expand OME metadata

studio/app/optinist/microscopes/IsxdReader.py

@@ -71,7 +71,10 @@ def _build_ome_metadata(self, original_metadata: dict) -> OMEDataModel:
             size_x=spacing["width"],
             size_y=spacing["height"],
             size_t=timing["num_samples"],
-            size_c=0,
+            size_z=0,  # Note: currently unsettled
+            size_c=0,  # Note: currently unsettled
+            acquisition_date=timing["start"],
+            objective_model=None,  # Note: currently unsettled
             fps=(1000 / timing["period_msec"]),
         )
 

studio/app/optinist/microscopes/MicroscopeDataReaderBase.py

@@ -12,14 +12,12 @@ class OMEDataModel:
     image_name: str
     size_x: int  # width
     size_y: int  # height
-    size_t: int  # time
-    size_c: int  # TODO: 要確認
-    fps: int  # frames_per_second  # TODO: OME標準の類似項目に合わせる
-
-    # TODO: 以下今後追加想定
-    # SizeZ: int
-    # AcquisitionDate: date
-    # Instrument/(Laser|Detector): str
+    size_t: int  # time frames
+    size_z: int  # axis z frames
+    size_c: int  # channels
+    acquisition_date: str
+    objective_model: str  # objective lens model
+    fps: int  # frames_per_second  # Note: extended from OME format
 
 
 class MicroscopeDataReaderBase(metaclass=ABCMeta):

studio/app/optinist/microscopes/ND2Reader.py

@@ -2,6 +2,7 @@
 import json
 import os
 import platform
+import re
 from enum import Enum, IntEnum
 
 import numpy as np
@@ -167,22 +168,33 @@ def _build_ome_metadata(self, original_metadata: dict) -> OMEDataModel:
         """
 
         attributes = original_metadata["attributes"]
+        metadata = original_metadata["metadata"]
+        textinfo = original_metadata["textinfo"]
         experiments = original_metadata["experiments"]
+        first_experiment_parameters = experiments[0]["parameters"]
+        metadata_ch0_microscope = metadata["channels"][0]["microscope"]
 
         # experiment, periods, の参照は先頭データの内容から取得
-        if (experiments is not None) and ("periods" in experiments[0]["parameters"]):
-            period_ms = float(experiments[0]["parameters"]["periods"][0]["periodMs"])
-            fps = (1000 / period_ms) if period_ms > 0 else 0
+        if "periods" in first_experiment_parameters:
+            try:
+                fps = (
+                    1000
+                    / first_experiment_parameters["periods"][0]["periodDiff"]["avg"]
+                )
+            except:  # noqa: E722
+                fps = 1000 / first_experiment_parameters["periodDiff"]["avg"]
         else:
-            period_ms = 0
             fps = 0
 
         omeData = OMEDataModel(
             image_name=original_metadata["data_name"],
             size_x=attributes["widthPx"],
             size_y=attributes["heightPx"],
             size_t=attributes["sequenceCount"],
-            size_c=0,
+            size_z=0,  # size_z は後続処理で計算・設定する
+            size_c=len(metadata["channels"]),
+            acquisition_date=re.sub(" +", " ", textinfo["date"]),
+            objective_model=metadata_ch0_microscope.get("objectiveName", None),
             fps=fps,
         )
 
@@ -223,6 +235,9 @@ def _build_lab_specific_metadata(self, original_metadata: dict) -> dict:
                 z_slicenum = experiments[0]["count"]
                 z_interval = experiments[0]["parameters"]["stepUm"]
 
+        # ※ome_metadata の一部項目をアップデート
+        self.ome_metadata.size_z = z_slicenum
+
         # ----------------------------------------
         # Lab固有metadata変数構築
         # ----------------------------------------

studio/app/optinist/microscopes/OIRReader.py

@@ -207,6 +207,9 @@ def _build_ome_metadata(self, original_metadata: dict) -> OMEDataModel:
 
         rect = original_metadata["rect"]
         axis_info = original_metadata["axis_info"]
+        channel_info = original_metadata["channel_info"]
+        objective_lens_info = original_metadata["objective_lens_info"]
+        file_creation_time = original_metadata["file_creation_time"]
 
         # get sequence counts
         # Note: Use the largest sequence count for each axis.
@@ -215,14 +218,24 @@ def _build_ome_metadata(self, original_metadata: dict) -> OMEDataModel:
             axes_sequence_counts.append(axis["max"])
         sequence_count = max(axes_sequence_counts)
 
-        fps = 0  # TODO: 今後計算対象予定
+        # get axis z frame count
+        nZLoop = axis_info["ZSTACK"]["max"] if "ZSTACK" in axis_info else 1
+
+        # get fps
+        # TODO: fps の取得には、FrameManager経由
+        #   (FrameManager.m_vecAxisPosition[].GetPosition) での
+        #   アクセスが必要となる模様. 今後計算対象予定.
+        fps = 0
 
         omeData = OMEDataModel(
             image_name=original_metadata["data_name"],
             size_x=rect["width"],
             size_y=rect["height"],
             size_t=sequence_count,
-            size_c=0,
+            size_z=nZLoop,
+            size_c=len(channel_info),
+            acquisition_date=file_creation_time["creation_time"],
+            objective_model=objective_lens_info["name"],
             fps=fps,
         )