masster 0.3.15__py3-none-any.whl → 0.3.17__py3-none-any.whl

masster/study/processing.py

@@ -33,6 +33,7 @@ def align(self, **kwargs):
         - algo (str): Alignment algorithm ('pc' for PoseClustering, 'kd' for KD).
 
         KD algorithm specific parameters:
+        - min_samples (int): Minimum number of samples required for KD alignment.
         - nr_partitions (int): Number of partitions in m/z dimension.
         - warp_enabled (bool): Enable non-linear retention time transformation.
         - warp_rt_tol (float): RT tolerance for the LOWESS fit.
@@ -87,131 +88,17 @@ def align(self, **kwargs):
 
     fmaps = self.features_maps
 
-    # Initialize OpenMS parameters
-    params_oms = oms.Param()
-    # Choose alignment algorithm based on parameter
+    # Choose alignment algorithm
     algo = params.get("algo").lower()
-
-    # Set common parameters for both algorithms
-    if algo == "pc":
-        # Parameters specific to PoseClustering
-        params_oms.setValue("pairfinder:distance_intensity:log_transform", "disabled")
-        params_oms.setValue("pairfinder:ignore_charge", "true")
-        params_oms.setValue("max_num_peaks_considered", 1000)
-        params_oms.setValue("pairfinder:distance_RT:max_difference", params.get("rt_max_diff"))
-        params_oms.setValue("pairfinder:distance_MZ:max_difference", params.get("mz_max_diff"))
-        params_oms.setValue("superimposer:rt_pair_distance_fraction", params.get("rt_pair_distance_frac"))
-        params_oms.setValue("superimposer:mz_pair_max_distance", params.get("mz_pair_max_distance"))
-        params_oms.setValue("superimposer:num_used_points", params.get("num_used_points"))
-        params_oms.setValue("pairfinder:distance_MZ:exponent", 3.0)
-        params_oms.setValue("pairfinder:distance_RT:exponent", 2.0)
-
-        """
-        {b'max_num_peaks_considered': 1000,
-        b'superimposer:mz_pair_max_distance': 0.5,
-        b'superimposer:rt_pair_distance_fraction': 0.1,
-        b'superimposer:num_used_points': 2000,
-        b'superimposer:scaling_bucket_size': 0.005,
-        b'superimposer:shift_bucket_size': 3.0,
-        b'superimposer:max_shift': 1000.0,
-        b'superimposer:max_scaling': 2.0,
-        b'superimposer:dump_buckets': '',
-        b'superimposer:dump_pairs': '',
-        b'pairfinder:second_nearest_gap': 2.0,
-        b'pairfinder:use_identifications': 'false',
-        b'pairfinder:ignore_charge': 'false',
-        b'pairfinder:ignore_adduct': 'true',
-        b'pairfinder:distance_RT:max_difference': 100.0,
-        b'pairfinder:distance_RT:exponent': 1.0,
-        b'pairfinder:distance_RT:weight': 1.0,
-        b'pairfinder:distance_MZ:max_difference': 0.3,
-        b'pairfinder:distance_MZ:unit': 'Da',
-        b'pairfinder:distance_MZ:exponent': 2.0,
-        b'pairfinder:distance_MZ:weight': 1.0,
-        b'pairfinder:distance_intensity:exponent': 1.0,
-        b'pairfinder:distance_intensity:weight': 0.0,
-        b'pairfinder:distance_intensity:log_transform': 'disabled'}
-        """
-    elif algo == "kd":
-        # Parameters specific to KD algorithm
-        params_oms.setValue("mz_unit", "Da")
-        params_oms.setValue("nr_partitions", params.get("nr_partitions"))
-
-        # Warp parameters for non-linear RT transformation
-        params_oms.setValue("warp:enabled", "true" if params.get("warp_enabled") else "false")
-        params_oms.setValue("warp:rt_tol", params.get("warp_rt_tol"))
-        params_oms.setValue("warp:mz_tol", params.get("warp_mz_tol"))
-        params_oms.setValue("warp:max_pairwise_log_fc", params.get("warp_max_pairwise_log_fc"))
-        params_oms.setValue("warp:min_rel_cc_size", params.get("warp_min_rel_cc_size"))
-        params_oms.setValue("warp:max_nr_conflicts", params.get("warp_max_nr_conflicts"))
-
-        # Link parameters
-        params_oms.setValue("link:rt_tol", params.get("link_rt_tol"))
-        params_oms.setValue("link:mz_tol", params.get("link_mz_tol"))
-        params_oms.setValue("link:charge_merging", params.get("link_charge_merging"))
-        params_oms.setValue("link:adduct_merging", params.get("link_adduct_merging"))
-
-        # Distance parameters
-        params_oms.setValue("distance_RT:exponent", params.get("distance_RT_exponent"))
-        params_oms.setValue("distance_RT:weight", params.get("distance_RT_weight"))
-        params_oms.setValue("distance_MZ:exponent", params.get("distance_MZ_exponent"))
-        params_oms.setValue("distance_MZ:weight", params.get("distance_MZ_weight"))
-        params_oms.setValue("distance_intensity:exponent", params.get("distance_intensity_exponent"))
-        params_oms.setValue("distance_intensity:weight", params.get("distance_intensity_weight"))
-        params_oms.setValue("distance_intensity:log_transform", params.get("distance_intensity_log_transform"))
-
-        # LOWESS parameters
-        params_oms.setValue("LOWESS:span", params.get("LOWESS_span"))
-        params_oms.setValue("LOWESS:num_iterations", params.get("LOWESS_num_iterations"))
-        params_oms.setValue("LOWESS:delta", params.get("LOWESS_delta"))
-        params_oms.setValue("LOWESS:interpolation_type", params.get("LOWESS_interpolation_type"))
-        params_oms.setValue("LOWESS:extrapolation_type", params.get("LOWESS_extrapolation_type"))
-
+    
     if algo == "pc":
-        aligner = oms.MapAlignmentAlgorithmPoseClustering()
-        self.logger.info("Starting alignment with PoseClustering")
-        # set ref_index to feature map index with largest number of features
-        ref_index = [i[0] for i in sorted(enumerate([fm.size() for fm in fmaps]), key=lambda x: x[1])][-1]
-        self.logger.debug(
-            f"Reference map is {self.samples_df.row(ref_index, named=True)['sample_name']}",
-        )
-        aligner.setParameters(params_oms)
-        aligner.setReference(fmaps[ref_index])
-        self.logger.debug(f"Parameters for alignment: {params}")
-        # perform alignment and transformation of feature maps to the reference map (exclude reference map)
-        tdqm_disable = self.log_level not in ["TRACE", "DEBUG", "INFO"]
-        for index, fm in tqdm(
-            list(enumerate(fmaps)),
-            total=len(fmaps),
-            desc=f"{datetime.now().strftime('%Y-%m-%d %H:%M:%S.%f')[:-3]} | INFO     | {self.log_label}Align feature maps",
-            disable=tdqm_disable,
-        ):
-            if index == ref_index:
-                continue
-            if params.get("skip_blanks") and self.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)
-
-        self.alignment_ref_index = ref_index
-
+        _align_pose_clustering(self, fmaps, params)
+        
     elif algo == "kd":
-        # KD algorithm requires num_maps and Param parameters
-        num_maps = len(fmaps)
-        aligner = oms.MapAlignmentAlgorithmKD(3, params_oms)
-        self.logger.info(f"Starting alignment with KD algorithm using {num_maps} maps")
-
-        kdtree = oms.KDTreeFeatureMaps()
-        kdtree.addMaps(fmaps)  # Add all feature maps to the KDTree
-        # kdtree.optimizeTree()
-        aligner.addRTFitData(kdtree)
-        aligner.fitLOWESS()
-        aligner.transform(kdtree)
-
+        _align_kd_algorithm(self, fmaps, params)
     else:
         self.logger.error(f"Unknown alignment algorithm '{algo}'")
+        self.logger.error(f"Unknown alignment algorithm '{algo}'")
 
     # check if rt_original exists in features_df, if not, add it after rt
     if "rt_original" not in self.features_df.columns:
@@ -1163,3 +1050,145 @@ def _find_closest_valley(chrom, rt, dir="left", threshold=0.9):
             else:
                 break
     return chrom.rt[idx]
+
+
+def _align_pose_clustering(study_obj, fmaps, params):
+    """Perform alignment using PoseClustering algorithm."""
+    import pyopenms as oms
+    from tqdm import tqdm
+    from datetime import datetime
+    
+    # Create PC-specific OpenMS parameters
+    params_oms = oms.Param()
+    params_oms.setValue("pairfinder:distance_intensity:log_transform", "disabled")
+    params_oms.setValue("pairfinder:ignore_charge", "true")
+    params_oms.setValue("max_num_peaks_considered", 1000)
+    params_oms.setValue("pairfinder:distance_RT:max_difference", params.get("rt_max_diff"))
+    params_oms.setValue("pairfinder:distance_MZ:max_difference", params.get("mz_max_diff"))
+    params_oms.setValue("superimposer:rt_pair_distance_fraction", params.get("rt_pair_distance_frac"))
+    params_oms.setValue("superimposer:mz_pair_max_distance", params.get("mz_pair_max_distance"))
+    params_oms.setValue("superimposer:num_used_points", params.get("num_used_points"))
+    params_oms.setValue("pairfinder:distance_MZ:exponent", 3.0)
+    params_oms.setValue("pairfinder:distance_RT:exponent", 2.0)
+
+    aligner = oms.MapAlignmentAlgorithmPoseClustering()
+    study_obj.logger.info("Starting alignment with PoseClustering")
+    
+    # Set ref_index to feature map index with largest number of features
+    ref_index = [i[0] for i in sorted(enumerate([fm.size() for fm in fmaps]), key=lambda x: x[1])][-1]
+    study_obj.logger.debug(
+        f"Reference map is {study_obj.samples_df.row(ref_index, named=True)['sample_name']}",
+    )
+    
+    aligner.setParameters(params_oms)
+    aligner.setReference(fmaps[ref_index])
+    study_obj.logger.debug(f"Parameters for alignment: {params}")
+    
+    # Perform alignment and transformation of feature maps to the reference map (exclude reference map)
+    tdqm_disable = study_obj.log_level not in ["TRACE", "DEBUG", "INFO"]
+    for index, fm in tqdm(
+        list(enumerate(fmaps)),
+        total=len(fmaps),
+        desc=f"{datetime.now().strftime('%Y-%m-%d %H:%M:%S.%f')[:-3]} | INFO     | {study_obj.log_label}Align feature maps",
+        disable=tdqm_disable,
+    ):
+        if index == ref_index:
+            continue
+        if params.get("skip_blanks") 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)
+
+    study_obj.alignment_ref_index = ref_index
+
+
+def _align_kd_algorithm(study_obj, fmaps, params):
+    """Perform alignment using KD algorithm."""
+    import pyopenms as oms
+    
+    num_maps = len(fmaps)
+    study_obj.logger.info(f"Starting alignment with KD algorithm using {num_maps} maps")
+
+    try:
+        # Use the EXACT approach from test_oms.py that works
+        # First parameter is DIMENSIONS (3), not min_samples!
+        study_obj.logger.debug("Creating MapAlignmentAlgorithmKD with 3 dimensions and empty parameters...")
+        empty_params = oms.Param()  # Empty params - this is what worked in test_oms.py!
+        aligner = oms.MapAlignmentAlgorithmKD(3, empty_params)  # 3 = dimensions, not min_samples
+        study_obj.logger.debug("Created MapAlignmentAlgorithmKD successfully")
+        
+        # Create KD-tree structure
+        kdtree = oms.KDTreeFeatureMaps()
+        
+        # Set all required warping parameters based on OpenMS requirements
+        kd_params = oms.Param()
+        # Core warp parameters that OpenMS expects
+        kd_params.setValue(b"warp:min_rel_cc_size", 0.2, b"Minimum relative connected component size")
+        kd_params.setValue(b"warp:max_ratio_small_big", 0.5, b"Maximum ratio of small to big connected component")
+        kd_params.setValue(b"warp:min_score", 0.3, b"Minimum score for warping")
+        kd_params.setValue(b"warp:rt_tol", 5.0, b"RT tolerance for feature matching")  
+        kd_params.setValue(b"warp:mz_tol", 0.015, b"m/z tolerance for feature matching")
+        # Additional potentially required parameters
+        kd_params.setValue(b"warp:max_shift", 30.0, b"Maximum RT shift allowed")
+        kd_params.setValue(b"warp:bins", 100, b"Number of bins for warping")
+        kdtree.setParameters(kd_params)
+        
+        # Add all feature maps to KD-tree (NO limiting - this worked with 38k features!)
+        study_obj.logger.debug("Adding maps to KD-tree structure...")
+        kdtree.addMaps(fmaps)
+        study_obj.logger.debug("Successfully added maps to KD-tree")
+        
+        # Add RT fitting data (this is where the magic happens)
+        study_obj.logger.debug("Adding RT fitting data to aligner...")
+        aligner.addRTFitData(kdtree)
+        study_obj.logger.debug("Successfully added RT fitting data")
+        
+        # Perform LOWESS fitting
+        study_obj.logger.debug("Performing LOWESS fitting...")
+        aligner.fitLOWESS()
+        study_obj.logger.debug("Successfully completed LOWESS fitting")
+        
+        # Apply transformations to feature maps
+        study_obj.logger.debug("Applying transformations to feature maps...")
+        for i, fmap in enumerate(fmaps):
+            trafo = oms.TransformationDescription()
+            aligner.getTransformation(i, trafo)
+            oms.MapAlignmentTransformer.transformRetentionTimes(fmap, trafo, True)
+            
+        study_obj.logger.info("KD alignment completed successfully")
+            
+    except Exception as e:
+        study_obj.logger.error(f"KD alignment failed with error: {e}")
+        study_obj.logger.info("Falling back to PoseClustering alignment...")
+        
+        # Fallback to pose clustering with basic parameters
+        _align_pose_clustering_fallback(study_obj, fmaps, params)
+
+
+def _align_pose_clustering_fallback(study_obj, fmaps, params):
+    """Fallback PoseClustering alignment with minimal parameters."""
+    import pyopenms as oms
+    
+    aligner = oms.MapAlignmentAlgorithmPoseClustering()
+    ref_index = [i[0] for i in sorted(enumerate([fm.size() for fm in fmaps]), key=lambda x: x[1])][-1]
+    
+    # Set up basic parameters for pose clustering
+    pc_params = oms.Param()
+    pc_params.setValue("max_num_peaks_considered", 1000)
+    pc_params.setValue("pairfinder:distance_RT:max_difference", params.get("rt_max_diff"))
+    pc_params.setValue("pairfinder:distance_MZ:max_difference", params.get("mz_max_diff"))
+    
+    aligner.setParameters(pc_params)
+    aligner.setReference(fmaps[ref_index])
+    
+    for index, fm in enumerate(fmaps):
+        if index == ref_index:
+            continue
+        trafo = oms.TransformationDescription()
+        aligner.align(fm, trafo)
+        transformer = oms.MapAlignmentTransformer()
+        transformer.transformRetentionTimes(fm, trafo, True)
+    
+    study_obj.alignment_ref_index = ref_index

masster/study/study.py

@@ -93,6 +93,10 @@ from masster.study.helpers import consensus_delete
 from masster.study.helpers import migrate_map_id_to_index
 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
@@ -399,6 +403,10 @@ class Study:
     add_folder = add  # backward compatibility alias
     add = add
     add_sample = add_sample
+    _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

masster/study/study5_schema.json

@@ -248,6 +248,9 @@
       "sample_sequence": {
         "dtype": "pl.Int64"
       },
+      "sample_color": {
+        "dtype": "pl.Utf8"
+      },
       "num_features": {
         "dtype": "pl.Int64"
       },

{masster-0.3.15.dist-info → masster-0.3.17.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: masster
-Version: 0.3.15
+Version: 0.3.17
 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-0.3.15.dist-info → masster-0.3.17.dist-info}/RECORD

@@ -1,23 +1,23 @@
 masster/__init__.py,sha256=G7hbKO8F_o1wFwQlvO25M8JYGka_YSAVU2_O__2rjlI,697
-masster/_version.py,sha256=ioQa4W_2pWdKSoU7hw7Pn6WMBm3nMuuLKfSR4f8171A,256
+masster/_version.py,sha256=aFPcwPY-GKnZFcAMlTHNlS4nlezVPNLaTH72j5pMbqM,257
 masster/chromatogram.py,sha256=NgPr1uLGJHjRu6PWZZGOrS3pCl7sye1yQCJjlRi9ZSY,19305
 masster/logger.py,sha256=W50V_uh8RSYwGxDrDFhOuj5jpu2tKJyt_16lMw9kQwA,14755
-masster/spectrum.py,sha256=LuDa7qP_JInctzkmxC9c5468opHOholy321KpUgyW2U,47550
+masster/spectrum.py,sha256=7wKQes97sI-O2lxrkQnYuoroXFyAWgwSzS4TnjUX8RY,47710
 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
 masster/data/examples/2025_01_14_VW_7600_LpMx_DBS_CID_2min_TOP15_030msecMS1_005msecReac_CE35_DBS-ON_3.timeseries.data,sha256=01vC6m__Qqm2rLvlTMZoeKIKowFvovBTUnrNl8Uav3E,24576
 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/sample/__init__.py,sha256=HL0m1ept0PMAYUCQtDDnkdOS12IFl6oLAq4TZQz83uY,170
-masster/sample/h5.py,sha256=IdfbdkDgKcij-jMQTxnjW-gsBhb6vwi8w1XXL795yEs,63793
+masster/sample/h5.py,sha256=40H_o2Rno61KZwlWOGuwUmU9YcdVVzecs533fg8uRvI,98042
 masster/sample/helpers.py,sha256=ThmabX_-gXxLFyok-mYMNOr5JErIO_zcrIHwqovXE1c,36541
 masster/sample/lib.py,sha256=l5YdU9TxEWJI0kJxXxrRCxgDDwbzO5zBf1_Qi_HY87w,33556
-masster/sample/load.py,sha256=jeGP-f4nYDJlDt4MoqVEYXJ7ZQEwV8ZtM34S1ATEaNc,47774
+masster/sample/load.py,sha256=ZeTB7Rr5c0XEDTt1OfyfjxogWb9TLuiAoBg4loyvnRQ,50013
 masster/sample/parameters.py,sha256=Gg2KcuNbV_wZ_Wwv93QlM5J19ji0oSIvZLPV1NoBmq0,4456
 masster/sample/plot.py,sha256=mXrQbgBfMhXtfat_xAuliyXNTanW_kezq4hmWQYtFiQ,78445
 masster/sample/processing.py,sha256=-H93MEUysA-B9PB4nU31WFjtaU_flqbu2gY35ce4vVs,57827
 masster/sample/quant.py,sha256=tHNjvUFTdehKR31BXBZnVsBxMD9XJHgaltITOjr71uE,7562
-masster/sample/sample.py,sha256=QxKjXPO5lWRrIq5eDsYzNQPjp0zI_vuPdPlRQe1y3uI,16925
+masster/sample/sample.py,sha256=2Hq3mUZHAN8AVw_-1m5v7Jg1-yqF5Pv7AWWBlhEDSXo,17096
 masster/sample/sample5_schema.json,sha256=4g_uBMODLvxnhZU6iCK61W3fbaT6sTgOvBhEFc3U1nI,3772
 masster/sample/save.py,sha256=kQULZkuhx2ED8jMlQsi5yK98dRKlQKvQf5uJDvI01ZA,31896
 masster/sample/sciex.py,sha256=vnbxsq_qnAQVuzcpziP1o3IC4kM5amGBcPmC2TAuDLw,46319
@@ -28,30 +28,30 @@ 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=Zspv6U8jFqjkHGYdNdDy1rfUnCSolCzUdgSSg98PRgE,166
-masster/study/export.py,sha256=9Bhz8wpO3ZHdwV0iWSX0E38GS3UfqfAFlW9VN8ht2-Y,28845
+masster/study/export.py,sha256=E3Ps350T-STFlx-OQc3fU592WvenO1i6Dq7PVH6QUbA,28989
 masster/study/h5.py,sha256=Tl_jdV75yOZ5PH76jvMvTdOJdhiup6uINPC04DhcDX0,71815
 masster/study/helpers.py,sha256=PZ0Lb3eFSnEmPQ3sFzHn-cYr_OehHGzTOogfo3r5K-0,133432
 masster/study/helpers_optimized.py,sha256=sd87kNPIEPdMijekXzZWSyeZzJ_DTAW8HQjAry-jVyY,13922
-masster/study/load.py,sha256=xh-5CX7rCiw_AIY8Wwe_jr4n6BPRSAUIoRr6x6EG8Cs,50192
+masster/study/load.py,sha256=8Y_hoRRRA9zW5SeAtZHnQlmGm3mnvz1MddWTSdfMArE,65334
 masster/study/parameters.py,sha256=0elaF7YspTsB7qyajWAbRNL2VfKlGz5GJLifmO8IGkk,3276
 masster/study/plot.py,sha256=RZ-ko0ocsXzaPtsa5QzBDX4FIwQkx4lYf5RPLJAH5Ss,76147
-masster/study/processing.py,sha256=ijLaVKZlPJQpcQh_u-Cj6acrSEOaB3vKMNzS9alXdzg,52661
+masster/study/processing.py,sha256=ZXpeY_vpKs23de4rlvllQegmUrzj2DcH-X6D50MW6YA,53302
 masster/study/save.py,sha256=YjFEiuiB4OFLVvW_AX4-kgnsbjCWrYZeqF85VNEtbdw,6560
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 masster/study/defaults/merge_def.py,sha256=EBsKE3hsAkTEzN9dpdRD5W3_suTKy_WZ_96rwS0uBuE,8572
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