- read metadata into ome structure
- pytest - use pathlib - series as part of the path: path/PosN - summary only shows some available metadata - allow dict in Imread[dict(c=c, z=z, t=t)] - bfread in different process so the user can start another jvm - deal with multiple images (series/positions) in czi files - use jpype instead of javabridge/bioformats - poetry for install
This commit is contained in:
Wim Pomp
@@ -1,85 +1,110 @@
|
||||
from ndbioimage import Imread, XmlData
|
||||
import os
|
||||
from abc import ABC
|
||||
|
||||
import tifffile
|
||||
import yaml
|
||||
import json
|
||||
import re
|
||||
from ndbioimage import Imread
|
||||
from pathlib import Path
|
||||
from functools import cached_property
|
||||
from ome_types import model
|
||||
from itertools import product
|
||||
from datetime import datetime
|
||||
|
||||
|
||||
class Reader(Imread):
|
||||
class Reader(Imread, ABC):
|
||||
priority = 10
|
||||
|
||||
@staticmethod
|
||||
def _can_open(path):
|
||||
return isinstance(path, str) and os.path.splitext(path)[1] == ''
|
||||
return isinstance(path, Path) and path.suffix == ""
|
||||
|
||||
def __metadata__(self):
|
||||
filelist = sorted([file for file in os.listdir(self.path) if re.search(r'^img_\d{3,}.*\d{3,}.*\.tif$', file)])
|
||||
def get_metadata(self, c, z, t):
|
||||
with tifffile.TiffFile(self.filedict[c, z, t]) as tif:
|
||||
return {key: yaml.safe_load(value) for key, value in tif.pages[0].tags[50839].value.items()}
|
||||
|
||||
try:
|
||||
with tifffile.TiffFile(os.path.join(self.path, filelist[0])) as tif:
|
||||
self.metadata = XmlData({key: yaml.safe_load(value)
|
||||
for key, value in tif.pages[0].tags[50839].value.items()})
|
||||
except Exception: # fallback
|
||||
with open(os.path.join(self.path, 'metadata.txt'), 'r') as metadatafile:
|
||||
self.metadata = XmlData(json.loads(metadatafile.read()))
|
||||
@cached_property
|
||||
def ome(self):
|
||||
ome = model.OME()
|
||||
metadata = self.get_metadata(0, 0, 0)
|
||||
ome.experimenters.append(
|
||||
model.Experimenter(id="Experimenter:0", user_name=metadata["Info"]["Summary"]["UserName"]))
|
||||
objective_str = metadata["Info"]["ZeissObjectiveTurret-Label"]
|
||||
ome.instruments.append(model.Instrument())
|
||||
ome.instruments[0].objectives.append(
|
||||
model.Objective(
|
||||
id="Objective:0", manufacturer="Zeiss", model=objective_str,
|
||||
nominal_magnification=float(re.findall(r"(\d+)x", objective_str)[0]),
|
||||
lens_na=float(re.findall(r"/(\d\.\d+)", objective_str)[0]),
|
||||
immersion=model.objective.Immersion.OIL if 'oil' in objective_str.lower() else None))
|
||||
tubelens_str = metadata["Info"]["ZeissOptovar-Label"]
|
||||
ome.instruments[0].objectives.append(
|
||||
model.Objective(
|
||||
id="Objective:Tubelens:0", manufacturer="Zeiss", model=tubelens_str,
|
||||
nominal_magnification=float(re.findall(r"\d?\d*[,.]?\d+(?=x$)", tubelens_str)[0].replace(",", "."))))
|
||||
ome.instruments[0].detectors.append(
|
||||
model.Detector(
|
||||
id="Detector:0", amplification_gain=100))
|
||||
ome.instruments[0].filter_sets.append(
|
||||
model.FilterSet(id='FilterSet:0', model=metadata["Info"]["ZeissReflectorTurret-Label"]))
|
||||
|
||||
pxsize = metadata["Info"]["PixelSizeUm"]
|
||||
pxsize_cam = 6.5 if 'Hamamatsu' in metadata["Info"]["Core-Camera"] else None
|
||||
if pxsize == 0:
|
||||
pxsize = pxsize_cam / ome.instruments[0].objectives[0].nominal_magnification
|
||||
pixel_type = metadata["Info"]["PixelType"].lower()
|
||||
if pixel_type.startswith("gray"):
|
||||
pixel_type = "uint" + pixel_type[4:]
|
||||
else:
|
||||
pixel_type = "uint16" # assume
|
||||
|
||||
size_c, size_z, size_t = [max(i) + 1 for i in zip(*self.filedict.keys())]
|
||||
t0 = datetime.strptime(metadata["Info"]["Time"], "%Y-%m-%d %H:%M:%S %z")
|
||||
ome.images.append(
|
||||
model.Image(
|
||||
pixels=model.Pixels(
|
||||
size_c=size_c, size_z=size_z, size_t=size_t,
|
||||
size_x=metadata['Info']['Width'], size_y=metadata['Info']['Height'],
|
||||
dimension_order="XYCZT", type=pixel_type, physical_size_x=pxsize, physical_size_y=pxsize,
|
||||
physical_size_z=metadata["Info"]["Summary"]["z-step_um"]),
|
||||
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, exposure_time=metadata["Info"]["Exposure-ms"] / 1000,
|
||||
delta_t=(datetime.strptime(self.get_metadata(c, z, t)["Info"]["Time"],
|
||||
"%Y-%m-%d %H:%M:%S %z") - t0).seconds))
|
||||
|
||||
# compare channel names from metadata with filenames
|
||||
cnamelist = self.metadata.search('ChNames')
|
||||
cnamelist = [c for c in cnamelist if any([c in f for f in filelist])]
|
||||
pattern_c = re.compile(r"img_\d{3,}_(.*)_\d{3,}$")
|
||||
for c in range(size_c):
|
||||
ome.images[0].pixels.channels.append(
|
||||
model.Channel(
|
||||
id=f"Channel:{c}", name=pattern_c.findall(self.filedict[c, 0, 0].stem)[0],
|
||||
detector_settings=model.DetectorSettings(
|
||||
id="Detector:0", binning=metadata["Info"]["Hamamatsu_sCMOS-Binning"]),
|
||||
filter_set_ref=model.FilterSetRef(id='FilterSet:0')))
|
||||
return ome
|
||||
|
||||
self.filedict = {}
|
||||
maxc = 0
|
||||
maxz = 0
|
||||
maxt = 0
|
||||
for file in filelist:
|
||||
T = re.search(r'(?<=img_)\d{3,}', file)
|
||||
Z = re.search(r'\d{3,}(?=\.tif$)', file)
|
||||
C = file[T.end() + 1:Z.start() - 1]
|
||||
t = int(T.group(0))
|
||||
z = int(Z.group(0))
|
||||
if C in cnamelist:
|
||||
c = cnamelist.index(C)
|
||||
else:
|
||||
c = len(cnamelist)
|
||||
cnamelist.append(C)
|
||||
|
||||
self.filedict[(c, z, t)] = file
|
||||
if c > maxc:
|
||||
maxc = c
|
||||
if z > maxz:
|
||||
maxz = z
|
||||
if t > maxt:
|
||||
maxt = t
|
||||
self.cnamelist = [str(cname) for cname in cnamelist]
|
||||
|
||||
X = self.metadata.search('Width')[0]
|
||||
Y = self.metadata.search('Height')[0]
|
||||
self.shape = (int(X), int(Y), maxc + 1, maxz + 1, maxt + 1)
|
||||
|
||||
self.pxsize = self.metadata.re_search(r'(?i)pixelsize_?um', 0)[0]
|
||||
if self.zstack:
|
||||
self.deltaz = self.metadata.re_search(r'(?i)z-step_?um', 0)[0]
|
||||
if self.timeseries:
|
||||
self.settimeinterval = self.metadata.re_search(r'(?i)interval_?ms', 0)[0] / 1000
|
||||
if 'Hamamatsu' in self.metadata.search('Core-Camera', '')[0]:
|
||||
self.pxsizecam = 6.5
|
||||
self.title = self.metadata.search('Prefix')[0]
|
||||
self.acquisitiondate = self.metadata.search('Time')[0]
|
||||
self.exposuretime = [i / 1000 for i in self.metadata.search('Exposure-ms')]
|
||||
self.objective = self.metadata.search('ZeissObjectiveTurret-Label')[0]
|
||||
self.optovar = []
|
||||
for o in self.metadata.search('ZeissOptovar-Label'):
|
||||
a = re.search(r'\d?\d*[,.]?\d+(?=x$)', o)
|
||||
if hasattr(a, 'group'):
|
||||
self.optovar.append(float(a.group(0).replace(',', '.')))
|
||||
if self.pxsize == 0:
|
||||
self.magnification = int(re.findall(r'(\d+)x', self.objective)[0]) * self.optovar[0]
|
||||
self.pxsize = self.pxsizecam / self.magnification
|
||||
def open(self):
|
||||
if not self.path.name.startswith("Pos"):
|
||||
path = self.path / f"Pos{self.series}"
|
||||
else:
|
||||
self.magnification = self.pxsizecam / self.pxsize
|
||||
self.pcf = self.shape[2] * self.metadata.re_search(r'(?i)conversion\sfactor\scoeff', 1)
|
||||
self.filter = self.metadata.search('ZeissReflectorTurret-Label', self.filter)[0]
|
||||
path = self.path
|
||||
|
||||
filelist = sorted([file for file in path.iterdir() if re.search(r'^img_\d{3,}.*\d{3,}.*\.tif$', 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()}
|
||||
|
||||
# compare channel names from metadata with filenames
|
||||
cnamelist = metadata["Info"]["Summary"]["ChNames"]
|
||||
cnamelist = [c for c in cnamelist if any([c in f.name for f in filelist])]
|
||||
|
||||
pattern_t = re.compile(r"img_(\d{3,})")
|
||||
pattern_c = re.compile(r"img_\d{3,}_(.*)_\d{3,}$")
|
||||
pattern_z = re.compile(r"(\d{3,})$")
|
||||
self.filedict = {(int(pattern_t.findall(file.stem)[0]),
|
||||
int(pattern_z.findall(file.stem)[0]),
|
||||
cnamelist.index(pattern_c.findall(file.stem)[0])): file for file in filelist}
|
||||
|
||||
def __frame__(self, c=0, z=0, t=0):
|
||||
return tifffile.imread(os.path.join(self.path, self.filedict[(c, z, t)]))
|
||||
return tifffile.imread(self.path / self.filedict[(c, z, t)])
|
||||
|
||||
Reference in New Issue
Block a user