masster 0.3.7__py3-none-any.whl → 0.3.9__py3-none-any.whl

masster/sample/defaults/find_features_def.py

@@ -90,6 +90,30 @@ class find_features_defaults:
     eic_mz_tol: float = 0.01
     eic_rt_tol: float = 10.0
 
+    # Additional OpenMS FeatureFinderMetabo parameters
+    threads: int = 1
+    no_progress: bool = False
+    debug: bool = False
+    min_sample_rate: float = 0.5
+    min_trace_length: int = 5
+    min_fwhm: float = 1.0
+    max_fwhm: float = 60.0
+    
+    # Additional Mass Trace Detection parameters
+    trace_termination_criterion: str = "outlier"
+    reestimate_mt_sd: bool = True
+    quant_method: str = "area"
+    
+    # Additional Elution Peak Detection parameters
+    enabled: bool = True
+    
+    # Additional Feature Finding parameters
+    local_rt_range: float = 10.0
+    local_mz_range: float = 6.5
+    charge_lower_bound: int = 1
+    charge_upper_bound: int = 3
+    report_smoothed_intensities: bool = False
+
     # Parameter metadata for validation and description
     _param_metadata: dict[str, dict[str, Any]] = field(
         default_factory=lambda: {
@@ -192,6 +216,90 @@ class find_features_defaults:
                 "min_value": 1.0,
                 "max_value": 60.0,
             },
+            "threads": {
+                "dtype": int,
+                "description": "Number of threads to use for parallel processing",
+                "min_value": 1,
+                "max_value": 64,
+            },
+            "no_progress": {
+                "dtype": bool,
+                "description": "Disable progress logging",
+            },
+            "debug": {
+                "dtype": bool,
+                "description": "Enable debug mode for detailed logging",
+            },
+            "min_sample_rate": {
+                "dtype": float,
+                "description": "Minimum sample rate for mass trace detection",
+                "min_value": 0.1,
+                "max_value": 1.0,
+            },
+            "min_trace_length": {
+                "dtype": int,
+                "description": "Minimum trace length in number of spectra",
+                "min_value": 2,
+                "max_value": 100,
+            },
+            "min_fwhm": {
+                "dtype": float,
+                "description": "Minimum full width at half maximum for peaks (seconds)",
+                "min_value": 0.1,
+                "max_value": 10.0,
+            },
+            "max_fwhm": {
+                "dtype": float,
+                "description": "Maximum full width at half maximum for peaks (seconds)",
+                "min_value": 1.0,
+                "max_value": 300.0,
+            },
+            "trace_termination_criterion": {
+                "dtype": str,
+                "description": "Criterion for mass trace termination",
+                "allowed_values": ["outlier", "sample_rate"],
+            },
+            "reestimate_mt_sd": {
+                "dtype": bool,
+                "description": "Whether to re-estimate mass trace standard deviation",
+            },
+            "quant_method": {
+                "dtype": str,
+                "description": "Quantification method for features",
+                "allowed_values": ["area", "height"],
+            },
+            "enabled": {
+                "dtype": bool,
+                "description": "Whether elution peak detection is enabled",
+            },
+            "local_rt_range": {
+                "dtype": float,
+                "description": "Local retention time range for feature finding (seconds)",
+                "min_value": 1.0,
+                "max_value": 100.0,
+            },
+            "local_mz_range": {
+                "dtype": float,
+                "description": "Local m/z range for feature finding (Da)",
+                "min_value": 1.0,
+                "max_value": 20.0,
+            },
+            "charge_lower_bound": {
+                "dtype": int,
+                "description": "Lower bound for charge state detection",
+                "min_value": 1,
+                "max_value": 10,
+            },
+            "charge_upper_bound": {
+                "dtype": int,
+                "description": "Upper bound for charge state detection",
+                "min_value": 1,
+                "max_value": 10,
+            },
+            "report_smoothed_intensities": {
+                "dtype": bool,
+                "description": "Whether to report smoothed intensities for features",
+            },
         },
     )
 

masster/sample/processing.py

@@ -569,6 +569,22 @@ def find_features(self, **kwargs):
             else:
                 self.logger.warning(f"Unknown parameter {key} ignored")
 
+    # Set global parameters
+    if hasattr(params, 'threads') and params.threads is not None:
+        try:
+            # Try setting via OpenMP environment variable first (newer approach)
+            import os
+            os.environ['OMP_NUM_THREADS'] = str(params.threads)
+            self.logger.debug(f"Set thread count to {params.threads} via OMP_NUM_THREADS")
+        except Exception:
+            self.logger.warning(f"Could not set thread count to {params.threads} - using default")
+    
+    # Set debug mode if enabled
+    if hasattr(params, 'debug') and params.debug:
+        self.logger.debug("Debug mode enabled")
+    elif hasattr(params, 'no_progress') and params.no_progress:
+        self.logger.debug("No progress mode enabled")
+    
     self.logger.info("Starting feature detection...")
     self.logger.debug(
         f"Parameters: chrom_fwhm={params.get('chrom_fwhm')}, noise={params.get('noise')}, tol_ppm={params.get('tol_ppm')}",
@@ -609,6 +625,13 @@ def find_features(self, **kwargs):
         int(params.get("trace_termination_outliers")),
     )
     mtd_par.setValue("chrom_peak_snr", float(params.get("chrom_peak_snr")))
+    
+    # Additional MTD parameters
+    mtd_par.setValue("min_sample_rate", float(params.get("min_sample_rate")))
+    mtd_par.setValue("min_trace_length", float(params.get("min_trace_length")))
+    mtd_par.setValue("trace_termination_criterion", params.get("trace_termination_criterion"))
+    mtd_par.setValue("reestimate_mt_sd", "true" if params.get("reestimate_mt_sd") else "false")
+    mtd_par.setValue("quant_method", params.get("quant_method"))
 
     mtd.setParameters(mtd_par)  # set the new parameters
     mtd.run(exp, mass_traces, 0)  # run mass trace detection
@@ -627,6 +650,13 @@ def find_features(self, **kwargs):
         epd_par.setValue("masstrace_snr_filtering", "true")
     if params.get("mz_scoring_13C"):
         epd_par.setValue("mz_scoring_13C", "true")
+    
+    # Additional EPD parameters
+    epd_par.setValue("enabled", "true" if params.get("enabled") else "false")
+    
+    # Set min/max FWHM parameters
+    epd_par.setValue("min_fwhm", float(params.get("min_fwhm")))
+    epd_par.setValue("max_fwhm", float(params.get("max_fwhm")))
 
     epd.setParameters(epd_par)
     epd.detectPeaks(mass_traces, mass_traces_deconvol)
@@ -654,6 +684,16 @@ def find_features(self, **kwargs):
         "report_chromatograms",
         "true" if params.get("report_chromatograms") else "false",
     )
+    
+    # Additional FFM parameters
+    ffm_par.setValue("local_rt_range", float(params.get("local_rt_range")))
+    ffm_par.setValue("local_mz_range", float(params.get("local_mz_range")))
+    ffm_par.setValue("charge_lower_bound", int(params.get("charge_lower_bound")))
+    ffm_par.setValue("charge_upper_bound", int(params.get("charge_upper_bound")))
+    ffm_par.setValue(
+        "report_smoothed_intensities",
+        "true" if params.get("report_smoothed_intensities") else "false",
+    )
 
     ffm.setParameters(ffm_par)
     self.logger.debug("Running feature finding with parameters:")

masster/study/study.py

@@ -126,6 +126,12 @@ from masster.study.defaults.integrate_chrom_def import integrate_chrom_defaults
 from masster.study.defaults.integrate_def import integrate_defaults
 from masster.study.defaults.merge_def import merge_defaults
 
+# Import sample defaults
+from masster.sample.defaults.sample_def import sample_defaults
+from masster.sample.defaults.find_features_def import find_features_defaults
+from masster.sample.defaults.find_adducts_def import find_adducts_defaults
+from masster.sample.defaults.get_spectrum_def import get_spectrum_defaults
+
 
 class Study:
     """
@@ -164,6 +170,19 @@ 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
+    find_features_defaults = find_features_defaults
+    find_adducts_defaults = find_adducts_defaults
+    find_ms2_defaults = find_ms2_defaults
+    get_spectrum_defaults = get_spectrum_defaults
+    export_mgf_defaults = export_mgf_defaults
+    align_defaults = align_defaults
+    merge_defaults = merge_defaults
+    integrate_defaults = integrate_defaults
+    integrate_chrom_defaults = integrate_chrom_defaults
 
     def __init__(
         self,

{masster-0.3.7.dist-info → masster-0.3.9.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: masster
-Version: 0.3.7
+Version: 0.3.9
 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-0.3.7.dist-info → masster-0.3.9.dist-info}/RECORD

@@ -17,7 +17,7 @@ masster/sample/lib.py,sha256=9r2XlF_BaJ4WNAsQo8hElieRLwsAv0yrbYq4DJ0iVOM,33496
 masster/sample/load.py,sha256=y-KUJ2nCFX_06FHPUOh-CzRRvaTx14xNcXoL19bU8qY,47562
 masster/sample/parameters.py,sha256=Gg2KcuNbV_wZ_Wwv93QlM5J19ji0oSIvZLPV1NoBmq0,4456
 masster/sample/plot.py,sha256=uUJAd2qxhVG6Ev2hLuU406zFA2TDkkBz2MG12P9fLik,71449
-masster/sample/processing.py,sha256=NjNLt47Fy0UF3Xs35NBhADg57qTC6Lfa4Xz8Y30v83A,58250
+masster/sample/processing.py,sha256=AZdqEzOu4D_0B-3KCrvEr3wZ67taWpfZqFAIHeslf3s,60265
 masster/sample/quant.py,sha256=tHNjvUFTdehKR31BXBZnVsBxMD9XJHgaltITOjr71uE,7562
 masster/sample/sample.py,sha256=ekS-qBfzx3_Lb2KLMu-s90owRlk3lK4616mmiAiiHTc,16726
 masster/sample/sample5_schema.json,sha256=3SPFQZH4SooLYUt_lW-PCOE9rHnl56Vhc2XG-r1nyEQ,3586
@@ -25,7 +25,7 @@ masster/sample/save.py,sha256=o9eFSqqr7KYwvCD3gOJt_nZ4h3pkflWqs0n0oSLM-sU,31970
 masster/sample/sciex.py,sha256=q6PdcjCtV2PWnJiXuvfISu09zjkaTR_fvHvWN9OvOcM,46870
 masster/sample/defaults/__init__.py,sha256=A09AOP44cxD_oYohyt7XFUho0zndRcrzVD4DUaGnKH4,447
 masster/sample/defaults/find_adducts_def.py,sha256=6CcGRlz4VeosoBT_W0bkR1Kjj11Rq3QvuuOnkizIZyk,11630
-masster/sample/defaults/find_features_def.py,sha256=d9LQsS7QEj2SIvhz_N55Zk80V2MOI5HlB4EylGDgG_4,13878
+masster/sample/defaults/find_features_def.py,sha256=Qh-_HT2uPn7xdG7p-j0nOvS2kMammxQYyD0Hl8L_Zcw,17924
 masster/sample/defaults/find_ms2_def.py,sha256=KTELMAnioGLYbhzAwOgK14TZqboPEvzeBN0HC-v0Z5A,9872
 masster/sample/defaults/get_spectrum_def.py,sha256=o62p31PhGd-LiIkTOzKQhwPtnO2AtQDHcPu-O-YoQPs,11460
 masster/sample/defaults/sample_def.py,sha256=t8vrb8MoBBsFQcRzlaT0-q0hAssOxWO7vhCAJU3_THs,14068
@@ -39,7 +39,7 @@ masster/study/parameters.py,sha256=0elaF7YspTsB7qyajWAbRNL2VfKlGz5GJLifmO8IGkk,3
 masster/study/plot.py,sha256=NW31XdM9Bf5wNvIAs-56AIoPA8VLTqBzr6qJInfZmhc,25159
 masster/study/processing.py,sha256=BQuSBO7O8iTlCjXenECyg0_PAsPF1NNiUllypuemPZI,46101
 masster/study/save.py,sha256=bcRADWTvhTER9WRkT9zNU5mDUPQZkZB2cuJwpRsYmrM,6589
-masster/study/study.py,sha256=5cgJaSOSrGnM3rqXAe3YdNkbWoT1ze6KGt-83nTq-AM,28144
+masster/study/study.py,sha256=4jItwNGUZUv9uDwAcfFYT3GRh-ACJ1bddSGQaiQs6YM,29002
 masster/study/study5_schema.json,sha256=A_xDPzB97xt2EFeQsX9j8Ut7yC4_DS7BZ24ucotOXIw,5103
 masster/study/defaults/__init__.py,sha256=m3Z5KXGqsTdh7GjYzZoENERt39yRg0ceVRV1DeCt1P0,610
 masster/study/defaults/align_def.py,sha256=9aM7kY4_ecgG8QC6v57AASiRRkPxwG77r3-PlQ2BkHk,9139
@@ -52,8 +52,8 @@ masster/study/defaults/integrate_chrom_def.py,sha256=Rih3-vat7fHGVfIvRitjNJJI3zL
 masster/study/defaults/integrate_def.py,sha256=Vf4SAzdBfnsSZ3IRaF0qZvWu3gMDPHdgPfMYoPKeWv8,7246
 masster/study/defaults/merge_def.py,sha256=EBsKE3hsAkTEzN9dpdRD5W3_suTKy_WZ_96rwS0uBuE,8572
 masster/study/defaults/study_def.py,sha256=hj8bYtEPwzdowC95yfyoCFt6fZkQePLjpJtmpNz9Z5M,9533
-masster-0.3.7.dist-info/METADATA,sha256=O5N1DYy-vg2mHR5HVrW7bhjfk9ckdQC0SuaFRKAiXjo,44292
-masster-0.3.7.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-masster-0.3.7.dist-info/entry_points.txt,sha256=ZHguQ_vPmdbpqq2uGtmEOLJfgP-DQ1T0c07Lxh30wc8,58
-masster-0.3.7.dist-info/licenses/LICENSE,sha256=bx5iLIKjgAdYQ7sISn7DsfHRKkoCUm1154sJJKhgqnU,35184
-masster-0.3.7.dist-info/RECORD,,
+masster-0.3.9.dist-info/METADATA,sha256=FXWOvACxtEV0Svzws7jY8fKf4v6xmgzZ-Drgc2O_n-0,44292
+masster-0.3.9.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+masster-0.3.9.dist-info/entry_points.txt,sha256=ZHguQ_vPmdbpqq2uGtmEOLJfgP-DQ1T0c07Lxh30wc8,58
+masster-0.3.9.dist-info/licenses/LICENSE,sha256=bx5iLIKjgAdYQ7sISn7DsfHRKkoCUm1154sJJKhgqnU,35184
+masster-0.3.9.dist-info/RECORD,,