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- slice notation for time argument on command line

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- fix seqread can_open
This commit is contained in:
Wim Pomp
2024-09-24 13:23:04 +02:00
parent eea24e17ef
commit 814bb0da85
3 changed files with 21 additions and 16 deletions
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18
ndbioimage/readers/seqread.py
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@@ -46,11 +46,9 @@ class Reader(AbstractReader, ABC):
@staticmethod
def _can_open(path):
if isinstance(path, Path) and path.is_dir():
files = [file for file in path.iterdir() if file.name.lower().startswith('pos')]
return len(files) > 0 and files[0].is_dir()
else:
return False
pat = re.compile(r'(?:\d+-)?Pos.*', re.IGNORECASE)
return (isinstance(path, Path) and path.is_dir() and
(pat.match(path.name) or any(file.is_dir() and pat.match(file.stem) for file in path.iterdir())))
def get_ome(self):
ome = model.OME()
@@ -104,7 +102,7 @@ class Reader(AbstractReader, ABC):
the_c=c, the_z=z, the_t=t, exposure_time=metadata['Info']['Exposure-ms'] / 1000))
# compare channel names from metadata with filenames
pattern_c = re.compile(r'img_\d{3,}_(.*)_\d{3,}$')
pattern_c = re.compile(r'img_\d{3,}_(.*)_\d{3,}$', re.IGNORECASE)
for c in range(size_c):
ome.images[0].pixels.channels.append(
model.Channel(
@@ -115,13 +113,13 @@ class Reader(AbstractReader, ABC):
return ome
def open(self):
pat = re.compile(r'(?:\d+-)?Pos.*')
pat = re.compile(r'(?:\d+-)?Pos.*', re.IGNORECASE)
if pat.match(self.path.name) is None:
path = sorted(file for file in self.path.iterdir() if pat.match(file.name))[self.series]
else:
path = self.path
pat = re.compile(r'^img_\d{3,}.*\d{3,}.*\.(tif|TIF)$')
pat = re.compile(r'^img_\d{3,}.*\d{3,}.*\.tif$', re.IGNORECASE)
filelist = sorted([file for file in path.iterdir() if pat.search(file.name)])
with tifffile.TiffFile(self.path / filelist[0]) as tif:
metadata = {key: yaml.safe_load(value) for key, value in tif.pages[0].tags[50839].value.items()}
@@ -130,9 +128,9 @@ class Reader(AbstractReader, ABC):
cnamelist = metadata['Info']['Summary']['ChNames']
cnamelist = [c for c in cnamelist if any([c in f.name for f in filelist])]
pattern_c = re.compile(r'img_\d{3,}_(.*)_\d{3,}$')
pattern_c = re.compile(r'img_\d{3,}_(.*)_\d{3,}$', re.IGNORECASE)
pattern_z = re.compile(r'(\d{3,})$')
pattern_t = re.compile(r'img_(\d{3,})')
pattern_t = re.compile(r'img_(\d{3,})', re.IGNORECASE)
self.filedict = {(cnamelist.index(pattern_c.findall(file.stem)[0]), # noqa
int(pattern_z.findall(file.stem)[0]),
int(pattern_t.findall(file.stem)[0])): file for file in filelist}