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93 lines
2.7 KiB
93 lines
2.7 KiB
from pims import FramesSequenceND, Frame
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import numpy as np
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from nd2reader.exc import NoImageError
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from nd2reader.parser import get_parser
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import six
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class ND2Reader(FramesSequenceND):
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"""
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PIMS wrapper for the ND2 reader
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"""
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def __init__(self, filename):
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self.filename = filename
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# first use the parser to parse the file
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self._fh = open(filename, "rb")
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self._parser = get_parser(self._fh)
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self._metadata = self._parser.metadata
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self._roi_metadata = self._parser.roi_metadata
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# Set data type
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self._dtype = self._get_dtype_from_metadata()
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# Setup the axes
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self._init_axis('x', self._metadata.width)
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self._init_axis('y', self._metadata.height)
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self._init_axis('c', len(self._metadata.channels))
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self._init_axis('t', len(self._metadata.frames))
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self._init_axis('z', len(self._metadata.z_levels))
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# provide the default
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self.iter_axes = 't'
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def _get_dtype_from_metadata(self):
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"""
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Determine the data type from the metadata.
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:return:
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"""
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bit_depth = self._parser.raw_metadata.image_attributes[six.b('SLxImageAttributes')][six.b('uiBpcInMemory')]
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if bit_depth <= 16:
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self._dtype = np.float16
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elif bit_depth <= 32:
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self._dtype = np.float32
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else:
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self._dtype = np.float64
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return self._dtype
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@classmethod
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def class_exts(cls):
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return {'nd2'} | super(ND2Reader, cls).class_exts()
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def close(self):
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if self._fh is not None:
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self._fh.close()
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def get_frame_2D(self, c, t, z):
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"""
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Gets a given frame using the parser
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:param c:
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:param t:
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:param z:
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:return:
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"""
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c_name = self._metadata.channels[c]
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try:
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image = self._parser.driver.get_image_by_attributes(t, 0, c_name, z, self._metadata.width,
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self._metadata.height)
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except (TypeError, NoImageError):
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return Frame([])
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else:
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return Frame(image, frame_no=image.frame_number, metadata=self._get_frame_metadata())
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def _get_frame_metadata(self):
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"""
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Get the metadata for one frame
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:return:
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"""
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frame_metadata = {
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"height": self._metadata.height,
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"width": self._metadata.width,
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"date": self._metadata.date,
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"pixel_microns": self._metadata.pixel_microns,
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"rois": self._roi_metadata
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}
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return frame_metadata
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@property
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def pixel_type(self):
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return self._dtype
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