masster 0.4.21__py3-none-any.whl → 0.4.22__py3-none-any.whl

masster/_version.py

@@ -1,7 +1,7 @@
 from __future__ import annotations
 
 
-__version__ = "0.4.21"
+__version__ = "0.4.22"
 
 
 def get_version():

masster/sample/save.py

@@ -344,7 +344,6 @@ def export_mgf(
         tdqm_disable = self.log_level not in ["TRACE", "DEBUG", "INFO"]
         
         # First pass: Export MS1 spectra for ALL features with ms1_spec data
-        print("Exporting MS1 spectra...")
         for row in tqdm(
             features_list,
             total=len(features_list),
@@ -398,7 +397,6 @@ def export_mgf(
                 ms1_fallback_count += 1
         
         # Second pass: Export MS2 spectra for features with MS2 data
-        print("Exporting MS2 spectra...")
         for row in tqdm(
             features_list,
             total=len(features_list),

masster/study/export.py

@@ -498,7 +498,7 @@ def export_mgf(self, **kwargs):
     self.logger.info(f"Exported {len(mgf_data)} spectra to {filename}")
 
 
-def export_mztab(self, filename: str = None, include_mgf=True, **kwargs) -> None:
+def export_mztab(self, filename: str | None = None, include_mgf=True, **kwargs) -> None:
     """
     Export the study as a fully compliant mzTab-M file.
 
@@ -1184,7 +1184,7 @@ def export_mztab(self, filename: str = None, include_mgf=True, **kwargs) -> None
     self.logger.info(f"Exported mzTab-M to {filename}")
 
 
-def export_xlsx(self, filename: str = None) -> None:
+def export_xlsx(self, filename: str | None = None) -> None:
     """
     Export the study data to an Excel workbook with multiple worksheets.
 
@@ -1295,7 +1295,7 @@ def export_xlsx(self, filename: str = None) -> None:
         self.logger.error(f"Error writing Excel file: {e}")
 
 
-def export_parquet(self, filename: str = None) -> None:
+def export_parquet(self, filename: str | None = None) -> None:
     """
     Export the study data to multiple Parquet files with different suffixes.
 

masster/study/load.py

@@ -1257,17 +1257,53 @@ def load_features(self):
         feature_map = oms.FeatureMap()
 
         # Convert DataFrame features to OpenMS Features
+        # Keep track of next available feature_id for this sample
+        next_feature_id = 1
+        used_feature_ids = set()
+        
+        # First pass: collect existing feature_ids to avoid conflicts
+        for feature_row in sample_features.iter_rows(named=True):
+            if feature_row["feature_id"] is not None:
+                used_feature_ids.add(int(feature_row["feature_id"]))
+                
+        # Find the next available feature_id
+        while next_feature_id in used_feature_ids:
+            next_feature_id += 1
+        
         for feature_row in sample_features.iter_rows(named=True):
             feature = oms.Feature()
 
             # Set properties from DataFrame (handle missing values gracefully)
             try:
-                feature.setUniqueId(int(feature_row["feature_id"]))
+                # Skip features with missing critical data
+                if feature_row["mz"] is None:
+                    self.logger.warning("Skipping feature due to missing mz")
+                    continue
+                if feature_row["rt"] is None:
+                    self.logger.warning("Skipping feature due to missing rt")
+                    continue
+                if feature_row["inty"] is None:
+                    self.logger.warning("Skipping feature due to missing inty")
+                    continue
+                
+                # Handle missing feature_id by generating a new one
+                if feature_row["feature_id"] is None:
+                    feature_id = next_feature_id
+                    next_feature_id += 1
+                    self.logger.debug(f"Generated new feature_id {feature_id} for feature with missing ID")
+                else:
+                    feature_id = int(feature_row["feature_id"])
+                
+                feature.setUniqueId(feature_id)
                 feature.setMZ(float(feature_row["mz"]))
                 feature.setRT(float(feature_row["rt"]))
                 feature.setIntensity(float(feature_row["inty"]))
-                feature.setOverallQuality(float(feature_row["quality"]))
-                feature.setCharge(int(feature_row["charge"]))
+                
+                # Handle optional fields that might be None
+                if feature_row.get("quality") is not None:
+                    feature.setOverallQuality(float(feature_row["quality"]))
+                if feature_row.get("charge") is not None:
+                    feature.setCharge(int(feature_row["charge"]))
 
                 # Add to feature map
                 feature_map.push_back(feature)

masster/study/plot.py

@@ -1724,221 +1724,154 @@ def plot_consensus_stats(
     self,
     filename=None,
     width=1200,
-    height=1200,
+    height=None,
     alpha=0.6,
-    markersize=3,
+    bins=30,
+    n_cols=4,
 ):
     """
-    Plot a scatter plot matrix (SPLOM) of consensus statistics using Bokeh.
-
+    Plot histograms/distributions for all numeric columns in consensus_df.
+    
     Parameters:
         filename (str, optional): Output filename for saving the plot
         width (int): Overall width of the plot (default: 1200)
-        height (int): Overall height of the plot (default: 1200)
-        alpha (float): Point transparency (default: 0.6)
-        markersize (int): Size of points (default: 5)
+        height (int, optional): Overall height of the plot (auto-calculated if None)
+        alpha (float): Histogram transparency (default: 0.6)
+        bins (int): Number of histogram bins (default: 30)
+        n_cols (int): Number of columns in the grid layout (default: 4)
     """
     from bokeh.layouts import gridplot
-    from bokeh.models import ColumnDataSource, HoverTool
-    from bokeh.plotting import figure, show, output_file
+    from bokeh.plotting import figure
+    import polars as pl
+    import numpy as np
 
     # Check if consensus_df exists and has data
     if self.consensus_df is None or self.consensus_df.is_empty():
         self.logger.error("No consensus data available. Run merge/find_consensus first.")
         return
 
-    # Define the columns to plot
-    columns = [
-        "rt",
-        "mz",
-        "number_samples",
-        "log10_quality",
-        "mz_delta_mean",
-        "rt_delta_mean",
-        "chrom_coherence_mean",
-        "chrom_prominence_scaled_mean",
-        "inty_mean",
-        "number_ms2",
-    ]
-
-    # Check which columns exist in the dataframe and compute missing ones
-    available_columns = self.consensus_df.columns
+    # Get all columns and their data types - work with original dataframe
     data_df = self.consensus_df.clone()
 
-    # Add log10_quality if quality exists
-    if "quality" in available_columns and "log10_quality" not in available_columns:
-        data_df = data_df.with_columns(
-            pl.col("quality").log10().alias("log10_quality"),
-        )
-
-    # Filter columns that actually exist
-    final_columns = [col for col in columns if col in data_df.columns]
-
-    if len(final_columns) < 2:
-        self.logger.error(f"Need at least 2 columns for SPLOM. Available: {final_columns}")
+    # Identify numeric columns (excluding ID columns that are typically strings)
+    id_columns = ["consensus_uid", "consensus_id", "uid", "id"]
+    numeric_columns = []
+    
+    for col in data_df.columns:
+        if col not in id_columns:
+            dtype = data_df[col].dtype
+            # Check if column is numeric (int, float, or can be converted to numeric)
+            if dtype in [pl.Int8, pl.Int16, pl.Int32, pl.Int64, 
+                        pl.UInt8, pl.UInt16, pl.UInt32, pl.UInt64,
+                        pl.Float32, pl.Float64]:
+                numeric_columns.append(col)
+
+    if len(numeric_columns) == 0:
+        self.logger.error("No numeric columns found in consensus_df for plotting distributions.")
         return
 
-    self.logger.debug(f"Creating SPLOM with columns: {final_columns}")
-
-    # Add important ID columns for tooltips even if not plotting them
-    tooltip_columns = []
-    for id_col in ["consensus_uid", "consensus_id"]:
-        if id_col in data_df.columns and id_col not in final_columns:
-            tooltip_columns.append(id_col)
+    self.logger.debug(f"Creating distribution plots for {len(numeric_columns)} numeric columns: {numeric_columns}")
 
-    # Select plotting columns plus tooltip columns
-    all_columns = final_columns + tooltip_columns
-    data_pd = data_df.select(all_columns).to_pandas()
+    # Work directly with Polars - no conversion to pandas needed
+    data_df_clean = data_df.select(numeric_columns)
 
-    # Remove any infinite or NaN values
-    data_pd = data_pd.replace([np.inf, -np.inf], np.nan).dropna()
-
-    if data_pd.empty:
-        self.logger.error("No valid data after removing NaN/infinite values.")
+    # Check if all numeric columns are empty
+    all_columns_empty = True
+    for col in numeric_columns:
+        # Check if column has any non-null, finite values
+        non_null_count = data_df_clean[col].filter(
+            data_df_clean[col].is_not_null() & 
+            (data_df_clean[col].is_finite() if data_df_clean[col].dtype in [pl.Float32, pl.Float64] else pl.lit(True))
+        ).len()
+        
+        if non_null_count > 0:
+            all_columns_empty = False
+            break
+    
+    if all_columns_empty:
+        self.logger.error("All numeric columns contain only NaN/infinite values.")
         return
 
-    source = ColumnDataSource(data_pd)
-
-    n_vars = len(final_columns)
-
-    # Fixed dimensions - override user input to ensure consistent layout
-    total_width = 1200
-    total_height = 1200
-
-    # Calculate plot sizes to ensure uniform inner plot areas
-    # First column needs extra width for y-axis labels
-    plot_width_first = 180  # Wider to account for y-axis labels
-    plot_width_others = 120  # Standard width for other columns
-    plot_height_normal = 120  # Standard height
-    plot_height_last = 155  # Taller last row to accommodate x-axis labels while keeping inner plot area same size
+    # Calculate grid dimensions
+    n_plots = len(numeric_columns)
+    n_rows = (n_plots + n_cols - 1) // n_cols  # Ceiling division
+    
+    # Auto-calculate height if not provided
+    if height is None:
+        plot_height = 300
+        height = plot_height * n_rows + 100  # Add some padding
+    else:
+        plot_height = (height - 100) // n_rows  # Subtract padding and divide
+    
+    plot_width = (width - 100) // n_cols  # Subtract padding and divide
 
-    # Create grid of plots with variable outer sizes but equal inner areas
+    # Create plots grid
     plots = []
-
-    for i, y_var in enumerate(final_columns):
-        row = []
-        for j, x_var in enumerate(final_columns):
-            # Determine if this plot needs axis labels
-            has_x_label = i == n_vars - 1  # bottom row
-            has_y_label = j == 0  # left column
-
-            # First column wider to accommodate y-axis labels, ensuring equal inner plot areas
-            current_width = plot_width_first if has_y_label else plot_width_others
-            current_height = plot_height_last if has_x_label else plot_height_normal
-
-            p = figure(
-                width=current_width,
-                height=current_height,
-                title=None,  # No title on any plot
-                toolbar_location=None,
-                # Adjusted borders - first column has more space, others minimal
-                min_border_left=70 if has_y_label else 15,
-                min_border_bottom=50 if has_x_label else 15,
-                min_border_right=15,
-                min_border_top=15,
-            )
-
-            # Ensure subplot background and border are explicitly white so the plot looks
-            # correct in dark and light themes.
-            p.outline_line_color = None
-            p.border_fill_color = "white"
-            p.border_fill_alpha = 1.0
-            p.background_fill_color = "white"
-
-            # Remove axis lines to eliminate black lines between plots
-            p.xaxis.axis_line_color = None
-            p.yaxis.axis_line_color = None
-
-            # Keep subtle grid lines for data reference
-            p.grid.visible = True
-            p.grid.grid_line_color = "#E0E0E0"  # Light gray grid lines
-
-            # Set axis labels and formatting
-            if has_x_label:  # bottom row
-                p.xaxis.axis_label = x_var
-                p.xaxis.axis_label_text_font_size = "12pt"
-                p.xaxis.major_label_text_font_size = "9pt"
-                p.xaxis.axis_label_standoff = 15
-            else:
-                p.xaxis.major_label_text_font_size = "0pt"
-                p.xaxis.minor_tick_line_color = None
-                p.xaxis.major_tick_line_color = None
-
-            if has_y_label:  # left column
-                p.yaxis.axis_label = y_var
-                p.yaxis.axis_label_text_font_size = "10pt"  # Smaller y-axis title
-                p.yaxis.major_label_text_font_size = "8pt"
-                p.yaxis.axis_label_standoff = 12
-            else:
-                p.yaxis.major_label_text_font_size = "0pt"
-                p.yaxis.minor_tick_line_color = None
-                p.yaxis.major_tick_line_color = None
-
-            if i == j:
-                # Diagonal: histogram
-                hist, edges = np.histogram(data_pd[x_var], bins=30)
-                p.quad(
-                    top=hist,
-                    bottom=0,
-                    left=edges[:-1],
-                    right=edges[1:],
-                    fill_color="green",
-                    line_color="white",
-                    alpha=alpha,
-                )
-            else:
-                # Off-diagonal: scatter plot
-                scatter = p.scatter(
-                    x=x_var,
-                    y=y_var,
-                    size=markersize,
-                    alpha=alpha,
-                    color="blue",
-                    source=source,
-                )
-
-                # Add hover tool
-                hover = HoverTool(
-                    tooltips=[
-                        (x_var, f"@{x_var}{{0.0000}}"),
-                        (y_var, f"@{y_var}{{0.0000}}"),
-                        (
-                            "consensus_uid",
-                            "@consensus_uid"
-                            if "consensus_uid" in data_pd.columns
-                            else "@consensus_id"
-                            if "consensus_id" in data_pd.columns
-                            else "N/A",
-                        ),
-                        ("rt", "@rt{0.00}" if "rt" in data_pd.columns else "N/A"),
-                        ("mz", "@mz{0.0000}" if "mz" in data_pd.columns else "N/A"),
-                    ],
-                    renderers=[scatter],
-                )
-                p.add_tools(hover)
-
-            row.append(p)
-        plots.append(row)
-
-    # Link axes for same variables
-    for i in range(n_vars):
-        for j in range(n_vars):
-            if i != j:  # Don't link diagonal plots
-                # Link x-axis to other plots in same column
-                for k in range(n_vars):
-                    if k != i and k != j:
-                        plots[i][j].x_range = plots[k][j].x_range
-
-                # Link y-axis to other plots in same row
-                for k in range(n_vars):
-                    if k != j and k != i:
-                        plots[i][j].y_range = plots[i][k].y_range
-
-    # Create grid layout and force overall background/border to white so the outer
-    # container doesn't show dark UI colors in night mode.
+    current_row = []
+    
+    for i, col in enumerate(numeric_columns):
+        # Create histogram for this column
+        p = figure(
+            width=plot_width,
+            height=plot_height,
+            title=col,
+            toolbar_location="above",
+            tools="pan,wheel_zoom,box_zoom,reset,save"
+        )
+        
+        # Set white background
+        p.background_fill_color = "white"
+        p.border_fill_color = "white"
+        
+        # Calculate histogram using Polars
+        # Get valid (non-null, finite) values for this column
+        if data_df_clean[col].dtype in [pl.Float32, pl.Float64]:
+            valid_values = data_df_clean.filter(
+                data_df_clean[col].is_not_null() & data_df_clean[col].is_finite()
+            )[col]
+        else:
+            valid_values = data_df_clean.filter(data_df_clean[col].is_not_null())[col]
+        
+        if valid_values.len() == 0:
+            self.logger.warning(f"No valid values for column {col}")
+            continue
+        
+        # Convert to numpy for histogram calculation
+        values_array = valid_values.to_numpy()
+        hist, edges = np.histogram(values_array, bins=bins)
+        
+        # Create histogram bars
+        p.quad(
+            top=hist,
+            bottom=0,
+            left=edges[:-1],
+            right=edges[1:],
+            fill_color="steelblue",
+            line_color="white",
+            alpha=alpha,
+        )
+        
+        # Style the plot
+        p.title.text_font_size = "12pt"
+        p.xaxis.axis_label = col
+        p.yaxis.axis_label = "Count"
+        p.grid.visible = True
+        p.grid.grid_line_color = "#E0E0E0"
+        
+        current_row.append(p)
+        
+        # If we've filled a row or reached the end, add the row to plots
+        if len(current_row) == n_cols or i == n_plots - 1:
+            # Fill remaining spots in the last row with None if needed
+            while len(current_row) < n_cols and i == n_plots - 1:
+                current_row.append(None)
+            plots.append(current_row)
+            current_row = []
+
+    # Create grid layout
     grid = gridplot(plots)
-
-    # Set overall background and border to white when supported
+    
+    # Set overall background to white
     if hasattr(grid, "background_fill_color"):
         grid.background_fill_color = "white"
     if hasattr(grid, "border_fill_color"):

masster/study/processing.py

@@ -15,6 +15,85 @@ from masster.study.defaults import (
 )
 
 
+def _generate_feature_maps_on_demand_for_align(study):
+    """
+    Generate feature maps on-demand from study.features_df for alignment operations.
+    Returns temporary feature maps that are not cached in the study.
+    
+    Args:
+        study: Study object containing features_df and samples_df
+    
+    Returns:
+        list: List of temporary FeatureMap objects
+    """
+    import polars as pl
+    import pyopenms as oms
+    
+    if study.features_df is None or len(study.features_df) == 0:
+        study.logger.error("No features_df available for generating feature maps")
+        return []
+    
+    temp_feature_maps = []
+    
+    # Process each sample in order
+    for sample_index, row_dict in enumerate(study.samples_df.iter_rows(named=True)):
+        sample_uid = row_dict["sample_uid"]
+        sample_name = row_dict["sample_name"]
+        
+        # Get features for this sample from features_df
+        sample_features = study.features_df.filter(pl.col("sample_uid") == sample_uid)
+        
+        # Create new FeatureMap
+        feature_map = oms.FeatureMap()
+        
+        # Convert DataFrame features to OpenMS Features
+        for feature_row in sample_features.iter_rows(named=True):
+            feature = oms.Feature()
+            
+            # Set properties from DataFrame (handle missing values gracefully)
+            try:
+                # Skip features with missing critical data
+                if feature_row["mz"] is None:
+                    study.logger.warning("Skipping feature due to missing mz")
+                    continue
+                if feature_row["rt"] is None:
+                    study.logger.warning("Skipping feature due to missing rt")
+                    continue
+                if feature_row["inty"] is None:
+                    study.logger.warning("Skipping feature due to missing inty")
+                    continue
+                
+                # Handle missing feature_id by generating a new one
+                if feature_row["feature_id"] is None:
+                    # Use a simple incremental ID for alignment purposes
+                    feature_id = len(temp_feature_maps) * 100000 + feature_map.size() + 1
+                    study.logger.debug(f"Generated new feature_id {feature_id} for feature with missing ID in sample {sample_name}")
+                else:
+                    feature_id = int(feature_row["feature_id"])
+                
+                feature.setUniqueId(feature_id)
+                feature.setMZ(float(feature_row["mz"]))
+                feature.setRT(float(feature_row["rt"]))
+                feature.setIntensity(float(feature_row["inty"]))
+                
+                # Handle optional fields that might be None
+                if feature_row.get("quality") is not None:
+                    feature.setOverallQuality(float(feature_row["quality"]))
+                if feature_row.get("charge") is not None:
+                    feature.setCharge(int(feature_row["charge"]))
+
+                # Add to feature map
+                feature_map.push_back(feature)
+            except (ValueError, TypeError) as e:
+                study.logger.warning(f"Skipping feature due to conversion error: {e}")
+                continue
+        
+        temp_feature_maps.append(feature_map)
+    
+    study.logger.debug(f"Generated {len(temp_feature_maps)} temporary feature maps from features_df for alignment")
+    return temp_feature_maps
+
+
 def align(self, **kwargs):
     """Align feature maps using pose clustering or KD algorithm and update feature RTs.
 
@@ -90,13 +169,9 @@ def align(self, **kwargs):
     self.store_history(["align"], params.to_dict())
     self.logger.debug("Parameters stored to align")
 
-    if len(self.features_maps) < len(self.samples_df):
-        self.features_maps = []
-        self.load_features()
-
-    # self.logger.debug("Starting alignment")
-
-    fmaps = self.features_maps
+    # Generate temporary feature maps on-demand from features_df instead of using cached data
+    self.logger.debug("Generating feature maps on-demand from features_df for alignment")
+    fmaps = _generate_feature_maps_on_demand_for_align(self)
 
     # Choose alignment algorithm
     algorithm = params.get("algorithm").lower()
@@ -108,6 +183,9 @@ def align(self, **kwargs):
         _align_kd_algorithm(self, fmaps, params)
     else:
         self.logger.error(f"Unknown alignment algorithm '{algorithm}'")
+        # Clean up temporary feature maps to release memory
+        del fmaps
+        return
 
     # check if rt_original exists in features_df, if not, add it after rt
     if "rt_original" not in self.features_df.columns:
@@ -256,6 +334,10 @@ def align(self, **kwargs):
     if params.get("save_features"):
         self.save_samples()
 
+    # Clean up temporary feature maps to release memory
+    del fmaps
+    self.logger.debug("Temporary feature maps deleted to release memory")
+
 
 def find_ms2(self, **kwargs):
     """
@@ -787,10 +869,22 @@ def _align_pose_clustering(study_obj, fmaps, params):
             and study_obj.samples_df.row(index, named=True)["sample_type"] == "blank"
         ):
             continue
-        trafo = oms.TransformationDescription()
-        aligner.align(fm, trafo)
-        transformer = oms.MapAlignmentTransformer()
-        transformer.transformRetentionTimes(fm, trafo, True)
+        
+        # Skip feature maps with insufficient data points for alignment
+        if fm.size() < 2:
+            sample_name = study_obj.samples_df.row(index, named=True)["sample_name"]
+            study_obj.logger.warning(f"Skipping alignment for sample '{sample_name}' - insufficient features ({fm.size()} features)")
+            continue
+            
+        try:
+            trafo = oms.TransformationDescription()
+            aligner.align(fm, trafo)
+            transformer = oms.MapAlignmentTransformer()
+            transformer.transformRetentionTimes(fm, trafo, True)
+        except RuntimeError as e:
+            sample_name = study_obj.samples_df.row(index, named=True)["sample_name"]
+            study_obj.logger.warning(f"Failed to align sample '{sample_name}': {e}")
+            continue
 
     study_obj.alignment_ref_index = ref_index
 

masster/wizard/wizard.py

@@ -127,7 +127,7 @@ class wizard_def:
     
     # === Feature Detection ===
     chrom_fwhm: float = 0.5
-    noise_threshold: float = 200.0
+    noise: float = 50.0
     chrom_peak_snr: float = 5.0
     tol_ppm: float = 10.0
     detector_type: str = "unknown"  # Detected detector type ("orbitrap", "quadrupole", "unknown")
@@ -307,15 +307,15 @@ class Wizard:
         """
         try:
             # Find first file
-            for extension in ['.wiff', '.raw', '.mzML', '.d']:
+            for extension in ['.wiff', '.raw', '.mzML']:
                 pattern = f"**/*{extension}" if True else f"*{extension}"  # search_subfolders=True
                 files = list(self.source_path.rglob(pattern))
                 if files:
                     first_file = files[0]
                     break
             else:
-                return None
-            
+                return 'positive'
+
             # Only implement for .wiff files initially (most common format)
             if first_file.suffix.lower() == '.wiff':
                 from masster.sample.load import _wiff_to_dict
@@ -337,7 +337,7 @@ class Wizard:
             # Silently fall back to default if inference fails
             pass
             
-        return None
+        return 'positive'
 
     @property
     def polarity(self) -> str:
@@ -543,9 +543,9 @@ class Wizard:
             '        sample = Sample(log_label=sample_name)',
             '        sample.load(filename=str(raw_file))',
             '        sample.find_features(',
-            '            noise=PARAMS[\'noise_threshold\'],',
-            '            chrom_fwhm=PARAMS[\'smoothing_width\'],',
-            '            chrom_peak_snr=PARAMS[\'peak_threshold\']',
+            '            noise=PARAMS[\'noise\'],',
+            '            chrom_fwhm=PARAMS[\'chrom_fwhm\'],',
+            '            chrom_peak_snr=PARAMS[\'chrom_peak_snr\']',
             '        )',
             '        sample.find_adducts(adducts=PARAMS[\'adducts\'])',
             '        sample.find_ms2()',

{masster-0.4.21.dist-info → masster-0.4.22.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: masster
-Version: 0.4.21
+Version: 0.4.22
 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-0.4.21.dist-info → masster-0.4.22.dist-info}/RECORD

@@ -1,5 +1,5 @@
 masster/__init__.py,sha256=ueZ224WPNRRjQEYTaQUol818nwQgJwB93HbEfmtPRmg,1041
-masster/_version.py,sha256=y5IX-RaakVoxIcxnpOMo4HnIGk-qPigff8Q07QC6yJU,257
+masster/_version.py,sha256=vQFUBi9UR5DFflCbwobRTLg-jW9TsSQB1GlM1tfxYuc,257
 masster/chromatogram.py,sha256=iYpdv8C17zVnlWvOFgAn9ns2uFGiF-GgoYf5QVVAbHs,19319
 masster/logger.py,sha256=tR65N23zfrNpcZNbZm2ot_Aual9XrGB1MWjLrovZkMs,16749
 masster/spectrum.py,sha256=XJSUrqXZSzfpWnD8v5IMClXMRZLKLYIk014qaMOS9_k,49738
@@ -28,7 +28,7 @@ masster/sample/processing.py,sha256=A1u5u7lGG0HR_ciUhJFmmwgugher7_AZQopNnbu65Bs,
 masster/sample/quant.py,sha256=tHNjvUFTdehKR31BXBZnVsBxMD9XJHgaltITOjr71uE,7562
 masster/sample/sample.py,sha256=uQP5DLdsRSC2YwZZvspsL9rgl_HefB-oxrL2dpgg_fc,19788
 masster/sample/sample5_schema.json,sha256=H5e2T6rHIDzul2kp_yP-ILUUWUpW08wP2pEQjMR0nSk,3977
-masster/sample/save.py,sha256=MfgHGiR2ofLyVp_rP9FIu7mUG3A6PEZHSscMypSTH7M,36425
+masster/sample/save.py,sha256=2yQtcQcRJjgAKPImTydj7LpyyMop_Q9JKRlNEK4yU6k,36339
 masster/sample/sciex.py,sha256=vnbxsq_qnAQVuzcpziP1o3IC4kM5amGBcPmC2TAuDLw,46319
 masster/sample/defaults/__init__.py,sha256=A09AOP44cxD_oYohyt7XFUho0zndRcrzVD4DUaGnKH4,447
 masster/sample/defaults/find_adducts_def.py,sha256=Bu2KiBJRxD0SAnOPNMm_Nk-6fx6QYoRXjFNGzz-0_o0,13570
@@ -37,15 +37,15 @@ masster/sample/defaults/find_ms2_def.py,sha256=KTELMAnioGLYbhzAwOgK14TZqboPEvzeB
 masster/sample/defaults/get_spectrum_def.py,sha256=o62p31PhGd-LiIkTOzKQhwPtnO2AtQDHcPu-O-YoQPs,11460
 masster/sample/defaults/sample_def.py,sha256=keoXyMyrm_iLgbYqfIbqCpJ3XHBVlNwCNmb5iMQL0iY,14579
 masster/study/__init__.py,sha256=55axdFuqRX4aXtJ8ocnhcLB32fNtmmJpCi58moO0r4g,237
-masster/study/export.py,sha256=CKrmje4_cQAJnQjQsB5u3mXkvDDbxKkAJO8e_MoeB38,59270
+masster/study/export.py,sha256=c-UQPYRwNBde8E1cYOB-0ZZz2tBDTwglRMlPfSKYB0w,59291
 masster/study/h5.py,sha256=eINlVmcJuntwbkkZHwzm10c63Kg7zib49vkzLDj1PyU,84790
 masster/study/helpers.py,sha256=6nDTNlsZbZWf9L6D5qzK2TUO2y7UBq51Ftj8N4bkIAk,160260
 masster/study/id.py,sha256=6NUBBKZCFOU1wlDKM0eXQeOIStSZCRNJ_3x7ZaIHzmM,55263
-masster/study/load.py,sha256=CQQY_7BzagE3oQTdDlqNyfuMdVWIAft-M4a2WCFnxp0,70695
+masster/study/load.py,sha256=mI6UyErlj3vIzSuG93fOjsxA7IIDCaiKfcuAcc2538o,72425
 masster/study/merge.py,sha256=3R_Dg6l2mnJUu3gFVAgrAN5hFSQyfHbqYPmc2cUfJqQ,159232
 masster/study/parameters.py,sha256=0elaF7YspTsB7qyajWAbRNL2VfKlGz5GJLifmO8IGkk,3276
-masster/study/plot.py,sha256=G9eStCUPxJTHrQk9TZpivk5rYxO1vbu5Yba6rP8NELM,90649
-masster/study/processing.py,sha256=WOcBdQ1agayASLkrtJ9GfUT0mgCJZVNnbuT77-J-KDY,52011
+masster/study/plot.py,sha256=OGUa_dDTD2QydbLg-4APRZc7Jx1kk9eXC9-GOLLgI1I,87666
+masster/study/processing.py,sha256=p0d-DyxA0YI6K9OPQZYTEs00DC6obr6-kLHPVWljEO0,56437
 masster/study/save.py,sha256=BANh9F1s-q7MclO1Mq_-v4xQyHeloEgmoPgRDVc-9aE,9037
 masster/study/study.py,sha256=rk-pJNg80N6xbROa9fqPfwVxFgzL_FLoSUNOTYeD5E0,40116
 masster/study/study5_schema.json,sha256=ghBeAXFS4a4Uavdn6TUVs9GaR1QOTnADCjQTOkN0tjU,7563
@@ -64,9 +64,9 @@ masster/study/defaults/study_def.py,sha256=h8dYbi9xv0sesCSQik49Z53IkskMmNtW6ixl7
 masster/wizard/README.md,sha256=mL1A3YWJZOefpJ6D0-HqGLkVRmUlOpwyVFdvJBeeoZM,14149
 masster/wizard/__init__.py,sha256=a2hcZnHASjfuw1lqZhZnvTR58rc33rRnoGAY_JfvGhI,683
 masster/wizard/example.py,sha256=xEZFTH9UZ8HKOm6s3JL8Js0Uw5ChnISWBHSZCL32vsM,7983
-masster/wizard/wizard.py,sha256=498u3rvYNC0mb0kDG7T71E8TKwMk2s1KKzHgDBn76c4,37698
-masster-0.4.21.dist-info/METADATA,sha256=BuBxOoHsoKYPLa5Jy6a2SPIUNDv9uCnujAbB7ibMqJU,44207
-masster-0.4.21.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-masster-0.4.21.dist-info/entry_points.txt,sha256=ZHguQ_vPmdbpqq2uGtmEOLJfgP-DQ1T0c07Lxh30wc8,58
-masster-0.4.21.dist-info/licenses/LICENSE,sha256=bx5iLIKjgAdYQ7sISn7DsfHRKkoCUm1154sJJKhgqnU,35184
-masster-0.4.21.dist-info/RECORD,,
+masster/wizard/wizard.py,sha256=esgaifLRyaGxytif9qOkTy-21VxlUQxrvl47K-l-BpE,37666
+masster-0.4.22.dist-info/METADATA,sha256=CXrrzzCC5cZ_G9plLZyCtiNpTXevD0wPuUNm0mIy-a4,44207
+masster-0.4.22.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+masster-0.4.22.dist-info/entry_points.txt,sha256=ZHguQ_vPmdbpqq2uGtmEOLJfgP-DQ1T0c07Lxh30wc8,58
+masster-0.4.22.dist-info/licenses/LICENSE,sha256=bx5iLIKjgAdYQ7sISn7DsfHRKkoCUm1154sJJKhgqnU,35184
+masster-0.4.22.dist-info/RECORD,,