from pims import FramesSequenceND, Frame from nd2reader.exceptions import NoImageError from nd2reader.parser import Parser class ND2Reader(FramesSequenceND): """ PIMS wrapper for the ND2 parser """ def __init__(self, filename): self.filename = filename # first use the parser to parse the file self._fh = open(filename, "rb") self._parser = Parser(self._fh) # Setup metadata self.metadata = self._parser.metadata # Set data type self._dtype = self._parser.get_dtype_from_metadata() # Setup the axes self._setup_axes() @classmethod def class_exts(cls): """ So PIMS open function can use this reader for opening .nd2 files :return: """ return {'nd2'} | super(ND2Reader, cls).class_exts() def close(self): """ Correctly close the file handle :return: """ if self._fh is not None: self._fh.close() def get_frame_2D(self, c, t, z): """ Gets a given frame using the parser :param c: :param t: :param z: :return: """ c_name = self.metadata["channels"][c] try: image = self._parser.get_image_by_attributes(t, 0, c_name, z, self.metadata["width"], self.metadata["height"]) except (TypeError, NoImageError): return Frame([]) else: return image @property def pixel_type(self): """ Return the pixel data type :return: """ return self._dtype def _setup_axes(self): """ Setup the xyctz axes, iterate over t axis by default :return: """ self._init_axis('x', self.metadata["width"]) self._init_axis('y', self.metadata["height"]) self._init_axis('c', len(self.metadata["channels"])) self._init_axis('t', len(self.metadata["frames"])) self._init_axis('z', len(self.metadata["z_levels"])) # provide the default self.iter_axes = 't'