- bump ome-types to 0.4

ndbioimage/readers/cziread.py

@@ -73,9 +73,9 @@ class Reader(AbstractReader, ABC):
 
         for detector in instrument.find("Detectors"):
             try:
-                detector_type = model.detector.Type(text(detector.find("Type")).upper() or "")
+                detector_type = model.Detector_Type(text(detector.find("Type")).upper() or "")
             except ValueError:
-                detector_type = model.detector.Type.OTHER
+                detector_type = model.Detector_Type.OTHER
 
             ome.instruments[0].detectors.append(
                 model.Detector(
@@ -123,8 +123,8 @@ class Reader(AbstractReader, ABC):
         objective_settings = image.find("ObjectiveSettings")
         scenes = image.find("Dimensions").find("S").find("Scenes")
         center_position = [float(pos) for pos in text(scenes[0].find("CenterPosition")).split(',')]
-        um = model.simple_types.UnitsLength.MICROMETER
+        um = model.UnitsLength.MICROMETER
-        nm = model.simple_types.UnitsLength.NANOMETER
+        nm = model.UnitsLength.NANOMETER
 
         ome.images.append(
             model.Image(
@@ -163,9 +163,9 @@ class Reader(AbstractReader, ABC):
             laser_scan_info = channel.find("LaserScanInfo")
             detector = detector_settings.find("Detector")
             try:
-                binning = model.simple_types.Binning(text(detector_settings.find("Binning")))
+                binning = model.Binning(text(detector_settings.find("Binning")))
             except ValueError:
-                binning = model.simple_types.Binning.OTHER
+                binning = model.Binning.OTHER
 
             light_sources_settings = channel.find("LightSourcesSettings")
             # no space in ome for multiple lightsources simultaneously
@@ -182,7 +182,7 @@ class Reader(AbstractReader, ABC):
                     id=f"Channel:0:{idx}",
                     name=channel.attrib["Name"],
                     acquisition_mode=text(channel.find("AcquisitionMode")),
-                    color=model.simple_types.Color(text(channels_ds[channel.attrib["Id"]].find("Color"))),
+                    color=model.Color(text(channels_ds[channel.attrib["Id"]].find("Color"))),
                     detector_settings=model.DetectorSettings(
                         id=detector.attrib["Id"].replace(" ", ""),
                         binning=binning),
@@ -239,9 +239,9 @@ class Reader(AbstractReader, ABC):
 
         for detector in instrument.find("Detectors"):
             try:
-                detector_type = model.detector.Type(text(detector.find("Type")).upper() or "")
+                detector_type = model.Detector_Type(text(detector.find("Type")).upper() or "")
             except ValueError:
-                detector_type = model.detector.Type.OTHER
+                detector_type = model.Detector_Type.OTHER
 
             ome.instruments[0].detectors.append(
                 model.Detector(
@@ -306,8 +306,8 @@ class Reader(AbstractReader, ABC):
         objective_settings = image.find("ObjectiveSettings")
         scenes = image.find("Dimensions").find("S").find("Scenes")
         positions = scenes[0].find("Positions")[0]
-        um = model.simple_types.UnitsLength.MICROMETER
+        um = model.UnitsLength.MICROMETER
-        nm = model.simple_types.UnitsLength.NANOMETER
+        nm = model.UnitsLength.NANOMETER
 
         ome.images.append(
             model.Image(
@@ -351,9 +351,9 @@ class Reader(AbstractReader, ABC):
             laser_scan_info = channel.find("LaserScanInfo")
             detector = detector_settings.find("Detector")
             try:
-                binning = model.simple_types.Binning(text(detector_settings.find("Binning")))
+                binning = model.Binning(text(detector_settings.find("Binning")))
             except ValueError:
-                binning = model.simple_types.Binning.OTHER
+                binning = model.Binning.OTHER
 
             filterset = text(channels_ts[key].find("BeamSplitters")[0].find("Filter"))
             filterset_idx = [filterset.model for filterset in ome.instruments[0].filter_sets].index(filterset)
@@ -375,7 +375,7 @@ class Reader(AbstractReader, ABC):
                     id=f"Channel:0:{idx}",
                     name=channel.attrib["Name"],
                     acquisition_mode=text(channel.find("AcquisitionMode")),
-                    color=model.simple_types.Color(text(channels_ds[channel.attrib["Id"]].find("Color"))),
+                    color=model.Color(text(channels_ds[channel.attrib["Id"]].find("Color"))),
                     detector_settings=model.DetectorSettings(id=detector.attrib["Id"], binning=binning),
                     emission_wavelength=text(channel.find("EmissionWavelength")),
                     excitation_wavelength=light_source_settings.wavelength,

ndbioimage/readers/fijiread.py

@@ -45,7 +45,7 @@ class Reader(AbstractReader, ABC):
         size_y, size_x = self.reader.pages[0].shape
         size_c, size_z = 1, 1
         size_t = int(np.floor((self.reader.filehandle.size - self.reader.pages[0].dataoffsets[0]) / self.count))
-        pixel_type = model.simple_types.PixelType(self.reader.pages[0].dtype.name)
+        pixel_type = model.PixelType(self.reader.pages[0].dtype.name)
         ome = model.OME()
         ome.instruments.append(model.Instrument())
         ome.images.append(

ndbioimage/readers/ndread.py

@@ -19,12 +19,12 @@ class Reader(AbstractReader, ABC):
             return size_x, size_y, size_c, size_z, size_t
         size_x, size_y, size_c, size_z, size_t = shape(*self.array.shape)
         try:
-            pixel_type = model.simple_types.PixelType(self.array.dtype.name)
+            pixel_type = model.PixelType(self.array.dtype.name)
         except ValueError:
             if self.array.dtype.name.startswith('int'):
-                pixel_type = model.simple_types.PixelType('int32')
+                pixel_type = model.PixelType('int32')
             else:
-                pixel_type = model.simple_types.PixelType('float')
+                pixel_type = model.PixelType('float')
 
         ome = model.OME()
         ome.instruments.append(model.Instrument())

ndbioimage/readers/seqread.py

@@ -4,7 +4,7 @@ import re
 from pathlib import Path
 from functools import cached_property
 from ome_types import model
-from ome_types._base_type import quantity_property
+from ome_types.units import _quantity_property
 from itertools import product
 from datetime import datetime
 from abc import ABC
@@ -25,7 +25,7 @@ class Plane(model.Plane):
     def __init__(self, t0, file, **kwargs):
         super().__init__(**kwargs)
         setattr(self.__class__, 'delta_t', lazy_property(self.get_delta_t, 'delta_t', 't0', 'file'))
-        setattr(self.__class__, 'delta_t_quantity', quantity_property('delta_t'))
+        setattr(self.__class__, 'delta_t_quantity', _quantity_property('delta_t'))
         self.__dict__['t0'] = t0
         self.__dict__['file'] = file
 
@@ -57,7 +57,7 @@ class Reader(AbstractReader, ABC):
                 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))
+                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(

pyproject.toml

@@ -17,7 +17,7 @@ pandas = "*"
 tifffile = "*"
 czifile = "*"
 tiffwrite = "*"
-ome-types = "*"
+ome-types = "^0.4"
 pint = "*"
 tqdm = "*"
 lxml = "*"