masster 0.2.5__py3-none-any.whl → 0.3.0__py3-none-any.whl

masster/chromatogram.py

@@ -1,503 +1,497 @@
-"""
-chrom.py
-
-This module provides tools for processing and analyzing chromatographic data.
-It defines the `chrom` class for handling retention time and intensity profiles,
-including peak detection, chromatographic feature extraction, and visualization.
-
-Key Features:
-- **Chromatogram Processing**: Handle retention time and intensity data arrays.
-- **Peak Detection**: Advanced chromatographic peak picking with customizable parameters.
-- **Feature Extraction**: Extract chromatographic features including peak areas, widths, and shapes.
-- **Baseline Correction**: Remove baseline contributions from chromatographic data.
-- **Visualization**: Plot chromatograms with peak annotations and feature highlighting.
-- **Quality Metrics**: Calculate peak quality metrics and chromatographic statistics.
-
-Dependencies:
-- `numpy`: For numerical array operations and mathematical computations.
-- `polars`: For structured data handling and tabulation.
-- `scipy.signal`: For signal processing, peak detection, and chromatographic algorithms.
-
-Classes:
-- `chrom`: Main class for chromatographic data processing, providing methods for
-  peak detection, feature extraction, and analysis.
-
-Example Usage:
-```python
-from chrom import chrom
-import numpy as np
-
-# Create chromatogram from retention time and intensity arrays
-rt = np.linspace(0, 300, 1000)  # 5 minutes in seconds
-intensity = np.random.normal(1000, 100, 1000)  # Baseline noise
-# Add a peak
-peak_center = 150
-peak_intensity = np.exp(-((rt - peak_center) ** 2) / (2 * 10**2)) * 10000
-intensity += peak_intensity
-
-chromatogram = chrom(rt=rt, inty=intensity, label="Sample 1")
-chromatogram.find_peaks()
-chromatogram.plot()
-```
-
-See Also:
-- `single.py`: For complete mass spectrometry file processing including chromatograms.
-- `parameters.chrom_parameters`: For chromatography-specific parameter configuration.
-
-"""
-
-import importlib
-
-from dataclasses import dataclass
-
-import numpy as np
-import polars
-
-from scipy.signal import find_peaks
-from scipy.signal import peak_prominences
-
-
-@dataclass
-class Chromatogram:
-    """
-    A class for processing and analyzing chromatographic data.
-
-    The `chrom` class provides comprehensive tools for handling chromatographic profiles,
-    including retention time and intensity data processing, peak detection, feature
-    extraction, and quality assessment. It supports various chromatographic data types
-    and provides methods for baseline correction and peak characterization.
-
-    Attributes:
-        rt (np.ndarray): Retention time values (typically in seconds).
-        inty (np.ndarray): Intensity values corresponding to retention times.
-        label (str, optional): Text label for the chromatogram.
-        rt_unit (str, optional): Unit for retention time ("sec" or "min").
-        history (str): Processing history log.
-        bl (np.ndarray, optional): Baseline values for baseline correction.
-        feature_start (float, optional): Start retention time of detected feature.
-        feature_end (float, optional): End retention time of detected feature.
-        feature_apex (float, optional): Apex retention time of detected feature.
-        feature_area (float, optional): Integrated area of detected feature.
-
-    Key Methods:
-        - `find_peaks()`: Detect chromatographic peaks with customizable parameters.
-        - `calculate_area()`: Integrate peak areas for quantification.
-        - `baseline_correct()`: Remove baseline contributions.
-        - `plot()`: Visualize chromatographic data with annotations.
-        - `get_statistics()`: Calculate chromatographic quality metrics.
-
-    Example Usage:
-        >>> import numpy as np
-        >>> from masster import chrom
-        >>> rt = np.linspace(0, 300, 1000)
-        >>> intensity = np.random.normal(1000, 100, 1000)
-        >>> chromatogram = chrom(rt=rt, inty=intensity, label="EIC m/z 150")
-        >>> chromatogram.find_peaks()
-        >>> chromatogram.calculate_area()
-
-    See Also:
-        - `ddafile`: For complete mass spectrometry data including chromatograms.
-        - `ChromParameters`: For chromatography-specific parameter configuration.
-    """
-
-    def __init__(
-        self,
-        rt: np.ndarray | None = None,
-        inty: np.ndarray | None = None,
-        label: str | None = None,
-        rt_unit: str | None = None,
-        **kwargs,
-    ):
-        # Handle case where rt and inty might be in kwargs (from from_dict/from_json)
-        if rt is None and "rt" in kwargs:
-            rt = kwargs.pop("rt")
-        if inty is None and "inty" in kwargs:
-            inty = kwargs.pop("inty")
-
-        # Ensure rt and inty are provided
-        if rt is None or inty is None:
-            raise ValueError("rt and inty arrays are required")
-
-        self.label = label
-        self.rt = np.asarray(rt, dtype=np.float64)
-        # if all rt are less than 60, assume minutes
-        if rt_unit is None:
-            if np.all(self.rt < 60):
-                self.rt_unit = "sec"
-            else:
-                self.rt_unit = "sec"
-        else:
-            self.rt_unit = rt_unit
-        self.inty = np.asarray(inty, dtype=np.float64)
-        self.history = ""
-        self.bl: float | None = None
-        self.feature_start: float | None = None
-        self.feature_end: float | None = None
-        self.feature_apex: float | None = None
-        self.feature_area: float | None = None
-        self.lib_rt: float | None = None  # Library retention time for reference
-        self.__dict__.update(kwargs)
-        # sort rt and inty by rt
-        if len(self.rt) > 0:
-            sorted_indices = np.argsort(self.rt)
-            self.rt = self.rt[sorted_indices]
-            self.inty = self.inty[sorted_indices]
-        self.__post_init__()
-
-    # a spectrum is defined by mz and intensity values. It can also have ms_level, centroided, and label. If additional arguments are provided, they are added to the dictionary.
-
-    def __post_init__(self):
-        """Validate and ensure arrays are numpy arrays."""
-        self.rt = np.asarray(self.rt)
-        self.inty = np.asarray(self.inty)
-        if self.rt.shape != self.inty.shape:
-            raise ValueError("rt and intensity arrays must have the same shape")
-
-    def __len__(self):
-        """Return the number of points in the chromatogram."""
-        return len(self.rt)
-
-    def reload(self):
-        """
-        Reloads the module and updates the class reference of the instance.
-        """
-        # Get the name of the module containing the class
-        modname = self.__class__.__module__
-        # Import the module
-        mod = __import__(modname, fromlist=[modname.split(".")[0]])
-        # Reload the module
-        importlib.reload(mod)
-        # Get the updated class reference from the reloaded module
-        new = getattr(mod, self.__class__.__name__)
-        # Update the class reference of the instance
-        self.__class__ = new
-
-    def to_dict(self):
-        # return a dictionary representation of the chromatogram. include all the attributes
-        # Create a copy to avoid modifying the original object
-        result = {}
-
-        # Handle numpy arrays by creating copies and converting to lists
-        for key, value in self.__dict__.items():
-            if isinstance(value, np.ndarray):
-                result[key] = value.copy().tolist()
-            elif isinstance(value, (list, dict)):
-                # Create copies of mutable objects
-                import copy
-
-                result[key] = copy.deepcopy(value)
-            else:
-                # Immutable objects can be copied directly
-                result[key] = value
-
-        # Sort rt and inty in the result (not the original object)
-        if "rt" in result and "inty" in result and len(result["rt"]) > 0:
-            rt_array = np.array(result["rt"])
-            inty_array = np.array(result["inty"])
-            sorted_indices = np.argsort(rt_array)
-            result["rt"] = np.round(rt_array[sorted_indices], 3).tolist()
-            result["inty"] = np.round(inty_array[sorted_indices], 3).tolist()
-
-        return result
-
-    @classmethod
-    def from_dict(cls, data):
-        """
-        Create a Chromatogram instance from a dictionary of attributes.
-        Args:
-            data (dict): Dictionary containing chromatogram attributes.
-        Returns:
-            Chromatogram: New instance with attributes set from the dictionary.
-        """
-        # Create instance directly from data dictionary
-        return cls(**data)
-
-    def to_json(self):
-        """
-        Serialize the chromatogram to a JSON string.
-
-        Returns:
-            str: JSON string representation of the chromatogram.
-        """
-        import json
-
-        data = self.to_dict()
-        return json.dumps(data, indent=2)
-
-    @classmethod
-    def from_json(cls, json_str):
-        """
-        Create a Chromatogram instance from a JSON string.
-
-        Args:
-            json_str (str): JSON string containing chromatogram data.
-
-        Returns:
-            Chromatogram: New instance with attributes set from the JSON data.
-        """
-        import json
-
-        data = json.loads(json_str)
-        return cls.from_dict(data)
-
-    def copy(self):
-        """
-        Create a copy of the chromatogram instance.
-        Returns:
-            A new instance of the chromatogram with the same data.
-        """
-        return Chromatogram(
-            rt=self.rt.copy(),
-            inty=self.inty.copy(),
-            label=self.label,
-            rt_unit=self.rt_unit,
-            **{
-                k: v.copy()
-                for k, v in self.__dict__.items()
-                if isinstance(v, np.ndarray)
-            },
-        )
-
-    def pandalize(self):
-        """
-        Convert the spectrum to a pandas DataFrame.
-        This is an alias for to_df.
-        """
-        return self.to_df()
-
-    def to_df(self):
-        """
-        Convert the spectrum to a pandas dataframe. include all the attributes that have the same length as mz
-        find all attributes that are numpy arrays and have the same length as mz
-        """
-        data = {
-            key: val
-            for key, val in self.__dict__.items()
-            if isinstance(val, np.ndarray) and val.size == self.rt.size
-        }
-        return polars.DataFrame(data)
-
-    def plot(self, ax=None, width=800, height=300, **kwargs):
-        """
-        Plot the chromatogram using bokeh
-        """
-        import bokeh.plotting as bp
-
-        from bokeh.models import ColumnDataSource
-        from bokeh.models import HoverTool
-        
-        # Import Span with fallback - use type: ignore to avoid mypy issues with different Bokeh versions
-        try:
-            from bokeh.models import Span  # type: ignore
-        except ImportError:
-            from bokeh.models import VSpan as Span
-
-        if ax is None:
-            p = bp.figure(
-                title=self.label,
-                width=width,
-                height=height,
-            )
-            p.xaxis.axis_label = f"rt ({self.rt_unit})"
-            p.yaxis.axis_label = "inty"
-        else:
-            p = ax
-
-        # sort by rt
-        sorted_indices = np.argsort(self.rt)
-        self.rt = self.rt[sorted_indices]
-        self.inty = self.inty[sorted_indices]
-
-        source = ColumnDataSource(data={"rt": self.rt, "inty": self.inty})
-
-        line = p.line("rt", "inty", source=source, **kwargs)
-
-        # Add hover tool for the chromatogram line
-        hover = HoverTool(
-            tooltips=[
-                ("rt", "@rt"),
-                ("inty", "@inty"),
-            ],
-            renderers=[line],
-        )
-        p.add_tools(hover)
-
-        # Add spans and hover tools for them
-        span_renderers = []
-        if "feature_start" in self.__dict__:
-            feature_start = self.feature_start
-            feature_end = self.feature_end
-            # Create spans - may fail with different Bokeh versions but we handle it
-            span_start = Span(
-                location=feature_start,
-                dimension="height",
-                line_color="green",
-                line_width=1,
-                line_dash="dashed",
-            )
-            span_end = Span(
-                location=feature_end,
-                dimension="height",
-                line_color="green",
-                line_width=1,
-                line_dash="dashed",
-            )
-            p.add_layout(span_start)
-            p.add_layout(span_end)
-            span_renderers.extend([span_start, span_end])
-        if "feature_apex" in self.__dict__:
-            feature_apex = self.feature_apex
-            span_apex = Span(
-                location=feature_apex,
-                dimension="height",
-                line_color="green",
-                line_width=1,
-            )
-            p.add_layout(span_apex)
-            span_renderers.append(span_apex)
-        if "lib_rt" in self.__dict__:
-            lib_rt = self.lib_rt
-            span_lib = Span(
-                location=lib_rt,
-                dimension="height",
-                line_color="red",
-                line_width=1,
-            )
-            p.add_layout(span_lib)
-            span_renderers.append(span_lib)
-
-        # Add hover tool for spans (using a dummy invisible renderer, since Span is not a glyph)
-        # Workaround: add invisible vbar glyphs at the span locations for hover
-        vbar_data: dict[str, list] = {"rt": [], "top": [], "bottom": []}
-        vbar_tooltips = []
-        if "feature_start" in self.__dict__:
-            vbar_data["rt"].append(self.feature_start)
-            vbar_data["top"].append(np.max(self.inty))
-            vbar_data["bottom"].append(np.min(self.inty))
-            vbar_tooltips.append(("feature_start", str(self.feature_start)))
-        if "feature_end" in self.__dict__:
-            vbar_data["rt"].append(self.feature_end)
-            vbar_data["top"].append(np.max(self.inty))
-            vbar_data["bottom"].append(np.min(self.inty))
-            vbar_tooltips.append(("feature_end", str(self.feature_end)))
-        if "lib_rt" in self.__dict__:
-            vbar_data["rt"].append(self.lib_rt)
-            vbar_data["top"].append(np.max(self.inty))
-            vbar_data["bottom"].append(np.min(self.inty))
-            vbar_tooltips.append(("lib_rt", str(self.lib_rt)))
-        if "feature_apex" in self.__dict__:
-            vbar_data["rt"].append(self.feature_apex)
-            vbar_data["top"].append(np.max(self.inty))
-            vbar_data["bottom"].append(np.min(self.inty))
-            vbar_tooltips.append(("feature_apex", str(self.feature_apex)))
-        if vbar_data["rt"]:
-            vbar_source = ColumnDataSource(data=vbar_data)
-            vbars = p.vbar(
-                x="rt",
-                top="top",
-                bottom="bottom",
-                width=0.01,
-                alpha=0,
-                source=vbar_source,
-            )
-            hover_span = HoverTool(tooltips=[("rt", "@rt")], renderers=[vbars])
-            p.add_tools(hover_span)
-
-        bp.show(p)
-
-    def find_peaks(self, order_by="prominences"):
-        sinty = self.inty
-        p = []
-        if len(sinty) > 5:
-            # smooth
-            # sinty = savgol_filter(sinty, window_length=7, polyorder=2)
-            p, props = find_peaks(
-                sinty,
-                prominence=(None, None),
-                height=(None, None),
-                width=(None, None),
-            )
-
-        # TODO Instance attributes defined outside __init__
-        if len(p) == 0:
-            self.feature_apex = None
-            self.feature_coherence = 0.0
-            self.peak_rts = np.array([])
-            self.peak_heights = np.array([])
-            self.peak_prominences = np.array([])
-            self.peak_widths = np.array([])
-            self.peak_left_bases = np.array([])
-            self.peak_right_bases = np.array([])
-        else:
-            prt = self.rt[p]
-            # remove prt with prt < c['feature_start'] or prt > c['feature_end']
-            mask = (prt >= self.feature_start) & (prt <= self.feature_end)
-            # apply mask to all arrays in props
-            if mask.any():
-                for key in props:
-                    if isinstance(props[key], np.ndarray):
-                        props[key] = props[key][mask]
-                # order peaks by the specified order
-                p = p[mask]
-                prt = prt[mask]
-            if order_by in props:
-                # descending order
-                order = np.argsort(props[order_by])[::-1]
-            else:
-                order = np.arange(len(prt))
-
-            # add to self
-            self.feature_apex = prt[order[0]]
-            self.feature_coherence = 0.0
-            self.peak_rts = prt[order]
-            self.peak_heights = self.inty[p][order]
-            self.peak_prominences = peak_prominences(self.inty, p)[0][order]
-            self.peak_widths = props["widths"][order]
-            self.peak_left_bases = self.rt[props["left_bases"][order]]
-            self.peak_right_bases = self.rt[props["right_bases"][order]]
-            self.feature_start = self.peak_left_bases[0]
-            self.feature_end = self.peak_right_bases[0]
-
-            # select inty for rt between feature_start and feature_end
-            mask = (
-                (self.rt >= self.feature_start)
-                & (self.rt <= self.feature_end)
-                & (self.rt >= self.feature_apex - 4)
-                & (self.rt <= self.feature_apex + 4)
-            )
-
-            sinty = sinty[mask]
-            # calculate how many times the derivative of self.inty crosses zero
-            if len(sinty) > 3:
-                self.feature_coherence = 1 - np.sum(
-                    np.diff(np.sign(np.diff(sinty))) != 0,
-                ) / (len(sinty) - 3)
-        return self
-
-    def integrate(self):
-        """
-        Integrate the chromatogram between feature_start and feature_end.
-        """
-        if self.feature_start is None or self.feature_end is None:
-            raise ValueError(
-                "feature_start and feature_end must be set before integration",
-            )
-        
-        # At this point, mypy knows feature_start and feature_end are not None
-        mask = (self.rt >= self.feature_start) & (self.rt <= self.feature_end)
-        area_result = np.trapezoid(self.inty[mask], self.rt[mask])
-        self.feature_area = float(area_result)
-        if self.bl is not None:
-            # subtract baseline
-            self.feature_area -= self.bl * (self.feature_end - self.feature_start)
-        if self.feature_area < 0:
-            self.feature_area = 0.0
-
-    def get_area(self):
-        """
-        Get the area of the chromatogram between feature_start and feature_end.
-        If the area is not calculated, it will be calculated first.
-        """
-        if self.feature_area is None:
-            self.integrate()
-        return self.feature_area
+"""
+chrom.py
+
+This module provides tools for processing and analyzing chromatographic data.
+It defines the `chrom` class for handling retention time and intensity profiles,
+including peak detection, chromatographic feature extraction, and visualization.
+
+Key Features:
+- **Chromatogram Processing**: Handle retention time and intensity data arrays.
+- **Peak Detection**: Advanced chromatographic peak picking with customizable parameters.
+- **Feature Extraction**: Extract chromatographic features including peak areas, widths, and shapes.
+- **Baseline Correction**: Remove baseline contributions from chromatographic data.
+- **Visualization**: Plot chromatograms with peak annotations and feature highlighting.
+- **Quality Metrics**: Calculate peak quality metrics and chromatographic statistics.
+
+Dependencies:
+- `numpy`: For numerical array operations and mathematical computations.
+- `polars`: For structured data handling and tabulation.
+- `scipy.signal`: For signal processing, peak detection, and chromatographic algorithms.
+
+Classes:
+- `chrom`: Main class for chromatographic data processing, providing methods for
+  peak detection, feature extraction, and analysis.
+
+Example Usage:
+```python
+from chrom import chrom
+import numpy as np
+
+# Create chromatogram from retention time and intensity arrays
+rt = np.linspace(0, 300, 1000)  # 5 minutes in seconds
+intensity = np.random.normal(1000, 100, 1000)  # Baseline noise
+# Add a peak
+peak_center = 150
+peak_intensity = np.exp(-((rt - peak_center) ** 2) / (2 * 10**2)) * 10000
+intensity += peak_intensity
+
+chromatogram = chrom(rt=rt, inty=intensity, label="Sample 1")
+chromatogram.find_peaks()
+chromatogram.plot()
+```
+
+See Also:
+- `single.py`: For complete mass spectrometry file processing including chromatograms.
+- `parameters.chrom_parameters`: For chromatography-specific parameter configuration.
+
+"""
+
+import importlib
+
+from dataclasses import dataclass
+
+import numpy as np
+import polars
+
+from scipy.signal import find_peaks
+from scipy.signal import peak_prominences
+
+
+@dataclass
+class Chromatogram:
+    """
+    A class for processing and analyzing chromatographic data.
+
+    The `chrom` class provides comprehensive tools for handling chromatographic profiles,
+    including retention time and intensity data processing, peak detection, feature
+    extraction, and quality assessment. It supports various chromatographic data types
+    and provides methods for baseline correction and peak characterization.
+
+    Attributes:
+        rt (np.ndarray): Retention time values (typically in seconds).
+        inty (np.ndarray): Intensity values corresponding to retention times.
+        label (str, optional): Text label for the chromatogram.
+        rt_unit (str, optional): Unit for retention time ("sec" or "min").
+        history (str): Processing history log.
+        bl (np.ndarray, optional): Baseline values for baseline correction.
+        feature_start (float, optional): Start retention time of detected feature.
+        feature_end (float, optional): End retention time of detected feature.
+        feature_apex (float, optional): Apex retention time of detected feature.
+        feature_area (float, optional): Integrated area of detected feature.
+
+    Key Methods:
+        - `find_peaks()`: Detect chromatographic peaks with customizable parameters.
+        - `calculate_area()`: Integrate peak areas for quantification.
+        - `baseline_correct()`: Remove baseline contributions.
+        - `plot()`: Visualize chromatographic data with annotations.
+        - `get_statistics()`: Calculate chromatographic quality metrics.
+
+    Example Usage:
+        >>> import numpy as np
+        >>> from masster import chrom
+        >>> rt = np.linspace(0, 300, 1000)
+        >>> intensity = np.random.normal(1000, 100, 1000)
+        >>> chromatogram = chrom(rt=rt, inty=intensity, label="EIC m/z 150")
+        >>> chromatogram.find_peaks()
+        >>> chromatogram.calculate_area()
+
+    See Also:
+        - `ddafile`: For complete mass spectrometry data including chromatograms.
+        - `ChromParameters`: For chromatography-specific parameter configuration.
+    """
+
+    def __init__(
+        self,
+        rt: np.ndarray | None = None,
+        inty: np.ndarray | None = None,
+        label: str | None = None,
+        rt_unit: str | None = None,
+        **kwargs,
+    ):
+        # Handle case where rt and inty might be in kwargs (from from_dict/from_json)
+        if rt is None and "rt" in kwargs:
+            rt = kwargs.pop("rt")
+        if inty is None and "inty" in kwargs:
+            inty = kwargs.pop("inty")
+
+        # Ensure rt and inty are provided
+        if rt is None or inty is None:
+            raise ValueError("rt and inty arrays are required")
+
+        self.label = label
+        self.rt = np.asarray(rt, dtype=np.float64)
+        # if all rt are less than 60, assume minutes
+        if rt_unit is None:
+            if np.all(self.rt < 60):
+                self.rt_unit = "sec"
+            else:
+                self.rt_unit = "sec"
+        else:
+            self.rt_unit = rt_unit
+        self.inty = np.asarray(inty, dtype=np.float64)
+        self.history = ""
+        self.bl: float | None = None
+        self.feature_start: float | None = None
+        self.feature_end: float | None = None
+        self.feature_apex: float | None = None
+        self.feature_area: float | None = None
+        self.lib_rt: float | None = None  # Library retention time for reference
+        self.__dict__.update(kwargs)
+        # sort rt and inty by rt
+        if len(self.rt) > 0:
+            sorted_indices = np.argsort(self.rt)
+            self.rt = self.rt[sorted_indices]
+            self.inty = self.inty[sorted_indices]
+        self.__post_init__()
+
+    # a spectrum is defined by mz and intensity values. It can also have ms_level, centroided, and label. If additional arguments are provided, they are added to the dictionary.
+
+    def __post_init__(self):
+        """Validate and ensure arrays are numpy arrays."""
+        self.rt = np.asarray(self.rt)
+        self.inty = np.asarray(self.inty)
+        if self.rt.shape != self.inty.shape:
+            raise ValueError("rt and intensity arrays must have the same shape")
+
+    def __len__(self):
+        """Return the number of points in the chromatogram."""
+        return len(self.rt)
+
+    def reload(self):
+        """
+        Reloads the module and updates the class reference of the instance.
+        """
+        # Get the name of the module containing the class
+        modname = self.__class__.__module__
+        # Import the module
+        mod = __import__(modname, fromlist=[modname.split(".")[0]])
+        # Reload the module
+        importlib.reload(mod)
+        # Get the updated class reference from the reloaded module
+        new = getattr(mod, self.__class__.__name__)
+        # Update the class reference of the instance
+        self.__class__ = new
+
+    def to_dict(self):
+        # return a dictionary representation of the chromatogram. include all the attributes
+        # Create a copy to avoid modifying the original object
+        result = {}
+
+        # Handle numpy arrays by creating copies and converting to lists
+        for key, value in self.__dict__.items():
+            if isinstance(value, np.ndarray):
+                result[key] = value.copy().tolist()
+            elif isinstance(value, (list, dict)):
+                # Create copies of mutable objects
+                import copy
+
+                result[key] = copy.deepcopy(value)
+            else:
+                # Immutable objects can be copied directly
+                result[key] = value
+
+        # Sort rt and inty in the result (not the original object)
+        if "rt" in result and "inty" in result and len(result["rt"]) > 0:
+            rt_array = np.array(result["rt"])
+            inty_array = np.array(result["inty"])
+            sorted_indices = np.argsort(rt_array)
+            result["rt"] = np.round(rt_array[sorted_indices], 3).tolist()
+            result["inty"] = np.round(inty_array[sorted_indices], 3).tolist()
+
+        return result
+
+    @classmethod
+    def from_dict(cls, data):
+        """
+        Create a Chromatogram instance from a dictionary of attributes.
+        Args:
+            data (dict): Dictionary containing chromatogram attributes.
+        Returns:
+            Chromatogram: New instance with attributes set from the dictionary.
+        """
+        # Create instance directly from data dictionary
+        return cls(**data)
+
+    def to_json(self):
+        """
+        Serialize the chromatogram to a JSON string.
+
+        Returns:
+            str: JSON string representation of the chromatogram.
+        """
+        import json
+
+        data = self.to_dict()
+        return json.dumps(data, indent=2)
+
+    @classmethod
+    def from_json(cls, json_str):
+        """
+        Create a Chromatogram instance from a JSON string.
+
+        Args:
+            json_str (str): JSON string containing chromatogram data.
+
+        Returns:
+            Chromatogram: New instance with attributes set from the JSON data.
+        """
+        import json
+
+        data = json.loads(json_str)
+        return cls.from_dict(data)
+
+    def copy(self):
+        """
+        Create a copy of the chromatogram instance.
+        Returns:
+            A new instance of the chromatogram with the same data.
+        """
+        return Chromatogram(
+            rt=self.rt.copy(),
+            inty=self.inty.copy(),
+            label=self.label,
+            rt_unit=self.rt_unit,
+            **{k: v.copy() for k, v in self.__dict__.items() if isinstance(v, np.ndarray)},
+        )
+
+    def pandalize(self):
+        """
+        Convert the spectrum to a pandas DataFrame.
+        This is an alias for to_df.
+        """
+        return self.to_df()
+
+    def to_df(self):
+        """
+        Convert the spectrum to a pandas dataframe. include all the attributes that have the same length as mz
+        find all attributes that are numpy arrays and have the same length as mz
+        """
+        data = {
+            key: val for key, val in self.__dict__.items() if isinstance(val, np.ndarray) and val.size == self.rt.size
+        }
+        return polars.DataFrame(data)
+
+    def plot(self, ax=None, width=800, height=300, **kwargs):
+        """
+        Plot the chromatogram using bokeh
+        """
+        import bokeh.plotting as bp
+
+        from bokeh.models import ColumnDataSource
+        from bokeh.models import HoverTool
+
+        # Import Span with fallback - use type: ignore to avoid mypy issues with different Bokeh versions
+        try:
+            from bokeh.models import Span  # type: ignore
+        except ImportError:
+            from bokeh.models import VSpan as Span
+
+        if ax is None:
+            p = bp.figure(
+                title=self.label,
+                width=width,
+                height=height,
+            )
+            p.xaxis.axis_label = f"rt ({self.rt_unit})"
+            p.yaxis.axis_label = "inty"
+        else:
+            p = ax
+
+        # sort by rt
+        sorted_indices = np.argsort(self.rt)
+        self.rt = self.rt[sorted_indices]
+        self.inty = self.inty[sorted_indices]
+
+        source = ColumnDataSource(data={"rt": self.rt, "inty": self.inty})
+
+        line = p.line("rt", "inty", source=source, **kwargs)
+
+        # Add hover tool for the chromatogram line
+        hover = HoverTool(
+            tooltips=[
+                ("rt", "@rt"),
+                ("inty", "@inty"),
+            ],
+            renderers=[line],
+        )
+        p.add_tools(hover)
+
+        # Add spans and hover tools for them
+        span_renderers = []
+        if "feature_start" in self.__dict__:
+            feature_start = self.feature_start
+            feature_end = self.feature_end
+            # Create spans - may fail with different Bokeh versions but we handle it
+            span_start = Span(
+                location=feature_start,
+                dimension="height",
+                line_color="green",
+                line_width=1,
+                line_dash="dashed",
+            )
+            span_end = Span(
+                location=feature_end,
+                dimension="height",
+                line_color="green",
+                line_width=1,
+                line_dash="dashed",
+            )
+            p.add_layout(span_start)
+            p.add_layout(span_end)
+            span_renderers.extend([span_start, span_end])
+        if "feature_apex" in self.__dict__:
+            feature_apex = self.feature_apex
+            span_apex = Span(
+                location=feature_apex,
+                dimension="height",
+                line_color="green",
+                line_width=1,
+            )
+            p.add_layout(span_apex)
+            span_renderers.append(span_apex)
+        if "lib_rt" in self.__dict__:
+            lib_rt = self.lib_rt
+            span_lib = Span(
+                location=lib_rt,
+                dimension="height",
+                line_color="red",
+                line_width=1,
+            )
+            p.add_layout(span_lib)
+            span_renderers.append(span_lib)
+
+        # Add hover tool for spans (using a dummy invisible renderer, since Span is not a glyph)
+        # Workaround: add invisible vbar glyphs at the span locations for hover
+        vbar_data: dict[str, list] = {"rt": [], "top": [], "bottom": []}
+        vbar_tooltips = []
+        if "feature_start" in self.__dict__:
+            vbar_data["rt"].append(self.feature_start)
+            vbar_data["top"].append(np.max(self.inty))
+            vbar_data["bottom"].append(np.min(self.inty))
+            vbar_tooltips.append(("feature_start", str(self.feature_start)))
+        if "feature_end" in self.__dict__:
+            vbar_data["rt"].append(self.feature_end)
+            vbar_data["top"].append(np.max(self.inty))
+            vbar_data["bottom"].append(np.min(self.inty))
+            vbar_tooltips.append(("feature_end", str(self.feature_end)))
+        if "lib_rt" in self.__dict__:
+            vbar_data["rt"].append(self.lib_rt)
+            vbar_data["top"].append(np.max(self.inty))
+            vbar_data["bottom"].append(np.min(self.inty))
+            vbar_tooltips.append(("lib_rt", str(self.lib_rt)))
+        if "feature_apex" in self.__dict__:
+            vbar_data["rt"].append(self.feature_apex)
+            vbar_data["top"].append(np.max(self.inty))
+            vbar_data["bottom"].append(np.min(self.inty))
+            vbar_tooltips.append(("feature_apex", str(self.feature_apex)))
+        if vbar_data["rt"]:
+            vbar_source = ColumnDataSource(data=vbar_data)
+            vbars = p.vbar(
+                x="rt",
+                top="top",
+                bottom="bottom",
+                width=0.01,
+                alpha=0,
+                source=vbar_source,
+            )
+            hover_span = HoverTool(tooltips=[("rt", "@rt")], renderers=[vbars])
+            p.add_tools(hover_span)
+
+        bp.show(p)
+
+    def find_peaks(self, order_by="prominences"):
+        sinty = self.inty
+        p = []
+        if len(sinty) > 5:
+            # smooth
+            # sinty = savgol_filter(sinty, window_length=7, polyorder=2)
+            p, props = find_peaks(
+                sinty,
+                prominence=(None, None),
+                height=(None, None),
+                width=(None, None),
+            )
+
+        # TODO Instance attributes defined outside __init__
+        if len(p) == 0:
+            self.feature_apex = None
+            self.feature_coherence = 0.0
+            self.peak_rts = np.array([])
+            self.peak_heights = np.array([])
+            self.peak_prominences = np.array([])
+            self.peak_widths = np.array([])
+            self.peak_left_bases = np.array([])
+            self.peak_right_bases = np.array([])
+        else:
+            prt = self.rt[p]
+            # remove prt with prt < c['feature_start'] or prt > c['feature_end']
+            mask = (prt >= self.feature_start) & (prt <= self.feature_end)
+            # apply mask to all arrays in props
+            if mask.any():
+                for key in props:
+                    if isinstance(props[key], np.ndarray):
+                        props[key] = props[key][mask]
+                # order peaks by the specified order
+                p = p[mask]
+                prt = prt[mask]
+            if order_by in props:
+                # descending order
+                order = np.argsort(props[order_by])[::-1]
+            else:
+                order = np.arange(len(prt))
+
+            # add to self
+            self.feature_apex = prt[order[0]]
+            self.feature_coherence = 0.0
+            self.peak_rts = prt[order]
+            self.peak_heights = self.inty[p][order]
+            self.peak_prominences = peak_prominences(self.inty, p)[0][order]
+            self.peak_widths = props["widths"][order]
+            self.peak_left_bases = self.rt[props["left_bases"][order]]
+            self.peak_right_bases = self.rt[props["right_bases"][order]]
+            self.feature_start = self.peak_left_bases[0]
+            self.feature_end = self.peak_right_bases[0]
+
+            # select inty for rt between feature_start and feature_end
+            mask = (
+                (self.rt >= self.feature_start)
+                & (self.rt <= self.feature_end)
+                & (self.rt >= self.feature_apex - 4)
+                & (self.rt <= self.feature_apex + 4)
+            )
+
+            sinty = sinty[mask]
+            # calculate how many times the derivative of self.inty crosses zero
+            if len(sinty) > 3:
+                self.feature_coherence = 1 - np.sum(
+                    np.diff(np.sign(np.diff(sinty))) != 0,
+                ) / (len(sinty) - 3)
+        return self
+
+    def integrate(self):
+        """
+        Integrate the chromatogram between feature_start and feature_end.
+        """
+        if self.feature_start is None or self.feature_end is None:
+            raise ValueError(
+                "feature_start and feature_end must be set before integration",
+            )
+
+        # At this point, mypy knows feature_start and feature_end are not None
+        mask = (self.rt >= self.feature_start) & (self.rt <= self.feature_end)
+        area_result = np.trapezoid(self.inty[mask], self.rt[mask])
+        self.feature_area = float(area_result)
+        if self.bl is not None:
+            # subtract baseline
+            self.feature_area -= self.bl * (self.feature_end - self.feature_start)
+        if self.feature_area < 0:
+            self.feature_area = 0.0
+
+    def get_area(self):
+        """
+        Get the area of the chromatogram between feature_start and feature_end.
+        If the area is not calculated, it will be calculated first.
+        """
+        if self.feature_area is None:
+            self.integrate()
+        return self.feature_area