masster 0.4.13__py3-none-any.whl → 0.4.16__py3-none-any.whl

masster/study/save.py

@@ -53,7 +53,7 @@ def save(self, filename=None, add_timestamp=True, compress=False):
             if hasattr(self, "samples_df") and not self.samples_df.is_empty()
             else 0
         )
-        self.logger.info(
+        self.logger.debug(
             f"Saving study with {sample_count} samples and {feature_count} features to {filename}",
         )
 

masster/study/study.py

@@ -116,7 +116,11 @@ 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.processing import merge
+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 _finalize_merge
 from masster.study.processing import integrate
 from masster.study.processing import find_ms2
 from masster.study.parameters import store_history
@@ -146,7 +150,6 @@ from masster.study.defaults.align_def import align_defaults
 from masster.study.defaults.export_def import export_mgf_defaults
 from masster.study.defaults.fill_chrom_def import fill_chrom_defaults
 from masster.study.defaults.fill_def import fill_defaults
-from masster.study.defaults.find_consensus_def import find_consensus_defaults
 from masster.study.defaults.find_ms2_def import find_ms2_defaults
 from masster.study.defaults.integrate_chrom_def import integrate_chrom_defaults
 from masster.study.defaults.integrate_def import integrate_defaults
@@ -385,7 +388,6 @@ class Study:
     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
@@ -490,13 +492,18 @@ class Study:
     _format_adduct_name = _format_adduct_name
     _parse_element_counts = _parse_element_counts
     
+    # === Merge Helper Methods ===
+    _reset_consensus_data = _reset_consensus_data
+    _extract_consensus_features = _extract_consensus_features
+    _perform_adduct_grouping = _perform_adduct_grouping
+    _finalize_merge = _finalize_merge
+    
     # === Default Parameters ===
     study_defaults = study_defaults
     align_defaults = align_defaults
     export_mgf_defaults = export_mgf_defaults
     fill_chrom_defaults = fill_chrom_defaults
     fill_defaults = fill_defaults
-    find_consensus_defaults = find_consensus_defaults
     find_ms2_defaults = find_ms2_defaults
     integrate_chrom_defaults = integrate_chrom_defaults
     integrate_defaults = integrate_defaults
@@ -587,6 +594,51 @@ class Study:
         except Exception as e:
             self.logger.error(f"Failed to reload current module {current_module}: {e}")
 
+    def __dir__(self):
+        """
+        Custom __dir__ implementation to hide internal methods starting with '_' 
+        and backward compatibility aliases from tab completion and dir() calls, 
+        while keeping them accessible to class methods.
+        
+        Returns:
+            list: List of public attribute and method names (excluding internal and deprecated methods)
+        """
+        # Define backward compatibility aliases to hide
+        backward_compatibility_aliases = {
+            'add_folder',           # alias for add
+            '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
+        }
+        
+        # Get all attributes from the class
+        all_attrs = set()
+        
+        # Add attributes from the class and all its bases
+        for cls in self.__class__.__mro__:
+            all_attrs.update(cls.__dict__.keys())
+        
+        # Add instance attributes
+        all_attrs.update(self.__dict__.keys())
+        
+        # Filter out attributes starting with '_' (but keep special methods like __init__, __str__, etc.)
+        # Also filter out backward compatibility aliases
+        public_attrs = [
+            attr for attr in all_attrs 
+            if not attr.startswith('_') or attr.startswith('__') and attr.endswith('__')
+        ]
+        
+        # Remove backward compatibility aliases from the public attributes
+        public_attrs = [attr for attr in public_attrs if attr not in backward_compatibility_aliases]
+        
+        return sorted(public_attrs)
+
     def __str__(self):
         """
         Returns a string representation of the study.
@@ -632,11 +684,13 @@ class Study:
         samples count, and various statistics. Shows warning symbols for values
         that are out of normal range.
         """
-        # Cache DataFrame lengths and existence checks
-        consensus_df_len = (
-            len(self.consensus_df) if not self.consensus_df.is_empty() else 0
-        )
-        samples_df_len = len(self.samples_df) if not self.samples_df.is_empty() else 0
+        if self.consensus_df is None or self.consensus_df.is_empty():
+            self.consensus_df = pl.DataFrame()
+            consensus_df_len = 0
+        else:
+            consensus_df_len = len(self.consensus_df)
+
+        samples_df_len = len(self.samples_df) if (self.samples_df is not None and not self.samples_df.is_empty()) else 0
 
         # Calculate consensus statistics only if consensus_df exists and has data
         if consensus_df_len > 0:
@@ -658,7 +712,8 @@ class Study:
             max_samples = 0
 
         # Count only features where 'filled' == False
-        if not self.features_df.is_empty() and "filled" in self.features_df.columns:
+        if (self.features_df is not None and not self.features_df.is_empty() and 
+            "filled" in self.features_df.columns):
             unfilled_features_count = self.features_df.filter(
                 ~self.features_df["filled"],
             ).height
@@ -666,7 +721,8 @@ class Study:
             unfilled_features_count = 0
 
         # Calculate features in consensus vs not in consensus (only for unfilled features)
-        if not self.features_df.is_empty() and not self.consensus_mapping_df.is_empty():
+        if (self.features_df is not None and not self.features_df.is_empty() and 
+            self.consensus_mapping_df is not None and not self.consensus_mapping_df.is_empty()):
             # Get unfilled features only
             unfilled_features = (
                 self.features_df.filter(~self.features_df["filled"])
@@ -720,6 +776,7 @@ class Study:
         if (
             consensus_df_len > 0
             and samples_df_len > 0
+            and self.features_df is not None
             and not self.features_df.is_empty()
         ):
             # Ensure matching data types for join keys
@@ -745,7 +802,8 @@ class Study:
                     )
 
             # Use more efficient counting - count non-null chroms only for features in consensus mapping
-            if not self.consensus_mapping_df.is_empty():
+            if (self.consensus_mapping_df is not None and 
+                not self.consensus_mapping_df.is_empty()):
                 non_null_chroms = (
                     self.features_df.join(
                         self.consensus_mapping_df.select("feature_uid"),
@@ -767,16 +825,16 @@ class Study:
             chrom_completeness = 0
 
         # Calculate consensus features with MS2 (count unique consensus_uids with MS2)
-        if not self.consensus_ms2.is_empty():
+        if self.consensus_ms2 is not None and not self.consensus_ms2.is_empty():
             consensus_with_ms2_count = self.consensus_ms2["consensus_uid"].n_unique()
         else:
             consensus_with_ms2_count = 0
 
-        if not self.consensus_df.is_empty():
+        if self.consensus_df is not None and not self.consensus_df.is_empty():
             # Compute RT spread using only consensus rows with number_samples >= half the number of samples
             threshold = (
                 self.consensus_df.select(pl.col("number_samples").max()).item() / 2
-                if not self.samples_df.is_empty()
+                if (self.samples_df is not None and not self.samples_df.is_empty())
                 else 0
             )
             filtered = self.consensus_df.filter(pl.col("number_samples") >= threshold)
@@ -803,16 +861,16 @@ class Study:
 
         # Total MS2 spectra count
         total_ms2_count = (
-            len(self.consensus_ms2) if not self.consensus_ms2.is_empty() else 0
+            len(self.consensus_ms2) if (self.consensus_ms2 is not None and not self.consensus_ms2.is_empty()) else 0
         )
 
         # Estimate memory usage
         memory_usage = (
-            self.samples_df.estimated_size()
-            + self.features_df.estimated_size()
-            + self.consensus_df.estimated_size()
-            + self.consensus_ms2.estimated_size()
-            + self.consensus_mapping_df.estimated_size()
+            (self.samples_df.estimated_size() if self.samples_df is not None else 0)
+            + (self.features_df.estimated_size() if self.features_df is not None else 0)
+            + (self.consensus_df.estimated_size() if self.consensus_df is not None else 0)
+            + (self.consensus_ms2.estimated_size() if self.consensus_ms2 is not None else 0)
+            + (self.consensus_mapping_df.estimated_size() if self.consensus_mapping_df is not None else 0)
         )
 
         # Add warning symbols for out-of-range values

masster/wizard/README.md

@@ -0,0 +1,373 @@
+# Wizard Class Documentation
+
+The `Wizard` class provides comprehensive automation for mass spectrometry data processing, from raw files to final study results. It handles the complete workflow with minimal user intervention while providing intelligent resume capabilities, parallel processing optimization, and adaptive output formats.
+
+## Quick Start
+
+### Basic Usage
+
+```python
+from masster import Wizard
+
+# Create wizard with minimal configuration
+wizard = Wizard(
+    data_source="./raw_data",      # Directory with raw files
+    study_folder="./processed",    # Output directory  
+    polarity="positive",           # or "negative"
+    num_cores=4                    # CPU cores to use
+)
+
+# Run complete pipeline
+success = wizard.run_full_pipeline()
+
+if success:
+    wizard.info()  # Print summary
+```
+
+### Advanced Configuration
+
+```python
+from masster import Wizard, wizard_def
+
+# Create custom parameters
+params = wizard_def(
+    data_source="./raw_data",
+    study_folder="./processed_advanced",
+    polarity="negative",
+    num_cores=8,
+    
+    # File discovery
+    file_extensions=[".wiff", ".raw", ".mzML"],
+    search_subfolders=True,
+    skip_patterns=["blank", "QC", "test"],
+    
+    # Processing parameters
+    adducts=["H-1:-:0.95", "Cl:-:0.05", "CH2O2:0:0.2"],
+    chrom_fwhm=0.15,
+    noise_threshold=5e4,
+    
+    # Study assembly
+    rt_tolerance=1.0,
+    mz_tolerance=0.008,
+    min_samples_for_merge=30,
+    
+    # Output options
+    export_formats=["csv", "xlsx", "mgf", "parquet"],
+    generate_plots=True,
+    compress_output=True,
+)
+
+wizard = Wizard(params=params)
+wizard.run_full_pipeline()
+```
+
+## Key Features
+
+### 🔄 Automated Pipeline
+- **Raw Data Discovery**: Automatically finds and validates raw MS files
+- **Batch Conversion**: Parallel conversion to sample5 format with optimized parameters
+- **Study Assembly**: Creates study from processed samples with quality filtering
+- **Feature Alignment**: Cross-sample alignment using configurable algorithms
+- **Consensus Generation**: Merges aligned features with statistical validation
+- **Results Export**: Multiple output formats for downstream analysis
+
+### 💾 Intelligent Resume
+- **Checkpoint System**: Automatically saves progress at key points
+- **File Tracking**: Remembers which files have been processed successfully  
+- **Smart Recovery**: Resumes from last successful step after interruption
+- **Validation**: Verifies existing outputs before skipping
+
+### ⚡ Performance Optimization
+- **Parallel Processing**: Utilizes multiple CPU cores efficiently
+- **Memory Management**: Adaptive batch sizing based on available memory
+- **Process Isolation**: Prevents memory leaks in long-running jobs
+- **Adaptive Compression**: Optimizes output format based on study size
+
+### 📊 Comprehensive Logging
+- **Progress Tracking**: Real-time status updates with time estimates
+- **Detailed Logs**: Complete processing history saved to files
+- **Error Reporting**: Clear error messages with recovery suggestions
+- **Performance Metrics**: Processing times and resource usage statistics
+
+## Pipeline Steps
+
+### 1. File Discovery
+- Searches for raw MS files (`.wiff`, `.raw`, `.mzML`, `.d`)
+- Applies skip patterns to exclude unwanted files
+- Validates file integrity and accessibility
+- Reports file sizes and estimates processing time
+
+### 2. Sample5 Conversion
+- **Feature Detection**: Two-pass algorithm with configurable parameters
+- **Adduct Detection**: Automated adduct grouping based on polarity
+- **MS2 Linking**: Associates fragmentation spectra with features
+- **Quality Control**: Validates outputs and reports statistics
+- **Parallel Processing**: Utilizes multiple CPU cores with batch optimization
+
+### 3. Study Assembly
+- **Sample Loading**: Imports all processed sample5 files
+- **Quality Filtering**: Removes low-quality features based on coherence/prominence
+- **Metadata Organization**: Organizes sample information and experimental design
+- **Memory Optimization**: Efficient data structures for large studies
+
+### 4. Feature Alignment
+- **RT Alignment**: Corrects retention time shifts between samples
+- **Mass Alignment**: Accounts for mass calibration differences  
+- **Algorithm Selection**: Supports KD-tree, QT-clustering, and chunked methods
+- **Validation**: Reports alignment statistics and quality metrics
+
+### 5. Consensus Generation
+- **Feature Merging**: Groups aligned features into consensus features
+- **Statistical Validation**: Applies minimum sample requirements
+- **Gap Filling**: Extracts chromatograms for missing values
+- **MS2 Integration**: Links consensus features to MS2 spectra
+
+### 6. Visualization & Export
+- **Interactive Plots**: 2D feature maps, PCA plots, alignment visualizations
+- **Multiple Formats**: CSV, Excel, MGF, Parquet exports
+- **Study Archival**: Compressed study5 format for long-term storage
+- **Metadata Export**: Complete processing parameters and statistics
+
+## Configuration Options
+
+### Core Parameters
+
+| Parameter | Type | Default | Description |
+|-----------|------|---------|-------------|
+| `data_source` | str | **required** | Directory containing raw data files |
+| `study_folder` | str | **required** | Output directory for processed study |
+| `polarity` | str | `"positive"` | Ion polarity mode (`"positive"` or `"negative"`) |
+| `num_cores` | int | `4` | Number of CPU cores for parallel processing |
+| `adducts` | List[str] | auto-set | Adduct specifications (set based on polarity) |
+
+### File Discovery
+
+| Parameter | Type | Default | Description |
+|-----------|------|---------|-------------|
+| `file_extensions` | List[str] | `[".wiff", ".raw", ".mzML", ".d"]` | File types to search for |
+| `search_subfolders` | bool | `True` | Search subdirectories recursively |
+| `skip_patterns` | List[str] | `["blank", "QC", "test"]` | Filename patterns to skip |
+| `max_file_size_gb` | float | `4.0` | Maximum file size warning threshold |
+
+### Processing Parameters
+
+| Parameter | Type | Default | Description |
+|-----------|------|---------|-------------|
+| `batch_size` | int | `8` | Files processed per batch |
+| `memory_limit_gb` | float | `16.0` | Memory usage limit |
+| `chrom_fwhm` | float | `0.2` | Expected chromatographic peak width (s) |
+| `noise_threshold` | float | `1e5` | Intensity threshold for peak detection |
+| `chrom_peak_snr` | float | `5.0` | Signal-to-noise ratio requirement |
+| `tol_ppm` | float | `10.0` | Mass tolerance (ppm) |
+
+### Study Assembly
+
+| Parameter | Type | Default | Description |
+|-----------|------|---------|-------------|
+| `rt_tolerance` | float | `1.5` | RT tolerance for alignment (seconds) |
+| `mz_tolerance` | float | `0.01` | m/z tolerance for alignment (Da) |
+| `alignment_algorithm` | str | `"kd"` | Alignment algorithm (`"kd"`, `"qt"`, `"chunked"`) |
+| `merge_method` | str | `"chunked"` | Merge algorithm for consensus generation |
+| `min_samples_for_merge` | int | `50` | Minimum samples required for consensus |
+
+### Output & Logging
+
+| Parameter | Type | Default | Description |
+|-----------|------|---------|-------------|
+| `generate_plots` | bool | `True` | Generate visualization plots |
+| `export_formats` | List[str] | `["csv", "mgf", "xlsx"]` | Output formats to generate |
+| `compress_output` | bool | `True` | Compress final study file |
+| `adaptive_compression` | bool | `True` | Adapt compression based on study size |
+| `log_level` | str | `"INFO"` | Logging detail level |
+| `log_to_file` | bool | `True` | Save logs to file |
+
+### Resume & Recovery
+
+| Parameter | Type | Default | Description |
+|-----------|------|---------|-------------|
+| `resume_enabled` | bool | `True` | Enable automatic resume capability |
+| `force_reprocess` | bool | `False` | Force reprocessing of existing files |
+| `backup_enabled` | bool | `True` | Create backups of intermediate results |
+| `checkpoint_interval` | int | `10` | Save progress every N files |
+| `cleanup_temp_files` | bool | `True` | Remove temporary files after completion |
+
+## Methods
+
+### Pipeline Control
+
+#### `run_full_pipeline() -> bool`
+Executes the complete processing pipeline in sequence. Returns `True` if successful.
+
+#### Individual Steps
+- `discover_files() -> List[Path]` - Find raw data files
+- `convert_to_sample5(file_list=None) -> bool` - Convert to sample5 format
+- `assemble_study() -> bool` - Create study from sample5 files
+- `align_and_merge() -> bool` - Perform feature alignment and merging
+- `generate_plots() -> bool` - Create visualization plots
+- `export_results() -> bool` - Export in requested formats
+- `save_study() -> bool` - Save final study file
+- `cleanup_temp_files() -> bool` - Remove temporary files
+
+### Status & Information
+
+#### `info()`
+Prints comprehensive wizard status including progress, timings, and results.
+
+#### `get_status() -> Dict[str, Any]`
+Returns detailed status dictionary with current step, processed files, timing, and parameters.
+
+## Error Handling & Recovery
+
+### Common Issues and Solutions
+
+**Memory Errors**
+- Reduce `batch_size` parameter
+- Increase `memory_limit_gb` if available
+- Use `merge_method="chunked"` for large studies
+- Enable `cleanup_temp_files=True`
+
+**File Access Errors**
+- Check file permissions on source and destination folders
+- Verify network connectivity for remote file systems
+- Ensure sufficient disk space in output directory
+- Close any applications that might lock files
+
+**Processing Failures** 
+- Check individual file integrity
+- Review `skip_patterns` to exclude problematic files
+- Examine detailed logs in `wizard.log` and `processing.log`
+- Try processing failed files individually for debugging
+
+**Resume Issues**
+- Delete `wizard_checkpoint.json` to force fresh start
+- Verify output directory permissions
+- Check for corrupted intermediate files
+
+### Validation and Quality Control
+
+The Wizard includes built-in validation at each step:
+
+- **File Validation**: Checks file accessibility and format compatibility
+- **Processing Validation**: Verifies sample5 outputs can be loaded
+- **Study Validation**: Ensures study assembly completed successfully  
+- **Alignment Validation**: Reports alignment statistics and warnings
+- **Export Validation**: Confirms all requested outputs were created
+
+## Performance Guidelines
+
+### System Requirements
+- **Minimum**: 4 CPU cores, 8 GB RAM
+- **Recommended**: 8+ CPU cores, 16+ GB RAM  
+- **Large Studies**: 16+ CPU cores, 32+ GB RAM
+- **Storage**: SSD recommended, ~2-3x raw data size free space
+
+### Optimization Tips
+
+**For Small Studies (< 50 samples)**
+- Use `num_cores = 4-6`
+- Set `batch_size = 4-8`  
+- Use `merge_method = "kd"`
+- Enable all export formats
+
+**For Large Studies (100+ samples)**
+- Use `num_cores = 8-16`
+- Set `batch_size = 16-32`
+- Use `merge_method = "chunked"`
+- Enable `adaptive_compression = True`
+- Consider processing in polarity-specific batches
+
+**For Very Large Studies (500+ samples)**
+- Process positive/negative modes separately
+- Use `memory_limit_gb = 64+`
+- Set `checkpoint_interval = 50`
+- Enable `cleanup_temp_files = True`
+- Consider cluster/cloud processing
+
+## Integration Examples
+
+### With Existing Workflows
+
+```python
+# Integration with custom preprocessing
+wizard = Wizard(data_source="./preprocessed", ...)
+
+# Skip conversion if already done
+if not wizard.study_folder_path.glob("*.sample5"):
+    wizard.convert_to_sample5()
+
+# Continue with study-level processing
+wizard.assemble_study()
+wizard.align_and_merge() 
+wizard.export_results()
+```
+
+### Batch Processing Multiple Studies
+
+```python
+studies = [
+    {"source": "./batch1", "output": "./results/batch1", "polarity": "pos"},
+    {"source": "./batch2", "output": "./results/batch2", "polarity": "neg"},
+]
+
+for study_config in studies:
+    wizard = Wizard(**study_config, num_cores=8)
+    success = wizard.run_full_pipeline()
+    
+    if success:
+        print(f"✅ {study_config['output']} completed")
+    else:
+        print(f"❌ {study_config['output']} failed")
+```
+
+### Custom Processing Steps
+
+```python
+wizard = Wizard(...)
+
+# Standard conversion
+wizard.convert_to_sample5()
+
+# Custom study assembly with specific parameters
+wizard.assemble_study()
+
+# Custom filtering before alignment
+if hasattr(wizard.study, 'features_filter'):
+    selection = wizard.study.features_select(
+        chrom_coherence=0.5,  # Higher quality threshold
+        chrom_prominence_scaled=2.0
+    )
+    wizard.study.features_filter(selection)
+
+# Continue with standard pipeline  
+wizard.align_and_merge()
+wizard.generate_plots()
+```
+
+## Output Files
+
+The Wizard generates several types of output files:
+
+### Primary Results
+- `final_study.study5` - Complete study in masster native format
+- `consensus_features.csv` - Feature table with RT, m/z, intensity data
+- `study_results.xlsx` - Multi-sheet Excel workbook with results and metadata
+- `consensus_ms2.mgf` - MS2 spectra for database searching
+
+### Visualizations
+- `alignment_plot.html` - Interactive alignment visualization
+- `consensus_2d.html` - 2D feature map of consensus features
+- `pca_plot.html` - Principal component analysis plot
+- `consensus_stats.html` - Study statistics and quality metrics
+
+### Processing Logs
+- `wizard.log` - Detailed processing log with debug information
+- `processing.log` - Simple progress log with timestamps
+- `study_metadata.txt` - Study summary with parameters and statistics
+
+### Individual Sample Outputs (if enabled)
+- `sample_name.sample5` - Processed sample in masster format
+- `sample_name.features.csv` - Individual sample feature table
+- `sample_name.mgf` - Individual sample MS2 spectra
+- `sample_name_2d.html` - Individual sample 2D plot
+
+The Wizard provides a complete, automated solution for mass spectrometry data processing while maintaining flexibility for custom workflows and providing robust error handling and recovery capabilities.

masster/wizard/__init__.py

@@ -0,0 +1,11 @@
+"""
+Wizard module for automated processing of mass spectrometry studies.
+
+This module provides the Wizard class for fully automated processing of MS data
+from raw files to final study results, including batch conversion, assembly,
+alignment, merging, plotting, and export.
+"""
+
+from .wizard import Wizard, wizard_def
+
+__all__ = ["Wizard", "wizard_def"]