def execute(self, slot, subindex, rroi, result):
self.progressSignal(0)
# Save the axistags as a dataset attribute
self.d.attrs['axistags'] = self.Image.meta.axistags.toJSON()
def handle_block_result(roi, data):
slicing = roiToSlice(*roi)
if data.flags.c_contiguous:
self.d.write_direct(data.view(numpy.ndarray), dest_sel=slicing)
else:
self.d[slicing] = data
batch_size = None
if self.BatchSize.ready():
batch_size = self.BatchSize.value
requester = BigRequestStreamer(self.Image,
roiFromShape(self.Image.meta.shape),
batchSize=batch_size)
requester.resultSignal.subscribe(handle_block_result)
requester.progressSignal.subscribe(self.progressSignal)
requester.execute()
# Be paranoid: Flush right now.
self.f.file.flush()
# We're finished.
result[0] = True
self.progressSignal(100)
def execute(self, slot, subindex, rroi, result):
self.progressSignal(0)
# Save the axistags as a dataset attribute
self.d.attrs['axistags'] = self.Image.meta.axistags.toJSON()
def handle_block_result(roi, data):
slicing = roiToSlice(*roi)
if data.flags.c_contiguous:
self.d.write_direct(data.view(numpy.ndarray), dest_sel=slicing)
else:
self.d[slicing] = data
batch_size = None
if self.BatchSize.ready():
batch_size = self.BatchSize.value
requester = BigRequestStreamer( self.Image, roiFromShape( self.Image.meta.shape ), batchSize=batch_size )
requester.resultSignal.subscribe( handle_block_result )
requester.progressSignal.subscribe( self.progressSignal )
requester.execute()
# Be paranoid: Flush right now.
self.f.file.flush()
# We're finished.
result[0] = True
self.progressSignal(100)
def run_export(self):
"""
Request the volume in slices (running in parallel), and write each slice to a separate image.
"""
# Make the directory first if necessary
export_dir = os.path.split(self.FilepathPattern.value)[0]
if not os.path.exists(export_dir):
os.makedirs(export_dir)
# Sliceshape is the same as the input shape, except for the sliced dimension
tagged_sliceshape = self.Input.meta.getTaggedShape()
tagged_sliceshape[self._volume_axes[0]] = 1
slice_shape = (tagged_sliceshape.values())
# Use a request streamer to automatically request a constant batch of 4 active requests.
streamer = BigRequestStreamer( self.Input,
roiFromShape( self.Input.meta.shape ),
slice_shape,
batchSize=4 )
# Write the slices as they come in (possibly out-of-order, but probably not.
streamer.resultSignal.subscribe( self._write_slice )
streamer.progressSignal.subscribe( self.progressSignal )
logger.debug("Starting Stack Export with slicing shape: {}".format( slice_shape ))
streamer.execute()
def run_export(self):
"""
Request the volume in slices (running in parallel), and write each slice to a separate image.
"""
# Make the directory first if necessary
export_dir = os.path.split(self.FilepathPattern.value)[0]
if not os.path.exists(export_dir):
os.makedirs(export_dir)
# Sliceshape is the same as the input shape, except for the sliced dimension
tagged_sliceshape = self.Input.meta.getTaggedShape()
tagged_sliceshape[self._volume_axes[0]] = 1
slice_shape = (tagged_sliceshape.values())
# Use a request streamer to automatically request a constant batch of 4 active requests.
streamer = BigRequestStreamer( self.Input,
roiFromShape( self.Input.meta.shape ),
slice_shape,
batchSize=4 )
# Write the slices as they come in (possibly out-of-order, but probably not.
streamer.resultSignal.subscribe( self._write_slice )
streamer.progressSignal.subscribe( self.progressSignal )
logger.debug("Starting Stack Export with slicing shape: {}".format( slice_shape ))
streamer.execute()
def run_export(self):
"""
Request the volume in slices (running in parallel), and write each slice to a separate image.
"""
# Make the directory first if necessary
export_dir = os.path.split(self.FilepathPattern.value)[0]
if not os.path.exists(export_dir):
os.makedirs(export_dir)
# Sliceshape is the same as the input shape, except for the sliced dimension
tagged_sliceshape = self.Input.meta.getTaggedShape()
tagged_sliceshape[self._volume_axes[0]] = 1
slice_shape = (list(tagged_sliceshape.values()))
parallel_requests = 4
# If ram usage info is available, make a better guess about how many requests we can launch in parallel
ram_usage_per_requested_pixel = self.Input.meta.ram_usage_per_requested_pixel
if ram_usage_per_requested_pixel is not None:
pixels_per_slice = numpy.prod(slice_shape)
if 'c' in tagged_sliceshape:
pixels_per_slice //= tagged_sliceshape['c']
ram_usage_per_slice = pixels_per_slice * ram_usage_per_requested_pixel
# Fudge factor: Reduce RAM usage by a bit
available_ram = psutil.virtual_memory().available
available_ram *= 0.5
parallel_requests = int(available_ram // ram_usage_per_slice)
if parallel_requests < 1:
raise MemoryError(
'Not enough RAM to export to the selected format. '
'Consider exporting to hdf5 (h5).'
)
streamer = BigRequestStreamer( self.Input,
roiFromShape( self.Input.meta.shape ),
slice_shape,
parallel_requests )
# Write the slices as they come in (possibly out-of-order, but probably not)
streamer.resultSignal.subscribe( self._write_slice )
streamer.progressSignal.subscribe( self.progressSignal )
logger.debug("Starting Stack Export with slicing shape: {}".format( slice_shape ))
streamer.execute()
def run_export(self):
"""
Request the volume in slices (running in parallel), and write each slice to a separate image.
"""
# Make the directory first if necessary
export_dir = os.path.split(self.FilepathPattern.value)[0]
if not os.path.exists(export_dir):
os.makedirs(export_dir)
# Sliceshape is the same as the input shape, except for the sliced dimension
tagged_sliceshape = self.Input.meta.getTaggedShape()
tagged_sliceshape[self._volume_axes[0]] = 1
slice_shape = list(tagged_sliceshape.values())
parallel_requests = 4
# If ram usage info is available, make a better guess about how many requests we can launch in parallel
ram_usage_per_requested_pixel = self.Input.meta.ram_usage_per_requested_pixel
if ram_usage_per_requested_pixel is not None:
pixels_per_slice = numpy.prod(slice_shape)
if "c" in tagged_sliceshape:
pixels_per_slice //= tagged_sliceshape["c"]
ram_usage_per_slice = pixels_per_slice * ram_usage_per_requested_pixel
# Fudge factor: Reduce RAM usage by a bit
available_ram = psutil.virtual_memory().available
available_ram *= 0.5
parallel_requests = int(available_ram // ram_usage_per_slice)
if parallel_requests < 1:
raise MemoryError(
"Not enough RAM to export to the selected format. " "Consider exporting to hdf5 (h5)."
)
streamer = BigRequestStreamer(self.Input, roiFromShape(self.Input.meta.shape), slice_shape, parallel_requests)
# Write the slices as they come in (possibly out-of-order, but probably not)
streamer.resultSignal.subscribe(self._write_slice)
streamer.progressSignal.subscribe(self.progressSignal)
logger.debug(f"Starting Stack Export with slicing shape: {slice_shape}")
streamer.execute()
def execute(self, slot, subindex, rroi, result):
self.progressSignal(0)
# Save the axistags as a dataset attribute
self.d.attrs["axistags"] = self.Image.meta.axistags.toJSON()
if isinstance(self.d, h5py.Dataset):
for index, tag in enumerate(self.Image.meta.axistags):
self.d.dims[index].label = tag.key
else: # if n5 dataset, apply neuroglancer's axes tags convention
self.d.attrs["axes"] = "".join(
tag.key for tag in self.Image.meta.axistags)[::-1]
drange = self.Image.meta.get("drange")
if drange:
self.d.attrs["drange"] = drange
def handle_block_result(roi, data):
slicing = roiToSlice(*roi)
if data.flags.c_contiguous:
self.d.write_direct(data.view(numpy.ndarray), dest_sel=slicing)
else:
self.d[slicing] = data
batch_size = None
if self.BatchSize.ready():
batch_size = self.BatchSize.value
requester = BigRequestStreamer(self.Image,
roiFromShape(self.Image.meta.shape),
batchSize=batch_size)
requester.resultSignal.subscribe(handle_block_result)
requester.progressSignal.subscribe(self.progressSignal)
requester.execute()
# Be paranoid: Flush right now.
if isinstance(self.f, h5py.File):
self.f.file.flush() # not available in z5py
# We're finished.
result[0] = True
self.progressSignal(100)