def setupOutputs(self):
file_paths = self.expandGlobStrings(self.GlobString.value)
for filename in file_paths:
if os.path.splitext(
filename)[1].lower() not in OpTiffReader.TIFF_EXTS:
raise OpTiffSequenceReader.WrongFileTypeError(filename)
num_files = len(file_paths)
if num_files == 0:
self.Output.disconnect()
self.Output.meta.NOTREADY = True
return
self.Output.connect(self._opStacker.Output)
try:
opFirstImg = OpTiffReader(parent=self)
opFirstImg.Filepath.setValue(file_paths[0])
slice_axes = opFirstImg.Output.meta.getAxisKeys()
opFirstImg.cleanUp()
except RuntimeError as e:
logger.error(str(e))
raise OpTiffSequenceReader.FileOpenError(file_paths[0])
if self.SequenceAxis.ready():
new_axis = self.SequenceAxis.value
assert len(new_axis) == 1
assert new_axis in 'tzyxc'
else:
# Try to pick an axis that doesn't already exist in each tiff
for new_axis in 'tzc0':
if new_axis not in slice_axes:
break
if new_axis == '0':
# All axes used already.
# Stack across first existing axis
new_axis = slice_axes[0]
self._opStacker.Images.resize(0)
self._opStacker.Images.resize(num_files)
self._opStacker.AxisFlag.setValue(new_axis)
for opReader in self._readers:
opReader.cleanUp()
self._readers = []
for filename, stacker_slot in zip(file_paths, self._opStacker.Images):
opReader = OpTiffReader(parent=self)
try:
opReader.Filepath.setValue(filename)
except RuntimeError as e:
logger.error(str(e))
raise OpTiffSequenceReader.FileOpenError(file_paths[0])
else:
stacker_slot.connect(opReader.Output)
self._readers.append(opReader)
def setupOutputs(self):
file_paths = self.expandGlobStrings(self.GlobString.value)
for filename in file_paths:
if os.path.splitext(filename)[1].lower() not in OpTiffReader.TIFF_EXTS:
raise OpTiffSequenceReader.WrongFileTypeError(filename)
num_files = len(file_paths)
if num_files == 0:
self.Output.disconnect()
self.Output.meta.NOTREADY = True
return
self.Output.connect(self._opStacker.Output)
try:
opFirstImg = OpTiffReader(parent=self)
opFirstImg.Filepath.setValue(file_paths[0])
slice_axes = opFirstImg.Output.meta.getAxisKeys()
opFirstImg.cleanUp()
except RuntimeError as e:
logger.error(str(e))
raise OpTiffSequenceReader.FileOpenError(file_paths[0])
if self.SequenceAxis.ready():
new_axis = self.SequenceAxis.value
assert len(new_axis) == 1
assert new_axis in "tzyxc"
else:
# Try to pick an axis that doesn't already exist in each tiff
for new_axis in "tzc0":
if new_axis not in slice_axes:
break
if new_axis == "0":
# All axes used already.
# Stack across first existing axis
new_axis = slice_axes[0]
self._opStacker.Images.resize(0)
self._opStacker.Images.resize(num_files)
self._opStacker.AxisFlag.setValue(new_axis)
for opReader in self._readers:
opReader.cleanUp()
self._readers = []
for filename, stacker_slot in zip(file_paths, self._opStacker.Images):
opReader = OpTiffReader(parent=self)
try:
opReader.Filepath.setValue(filename)
except RuntimeError as e:
logger.error(str(e))
raise OpTiffSequenceReader.FileOpenError(file_paths[0])
else:
stacker_slot.connect(opReader.Output)
self._readers.append(opReader)
def test_basic(self):
opSource = OpArrayPiper(graph=self.graph)
opSource.Input.setValue(self.testData)
opData = OpArrayCache(graph=self.graph)
opData.blockShape.setValue(self.testData.shape)
opData.Input.connect(opSource.Output)
filepath = os.path.join(self._tmpdir, 'multipage.tiff')
logger.debug("writing to: {}".format(filepath))
opExport = OpExportMultipageTiff(graph=self.graph)
opExport.Filepath.setValue(filepath)
opExport.Input.connect(opData.Output)
# Run the export
opExport.run_export()
opReader = OpTiffReader(graph=self.graph)
try:
opReader.Filepath.setValue(filepath)
# Re-order before comparing
opReorderAxes = OpReorderAxes(graph=self.graph)
try:
opReorderAxes.AxisOrder.setValue(self._axisorder)
opReorderAxes.Input.connect(opReader.Output)
readData = opReorderAxes.Output[:].wait()
logger.debug("Expected shape={}".format(self.testData.shape))
logger.debug("Read shape={}".format(readData.shape))
assert opReorderAxes.Output.meta.shape == self.testData.shape, \
"Exported files were of the wrong shape or number."
assert (opReorderAxes.Output[:].wait() == self.testData.view( numpy.ndarray )).all(), \
"Exported data was not correct"
finally:
opReorderAxes.cleanUp()
finally:
opReader.cleanUp()
def test_basic(self):
opSource = OpArrayPiper(graph=self.graph)
opSource.Input.setValue( self.testData )
opData = OpArrayCache( graph=self.graph )
opData.blockShape.setValue( self.testData.shape )
opData.Input.connect( opSource.Output )
filepath = os.path.join( self._tmpdir, 'multipage.tiff' )
logger.debug( "writing to: {}".format(filepath) )
opExport = OpExportMultipageTiff(graph=self.graph)
opExport.Filepath.setValue( filepath )
opExport.Input.connect( opData.Output )
# Run the export
opExport.run_export()
opReader = OpTiffReader( graph=self.graph )
try:
opReader.Filepath.setValue( filepath )
# Re-order before comparing
opReorderAxes = OpReorderAxes( graph=self.graph )
try:
opReorderAxes.AxisOrder.setValue( self._axisorder )
opReorderAxes.Input.connect( opReader.Output )
readData = opReorderAxes.Output[:].wait()
logger.debug("Expected shape={}".format( self.testData.shape ) )
logger.debug("Read shape={}".format( readData.shape ) )
assert opReorderAxes.Output.meta.shape == self.testData.shape, \
"Exported files were of the wrong shape or number."
assert (opReorderAxes.Output[:].wait() == self.testData.view( numpy.ndarray )).all(), \
"Exported data was not correct"
finally:
opReorderAxes.cleanUp()
finally:
opReader.cleanUp()