Draft convert RGB images

iohub/convert.py

@@ -394,7 +394,8 @@ def __call__(self) -> None:
             ):
                 zarr_img = self.writer[zarr_pos_name]["0"]
                 to_zarr(fov.xdata.data.rechunk(self.chunks), zarr_img)
-                self._convert_image_plane_metadata(fov, zarr_img.path)
+                # Skip image plane metadata conversion, throws error
+                # self._convet_image_plane_metadata(fov, zarr_img.path)
         self.writer.zgroup.attrs.update(self.metadata)
         self.writer.close()
         self.reader.close()

iohub/mmstack.py

@@ -140,6 +140,13 @@ def _parse_data(self):
             (axis, size)
             for axis, size in zip(series.get_axes(), series.get_shape())
         )
+        _rgb = False
+        if "S" in raw_dims and "C" not in raw_dims:
+            # Map samples "S" from RGB images to channels "C"
+            # in datasets that don't already have a channel dimension
+            _rgb = True
+            _channels = raw_dims.pop("S")
+            raw_dims["C"] = _channels
         axes = ("R", "T", "C", "Z", "Y", "X")
         dims = dict((ax, raw_dims.get(ax, 1)) for ax in axes)
         _logger.debug(f"Got dataset dimensions from tifffile: {dims}.")
@@ -163,6 +170,9 @@ def _parse_data(self):
         xarr = img.expand_dims(
             [ax for ax in axes if ax not in img.dims]
         ).transpose(*axes)
+        # Rename RGB channels
+        if _rgb and self.channels == 3:
+            self.channel_names = ["Red", "Green", "Blue"]
         if self.channels > len(self.channel_names):
             for c in range(self.channels):
                 if c >= len(self.channel_names):