How to use the tifffile.TiffSequence._ParseError function in tifffile

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github flika-org / flika / tifffile.py View on Github external
def _parse(self):
        """Get axes and shape from file names."""
        if not self.pattern:
            raise self._ParseError("invalid pattern")
        pattern = re.compile(self.pattern, re.IGNORECASE | re.VERBOSE)
        matches = pattern.findall(self.files[0])
        if not matches:
            raise self._ParseError("pattern doesn't match file names")
        matches = matches[-1]
        if len(matches) % 2:
            raise self._ParseError("pattern doesn't match axis name and index")
        axes = ''.join(m for m in matches[::2] if m)
        if not axes:
            raise self._ParseError("pattern doesn't match file names")

        indices = []
        for fname in self.files:
            matches = pattern.findall(fname)[-1]
            if axes != ''.join(m for m in matches[::2] if m):
                raise ValueError("axes don't match within the image sequence")
            indices.append([int(m) for m in matches[1::2] if m])
        shape = tuple(numpy.max(indices, axis=0))
        start_index = tuple(numpy.min(indices, axis=0))
        shape = tuple(i-j+1 for i, j in zip(shape, start_index))
        if numpy.prod(shape) != len(self.files):
            warnings.warn("files are missing. Missing data are zeroed")

        self.axes = axes.upper()
        self.shape = shape
        self._indices = indices
github flika-org / flika / tifffile.py View on Github external
def _parse(self):
        """Get axes and shape from file names."""
        if not self.pattern:
            raise self._ParseError("invalid pattern")
        pattern = re.compile(self.pattern, re.IGNORECASE | re.VERBOSE)
        matches = pattern.findall(self.files[0])
        if not matches:
            raise self._ParseError("pattern doesn't match file names")
        matches = matches[-1]
        if len(matches) % 2:
            raise self._ParseError("pattern doesn't match axis name and index")
        axes = ''.join(m for m in matches[::2] if m)
        if not axes:
            raise self._ParseError("pattern doesn't match file names")

        indices = []
        for fname in self.files:
            matches = pattern.findall(fname)[-1]
            if axes != ''.join(m for m in matches[::2] if m):
                raise ValueError("axes don't match within the image sequence")
            indices.append([int(m) for m in matches[1::2] if m])
        shape = tuple(numpy.max(indices, axis=0))
        start_index = tuple(numpy.min(indices, axis=0))
        shape = tuple(i-j+1 for i, j in zip(shape, start_index))
github flika-org / flika / tifffile.py View on Github external
def _parse(self):
        """Get axes and shape from file names."""
        if not self.pattern:
            raise self._ParseError("invalid pattern")
        pattern = re.compile(self.pattern, re.IGNORECASE | re.VERBOSE)
        matches = pattern.findall(self.files[0])
        if not matches:
            raise self._ParseError("pattern doesn't match file names")
        matches = matches[-1]
        if len(matches) % 2:
            raise self._ParseError("pattern doesn't match axis name and index")
        axes = ''.join(m for m in matches[::2] if m)
        if not axes:
            raise self._ParseError("pattern doesn't match file names")

        indices = []
        for fname in self.files:
            matches = pattern.findall(fname)[-1]
            if axes != ''.join(m for m in matches[::2] if m):
                raise ValueError("axes don't match within the image sequence")
github flika-org / flika / tifffile.py View on Github external
def _parse(self):
        """Get axes and shape from file names."""
        if not self.pattern:
            raise self._ParseError("invalid pattern")
        pattern = re.compile(self.pattern, re.IGNORECASE | re.VERBOSE)
        matches = pattern.findall(self.files[0])
        if not matches:
            raise self._ParseError("pattern doesn't match file names")
        matches = matches[-1]
        if len(matches) % 2:
            raise self._ParseError("pattern doesn't match axis name and index")
        axes = ''.join(m for m in matches[::2] if m)
        if not axes:
            raise self._ParseError("pattern doesn't match file names")

        indices = []
        for fname in self.files:
            matches = pattern.findall(fname)[-1]
            if axes != ''.join(m for m in matches[::2] if m):
                raise ValueError("axes don't match within the image sequence")
            indices.append([int(m) for m in matches[1::2] if m])
        shape = tuple(numpy.max(indices, axis=0))
        start_index = tuple(numpy.min(indices, axis=0))
        shape = tuple(i-j+1 for i, j in zip(shape, start_index))
        if numpy.prod(shape) != len(self.files):
            warnings.warn("files are missing. Missing data are zeroed")