def test_regionradii(self):
# Create a volume of flat superpixels, where every slice
# is the same (except for the actual sp ids)
num_sp_per_slice = 200
slice_superpixels = generate_random_voronoi((100,200), num_sp_per_slice)
superpixels = np.zeros( shape=((10,) + slice_superpixels.shape), dtype=np.uint32 )
for z in range(10):
superpixels[z] = slice_superpixels + z*num_sp_per_slice
superpixels = vigra.taggedView(superpixels, 'zyx')
rag_flat = Rag( superpixels, flat_superpixels=True )
values = np.random.random(size=(superpixels.shape)).astype(np.float32)
values = vigra.taggedView(values, 'zyx')
flat_features_df = rag_flat.compute_features(values, ['standard_flatedge_regionradii'], edge_group='z')
# Now compute the radii using a normal 'dense' rag
rag_dense = Rag( superpixels )
dense_features_df = rag_dense.compute_features(values, ['edgeregion_edge_regionradii'])
# Both methods should be reasonably close.
combined_features_df = pd.merge(flat_features_df, dense_features_df, how='left', on=['sp1', 'sp2'])
assert np.isclose(combined_features_df['standard_flatedge_regionradii_0'], combined_features_df['edgeregion_edge_regionradii_0'], atol=0.001).all()
assert np.isclose(combined_features_df['standard_flatedge_regionradii_1'], combined_features_df['edgeregion_edge_regionradii_1'], atol=0.001).all()
def test_quantiles(self):
# Create a volume of flat superpixels, where every slice
# is the same (except for the actual sp ids)
num_sp_per_slice = 200
slice_superpixels = generate_random_voronoi((100,200), num_sp_per_slice)
superpixels = np.zeros( shape=((10,) + slice_superpixels.shape), dtype=np.uint32 )
for z in range(10):
superpixels[z] = slice_superpixels + z*num_sp_per_slice
superpixels = vigra.taggedView(superpixels, 'zyx')
rag_flat = Rag( superpixels, flat_superpixels=True )
values = np.random.random(size=(superpixels.shape)).astype(np.float32)
values = vigra.taggedView(values, 'zyx')
flat_features_df = rag_flat.compute_features(values, ['standard_flatedge_quantiles'], edge_group='z')
flat_features_df2 = rag_flat.compute_features(values, ['standard_edge_quantiles'], edge_group='yx')
# Rename columns
flat_features_df2.columns = flat_features_df.columns.values
flat_features_df = pd.concat( (flat_features_df, flat_features_df2), axis=0 )
# Now compute the quantiles using a normal 'dense' rag
rag_dense = Rag( superpixels )
dense_features_df = rag_dense.compute_features(values, ['standard_edge_quantiles'])
all_features_df = pd.merge(dense_features_df, flat_features_df, how='left', on=['sp1', 'sp2'])
assert (all_features_df['standard_edge_quantiles_0'] == all_features_df['standard_flatedge_quantiles_0']).all()
assert (all_features_df['standard_edge_quantiles_100'] == all_features_df['standard_flatedge_quantiles_100']).all()
# Due to the way histogram ranges are computed, we can't expect quantiles_10 to match closely
# ... but quantiles_50 seems to be good.
assert np.isclose(all_features_df['standard_edge_quantiles_50'], all_features_df['standard_edge_quantiles_50']).all()
def deepDetexturize(
srcImg,
img,
nIteration=10,
**kwargs
):
hist=img.copy()
mixIn=None
for i in range(nIteration):
newImg = detexturize(img=hist,**kwargs)
newImgIter = newImg.copy()
newImgIter = vigra.taggedView(newImgIter,'xyc')
if i == 0:
mixIn=newImg.copy()
if i !=0 :
newImg = numpy.concatenate([newImg,mixIn],axis=2)
newImg = vigra.taggedView(newImg,'xyc')
hist = histogram(newImg,r=2,sigma=[3.0,3.0])
f = pylab.figure()
for n, iterImg in enumerate([srcImg,newImgIter]):
#f.add_subplot(2, 1, n) # this line outputs images on top of each other
f.add_subplot(1, 2, n) # this line outputs images side-by-side
if iterImg.ndim==2:
pylab.imshow(numpy.swapaxes(norm01(iterImg),0,1),cmap='gray')
else :
pylab.imshow(numpy.swapaxes(norm01(iterImg),0,1))
pylab.show()
def testBasic(self):
features = numpy.indices( (100,100) ).astype(numpy.float) + 0.5
features = numpy.rollaxis(features, 0, 3)
features = vigra.taggedView(features, 'xyc')
labels = numpy.zeros( (100,100,1), dtype=numpy.uint8 )
labels = vigra.taggedView(labels, 'xyc')
labels[10,10] = 1
labels[10,11] = 1
labels[20,20] = 2
labels[20,21] = 2
graph = Graph()
opTrain = OpTrainClassifierBlocked( graph=graph )
opTrain.ClassifierFactory.setValue( VigraRfLazyflowClassifierFactory(10) )
opTrain.Images.resize(1)
opTrain.Labels.resize(1)
opTrain.nonzeroLabelBlocks.resize(1)
opTrain.Images[0].setValue( features )
opTrain.Labels[0].setValue( labels )
opTrain.nonzeroLabelBlocks[0].setValue(0) # Dummy for now (not used by operator yet)
opTrain.MaxLabel.setValue(2)
opTrain.Labels[0].setDirty( numpy.s_[10:11, 10:12] )
opTrain.Labels[0].setDirty( numpy.s_[20:21, 20:22] )
opTrain.Labels[0].setDirty( numpy.s_[30:31, 30:32] )
trained_classifier = opTrain.Classifier.value
# This isn't much of a test at the moment...
assert isinstance( trained_classifier, VigraRfLazyflowClassifier )
def testBasic2(self):
a = numpy.ones((100, 101, 102))
a = a[..., None]
a = vigra.taggedView(a, "tyxc")
graph = Graph()
opPrep = OpArrayPiper(graph=graph)
opPrep.Input.setValue(a)
op = OpNansheExtractF0Cached(graph=graph)
op.Input.connect(opPrep.Output)
op.HalfWindowSize.setValue(20)
op.WhichQuantile.setValue(0.5)
op.TemporalSmoothingGaussianFilterStdev.setValue(5.0)
op.SpatialSmoothingGaussianFilterStdev.setValue(5.0)
op.Bias.setValue(100)
op.BiasEnabled.setValue(True)
b = op.dF_F[...].wait()
b = vigra.taggedView(b, "tyxc")
assert(a.shape == b.shape)
assert((b == 0).all())
def setUp(self):
self.nx = 50
self.ny = 51
self.nz = 52
self.nc = 3
clusters = self.generateData((self.nx, self.ny, self.nz))
self.data = clusters[0] + clusters[1] + clusters[2] + clusters[3] + clusters[4]
self.data = self.data.reshape(self.data.shape+(1,))
self.data = vigra.taggedView(self.data, axistags='xyzc')
self.minSize = 5 # first cluster doesn't pass this
self.maxSize = 30 # fourth and fifth cluster don't pass this
self.highThreshold = 0.65 # third cluster doesn't pass
self.lowThreshold = 0.1
# Replicate the 4d data for multiple time slices
self.data5d = numpy.concatenate(3*(self.data[numpy.newaxis, ...],),
axis=0)
self.data5d = vigra.taggedView(self.data5d, axistags="txyzc")
self.sigma = {'x': 0.3, 'y': 0.3, 'z': 0.3}
#pre-smooth 4d data
self.data = vigra.filters.gaussianSmoothing(
self.data.astype(numpy.float32), 0.3)
def testMargin(self):
graph = Graph()
vol = np.zeros((100, 110, 10), dtype=np.float32)
# draw a big plus sign
vol[50:70, :, :] = 1.0
vol[:, 60:80, :] = 1.0
vol = vigra.taggedView(vol, axistags="xyz").withAxes(*"txyzc")
labels = np.zeros((100, 110, 10), dtype=np.uint32)
labels[45:75, 55:85, 3:4] = 1
labels = vigra.taggedView(labels, axistags="xyz").withAxes(*"txyzc")
op = OpObjectsSegment(graph=graph)
piper = OpArrayPiper(graph=graph)
piper.Input.setValue(vol)
op.Prediction.connect(piper.Output)
op.LabelImage.setValue(labels)
# without margin
op.Margin.setValue(np.asarray((0, 0, 0)))
out = op.Output[...].wait()
out = vigra.taggedView(out, axistags=op.Output.meta.axistags)
out = out.withAxes(*"xyz")
vol = vol.withAxes(*"xyz")
assert_array_equal(out[50:70, 60:80, 3] > 0, vol[50:70, 60:80, 3] > 0.5)
assert np.all(out[:45, ...] == 0)
# with margin
op.Margin.setValue(np.asarray((5, 5, 0)))
out = op.Output[...].wait()
out = vigra.taggedView(out, axistags=op.Output.meta.axistags)
out = out.withAxes(*"xyz")
assert_array_equal(out[45:75, 55:85, 3] > 0, vol[45:75, 55:85, 3] > 0.5)
assert np.all(out[:40, ...] == 0)
def testBasic3(self):
a = numpy.ones((1, 100, 101))
a = a[..., None]
a = vigra.taggedView(a, "tyxc")
r = numpy.array([[0, 0, 0], [1, 3, 4]]).T.copy()
ar = a.copy()
for each_r in r:
nanshe.util.xnumpy.index_axis_at_pos(nanshe.util.xnumpy.index_axis_at_pos(ar, 0, each_r[0]), -1, each_r[-1])[:] = 0
graph = Graph()
opPrep = OpArrayPiper(graph=graph)
opPrep.Input.setValue(ar)
op = OpNansheRemoveZeroedLinesCached(graph=graph)
op.Input.connect(opPrep.Output)
op.ErosionShape.setValue([21, 1])
op.DilationShape.setValue([1, 3])
b = op.Output[...].wait()
b = vigra.taggedView(b, "tyxc")
assert((a == b).all())
def testOptimalInit(self):
x = np.asarray([0, 0, 1, 1, .5])
y = np.asarray([0, 1, 0, 1, .5])
vol = np.zeros((5, 2), dtype=np.float32)
vol[:, 0] = x
vol[:, 1] = y
vol = vigra.taggedView(vol, axistags='tc')
z = x*(1-y) + y*(1-x)
z = vigra.taggedView(z[:, np.newaxis], axistags='tc')
nvis = 2
ncent = 5
layers = [Sigmoid(layer_name='bumps', irange=0, dim=2*nvis*ncent),
Sigmoid(layer_name='cents', irange=0, dim=ncent),
Linear(layer_name='out', irange=0, dim=1)]
mlp = MLP(layers=layers, nvis=nvis)
init = OptimalInitializer.build({}, graph=Graph())
init.Data.setValue(vol)
init.Target.setValue(z)
init.init_model(mlp)
op = OpForwardLayers(layers[:], graph=Graph())
op.Input.setValue(vol)
z_pred = op.Output[..., 0].wait().squeeze()
assert max(z_pred[0], z_pred[3]) < z_pred[4]
assert min(z_pred[1], z_pred[2]) > z_pred[4]
def testCircular(self):
g = Graph()
op = OpLazyCC(graph=g)
op.ChunkShape.setValue((3, 3, 1))
vol = np.asarray(
[
[0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 1, 1, 1, 0, 1, 1, 1, 0],
[0, 1, 0, 0, 0, 0, 0, 1, 0],
[0, 1, 0, 0, 0, 0, 0, 1, 0],
[0, 1, 0, 0, 0, 0, 0, 1, 0],
[0, 1, 0, 0, 0, 0, 0, 1, 0],
[0, 1, 0, 0, 0, 0, 0, 1, 0],
[0, 1, 1, 1, 1, 1, 1, 1, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0],
],
dtype=np.uint8,
)
vol1 = vigra.taggedView(vol, axistags="yx")
vol2 = vigra.taggedView(vol, axistags="xy")
vol3 = vigra.taggedView(np.flipud(vol), axistags="yx")
vol4 = vigra.taggedView(np.flipud(vol), axistags="xy")
for v in (vol1, vol2, vol3, vol4):
op.Input.setValue(v)
for x in [0, 3, 6]:
for y in [0, 3, 6]:
if x == 3 and y == 3:
continue
op.Input.setDirty(slice(None))
out = op.Output[x : x + 3, y : y + 3].wait()
print(out.squeeze())
assert out.max() == 1
def process_timestep( t ):
# Request input and resize it.
# FIXME: This is not quite correct. We should request a halo that is wide enough
# for the BSpline used by resize(). See vigra docs for BSlineBase.radius()
step_input_roi = copy.copy(input_roi)
step_input_roi[0][0] = t
step_input_roi[1][0] = t+1
step_input_data = self.Input( *step_input_roi ).wait()
step_input_data = vigra.taggedView( step_input_data, 'tzyxc' )
step_shape_4d = numpy.array(step_input_data[0].shape)
step_shape_4d_nochannel = step_shape_4d[:-1]
squeezed_slicing = numpy.where(step_shape_4d_nochannel == 1, 0, slice(None))
squeezed_slicing = tuple(squeezed_slicing) + (slice(None),)
step_input_squeezed = step_input_data[0][squeezed_slicing]
result_step = result[t][squeezed_slicing]
# vigra assumes wrong axis order if we don't specify one explicitly here...
result_step = vigra.taggedView( result_step, step_input_squeezed.axistags )
if self.Input.meta.dtype == numpy.float32:
vigra.sampling.resize( step_input_squeezed, out=result_step )
else:
step_input_squeezed = step_input_squeezed.astype( numpy.float32 )
result_float = vigra.sampling.resize(step_input_squeezed, shape=result_step.shape[:-1])
result_step[:] = result_float.round()
def relabel(key_label_mapping):
import numpy
(subvolume, labels) = key_label_mapping
# grab broadcast offset
offset = numpy.uint64( subvolume_offsets.value[subvolume.sv_index] )
# check for body mask labels and protect from renumber
fix_bodies = []
labels = labels + offset
# make sure 0 is 0
labels[labels == offset] = 0
# create default map
labels_view = vigra.taggedView(labels.astype(numpy.uint64), 'zyx')
mapping_col = numpy.sort( vigra.analysis.unique(labels_view) )
label_mappings = dict(zip(mapping_col, mapping_col))
# create maps from merge list
for mapping in master_merge_list.value:
if mapping[0] in label_mappings:
label_mappings[mapping[0]] = mapping[1]
# apply maps
new_labels = numpy.empty_like( labels, dtype=numpy.uint64 )
new_labels_view = vigra.taggedView(new_labels, 'zyx')
vigra.analysis.applyMapping(labels_view, label_mappings, allow_incomplete_mapping=True, out=new_labels_view)
return (subvolume, new_labels)
def testBasic2(self):
a = numpy.zeros((2,2,2,), dtype=int)
a[1,1,1] = 1
a[0,0,0] = 1
a = a[..., None]
a = vigra.taggedView(a, "tyxc")
expected_b = a.astype(float)
expected_b = vigra.taggedView(expected_b, "tyxc")
graph = Graph()
op = OpConvertTypeCached(graph=graph)
opPrep = OpArrayPiper(graph=graph)
opPrep.Input.setValue(a)
op.Input.connect(opPrep.Output)
op.Dtype.setValue(float)
b = op.Output[...].wait()
b = vigra.taggedView(b, "tyxc")
assert((b == expected_b).all())
def execute(self, slot, subindex, roi, result):
window = self.WindowSize.value
if slot is self.Output:
padding_size = max(window - 1 - roi.start[0], 0)
padding = np.zeros((padding_size,), dtype=np.float32)
new_start = (roi.start[0] - window + 1 + padding_size,)
new_stop = (roi.stop[0],)
new_roi = SubRegion(self.Input, start=new_start, stop=new_stop)
input_data = self.Input.get(new_roi).wait()
input_data = vigra.taggedView(input_data,
axistags=self.Input.meta.axistags)
input_data = input_data.withAxes('t').view(np.ndarray)
input_data = np.concatenate((padding, input_data))
res_view = vigra.taggedView(result,
axistags=self.Output.meta.axistags)
res_view = res_view.withAxes('t')
self.apply_window_function(input_data, window, res_view)
elif slot is self.Valid:
result[:] = 1
first_valid_index = window - 1
num_invalid = first_valid_index - roi.start[0]
if num_invalid > 0:
result[:num_invalid] = 0
def test4dAnd5d(self):
g = Graph()
oper = OpThresholdTwoLevels5d(graph=g)
oper.InputImage.setValue(self.data.withAxes(*'txyzc'))
oper.MinSize.setValue(self.minSize)
oper.MaxSize.setValue(self.maxSize)
oper.HighThreshold.setValue(self.highThreshold)
oper.LowThreshold.setValue(self.lowThreshold)
output = oper.Output[:].wait()
output = vigra.taggedView(output, axistags=oper.Output.meta.axistags)
self.checkResult(output)
oper5d = OpThresholdTwoLevels(graph=g)
oper5d.InputImage.setValue(self.data5d)
oper5d.MinSize.setValue(self.minSize)
oper5d.MaxSize.setValue(self.maxSize)
oper5d.HighThreshold.setValue(self.highThreshold)
oper5d.LowThreshold.setValue(self.lowThreshold)
oper5d.SmootherSigma.setValue({'x': 0, 'y': 0, 'z': 0})
oper5d.Channel.setValue(0)
oper5d.CurOperator.setValue(1)
out5d = oper5d.Output[0:1, ...].wait()
out5d = vigra.taggedView(out5d, axistags=oper5d.Output.meta.axistags)
self.checkResult(out5d)
numpy.testing.assert_array_equal(out5d, output)
def execute(self, slot, subindex, roi, result):
assert len(roi.start) == len(roi.stop) == len(self.Output.meta.shape)
assert slot == self.Output
t_ind = self.RawVolume.axistags.index('t')
assert t_ind < len(self.RawVolume.meta.shape)
# loop over requested time slices
for res_t_ind, t in enumerate(xrange(roi.start[t_ind],
roi.stop[t_ind])):
# Process entire spatial volume
s = [slice(None) for i in range(len(self.RawVolume.meta.shape))]
s[t_ind] = slice(t, t+1)
s = tuple(s)
rawVolume = self.RawVolume[s].wait()
rawVolume = vigra.taggedView(
rawVolume, axistags=self.RawVolume.meta.axistags)
labelVolume = self.LabelVolume[s].wait()
labelVolume = vigra.taggedView(
labelVolume, axistags=self.LabelVolume.meta.axistags)
# Convert to 4D (preserve axis order)
axes4d = self.RawVolume.meta.getTaggedShape().keys()
axes4d = filter(lambda k: k in 'xyzc', axes4d)
rawVolume = rawVolume.withAxes(*axes4d)
labelVolume = labelVolume.withAxes(*axes4d)
acc = self._extract(rawVolume4d, labelVolume4d)
result[res_t_ind] = acc
return result
def testAgainstOwn(self):
g = Graph()
oper = OpThresholdTwoLevels(graph=g)
oper.InputImage.setValue(self.data5d)
oper.MinSize.setValue(self.minSize)
oper.MaxSize.setValue(self.maxSize)
oper.HighThreshold.setValue(self.highThreshold)
oper.LowThreshold.setValue(self.lowThreshold)
oper.SmootherSigma.setValue({'x': 0, 'y': 0, 'z': 0})
oper.CurOperator.setValue(1)
output = oper.Output[0, ..., 0].wait()
output = vigra.taggedView(output, axistags=oper.Output.meta.axistags)
output = output.withAxes(*'xyz')
output2 = self.thresholdTwoLevels(self.data5d[0, ..., 0])
output2 = vigra.taggedView(output2, axistags='xyz')
ref = output*output2
idx = np.where(ref != output)
print(oper.Output.meta.getTaggedShape())
print(output.shape)
print(idx)
print(output[idx])
print(output2[idx])
numpy.testing.assert_array_almost_equal(ref, output)
def _label(self, roi, result):
result = vigra.taggedView(result, axistags=self.Output.meta.axistags)
# get the background values
bg = self.Background[...].wait()
bg = vigra.taggedView(bg, axistags=self.Background.meta.axistags)
bg = bg.withAxes(*'ct')
assert np.all(self.Background.meta.shape[3:] ==
self.Input.meta.shape[3:]),\
"Shape of background values incompatible to shape of Input"
# do labeling in parallel over channels and time slices
pool = RequestPool()
start = np.asarray(roi.start, dtype=np.int)
stop = np.asarray(roi.stop, dtype=np.int)
for ti, t in enumerate(range(roi.start[4], roi.stop[4])):
start[4], stop[4] = t, t+1
for ci, c in enumerate(range(roi.start[3], roi.stop[3])):
start[3], stop[3] = c, c+1
newRoi = SubRegion(self.Output,
start=tuple(start), stop=tuple(stop))
resView = result[..., ci, ti].withAxes(*'xyz')
req = Request(partial(self._label3d, newRoi,
bg[c, t], resView))
pool.add(req)
logger.debug(
"{}: Computing connected components for ROI {} ...".format(
self.name, roi))
pool.wait()
pool.clean()
logger.debug("{}: Connected components computed.".format(
self.name))
def execute(self, slot, subindex, roi, result):
if slot == self.Detector:
result = self.dumps()
return result
# sanity check
assert self.DetectionMethod.value in ['svm', 'classic'], \
"Unknown detection method '{}'".format(self.DetectionMethod.value)
# prefill result
resultZYXCT = vigra.taggedView(
result, self.InputVolume.meta.axistags).withAxes(*'zyxct')
# acquire data
data = self.InputVolume.get(roi).wait()
dataZYXCT = vigra.taggedView(
data, self.InputVolume.meta.axistags).withAxes(*'zyxct')
# walk over time and channel axes
for t in range(dataZYXCT.shape[4]):
for c in range(dataZYXCT.shape[3]):
resultZYXCT[..., c, t] = \
self._detectMissing(dataZYXCT[..., c, t])
return result
def testBasic(self):
features = numpy.indices((100, 100)).astype(numpy.float32) + 0.5
features = numpy.rollaxis(features, 0, 3)
features = vigra.taggedView(features, "xyc")
labels = numpy.zeros((100, 100, 1), dtype=numpy.uint8)
labels = vigra.taggedView(labels, "xyc")
labels[10, 10] = 1
labels[10, 11] = 1
labels[20, 20] = 2
labels[20, 21] = 2
graph = Graph()
opFeatureMatrixCache = OpFeatureMatrixCache(graph=graph)
opFeatureMatrixCache.FeatureImage.setValue(features)
opFeatureMatrixCache.LabelImage.setValue(labels)
opFeatureMatrixCache.LabelImage.setDirty(numpy.s_[10:11, 10:12])
opFeatureMatrixCache.LabelImage.setDirty(numpy.s_[20:21, 20:22])
opFeatureMatrixCache.LabelImage.setDirty(numpy.s_[30:31, 30:32])
opTrain = OpTrainClassifierFromFeatureVectors(graph=graph)
opTrain.ClassifierFactory.setValue(ParallelVigraRfLazyflowClassifierFactory(100))
opTrain.MaxLabel.setValue(2)
opTrain.LabelAndFeatureMatrix.connect(opFeatureMatrixCache.LabelAndFeatureMatrix)
assert opTrain.Classifier.ready()
trained_classifier = opTrain.Classifier.value
# This isn't much of a test at the moment...
assert isinstance(
trained_classifier, ParallelVigraRfLazyflowClassifier
), "classifier is of the wrong type: {}".format(type(trained_classifier))
def testBasic2(self):
a = numpy.zeros((2,2,2,))
a[1,1,1] = 1
a[0,0,0] = 1
a = a[..., None]
a = vigra.taggedView(a, "tyxc")
expected_b = a.mean(axis=0)
expected_b = vigra.taggedView(expected_b, "yxc")
graph = Graph()
op = OpMeanProjectionCached(graph=graph)
opPrep = OpArrayPiper(graph=graph)
opPrep.Input.setValue(a)
op.Input.connect(opPrep.Output)
op.Axis.setValue(0)
b = op.Output[...].wait()
b = vigra.taggedView(b, "yxc")
assert((b == expected_b).all())
def test2():
vol = np.zeros((2, 3, 4, 5, 6), dtype=np.uint8)
vol1 = vigra.taggedView(vol, axistags='txyzc')
vol2 = vigra.taggedView(vol, axistags='czyxt')
g = Graph()
pipe1 = OpArrayPiper(graph=g)
pipe1.Input.setValue(vol1)
pipe2 = OpArrayPiper(graph=g)
pipe2.Input.setValue(vol2)
op = OpThresholdTwoLevels(graph=g)
printer = Printer(graph=g)
printer.Input.connect(op.Output)
op.InputImage.connect(pipe1.Output)
#print(op.Output.meta.getTaggedShape())
#print(op.CachedOutput.meta.getTaggedShape())
print("")
#op.InputImage.connect(pipe2.Output)
op.InputImage.meta.axistags = vol2.axistags
op.InputImage._sig_changed()
def testBasic(self):
features = numpy.indices( (100,100) ).astype(numpy.float32) + 0.5
features = numpy.rollaxis(features, 0, 3)
features = vigra.taggedView(features, 'xyc')
labels = numpy.zeros( (100,100,1), dtype=numpy.uint8 )
labels = vigra.taggedView(labels, 'xyc')
labels[10,10] = 1
labels[10,11] = 1
labels[20,20] = 2
labels[20,21] = 2
graph = Graph()
opFeatureMatrixCache = OpFeatureMatrixCache(graph=graph)
opFeatureMatrixCache.FeatureImage.setValue(features)
opFeatureMatrixCache.LabelImage.setValue(labels)
opFeatureMatrixCache.NonZeroLabelBlocks.setValue(0)
labels_and_features = opFeatureMatrixCache.LabelAndFeatureMatrix.value
assert labels_and_features.shape == (0,3), "Empty feature matrix has wrong shape: {}".format( labels_and_features.shape )
opFeatureMatrixCache.LabelImage.setDirty( numpy.s_[10:11, 10:12] )
opFeatureMatrixCache.LabelImage.setDirty( numpy.s_[20:21, 20:22] )
opFeatureMatrixCache.LabelImage.setDirty( numpy.s_[30:31, 30:32] )
labels_and_features = opFeatureMatrixCache.LabelAndFeatureMatrix.value
assert labels_and_features.shape == (4,3)
assert (labels_and_features[:,0] == 1).sum() == 2
assert (labels_and_features[:,0] == 2).sum() == 2
# Can't check for equality because feature blocks can be in a random order.
# Just check that all features are present, regardless of order.
for feature_vec in [[10.5, 10.5], [10.5, 11.5], [20.5, 20.5], [20.5, 21.5]]:
assert feature_vec in labels_and_features[:,1:]
def testFunnyAxes(self):
vol = self.data.withAxes(*'ztxcy')
g = Graph()
oper = OpThresholdOneLevel(graph=g)
oper.MinSize.setValue(self.minSize)
oper.MaxSize.setValue(self.maxSize)
oper.Threshold.setValue(0.5)
oper.InputImage.setValue(vol)
output = oper.Output[:].wait()
assert numpy.all(output.shape == vol.shape)
clusters = self.generateData((self.nx, self.ny, self.nz, self.nc))
output = vigra.taggedView(output, axistags=oper.Output.meta.axistags)
output = output.withAxes(*'xyzc')
cluster1 = numpy.logical_and(output, clusters[0])
assert numpy.any(cluster1 != 0)
oper.MinSize.setValue(5)
output = oper.Output[:].wait()
cluster1 = numpy.logical_and(output, clusters[0])
assert numpy.all(cluster1 == 0)
cluster4 = numpy.logical_and(output.squeeze(), clusters[3])
assert numpy.all(cluster4 == 0)
cluster5 = numpy.logical_and(output.squeeze(), clusters[2])
assert numpy.all(cluster5 == 0)
oper.Threshold.setValue(0.2)
output = oper.Output[:].wait()
output = vigra.taggedView(output, axistags=oper.Output.meta.axistags)
output = output.withAxes(*'xyzc')
cluster5 = numpy.logical_and(output.squeeze(), clusters[2])
assert numpy.any(cluster5 != 0)
def testSingletonZ(self):
vol = np.zeros((82, 70, 1, 5, 5), dtype=np.uint8)
vol = vigra.taggedView(vol, axistags='xyzct')
blocks = np.zeros(vol.shape, dtype=np.uint8)
blocks[30:50, 40:60, :, 2:4, 3:5] = 1
blocks[30:50, 40:60, :, 2:4, 0:2] = 2
blocks[60:70, 30:40, :, :, :] = 3
vol[blocks == 1] = 255
vol[blocks == 2] = 255
vol[blocks == 3] = 255
op = OpLabelVolume(graph=Graph())
op.Method.setValue(self.method)
op.Input.setValue(vol)
out = op.Output[...].wait()
tags = op.Output.meta.getTaggedShape()
print(tags)
out = vigra.taggedView(out, axistags="".join([s for s in tags]))
for c in range(out.shape[3]):
for t in range(out.shape[4]):
print("t={}, c={}".format(t, c))
assertEquivalentLabeling(blocks[..., c, t], out[..., c, t])
def setUp(self):
g = Graph()
rawimg = np.random.randint(0, 255, (2, 10, 10, 10, 1))
binimg = rawimg>100
cc0 = vigra.analysis.labelVolumeWithBackground(binimg[0,:, :, :, 0].astype(np.uint8))
cc1 = vigra.analysis.labelVolumeWithBackground(binimg[1,:, :, :, 0].astype(np.uint8))
nobj = np.max(cc0)+1+np.max(cc1)+1
segmimg = np.zeros(rawimg.shape, cc0.dtype)
segmimg[0,:, : , :, 0] = cc0[:]
segmimg[1,:, :, :,0] = cc1[:]
rawimg = vigra.taggedView(rawimg, 'txyzc')
binimg = vigra.taggedView(rawimg, 'txyzc')
segmimg = vigra.taggedView(segmimg, 'txyzc')
self.features = {"Bad Plugin": {"bad_feature_1": {}, "bad_feature_2":{}}}
self.featureArrays = {0: {"Bad Plugin":{"bad_feature_1": np.array(range(nobj)), \
"bad_feature_2": np.array(range(nobj))}},
1: {"Bad Plugin":{"bad_feature_1": np.array(range(nobj)), \
"bad_feature_2": np.array(range(nobj))}}}
self.op = OpObjectClassification(graph = g)
self.op.RawImages.setValues([rawimg])
self.op.BinaryImages.setValues([binimg])
self.op.SegmentationImages.setValues([segmimg])
self.op.ObjectFeatures.setValues([self.featureArrays])
self.op.ComputedFeatureNames.setValue(self.features)
self.op.SelectedFeatures.setValue(self.features)
def testBasic2(self):
a = numpy.eye(3, dtype = numpy.float32)
a = a[None, ..., None]
a = vigra.taggedView(a, "tyxc")
expected_b = numpy.array([[ 0.59375, -0.375 , -0.34375],
[-0.375 , 0.625 , -0.375 ],
[-0.34375, -0.375 , 0.59375]], dtype=numpy.float32)
expected_b = expected_b[None, ..., None]
expected_b = vigra.taggedView(expected_b, "tyxc")
graph = Graph()
opPrep = OpArrayPiper(graph=graph)
opPrep.Input.setValue(a)
op = OpNansheWaveletTransform(graph=graph)
op.Input.connect(opPrep.Output)
op.Scale.setValue((0, 1, 1))
b = op.Output[...].wait()
b = vigra.taggedView(b, "tyxc")
assert((b == expected_b).all())
def testMinimalRequest():
"""
Make sure that unneeded slices are not requested by the stacker.
"""
graph = Graph()
ops = []
for op in range(10):
data = numpy.random.random( (100,100) )
data = vigra.taggedView( data, 'yx' )
meta = MetaDict( { 'shape' : data.shape,
'dtype' : data.dtype,
'axistags' : data.axistags } )
opData = OpTrackedOutputProvider( data, meta, graph=graph )
ops.append( opData )
opStacker = OpMultiArrayStacker(graph=graph)
opStacker.AxisFlag.setValue('z')
opStacker.AxisIndex.setValue(0)
opStacker.Images.resize( len(ops) )
for islot, opData in zip( opStacker.Images, ops ):
islot.connect( opData.Output )
assert opStacker.Output.meta.getTaggedShape()['z'] == len(ops)
stacked_data = opStacker.Output[3:5,:,:].wait()
assert stacked_data.shape == (2, 100, 100)
stacked_data = vigra.taggedView( stacked_data, 'zyx' )
expected_data = numpy.concatenate( (ops[3]._data[numpy.newaxis, :], ops[4]._data[numpy.newaxis, :]) )
expected_data = vigra.taggedView( expected_data, 'zyx' )
assert (stacked_data == expected_data).all(), "Stacker returned the wrong data"
for index, op in enumerate(ops):
assert len(op.requested_rois) == 0 or index in range(3,5), "Stacker requested more data than it needed."
def test1():
vol = np.zeros((1, 2, 3, 4, 5), dtype=np.uint8)
vol1 = vigra.taggedView(vol, axistags='txyzc')
vol2 = vigra.taggedView(vol, axistags='czyxt')
g = Graph()
pipe1 = OpArrayPiper(graph=g)
pipe1.Input.setValue(vol1)
pipe2 = OpArrayPiper(graph=g)
pipe2.Input.setValue(vol2)
slicer = OpMultiArraySlicer(graph=g)
slicer.AxisFlag.setValue('c')
op = OperatorWrapper(TestOp, graph=g)
op.Input.connect(slicer.Slices)
stacker = OpMultiArrayStacker(graph=g)
stacker.AxisFlag.setValue('c')
stacker.Images.connect(op.Output)
stacker.AxisIndex.setValue(0)
slicer.Input.connect(pipe1.Output)
print(stacker.Output.meta.getTaggedShape())
print()
stacker.AxisIndex.setValue(0)
slicer.Input.connect(pipe2.Output)
print(stacker.Output.meta.getTaggedShape())
def _execute_HYSTERESIS(self, roi, result):
self._execute_SIMPLE(roi, result)
final_labels = vigra.taggedView( result, self.Output.meta.axistags )
core_labels = self.CoreLabels(roi.start, roi.stop).wait()
core_labels = vigra.taggedView( core_labels, self.CoreLabels.meta.axistags )
select_labels(core_labels, final_labels) # Edits final_labels in-place
def testBasic2(self):
a = numpy.ones((100, 101, 102))
a = a[..., None]
a = vigra.taggedView(a, "tyxc")
graph = Graph()
opPrep = OpArrayPiper(graph=graph)
opPrep.Input.setValue(a)
op = OpNansheEstimateF0Cached(graph=graph)
op.Input.connect(opPrep.Output)
op.HalfWindowSize.setValue(20)
op.WhichQuantile.setValue(0.5)
op.TemporalSmoothingGaussianFilterStdev.setValue(5.0)
op.SpatialSmoothingGaussianFilterStdev.setValue(5.0)
b = op.Output[...].wait()
b = vigra.taggedView(b, "tyxc")
assert(a.shape == b.shape)
assert((b == 1).all())
def testReconnect(self):
"""
Can we connect an image, then replace it with a differently-ordered image?
"""
predRaw = np.zeros((20, 22, 21, 3), dtype=np.uint32)
pred1 = vigra.taggedView(predRaw, axistags='zyxc')
pred2 = vigra.taggedView(predRaw, axistags='tyxc')
oper5d = OpThresholdTwoLevels(graph=Graph())
oper5d.InputImage.setValue(pred1)
oper5d.MinSize.setValue(self.minSize)
oper5d.MaxSize.setValue(self.maxSize)
oper5d.HighThreshold.setValue(self.highThreshold)
oper5d.LowThreshold.setValue(self.lowThreshold)
oper5d.SmootherSigma.setValue(self.sigma)
oper5d.Channel.setValue(0)
oper5d.CoreChannel.setValue(0)
oper5d.CurOperator.setValue(1)
out5d = oper5d.CachedOutput[:].wait()
oper5d.InputImage.disconnect() # FIXME: Why is this line necessary? Ideally, it shouldn't be...
oper5d.InputImage.setValue(pred2)
out5d = oper5d.CachedOutput[:].wait()
def testSingletonZ(self):
vol = np.zeros((82, 70, 1, 5, 5), dtype=np.uint8)
vol = vigra.taggedView(vol, axistags="xyzct")
blocks = np.zeros(vol.shape, dtype=np.uint8)
blocks[30:50, 40:60, :, 2:4, 3:5] = 1
blocks[30:50, 40:60, :, 2:4, 0:2] = 2
blocks[60:70, 30:40, :, :, :] = 3
vol[blocks == 1] = 255
vol[blocks == 2] = 255
vol[blocks == 3] = 255
op = OpLabelVolume(graph=Graph())
op.Method.setValue(self.method)
op.Input.setValue(vol)
out = op.Output[...].wait()
tags = op.Output.meta.getTaggedShape()
out = vigra.taggedView(out, axistags="".join([s for s in tags]))
for c in range(out.shape[3]):
for t in range(out.shape[4]):
assertEquivalentLabeling(blocks[..., c, t], out[..., c, t])
def _execute_bbox(self, roi, result):
cc = self.LabelImage.get(roi).wait()
cc = vigra.taggedView(cc, axistags=self.LabelImage.meta.axistags)
cc = cc.withAxes(*'xyz')
logger.debug("computing bboxes...")
feats = vigra.analysis.extractRegionFeatures(
cc.astype(np.float32),
cc.astype(np.uint32),
features=["Count", "Coord<Minimum>", "Coord<Maximum>"])
feats_dict = {}
feats_dict["Coord<Minimum>"] = feats["Coord<Minimum>"]
feats_dict["Coord<Maximum>"] = feats["Coord<Maximum>"]
feats_dict["Count"] = feats["Count"]
return feats_dict
def execute(self, slot, subindex, roi, result):
if slot == self.Detector:
result = self.dumps()
return result
# sanity check
assert self.DetectionMethod.value in ["svm", "classic"], "Unknown detection method '{}'".format(
self.DetectionMethod.value
)
# prefill result
resultZYXCT = vigra.taggedView(result, self.InputVolume.meta.axistags).withAxes(*"zyxct")
# acquire data
data = self.InputVolume.get(roi).wait()
dataZYXCT = vigra.taggedView(data, self.InputVolume.meta.axistags).withAxes(*"zyxct")
# walk over time and channel axes
for t in range(dataZYXCT.shape[4]):
for c in range(dataZYXCT.shape[3]):
resultZYXCT[..., c, t] = self._detectMissing(dataZYXCT[..., c, t])
return result
def testOpSelectLabels(self):
op = OpSelectLabels(graph=Graph())
small = numpy.asarray(
[[0, 0, 0],
[0, 1, 0],
[0, 0, 0]]).astype(np.uint32)
big = numpy.asarray(
[[0, 1, 0],
[1, 1, 1],
[0, 1, 0]]).astype(np.uint32)
small = vigra.taggedView(small[:,:,None], 'yxc')
big = vigra.taggedView(big[:,:,None], 'yxc')
op.BigLabels.setValue(big)
op.SmallLabels.setValue(small)
out = op.Output[...].wait()
numpy.testing.assert_array_equal(out, big)
op.BigLabels.setValue(big)
op.SmallLabels.setValue(small*0)
out = op.Output[...].wait()
numpy.testing.assert_array_equal(out, big*0)
def testReconnectWithoutRequest(self):
vol = numpy.zeros((200, 100, 50), dtype=numpy.float32)
vol1 = vigra.taggedView(vol, axistags='xyz')
vol2 = vigra.taggedView(vol, axistags='zyx').withAxes(*'xyz')
graph = Graph()
opData1 = OpArrayPiper(graph=graph)
opData1.Input.setValue(vol1)
op = OpCompressedCache(graph=graph)
op.Input.connect(opData1.Output)
op.BlockShape.setValue((200, 100, 10))
out = op.Output[...].wait().view(numpy.ndarray)
assert (out == vol).all(), "Incorrect output!"
op.BlockShape.setValue((50, 100, 10))
# Older versions of OpCompressedCache threw an exception here because
# we tried to access the cache after changing the blockshape.
# But in the current version, we claim that's okay.
out = op.Output[...].wait()
assert (out == vol).all(), "Incorrect output!"
def _prepare_data_zyx(self):
file_base = self._tmp_dir + "/rand_3d"
X, Y = (100, 100)
Z = 10
rand_data_3d = numpy.random.random((Z, Y, X))
rand_data_3d *= 256
rand_data_3d = rand_data_3d.astype(numpy.uint8)
rand_data_3d = vigra.taggedView(rand_data_3d, 'zyx')
for z in range(Z):
file_name = file_base + "_z{}.tiff".format(z)
vigra.impex.writeImage(rand_data_3d[z, :, :], file_name)
return (rand_data_3d, file_base + "*.tiff")
def test_3d(self, tmp_path):
data = numpy.random.randint(0, 255,
(50, 100, 200, 3)).astype(numpy.uint8)
tiff_path = str(tmp_path / "test-3d.tiff")
for z_slice in data:
vigra.impex.writeImage(vigra.taggedView(z_slice, "yxc"),
tiff_path,
dtype="NATIVE",
mode="a")
op = OpTiffReader(graph=Graph())
op.Filepath.setValue(tiff_path)
assert op.Output.ready()
assert (op.Output[20:30, 50:100, 50:150].wait() == data[20:30, 50:100,
50:150]).all()
def testPatchDetection(self):
vol = vigra.taggedView(np.ones((5, 5), dtype=np.uint8) * 128,
axistags=vigra.defaultAxistags('xy'))
vol[2:5, 2:5] = 0
expected = np.zeros((5, 5))
expected[3:5, 3:5] = 1
self.op.PatchSize.setValue(2)
self.op.HaloSize.setValue(1)
self.op.DetectionMethod.setValue('classic')
self.op.InputVolume.setValue(vol)
out = self.op.Output[:].wait()
assert_array_equal(expected[3:5, 3:5], out[3:5, 3:5])
def setUp(self):
self.nz = 50
self.ny = 51
self.nx = 52
self.nc = 3
clusters = self.generateData((self.nz, self.ny, self.nx))
self.data = clusters[0] + clusters[1] + clusters[2] + clusters[3] + clusters[4]
self.data = self.data.reshape(self.data.shape + (1,))
self.data = vigra.taggedView(self.data, axistags="zyxc")
self.minSize = 5 # first cluster doesn't pass this
self.maxSize = 30 # fourth and fifth cluster don't pass this
self.highThreshold = 0.65 # third cluster doesn't pass
self.lowThreshold = 0.1
# Replicate the 4d data for multiple time slices
self.data5d = numpy.concatenate(3 * (self.data[numpy.newaxis, ...],), axis=0)
self.data5d = vigra.taggedView(self.data5d, axistags="tzyxc")
self.sigma = {"z": 0.3, "y": 0.3, "x": 0.3}
# pre-smooth 4d data
self.data = vigra.filters.gaussianSmoothing(self.data.astype(numpy.float32), 0.3)
def testBasic(self):
features = numpy.indices((100, 100)).astype(numpy.float32) + 0.5
features = numpy.rollaxis(features, 0, 3)
features = vigra.taggedView(features, 'xyc')
labels = numpy.zeros((100, 100, 1), dtype=numpy.uint8)
labels = vigra.taggedView(labels, 'xyc')
labels[10, 10] = 1
labels[10, 11] = 1
labels[20, 20] = 2
labels[20, 21] = 2
graph = Graph()
opFeatureMatrixCache = OpFeatureMatrixCache(graph=graph)
opFeatureMatrixCache.FeatureImage.setValue(features)
opFeatureMatrixCache.LabelImage.setValue(labels)
opFeatureMatrixCache.NonZeroLabelBlocks.setValue(0)
opFeatureMatrixCache.LabelImage.setDirty(numpy.s_[10:11, 10:12])
opFeatureMatrixCache.LabelImage.setDirty(numpy.s_[20:21, 20:22])
opFeatureMatrixCache.LabelImage.setDirty(numpy.s_[30:31, 30:32])
opTrain = OpTrainClassifierFromFeatureVectors(graph=graph)
opTrain.ClassifierFactory.setValue(
ParallelVigraRfLazyflowClassifierFactory(100))
opTrain.MaxLabel.setValue(2)
opTrain.LabelAndFeatureMatrix.connect(
opFeatureMatrixCache.LabelAndFeatureMatrix)
assert opTrain.Classifier.ready()
trained_classifer = opTrain.Classifier.value
# This isn't much of a test at the moment...
assert isinstance( trained_classifer, ParallelVigraRfLazyflowClassifier ), \
"classifier is of the wrong type: {}".format(type(trained_classifer))
def test(self):
"""
Test use-case from https://github.com/ilastik/lazyflow/issues/111
"""
data = numpy.zeros((20, 20))
data = vigra.taggedView(data, 'xy')
op = OpArrayCache(graph=Graph())
op.Input.setValue(data)
assert (op.Output[0:20, 0:20].wait() == 0).all()
# Should not crash...
op.Input[0:20, 0:20] = numpy.ones((20, 20))
assert (op.Output[0:20, 0:20].wait() == 1).all()
def _label(self, roi, result):
result = vigra.taggedView(result, axistags=self.Output.meta.axistags)
# get the background values
bg = self.Background[...].wait()
bg = vigra.taggedView(bg, axistags=self.Background.meta.axistags)
bg = bg.withAxes(*'ct')
assert np.all(self.Background.meta.shape[0] ==
self.Input.meta.shape[0]),\
"Shape of background values incompatible to shape of Input"
assert np.all(self.Background.meta.shape[4] ==
self.Input.meta.shape[4]),\
"Shape of background values incompatible to shape of Input"
# do labeling in parallel over channels and time slices
pool = RequestPool()
start = np.asarray(roi.start, dtype=np.int)
stop = np.asarray(roi.stop, dtype=np.int)
for ti, t in enumerate(range(roi.start[0], roi.stop[0])):
start[0], stop[0] = t, t + 1
for ci, c in enumerate(range(roi.start[4], roi.stop[4])):
start[4], stop[4] = c, c + 1
newRoi = SubRegion(self.Output,
start=tuple(start),
stop=tuple(stop))
resView = result[ti, ..., ci].withAxes(*'xyz')
req = Request(partial(self._label3d, newRoi, bg[c, t],
resView))
pool.add(req)
logger.debug(
"{}: Computing connected components for ROI {} ...".format(
self.name, roi))
pool.wait()
pool.clean()
logger.debug("{}: Connected components computed.".format(self.name))
def execute(self, slot, subindex, roi, result):
assert slot == self.Output, "Unknown slot requested: {}".format(slot)
for i in (0, 4):
assert roi.stop[i] - roi.start[i] == 1,\
"Invalid roi for graph-cut: {}".format(str(roi))
# request the prediction image
pred = self.Prediction.get(roi).wait()
pred = vigra.taggedView(pred, axistags=self.Prediction.meta.axistags)
pred = pred.withAxes(*'zyx')
# prepare result
resView = vigra.taggedView(result, axistags=self.Output.meta.axistags)
resView = resView.withAxes(*'zyx')
logger.info("Executing graph cut ... (this might take a while)")
threshold_binary = segmentGC(pred, self.Beta.value)
threshold_binary = vigra.taggedView(threshold_binary, 'zyx')
logger.info("Graph-cut done")
# label the segmentation so that this operator is consistent with
# the other thresholding operators
vigra.analysis.labelVolumeWithBackground(
threshold_binary.astype(np.uint8), out=resView)
def testMargin(self):
graph = Graph()
vol = np.zeros((100, 110, 10), dtype=np.float32)
# draw a big plus sign
vol[50:70, :, :] = 1.0
vol[:, 60:80, :] = 1.0
vol = vigra.taggedView(vol, axistags='zyx').withAxes(*'tzyxc')
labels = np.zeros((100, 110, 10), dtype=np.uint32)
labels[45:75, 55:85, 3:4] = 1
labels = vigra.taggedView(labels,
axistags='zyx').withAxes(*'tzyxc')
op = OpObjectsSegment(graph=graph)
piper = OpArrayPiper(graph=graph)
piper.Input.setValue(vol)
op.Prediction.connect(piper.Output)
op.LabelImage.setValue(labels)
# without margin
op.MarginZYX.setValue(np.asarray((0, 0, 0)))
out = op.Output[...].wait()
out = vigra.taggedView(out, axistags=op.Output.meta.axistags)
out = out.withAxes(*'zyx')
vol = vol.withAxes(*'zyx')
assert_array_equal(out[50:70, 60:80, 3] > 0,
vol[50:70, 60:80, 3] > .5)
assert np.all(out[:45, ...] == 0)
# with margin
op.MarginZYX.setValue(np.asarray((5, 5, 0)))
out = op.Output[...].wait()
out = vigra.taggedView(out, axistags=op.Output.meta.axistags)
out = out.withAxes(*'zyx')
assert_array_equal(out[45:75, 55:85, 3] > 0,
vol[45:75, 55:85, 3] > .5)
assert np.all(out[:40, ...] == 0)
def testCompressed(self):
graph = Graph()
opDataProvider = OpArrayPiperWithAccessCount(graph=graph)
opCache = OpUnblockedArrayCache(graph=graph)
opCache.CompressionEnabled.setValue(True)
data = np.random.random((100, 100, 100)).astype(np.float32)
opDataProvider.Input.setValue(vigra.taggedView(data, 'zyx'))
opCache.Input.connect(opDataProvider.Output)
roi = ((30, 30, 30), (50, 50, 50))
cache_data = opCache.Output(*roi).wait()
assert (cache_data == data[roiToSlice(*roi)]).all()
assert opDataProvider.accessCount == 1
# Request the same data a second time.
# Access count should not change.
cache_data = opCache.Output(*roi).wait()
assert (cache_data == data[roiToSlice(*roi)]).all()
assert opDataProvider.accessCount == 1
# Now invalidate a part of the data
# The cache will discard it, so the access count should increase.
opDataProvider.Input.setDirty((30, 30, 30), (31, 31, 31))
cache_data = opCache.Output(*roi).wait()
assert (cache_data == data[roiToSlice(*roi)]).all()
assert opDataProvider.accessCount == 2
# Repeat this next part just for safety
for _ in range(10):
# Make sure the cache is empty
opDataProvider.Input.setDirty((30, 30, 30), (31, 31, 31))
opDataProvider.accessCount = 0
# Create many requests for the same data.
# Upstream data should only be accessed ONCE.
pool = RequestPool()
for _ in range(10):
pool.add(opCache.Output(*roi))
pool.wait()
assert opDataProvider.accessCount == 1
# Also, make sure requests for INNER rois of stored blocks are also serviced from memory
opDataProvider.accessCount = 0
inner_roi = ((35, 35, 35), (45, 45, 45))
cache_data = opCache.Output(*inner_roi).wait()
assert (cache_data == data[roiToSlice(*inner_roi)]).all()
assert opDataProvider.accessCount == 0
def calc_std_features(data_filename, output_filename, n_images, sigmas):
#return type: none but produces file with name output_filename containing feature_array [x,y,t,c, type_feature, sigmas]
#data_filename: name of file with dataset 'data' in shape [t,x,y,c] to calculate features on
#output_filename: name of file with dataset 'data' in shape [x,y,n_images, cDim, 7, len(sigmas)]
#n_images: compute convolutions on first n_images of data_filename
#sigmas: sigmas for following features: sigmasGaussian, sigmasLoG, sigmasGGM, sigmasSTE, sigmasHoGE
#open data file
rawdataF = h5py.File(data_filename, 'r')
xDim = rawdataF['data'].shape[1]
yDim = rawdataF['data'].shape[2]
cDim = rawdataF['data'].shape[3]
outF = h5py.File(output_filename, 'w')
#number of features types: 7 because STE and HoGE consists of two eigenvalues
n_feat_types = 7
outF.create_dataset(
"data", (xDim, yDim, n_images, cDim, n_feat_types, len(sigmas)),
dtype=np.float32,
compression='gzip')
for t in np.arange(n_images):
data = np.zeros((xDim, yDim, cDim), dtype=np.float32)
data = rawdataF['data'][t, :, :, :]
print data.shape
#rawdata = rawdata.swapaxes(0,2).swapaxes(0,1)
rawdata = vg.taggedView(data.astype(np.float32), "xyc")
features = np.zeros((xDim, yDim, cDim, n_feat_types, len(sigmas)),
dtype=np.float32)
for c in np.arange(cDim):
for i, sigma in enumerate(sigmas):
features[:, :, c, 0, i] = vg.filters.gaussianSmoothing(
rawdata[:, :, c], sigma)
features[:, :, c, 1, i] = vg.filters.laplacianOfGaussian(
rawdata[:, :, c], sigma)
features[:, :, c, 2, i] = vg.filters.gaussianGradientMagnitude(
rawdata[:, :, c], sigma)
data1 = vg.filters.structureTensorEigenvalues(
rawdata[:, :, c], sigma, sigma)
features[:, :, c, 3, i] = data1[:, :, 0]
features[:, :, c, 4, i] = data1[:, :, 1]
data2 = vg.filters.hessianOfGaussianEigenvalues(
rawdata[:, :, c], sigma)
features[:, :, c, 5, i] = data2[:, :, 0]
features[:, :, c, 6, i] = data2[:, :, 1]
outF['data'][:, :, t, :, :, :] = features[:, :, :, :, :]
outF.close()
rawdataF.close()
return features
def testCacheApi(self):
graph = Graph()
opDataProvider = OpArrayPiperWithAccessCount(graph=graph)
opCache = OpUnblockedArrayCache(graph=graph)
data = np.random.random((100, 100, 100)).astype(np.float32)
opDataProvider.Input.setValue(vigra.taggedView(data, 'zyx'))
opCache.Input.connect(opDataProvider.Output)
opCache.Output[10:20, 20:40, 50:100].wait()
opCache.Output[11:21, 22:43, 53:90].wait()
l = opCache.getBlockAccessTimes()
assert len(l) == 2
for k, t in l:
assert t > 0.0
def test_attempt_drop_nonsingleton_axis(self):
"""
Attempt to configure the operator with invalid settings by trying to drop a non-singleton axis.
The execute method should assert in that case.
"""
data = numpy.zeros( (100,100,100), dtype=numpy.uint8 )
data = vigra.taggedView( data, vigra.defaultAxistags('xyz') )
op = OpReorderAxes( graph=Graph() )
op.Input.setValue( data )
# Attempt to drop some axes that can't be dropped.
op.AxisOrder.setValue( 'txc' )
# Make sure this results in an error.
self.assertRaises( AssertionError, op.Output[:].wait )
def testStrangeAxesWithout(self):
pred = np.zeros((20, 22, 21, 3), dtype=np.uint32)
pred = vigra.taggedView(pred, axistags='tyxc')
oper5d = OpThresholdTwoLevels(graph=Graph())
oper5d.InputImage.setValue(pred)
oper5d.MinSize.setValue(self.minSize)
oper5d.MaxSize.setValue(self.maxSize)
oper5d.HighThreshold.setValue(self.highThreshold)
oper5d.LowThreshold.setValue(self.lowThreshold)
oper5d.SmootherSigma.setValue(self.sigma)
oper5d.Channel.setValue(0)
oper5d.CurOperator.setValue(2)
oper5d.UsePreThreshold.setValue(False)
out5d = oper5d.CachedOutput[:].wait()
def allPairsOfShortestPath(graph, weights):
pathFinder = vigra.graphs.ShortestPathPathDijkstra(graph)
distances = numpy.zeros([graph.nodeNum] * 2)
for ni, node in enumerate(graph.nodeIter()):
pathFinder.run(weights**1, node)
d = pathFinder.distances()**1
distances[ni, :] = d[:]
ggf = graph.projectNodeFeaturesToGridGraph(d)
ggf = vigra.taggedView(ggf, 'xy')
if ni < 1:
vigra.imshow(ggf)
vigra.show()
print distances.min(), distances.max()
return distances
def test_2d(self):
graph = Graph()
data2d = numpy.random.random((2,100,100,1,3))
data2d = vigra.taggedView(data2d, axistags='txyzc')
# Define operators
opFeatures = OpFeatureSelection(graph=graph)
opFeatures.Scales.connect(self.opFeatures.Scales[0])
opFeatures.FeatureIds.connect(self.opFeatures.FeatureIds[0])
opFeatures.SelectionMatrix.connect(self.opFeatures.SelectionMatrix[0])
# Set input data
opFeatures.InputImage.setValue(data2d)
# Compute results for the top slice only
topSlice = [0, slice(None), slice(None), 0, slice(None)]
result = opFeatures.OutputImage[topSlice].wait()
def __init__(self,
*,
preloaded_array: numpy.ndarray,
axistags: AxisTags = None,
nickname: str = "",
**info_kwargs):
self.preloaded_array = vigra.taggedView(
preloaded_array, axistags
or get_default_axisordering(preloaded_array.shape))
super().__init__(
nickname=nickname
or "preloaded-{}-array".format(self.preloaded_array.dtype.name),
default_tags=self.preloaded_array.axistags,
laneShape=preloaded_array.shape,
laneDtype=preloaded_array.dtype,
**info_kwargs,
)
def test_attempt_drop_nonsingleton_axis(self):
"""
Attempt to configure the operator with invalid settings by trying to drop a non-singleton axis.
The execute method should assert in that case.
"""
data = numpy.zeros((100, 100, 100), dtype=numpy.uint8)
data = vigra.taggedView(data, vigra.defaultAxistags("xyz"))
# Attempt to drop some axes that can't be dropped.
op = OpReorderAxes(graph=Graph(), Input=data, AxisOrder="txc")
# Make sure this results in an error.
req = op.Output[:]
req.notify_failed(
lambda *args: None
) # We expect an exception here, so disable the default fail handler to hide the traceback
self.assertRaises(AssertionError, req.wait)
def processSingleObject(i):
logger.debug("processing object {}".format(i))
# maxs are inclusive, so we need to add 1
xmin = max(mins[i][0] - margin[0], 0)
ymin = max(mins[i][1] - margin[1], 0)
zmin = max(mins[i][2] - margin[2], 0)
xmax = min(maxs[i][0] + margin[0] + 1, cc.shape[0])
ymax = min(maxs[i][1] + margin[1] + 1, cc.shape[1])
zmax = min(maxs[i][2] + margin[2] + 1, cc.shape[2])
ccbox = cc[xmin:xmax, ymin:ymax, zmin:zmax]
resbox = resultXYZ[xmin:xmax, ymin:ymax, zmin:zmax]
nVoxels = ccbox.size
if nVoxels > MAXBOXSIZE:
#problem too large to run graph cut, assign to seed
logger.warn("Object {} too large for graph cut.".format(i))
resbox[ccbox == i] = 1
return
probbox = pred[xmin:xmax, ymin:ymax, zmin:zmax]
gcsegm = segmentGC(probbox, beta)
gcsegm = vigra.taggedView(gcsegm, axistags='xyz')
ccsegm = vigra.analysis.labelVolumeWithBackground(
gcsegm.astype(np.uint8))
# Extended bboxes of different objects might overlap.
# To avoid conflicting segmentations, we find all connected
# components in the results and only take the one, which
# overlaps with the object "core" or "seed", defined by the
# pre-thresholding
seed = ccbox == i
filtered = seed * ccsegm
passed = vigra.analysis.unique(filtered)
passed.sort()
assert len(passed.shape) == 1
if passed.size > 2:
logger.warn("ambiguous label assignment for region {}".format(
(xmin, xmax, ymin, ymax, zmin, zmax)))
resbox[ccbox == i] = 1
elif passed.size <= 1:
logger.warn("box {} segmented out with beta {}".format(
i, beta))
else:
# assign to the overlap region
label = passed[1] # 0 is background
resbox[ccsegm == label] = 1
def distance_transform(mask, background=False, smoothing=0.0, negate=False):
"""
Compute the distance transform of voxels inside (or outside) the given mask,
with smoothing and negation post-processing options as a convenience.
"""
mask = mask.astype(bool, copy=False)
mask = vigra.taggedView(mask, 'zyx').astype(np.uint32)
dt = vigra.filters.distanceTransform(mask, background=background)
del mask
if smoothing > 0.0:
vigra.filters.gaussianSmoothing(dt, smoothing, dt, window_size=2.0)
if negate:
dt[:] *= -1
return dt
def testSimpleUsage(self):
n = self.vol.shape[2]
op = OpMultiArrayStacker(graph=self.g)
op.AxisFlag.setValue('z')
provider = OperatorWrapper(OpArrayPiper, graph=self.g)
vol = self.vol
op.Images.connect(provider.Output)
provider.Input.resize(n)
for i in range(n):
provider.Input[i].setValue(vol[..., i])
out = op.Output[...].wait()
out = vigra.taggedView(out, axistags='xyz')
numpy.testing.assert_array_equal(out, vol)
def test_tzyxc(self):
expected_volume_tzyxc, globstring = self._prepare_data(
"rand_4dc", (5, 10, 50, 100, 3), "tzyxc", "t")
graph = Graph()
op = OpStackLoader(graph=graph)
op.globstring.setValue(globstring)
assert len(op.stack.meta.axistags) == 5
assert op.stack.meta.getAxisKeys() == list("tzyxc")
assert op.stack.meta.dtype == expected_volume_tzyxc.dtype
vol_from_stack_tzyxc = op.stack[:].wait()
vol_from_stack_tzyxc = vigra.taggedView(vol_from_stack_tzyxc, "tzyxc")
assert (vol_from_stack_tzyxc == expected_volume_tzyxc
).all(), "4D+c Volume from stack did not match expected data."
def execute(self, slot, subindex, roi, result):
rag = self.Rag.value
channel_feature_names = self.FeatureNames.value
edge_feature_dfs = []
for c in range(self.VoxelData.meta.shape[-1]):
channel_name = self.VoxelData.meta.channel_names[c]
if channel_name not in channel_feature_names:
continue
feature_names = [
decodeToStringIfBytes(f)
for f in channel_feature_names[channel_name]
]
if not feature_names:
# No features selected for this channel
continue
voxel_data = self.VoxelData[..., c:c + 1].wait()
voxel_data = vigra.taggedView(voxel_data,
self.VoxelData.meta.axistags)
voxel_data = voxel_data[..., 0] # drop channel
edge_features_df = rag.compute_features(voxel_data, feature_names)
#if np.isnan(edge_features_df.values).any():
# raise RuntimeError("Whoa, why are there NaN values in the feature matrix?")
edge_features_df = edge_features_df.iloc[:,
2:] # Discard columns [sp1, sp2]
# Prefix all column names with the channel name, to guarantee uniqueness
# (Generally a nice feature, but also required for serialization.)
edge_features_df.columns = [
channel_name + ' ' + feature_name
for feature_name in edge_features_df.columns.values
]
edge_feature_dfs.append(edge_features_df)
# Could use join() or merge() here, but we know the rows are already in the right order, and concat() should be faster.
all_edge_features_df = pd.DataFrame(rag.edge_ids,
columns=['sp1', 'sp2'])
all_edge_features_df = pd.concat([all_edge_features_df] +
edge_feature_dfs,
axis=1,
copy=False)
result[0] = all_edge_features_df