- slice notation for time argument on command line

- fix seqread can_open

ndbioimage/__init__.py

@@ -978,13 +978,20 @@ class Imread(np.lib.mixins.NDArrayOperatorsMixin, ABC):
 
     def save_as_movie(self, fname: Path | str = None,
                       c: int | Sequence[int] = None, z: int | Sequence[int] = None,  # noqa
-                      t: int | Sequence[int] = None,  # noqa
+                      t: str | int | Sequence[int] = None,  # noqa
                       colors: tuple[str] = None, brightnesses: tuple[float] = None,
                       scale: int = None, bar: bool = True) -> None:
         """ saves the image as a mp4 or mkv file """
         from matplotlib.colors import to_rgb
         from skvideo.io import FFmpegWriter
 
+        if t is None:
+            t = np.arange(self.shape['t'])
+        elif isinstance(t, str):
+            t = eval(f"np.arange(self.shape['t'])[{t}]")
+        elif np.isscalar(t):
+            t = (t,)
+
         def get_ab(tyx: Imread, p: tuple[float, float] = (1, 99)) -> tuple[float, float]:
             s = tyx.flatten()
             s = s[s > 0]
@@ -1014,9 +1021,9 @@ class Imread(np.lib.mixins.NDArrayOperatorsMixin, ABC):
                             '-vf': f'setpts={25 / 7}*PTS,scale={shape_x}:{shape_y}:flags=neighbor'}
         ) as movie:
             im = self.transpose('tzcyx')
-            for t in trange(self.shape['t'], desc='Saving movie', disable=not bar):
+            for ti in tqdm(t, desc='Saving movie', disable=not bar):
                 movie.writeFrame(np.max([cframe(yx, c, a, b / s, scale)
-                                         for yx, a, b, c, s in zip(im[t].max('z'), *ab, colors, brightnesses)], 0))
+                                         for yx, a, b, c, s in zip(im[ti].max('z'), *ab, colors, brightnesses)], 0))
 
     def save_as_tiff(self, fname: Path | str = None, c: int | Sequence[int] = None, z: int | Sequence[int] = None,
                      t: int | Sequence[int] = None, split: bool = False, bar: bool = True, pixel_type: str = 'uint16',
@@ -1311,7 +1318,7 @@ def main() -> None:
     parser.add_argument('-r', '--register', help='register channels', action='store_true')
     parser.add_argument('-c', '--channel', help='channel', type=int, default=None)
     parser.add_argument('-z', '--zslice', help='z-slice', type=int, default=None)
-    parser.add_argument('-t', '--time', help='time', type=int, default=None)
+    parser.add_argument('-t', '--time', help='time', type=str, default=None)
     parser.add_argument('-s', '--split', help='split channels', action='store_true')
     parser.add_argument('-f', '--force', help='force overwrite', action='store_true')
     parser.add_argument('-C', '--movie-colors', help='colors for channels in movie', type=str, nargs='*')

ndbioimage/readers/seqread.py

@@ -46,11 +46,9 @@ class Reader(AbstractReader, ABC):
 
     @staticmethod
     def _can_open(path):
-        if isinstance(path, Path) and path.is_dir():
+        pat = re.compile(r'(?:\d+-)?Pos.*', re.IGNORECASE)
-            files = [file for file in path.iterdir() if file.name.lower().startswith('pos')]
+        return (isinstance(path, Path) and path.is_dir() and
-            return len(files) > 0 and files[0].is_dir()
+                (pat.match(path.name) or any(file.is_dir() and pat.match(file.stem) for file in path.iterdir())))
-        else:
-            return False
 
     def get_ome(self):
         ome = model.OME()
@@ -104,7 +102,7 @@ class Reader(AbstractReader, ABC):
                       the_c=c, the_z=z, the_t=t, exposure_time=metadata['Info']['Exposure-ms'] / 1000))
 
         # compare channel names from metadata with filenames
-        pattern_c = re.compile(r'img_\d{3,}_(.*)_\d{3,}$')
+        pattern_c = re.compile(r'img_\d{3,}_(.*)_\d{3,}$', re.IGNORECASE)
         for c in range(size_c):
             ome.images[0].pixels.channels.append(
                 model.Channel(
@@ -115,13 +113,13 @@ class Reader(AbstractReader, ABC):
         return ome
 
     def open(self):
-        pat = re.compile(r'(?:\d+-)?Pos.*')
+        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]
         else:
             path = self.path
 
-        pat = re.compile(r'^img_\d{3,}.*\d{3,}.*\.(tif|TIF)$')
+        pat = re.compile(r'^img_\d{3,}.*\d{3,}.*\.tif$', re.IGNORECASE)
         filelist = sorted([file for file in path.iterdir() if pat.search(file.name)])
         with tifffile.TiffFile(self.path / filelist[0]) as tif:
             metadata = {key: yaml.safe_load(value) for key, value in tif.pages[0].tags[50839].value.items()}
@@ -130,9 +128,9 @@ class Reader(AbstractReader, ABC):
         cnamelist = metadata['Info']['Summary']['ChNames']
         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,}$')
+        pattern_c = re.compile(r'img_\d{3,}_(.*)_\d{3,}$', re.IGNORECASE)
         pattern_z = re.compile(r'(\d{3,})$')
-        pattern_t = re.compile(r'img_(\d{3,})')
+        pattern_t = re.compile(r'img_(\d{3,})', re.IGNORECASE)
         self.filedict = {(cnamelist.index(pattern_c.findall(file.stem)[0]),  # noqa
                           int(pattern_z.findall(file.stem)[0]),
                           int(pattern_t.findall(file.stem)[0])): file for file in filelist}

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "ndbioimage"
-version = "2024.9.1"
+version = "2024.9.2"
 description = "Bio image reading, metadata and some affine registration."
 authors = ["W. Pomp <w.pomp@nki.nl>"]
 license = "GPLv3"
@@ -22,7 +22,7 @@ pint = "*"
 tqdm = "*"
 lxml = "*"
 pyyaml = "*"
-parfor = ">=2024.9.1"
+parfor = ">=2024.9.2"
 JPype1 = "*"
 SimpleITK-SimpleElastix = [
     { version = "*", python = "<3.12" },