masster 0.5.5__py3-none-any.whl → 0.5.6__py3-none-any.whl

masster/sample/adducts.py

@@ -473,7 +473,7 @@ def find_adducts(self, **kwargs):
     self.logger.debug(f"Min probability threshold: {min_probability}")
 
     # Generate comprehensive adduct specifications using the Sample method
-    adducts_df = _get_adducts(self, 
+    adducts_df = self._get_adducts( 
         adducts_list=adducts_list,
         charge_min=charge_min,
         charge_max=charge_max,

masster/sample/helpers.py

@@ -358,7 +358,7 @@ def get_eic(self, mz, mz_tol=None):
         return None
 
 
-def select(
+def features_select(
     self,
     mz=None,
     rt=None,
@@ -372,6 +372,7 @@ def select(
     height_scaled=None,
     prominence=None,
     height=None,
+    uids=None,
 ):
     """
     Select features based on specified criteria and return the filtered DataFrame.
@@ -389,6 +390,7 @@ def select(
         height_scaled: scaled height filter (tuple for range, single value for minimum)
         prominence: prominence filter (tuple for range, single value for minimum)
         height: height filter (tuple for range, single value for minimum)
+        uids: feature UID filter (list of feature UIDs, polars/pandas DataFrame with feature_uid/feature_id column, or None for all features)
 
     Returns:
         polars.DataFrame: Filtered features DataFrame
@@ -398,6 +400,20 @@ def select(
         # self.logger.info("No features found. R")
         return
     feats = self.features_df.clone()
+    
+    # Filter by feature UIDs if provided
+    if uids is not None:
+        feature_uids_to_keep = self._get_feature_uids(features=uids, verbose=True)
+        if not feature_uids_to_keep:
+            self.logger.warning("No valid feature UIDs provided.")
+            return feats.limit(0)  # Return empty DataFrame with same structure
+        
+        feats_len_before_filter = len(feats)
+        feats = feats.filter(pl.col("feature_uid").is_in(feature_uids_to_keep))
+        self.logger.debug(
+            f"Selected features by UIDs. Features removed: {feats_len_before_filter - len(feats)}",
+        )
+    
     if coherence is not None:
         has_coherence = "chrom_coherence" in self.features_df.columns
         if not has_coherence:

masster/sample/plot.py

@@ -57,12 +57,78 @@ from holoviews import dim
 from holoviews.plotting.util import process_cmap
 from matplotlib.colors import rgb2hex
 
+# Import cmap for colormap handling
+try:
+    from cmap import Colormap
+except ImportError:
+    Colormap = None
+
 # Parameters removed - using hardcoded defaults
 
 
 hv.extension("bokeh")
 
 
+def _process_cmap(cmap, fallback="viridis", logger=None):
+    """
+    Process colormap using the cmap package, similar to study's implementation.
+    
+    Parameters:
+        cmap: Colormap specification (string name, cmap.Colormap object, or None)
+        fallback: Fallback colormap name if cmap processing fails
+        logger: Logger for warnings (optional)
+        
+    Returns:
+        list: List of hex color strings for the colormap
+    """
+    # Handle None case
+    if cmap is None:
+        cmap = "viridis"
+    elif cmap == "grey":
+        cmap = "Greys256"
+    elif cmap == "iridescent":
+        cmap = "iridescent_r"
+    
+    # If cmap package is not available, fall back to process_cmap
+    if Colormap is None:
+        if logger:
+            logger.warning("cmap package not available, using holoviews process_cmap")
+        return process_cmap(cmap, provider="bokeh")
+    
+    try:
+        # Handle colormap using cmap.Colormap
+        if isinstance(cmap, str):
+            colormap = Colormap(cmap)
+            # Generate 256 colors and convert to hex
+            import matplotlib.colors as mcolors
+            colors = colormap(np.linspace(0, 1, 256))
+            palette = [mcolors.rgb2hex(color) for color in colors]
+        else:
+            colormap = cmap
+            # Try to use to_bokeh() method first
+            try:
+                palette = colormap.to_bokeh()
+                # Ensure we got a color palette, not another mapper
+                if not isinstance(palette, (list, tuple)):
+                    # Fall back to generating colors manually
+                    import matplotlib.colors as mcolors
+                    colors = colormap(np.linspace(0, 1, 256))
+                    palette = [mcolors.rgb2hex(color) for color in colors]
+            except AttributeError:
+                # Fall back to generating colors manually
+                import matplotlib.colors as mcolors
+                colors = colormap(np.linspace(0, 1, 256))
+                palette = [mcolors.rgb2hex(color) for color in colors]
+        
+        return palette
+        
+    except (AttributeError, ValueError, TypeError) as e:
+        # Fallback to process_cmap if cmap interpretation fails
+        if logger:
+            logger.warning(f"Could not interpret colormap '{cmap}': {e}, falling back to {fallback}")
+        return process_cmap(fallback, provider="bokeh")
+
+
 def _is_notebook_environment():
     """
     Detect if code is running in a notebook environment (Jupyter, JupyterLab, or Marimo).
@@ -462,10 +528,8 @@ def plot_2d(
         self.logger.error("No MS1 data available.")
         return
 
-    if cmap is None:
-        cmap = "iridescent_r"
-    elif cmap == "grey":
-        cmap = "Greys256"
+    # Process colormap using the cmap package
+    cmap_palette = _process_cmap(cmap, fallback="iridescent_r", logger=self.logger)
 
     # get columns rt, mz, inty from self.ms1_df, It's polars DataFrame
     spectradf = self.ms1_df.select(["rt", "mz", "inty"])
@@ -585,7 +649,7 @@ def plot_2d(
         dynamic=dyn,  # alpha=10,                min_alpha=0,
     ).opts(
         active_tools=["box_zoom"],
-        cmap=process_cmap(cmap, provider="bokeh"),  # blues
+        cmap=cmap_palette,
         tools=["hover"],
         hooks=[new_bounds_hook],
         width=width,
@@ -1003,10 +1067,8 @@ def plot_2d_oracle(
         print("Please load a file first.")
         return
 
-    if cmap is None or cmap == "grey":
-        cmap = "Greys256"
-    elif cmap == "iridescent":
-        cmap = "iridescent_r"
+    # Process colormap using the cmap package
+    cmap_palette = _process_cmap(cmap, fallback="Greys256", logger=self.logger)
 
     # get columns rt, mz, inty from self.ms1_df, It's polars DataFrame
     spectradf = self.ms1_df.to_pandas()
@@ -1057,7 +1119,7 @@ def plot_2d_oracle(
         dynamic=dyn,  # alpha=10,                min_alpha=0,
     ).opts(
         active_tools=["box_zoom"],
-        cmap=process_cmap(cmap, provider="bokeh"),  # blues
+        cmap=cmap_palette,
         tools=["hover"],
         hooks=[new_bounds_hook],
         width=1000,
@@ -1183,13 +1245,45 @@ def plot_2d_oracle(
 
     if cvalues is not None:
         num_colors = len(cvalues)
-        cmap = "rainbow"
-        cmap_provider = "colorcet"
-        cm = process_cmap(cmap, ncolors=num_colors, provider=cmap_provider)
-        colors = [
-            rgb2hex(cm[int(i * (len(cm) - 1) / (num_colors - 1))]) if num_colors > 1 else rgb2hex(cm[0])
-            for i in range(num_colors)
-        ]
+        
+        # Use cmap package for categorical colormap
+        try:
+            if Colormap is not None:
+                # Use rainbow colormap for categorical data
+                colormap = Colormap("rainbow")
+                colors = []
+                for i in range(num_colors):
+                    # Generate evenly spaced colors across the colormap
+                    t = i / (num_colors - 1) if num_colors > 1 else 0.5
+                    color = colormap(t)
+                    # Convert to hex
+                    import matplotlib.colors as mcolors
+                    # Convert color to hex - handle different color formats
+                    if hasattr(color, '__len__') and len(color) >= 3:
+                        # It's an array-like color (RGB or RGBA)
+                        colors.append(mcolors.rgb2hex(color[:3]))
+                    else:
+                        # It's a single value, convert to RGB
+                        colors.append(mcolors.rgb2hex([color, color, color]))
+            else:
+                # Fallback to original method
+                cmap = "rainbow"
+                cmap_provider = "colorcet"
+                cm = process_cmap(cmap, ncolors=num_colors, provider=cmap_provider)
+                colors = [
+                    rgb2hex(cm[int(i * (len(cm) - 1) / (num_colors - 1))]) if num_colors > 1 else rgb2hex(cm[0])
+                    for i in range(num_colors)
+                ]
+        except Exception:
+            # Final fallback to original method
+            cmap = "rainbow"
+            cmap_provider = "colorcet" 
+            cm = process_cmap(cmap, ncolors=num_colors, provider=cmap_provider)
+            colors = [
+                rgb2hex(cm[int(i * (len(cm) - 1) / (num_colors - 1))]) if num_colors > 1 else rgb2hex(cm[0])
+                for i in range(num_colors)
+            ]
+        
         # assign color to each row based on id_class. If id_class is null, assign 'black'
         feats["color"] = "black"
 
@@ -1577,10 +1671,8 @@ def plot_ms2_cycle(
         print("Cycle number not found in scans_df.")
         return
 
-    if cmap is None:
-        cmap = "iridescent_r"
-    elif cmap == "grey":
-        cmap = "Greys256"
+    # Process colormap using the cmap package
+    cmap_palette = _process_cmap(cmap, fallback="iridescent_r", logger=self.logger)
 
     # find all scans in cycle
     scans = self.scans_df.filter(pl.col("cycle") == cycle)
@@ -1645,7 +1737,7 @@ def plot_ms2_cycle(
         dynamic=raster_dynamic,  # alpha=10,                min_alpha=0,
     ).opts(
         active_tools=["box_zoom"],
-        cmap=process_cmap(cmap, provider="bokeh"),  # blues
+        cmap=cmap_palette,
         tools=["hover"],
         hooks=[new_bounds_hook],
         width=1000,

masster/sample/sample.py

@@ -57,10 +57,11 @@ from masster.sample.helpers import _get_scan_uids
 from masster.sample.helpers import _get_feature_uids
 # from masster.sample.helpers import _features_sync - made internal only
 from masster.sample.adducts import find_adducts
+from masster.sample.adducts import _get_adducts
 # Removed _get_adducts - only used in study modules
 from masster.sample.helpers import features_delete
 from masster.sample.helpers import features_filter
-from masster.sample.helpers import select
+from masster.sample.helpers import features_select
 from masster.sample.helpers import select_closest_scan
 from masster.sample.helpers import get_dda_stats
 from masster.sample.helpers import get_feature
@@ -110,6 +111,7 @@ from masster.sample.save import export_chrom
 from masster.sample.save import export_dda_stats
 from masster.sample.save import export_features
 from masster.sample.save import export_mgf
+from masster.sample.save import export_xlsx
 from masster.sample.save import save
 # Removed internal-only import: _save_featureXML
 
@@ -139,7 +141,6 @@ class Sample:
 
                      Core initialization parameters:
                      - file (str, optional): The file path or file object to be loaded
-                     - ondisk (bool): Whether to keep data on disk or load into memory. Default is False
                      - label (str, optional): An optional label to identify the file or dataset
                      - log_level (str): The logging level to be set for the logger. Defaults to 'INFO'
                      - log_label (str, optional): Optional label for the logger
@@ -221,11 +222,12 @@ class Sample:
     save = save
     find_features = find_features
     find_adducts = find_adducts
+    _get_adducts= _get_adducts
     find_iso = find_iso
     find_ms2 = find_ms2
     get_spectrum = get_spectrum
     filter = features_filter
-    select = select
+    select = features_select
     features_filter = filter  # New function that keeps only specified features
     filter_features = filter
     features_select = select
@@ -238,6 +240,7 @@ class Sample:
     get_parameters_property = get_parameters_property
     set_parameters_property = set_parameters_property
     export_features = export_features
+    export_xlsx = export_xlsx
     export_mgf = export_mgf
     export_chrom = export_chrom
     export_dda_stats = export_dda_stats

masster/sample/save.py

@@ -105,7 +105,7 @@ def save(self, filename=None):
     self._save_sample5(filename=filename)
     self.file_path = filename
 
-
+'''
 def _save_featureXML(self, filename="features.featureXML"):
     if self._oms_features_map is None:
         self.logger.warning("No features found.")
@@ -114,7 +114,7 @@ def _save_featureXML(self, filename="features.featureXML"):
     fh.store(filename, self._oms_features_map)
     self.logger.debug(f"Features Map saved to {filename}")
 
-
+'''
 def export_features(self, filename="features.csv"):
     """
     Export the features DataFrame to a CSV or Excel file.
@@ -827,6 +827,60 @@ def export_dda_stats(self, filename="stats.csv"):
     self.logger.info(f"DDA statistics exported to {filename}")
 
 
+def export_xlsx(self, filename="features.xlsx"):
+    """
+    Export the features DataFrame to an Excel file.
+
+    This method exports the features DataFrame (features_df) to an Excel (.xlsx) file.
+    Columns with data types 'List' or 'Object' are excluded from the export to ensure
+    compatibility with Excel format. A boolean column 'has_ms2' is added to indicate
+    whether MS2 data is available for each feature.
+
+    Parameters:
+        filename (str): The path to the output Excel file. Must end with '.xlsx' or '.xls'.
+                        Defaults to 'features.xlsx'.
+
+    Raises:
+        ValueError: If filename doesn't end with '.xlsx' or '.xls'
+
+    Side Effects:
+        Writes the exported data to the specified Excel file and logs the export operation.
+    """
+    if self.features_df is None:
+        self.logger.warning("No features found. Cannot export to Excel.")
+        return
+
+    # Validate filename extension
+    if not filename.lower().endswith(('.xlsx', '.xls')):
+        raise ValueError("Filename must end with '.xlsx' or '.xls' for Excel export")
+    
+    filename = os.path.abspath(filename)
+    
+    # Clone the DataFrame to avoid modifying the original
+    clean_df = self.features_df.clone()
+    
+    # Add a column has_ms2=True if column ms2_scans is not None
+    if "ms2_scans" in clean_df.columns:
+        clean_df = clean_df.with_columns(
+            (pl.col("ms2_scans").is_not_null()).alias("has_ms2")
+        )
+    
+    # Filter out columns with List or Object data types that can't be exported to Excel
+    exportable_columns = [
+        col for col in clean_df.columns
+        if clean_df[col].dtype not in (pl.List, pl.Object)
+    ]
+    
+    clean_df = clean_df.select(exportable_columns)
+    
+    # Convert to pandas and export to Excel
+    pandas_df = clean_df.to_pandas()
+    pandas_df.to_excel(filename, index=False)
+    
+    self.logger.info(f"Features exported to {filename} (Excel format)")
+    self.logger.debug(f"Exported {len(clean_df)} features with {len(exportable_columns)} columns")
+
+
 def export_chrom(self, filename="chrom.csv"):
     # saves self.chrom_df to a csv file. Remove the scan_uid and chrom columns if the file already exists
     if self.chrom_df is None:

masster/spectrum.py

@@ -827,8 +827,11 @@ class Spectrum:
                 inty = inty[idx]
             p.line(mz, inty, line_color="black", legend_label=label)
         else:
-            data = self.to_dict()
-            data = {key: val for key, val in data.items() if isinstance(val, np.ndarray) and val.size == mz.size}
+            # Build data dictionary from spectrum attributes (numpy arrays)
+            data = {}
+            for key, val in self.__dict__.items():
+                if isinstance(val, np.ndarray) and val.size == mz.size:
+                    data[key] = val
             if ylog:
                 data["zeros"] = np.ones_like(mz)
             else:

{masster-0.5.5.dist-info → masster-0.5.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: masster
-Version: 0.5.5
+Version: 0.5.6
 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-0.5.5.dist-info → masster-0.5.6.dist-info}/RECORD

@@ -1,8 +1,8 @@
 masster/__init__.py,sha256=ueZ224WPNRRjQEYTaQUol818nwQgJwB93HbEfmtPRmg,1041
-masster/_version.py,sha256=gwA0FHD4Z-_YF_DHvv1fia5KlwKC04Tq47mBa_FkOEo,256
+masster/_version.py,sha256=rLineW-O0OSBF7JBd31acdcshluNBFss77bXVJCx5BY,256
 masster/chromatogram.py,sha256=iYpdv8C17zVnlWvOFgAn9ns2uFGiF-GgoYf5QVVAbHs,19319
 masster/logger.py,sha256=tR65N23zfrNpcZNbZm2ot_Aual9XrGB1MWjLrovZkMs,16749
-masster/spectrum.py,sha256=XJSUrqXZSzfpWnD8v5IMClXMRZLKLYIk014qaMOS9_k,49738
+masster/spectrum.py,sha256=TWIgDcl0lveG40cLVZTWGp8-FxMolu-P8EjZyRBtXL4,49850
 masster/data/dda/20250530_VH_IQX_KW_RP_HSST3_100mm_12min_pos_v4_DDA_OT_C-MiLUT_QC_dil2_01_20250602151849.sample5,sha256=LdJMF8uLoDm9ixZNHBoOzBH6hX7NGY7vTvqa2Pzetb8,6539174
 masster/data/dda/20250530_VH_IQX_KW_RP_HSST3_100mm_12min_pos_v4_DDA_OT_C-MiLUT_QC_dil3_01_20250602150634.sample5,sha256=hWUfslGoOTiQw59jENSBXP4sa6DdkbOi40FJ68ep61Q,6956773
 masster/data/dda/20250530_VH_IQX_KW_RP_HSST3_100mm_12min_pos_v4_MS1_C-MiLUT_C008_v6_r38_01.sample5,sha256=dSd2cIgYYdRcNSzkhqlZCeWKi3x8Hhhcx8BFMuiVG4c,11382948
@@ -10,6 +10,7 @@ masster/data/dda/20250530_VH_IQX_KW_RP_HSST3_100mm_12min_pos_v4_MS1_C-MiLUT_C008
 masster/data/dda/20250530_VH_IQX_KW_RP_HSST3_100mm_12min_pos_v4_MS1_C-MiLUT_C017_v5_r99_01.sample5,sha256=h2OOAWWTwKXzTNewhiYeL-cMYdp_JYLPya8Q9Nv9Lvw,12389587
 masster/data/libs/aa.csv,sha256=Sja1DyMsiaM2NfLcct4kAAcXYwPCukJJW8sDkup9w_c,1924
 masster/data/libs/ccm.csv,sha256=Q6nylV1152uTpX-ydqWeGrc6L9kgv45xN_fBZ4f7Tvo,12754
+masster/data/libs/hilic.csv,sha256=Ao2IN9t7GiFWEBJg21TmNJZjTbyHC3e0dJcfftAKsM4,671265
 masster/data/libs/urine.csv,sha256=iRrR4N8Wzb8KDhHJA4LqoQC35pp93FSaOKvXPrgFHis,653736
 masster/data/wiff/2025_01_14_VW_7600_LpMx_DBS_CID_2min_TOP15_030msecMS1_005msecReac_CE35_DBS-ON_3.timeseries.data,sha256=01vC6m__Qqm2rLvlTMZoeKIKowFvovBTUnrNl8Uav3E,24576
 masster/data/wiff/2025_01_14_VW_7600_LpMx_DBS_CID_2min_TOP15_030msecMS1_005msecReac_CE35_DBS-ON_3.wiff,sha256=go5N9gAM1rn4PZAVaoCmdteY9f7YGEM9gyPdSmkQ8PE,1447936
@@ -18,18 +19,18 @@ masster/data/wiff/2025_01_14_VW_7600_LpMx_DBS_CID_2min_TOP15_030msecMS1_005msecR
 masster/lib/__init__.py,sha256=TcePNx3SYZHz6763TL9Sg4gUNXaRWjlrOtyS6vsu-hg,178
 masster/lib/lib.py,sha256=SSN06UtiM-hIdjS3eCiIHsJ_8S4YHRGOLGmdPIh-efo,27481
 masster/sample/__init__.py,sha256=HL0m1ept0PMAYUCQtDDnkdOS12IFl6oLAq4TZQz83uY,170
-masster/sample/adducts.py,sha256=5aEZPVcjGywCsN06ZuUWIi7h1817NsUp6o8L26P0bpY,32592
+masster/sample/adducts.py,sha256=nl5KEuat0hvktgar6Ca4PbY8JXt9SD05EeTn0HOKt64,32592
 masster/sample/h5.py,sha256=tlTPGrT9AMUhduvY_YPDzk6dZF5dI-9NRc1xeiuze5c,115442
-masster/sample/helpers.py,sha256=avW7gKT1wH47NUU0tEB3hkzm6ayQdfHpWR730kgWPSI,41342
+masster/sample/helpers.py,sha256=27eZFFidr02-DlSi4-eF4bpSk_y-qU3eoFCAOshRO20,42138
 masster/sample/lib.py,sha256=E-j9c3Wd8f9a-H8xj7CAOwlA8KcyXPoFyYm3c8r7LtI,33755
 masster/sample/load.py,sha256=swjRBCoFGni9iPztHIKPVB5ru_xDMVryB_inPXdujTw,51819
 masster/sample/parameters.py,sha256=Gg2KcuNbV_wZ_Wwv93QlM5J19ji0oSIvZLPV1NoBmq0,4456
-masster/sample/plot.py,sha256=0v4FzO_yzpUdATjdHZU4YO7UoW73Xlf51vVQByQ33X0,82574
+masster/sample/plot.py,sha256=vA37dwmpeymVW8xobrsLhsD7X8x7EQIOw50Csiica84,86675
 masster/sample/processing.py,sha256=CjaLCElDKECeCvYWqzT5EH_-rPQ0Y4A30zKjZfqmS5s,55915
 masster/sample/quant.py,sha256=tHNjvUFTdehKR31BXBZnVsBxMD9XJHgaltITOjr71uE,7562
-masster/sample/sample.py,sha256=O2PY7DnRx7VkASBU4qKQcTqND1aRfd0OCjKK9Rjn5uw,20574
+masster/sample/sample.py,sha256=VhQik_ev1liRqGUtbZvV1NOjfFzgfZI1orfQT87gai4,20643
 masster/sample/sample5_schema.json,sha256=H5e2T6rHIDzul2kp_yP-ILUUWUpW08wP2pEQjMR0nSk,3977
-masster/sample/save.py,sha256=q1DjzVCB2FsTi9Sk-szd2-Nr7kPbqqFhJpjAWNfSCno,36536
+masster/sample/save.py,sha256=IwWfcsmWLWM-2ASdhHXWAiPyrZBv5JUynvciNPppDUs,38643
 masster/sample/sciex.py,sha256=vnbxsq_qnAQVuzcpziP1o3IC4kM5amGBcPmC2TAuDLw,46319
 masster/sample/defaults/__init__.py,sha256=A09AOP44cxD_oYohyt7XFUho0zndRcrzVD4DUaGnKH4,447
 masster/sample/defaults/find_adducts_def.py,sha256=Bu2KiBJRxD0SAnOPNMm_Nk-6fx6QYoRXjFNGzz-0_o0,13570
@@ -66,8 +67,8 @@ masster/wizard/README.md,sha256=mL1A3YWJZOefpJ6D0-HqGLkVRmUlOpwyVFdvJBeeoZM,1414
 masster/wizard/__init__.py,sha256=a2hcZnHASjfuw1lqZhZnvTR58rc33rRnoGAY_JfvGhI,683
 masster/wizard/example.py,sha256=xEZFTH9UZ8HKOm6s3JL8Js0Uw5ChnISWBHSZCL32vsM,7983
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