Пример #1
0
    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
Пример #2
0
    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