class TestOutputOutputConnection(object):
def setUp(self):
self.g = Graph()
self.op = OpOuter(graph=self.g)
def tearDown(self):
self.g.stopGraph()
def test_value(self):
"""
This test checks, that requests produce correct
results in the case of output-output connections
(the o-o connection exists inside the OpOuter...
"""
self.op.Input.setValue(True)
result = self.op.Output[:].wait()[0]
assert result == True, "result = %r" % result
self.op.Input.setValue(False)
result = self.op.Output[:].wait()[0]
assert result == False, "result = %r" % result
def test_execute(self):
"""
This test checks that the execute method of the outer
operator is not called, when the output slot of the
op is connect to the output slot of another (inner) operator
"""
self.op.Input.setValue(True)
self.op._was_executed = False
result = self.op.Output[:].wait()[0]
assert self.op._was_executed is False
class TestSlot_notifyMetaChanged(object):
def setUp(self):
self.g = Graph()
def tearDown(self):
self.g.stopGraph()
def test_inputslot_changed(self):
# test that the changed callback is called
# when the slot meta information changes
ops = OpS(graph=self.g)
opa = OpA(graph=self.g)
upval = [False]
def callBack(slot):
upval[0] = True
# test normal InputSlot
opa.Input1.notifyMetaChanged(callBack)
opa.Input1.connect(ops.Output1)
assert upval[0] == True
upval[0] = False
opa.Input1.connect(ops.Output2)
assert upval[0] == True
# test InputSlot with default value
upval[0] = False
opa.Input3.notifyMetaChanged(callBack)
opa.Input3.connect(ops.Output1)
assert upval[0] == True
upval[0] = False
def __init__(self, argv):
QMainWindow.__init__(self)
#Normalize the data if true
self._normalize_data=True
if 'notnormalize' in sys.argv:
print sys.argv
self._normalize_data=False
sys.argv.remove('notnormalize')
self.opPredict = None
self.opTrain = None
self.opThreshold = None
self._colorTable16 = self._createDefault16ColorColorTable()
#self.g = Graph(7, 2048*1024**2*5)
self.g = Graph()
self.fixableOperators = []
self.featureDlg=None
#The old ilastik provided the following scale names:
#['Tiny', 'Small', 'Medium', 'Large', 'Huge', 'Megahuge', 'Gigahuge']
#The corresponding scales are:
self.featScalesList=[0.3, 0.7, 1, 1.6, 3.5, 5.0, 10.0]
self.initUic()
#if the filename was specified on command line, load it
if len(sys.argv) >= 2:
def loadFile():
self._openFile(sys.argv[1:])
QTimer.singleShot(0, loadFile)
class TestMultiInputInputConnection(object):
def setUp(self):
self.g = Graph()
self.op = OpC(graph=self.g)
def tearDown(self):
self.g.stopGraph()
def test_wrapping(self):
opm = operators.Op5ToMulti(graph=self.g)
opm.Input0.setValue(1)
self.op.Input.connect(opm.Outputs)
assert len(self.op.internalOp.Output) == 1
assert self.op.internalOp.Output[0].meta.shape is not None
assert self.op.internalOp.Output[0].value == 1
class TestInputInputConnection(object):
def setUp(self):
self.g = Graph()
self.op = OpA(graph=self.g)
def tearDown(self):
self.g.stopGraph()
def test_value(self):
self.op.Input.setValue(True)
result = self.op.Output[:].allocate().wait()[0]
assert result == True, "result = %r" % result
self.op.Input.setValue(False)
result = self.op.Output[:].allocate().wait()[0]
assert result == False, "result = %r" % result
def test_disconnect(self):
self.op.internalOp.Input.disconnect()
self.op.internalOp.Input.connect(self.op.Input)
def test_wrapping(self):
opm = operators.Op5ToMulti(graph=self.g)
opm.Input0.setValue(1)
op = OperatorWrapper( OpA, graph=self.g )
op.Input.connect(opm.Outputs)
result = op.Output[0][:].allocate().wait()[0]
assert result == 1
opm.Input1.setValue(2)
result = op.Output[1][:].allocate().wait()[0]
assert result == 2
# Note: operator wrappers do not "restore" back to unwrapped operators after disconnect
# (That was their behavior at some point, but no longer.)
op.Input.disconnect()
op.Input.resize(0)
op.Input.setValue(2)
assert len(op.Input) == 0
assert len(op.Output) == 0
def testReportGeneration(self):
graph = Graph()
sampleData = numpy.random.randint(0, 256, size=(50, 50, 50))
sampleData = sampleData.astype(numpy.uint8)
sampleData = vigra.taggedView(sampleData, axistags="xyz")
opData = OpArrayPiper(graph=graph)
opData.Input.setValue(sampleData)
op = OpCompressedCache(parent=None, graph=graph)
op.BlockShape.setValue((25, 25, 25))
op.Input.connect(opData.Output)
before = time.time()
assert op.Output.ready()
assert op.usedMemory() == 0.0, "cache must not be filled at this point"
op.Output[...].wait()
assert op.usedMemory() > 0.0, "cache must contain data at this point"
after = time.time()
r = MemInfoNode()
op.generateReport(r)
# not sure how good this can be compressed, but the cache
# should hold memory by now
assert r.usedMemory > 0
# check sanity of last access time
assert r.lastAccessTime >= before, str(r.lastAccessTime)
assert r.lastAccessTime <= after, str(r.lastAccessTime)
assert r.fractionOfUsedMemoryDirty == 0.0
opData.Input.setDirty((slice(0, 25), slice(0, 25), slice(0, 25)))
assert op.fractionOfUsedMemoryDirty() < 1.0
assert op.fractionOfUsedMemoryDirty() > 0
opData.Input.setDirty(slice(None))
assert op.fractionOfUsedMemoryDirty() == 1.0
def test_3d_with_compression(self, tmp_path):
"""
This tests that we can read a compressed (LZW) TIFF file.
Note: It would be nice to test JPEG compression here, but strangely when vigra
writes a JPEG-compressed TIFF, it is somehow messed up. The image has two image
'series' in it, so the thing seems to have twice as many planes as it should.
Furthermore, vigra doesn't seem to read it back correctly, or maybe I'm missing something...
"""
data = numpy.random.randint(0, 255, (50, 100, 200, 3), dtype="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",
compression="LZW",
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 __init__(
self,
*,
filePath: str,
project_file: h5py.File = None,
sequence_axis: str = None,
nickname: str = "",
drange: Tuple[Number, Number] = None,
**info_kwargs,
):
"""
sequence_axis: Axis along which to stack (only applicable for stacks).
"""
self.sequence_axis = sequence_axis
self.base_dir = str(Path(project_file.filename).absolute().parent) if project_file else os.getcwd()
assert os.path.isabs(self.base_dir) # FIXME: if file_project was opened as a relative path, this would break
self.expanded_paths = self.expand_path(filePath, cwd=self.base_dir)
assert len(self.expanded_paths) == 1 or self.sequence_axis
if len({PathComponents(ep).extension for ep in self.expanded_paths}) > 1:
raise Exception(f"Multiple extensions unsupported as a single data source: {self.expanded_paths}")
self.filePath = os.path.pathsep.join(self.expanded_paths)
op_reader = OpInputDataReader(
graph=Graph(), WorkingDirectory=self.base_dir, FilePath=self.filePath, SequenceAxis=self.sequence_axis
)
meta = op_reader.Output.meta.copy()
op_reader.cleanUp()
super().__init__(
default_tags=meta.axistags,
nickname=nickname or self.create_nickname(self.expanded_paths),
laneShape=meta.shape,
laneDtype=meta.dtype,
drange=drange or meta.get("drange"),
**info_kwargs,
)
def test_hysteresis(self):
data = self.data
core_binary = (data == 5)
core_labels = np.empty_like(data, dtype=np.uint32)
core_labels[0, ..., 0] = vigra.analysis.labelMultiArrayWithBackground(
core_binary[0, ..., 0].astype(np.uint8))
op = OpLabeledThreshold(graph=Graph())
op.Method.setValue(ThresholdMethod.HYSTERESIS)
op.FinalThreshold.setValue(0.5)
op.Input.setValue(data.copy())
op.CoreLabels.setValue(core_labels)
result = op.Output[:].wait()
label_values = np.unique(result)[1:]
assert len(label_values) == 1
expected_result = np.where(data, label_values[0], 0)
expected_result[0, :, 5:, 0, 0] = 0 # Right half won't survive
#print expected_result[0,:,:,0,0]
#print result[0,:,:,0,0]
assert (result == expected_result).all()
def create_input(cls, filepath, input_axes, outmin=None, outmax=None, dtype=None):
""" Creates a file from the data at 'filepath' that has 'input_axes' """
basename = os.path.basename(filepath)
reader = OpInputDataReader(graph=Graph())
assert os.path.exists(filepath), '{} not found'.format(filepath)
reader.FilePath.setValue(os.path.abspath(filepath))
writer = OpFormattedDataExport(parent=reader)
if outmin is not None:
writer.ExportMin.setValue(outmin)
if outmax is not None:
writer.ExportMax.setValue(outmax)
if dtype is not None:
writer.ExportDtype.setValue(dtype)
writer.OutputAxisOrder.setValue(input_axes)
writer.Input.connect(reader.Output)
writer.OutputFilenameFormat.setValue(os.path.join(
cls.dir, basename.split('.')[0] + '_' + input_axes))
writer.TransactionSlot.setValue(True)
input_path = writer.ExportPath.value
writer.run_export()
return input_path
def __init__(self, headless, workflow_cmdline_args, *args, **kwargs):
# Create a graph to be shared by all operators
graph = Graph()
super(StopWatchWorkflow, self).__init__(headless,
graph=graph,
*args,
**kwargs)
#self.name = OperatorWrapper(OpName( graph=graph)
#self.name.Output[0].setValue("void")
self._applets = []
# Create applets
self.dataSelectionApplet = DataSelectionApplet(
self,
"Input Data",
"Input Data",
supportIlastik05Import=True,
batchDataGui=False)
self.stopWatchApplet = StopWatchApplet(self, "Stop Watch",
"Stop Watch")
self._applets.append(self.dataSelectionApplet)
self._applets.append(self.stopWatchApplet)
def test_graphcut(self):
if _has_graphcut:
data = self.data
# Core labels don't matter in this graphcut test
#core_binary = (data == 5)
core_labels = np.empty_like(data, dtype=np.uint32)
#core_labels[0,...,0] = vigra.analysis.labelMultiArrayWithBackground(core_binary[0,...,0].astype(np.uint8))
op = OpLabeledThreshold(graph=Graph())
op.Method.setValue(ThresholdMethod.GRAPHCUT)
op.FinalThreshold.setValue(0.5)
op.Input.setValue(data.copy())
op.CoreLabels.setValue(core_labels)
op.GraphcutBeta.setValue(0.5) # High enough to fill the hole in the third segment
result = op.Output[:].wait()
result_yx = result[0,:,:,0,0]
#print result_yx
label_values = np.unique(result)[1:]
assert len(label_values) == 3
assert len(np.unique(result_yx[1:12, 1:5])) == 1 # Same as 'simple'
assert len(np.unique(result_yx[7:10, 6:9])) == 1 # Almost same as simple, but with the hole filled in.
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 testSetInSlot(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)
# Write two blocks
opCache.Input[10:20, 10:20, 10:20] = 2 * np.ones((10, 10, 10), dtype=np.float32)
opCache.Input[20:30, 20:30, 20:30] = 3 * np.ones((10, 10, 10), dtype=np.float32)
# They should be valid now
assert opCache.CleanBlocks.value == [tuple(make_key[10:20, 10:20, 10:20]), tuple(make_key[20:30, 20:30, 20:30])]
assert (opCache.Output[10:20, 10:20, 10:20].wait() == 2).all()
assert (opCache.Output[20:30, 20:30, 20:30].wait() == 3).all()
# Mark a big dirty area
opDataProvider.Input.setDirty((10, 10, 10), (40, 40, 40))
# No blocks left in the cache
assert opCache.CleanBlocks.value == []
def testDirtyPropagation(self):
g = Graph()
vol = np.asarray(
[[0, 0, 0, 0], [0, 0, 1, 1], [0, 1, 0, 1], [0, 1, 0, 1]],
dtype=np.uint8)
vol = vigra.taggedView(vol, axistags='xy').withAxes(*'xyz')
chunkShape = (2, 2, 1)
opCache = OpCompressedCache(graph=g)
opCache.Input.setValue(vol)
opCache.BlockShape.setValue(chunkShape)
op = OpLazyCC(graph=g)
op.Input.connect(opCache.Output)
op.ChunkShape.setValue(chunkShape)
out1 = op.Output[:2, :2].wait()
assert np.all(out1 == 0)
opCache.Input[0:1, 0:1, 0:1] = np.asarray([[[1]]], dtype=np.uint8)
out2 = op.Output[:1, :1].wait()
assert np.all(out2 > 0)
def testEvenFunnierAxes(self):
vol = numpy.random.randint(0, 255, size=(5, 17, 31, 42, 11))
vol = vol.astype(numpy.uint8)
# don't care about corner cases
vol[vol == 128] = 129
vol[vol == 127] = 126
desiredResult = numpy.where(vol > 128, 1, 0)
vol = vigra.taggedView(vol, axistags='xtycz')
oper5d = OpThresholdTwoLevels(graph=Graph())
oper5d.InputImage.setValue(vol)
oper5d.MinSize.setValue(1)
oper5d.MaxSize.setValue(vol.size)
oper5d.LowThreshold.setValue(128)
oper5d.SmootherSigma.setValue({'z': 0.0, 'y': 0.0, 'x': 0.0})
oper5d.CurOperator.setValue(self.curOperator)
#for i in range(vol.shape[3]):
for i in range(2, 5): # just test some sample slices (runtime :)
oper5d.Channel.setValue(i)
oper5d.CoreChannel.setValue(i)
out5d = oper5d.Output[:].wait()
out5d[out5d > 0] = 1
numpy.testing.assert_array_equal(out5d.squeeze(), desiredResult[..., i, :])
def test_xyz_stack_c(self):
# expected_volume_zyxc, globstring = self._prepare_data_zyx_stack_c()
expected_volume, globstring = self._prepare_data(
'rand_3d_stack_c',
(2, 3, 5, 4),
'czxy',
'c'
)
graph = Graph()
op = OpStackLoader(graph=graph)
op.SequenceAxis.setValue('c')
op.globstring.setValue(globstring)
assert len(op.stack.meta.axistags) == 4
assert op.stack.meta.getAxisKeys() == list('czyx')
assert op.stack.meta.dtype == expected_volume.dtype
volume_from_stack = op.stack[:].wait()
volume_from_stack = vigra.taggedView(volume_from_stack, 'czyx')
volume_from_stack = volume_from_stack.withAxes(*'czxy')
assert (volume_from_stack == expected_volume).all(), \
"3D Volume stacked along c did not match expected data."
def testReconnectWithoutRequest_masked(self):
vol = numpy.ma.zeros((200, 100, 50), dtype=numpy.float32)
vol.set_fill_value(numpy.float32(numpy.nan))
vol[0] = numpy.ma.masked
vol1 = vol
vol2 = vol1.T
graph = Graph()
opData1 = OpArrayPiper(graph=graph)
opData1.Input.meta.has_mask = True
opData1.Input.meta.axistags = vigra.defaultAxistags('xyz')
opData1.Input.setValue(vol1)
op = OpCompressedCache(graph=graph)
op.Input.connect(opData1.Output)
op.BlockShape.setValue((200, 100, 10))
out = op.Output[...].wait()
assert (out == vol).all() and \
(out.mask == vol.mask).all() and \
((out.fill_value == vol.fill_value) |
(numpy.isnan(out.fill_value) & numpy.isnan(vol.fill_value))).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() and \
(out.mask == vol.mask).all() and \
((out.fill_value == vol.fill_value) |
(numpy.isnan(out.fill_value) & numpy.isnan(vol.fill_value))).all(),\
"Incorrect output!"
def setUp(self):
segimg = segImage()
binimg = (segimg>0).astype(np.uint8)
labels = {0 : np.array([0, 1, 2]),
1 : np.array([0, 1, 1, 2])}
rawimg = np.indices(segimg.shape).sum(0).astype(np.float32)
rawimg = rawimg.view(vigra.VigraArray)
rawimg.axistags = vigra.defaultAxistags('txyzc')
g = Graph()
features = {"Standard Object Features": {"Count":{}, "RegionCenter":{}, "Coord<Principal<Kurtosis>>":{}, \
"Coord<Minimum>":{}, "Coord<Maximum>":{}, "Mean":{}, \
"Mean in neighborhood":{"margin":(30, 30, 1)}}}
sel_features = {"Standard Object Features": {"Count":{}, "Mean":{}, "Mean in neighborhood":{"margin":(30, 30, 1)}, "Variance":{}}}
self.extrOp = OpObjectExtraction(graph=g)
self.extrOp.BinaryImage.setValue(binimg)
self.extrOp.RawImage.setValue(rawimg)
self.extrOp.Features.setValue(features)
assert self.extrOp.RegionFeatures.ready()
self.trainop = OpObjectTrain(graph=g)
self.trainop.Features.resize(1)
self.trainop.Features.connect(self.extrOp.RegionFeatures)
self.trainop.SelectedFeatures.setValue(sel_features)
self.trainop.LabelsCount.setValue(2)
self.trainop.Labels.resize(1)
self.trainop.Labels.setValues([labels])
self.trainop.FixClassifier.setValue(False)
self.trainop.ForestCount.setValue(1)
assert self.trainop.Classifier.ready()
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 testBasic(self):
graph = Graph()
op = OpTiledVolumeReader(graph=graph)
op.DescriptionFilePath.setValue(
self.data_setup.VOLUME_DESCRIPTION_FILE)
op.tiled_volume.TEST_MODE = True
roi = numpy.array([(10, 150, 100), (30, 550, 550)])
result_out = op.Output(*roi).wait()
# We expect a channel dimension to be added automatically...
assert (result_out.shape == roi[1] - roi[0]).all()
ref_path_comp = PathComponents(self.data_setup.REFERENCE_VOL_PATH)
with h5py.File(ref_path_comp.externalPath, "r") as f:
ref_data = f[ref_path_comp.internalPath][:]
expected = ref_data[roiToSlice(*roi)]
# numpy.save('/tmp/expected.npy', expected)
# numpy.save('/tmp/result_out.npy', result_out)
# We can't expect the pixels to match exactly because compression was used to create the tiles...
assert (expected == result_out).all()
def testNoOp(self):
oper5d = OpThresholdTwoLevels(graph=Graph())
oper5d.InputImage.setValue(self.data5d)
oper5d.MinSize.setValue(1)
oper5d.MaxSize.setValue(self.data5d.size)
oper5d.LowThreshold.setValue(-0.01)
oper5d.SmootherSigma.setValue({'z': 0.0, 'y': 0.0, 'x': 0.0})
oper5d.Channel.setValue(0)
oper5d.CoreChannel.setValue(0)
oper5d.CurOperator.setValue(self.curOperator)
out5d = oper5d.Output[:].wait()
numpy.testing.assert_array_equal(out5d.shape, self.data5d.shape)
# the image should be white, because of negative threshold
assert numpy.all(out5d > 0),\
"{}% elements <= 0".format((out5d <= 0).sum()/float(out5d.size)*100)
oper5d.LowThreshold.setValue(1.01)
out5d = oper5d.Output[:].wait()
# the image should be black, because of threshold larger than 1
assert numpy.all(out5d == 0),\
"{}% elements > 0".format((out5d > 0).sum()/float(out5d.size)*100)
def testBasic(self):
tmpdir = tempfile.mkdtemp()
try:
filepath = tmpdir + "/random_data.klb"
shape = (1, 1, 30, 40, 50)
data_tczyx = np.indices(shape).sum(0).astype(np.uint8)
pyklb.writefull(data_tczyx,
filepath,
blocksize_xyzct=np.array([10, 10, 10, 1, 1],
dtype=np.uint32))
readback = pyklb.readroi(filepath, (0, 0, 0, 0, 0),
np.array(shape) - 1)
op = OpKlbReader(graph=Graph())
op.FilePath.setValue(filepath)
assert op.Output.meta.shape == shape
assert op.Output.meta.dtype == np.uint8
read_data = op.Output[:].wait()
assert (read_data == data_tczyx).all()
finally:
shutil.rmtree(tmpdir)
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 test_lzw_compressed_file(self):
"""
This test is loosely related to
https://github.com/ilastik/ilastik/issues/1415
Tests whether lzw compressed tiff files can be read.
"""
import os
basepath = os.path.split(__file__)[0]
compressed_tiff_file = '{}/data/inputdata/compressed_lzw.tiff'.format(
basepath)
# generate checker-board, as in the file
data = numpy.zeros((10, 20, 3)).astype(numpy.uint8)
for i in range(data.shape[0]):
if i % 2 == 0:
data[i, 1::2, :] = 255
else:
data[i, 0::2, :] = 255
op = OpTiffReader(graph=Graph())
op.Filepath.setValue(compressed_tiff_file)
assert op.Output.ready()
assert op.Output.meta.shape == data.shape
assert_array_equal(data, op.Output[:].wait())
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 testCleanup(self):
try:
CacheMemoryManager().disable()
sampleData = numpy.indices((100, 200, 150),
dtype=numpy.float32).sum(0)
sampleData = vigra.taggedView(sampleData, axistags="xyz")
graph = Graph()
opData = OpArrayPiper(graph=graph)
opData.Input.setValue(sampleData)
op = OpCompressedCache(graph=graph)
# logger.debug("Setting block shape...")
op.BlockShape.setValue([100, 75, 50])
op.Input.connect(opData.Output)
x = op.Output[...].wait()
op.Input.disconnect()
r = weakref.ref(op)
del op
gc.collect()
assert r(
) is None, "OpBlockedArrayCache was not cleaned up correctly"
finally:
CacheMemoryManager().enable()
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 setUp(self):
self.g = Graph()
self.op = OpOuter(graph=self.g)
non_singleton_dims = filter(lambda (k, v): k != 'c' and v > 1,
tagged_shape.items())
assert len(non_singleton_dims) <= 2, \
"Image to export must have no more than 2 non-singleton dimensions.\n"\
"You are attempting to export a {}D result into a 2D file format."\
.format( len(non_singleton_dims) )
data = self._opExportToArray.run_export_to_array()
data = vigra.taggedView(data, self.Input.meta.axistags)
data = data.squeeze()
if len(data.shape) == 1 or len(
data.shape) == 2 and data.axistags.channelIndex < 2:
data = data[numpy.newaxis, :]
assert len(data.shape) == 2 or (len(data.shape) == 3 and data.axistags.channelIndex < 3), \
"Image has shape {}, channelIndex is {}".format(data.shape, data.axistags.channelIndex)
vigra.impex.writeImage(data, self.Filepath.value)
if __name__ == "__main__":
a = numpy.random.random((1, 100, 1, 100, 1)) * 255
a = a.astype(numpy.uint8)
a = vigra.taggedView(a, vigra.defaultAxistags('txyzc'))
from lazyflow.graph import Graph
op = OpExport2DImage(graph=Graph())
op.Input.setValue(a)
op.Filepath.setValue('/tmp/test.png')
op.run_export()
class TestSlot_notifyDisconnect(object):
def setUp(self):
self.g = Graph()
def tearDown(self):
self.g.stopGraph()
def test_disconnect(self):
# test that the notifyConnect callback is called
# when the slot is connected
ops = OpS(graph=self.g)
opa = OpA(graph=self.g)
upval = [False]
def callBack(slot):
upval[0] = True
# check the disconnect callback is called upon disconnect
opa.Input1.connect(ops.Output1)
opa.Input1.notifyDisconnect(callBack)
opa.Input1.disconnect()
assert upval[0] == True
# check the disconnect callback is called upon reconnect
opa.Input1.connect(ops.Output1)
upval[0] = False
opa.Input1.connect(ops.Output2)
assert upval[0] == True
# check the disconnect callback is called upon setValue when being already connected
opa.Input1.connect(ops.Output1)
upval[0] = False
opa.Input1.disconnect()
opa.Input1.setValue(19)
assert upval[0] == True
def test_no_disconnect(self):
ops = OpS(graph=self.g)
opa = OpA(graph=self.g)
upval = [False]
def callBack(slot):
upval[0] = True
opa.Input1.notifyDisconnect(callBack)
# check the disconnect callback is not called when reconnecting to the same slot
opa.Input1.connect(ops.Output1)
upval[0] = False
opa.Input1.connect(ops.Output1)
assert upval[0] == False
# check the disconnect callback is not called when setting the same value again
opa.Input1.disconnect()
opa.Input1.setValue(10)
upval[0] = False
opa.Input1.setValue(10)
assert upval[0] == False
def test_unregister_disconnect(self):
# check that unregistering a disconnect callback works
ops = OpS(graph=self.g)
opa = OpA(graph=self.g)
upval = [False]
def callBack(slot):
upval[0] = True
opa.Input1.connect(ops.Output1)
opa.Input1.notifyDisconnect(callBack)
opa.Input1.unregisterDisconnect(callBack)
opa.Input1.disconnect()
assert upval[0] == False
shape = tuple(self._slot.meta.shape)
axes = "".join(self._slot.meta.getAxisKeys())
dtype = self._slot.meta.dtype.__name__
else:
shape = axes = dtype = ""
if not sip.isdeleted(self.shapeEdit):
self.shapeEdit.setText(str(shape))
self.axisOrderEdit.setText(axes)
self.dtypeEdit.setText(dtype)
if __name__ == "__main__":
import numpy
import vigra
from PyQt4.QtGui import QApplication
from lazyflow.graph import Graph
from lazyflow.operators import OpArrayCache
data = numpy.zeros((10, 20, 30, 3), dtype=numpy.float32)
data = vigra.taggedView(data, 'zyxc')
op = OpArrayCache(graph=Graph())
op.Input.setValue(data)
app = QApplication([])
w = SlotMetaInfoDisplayWidget(None)
w.initSlot(op.Output)
w.show()
app.exec_()
# when the dot happen to be in the centre of the movable squere in the
# image then we show a one on the top left corner
# ===========================================================================
from ilastik.widgets.boxListView import BoxListView
from PyQt5.QtWidgets import QWidget
app = QApplication([])
boxListModel = BoxListModel()
h, w = (500, 500)
LV = BoxListView()
LV.setModel(boxListModel)
LV._table.setShowGrid(True)
g = Graph()
cron = QTimer()
cron.start(500 * 100)
op = OpArrayPiper2(graph=g) # Generate random noise
shape = (1, w, h, 1, 1)
# array = np.random.randint(0,255,500*500).reshape(shape).astype(np.uint8)
import scipy
array = scipy.misc.lena().astype(np.uint8)
array = vigra.sampling.resize(array.astype(np.float32), (h, w)).reshape(shape).astype(np.uint8)
op.Input.setValue(array)
def do():
def __init__( self, shell, headless, workflow_cmdline_args, project_creation_args, *args, **kwargs ):
graph = kwargs['graph'] if 'graph' in kwargs else Graph()
if 'graph' in kwargs: del kwargs['graph']
super(StructuredTrackingWorkflowBase, self).__init__(shell, headless, workflow_cmdline_args, project_creation_args, graph=graph, *args, **kwargs)
data_instructions = 'Use the "Raw Data" tab to load your intensity image(s).\n\n'
if self.fromBinary:
data_instructions += 'Use the "Binary Image" tab to load your segmentation image(s).'
else:
data_instructions += 'Use the "Prediction Maps" tab to load your pixel-wise probability image(s).'
# Create applets
self.dataSelectionApplet = DataSelectionApplet(self,
"Input Data",
"Input Data",
batchDataGui=False,
forceAxisOrder=['txyzc'],
instructionText=data_instructions,
max_lanes=1)
opDataSelection = self.dataSelectionApplet.topLevelOperator
if self.fromBinary:
opDataSelection.DatasetRoles.setValue( ['Raw Data', 'Binary Image'] )
else:
opDataSelection.DatasetRoles.setValue( ['Raw Data', 'Prediction Maps'] )
if not self.fromBinary:
self.thresholdTwoLevelsApplet = ThresholdTwoLevelsApplet( self,"Threshold and Size Filter","ThresholdTwoLevels" )
self.divisionDetectionApplet = ObjectClassificationApplet(workflow=self,
name="Division Detection (optional)",
projectFileGroupName="DivisionDetection",
selectedFeatures=configConservation.selectedFeaturesDiv)
self.cellClassificationApplet = ObjectClassificationApplet(workflow=self,
name="Object Count Classification",
projectFileGroupName="CountClassification",
selectedFeatures=configConservation.selectedFeaturesObjectCount)
self.trackingFeatureExtractionApplet = TrackingFeatureExtractionApplet(name="Object Feature Computation",workflow=self, interactive=False)
self.objectExtractionApplet = ObjectExtractionApplet(name="Object Feature Computation",workflow=self, interactive=False)
self.annotationsApplet = AnnotationsApplet( name="Training", workflow=self )
opAnnotations = self.annotationsApplet.topLevelOperator
self.trackingApplet = StructuredTrackingApplet( name="Tracking - Structured Learning", workflow=self )
opStructuredTracking = self.trackingApplet.topLevelOperator
if SOLVER=="CPLEX" or SOLVER=="GUROBI":
self._solver="ILP"
elif SOLVER=="DPCT":
self._solver="Flow-based"
else:
self._solver=None
opStructuredTracking._solver = self._solver
self.default_tracking_export_filename = '{dataset_dir}/{nickname}-tracking_exported_data.csv'
self.dataExportTrackingApplet = TrackingBaseDataExportApplet(self, "Tracking Result Export",default_export_filename=self.default_tracking_export_filename)
opDataExportTracking = self.dataExportTrackingApplet.topLevelOperator
opDataExportTracking.SelectionNames.setValue( ['Tracking-Result', 'Merger-Result', 'Object-Identities'] )
opDataExportTracking.WorkingDirectory.connect( opDataSelection.WorkingDirectory )
self.dataExportTrackingApplet.set_exporting_operator(opStructuredTracking)
self.dataExportTrackingApplet.prepare_lane_for_export = self.prepare_lane_for_export
self.dataExportTrackingApplet.post_process_lane_export = self.post_process_lane_export
# configure export settings
settings = {'file path': self.default_tracking_export_filename, 'compression': {}, 'file type': 'h5'}
selected_features = ['Count', 'RegionCenter', 'RegionRadii', 'RegionAxes']
opStructuredTracking.ExportSettings.setValue( (settings, selected_features) )
self._applets = []
self._applets.append(self.dataSelectionApplet)
if not self.fromBinary:
self._applets.append(self.thresholdTwoLevelsApplet)
self._applets.append(self.trackingFeatureExtractionApplet)
self._applets.append(self.divisionDetectionApplet)
self.batchProcessingApplet = BatchProcessingApplet(self, "Batch Processing", self.dataSelectionApplet, self.dataExportTrackingApplet)
self._applets.append(self.cellClassificationApplet)
self._applets.append(self.objectExtractionApplet)
self._applets.append(self.annotationsApplet)
self._applets.append(self.trackingApplet)
self._applets.append(self.dataExportTrackingApplet)
if self.divisionDetectionApplet:
opDivDetection = self.divisionDetectionApplet.topLevelOperator
opDivDetection.SelectedFeatures.setValue(configConservation.selectedFeaturesDiv)
opDivDetection.LabelNames.setValue(['Not Dividing', 'Dividing'])
opDivDetection.AllowDeleteLabels.setValue(False)
opDivDetection.AllowAddLabel.setValue(False)
opDivDetection.EnableLabelTransfer.setValue(False)
opCellClassification = self.cellClassificationApplet.topLevelOperator
opCellClassification.SelectedFeatures.setValue(configConservation.selectedFeaturesObjectCount )
opCellClassification.SuggestedLabelNames.setValue( ['False Detection',] + [str(1) + ' Object'] + [str(i) + ' Objects' for i in range(2,10) ] )
opCellClassification.AllowDeleteLastLabelOnly.setValue(True)
opCellClassification.EnableLabelTransfer.setValue(False)
if workflow_cmdline_args:
if '--testFullAnnotations' in workflow_cmdline_args:
self.testFullAnnotations = True
else:
self.testFullAnnotations = False
self._data_export_args, unused_args = self.dataExportTrackingApplet.parse_known_cmdline_args( workflow_cmdline_args )
self._batch_input_args, unused_args = self.batchProcessingApplet.parse_known_cmdline_args( workflow_cmdline_args )
else:
unused_args = None
self._data_export_args = None
self._batch_input_args = None
self.testFullAnnotations = False
if unused_args:
logger.warning("Unused command-line args: {}".format( unused_args ))
def __init__(self, shell, headless, workflow_cmdline_args,
project_creation_args, *args, **kwargs):
# Create a graph to be shared by all operators
graph = Graph()
super(NNClassificationWorkflow, self).__init__(shell,
headless,
workflow_cmdline_args,
project_creation_args,
graph=graph,
*args,
**kwargs)
self._applets = []
self._workflow_cmdline_args = workflow_cmdline_args
# Parse workflow-specific command-line args
parser = argparse.ArgumentParser()
# parser.add_argument('--print-labels-by-slice', help="Print the number of labels for each Z-slice of each image.", action="store_true")
# Parse the creation args: These were saved to the project file when this project was first created.
parsed_creation_args, unused_args = parser.parse_known_args(
project_creation_args)
# Parse the cmdline args for the current session.
parsed_args, unused_args = parser.parse_known_args(
workflow_cmdline_args)
# self.print_labels_by_slice = parsed_args.print_labels_by_slice
data_instructions = (
"Select your input data using the 'Raw Data' tab shown on the right.\n\n"
"Power users: Optionally use the 'Prediction Mask' tab to supply a binary image that tells ilastik where it should avoid computations you don't need."
)
# Applets for training (interactive) workflow
self.dataSelectionApplet = self.createDataSelectionApplet()
opDataSelection = self.dataSelectionApplet.topLevelOperator
# see role constants, above
opDataSelection.DatasetRoles.setValue(
NNClassificationWorkflow.ROLE_NAMES)
self.nnClassificationApplet = NNClassApplet(self, "NNClassApplet")
self.dataExportApplet = NNClassificationDataExportApplet(
self, "Data Export")
# Configure global DataExport settings
opDataExport = self.dataExportApplet.topLevelOperator
opDataExport.WorkingDirectory.connect(opDataSelection.WorkingDirectory)
opDataExport.SelectionNames.setValue(self.EXPORT_NAMES)
self.batchProcessingApplet = BatchProcessingApplet(
self, "Batch Processing", self.dataSelectionApplet,
self.dataExportApplet)
# Expose for shell
self._applets.append(self.dataSelectionApplet)
self._applets.append(self.nnClassificationApplet)
self._applets.append(self.dataExportApplet)
self._applets.append(self.batchProcessingApplet)
if unused_args:
# We parse the export setting args first. All remaining args are considered input files by the input applet.
self._batch_export_args, unused_args = self.dataExportApplet.parse_known_cmdline_args(
unused_args)
self._batch_input_args, unused_args = self.batchProcessingApplet.parse_known_cmdline_args(
unused_args)
else:
self._batch_input_args = None
self._batch_export_args = None
if unused_args:
logger.warn("Unused command-line args: {}".format(unused_args))
self.progressSignal(100)
def propagateDirty(self, slot, subindex, roi):
# The output from this operator isn't generally connected to other operators.
# If someone is using it that way, we'll assume that the user wants to know that
# the input image has become dirty and may need to be written to disk again.
self.WriteImage.setDirty(slice(None))
if __name__ == "__main__":
from lazyflow.graph import Graph
import h5py
import sys
traceLogger.addHandler(logging.StreamHandler(sys.stdout))
traceLogger.setLevel(logging.DEBUG)
traceLogger.debug("HELLO")
f = h5py.File("/tmp/flyem_sample_stack.h5", "r")
internalPath = "volume/data"
# OpStackToH5Writer
graph = Graph()
opStackToH5 = OpStackToH5Writer()
opStackToH5.GlobString.setValue("/tmp/flyem_sample_stack/*.png")
opStackToH5.hdf5Group.setValue(f)
opStackToH5.hdf5Path.setValue(internalPath)
success = opStackToH5.WriteImage.value
assert success
def generate_trained_project_file(new_project_path,
raw_data_paths,
label_data_paths,
feature_selections,
classifier_factory=None):
"""
Create a new project file from scratch, add the given raw data files,
inject the corresponding labels, configure the given feature selections,
and (if provided) override the classifier type ('factory').
Finally, request the classifier object from the pipeline (which forces training),
and save the project.
new_project_path: Where to save the new project file
raw_data_paths: A list of paths to the raw data images to train with
label_data_paths: A list of paths to the label image data to train with
feature_selections: A matrix of bool, representing the selected features
classifier_factory: Override the classifier type. Must be a subclass of either:
- lazyflow.classifiers.LazyflowVectorwiseClassifierFactoryABC
- lazyflow.classifiers.LazyflowPixelwiseClassifierFactoryABC
"""
assert len(raw_data_paths) == len(
label_data_paths
), "Number of label images must match number of raw images."
import ilastik_main
from ilastik.workflows.pixelClassification import PixelClassificationWorkflow
from lazyflow.graph import Graph
from lazyflow.operators.ioOperators import OpInputDataReader
from lazyflow.roi import roiToSlice, roiFromShape
##
## CREATE PROJECT
##
# Manually configure the arguments to ilastik, as if they were parsed from the command line.
# (Start with empty args and fill in below.)
ilastik_args = ilastik_main.parse_args([])
ilastik_args.new_project = new_project_path
ilastik_args.headless = True
ilastik_args.workflow = "Pixel Classification"
shell = ilastik_main.main(ilastik_args)
assert isinstance(shell.workflow, PixelClassificationWorkflow)
##
## CONFIGURE GRAYSCALE INPUT
##
data_selection_applet = shell.workflow.dataSelectionApplet
# To configure data selection, start with empty cmdline args and manually fill them in
data_selection_args, _ = data_selection_applet.parse_known_cmdline_args(
[], PixelClassificationWorkflow.ROLE_NAMES)
data_selection_args.raw_data = raw_data_paths
data_selection_args.preconvert_stacks = True
# Simplest thing here is to configure using cmd-line interface
data_selection_applet.configure_operator_with_parsed_args(
data_selection_args)
##
## APPLY FEATURE MATRIX (from matrix above)
##
opFeatures = shell.workflow.featureSelectionApplet.topLevelOperator
opFeatures.Scales.setValue(ScalesList)
opFeatures.FeatureIds.setValue(FeatureIds)
opFeatures.SelectionMatrix.setValue(feature_selections)
##
## CUSTOMIZE CLASSIFIER TYPE
##
opPixelClassification = shell.workflow.pcApplet.topLevelOperator
if classifier_factory is not None:
opPixelClassification.ClassifierFactory.setValue(classifier_factory)
##
## READ/APPLY LABEL VOLUMES
##
# Read each label volume and inject the label data into the appropriate training slot
cwd = os.getcwd()
max_label_class = 0
for lane, label_data_path in enumerate(label_data_paths):
graph = Graph()
opReader = OpInputDataReader(graph=graph)
try:
opReader.WorkingDirectory.setValue(cwd)
opReader.FilePath.setValue(label_data_path)
print("Reading label volume: {}".format(label_data_path))
label_volume = opReader.Output[:].wait()
finally:
opReader.cleanUp()
raw_shape = opPixelClassification.InputImages[lane].meta.shape
if label_volume.ndim != len(raw_shape):
# Append a singleton channel axis
assert label_volume.ndim == len(raw_shape) - 1
label_volume = label_volume[..., None]
# Auto-calculate the max label value
max_label_class = max(max_label_class, label_volume.max())
print("Applying label volume to lane #{}".format(lane))
entire_volume_slicing = roiToSlice(*roiFromShape(label_volume.shape))
opPixelClassification.LabelInputs[lane][
entire_volume_slicing] = label_volume
assert max_label_class > 1, "Not enough label classes were found in your label data."
label_names = list(map(str, list(range(max_label_class))))
opPixelClassification.LabelNames.setValue(label_names)
##
## TRAIN CLASSIFIER
##
# Make sure the caches in the pipeline are not 'frozen'.
# (This is the equivalent of 'live update' mode in the GUI.)
opPixelClassification.FreezePredictions.setValue(False)
# Request the classifier object from the pipeline.
# This forces the pipeline to produce (train) the classifier.
_ = opPixelClassification.Classifier.value
##
## SAVE PROJECT
##
# save project file (includes the new classifier).
shell.projectManager.saveProject(force_all_save=False)
class TestSlot_notifyConnect(object):
def setUp(self):
self.g = Graph()
def tearDown(self):
self.g.stopGraph()
def test_connect(self):
# test that the notifyConnect callback is called
# when the slot is connected
ops = OpS(graph=self.g)
opa = OpA(graph=self.g)
opa.Input2.connect(ops.Output2)
upval = [False]
def callBack(slot):
upval[0] = True
# check the connect callback is called
opa.Input1._notifyConnect(callBack)
opa.Input1.connect(ops.Output1)
assert upval[0] == True
# check the connect callback is called for a slot with default value
upval[0] = False
opa.Input3._notifyConnect(callBack)
opa.Input3.connect(ops.Output3)
assert upval[0] == True
# check the connect callback is called for a multi inputslot
upval[0] = False
opa.Input4._notifyConnect(callBack)
opa.Input4.connect(ops.Output4)
assert upval[0] == True
def test_no_connect(self):
ops = OpS(graph=self.g)
opa = OpA(graph=self.g)
upval = [False]
def callBack(slot):
upval[0] = True
opa.Input1._notifyConnect(callBack)
# check the connect callback is not called when reconnecting to the same slot
opa.Input1.connect(ops.Output1)
upval[0] = False
opa.Input1.connect(ops.Output1)
assert upval[0] == False
# check the connect callback is not called when setting the same value again
opa.Input1.disconnect()
opa.Input1.setValue(10)
upval[0] = False
opa.Input1.setValue(10)
assert upval[0] == False
def test_unregister_connect(self):
# check that unregistering a connect callback works
ops = OpS(graph=self.g)
opa = OpA(graph=self.g)
upval = [False]
def callBack(slot):
upval[0] = True
opa.Input1._notifyConnect(callBack)
opa.Input1._unregisterConnect(callBack)
opa.Input1.connect(ops.Output1)
assert upval[0] == False
class Main(QMainWindow):
haveData = pyqtSignal()
dataReadyToView = pyqtSignal()
def __init__(self, argv):
QMainWindow.__init__(self)
#Normalize the data if true
self._normalize_data=True
if 'notnormalize' in sys.argv:
print sys.argv
self._normalize_data=False
sys.argv.remove('notnormalize')
self.opPredict = None
self.opTrain = None
self.opThreshold = None
self._colorTable16 = self._createDefault16ColorColorTable()
#self.g = Graph(7, 2048*1024**2*5)
self.g = Graph()
self.fixableOperators = []
self.featureDlg=None
#The old ilastik provided the following scale names:
#['Tiny', 'Small', 'Medium', 'Large', 'Huge', 'Megahuge', 'Gigahuge']
#The corresponding scales are:
self.featScalesList=[0.3, 0.7, 1, 1.6, 3.5, 5.0, 10.0]
self.initUic()
#if the filename was specified on command line, load it
if len(sys.argv) >= 2:
def loadFile():
self._openFile(sys.argv[1:])
QTimer.singleShot(0, loadFile)
def setIconToViewMenu(self):
self.actionOnly_for_current_view.setIcon(QIcon(self.editor.imageViews[self.editor._lastImageViewFocus]._hud.axisLabel.pixmap()))
def initUic(self):
p = os.path.split(__file__)[0]+'/'
if p == "/": p = "."+p
uic.loadUi(p+"MainWindow_cc.ui", self)
#connect the window and graph creation to the opening of the file
self.actionOpen.triggered.connect(self.openFile)
self.actionQuit.triggered.connect(qApp.quit)
def toggleDebugPatches(show):
self.editor.showDebugPatches = show
def fitToScreen():
shape = self.editor.posModel.shape
for i, v in enumerate(self.editor.imageViews):
s = list(copy.copy(shape))
del s[i]
v.changeViewPort(v.scene().data2scene.mapRect(QRectF(0,0,*s)))
def fitImage():
if hasattr(self.editor, '_lastImageViewFocus'):
self.editor.imageViews[self.editor._lastImageViewFocus].fitImage()
def restoreImageToOriginalSize():
if hasattr(self.editor, '_lastImageViewFocus'):
self.editor.imageViews[self.editor._lastImageViewFocus].doScaleTo()
def rubberBandZoom():
if hasattr(self.editor, '_lastImageViewFocus'):
if not self.editor.imageViews[self.editor._lastImageViewFocus]._isRubberBandZoom:
self.editor.imageViews[self.editor._lastImageViewFocus]._isRubberBandZoom = True
self.editor.imageViews[self.editor._lastImageViewFocus]._cursorBackup = self.editor.imageViews[self.editor._lastImageViewFocus].cursor()
self.editor.imageViews[self.editor._lastImageViewFocus].setCursor(Qt.CrossCursor)
else:
self.editor.imageViews[self.editor._lastImageViewFocus]._isRubberBandZoom = False
self.editor.imageViews[self.editor._lastImageViewFocus].setCursor(self.editor.imageViews[self.editor._lastImageViewFocus]._cursorBackup)
def hideHud():
if self.editor.imageViews[0]._hud.isVisible():
hide = False
else:
hide = True
for i, v in enumerate(self.editor.imageViews):
v.hideHud(hide)
def toggleSelectedHud():
if hasattr(self.editor, '_lastImageViewFocus'):
self.editor.imageViews[self.editor._lastImageViewFocus].toggleHud()
def centerAllImages():
for i, v in enumerate(self.editor.imageViews):
v.centerImage()
def centerImage():
if hasattr(self.editor, '_lastImageViewFocus'):
self.editor.imageViews[self.editor._lastImageViewFocus].centerImage()
self.actionOnly_for_current_view.setEnabled(True)
self.actionCenterAllImages.triggered.connect(centerAllImages)
self.actionCenterImage.triggered.connect(centerImage)
self.actionToggleAllHuds.triggered.connect(hideHud)
self.actionToggleSelectedHud.triggered.connect(toggleSelectedHud)
self.actionShowDebugPatches.toggled.connect(toggleDebugPatches)
self.actionFitToScreen.triggered.connect(fitToScreen)
self.actionFitImage.triggered.connect(fitImage)
self.actionReset_zoom.triggered.connect(restoreImageToOriginalSize)
self.actionRubberBandZoom.triggered.connect(rubberBandZoom)
self.haveData.connect(self.initGraph)
self.dataReadyToView.connect(self.initEditor)
self.layerstack = LayerStackModel()
model = LabelListModel()
self.labelListView.setModel(model)
self.labelListModel=model
self.labelListModel.rowsAboutToBeRemoved.connect(self.onLabelAboutToBeRemoved)
self.labelListModel.labelSelected.connect(self.switchLabel)
def onDataChanged(topLeft, bottomRight):
firstRow = topLeft.row()
lastRow = bottomRight.row()
firstCol = topLeft.column()
lastCol = bottomRight.column()
if lastCol == firstCol == 0:
assert(firstRow == lastRow) #only one data item changes at a time
#in this case, the actual data (for example color) has changed
self.switchColor(firstRow+1, self.labelListModel[firstRow].color)
self.editor.scheduleSlicesRedraw()
else:
#this column is used for the 'delete' buttons, we don't care
#about data changed here
pass
self.labelListModel.dataChanged.connect(onDataChanged)
self.AddLabelButton.clicked.connect(self.addLabel)
self.SelectFeaturesButton.clicked.connect(self.onFeatureButtonClicked)
self.StartClassificationButton.clicked.connect(self.startClassification)
self.StartClassificationButton.setEnabled(False)
self.checkInteractive.setEnabled(False)
self.checkInteractive.toggled.connect(self.toggleInteractive)
self.interactionComboBox.currentIndexChanged.connect(self.changeInteractionMode)
self.interactionComboBox.setEnabled(False)
self.AddThresholdButton.clicked.connect(self.addThresholdOperator)
self.AddThresholdButton.setEnabled(False)
self.CCButton.clicked.connect(self.addCCOperator)
self.CCButton.setEnabled(False)
self._initFeatureDlg()
def toggleInteractive(self, checked):
print "toggling interactive mode to '%r'" % checked
#Check if the number of labels in the layer stack is equals to the number of Painted labels
if checked==True:
labels =numpy.unique(numpy.asarray(self.opLabels.outputs["nonzeroValues"][:].allocate().wait()[0]))
nPaintedLabels=labels.shape[0]
nLabelsLayers = self.labelListModel.rowCount()
selectedFeatures = numpy.asarray(self.featureDlg.featureTableWidget.createSelectedFeaturesBoolMatrix())
if nPaintedLabels!=nLabelsLayers:
self.checkInteractive.setCheckState(0)
mexBox=QMessageBox()
mexBox.setText("Did you forget to paint some labels?")
mexBox.setInformativeText("Painted Labels %d \nNumber Active Labels Layers %d"%(nPaintedLabels,self.labelListModel.rowCount()))
mexBox.exec_()
return
if (selectedFeatures==0).all():
self.checkInteractive.setCheckState(0)
mexBox=QMessageBox()
mexBox.setText("The are no features selected ")
mexBox.exec_()
return
else:
self.g.stopGraph()
self.g.resumeGraph()
self.AddLabelButton.setEnabled(not checked)
self.SelectFeaturesButton.setEnabled(not checked)
for o in self.fixableOperators:
o.inputs["fixAtCurrent"].setValue(not checked)
self.labelListModel.allowRemove(not checked)
self.editor.scheduleSlicesRedraw()
def changeInteractionMode( self, index ):
modes = {0: "navigation", 1: "brushing"}
self.editor.setInteractionMode( modes[index] )
self.interactionComboBox.setCurrentIndex(index)
print "interaction mode switched to", modes[index]
def switchLabel(self, row):
print "switching to label=%r" % (self.labelListModel[row])
#+1 because first is transparent
#FIXME: shouldn't be just row+1 here
self.editor.brushingModel.setDrawnNumber(row+1)
self.editor.brushingModel.setBrushColor(self.labelListModel[row].color)
def switchColor(self, row, color):
print "label=%d changes color to %r" % (row, color)
self.labellayer.colorTable[row]=color.rgba()
self.editor.brushingModel.setBrushColor(color)
self.editor.scheduleSlicesRedraw()
def addLabel(self):
color = QColor(numpy.random.randint(0,255), numpy.random.randint(0,255), numpy.random.randint(0,255))
numLabels = len(self.labelListModel)
if numLabels < len(self._colorTable16):
color = self._colorTable16[numLabels]
self.labellayer.colorTable.append(color.rgba())
self.labelListModel.insertRow(self.labelListModel.rowCount(), Label("Label %d" % (self.labelListModel.rowCount() + 1), color))
nlabels = self.labelListModel.rowCount()
if self.opPredict is not None:
print "Label added, changing predictions"
#re-train the forest now that we have more labels
self.opPredict.inputs['LabelsCount'].setValue(nlabels)
self.addPredictionLayer(nlabels-1, self.labelListModel._labels[nlabels-1])
#make the new label selected
index = self.labelListModel.index(nlabels-1, 1)
self.labelListModel._selectionModel.select(index, QItemSelectionModel.ClearAndSelect)
#FIXME: this should watch for model changes
#drawing will be enabled when the first label is added
self.changeInteractionMode( 1 )
self.interactionComboBox.setEnabled(True)
def onLabelAboutToBeRemoved(self, parent, start, end):
#the user deleted a label, reshape prediction and remove the layer
#the interface only allows to remove one label at a time?
nout = start-end+1
ncurrent = self.labelListModel.rowCount()
print "removing", nout, "out of ", ncurrent
if self.opPredict is not None:
self.opPredict.inputs['LabelsCount'].setValue(ncurrent-nout)
for il in range(start, end+1):
labelvalue = self.labelListModel._labels[il]
self.removePredictionLayer(labelvalue)
self.opLabels.inputs["deleteLabel"].setValue(il+1)
self.editor.scheduleSlicesRedraw()
def startClassification(self):
if self.opTrain is None:
#initialize all classification operators
print "initializing classification..."
opMultiL = Op5ToMulti(self.g)
opMultiL.inputs["Input0"].connect(self.opLabels.outputs["Output"])
opMultiLblocks = Op5ToMulti(self.g)
opMultiLblocks.inputs["Input0"].connect(self.opLabels.outputs["nonzeroBlocks"])
self.opTrain = OpTrainRandomForestBlocked(self.g)
self.opTrain.inputs['Labels'].connect(opMultiL.outputs["Outputs"])
self.opTrain.inputs['Images'].connect(self.opFeatureCache.outputs["Output"])
self.opTrain.inputs["nonzeroLabelBlocks"].connect(opMultiLblocks.outputs["Outputs"])
self.opTrain.inputs['fixClassifier'].setValue(False)
opClassifierCache = OpArrayCache(self.g)
opClassifierCache.inputs["Input"].connect(self.opTrain.outputs['Classifier'])
################## Prediction
self.opPredict=OpPredictRandomForest(self.g)
nclasses = self.labelListModel.rowCount()
self.opPredict.inputs['LabelsCount'].setValue(nclasses)
self.opPredict.inputs['Classifier'].connect(opClassifierCache.outputs['Output'])
self.opPredict.inputs['Image'].connect(self.opPF.outputs["Output"])
pCache = OpSlicedBlockedArrayCache(self.g)
pCache.inputs["fixAtCurrent"].setValue(False)
pCache.inputs["innerBlockShape"].setValue(((1,256,256,1,2),(1,256,1,256,2),(1,1,256,256,2)))
pCache.inputs["outerBlockShape"].setValue(((1,256,256,4,2),(1,256,4,256,2),(1,4,256,256,2)))
pCache.inputs["Input"].connect(self.opPredict.outputs["PMaps"])
self.pCache = pCache
#add prediction results for all classes as separate channels
for icl in range(nclasses):
self.addPredictionLayer(icl, self.labelListModel._labels[icl])
self.StartClassificationButton.setEnabled(False)
self.checkInteractive.setEnabled(True)
self.AddThresholdButton.setEnabled(True)
def addPredictionLayer(self, icl, ref_label):
selector=OpSingleChannelSelector(self.g)
selector.inputs["Input"].connect(self.pCache.outputs['Output'])
selector.inputs["Index"].setValue(icl)
if self.checkInteractive.isChecked():
self.pCache.inputs["fixAtCurrent"].setValue(False)
else:
self.pCache.inputs["fixAtCurrent"].setValue(True)
predictsrc = LazyflowSource(selector.outputs["Output"][0])
def srcName(newName):
predictsrc.setObjectName("Prediction for %s" % ref_label.name)
srcName("")
predictLayer = AlphaModulatedLayer(predictsrc, tintColor=ref_label.color)
predictLayer.nameChanged.connect(srcName)
def setLayerColor(c):
print "as the color of label '%s' has changed, setting layer's '%s' tint color to %r" % (ref_label.name, predictLayer.name, c)
predictLayer.tintColor = c
ref_label.colorChanged.connect(setLayerColor)
def setLayerName(n):
newName = "Prediction for %s" % ref_label.name
print "as the name of label '%s' has changed, setting layer's '%s' name to '%s'" % (ref_label.name, predictLayer.name, newName)
predictLayer.name = newName
setLayerName(ref_label.name)
ref_label.nameChanged.connect(setLayerName)
predictLayer.ref_object = ref_label
#make sure that labels (index = 0) stay on top!
self.layerstack.insert(1, predictLayer )
self.fixableOperators.append(self.pCache)
def removePredictionLayer(self, ref_label):
for il, layer in enumerate(self.layerstack):
if layer.ref_object==ref_label:
print "found the prediction", layer.ref_object, ref_label
self.layerstack.removeRows(il, 1)
break
def addThresholdOperator(self):
if self.opThreshold is None:
self.opThreshold = OpThreshold(self.g)
self.opThreshold.inputs["Input"].connect(self.pCache.outputs["Output"])
#channel, value = ThresholdDlg(self.labelListModel._labels)
channel = 0
value = 0.5
ref_label = self.labelListModel._labels[channel]
self.opThreshold.inputs["Channel"].setValue(channel)
self.opThreshold.inputs["Threshold"].setValue(value)
threshsrc = LazyflowSource(self.opThreshold.outputs["Output"][0])
threshsrc.setObjectName("Threshold for %s" % ref_label.name)
transparent = QColor(0,0,0,0)
white = QColor(255,255,255)
colorTable = [transparent.rgba(), white.rgba()]
threshLayer = ColortableLayer(threshsrc, colorTable = colorTable )
threshLayer.name = "Threshold for %s" % ref_label.name
self.layerstack.insert(1, threshLayer)
self.CCButton.setEnabled(True)
def addCCOperator(self):
self.opCC = OpConnectedComponents(self.g)
self.opCC.inputs["Input"].connect(self.opThreshold.outputs["Output"])
#we shouldn't have to define these. But just in case...
self.opCC.inputs["Neighborhood"].setValue(6)
self.opCC.inputs["Background"].setValue(0)
ccsrc = LazyflowSource(self.opCC.outputs["Output"][0])
ccsrc.setObjectName("Connected Components")
ctb = colortables.create_default_16bit()
ctb.insert(0, QColor(0, 0, 0, 0).rgba()) # make background transparent
ccLayer = ColortableLayer(ccsrc, ctb)
ccLayer.name = "Connected Components"
self.layerstack.insert(1, ccLayer)
def openFile(self):
fileNames = QFileDialog.getOpenFileNames(self, "Open Image", os.path.abspath(__file__), "Numpy and h5 files (*.npy *.h5)")
if fileNames.count() == 0:
return
self._openFile(fileNames)
def _openFile(self, fileNames):
self.inputProvider = None
fName, fExt = os.path.splitext(str(fileNames[0]))
print "Opening Files %r" % fileNames
if fExt=='.npy':
fileName = fileNames[0]
if len(fileNames)>1:
print "WARNING: only the first file will be read, multiple file prediction not supported yet"
fName, fExt = os.path.splitext(str(fileName))
self.raw = numpy.load(str(fileName))
self.min, self.max = numpy.min(self.raw), numpy.max(self.raw)
self.inputProvider = OpArrayPiper(self.g)
self.raw = self.raw.view(vigra.VigraArray)
self.raw.axistags = vigra.AxisTags(
vigra.AxisInfo('t',vigra.AxisType.Time),
vigra.AxisInfo('x',vigra.AxisType.Space),
vigra.AxisInfo('y',vigra.AxisType.Space),
vigra.AxisInfo('z',vigra.AxisType.Space),
vigra.AxisInfo('c',vigra.AxisType.Channels))
self.inputProvider.inputs["Input"].setValue(self.raw)
elif fExt=='.h5':
readerNew=OpH5ReaderBigDataset(self.g)
readerNew.inputs["Filenames"].setValue(fileNames)
readerNew.inputs["hdf5Path"].setValue("volume/data")
readerCache = OpSlicedBlockedArrayCache(self.g)
readerCache.inputs["fixAtCurrent"].setValue(False)
readerCache.inputs["innerBlockShape"].setValue(((1,256,256,1,2),(1,256,1,256,2),(1,1,256,256,2)))
readerCache.inputs["outerBlockShape"].setValue(((1,256,256,4,2),(1,256,4,256,2),(1,4,256,256,2)))
readerCache.inputs["Input"].connect(readerNew.outputs["Output"])
self.inputProvider = OpArrayPiper(self.g)
self.inputProvider.inputs["Input"].connect(readerCache.outputs["Output"])
else:
raise RuntimeError("opening filenames=%r not supported yet" % fileNames)
self.haveData.emit()
def initGraph(self):
shape = self.inputProvider.outputs["Output"].shape
srcs = []
minMax = []
normalize = []
print "* Data has shape=%r" % (shape,)
#create a layer for each channel of the input:
slicer=OpMultiArraySlicer2(self.g)
slicer.inputs["Input"].connect(self.inputProvider.outputs["Output"])
slicer.inputs["AxisFlag"].setValue('c')
nchannels = shape[-1]
for ich in xrange(nchannels):
data=slicer.outputs['Slices'][ich][:].allocate().wait()
#find the minimum and maximum value for normalization
mm = (numpy.min(data), numpy.max(data))
print " - channel %d: min=%r, max=%r" % (ich, mm[0], mm[1])
minMax.append(mm)
if self._normalize_data:
normalize.append(mm)
else:
normalize.append((0,255))
layersrc = LazyflowSource(slicer.outputs['Slices'][ich], priority = 100)
layersrc.setObjectName("raw data channel=%d" % ich)
srcs.append(layersrc)
#FIXME: we shouldn't merge channels automatically, but for now it's prettier
layer1 = None
if nchannels == 1:
layer1 = GrayscaleLayer(srcs[0], range=minMax[0], normalize=normalize[0])
print " - showing raw data as grayscale"
elif nchannels==2:
layer1 = RGBALayer(red = srcs[0], normalizeR=normalize[0],
green = srcs[1], normalizeG=normalize[1], range=minMax[0:2]+[(0,255), (0,255)])
print " - showing channel 1 as red, channel 2 as green"
elif nchannels==3:
layer1 = RGBALayer(red = srcs[0], normalizeR=normalize[0],
green = srcs[1], normalizeG=normalize[1],
blue = srcs[2], normalizeB=normalize[2],
range = minMax[0:3])
print " - showing channel 1 as red, channel 2 as green, channel 3 as blue"
else:
print "only 1,2 or 3 channels supported so far"
return
print
layer1.name = "Input data"
layer1.ref_object = None
self.layerstack.append(layer1)
opImageList = Op5ToMulti(self.g)
opImageList.inputs["Input0"].connect(self.inputProvider.outputs["Output"])
#init the features operator
opPF = OpPixelFeaturesPresmoothed(self.g)
opPF.inputs["Input"].connect(opImageList.outputs["Outputs"])
opPF.inputs["Scales"].setValue(self.featScalesList)
self.opPF=opPF
#Caches the features
opFeatureCache = OpBlockedArrayCache(self.g)
opFeatureCache.inputs["innerBlockShape"].setValue((1,32,32,32,16))
opFeatureCache.inputs["outerBlockShape"].setValue((1,128,128,128,64))
opFeatureCache.inputs["Input"].connect(opPF.outputs["Output"])
opFeatureCache.inputs["fixAtCurrent"].setValue(False)
self.opFeatureCache=opFeatureCache
self.initLabels()
self.dataReadyToView.emit()
def initLabels(self):
#Add the layer to draw the labels, but don't add any labels
shape=self.inputProvider.outputs["Output"].shape
self.opLabels = OpBlockedSparseLabelArray(self.g)
self.opLabels.inputs["shape"].setValue(shape[:-1] + (1,))
self.opLabels.inputs["blockShape"].setValue((1, 32, 32, 32, 1))
self.opLabels.inputs["eraser"].setValue(100)
self.labelsrc = LazyflowSinkSource(self.opLabels, self.opLabels.outputs["Output"], self.opLabels.inputs["Input"])
self.labelsrc.setObjectName("labels")
transparent = QColor(0,0,0,0)
self.labellayer = ColortableLayer(self.labelsrc, colorTable = [transparent.rgba()] )
self.labellayer.name = "Labels"
self.labellayer.ref_object = None
self.layerstack.append(self.labellayer)
def initEditor(self):
shape=self.inputProvider.outputs["Output"].shape
self.editor = VolumeEditor(self.layerstack, labelsink=self.labelsrc)
self.editor.dataShape = shape
self.editor.newImageView2DFocus.connect(self.setIconToViewMenu)
#drawing will be enabled when the first label is added
self.editor.setInteractionMode( 'navigation' )
self.volumeEditorWidget.init(self.editor)
model = self.editor.layerStack
self.layerWidget.init(model)
self.UpButton.clicked.connect(model.moveSelectedUp)
model.canMoveSelectedUp.connect(self.UpButton.setEnabled)
self.DownButton.clicked.connect(model.moveSelectedDown)
model.canMoveSelectedDown.connect(self.DownButton.setEnabled)
self.DeleteButton.clicked.connect(model.deleteSelected)
model.canDeleteSelected.connect(self.DeleteButton.setEnabled)
self.opLabels.inputs["eraser"].setValue(self.editor.brushingModel.erasingNumber)
def _createDefault16ColorColorTable(self):
c = []
c.append(QColor(0, 0, 255))
c.append(QColor(255, 255, 0))
c.append(QColor(255, 0, 0))
c.append(QColor(0, 255, 0))
c.append(QColor(0, 255, 255))
c.append(QColor(255, 0, 255))
c.append(QColor(255, 105, 180)) #hot pink
c.append(QColor(102, 205, 170)) #dark aquamarine
c.append(QColor(165, 42, 42)) #brown
c.append(QColor(0, 0, 128)) #navy
c.append(QColor(255, 165, 0)) #orange
c.append(QColor(173, 255, 47)) #green-yellow
c.append(QColor(128,0, 128)) #purple
c.append(QColor(192, 192, 192)) #silver
c.append(QColor(240, 230, 140)) #khaki
c.append(QColor(69, 69, 69)) # dark grey
return c
def onFeatureButtonClicked(self):
self.featureDlg.show()
def onDlgAccepted():
self.StartClassificationButton.setEnabled(True)
self.featureDlg.accepted.connect(onDlgAccepted)
def _onFeaturesChosen(self):
selectedFeatures = self.featureDlg.featureTableWidget.createSelectedFeaturesBoolMatrix()
print "new feature set:", selectedFeatures
self.opPF.inputs['Matrix'].setValue(numpy.asarray(selectedFeatures))
def _initFeatureDlg(self):
dlg = self.featureDlg = FeatureDlg()
dlg.setWindowTitle("Features")
dlg.createFeatureTable({"Features": [FeatureEntry("Gaussian smoothing"), \
FeatureEntry("Laplacian of Gaussian"), \
FeatureEntry("Structure Tensor Eigenvalues"), \
FeatureEntry("Hessian of Gaussian EV"), \
FeatureEntry("Gaussian Gradient Magnitude"), \
FeatureEntry("Difference Of Gaussian")]}, \
self.featScalesList)
dlg.setImageToPreView(None)
m = [[1,0,0,0,0,0,0],[1,0,0,0,0,0,0],[0,0,0,0,0,0,0],[1,0,0,0,0,0,0],[1,0,0,0,0,0,0],[1,0,0,0,0,0,0]]
dlg.featureTableWidget.setSelectedFeatureBoolMatrix(m)
dlg.accepted.connect(self._onFeaturesChosen)
def testFullAllocate():
nx = 5
ny = 10
nz = 2
nc = 7
stack = vigra.VigraArray((nx, ny, nz, nc), axistags=vigra.defaultAxistags('xyzc'))
stack[...] = numpy.random.rand(nx, ny, nz, nc)
g = Graph()
#assume that the slicer works
slicerX = OpMultiArraySlicer(graph=g)
slicerX.inputs["Input"].setValue(stack)
slicerX.inputs["AxisFlag"].setValue('x')
#insert the x dimension
stackerX = OpMultiArrayStacker(graph=g)
stackerX.inputs["AxisFlag"].setValue('x')
stackerX.inputs["AxisIndex"].setValue(0)
stackerX.inputs["Images"].connect(slicerX.outputs["Slices"])
newdata = stackerX.outputs["Output"][:].wait()
assert_array_equal(newdata, stack.view(numpy.ndarray))
print "1st part ok................."
#merge stuff that already has an x dimension
stack2 = vigra.VigraArray((nx-1, ny, nz, nc), axistags=vigra.defaultAxistags('xyzc'))
stack2[...] = numpy.random.rand(nx-1, ny, nz, nc)
opMulti = Op5ToMulti(graph=g)
opMulti.inputs["Input0"].setValue(stack)
opMulti.inputs["Input1"].setValue(stack2)
#print "OPMULTI: ", len(opMulti.outputs["Outputs"])
stackerX2 = OpMultiArrayStacker(graph=g)
stackerX2.inputs["Images"].connect(opMulti.outputs["Outputs"])
stackerX2.inputs["AxisFlag"].setValue('x')
stackerX2.inputs["AxisIndex"].setValue(0)
#print "STACKER: ", stackerX2.outputs["Output"].meta.shape
newdata = stackerX2.outputs["Output"][:].wait()
bothstacks = numpy.concatenate((stack, stack2), axis=0)
assert_array_equal(newdata, bothstacks.view(numpy.ndarray))
#print newdata.shape, bothstacks.shape
print "2nd part ok................."
#print "------------------------------------------------------------"
#print "------------------------------------------------------------"
#print "------------------------------------------------------------"
##### channel
#assume that the slicer works
slicerC = OpMultiArraySlicer(graph=g)
slicerC.inputs["Input"].setValue(stack)
slicerC.inputs["AxisFlag"].setValue('c')
#insert the c dimension
stackerC = OpMultiArrayStacker(graph=g)
stackerC.inputs["AxisFlag"].setValue('c')
stackerC.inputs["AxisIndex"].setValue(3)
stackerC.inputs["Images"].connect(slicerC.outputs["Slices"])
newdata = stackerC.outputs["Output"][:].wait()
assert_array_equal(newdata, stack.view(numpy.ndarray))
print "3rd part ok................."
#print "STACKER: ", stackerC.outputs["Output"].meta.shape
#merge stuff that already has an x dimension
stack3 = vigra.VigraArray((nx, ny, nz, nc-1), axistags=vigra.defaultAxistags('xyzc'))
stack3[...] = numpy.random.rand(nx, ny, nz, nc-1)
opMulti = Op5ToMulti(graph=g)
opMulti.inputs["Input0"].setValue(stack)
opMulti.inputs["Input1"].setValue(stack3)
stackerC2 = OpMultiArrayStacker(graph=g)
stackerC2.inputs["AxisFlag"].setValue('c')
stackerC2.inputs["AxisIndex"].setValue(3)
stackerC2.inputs["Images"].connect(opMulti.outputs["Outputs"])
newdata = stackerC2.outputs["Output"][:].wait()
bothstacks = numpy.concatenate((stack, stack3), axis=3)
assert_array_equal(newdata, bothstacks.view(numpy.ndarray))
print "4th part ok................."
g.finalize()
def setUp(self):
self.g = Graph()
self.op = OpA(graph=self.g)
def setUp(self):
self.g = Graph()