Fixed issue #21 (when an existing file was opened with mode "w", it was not initialized)

src/robofish/io/file.py

@@ -176,8 +176,19 @@ class File(h5py.File):
             # x        Create file, fail if exists
             # a        Read/write if exists, create otherwise
             logging.info(f"Opening File {path}")
-            initialize = not Path(path).exists()
+
+            assert mode in ["r", "r+", "w", "x", "a"], f"Unknown mode {mode}."
+
+            # If the file does not exist or if it should be truncated with mode=w, initialize it.
+            if Path(path).exists() and mode != "w":
+                initialize = False
+            else:
+                initialize = True
+
+            try:
                 super().__init__(path, mode, libver=("earliest", "v110"))
+            except OSError as e:
+                raise OSError(f"Could not open file {path} with mode {mode}.\n{e}")
 
         if initialize:
             assert world_size_cm is not None and format_version is not None
@@ -264,13 +275,30 @@ class File(h5py.File):
 
         sampling = self["samplings"].create_group(name)
 
-        if frequency_hz is not None:
-            sampling.attrs["frequency_hz"] = (np.float32)(frequency_hz)
         if monotonic_time_points_us is not None:
+
+            monotonic_time_points_us = np.array(
+                monotonic_time_points_us, dtype=np.int64
+            )
             sampling.create_dataset(
-                "monotonic_time_points_us",
-                data=np.array(monotonic_time_points_us, dtype=np.int64),
+                "monotonic_time_points_us", data=monotonic_time_points_us
             )
+            if frequency_hz is None:
+                diff = np.diff(monotonic_time_points_us)
+                if np.all(diff == diff[0]) and diff[0] > 0:
+                    frequency_hz = 1e6 / diff[0]
+                    warnings.warn(
+                        f"The frequency_hz of {frequency_hz:.2f}hz was calculated automatically by robofish.io. The safer variant is to pass it using frequency_hz.\nThis is important when using fish_models with the files."
+                    )
+
+                else:
+                    warnings.warn(
+                        "The frequency_hz could not be calculated automatically. When using fish_models, the file will access frequency_hz."
+                    )
+
+        if frequency_hz is not None:
+            sampling.attrs["frequency_hz"] = (np.float32)(frequency_hz)
+
         if calendar_time_points is not None:
 
             def format_calendar_time_point(p):
@@ -314,8 +342,9 @@ class File(h5py.File):
 
     @property
     def default_sampling(self):
-        if not "samplings" in self:
-            print("Wassss?", self)
+        assert (
+            "samplings" in self
+        ), "The file does not have a group 'sampling' which is required."
         if "default" in self["samplings"].attrs:
             return self["samplings"].attrs["default"]
         return None