def addHocViewer(grayData=None, segData=None, title="viewer", visu=True):
if visu:
app = QApp.Instance().app
v = Viewer()
if grayData is not None:
for name in grayData.keys():
data = grayData[name]
if _hasVigra:
if isinstance(data, vigra.arraytypes.VigraArray):
v.addGrayscaleLayer(data.view(numpy.ndarray),
name=name)
else:
v.addGrayscaleLayer(data, name=name)
else:
v.addGrayscaleLayer(data, name=name)
if segData is not None:
for name in segData.keys():
data = segData[name]
if _hasVigra:
if isinstance(data, vigra.arraytypes.VigraArray):
v.addColorTableLayer(data.view(numpy.ndarray),
name=name)
else:
v.addColorTableLayer(data, name=name)
else:
v.addGrayscaleLayer(data, name=name)
v.setWindowTitle(title)
v.showMaximized()
app.exec_()
def addHocViewer(grayData=None, segData=None, title="viewer", visu=True):
if visu:
app = QApp.Instance().app
v = Viewer()
if grayData is not None:
for name in grayData.keys():
data = grayData[name]
if hasVigra:
if isinstance(data, vigra.arraytypes.VigraArray):
v.addGrayscaleLayer(data.view(numpy.ndarray), name=name)
else:
v.addGrayscaleLayer(data, name=name)
else:
v.addGrayscaleLayer(data, name=name)
if segData is not None:
for name in segData.keys():
data = segData[name]
if hasVigra:
if isinstance(data, vigra.arraytypes.VigraArray):
v.addColorTableLayer(data.view(numpy.ndarray), name=name)
else:
v.addColorTableLayer(data, name=name)
else:
v.addGrayscaleLayer(data, name=name)
v.setWindowTitle(title)
v.showMaximized()
app.exec_()
l1 = v.addGrayscaleLayer(raw, name="raw", direct=True)
l1.visible = direct
colortable = [
QColor(0, 0, 0, 0).rgba(),
QColor(255, 0, 0).rgba(),
QColor(0, 255, 0).rgba(),
QColor(0, 0, 255).rgba()
]
s = ((raw // 64)).astype(numpy.uint8)
def onClick(layer, pos5D, pos):
print("here i am: ", pos5D, s[pos5D])
l2 = v.addColorTableLayer(s,
clickFunctor=onClick,
name="thresh",
colortable=colortable,
direct=direct)
l2.colortableIsRandom = True
l2.zeroIsTransparent = True
l2.visible = False
v.addClickableSegmentationLayer(s, "click it", direct=True)
v.show()
app.exec_()
print "seg "
labels = vigra.readHDF5(lPath, 'data')
labelsS = vigra.readHDF5(lsPath, 'data')
#labelsSS = vigra.readHDF5(lssPath, 'data')
labelsPS = vigra.readHDF5(
"/mnt/CLAWS1/tbeier/data/stack_with_holes/lps.h5", 'data')
print ew.shape
print "datashape", data.shape
print "resshape", smoothedT.shape
app = QApplication(sys.argv)
v = Viewer()
v.addGrayscaleLayer(data, name="raw")
v.addGrayscaleLayer(smoothedT, name="smoothedT")
v.addGrayscaleLayer(ew, name="hessian ew")
v.addGrayscaleLayer(ews, name="hessian ews")
v.addGrayscaleLayer(ewss, name="hessian ewss")
v.addGrayscaleLayer(pEws, name="hessian p80ews")
#v.addGrayscaleLayer(dd, name="diff ews")
v.addColorTableLayer(labels, name="labels")
v.addColorTableLayer(labelsS, name="labelsS")
#v.addColorTableLayer(labelsSS, name="labelsSS")
v.addColorTableLayer(labelsPS, name="labelsPS")
v.setWindowTitle("stack with holes")
v.showMaximized()
app.exec_()
item1.setPath(path1)
# Create images
back = (numpy.ones((100, 200, 300)) * 0).astype(numpy.uint8)
back[0:60, 0:60, 0:60] = 255
back[40:80, 40:80, 40:80] = 120
back[40:100, 40:100, 0:40] = 80
back[0:45, 50:100, 0:100] = 200
ol = (numpy.zeros((100, 200, 300))).astype(numpy.uint8)
# ol[0:99, 0:99, 0:99] = 120
# ol[0:99, 120:140, 0:99] = 255
ol[:] = back
back.shape = (1,)+back.shape+(1,)
ol.shape = (1,)+ol.shape+(1,)
# Add layers
l1 = v.addGrayscaleLayer(back, name="back")
l1.visible = True
l2 = v.addColorTableLayer(ol, name="overlay")
# Add the path to the graphics scene
# v.editor.imageScenes[0].addItem(item1)
# v.editor.imageScenes[1].addItem(item1)
v.editor.imageScenes[2].addItem(item1)
v.setWindowTitle("Clickable Border Viewer")
v.show()
app.exec_()
#load data
f = h5py.File(fname, 'r')
raw = f[gname].value
assert raw.ndim == 3
assert raw.dtype == numpy.uint8
f.close()
app = QApplication([])
v = Viewer()
direct = True
raw.shape = (1,)+raw.shape+(1,)
l1 = v.addGrayscaleLayer(raw, name="raw", direct=True)
l1.visible = direct
colortable = [QColor(0,0,0,0).rgba(), QColor(255,0,0).rgba(), QColor(0,255,0).rgba(), QColor(0,0,255).rgba()]
s = ((raw/64)).astype(numpy.uint8)
def onClick(layer, pos5D, pos):
print "here i am: ", pos5D, s[pos5D]
l2 = v.addColorTableLayer(s, clickFunctor=onClick, name="thresh", colortable=colortable, direct=direct)
l2.colortableIsRandom = True
l2.zeroIsTransparent = True
l2.visible = False
v.addClickableSegmentationLayer(s, "click it", direct=True)
v.show()
app.exec_()
labelsS = vigra.readHDF5(lsPath, 'data')
#labelsSS = vigra.readHDF5(lssPath, 'data')
labelsPS = vigra.readHDF5("/mnt/CLAWS1/tbeier/data/stack_with_holes/lps.h5", 'data')
print ew.shape
print "datashape",data.shape
print "resshape",smoothedT.shape
app = QApplication(sys.argv)
v = Viewer()
v.addGrayscaleLayer(data, name="raw")
v.addGrayscaleLayer(smoothedT, name="smoothedT")
v.addGrayscaleLayer(ew, name="hessian ew")
v.addGrayscaleLayer(ews, name="hessian ews")
v.addGrayscaleLayer(ewss, name="hessian ewss")
v.addGrayscaleLayer(pEws, name="hessian p80ews")
#v.addGrayscaleLayer(dd, name="diff ews")
v.addColorTableLayer(labels, name="labels")
v.addColorTableLayer(labelsS, name="labelsS")
#v.addColorTableLayer(labelsSS, name="labelsSS")
v.addColorTableLayer(labelsPS, name="labelsPS")
v.setWindowTitle("stack with holes")
v.showMaximized()
app.exec_()
##-----
app = QApplication(sys.argv)
v = Viewer()
graph = Graph()
def mkH5source(fname, gname):
h5file = h5py.File(fname)
source = OpStreamingHdf5Reader(graph=graph)
source.Hdf5File.setValue(h5file)
source.InternalPath.setValue(gname)
op = OpCompressedCache(parent=None, graph=graph)
op.BlockShape.setValue([100, 100, 100])
op.Input.connect(source.OutputImage)
return op.Output
rawSource = mkH5source("raw.h5", "raw")
segSource = mkH5source("seg.h5", "seg")
v.addGrayscaleLayer(rawSource, name="raw")
v.addColorTableLayer(segSource, name="seg")
v.setWindowTitle("streaming viewer")
v.showMaximized()
app.exec_()
item1 = ClickablePathItem(v.editor.imageScenes[2], clickable_width=11)
item1.set_path_from_coordinates(c_x, c_y)
# Create images
back = (numpy.ones((100, 200, 300)) * 0).astype(numpy.uint8)
back[0:60, 0:60, 0:60] = 255
back[40:80, 40:80, 40:80] = 120
back[40:100, 40:100, 0:40] = 80
back[0:45, 50:100, 0:100] = 200
ol = (numpy.zeros((100, 200, 300))).astype(numpy.uint8)
# ol[0:99, 0:99, 0:99] = 120
# ol[0:99, 120:140, 0:99] = 255
ol[:] = back
back.shape = (1,)+back.shape+(1,)
ol.shape = (1,)+ol.shape+(1,)
# Add layers
l1 = v.addGrayscaleLayer(back, name="back")
l1.visible = True
l2 = v.addColorTableLayer(ol, name="overlay")
# Add the path to the graphics scene
# v.editor.imageScenes[0].addItem(item1)
# v.editor.imageScenes[1].addItem(item1)
# v.editor.imageScenes[2].addItem(item1)
v.setWindowTitle("Clickable Border Viewer")
v.show()
app.exec_()
##-----
app = QApplication(sys.argv)
v = Viewer()
graph = Graph()
def mkH5source(fname, gname):
h5file = h5py.File(fname)
source = OpStreamingH5N5Reader(graph=graph)
source.H5N5File.setValue(h5file)
source.InternalPath.setValue(gname)
op = OpCompressedCache(parent=None, graph=graph)
op.BlockShape.setValue([100, 100, 100])
op.Input.connect(source.OutputImage)
return op.Output
rawSource = mkH5source("raw.h5", "raw")
segSource = mkH5source("seg.h5", "seg")
v.addGrayscaleLayer(rawSource, name="raw")
v.addColorTableLayer(segSource, name="seg")
v.setWindowTitle("streaming viewer")
v.showMaximized()
app.exec_()
