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- read the correct metadata for series > 0

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Wim Pomp
2024-03-18 16:43:26 +01:00
parent 110cb6d9c1
commit 5345e38d3c
2 changed files with 5 additions and 5 deletions
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8
ndbioimage/__init__.py
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@@ -987,7 +987,7 @@ class AbstractReader(Imread, metaclass=ABCMeta):
self.open()
# extract some metadata from ome
instrument = self.ome.instruments[0] if self.ome.instruments else None
image = self.ome.images[0]
image = self.ome.images[self.series]
pixels = image.pixels
self.shape = pixels.size_y, pixels.size_x, pixels.size_c, pixels.size_z, pixels.size_t
self.dtype = pixels.type.value if dtype is None else dtype
@@ -1003,8 +1003,8 @@ class AbstractReader(Imread, metaclass=ABCMeta):
self.deltaz_um = None if self.deltaz is None else self.deltaz.to(self.ureg.um).m
else:
self.deltaz = self.deltaz_um = None
if self.ome.images[0].objective_settings:
self.objective = find(instrument.objectives, id=self.ome.images[0].objective_settings.id)
if self.ome.images[self.series].objective_settings:
self.objective = find(instrument.objectives, id=self.ome.images[self.series].objective_settings.id)
else:
self.objective = None
try:
@@ -1107,7 +1107,7 @@ class AbstractReader(Imread, metaclass=ABCMeta):
p = re.compile(r'(\d+):(\d+)$')
try:
self.track, self.detector = zip(*[[int(i) for i in p.findall(find(
self.ome.images[0].pixels.channels, id=f'Channel:{c}').detector_settings.id)[0]]
self.ome.images[self.series].pixels.channels, id=f'Channel:{c}').detector_settings.id)[0]]
for c in range(self.shape['c'])])
except Exception:
pass