Source code for nd2reader.reader

from pims import Frame
from pims.base_frames import FramesSequenceND

from nd2reader.exceptions import EmptyFileError
from nd2reader.parser import Parser
import numpy as np

[docs]class ND2Reader(FramesSequenceND): """PIMS wrapper for the ND2 parser. This is the main class: use this to process your .nd2 files. """ class_priority = 12 def __init__(self, filename): super(self.__class__, self).__init__() 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() # Other properties self._timesteps = None
[docs] @classmethod def class_exts(cls): """Let PIMS open function use this reader for opening .nd2 files """ return {'nd2'} | super(ND2Reader, cls).class_exts()
[docs] def close(self): """Correctly close the file handle """ if self._fh is not None: self._fh.close()
def _get_default(self, coord): try: return self.default_coords[coord] except KeyError: return 0
[docs] def get_frame_2D(self, c=0, t=0, z=0, x=0, y=0, v=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 v: The field of view index Returns: pims.Frame: The requested frame """ # This needs to be set to width/height to return an image x = self.metadata["width"] y = self.metadata["height"] return self._parser.get_image_by_attributes(t, v, c, z, y, x)
@property def parser(self): """ Returns the parser object. Returns: Parser: the parser object """ return self._parser @property def pixel_type(self): """Return the pixel data type Returns: dtype: the pixel data type """ return self._dtype @property def timesteps(self): """Get the timesteps of the experiment Returns: np.ndarray: an array of times in milliseconds. """ if self._timesteps is None: return self.get_timesteps() return self._timesteps @property def events(self): """Get the events of the experiment Returns: iterator of events as dict """ return self._get_metadata_property("events") @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'] if total_duration == 0: raise ValueError('Total measurement duration could not be determined from loops') return self.metadata['num_frames'] / (total_duration/1000.0) def _get_metadata_property(self, key, default=None): if self.metadata is None: return default if key not in self.metadata: return default if self.metadata[key] is None: return default return self.metadata[key] def _setup_axes(self): """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) if len(self.sizes) == 0: raise EmptyFileError("No axes were found for this .nd2 file.") # provide the default self.iter_axes = self._guess_default_iter_axis() self._register_get_frame(self.get_frame_2D, 'yx') def _init_axis_if_exists(self, axis, size, min_size=1): if size >= min_size: self._init_axis(axis, size) def _guess_default_iter_axis(self): """ Guesses the default axis to iterate over based on axis sizes. Returns: the axis to iterate over """ priority = ['t', 'z', 'c', 'v'] found_axes = [] for axis in priority: try: current_size = self.sizes[axis] except KeyError: continue if current_size > 1: return axis found_axes.append(axis) return found_axes[0]
[docs] def get_timesteps(self): """Get the timesteps of the experiment Returns: np.ndarray: an array of times in milliseconds. """ 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 return self._timesteps