Fix bug determining number of rows and cols (#214)

* fix bug determining number of rows and cols

* add another XY Stage variation

* add docs and fix style

Author: ieivanov

iohub/convert.py

@@ -180,32 +180,41 @@ def _make_default_grid(self):
             )
 
     def _get_position_coords(self):
-        row_max = 0
-        col_max = 0
-        coords_list = []
+        """Get the position coordinates from the reader metadata.
+
+        Raises:
+            ValueError: If stage positions are not available.
+
+        Returns:
+            list: XY stage position coordinates.
+            int: Number of grid rows.
+            int: Number of grid columns.
+        """
+        rows = set()
+        cols = set()
+        xy_coords = []
 
-        # TODO: read rows, cols directly from XY corods
         # TODO: account for non MM2gamma meta?
         if not self.reader.stage_positions:
             raise ValueError("Stage positions not available.")
         for idx, pos in enumerate(self.reader.stage_positions):
-            stage_pos = pos.get("XYStage") or pos.get("XY")
+            stage_pos = (
+                pos.get("XYStage") or pos.get("XY") or pos.get("XY Stage")
+            )
             if stage_pos is None:
                 raise ValueError(
                     f"Stage position is not available for position {idx}"
                 )
-            coords_list.append(stage_pos)
+            xy_coords.append(stage_pos)
             try:
-                row = pos["GridRow"]
-                col = pos["GridCol"]
+                rows.add(pos["GridRow"])
+                cols.add(pos["GridCol"])
             except KeyError:
                 raise ValueError(
                     f"Grid indices not available for position {idx}"
                 )
-            row_max = row if row > row_max else row_max
-            col_max = col if col > col_max else col_max
 
-        return coords_list, row_max + 1, col_max + 1
+        return xy_coords, len(rows), len(cols)
 
     def _get_pos_names(self):
         """Append a list of pos names in ascending order