masster 0.5.13__py3-none-any.whl → 0.5.15__py3-none-any.whl

masster/study/id.py

@@ -145,16 +145,61 @@ def lib_load(
                 column_order.append("quant_group")
             elif col == "formula" and "iso" in columns_list and "iso" not in column_order:
                 column_order.append("iso")
-    
-    # Apply the column ordering
-    filtered_lf = filtered_lf.select(column_order)
 
+    
     # Add to existing lib_df instead of replacing
     if (
         hasattr(study, "lib_df")
         and study.lib_df is not None
         and not study.lib_df.is_empty()
     ):
+        # Check for schema compatibility and handle mismatches
+        existing_cols = set(study.lib_df.columns)
+        new_cols = set(filtered_lf.columns)
+        
+        # If schemas don't match, we need to align them
+        if existing_cols != new_cols:
+            # Get union of all columns
+            all_cols = existing_cols.union(new_cols)
+            
+            # Add missing columns to existing data with appropriate defaults
+            for col in new_cols - existing_cols:
+                if col == "probability":
+                    # Add probability column to existing data - try to calculate from adduct
+                    if "adduct" in study.lib_df.columns:
+                        try:
+                            adduct_prob_map = _get_adduct_probabilities(study)
+                            study.lib_df = study.lib_df.with_columns(
+                                pl.col("adduct").map_elements(
+                                    lambda adduct: adduct_prob_map.get(adduct, 1.0) if adduct is not None else 1.0,
+                                    return_dtype=pl.Float64
+                                ).alias("probability")
+                            )
+                        except Exception:
+                            study.lib_df = study.lib_df.with_columns(pl.lit(1.0).alias("probability"))
+                    else:
+                        study.lib_df = study.lib_df.with_columns(pl.lit(1.0).alias("probability"))
+                elif col == "iso":
+                    study.lib_df = study.lib_df.with_columns(pl.lit(0).cast(pl.Int64).alias("iso"))
+                elif col == "quant_group":
+                    # Set quant_group using cmpd_uid or lib_uid
+                    if "cmpd_uid" in study.lib_df.columns:
+                        study.lib_df = study.lib_df.with_columns(pl.col("cmpd_uid").cast(pl.Int64).alias("quant_group"))
+                    else:
+                        study.lib_df = study.lib_df.with_columns(pl.col("lib_uid").cast(pl.Int64).alias("quant_group"))
+                else:
+                    # Default to null for other columns
+                    study.lib_df = study.lib_df.with_columns(pl.lit(None).alias(col))
+            
+            # Add missing columns to new data with appropriate defaults
+            for col in existing_cols - new_cols:
+                if col not in ["probability", "iso", "quant_group"]:  # These should already be handled
+                    filtered_lf = filtered_lf.with_columns(pl.lit(None).alias(col))
+        
+        # Ensure column order matches for concatenation - use existing column order
+        existing_column_order = list(study.lib_df.columns)
+        filtered_lf = filtered_lf.select(existing_column_order)
+        
         # Concatenate with existing data
         study.lib_df = pl.concat([study.lib_df, filtered_lf])
     else:
@@ -209,8 +254,19 @@ def _setup_identify_parameters(params, kwargs):
 
     # Override parameters with any provided kwargs
     if kwargs:
+        # Handle parameter name mapping for backwards compatibility
+        param_mapping = {
+            'rt_tolerance': 'rt_tol',
+            'mz_tolerance': 'mz_tol'
+        }
+        
         for param_name, value in kwargs.items():
-            if hasattr(params, param_name):
+            # Check if we need to map the parameter name
+            mapped_name = param_mapping.get(param_name, param_name)
+            
+            if hasattr(params, mapped_name):
+                setattr(params, mapped_name, value)
+            elif hasattr(params, param_name):
                 setattr(params, param_name, value)
     
     return params
@@ -319,9 +375,13 @@ def _perform_identification_matching(consensus_to_process, study, effective_mz_t
                     else None
                 )
 
-                # Get adduct probability from cached map
+                # Get library probability as base score, then multiply by adduct probability
+                lib_probability = match_row.get("probability", 1.0) if match_row.get("probability") is not None else 1.0
                 adduct = match_row.get("adduct")
-                score = adduct_prob_map.get(adduct, 1.0) if adduct else 1.0
+                adduct_probability = adduct_prob_map.get(adduct, 1.0) if adduct else 1.0
+                score = lib_probability * adduct_probability
+                # Scale to 0-100 and round to 1 decimal place
+                score = round(score * 100.0, 1)
 
                 match_results.append({
                     "lib_uid": match_row.get("lib_uid"),
@@ -337,7 +397,11 @@ def _perform_identification_matching(consensus_to_process, study, effective_mz_t
 
 
 def _find_matches_vectorized(lib_df, cons_mz, cons_rt, mz_tol, rt_tol, logger, cons_uid):
-    """Find library matches using optimized vectorized operations."""
+    """
+    Find library matches using optimized vectorized operations.
+    
+    FIXED VERSION: Prevents incorrect matching of same compound to different m/z values.
+    """
     # Filter by m/z tolerance using vectorized operations
     matches = lib_df.filter(
         (pl.col("mz") >= cons_mz - mz_tol) & (pl.col("mz") <= cons_mz + mz_tol)
@@ -345,43 +409,78 @@ def _find_matches_vectorized(lib_df, cons_mz, cons_rt, mz_tol, rt_tol, logger, c
 
     initial_match_count = len(matches)
 
-    # Apply RT filter if available
+    # Apply RT filter if available - STRICT VERSION (no fallback)
     if rt_tol is not None and cons_rt is not None and not matches.is_empty():
-        rt_matches = matches.filter(
-            pl.col("rt").is_not_null() &
-            (pl.col("rt") >= cons_rt - rt_tol) &
-            (pl.col("rt") <= cons_rt + rt_tol)
-        )
+        # First, check if any m/z matches have RT data
+        rt_candidates = matches.filter(pl.col("rt").is_not_null())
         
-        if not rt_matches.is_empty():
-            matches = rt_matches
+        if not rt_candidates.is_empty():
+            # Apply RT filtering to candidates with RT data
+            rt_matches = rt_candidates.filter(
+                (pl.col("rt") >= cons_rt - rt_tol) &
+                (pl.col("rt") <= cons_rt + rt_tol)
+            )
+            
+            if not rt_matches.is_empty():
+                matches = rt_matches
+                if logger:
+                    logger.debug(
+                        f"Consensus {cons_uid}: {initial_match_count} m/z matches, {len(rt_candidates)} with RT, {len(matches)} after RT filter"
+                    )
+            else:
+                # NO FALLBACK - if RT filtering finds no matches, return empty
+                matches = rt_matches  # This is empty
+                if logger:
+                    logger.debug(
+                        f"Consensus {cons_uid}: RT filtering eliminated all {len(rt_candidates)} candidates (rt_tol={rt_tol}s) - no matches returned"
+                    )
+        else:
+            # No RT data in library matches - return empty if strict RT filtering requested
             if logger:
                 logger.debug(
-                    f"Consensus {cons_uid}: {initial_match_count} m/z matches, {len(matches)} after RT filter"
+                    f"Consensus {cons_uid}: {initial_match_count} m/z matches but none have library RT data - no matches returned due to RT filtering"
                 )
+            matches = pl.DataFrame()  # Return empty DataFrame
+
+    # FIX 1: Add stricter m/z validation - prioritize more accurate matches
+    if not matches.is_empty():
+        strict_mz_tol = mz_tol * 0.5  # Use 50% of tolerance as strict threshold
+        strict_matches = matches.filter(
+            (pl.col("mz") >= cons_mz - strict_mz_tol) & (pl.col("mz") <= cons_mz + strict_mz_tol)
+        )
+        
+        if not strict_matches.is_empty():
+            # Use strict matches if available
+            matches = strict_matches
+            if logger:
+                logger.debug(f"Consensus {cons_uid}: Using {len(matches)} strict m/z matches (within {strict_mz_tol:.6f} Da)")
         else:
             if logger:
-                logger.debug(
-                    f"Consensus {cons_uid}: {initial_match_count} m/z matches, 0 after RT filter - using m/z matches only"
-                )
+                logger.debug(f"Consensus {cons_uid}: No strict matches, using {len(matches)} loose matches")
 
-    # Optimized deduplication using Polars operations
+    # FIX 2: Improved deduplication - prioritize by m/z accuracy
     if not matches.is_empty() and len(matches) > 1:
         if "formula" in matches.columns and "adduct" in matches.columns:
             pre_dedup_count = len(matches)
             
-            # Use Polars group_by with maintain_order for consistent results
+            # Calculate m/z error for sorting
+            matches = matches.with_columns([
+                (pl.col("mz") - cons_mz).abs().alias("mz_error_abs")
+            ])
+            
+            # Group by formula and adduct, but keep the most accurate m/z match
             matches = (
                 matches
-                .sort("lib_uid")  # Ensure consistent ordering
+                .sort(["mz_error_abs", "lib_uid"])  # Sort by m/z accuracy first, then lib_uid for consistency
                 .group_by(["formula", "adduct"], maintain_order=True)
                 .first()
+                .drop("mz_error_abs")  # Remove the temporary column
             )
             
             post_dedup_count = len(matches)
             if logger and post_dedup_count < pre_dedup_count:
                 logger.debug(
-                    f"Consensus {cons_uid}: deduplicated {pre_dedup_count} to {post_dedup_count} matches"
+                    f"Consensus {cons_uid}: deduplicated {pre_dedup_count} to {post_dedup_count} matches (m/z accuracy prioritized)"
                 )
 
     return matches
@@ -617,7 +716,11 @@ def _apply_scoring_adjustments(study, params):
 
 
 def _update_consensus_id_columns(study, logger=None):
-    """Update consensus_df with top-scoring identification results using safe in-place updates."""
+    """
+    Update consensus_df with top-scoring identification results using safe in-place updates.
+    
+    FIXED VERSION: Prevents same compound from being assigned to vastly different m/z values.
+    """
     try:
         if not hasattr(study, "id_df") or study.id_df is None or study.id_df.is_empty():
             if logger:
@@ -634,14 +737,47 @@ def _update_consensus_id_columns(study, logger=None):
                 logger.debug("No consensus data available")  
             return
 
-        # Get library columns we need
-        lib_columns = ["lib_uid", "name", "adduct"]
+        # Get library columns we need (include mz for validation)
+        lib_columns = ["lib_uid", "name", "adduct", "mz"]
         if "class" in study.lib_df.columns:
             lib_columns.append("class")
 
-        # Get top-scoring identification for each consensus feature
+        # FIX 1: Join identification results with consensus m/z for validation
+        id_with_consensus = study.id_df.join(
+            study.consensus_df.select(["consensus_uid", "mz"]),
+            on="consensus_uid",
+            how="left",
+            suffix="_consensus"
+        )
+
+        # FIX 2: Validate m/z accuracy - filter out poor matches
+        id_with_lib = id_with_consensus.join(
+            study.lib_df.select(["lib_uid", "mz"]),
+            on="lib_uid",
+            how="left",
+            suffix="_lib"
+        )
+        
+        # Calculate actual m/z error and filter out excessive errors
+        id_validated = id_with_lib.with_columns([
+            (pl.col("mz") - pl.col("mz_lib")).abs().alias("actual_mz_error")
+        ])
+        
+        # Filter out matches with excessive m/z error
+        max_reasonable_error = 0.02  # 20 millidalton maximum error
+        id_validated = id_validated.filter(
+            (pl.col("actual_mz_error") <= max_reasonable_error) | pl.col("actual_mz_error").is_null()
+        )
+        
+        if logger:
+            original_count = len(id_with_consensus)
+            validated_count = len(id_validated)
+            if validated_count < original_count:
+                logger.warning(f"Filtered out {original_count - validated_count} identifications with excessive m/z error (>{max_reasonable_error:.3f} Da)")
+
+        # Get top-scoring identification for each consensus feature (from validated results)
         top_ids = (
-            study.id_df
+            id_validated
             .sort(["consensus_uid", "score"], descending=[False, True])
             .group_by("consensus_uid", maintain_order=True)
             .first()
@@ -656,6 +792,37 @@ def _update_consensus_id_columns(study, logger=None):
             .rename({"name": "id_top_name"})
         )
 
+        # FIX 3: Check for conflicts where same compound+adduct assigned to very different m/z
+        if not top_ids.is_empty():
+            compound_groups = (
+                top_ids
+                .join(study.consensus_df.select(["consensus_uid", "mz"]), on="consensus_uid", how="left")
+                .group_by(["id_top_name", "id_top_adduct"])
+                .agg([
+                    pl.col("consensus_uid").count().alias("count"),
+                    pl.col("mz").min().alias("mz_min"),
+                    pl.col("mz").max().alias("mz_max")
+                ])
+                .with_columns([
+                    (pl.col("mz_max") - pl.col("mz_min")).alias("mz_range")
+                ])
+            )
+            
+            # Find problematic assignments (same compound+adduct with >0.1 Da m/z range)
+            problematic = compound_groups.filter(
+                (pl.col("count") > 1) & (pl.col("mz_range") > 0.1)
+            )
+            
+            if not problematic.is_empty() and logger:
+                for row in problematic.iter_rows(named=True):
+                    name = row["id_top_name"]
+                    adduct = row["id_top_adduct"] 
+                    count = row["count"]
+                    mz_range = row["mz_range"]
+                    logger.warning(
+                        f"Identification conflict detected: '{name}' ({adduct}) assigned to {count} features with {mz_range:.4f} Da m/z range"
+                    )
+
         # Ensure we have the id_top columns in consensus_df
         for col_name, dtype in [
             ("id_top_name", pl.String),
@@ -783,7 +950,7 @@ def identify(study, features=None, params=None, **kwargs):
     if logger:
         features_with_matches = len([r for r in results if len(r["matches"]) > 0])
         total_matches = sum(len(r["matches"]) for r in results)
-        logger.info(
+        logger.success(
             f"Identification completed: {features_with_matches}/{consensus_count} features matched, {total_matches} total identifications",
         )
 
@@ -806,6 +973,8 @@ def get_id(study, features=None) -> pl.DataFrame:
         - mz (consensus feature m/z)
         - rt (consensus feature RT)
         - name (compound name from library)
+        - shortname (short name from library, if available)
+        - class (compound class from library, if available)
         - formula (molecular formula from library)
         - adduct (adduct type from library)
         - smiles (SMILES notation from library)
@@ -873,6 +1042,8 @@ def get_id(study, features=None) -> pl.DataFrame:
     lib_cols = [
         "lib_uid",
         "name",
+        "shortname",
+        "class",
         "formula",
         "adduct",
         "smiles",
@@ -901,6 +1072,8 @@ def get_id(study, features=None) -> pl.DataFrame:
         "cmpd_uid" if "cmpd_uid" in result_df.columns else None,
         "lib_uid",
         "name" if "name" in result_df.columns else None,
+        "shortname" if "shortname" in result_df.columns else None,
+        "class" if "class" in result_df.columns else None,
         "formula" if "formula" in result_df.columns else None,
         "adduct" if "adduct" in result_df.columns else None,
         "mz" if "mz" in result_df.columns else None,
@@ -952,6 +1125,8 @@ def get_id(study, features=None) -> pl.DataFrame:
                 "cmpd_uid",
                 "lib_uid",
                 "name",
+                "shortname",
+                "class",
                 "formula",
                 "adduct",
                 "mz",
@@ -1094,7 +1269,7 @@ def id_reset(study):
         del study.history["identify"]
 
     if logger:
-        logger.success("Identification data reset completed")
+        logger.info("Identification data reset completed")
 
 
 def lib_reset(study):
@@ -1123,11 +1298,33 @@ def lib_reset(study):
             logger.debug("Checking for consensus features created by lib_to_consensus()")
         
         try:
-            # Filter for features with number_samples = -1 or 0
-            # Since consensus_select doesn't support list of discrete values, use direct filtering
-            lib_consensus_features = study.consensus_df.filter(
-                (pl.col("number_samples") == -1) | (pl.col("number_samples") == 0)
-            )
+            # Filter for features created by lib_to_consensus()
+            # These can be identified by:
+            # 1. number_samples < 1 (set to 0.0 by lib_to_consensus)
+            # 2. AND have corresponding entries in consensus_mapping_df with sample_uid = 0 (virtual sample)
+            
+            # First check if we have any features with number_samples < 1
+            potential_lib_features = study.consensus_df.filter(pl.col("number_samples") < 1)
+            
+            if potential_lib_features is not None and not potential_lib_features.is_empty():
+                # Further filter by checking if they have sample_uid = 0 in consensus_mapping_df
+                # This ensures we only remove library-derived features, not legitimate features with 0 samples
+                if hasattr(study, "consensus_mapping_df") and not study.consensus_mapping_df.is_empty():
+                    lib_consensus_uids = study.consensus_mapping_df.filter(
+                        pl.col("sample_uid") == 0
+                    )["consensus_uid"].unique().to_list()
+                    
+                    if lib_consensus_uids:
+                        lib_consensus_features = potential_lib_features.filter(
+                            pl.col("consensus_uid").is_in(lib_consensus_uids)
+                        )
+                    else:
+                        lib_consensus_features = pl.DataFrame()  # No library features found
+                else:
+                    # If no consensus_mapping_df, fall back to number_samples < 1 only
+                    lib_consensus_features = potential_lib_features
+            else:
+                lib_consensus_features = pl.DataFrame()  # No features with number_samples < 1
             
             if lib_consensus_features is not None and not lib_consensus_features.is_empty():
                 num_lib_features = len(lib_consensus_features)
@@ -1199,7 +1396,7 @@ def lib_reset(study):
             del study.history["lib_to_consensus"]
 
     if logger:
-        logger.success("Library and identification data reset completed")
+        logger.info("Library and identification data reset completed")
 
 
 def _get_adducts(study, adducts_list: list | None = None, **kwargs):
@@ -1306,7 +1503,8 @@ def _get_adducts(study, adducts_list: list | None = None, **kwargs):
 
     # 1. Single adducts (filter out neutral adducts with charge == 0)
     for spec in base_specs:
-        if charge_min <= spec["charge"] <= charge_max and spec["charge"] != 0:
+        # Study-level filtering: exclude neutral adducts (charge=0) but use abs() for charged adducts
+        if spec["charge"] != 0 and charge_min <= abs(spec["charge"]) <= charge_max:
             formatted_name = _format_adduct_name([spec])
             combinations_list.append(
                 {
@@ -1324,7 +1522,7 @@ def _get_adducts(study, adducts_list: list | None = None, **kwargs):
         base_charge = spec["charge"]
         for multiplier in range(2, min(max_combinations + 1, 4)):  # Up to 3x multiplier
             total_charge = base_charge * multiplier
-            if charge_min <= total_charge <= charge_max and total_charge != 0:
+            if charge_min <= abs(total_charge) <= charge_max and total_charge != 0:
                 components = [spec] * multiplier
                 formatted_name = _format_adduct_name(components)
                 probability_multiplied = float(spec["probability"]) ** multiplier
@@ -1346,7 +1544,7 @@ def _get_adducts(study, adducts_list: list | None = None, **kwargs):
         for pos_spec in positive_specs[:2]:  # Limit to first 2 positive specs
             for neut_spec in neutral_specs[:1]:  # Only 1 neutral loss
                 total_charge = pos_spec["charge"] + neut_spec["charge"]
-                if charge_min <= total_charge <= charge_max and total_charge != 0:
+                if charge_min <= abs(total_charge) <= charge_max and total_charge != 0:
                     components = [pos_spec, neut_spec]
                     formatted_name = _format_adduct_name(components)
                     combinations_list.append(