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- pyproject towards PEP621

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- catch errors reading metadata in tifread
- read dimension order from ome
This commit is contained in:
Wim Pomp
2025-03-19 15:04:57 +01:00
parent 6daa372ccf
commit 0ac22aff87
4 changed files with 85 additions and 75 deletions
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97
ndbioimage/readers/tifread.py
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@@ -6,9 +6,10 @@ from pathlib import Path
import numpy as np
import tifffile
import yaml
from ome_types import model
import warnings
from ome_types import model, from_xml
from .. import AbstractReader
from .. import AbstractReader, try_default
class Reader(AbstractReader, ABC):
@@ -25,61 +26,75 @@ class Reader(AbstractReader, ABC):
@cached_property
def metadata(self):
return {key: yaml.safe_load(value) if isinstance(value, str) else value
return {key: try_default(yaml.safe_load, value, value) if isinstance(value, str) else value
for key, value in self.reader.imagej_metadata.items()}
def get_ome(self):
page = self.reader.pages[0]
size_y = page.imagelength
size_x = page.imagewidth
if self.p_ndim == 3:
size_c = page.samplesperpixel
size_t = self.metadata.get('frames', 1) # // C
if self.reader.is_ome:
with warnings.catch_warnings():
warnings.simplefilter('ignore', category=UserWarning)
return from_xml(self.reader.ome_metadata)
else:
size_c = self.metadata.get('channels', 1)
size_t = self.metadata.get('frames', 1)
size_z = self.metadata.get('slices', 1)
if 282 in page.tags and 296 in page.tags and page.tags[296].value == 1:
f = page.tags[282].value
pxsize = f[1] / f[0]
else:
pxsize = None
page = self.reader.pages[0]
size_y = page.imagelength
size_x = page.imagewidth
if self.p_ndim == 3:
size_c = page.samplesperpixel
size_t = self.metadata.get('frames', 1) # // C
else:
size_c = self.metadata.get('channels', 1)
size_t = self.metadata.get('frames', 1)
size_z = self.metadata.get('slices', 1)
if 282 in page.tags and 296 in page.tags and page.tags[296].value == 1:
f = page.tags[282].value
pxsize = f[1] / f[0]
else:
pxsize = None
dtype = page.dtype.name
if dtype not in ('int8', 'int16', 'int32', 'uint8', 'uint16', 'uint32',
'float', 'double', 'complex', 'double-complex', 'bit'):
dtype = 'float'
dtype = page.dtype.name
if dtype not in ('int8', 'int16', 'int32', 'uint8', 'uint16', 'uint32',
'float', 'double', 'complex', 'double-complex', 'bit'):
dtype = 'float'
interval_t = self.metadata.get('interval', 0)
interval_t = self.metadata.get('interval', 0)
ome = model.OME()
ome.instruments.append(model.Instrument(id='Instrument:0'))
ome.instruments[0].objectives.append(model.Objective(id='Objective:0'))
ome.images.append(
model.Image(
id='Image:0',
pixels=model.Pixels(
id='Pixels:0',
size_c=size_c, size_z=size_z, size_t=size_t, size_x=size_x, size_y=size_y,
dimension_order='XYCZT', type=dtype, # type: ignore
physical_size_x=pxsize, physical_size_y=pxsize),
objective_settings=model.ObjectiveSettings(id='Objective:0')))
for c, z, t in product(range(size_c), range(size_z), range(size_t)):
ome.images[0].pixels.planes.append(model.Plane(the_c=c, the_z=z, the_t=t, delta_t=interval_t * t))
return ome
ome = model.OME()
ome.instruments.append(model.Instrument(id='Instrument:0'))
ome.instruments[0].objectives.append(model.Objective(id='Objective:0'))
ome.images.append(
model.Image(
id='Image:0',
pixels=model.Pixels(
id='Pixels:0',
size_c=size_c, size_z=size_z, size_t=size_t, size_x=size_x, size_y=size_y,
dimension_order='XYCZT', type=dtype, # type: ignore
physical_size_x=pxsize, physical_size_y=pxsize),
objective_settings=model.ObjectiveSettings(id='Objective:0')))
for c, z, t in product(range(size_c), range(size_z), range(size_t)):
ome.images[0].pixels.planes.append(model.Plane(the_c=c, the_z=z, the_t=t, delta_t=interval_t * t))
return ome
def open(self):
self.reader = tifffile.TiffFile(self.path)
page = self.reader.pages[0]
page = self.reader.pages.first
self.p_ndim = page.ndim # noqa
if self.p_ndim == 3:
self.p_transpose = [i for i in [page.axes.find(j) for j in 'SYX'] if i >= 0] # noqa
else:
self.p_transpose = [i for i in [page.axes.find(j) for j in 'YX'] if i >= 0] # noqa
def close(self):
self.reader.close()
def __frame__(self, c, z, t):
def __frame__(self, c: int, z: int, t: int):
dimension_order = self.ome.images[0].pixels.dimension_order.value
if self.p_ndim == 3:
return np.transpose(self.reader.asarray(z + t * self.base_shape['z']), self.p_transpose)[c]
axes = ''.join([ax.lower() for ax in dimension_order if ax.lower() in 'zt'])
ct = {'z': z, 't': t}
n = sum([ct[ax] * np.prod(self.base_shape[axes[:i]]) for i, ax in enumerate(axes)])
return np.transpose(self.reader.asarray(int(n)), self.p_transpose)[int(c)]
else:
return self.reader.asarray(c + z * self.base_shape['c'] + t * self.base_shape['c'] * self.base_shape['z'])
axes = ''.join([ax.lower() for ax in dimension_order if ax.lower() in 'czt'])
czt = {'c': c, 'z': z, 't': t}
n = sum([czt[ax] * np.prod(self.base_shape[axes[:i]]) for i, ax in enumerate(axes)])
return np.transpose(self.reader.asarray(int(n)), self.p_transpose)

2
ndbioimage/transform.txt
View File

@@ -1,6 +1,4 @@
#Insight Transform File V1.0
#Transform 0
Transform: CompositeTransform_double_2_2
#Transform 1
Transform: AffineTransform_double_2_2
Parameters: 1 0 0 1 0 0

2
ndbioimage/transforms.py
View File

@@ -299,7 +299,7 @@ class Transform:
new.shape = [float(t) for t in transform['Size']]
new.origin = [(t - 1) / 2 for t in new.shape]
else:
raise NotImplementedError(f'{kind} tranforms not implemented (yet)')
raise NotImplementedError(f'{kind} transforms not implemented (yet)')
new.dparameters = 6 * [np.nan]
return new