime = True
if self.xview:
imgScaleFactor = 1. / freader.scaleFactor
self.data = self.dataswappedX
self.ROI = np.swapaxes(np.swapaxes(ROI, 0, 1), 1, 2)[:, ::-1, ::-1]
self.xscale = self.ConstPixelSpacing[1]
self.yscale = self.ConstPixelSpacing[2]
elif self.yview:
imgScaleFactor = 1. / freader.scaleFactor
self.data = self.dataswappedY
self.ROI = np.swapaxes(ROI, 0, 2)[:, :, ::-1]
self.xscale = self.ConstPixelSpacing[0]
self.yscale = self.ConstPixelSpacing[2]
else:
imgScaleFactor = 1.
self.data = self.dataZ
self.ROI = ROI
self.xscale = self.ConstPixelSpacing[0]
self.yscale = self.ConstPixelSpacing[1]
self.xshift = 0
self.yshift = 0
if self.verbose:
print("data len:", len(self.data))
self.updatemain()
self.rois = [None] * len(self.data)
self.button_next = QtGui.QPushButton('Next', self)
self.button_prev = QtGui.QPushButton('Prev', self)
self.button_next.clicked.connect(self.nextimg)
self.button_prev.clicked.connect(self.previmg)
# layout = QtGui.QVBoxLayout(self)
# layout = QtGui.QGridLayout(self)
layout = QtGui.QGridLayout(widgetWindow)
layout.addWidget(self.button_next, 1, 1)
layout.addWidget(self.button_prev, 2, 1)
self.button_setroi = QtGui.QPushButton('Set ROI', self)
self.button_setroi.clicked.connect(self.setROI)
layout.addWidget(self.button_setroi, 12, 1)
self.button_delroi = QtGui.QPushButton('Del ROI', self)
self.button_delroi.clicked.connect(self.delROI)
layout.addWidget(self.button_delroi, 13, 1)
label = QtGui.QLabel(
"Click on a line segment to add a new handle. Right click on a handle to remove."
)
# label.setAlignment(Qt.AlignCenter)
layout.addWidget(label, 0, 0)
self.label_layer = QtGui.QLabel("layer: " + str(self.layer + 1) + "/" +
str(len(self.data)))
self.label_shape = QtGui.QLabel("shape: " + str(self.arr.shape))
self.label_size = QtGui.QLabel("size: " + str(self.arr.size))
self.label_min = QtGui.QLabel("min: " + str(self.arr.min()))
self.label_max = QtGui.QLabel("max: " + str(self.arr.max()))
self.label_mean = QtGui.QLabel("mean: " + str(self.arr.mean()))
self.label_sd = QtGui.QLabel("sd: " + str(ndimage.mean(self.arr)))
self.label_sum = QtGui.QLabel("sum: " + str(ndimage.sum(self.arr)))
layout.addWidget(self.label_layer, 3, 1)
layout.addWidget(self.label_shape, 4, 1)
layout.addWidget(self.label_size, 5, 1)
layout.addWidget(self.label_min, 6, 1)
layout.addWidget(self.label_max, 7, 1)
layout.addWidget(self.label_mean, 8, 1)
layout.addWidget(self.label_sd, 9, 1)
layout.addWidget(self.label_sum, 10, 1)
self.roisSetted = 0
self.label2_roisSetted = QtGui.QLabel("ROI setted: 0")
self.label2_shape = QtGui.QLabel()
self.label2_size = QtGui.QLabel()
self.label2_min = QtGui.QLabel()
self.label2_max = QtGui.QLabel()
self.label2_mean = QtGui.QLabel()
self.label2_sd = QtGui.QLabel()
self.label2_sum = QtGui.QLabel()
layout.addWidget(self.label2_roisSetted, 14, 1)
layout.addWidget(self.label2_shape, 15, 1)
layout.addWidget(self.label2_size, 16, 1)
layout.addWidget(self.label2_min, 17, 1)
layout.addWidget(self.label2_max, 18, 1)
layout.addWidget(self.label2_mean, 19, 1)
layout.addWidget(self.label2_sd, 20, 1)
layout.addWidget(self.label2_sum, 21, 1)
self.p1 = pg.PlotWidget()
self.p1.setAspectLocked(True, imgScaleFactor)
self.p1.addItem(self.img1a)
# imv = pg.ImageView(imageItem=img1a)
layout.addWidget(self.p1, 1, 0, 10, 1)
# self.slider = QtGui.QSlider(QtCore.Qt.Horizontal)
self.slider = QtGui.QScrollBar(QtCore.Qt.Horizontal)
self.slider.setMinimum(1)
self.slider.setMaximum(len(self.data))
self.slider.setValue(self.layer + 1)
self.slider.setSingleStep(1)
self.slider.setFocus()
self.slider.setFocusPolicy(QtCore.Qt.StrongFocus)
# self.slider.setTickPosition(QtGui.QSlider.TicksBelow)
# self.slider.setTickInterval(5)
# self.slider.sliderMoved.connect(self.slider_jump_to)
self.slider.valueChanged.connect(self.slider_jump_to)
layout.addWidget(self.slider, 11, 0)
self.statusBar = MyStatusBar()
self.statusBar.setSize(len(self.data))
layout.addWidget(self.statusBar, 12, 0)
self.img1b = pg.ImageItem()
# self.img1a.scale(self.xscale, self.yscale)
# self.img1a.translate(self.xshift, self.yshift)
# self.img1b.scale(self.xscale, self.yscale)
# self.img1b.translate(self.xshift, self.yshift)
if not args.filterROI:
self.roi = pg.PolyLineROI([[80, 60], [90, 30], [60, 40]],
pen=(6, 9),
closed=True)
else:
self.rois = roi2myroi(self.ROI)
if self.rois[self.layer]:
self.roi = self.rois[self.layer]
else:
self.roi = pg.PolyLineROI([[80, 60], [90, 30], [60, 40]],
pen=(6, 9),
closed=True)
# for simplex in hull.simplices:
# if self.rois[self.layer]:
# self.roi = self.rois[self.layer]
self.p2 = pg.PlotWidget()
# self.p2.disableAutoRange('xy')
self.p2.setAspectLocked(True, imgScaleFactor)
self.p2.addItem(self.img1b)
# if not args.filterROI:
self.p1.addItem(self.roi)
self.roi.sigRegionChanged.connect(self.update)
layout.addWidget(self.p2, 13, 0, 10, 1)
def __init__(self):
# QtGui.QWidget.__init__(self)
super(Window_dicom_roi_RGB, self).__init__()
# self.setGeometry(50, 50, 500, 300)
self.setWindowTitle("DICOM roi (vRGB)")
# self.setWindowIcon(QtGui.QIcon('pythonlogo.png'))
widgetWindow = QtGui.QWidget(self)
self.setCentralWidget(widgetWindow)
outfname="roi.txt"
self.inpath="."
parser = argparse.ArgumentParser()
parser.add_argument("-v", "--verbose", help="increase output verbosity",
action="store_true")
parser.add_argument("-i", "--inputpath", help="path of the DICOM directory (default ./)")
parser.add_argument("-o", "--outfile", help="define output file name (default roi.txt)")
parser.add_argument("-l", "--layer", help="select layer",
type=int)
parser.add_argument("-f", "--filterROI", help="filter the image with a ROI (folder path, nrrd file supported)")
parser.add_argument("-c","--colorRange", help="highlight a color range (expects sometghin like 100:200)")
parser.add_argument("-r","--raw", help="do not normalize",action="store_true")
group = parser.add_mutually_exclusive_group()
group.add_argument("-y", "--yview", help="swap axes",
action="store_true")
group.add_argument("-x", "--xview", help="swap axes",
action="store_true")
args = parser.parse_args()
self.layer=0
if args.outfile:
outfname = args.outfile
if args.inputpath:
self.inpath = args.inputpath
if args.layer:
self.layer = args.layer
openFile = QtGui.QAction("&Open ROI File", self)
openFile.setShortcut("Ctrl+O")
openFile.setStatusTip('Open ROI File')
openFile.triggered.connect(self.file_open)
saveFile = QtGui.QAction("&Save ROI on File", self)
saveFile.setShortcut("Ctrl+S")
saveFile.setStatusTip('Save ROI on File')
saveFile.triggered.connect(self.file_save)
# self.statusBar()
mainMenu = self.menuBar()
fileMenu = mainMenu.addMenu('&ROI')
# fileMenu.addAction(extractAction)
fileMenu.addAction(openFile)
fileMenu.addAction(saveFile)
self.verbose = args.verbose
freader = FileReader(self.inpath, args.filterROI, args.verbose)
# dataRGB, unusedROI = read_files(inpath, False, args.verbose, False)
dataRGB, unusedROI = freader.read(False)
self.scaleFactor = freader.scaleFactor
if not args.raw:
thisNormalizer = Normalizer(self.verbose)
thisNormalizer.setRootOutput()
self.dataZ = thisNormalizer.match_all(dataRGB)
thisNormalizer.writeRootOutputOnFile("checkNorm.root")
else:
self.dataZ = dataRGB
if args.colorRange:
self.dataZ = highlight_color(dataRGB,args.colorRange,args.verbose)
# self.dataZ = np.swapaxes(dataRGB[:,:,:,:],0,1)
#
# self.data = dataRGB[:,:,::-1,:]
#dataswappedX = np.swapaxes(np.swapaxes(self.data,0,1),1,2)
self.dataswappedX = np.swapaxes(np.swapaxes(self.dataZ,0,1),1,2)[:,::-1,::-1,:]
self.dataswappedY = np.swapaxes(self.dataZ,0,2)[:,:,::-1,:]
if args.verbose:
print("shape:", self.dataZ.shape)
print("shape of a channel:", self.dataZ[:,:,:,0].shape)
print("layer: ",self.layer)
self.xview = args.xview
self.yview = args.yview
self.img1a = pg.ImageItem()
self.arr = None
self.firsttime = True
if self.xview:
imgScaleFactor= 1./freader.scaleFactor
self.data = self.dataswappedX
elif self.yview:
imgScaleFactor= 1./freader.scaleFactor
self.data = self.dataswappedY
else:
imgScaleFactor= 1.
self.data = self.dataZ
if self.verbose:
print("data len:",len(self.data[:,:,:,0]))
self.updatemain()
self.rois = [None]*len(self.data[:,:,:,0])
self.button_next = QtGui.QPushButton('Next', self)
self.button_prev = QtGui.QPushButton('Prev', self)
self.button_next.clicked.connect(self.nextimg)
self.button_prev.clicked.connect(self.previmg)
# layout = QtGui.QVBoxLayout(self)
# layout = QtGui.QGridLayout(self)
layout = QtGui.QGridLayout(widgetWindow)
layout.addWidget(self.button_next,1,1)
layout.addWidget(self.button_prev,2,1)
self.button_setroi = QtGui.QPushButton('Set ROI', self)
self.button_setroi.clicked.connect(self.setROI)
layout.addWidget(self.button_setroi,12,1)
self.button_delroi = QtGui.QPushButton('Del ROI', self)
self.button_delroi.clicked.connect(self.delROI)
layout.addWidget(self.button_delroi,13,1)
label = QtGui.QLabel("Click on a line segment to add a new handle. Right click on a handle to remove.")
# label.setAlignment(Qt.AlignCenter)
layout.addWidget(label,0,0)
self.label_layer = QtGui.QLabel("layer: "+str(self.layer+1)+"/"+str(len(self.data[:,:,:,0])))
self.label_shape = QtGui.QLabel("shape: "+str(self.arr[:,:,0].shape))
self.label_size = QtGui.QLabel("size: "+str(self.arr[:,:,0].size))
self.label_min = QtGui.QLabel("min: "+str(self.arr[:,:,0].min()))
self.label_max = QtGui.QLabel("max: "+str(self.arr[:,:,0].max()))
self.label_mean = QtGui.QLabel("mean: "+str(self.arr[:,:,0].mean()))
self.label_sd = QtGui.QLabel("sd: "+str(ndimage.standard_deviation(self.arr[:,:,0])))
self.label_sum = QtGui.QLabel("sum: "+str(ndimage.sum(self.arr[:,:,0])))
layout.addWidget(self.label_layer,3,1)
layout.addWidget(self.label_shape,4,1)
layout.addWidget(self.label_size,5,1)
layout.addWidget(self.label_min,6,1)
layout.addWidget(self.label_max,7,1)
layout.addWidget(self.label_mean,8,1)
layout.addWidget(self.label_sd,9,1)
layout.addWidget(self.label_sum,10,1)
self.roisSetted = 0
self.label2_roisSetted = QtGui.QLabel("ROI setted: 0")
self.label2_shape = QtGui.QLabel()
self.label2_size = QtGui.QLabel()
self.label2_min = QtGui.QLabel()
self.label2_max = QtGui.QLabel()
self.label2_mean = QtGui.QLabel()
self.label2_sd = QtGui.QLabel()
self.label2_sum = QtGui.QLabel()
layout.addWidget(self.label2_roisSetted,14,1)
layout.addWidget(self.label2_shape,15,1)
layout.addWidget(self.label2_size,16,1)
layout.addWidget(self.label2_min,17,1)
layout.addWidget(self.label2_max,18,1)
layout.addWidget(self.label2_mean,19,1)
layout.addWidget(self.label2_sd,20,1)
layout.addWidget(self.label2_sum,21,1)
self.p1 = pg.PlotWidget()
self.p1.setAspectLocked(True,imgScaleFactor)
self.p1.addItem(self.img1a)
# imv = pg.ImageView(imageItem=img1a)
layout.addWidget(self.p1,1,0,10,1)
# self.slider = QtGui.QSlider(QtCore.Qt.Horizontal)
self.slider = QtGui.QScrollBar(QtCore.Qt.Horizontal)
self.slider.setMinimum(1)
self.slider.setMaximum(len(self.data[:,:,:,0]))
self.slider.setValue(self.layer+1)
self.slider.setSingleStep(1)
self.slider.setFocus()
self.slider.setFocusPolicy(QtCore.Qt.StrongFocus)
# self.slider.setTickPosition(QtGui.QSlider.TicksBelow)
# self.slider.setTickInterval(5)
# self.slider.sliderMoved.connect(self.slider_jump_to)
self.slider.valueChanged.connect(self.slider_jump_to)
layout.addWidget(self.slider,11,0)
self.img1b = pg.ImageItem()
self.roi = pg.PolyLineROI([[80, 60], [90, 30], [60, 40]], pen=(6,9), closed=True)
# if self.rois[self.layer]:
# self.roi = self.rois[self.layer]
self.p2 = pg.PlotWidget()
# self.p2.disableAutoRange('xy')
self.p2.setAspectLocked(True,imgScaleFactor)
self.p2.addItem(self.img1b)
self.p1.addItem(self.roi)
self.roi.sigRegionChanged.connect(self.update)
layout.addWidget(self.p2,12,0,10,1)
patientID = patID
print("working on patient: "+patientID)
print("in the directory: "+pathT2)
if os.path.isdir(pathT2):
print("T2 dir found.")
pathROI = analasisysdir + "ROI/"
if os.path.isdir(pathROI):
print("ROI dir found.")
infos = info_file_parser(analasisysdir + "info2.txt")
timeflag = timeflagconverter_string2int(infos["time"])
ypT = int(infos["ypT"])
ypT2 = int(infos["ypT2"])
# # data, ROI = read_files(pathT2, pathROI, args.verbose, True)
freader = FileReader(pathT2, pathROI, args.verbose)
try:
data, ROI = freader.read(raw=True)
except NotImplementedError:
data = freader.readUsingGDCM(raw=True)
ROI = freader.readROI()
except ValueError:
print("Data not read. Check folders")
continue
roinorm=False
if args.verbose:
print("dicom file read")
if args.norm:
def setExternalTemplate(self, dcmfile):
freader = FileReader(dcmfile, False, self.verbose)
dataRGB, unusedROI = freader.read(False)
self.externalTemplateSetted = True
self.externalTemplate = dataRGB[:,:,0]
self.NormLayer = -1
patientID[:63] = patID
print("working on patient: "+patientID)
print("in the directory: "+pathT2)
if os.path.isdir(pathT2):
print("T2 dir found.")
pathROI = analasisysdir + "ROI/"
if os.path.isdir(pathROI):
print("ROI dir found.")
infos = info_file_parser(analasisysdir + "info2.txt")
timeflag[0] = timeflagconverter_string2int(infos["time"])
ypT[0] = int(infos["ypT"])
ypT2[0] = int(infos["ypT2"])
# # data, ROI = read_files(pathT2, pathROI, args.verbose, True)
freader = FileReader(pathT2, pathROI, args.verbose)
try:
data, ROI = freader.read(raw=True)
except NotImplementedError:
# data = freader.readUsingGDCM(raw=True)
dataTMP = freader.readUsingGDCM(raw=False)
data = dataTMP[:,:,:,0]
ROI = freader.readROI()
except ValueError:
continue
roinorm=False
if args.verbose:
print("dicom file read")
def setExternalTemplate(self, dcmfile):
freader = FileReader(dcmfile, False, self.verbose)
dataRGB, unusedROI = freader.read(False)
self.externalTemplateSetted = True
self.externalTemplate = dataRGB[:, :, 0]
self.NormLayer = -1
