fix bug reading dragonfly acquisitions

iohub/mmstack.py

@@ -12,6 +12,7 @@
 from numpy.typing import ArrayLike
 from tifffile import TiffFile
 from xarray import DataArray
+from natsort import natsorted
 
 from iohub.mm_fov import MicroManagerFOV, MicroManagerFOVMapping
 
@@ -126,6 +127,7 @@ def _parse_data(self):
         self._store = series.aszarr()
         _logger.debug(f"Opened {self._store}.")
         data = da.from_zarr(zarr.open(self._store))
+        data = data[:self.positions] # not all positions may have been acquires
         self.dtype = data.dtype
         img = DataArray(data, dims=raw_dims, name=self.dirname)
         xarr = img.expand_dims(
@@ -150,7 +152,7 @@ def xdata(self):
         return self._xdata
 
     def __len__(self) -> int:
-        return self.positions
+        return len(self.xdata.keys())
 
     def __getitem__(self, key: str | int) -> MMOmeTiffFOV:
         key = _normalize_mm_pos_key(key)
@@ -218,15 +220,14 @@ def _set_mm_meta(self, mm_meta: dict) -> None:
             mm_version == "2.0.1 20220920"
             and self._mm_meta["Summary"]["Prefix"] == "raw_data"
         ):
-            file_names = set(
-                [(key[0], val[0]) for key, val in self.coord_map.items()]
-            )
+            files = natsorted(self.root.glob("*.ome.tif"))
+            self.positions = len(files)  # not all positions are saved
 
             if self._mm_meta["Summary"]["Positions"] > 1:
                 self._stage_positions = [None] * self.positions
 
-                for p_idx, file_name in file_names:
-                    site_idx = int(file_name.split("_")[-1].split("-")[0])
+                for p_idx, file_name in enumerate(files):
+                    site_idx = int(str(file_name).split("_")[-1].split("-")[0])
                     pos = self._simplify_stage_position(
                         self._mm_meta["Summary"]["StagePositions"][site_idx]
                     )