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80 lines
2.1 KiB
80 lines
2.1 KiB
from pims import FramesSequenceND, Frame
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from nd2reader.exc import NoImageError
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from nd2reader.nd2parser import ND2Parser
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class ND2Reader(FramesSequenceND):
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"""
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PIMS wrapper for the ND2 parser
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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 = ND2Parser(self._fh)
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# Setup metadata
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self.metadata = self._parser.metadata
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# Set data type
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self._dtype = self._parser.get_dtype_from_metadata()
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# Setup the axes
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self._setup_axes()
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@classmethod
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def class_exts(cls):
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"""
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So PIMS open function can use this reader for opening .nd2 files
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:return:
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"""
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return {'nd2'} | super(ND2Reader, cls).class_exts()
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def close(self):
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"""
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Correctly close the file handle
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:return:
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"""
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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.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 image
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@property
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def pixel_type(self):
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"""
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Return the pixel data type
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:return:
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"""
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return self._dtype
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def _setup_axes(self):
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"""
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Setup the xyctz axes, iterate over t axis by default
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:return:
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"""
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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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