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- do_copy class attribute to force copy of ome

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- more ome parts optional
- reading closed file raises an error
This commit is contained in:
Wim Pomp
2023-07-11 17:20:03 +02:00
parent b629f98727
commit dbe80c495b
5 changed files with 35 additions and 13 deletions
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1
.gitignore vendored
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@@ -6,3 +6,4 @@
.idea
/.pytest_cache/
/ndbioimage/_version.py
/ndbioimage/jars

28
ndbioimage/__init__.py
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@@ -423,6 +423,7 @@ class Imread(np.lib.mixins.NDArrayOperatorsMixin, metaclass=ABCMeta):
priority = 99
do_not_pickle = 'base', 'copies', 'cache'
do_not_copy = 'extrametadata'
do_copy = 'ome'
ureg = ureg
@staticmethod
@@ -472,6 +473,11 @@ class Imread(np.lib.mixins.NDArrayOperatorsMixin, metaclass=ABCMeta):
else subclass.do_not_copy if hasattr(subclass, 'do_not_copy') else ()
subclass.do_not_copy = set(do_not_copy).union(set(subclass_do_not_copy))
do_copy = (cls.do_copy,) if isinstance(cls.do_copy, str) else cls.do_copy
subclass_do_copy = (subclass.do_copy,) if isinstance(subclass.do_copy, str) \
else subclass.do_copy if hasattr(subclass, 'do_copy') else ()
subclass.do_copy = set(do_copy).union(set(subclass_do_copy))
return super().__new__(subclass)
@staticmethod
@@ -519,13 +525,17 @@ class Imread(np.lib.mixins.NDArrayOperatorsMixin, metaclass=ABCMeta):
self.open()
# extract some metadata from ome
instrument = self.ome.instruments[0]
instrument = self.ome.instruments[0] if self.ome.instruments else None
image = self.ome.images[0]
pixels = image.pixels
self.shape = pixels.size_x, pixels.size_y, pixels.size_c, pixels.size_z, pixels.size_t
self.pxsize = pixels.physical_size_x_quantity
try:
self.exposuretime = tuple(find(image.pixels.planes, the_c=c).exposure_time_quantity
for c in range(self.shape['c']))
except AttributeError:
self.exposuretime = ()
if self.zstack:
self.deltaz = image.pixels.physical_size_z_quantity
self.deltaz_um = None if self.deltaz is None else self.deltaz.to(self.ureg.um).m
@@ -535,16 +545,22 @@ class Imread(np.lib.mixins.NDArrayOperatorsMixin, metaclass=ABCMeta):
self.objective = find(instrument.objectives, id=self.ome.images[0].objective_settings.id)
else:
self.objective = None
try:
t0 = find(image.pixels.planes, the_c=0, the_t=0, the_z=0).delta_t
t1 = find(image.pixels.planes, the_c=0, the_t=self.shape['t'] - 1, the_z=0).delta_t
self.timeinterval = (t1 - t0) / (self.shape['t'] - 1) if self.shape['t'] > 1 else None
except AttributeError:
self.timeinterval = None
try:
self.binning = [int(i) for i in image.pixels.channels[0].detector_settings.binning.value.split('x')]
self.pxsize *= self.binning[0]
except (Exception,):
except (AttributeError, IndexError):
self.binning = None
self.cnamelist = [channel.name for channel in image.pixels.channels]
try:
optovars = [objective for objective in instrument.objectives if 'tubelens' in objective.id.lower()]
except AttributeError:
optovars = []
if len(optovars) == 0:
self.tubelens = None
else:
@@ -607,7 +623,7 @@ class Imread(np.lib.mixins.NDArrayOperatorsMixin, metaclass=ABCMeta):
try:
sigma = []
for c, d in enumerate(self.detector):
emission = np.hstack(self.laserwavelengths[c]) + 22 * ureg.nm
emission = (np.hstack(self.laserwavelengths[c]) + 22) * ureg.nm
sigma.append([emission[emission > s].max(initial=0), emission[emission < s].max(initial=0)][d])
sigma = np.hstack(sigma)
sigma[sigma == 0] = 600 * ureg.nm
@@ -705,7 +721,7 @@ class Imread(np.lib.mixins.NDArrayOperatorsMixin, metaclass=ABCMeta):
s.append(f'pixel size: {1000 * self.pxsize_um:.2f} nm')
if self.zstack and self.deltaz_um:
s.append(f'z-interval: {1000 * self.deltaz_um:.2f} nm')
if self.exposuretime_s[0]:
if self.exposuretime_s:
s.append(f'exposuretime: {self.exposuretime_s[0]:.2f} s')
if self.timeseries and self.timeinterval:
s.append(f'time interval: {self.timeinterval:.3f} s')
@@ -749,6 +765,8 @@ class Imread(np.lib.mixins.NDArrayOperatorsMixin, metaclass=ABCMeta):
def __getitem__(self, n):
""" slice like a numpy array but return an Imread instance """
if self.isclosed:
raise IOError("file is closed")
if isinstance(n, (slice, Number)): # None = :
n = (n,)
elif isinstance(n, type(Ellipsis)):
@@ -872,7 +890,7 @@ class Imread(np.lib.mixins.NDArrayOperatorsMixin, metaclass=ABCMeta):
new.copies = []
new.base = self
for key, value in self.__dict__.items():
if key not in self.do_not_copy and not hasattr(new, key):
if key in self.do_copy or (key not in self.do_not_copy and not hasattr(new, key)):
new.__dict__[key] = value
self.copies.append(new)
return new

3
ndbioimage/readers/__init__.py
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@@ -1,2 +1,3 @@
from pathlib import Path
__all__ = [file.stem for file in Path(__file__).parent.iterdir() if file.suffix == ".py" and not file == Path(__file__)]
__all__ = [file.stem for file in Path(__file__).parent.iterdir()
if file.suffix == ".py" and not file == Path(__file__) and not file.stem.startswith('.')]

1
ndbioimage/readers/bfread.py
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@@ -14,6 +14,7 @@ class JVMReader:
if not bf_jar.exists():
print('Downloading bioformats_package.jar.')
url = 'https://downloads.openmicroscopy.org/bio-formats/latest/artifacts/bioformats_package.jar'
bf_jar.parent.mkdir(exist_ok=True)
bf_jar.write_bytes(request.urlopen(url).read())
mp = multiprocessing.get_context('spawn')

3
pyproject.toml
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@@ -1,6 +1,6 @@
[tool.poetry]
name = "ndbioimage"
version = "2023.7.1"
version = "2023.7.2"
description = "Bio image reading, metadata and some affine registration."
authors = ["W. Pomp <w.pomp@nki.nl>"]
license = "GPLv3"
@@ -8,6 +8,7 @@ readme = "README.md"
keywords = ["bioformats", "imread", "numpy", "metadata"]
include = ["transform.txt"]
repository = "https://github.com/wimpomp/ndbioimage"
exclude = [ "ndbioimage/jars" ]
[tool.poetry.dependencies]
python = "^3.8"