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

masster/sample/save.py

@@ -1,736 +1,737 @@
-"""
-_export.py
-
-This module provides data export functionality for mass spectrometry analysis results.
-It handles saving processed data in various formats for downstream analysis, sharing,
-and archival purposes, including spectrum files, feature tables, and custom formats.
-
-Key Features:
-- **Multi-Format Export**: Save data as MGF, mzML, CSV, FeatureXML, and custom formats.
-- **Spectrum Export**: Export MS/MS spectra for database searching and identification.
-- **Feature Export**: Save detected features with quantitative information.
-- **Custom Formats**: Support for compressed pickle formats (mzpkl) for fast storage.
-- **Metadata Preservation**: Maintain acquisition parameters and processing history.
-- **Batch Export**: Export multiple samples or studies simultaneously.
-
-Dependencies:
-- `pyopenms`: For standard mass spectrometry file format export.
-- `polars` and `pandas`: For tabular data export and manipulation.
-- `numpy`: For numerical array operations.
-- `pickle` and `bz2`: For custom format compression and serialization.
-- `loguru`: For logging export operations and error handling.
-
-Functions:
-- `save()`: Main export function with format detection.
-- `save_mzpkl()`: Export to compressed pickle format for fast loading.
-- `save_featureXML()`: Export features in OpenMS FeatureXML format.
-- `export_mgf()`: Export MS/MS spectra in MGF format for database searching.
-- `export_csv()`: Export features and metadata in CSV format.
-
-Supported Export Formats:
-- MGF (Mascot Generic Format) for MS/MS spectra
-- mzML (open standard format) for spectral data
-- CSV for tabular feature data
-- FeatureXML (OpenMS format) for feature data
-- mzpkl (custom compressed format) for complete analysis results
-
-Example Usage:
-```python
-from _export import save, export_mgf
-
-# Save complete analysis in custom format
-save(self, filename="analysis_results.mzpkl")
-
-# Export MS/MS spectra for database searching
-export_mgf(self, filename="ms2_spectra.mgf", export_type="all")
-
-# Export feature table
-export_csv(self, filename="features.csv", data_type="features")
-```
-
-See Also:
-- `parameters._export_parameters`: For export-specific parameter configuration.
-- `_import.py`: For data import functionality.
-- `single.py`: For using export methods with ddafile class.
-
-"""
-
-import os
-
-from datetime import datetime
-
-import numpy as np
-import pandas as pd
-import polars as pl
-import pyopenms as oms
-
-from tqdm import tqdm
-
-# Parameters removed - using hardcoded defaults
-from masster.spectrum import combine_peaks
-
-
-def save(self, filename=None):
-    """
-    Save the current object to a file in the '.sample5' format.
-
-    If `filename` is not provided, the method attempts to use `self.file_path` as the base name,
-    replacing its extension with '.sample5'. If neither `filename` nor `self.file_path` is available,
-    a ValueError is raised.
-
-    If `filename` is provided and `self.file_path` is an absolute path, the extension of `filename`
-    is replaced with '.sample5'. Otherwise, if `self.file_path` is available, its extension is replaced
-    with '.sample5'. If neither is available, a ValueError is raised.
-
-    Parameters:
-        filename (str, optional): The name of the file to save to. If not provided, uses `self.file_path`.
-
-    Returns:
-        None
-    """
-    if filename is None:
-        # save to default file name
-        if self.file_path is not None:
-            filename = os.path.splitext(self.file_path)[0] + ".sample5"
-        else:
-            raise ValueError("either filename or file_path must be provided")
-    else:
-        # check if filename includes an absolute path
-        if os.path.isabs(self.file_path):
-            filename = os.path.splitext(filename)[0] + ".sample5"
-        elif self.file_path is not None:
-            filename = os.path.splitext(self.file_path)[0] + ".sample5"
-        else:
-            raise ValueError("either filename or file_path must be provided")
-    self._save_sample5(filename=filename)
-
-
-def _save_featureXML(self, filename="features.featureXML"):
-    if self.features is None:
-        self.logger.warning("No features found.")
-        return
-    fh = oms.FeatureXMLFile()
-    fh.store(filename, self.features)
-    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.
-
-    This method clones the internal features DataFrame, adds a boolean column 'has_ms2' indicating
-    whether the 'ms2_scans' column is not null, and exports the resulting DataFrame to the specified file.
-    Columns with data types 'List' or 'Object' are excluded from the export.
-
-    Parameters:
-        filename (str): The path to the output file. If the filename ends with '.xls' or '.xlsx',
-                        the data is exported in Excel format; otherwise, it is exported as CSV.
-                        Defaults to 'features.csv'.
-
-    Side Effects:
-        Writes the exported data to the specified file and logs the export operation.
-    """
-    # clone df
-    clean_df = self.features_df.clone()
-    filename = os.path.abspath(filename)
-    # add a column has_ms2=True if colum 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")
-        )
-    clean_df = self.features_df.select([
-        col for col in self.features_df.columns if self.features_df[col].dtype not in (pl.List, pl.Object)
-    ])
-    if filename.lower().endswith((".xls", ".xlsx")):
-        clean_df.to_pandas().to_excel(filename, index=False)
-        self.logger.info(f"Features exported to {filename} (Excel format)")
-    else:
-        clean_df.write_csv(filename)
-        self.logger.info(f"Features exported to {filename}")
-
-
-def export_mgf(
-    self,
-    filename: str = "features.mgf",
-    use_cache=True,
-    selection="best",
-    split_energy=True,
-    merge=False,
-    mz_start=None,
-    mz_end=None,
-    rt_start=None,
-    rt_end=None,
-    include_all_ms1=False,
-    full_ms1=False,
-    centroid=True,
-    inty_min=float("-inf"),
-    q1_ratio_min=None,
-    q1_ratio_max=None,
-    eic_corr_min=None,
-    deisotope=True,
-    precursor_trim=10.0,
-    centroid_algo=None,
-):
-    """
-    Export features as an MGF file with MS1 and MS2 spectra.
-
-    Iterates over all features in `self.features_df` (or `self.features` if the former is None),
-    retrieves the corresponding MS1 and MS2 spectra, applies peak filtering, and writes them in MGF format.
-
-    Args:
-        filename (str, optional): Output MGF file name. Defaults to "features.mgf".
-        use_cache (bool, optional): Use cached MS2 spectra from the features DataFrame. Defaults to False.
-        selection (str, optional): "best" for first scan, "all" for every scan. Defaults to "best".
-        split_energy (bool, optional): Process MS2 scans by unique energy. Defaults to False.
-        merge (bool, optional): If selection="all", merge MS2 scans into one spectrum. Defaults to False.
-        mz_start (float, optional): Minimum m/z for feature selection.
-        mz_end (float, optional): Maximum m/z for feature selection.
-        rt_start (float, optional): Minimum RT for feature selection.
-        rt_end (float, optional): Maximum RT for feature selection.
-        include_all_ms1 (bool, optional): Include MS1 spectra even if no MS2 scan. Defaults to False.
-        full_ms1 (bool, optional): Export full MS1 spectrum or trim around precursor. Defaults to False.
-        centroid (bool, optional): Centroid the spectrum. Defaults to True.
-        inty_min (float, optional): Minimum intensity threshold for peaks.
-        q1_ratio_min (float, optional): Minimum q1_ratio for peaks.
-        q1_ratio_max (float, optional): Maximum q1_ratio for peaks.
-        eic_corr_min (float, optional): Minimum EIC correlation for peaks.
-        deisotope (bool, optional): Perform deisotoping. Defaults to True.
-        verbose (bool, optional): Print summary after export. Defaults to False.
-        precursor_trim (int, optional): Trimming parameter for precursor peaks. Defaults to -10.
-        centroid_algo (str, optional): Centroiding algorithm to use.
-
-    Returns:
-        None
-
-    Notes:
-        - If neither `self.features_df` nor `self.features` are available, the method logs a warning and returns.
-        - Uses internal helpers for peak filtering and MGF formatting.
-        - For each feature, writes MS1 spectrum first, then MS2 spectra if available.
-    """
-
-    if self.features_df is None:
-        if self.features is None:
-            self.logger.warning("Please find features first.")
-            return
-        else:
-            self.features_df = self.features.get_df()
-    
-    # Apply filtering at DataFrame level for better performance
-    features = self.features_df
-    if mz_start is not None:
-        features = features.filter(pl.col("mz") >= mz_start)
-    if mz_end is not None:
-        features = features.filter(pl.col("mz") <= mz_end)
-    if rt_start is not None:
-        features = features.filter(pl.col("rt") >= rt_start)
-    if rt_end is not None:
-        features = features.filter(pl.col("rt") <= rt_end)
-    if not include_all_ms1:
-        features = features.filter(pl.col("ms2_scans").is_not_null())
-    
-    # Convert to list of dictionaries for faster iteration
-    features_list = features.to_dicts()
-
-    def filter_peaks(spec, inty_min=None, q1_min=None, eic_min=None, q1_max=None):
-        # create a copy of the spectrum
-        spec = spec.copy()
-        spec_len = len(spec.mz)
-        mask = [True] * spec_len
-        if inty_min is not None and inty_min > 0:
-            mask = np.array(mask) & (spec.inty >= inty_min)
-        # check if q1_ratio is an attribute of spec
-        if q1_min is not None and hasattr(spec, "q1_ratio"):
-            mask = mask & (spec.q1_ratio >= q1_min)
-        # check if eic_corr is an attribute of spec
-        if q1_max is not None and hasattr(spec, "q1_ratio"):
-            mask = mask & (spec.q1_ratio <= q1_max)
-        # check if eic_corr is an attribute of spec
-        if eic_min is not None and hasattr(spec, "eic_corr"):
-            mask = mask & (spec.eic_corr >= eic_min)
-        # apply mask to all attributes of spec with the same length as mz
-        for attr in spec.__dict__:
-            # check it attr is a list or an array:
-            if isinstance(getattr(spec, attr), list) or isinstance(
-                getattr(spec, attr),
-                np.ndarray,
-            ):
-                # check if attr has attribute 0 and its length is equal to spec_len:
-                if hasattr(getattr(spec, attr), "__len__"):
-                    if len(getattr(spec, attr)) == spec_len:
-                        setattr(spec, attr, getattr(spec, attr)[mask])
-        return spec
-
-    def write_ion(f, title, fid, mz, rt, charge, spect):
-        if spect is None:
-            return
-        f.write(f"BEGIN IONS\nTITLE={title}\n")
-        f.write(f"FEATURE_ID={fid}\n")
-        f.write(f"CHARGE={charge}\nPEPMASS={mz}\nRTINSECONDS={rt}\n")
-        if spect.ms_level is None:
-            f.write("MSLEVEL=1\n")
-        else:
-            f.write(f"MSLEVEL={spect.ms_level}\n")
-        if spect.ms_level is not None:
-            if spect.ms_level > 1 and hasattr(spect, "energy"):
-                f.write(f"ENERGY={spect.energy}\n")
-        # Use list comprehension for better performance
-        peak_lines = [f"{mz_val:.5f} {inty_val:.0f}\n" for mz_val, inty_val in zip(spect.mz, spect.inty, strict=False)]
-        f.writelines(peak_lines)
-        f.write("END IONS\n\n")
-
-    if centroid_algo is None:
-        if hasattr(self.parameters, "centroid_algo"):
-            centroid_algo = self.parameters.centroid_algo
-        else:
-            centroid_algo = "cr"
-
-    # count how many features have charge < 0
-    if self.features_df.filter(pl.col("charge") < 0).shape[0]- self.features_df.filter(pl.col("charge") > 0).shape[0] > 0:
-        preferred_charge = -1
-    else:
-        preferred_charge = 1
-
-    c = 0
-    skip = 0
-    # check if features is empty
-    if len(features_list) == 0:
-        self.logger.warning("No features found.")
-        return
-    filename = os.path.abspath(filename)
-    with open(filename, "w", encoding="utf-8") as f:
-        tdqm_disable = self.log_level not in ["TRACE", "DEBUG", "INFO"]
-        for row in tqdm(
-            features_list,
-            total=len(features_list),
-            desc=f"{datetime.now().strftime('%Y-%m-%d %H:%M:%S.%f')[:-3]} | INFO     | {self.log_label}Export MGF",
-            disable=tdqm_disable,
-        ):
-            # Pre-calculate common values
-            feature_uid = row["feature_uid"]
-            mz = row["mz"]
-            rt = row["rt"]
-            rt_str = f"{rt:.2f}"
-            mz_str = f"{mz:.4f}"
-            
-            # Filtering is now done at DataFrame level, so we can skip these checks
-            if row["ms2_scans"] is None and not include_all_ms1:
-                skip = skip + 1
-                continue
-
-            # write MS1 spectrum
-            ms1_scan_uid = self.find_closest_scan(rt=rt)["scan_uid"]
-            spect = self.get_spectrum(
-                ms1_scan_uid,
-                centroid=centroid,
-                deisotope=deisotope,
-                centroid_algo=centroid_algo,
-            )
-
-            spect = filter_peaks(spect, inty_min=inty_min)
-
-            if not full_ms1:
-                # trim spectrum to region around the precursor, it's wide to potentially identify adducts
-                spect = spect.trim(
-                    mz_min=mz - 50,
-                    mz_max=mz + 50,
-                )
-
-            charge = preferred_charge
-            if row["charge"] is not None and row["charge"] != 0:
-                    charge = row["charge"]
-
-            write_ion(
-                f,
-                f"feature_uid:{feature_uid}, rt:{rt_str}, mz:{mz_str}",
-                feature_uid,
-                mz,
-                rt,
-                charge,
-                spect,
-            )
-
-            if row["ms2_scans"] is None:
-                continue
-            elif use_cache:
-                spect = row["ms2_specs"]
-                if spect is None:
-                    # No cached spectra, fall through to fetch from scan_uid
-                    use_cache = False
-                else:
-                    # check if spec is a list of spectra
-                    if isinstance(spect, list):
-                        if selection == "best":
-                            s = spect[0]
-                            scan_uid = row["ms2_scans"][0]
-                            s.energy = self.get_spectrum(scan_uid).energy
-                            spect = [s]
-                            scan_uids = [scan_uid]
-                        else:
-                            scan_uids = row["ms2_scans"]
-
-                        for i, s in enumerate(spect):
-                            if s is None:
-                                print(
-                                    f"No MS2 spectrum for feature {feature_uid} is cached.",
-                                )
-                                continue
-                            # check if s is a spectrum
-                            if type(s).__name__ == "Spectrum":
-                                s = filter_peaks(
-                                    s,
-                                    inty_min=inty_min,
-                                    q1_min=q1_ratio_min,
-                                    eic_min=eic_corr_min,
-                                    q1_max=q1_ratio_max,
-                                )
-                                # Get the corresponding scan_uid from the list
-                                current_scan_uid = scan_uids[i] if i < len(scan_uids) else "unknown"
-                                write_ion(
-                                    f,
-                                    f"fid:{feature_uid}, rt:{rt_str}, mz:{mz_str}, scan_uid:{current_scan_uid}",
-                                    feature_uid,
-                                    mz,
-                                    rt,
-                                    charge,
-                                    s,
-                                )
-                                c += 1
-                        continue  # Skip the rest of the processing for this feature
-            
-            # If we reach here, either use_cache=False or no cached spectra were available
-            if split_energy:
-                # get energy of all scans with scan_uid in ms2_scans by fetching them
-                ms2_scan_uids = row["ms2_scans"]
-                if isinstance(ms2_scan_uids, list) and len(ms2_scan_uids) > 0:
-                    # Fetch spectra to get energy information
-                    spectra_with_energy = []
-                    for scan_uid in ms2_scan_uids:
-                        spec = self.get_spectrum(scan_uid)
-                        if spec is not None:
-                            spectra_with_energy.append((scan_uid, spec.energy if hasattr(spec, 'energy') else 0))
-                    
-                    # Group by energy
-                    energy_groups: dict[float, list[int]] = {}
-                    for scan_uid, energy in spectra_with_energy:
-                        if energy not in energy_groups:
-                            energy_groups[energy] = []
-                        energy_groups[energy].append(scan_uid)
-                    
-                    for energy, scan_uids_for_energy in energy_groups.items():
-                        if selection == "best":
-                            # Keep only the first scan for this energy
-                            scan_uids_for_energy = [scan_uids_for_energy[0]]
-                        
-                        for scan_uid in scan_uids_for_energy:
-                            spect = self.get_spectrum(
-                                scan_uid,
-                                centroid=centroid,
-                                deisotope=deisotope,
-                                precursor_trim=precursor_trim,
-                                centroid_algo=centroid_algo,
-                            )
-                            spect = filter_peaks(
-                                spect,
-                                inty_min=inty_min,
-                                q1_min=q1_ratio_min,
-                                eic_min=eic_corr_min,
-                                q1_max=q1_ratio_max,
-                            )
-                            write_ion(
-                                f,
-                                f"fid:{feature_uid}, rt:{rt_str}, mz:{mz_str}, scan_uid:{scan_uid}, energy:{energy}",
-                                feature_uid,
-                                mz,
-                                rt,
-                                charge,
-                                spect,
-                            )
-                            c += 1
-            else:
-                if selection == "best":
-                    ms2_scans = row["ms2_scans"][0]
-                    spect = self.get_spectrum(
-                        ms2_scans,
-                        centroid=centroid,
-                        deisotope=deisotope,
-                        precursor_trim=precursor_trim,
-                        centroid_algo=centroid_algo,
-                    )
-                    spect = filter_peaks(
-                        spect,
-                        inty_min=inty_min,
-                        q1_min=q1_ratio_min,
-                        eic_min=eic_corr_min,
-                        q1_max=q1_ratio_max,
-                    )
-                    write_ion(
-                        f,
-                        f"fid:{feature_uid}, rt:{rt_str}, mz:{mz_str}, scan_uid:{ms2_scans}",
-                        feature_uid,
-                        mz,
-                        rt,
-                        charge,
-                        spect,
-                    )
-                    c += 1
-                elif selection == "all":
-                    if merge:
-                        specs = []
-                        for ms2_scans in row["ms2_scans"]:
-                            specs.append(
-                                self.get_spectrum(
-                                    ms2_scans,
-                                    centroid=centroid,
-                                    deisotope=deisotope,
-                                    precursor_trim=precursor_trim,
-                                ),
-                            )
-                        spect = combine_peaks(specs)
-                        if centroid:
-                            spect = spect.denoise()
-                            if spect.ms_level == 1:
-                                spect = spect.centroid(
-                                    tolerance=self.parameters["mz_tol_ms1_da"],
-                                    ppm=self.parameters["mz_tol_ms1_ppm"],
-                                    min_points=self.parameters["centroid_min_points_ms1"],
-                                    algo=centroid_algo,
-                                )
-                            elif spect.ms_level == 2:
-                                spect = spect.centroid(
-                                    tolerance=self.parameters["mz_tol_ms2_da"],
-                                    ppm=self.parameters["mz_tol_ms2_ppm"],
-                                    min_points=self.parameters["centroid_min_points_ms2"],
-                                    algo=centroid_algo,
-                                )
-                        if deisotope:
-                            spect = spect.deisotope()
-                        title = f"fid:{feature_uid}, rt:{rt_str}, mz:{mz_str}, merged"
-                        spect = filter_peaks(
-                            spect,
-                            inty_min=inty_min,
-                            q1_min=q1_ratio_min,
-                            eic_min=eic_corr_min,
-                            q1_max=q1_ratio_max,
-                        )
-                        write_ion(
-                            f,
-                            title,
-                            feature_uid,
-                            mz,
-                            rt,
-                            charge,
-                            spect,
-                        )
-                        c += 1
-                    else:
-                        for ms2_scans in row["ms2_scans"]:
-                            spect = self.get_spectrum(
-                                ms2_scans,
-                                centroid=centroid,
-                                deisotope=deisotope,
-                                precursor_trim=precursor_trim,
-                                centroid_algo=centroid_algo,
-                            )
-                            spect = filter_peaks(
-                                spect,
-                                inty_min=inty_min,
-                                q1_min=q1_ratio_min,
-                                eic_min=eic_corr_min,
-                                q1_max=q1_ratio_max,
-                            )
-                            write_ion(
-                                f,
-                                f"fid:{feature_uid}, rt:{rt_str}, mz:{mz_str}, scan_uid:{ms2_scans}",
-                                feature_uid,
-                                mz,
-                                rt,
-                                charge,
-                                spect,
-                            )
-                            c += 1
-
-    self.logger.info(f"Exported {c} features to {filename}")
-
-    # Handle None values in logging
-    inty_min_str = f"{inty_min:.3f}" if inty_min != float("-inf") else "None"
-    q1_ratio_min_str = f"{q1_ratio_min:.3f}" if q1_ratio_min is not None else "None"
-    eic_corr_min_str = f"{eic_corr_min:.3f}" if eic_corr_min is not None else "None"
-    
-    self.logger.debug(
-        f"MGF created with int>{inty_min_str}, q1_ratio>{q1_ratio_min_str}, eic_corr>{eic_corr_min_str}",
-    )
-    self.logger.debug(
-        f"- Exported {c} MS2 spectra for {len(features_list) - skip} precursors. Average spectra/feature is {c / (len(features_list) - skip + 0.000000001):.0f}",
-    )
-    self.logger.debug(
-        f"- Skipped {skip} features because no MS2 scans were available.",
-    )
-
-
-def export_dda_stats(self, filename="stats.csv"):
-    """
-    Save DDA statistics into a CSV file.
-
-    This method computes basic statistics from the DDA analysis, such as:
-        - Total number of MS1 scans.
-        - Total number of MS2 scans.
-        - Total number of detected features.
-        - Number of features linked with MS2 data.
-        - Average cycle time (if available in the scans data).
-
-    The resulting statistics are saved in CSV format.
-
-    Parameters:
-        filename (str): The name/path of the CSV file to be saved. Defaults to "stats.csv".
-
-    Returns:
-        None
-    """
-    # Compute counts from scans_df and features_df
-    ms1_count = len(self.scans_df.filter(pl.col("ms_level") == 1))
-    ms2_count = len(self.scans_df.filter(pl.col("ms_level") == 2))
-    features_count = len(self.features_df) if self.features_df is not None else 0
-    features_with_ms2 = (
-        self.features_df.filter(pl.col("ms2_scans").is_not_null()).height if self.features_df is not None else 0
-    )
-
-    # Initialize a dictionary to hold statistics
-    stats = {
-        "MS1_scans": ms1_count,
-        "MS2_scans": ms2_count,
-        "Total_features": features_count,
-        "Features_with_MS2": features_with_ms2,
-    }
-
-    # Calculate the average cycle time if available.
-    if "time_cycle" in self.scans_df.columns:
-        ms1_df = self.scans_df.filter(pl.col("ms_level") == 1)
-        avg_cycle_time = ms1_df["time_cycle"].mean()
-        stats["Average_cycle_time"] = avg_cycle_time if avg_cycle_time is not None else ""
-    else:
-        stats["Average_cycle_time"] = 0
-
-    # Convert stats dict to a Pandas DataFrame and save as CSV.
-    df_stats = pd.DataFrame(list(stats.items()), columns=["Metric", "Value"])
-    df_stats.to_csv(filename, index=False)
-    lines = []
-    lines.append(f"Filename,{self.file_path}")
-    lines.append(
-        f"Number of cycles,{len(self.scans_df.filter(pl.col('ms_level') == 1))}",
-    )
-    lines.append(
-        f"Number of MS2 scans,{len(self.scans_df.filter(pl.col('ms_level') == 2))}",
-    )
-    # retrieve scans with mslevel 1 from
-    ms1 = self.scans_df.filter(pl.col("ms_level") == 1)
-    lines.append(f"Maximal number of MS2 scans per cycle (N),{ms1['ms2_n'].max()}")
-    # average number of MS2 scans per cycle, skip null values
-    ms2n_mean = ms1.filter(pl.col("ms2_n") >= 0)["ms2_n"].mean()
-    lines.append(f"Average number of MS2 scans per cycle,{ms2n_mean:.0f}")
-    lines.append(f"Maximal cycle time,{ms1['time_cycle'].max():.3f}")
-    # find spectra with ms2_n = 0
-    ms1_ms2_0 = ms1.filter(pl.col("ms2_n") == 0)
-    if len(ms1_ms2_0) > 0:
-        lines.append(
-            f"Average cycle time at MS1-only,{ms1_ms2_0['time_cycle'].mean():.3f}",
-        )
-    else:
-        lines.append("Average cycle time at MS1-only,")
-    # find spectra with ms2_n = 1
-    ms1_ms2_1 = ms1.filter(pl.col("ms2_n") == 1)
-    if len(ms1_ms2_1) > 0:
-        lines.append(
-            f"Average cycle time with 1 MS2,{ms1_ms2_1['time_cycle'].mean():.3f}",
-        )
-    else:
-        lines.append("Average cycle time with 1 MS2,")
-    # find spectra with ms2_n = 2
-    ms1_ms2_2 = ms1.filter(pl.col("ms2_n") == 2)
-    if len(ms1_ms2_2) > 0:
-        lines.append(
-            f"Average cycle time with 2 MS2,{ms1_ms2_2['time_cycle'].mean():.3f}",
-        )
-    else:
-        lines.append("Average cycle time with 2 MS2,")
-    # find spectra with ms2_n = 2
-    ms1_ms2_3 = ms1.filter(pl.col("ms2_n") == 3)
-    if len(ms1_ms2_3) > 0:
-        lines.append(
-            f"Average cycle time with 3 MS2,{ms1_ms2_3['time_cycle'].mean():.3f}",
-        )
-    else:
-        lines.append("Average cycle time with 3 MS2,")
-    max_ms2_n = ms1["ms2_n"].max()
-    ms1_ms2_n1 = ms1.filter(pl.col("ms2_n") == max_ms2_n - 1)
-    if len(ms1_ms2_n1) > 0:
-        lines.append(
-            f"Average cycle time with N-1 MS2,{ms1_ms2_n1['time_cycle'].mean():.3f}",
-        )
-    else:
-        lines.append("Average cycle time with N-1 MS2,")
-    # find specgtra with maximal ms2_n
-    ms1_max_ms2_n = ms1.filter(pl.col("ms2_n") == max_ms2_n)
-    lines.append(
-        f"Average cycle time with N MS2,{ms1_max_ms2_n['time_cycle'].mean():.3f}",
-    )
-    # average time_MS1, skip null values
-    a = ms1.filter(pl.col("time_ms1_to_ms1") >= 0)["time_ms1_to_ms1"].mean()
-    if a is not None:
-        lines.append(f"Average MS1-to-MS1 scan time,{a:.3f}")
-    else:
-        lines.append("Average MS1-to-MS1 scan time,")
-    a = ms1.filter(pl.col("time_ms1_to_ms2") >= 0)["time_ms1_to_ms2"].mean()
-    if a is not None:
-        lines.append(f"Average MS1-to-MS2 scan time,{a:.3f}")
-    else:
-        lines.append("Average MS1-to-MS2 scan time,")
-    ms2_mean = ms1.filter(pl.col("time_ms2_to_ms2") >= 0)["time_ms2_to_ms2"].mean()
-    if ms2_mean is not None:
-        lines.append(f"Average MS2-to-MS2 scan time,{ms2_mean:.3f}")
-    else:
-        lines.append("Average MS2-to-MS2 scan time,")
-    a = ms1.filter(pl.col("time_ms2_to_ms1") >= 0)["time_ms2_to_ms1"].mean()
-    if a is not None:
-        lines.append(f"Average MS2-to-MS1 scan time,{a:.3f}")
-    else:
-        lines.append("Average MS2-to-MS1 scan time,")
-    # number of features
-    if self.features_df is not None:
-        lines.append(f"Number of features,{self.features_df.height}")
-        a = self.features_df.filter(pl.col("ms2_scans").is_not_null()).height
-        lines.append(f"Number of features with MS2 data,{a}")
-        b = self.scans_df.filter(pl.col("feature_uid") >= 0).height
-        lines.append(f"Number of MS2 scans with features,{b}")
-        if a > 0:
-            lines.append(f"Redundancy of MS2 scans with features,{b / a:.3f}")
-        else:
-            lines.append("Redundancy of MS2 scans with features,")
-    else:
-        lines.append("Number of features,")
-        lines.append("Number of features with MS2 data,")
-        lines.append("Number of MS2 scans with features,")
-        lines.append("Redundancy of MS2 scans with features,")
-
-    # write to file
-    with open(filename, "w") as f:
-        for line in lines:
-            f.write(line + "\n")
-
-    self.logger.info(f"DDA statistics exported to {filename}")
-
-
-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:
-        self.logger.warning("No chromatogram definitions found.")
-        return
-    data = self.chrom_df.clone()
-    # Convert to pandas for CSV export
-    if hasattr(data, "to_pandas"):
-        data = data.to_pandas()
-    # remove scan_uid and chrom columns if they exist
-    if "scan_uid" in data.columns:
-        data = data.drop("scan_uid")
-    if "chrom" in data.columns:
-        data = data.drop("chrom")
-    data.to_csv(filename, index=False)
+"""
+_export.py
+
+This module provides data export functionality for mass spectrometry analysis results.
+It handles saving processed data in various formats for downstream analysis, sharing,
+and archival purposes, including spectrum files, feature tables, and custom formats.
+
+Key Features:
+- **Multi-Format Export**: Save data as MGF, mzML, CSV, FeatureXML, and custom formats.
+- **Spectrum Export**: Export MS/MS spectra for database searching and identification.
+- **Feature Export**: Save detected features with quantitative information.
+- **Custom Formats**: Support for compressed pickle formats (mzpkl) for fast storage.
+- **Metadata Preservation**: Maintain acquisition parameters and processing history.
+- **Batch Export**: Export multiple samples or studies simultaneously.
+
+Dependencies:
+- `pyopenms`: For standard mass spectrometry file format export.
+- `polars` and `pandas`: For tabular data export and manipulation.
+- `numpy`: For numerical array operations.
+- `pickle` and `bz2`: For custom format compression and serialization.
+- `loguru`: For logging export operations and error handling.
+
+Functions:
+- `save()`: Main export function with format detection.
+- `save_mzpkl()`: Export to compressed pickle format for fast loading.
+- `save_featureXML()`: Export features in OpenMS FeatureXML format.
+- `export_mgf()`: Export MS/MS spectra in MGF format for database searching.
+- `export_csv()`: Export features and metadata in CSV format.
+
+Supported Export Formats:
+- MGF (Mascot Generic Format) for MS/MS spectra
+- mzML (open standard format) for spectral data
+- CSV for tabular feature data
+- FeatureXML (OpenMS format) for feature data
+- mzpkl (custom compressed format) for complete analysis results
+
+Example Usage:
+```python
+from _export import save, export_mgf
+
+# Save complete analysis in custom format
+save(self, filename="analysis_results.mzpkl")
+
+# Export MS/MS spectra for database searching
+export_mgf(self, filename="ms2_spectra.mgf", export_type="all")
+
+# Export feature table
+export_csv(self, filename="features.csv", data_type="features")
+```
+
+See Also:
+- `parameters._export_parameters`: For export-specific parameter configuration.
+- `_import.py`: For data import functionality.
+- `single.py`: For using export methods with ddafile class.
+
+"""
+
+import os
+
+from datetime import datetime
+
+import numpy as np
+import pandas as pd
+import polars as pl
+import pyopenms as oms
+
+from tqdm import tqdm
+
+# Parameters removed - using hardcoded defaults
+from masster.spectrum import combine_peaks
+
+
+def save(self, filename=None):
+    """
+    Save the current object to a file in the '.sample5' format.
+
+    If `filename` is not provided, the method attempts to use `self.file_path` as the base name,
+    replacing its extension with '.sample5'. If neither `filename` nor `self.file_path` is available,
+    a ValueError is raised.
+
+    If `filename` is provided and `self.file_path` is an absolute path, the extension of `filename`
+    is replaced with '.sample5'. Otherwise, if `self.file_path` is available, its extension is replaced
+    with '.sample5'. If neither is available, a ValueError is raised.
+
+    Parameters:
+        filename (str, optional): The name of the file to save to. If not provided, uses `self.file_path`.
+
+    Returns:
+        None
+    """
+    if filename is None:
+        # save to default file name
+        if self.file_path is not None:
+            filename = os.path.splitext(self.file_path)[0] + ".sample5"
+        else:
+            raise ValueError("either filename or file_path must be provided")
+    else:
+        # check if filename includes an absolute path
+        if os.path.isabs(self.file_path):
+            filename = os.path.splitext(filename)[0] + ".sample5"
+        elif self.file_path is not None:
+            filename = os.path.splitext(self.file_path)[0] + ".sample5"
+        else:
+            raise ValueError("either filename or file_path must be provided")
+    self._save_sample5(filename=filename)
+    self.file_path = filename
+
+
+def _save_featureXML(self, filename="features.featureXML"):
+    if self.features is None:
+        self.logger.warning("No features found.")
+        return
+    fh = oms.FeatureXMLFile()
+    fh.store(filename, self.features)
+    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.
+
+    This method clones the internal features DataFrame, adds a boolean column 'has_ms2' indicating
+    whether the 'ms2_scans' column is not null, and exports the resulting DataFrame to the specified file.
+    Columns with data types 'List' or 'Object' are excluded from the export.
+
+    Parameters:
+        filename (str): The path to the output file. If the filename ends with '.xls' or '.xlsx',
+                        the data is exported in Excel format; otherwise, it is exported as CSV.
+                        Defaults to 'features.csv'.
+
+    Side Effects:
+        Writes the exported data to the specified file and logs the export operation.
+    """
+    # clone df
+    clean_df = self.features_df.clone()
+    filename = os.path.abspath(filename)
+    # add a column has_ms2=True if colum 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")
+        )
+    clean_df = self.features_df.select([
+        col for col in self.features_df.columns if self.features_df[col].dtype not in (pl.List, pl.Object)
+    ])
+    if filename.lower().endswith((".xls", ".xlsx")):
+        clean_df.to_pandas().to_excel(filename, index=False)
+        self.logger.info(f"Features exported to {filename} (Excel format)")
+    else:
+        clean_df.write_csv(filename)
+        self.logger.info(f"Features exported to {filename}")
+
+
+def export_mgf(
+    self,
+    filename: str = "features.mgf",
+    use_cache=True,
+    selection="best",
+    split_energy=True,
+    merge=False,
+    mz_start=None,
+    mz_end=None,
+    rt_start=None,
+    rt_end=None,
+    include_all_ms1=False,
+    full_ms1=False,
+    centroid=True,
+    inty_min=float("-inf"),
+    q1_ratio_min=None,
+    q1_ratio_max=None,
+    eic_corr_min=None,
+    deisotope=True,
+    precursor_trim=10.0,
+    centroid_algo=None,
+):
+    """
+    Export features as an MGF file with MS1 and MS2 spectra.
+
+    Iterates over all features in `self.features_df` (or `self.features` if the former is None),
+    retrieves the corresponding MS1 and MS2 spectra, applies peak filtering, and writes them in MGF format.
+
+    Args:
+        filename (str, optional): Output MGF file name. Defaults to "features.mgf".
+        use_cache (bool, optional): Use cached MS2 spectra from the features DataFrame. Defaults to False.
+        selection (str, optional): "best" for first scan, "all" for every scan. Defaults to "best".
+        split_energy (bool, optional): Process MS2 scans by unique energy. Defaults to False.
+        merge (bool, optional): If selection="all", merge MS2 scans into one spectrum. Defaults to False.
+        mz_start (float, optional): Minimum m/z for feature selection.
+        mz_end (float, optional): Maximum m/z for feature selection.
+        rt_start (float, optional): Minimum RT for feature selection.
+        rt_end (float, optional): Maximum RT for feature selection.
+        include_all_ms1 (bool, optional): Include MS1 spectra even if no MS2 scan. Defaults to False.
+        full_ms1 (bool, optional): Export full MS1 spectrum or trim around precursor. Defaults to False.
+        centroid (bool, optional): Centroid the spectrum. Defaults to True.
+        inty_min (float, optional): Minimum intensity threshold for peaks.
+        q1_ratio_min (float, optional): Minimum q1_ratio for peaks.
+        q1_ratio_max (float, optional): Maximum q1_ratio for peaks.
+        eic_corr_min (float, optional): Minimum EIC correlation for peaks.
+        deisotope (bool, optional): Perform deisotoping. Defaults to True.
+        verbose (bool, optional): Print summary after export. Defaults to False.
+        precursor_trim (int, optional): Trimming parameter for precursor peaks. Defaults to -10.
+        centroid_algo (str, optional): Centroiding algorithm to use.
+
+    Returns:
+        None
+
+    Notes:
+        - If neither `self.features_df` nor `self.features` are available, the method logs a warning and returns.
+        - Uses internal helpers for peak filtering and MGF formatting.
+        - For each feature, writes MS1 spectrum first, then MS2 spectra if available.
+    """
+
+    if self.features_df is None:
+        if self.features is None:
+            self.logger.warning("Please find features first.")
+            return
+        else:
+            self.features_df = self.features.get_df()
+    
+    # Apply filtering at DataFrame level for better performance
+    features = self.features_df
+    if mz_start is not None:
+        features = features.filter(pl.col("mz") >= mz_start)
+    if mz_end is not None:
+        features = features.filter(pl.col("mz") <= mz_end)
+    if rt_start is not None:
+        features = features.filter(pl.col("rt") >= rt_start)
+    if rt_end is not None:
+        features = features.filter(pl.col("rt") <= rt_end)
+    if not include_all_ms1:
+        features = features.filter(pl.col("ms2_scans").is_not_null())
+    
+    # Convert to list of dictionaries for faster iteration
+    features_list = features.to_dicts()
+
+    def filter_peaks(spec, inty_min=None, q1_min=None, eic_min=None, q1_max=None):
+        # create a copy of the spectrum
+        spec = spec.copy()
+        spec_len = len(spec.mz)
+        mask = [True] * spec_len
+        if inty_min is not None and inty_min > 0:
+            mask = np.array(mask) & (spec.inty >= inty_min)
+        # check if q1_ratio is an attribute of spec
+        if q1_min is not None and hasattr(spec, "q1_ratio"):
+            mask = mask & (spec.q1_ratio >= q1_min)
+        # check if eic_corr is an attribute of spec
+        if q1_max is not None and hasattr(spec, "q1_ratio"):
+            mask = mask & (spec.q1_ratio <= q1_max)
+        # check if eic_corr is an attribute of spec
+        if eic_min is not None and hasattr(spec, "eic_corr"):
+            mask = mask & (spec.eic_corr >= eic_min)
+        # apply mask to all attributes of spec with the same length as mz
+        for attr in spec.__dict__:
+            # check it attr is a list or an array:
+            if isinstance(getattr(spec, attr), list) or isinstance(
+                getattr(spec, attr),
+                np.ndarray,
+            ):
+                # check if attr has attribute 0 and its length is equal to spec_len:
+                if hasattr(getattr(spec, attr), "__len__"):
+                    if len(getattr(spec, attr)) == spec_len:
+                        setattr(spec, attr, getattr(spec, attr)[mask])
+        return spec
+
+    def write_ion(f, title, fid, mz, rt, charge, spect):
+        if spect is None:
+            return
+        f.write(f"BEGIN IONS\nTITLE={title}\n")
+        f.write(f"FEATURE_ID={fid}\n")
+        f.write(f"CHARGE={charge}\nPEPMASS={mz}\nRTINSECONDS={rt}\n")
+        if spect.ms_level is None:
+            f.write("MSLEVEL=1\n")
+        else:
+            f.write(f"MSLEVEL={spect.ms_level}\n")
+        if spect.ms_level is not None:
+            if spect.ms_level > 1 and hasattr(spect, "energy"):
+                f.write(f"ENERGY={spect.energy}\n")
+        # Use list comprehension for better performance
+        peak_lines = [f"{mz_val:.5f} {inty_val:.0f}\n" for mz_val, inty_val in zip(spect.mz, spect.inty, strict=False)]
+        f.writelines(peak_lines)
+        f.write("END IONS\n\n")
+
+    if centroid_algo is None:
+        if hasattr(self.parameters, "centroid_algo"):
+            centroid_algo = self.parameters.centroid_algo
+        else:
+            centroid_algo = "cr"
+
+    # count how many features have charge < 0
+    if self.features_df.filter(pl.col("charge") < 0).shape[0]- self.features_df.filter(pl.col("charge") > 0).shape[0] > 0:
+        preferred_charge = -1
+    else:
+        preferred_charge = 1
+
+    c = 0
+    skip = 0
+    # check if features is empty
+    if len(features_list) == 0:
+        self.logger.warning("No features found.")
+        return
+    filename = os.path.abspath(filename)
+    with open(filename, "w", encoding="utf-8") as f:
+        tdqm_disable = self.log_level not in ["TRACE", "DEBUG", "INFO"]
+        for row in tqdm(
+            features_list,
+            total=len(features_list),
+            desc=f"{datetime.now().strftime('%Y-%m-%d %H:%M:%S.%f')[:-3]} | INFO     | {self.log_label}Export MGF",
+            disable=tdqm_disable,
+        ):
+            # Pre-calculate common values
+            feature_uid = row["feature_uid"]
+            mz = row["mz"]
+            rt = row["rt"]
+            rt_str = f"{rt:.2f}"
+            mz_str = f"{mz:.4f}"
+            
+            # Filtering is now done at DataFrame level, so we can skip these checks
+            if row["ms2_scans"] is None and not include_all_ms1:
+                skip = skip + 1
+                continue
+
+            # write MS1 spectrum
+            ms1_scan_uid = self.select_closest_scan(rt=rt)["scan_uid"][0]
+            spect = self.get_spectrum(
+                ms1_scan_uid,
+                centroid=centroid,
+                deisotope=deisotope,
+                centroid_algo=centroid_algo,
+            )
+
+            spect = filter_peaks(spect, inty_min=inty_min)
+
+            if not full_ms1:
+                # trim spectrum to region around the precursor, it's wide to potentially identify adducts
+                spect = spect.trim(
+                    mz_min=mz - 50,
+                    mz_max=mz + 50,
+                )
+
+            charge = preferred_charge
+            if row["charge"] is not None and row["charge"] != 0:
+                    charge = row["charge"]
+
+            write_ion(
+                f,
+                f"feature_uid:{feature_uid}, rt:{rt_str}, mz:{mz_str}",
+                feature_uid,
+                mz,
+                rt,
+                charge,
+                spect,
+            )
+
+            if row["ms2_scans"] is None:
+                continue
+            elif use_cache:
+                spect = row["ms2_specs"]
+                if spect is None:
+                    # No cached spectra, fall through to fetch from scan_uid
+                    use_cache = False
+                else:
+                    # check if spec is a list of spectra
+                    if isinstance(spect, list):
+                        if selection == "best":
+                            s = spect[0]
+                            scan_uid = row["ms2_scans"][0]
+                            s.energy = self.get_spectrum(scan_uid).energy
+                            spect = [s]
+                            scan_uids = [scan_uid]
+                        else:
+                            scan_uids = row["ms2_scans"]
+
+                        for i, s in enumerate(spect):
+                            if s is None:
+                                print(
+                                    f"No MS2 spectrum for feature {feature_uid} is cached.",
+                                )
+                                continue
+                            # check if s is a spectrum
+                            if type(s).__name__ == "Spectrum":
+                                s = filter_peaks(
+                                    s,
+                                    inty_min=inty_min,
+                                    q1_min=q1_ratio_min,
+                                    eic_min=eic_corr_min,
+                                    q1_max=q1_ratio_max,
+                                )
+                                # Get the corresponding scan_uid from the list
+                                current_scan_uid = scan_uids[i] if i < len(scan_uids) else "unknown"
+                                write_ion(
+                                    f,
+                                    f"fid:{feature_uid}, rt:{rt_str}, mz:{mz_str}, scan_uid:{current_scan_uid}",
+                                    feature_uid,
+                                    mz,
+                                    rt,
+                                    charge,
+                                    s,
+                                )
+                                c += 1
+                        continue  # Skip the rest of the processing for this feature
+            
+            # If we reach here, either use_cache=False or no cached spectra were available
+            if split_energy:
+                # get energy of all scans with scan_uid in ms2_scans by fetching them
+                ms2_scan_uids = row["ms2_scans"]
+                if isinstance(ms2_scan_uids, list) and len(ms2_scan_uids) > 0:
+                    # Fetch spectra to get energy information
+                    spectra_with_energy = []
+                    for scan_uid in ms2_scan_uids:
+                        spec = self.get_spectrum(scan_uid)
+                        if spec is not None:
+                            spectra_with_energy.append((scan_uid, spec.energy if hasattr(spec, 'energy') else 0))
+                    
+                    # Group by energy
+                    energy_groups: dict[float, list[int]] = {}
+                    for scan_uid, energy in spectra_with_energy:
+                        if energy not in energy_groups:
+                            energy_groups[energy] = []
+                        energy_groups[energy].append(scan_uid)
+                    
+                    for energy, scan_uids_for_energy in energy_groups.items():
+                        if selection == "best":
+                            # Keep only the first scan for this energy
+                            scan_uids_for_energy = [scan_uids_for_energy[0]]
+                        
+                        for scan_uid in scan_uids_for_energy:
+                            spect = self.get_spectrum(
+                                scan_uid,
+                                centroid=centroid,
+                                deisotope=deisotope,
+                                precursor_trim=precursor_trim,
+                                centroid_algo=centroid_algo,
+                            )
+                            spect = filter_peaks(
+                                spect,
+                                inty_min=inty_min,
+                                q1_min=q1_ratio_min,
+                                eic_min=eic_corr_min,
+                                q1_max=q1_ratio_max,
+                            )
+                            write_ion(
+                                f,
+                                f"fid:{feature_uid}, rt:{rt_str}, mz:{mz_str}, scan_uid:{scan_uid}, energy:{energy}",
+                                feature_uid,
+                                mz,
+                                rt,
+                                charge,
+                                spect,
+                            )
+                            c += 1
+            else:
+                if selection == "best":
+                    ms2_scans = row["ms2_scans"][0]
+                    spect = self.get_spectrum(
+                        ms2_scans,
+                        centroid=centroid,
+                        deisotope=deisotope,
+                        precursor_trim=precursor_trim,
+                        centroid_algo=centroid_algo,
+                    )
+                    spect = filter_peaks(
+                        spect,
+                        inty_min=inty_min,
+                        q1_min=q1_ratio_min,
+                        eic_min=eic_corr_min,
+                        q1_max=q1_ratio_max,
+                    )
+                    write_ion(
+                        f,
+                        f"fid:{feature_uid}, rt:{rt_str}, mz:{mz_str}, scan_uid:{ms2_scans}",
+                        feature_uid,
+                        mz,
+                        rt,
+                        charge,
+                        spect,
+                    )
+                    c += 1
+                elif selection == "all":
+                    if merge:
+                        specs = []
+                        for ms2_scans in row["ms2_scans"]:
+                            specs.append(
+                                self.get_spectrum(
+                                    ms2_scans,
+                                    centroid=centroid,
+                                    deisotope=deisotope,
+                                    precursor_trim=precursor_trim,
+                                ),
+                            )
+                        spect = combine_peaks(specs)
+                        if centroid:
+                            spect = spect.denoise()
+                            if spect.ms_level == 1:
+                                spect = spect.centroid(
+                                    tolerance=self.parameters["mz_tol_ms1_da"],
+                                    ppm=self.parameters["mz_tol_ms1_ppm"],
+                                    min_points=self.parameters["centroid_min_points_ms1"],
+                                    algo=centroid_algo,
+                                )
+                            elif spect.ms_level == 2:
+                                spect = spect.centroid(
+                                    tolerance=self.parameters["mz_tol_ms2_da"],
+                                    ppm=self.parameters["mz_tol_ms2_ppm"],
+                                    min_points=self.parameters["centroid_min_points_ms2"],
+                                    algo=centroid_algo,
+                                )
+                        if deisotope:
+                            spect = spect.deisotope()
+                        title = f"fid:{feature_uid}, rt:{rt_str}, mz:{mz_str}, merged"
+                        spect = filter_peaks(
+                            spect,
+                            inty_min=inty_min,
+                            q1_min=q1_ratio_min,
+                            eic_min=eic_corr_min,
+                            q1_max=q1_ratio_max,
+                        )
+                        write_ion(
+                            f,
+                            title,
+                            feature_uid,
+                            mz,
+                            rt,
+                            charge,
+                            spect,
+                        )
+                        c += 1
+                    else:
+                        for ms2_scans in row["ms2_scans"]:
+                            spect = self.get_spectrum(
+                                ms2_scans,
+                                centroid=centroid,
+                                deisotope=deisotope,
+                                precursor_trim=precursor_trim,
+                                centroid_algo=centroid_algo,
+                            )
+                            spect = filter_peaks(
+                                spect,
+                                inty_min=inty_min,
+                                q1_min=q1_ratio_min,
+                                eic_min=eic_corr_min,
+                                q1_max=q1_ratio_max,
+                            )
+                            write_ion(
+                                f,
+                                f"fid:{feature_uid}, rt:{rt_str}, mz:{mz_str}, scan_uid:{ms2_scans}",
+                                feature_uid,
+                                mz,
+                                rt,
+                                charge,
+                                spect,
+                            )
+                            c += 1
+
+    self.logger.info(f"Exported {c} features to {filename}")
+
+    # Handle None values in logging
+    inty_min_str = f"{inty_min:.3f}" if inty_min != float("-inf") else "None"
+    q1_ratio_min_str = f"{q1_ratio_min:.3f}" if q1_ratio_min is not None else "None"
+    eic_corr_min_str = f"{eic_corr_min:.3f}" if eic_corr_min is not None else "None"
+    
+    self.logger.debug(
+        f"MGF created with int>{inty_min_str}, q1_ratio>{q1_ratio_min_str}, eic_corr>{eic_corr_min_str}",
+    )
+    self.logger.debug(
+        f"- Exported {c} MS2 spectra for {len(features_list) - skip} precursors. Average spectra/feature is {c / (len(features_list) - skip + 0.000000001):.0f}",
+    )
+    self.logger.debug(
+        f"- Skipped {skip} features because no MS2 scans were available.",
+    )
+
+
+def export_dda_stats(self, filename="stats.csv"):
+    """
+    Save DDA statistics into a CSV file.
+
+    This method computes basic statistics from the DDA analysis, such as:
+        - Total number of MS1 scans.
+        - Total number of MS2 scans.
+        - Total number of detected features.
+        - Number of features linked with MS2 data.
+        - Average cycle time (if available in the scans data).
+
+    The resulting statistics are saved in CSV format.
+
+    Parameters:
+        filename (str): The name/path of the CSV file to be saved. Defaults to "stats.csv".
+
+    Returns:
+        None
+    """
+    # Compute counts from scans_df and features_df
+    ms1_count = len(self.scans_df.filter(pl.col("ms_level") == 1))
+    ms2_count = len(self.scans_df.filter(pl.col("ms_level") == 2))
+    features_count = len(self.features_df) if self.features_df is not None else 0
+    features_with_ms2 = (
+        self.features_df.filter(pl.col("ms2_scans").is_not_null()).height if self.features_df is not None else 0
+    )
+
+    # Initialize a dictionary to hold statistics
+    stats = {
+        "MS1_scans": ms1_count,
+        "MS2_scans": ms2_count,
+        "Total_features": features_count,
+        "Features_with_MS2": features_with_ms2,
+    }
+
+    # Calculate the average cycle time if available.
+    if "time_cycle" in self.scans_df.columns:
+        ms1_df = self.scans_df.filter(pl.col("ms_level") == 1)
+        avg_cycle_time = ms1_df["time_cycle"].mean()
+        stats["Average_cycle_time"] = avg_cycle_time if avg_cycle_time is not None else ""
+    else:
+        stats["Average_cycle_time"] = 0
+
+    # Convert stats dict to a Pandas DataFrame and save as CSV.
+    df_stats = pd.DataFrame(list(stats.items()), columns=["Metric", "Value"])
+    df_stats.to_csv(filename, index=False)
+    lines = []
+    lines.append(f"Filename,{self.file_path}")
+    lines.append(
+        f"Number of cycles,{len(self.scans_df.filter(pl.col('ms_level') == 1))}",
+    )
+    lines.append(
+        f"Number of MS2 scans,{len(self.scans_df.filter(pl.col('ms_level') == 2))}",
+    )
+    # retrieve scans with mslevel 1 from
+    ms1 = self.scans_df.filter(pl.col("ms_level") == 1)
+    lines.append(f"Maximal number of MS2 scans per cycle (N),{ms1['ms2_n'].max()}")
+    # average number of MS2 scans per cycle, skip null values
+    ms2n_mean = ms1.filter(pl.col("ms2_n") >= 0)["ms2_n"].mean()
+    lines.append(f"Average number of MS2 scans per cycle,{ms2n_mean:.0f}")
+    lines.append(f"Maximal cycle time,{ms1['time_cycle'].max():.3f}")
+    # find spectra with ms2_n = 0
+    ms1_ms2_0 = ms1.filter(pl.col("ms2_n") == 0)
+    if len(ms1_ms2_0) > 0:
+        lines.append(
+            f"Average cycle time at MS1-only,{ms1_ms2_0['time_cycle'].mean():.3f}",
+        )
+    else:
+        lines.append("Average cycle time at MS1-only,")
+    # find spectra with ms2_n = 1
+    ms1_ms2_1 = ms1.filter(pl.col("ms2_n") == 1)
+    if len(ms1_ms2_1) > 0:
+        lines.append(
+            f"Average cycle time with 1 MS2,{ms1_ms2_1['time_cycle'].mean():.3f}",
+        )
+    else:
+        lines.append("Average cycle time with 1 MS2,")
+    # find spectra with ms2_n = 2
+    ms1_ms2_2 = ms1.filter(pl.col("ms2_n") == 2)
+    if len(ms1_ms2_2) > 0:
+        lines.append(
+            f"Average cycle time with 2 MS2,{ms1_ms2_2['time_cycle'].mean():.3f}",
+        )
+    else:
+        lines.append("Average cycle time with 2 MS2,")
+    # find spectra with ms2_n = 2
+    ms1_ms2_3 = ms1.filter(pl.col("ms2_n") == 3)
+    if len(ms1_ms2_3) > 0:
+        lines.append(
+            f"Average cycle time with 3 MS2,{ms1_ms2_3['time_cycle'].mean():.3f}",
+        )
+    else:
+        lines.append("Average cycle time with 3 MS2,")
+    max_ms2_n = ms1["ms2_n"].max()
+    ms1_ms2_n1 = ms1.filter(pl.col("ms2_n") == max_ms2_n - 1)
+    if len(ms1_ms2_n1) > 0:
+        lines.append(
+            f"Average cycle time with N-1 MS2,{ms1_ms2_n1['time_cycle'].mean():.3f}",
+        )
+    else:
+        lines.append("Average cycle time with N-1 MS2,")
+    # find specgtra with maximal ms2_n
+    ms1_max_ms2_n = ms1.filter(pl.col("ms2_n") == max_ms2_n)
+    lines.append(
+        f"Average cycle time with N MS2,{ms1_max_ms2_n['time_cycle'].mean():.3f}",
+    )
+    # average time_MS1, skip null values
+    a = ms1.filter(pl.col("time_ms1_to_ms1") >= 0)["time_ms1_to_ms1"].mean()
+    if a is not None:
+        lines.append(f"Average MS1-to-MS1 scan time,{a:.3f}")
+    else:
+        lines.append("Average MS1-to-MS1 scan time,")
+    a = ms1.filter(pl.col("time_ms1_to_ms2") >= 0)["time_ms1_to_ms2"].mean()
+    if a is not None:
+        lines.append(f"Average MS1-to-MS2 scan time,{a:.3f}")
+    else:
+        lines.append("Average MS1-to-MS2 scan time,")
+    ms2_mean = ms1.filter(pl.col("time_ms2_to_ms2") >= 0)["time_ms2_to_ms2"].mean()
+    if ms2_mean is not None:
+        lines.append(f"Average MS2-to-MS2 scan time,{ms2_mean:.3f}")
+    else:
+        lines.append("Average MS2-to-MS2 scan time,")
+    a = ms1.filter(pl.col("time_ms2_to_ms1") >= 0)["time_ms2_to_ms1"].mean()
+    if a is not None:
+        lines.append(f"Average MS2-to-MS1 scan time,{a:.3f}")
+    else:
+        lines.append("Average MS2-to-MS1 scan time,")
+    # number of features
+    if self.features_df is not None:
+        lines.append(f"Number of features,{self.features_df.height}")
+        a = self.features_df.filter(pl.col("ms2_scans").is_not_null()).height
+        lines.append(f"Number of features with MS2 data,{a}")
+        b = self.scans_df.filter(pl.col("feature_uid") >= 0).height
+        lines.append(f"Number of MS2 scans with features,{b}")
+        if a > 0:
+            lines.append(f"Redundancy of MS2 scans with features,{b / a:.3f}")
+        else:
+            lines.append("Redundancy of MS2 scans with features,")
+    else:
+        lines.append("Number of features,")
+        lines.append("Number of features with MS2 data,")
+        lines.append("Number of MS2 scans with features,")
+        lines.append("Redundancy of MS2 scans with features,")
+
+    # write to file
+    with open(filename, "w") as f:
+        for line in lines:
+            f.write(line + "\n")
+
+    self.logger.info(f"DDA statistics exported to {filename}")
+
+
+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:
+        self.logger.warning("No chromatogram definitions found.")
+        return
+    data = self.chrom_df.clone()
+    # Convert to pandas for CSV export
+    if hasattr(data, "to_pandas"):
+        data = data.to_pandas()
+    # remove scan_uid and chrom columns if they exist
+    if "scan_uid" in data.columns:
+        data = data.drop("scan_uid")
+    if "chrom" in data.columns:
+        data = data.drop("chrom")
+    data.to_csv(filename, index=False)