Ejemplo n.º 1
0
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)
Ejemplo n.º 2
0
#     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))
Ejemplo n.º 3
0
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.
Ejemplo n.º 4
0
#     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)):
Ejemplo n.º 5
0
    "--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()
Ejemplo n.º 6
0
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.