- bugfix: reading wrong frame in some cases when opened with custom axes argument

- some more try except in czi metadata reading
- bugfix: Pos pattern in seqread

ndbioimage/__init__.py

@@ -1200,6 +1200,7 @@ class AbstractReader(Imread, metaclass=ABCMeta):
         image = self.ome.images[self.series if len(self.ome.images) > 1 else 0]
         pixels = image.pixels
         self.shape = pixels.size_y, pixels.size_x, pixels.size_c, pixels.size_z, pixels.size_t
+        self.base_shape = Shape((pixels.size_y, pixels.size_x, pixels.size_c, pixels.size_z, pixels.size_t), 'yxczt')
         self.dtype = pixels.type.value if dtype is None else dtype
         self.pxsize = pixels.physical_size_x_quantity
         try:

ndbioimage/readers/cziread.py

@@ -184,7 +184,7 @@ class Reader(AbstractReader, ABC):
         return OmeParse.get_ome(self.reader, self.filedict)
 
     def __frame__(self, c: int = 0, z: int = 0, t: int = 0) -> np.ndarray:
-        f = np.zeros(self.base.shape['yx'], self.dtype)
+        f = np.zeros(self.base_shape['yx'], self.dtype)
         if (c, z, t) in self.filedict:
             directory_entries = self.filedict[c, z, t]
             x_min = min([f.start[f.axes.index('X')] for f in directory_entries])
@@ -340,11 +340,14 @@ class OmeParse:
         if self.version == '1.0':
             for idx, tube_lens in enumerate({self.text(track_setup.find('TubeLensPosition'))
                                              for track_setup in self.multi_track_setup}):
+                try:
+                    nominal_magnification = float(re.findall(r'\d+[,.]\d*', tube_lens)[0].replace(',', '.'))
+                except Exception:  # noqa
+                    nominal_magnification = 1.0
+
                 self.ome.instruments[0].objectives.append(
                     model.Objective(id=f'Objective:Tubelens:{idx}', model=tube_lens,
-                                    nominal_magnification=float(
-                                        re.findall(r'\d+[,.]\d*', tube_lens)[0].replace(',', '.'))
-                                    ))
+                                    nominal_magnification=nominal_magnification))
         elif self.version in ('1.1', '1.2'):
             for tubelens in self.instrument.find('TubeLenses'):
                 try:
@@ -362,6 +365,7 @@ class OmeParse:
     def get_light_sources(self) -> None:
         if self.version == '1.0':
             for light_source in self.def_list(self.instrument.find('LightSources')):
+                try:
                     if light_source.find('LightSourceType').find('Laser') is not None:
                         self.ome.instruments[0].lasers.append(
                             model.Laser(
@@ -370,14 +374,19 @@ class OmeParse:
                                 power=float(self.text(light_source.find('Power'))),
                                 wavelength=float(
                                     self.text(light_source.find('LightSourceType').find('Laser').find('Wavelength')))))
+                except AttributeError:
+                    pass
         elif self.version in ('1.1', '1.2'):
             for light_source in self.def_list(self.instrument.find('LightSources')):
+                try:
                     if light_source.find('LightSourceType').find('Laser') is not None:
                         self.ome.instruments[0].lasers.append(
                             model.Laser(
                                 id=f"LightSource:{light_source.attrib['Id']}",
                                 power=float(self.text(light_source.find('Power'))),
                                 wavelength=float(light_source.attrib['Id'][-3:])))
+                except AttributeError:
+                    pass
 
     def get_filters(self) -> None:
         if self.version == '1.0':

ndbioimage/readers/fijiread.py

@@ -26,7 +26,7 @@ class Reader(AbstractReader, ABC):
 
     def __frame__(self, c, z, t):  # Override this, return the frame at c, z, t
         self.reader.filehandle.seek(self.offset + t * self.count)
-        return np.reshape(unpack(self.fmt, self.reader.filehandle.read(self.count)), self.shape['yx'])
+        return np.reshape(unpack(self.fmt, self.reader.filehandle.read(self.count)), self.base_shape['yx'])
 
     def open(self):
         warn(f'File {self.path.name} is probably damaged, opening with fijiread.')

ndbioimage/readers/seqread.py

@@ -114,9 +114,15 @@ class Reader(AbstractReader, ABC):
         return ome
 
     def open(self):
-        pat = re.compile(r'(?:\d+-)?Pos.*', re.IGNORECASE)
-        if pat.match(self.path.name) is None:
-            path = sorted(file for file in self.path.iterdir() if pat.match(file.name))[self.series]
+        # /some_path/Pos4: path = /some_path, series = 4
+        # /some_path/5-Pos_001_005: path = /some_path/5-Pos_001_005, series = 0
+        if re.match(r'(?:\d+-)?Pos.*', self.path.name, re.IGNORECASE) is None:
+            pat = re.compile(rf'^(?:\d+-)?Pos{self.series}$', re.IGNORECASE)
+            files = sorted(file for file in self.path.iterdir() if pat.match(file.name))
+            if len(files):
+                path = files[0]
+            else:
+                raise FileNotFoundError(self.path / pat.pattern)
         else:
             path = self.path
 

ndbioimage/readers/tifread.py

@@ -80,6 +80,6 @@ class Reader(AbstractReader, ABC):
 
     def __frame__(self, c, z, t):
         if self.p_ndim == 3:
-            return np.transpose(self.reader.asarray(z + t * self.base.shape['z']), self.p_transpose)[c]
+            return np.transpose(self.reader.asarray(z + t * self.base_shape['z']), self.p_transpose)[c]
         else:
-            return self.reader.asarray(c + z * self.base.shape['c'] + t * self.base.shape['c'] * self.base.shape['z'])
+            return self.reader.asarray(c + z * self.base_shape['c'] + t * self.base_shape['c'] * self.base_shape['z'])

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "ndbioimage"
-version = "2025.1.0"
+version = "2025.1.1"
 description = "Bio image reading, metadata and some affine registration."
 authors = ["W. Pomp <w.pomp@nki.nl>"]
 license = "GPLv3"