From 4563908254d4683197a72ba0a293382997825a75 Mon Sep 17 00:00:00 2001
From: "w.pomp" <w.pomp@nki.nl>
Date: Tue, 3 Mar 2026 15:56:27 +0100
Subject: [PATCH] - make paths absolute if possible - seqfind: read some
 metadata from display_and_comments.txt if needed and present

---
 ndbioimage/__init__.py        |  6 ++++--
 ndbioimage/readers/seqread.py | 20 +++++++++++++++-----
 pyproject.toml                |  2 +-
 3 files changed, 20 insertions(+), 8 deletions(-)

diff --git a/ndbioimage/__init__.py b/ndbioimage/__init__.py
index 9a5a27f..c0f31de 100755
--- a/ndbioimage/__init__.py
+++ b/ndbioimage/__init__.py
@@ -1306,9 +1306,11 @@ class Imread(np.lib.mixins.NDArrayOperatorsMixin, ABC):
     @staticmethod
     def split_path_series(path: Path | str) -> tuple[Path, int]:
         if isinstance(path, str):
-            path = Path(path)
+            path = Path(path).absolute()
         if isinstance(path, Path) and path.name.startswith("Pos") and path.name.lstrip("Pos").isdigit():
-            return path.parent, int(path.name.lstrip("Pos"))
+            return path.absolute().parent, int(path.name.lstrip("Pos"))
+        if isinstance(path, Path):
+            return path.absolute(), 0
         return path, 0
 
     def view(self, *args: Any, **kwargs: Any) -> View:
diff --git a/ndbioimage/readers/seqread.py b/ndbioimage/readers/seqread.py
index ee72d8f..5fd83ed 100644
--- a/ndbioimage/readers/seqread.py
+++ b/ndbioimage/readers/seqread.py
@@ -1,4 +1,5 @@
 import re
+import warnings
 from abc import ABC
 from datetime import datetime
 from itertools import product
@@ -59,9 +60,10 @@ class Reader(AbstractReader, ABC):
         ome = model.OME()
         with tifffile.TiffFile(self.filedict[0, 0, 0]) as tif:
             metadata = {key: yaml.safe_load(value) for key, value in tif.pages[0].tags[50839].value.items()}
-        ome.experimenters.append(
-            model.Experimenter(id="Experimenter:0", user_name=metadata["Info"]["Summary"]["UserName"])
-        )
+        if "Summary" in metadata["Info"] and "UserName" in metadata["Info"]["Summary"]:
+            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(
@@ -112,7 +114,7 @@ class Reader(AbstractReader, ABC):
                     type=pixel_type,
                     physical_size_x=pxsize,
                     physical_size_y=pxsize,
-                    physical_size_z=metadata["Info"]["Summary"]["z-step_um"],
+                    physical_size_z=metadata["Info"]["Summary"]["z-step_um"] if "Summary" in metadata["Info"] else None,
                 ),
                 objective_settings=model.ObjectiveSettings(id="Objective:0"),
             )
@@ -164,7 +166,15 @@ class Reader(AbstractReader, ABC):
             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"]
+        if "Summary" in metadata["Info"] and "ChNames" in metadata["Info"]["Summary"]:
+            cnamelist = metadata["Info"]["Summary"]["ChNames"]
+        elif (self.path.parent / "display_and_comments.txt").exists():
+            warnings.warn(f"{self.path} is missing some metadata")
+            with open(self.path.parent / "display_and_comments.txt") as f:
+                cnamelist = [channel["Name"] for channel in yaml.safe_load(f)["Channels"]]
+        else:
+            raise ValueError("could not find metadata describing the order of the channels")
+
         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,}$", re.IGNORECASE)
diff --git a/pyproject.toml b/pyproject.toml
index add0b61..c8bfc7c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [project]
 name = "ndbioimage"
-version = "2026.1.2"
+version = "2026.3.0"
 description = "Bio image reading, metadata and some affine registration."
 authors = [
     { name = "W. Pomp", email = "w.pomp@nki.nl" }