You can not select more than 25 topics
Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.
81 lines
2.1 KiB
81 lines
2.1 KiB
from pims import FramesSequenceND
|
|
from nd2reader.parser import Parser
|
|
|
|
|
|
class ND2Reader(FramesSequenceND):
|
|
"""
|
|
PIMS wrapper for the ND2 parser
|
|
"""
|
|
def __init__(self, filename):
|
|
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()
|
|
|
|
@classmethod
|
|
def class_exts(cls):
|
|
"""
|
|
So PIMS open function can use this reader for opening .nd2 files
|
|
:return:
|
|
"""
|
|
return {'nd2'} | super(ND2Reader, cls).class_exts()
|
|
|
|
def close(self):
|
|
"""
|
|
Correctly close the file handle
|
|
:return:
|
|
"""
|
|
if self._fh is not None:
|
|
self._fh.close()
|
|
|
|
def get_frame(self, i):
|
|
"""
|
|
Return one frame
|
|
:param i:
|
|
:return:
|
|
"""
|
|
c_name = self.metadata["channels"][0]
|
|
return self._parser.get_image_by_attributes(i, 0, c_name, 0, self.metadata["height"], self.metadata["width"])
|
|
|
|
def get_frame_2D(self, c, t, z):
|
|
"""
|
|
Gets a given frame using the parser
|
|
:param c:
|
|
:param t:
|
|
:param z:
|
|
:return:
|
|
"""
|
|
c_name = self.metadata["channels"][c]
|
|
return self._parser.get_image_by_attributes(t, 0, c_name, z, self.metadata["height"], self.metadata["width"])
|
|
|
|
@property
|
|
def pixel_type(self):
|
|
"""
|
|
Return the pixel data type
|
|
:return:
|
|
"""
|
|
return self._dtype
|
|
|
|
def _setup_axes(self):
|
|
"""
|
|
Setup the xyctz axes, iterate over t axis by default
|
|
:return:
|
|
"""
|
|
self._init_axis('x', self.metadata["width"])
|
|
self._init_axis('y', self.metadata["height"])
|
|
self._init_axis('c', len(self.metadata["channels"]))
|
|
self._init_axis('t', len(self.metadata["frames"]))
|
|
self._init_axis('z', len(self.metadata["z_levels"]))
|
|
|
|
# provide the default
|
|
self.iter_axes = 't'
|