109 lines
4.4 KiB
Python
109 lines
4.4 KiB
Python
import re
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import warnings
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from abc import ABC
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from functools import cached_property
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from itertools import product
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from pathlib import Path
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import numpy as np
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import tifffile
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import yaml
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from lfdfiles import TiffFile
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from ome_types import from_xml, model
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from .. import AbstractReader, try_default
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class Reader(AbstractReader, ABC):
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priority = 0
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do_not_pickle = 'reader'
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@staticmethod
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def _can_open(path):
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if isinstance(path, Path) and path.suffix in ('.tif', '.tiff'):
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with tifffile.TiffFile(path) as tif:
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return tif.is_imagej and tif.pages[-1]._nextifd() == 0 # noqa
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else:
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return False
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@cached_property
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def metadata(self):
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return {key: try_default(yaml.safe_load, value, value) if isinstance(value, str) else value
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for key, value in self.reader.imagej_metadata.items()}
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def get_ome(self):
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if self.reader.is_ome:
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match = re.match(r'^(.*)(pos.*)$', self.path.stem, flags=re.IGNORECASE)
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if match is not None and len(match.groups()) == 2:
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a, b = match.groups()
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file0 = TiffFile(self.path.with_stem(a + re.sub(r'\d', '0', b)))
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with warnings.catch_warnings():
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warnings.simplefilter('ignore', category=UserWarning)
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ome = from_xml(file0.ome_metadata)
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ome.images = [image for image in ome.images if self.path.stem[:len(image.name)] == image.name]
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return ome
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page = self.reader.pages[0]
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size_y = page.imagelength
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size_x = page.imagewidth
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if self.p_ndim == 3:
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size_c = page.samplesperpixel
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size_t = self.metadata.get('frames', 1) # // C
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else:
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size_c = self.metadata.get('channels', 1)
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size_t = self.metadata.get('frames', 1)
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size_z = self.metadata.get('slices', 1)
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if 282 in page.tags and 296 in page.tags and page.tags[296].value == 1:
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f = page.tags[282].value
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pxsize = f[1] / f[0]
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else:
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pxsize = None
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dtype = page.dtype.name
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if dtype not in ('int8', 'int16', 'int32', 'uint8', 'uint16', 'uint32',
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'float', 'double', 'complex', 'double-complex', 'bit'):
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dtype = 'float'
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interval_t = self.metadata.get('interval', 0)
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ome = model.OME()
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ome.instruments.append(model.Instrument(id='Instrument:0'))
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ome.instruments[0].objectives.append(model.Objective(id='Objective:0'))
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ome.images.append(
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model.Image(
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id='Image:0',
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pixels=model.Pixels(
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id='Pixels:0',
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size_c=size_c, size_z=size_z, size_t=size_t, size_x=size_x, size_y=size_y,
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dimension_order='XYCZT', type=dtype, # type: ignore
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physical_size_x=pxsize, physical_size_y=pxsize),
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objective_settings=model.ObjectiveSettings(id='Objective:0')))
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for c, z, t in product(range(size_c), range(size_z), range(size_t)):
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ome.images[0].pixels.planes.append(model.Plane(the_c=c, the_z=z, the_t=t, delta_t=interval_t * t))
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return ome
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def open(self):
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self.reader = tifffile.TiffFile(self.path)
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page = self.reader.pages.first
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self.p_ndim = page.ndim # noqa
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if self.p_ndim == 3:
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self.p_transpose = [i for i in [page.axes.find(j) for j in 'SYX'] if i >= 0] # noqa
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else:
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self.p_transpose = [i for i in [page.axes.find(j) for j in 'YX'] if i >= 0] # noqa
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def close(self):
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self.reader.close()
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def __frame__(self, c: int, z: int, t: int):
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dimension_order = self.ome.images[0].pixels.dimension_order.value
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if self.p_ndim == 3:
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axes = ''.join([ax.lower() for ax in dimension_order if ax.lower() in 'zt'])
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ct = {'z': z, 't': t}
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n = sum([ct[ax] * np.prod(self.base_shape[axes[:i]]) for i, ax in enumerate(axes)])
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return np.transpose(self.reader.asarray(int(n)), self.p_transpose)[int(c)]
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else:
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axes = ''.join([ax.lower() for ax in dimension_order if ax.lower() in 'czt'])
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czt = {'c': c, 'z': z, 't': t}
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n = sum([czt[ax] * np.prod(self.base_shape[axes[:i]]) for i, ax in enumerate(axes)])
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return np.transpose(self.reader.asarray(int(n)), self.p_transpose)
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