masster 0.3.14__tar.gz → 0.3.16__tar.gz

{masster-0.3.14 → masster-0.3.16}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: masster
-Version: 0.3.14
+Version: 0.3.16
 Summary: Mass spectrometry data analysis package
 Project-URL: homepage, https://github.com/zamboni-lab/masster
 Project-URL: repository, https://github.com/zamboni-lab/masster

{masster-0.3.14 → masster-0.3.16}/pyproject.toml

@@ -1,7 +1,7 @@
 
 [project]
 name = "masster"
-version = "0.3.14"
+version = "0.3.16"
 description = "Mass spectrometry data analysis package"
 authors = [
     { name = "Zamboni Lab" }

{masster-0.3.14 → masster-0.3.16}/src/masster/_version.py

@@ -1,7 +1,7 @@
 from __future__ import annotations
 
 
-__version__ = "0.3.14"
+__version__ = "0.3.16"
 
 
 def get_version():

{masster-0.3.14 → masster-0.3.16}/src/masster/sample/h5.py

@@ -897,6 +897,583 @@ def _load_sample5(self, filename: str, map: bool = True):
     self.logger.info(f"Sample loaded successfully from {filename}")
 
 
+def _load_sample5_study(self, filename: str, map: bool = True):
+    """
+    Optimized variant of _load_sample5 for study loading that skips reading ms1_df.
+    
+    This is used when adding samples to studies where ms1_df data is not needed,
+    improving loading throughput by skipping the potentially large ms1_df dataset.
+
+    Args:
+        filename (str): Path to the sample5 HDF5 file to load.
+        map (bool, optional): Whether to map featureXML file if available. Defaults to True.
+
+    Returns:
+        None (modifies self in place)
+
+    Notes:
+        - Same as _load_sample5 but skips ms1_df loading for better performance
+        - Sets ms1_df = None explicitly
+        - Suitable for study workflows where MS1 spectral data is not required
+    """
+    # Load schema for proper DataFrame reconstruction
+    schema_path = os.path.join(os.path.dirname(__file__), "sample5_schema.json")
+    try:
+        with open(schema_path) as f:
+            schema = json.load(f)
+    except FileNotFoundError:
+        self.logger.warning(
+            f"Schema file {schema_path} not found. Using default types.",
+        )
+        schema = {}
+
+    with h5py.File(filename, "r") as f:
+        # Load metadata
+        if "metadata" in f:
+            metadata_group = f["metadata"]
+            self.file_path = decode_metadata_attr(metadata_group.attrs.get("file_path", ""))
+
+            # Load file_source if it exists, otherwise set it equal to file_path
+            if "file_source" in metadata_group.attrs:
+                self.file_source = decode_metadata_attr(metadata_group.attrs.get("file_source", ""))
+            else:
+                self.file_source = self.file_path
+
+            self.file_type = decode_metadata_attr(metadata_group.attrs.get("file_type", ""))
+            self.label = decode_metadata_attr(metadata_group.attrs.get("label", ""))
+
+            # Load parameters from JSON in metadata
+            loaded_data = load_parameters_from_metadata(metadata_group)
+
+            # Always create a fresh sample_defaults object
+            from masster.sample.defaults.sample_def import sample_defaults
+
+            self.parameters = sample_defaults()
+
+            # Initialize history and populate from loaded data
+            self.history = {}
+            if loaded_data is not None and isinstance(loaded_data, dict):
+                # Store the loaded data in history
+                self.history = loaded_data
+                # If there are sample parameters in the history, use them to update defaults
+                if "sample" in loaded_data:
+                    sample_params = loaded_data["sample"]
+                    if isinstance(sample_params, dict):
+                        self.parameters.set_from_dict(sample_params, validate=False)
+
+        # Load scans_df
+        if "scans" in f:
+            scans_group = f["scans"]
+            data: dict[str, Any] = {}
+            missing_columns = []
+            for col in schema.get("scans_df", {}).get("columns", []):
+                if col not in scans_group:
+                    self.logger.debug(f"Column '{col}' not found in sample5/scans.")
+                    data[col] = None
+                    missing_columns.append(col)
+                    continue
+
+                dtype = schema["scans_df"]["columns"][col].get("dtype", "native")
+                match dtype:
+                    case "pl.Object":
+                        self.logger.debug(f"Unexpected Object column '{col}'")
+                        data[col] = None
+                        missing_columns.append(col)
+
+                    case _:
+                        data[col] = scans_group[col][:]
+
+            # create polars DataFrame from data
+            if data:
+                self.scans_df = pl.DataFrame(data)
+
+                # Convert "None" strings and NaN values to proper null values
+                for col in self.scans_df.columns:
+                    if self.scans_df[col].dtype == pl.Utf8:  # String columns
+                        self.scans_df = self.scans_df.with_columns([
+                            pl.when(pl.col(col).is_in(["None", "", "null", "NULL"]))
+                            .then(None)
+                            .otherwise(pl.col(col))
+                            .alias(col),
+                        ])
+                    elif self.scans_df[col].dtype in [
+                        pl.Float64,
+                        pl.Float32,
+                    ]:  # Float columns
+                        self.scans_df = self.scans_df.with_columns([
+                            pl.col(col).fill_nan(None).alias(col),
+                        ])
+
+                # update all columns with schema types
+                for col in self.scans_df.columns:
+                    if col in schema.get("scans_df", {}).get("columns", {}):
+                        try:
+                            dtype_str = schema["scans_df"]["columns"][col]["dtype"]
+                            # Convert dtype string to actual polars dtype
+                            if dtype_str.startswith("pl."):
+                                # Skip Object columns - they're already properly reconstructed
+                                if "Object" in dtype_str:
+                                    continue
+                                # Handle different polars data types
+                                if "Int" in dtype_str:
+                                    # Convert to numeric first, handling different input types
+                                    if self.scans_df[col].dtype == pl.Utf8:
+                                        # String data - convert to integer
+                                        self.scans_df = self.scans_df.with_columns(
+                                            pl.col(col).str.to_integer().cast(eval(dtype_str)),
+                                        )
+                                    elif self.scans_df[col].dtype in [
+                                        pl.Float64,
+                                        pl.Float32,
+                                    ]:
+                                        # Float data - cast to integer
+                                        self.scans_df = self.scans_df.with_columns(
+                                            pl.col(col).cast(eval(dtype_str)),
+                                        )
+                                    else:
+                                        # Try direct casting
+                                        self.scans_df = self.scans_df.with_columns(
+                                            pl.col(col).cast(eval(dtype_str)),
+                                        )
+                                elif "Float" in dtype_str:
+                                    # Convert to float, handling different input types
+                                    if self.scans_df[col].dtype == pl.Utf8:
+                                        # String data - convert to float
+                                        self.scans_df = self.scans_df.with_columns(
+                                            pl.col(col).str.to_decimal().cast(eval(dtype_str)),
+                                        )
+                                    else:
+                                        # Try direct casting
+                                        self.scans_df = self.scans_df.with_columns(
+                                            pl.col(col).cast(eval(dtype_str)),
+                                        )
+                                elif "Utf8" in dtype_str:
+                                    # Ensure it's string type
+                                    self.scans_df = self.scans_df.with_columns(
+                                        pl.col(col).cast(pl.Utf8),
+                                    )
+                                else:
+                                    # Handle special cases and try direct casting for other types
+                                    current_dtype = self.scans_df[col].dtype
+                                    target_dtype = eval(dtype_str)
+
+                                    # Handle binary data that might need string conversion first
+                                    if "Binary" in str(current_dtype):
+                                        # Convert binary to string first, then to target type
+                                        if target_dtype == pl.Utf8:
+                                            self.scans_df = self.scans_df.with_columns(
+                                                pl.col(col)
+                                                .map_elements(
+                                                    lambda x: x.decode("utf-8") if isinstance(x, bytes) else str(x),
+                                                    return_dtype=pl.Utf8,
+                                                )
+                                                .cast(target_dtype),
+                                            )
+                                        elif "Int" in str(target_dtype):
+                                            self.scans_df = self.scans_df.with_columns(
+                                                pl.col(col)
+                                                .map_elements(
+                                                    lambda x: x.decode("utf-8") if isinstance(x, bytes) else str(x),
+                                                    return_dtype=pl.Utf8,
+                                                )
+                                                .str.to_integer()
+                                                .cast(target_dtype),
+                                            )
+                                        elif "Float" in str(target_dtype):
+                                            self.scans_df = self.scans_df.with_columns(
+                                                pl.col(col)
+                                                .map_elements(
+                                                    lambda x: x.decode("utf-8") if isinstance(x, bytes) else str(x),
+                                                    return_dtype=pl.Utf8,
+                                                )
+                                                .str.to_decimal()
+                                                .cast(target_dtype),
+                                            )
+                                        else:
+                                            # Try direct casting
+                                            self.scans_df = self.scans_df.with_columns(
+                                                pl.col(col).cast(target_dtype),
+                                            )
+                                    else:
+                                        # Try direct casting for non-binary types
+                                        self.scans_df = self.scans_df.with_columns(
+                                            pl.col(col).cast(target_dtype),
+                                        )
+                        except Exception as e:
+                            self.logger.warning(
+                                f"Failed to cast column '{col}' in scans_df: {e}",
+                            )
+                    else:
+                        self.logger.warning(
+                            f"Column '{col}' in scans_df not found in schema, keeping original type.",
+                        )
+
+            # Ensure column order matches schema order
+            if "scans_df" in schema and "columns" in schema["scans_df"]:
+                schema_column_order = list(schema["scans_df"]["columns"].keys())
+                # Only reorder columns that exist in both schema and DataFrame
+                existing_columns = [col for col in schema_column_order if col in self.scans_df.columns]
+                if existing_columns:
+                    self.scans_df = self.scans_df.select(existing_columns)
+
+            else:
+                self.scans_df = None
+        else:
+            self.scans_df = None
+
+        # Load features_df
+        if "features" in f:
+            features_group = f["features"]
+            # columns = list(features_group.attrs.get('columns', []))
+            data = {}
+            missing_columns = []
+            for col in schema.get("features_df", {}).get("columns", []):
+                if col not in features_group:
+                    self.logger.debug(
+                        f"Column '{col}' not found in sample5/features.",
+                    )
+                    data[col] = None
+                    missing_columns.append(col)
+                    continue
+
+                dtype = schema["features_df"]["columns"][col].get("dtype", "native")
+                match dtype:
+                    case "pl.Object":
+                        match col:
+                            case "chrom":
+                                data_col = features_group[col][:]
+                                # Convert JSON strings back to Chromatogram objects
+                                reconstructed_data: list[Any] = []
+                                for item in data_col:
+                                    if isinstance(item, bytes):
+                                        item = item.decode("utf-8")
+
+                                    if item == "None" or item == "":
+                                        reconstructed_data.append(None)
+                                    else:
+                                        try:
+                                            reconstructed_data.append(
+                                                Chromatogram.from_json(item),
+                                            )
+                                        except (json.JSONDecodeError, ValueError):
+                                            reconstructed_data.append(None)
+
+                                data[col] = reconstructed_data
+                            case "ms2_scans":
+                                data_col = features_group[col][:]
+                                # Convert JSON strings back to list objects
+                                reconstructed_data = []
+                                for item in data_col:
+                                    if isinstance(item, bytes):
+                                        item = item.decode("utf-8")
+
+                                    if item == "None" or item == "":
+                                        reconstructed_data.append(None)
+                                    else:
+                                        try:
+                                            reconstructed_data.append(json.loads(item))
+                                        except json.JSONDecodeError:
+                                            reconstructed_data.append(None)
+
+                                data[col] = reconstructed_data
+                            case "ms2_specs":
+                                data_col = features_group[col][:]
+                                # Convert JSON strings back to list of Spectrum objects
+                                reconstructed_data = []
+                                for item in data_col:
+                                    if isinstance(item, bytes):
+                                        item = item.decode("utf-8")
+
+                                    if item == "None" or item == "":
+                                        reconstructed_data.append(None)
+                                    else:
+                                        try:
+                                            spectrum_list = []
+                                            for spec_data in json.loads(item):
+                                                if spec_data is not None:
+                                                    spectrum = Spectrum.from_json(spec_data)
+                                                    spectrum_list.append(spectrum)
+                                                else:
+                                                    spectrum_list.append(None)
+                                            reconstructed_data.append(spectrum_list)
+                                        except (json.JSONDecodeError, ValueError, TypeError):
+                                            reconstructed_data.append(None)
+
+                                data[col] = reconstructed_data
+                            case _:
+                                # Handle other Object columns as raw data
+                                data[col] = features_group[col][:]
+
+                    case _:
+                        data[col] = features_group[col][:]
+
+            # create polars DataFrame from data
+            if data:
+                self.features_df = pl.DataFrame(data, strict=False)
+
+                # Convert "None" strings and NaN values to proper null values for regular columns first
+                for col in self.features_df.columns:
+                    # Skip Object columns - they're already properly reconstructed
+                    if col in schema.get("features_df", {}).get("columns", {}):
+                        if "Object" in schema["features_df"]["columns"][col].get("dtype", ""):
+                            continue
+
+                    if self.features_df[col].dtype == pl.Utf8:  # String columns
+                        self.features_df = self.features_df.with_columns([
+                            pl.when(pl.col(col).is_in(["None", "", "null", "NULL"]))
+                            .then(None)
+                            .otherwise(pl.col(col))
+                            .alias(col),
+                        ])
+                    elif self.features_df[col].dtype in [
+                        pl.Float64,
+                        pl.Float32,
+                    ]:  # Float columns
+                        self.features_df = self.features_df.with_columns([
+                            pl.col(col).fill_nan(None).alias(col),
+                        ])
+
+                # update all columns with schema types
+                for col in self.features_df.columns:
+                    if col in schema.get("features_df", {}).get("columns", {}):
+                        try:
+                            dtype_str = schema["features_df"]["columns"][col]["dtype"]
+                            # Convert dtype string to actual polars dtype
+                            if dtype_str.startswith("pl."):
+                                # Skip Object columns - they're already properly reconstructed
+                                if "Object" in dtype_str:
+                                    continue
+                                # Handle different polars data types
+                                if "Int" in dtype_str:
+                                    # Convert to numeric first, handling different input types
+                                    if self.features_df[col].dtype == pl.Utf8:
+                                        # String data - convert to integer
+                                        self.features_df = self.features_df.with_columns(
+                                            pl.col(col).str.to_integer().cast(eval(dtype_str)),
+                                        )
+                                    elif self.features_df[col].dtype in [
+                                        pl.Float64,
+                                        pl.Float32,
+                                    ]:
+                                        # Float data - cast to integer with null handling for NaN values
+                                        self.features_df = self.features_df.with_columns(
+                                            pl.col(col).cast(eval(dtype_str), strict=False),
+                                        )
+                                    else:
+                                        # Handle special cases and try direct casting for other types
+                                        current_dtype = self.features_df[col].dtype
+                                        target_dtype = eval(dtype_str)
+
+                                        # Handle binary data that might need string conversion first
+                                        if "Binary" in str(current_dtype):
+                                            # Convert binary to string first, then to target type
+                                            if target_dtype == pl.Utf8:
+                                                self.features_df = self.features_df.with_columns(
+                                                    pl.col(col)
+                                                    .map_elements(
+                                                        lambda x: x.decode("utf-8") if isinstance(x, bytes) else str(x),
+                                                        return_dtype=pl.Utf8,
+                                                    )
+                                                    .cast(target_dtype),
+                                                )
+                                            elif "Int" in str(target_dtype):
+                                                self.features_df = self.features_df.with_columns(
+                                                    pl.col(col)
+                                                    .map_elements(
+                                                        lambda x: x.decode("utf-8") if isinstance(x, bytes) else str(x),
+                                                        return_dtype=pl.Utf8,
+                                                    )
+                                                    .str.to_integer()
+                                                    .cast(target_dtype),
+                                                )
+                                            elif "Float" in str(target_dtype):
+                                                self.features_df = self.features_df.with_columns(
+                                                    pl.col(col)
+                                                    .map_elements(
+                                                        lambda x: x.decode("utf-8") if isinstance(x, bytes) else str(x),
+                                                        return_dtype=pl.Utf8,
+                                                    )
+                                                    .str.to_decimal()
+                                                    .cast(target_dtype),
+                                                )
+                                            else:
+                                                # Try direct casting
+                                                self.features_df = self.features_df.with_columns(
+                                                    pl.col(col).cast(target_dtype),
+                                                )
+                                        else:
+                                            # Try direct casting for non-binary types
+                                            self.features_df = self.features_df.with_columns(
+                                                pl.col(col).cast(target_dtype),
+                                            )
+                                elif "Float" in dtype_str:
+                                    # Convert to float, handling different input types
+                                    if self.features_df[col].dtype == pl.Utf8:
+                                        # String data - convert to float
+                                        self.features_df = self.features_df.with_columns(
+                                            pl.col(col).str.to_decimal().cast(eval(dtype_str)),
+                                        )
+                                    else:
+                                        # Handle special cases and try direct casting for other types
+                                        current_dtype = self.features_df[col].dtype
+                                        target_dtype = eval(dtype_str)
+
+                                        # Handle binary data that might need string conversion first
+                                        if "Binary" in str(current_dtype):
+                                            # Convert binary to string first, then to target type
+                                            if target_dtype == pl.Utf8:
+                                                self.features_df = self.features_df.with_columns(
+                                                    pl.col(col)
+                                                    .map_elements(
+                                                        lambda x: x.decode("utf-8") if isinstance(x, bytes) else str(x),
+                                                        return_dtype=pl.Utf8,
+                                                    )
+                                                    .cast(target_dtype),
+                                                )
+                                            elif "Int" in str(target_dtype):
+                                                self.features_df = self.features_df.with_columns(
+                                                    pl.col(col)
+                                                    .map_elements(
+                                                        lambda x: x.decode("utf-8") if isinstance(x, bytes) else str(x),
+                                                        return_dtype=pl.Utf8,
+                                                    )
+                                                    .str.to_integer()
+                                                    .cast(target_dtype),
+                                                )
+                                            elif "Float" in str(target_dtype):
+                                                self.features_df = self.features_df.with_columns(
+                                                    pl.col(col)
+                                                    .map_elements(
+                                                        lambda x: x.decode("utf-8") if isinstance(x, bytes) else str(x),
+                                                        return_dtype=pl.Utf8,
+                                                    )
+                                                    .str.to_decimal()
+                                                    .cast(target_dtype),
+                                                )
+                                            else:
+                                                # Try direct casting
+                                                self.features_df = self.features_df.with_columns(
+                                                    pl.col(col).cast(target_dtype),
+                                                )
+                                        else:
+                                            # Try direct casting for non-binary types
+                                            self.features_df = self.features_df.with_columns(
+                                                pl.col(col).cast(target_dtype),
+                                            )
+                                elif "Utf8" in dtype_str:
+                                    # Ensure it's string type
+                                    self.features_df = self.features_df.with_columns(
+                                        pl.col(col).cast(pl.Utf8),
+                                    )
+                                else:
+                                    # Handle special cases and try direct casting for other types
+                                    current_dtype = self.features_df[col].dtype
+                                    target_dtype = eval(dtype_str)
+
+                                    # Handle binary data that might need string conversion first
+                                    if "Binary" in str(current_dtype):
+                                        # Convert binary to string first, then to target type
+                                        if target_dtype == pl.Utf8:
+                                            self.features_df = self.features_df.with_columns(
+                                                pl.col(col)
+                                                .map_elements(
+                                                    lambda x: x.decode("utf-8") if isinstance(x, bytes) else str(x),
+                                                    return_dtype=pl.Utf8,
+                                                )
+                                                .cast(target_dtype),
+                                            )
+                                        elif "Int" in str(target_dtype):
+                                            self.features_df = self.features_df.with_columns(
+                                                pl.col(col)
+                                                .map_elements(
+                                                    lambda x: x.decode("utf-8") if isinstance(x, bytes) else str(x),
+                                                    return_dtype=pl.Utf8,
+                                                )
+                                                .str.to_integer()
+                                                .cast(target_dtype),
+                                            )
+                                        elif "Float" in str(target_dtype):
+                                            self.features_df = self.features_df.with_columns(
+                                                pl.col(col)
+                                                .map_elements(
+                                                    lambda x: x.decode("utf-8") if isinstance(x, bytes) else str(x),
+                                                    return_dtype=pl.Utf8,
+                                                )
+                                                .str.to_decimal()
+                                                .cast(target_dtype),
+                                            )
+                                        else:
+                                            # Try direct casting
+                                            self.features_df = self.features_df.with_columns(
+                                                pl.col(col).cast(target_dtype),
+                                            )
+                                    else:
+                                        # Try direct casting for non-binary types
+                                        self.features_df = self.features_df.with_columns(
+                                            pl.col(col).cast(target_dtype),
+                                        )
+                        except Exception as e:
+                            self.logger.warning(
+                                f"Failed to cast column '{col}' in features_df: {e}",
+                            )
+                    else:
+                        self.logger.warning(
+                            f"Column '{col}' in features_df not found in schema, keeping original type.",
+                        )
+
+                # FINAL null conversion pass - after all type casting is done
+                # This ensures "None" strings introduced by failed conversions are properly handled
+                for col in self.features_df.columns:
+                    if self.features_df[col].dtype == pl.Utf8:  # String columns
+                        self.features_df = self.features_df.with_columns([
+                            pl.when(pl.col(col).is_in(["None", "", "null", "NULL"]))
+                            .then(None)
+                            .otherwise(pl.col(col))
+                            .alias(col),
+                        ])
+                    # Float columns
+                    elif self.features_df[col].dtype in [pl.Float64, pl.Float32]:
+                        self.features_df = self.features_df.with_columns([
+                            pl.col(col).fill_nan(None).alias(col),
+                        ])
+
+                # Ensure column order matches schema order
+                if "features_df" in schema and "columns" in schema["features_df"]:
+                    schema_column_order = list(schema["features_df"]["columns"].keys())
+                    # Only reorder columns that exist in both schema and DataFrame
+                    existing_columns = [col for col in schema_column_order if col in self.features_df.columns]
+                    if existing_columns:
+                        self.features_df = self.features_df.select(existing_columns)
+
+            else:
+                self.features_df = None
+        else:
+            self.features_df = None
+
+        # OPTIMIZED: Skip loading ms1_df for study use - set to None for performance
+        self.ms1_df = None
+
+        # Parameters are now loaded from metadata JSON (see above)
+        # Lib and lib_match are no longer saved/loaded
+
+    if map:
+        featureXML = filename.replace(".sample5", ".featureXML")
+        if os.path.exists(featureXML):
+            self._load_featureXML(featureXML)
+            self._features_sync()
+        else:
+            self.logger.warning(
+                f"Feature XML file {featureXML} not found, skipping loading.",
+            )
+
+    # set self.file_path to *.sample5
+    self.file_path = filename
+    # set self.label to basename without extension
+    if self.label is None or self.label == "":
+        self.label = os.path.splitext(os.path.basename(filename))[0]
+    self.logger.info(f"Sample loaded successfully from {filename} (optimized for study)")
+
+
 def load_schema(schema_path: str) -> Dict[str, Any]:
     """
     Load schema from JSON file with error handling.

{masster-0.3.14 → masster-0.3.16}/src/masster/sample/helpers.py

@@ -281,7 +281,7 @@ def select_closest_scan(
     return scan
 
 
-def get_eic(self, mz, mz_tol=0.01):
+def get_eic(self, mz, mz_tol=None):
     """
     Extract an extracted ion chromatogram (EIC) from `ms1_df` for a target m/z ± mz_tol.
 
@@ -291,11 +291,18 @@ def get_eic(self, mz, mz_tol=0.01):
 
     Parameters:
         mz (float): target m/z value
-        mz_tol (float): tolerance around mz (default 0.01)
+        mz_tol (float): tolerance around mz. If None, uses self.parameters.eic_mz_tol or defaults to 0.01
 
     Returns:
         polars.DataFrame or None: chromatogram with columns ['rt', 'inty'] or None if not available
     """
+    # Use default mz_tol from sample parameters if not provided
+    if mz_tol is None:
+        if hasattr(self, 'parameters') and hasattr(self.parameters, 'eic_mz_tol'):
+            mz_tol = self.parameters.eic_mz_tol
+        else:
+            mz_tol = 0.01  # fallback default
+
     # Validate ms1_df
     if not hasattr(self, "ms1_df") or self.ms1_df is None:
         if hasattr(self, "logger"):