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64 lines
2.0 KiB
64 lines
2.0 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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from nd2reader.version import get_version
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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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major_version, minor_version = get_version(self._fh)
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self._parser = get_parser(self._fh, major_version, minor_version)
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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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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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# 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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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)
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@property
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def pixel_type(self):
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return self._dtype
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