def read(self, fname, frame=None):
"""
Wrapper for TiffIO.
"""
infile = self._open(fname, "rb")
self._readheader(infile)
infile.seek(0)
self.lib = None
try:
tiffIO = TiffIO(infile)
if tiffIO.getNumberOfImages() > 0:
# No support for now of multi-frame tiff images
self.data = tiffIO.getImage(0)
self.header = tiffIO.getInfo(0)
except Exception as error:
logger.warning("Unable to read %s with TiffIO due to %s, trying PIL" % (fname, error))
else:
if self.data.ndim == 2:
self.dim2, self.dim1 = self.data.shape
elif self.data.ndim == 3:
self.dim2, self.dim1, ncol = self.data.shape
logger.warning("Third dimension is the color")
else:
logger.warning("dataset has %s dimensions (%s), check for errors !!!!", self.data.ndim, self.data.shape)
self.lib = "TiffIO"
if self.lib is None:
if Image:
try:
infile.seek(0)
self.pilimage = Image.open(infile)
except Exception:
logger.error("Error in opening %s with PIL" % fname)
self.lib = None
infile.seek(0)
else:
self.lib = "PIL"
self.dim1, self.dim2 = self.pilimage.size
if self.pilimage.mode in PIL_TO_NUMPY:
self.data = numpy.fromstring(self.pilimage.tostring(), PIL_TO_NUMPY[self.pilimage.mode])
else: # probably RGB or RGBA images: rely on PIL to convert it to greyscale float.
self.data = numpy.fromstring(self.pilimage.convert("F").tostring(), numpy.float32)
self.data.shape = (self.dim2, self.dim1)
else:
logger.error("Error in opening %s: no tiff reader managed to read the file.", fname)
self.lib = None
infile.seek(0)
self.bpp = len(numpy.zeros(1, dtype=self.data.dtype).tostring())
self.bytecode = self.data.dtype.name
self.resetvals()
return self
def read(self, fname, frame=None):
"""
Wrapper for TiffIO.
"""
infile = self._open(fname, "rb")
self._readheader(infile)
infile.seek(0)
self.lib = None
try:
tiffIO = TiffIO(infile)
if tiffIO.getNumberOfImages() > 0:
# No support for now of multi-frame tiff images
self.data = tiffIO.getImage(0)
self.header = tiffIO.getInfo(0)
except Exception as error:
logger.warning("Unable to read %s with TiffIO due to %s, trying PIL" % (fname, error))
else:
if self.data.ndim == 2:
self.dim2, self.dim1 = self.data.shape
elif self.data.ndim == 3:
self.dim2, self.dim1, ncol = self.data.shape
logger.warning("Third dimension is the color")
else:
logger.warning("dataset has %s dimensions (%s), check for errors !!!!", self.data.ndim, self.data.shape)
self.lib = "TiffIO"
if (self.lib is None):
if Image:
try:
infile.seek(0)
self.pilimage = Image.open(infile)
except Exception:
logger.error("Error in opening %s with PIL" % fname)
self.lib = None
infile.seek(0)
else:
self.lib = "PIL"
dim1, dim2 = self.pilimage.size
if self.pilimage.mode in PIL_TO_NUMPY:
dtype = PIL_TO_NUMPY[self.pilimage.mode]
pilimage = self.pilimage
else:
dtype = numpy.float32
pilimage = self.pilimage.convert("F")
try:
data = numpy.asarray(pilimage, dtype)
except: # PIL does not support buffer interface (yet)
if "tobytes" in dir(pilimage):
data = numpy.fromstring(pilimage.tobytes(), dtype=dtype)
else:
data = numpy.fromstring(pilimage.tostring(), dtype=dtype)
# byteswap ?
if numpy.dtype(dtype).itemsize > 1:
if (numpy.little_endian and "B" in self.pilimage.mode) or\
(not numpy.little_endian and self.pilimage.mode.endswith("L")):
data.byteswap(True)
self.data = data.reshape((dim2, dim1))
else:
logger.error("Error in opening %s: no tiff reader managed to read the file.", fname)
self.lib = None
infile.seek(0)
self.resetvals()
return self