def show():
import numpy as np
import sys , h5py ; from numpy import float32 , uint8
from vigra.filters import hessianOfGaussianEigenvalues , gaussianSmoothing
from vigra.analysis import watersheds
from vigra.analysis import labelVolumeWithBackground, extendedLocalMinima3D
from PyQt4.QtCore import QTimer ; from PyQt4 . QtGui import QApplication
app = QApplication ( sys.argv )
from volumina.api import Viewer
v = Viewer ()
v . title = " Volumina Demo "
v . showMaximized ()
print "blubb"
print a
data = np.random.random((50,50,50))
v . addGrayscaleLayer ( data , name =" raw data ")
t = QTimer ()
t.setInterval (200)
app.exec_ ()
def view(data, labels=None, layer_types=None):
"""
"""
if labels is not None:
assert len(labels) == len(data)
if layer_types is not None:
assert len(layer_types) == len(data)
assert all(ltype in ('Grayscale', 'RandomColors', 'Red', 'Green', 'Blue')
for ltype in layer_types)
app = QApplication(sys.argv)
from volumina.api import Viewer
v = Viewer()
v.title = "Volumina Viewer"
v.showMaximized()
for i, d in enumerate(data):
layer_name = layer_name = "layer_" + str(i) if labels is None else labels[i]
if layer_types is None:
_dtype_to_layer(v, d, layer_name)
else:
_name_to_layer(v, d, layer_types[i], layer_name)
app.exec_()
def volumina_n_layer(data, labels = None):
app = QApplication(sys.argv)
import volumina
from volumina.api import Viewer
v = Viewer ()
v.title = " Volumina Demo "
v.showMaximized ()
for ind, d in enumerate(data):
layer_name = "layer_" + str(ind)
if labels is not None:
layer_name = labels[ind]
# get data type of the elements d, to determine
# if we use a grayscale overlay (float32) or a randomcolors overlay (uint) for labels
data_type = d.dtype
if data_type == np.float32 or data_type == np.float64:
v.addGrayscaleLayer(d , name = layer_name)
else:
v.addRandomColorsLayer(d.astype(np.uint32), name = layer_name)
app.exec_()
def streaming_n_layer(files, keys, labels=None, block_shape=[100, 100, 100]):
from volumina.api import Viewer
from volumina.pixelpipeline.datasources import LazyflowSource
from lazyflow.graph import Graph
from lazyflow.operators.ioOperators.opStreamingHdf5Reader import OpStreamingHdf5Reader
from lazyflow.operators import OpCompressedCache
app = QApplication(sys.argv)
v = Viewer()
graph = Graph()
def mkH5source(fname, gname):
h5file = h5py.File(fname)
dtype = h5file[gname].dtype
source = OpStreamingHdf5Reader(graph=graph)
source.Hdf5File.setValue(h5file)
source.InternalPath.setValue(gname)
op = OpCompressedCache(parent=None, graph=graph)
op.BlockShape.setValue(block_shape)
op.Input.connect(source.OutputImage)
return op.Output, dtype
#rawSource = mkH5source(data[0], keys[0])
#v.addGrayscaleLayer(rawSource, name = 'raw')
for i, f in enumerate(files):
if labels is not None:
layer_name = labels[i]
else:
layer_name = "layer_%i" % (i)
source, dtype = mkH5source(f, keys[i])
if np.dtype(dtype) in (np.dtype('uint8'), np.dtype('float32'),
np.dtype('float64')):
v.addGrayscaleLayer(source, name=layer_name)
else:
v.addRandomColorsLayer(source, name=layer_name)
v.setWindowTitle("Streaming Viewer")
v.showNormal()
app.exec_()
def volumina_viewer():
app = QApplication(sys.argv)
v = Viewer()
v.editor.setInteractionMode("navigation")
yield v
try:
signal.signal(signal.SIGINT, lambda *_: app.quit())
app.exec_()
finally:
app.quit()
def view(dset):
from volumina.api import Viewer
from PyQt4.QtGui import QApplication
app = QApplication([])
v = Viewer()
if isinstance(dset, str):
f = h5py.File(dset, 'r')
d = f["volume/data"].value
f.close()
v.setWindowTitle(dset)
v.addGrayscaleLayer(d, name="raw")
elif isinstance(dset, numpy.ndarray):
v.addGrayscaleLayer(dset, name="raw")
else:
raise RuntimeError("%r" % dset)
v.showMaximized()
app.exec_()
def volumina_single_layer(data): app = QApplication (sys.argv) from volumina.api import Viewer v = Viewer () v.title = " Volumina Demo " v.showMaximized () v.addGrayscaleLayer (data , name =" raw data ") app . exec_ ()
def view_HDF5(inpaths):
app = QApplication(sys.argv)
v = Viewer()
for inpath in inpaths:
if "n_1_" in inpath:
prefix = "n_1_"
elif "n_2_" in inpath:
prefix = "n_2_"
else:
prefix = ""
if "h5" in inpath:
#data = vigra.readHDF5(inpath, "data")
print
print "inpath", inpath
data = read_h5(inpath)
file = inpath.split("/")[-1]
name = prefix + file.split(".")[0]
if "prob_files" in inpath or "seeds" in inpath or "trimap" in inpath:
data = binarize_predict(data)
file = inpath.split("/")[-2] + "_" + inpath.split("/")[-1]
name = prefix + file.split(".")[0]
print "type", type(data)
if "test_data" in inpath or "prob_files" in inpath or "seeds" in inpath or "trimap" in inpath:
v.addGrayscaleLayer(data, name=name)
# if "trimaps" in inpath or "dense" in inpath or "sup_maps" in inpath or "seg_maps" in inpath:
# v.addRandomColorsLayer(255*data, name=name+"_color")
else:
v.addRandomColorsLayer(255*data, name=name+"_color")
if "png" in inpath:
img = vigra.impex.readImage(inpath)
img = np.asarray(img)
file = inpath.split("/")[-1]
name = file.split(".")[0]
print "type",type(img)
v.addGrayscaleLayer(img, name=name)
#v.addRandomColorsLayer(255*img, name=name+"color")
v.showMaximized()
app.exec_()
def showStuff(raw_name,
pred_viewer1,
pred_viewer2,
cutout_name,
one_extra=None):
# display the raw and annotations for cremi challenge data
raw = vigra.impex.readHDF5(indir + datasets[raw_name], "data", order='C')
# raw_old = vigra.readHDF5(indir+datasets["raw_bad"], "data", order = 'C')
defect_prediction_128 = vigra.impex.readHDF5(indir +
datasets[pred_viewer2],
"data",
order='C')
defect_prediction_150 = vigra.impex.readHDF5(indir +
datasets[pred_viewer1],
"data",
order='C')
cutout_from_150_pred = vigra.impex.readHDF5(indir + datasets[cutout_name],
"data",
order='C')
####################################################################################################################
# only used for fast testing stuff
#change_one = vigra.readHDF5(indir+datasets["segmentation_on_equalized_image"], "data", order = 'C')
#pdb.set_trace()
#defect_prediction_150[1,:,:] = change_one[0,:,:,0]
####################################################################################################################
# defect_prediction_150 = gt[..., 0]
cutout = numpy.asarray(cutout_from_150_pred)
rawdata = numpy.asarray(raw)
# rawdata_old = numpy.asarray(raw_old)
# op5ify
# shape5d = rawdata.shape
shape5d = (1, ) + rawdata.shape + (1, )
print shape5d, rawdata.shape, rawdata.dtype
app = QApplication([])
v = Viewer()
direct = False
# layer for raw data
rawdata = numpy.reshape(rawdata, shape5d)
rawsource = ArraySource(rawdata)
v.dataShape = shape5d
lraw = GrayscaleLayer(rawsource, direct=direct)
lraw.visible = True
lraw.name = "raw"
v.layerstack.append(lraw)
# layer for cutout regions from raw data
cutout = numpy.reshape(cutout, shape5d)
cutoutsource = ArraySource(cutout)
lcutout = GrayscaleLayer(cutoutsource, direct=direct)
lcutout.visible = False
lcutout.name = "cut_out"
v.layerstack.append(lcutout)
# layer for first prediction result
defect_prediction_128 = numpy.reshape(defect_prediction_128, shape5d)
synsource = ArraySource(defect_prediction_128)
ct = create_random_16bit()
ct[0] = 0
lsyn = ColortableLayer(synsource, ct)
lsyn.name = pred_viewer2
lsyn.visible = False
v.layerstack.append(lsyn)
# layer for second prediction result
segm = numpy.reshape(defect_prediction_150, shape5d)
segsource = ArraySource(segm)
ct = create_random_16bit()
ct[0] = 0
lseg = ColortableLayer(segsource, ct)
lseg.name = pred_viewer1
lseg.visible = False
v.layerstack.append(lseg)
if one_extra is None:
v.showMaximized()
app.exec_()
if one_extra is not None:
# layer for third prediction result
extra_prediction = vigra.readHDF5(indir + datasets[one_extra],
"data",
order='C')
extra_pred_reshaped = numpy.reshape(extra_prediction, shape5d)
segsource = ArraySource(extra_pred_reshaped)
ct = create_random_16bit()
ct[0] = 0
# ct = create_default_16bit()
lseg = ColortableLayer(segsource, ct)
lseg.name = one_extra
lseg.visible = False
v.layerstack.append(lseg)
v.showMaximized()
app.exec_()
a = np.zeros(500 * 500).reshape(500, 500).astype(np.uint8)
ii = np.random.randint(0, 500, 1)
jj = np.random.randint(0, 500, 1)
a[ii, jj] = 1
a = vigra.filters.discDilation(a, radius=20)
array[:] = a.reshape(shape).view(np.ndarray) * 255
op.Input.setDirty()
do()
cron.timeout.connect(do)
ds = createDataSource(op.Output)
layer = ColortableLayer(ds, jet())
mainwin = Viewer()
mainwin.layerstack.append(layer)
mainwin.dataShape = (1, h, w, 1, 1)
print(mainwin.centralWidget())
BoxContr = BoxController(mainwin.editor, op.Output, boxListModel)
BoxInt = BoxInterpreter(mainwin.editor.navInterpret, mainwin.editor.posModel, BoxContr, mainwin.centralWidget())
mainwin.editor.setNavigationInterpreter(BoxInt)
# boxListModel.boxRemoved.connect(BoxContr.deleteItem)
LV.show()
mainwin.show()
app.exec_()
nlm2 = vigra.readHDF5(pnlm2, 'data')
tvbi2 = vigra.readHDF5(ptvbi2, 'data')
tvbai20 = vigra.readHDF5(ptvbai20, 'data')
tvc5 = vigra.readHDF5(ptvc5, 'data')
m1 = vigra.readHDF5(pm1, 'data')
m2 = vigra.readHDF5(pm2, 'data')
m3 = vigra.readHDF5(pm3, 'data')
g1 = vigra.readHDF5(pg1, 'data')
gf5 = vigra.readHDF5(pgf5, 'data')
gm3 = vigra.readHDF5(pgm3, 'data')
diff = gf5-data
app = QApplication(sys.argv)
v = Viewer()
print "add layers"
v.addGrayscaleLayer(data, name="raw")
v.addGrayscaleLayer(nlm, name="non local mean")
v.addGrayscaleLayer(nlm2, name="non local mean (on presmoothed)")
v.addGrayscaleLayer(tvbi2, name="tv bregman 2.0 isotropic")
v.addGrayscaleLayer(tvbai20, name="tv bregman 20.0 anisotropic")
v.addGrayscaleLayer(tvc5, name="tv Chambolle 2.0")
v.addGrayscaleLayer(m1, name="median 1")
v.addGrayscaleLayer(m2, name="median 2")
v.addGrayscaleLayer(m3, name="median 3")
v.addGrayscaleLayer(g1.view(numpy.ndarray), name="gauss 1")
v.addGrayscaleLayer(gf5.view(numpy.ndarray), name="gauss guided filter 5")
v.addGrayscaleLayer(gm3.view(numpy.ndarray), name="median guided filter 3")
x = args[0].find(".h5")
fname = args[0][:x+3]
gname = args[0][x+4:]
#load data
try:
f = h5py.File(fname, 'r')
except:
raise RuntimeError("Could not load '%s'" % fname)
raw = f[gname].value.squeeze()
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)
#######################################################################################################################
skeletons = Skeletons()
e = SkeletonInterpreter(v.editor, skeletons, v)
v.editor.eventSwitch.interpreter = e
v.show()
app.exec_()
x = args[0].find(".h5")
fname = args[0][: x + 3]
gname = args[0][x + 4 :]
# load data
try:
f = h5py.File(fname, "r")
except:
raise RuntimeError("Could not load '%s'" % fname)
raw = f[gname][()].squeeze()
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)
#######################################################################################################################
skeletons = Skeletons()
e = SkeletonInterpreter(v.editor, skeletons, v)
v.editor.eventSwitch.interpreter = e
v.show()
v.raise_()
#array[:] = np.random.randint(0,255,500*500).reshape(shape).astype(np.uint8)
a = np.zeros(500*500).reshape(500,500).astype(np.uint8)
ii=np.random.randint(0,500,1)
jj=np.random.randint(0,500,1)
a[ii,jj]=1
a=vigra.filters.discDilation(a,radius=20)
array[:]=a.reshape(shape).view(np.ndarray)*255
op.Input.setDirty()
do()
cron.connect(cron, SIGNAL('timeout()'), do)
ds = LazyflowSource( op.Output )
layer = ColortableLayer(ds,jet())
mainwin=Viewer()
def _addNewLabel():
"""
Add a new label to the label list GUI control.
Return the new number of labels in the control.
"""
erase=Label( "Dummy",QColor(255,255,255))
label = Label( "Foreground",QColor(255,0,0))
back = Label( "Background",QColor(0,255,0))
newRow = labelListModel.rowCount()
labelListModel.insertRow( newRow, erase )
newRow = labelListModel.rowCount()
import skneuro
import vigra
from volumina.api import Viewer
from PyQt4.QtGui import QApplication
import skneuro.denoising as dn
p = '/home/tbeier/Desktop/blocks/data_sub_3.h5'
data = vigra.impex.readHDF5(p,'data')[0:200,:,0:200].astype('uint8').squeeze()
app = QApplication(sys.argv)
v = Viewer()
v.addGrayscaleLayer(data, name="raw")
with vigra.Timer("get ranks 8*2"):
a = dn.ballRankOrder(data,
radius=12,
takeNth=2,
ranks=(0.01,0.1, 0.5, 0.9, 0.99),
useHistogram=True,
minVal=0.0,
maxVal=255.0,
nBins=256)
if event.type() == QEvent.GraphicsSceneMousePress:
if event.button() == QtCore.Qt.LeftButton:
# print "MyPathItem left click event detected!"
pen = QPen(QColor(0, 255, 255))
self.visiblePath.setPen(pen)
if event.button() == Qt.RightButton:
# print "MyPathItem right click event detected!"
pen = QPen(QColor(255, 255, 0))
self.visiblePath.setPen(pen)
app = QtGui.QApplication([])
v = Viewer()
c_x = numpy.array([10, 20, 40, 80])
c_y = numpy.array([80, 90, 100, 110])
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
for n, arr in enumerate(imgs):
arr = arr.squeeze()
f.add_subplot(1, len(imgs), n)
pylab.imshow(arr.swapaxes(0,1))
pylab.show()
else:
if False:
pmapSmooth2 = dn.diffusion3d(p.copy()*255.0, param)
vigra.impex.writeHDF5(pmapSmooth2, "sub.h5", "dc_1.00_2.50")
if True :
pmapSmooth1 = vigra.impex.readHDF5("sub.h5", "dc_0.75_2")
pmapSmooth2 = vigra.impex.readHDF5("sub.h5", "dc_1.00_2.50")
app = QApplication(sys.argv)
v = Viewer()
v.addGrayscaleLayer(pmapSmooth1, name="pmapSmooth_0.75_2.00")
v.addGrayscaleLayer(pmapSmooth2, name="pmapSmooth_1.00_2.50")
v.addGrayscaleLayer(p, name="pmap")
v.addGrayscaleLayer(d, name="raw")
#v.addGrayscaleLayer(bf.grayscaleErosion(data,sigma=2.5), name="e")
#v.addGrayscaleLayer(dt, name="dt")
v.setWindowTitle("data")
v.showMaximized()
from PyQt5.QtWidgets import QApplication
f = h5py.File("raw.h5", "w")
d = (255 * numpy.random.random((100, 200, 300))).astype(numpy.uint8)
f.create_dataset("raw", data=d)
f.close()
f = h5py.File("seg.h5", "w")
d = (10 * numpy.random.random((100, 200, 300))).astype(numpy.uint32)
f.create_dataset("seg", data=d)
f.close()
##-----
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
import numpy
import skneuro
import vigra
from volumina.api import Viewer
from PyQt4.QtGui import QApplication
import skneuro.denoising as dn
p = '/home/tbeier/Desktop/blocks/data_sub_3.h5'
data = vigra.impex.readHDF5(p, 'data')[0:200, :,
0:200].astype('uint8').squeeze()
app = QApplication(sys.argv)
v = Viewer()
v.addGrayscaleLayer(data, name="raw")
with vigra.Timer("get ranks 8*2"):
a = dn.ballRankOrder(data,
radius=12,
takeNth=2,
ranks=(0.01, 0.1, 0.5, 0.9, 0.99),
useHistogram=True,
minVal=0.0,
maxVal=255.0,
nBins=256)
v.addGrayscaleLayer(a, name="0.5 8* 2")
v.setWindowTitle("data")
v.showMaximized()
app.exec_()
from volumina.api import Viewer
from volumina.colortables import default16_new
from volumina.pixelpipeline.datasources import ArraySinkSource, ArraySource
from volumina.layer import ColortableLayer, GrayscaleLayer
from PyQt5.QtWidgets import QApplication
SHAPE = (1, 600, 800, 1, 1) # volumina expects 5d txyzc
data_arr = (255 * numpy.random.random(SHAPE)).astype(numpy.uint8)
label_arr = numpy.zeros(SHAPE, dtype=numpy.uint8)
##-----
app = QApplication(sys.argv)
v = Viewer()
data_src = ArraySource(data_arr)
data_layer = GrayscaleLayer(data_src)
data_layer.name = "Raw"
data_layer.numberOfChannels = 1
label_src = ArraySinkSource(label_arr)
label_layer = ColortableLayer(label_src,
colorTable=default16_new,
direct=False)
label_layer.name = "Labels"
label_layer.ref_object = None
assert SHAPE == label_arr.shape == data_arr.shape
v.dataShape = SHAPE
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 eventFilter(self, QObject, QEvent):
if (QEvent.type() == QtCore.QEvent.MouseButtonRelease
and QObject is self):
pos = QEvent.pos()
print('mouse button release: (%d, %d)' % (pos.x(), pos.y()))
return Viewer.eventFilter(self, QObject, QEvent)
#array[:] = np.random.randint(0,255,500*500).reshape(shape).astype(np.uint8)
a = np.zeros(500 * 500).reshape(500, 500).astype(np.uint8)
ii = np.random.randint(0, 500, 1)
jj = np.random.randint(0, 500, 1)
a[ii, jj] = 1
a = vigra.filters.discDilation(a, radius=20)
array[:] = a.reshape(shape).view(np.ndarray) * 255
op.Input.setDirty()
do()
cron.timeout.connect(do)
ds = createDataSource(op.Output)
layer = ColortableLayer(ds, jet())
mainwin = Viewer()
def _addNewLabel():
"""
Add a new label to the label list GUI control.
Return the new number of labels in the control.
"""
erase = Label("Dummy", QColor(255, 255, 255))
label = Label("Foreground", QColor(255, 0, 0))
back = Label("Background", QColor(0, 255, 0))
newRow = labelListModel.rowCount()
labelListModel.insertRow(newRow, erase)
newRow = labelListModel.rowCount()
labelListModel.insertRow(newRow, label)
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()
if len(args) != 1:
parser.error("no hdf5 dataset supplied")
x = args[0].find(".h5")
fname = args[0][:x+3]
gname = args[0][x+4:]
#load data
f = h5py.File(fname, 'r')
raw = f[gname].value.squeeze()
assert raw.ndim == 3
assert raw.dtype == numpy.uint8
f.close()
app = QApplication([])
v = Viewer()
direct = True
raw.shape = (1,)+raw.shape+(1,)
def addLayers(v, direct):
l1 = v.addGrayscaleLayer(raw, name="raw direct=%r" % direct, direct=direct)
l1.visible = direct
colortable = [QColor(0,0,0,0).rgba(), QColor(255,0,0).rgba()]
l2 = v.addColorTableLayer((raw>128).astype(numpy.uint8), name="thresh direct=%r" % direct, colortable=colortable, direct=direct)
l2.visible = direct
return (l1, l2)
directLayers = addLayers(v, True)
indirectLayers = addLayers(v, False)
if len(args) != 1:
parser.error("no hdf5 dataset supplied")
x = args[0].find(".h5")
fname = args[0][:x+3]
gname = args[0][x+4:]
#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
# This program is free software; you can redistribute it and/or # modify it under the terms of the GNU General Public License # as published by the Free Software Foundation; either version 2 # of the License, or (at your option) any later version. # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # You should have received a copy of the GNU General Public License # along with this program; if not, write to the Free Software Foundation, # Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. # # Copyright 2011-2014, the ilastik developers from volumina.api import Viewer from PyQt4.QtGui import QApplication import numpy app = QApplication([]) v = Viewer() a = (255*numpy.random.random((1, 50,60,70,10) )).astype(numpy.uint8) v.addGrayscaleLayer(a, name="raw") v.showMaximized() app.exec_()
f = pylab.figure()
for n, arr in enumerate(imgs):
arr = arr.squeeze()
f.add_subplot(1, len(imgs), n)
pylab.imshow(arr.swapaxes(0, 1))
pylab.show()
else:
if False:
pmapSmooth2 = dn.diffusion3d(p.copy() * 255.0, param)
vigra.impex.writeHDF5(pmapSmooth2, "sub.h5", "dc_1.00_2.50")
if True:
pmapSmooth1 = vigra.impex.readHDF5("sub.h5", "dc_0.75_2")
pmapSmooth2 = vigra.impex.readHDF5("sub.h5", "dc_1.00_2.50")
app = QApplication(sys.argv)
v = Viewer()
v.addGrayscaleLayer(pmapSmooth1, name="pmapSmooth_0.75_2.00")
v.addGrayscaleLayer(pmapSmooth2, name="pmapSmooth_1.00_2.50")
v.addGrayscaleLayer(p, name="pmap")
v.addGrayscaleLayer(d, name="raw")
#v.addGrayscaleLayer(bf.grayscaleErosion(data,sigma=2.5), name="e")
#v.addGrayscaleLayer(dt, name="dt")
v.setWindowTitle("data")
v.showMaximized()
app.exec_()
sys.exit()
from volumina.api import Viewer from PyQt4.QtGui import QApplication import numpy app = QApplication([]) v = Viewer() a = (255*numpy.random.random((1, 50,60,70,10) )).astype(numpy.uint8) v.addGrayscaleLayer(a, name="raw") v.showMaximized() app.exec_()
if event.button() == QtCore.Qt.LeftButton:
# print "MyPathItem left click event detected!"
pen = QPen(QColor(0, 255, 255))
pen.setWidth(5)
self.setPen(pen)
if event.button() == Qt.RightButton:
# print "MyPathItem right click event detected!"
pen = QPen(QColor(255, 255, 0))
pen.setWidth(5)
self.setPen(pen)
app = QtGui.QApplication([])
v = Viewer()
xFwd = numpy.array([10, 20, 40, 80])
xRev = xFwd[::-1]
x = numpy.concatenate([xFwd, xRev])
yFwd = numpy.array([80, 90, 100, 110])
yRev = yFwd[::-1]
y = numpy.concatenate([yFwd, yRev])
path1 = arrayToQPath(x, y)
item1 = ClickablePathItem()
item1.setPath(path1)
# Create images
back = (numpy.ones((100, 200, 300)) * 0).astype(numpy.uint8)
back[0:60, 0:60, 0:60] = 255
a = np.zeros(500*500).reshape(500,500).astype(np.uint8)
ii=np.random.randint(0,500,1)
jj=np.random.randint(0,500,1)
a[ii,jj]=1
a=vigra.filters.discDilation(a,radius=20)
array[:]=a.reshape(shape).view(np.ndarray)*255
op.Input.setDirty()
do()
cron.connect(cron, SIGNAL('timeout()'), do)
ds = LazyflowSource( op.Output )
layer = ColortableLayer(ds,jet())
mainwin=Viewer()
mainwin.layerstack.append(layer)
mainwin.dataShape=(1,h,w,1,1)
print mainwin.centralWidget()
BoxContr=BoxController(mainwin.editor,op.Output,boxListModel)
BoxInt=BoxInterpreter(mainwin.editor.navInterpret,mainwin.editor.posModel,BoxContr,mainwin.centralWidget())
mainwin.editor.setNavigationInterpreter(BoxInt)
# boxListModel.boxRemoved.connect(BoxContr.deleteItem)
LV.show()
mainwin.show()
def addHocViewer(grayData=None, segData=None, title="viewer", visu=True):
if visu:
app = QApp.Instance().app
v = Viewer()
if grayData is not None:
for data, name in grayData:
if isinstance(data, vigra.arraytypes.VigraArray):
v.addGrayscaleLayer(data.view(numpy.ndarray), name=name)
else:
v.addGrayscaleLayer(data, name=name)
if segData is not None:
for data, name in segData:
if isinstance(data, vigra.arraytypes.VigraArray):
v.addColorTableLayer(data.view(numpy.ndarray), name=name)
else:
v.addColorTableLayer(data, name=name)
v.setWindowTitle(title)
v.showMaximized()
app.exec_()
def showStuff(raw_name, pred_viewer1, pred_viewer2, cutout_name, one_extra = None):
# display the raw and annotations for cremi challenge data
raw = vigra.impex.readHDF5(indir+datasets[raw_name], "data", order = 'C')
# raw_old = vigra.readHDF5(indir+datasets["raw_bad"], "data", order = 'C')
defect_prediction_128 = vigra.impex.readHDF5(indir+datasets[pred_viewer2], "data", order = 'C')
defect_prediction_150 = vigra.impex.readHDF5(indir+datasets[pred_viewer1], "data", order = 'C')
cutout_from_150_pred = vigra.impex.readHDF5(indir+datasets[cutout_name], "data", order = 'C')
####################################################################################################################
# only used for fast testing stuff
#change_one = vigra.readHDF5(indir+datasets["segmentation_on_equalized_image"], "data", order = 'C')
#pdb.set_trace()
#defect_prediction_150[1,:,:] = change_one[0,:,:,0]
####################################################################################################################
# defect_prediction_150 = gt[..., 0]
cutout = numpy.asarray(cutout_from_150_pred)
rawdata = numpy.asarray(raw)
# rawdata_old = numpy.asarray(raw_old)
# op5ify
# shape5d = rawdata.shape
shape5d = (1,)+rawdata.shape+(1,)
print shape5d, rawdata.shape, rawdata.dtype
app = QApplication([])
v = Viewer()
direct = False
# layer for raw data
rawdata = numpy.reshape(rawdata, shape5d)
rawsource = ArraySource(rawdata)
v.dataShape = shape5d
lraw = GrayscaleLayer(rawsource, direct=direct)
lraw.visible = True
lraw.name = "raw"
v.layerstack.append(lraw)
# layer for cutout regions from raw data
cutout = numpy.reshape(cutout, shape5d)
cutoutsource = ArraySource(cutout)
lcutout = GrayscaleLayer(cutoutsource, direct = direct)
lcutout.visible = False
lcutout.name = "cut_out"
v.layerstack.append(lcutout)
# layer for first prediction result
defect_prediction_128 = numpy.reshape(defect_prediction_128, shape5d)
synsource = ArraySource(defect_prediction_128)
ct = create_random_16bit()
ct[0] = 0
lsyn = ColortableLayer(synsource, ct)
lsyn.name = pred_viewer2
lsyn.visible = False
v.layerstack.append(lsyn)
# layer for second prediction result
segm = numpy.reshape(defect_prediction_150, shape5d)
segsource = ArraySource(segm)
ct = create_random_16bit()
ct[0] = 0
lseg = ColortableLayer(segsource, ct)
lseg.name = pred_viewer1
lseg.visible = False
v.layerstack.append(lseg)
if one_extra is None:
v.showMaximized()
app.exec_()
if one_extra is not None:
# layer for third prediction result
extra_prediction = vigra.readHDF5(indir+datasets[one_extra], "data", order = 'C')
extra_pred_reshaped = numpy.reshape(extra_prediction, shape5d)
segsource = ArraySource(extra_pred_reshaped)
ct = create_random_16bit()
ct[0] = 0
# ct = create_default_16bit()
lseg = ColortableLayer(segsource, ct)
lseg.name = one_extra
lseg.visible = False
v.layerstack.append(lseg)
v.showMaximized()
app.exec_()
# array[:] = np.random.randint(0,255,500*500).reshape(shape).astype(np.uint8)
a = np.zeros(500 * 500).reshape(500, 500).astype(np.uint8)
ii = np.random.randint(0, 500, 1)
jj = np.random.randint(0, 500, 1)
a[ii, jj] = 1
a = vigra.filters.discDilation(a, radius=20)
array[:] = a.reshape(shape).view(np.ndarray) * 255
op.Input.setDirty()
do()
cron.connect(cron, SIGNAL("timeout()"), do)
ds = LazyflowSource(op.Output)
layer = ColortableLayer(ds, jet())
mainwin = Viewer()
def _addNewLabel():
"""
Add a new label to the label list GUI control.
Return the new number of labels in the control.
"""
erase = Label("Dummy", QColor(255, 255, 255))
label = Label("Foreground", QColor(255, 0, 0))
back = Label("Background", QColor(0, 255, 0))
newRow = labelListModel.rowCount()
labelListModel.insertRow(newRow, erase)
newRow = labelListModel.rowCount()
labelListModel.insertRow(newRow, label)
def volumina_double_layer(data, overlay): # get data type of the elements of overlay, to determine # if we use a grayscale overlay (float32) or a randomcolors overlay (uint) for labels mask = [] for i in range( len(overlay.shape) ): mask.append(0) mask = tuple(mask) data_type = type(overlay[mask]) app = QApplication (sys.argv) from volumina.api import Viewer v = Viewer () v.title = " Volumina Demo " v.showMaximized () v.addGrayscaleLayer(data , name = " raw data ") if data_type == np.float32: v.addGrayscaleLayer(overlay , name = " overlay ") else: v.addRandomColorsLayer(overlay, name = " overlay ") app . exec_ ()
sigma = float(sigma)
return (-1.0 / sigma) * gauss(x, mean, sigma) + ((
(-x + mean) / sigma)**2) * gauss(x, mean, sigma)
for x in range(patchSize[0]):
for y in range(patchSize[1]):
for z in range(patchSize[2]):
dgx = gauss2d(x, radius[0], sigma[0])
gy = gauss(y, radius[1], sigma[1])
gz = gauss(z, radius[2], sigma[2])
kernel[x, y, z] = dgx * gy * gz
return kernel
kernel = makeFilter(radius, sigma)
kernel /= numpy.sum(kernel)
kernel -= kernel.min()
kernel /= kernel.max()
app = QApplication(sys.argv)
v = Viewer()
v.addGrayscaleLayer(kernel, name="raw")
v.setWindowTitle("kernel")
v.showMaximized()
app.exec_()
def volumina_flexible_layer(data, layer_types, labels=None):
assert len(layer_types) == len(data)
app = QApplication (sys.argv)
import volumina
from volumina.api import Viewer
v = Viewer ()
v.title = " Volumina Demo "
v.showMaximized ()
for i, d in enumerate(data):
layer_name = "layer_" + str(i)
if labels is not None:
layer_name = labels[i]
# get data type of the elements d, to determine
# if we use a grayscale overlay (float32) or a randomcolors overlay (uint) for labels
data_type = d.dtype
if layer_types[i] == 'Grayscale':
v.addGrayscaleLayer(d , name = layer_name)
elif layer_types[i] == 'RandomColors':
v.addRandomColorsLayer(d.astype(np.uint32), name=layer_name)
elif layer_types[i] == 'Red':
v.addAlphaModulatedLayer(d , name=layer_name, tintColor=QColor(255,0,0))
elif layer_types[i] == 'Green':
v.addAlphaModulatedLayer(d , name=layer_name, tintColor=QColor(0,255,0))
elif layer_types[i] == 'Blue':
v.addAlphaModulatedLayer(d , name=layer_name, tintColor=QColor(0,0,255))
else:
raise KeyError("Invalid Layer Type, %s!" % layer_types[i])
app.exec_()
a = np.zeros(500 * 500).reshape(500, 500).astype(np.uint8)
ii = np.random.randint(0, 500, 1)
jj = np.random.randint(0, 500, 1)
a[ii, jj] = 1
a = vigra.filters.discDilation(a, radius=20)
array[:] = a.reshape(shape).view(np.ndarray) * 255
op.Input.setDirty()
do()
cron.timeout.connect(do)
ds = LazyflowSource(op.Output)
layer = ColortableLayer(ds, jet())
mainwin = Viewer()
mainwin.layerstack.append(layer)
mainwin.dataShape = (1, h, w, 1, 1)
print(mainwin.centralWidget())
BoxContr = BoxController(mainwin.editor, op.Output, boxListModel)
BoxInt = BoxInterpreter(mainwin.editor.navInterpret,
mainwin.editor.posModel, BoxContr,
mainwin.centralWidget())
mainwin.editor.setNavigationInterpreter(BoxInt)
# boxListModel.boxRemoved.connect(BoxContr.deleteItem)
LV.show()
mainwin.show()
from PyQt4.QtGui import QApplication
f = h5py.File("raw.h5", 'w')
d = (255 * numpy.random.random((100, 200, 300))).astype(numpy.uint8)
f.create_dataset("raw", data=d)
f.close()
f = h5py.File("seg.h5", 'w')
d = (10 * numpy.random.random((100, 200, 300))).astype(numpy.uint32)
f.create_dataset("seg", data=d)
f.close()
##-----
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
#dd = ew-ews
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()
#array[:] = np.random.randint(0,255,500*500).reshape(shape).astype(np.uint8)
a = np.zeros(500 * 500).reshape(500, 500).astype(np.uint8)
ii = np.random.randint(0, 500, 1)
jj = np.random.randint(0, 500, 1)
a[ii, jj] = 1
a = vigra.filters.discDilation(a, radius=20)
array[:] = a.reshape(shape).view(np.ndarray) * 255
op.Input.setDirty()
do()
cron.connect(cron, SIGNAL('timeout()'), do)
ds = LazyflowSource(op.Output)
layer = ColortableLayer(ds, jet())
mainwin = Viewer()
mainwin.layerstack.append(layer)
mainwin.dataShape = (1, 500, 500, 1, 1)
print mainwin.centralWidget()
BoxContr = BoxController(mainwin.editor.imageScenes[2], op.Output,
boxListModel)
BoxInt = BoxInterpreter(mainwin.editor.navInterpret,
mainwin.editor._posModel, BoxContr,
mainwin.centralWidget())
mainwin.editor.setNavigationInterpreter(BoxInt)
# boxListModel.boxRemoved.connect(BoxContr.deleteItem)
LV.show()
mainwin.show()
if len(args) != 1:
parser.error("no hdf5 dataset supplied")
x = args[0].find(".h5")
fname = args[0][:x + 3]
gname = args[0][x + 4:]
# load data
f = h5py.File(fname, "r")
raw = f[gname].value.squeeze()
assert raw.ndim == 3
assert raw.dtype == numpy.uint8
f.close()
app = QApplication([])
v = Viewer()
direct = True
raw.shape = (1, ) + raw.shape + (1, )
def addLayers(v, direct):
l1 = v.addGrayscaleLayer(raw, name="raw direct=%r" % direct, direct=direct)
l1.visible = direct
colortable = [QColor(0, 0, 0, 0).rgba(), QColor(255, 0, 0).rgba()]
l2 = v.addColorTableLayer((raw > 128).astype(numpy.uint8),
name="thresh direct=%r" % direct,
colortable=colortable,
direct=direct)
l2.visible = direct
return (l1, l2)
def __init__(self):
Viewer.__init__(self)
self.installEventFilter(self)
if len(args) != 1:
parser.error("no hdf5 dataset supplied")
x = args[0].find(".h5")
fname = args[0][:x + 3]
gname = args[0][x + 4:]
# 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)
gt = vigra.readHDF5("/home/stamylew/volumes/groundtruth/dense_groundtruth/100p_cube1_dense_gt.h5", "data")
from volumina.api import Viewer
from volumina.pixelpipeline.datasources import LazyflowSource
import sys
from lazyflow.graph import Graph
from lazyflow.operators.ioOperators.opStreamingHdf5Reader import OpStreamingHdf5Reader
from lazyflow.operators import OpCompressedCache
from PyQt4.QtGui import QApplication
app = QApplication(sys.argv)
v = Viewer()
#raw layer
v.addGrayscaleLayer(raw, name="test")
#predict layer
#predict = np.array(predict[:,:,:,0,0]) * 255
#v.addColorTableLayer(predict.astype(np.float32), name="prediction")
v.addGrayscaleLayer(predict.astype(np.float32), name="org")
#trimap layer
tm = np.array(tm)*255
print np.unique(tm)
#v.addColorTableLayer(tm.astype(np.float32), name="trimap")
#v.addGrayscaleLayer(tm.astype(np.float32), name="tm")
