diff --git a/nd2reader/reader.py b/nd2reader/reader.py index 003f9a1..1a9e0c8 100644 --- a/nd2reader/reader.py +++ b/nd2reader/reader.py @@ -39,50 +39,18 @@ class ND2Reader(FramesSequenceND): if self._fh is not None: self._fh.close() - def get_frame(self, i): - """Return one frame + def _get_default(self, coord): + try: + return self.default_coords[coord] + except KeyError: + return 0 - Args: - i: The frame number - - Returns: - numpy.ndarray: The requested frame - - """ - fetch_all_channels = 'c' in self.bundle_axes - - if fetch_all_channels: - return self._get_frame_all_channels(i) - else: - return self.get_frame_2D(self.default_coords['c'], i, self.default_coords['z']) - - def _get_frame_all_channels(self, i): - """Get all color channels for this frame - - Args: - i: The frame number - - Returns: - numpy.ndarray: The requested frame, with all color channels. - - """ - frames = None - for c in range(len(self.metadata["channels"])): - try: - z = self.default_coords['z'] - except KeyError: - z = 0 - frame = self.get_frame_2D(c, i, z) - if frames is None: - frames = Frame([frame]) - else: - frames = np.concatenate((frames, [frame]), axis=0) - return frames - - def get_frame_2D(self, c, t, z): + def get_frame_2D(self, c=0, t=0, z=0, x=0, y=0): """Gets a given frame using the parser Args: + x: The x-index (pims expects this) + y: The y-index (pims expects this) c: The color channel number t: The frame number z: The z stack number @@ -92,7 +60,9 @@ class ND2Reader(FramesSequenceND): """ c_name = self.metadata["channels"][c] - return self._parser.get_image_by_attributes(t, 0, c_name, z, self.metadata["height"], self.metadata["width"]) + x = self.metadata["width"] if x <= 0 else x + y = self.metadata["height"] if y <= 0 else y + return self._parser.get_image_by_attributes(t, 0, c_name, z, y, x) @property def parser(self):