Source code for mesmerize.viewer.core.data_types

#!/usr/bin/env python3:
# -*- coding: utf-8 -*-
Created on Tue Dec 22 19:01:21 2017

@author: kushal

Chatzigeorgiou Group
Sars International Centre for Marine Molecular Biology

GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007

Just a clean simple & independent image data class which is the core of the work
envrionment in Mesmerize Viewer.

seq : 3D array (2D + time) of the image sequence
meta : meta data dictionary
Map : Stimulus map. Contains the definitions of the stimuli & the time that they
occured for the animal that was exposed to in this particular image sequence

import numpy as np

[docs]class ImgData: """Object that stores the image sequence and meta data from the imaging source"""
[docs] def __init__(self, seq: np.ndarray = None, meta: dict = None): """ :param seq: Image sequence as a numpy array, shape is [x, y, t] or [x, y, t, z] :param meta: Meta data dict from the imaging source. """ self.seq = None self._seq = None self.z = None self.z_max = None self._meta = None if seq is not None: self.ndim = seq.ndim if seq.ndim == 4: self._seq = seq self.seq = self._seq[:, :, :, 0] self.z = 0 self.z_max = self._seq.shape[3] - 1 else: self._seq = seq self.seq = self.seq = self._seq #: image sequence, shape is [x, y, t] or [x, y, t, z] else: self.ndim = None if meta is None: meta = {'origin': 'unknown', 'fps': 0, 'date': 'unknown', 'orig_meta': None } self.meta = meta.copy() #: Meta data dict from the imaging source
@property def meta(self) -> dict: return self._meta @meta.setter def meta(self, m: dict): reqs = ['origin', 'fps', 'date'] if not all(k in m.keys() for k in reqs): raise ValueError(f"Meta data dict must contain all of the following mandatory fields:\n{reqs}") self._meta = m def set_zlevel(self, z): if self._seq.ndim < 4: raise ValueError('Data are not 3D, cannot set z-level') self.z = z self.seq = self._seq[:, :, :, self.z] def clear(self): del self.seq del self._seq del self._meta self.seq = None self._seq = None self.meta = None