Move to alphatims

alpharaw/dia/normal_dia.py

@@ -2,11 +2,10 @@
 from collections import defaultdict
 
 import numpy as np
+from alphatims.alphatims_wrapper import convert_to_alphatims, remove_unused_peaks
 from alphatims.bruker import TimsTOF
 
 from alpharaw.ms_data_base import MSData_Base
-from alpharaw.utils.df_processing import remove_unused_peaks
-from alpharaw.utils.timstof import convert_to_alphatims
 
 
 class NormalDIAGrouper:

alpharaw/utils/df_processing.py

@@ -1,47 +1,7 @@
-from typing import Tuple
+"""Deprecated functions for processing dataframes in alpharaw."""
 
-import pandas as pd
-from alphabase.peptide.fragment import (
-    compress_fragment_indices,
-    remove_unused_fragments,
-)
 
-
-def remove_unused_peaks(
-    spectrum_df: pd.DataFrame,
-    peak_df: pd.DataFrame,
-) -> Tuple[pd.DataFrame, pd.DataFrame]:
-    """Removes unused peaks of removed spectra,
-    reannotates the peak_start_idx and peak_stop_idx
-
-    Parameters
-    ----------
-    spectrum_df : pd.DataFrame
-        Spectrum dataframe which contains peak_start_idx and peak_stop_idx columns
-
-    peak_df : pd.DataFrame
-        The peak dataframe which should be compressed by removing unused peaks.
-
-    Returns
-    -------
-    pd.DataFrame, pd.DataFrame
-        The reindexed spectrum DataFrame and the sliced peak DataFrame
-    """
-
-    spectrum_df, (peak_df,) = remove_unused_fragments(
-        spectrum_df,
-        (peak_df,),
-        frag_start_col="peak_start_idx",
-        frag_stop_col="peak_stop_idx",
+def remove_unused_peaks(*args, **kwargs):
+    raise DeprecationWarning(
+        "remove_unused_peaks has been moved to alphatims and will be removed from alpharaw in a future version."
     )
-    return spectrum_df, peak_df
-
-    spectrum_df = spectrum_df.sort_values(["peak_start_idx"], ascending=True)
-    frag_idx = spectrum_df[["peak_start_idx", "peak_stop_idx"]].values
-
-    new_frag_idx, fragment_pointer = compress_fragment_indices(frag_idx)
-
-    spectrum_df[["peak_start_idx", "peak_stop_idx"]] = new_frag_idx
-    spectrum_df = spectrum_df.sort_index()
-
-    return (spectrum_df, peak_df.iloc[fragment_pointer].copy().reset_index(drop=True))

alpharaw/utils/timstof.py

@@ -1,37 +1,7 @@
-import typing
+"""Deprecated functions for converting to alphatims format."""
 
-import pandas as pd
-from alphatims.bruker import TimsTOF
 
-from alpharaw.ms_data_base import MSData_Base
-from alpharaw.utils.df_processing import remove_unused_peaks
-from alpharaw.wrappers.alphatims_wrapper import AlphaTimsWrapper
-
-
-def convert_to_alphatims(
-    spec_df: pd.DataFrame,
-    peak_df: pd.DataFrame,
-    dda: bool = False,
-) -> typing.Tuple[MSData_Base, TimsTOF]:
-    """
-    Convert any spectrum dataframe or sliced spectrum dataframe
-    and its peak dataframe into AlphaTims' TimsTOF object (AlphaTimsWrapper).
-
-    Args:
-        spec_df (pd.DataFrame):
-            spectrum dataframe or sliced spectrum dataframe in AlphaRaw's format.
-        peak_df (pd.DataFrame):
-            peak dataframe in AlphaRaw's format by removing unused peaks in spec_df.
-        dda (bool):
-            if dda data.
-
-    Returns:
-        MSData_Base: AlphaRaw object
-        TimsTOF: AlphaTims' TimsTOF object (AlphaTimsWrapper).
-    """
-    spec_df, peak_df = remove_unused_peaks(spec_df, peak_df)
-    ms_data = MSData_Base()
-    ms_data.spectrum_df = spec_df
-    ms_data.peak_df = peak_df
-
-    return ms_data, AlphaTimsWrapper(ms_data, dda=dda)
+def convert_to_alphatims(*args, **kwargs):
+    raise DeprecationWarning(
+        "convert_to_alphatims has been moved to alphatims and will be removed from alpharaw in a future version."
+    )

alpharaw/viz/plot_utils.py

@@ -1,9 +1,6 @@
-import typing
-
 import numpy as np
 import pandas as pd
 import plotly.graph_objects as go
-from alphatims.bruker import TimsTOF
 
 
 def plot_scatter(
@@ -52,138 +49,15 @@ def plot_scatter(
     )
 
 
-alphatims_labels = {
-    "rt": "rt_values",
-    "im": "mobility_values",
-}
-
-
-def plot_line_tims(
-    tims_data: TimsTOF,
-    tims_raw_indices: np.ndarray,
-    tims_view_indices: np.array,
-    name: str,
-    legend_group: str,
-    marker_color: str,
-    view_dim: typing.Literal["rt", "im"] = "rt",  # or 'im'
-    intensity_scale: float = 1.0,
-    rt_unit: str = "minute",
-) -> go.Figure:
-    """
-    Plot an XIC line on alphatims `TimsTOF` data
-
-    Parameters
-    ----------
-    tims_data : TimsTOF
-        The alphatims `TimsTOF` object
-    tims_raw_indices : np.ndarray
-        Raw indices on `TimsTOF` object
-    tims_view_indices : np.array
-        View indices on `TimsTOF` object
-    name : str
-        Display name
-    legend_group : str
-        Lines will be grouped by `legend_group`
-    marker_color : str
-        Color of the scatter (x, y)
-    view_dim : "rt", "im", optional
-        View dimension, "rt" or "im", by default "rt"
-    rt_unit : str, optional
-        RT unit, by default "minute"
-
-    Returns
-    -------
-    go.Figure
-        Line plot
-    """
-    x_dimension = alphatims_labels[view_dim]
-
-    intensities = tims_data.bin_intensities(tims_raw_indices, [x_dimension])
-    if view_dim == "rt":
-        x_ticks = tims_data.rt_values[tims_view_indices]
-        intensities = intensities[tims_view_indices]
-        if rt_unit == "minute":
-            x_ticks /= 60.0
-    else:
-        x_ticks = tims_data.mobility_values[tims_view_indices]
-        intensities = intensities[tims_view_indices]
-
-    return plot_line(
-        x_ticks,
-        intensities * intensity_scale,
-        name=name,
-        marker_color=marker_color,
-        legend_group=legend_group,
-        x_text=view_dim.upper(),
+def plot_line_tims(*args, **kwargs) -> go.Figure:
+    raise DeprecationWarning(
+        "plot_line_tims has been moved to alphaviz and will be removed from alpharaw in a future version."
     )
 
 
-def plot_line_tims_fast(
-    tims_data: TimsTOF,
-    tims_raw_indices: np.ndarray,
-    tims_view_indices: np.array,
-    name: str,
-    legend_group: str,
-    marker_color: str,
-    view_dim: typing.Literal["rt", "im"] = "rt",
-    intensity_scale: float = 1.0,
-    rt_unit: str = "minute",
-    add_peak_area=True,
-) -> go.Figure:
-    """
-    Plot an XIC line on alphatims `TimsTOF` data
-
-    Parameters
-    ----------
-    tims_data : TimsTOF
-        The alphatims `TimsTOF` object
-    tims_raw_indices : np.ndarray
-        Raw indices on `TimsTOF` object
-    tims_view_indices : np.array
-        View indices on `TimsTOF` object
-    name : str
-        Display name
-    legend_group : str
-        Lines will be grouped by `legend_group`
-    marker_color : str
-        Color of the scatter (x, y)
-    view_dim : "rt", "im", optional
-        View dimension, "rt" or "im", by default "rt"
-    intensity_scale : float, optional
-        Intensity scale of mirror plot, by default 1.0
-    rt_unit : str, optional
-        RT unit, by default "minute"
-    add_peak_area : bool, optional
-        If add peak area in the hover text, by default True
-
-    Returns
-    -------
-    go.Figure
-        _description_
-    """
-    x_dimension = alphatims_labels[view_dim]
-
-    intensities = tims_data.bin_intensities(tims_raw_indices, [x_dimension])
-    if view_dim == "rt":
-        x_ticks = tims_data.rt_values[tims_view_indices]
-        intensities = intensities[tims_view_indices]
-        if rt_unit == "minute":
-            x_ticks /= 60.0
-    else:
-        x_ticks = tims_data.mobility_values[tims_view_indices]
-        intensities = intensities[tims_view_indices]
-
-    if add_peak_area:
-        peak_area = abs(np.trapz(y=intensities, x=x_ticks))
-
-    return plot_line(
-        x_ticks,
-        intensities * intensity_scale,
-        name=name,
-        marker_color=marker_color,
-        legend_group=legend_group,
-        x_text=view_dim.upper(),
-        other_info=f"Peak area: {peak_area:.2e}" if add_peak_area else "",
+def plot_line_tims_fast(*args, **kwargs) -> go.Figure:
+    raise DeprecationWarning(
+        "plot_line_tims_fast has been moved to alphaviz and will be removed from alpharaw in a future version."
     )