OpenCell reader extension (#197)

* stage positions parsing for opencell datasets

* formatting

* don't overwrite frames, slices, and channels in `_set_mm_meta`

* fix error getting stage position

iohub/convert.py

@@ -310,10 +310,10 @@ def _get_pos_names(self):
         if self.p > 1:
             self.pos_names = []
             for p in range(self.p):
-                name = (
-                    self.summary_metadata["StagePositions"][p].get("Label")
-                    or p
-                )
+                try:
+                    name = self.reader.stage_positions[p]["Label"]
+                except (IndexError, KeyError):
+                    name = p
                 self.pos_names.append(name)
         else:
             self.pos_names = ["0"]

iohub/multipagetiff.py

@@ -55,12 +55,12 @@ def __init__(self, folder: str, extract_data: bool = False):
         # Initialize MM attributes
         self.channel_names = []
 
-        # Read MM data
-        self._set_mm_meta()
-
         # Gather index map of file, page, byte offset
         self._gather_index_maps()
 
+        # Read MM data
+        self._set_mm_meta()
+
         # if extract data, create all of the virtual zarr stores up front
         if extract_data:
             for i in range(self.positions):
@@ -173,6 +173,29 @@ def _set_mm_meta(self):
                 for ch in self.mm_meta["Summary"].get("ChNames", []):
                     self.channel_names.append(ch)
 
+            # Parsing of data acquired with the OpenCell
+            # acquisition script on the Dragonfly miroscope
+            elif (
+                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()]
+                )
+
+                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])
+                        pos = self._simplify_stage_position(
+                            self.mm_meta["Summary"]["StagePositions"][site_idx]
+                        )
+                        self._stage_positions[p_idx] = pos
+
+                for ch in self.mm_meta["Summary"]["ChNames"]:
+                    self.channel_names.append(ch)
+
             else:
                 if self.mm_meta["Summary"]["Positions"] > 1:
                     self._stage_positions = []
@@ -186,15 +209,17 @@ def _set_mm_meta(self):
                 for ch in self.mm_meta["Summary"].get("ChNames", []):
                     self.channel_names.append(ch)
 
-            # dimensions based on mm metadata
-            # do not reflect final written dimensions
-            # these will change after data is loaded
             self.z_step_size = self.mm_meta["Summary"]["z-step_um"]
             self.height = self.mm_meta["Summary"]["Height"]
             self.width = self.mm_meta["Summary"]["Width"]
-            self.frames = self.mm_meta["Summary"]["Frames"]
-            self.slices = self.mm_meta["Summary"]["Slices"]
-            self.channels = self.mm_meta["Summary"]["Channels"]
+
+            # dimensions based on mm metadata
+            # do not reflect final written dimensions
+            # these set in _gather_index_maps
+            #
+            # self.frames = self.mm_meta["Summary"]["Frames"]
+            # self.slices = self.mm_meta["Summary"]["Slices"]
+            # self.channels = self.mm_meta["Summary"]["Channels"]
 
     def _simplify_stage_position(self, stage_pos: dict):
         """