def init_reader(self):
mdoptions = metadatatools.get_metadata_options(metadatatools.ALL)
self.rdr.setMetadataOptions(mdoptions)
self.rdr.setGroupFiles(False)
self.metadata = metadatatools.createOMEXMLMetadata()
self.rdr.setMetadataStore(self.metadata)
try:
self.rdr.setId(self.path)
except jutil.JavaException as e:
# logger.warn(e.message)
# for line in traceback.format_exc().split("\n"):
# logger.warn(line)
je = e.throwable
if has_omero_packages() and jutil.is_instance_of(
je, "Glacier2/PermissionDeniedException"):
# Handle at a higher level
raise
if jutil.is_instance_of(je, "loci/formats/FormatException"):
# je = jutil.call(je, "getCause",
# "()Ljava/lang/Throwable;")
# Handle at a higher level
raise
if jutil.is_instance_of(je, "java/io/FileNotFoundException"):
raise IOError(errno.ENOENT,
"The file, \"%s\", does not exist." % self.path,
self.path)
e2 = IOError(
errno.EINVAL,
"Could not load the file as an image (see log for details)",
self.path.encode('utf-8'))
raise e2
def __load_using_bioformats(path, c, z, t, series, index, rescale,
wants_max_intensity, channel_names):
FormatTools = make_format_tools_class()
ImageReader = make_image_reader_class()
ChannelSeparator = make_reader_wrapper_class(
"loci/formats/ChannelSeparator")
#
# Bioformats is more picky about slashes than Python
#
if sys.platform.startswith("win"):
path = path.replace("/", os.path.sep)
#
# Bypass the ImageReader and scroll through the class list. The
# goal here is to ask the FormatHandler if it thinks it could
# possibly parse the file, then only give the FormatReader access
# to the open file stream so it can't damage the file server.
#
# Pass 0 - allow access to stream if reader believes it is the correct
# reader no matter what the file contents.
# Pass 1 - allow access to stream if reader indicates that it supports
# files with this file's suffix.
# Pass 2 - allow all readers access to the stream
#
env = jutil.get_env()
with GetImageReader(path) as rdr:
mdoptions = metadatatools.get_metadata_options(metadatatools.ALL)
rdr.setMetadataOptions(mdoptions)
rdr.setGroupFiles(False)
metadata = metadatatools.createOMEXMLMetadata()
rdr.setMetadataStore(metadata)
rdr.setId(path)
width = rdr.getSizeX()
height = rdr.getSizeY()
pixel_type = rdr.getPixelType()
little_endian = rdr.isLittleEndian()
if pixel_type == FormatTools.INT8:
dtype = np.char
scale = 255
elif pixel_type == FormatTools.UINT8:
dtype = np.uint8
scale = 255
elif pixel_type == FormatTools.UINT16:
dtype = '<u2' if little_endian else '>u2'
scale = 65535
elif pixel_type == FormatTools.INT16:
dtype = '<i2' if little_endian else '>i2'
scale = 65535
elif pixel_type == FormatTools.UINT32:
dtype = '<u4' if little_endian else '>u4'
scale = 2**32
elif pixel_type == FormatTools.INT32:
dtype = '<i4' if little_endian else '>i4'
scale = 2**32 - 1
elif pixel_type == FormatTools.FLOAT:
dtype = '<f4' if little_endian else '>f4'
scale = 1
elif pixel_type == FormatTools.DOUBLE:
dtype = '<f8' if little_endian else '>f8'
scale = 1
max_sample_value = rdr.getMetadataValue('MaxSampleValue')
if max_sample_value is not None:
try:
scale = jutil.call(max_sample_value, 'intValue', '()I')
except:
bioformats.logger.warning(
"WARNING: failed to get MaxSampleValue for image. Intensities may be improperly scaled."
)
if series is not None:
rdr.setSeries(series)
if index is not None:
image = np.frombuffer(rdr.openBytes(index), dtype)
if len(image) / height / width in (3, 4):
n_channels = int(len(image) / height / width)
if rdr.isInterleaved():
image.shape = (height, width, n_channels)
else:
image.shape = (n_channels, height, width)
image = image.transpose(1, 2, 0)
else:
image.shape = (height, width)
elif rdr.isRGB() and rdr.isInterleaved():
index = rdr.getIndex(z, 0, t)
image = np.frombuffer(rdr.openBytes(index), dtype)
image.shape = (height, width, 3)
elif c is not None and rdr.getRGBChannelCount() == 1:
index = rdr.getIndex(z, c, t)
image = np.frombuffer(rdr.openBytes(index), dtype)
image.shape = (height, width)
elif rdr.getRGBChannelCount() > 1:
n_planes = rdr.getRGBChannelCount()
rdr = ChannelSeparator(rdr)
planes = [
np.frombuffer(rdr.openBytes(rdr.getIndex(z, i, t)), dtype)
for i in range(n_planes)
]
if len(planes) > 3:
planes = planes[:3]
elif len(planes) < 3:
# > 1 and < 3 means must be 2
# see issue #775
planes.append(np.zeros(planes[0].shape, planes[0].dtype))
image = np.dstack(planes)
image.shape = (height, width, 3)
elif rdr.getSizeC() > 1:
images = [
np.frombuffer(rdr.openBytes(rdr.getIndex(z, i, t)), dtype)
for i in range(rdr.getSizeC())
]
image = np.dstack(images)
image.shape = (height, width, rdr.getSizeC())
if not channel_names is None:
metadata = metadatatools.MetadataRetrieve(metadata)
for i in range(rdr.getSizeC()):
index = rdr.getIndex(z, 0, t)
channel_name = metadata.getChannelName(index, i)
if channel_name is None:
channel_name = metadata.getChannelID(index, i)
channel_names.append(channel_name)
elif rdr.isIndexed():
#
# The image data is indexes into a color lookup-table
# But sometimes the table is the identity table and just generates
# a monochrome RGB image
#
index = rdr.getIndex(z, 0, t)
image = np.frombuffer(rdr.openBytes(index), dtype)
if pixel_type in (FormatTools.INT16, FormatTools.UINT16):
lut = rdr.get16BitLookupTable()
lut = np.array([
env.get_short_array_elements(d)
for d in env.get_object_array_elements(lut)
]).transpose()
else:
lut = rdr.get8BitLookupTable()
lut = np.array([
env.get_byte_array_elements(d)
for d in env.get_object_array_elements(lut)
]).transpose()
image.shape = (height, width)
if not np.all(lut == np.arange(lut.shape[0])[:, np.newaxis]):
image = lut[image, :]
else:
index = rdr.getIndex(z, 0, t)
image = np.frombuffer(rdr.openBytes(index), dtype)
image.shape = (height, width)
rdr.close()
if rescale:
image = image.astype(np.float32) / float(scale)
if wants_max_intensity:
return image, scale
return image
def fn(path=path, c=c, z=z, t=t, series=series, index=index,
rescale=rescale, wants_max_intensity=wants_max_intensity,
channel_names=channel_names):
FormatTools = make_format_tools_class()
ImageReader = make_image_reader_class()
ChannelSeparator = make_reader_wrapper_class(
"loci/formats/ChannelSeparator")
#
# Bioformats is more picky about slashes than Python
#
if sys.platform.startswith("win"):
path = path.replace("/",os.path.sep)
#
# Bypass the ImageReader and scroll through the class list. The
# goal here is to ask the FormatHandler if it thinks it could
# possibly parse the file, then only give the FormatReader access
# to the open file stream so it can't damage the file server.
#
env = jutil.get_env()
class_list = get_class_list()
stream = jutil.make_instance('loci/common/RandomAccessInputStream',
'(Ljava/lang/String;)V', path)
filename = os.path.split(path)[1]
IFormatReader = make_iformat_reader_class()
rdr = None
for klass in env.get_object_array_elements(class_list.get_classes()):
wclass = jutil.get_class_wrapper(klass, True)
maybe_rdr = IFormatReader()
maybe_rdr.o = wclass.newInstance()
maybe_rdr.setGroupFiles(False)
if maybe_rdr.suffixNecessary:
if not maybe_rdr.isThisTypeSZ(filename, False):
continue
if maybe_rdr.suffixSufficient:
rdr = maybe_rdr
break
if (maybe_rdr.isThisTypeStream(stream)):
rdr = maybe_rdr
break
if rdr is None:
raise ValueError("Could not find a Bio-Formats reader for %s", path)
mdoptions = metadatatools.get_metadata_options(metadatatools.ALL)
rdr.setMetadataOptions(mdoptions)
metadata = metadatatools.createOMEXMLMetadata()
rdr.setMetadataStore(metadata)
rdr.setId(path)
width = rdr.getSizeX()
height = rdr.getSizeY()
pixel_type = rdr.getPixelType()
little_endian = rdr.isLittleEndian()
if pixel_type == FormatTools.INT8:
dtype = np.char
scale = 255
elif pixel_type == FormatTools.UINT8:
dtype = np.uint8
scale = 255
elif pixel_type == FormatTools.UINT16:
dtype = '<u2' if little_endian else '>u2'
scale = 65535
elif pixel_type == FormatTools.INT16:
dtype = '<i2' if little_endian else '>i2'
scale = 65535
elif pixel_type == FormatTools.UINT32:
dtype = '<u4' if little_endian else '>u4'
scale = 2**32
elif pixel_type == FormatTools.INT32:
dtype = '<i4' if little_endian else '>i4'
scale = 2**32-1
elif pixel_type == FormatTools.FLOAT:
dtype = '<f4' if little_endian else '>f4'
scale = 1
elif pixel_type == FormatTools.DOUBLE:
dtype = '<f8' if little_endian else '>f8'
scale = 1
max_sample_value = rdr.getMetadataValue('MaxSampleValue')
if max_sample_value is not None:
try:
scale = jutil.call(max_sample_value, 'intValue', '()I')
except:
bioformats.logger.warning("WARNING: failed to get MaxSampleValue for image. Intensities may be improperly scaled.")
if series is not None:
rdr.setSeries(series)
if index is not None:
image = np.frombuffer(rdr.openBytes(index), dtype)
if len(image) / height / width in (3,4):
image.shape = (height, width, int(len(image) / height / width))
else:
image.shape = (height, width)
elif rdr.isRGB() and rdr.isInterleaved():
index = rdr.getIndex(z,0,t)
image = np.frombuffer(rdr.openBytes(index), dtype)
image.shape = (height, width, 3)
elif c is not None and rdr.getRGBChannelCount() == 1:
index = rdr.getIndex(z,c,t)
image = np.frombuffer(rdr.openBytes(index), dtype)
image.shape = (height, width)
elif rdr.getRGBChannelCount() > 1:
rdr.close()
rdr = ImageReader()
rdr.allowOpenToCheckType(False)
rdr = ChannelSeparator(rdr)
rdr.setGroupFiles(False)
rdr.setId(path)
red_image, green_image, blue_image = [
np.frombuffer(rdr.openBytes(rdr.getIndex(z,i,t)),dtype)
for i in range(3)]
image = np.dstack((red_image, green_image, blue_image))
image.shape=(height,width,3)
elif rdr.getSizeC() > 1:
images = [np.frombuffer(rdr.openBytes(rdr.getIndex(z,i,t)), dtype)
for i in range(rdr.getSizeC())]
image = np.dstack(images)
image.shape = (height, width, rdr.getSizeC())
if not channel_names is None:
metadata = metadatatools.MetadataRetrieve(metadata)
for i in range(rdr.getSizeC()):
index = rdr.getIndex(z, 0, t)
channel_name = metadata.getChannelName(index, i)
if channel_name is None:
channel_name = metadata.getChannelID(index, i)
channel_names.append(channel_name)
else:
index = rdr.getIndex(z,0,t)
image = np.frombuffer(rdr.openBytes(index),dtype)
image.shape = (height,width)
rdr.close()
jutil.call(stream, 'close', '()V')
del rdr
#
# Run the Java garbage collector here.
#
jutil.static_call("java/lang/System", "gc","()V")
if rescale:
image = image.astype(np.float32) / float(scale)
if wants_max_intensity:
return image, scale
return image
def __load_using_bioformats(path, c, z, t, series, index, rescale,
wants_max_intensity, channel_names):
FormatTools = make_format_tools_class()
ImageReader = make_image_reader_class()
ChannelSeparator = make_reader_wrapper_class(
"loci/formats/ChannelSeparator")
#
# Bioformats is more picky about slashes than Python
#
if sys.platform.startswith("win"):
path = path.replace("/",os.path.sep)
#
# Bypass the ImageReader and scroll through the class list. The
# goal here is to ask the FormatHandler if it thinks it could
# possibly parse the file, then only give the FormatReader access
# to the open file stream so it can't damage the file server.
#
# Pass 0 - allow access to stream if reader believes it is the correct
# reader no matter what the file contents.
# Pass 1 - allow access to stream if reader indicates that it supports
# files with this file's suffix.
# Pass 2 - allow all readers access to the stream
#
env = jutil.get_env()
with GetImageReader(path) as rdr:
mdoptions = metadatatools.get_metadata_options(metadatatools.ALL)
rdr.setMetadataOptions(mdoptions)
rdr.setGroupFiles(False)
metadata = metadatatools.createOMEXMLMetadata()
rdr.setMetadataStore(metadata)
rdr.setId(path)
if series is not None:
rdr.setSeries(series)
width = rdr.getSizeX()
height = rdr.getSizeY()
pixel_type = rdr.getPixelType()
little_endian = rdr.isLittleEndian()
if pixel_type == FormatTools.INT8:
dtype = np.char
scale = 255
elif pixel_type == FormatTools.UINT8:
dtype = np.uint8
scale = 255
elif pixel_type == FormatTools.UINT16:
dtype = '<u2' if little_endian else '>u2'
scale = 65535
elif pixel_type == FormatTools.INT16:
dtype = '<i2' if little_endian else '>i2'
scale = 65535
elif pixel_type == FormatTools.UINT32:
dtype = '<u4' if little_endian else '>u4'
scale = 2**32
elif pixel_type == FormatTools.INT32:
dtype = '<i4' if little_endian else '>i4'
scale = 2**32-1
elif pixel_type == FormatTools.FLOAT:
dtype = '<f4' if little_endian else '>f4'
scale = 1
elif pixel_type == FormatTools.DOUBLE:
dtype = '<f8' if little_endian else '>f8'
scale = 1
max_sample_value = rdr.getMetadataValue('MaxSampleValue')
if max_sample_value is not None:
try:
scale = jutil.call(max_sample_value, 'intValue', '()I')
except:
bioformats.logger.warning("WARNING: failed to get MaxSampleValue for image. Intensities may be improperly scaled.")
if index is not None:
image = np.frombuffer(rdr.openBytes(index), dtype)
if len(image) / height / width in (3,4):
n_channels = int(len(image) / height / width)
if rdr.isInterleaved():
image.shape = (height, width, n_channels)
else:
image.shape = (n_channels, height, width)
image = image.transpose(1, 2, 0)
else:
image.shape = (height, width)
elif rdr.isRGB() and rdr.isInterleaved():
index = rdr.getIndex(z,0,t)
image = np.frombuffer(rdr.openBytes(index), dtype)
image.shape = (height, width, 3)
elif c is not None and rdr.getRGBChannelCount() == 1:
index = rdr.getIndex(z,c,t)
image = np.frombuffer(rdr.openBytes(index), dtype)
image.shape = (height, width)
elif rdr.getRGBChannelCount() > 1:
n_planes = rdr.getRGBChannelCount()
rdr = ChannelSeparator(rdr)
planes = [
np.frombuffer(rdr.openBytes(rdr.getIndex(z,i,t)),dtype)
for i in range(n_planes)]
if len(planes) > 3:
planes = planes[:3]
elif len(planes) < 3:
# > 1 and < 3 means must be 2
# see issue #775
planes.append(np.zeros(planes[0].shape, planes[0].dtype))
image = np.dstack(planes)
image.shape=(height,width,3)
elif rdr.getSizeC() > 1:
images = [np.frombuffer(rdr.openBytes(rdr.getIndex(z,i,t)), dtype)
for i in range(rdr.getSizeC())]
image = np.dstack(images)
image.shape = (height, width, rdr.getSizeC())
if not channel_names is None:
metadata = metadatatools.MetadataRetrieve(metadata)
for i in range(rdr.getSizeC()):
index = rdr.getIndex(z, 0, t)
channel_name = metadata.getChannelName(index, i)
if channel_name is None:
channel_name = metadata.getChannelID(index, i)
channel_names.append(channel_name)
elif rdr.isIndexed():
#
# The image data is indexes into a color lookup-table
# But sometimes the table is the identity table and just generates
# a monochrome RGB image
#
index = rdr.getIndex(z,0,t)
image = np.frombuffer(rdr.openBytes(index),dtype)
if pixel_type in (FormatTools.INT16, FormatTools.UINT16):
lut = rdr.get16BitLookupTable()
lut = np.array(
[env.get_short_array_elements(d)
for d in env.get_object_array_elements(lut)]).transpose()
else:
lut = rdr.get8BitLookupTable()
lut = np.array(
[env.get_byte_array_elements(d)
for d in env.get_object_array_elements(lut)]).transpose()
image.shape = (height, width)
if not np.all(lut == np.arange(lut.shape[0])[:, np.newaxis]):
image = lut[image, :]
else:
index = rdr.getIndex(z,0,t)
image = np.frombuffer(rdr.openBytes(index),dtype)
image.shape = (height,width)
rdr.close()
if rescale:
image = image.astype(np.float32) / float(scale)
if wants_max_intensity:
return image, scale
return image
