#!usr/bin/env python3 # -*- coding: latin-1 -*- """ The spectrum class offers a python object for mass spectrometry data. The spectrum object holds the basic information of the spectrum and offers methods to interrogate properties of the spectrum. Data, i.e. mass over charge (m/z) and intensity decoding is performed on demand and can be accessed via their properties, e.g. :py:attr:`~pymzml.spec.Spectrum.peaks`. The Spectrum class is used in the :py:class:`~pymzml.run.Reader` class. There each spectrum is accessible as a spectrum object. Theoretical spectra can also be created using the setter functions. For example, m/z values, intensities, and peaks can be set by the corresponding properties: :py:attr:`pymzml.spec.Spectrum.mz`, :py:attr:`pymzml.spec.Spectrum.i`, :py:attr:`pymzml.spec.Spectrum.peaks`. Similar to the spectrum class, the chromatogram class allows interrogation with profile data (time, intensity) in an total ion chromatogram. """ # Python mzML module - pymzml # Copyright (C) 2010-2019 M. Kösters, C. Fufezan # The MIT License (MIT) # Permission is hereby granted, free of charge, to any person obtaining a copy # of this software and associated documentation files (the "Software"), to deal # in the Software without restriction, including without limitation the rights # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell # copies of the Software, and to permit persons to whom the Software is # furnished to do so, subject to the following conditions: # The above copyright notice and this permission notice shall be included in all # copies or substantial portions of the Software. # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE # SOFTWARE. import math import re import sys import warnings import xml.etree.ElementTree as ElementTree import zlib from base64 import b64decode as b64dec from collections import defaultdict as ddict from functools import lru_cache from operator import itemgetter as itemgetter from struct import unpack import numpy as np try: DECON_DEP = True from ms_deisotope.deconvolution import deconvolute_peaks from ms_peak_picker import simple_peak except (ImportError, ModuleNotFoundError) as e: DECON_DEP = False pass from . import regex_patterns from .decoder import MSDecoder PROTON = 1.00727646677 ISOTOPE_AVERAGE_DIFFERENCE = 1.002 class MS_Spectrum(object): """ General spectrum class for data handling. """ # __slots__ = [ # # '_read_accessions', # # 'get_element_by_name', # # 'get_element_by_path', # # '_register', # # 'precursors', # # '_get_encoding_parameters', # # 'measured_precision', # # '_decode_to_numpy', # # '_median', # # 'to_string', # ] def __init__(self): """.""" pass def _read_accessions(self): """Set all required variables for this spectrum.""" self.accessions = {} for element in self.element.getiterator(): accession = element.get("accession") name = element.get("name") if accession is not None: self.accessions[name] = accession if "profile spectrum" in self.accessions.keys(): self._profile = True def get_element_by_name(self, name): """ Get element from the original tree by it's unit name. Arguments: name (str): unit name of the mzml element. Keyword Arguments: obo_version (str, optional): obo version number. """ iterator = self.element.iter() return_ele = None for ele in iterator: if ele.get("name", default=None) == name: return_ele = ele break return return_ele def get_element_by_path(self, hooks): """ Find elements in spectrum by its path. Arguments: hooks (list): list of parent elements for the target element. Returns: elements (list): list of XML objects found in the path Example: To access cvParam in scanWindow tag: >>> spec.get_element_by_path(['scanList', 'scan', 'scanWindowList', ... 'scanWindow', 'cvParam']) """ return_ele = None if len(hooks) > 0: path_array = ["."] for hook in hooks: path_array.append("{ns}{hook}".format(ns=self.ns, hook=hook)) path = "/".join(path_array) return_ele = self.element.findall(path) return return_ele def _register(self, decoded_tuple): d_type, array = decoded_tuple if d_type == "mz": self._mz = array elif d_type == "i": self._i = array elif d_type == "time": self._time = array else: raise Exception("Unknown data Type ({0})".format(d_type)) def _get_encoding_parameters(self, array_type): """ Find the correct parameter for decoding and return them as tuple. Arguments: array_type (str): data type of the array, e.g. m/z, time or intensity Returns: data (str) : encoded data comp (str) : compression method fType (str) : float precision d_array_length (str) : length of the data array """ numpress_encoding = False # array_type_accession = self.calling_instance.OT[array_type]["id"] b_data_string = "./{ns}binaryDataArrayList/{ns}binaryDataArray/{ns}cvParam[@name='{Acc}']/..".format( ns=self.ns, Acc=array_type ) float_type_string = "./{ns}cvParam[@accession='{Acc}']" b_data_array = self.element.find(b_data_string) comp = [] if b_data_array: for cvParam in b_data_array.iterfind("./{ns}cvParam".format(ns=self.ns)): if "compression" in cvParam.get("name"): if "numpress" in cvParam.get("name").lower(): numpress_encoding = True comp.append(cvParam.get("name")) d_array_length = self.element.get("defaultArrayLength") if not numpress_encoding: try: # 32-bit float f_type = b_data_array.find( float_type_string.format( ns=self.ns, Acc=self.calling_instance.OT["32-bit float"]["id"], ) ).get("name") except: # 64-bit Float f_type = b_data_array.find( float_type_string.format( ns=self.ns, Acc=self.calling_instance.OT["64-bit float"]["id"], ) ).get("name") else: # compression is numpress, dont need floattype here f_type = None data = b_data_array.find("./{ns}binary".format(ns=self.ns)) if data is not None: data = data.text else: data = None d_array_length = 0 f_type = "64-bit float" if data is not None: data = data.encode("utf-8") else: data = "" return (data, d_array_length, f_type, comp) @property def measured_precision(self): """ Set the measured and internal precision. Returns: value (float): measured Precision (e.g. 5e-6) """ return self._measured_precision @measured_precision.setter def measured_precision(self, value): self._measured_precision = value self.internal_precision = int(round(50000.0 / (value * 1e6))) return def _decode_to_numpy(self, data, d_array_length, float_type, comp): """ Decode the b64 encoded and packed strings from data as numpy arrays. Returns: data (np.ndarray): Returns the unpacked data as a tuple. Returns an empty list if there is no raw data or raises an exception if data could not be decoded. d_array_length just for compatibility """ out_data = b64dec(data) if len(out_data) != 0: if "zlib" in comp or "zlib compression" in comp: out_data = zlib.decompress(out_data) if ( "ms-np-linear" in comp or "ms-np-pic" in comp or "ms-np-slof" in comp or "MS-Numpress linear prediction compression" in comp or "MS-Numpress short logged float compression" in comp ): out_data = self._decodeNumpress_to_array(out_data, comp) if float_type == "32-bit float": # one character code may be sufficient too (f) f_type = np.float32 out_data = np.frombuffer(out_data, f_type) elif float_type == "64-bit float": # one character code may be sufficient too (d) f_type = np.float64 out_data = np.frombuffer(out_data, f_type) else: out_data = np.array([]) return out_data def _decode_to_tuple(self, data, d_array_length, float_type, comp): """ Decode b64 encoded and packed strings. Returns: data (tuple): Returns the unpacked data as a tuple. Returns an empty list if there is no raw data or raises an exception if data could not be decoded. """ dec_data = b64dec(data) if len(dec_data) != 0: if "zlib" in comp or "zlib compression" in comp: dec_data = zlib.decompress(dec_data) if set(["ms-np-linear", "ms-np-pic", "ms-np-slof"]) & set(comp): self._decodeNumpress(data, comp) # else: # print( # 'New data compression ({0}) detected, cant decompress'.format( # comp # ) # ) # sys.exit(1) if float_type == "32-bit float": f_type = "f" elif float_type == "64-bit float": f_type = "d" fmt = "{endian}{array_length}{float_type}".format( endian="<", array_length=d_array_length, float_type=f_type ) ret_data = unpack(fmt, dec_data) else: ret_data = [] return ret_data def _decodeNumpress_to_array(self, data, compression): """ Decode golomb-rice encoded data (aka numpress encoded data). Arguments: data (str) : Encoded data string compression (str) : Decompression algorithm to be used (valid are 'ms-np-linear', 'ms-np-pic', 'ms-np-slof') Returns: array (list): Returns the unpacked data as an array of floats. """ result = [] comp_ms_tags = [self.calling_instance.OT[comp]["id"] for comp in compression] data = np.frombuffer(data, dtype=np.uint8) if "MS:1002312" in comp_ms_tags: result = MSDecoder.decode_linear(data) elif "MS:1002313" in comp_ms_tags: result = MSDecoder.decode_pic(data) elif "MS:1002314" in comp_ms_tags: result = MSDecoder.decode_slof(data) return result def _median(self, data): """ Compute median. Arguments: data (list): list of numeric values Returns: median (float): median of the input data """ return np.median(data) def to_string(self, encoding="latin-1", method="xml"): """ Return string representation of the xml element the spectrum was initialized with. Keyword Arguments: encoding (str) : text encoding of the returned string.\n Default is latin-1. method (str) : text format of the returned string.\n Default is xml, alternatives are html and text. Returns: element (str) : xml string representation of the spectrum. """ return ElementTree.tostring(self.element, encoding=encoding, method=method) class Spectrum(MS_Spectrum): """ Spectrum class which inherits from class :py:attr:`pymzml.spec.MS_Spectrum` Arguments: element (xml.etree.ElementTree.Element): spectrum as xml element Keyword Arguments: measured_precision (float): in ppm, i.e. 5e-6 equals to 5 ppm. """ def __init__(self, element=ElementTree.Element(""), measured_precision=5e-6): __slots__ = [ "_centroided_peaks", "_centroided_peaks_sorted_by_i", "_deconvoluted_peaks", "_extreme_values", "_i", "_ID", "_id_dict", "_index", "_measured_precision", "_peaks", "_profile", "_reprofiled_peaks", "_t_mass_set", "_t_mz_set", "_time", "_transformed_mass_with_error", "_transformed_mz_with_error", "_transformed_peaks" "calling_instance" "element", "internal_precision" "noise_level_estimate", "selected_precursors", ] self._centroided_peaks = None self._centroided_peaks_sorted_by_i = None self._extreme_values = None self._i = None self._ID = None self._id_dict = None self._index = None self._ms_level = None self._mz = None self._peak_dict = { "raw": None, "centroided": None, "reprofiled": None, "deconvoluted": None, } self._selected_precursors = None self._profile = None self.reprofiled = False self._reprofiled_peaks = None self._scan_time = None self._scan_time_unit = None self._scan_time_in_minutes = None self._t_mass_set = None self._t_mz_set = None self._TIC = None self._precursors = None self._transformed_mass_with_error = None self._transformed_mz_with_error = None self._transformed_peaks = None self.calling_instance = None self.element = element self.measured_precision = measured_precision self.noise_level_estimate = {} self.ns = "" if self.element: self.ns = ( re.match(r"\{.*\}", element.tag).group(0) if re.match(r"\{.*\}", element.tag) else "" ) self._decode = self._decode_to_numpy self._array = np.array self._ms_deisotop_warning_printed = False def __del__(self): """ Clear self.element to limit RAM usage """ if self.element: self.element.clear() def __add__(self, other_spec): """ Adds two pymzml spectra Arguments: other_spec (Spectrum): spectrum to add to the current spectrum Returns: self (Spectrum): reference to the edited spectrum Example: >>> import pymzml >>> s = pymzml.spec.Spectrum( measuredPrescision = 20e-6 ) >>> file_to_read = "../mzML_example_files/xy.mzML.gz" >>> run = pymzml.run.Reader( ... file_to_read , ... MS1_Precision = 5e-6 , ... MSn_Precision = 20e-6 ... ) >>> for spec in run: ... s += spec """ assert isinstance(other_spec, Spectrum) if self._peak_dict["reprofiled"] is None: reprofiled = self._reprofile_Peaks() self.set_peaks(reprofiled, "reprofiled") if other_spec._peak_dict["reprofiled"] is None: other_spec.set_peaks(other_spec._reprofile_Peaks(), "reprofiled") for mz, i in other_spec.peaks("reprofiled"): self._peak_dict["reprofiled"][mz] += i return self def __sub__(self, other_spec): """ Subtracts two pymzml spectra. Arguments: other_spec (spec.Spectrum): spectrum to subtract from the current spectrum Returns: self (spec.Spectrum): returns self after other_spec was subtracted """ assert isinstance(other_spec, Spectrum) if self._peak_dict["reprofiled"] is None: self.set_peaks(self._reprofile_Peaks(), "reprofiled") for mz, i in other_spec.peaks("reprofiled"): self._peak_dict["reprofiled"][mz] -= i self.set_peaks(None, "centroided") self.set_peaks(None, "raw") return self def __mul__(self, value): """ Multiplies each intensity with a float, i.e. scales the spectrum. Arguments: value (int, float): value to multiply the intensities with Returns: self (spec.Spectrum): returns self after intensities were scaled by value """ assert isinstance(value, (int, float)) if self._peak_dict["raw"] is not None: self.set_peaks( np.column_stack( (self.peaks("raw")[:, 0], self.peaks("raw")[:, 1] * value) ), "raw", ) if self._peak_dict["centroided"] is not None: self.set_peaks( np.column_stack( (self.centroided_peaks[:, 0], self.centroided_peaks[:, 1] * value) ), "centroided", ) if self._peak_dict["reprofiled"] is not None: for mz in self._peak_dict["reprofiled"].keys(): self._peak_dict["reprofiled"][mz] *= float(value) return self def __truediv__(self, value): """ Divides each intensity by a float, i.e. scales the spectrum. Arguments: value (int, float): value to divide the intensities by Returns: self (spec.Spectrum): returns self after intensities were scaled by value. """ if self._peak_dict["reprofiled"] is not None: for mz, i in self.peaks("reprofiled"): self._peak_dict["reprofiled"][mz] /= float(value) if self._peak_dict["raw"] is not None: if len(self._peak_dict["raw"]) != 0: self.set_peaks( np.column_stack( ( self.peaks("raw")[:, 0], self.peaks("raw")[:, 1] / float(value), ) ), "raw", ) if self._peak_dict["centroided"] is not None: peaks = self._peak_dict["centroided"] scaled_peaks = peaks[:, 1] / value peaks[:, 1] = scaled_peaks self._peak_dict["centroided"] = peaks return self def __div__(self, value): """ Integer division is the same as __truediv__ for this class """ return self.__truediv__(value) def __repr__(self): """ Returns representative string for a spectrum object class """ return "<__main__.Spectrum object with native ID {0} at {1}>".format( self.ID, hex(id(self)) ) def __str__(self): """ Returns representative string for a spectrum object class """ return "<__main__.Spectrum object with native ID {0} at {1}>".format( self.ID, hex(id(self)) ) @lru_cache() def __getitem__(self, accession): """ Access spectrum XML information by tag name Args: accession(str): name of the XML tag Returns: value (float or str): value of the XML tag """ # TODO implement cache??? if accession == "id": return_val = self.ID else: if not accession.startswith("MS:"): try: accession = self.calling_instance.OT[accession]["id"] except TypeError: accession = "---" search_string = './/*[@accession="{0}"]'.format(accession) elements = [] for x in self.element.iterfind(search_string): val = x.attrib.get("value", "") try: val = float(val) except: pass elements.append(val) if len(elements) == 0: return_val = None elif len(elements) == 1: return_val = elements[0] else: return_val = elements if return_val == "": return_val = True return return_val def get(self, acc, default=None): """Mimic dicts get function. Args: acc (str): accession or obo tag to return default (None, optional): default value if acc is not found """ val = self[acc] if val is None: val = default return val def __contains__(self, value): """Check if MS tag or name can be found in spectrum. Args: value (str): MS tag or OBO name Returns: bool """ r = False if self[value] is not None: r = True return r @property def measured_precision(self): """ Sets the measured and internal precision Returns: value (float): measured precision (e.g. 5e-6) """ return self._measured_precision @measured_precision.setter def measured_precision(self, value): self._measured_precision = value self.internal_precision = int(round(50000.0 / (value * 1e6))) return @property def t_mz_set(self): """ Creates a set of integers out of transformed m/z values (including all values in the defined imprecision). This is used to accelerate has_peak function and similar. Returns: t_mz_set (set): set of transformed m/z values """ if self._t_mz_set is None: self._t_mz_set = set() for mz, i in self.peaks("centroided"): self._t_mz_set |= set( range( int( round( (mz - (mz * self.measured_precision)) * self.internal_precision ) ), int( round( (mz + (mz * self.measured_precision)) * self.internal_precision ) ) + 1, ) ) return self._t_mz_set @property def transformed_mz_with_error(self): """ Returns transformed m/z value with error Returns: tmz values (dict): Transformed m/z values in dictionary\n {\n m/z_with_error : [(m/z,intensity), ...], ...\n }\n """ if self._transformed_mz_with_error is None: self._transformed_mz_with_error = ddict(list) for mz, i in self.peaks("centroided"): for t_mz_with_error in range( int( round( (mz - (mz * self.measured_precision)) * self.internal_precision ) ), int( round( (mz + (mz * self.measured_precision)) * self.internal_precision ) ) + 1, ): self._transformed_mz_with_error[t_mz_with_error].append((mz, i)) return self._transformed_mz_with_error @property def transformed_peaks(self): """ m/z value is multiplied by the internal precision. Returns: Transformed peaks (list): Returns a list of peaks (tuples of mz and intensity). Float m/z values are adjusted by the internal precision to integers. """ if self._transformed_peaks is None: self._transformed_peaks = [ (self.transform_mz(mz), i) for mz, i in self.peaks("centroided") ] return self._transformed_peaks @property def TIC(self): """ Property to access the total ion current for this spectrum. Returns: TIC (float): Total Ion Current of the spectrum. """ if self._TIC is None: self._TIC = float( self.element.find( "./{ns}cvParam[@accession='MS:1000285']".format(ns=self.ns) ).get("value") ) # put hardcoded MS tags in minimum.py??? return self._TIC @property def ID(self): """ Access the native id (last number in the id attribute) of the spectrum. Returns: ID (str): native ID of the spectrum """ if self._ID is None: if self.element: match = regex_patterns.SPECTRUM_ID_PATTERN.search( self.element.get("id", None) ) if match: try: self._ID = int(match.group(1)) except ValueError: self._ID = match.group(1) else: self._ID = self.element.get("id") return self._ID @property def id_dict(self): """ Access to all entries stored the id attribute of a spectrum. Returns: id_dict (dict): key value pairs for all entries in id attribute of a spectrum """ if self._id_dict is None: tuples = [] match = regex_patterns.SPECTRUM_PATTERN3.match(self.element.attrib["id"]) if match is not None: captures = match.captures(1) for element in captures: k, v = element.strip().split("=") v = int(v) tuples.append([k, v]) self._id_dict = dict(tuples) else: self._id_dict = {} return self._id_dict @property def index(self): """ Access the index of the spectrum. Returns: index (int): index of the spectrum Note: This does not necessarily correspond to the native spectrum ID """ if self._index is None: self._index = self.element.get("index") try: self._index = int(self._index) except: pass return self._index @property def ms_level(self): """ Property to access the ms level. Returns: ms_level (int): """ if self._ms_level is None: sub_element = self.element.find( ".//{ns}cvParam[@accession='MS:1000511']".format(ns=self.ns) ) if sub_element is not None: self._ms_level = int( sub_element.get("value") ) # put hardcoded MS tags in minimum.py??? return self._ms_level @property def scan_time(self): """ Property to access the retention time and retention time unit. Please note, that we do not assume the retention time unit, if it is not correctly defined in the mzML. It is set to 'unicorns' in this case. Returns: scan_time (float): scan_time_unit (str): """ if self._scan_time is None or self._scan_time_unit is None: scan_time_ele = self.element.find( ".//*[@accession='MS:1000016']".format(ns=self.ns) ) self._scan_time = float(scan_time_ele.attrib.get("value")) self._scan_time_unit = scan_time_ele.get("unitName", "unicorns") return self._scan_time, self._scan_time_unit # @property def scan_time_in_minutes(self): """ Property to access the retention time in minutes. If the retention time unit is defined within the mzML, the retention time is converted into minutes and returned without the unit. Returns: scan_time (float): """ if self._scan_time_in_minutes is None: self._scan_time, time_unit = self.scan_time if self._scan_time_unit.lower() == "millisecond": self._scan_time_in_minutes = self._scan_time / 1000.0 / 60.0 if self._scan_time_unit.lower() == "second": self._scan_time_in_minutes = self._scan_time / 60.0 elif self._scan_time_unit.lower() == "minute": self._scan_time_in_minutes = self._scan_time elif self._scan_time_unit.lower() == "hour": self._scan_time_in_minutes = self._scan_time * 60.0 else: raise Exception("Time unit '{0}' unknown".format(self._scan_time_unit)) return self._scan_time_in_minutes @property def selected_precursors(self): """ Property to access the selected precursors of a MS2 spectrum. Returns a list of dicts containing the precursors mz and, if available intensity and charge for each precursor. Returns: selected_precursors (list): """ if self._selected_precursors is None: selected_precursor_mzs = self.element.findall( ".//*[@accession='MS:1000744']" ) selected_precursor_is = self.element.findall(".//*[@accession='MS:1000042']") selected_precursor_cs = self.element.findall(".//*[@accession='MS:1000041']") precursors = self.element.findall( "./{ns}precursorList/{ns}precursor".format(ns=self.ns) ) mz_values = [] i_values = [] charges = [] ids = [] for obj in selected_precursor_mzs: mz = obj.get("value") mz_values.append(float(mz)) for obj in selected_precursor_is: i = obj.get("value") i_values.append(float(i)) for obj in selected_precursor_cs: c = obj.get("value") charges.append(int(c)) for prec in precursors: spec_ref = prec.get("spectrumRef") if spec_ref is not None: ids.append( regex_patterns.SPECTRUM_ID_PATTERN.search(spec_ref).group(1) ) else: ids.append(None) # ids.append() self._selected_precursors = [] for pos, mz in enumerate(mz_values): dict_2_save = {"mz": mz} for key, list_of_values in [ ("i", i_values), ("charge", charges), ("precursor id", ids), ]: try: dict_2_save[key] = list_of_values[pos] except: continue self._selected_precursors.append(dict_2_save) return self._selected_precursors @property def precursors(self): """ List the precursor information of this spectrum, if available. Returns: precursor(list): list of precursor ids for this spectrum. """ self.deprecation_warning(sys._getframe().f_code.co_name) if not self._precursors: precursors = self.element.findall( "./{ns}precursorList/{ns}precursor".format(ns=self.ns) ) self._precursors = [] for prec in precursors: spec_ref = prec.get("spectrumRef") self._precursors.append( regex_patterns.SPECTRUM_ID_PATTERN.search(spec_ref).group(1) ) return self._precursors def remove_precursor_peak(self): peaks = self.peaks("centroided") for precursor in self.selected_precursors: mz = precursor["mz"] hp = self.has_peak(mz) if hp: for p in hp: peaks = peaks[(peaks[:, 0] != p[0])] self.set_peaks(peaks, "centroided") self.set_peaks(peaks, "raw") return peaks @property def mz(self): """ Returns the list of m/z values. If the m/z values are encoded, the function :func:`~spec.MS_Spectrum._decode` is used to decode the encoded data. The mz property can also be set, e.g. for theoretical data. However, it is recommended to use the peaks property to set mz and intensity tuples at same time. Returns: mz (list): list of m/z values of spectrum. """ if self._mz is None: params = self._get_encoding_parameters("m/z array") self._mz = self._decode(*params) return self._mz @mz.setter def mz(self, mz_list): """""" mz_list = np.array(mz_list, dtype=np.float64) mz_list.sort() self._mz = mz_list @property def i(self): """ Returns the list of the intensity values. If the intensity values are encoded, the function :func:`~spec.MS_Spectrum._decode` is used to decode the encoded data.\n The i property can also be set, e.g. for theoretical data. However, it is recommended to use the peaks property to set mz and intensity tuples at same time. Returns i (list): list of intensity values from the analyzed spectrum """ if self._i is None: params = self._get_encoding_parameters("intensity array") self._i = self._decode(*params) return self._i @i.setter def i(self, intensity_list): self._i = intensity_list def peaks(self, peak_type): """ Decode and return a list of mz/i tuples. Args: peak_type(str): currently supported types are: raw, centroided and reprofiled Returns: peaks (list or ndarray): list or numpy array of mz/i tuples or arrays """ if self._peak_dict[peak_type] is None: if self._peak_dict["raw"] is None: mz_params = self._get_encoding_parameters("m/z array") i_params = self._get_encoding_parameters("intensity array") mz = self._decode(*mz_params) i = self._decode(*i_params) arr = np.stack((mz, i), axis=-1) self._peak_dict[peak_type] = arr if peak_type == "raw": pass elif peak_type == "centroided": self._peak_dict["centroided"] = self._centroid_peaks() elif peak_type == "reprofiled": self._peak_dict["reprofiled"] = self._reprofile_Peaks() elif peak_type == "deconvoluted": self._peak_dict["deconvoluted"] = self._deconvolute_peaks() else: raise KeyError if not isinstance(self._peak_dict[peak_type], np.ndarray): peaks = self._array(self._peak_dict[peak_type]) else: peaks = self._peak_dict[peak_type] if peak_type == "reprofiled": peaks = list(self._peak_dict[peak_type].items()) peaks.sort(key=itemgetter(0)) return peaks @lru_cache() def get_array(self, arr_name): array_params = self._get_encoding_parameters(arr_name) array = self._decode(*array_params) if len(array) == 0: array = None _ = self.get_all_arrays_in_spec(not_found_array=arr_name) return array def get_tims_tof_ion_mobility( self, array_name="mean inverse reduced ion mobility array" ): arr = self.get_array(array_name) if arr is None: _ = self.get_all_arrays_in_spec(not_found_array=array_name) return arr def get_all_arrays_in_spec(self, not_found_array=None): b_data_string = "./{ns}binaryDataArrayList/{ns}binaryDataArray/{ns}cvParam[@unitCvRef='MS']".format( ns=self.ns ) b_data_arrays = self.element.findall(b_data_string) array_names = [arr.attrib["name"] for arr in b_data_arrays] formatted_array_names = [] for name in array_names: formatted_array_names.append("\t- {name}".format(name=name)) if not_found_array is not None: print( "Requested array ({not_found_array}) not found.\nAvailable arrays are:".format( not_found_array=not_found_array ) ) print("\n".join(formatted_array_names)) return array_names def _deconvolute_peaks(self, *args, **kwargs): if DECON_DEP is True: peaks = self.peaks("centroided") # pack peak matrix into expected structure peaks = [simple_peak(p[0], p[1], 0.01) for p in peaks] decon_result = deconvolute_peaks(peaks, *args, **kwargs) dpeaks = decon_result.peak_set # pack deconvoluted peak list into matrix structure dpeaks_mat = np.zeros((len(dpeaks), 3), dtype=float) for i, dp in enumerate(dpeaks): dpeaks_mat[i, :] = dp.neutral_mass, dp.intensity, dp.charge return dpeaks_mat else: if self._ms_deisotop_warning_printed is False: print( "ms_deisotope is missing, please install using pip install ms_deisotope" ) self._ms_deisotop_warning_printed = True def set_peaks(self, peaks, peak_type): """ Assign a custom peak array of type peak_type Args: peaks(list or ndarray): list or array of mz/i values peak_type(str): Either raw, centroided or reprofiled """ peak_type = peak_type.lower() # reset after changing peaks self._transformed_mass_with_error = None self._transformed_mz_with_error = None if peak_type == "raw": # if not isinstance(peaks, np.ndarray): # peaks = np.array(peaks) self._peak_dict["raw"] = peaks try: self._mz = self.peaks("raw")[:, 0] self._i = self.peaks("raw")[:, 1] except IndexError: self._mz = np.array([]) self._i = np.array([]) elif peak_type == "centroided": # if not isinstance(peaks, np.ndarray): # peaks = np.array(peaks) self._peak_dict["centroided"] = peaks try: self._mz = self.peaks("raw")[:, 0] self._i = self.peaks("raw")[:, 1] except IndexError: self._mz = np.array([]) self._i = np.array([]) elif peak_type == "reprofiled": try: self._peak_dict["reprofiled"] = peaks except TypeError: self._peak_dict["reprofiled"] = None elif peak_type == "deconvoluted": self._peak_dict["deconvoluted"] = peaks try: self._mz = self.peaks("raw")[:, 0] self._i = self.peaks("raw")[:, 1] except IndexError: self._mz = np.array([]) else: raise Exception( "Peak type is not suppported\n" 'Choose either "raw", "centroided" or "reprofiled"' ) def _centroid_peaks(self): """ Perform a Gauss fit to centroid the peaks for the property centroided_peaks. Returns: centroided_peaks (list): list of centroided m/z, i tuples """ try: profile_ot = self.calling_instance.OT.name.get("profile spectrum", None) if profile_ot is None: profile_ot = self.calling_instance.OT.name.get("profile mass spectrum", None) acc = profile_ot["id"] is_profile = ( True if self.element.find( ".//*[@accession='{acc}']".format(ns=self.ns, acc=acc) ) is not None else None ) except (TypeError, AttributeError) as e: # user creadted spectrum objects without xml and calling instance cant determine if they are reprofiled or not is_profile = None if is_profile is not None or self.reprofiled: # check if spec is a profile spec tmp = [] if self._peak_dict["reprofiled"] is not None: i_array = [i for mz, i in self.peaks("reprofiled")] mz_array = [mz for mz, i in self.peaks("reprofiled")] else: i_array = self.i mz_array = self.mz for pos, i in enumerate(i_array[:-1]): if pos <= 1: continue if 0 < i_array[pos - 1] < i > i_array[pos + 1] > 0: x1 = float(mz_array[pos - 1]) y1 = float(i_array[pos - 1]) x2 = float(mz_array[pos]) y2 = float(i_array[pos]) x3 = float(mz_array[pos + 1]) y3 = float(i_array[pos + 1]) if x2 - x1 > (x3 - x2) * 10 or (x2 - x1) * 10 < x3 - x2: continue if y3 == y1: y3 += 0.01 * y1 try: double_log = math.log(y2 / y1) / math.log(y3 / y1) mue = (double_log * (x1 * x1 - x3 * x3) - x1 * x1 + x2 * x2) / ( 2 * (x2 - x1) - 2 * double_log * (x3 - x1) ) c_squarred = ( x2 * x2 - x1 * x1 - 2 * x2 * mue + 2 * x1 * mue ) / (2 * math.log(y1 / y2)) A = y1 * math.exp((x1 - mue) * (x1 - mue) / (2 * c_squarred)) except ZeroDivisionError: continue tmp.append((mue, A)) return tmp else: return self.peaks("raw") def _reprofile_Peaks(self): """ Performs reprofiling for property reprofiled_peaks. Returns: reprofiled_peaks (list): list of reprofiled m/z, i tuples """ tmp = ddict(int) for mz, i in self.peaks("centroided"): # Let the measured precision be 2 sigma of the signal width # When using normal distribution # FWHM = 2 sqt(2 * ln(2)) sigma = 2.3548 sigma s = mz * self.measured_precision * 2 # in before 2 s2 = s * s floor = mz - 5.0 * s # Gauss curve +- 3 sigma ceil = mz + 5.0 * s ip = self.internal_precision / 4 # more spacing, i.e. less points describing the gauss curve # -> faster adding for _ in range(int(round(floor * ip)), int(round(ceil * ip)) + 1): if _ % int(5) == 0: a = float(_) / float(ip) y = i * math.exp(-1 * ((mz - a) * (mz - a)) / (2 * s2)) tmp[a] += y self.reprofiled = True self.set_peaks(None, "centroided") return tmp def _register(self, decoded_tuple): d_type, array = decoded_tuple if d_type == "mz": self._mz = array elif d_type == "i": self._i = array elif d_type == "time": self._time = array else: raise Exception("Unknown data Type ({0})".format(d_type)) def _mz_2_mass(self, mz, charge): """ Calculate the uncharged mass for a given mz value Arguments: mz (float) : m/z value charge(int) : charge Returns: mass (float): Returns mass of a given m/z value """ return (mz - PROTON) * charge def _set_params_from_reference_group(self, ref_element): ref = self.element.find("{ns}referenceableParamGroupRef".format(ns=self.ns)) if ref is not None: ref = ref.get("ref") ele = ref_element.find(".//*[@id='{ref}']".format(ref=ref, ns=self.ns)) if ele is not None and ref == ele.get("id"): for param in ele.getiterator(): self.element.append(ele) acc = param.get("accession") # Public functions def reduce(self, peak_type="raw", mz_range=(None, None)): """ Remove all m/z values outside the given range. Arguments: mz_range (tuple): tuple of min, max values Returns: peaks (list): list of mz, i tuples in the given range. """ arr = self.peaks(peak_type) peaks = arr[ np.where(np.logical_and(arr[:, 0] >= mz_range[0], arr[:, 0] <= mz_range[1])) ] self.set_peaks(peaks, peak_type) return peaks def remove_noise( self, mode="median", noise_level=None, signal_to_noise_threshold=1.0 ): """ Function to remove noise from peaks, centroided peaks and reprofiled peaks. Keyword arguments: mode (str): define mode for removing noise. Default = "median" (other modes: "mean", "mad") noise_level (float): noise threshold signal_to_noise_threshold (float): S/N threshold for a peak to be accepted Returns: reprofiled peaks (list): Returns a list with tuples of m/z-intensity pairs above the noise threshold """ # Thanks to JD Hogan for pointing it out! callPeaks = self.peaks("raw") # callcentPeaks = self.peaks("centroided") if noise_level is None: noise_level = self.estimated_noise_level(mode=mode) if len(self.peaks("centroided")) != 0: self._peak_dict["centroided"] = self.peaks("centroided")[ self.peaks("centroided")[:, 1] / noise_level >= signal_to_noise_threshold ] if len(self.peaks("raw")) != 0: self._peak_dict["raw"] = self.peaks("raw")[ self.peaks("raw")[:, 1] / noise_level >= signal_to_noise_threshold ] self._peak_dict["reprofiled"] = None return self def estimated_noise_level(self, mode="median"): """ Calculates noise threshold for function remove_noise. Different modes are available. Default is 'median' Keyword Arguments: mode (str): define mode for removing noise. Default = "median" (other modes: "mean", "mad") Returns: noise_level (float): estimate noise threshold """ if len(self.peaks("centroided")) == 0: # or is None? return 0 self.noise_level_estimate = {} if mode not in self.noise_level_estimate.keys(): if mode == "median": self.noise_level_estimate["median"] = np.median( self.peaks("centroided")[:, 1] ) elif mode == "mad": median = self.estimated_noise_level(mode="median") self.noise_level_estimate["mad"] = np.median( abs(self.peaks("centroided")[:, 1] - median) ) elif mode == "mean": self.noise_level_estimate["mean"] = sum( self.peaks("centroided")[:, 1] ) / float(len(self.peaks("centroided"))) else: print( "Do not understand noise level estimation method call with given mode: {0}".format( mode ) ) return_value = self.noise_level_estimate[mode] return return_value def highest_peaks(self, n): """ Function to retrieve the n-highest centroided peaks of the spectrum. Arguments: n (int): number of highest peaks to return. Returns: centroided peaks (list): list mz, i tupls with n-highest Example: >>> run = pymzml.run.Reader( ... "tests/data/example.mzML.gz", ... MS_precisions = { ... 1 : 5e-6, ... 2 : 20e-6 ... } ... ) >>> for spectrum in run: ... if spectrum.ms_level == 2: ... if spectrum.ID == 1770: ... for mz,i in spectrum.highest_peaks(5): ... print(mz, i) """ if self._centroided_peaks_sorted_by_i is None: self._centroided_peaks_sorted_by_i = self.peaks("centroided")[ self.peaks("centroided")[:, 1].argsort() ] return self._centroided_peaks_sorted_by_i[-n:] def ppm2abs(self, value, ppm_value, direction=1, factor=1): """ Returns the value plus (or minus, dependent on direction) the error (measured precision ) for this value. Arguments: value (float) : m/z value ppm_value (int) : ppm value Keyword Arguments: direction (int) : plus or minus the considered m/z value. The argument *direction* should be 1 or -1 factor (int) : multiplication factor for the imprecision. The argument *factor* should be bigger than 0 Returns: imprecision (float): imprecision for the given value """ result = value + (value * (ppm_value * factor)) * direction return result def extreme_values(self, key): """ Find extreme values, minimal and maximum m/z and intensity Arguments: key (str) : m/z : "mz" or intensity : "i" Returns: extrema (tuple) : tuple of minimal and maximum m/z or intensity """ available_extreme_values = ["mz", "i"] if key not in available_extreme_values: print( "Do not understand extreme request: '{0}'; available values are: {1}".format( key, available_extreme_values ) ) exit() if self._extreme_values is None: self._extreme_values = {} try: if key == "mz": all_mz_values = self.peaks("raw")[:, 0] self._extreme_values["mz"] = (all_mz_values.min(), all_mz_values.max()) self._extreme_values["mz"] = ( self.peaks("raw")[:, 0].min(), self.peaks("raw")[:, 0].max(), ) else: all_i_values = self.peaks("raw")[:, 1] self._extreme_values["i"] = ( self.peaks("raw")[:, 1].min(), self.peaks("raw")[:, 1].max(), ) except ValueError: # emtpy spectrum self._extreme_values[key] = () return self._extreme_values[key] def has_peak(self, mz2find): """ Checks if a Spectrum has a certain peak. Requires a m/z value as input and returns a list of peaks if the m/z value is found in the spectrum, otherwise ``[]`` is returned. Every peak is a tuple of m/z and intensity. Note: Multiple peaks may be found, depending on the defined precisions Arguments: mz2find (float): m/z value which should be found Returns: peaks (list): list of m/z, i tuples Example: >>> import pymzml >>> example_file = 'tests/data/example.mzML' >>> run = pymzml.run.Reader( ... example_file, ... MS_precisions = { ... 1 : 5e-6, ... 2 : 20e-6 ... } ... ) >>> for spectrum in run: ... if spectrum.ms_level == 2: ... peak_to_find = spectrum.has_peak(1016.5404) ... print(peak_to_find) [(1016.5404, 19141.735187697403)] """ value = self.transform_mz(mz2find) return self.transformed_mz_with_error[value] def has_overlapping_peak(self, mz): """ Checks if a spectrum has more than one peak for a given m/z value and within the measured precision Arguments: mz (float): m/z value which should be checked Returns: Boolean (bool): Returns ``True`` if a nearby peak is detected, otherwise ``False`` """ for minus_or_plus in [-1, 1]: target = self.ppm2abs(mz, self.measured_precision, minus_or_plus, 1) temp = self.has_peak(self.ppm2abs(mz, self.measured_precision)) if temp and len(temp) > 1: return True return False def similarity_to(self, spec2, round_precision=0): """ Compares two spectra and returns cosine Arguments: spec2 (Spectrum): another pymzml spectrum that is compared to the current spectrum. Keyword Arguments: round_precision (int): precision mzs are rounded to, i.e. round( mz, round_precision ) Returns: cosine (float): value between 0 and 1, i.e. the cosine between the two spectra. Note: Spectra data is transformed into an n-dimensional vector, where m/z values are binned in bins of 10 m/z and the intensities are added up. Then the cosine is calculated between those two vectors. The more similar the specs are, the closer the value is to 1. """ assert isinstance(spec2, Spectrum), "Spectrum 2 is not a pymzML spectrum" vector1 = ddict(int) vector2 = ddict(int) mzs = set() for mz, i in self.peaks("raw"): vector1[round(mz, round_precision)] += i mzs.add(round(mz, round_precision)) for mz, i in spec2.peaks("raw"): vector2[round(mz, round_precision)] += i mzs.add(round(mz, round_precision)) z = 0 n_v1 = 0 n_v2 = 0 for mz in mzs: int1 = vector1[mz] int2 = vector2[mz] z += int1 * int2 n_v1 += int1 * int1 n_v2 += int2 * int2 try: cosine = z / (math.sqrt(n_v1) * math.sqrt(n_v2)) except: cosine = 0.0 return cosine def transform_mz(self, value): """ pymzml uses an internal precision for different tasks. This precision depends on the measured precision and is calculated when :py:attr:`spec.Spectrum.measured_precision` is invoked. transform_mz can be used to transform m/z values into the internal standard. Arguments: value (float): m/z value Returns: transformed value (float): to internal standard transformed mz value this value can be used to probe internal dictionaries, lists or sets, e.g. :func:`pymzml.spec.Spectrum.t_mz_set` Example: >>> import pymzml >>> run = pymzml.run.Reader( ... "test.mzML.gz" , ... MS_precisions = { ... 1 : 5e-6, ... 2 : 20e-6 ... } ... ) >>> >>> for spectrum in run: ... if spectrum.ms_level == 2: ... peak_to_find = spectrum.has_deconvoluted_peak( ... 1044.5804 ... ) ... print(peak_to_find) [(1044.5596, 3809.4356300564586)] """ return int(round(value * self.internal_precision)) def deprecation_warning(self, function_name): deprecation_lookup = { "similarityTo": "similarity_to", "hasPeak": "has_peak", "extremeValues": "extreme_values", "transformMZ": "transform_mz", "hasOverlappingPeak": "has_overlapping_peak", "highestPeaks": "highest_peaks", "estimatedNoiseLevel": "estimated_noise_level", "removeNoise": "remove_noise", "newPlot": "new_plot", "centroidedPeaks": "peaks", "precursors": "selected_precursors", } warnings.warn( """ Function: "{0}" deprecated since version 1.0.0, please use new function: "{1}" """.format( function_name, deprecation_lookup.get(function_name, "not_defined_yet") ), DeprecationWarning, ) def similarityTo(self, spec2, round_precision=0): self.deprecation_warning(sys._getframe().f_code.co_name) return self.similarity_to(spec2, round_precision=round_precision) def hasPeak(self, mz): self.deprecation_warning(sys._getframe().f_code.co_name) return self.has_peak(mz) def extremeValues(self, key): self.deprecation_warning(sys._getframe().f_code.co_name) return self.extreme_values(key) def transformMZ(self, value): self.deprecation_warning(sys._getframe().f_code.co_name) return self.transform_mz(value) def hasOverlappingPeak(self, mz): self.deprecation_warning(sys._getframe().f_code.co_name) return self.has_overlapping_peak(mz) def highestPeaks(self, n): self.deprecation_warning(sys._getframe().f_code.co_name) return self.highest_peaks(n) def estimatedNoiseLevel(self, mode="median"): self.deprecation_warning(sys._getframe().f_code.co_name) return self.estimated_noise_level(mode=mode) def removeNoise(self, mode="median", noiseLevel=None): self.deprecation_warning(sys._getframe().f_code.co_name) return self.remove_noise(mode=mode, noise_level=noiseLevel) @property def centroidedPeaks(self): # self.deprecation_warning( sys._getframe().f_code.co_name ) return self.peaks("centroided") class Chromatogram(MS_Spectrum): """ Class for Chromatogram access and handling. """ def __init__(self, element, measured_precision=5e-6, param=None): """ Arguments: element (xml.etree.ElementTree.Element): spectrum as xml Element Keyword Arguments: measured_precision (float): in ppm, i.e. 5e-6 equals to 5 ppm. param (dict): parameter mapping for this spectrum """ __slots__ = [ "_measured_precision", "element", "noise_level_estimate", "_time", "_i", "_t_mass_set", "_peaks", "_t_mz_set", "_centroided_peaks", "_reprofiled_peaks", "_deconvoluted_peaks", "_profile", "_extreme_values", "_centroided_peaks_sorted_by_i", "_transformed_mz_with_error", "_transformed_mass_with_error", "_precursors", "_ID", "internal_precision", ] self._measured_precision = measured_precision self.element = element self.noise_level_estimate = {} # Property variables self._time = None self._ms_level = None self._i = None self._t_mass_set = None self._peaks = None self._t_mz_set = None self._centroided_peaks = None self._reprofiled_peaks = None self._deconvoluted_peaks = None self._profile = None self._extreme_values = None self._centroided_peaks_sorted_by_i = None self._transformed_mz_with_error = None self._transformed_mass_with_error = None self._precursors = None self._ID = None if self.element: # self._read_accessions() self.ns = ( re.match(r"\{.*\}", element.tag).group(0) if re.match(r"\{.*\}", element.tag) else "" ) # self._ns_paths = { # 'mz' : "{ns}binaryDataArrayList/" \ # "{ns}binaryDataArray/" \ # "{ns}cvParam[@accession='{Acc}']/..".format( # ns=self.ns, # Acc=self.accessions['time array'] # ), # 'i' : "{ns}binaryDataArrayList/" \ # "{ns}binaryDataArray/" \ # "{ns}cvParam[@accession='{Acc}']/..".format( # ns=self.ns, # Acc=self.accessions['intensity array'] # ), # 'time' : "{ns}binaryDataArrayList/" \ # "{ns}binaryDataArray/" \ # "{ns}cvParam[@accession='{Acc}']/..".format( # ns=self.ns, # Acc=self.accessions['time array'] # ), # 'float_type' : "./{ns}cvParam[@accession='{Acc}']" # } self._decode = self._decode_to_numpy # assign function to create numpy array to list??? self._array = np.array def __repr__(self): return "<__main__.Chromatogram object with native ID {0} at {1}>".format( self.ID, hex(id(self)) ) def __str__(self): return "<__main__.Chromatogram object with native ID {0} at {1}>".format( self.ID, hex(id(self)) ) @property def ID(self): if self._ID is None: self._ID = self.element.get("id") return self._ID @property def mz(self): """""" print("Chromatogram has no property mz.\nReturn retention time instead") return self.time @property def time(self): """ Returns the list of time values. If the time values are encoded, the function _decode() is used to decode the encoded data.\n The time property can also be set, e.g. for theoretical data. However, it is recommended to use the profile property to set time and intensity tuples at same time. Returns: time (list): list of time values from the analyzed chromatogram """ if self._time is None: params = self._get_encoding_parameters("time array") self._time = self._decode(*params) return self._time @property def i(self): if self._i is None: params = self._get_encoding_parameters("intensity array") self._i = self._decode(*params) return self._i @property def profile(self): """ Returns the list of peaks of the chromatogram as tuples (time, intensity). Returns: peaks (list): list of time, i tuples Example: >>> import pymzml >>> run = pymzml.run.Reader( ... spectra.mzMl.gz, ... MS_precisions = { ... 1 : 5e-6, ... 2 : 20e-6 ... } ... ) >>> for entry in run: ... if isinstance(entry, pymzml.spec.Chromatogram): ... for time, intensity in entry.peaks: ... print(time, intensity) Note: The peaks property can also be set, e.g. for theoretical data. It requires a list of time/intensity tuples. """ if self._profile is None: if self._time is None and self._i is None: self._profile = [] for pos, t in enumerate(self.time): self._profile.append([t, self.i[pos]]) # much faster than zip ... list(zip(self.mz, self.i)) elif self._time is not None and self._i is not None: self._profile = [] for pos, t in enumerate(self.time): self._profile.append([t, self.i[pos]]) elif self._profile is None: self._profile = [] return self._array(self._profile) @profile.setter def profile(self, tuple_list): if len(tuple_list) == 0: return # self._mz, self._i = map(list, zip(*tuple_list)) # same here .. zip is soooooo slow :) self._time = [] self._i = [] for time, i in tuple_list: self._time.append(time) self._i.append(i) self._peaks = tuple_list self._reprofiledPeaks = None self._centroidedPeaks = None return self def peaks(self): """ Return the list of peaks of the spectrum as tuples (time, intensity). Returns: peaks (list): list of time, intensity tuples Example: >>> import pymzml >>> run = pymzml.run.Reader( ... spectra.mzMl.gz, ... MS_precisions = { ... 1 : 5e-6, ... 2 : 20e-6 ... } ... ) >>> for entry in run: ... if isinstance(entry, pymzml.spec.Chromatogram): ... for time, intensity in entry.peaks: ... print(time, intensity) Note: The peaks property can also be set, e.g. for theoretical data. It requires a list of time/intensity tuples. """ return self.profile