def read_plist_roi_file(fname, nOfRois=0, shape=None, debug=False):
with open(fname, 'rb') as fp:
pl = plistlib.load(fp)
outrois = [None] * len(pl['Images'])
nRois = 0
for image in pl['Images']:
points = image['ROIs'][0]['Point_px']
outpoints = []
try:
imageHeight = image['ImageHeight']
except KeyError:
if shape is not None:
imageHeight = shape[1]
else:
raise IndexError(
"The image height is not indicated in the xml file, pass it as input"
)
imageIndex = image['ImageIndex']
for point in points:
if debug:
print(point, type(point))
px = float(point.split(",")[0][1:])
py = -float(point.split(",")[1][:-1])
if debug:
print(px, py)
outpoints.append([px, py])
if debug:
print(image['ImageIndex'], outpoints)
if imageIndex < len(outrois):
outrois[imageIndex] = pg.PolyLineROI(outpoints,
closed=True).saveState()
else:
outrois[nRois] = pg.PolyLineROI(outpoints,
closed=True).saveState()
nRois += 1
if nOfRois and nRois >= nOfRois:
break
return outrois, nRois
def roi2myroi(ROI, verbose=False):
rois = [None]*len(ROI)
firsttime = True
for layer in xrange(0, len(ROI)):
fetta = ROI[layer]
apoints = []
if fetta.max() > 0 :
for j, riga in enumerate(fetta):
for i, elemento in enumerate(riga):
if elemento:
thispoint = [i,j]
apoints.append(thispoint)
points = np.array(apoints)
if firsttime:
firsttime = False
for point in points:
print(point)
hull = ConvexHull(points)
rois[layer] = pg.PolyLineROI(hull.simplices.tolist(), pen=(6,9), closed=True).saveState()
return rois
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)
# elif args.yview:
# imv.setImage(dataswappedY, xvals=np.linspace(0, dataswappedY.shape[0], dataswappedY.shape[0] ))
# else:
# imv.setImage(data, xvals=np.linspace(0, data.shape[0], data.shape[0] ))
v1a.addItem(img1a)
img1b = pg.ImageItem()
v1b.addItem(img1b)
# v1a.disableAutoRange('xy')
v1a.autoRange()
#v1b.autoRange()
v1b.disableAutoRange('xy')
#rois = []
roi = pg.PolyLineROI([[80, 60], [90, 30], [60, 40]], pen=(6, 9), closed=True)
def update(roi):
thisroi = roi.getArrayRegion(arr, img1a).astype(int)
img1b.setImage(thisroi, levels=(0, arr.max()))
print(type(thisroi[0][0]))
print("shape: ", thisroi.shape)
print("size: ", thisroi.size)
print("min: ", thisroi.min())
print("max: ", thisroi.max())
print("mean: ", thisroi.mean())
print("mean: ", ndimage.mean(thisroi))
print("sd: ", ndimage.standard_deviation(thisroi))
print("sum: ", ndimage.sum(thisroi))