From 8a66c570a67ed08c7874789cd0084a919b597712 Mon Sep 17 00:00:00 2001
From: Wim Pomp <w.pomp@nki.nl>
Date: Tue, 13 Feb 2024 17:46:23 +0100
Subject: [PATCH] - Fix bug wrt. supporting non-file images. - Make layers
 optional in czi metadata. - Delta_t for tif.

---
 ndbioimage/__init__.py        | 4 ++--
 ndbioimage/readers/cziread.py | 4 ++--
 ndbioimage/readers/tifread.py | 4 +++-
 pyproject.toml                | 2 +-
 4 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/ndbioimage/__init__.py b/ndbioimage/__init__.py
index f80ef42..8aafc8e 100755
--- a/ndbioimage/__init__.py
+++ b/ndbioimage/__init__.py
@@ -962,11 +962,11 @@ class AbstractReader(Imread, metaclass=ABCMeta):
         if isinstance(path, str):
             path = Path(path)
         self.path, self.series = self.split_path_series(path)
-        if isinstance(path, Path):
+        if isinstance(path, Path) and path.exists():
             self.title = self.path.name
             self.acquisitiondate = datetime.fromtimestamp(self.path.stat().st_mtime).strftime('%y-%m-%dT%H:%M:%S')
         else:  # ndarray
-            self.title = 'ndarray'
+            self.title = self.__class__.__name__
             self.acquisitiondate = 'now'
 
         self.reader = None
diff --git a/ndbioimage/readers/cziread.py b/ndbioimage/readers/cziread.py
index 43d276b..72ea635 100644
--- a/ndbioimage/readers/cziread.py
+++ b/ndbioimage/readers/cziread.py
@@ -354,7 +354,7 @@ class Reader(AbstractReader, ABC):
                 model.Plane(the_c=c, the_z=z, the_t=t, delta_t=delta_ts[t], exposure_time=exposure_times[c]))
 
         idx = 0
-        for layer in metadata.find("Layers"):
+        for layer in metadata.find("Layers") or []:
             rectangle = layer.find("Elements").find("Rectangle")
             if rectangle is not None:
                 geometry = rectangle.find("Geometry")
@@ -552,7 +552,7 @@ class Reader(AbstractReader, ABC):
                             position_z=float(positions.attrib["Z"]), position_z_unit=um))
 
         idx = 0
-        for layer in metadata.find("Layers"):
+        for layer in [] if (ml := metadata.find("Layers")) is None else ml:
             rectangle = layer.find("Elements").find("Rectangle")
             if rectangle is not None:
                 geometry = rectangle.find("Geometry")
diff --git a/ndbioimage/readers/tifread.py b/ndbioimage/readers/tifread.py
index 69ae39a..fa6c68b 100644
--- a/ndbioimage/readers/tifread.py
+++ b/ndbioimage/readers/tifread.py
@@ -51,6 +51,8 @@ class Reader(AbstractReader, ABC):
                          'float', 'double', 'complex', 'double-complex', 'bit'):
             dtype = 'float'
 
+        interval_t = metadata.get('interval', 0)
+
         ome = model.OME()
         ome.instruments.append(model.Instrument(id='Instrument:0'))
         ome.instruments[0].objectives.append(model.Objective(id='Objective:0'))
@@ -63,7 +65,7 @@ class Reader(AbstractReader, ABC):
                     dimension_order="XYCZT", type=dtype, physical_size_x=pxsize, physical_size_y=pxsize),
                 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, delta_t=0))
+            ome.images[0].pixels.planes.append(model.Plane(the_c=c, the_z=z, the_t=t, delta_t=interval_t * t))
         return ome
 
     def open(self):
diff --git a/pyproject.toml b/pyproject.toml
index 17172a7..c7f9a64 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "ndbioimage"
-version = "2023.12.2"
+version = "2024.2.0"
 description = "Bio image reading, metadata and some affine registration."
 authors = ["W. Pomp <w.pomp@nki.nl>"]
 license = "GPLv3"