- bugfix in tifread reading files missing a dimension in metadata

- tiff: read spacing

.gitignore

@@ -11,3 +11,4 @@
 /poetry.lock
 /dist/
 /uv.lock
+.agentbridge

README.md

@@ -1,4 +1,4 @@
-[![Pytest](https://github.com/wimpomp/ndbioimage/actions/workflows/pytest.yml/badge.svg)](https://github.com/wimpomp/ndbioimage/actions/workflows/pytest.yml)
+[![Pytest](https://git.wimpomp.nl/wim/ndbioimage/actions/workflows/pytest.yml/badge.svg)](https://git.wimpomp.nl/wim/ndbioimage/actions?workflow=pytest.yml)
 
 # ndbioimage
 

ndbioimage/__init__.py

@@ -191,7 +191,8 @@ def get_positions(path: str | Path) -> Optional[list[int]]:
     return subclass.get_positions(AbstractReader.split_path_series(path)[0])
 
 
-class Imread(np.lib.mixins.NDArrayOperatorsMixin, ABC):
+# noinspection PyAbstractClass
+class Imread(np.lib.mixins.NDArrayOperatorsMixin):
     """class to read image files, while taking good care of important metadata,
     currently optimized for .czi files, but can open anything that bioformats can handle
         path: path to the image file
@@ -1528,6 +1529,12 @@ class AbstractReader(Imread, metaclass=ABCMeta):
             self.immersionN = 1
 
         p = re.compile(r"(\d+):(\d+)$")
+        if self.ome.structured_annotations is not None:
+            tirf_angles = {}
+            for annotation in self.ome.structured_annotations:
+                if annotation.description is not None and annotation.description.lower() == "tirfangle":
+                    tirf_angles[int(annotation.id.split(":")[1])] = annotation.value
+            self.tirfangle = [angle for track, angle in sorted(tirf_angles.items(), key=lambda x: x[0])]
         try:
             self.track, self.detector = zip(
                 *[

ndbioimage/readers/cziread.py

@@ -248,7 +248,7 @@ class Reader(AbstractReader, ABC):
         return [(i - j, i - j + k) for i, j, k in zip(directory_entry.start, start, directory_entry.shape)]
 
     @cached_property
-    def tiles(self):
+    def tiles(self) -> tuple[int, int]:
         columns = 1
         rows = 1
         xml = self.reader.metadata()
@@ -335,6 +335,7 @@ class OmeParse:
         self.get_light_sources()
         self.get_filters()
         self.get_pixels()
+        self.get_tirf_angle()
         self.get_channels()
         self.get_planes()
         self.get_annotations()
@@ -555,6 +556,18 @@ class OmeParse:
             elif self.size_z > 1 and distance.attrib["Id"] == "Z":
                 self.ome.images[0].pixels.physical_size_z = float(self.text(distance.find("Value"))) * 1e6
 
+    def get_tirf_angle(self) -> None:
+        if self.version == "1.0":
+            for track_setup in self.multi_track_setup:
+                tirf_angle = track_setup.find("TirfAngle")
+                if tirf_angle is not None:
+                    self.ome.structured_annotations.append(
+                        model.DoubleAnnotation(
+                            description="TirfAngle", id="Annotation:0", value=50 * float(tirf_angle.text)
+                        )
+                    )
+                    self.ome.images[0].annotation_refs.append(model.AnnotationRef(id="Annotation:0"))
+
     @cached_property
     def positions(self) -> tuple[float, float, Optional[float]]:
         if self.version == "1.0":
@@ -677,14 +690,12 @@ class OmeParse:
                 else:
                     light_source_settings = None
 
-                self.ome.images[0].pixels.channels.append(
-                    model.Channel(
+                channel = dict(
                     id=f"Channel:{idx}",
                     name=channel.attrib["Name"],
                     acquisition_mode=self.text(channel.find("AcquisitionMode")).replace(  # type: ignore
                         "SingleMoleculeLocalisation", "SingleMoleculeImaging"
                     ),
-                        color=color,
                     detector_settings=model.DetectorSettings(
                         id=detector.attrib["Id"].replace(" ", ""), binning=binning
                     ),
@@ -697,7 +708,11 @@ class OmeParse:
                     light_source_settings=light_source_settings,
                     samples_per_pixel=samples_per_pixel,
                 )
-                )
+
+                if color is not None:
+                    channel["color"] = color
+
+                self.ome.images[0].pixels.channels.append(model.Channel(**channel))
 
     def get_planes(self) -> None:
         try:

ndbioimage/readers/seqread.py

@@ -192,4 +192,4 @@ class Reader(AbstractReader, ABC):
         }
 
     def __frame__(self, c=0, z=0, t=0):
-        return tifffile.imread(self.path / self.filedict[(c, z, t)])
+        return tifffile.imread(self.path / self.filedict[c, z, t])

ndbioimage/readers/tifread.py

@@ -1,16 +1,18 @@
 import re
 import warnings
 from abc import ABC
+from contextlib import ExitStack
 from functools import cached_property
 from itertools import product
 from pathlib import Path
+from typing import Any
 
 import numpy as np
 import tifffile
 import yaml
-from ome_types import from_xml, model
+from ome_types import OME, from_xml, model
 
-from .. import AbstractReader, try_default
+from .. import AbstractReader, Shape, try_default
 
 
 class Reader(AbstractReader, ABC):
@@ -18,7 +20,7 @@ class Reader(AbstractReader, ABC):
     do_not_pickle = "reader"
 
     @staticmethod
-    def _can_open(path):
+    def _can_open(path) -> bool:
         if isinstance(path, Path) and path.suffix in (".tif", ".tiff"):
             with tifffile.TiffFile(path) as tif:
                 return tif.is_imagej and tif.pages[-1]._nextifd() == 0  # noqa
@@ -26,13 +28,13 @@ class Reader(AbstractReader, ABC):
             return False
 
     @cached_property
-    def metadata(self):
+    def metadata(self) -> dict[str, Any]:
         return {
             key: try_default(yaml.safe_load, value, value) if isinstance(value, str) else value
             for key, value in self.reader.imagej_metadata.items()
         }
 
-    def get_ome(self):
+    def get_ome(self) -> OME:
         if self.reader.is_ome:
             pos_number_pat = re.compile(r"\d+")
 
@@ -88,13 +90,17 @@ class Reader(AbstractReader, ABC):
         page = self.reader.pages[0]
         size_y = page.imagelength
         size_x = page.imagewidth
-        if self.p_ndim == 3:
-            size_c = page.samplesperpixel
-            size_t = self.metadata.get("frames", 1)  # // C
-        else:
-            size_c = self.metadata.get("channels", 1)
-            size_t = self.metadata.get("frames", 1)
-        size_z = self.metadata.get("slices", 1)
+        max_c = max_z = max_t = 0
+        if self.file_dict:
+            for ci, zi, ti in self.file_dict.keys():
+                max_c = max(max_c, ci)
+                max_z = max(max_z, zi)
+                max_t = max(max_t, ti)
+
+        size_c: int = self.mod_shape["c"] * (max_c + 1)  # type: ignore
+        size_z: int = self.mod_shape["z"] * (max_z + 1)  # type: ignore
+        size_t: int = self.mod_shape["t"] * (max_t + 1)  # type: ignore
+
         if 282 in page.tags and 296 in page.tags and page.tags[296].value == 1:
             f = page.tags[282].value
             pxsize = f[1] / f[0]
@@ -142,11 +148,18 @@ class Reader(AbstractReader, ABC):
         )
         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, delta_t=interval_t * t))
+        if (spacing := self.metadata.get("spacing")) is not None:
+            ome.images[0].pixels.physical_size_z = spacing
+        if (unit := self.metadata.get("unit")) is not None and unit.lower() != "micron":
+            raise ValueError(f"cannot parse unit {unit}")
+
         return ome
 
-    def open(self):
+    def open(self) -> None:
         if self.series != 0:
-            raise FileNotFoundError(f"Series {self.series} not found in {self.path}. Tifread only supports one series.")
+            raise FileNotFoundError(
+                f"Series {self.series} not found in {self.path}. Tifread only supports one series."
+            )
         self.reader = tifffile.TiffFile(self.path)
         page = self.reader.pages.first
         self.p_ndim = page.ndim  # noqa
@@ -154,19 +167,68 @@ class Reader(AbstractReader, ABC):
             self.p_transpose = [i for i in [page.axes.find(j) for j in "SYX"] if i >= 0]  # noqa
         else:
             self.p_transpose = [i for i in [page.axes.find(j) for j in "YX"] if i >= 0]  # noqa
+        self.file_dict = {}  # noqa
+        pat = re.compile(r"^.*?((?:_[czt]\d+)*)$", re.IGNORECASE)
+        if (m := pat.match(self.path.stem)) is not None:
+            m = m.group(1)
+            cpat = re.compile(r"_c(\d+)", re.IGNORECASE)
+            zpat = re.compile(r"_z(\d+)", re.IGNORECASE)
+            tpat = re.compile(r"_t(\d+)", re.IGNORECASE)
+            for file in self.path.parent.glob(
+                re.sub(m, re.sub(r"\d+", "*", m), self.path.stem, re.IGNORECASE) + self.path.suffix
+            ):
+                m = pat.match(file.stem)
+                if m:
+                    m = m.group(0)
+                    c = cpat.findall(m)
+                    z = zpat.findall(m)
+                    t = tpat.findall(m)
+                    c = int(c[0]) if len(c) else 0
+                    z = int(z[0]) if len(z) else 0
+                    t = int(t[0]) if len(t) else 0
+                    self.file_dict[c, z, t] = file.name
 
-    def close(self):
+        page = self.reader.pages[0]
+        if self.p_ndim == 3:
+            mod_c = page.samplesperpixel
+            mod_t = self.metadata.get("frames", 1)  # // C
+        else:
+            mod_c = self.metadata.get("channels", 1)
+            mod_t = self.metadata.get("frames", 1)
+
+        mod_z = self.metadata.get("slices")
+        if mod_z is None:
+            if self.metadata.get("spacing") is None:
+                mod_t = len(self.reader.pages)
+            else:
+                mod_z = len(self.reader.pages)
+
+        self.mod_shape = Shape((mod_c or 1, mod_z or 1, mod_t or 1), "czt")  # noqa
+
+    def close(self) -> None:
         self.reader.close()
 
-    def __frame__(self, c: int, z: int, t: int):
+    def __frame__(self, c: int, z: int, t: int) -> np.ndarray:
+        with ExitStack() as stack:
+            if self.file_dict:
+                filename = self.file_dict[
+                    c - c % self.mod_shape["c"], z - z % self.mod_shape["z"], t - t % self.mod_shape["t"]
+                ]
+                if self.reader.filename == filename:
+                    reader = self.reader
+                else:
+                    reader = stack.enter_context(tifffile.TiffFile(self.path.parent / filename))
+            else:
+                reader = self.reader
+
             dimension_order = self.ome.images[0].pixels.dimension_order.value
             if self.p_ndim == 3:
                 axes = "".join([ax.lower() for ax in dimension_order if ax.lower() in "zt"])
-            ct = {"z": z, "t": t}
-            n = sum([ct[ax] * np.prod(self.base_shape[axes[:i]]) for i, ax in enumerate(axes)])
-            return np.transpose(self.reader.asarray(int(n)), self.p_transpose)[int(c)]
+                ct = {"z": z % self.mod_shape["z"], "t": t % self.mod_shape["t"]}
+                n = sum([ct[ax] * np.prod(self.mod_shape[axes[:i]]) for i, ax in enumerate(axes)])
+                return np.transpose(reader.asarray(int(n)), self.p_transpose)[int(c % self.mod_shape["c"])]
             else:
                 axes = "".join([ax.lower() for ax in dimension_order if ax.lower() in "czt"])
-            czt = {"c": c, "z": z, "t": t}
-            n = sum([czt[ax] * np.prod(self.base_shape[axes[:i]]) for i, ax in enumerate(axes)])
-        return np.transpose(self.reader.asarray(int(n)), self.p_transpose)
+                czt = {"c": c % self.mod_shape["c"], "z": z % self.mod_shape["z"], "t": t % self.mod_shape["t"]}
+                n = sum([czt[ax] * np.prod(self.mod_shape[axes[:i]]) for i, ax in enumerate(axes)])
+                return np.transpose(reader.asarray(int(n)), self.p_transpose)

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "ndbioimage"
-version = "2026.4.0"
+version = "2026.9.0"
 description = "Bio image reading, metadata and some affine registration."
 authors = [
     { name = "W. Pomp", email = "w.pomp@nki.nl" }
@@ -24,8 +24,8 @@ dependencies = [
     "pyyaml",
     "SimpleITK-SimpleElastix; sys_platform != 'darwin'",
     "scikit-image",
-    "tifffile <= 2025.1.10",
-    "tiffwrite >= 2024.12.1",
+    "tifffile >= 2024.1.30, <= 2025.1.10",
+    "tiffwrite >= 2026.5.0",
     "tqdm",
 ]
 
@@ -35,7 +35,7 @@ write = ["matplotlib", "scikit-video"]
 bioformats = ["JPype1"]
 
 [project.urls]
-repository = "https://git.wimpomp.nl/wim/focusfeedbackgui"
+repository = "https://git.wimpomp.nl/wim/ndbioimage"
 
 [project.scripts]
 ndbioimage = "ndbioimage:main"