Merge branch 'v1_feature_branch' of github.com:OpenCOMPES/sed into v1_feature_branch

Author: rettigl

src/sed/core/config.py

@@ -242,3 +242,78 @@ def complete_dictionary(dictionary: dict, base_dictionary: dict) -> dict:
                     dictionary[k] = v
 
     return dictionary
+
+
+def _parse_env_file(file_path: Path) -> dict:
+    """Helper function to parse a .env file into a dictionary.
+
+    Args:
+        file_path (Path): Path to the .env file
+
+    Returns:
+        dict: Dictionary of environment variables from the file
+    """
+    env_content = {}
+    if file_path.exists():
+        with open(file_path) as f:
+            for line in f:
+                line = line.strip()
+                if line and "=" in line:
+                    key, val = line.split("=", 1)
+                    env_content[key.strip()] = val.strip()
+    return env_content
+
+
+def read_env_var(var_name: str) -> str | None:
+    """Read an environment variable from multiple locations in order:
+    1. OS environment variables
+    2. .env file in current directory
+    3. .env file in user config directory
+
+    Args:
+        var_name (str): Name of the environment variable to read
+
+    Returns:
+        str | None: Value of the environment variable or None if not found
+    """
+    # First check OS environment variables
+    value = os.getenv(var_name)
+    if value is not None:
+        logger.debug(f"Found {var_name} in OS environment variables")
+        return value
+
+    # Then check .env in current directory
+    local_vars = _parse_env_file(Path(".env"))
+    if var_name in local_vars:
+        logger.debug(f"Found {var_name} in ./.env file")
+        return local_vars[var_name]
+
+    # Finally check .env in user config directory
+    user_vars = _parse_env_file(USER_CONFIG_PATH / ".env")
+    if var_name in user_vars:
+        logger.debug(f"Found {var_name} in user config .env file")
+        return user_vars[var_name]
+
+    logger.debug(f"Environment variable {var_name} not found in any location")
+    return None
+
+
+def save_env_var(var_name: str, value: str) -> None:
+    """Save an environment variable to the .env file in the user config directory.
+    If the file exists, preserves other variables. If not, creates a new file.
+
+    Args:
+        var_name (str): Name of the environment variable to save
+        value (str): Value to save for the environment variable
+    """
+    env_path = USER_CONFIG_PATH / ".env"
+    env_content = _parse_env_file(env_path)
+
+    # Update or add new variable
+    env_content[var_name] = value
+
+    # Write all variables back to file
+    with open(env_path, "w") as f:
+        for key, val in env_content.items():
+            f.write(f"{key}={val}\n")
+    logger.debug(f"Environment variable {var_name} saved to .env file")

src/sed/core/config_model.py

@@ -14,7 +14,6 @@
 from pydantic import HttpUrl
 from pydantic import NewPath
 from pydantic import PositiveInt
-from pydantic import SecretStr
 
 from sed.loader.loader_interface import get_names_of_all_loaders
 
@@ -323,7 +322,6 @@ class MetadataModel(BaseModel):
     model_config = ConfigDict(extra="forbid")
 
     archiver_url: Optional[HttpUrl] = None
-    token: Optional[SecretStr] = None
     epics_pvs: Optional[Sequence[str]] = None
     fa_in_channel: Optional[str] = None
     fa_hor_channel: Optional[str] = None

src/sed/loader/flash/buffer_handler.py

@@ -2,6 +2,7 @@
 
 import os
 from pathlib import Path
+import time
 
 import dask.dataframe as dd
 import pyarrow.parquet as pq
@@ -20,7 +21,7 @@
 
 DF_TYP = ["electron", "timed"]
 
-logger = setup_logging(__name__)
+logger = setup_logging("flash_buffer_handler")
 
 
 class BufferFilePaths:
@@ -135,16 +136,15 @@ def __init__(
     def _schema_check(self, files: list[Path], expected_schema_set: set) -> None:
         """
         Checks the schema of the Parquet files.
-
-        Raises:
-            ValueError: If the schema of the Parquet files does not match the configuration.
         """
+        logger.debug(f"Checking schema for {len(files)} files")
         existing = [file for file in files if file.exists()]
         parquet_schemas = [pq.read_schema(file) for file in existing]
 
         for filename, schema in zip(existing, parquet_schemas):
             schema_set = set(schema.names)
             if schema_set != expected_schema_set:
+                logger.error(f"Schema mismatch in file: {filename}")
                 missing_in_parquet = expected_schema_set - schema_set
                 missing_in_config = schema_set - expected_schema_set
 
@@ -159,6 +159,7 @@ def _schema_check(self, files: list[Path], expected_schema_set: set) -> None:
                     f"{' '.join(errors)}. "
                     "Please check the configuration file or set force_recreate to True.",
                 )
+        logger.debug("Schema check passed successfully")
 
     def _create_timed_dataframe(self, df: dd.DataFrame) -> dd.DataFrame:
         """Creates the timed dataframe, optionally filtering by electron events.
@@ -185,35 +186,31 @@ def _create_timed_dataframe(self, df: dd.DataFrame) -> dd.DataFrame:
         return df_timed.loc[:, :, 0]
 
     def _save_buffer_file(self, paths: dict[str, Path]) -> None:
-        """
-        Creates the electron and timed buffer files from the raw H5 file.
-        First the dataframe is accessed and forward filled in the non-electron channels.
-        Then the data types are set. For the electron dataframe, all values not in the electron
-        channels are dropped. For the timed dataframe, only the train and pulse channels are taken
-        and it pulse resolved (no longer electron resolved). Both are saved as parquet files.
-
-        Args:
-            paths (dict[str, Path]): Dictionary containing the paths to the H5 and buffer files.
-        """
-        # Create a DataFrameCreator instance and get the h5 file
+        """Creates the electron and timed buffer files from the raw H5 file."""
+        logger.debug(f"Processing file: {paths['raw'].stem}")
+        start_time = time.time()
+        # Create DataFrameCreator and get get dataframe
         df = DataFrameCreator(config_dataframe=self._config, h5_path=paths["raw"]).df
 
-        # forward fill all the non-electron channels
+        # Forward fill non-electron channels
+        logger.debug(f"Forward filling {len(self.fill_channels)} channels")
         df[self.fill_channels] = df[self.fill_channels].ffill()
 
         # Save electron resolved dataframe
         electron_channels = get_channels(self._config, "per_electron")
         dtypes = get_dtypes(self._config, df.columns.values)
-        df.dropna(subset=electron_channels).astype(dtypes).reset_index().to_parquet(
-            paths["electron"],
-        )
+        electron_df = df.dropna(subset=electron_channels).astype(dtypes).reset_index()
+        logger.debug(f"Saving electron buffer with shape: {electron_df.shape}")
+        electron_df.to_parquet(paths["electron"])
 
         # Create and save timed dataframe
         df_timed = self._create_timed_dataframe(df)
         dtypes = get_dtypes(self._config, df_timed.columns.values)
-        df_timed.astype(dtypes).reset_index().to_parquet(paths["timed"])
+        timed_df = df_timed.astype(dtypes).reset_index()
+        logger.debug(f"Saving timed buffer with shape: {timed_df.shape}")
+        timed_df.to_parquet(paths["timed"])
 
-        logger.debug(f"Processed {paths['raw'].stem}")
+        logger.debug(f"Processed {paths['raw'].stem} in {time.time() - start_time:.2f}s")
 
     def _save_buffer_files(self, force_recreate: bool, debug: bool) -> None:
         """

src/sed/loader/flash/dataframe.py

@@ -14,6 +14,9 @@
 
 from sed.loader.flash.utils import get_channels
 from sed.loader.flash.utils import InvalidFileError
+from sed.core.logging import setup_logging
+
+logger = setup_logging("flash_dataframe_creator")
 
 
 class DataFrameCreator:
@@ -34,6 +37,7 @@ def __init__(self, config_dataframe: dict, h5_path: Path) -> None:
             config_dataframe (dict): The configuration dictionary with only the dataframe key.
             h5_path (Path): Path to the h5 file.
         """
+        logger.debug(f"Initializing DataFrameCreator for file: {h5_path}")
         self.h5_file = h5py.File(h5_path, "r")
         self.multi_index = get_channels(index=True)
         self._config = config_dataframe
@@ -76,6 +80,7 @@ def get_dataset_array(
             tuple[pd.Index, np.ndarray | h5py.Dataset]: A tuple containing the train ID
             pd.Index and the channel's data.
         """
+        logger.debug(f"Getting dataset array for channel: {channel}")
         # Get the data from the necessary h5 file and channel
         index_key, dataset_key = self.get_index_dataset_key(channel)
 
@@ -85,6 +90,7 @@ def get_dataset_array(
         if slice_:
             slice_index = self._config["channels"][channel].get("slice", None)
             if slice_index is not None:
+                logger.debug(f"Slicing dataset with index: {slice_index}")
                 dataset = np.take(dataset, slice_index, axis=1)
         # If np_array is size zero, fill with NaNs, fill it with NaN values
         # of the same shape as index
@@ -291,10 +297,14 @@ def df(self) -> pd.DataFrame:
         Returns:
             pd.DataFrame: The combined pandas DataFrame.
         """
-
+        logger.debug("Creating combined DataFrame")
         self.validate_channel_keys()
-        # been tested with merge, join and concat
-        # concat offers best performance, almost 3 times faster
+
         df = pd.concat((self.df_electron, self.df_pulse, self.df_train), axis=1).sort_index()
-        # all the negative pulse values are dropped as they are invalid
-        return df[df.index.get_level_values("pulseId") >= 0]
+        logger.debug(f"Created DataFrame with shape: {df.shape}")
+
+        # Filter negative pulse values
+        df = df[df.index.get_level_values("pulseId") >= 0]
+        logger.debug(f"Filtered DataFrame shape: {df.shape}")
+
+        return df

src/sed/loader/flash/loader.py

@@ -207,14 +207,14 @@ def get_files_from_run_id(  # type: ignore[override]
         # Return the list of found files
         return [str(file.resolve()) for file in files]
 
-    def parse_metadata(self, scicat_token: str = None) -> dict:
+    def parse_metadata(self, token: str = None) -> dict:
         """Uses the MetadataRetriever class to fetch metadata from scicat for each run.
 
         Returns:
             dict: Metadata dictionary
-            scicat_token (str, optional):: The scicat token to use for fetching metadata
+            token (str, optional):: The scicat token to use for fetching metadata
         """
-        metadata_retriever = MetadataRetriever(self._config["metadata"], scicat_token)
+        metadata_retriever = MetadataRetriever(self._config["metadata"], token)
         metadata = metadata_retriever.get_metadata(
             beamtime_id=self._config["core"]["beamtime_id"],
             runs=self.runs,
@@ -329,7 +329,9 @@ def read_dataframe(
             debug (bool, optional): Whether to run buffer creation in serial. Defaults to False.
             remove_invalid_files (bool, optional): Whether to exclude invalid files.
                 Defaults to False.
-            scicat_token (str, optional): The scicat token to use for fetching metadata.
+            token (str, optional): The scicat token to use for fetching metadata. If provided,
+                will be saved to .env file for future use. If not provided, will check environment
+                variables when collect_metadata is True.
             filter_timed_by_electron (bool, optional): When True, the timed dataframe will only
                 contain data points where valid electron events were detected. When False, all
                 timed data points are included regardless of electron detection. Defaults to True.
@@ -341,13 +343,14 @@ def read_dataframe(
         Raises:
             ValueError: If neither 'runs' nor 'files'/'raw_dir' is provided.
             FileNotFoundError: If the conversion fails for some files or no data is available.
+            ValueError: If collect_metadata is True and no token is available.
         """
         detector = kwds.pop("detector", "")
         force_recreate = kwds.pop("force_recreate", False)
         processed_dir = kwds.pop("processed_dir", None)
         debug = kwds.pop("debug", False)
         remove_invalid_files = kwds.pop("remove_invalid_files", False)
-        scicat_token = kwds.pop("scicat_token", None)
+        token = kwds.pop("token", None)
         filter_timed_by_electron = kwds.pop("filter_timed_by_electron", True)
 
         if len(kwds) > 0:
@@ -401,7 +404,7 @@ def read_dataframe(
         if self.instrument == "wespe":
             df, df_timed = wespe_convert(df, df_timed)
 
-        self.metadata.update(self.parse_metadata(scicat_token) if collect_metadata else {})
+        self.metadata.update(self.parse_metadata(token) if collect_metadata else {})
         self.metadata.update(bh.metadata)
 
         print(f"loading complete in {time.time() - t0: .2f} s")