- replace "" with ''
- bugfix in seqread finding images with pattern 00-Pos_000_000 - cache ome metadata - detect faulty time delta data in czi files - read ome from path.ome.xml if this file exists - add extract-ome command line option
This commit is contained in:
Wim Pomp
@@ -1,7 +1,6 @@
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import re
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from abc import ABC
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from datetime import datetime
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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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@@ -39,7 +38,7 @@ class Plane(model.Plane):
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def get_delta_t(t0, file):
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with tifffile.TiffFile(file) as tif:
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info = yaml.safe_load(tif.pages[0].tags[50839].value['Info'])
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return float((datetime.strptime(info["Time"], "%Y-%m-%d %H:%M:%S %z") - t0).seconds)
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return float((datetime.strptime(info['Time'], '%Y-%m-%d %H:%M:%S %z') - t0).seconds)
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class Reader(AbstractReader, ABC):
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@@ -49,86 +48,87 @@ class Reader(AbstractReader, ABC):
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def _can_open(path):
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return isinstance(path, Path) and path.is_dir()
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@cached_property
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def ome(self):
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def get_ome(self):
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ome = model.OME()
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with tifffile.TiffFile(self.filedict[0, 0, 0]) as tif:
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metadata = {key: yaml.safe_load(value) for key, value in tif.pages[0].tags[50839].value.items()}
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ome.experimenters.append(
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model.Experimenter(id="Experimenter:0", user_name=metadata["Info"]["Summary"]["UserName"]))
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objective_str = metadata["Info"]["ZeissObjectiveTurret-Label"]
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model.Experimenter(id='Experimenter:0', user_name=metadata['Info']['Summary']['UserName']))
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objective_str = metadata['Info']['ZeissObjectiveTurret-Label']
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ome.instruments.append(model.Instrument())
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ome.instruments[0].objectives.append(
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model.Objective(
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id="Objective:0", manufacturer="Zeiss", model=objective_str,
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nominal_magnification=float(re.findall(r"(\d+)x", objective_str)[0]),
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lens_na=float(re.findall(r"/(\d\.\d+)", objective_str)[0]),
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id='Objective:0', manufacturer='Zeiss', model=objective_str,
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nominal_magnification=float(re.findall(r'(\d+)x', objective_str)[0]),
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lens_na=float(re.findall(r'/(\d\.\d+)', objective_str)[0]),
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immersion=model.Objective_Immersion.OIL if 'oil' in objective_str.lower() else None))
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tubelens_str = metadata["Info"]["ZeissOptovar-Label"]
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tubelens_str = metadata['Info']['ZeissOptovar-Label']
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ome.instruments[0].objectives.append(
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model.Objective(
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id="Objective:Tubelens:0", manufacturer="Zeiss", model=tubelens_str,
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nominal_magnification=float(re.findall(r"\d?\d*[,.]?\d+(?=x$)", tubelens_str)[0].replace(",", "."))))
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id='Objective:Tubelens:0', manufacturer='Zeiss', model=tubelens_str,
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nominal_magnification=float(re.findall(r'\d?\d*[,.]?\d+(?=x$)', tubelens_str)[0].replace(',', '.'))))
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ome.instruments[0].detectors.append(
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model.Detector(
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id="Detector:0", amplification_gain=100))
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id='Detector:0', amplification_gain=100))
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ome.instruments[0].filter_sets.append(
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model.FilterSet(id='FilterSet:0', model=metadata["Info"]["ZeissReflectorTurret-Label"]))
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model.FilterSet(id='FilterSet:0', model=metadata['Info']['ZeissReflectorTurret-Label']))
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pxsize = metadata["Info"]["PixelSizeUm"]
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pxsize_cam = 6.5 if 'Hamamatsu' in metadata["Info"]["Core-Camera"] else None
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pxsize = metadata['Info']['PixelSizeUm']
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pxsize_cam = 6.5 if 'Hamamatsu' in metadata['Info']['Core-Camera'] else None
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if pxsize == 0:
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pxsize = pxsize_cam / ome.instruments[0].objectives[0].nominal_magnification
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pixel_type = metadata["Info"]["PixelType"].lower()
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if pixel_type.startswith("gray"):
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pixel_type = "uint" + pixel_type[4:]
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pixel_type = metadata['Info']['PixelType'].lower()
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if pixel_type.startswith('gray'):
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pixel_type = 'uint' + pixel_type[4:]
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else:
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pixel_type = "uint16" # assume
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pixel_type = 'uint16' # assume
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size_c, size_z, size_t = (max(i) + 1 for i in zip(*self.filedict.keys()))
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t0 = datetime.strptime(metadata["Info"]["Time"], "%Y-%m-%d %H:%M:%S %z")
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t0 = datetime.strptime(metadata['Info']['Time'], '%Y-%m-%d %H:%M:%S %z')
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ome.images.append(
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model.Image(
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pixels=model.Pixels(
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size_c=size_c, size_z=size_z, size_t=size_t,
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size_x=metadata['Info']['Width'], size_y=metadata['Info']['Height'],
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dimension_order="XYCZT", type=pixel_type, physical_size_x=pxsize, physical_size_y=pxsize,
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physical_size_z=metadata["Info"]["Summary"]["z-step_um"]),
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objective_settings=model.ObjectiveSettings(id="Objective:0")))
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dimension_order='XYCZT', type=pixel_type, physical_size_x=pxsize, physical_size_y=pxsize,
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physical_size_z=metadata['Info']['Summary']['z-step_um']),
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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(
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Plane(t0, self.filedict[c, z, t],
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the_c=c, the_z=z, the_t=t, exposure_time=metadata["Info"]["Exposure-ms"] / 1000))
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the_c=c, the_z=z, the_t=t, exposure_time=metadata['Info']['Exposure-ms'] / 1000))
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# compare channel names from metadata with filenames
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pattern_c = re.compile(r"img_\d{3,}_(.*)_\d{3,}$")
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pattern_c = re.compile(r'img_\d{3,}_(.*)_\d{3,}$')
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for c in range(size_c):
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ome.images[0].pixels.channels.append(
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model.Channel(
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id=f"Channel:{c}", name=pattern_c.findall(self.filedict[c, 0, 0].stem)[0],
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id=f'Channel:{c}', name=pattern_c.findall(self.filedict[c, 0, 0].stem)[0],
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detector_settings=model.DetectorSettings(
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id="Detector:0", binning=metadata["Info"]["Hamamatsu_sCMOS-Binning"]),
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id='Detector:0', binning=metadata['Info']['Hamamatsu_sCMOS-Binning']),
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filter_set_ref=model.FilterSetRef(id='FilterSet:0')))
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return ome
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def open(self):
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if re.match(r'(?:\d+-)?Pos.*', self.path.name) is None:
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path = self.path / f"Pos{self.series}"
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pat = re.compile(r'(?:\d+-)?Pos.*')
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if pat.match(self.path.name) is None:
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path = sorted(file for file in self.path.iterdir() if pat.match(file.name))[self.series]
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else:
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path = self.path
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filelist = sorted([file for file in path.iterdir() if re.search(r'^img_\d{3,}.*\d{3,}.*\.tif$', file.name)])
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pat = re.compile(r'^img_\d{3,}.*\d{3,}.*\.tif$')
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filelist = sorted([file for file in path.iterdir() if pat.search(file.name)])
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with tifffile.TiffFile(self.path / filelist[0]) as tif:
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metadata = {key: yaml.safe_load(value) for key, value in tif.pages[0].tags[50839].value.items()}
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# compare channel names from metadata with filenames
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cnamelist = metadata["Info"]["Summary"]["ChNames"]
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cnamelist = metadata['Info']['Summary']['ChNames']
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cnamelist = [c for c in cnamelist if any([c in f.name for f in filelist])]
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pattern_c = re.compile(r"img_\d{3,}_(.*)_\d{3,}$")
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pattern_z = re.compile(r"(\d{3,})$")
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pattern_t = re.compile(r"img_(\d{3,})")
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pattern_c = re.compile(r'img_\d{3,}_(.*)_\d{3,}$')
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pattern_z = re.compile(r'(\d{3,})$')
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pattern_t = re.compile(r'img_(\d{3,})')
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self.filedict = {(cnamelist.index(pattern_c.findall(file.stem)[0]), # noqa
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int(pattern_z.findall(file.stem)[0]),
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int(pattern_t.findall(file.stem)[0])): file for file in filelist}
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