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()
if args.outfile:
outfname = args.outfile
if args.inputpath:
inpath = args.inputpath
dataRGB, ROI = read_files(inpath, args.filterROI, args.verbose)
if args.verbose:
print(dataRGB.shape)
dataswappedY = np.swapaxes(dataRGB,0,2)
#dataswappedX = np.fliplr(np.swapaxes(np.swapaxes(dataRGB,0,1),1,2))
dataswappedX = np.swapaxes(np.swapaxes(dataRGB,0,1),1,2)
# dataM=np.multiply(data,ROI)
app = QtGui.QApplication([])
## Create window with ImageView widget
win = QtGui.QMainWindow()
win.resize(800,800)
# if len(infilesROI) != len(infiles):
# print("ERROR: in the directory ",inpath," there are ",len(infiles)," dicom files")
# print("while in the ROI directory ",inpathROI," there are ",len(infilesROI)," dicom files")
# dicomsROI=[]
# for infileROI in infilesROI:
# dicomsROI.append(dicom.read_file(infileROI))
# for i, thisROI in enumerate(dicomsROI):
# pix_arr = thisROI.pixel_array
# ROI[i] = pix_arr.T
# for i, thisdicom in enumerate(dicoms):
# pix_arr = thisdicom.pixel_array
# data[i] = pix_arr.T
data, ROI = read_files(inpath,args.filterROI, args.verbose, True)
outfile= ROOT.TFile(outfname,"RECREATE")
his, allhistos = make_histo(data,ROI)
his.Write()
for thishisto in allhistos:
thishisto.Write()
# histograms = []
# for i, fetta, fettaROI in enumerate(zip(data,ROI)):
# if fettaROI.max() > 0 :
# histogram = make_histo(fetta, fettaROI)
# histogram.SetName("h"+str(i))
# histogram.SetTitle("h"+str(i))
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()
layer = 0
if args.outfile:
outfname = args.outfile
if args.inputpath:
inpath = args.inputpath
if args.layer:
layer = args.layer
dataRGB, ROI = read_files(inpath, False, args.verbose, False)
data = dataRGB[:, :, ::-1, 0]
if args.verbose:
print(data.shape)
print("layer: ", layer)
dataswappedY = np.swapaxes(data, 0, 2)
dataswappedX = np.swapaxes(np.swapaxes(data, 0, 1), 1, 2)
## create GUI
app = QtGui.QApplication([])
w = pg.GraphicsWindow(size=(1280, 768), border=True)
w.setWindowTitle("dicom with ROI")
text = """Click on a line segment to add a new handle.
# if len(infilesROI) != len(infiles):
# print("ERROR: in the directory ",inpath," there are ",len(infiles)," dicom files")
# print("while in the ROI directory ",inpathROI," there are ",len(infilesROI)," dicom files")
# dicomsROI=[]
# for infileROI in infilesROI:
# dicomsROI.append(dicom.read_file(infileROI))
# for i, thisROI in enumerate(dicomsROI):
# pix_arr = thisROI.pixel_array
# ROI[i] = pix_arr.T
# for i, thisdicom in enumerate(dicoms):
# pix_arr = thisdicom.pixel_array
# data[i] = pix_arr.T
data, ROI = read_files(inpath, args.filterROI, args.verbose, True)
outfile = ROOT.TFile(outfname, "RECREATE")
if args.filterROI:
his, allhistos = make_histo(data, ROI)
his.Write()
else:
allhistos = make_histo_ofallpixels(data, "", args.verbose, args.normalize)
for thishisto in allhistos:
thishisto.Write()
# histograms = []
# for i, fetta, fettaROI in enumerate(zip(data,ROI)):
"--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()
if args.outfile:
outfname = args.outfile
if args.inputpath:
inpath = args.inputpath
dataRGB, ROI = read_files(inpath, args.filterROI, args.verbose)
if args.verbose:
print(dataRGB.shape)
dataswappedY = np.swapaxes(dataRGB, 0, 2)
#dataswappedX = np.fliplr(np.swapaxes(np.swapaxes(dataRGB,0,1),1,2))
dataswappedX = np.swapaxes(np.swapaxes(dataRGB, 0, 1), 1, 2)
# dataM=np.multiply(data,ROI)
app = QtGui.QApplication([])
## Create window with ImageView widget
win = QtGui.QMainWindow()
win.resize(800, 800)
imv = pg.ImageView()
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()
layer = 0
if args.outfile:
outfname = args.outfile
if args.inputpath:
inpath = args.inputpath
if args.layer:
layer = args.layer
dataRGB, ROI = read_files(inpath, False, args.verbose, False)
data = dataRGB[:, :, ::-1, 0]
if args.verbose:
print(data.shape)
print("layer: ", layer)
dataswappedY = np.swapaxes(data, 0, 2)
dataswappedX = np.swapaxes(np.swapaxes(data, 0, 1), 1, 2)
## create GUI
app = QtGui.QApplication([])
w = pg.GraphicsWindow(size=(1280, 768), border=True)
w.setWindowTitle('dicom with ROI')
text = """Click on a line segment to add a new handle.