masster 0.4.0__py3-none-any.whl → 0.4.1__py3-none-any.whl

masster/sample/load.py

@@ -47,10 +47,10 @@ import pyopenms as oms
 
 from tqdm import tqdm
 
-from master.chromatogram import Chromatogram
+from masster.chromatogram import Chromatogram
 
 # Parameters removed - using hardcoded defaults
-from master.spectrum import Spectrum
+from masster.spectrum import Spectrum
 
 
 def load(
@@ -177,7 +177,7 @@ def load_study(
 ):
     """
     Backward compatibility alias for load_noms1().
-
+    
     This method is deprecated. Use load_noms1() instead.
     """
     return self.load_noms1(filename=filename, ondisk=ondisk, type=type, label=label)
@@ -263,16 +263,12 @@ def _load_mzML(
             energy = None
         else:
             prec_mz = s.getPrecursors()[0].getMZ()
-            precursorIsolationWindowLowerMZ = s.getPrecursors()[
-                0
-            ].getIsolationWindowLowerOffset()
-            precursorIsolationWindowUpperMZ = s.getPrecursors()[
-                0
-            ].getIsolationWindowUpperOffset()
+            precursorIsolationWindowLowerMZ = s.getPrecursors()[0].getIsolationWindowLowerOffset()
+            precursorIsolationWindowUpperMZ = s.getPrecursors()[0].getIsolationWindowUpperOffset()
             prec_intyensity = s.getPrecursors()[0].getIntensity()
             # Try to get collision energy from meta values first, fallback to getActivationEnergy()
             try:
-                energy = s.getPrecursors()[0].getMetaValue("collision energy")
+                energy = s.getPrecursors()[0].getMetaValue('collision energy')
                 if energy is None or energy == 0.0:
                     energy = s.getPrecursors()[0].getActivationEnergy()
             except Exception:
@@ -556,12 +552,12 @@ def _load_wiff(
     filename=None,
 ):
     try:
-        # Use master's own implementation first
-        from master.sample.sciex import SciexWiffData as MasterSciexWiffData
+        # Use masster's own implementation first
+        from masster.sample.sciex import SciexWiffData as MassterSciexWiffData
 
-        SciexWiffDataClass = MasterSciexWiffData
+        SciexWiffDataClass = MassterSciexWiffData
     except ImportError:
-        # Fallback to alpharaw if master implementation fails
+        # Fallback to alpharaw if masster implementation fails
         from alpharaw.sciex import SciexWiffData as AlpharawSciexWiffData
 
         SciexWiffDataClass = AlpharawSciexWiffData
@@ -972,8 +968,8 @@ def index_file(self):
         try:
             from alpharaw.sciex import SciexWiffData
         except ImportError:
-            # Fallback to master's own implementation
-            from master.sample.sciex import SciexWiffData
+            # Fallback to masster's own implementation
+            from masster.sample.sciex import SciexWiffData
 
         raw_data = SciexWiffData(centroided=False)
         raw_data.keep_k_peaks_per_spec = self.parameters.max_points_per_spectrum
@@ -989,9 +985,7 @@ def index_file(self):
         self.logger.info("Index raw data...")
         raw_data.import_raw(self.file_source)
         self.file_obj = raw_data
-    elif os.path.exists(self.file_source) and self.file_source.lower().endswith(
-        ".mzml",
-    ):
+    elif os.path.exists(self.file_source) and self.file_source.lower().endswith(".mzml"):
         self.file_interface = "oms"
         omsexp: oms.OnDiscMSExperiment | oms.MSExperiment
         if self.ondisk:
@@ -1001,9 +995,7 @@ def index_file(self):
             omsexp = oms.MSExperiment()
             oms.MzMLFile().load(self.file_source, omsexp)
             self.file_obj = omsexp
-    elif os.path.exists(self.file_source) and self.file_source.lower().endswith(
-        ".sample5",
-    ):
+    elif os.path.exists(self.file_source) and self.file_source.lower().endswith(".sample5"):
         # this is an old save, try to see if
         if os.path.exists(self.file_source.replace(".sample5", ".wiff")):
             self.set_source(self.file_source.replace(".sample5", ".wiff"))
@@ -1017,9 +1009,7 @@ def index_file(self):
             )
         self.index_file()
     else:
-        raise FileNotFoundError(
-            f"File {self.file_source} not found. Did the path change? Consider running source().",
-        )
+        raise FileNotFoundError(f"File {self.file_source} not found. Did the path change? Consider running source().")
 
 
 def _load_ms2data(
@@ -1224,9 +1214,7 @@ def chrom_extract(
             scan_uid = trace["scan_uid"]
             # find all ms1 data with scan_uid and mz between q1-mz_tol and q1+mz_tol
             d = self.ms1_df.filter(
-                (pl.col("scan_uid").is_in(scan_uid))
-                & (pl.col("mz") >= q1 - mz_tol)
-                & (pl.col("mz") <= q1 + mz_tol),
+                (pl.col("scan_uid").is_in(scan_uid)) & (pl.col("mz") >= q1 - mz_tol) & (pl.col("mz") <= q1 + mz_tol),
             )
             # for all unique rt values, find the maximum inty
             eic_rt = d.group_by("rt").agg(pl.col("inty").max())
@@ -1245,9 +1233,7 @@ def chrom_extract(
             scan_uid = trace["scan_uid"]
             # find all ms2 data with scan_uid and mz between q3-mz_tol and q3+mz_tol
             d = self.ms2data.filter(
-                (pl.col("scan_uid").is_in(scan_uid))
-                & (pl.col("mz") >= q3 - mz_tol)
-                & (pl.col("mz") <= q3 + mz_tol),
+                (pl.col("scan_uid").is_in(scan_uid)) & (pl.col("mz") >= q3 - mz_tol) & (pl.col("mz") <= q3 + mz_tol),
             )
             # for all unique rt values, find the maximum inty
             eic_rt = d.group_by("rt").agg(pl.col("inty").max())

masster/sample/parameters.py

@@ -53,11 +53,7 @@ def get_parameters(self, keys):
     if keys[0] == "sample":
         if len(keys) == 1:
             # Return the whole sample_defaults object as dict
-            return (
-                self.parameters.to_dict()
-                if hasattr(self.parameters, "to_dict")
-                else None
-            )
+            return self.parameters.to_dict() if hasattr(self.parameters, "to_dict") else None
         else:
             # Get specific parameter from sample_defaults object
             param_name = keys[1]
@@ -89,7 +85,7 @@ def update_parameters(self, **kwargs):
                  - Individual parameter names and values (see sample_defaults for details)
     """
     # Import here to avoid circular imports
-    from master.sample.defaults.sample_def import (
+    from masster.sample.defaults.sample_def import (
         sample_defaults as SampleDefaults,
     )
 

masster/sample/plot.py

@@ -144,7 +144,7 @@ def _display_plot(plot_object, layout=None):
 def _handle_sample_plot_output(self, plot_obj, filename=None, plot_type="bokeh"):
     """
     Helper function to handle consistent save/display behavior for sample plots.
-
+    
     Parameters:
         plot_obj: The plot object (bokeh figure, holoviews layout, or panel object)
         filename: Optional filename to save the plot
@@ -153,24 +153,21 @@ def _handle_sample_plot_output(self, plot_obj, filename=None, plot_type="bokeh")
     if filename is not None:
         # Convert relative paths to absolute paths using sample folder as base
         import os
-
-        if hasattr(self, "folder") and self.folder and not os.path.isabs(filename):
+        if hasattr(self, 'folder') and self.folder and not os.path.isabs(filename):
             filename = os.path.join(self.folder, filename)
-
+        
         # Convert to absolute path for logging
         abs_filename = os.path.abspath(filename)
-
+        
         if filename.endswith(".html"):
             if plot_type == "panel":
                 plot_obj.save(filename, embed=True)  # type: ignore[attr-defined]
             elif plot_type == "holoviews":
                 import panel
-
                 panel.panel(plot_obj).save(filename, embed=True)  # type: ignore[attr-defined]
             elif plot_type == "bokeh":
                 from bokeh.plotting import output_file
                 from bokeh.io import save
-
                 output_file(filename)
                 save(plot_obj)
             self.logger.info(f"Plot saved to: {abs_filename}")
@@ -178,75 +175,61 @@ def _handle_sample_plot_output(self, plot_obj, filename=None, plot_type="bokeh")
             try:
                 if plot_type == "bokeh":
                     from bokeh.io.export import export_png
-
                     export_png(plot_obj, filename=filename)
                 elif plot_type in ["panel", "holoviews"]:
                     import holoviews as hv
-
                     hv.save(plot_obj, filename, fmt="png")
                 self.logger.info(f"Plot saved to: {abs_filename}")
             except Exception:
                 # Fall back to HTML if PNG export not available
-                html_filename = filename.replace(".png", ".html")
+                html_filename = filename.replace('.png', '.html')
                 abs_html_filename = os.path.abspath(html_filename)
                 if plot_type == "panel":
                     plot_obj.save(html_filename, embed=True)  # type: ignore[attr-defined]
                 elif plot_type == "holoviews":
                     import panel
-
                     panel.panel(plot_obj).save(html_filename, embed=True)  # type: ignore[attr-defined]
                 elif plot_type == "bokeh":
                     from bokeh.plotting import output_file
                     from bokeh.io import save
-
                     output_file(html_filename)
                     save(plot_obj)
-                self.logger.warning(
-                    f"PNG export not available, saved as HTML instead: {abs_html_filename}",
-                )
+                self.logger.warning(f"PNG export not available, saved as HTML instead: {abs_html_filename}")
         elif filename.endswith(".pdf"):
             # Try to save as PDF, fall back to HTML if not available
             try:
                 if plot_type == "bokeh":
                     from bokeh.io.export import export_pdf
-
                     export_pdf(plot_obj, filename=filename)
                 elif plot_type in ["panel", "holoviews"]:
                     import holoviews as hv
-
                     hv.save(plot_obj, filename, fmt="pdf")
                 self.logger.info(f"Plot saved to: {abs_filename}")
             except ImportError:
                 # Fall back to HTML if PDF export not available
-                html_filename = filename.replace(".pdf", ".html")
+                html_filename = filename.replace('.pdf', '.html')
                 abs_html_filename = os.path.abspath(html_filename)
                 if plot_type == "panel":
                     plot_obj.save(html_filename, embed=True)  # type: ignore[attr-defined]
                 elif plot_type == "holoviews":
                     import panel
-
                     panel.panel(plot_obj).save(html_filename, embed=True)  # type: ignore[attr-defined]
                 elif plot_type == "bokeh":
                     from bokeh.plotting import output_file
                     from bokeh.io import save
-
                     output_file(html_filename)
                     save(plot_obj)
-                self.logger.warning(
-                    f"PDF export not available, saved as HTML instead: {abs_html_filename}",
-                )
+                self.logger.warning(f"PDF export not available, saved as HTML instead: {abs_html_filename}")
         else:
             # Default to HTML for unknown extensions
             if plot_type == "panel":
                 plot_obj.save(filename, embed=True)  # type: ignore[attr-defined]
             elif plot_type == "holoviews":
                 import panel
-
                 panel.panel(plot_obj).save(filename, embed=True)  # type: ignore[attr-defined]
             elif plot_type == "bokeh":
                 from bokeh.plotting import output_file
                 from bokeh.io import save
-
                 output_file(filename)
                 save(plot_obj)
             self.logger.info(f"Plot saved to: {abs_filename}")
@@ -256,11 +239,9 @@ def _handle_sample_plot_output(self, plot_obj, filename=None, plot_type="bokeh")
             plot_obj.show()  # type: ignore[attr-defined]
         elif plot_type == "holoviews":
             import panel
-
             return panel.panel(plot_obj)
         elif plot_type == "bokeh":
             from bokeh.plotting import show
-
             show(plot_obj)
 
 
@@ -318,9 +299,7 @@ def plot_chrom(
         if isinstance(feature_uids, int):
             feature_uids = [feature_uids]
         # select only the features with feature_uid in feature_uids
-        feats = self.features_df[
-            self.features_df["feature_uid"].is_in(feature_uids)
-        ].clone()
+        feats = self.features_df[self.features_df["feature_uid"].is_in(feature_uids)].clone()
 
     # make sure feature_uid is a list of integers
 
@@ -396,7 +375,7 @@ def plot_chrom(
 
     layout = layout.cols(1)
     layout = panel.Column(layout)
-
+    
     # Use consistent save/display behavior
     self._handle_sample_plot_output(layout, filename, "panel")
 
@@ -494,13 +473,9 @@ def plot_2d(
     # keep only rt, mz, and inty
     spectradf = spectradf.select(["rt", "mz", "inty"])
     if mz_range is not None:
-        spectradf = spectradf.filter(
-            (pl.col("mz") >= mz_range[0]) & (pl.col("mz") <= mz_range[1]),
-        )
+        spectradf = spectradf.filter((pl.col("mz") >= mz_range[0]) & (pl.col("mz") <= mz_range[1]))
     if rt_range is not None:
-        spectradf = spectradf.filter(
-            (pl.col("rt") >= rt_range[0]) & (pl.col("rt") <= rt_range[1]),
-        )
+        spectradf = spectradf.filter((pl.col("rt") >= rt_range[0]) & (pl.col("rt") <= rt_range[1]))
     maxrt = spectradf["rt"].max()
     minrt = spectradf["rt"].min()
     maxmz = spectradf["mz"].max()
@@ -532,11 +507,7 @@ def plot_2d(
     def dynamic_sizing_hook(plot, element):
         """Hook to convert size-based markers to radius-based for dynamic behavior"""
         try:
-            if (
-                use_dynamic_sizing
-                and hasattr(plot, "state")
-                and hasattr(plot.state, "renderers")
-            ):
+            if use_dynamic_sizing and hasattr(plot, "state") and hasattr(plot.state, "renderers"):
                 from bokeh.models import Circle
 
                 for renderer in plot.state.renderers:
@@ -847,38 +818,20 @@ def plot_2d(
 
             if feature_points_4 is not None:
                 updated_points_4 = feature_points_4.opts(size=size_val)
-                feature_overlay = (
-                    updated_points_4
-                    if feature_overlay is None
-                    else feature_overlay * updated_points_4
-                )
+                feature_overlay = updated_points_4 if feature_overlay is None else feature_overlay * updated_points_4
             if feature_points_3 is not None:
                 updated_points_3 = feature_points_3.opts(size=size_val)
-                feature_overlay = (
-                    updated_points_3
-                    if feature_overlay is None
-                    else feature_overlay * updated_points_3
-                )
+                feature_overlay = updated_points_3 if feature_overlay is None else feature_overlay * updated_points_3
             if feature_points_1 is not None:
                 updated_points_1 = feature_points_1.opts(size=size_val)
-                feature_overlay = (
-                    updated_points_1
-                    if feature_overlay is None
-                    else feature_overlay * updated_points_1
-                )
+                feature_overlay = updated_points_1 if feature_overlay is None else feature_overlay * updated_points_1
             if not show_only_features_with_ms2 and feature_points_2 is not None:
                 updated_points_2 = feature_points_2.opts(size=size_val)
-                feature_overlay = (
-                    updated_points_2
-                    if feature_overlay is None
-                    else feature_overlay * updated_points_2
-                )
+                feature_overlay = updated_points_2 if feature_overlay is None else feature_overlay * updated_points_2
             if feature_points_iso is not None:
                 updated_points_iso = feature_points_iso.opts(size=size_val)
                 feature_overlay = (
-                    updated_points_iso
-                    if feature_overlay is None
-                    else feature_overlay * updated_points_iso
+                    updated_points_iso if feature_overlay is None else feature_overlay * updated_points_iso
                 )
 
             # Combine with the static raster background
@@ -908,12 +861,7 @@ def plot_2d(
 
         # Create the slider widget row with clear styling
         slider_widget = on.Row(
-            on.pane.HTML(
-                "<b>Marker Size Control:</b>",
-                width=150,
-                height=40,
-                margin=(5, 10),
-            ),
+            on.pane.HTML("<b>Marker Size Control:</b>", width=150, height=40, margin=(5, 10)),
             size_slider,
             height=60,
             margin=10,
@@ -979,7 +927,7 @@ def plot_2d(
         layout = panel.Column(overlay)
 
     if filename is not None:
-        # Use consistent save/display behavior
+        # Use consistent save/display behavior  
         self._handle_sample_plot_output(layout, filename, "panel")
         return None
     else:
@@ -1060,13 +1008,9 @@ def plot_2d_oracle(
     # keep only rt, mz, and inty
     spectradf = spectradf[["rt", "mz", "inty"]]
     if mz_range is not None:
-        spectradf = spectradf[
-            (spectradf["mz"] >= mz_range[0]) & (spectradf["mz"] <= mz_range[1])
-        ]
+        spectradf = spectradf[(spectradf["mz"] >= mz_range[0]) & (spectradf["mz"] <= mz_range[1])]
     if rt_range is not None:
-        spectradf = spectradf[
-            (spectradf["rt"] >= rt_range[0]) & (spectradf["rt"] <= rt_range[1])
-        ]
+        spectradf = spectradf[(spectradf["rt"] >= rt_range[0]) & (spectradf["rt"] <= rt_range[1])]
 
     maxrt = spectradf["rt"].max()
     minrt = spectradf["rt"].min()
@@ -1189,8 +1133,7 @@ def plot_2d_oracle(
         # iterate over the rows and find the feature_uid in feats by looking at the closest rt and mz
         for i, row in oracle_data.iterrows():
             candidates = feats[
-                (abs(feats["rt"] - row["rt"]) < 1)
-                & (abs(feats["mz"] - row["precursor"]) < 0.005)
+                (abs(feats["rt"] - row["rt"]) < 1) & (abs(feats["mz"] - row["precursor"]) < 0.005)
             ].copy()
             if len(candidates) > 0:
                 # sort by delta rt
@@ -1236,9 +1179,7 @@ def plot_2d_oracle(
         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])
+            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'
@@ -1868,9 +1809,7 @@ def plot_ms2_q1(
     scans = self.scans_df.filter(pl.col("cycle") == cycle)
     scans = scans.filter(pl.col("ms_level") == 2)
     # find the scan in cycle whose 'prec_mz' is the closest to the feature['mz']
-    scan_uid = scans[(scans["prec_mz"] - feature["mz"]).abs().arg_sort()[:1]][
-        "scan_uid"
-    ][0]
+    scan_uid = scans[(scans["prec_mz"] - feature["mz"]).abs().arg_sort()[:1]]["scan_uid"][0]
     # get q1_width scans before and after the scan_uid
     scans = self.scans_df.filter(pl.col("scan_uid") >= scan_uid - q1_width)
     scans = scans.filter(pl.col("scan_uid") <= scan_uid + q1_width)
@@ -2134,7 +2073,7 @@ def plot_tic(
         return
 
     # Import helper locally to avoid circular imports
-    from master.study.helpers import get_tic
+    from masster.study.helpers import get_tic
 
     # Delegate TIC computation to study helper which handles ms1_df and scans_df fallbacks
     try:
@@ -2189,7 +2128,7 @@ def plot_bpc(
         return
 
     # Import helper locally to avoid circular imports
-    from master.study.helpers import get_bpc
+    from masster.study.helpers import get_bpc
 
     # Delegate BPC computation to study helper
     try: