masster 0.3.10__py3-none-any.whl → 0.3.12__py3-none-any.whl

masster/study/study.py

@@ -50,6 +50,7 @@ import os
 import sys
 
 import polars as pl
+import numpy as np
 
 # Study-specific imports
 from masster.study.h5 import _load_study5
@@ -66,6 +67,7 @@ from masster.study.helpers import restore_features
 from masster.study.helpers import restore_chrom
 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_consensus
 from masster.study.helpers import get_consensus_matches
 from masster.study.helpers import get_consensus_matrix
@@ -75,6 +77,8 @@ 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 name_replace
+from masster.study.helpers import name_reset
 from masster.study.helpers import features_select
 from masster.study.helpers import features_filter
 from masster.study.helpers import features_delete
@@ -92,12 +96,16 @@ from masster.study.load import _load_consensusXML
 from masster.study.load import load_features
 from masster.study.load import sanitize
 from masster.study.plot import plot_alignment
-from masster.study.plot import plot_alignment_bokeh
-from masster.study.plot import plot_chrom
 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_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.processing import filter_consensus
 from masster.study.processing import merge
 from masster.study.processing import integrate
 from masster.study.processing import find_ms2
@@ -170,7 +178,7 @@ class Study:
         - `ddafile`: For individual sample processing before study-level analysis.
         - `StudyParameters`: For configuring study-specific parameters.
     """
-    
+
     # Defaults class attributes
     study_defaults = study_defaults
     sample_defaults = sample_defaults
@@ -219,15 +227,15 @@ class Study:
         # Handle filename parameter for automatic loading
         auto_load_filename = None
         if filename is not None:
-            if not filename.endswith('.study5'):
+            if not filename.endswith(".study5"):
                 raise ValueError("filename must be a .study5 file")
             if not os.path.exists(filename):
                 raise FileNotFoundError(f"Study file not found: {filename}")
-            
+
             # Set folder to the directory containing the file if not already specified
-            if 'folder' not in kwargs:
-                kwargs['folder'] = os.path.dirname(os.path.abspath(filename))
-            
+            if "folder" not in kwargs:
+                kwargs["folder"] = os.path.dirname(os.path.abspath(filename))
+
             auto_load_filename = filename
 
         # Check if a study_defaults instance was passed
@@ -257,7 +265,7 @@ class Study:
         self.log_level = params.log_level.upper() if params.log_level else "INFO"
         self.log_label = params.log_label + " | " if params.log_label else ""
         self.log_sink = params.log_sink
-        
+
         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)
@@ -308,80 +316,91 @@ class Study:
         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  
+
+    # Attach module functions as class methods
     load = load
-    save = save 
-    save_consensus = save_consensus 
-    save_samples = save_samples 
-    align = align 
-    fill_single = fill_single 
+    save = save
+    save_consensus = save_consensus
+    save_samples = save_samples
+    align = align
+    fill_single = fill_single
     fill_chrom_single = fill_single  # Backward compatibility alias
-    merge = merge 
+    merge = merge
     find_consensus = merge  # Backward compatibility alias
-    find_ms2 = find_ms2 
+    find_ms2 = find_ms2
     integrate = integrate
     integrate_chrom = integrate  # Backward compatibility alias
-    store_history = store_history 
-    get_parameters = get_parameters 
-    update_parameters = update_parameters 
-    get_parameters_property = get_parameters_property 
-    set_parameters_property = set_parameters_property 
-    plot_alignment = plot_alignment 
-    plot_alignment_bokeh = plot_alignment_bokeh 
-    plot_chrom = plot_chrom 
-    plot_consensus_2d = plot_consensus_2d 
-    plot_samples_2d = plot_samples_2d 
-    get_consensus = get_consensus 
-    get_chrom = get_chrom 
-    get_consensus_matches = get_consensus_matches 
-    compress = compress 
+    store_history = store_history
+    get_parameters = get_parameters
+    update_parameters = update_parameters
+    get_parameters_property = get_parameters_property
+    set_parameters_property = set_parameters_property
+    plot_alignment = plot_alignment
+    plot_chrom = plot_chrom
+    plot_consensus_2d = plot_consensus_2d
+    plot_consensus_stats = plot_consensus_stats
+    plot_pca = plot_pca
+    plot_samples_2d = plot_samples_2d
+    plot_bpc = plot_bpc
+    plot_rt_correction = plot_rt_correction
+    plot_tic = plot_tic
+    plot_eic = plot_eic
+    get_consensus = get_consensus
+    get_chrom = get_chrom
+    get_sample = get_sample
+    get_consensus_matches = get_consensus_matches
+    compress = compress
     compress_features = compress_features
     compress_ms2 = compress_ms2
     compress_chrom = compress_chrom
-    restore_features = restore_features 
+    restore_features = restore_features
     restore_chrom = restore_chrom
-    fill_reset = fill_reset 
-    align_reset = align_reset 
+    fill_reset = fill_reset
+    align_reset = align_reset
     set_source = set_source
+    name_replace = name_replace
+    name_reset = name_reset
     features_select = features_select
     features_filter = features_filter
     features_delete = features_delete
     consensus_select = consensus_select
     consensus_filter = consensus_filter
     consensus_delete = consensus_delete
-    filter_consensus = consensus_filter 
+    filter_consensus = consensus_filter
     select_consensus = consensus_select
     filter_features = features_filter
     select_features = features_select
     consensus_find = merge
-    filter_features = features_filter    
+    filter_features = features_filter
 
     # Additional method assignments for all imported functions
-    add_folder = add # backward compatibility alias
-    add = add 
+    add_folder = add  # backward compatibility alias
+    add = add
     add_sample = add_sample
-    _load_study5 = _load_study5 
-    _save_study5 = _save_study5 
-    _save_study5_compressed = _save_study5_compressed 
-    _get_consensus_uids = _get_consensus_uids 
-    _get_feature_uids = _get_feature_uids 
-    _get_sample_uids = _get_sample_uids 
-    get_consensus_matrix = get_consensus_matrix 
-    get_gaps_matrix = get_gaps_matrix 
-    get_gaps_stats = get_gaps_stats 
+    _load_study5 = _load_study5
+    _save_study5 = _save_study5
+    _save_study5_compressed = _save_study5_compressed
+    _get_consensus_uids = _get_consensus_uids
+    _get_feature_uids = _get_feature_uids
+    _get_sample_uids = _get_sample_uids
+    get_consensus_matrix = get_consensus_matrix
+    get_gaps_matrix = get_gaps_matrix
+    get_gaps_stats = get_gaps_stats
     get_orphans = get_orphans
-    set_folder = set_folder 
-    fill = fill 
+    set_folder = set_folder
+    fill = fill
     fill_chrom = fill  # Backward compatibility alias
-    _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 
-    sanitize = sanitize 
-    _save_consensusXML = _save_consensusXML 
-    export_mgf = export_mgf 
+    _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
+    sanitize = sanitize
+    _save_consensusXML = _save_consensusXML
+    export_mgf = export_mgf
     export_mztab = export_mztab
     _get_mgf_df = _get_mgf_df  # New function for MGF data extraction
 
@@ -404,13 +423,13 @@ class Study:
         This ensures that the instance uses the latest implementation without restarting the interpreter.
         """
         # Reset logger configuration flags to allow proper reconfiguration after reload
-        '''        try:
+        """        try:
             import masster.sample.logger as logger_module
 
             if hasattr(logger_module, "_STUDY_LOGGER_CONFIGURED"):
                 logger_module._STUDY_LOGGER_CONFIGURED = False
         except Exception:
-            pass'''
+            pass"""
 
         # Get the base module name (masster)
         base_modname = self.__class__.__module__.split(".")[0]
@@ -508,7 +527,7 @@ class Study:
         # 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
-        
+
         # Calculate consensus statistics only if consensus_df exists and has data
         if consensus_df_len > 0:
             # Execute the aggregation once
@@ -525,40 +544,44 @@ class Study:
             min_samples = 0
             mean_samples = 0
             max_samples = 0
-        
+
         # Count only features where 'filled' == False
-        if 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
+        if 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
         else:
             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():
             # Get unfilled features only
-            unfilled_features = self.features_df.filter(~self.features_df['filled']) if 'filled' in self.features_df.columns else self.features_df
-            
+            unfilled_features = (
+                self.features_df.filter(~self.features_df["filled"])
+                if "filled" in self.features_df.columns
+                else self.features_df
+            )
+
             # Ensure the column and list have matching data types
-            consensus_feature_uids = self.consensus_mapping_df['feature_uid'].to_list()
-            
+            consensus_feature_uids = self.consensus_mapping_df["feature_uid"].to_list()
+
             # Check if we need to cast either side to match types
-            unfilled_dtype = unfilled_features['feature_uid'].dtype
-            consensus_dtype = self.consensus_mapping_df['feature_uid'].dtype
-            
+            unfilled_dtype = unfilled_features["feature_uid"].dtype
+            consensus_dtype = self.consensus_mapping_df["feature_uid"].dtype
+
             if unfilled_dtype != consensus_dtype:
                 # Cast both to Int64 if possible, otherwise keep as string
                 try:
-                    unfilled_features = unfilled_features.with_columns(pl.col('feature_uid').cast(pl.Int64))
+                    unfilled_features = unfilled_features.with_columns(pl.col("feature_uid").cast(pl.Int64))
                     consensus_feature_uids = [int(uid) for uid in consensus_feature_uids]
                 except Exception:
                     # If casting fails, ensure both are strings
-                    unfilled_features = unfilled_features.with_columns(pl.col('feature_uid').cast(pl.Utf8))
+                    unfilled_features = unfilled_features.with_columns(pl.col("feature_uid").cast(pl.Utf8))
                     consensus_feature_uids = [str(uid) for uid in consensus_feature_uids]
 
             # Count unfilled features that are in consensus
             in_consensus_count = unfilled_features.filter(
-                pl.col('feature_uid').is_in(consensus_feature_uids)
+                pl.col("feature_uid").is_in(consensus_feature_uids),
             ).height
-            
+
             # Calculate ratios that sum to 100%
             total_unfilled = unfilled_features.height
             ratio_in_consensus_to_total = (in_consensus_count / total_unfilled * 100) if total_unfilled > 0 else 0
@@ -572,16 +595,20 @@ class Study:
             # Ensure matching data types for join keys
             features_dtype = self.features_df["feature_uid"].dtype
             consensus_dtype = self.consensus_mapping_df["feature_uid"].dtype
-            
+
             if features_dtype != consensus_dtype:
                 # Try to cast both to Int64, fallback to string if needed
                 try:
                     self.features_df = self.features_df.with_columns(pl.col("feature_uid").cast(pl.Int64))
-                    self.consensus_mapping_df = self.consensus_mapping_df.with_columns(pl.col("feature_uid").cast(pl.Int64))
+                    self.consensus_mapping_df = self.consensus_mapping_df.with_columns(
+                        pl.col("feature_uid").cast(pl.Int64)
+                    )
                 except Exception:
                     # If casting to Int64 fails, cast both to string
                     self.features_df = self.features_df.with_columns(pl.col("feature_uid").cast(pl.Utf8))
-                    self.consensus_mapping_df = self.consensus_mapping_df.with_columns(pl.col("feature_uid").cast(pl.Utf8))
+                    self.consensus_mapping_df = self.consensus_mapping_df.with_columns(
+                        pl.col("feature_uid").cast(pl.Utf8)
+                    )
 
             # Use more efficient counting - count non-null chroms only for features in consensus mapping
             if not self.consensus_mapping_df.is_empty():
@@ -599,21 +626,33 @@ class Study:
             else:
                 non_null_chroms = 0
             total_possible = samples_df_len * consensus_df_len
-            chrom_completeness = (
-                non_null_chroms / total_possible if total_possible > 0 else 0
-            )
+            chrom_completeness = non_null_chroms / total_possible if total_possible > 0 else 0
         else:
             chrom_completeness = 0
-        
+
         # Calculate consensus features with MS2 (count unique consensus_uids with MS2)
         if 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():
+            # Compute RT spread using only consensus rows with number_samples >= half the number of samples
+            threshold = len(self.samples_df) / 2 if not self.samples_df.is_empty() else 0
+            filtered = self.consensus_df.filter(pl.col("number_samples") >= threshold)
+            if filtered.is_empty():
+                rt_spread = -1.0
+            else:
+                rt_spread_row = filtered.select((pl.col("rt_max") - pl.col("rt_min")).mean()).row(0)
+                rt_spread = float(rt_spread_row[0]) if rt_spread_row and rt_spread_row[0] is not None else 0.0
+        else:
+            rt_spread = -1.0
+
         # Calculate percentage of consensus features with MS2
-        consensus_with_ms2_percentage = (consensus_with_ms2_count / consensus_df_len * 100) if consensus_df_len > 0 else 0
-        
+        consensus_with_ms2_percentage = (
+            (consensus_with_ms2_count / consensus_df_len * 100) if consensus_df_len > 0 else 0
+        )
+
         # Total MS2 spectra count
         total_ms2_count = len(self.consensus_ms2) if not self.consensus_ms2.is_empty() else 0
 
@@ -632,19 +671,45 @@ class Study:
             f"Samples:                {samples_df_len}\n"
             f"Features:               {unfilled_features_count}\n"
             f"- in consensus:         {ratio_in_consensus_to_total:.0f}%\n"
-            f"- not in consensus:     {ratio_not_in_consensus_to_total:.0f}%\n"            
+            f"- not in consensus:     {ratio_not_in_consensus_to_total:.0f}%\n"
             f"Consensus:              {consensus_df_len}\n"
+            f"- RT spread:            {rt_spread:.3f}s\n"
             f"- Min samples count:    {min_samples:.0f}\n"
             f"- Mean samples count:   {mean_samples:.0f}\n"
-            f"- Max samples count:    {max_samples:.0f}\n"            
+            f"- Max samples count:    {max_samples:.0f}\n"
             f"- with MS2:             {consensus_with_ms2_percentage:.0f}%\n"
             f"- total MS2:            {total_ms2_count}\n"
-            f"Chrom completeness:     {chrom_completeness*100:.0f}%\n"
-            f"Memory usage:           {memory_usage / (1024 ** 2):.2f} MB\n"
+            f"Chrom completeness:     {chrom_completeness * 100:.0f}%\n"
+            f"Memory usage:           {memory_usage / (1024**2):.2f} MB\n"
         )
 
         print(summary)
 
+    def _ensure_features_df_schema_order(self):
+        """
+        Ensure features_df columns are ordered according to study5_schema.json.
+        
+        This method should be called after operations that might scramble the column order.
+        """
+        if self.features_df is None or self.features_df.is_empty():
+            return
+        
+        try:
+            import os
+            import json
+            from masster.study.h5 import _reorder_columns_by_schema
+            
+            # Load schema
+            schema_path = os.path.join(os.path.dirname(__file__), "study5_schema.json")
+            with open(schema_path, 'r') as f:
+                schema = json.load(f)
+            
+            # Reorder columns to match schema
+            self.features_df = _reorder_columns_by_schema(self.features_df, schema, 'features_df')
+            
+        except Exception as e:
+            self.logger.warning(f"Failed to reorder features_df columns: {e}")
+
 
 if __name__ == "__main__":
     # This block is executed when the script is run directly

masster/study/study5_schema.json

@@ -136,12 +136,12 @@
       "feature_uid": {
         "dtype": "pl.Int64"
       },
-      "sample_uid": {
-        "dtype": "pl.Int32"
-      },
       "feature_id": {
         "dtype": "pl.Utf8"
       },
+      "sample_uid": {
+        "dtype": "pl.Int32"
+      },
       "mz": {
         "dtype": "pl.Float64"
       },
@@ -181,24 +181,24 @@
       "iso_of": {
         "dtype": "pl.Int64"
       },
-      "adduct_group": {
-        "dtype": "pl.Int64"
-      },
       "adduct": {
         "dtype": "pl.Utf8"
       },
       "adduct_mass": {
         "dtype": "pl.Float64"
       },
+      "adduct_group": {
+        "dtype": "pl.Int64"
+      },
+      "chrom": {
+        "dtype": "pl.Object"
+      },
       "filled": {
         "dtype": "pl.Boolean"
       },
       "chrom_area": {
         "dtype": "pl.Float64"
       },
-      "chrom": {
-        "dtype": "pl.Object"
-      },
       "chrom_coherence": {
         "dtype": "pl.Float64"
       },
@@ -221,24 +221,24 @@
   },
   "samples_df": {
     "columns": {
+      "sample_uid": {
+        "dtype": "pl.Int64"
+      },
       "map_id": {
         "dtype": "pl.Utf8"
       },
-      "sample_name": {
+      "file_source": {
         "dtype": "pl.Utf8"
       },
-      "sample_path": {
+      "sample_name": {
         "dtype": "pl.Utf8"
       },
-      "file_source": {
+      "sample_path": {
         "dtype": "pl.Utf8"
       },
       "sample_type": {
         "dtype": "pl.Utf8"
       },
-      "sample_uid": {
-        "dtype": "pl.Int64"
-      },
       "size": {
         "dtype": "pl.Int64"
       },

{masster-0.3.10.dist-info → masster-0.3.12.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: masster
-Version: 0.3.10
+Version: 0.3.12
 Summary: Mass spectrometry data analysis package
 Project-URL: homepage, https://github.com/zamboni-lab/masster
 Project-URL: repository, https://github.com/zamboni-lab/masster

{masster-0.3.10.dist-info → masster-0.3.12.dist-info}/RECORD

@@ -1,7 +1,7 @@
 masster/__init__.py,sha256=G7hbKO8F_o1wFwQlvO25M8JYGka_YSAVU2_O__2rjlI,697
 masster/_version.py,sha256=ioQa4W_2pWdKSoU7hw7Pn6WMBm3nMuuLKfSR4f8171A,256
 masster/chromatogram.py,sha256=NgPr1uLGJHjRu6PWZZGOrS3pCl7sye1yQCJjlRi9ZSY,19305
-masster/logger.py,sha256=iJGDtqR0nzW4cMb_fPOwoytpgrpnlSkuH5MIhgK90Xk,14733
+masster/logger.py,sha256=W50V_uh8RSYwGxDrDFhOuj5jpu2tKJyt_16lMw9kQwA,14755
 masster/spectrum.py,sha256=LuDa7qP_JInctzkmxC9c5468opHOholy321KpUgyW2U,47550
 masster/data/examples/2025_01_14_VW_7600_LpMx_DBS_CID_2min_TOP15_030msecMS1_005msecReac_CE35_DBS-ON_3.featureXML,sha256=033IjCWBaYVymnPhVHneytilC-XIa6T-6wkeBB0BXvc,10980374
 masster/data/examples/2025_01_14_VW_7600_LpMx_DBS_CID_2min_TOP15_030msecMS1_005msecReac_CE35_DBS-ON_3.mzML,sha256=3RS_crLN-aoPSacMYaQ45sxszmp_EcQElrg8tiuAQyA,39741920
@@ -10,50 +10,52 @@ masster/data/examples/2025_01_14_VW_7600_LpMx_DBS_CID_2min_TOP15_030msecMS1_005m
 masster/data/examples/2025_01_14_VW_7600_LpMx_DBS_CID_2min_TOP15_030msecMS1_005msecReac_CE35_DBS-ON_3.wiff,sha256=go5N9gAM1rn4PZAVaoCmdteY9f7YGEM9gyPdSmkQ8PE,1447936
 masster/data/examples/2025_01_14_VW_7600_LpMx_DBS_CID_2min_TOP15_030msecMS1_005msecReac_CE35_DBS-ON_3.wiff.scan,sha256=ahi1Y3UhAj9Bj4Q2MlbgPekNdkJvMOoMXVOoR6CeIxc,13881220
 masster/data/examples/2025_01_14_VW_7600_LpMx_DBS_CID_2min_TOP15_030msecMS1_005msecReac_CE35_DBS-ON_3.wiff2,sha256=TFB0HW4Agkig6yht7FtgjUdbXax8jjKaHpSZSvuU5vs,3252224
+masster/docs/SCX_API_Documentation.md,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+masster/docs/SCX_DLL_Analysis.md,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 masster/sample/__init__.py,sha256=HL0m1ept0PMAYUCQtDDnkdOS12IFl6oLAq4TZQz83uY,170
-masster/sample/h5.py,sha256=aGj3vJsM08wiWFKryRCn5ROKBSRX85vE0Z-jiPSqLjI,63817
-masster/sample/helpers.py,sha256=OEgvR3bptA-tEqHAFVPjWpbagKXAU1h0bePPi9ttHa4,34842
+masster/sample/h5.py,sha256=IdfbdkDgKcij-jMQTxnjW-gsBhb6vwi8w1XXL795yEs,63793
+masster/sample/helpers.py,sha256=U2VyboRdTsQbOefCy7VXh6PlSQtEsR6BK5QF2jGUd94,36208
 masster/sample/lib.py,sha256=l5YdU9TxEWJI0kJxXxrRCxgDDwbzO5zBf1_Qi_HY87w,33556
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