masster 0.4.21__py3-none-any.whl → 0.5.0__py3-none-any.whl

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.
 
@@ -87,16 +166,12 @@ def align(self, **kwargs):
     # end of parameter initialization
 
     # Store parameters in the Study object
-    self.store_history(["align"], params.to_dict())
+    self.update_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):
     """
@@ -288,7 +370,7 @@ def find_ms2(self, **kwargs):
     # end of parameter initialization
 
     # Store parameters in the Study object
-    self.store_history(["find_ms2"], params.to_dict())
+    self.update_history(["find_ms2"], params.to_dict())
     self.logger.debug("Parameters stored to find_ms2")
 
     data = []
@@ -469,7 +551,7 @@ def _integrate_chrom_impl(self, **kwargs):
     # end of parameter initialization
 
     # Store parameters in the Study object
-    self.store_history(["integrate_chrom"], params.to_dict())
+    self.update_history(["integrate_chrom"], params.to_dict())
     self.logger.debug("Parameters stored to integrate_chrom")
 
     # Get parameter values for use in the method
@@ -687,7 +769,7 @@ def integrate(self, **kwargs):
     # end of parameter initialization
 
     # Store parameters in the Study object
-    self.store_history(["integrate"], params.to_dict())
+    self.update_history(["integrate"], params.to_dict())
     self.logger.debug("Parameters stored to integrate")
 
     # Call the original integrate_chrom function with extracted parameters
@@ -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/study/save.py

@@ -59,13 +59,16 @@ def save(self, filename=None, add_timestamp=True, compress=False):
 
     # Use compressed mode for large datasets
     if compress:
-        self._save_study5_compressed(filename)
+        from masster.study.h5 import _save_study5_compressed
+        _save_study5_compressed(self, filename)
     else:
-        self._save_study5(filename)
+        from masster.study.h5 import _save_study5
+        _save_study5(self, filename)
 
     if self.consensus_map is not None:
         # save the features as a separate file
-        self._save_consensusXML(filename=filename.replace(".study5", ".consensusXML"))
+        from masster.study.save import _save_consensusXML
+        _save_consensusXML(self, filename=filename.replace(".study5", ".consensusXML"))
     self.filename = filename
 
 
@@ -211,4 +214,5 @@ def save_consensus(self, **kwargs):
     if self.consensus_map is None:
         self.logger.error("No consensus map found.")
         return
-    self._save_consensusXML(**kwargs)
+    from masster.study.save import _save_consensusXML
+    _save_consensusXML(self, **kwargs)

masster/study/study.py

@@ -52,36 +52,26 @@ import sys
 import polars as pl
 
 # Study-specific imports
-from masster.study.h5 import _load_study5
-from masster.study.h5 import _save_study5
-from masster.study.h5 import _save_study5_compressed
-from masster.study.h5 import _load_ms1
+from masster.study.analysis import analyze_umap
 from masster.study.helpers import _get_consensus_uids
-from masster.study.helpers import _get_feature_uids
-from masster.study.helpers import _get_sample_uids
-from masster.study.helpers import _ensure_features_df_schema_order
+from masster.study.helpers import _get_features_uids
+from masster.study.helpers import _get_samples_uids
 from masster.study.helpers import compress
-from masster.study.helpers import compress_features
-from masster.study.helpers import compress_ms2
-from masster.study.helpers import compress_chrom
-from masster.study.helpers import restore_features
-from masster.study.helpers import restore_chrom
-from masster.study.helpers import restore_ms2
 from masster.study.helpers import decompress
 from masster.study.helpers import fill_reset
 from masster.study.helpers import get_chrom
-from masster.study.helpers import get_sample
+from masster.study.helpers import get_samples
 from masster.study.helpers import get_consensus
 from masster.study.helpers import get_consensus_matches
 from masster.study.helpers import get_consensus_matrix
 from masster.study.helpers import get_orphans
+from masster.study.helpers import get_sample_stats
 from masster.study.helpers import get_gaps_matrix
 from masster.study.helpers import get_gaps_stats
 from masster.study.helpers import align_reset
-from masster.study.helpers import set_folder
-from masster.study.helpers import set_source
-from masster.study.helpers import sample_color
-from masster.study.helpers import sample_color_reset
+from masster.study.helpers import set_study_folder
+from masster.study.helpers import set_samples_source
+from masster.study.helpers import set_samples_color
 from masster.study.helpers import sample_name_replace
 from masster.study.helpers import sample_name_reset
 from masster.study.helpers import samples_select
@@ -94,61 +84,34 @@ from masster.study.helpers import consensus_filter
 from masster.study.helpers import consensus_delete
 from masster.study.load import add
 from masster.study.load import add_sample
-from masster.study.load import _add_samples_batch
-from masster.study.load import _add_sample_optimized
-from masster.study.load import _add_sample_standard
-from masster.study.load import _sample_color_reset_optimized
-from masster.study.load import fill_single
 from masster.study.load import fill
-from masster.study.load import _process_sample_for_parallel_fill
-from masster.study.load import _get_missing_consensus_sample_combinations
 from masster.study.load import load
-from masster.study.load import _load_consensusXML
-from masster.study.load import load_features
-from masster.study.load import sanitize
+from masster.study.load import _load_features
 from masster.study.plot import plot_alignment
 from masster.study.plot import plot_consensus_2d
 from masster.study.plot import plot_samples_2d
 from masster.study.plot import plot_consensus_stats
 from masster.study.plot import plot_chrom
-from masster.study.plot import plot_pca
+from masster.study.plot import plot_samples_pca
+from masster.study.plot import plot_samples_umap
 from masster.study.plot import plot_bpc
 from masster.study.plot import plot_tic
 from masster.study.plot import plot_eic
 from masster.study.plot import plot_rt_correction
 from masster.study.processing import align
 from masster.study.merge import merge
-from masster.study.merge import _reset_consensus_data
-from masster.study.merge import _extract_consensus_features
-from masster.study.merge import _perform_adduct_grouping
-from masster.study.merge import _consensus_cleanup
-from masster.study.merge import _identify_adduct_by_mass_shift
-from masster.study.merge import _finalize_merge
-from masster.study.merge import _count_tight_clusters
 from masster.study.processing import integrate
 from masster.study.processing import find_ms2
 from masster.study.processing import find_iso
 from masster.study.processing import reset_iso
-from masster.study.parameters import store_history
+from masster.study.parameters import update_history
 from masster.study.parameters import get_parameters
 from masster.study.parameters import update_parameters
 from masster.study.parameters import get_parameters_property
 from masster.study.parameters import set_parameters_property
-from masster.study.save import save, save_consensus, _save_consensusXML, save_samples
-from masster.study.export import (
-    export_mgf,
-    export_mztab,
-    export_xlsx,
-    export_parquet,
-    _get_mgf_df,
-)
+from masster.study.save import save, save_consensus, save_samples
+from masster.study.export import export_mgf, export_mztab, export_xlsx, export_parquet
 from masster.study.id import lib_load, identify, get_id, id_reset, lib_reset
-from masster.study.id import (
-    _get_adducts,
-    _calculate_formula_mass_shift,
-    _format_adduct_name,
-    _parse_element_counts,
-)
 
 from masster.logger import MassterLogger
 from masster.study.defaults.study_def import study_defaults
@@ -253,8 +216,24 @@ class Study:
                      For backward compatibility, original signature is supported:
                      Study(folder=..., label=..., log_level=..., log_label=..., log_sink=...)
         """
-        # Initialize default parameters
+        # ===== PARAMETER INITIALIZATION =====
+        auto_load_filename = self._init_parameters(filename, kwargs)
+        
+        # ===== DATA STRUCTURES INITIALIZATION =====
+        self._init_data_structures()
+        
+        # ===== LOGGER INITIALIZATION =====
+        self._init_logger()
+        
+        # ===== AUTO-LOAD FILE IF PROVIDED =====
+        if auto_load_filename is not None:
+            self.load(filename=auto_load_filename)
+
+        # ===== SAMPLE CACHE =====
+        self._samples_cache = {}
 
+    def _init_parameters(self, filename, kwargs):
+        """Initialize parameters and handle filename for auto-loading."""
         # Handle filename parameter for automatic loading
         auto_load_filename = None
         if filename is not None:
@@ -281,13 +260,11 @@ class Study:
                 if hasattr(params, key):
                     params.set(key, value, validate=True)
 
-        # Keeps a pointer to study5 whenever it's saved or loaded
-        self.filename = None
-
-        # Store parameter instance for method access
+        # Store parameter instance and initialize history
+        self.filename = None  # Keeps a pointer to study5 whenever it's saved or loaded
         self.parameters = params
         self.history = {}
-        self.store_history(["study"], params.to_dict())
+        self.update_history(["study"], params.to_dict())
 
         # Set instance attributes (ensure proper string values for logger)
         self.folder = params.folder
@@ -301,10 +278,15 @@ class Study:
         self.log_label = params.log_label + " | " if params.log_label else ""
         self.log_sink = params.log_sink
 
+        # Create folder if it doesn't exist
         if self.folder is not None and not os.path.exists(self.folder):
-            # create the folder if it does not exist
             os.makedirs(self.folder)
+            
+        return auto_load_filename
 
+    def _init_data_structures(self):
+        """Initialize all data structures used by the Study."""
+        # Sample information DataFrame
         self.samples_df = pl.DataFrame(
             {
                 "sample_uid": [],
@@ -337,21 +319,24 @@ class Study:
                 "num_ms2": pl.Int64,
             },
         )
+        
+        # Feature-related data structures
         self.features_maps = []
         self.features_df = pl.DataFrame()
+        
+        # Consensus-related data structures
         self.consensus_ms2 = pl.DataFrame()
         self.consensus_df = pl.DataFrame()
         self.consensus_map = None
         self.consensus_mapping_df = pl.DataFrame()
         self.alignment_ref_index = None
 
-        # Library DataFrame (populated by lib_load)
-        self.lib_df = pl.DataFrame()
+        # Library and identification data structures
+        self.lib_df = pl.DataFrame()  # populated by lib_load
+        self.id_df = pl.DataFrame()   # populated by identify
 
-        # Identification results DataFrame (populated by identify)
-        self.id_df = pl.DataFrame()
-
-        # Initialize independent logger
+    def _init_logger(self):
+        """Initialize the logger for this Study instance."""
         self.logger = MassterLogger(
             instance_type="study",
             level=self.log_level.upper(),
@@ -361,85 +346,68 @@ class Study:
         self.logger.debug(f"Study folder: {self.folder}")
         self.logger.debug(f"Polarity: {self.polarity}")
 
-        # Auto-load study file if filename was provided
-        if auto_load_filename is not None:
-            self.load(filename=auto_load_filename)
-
-        # cache for Sample instances created/loaded by this Study
-        self._samples_cache = {}
-
-    # ===== ATTACH MODULE FUNCTIONS AS CLASS METHODS =====
-    
     # === File I/O Operations ===
     load = load
     save = save
     save_consensus = save_consensus
     save_samples = save_samples
-    sanitize = sanitize
-    set_folder = set_folder
+    set_study_folder = set_study_folder
     
     # === Sample Management ===
     add = add
-    add_folder = add  # backward compatibility alias
     add_sample = add_sample
     
     # === Core Processing Operations ===
     align = align
-    merge = merge
-    find_consensus = merge  # Backward compatibility alias
+    merge = merge   
+    
     find_ms2 = find_ms2
     find_iso = find_iso
     reset_iso = reset_iso
     iso_reset = reset_iso
     integrate = integrate
-    integrate_chrom = integrate  # Backward compatibility alias
+    
     fill = fill
-    fill_chrom = fill  # Backward compatibility alias
-    fill_single = fill_single
-    fill_chrom_single = fill_single  # Backward compatibility alias
+    
     # === Data Retrieval and Access ===
     get_consensus = get_consensus
     get_chrom = get_chrom
-    get_sample = get_sample
+    get_samples = get_samples
     get_consensus_matches = get_consensus_matches
     get_consensus_matrix = get_consensus_matrix
     get_gaps_matrix = get_gaps_matrix
     get_gaps_stats = get_gaps_stats
     get_orphans = get_orphans
+    get_sample_stats = get_sample_stats
     
     # === Data Selection and Filtering ===
     samples_select = samples_select
     samples_delete = samples_delete
+    
     features_select = features_select
     features_filter = features_filter
     features_delete = features_delete
     consensus_select = consensus_select
     consensus_filter = consensus_filter
     consensus_delete = consensus_delete
-    # Backward compatibility aliases
-    filter_consensus = consensus_filter
-    select_consensus = consensus_select
-    filter_features = features_filter
-    select_features = features_select
-    consensus_find = merge
-    
-    # === Sample Metadata and Styling ===
-    set_source = set_source
-    sample_color = sample_color
-    sample_color_reset = sample_color_reset
-    reset_sample_color = sample_color_reset
-    name_replace = sample_name_replace
-    name_reset = sample_name_reset
-    reset_name = sample_name_reset
 
+    # === Sample Metadata and Styling ===
+    set_samples_source = set_samples_source
+    set_samples_color = set_samples_color
+       
+    samples_name_replace = sample_name_replace
+    samples_name_reset = sample_name_reset
+    
+    # Backward compatibility aliases for renamed methods
+    set_folder = set_study_folder
+    set_source = set_samples_source  
+    #sample_color = set_samples_color
+    #get_sample = get_samples
+    #load_features = _load_features
+    store_history = update_history
+    
     # === Data Compression and Storage ===
     compress = compress
-    compress_features = compress_features
-    compress_ms2 = compress_ms2
-    compress_chrom = compress_chrom
-    restore_features = restore_features
-    restore_chrom = restore_chrom
-    restore_ms2 = restore_ms2
     decompress = decompress
     
     # === Reset Operations ===
@@ -453,12 +421,16 @@ class Study:
     plot_chrom = plot_chrom
     plot_consensus_2d = plot_consensus_2d
     plot_consensus_stats = plot_consensus_stats
-    plot_pca = plot_pca
+    plot_samples_pca = plot_samples_pca
+    plot_samples_umap = plot_samples_umap
     plot_samples_2d = plot_samples_2d
     plot_bpc = plot_bpc
     plot_rt_correction = plot_rt_correction
     plot_tic = plot_tic
     plot_eic = plot_eic
+
+    # === Analysis Operations ===
+    analyze_umap = analyze_umap
     
     # === Export Operations ===
     export_mgf = export_mgf
@@ -476,45 +448,23 @@ class Study:
     reset_lib = lib_reset
 
     # === Parameter Management ===
-    store_history = store_history
+    update_history = update_history
     get_parameters = get_parameters
     update_parameters = update_parameters
     get_parameters_property = get_parameters_property
     set_parameters_property = set_parameters_property
     
     # === Private/Internal Methods ===
-    _add_samples_batch = _add_samples_batch
-    _add_sample_optimized = _add_sample_optimized
-    _add_sample_standard = _add_sample_standard
-    _sample_color_reset_optimized = _sample_color_reset_optimized
-    _load_study5 = _load_study5
-    _save_study5 = _save_study5
-    _save_study5_compressed = _save_study5_compressed
-    _load_ms1 = _load_ms1
     _get_consensus_uids = _get_consensus_uids
-    _get_feature_uids = _get_feature_uids
-    _get_sample_uids = _get_sample_uids
-    _ensure_features_df_schema_order = _ensure_features_df_schema_order
-    _process_sample_for_parallel_fill = _process_sample_for_parallel_fill
-    _get_missing_consensus_sample_combinations = (
-        _get_missing_consensus_sample_combinations
-    )
-    _load_consensusXML = _load_consensusXML
-    load_features = load_features
-    _save_consensusXML = _save_consensusXML
-    _get_mgf_df = _get_mgf_df
-    _get_adducts = _get_adducts
-    _calculate_formula_mass_shift = _calculate_formula_mass_shift
-    _format_adduct_name = _format_adduct_name
-    _parse_element_counts = _parse_element_counts
+    _get_features_uids = _get_features_uids
+    _get_samples_uids = _get_samples_uids
+    _load_features = _load_features
+    
+    # Note: _load_study5 and _save_study5 are not exposed as class methods
+    # They are used internally by load() and save() methods only
     
     # === Merge Helper Methods ===
-    _reset_consensus_data = _reset_consensus_data
-    _extract_consensus_features = _extract_consensus_features
-    _perform_adduct_grouping = _perform_adduct_grouping
-    _consensus_cleanup = _consensus_cleanup
-    _identify_adduct_by_mass_shift = _identify_adduct_by_mass_shift
-    _finalize_merge = _finalize_merge
+    # (All merge helper methods are now internal to the merge module)
     
     # === Default Parameters ===
     study_defaults = study_defaults
@@ -627,16 +577,24 @@ class Study:
             'find_consensus',       # alias for merge  
             'integrate_chrom',      # alias for integrate
             'fill_chrom',           # alias for fill
-            'fill_chrom_single',    # alias for fill_single
             'filter_consensus',     # alias for consensus_filter
             'select_consensus',     # alias for consensus_select
             'filter_features',      # alias for features_filter
             'select_features',      # alias for features_select
             'consensus_find',       # alias for merge
+            # Backward compatibility for renamed methods
+            'set_folder',           # alias for set_study_folder
+            'set_source',           # alias for set_samples_source
+            'sample_color',         # alias for set_samples_color
+            'get_sample',           # alias for get_samples
+            'load_features',        # alias for _load_features
+            'store_history',        # alias for update_history
+            'sample_color_reset',   # alias for set_samples_color(by=None)
+            'reset_sample_color',   # alias for sample_color_reset
         }
         
         # Get all attributes from the class
-        all_attrs = set()
+        all_attrs: set[str] = set()
         
         # Add attributes from the class and all its bases
         for cls in self.__class__.__mro__:
@@ -895,8 +853,9 @@ class Study:
         tight_clusters_count = 0
         if consensus_df_len > 0:
             try:
+                from masster.study.merge import _count_tight_clusters
                 tight_clusters_count = _count_tight_clusters(self, mz_tol=0.04, rt_tol=0.3)
-            except Exception as e:
+            except Exception:
                 # If tight clusters calculation fails, just use 0
                 tight_clusters_count = 0
 
@@ -952,7 +911,6 @@ class Study:
 
         print(summary)
 
-
 if __name__ == "__main__":
     # This block is executed when the script is run directly
     pass

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()',