From 0b8ae27dde3ddbcc4896e76a33d3541702087c6c Mon Sep 17 00:00:00 2001 From: Gabriele Girelli Date: Mon, 31 Aug 2020 10:32:38 +0200 Subject: [PATCH] Allowed for fh to be either str or IO, and formatted with black. --- nd2reader/reader.py | 90 +++++++++++++++++++++++++++------------------ 1 file changed, 55 insertions(+), 35 deletions(-) diff --git a/nd2reader/reader.py b/nd2reader/reader.py index e711ca3..5e524eb 100644 --- a/nd2reader/reader.py +++ b/nd2reader/reader.py @@ -14,41 +14,46 @@ class ND2Reader(FramesSequenceND): class_priority = 12 def __init__(self, fh): + """ + Arguments: + fh {str} -- absolute path to .nd2 file + fh {IO} -- input buffer handler (opened with "rb" mode) + """ super(ND2Reader, self).__init__() - self._fh = fh - self.filename = "" + if isinstance(fh, str): + if not fh.endswith(".nd2"): + raise InvalidFileType( + ("The file %s you want to read with nd2reader" % fh) + + " does not have extension .nd2." + ) - self._parser = Parser(self._fh) + self = ND2Reader(open(fh, "rb")) + self.filename = fh + else: + self._fh = fh + self.filename = "" - # Setup metadata - self.metadata = self._parser.metadata + self._parser = Parser(self._fh) - # Set data type - self._dtype = self._parser.get_dtype_from_metadata() + # Setup metadata + self.metadata = self._parser.metadata - # Setup the axes - self._setup_axes() + # Set data type + self._dtype = self._parser.get_dtype_from_metadata() - # Other properties - self._timesteps = None + # Setup the axes + self._setup_axes() - @staticmethod - def from_file(filename): - if not filename.endswith(".nd2"): - raise InvalidFileType("The file %s you want to read with nd2reader does not have extension .nd2." % filename) + # Other properties + self._timesteps = None - nd2r = ND2Reader(open(filename, "rb")) - nd2r.filename = filename - - return nd2r - @classmethod def class_exts(cls): """Let PIMS open function use this reader for opening .nd2 files """ - return {'nd2'} | super(ND2Reader, cls).class_exts() + return {"nd2"} | super(ND2Reader, cls).class_exts() def close(self): """Correctly close the file handle @@ -125,22 +130,24 @@ class ND2Reader(FramesSequenceND): @property def frame_rate(self): """The (average) frame rate - + Returns: float: the (average) frame rate in frames per second """ total_duration = 0.0 - for loop in self.metadata['experiment']['loops']: - total_duration += loop['duration'] + for loop in self.metadata["experiment"]["loops"]: + total_duration += loop["duration"] if total_duration == 0: total_duration = self.timesteps[-1] if total_duration == 0: - raise ValueError('Total measurement duration could not be determined from loops') + raise ValueError( + "Total measurement duration could not be determined from loops" + ) - return self.metadata['num_frames'] / (total_duration/1000.0) + return self.metadata["num_frames"] / (total_duration / 1000.0) def _get_metadata_property(self, key, default=None): if self.metadata is None: @@ -158,12 +165,22 @@ class ND2Reader(FramesSequenceND): """Setup the xyctz axes, iterate over t axis by default """ - self._init_axis_if_exists('x', self._get_metadata_property("width", default=0)) - self._init_axis_if_exists('y', self._get_metadata_property("height", default=0)) - self._init_axis_if_exists('c', len(self._get_metadata_property("channels", default=[])), min_size=2) - self._init_axis_if_exists('t', len(self._get_metadata_property("frames", default=[]))) - self._init_axis_if_exists('z', len(self._get_metadata_property("z_levels", default=[])), min_size=2) - self._init_axis_if_exists('v', len(self._get_metadata_property("fields_of_view", default=[])), min_size=2) + self._init_axis_if_exists("x", self._get_metadata_property("width", default=0)) + self._init_axis_if_exists("y", self._get_metadata_property("height", default=0)) + self._init_axis_if_exists( + "c", len(self._get_metadata_property("channels", default=[])), min_size=2 + ) + self._init_axis_if_exists( + "t", len(self._get_metadata_property("frames", default=[])) + ) + self._init_axis_if_exists( + "z", len(self._get_metadata_property("z_levels", default=[])), min_size=2 + ) + self._init_axis_if_exists( + "v", + len(self._get_metadata_property("fields_of_view", default=[])), + min_size=2, + ) if len(self.sizes) == 0: raise EmptyFileError("No axes were found for this .nd2 file.") @@ -171,7 +188,7 @@ class ND2Reader(FramesSequenceND): # provide the default self.iter_axes = self._guess_default_iter_axis() - self._register_get_frame(self.get_frame_2D, 'yx') + self._register_get_frame(self.get_frame_2D, "yx") def _init_axis_if_exists(self, axis, size, min_size=1): if size >= min_size: @@ -183,7 +200,7 @@ class ND2Reader(FramesSequenceND): Returns: the axis to iterate over """ - priority = ['t', 'z', 'c', 'v'] + priority = ["t", "z", "c", "v"] found_axes = [] for axis in priority: try: @@ -208,6 +225,9 @@ class ND2Reader(FramesSequenceND): if self._timesteps is not None and len(self._timesteps) > 0: return self._timesteps - self._timesteps = np.array(list(self._parser._raw_metadata.acquisition_times), dtype=np.float) * 1000.0 + self._timesteps = ( + np.array(list(self._parser._raw_metadata.acquisition_times), dtype=np.float) + * 1000.0 + ) return self._timesteps