corems.mass_spectrum.input.coremsHDF5
1import json 2 3from pandas import DataFrame 4import h5py 5from io import BytesIO 6from s3path import S3Path 7 8from corems.encapsulation.input.parameter_from_json import _set_dict_data_ms 9from corems.mass_spectrum.input.massList import ReadCoremsMasslist 10from corems.mass_spectrum.factory.MassSpectrumClasses import MassSpecCentroid 11from corems.encapsulation.factory.parameters import default_parameters 12 13 14class ReadCoreMSHDF_MassSpectrum(ReadCoremsMasslist): 15 """Class for reading mass spectrum data from a CoreMS HDF5 file. 16 17 Attributes 18 ---------- 19 h5pydata : h5py.File 20 The HDF5 file object. 21 scans : list 22 List of scan labels in the HDF5 file. 23 24 Parameters 25 ---------- 26 file_location : str or S3Path 27 The path to the CoreMS HDF5 file. 28 29 Methods 30 ------- 31 * load_raw_data(mass_spectrum, scan_index=0) Load raw data into the mass spectrum object. 32 * get_mass_spectrum(scan_number=0, time_index=-1, auto_process=True, load_settings=True, load_raw=True).Get a mass spectrum object. 33 * load_settings(mass_spectrum, scan_index=0, time_index=-1). Load settings into the mass spectrum object. 34 * get_dataframe(scan_index=0, time_index=-1). Get a pandas DataFrame representing the mass spectrum. 35 * get_time_index_to_pull(scan_label, time_index). Get the time index to pull from the HDF5 file. 36 * get_high_level_attr_data(attr_str). Get high-level attribute data from the HDF5 file. 37 * get_scan_group_attr_data(scan_index, time_index, attr_group, attr_srt=None). Get scan group attribute data from the HDF5 file. 38 * get_raw_data_attr_data(scan_index, attr_group, attr_str). Get raw data attribute data from the HDF5 file. 39 * get_output_parameters(polarity, scan_index=0). Get the output parameters for the mass spectrum. 40 """ 41 42 def __init__(self, file_location): 43 super().__init__(file_location) 44 45 if isinstance(self.file_location, S3Path): 46 data = BytesIO(self.file_location.open("rb").read()) 47 else: 48 data = self.file_location 49 50 self.h5pydata = h5py.File(data, "r") 51 52 self.scans = list(self.h5pydata.keys()) 53 54 def close(self): 55 """Close the underlying HDF5 file handle.""" 56 if self.h5pydata and self.h5pydata.id.valid: 57 self.h5pydata.close() 58 59 def __enter__(self): 60 return self 61 62 def __exit__(self, *args): 63 self.close() 64 65 def load_raw_data(self, mass_spectrum, scan_index=0): 66 """ 67 Load raw data into the mass spectrum object. 68 69 Parameters 70 ---------- 71 mass_spectrum : MassSpecCentroid 72 The mass spectrum object to load the raw data into. 73 scan_index : int, optional 74 The index of the scan to load the raw data from. Default is 0. 75 """ 76 77 scan_label = self.scans[scan_index] 78 79 # Check if the "raw_ms" dataset exists and has data 80 if "raw_ms" in self.h5pydata[scan_label] and self.h5pydata[scan_label]["raw_ms"].shape is not None: 81 mz_profile = self.h5pydata[scan_label]["raw_ms"][0] 82 83 abundance_profile = self.h5pydata[scan_label]["raw_ms"][1] 84 85 mass_spectrum.mz_exp_profile = mz_profile 86 87 mass_spectrum.abundance_profile = abundance_profile 88 89 def get_mass_spectrum( 90 self, 91 scan_number=0, 92 time_index=-1, 93 auto_process=True, 94 load_settings=True, 95 load_raw=True, 96 load_molecular_formula=True, 97 ): 98 """ 99 Instantiate a mass spectrum object from the CoreMS HDF5 file. 100 Note that this always returns a centroid mass spectrum object; functionality for profile and 101 frequency mass spectra is not yet implemented. 102 103 Parameters 104 ---------- 105 scan_number : int, optional 106 The index of the scan to retrieve the mass spectrum from. Default is 0. 107 time_index : int, optional 108 The index of the time point to retrieve the mass spectrum from. Default is -1. 109 auto_process : bool, optional 110 Whether to automatically process the mass spectrum. Default is True. 111 load_settings : bool, optional 112 Whether to load the settings into the mass spectrum object. Default is True. 113 load_raw : bool, optional 114 Whether to load the raw data into the mass spectrum object. Default is True. 115 load_molecular_formula : bool, optional 116 Whether to load the molecular formula into the mass spectrum object. 117 Default is True. 118 119 Returns 120 ------- 121 MassSpecCentroid 122 The mass spectrum object. 123 124 Raises 125 ------ 126 ValueError 127 If the CoreMS file is not valid. 128 If the mass spectrum has not been processed and load_molecular_formula is True. 129 """ 130 if "mass_spectra" in self.scans[0]: 131 scan_index = self.scans.index("mass_spectra/" + str(scan_number)) 132 else: 133 scan_index = self.scans.index(str(scan_number)) 134 dataframe = self.get_dataframe(scan_index, time_index=time_index) 135 if dataframe["Molecular Formula"].any() and not dataframe["C"].any(): 136 cols = dataframe.columns.tolist() 137 cols = cols[cols.index("Molecular Formula") + 1 :] 138 for index, row in dataframe.iterrows(): 139 if row["Molecular Formula"] is not None: 140 og_formula = row["Molecular Formula"] 141 for col in cols: 142 if "col" in og_formula: 143 # get the digit after the element ("col") in the molecular formula and set it to the dataframe 144 row[col] = int(og_formula.split(col)[1].split(" ")[0]) 145 146 if not set( 147 ["H/C", "O/C", "Heteroatom Class", "Ion Type", "Is Isotopologue"] 148 ).issubset(dataframe.columns): 149 raise ValueError( 150 "%s it is not a valid CoreMS file" % str(self.file_location) 151 ) 152 153 dataframe.rename(columns=self.parameters.header_translate, inplace=True) 154 155 # Cast m/z, and 'Peak Height' to float 156 dataframe["m/z"] = dataframe["m/z"].astype(float) 157 dataframe["Peak Height"] = dataframe["Peak Height"].astype(float) 158 159 polarity = dataframe["Ion Charge"].values[0] 160 161 output_parameters = self.get_output_parameters(polarity, scan_index=scan_index) 162 163 mass_spec_obj = MassSpecCentroid( 164 dataframe.to_dict(orient="list"), output_parameters, auto_process=False 165 ) 166 167 if auto_process: 168 # Set the settings on the mass spectrum object to relative abuncance of 0 so all peaks get added 169 mass_spec_obj.settings.noise_threshold_method = "absolute_abundance" 170 mass_spec_obj.settings.noise_threshold_absolute_abundance = 0 171 mass_spec_obj.process_mass_spec() 172 173 if load_settings: 174 # Load settings into the mass spectrum object 175 self.load_settings( 176 mass_spec_obj, scan_index=scan_index, time_index=time_index 177 ) 178 179 if load_raw: 180 self.load_raw_data(mass_spec_obj, scan_index=scan_index) 181 182 if load_molecular_formula: 183 if not auto_process: 184 raise ValueError( 185 "Can only add molecular formula if the mass spectrum has been processed" 186 ) 187 else: 188 self.add_molecular_formula(mass_spec_obj, dataframe) 189 190 return mass_spec_obj 191 192 def load_settings(self, mass_spectrum, scan_index=0, time_index=-1): 193 """ 194 Load settings into the mass spectrum object. 195 196 Parameters 197 ---------- 198 mass_spectrum : MassSpecCentroid 199 The mass spectrum object to load the settings into. 200 scan_index : int, optional 201 The index of the scan to load the settings from. Default is 0. 202 time_index : int, optional 203 The index of the time point to load the settings from. Default is -1. 204 """ 205 206 loaded_settings = {} 207 loaded_settings["MoleculaSearch"] = self.get_scan_group_attr_data( 208 scan_index, time_index, "MoleculaSearchSetting" 209 ) 210 loaded_settings["MassSpecPeak"] = self.get_scan_group_attr_data( 211 scan_index, time_index, "MassSpecPeakSetting" 212 ) 213 loaded_settings["MassSpectrum"] = self.get_scan_group_attr_data( 214 scan_index, time_index, "MassSpectrumSetting" 215 ) 216 loaded_settings["Transient"] = self.get_scan_group_attr_data( 217 scan_index, time_index, "TransientSetting" 218 ) 219 220 _set_dict_data_ms(loaded_settings, mass_spectrum) 221 222 def get_dataframe(self, scan_index=0, time_index=-1): 223 """ 224 Get a pandas DataFrame representing the mass spectrum. 225 226 Parameters 227 ---------- 228 scan_index : int, optional 229 The index of the scan to retrieve the DataFrame from. Default is 0. 230 time_index : int, optional 231 The index of the time point to retrieve the DataFrame from. Default is -1. 232 233 Returns 234 ------- 235 DataFrame 236 The pandas DataFrame representing the mass spectrum. 237 """ 238 239 columnsLabels = self.get_scan_group_attr_data( 240 scan_index, time_index, "ColumnsLabels" 241 ) 242 243 scan_label = self.scans[scan_index] 244 245 index_to_pull = self.get_time_index_to_pull(scan_label, time_index) 246 247 corems_table_data = self.h5pydata[scan_label][index_to_pull] 248 249 list_dict = [] 250 for row in corems_table_data: 251 data_dict = {} 252 for data_index, data in enumerate(row): 253 label = columnsLabels[data_index] 254 # if data starts with a b' it is a byte string, so decode it 255 if isinstance(data, bytes): 256 data = data.decode("utf-8") 257 if data == "nan": 258 data = None 259 data_dict[label] = data 260 261 list_dict.append(data_dict) 262 263 # Reorder the columns from low to high "Index" to match the order of the dataframe 264 df = DataFrame(list_dict) 265 # set the "Index" column to int so it sorts correctly 266 df["Index"] = df["Index"].astype(int) 267 df = df.sort_values(by="Index") 268 # Reset index to match the "Index" column 269 df = df.set_index("Index", drop=False) 270 271 return df 272 273 def get_time_index_to_pull(self, scan_label, time_index): 274 """ 275 Get the time index to pull from the HDF5 file. 276 277 Parameters 278 ---------- 279 scan_label : str 280 The label of the scan. 281 time_index : int 282 The index of the time point. 283 284 Returns 285 ------- 286 str 287 The time index to pull. 288 """ 289 290 time_data = sorted( 291 [(i, int(i)) for i in self.h5pydata[scan_label].keys() if i != "raw_ms"], 292 key=lambda m: m[1], 293 ) 294 295 index_to_pull = time_data[time_index][0] 296 297 return index_to_pull 298 299 def get_high_level_attr_data(self, attr_str): 300 """ 301 Get high-level attribute data from the HDF5 file. 302 303 Parameters 304 ---------- 305 attr_str : str 306 The attribute string. 307 308 Returns 309 ------- 310 dict 311 The attribute data. 312 313 Raises 314 ------ 315 KeyError 316 If the attribute string is not found in the HDF5 file. 317 """ 318 319 return self.h5pydata.attrs[attr_str] 320 321 def get_scan_group_attr_data( 322 self, scan_index, time_index, attr_group, attr_srt=None 323 ): 324 """ 325 Get scan group attribute data from the HDF5 file. 326 327 Parameters 328 ---------- 329 scan_index : int 330 The index of the scan. 331 time_index : int 332 The index of the time point. 333 attr_group : str 334 The attribute group. 335 attr_srt : str, optional 336 The attribute string. Default is None. 337 338 Returns 339 ------- 340 dict 341 The attribute data. 342 343 Notes 344 ----- 345 This method retrieves attribute data from the HDF5 file for a specific scan and time point. 346 The attribute data is stored in the specified attribute group. 347 If an attribute string is provided, only the corresponding attribute value is returned. 348 If no attribute string is provided, all attribute data in the group is returned as a dictionary. 349 """ 350 # Get index of self.scans where scan_index_str is found 351 scan_label = self.scans[scan_index] 352 353 index_to_pull = self.get_time_index_to_pull(scan_label, time_index) 354 355 if attr_srt: 356 return json.loads( 357 self.h5pydata[scan_label][index_to_pull].attrs[attr_group] 358 )[attr_srt] 359 360 else: 361 data = self.h5pydata[scan_label][index_to_pull].attrs.get(attr_group) 362 if data: 363 return json.loads(data) 364 else: 365 return {} 366 367 def get_raw_data_attr_data(self, scan_index, attr_group, attr_str): 368 """ 369 Get raw data attribute data from the HDF5 file. 370 371 Parameters 372 ---------- 373 scan_index : int 374 The index of the scan. 375 attr_group : str 376 The attribute group. 377 attr_str : str 378 The attribute string. 379 380 Returns 381 ------- 382 dict 383 The attribute data. 384 385 Raises 386 ------ 387 KeyError 388 If the attribute string is not found in the attribute group. 389 390 Notes 391 ----- 392 This method retrieves the attribute data associated with a specific scan, attribute group, and attribute string 393 from the HDF5 file. It returns the attribute data as a dictionary. 394 395 Example usage: 396 >>> data = get_raw_data_attr_data(0, "group1", "attribute1") 397 >>> print(data) 398 {'key1': 'value1', 'key2': 'value2'} 399 """ 400 scan_label = self.scans[scan_index] 401 402 # First try to get from raw_ms dataset attributes (backward compatibility) 403 if "raw_ms" in self.h5pydata[scan_label] and attr_group in self.h5pydata[scan_label]["raw_ms"].attrs: 404 try: 405 return json.loads(self.h5pydata[scan_label]["raw_ms"].attrs[attr_group])[attr_str] 406 except KeyError: 407 attr_str = attr_str.replace("baseline", "baselise") 408 return json.loads(self.h5pydata[scan_label]["raw_ms"].attrs[attr_group])[attr_str] 409 410 # If not found in raw_ms, try to get from scan group attributes (new format) 411 elif attr_group in self.h5pydata[scan_label].attrs: 412 try: 413 return json.loads(self.h5pydata[scan_label].attrs[attr_group])[attr_str] 414 except KeyError: 415 attr_str = attr_str.replace("baseline", "baselise") 416 return json.loads(self.h5pydata[scan_label].attrs[attr_group])[attr_str] 417 418 else: 419 raise KeyError(f"Attribute group '{attr_group}' not found in either raw_ms dataset or scan group for scan {scan_label}") 420 421 def get_output_parameters(self, polarity, scan_index=0): 422 """ 423 Get the output parameters for the mass spectrum. 424 425 Parameters 426 ---------- 427 polarity : str 428 The polarity of the mass spectrum. 429 scan_index : int, optional 430 The index of the scan. Default is 0. 431 432 Returns 433 ------- 434 dict 435 The output parameters. 436 """ 437 438 d_params = default_parameters(self.file_location) 439 d_params["filename_path"] = self.file_location 440 d_params["polarity"] = self.get_raw_data_attr_data( 441 scan_index, "MassSpecAttrs", "polarity" 442 ) 443 d_params["rt"] = self.get_raw_data_attr_data(scan_index, "MassSpecAttrs", "rt") 444 445 d_params["tic"] = self.get_raw_data_attr_data( 446 scan_index, "MassSpecAttrs", "tic" 447 ) 448 449 d_params["mobility_scan"] = self.get_raw_data_attr_data( 450 scan_index, "MassSpecAttrs", "mobility_scan" 451 ) 452 d_params["mobility_rt"] = self.get_raw_data_attr_data( 453 scan_index, "MassSpecAttrs", "mobility_rt" 454 ) 455 d_params["Aterm"] = self.get_raw_data_attr_data( 456 scan_index, "MassSpecAttrs", "Aterm" 457 ) 458 d_params["Bterm"] = self.get_raw_data_attr_data( 459 scan_index, "MassSpecAttrs", "Bterm" 460 ) 461 d_params["Cterm"] = self.get_raw_data_attr_data( 462 scan_index, "MassSpecAttrs", "Cterm" 463 ) 464 d_params["baseline_noise"] = self.get_raw_data_attr_data( 465 scan_index, "MassSpecAttrs", "baseline_noise" 466 ) 467 d_params["baseline_noise_std"] = self.get_raw_data_attr_data( 468 scan_index, "MassSpecAttrs", "baseline_noise_std" 469 ) 470 471 d_params["analyzer"] = self.get_high_level_attr_data("analyzer") 472 d_params["instrument_label"] = self.get_high_level_attr_data("instrument_label") 473 d_params["sample_name"] = self.get_high_level_attr_data("sample_name") 474 475 return d_params
15class ReadCoreMSHDF_MassSpectrum(ReadCoremsMasslist): 16 """Class for reading mass spectrum data from a CoreMS HDF5 file. 17 18 Attributes 19 ---------- 20 h5pydata : h5py.File 21 The HDF5 file object. 22 scans : list 23 List of scan labels in the HDF5 file. 24 25 Parameters 26 ---------- 27 file_location : str or S3Path 28 The path to the CoreMS HDF5 file. 29 30 Methods 31 ------- 32 * load_raw_data(mass_spectrum, scan_index=0) Load raw data into the mass spectrum object. 33 * get_mass_spectrum(scan_number=0, time_index=-1, auto_process=True, load_settings=True, load_raw=True).Get a mass spectrum object. 34 * load_settings(mass_spectrum, scan_index=0, time_index=-1). Load settings into the mass spectrum object. 35 * get_dataframe(scan_index=0, time_index=-1). Get a pandas DataFrame representing the mass spectrum. 36 * get_time_index_to_pull(scan_label, time_index). Get the time index to pull from the HDF5 file. 37 * get_high_level_attr_data(attr_str). Get high-level attribute data from the HDF5 file. 38 * get_scan_group_attr_data(scan_index, time_index, attr_group, attr_srt=None). Get scan group attribute data from the HDF5 file. 39 * get_raw_data_attr_data(scan_index, attr_group, attr_str). Get raw data attribute data from the HDF5 file. 40 * get_output_parameters(polarity, scan_index=0). Get the output parameters for the mass spectrum. 41 """ 42 43 def __init__(self, file_location): 44 super().__init__(file_location) 45 46 if isinstance(self.file_location, S3Path): 47 data = BytesIO(self.file_location.open("rb").read()) 48 else: 49 data = self.file_location 50 51 self.h5pydata = h5py.File(data, "r") 52 53 self.scans = list(self.h5pydata.keys()) 54 55 def close(self): 56 """Close the underlying HDF5 file handle.""" 57 if self.h5pydata and self.h5pydata.id.valid: 58 self.h5pydata.close() 59 60 def __enter__(self): 61 return self 62 63 def __exit__(self, *args): 64 self.close() 65 66 def load_raw_data(self, mass_spectrum, scan_index=0): 67 """ 68 Load raw data into the mass spectrum object. 69 70 Parameters 71 ---------- 72 mass_spectrum : MassSpecCentroid 73 The mass spectrum object to load the raw data into. 74 scan_index : int, optional 75 The index of the scan to load the raw data from. Default is 0. 76 """ 77 78 scan_label = self.scans[scan_index] 79 80 # Check if the "raw_ms" dataset exists and has data 81 if "raw_ms" in self.h5pydata[scan_label] and self.h5pydata[scan_label]["raw_ms"].shape is not None: 82 mz_profile = self.h5pydata[scan_label]["raw_ms"][0] 83 84 abundance_profile = self.h5pydata[scan_label]["raw_ms"][1] 85 86 mass_spectrum.mz_exp_profile = mz_profile 87 88 mass_spectrum.abundance_profile = abundance_profile 89 90 def get_mass_spectrum( 91 self, 92 scan_number=0, 93 time_index=-1, 94 auto_process=True, 95 load_settings=True, 96 load_raw=True, 97 load_molecular_formula=True, 98 ): 99 """ 100 Instantiate a mass spectrum object from the CoreMS HDF5 file. 101 Note that this always returns a centroid mass spectrum object; functionality for profile and 102 frequency mass spectra is not yet implemented. 103 104 Parameters 105 ---------- 106 scan_number : int, optional 107 The index of the scan to retrieve the mass spectrum from. Default is 0. 108 time_index : int, optional 109 The index of the time point to retrieve the mass spectrum from. Default is -1. 110 auto_process : bool, optional 111 Whether to automatically process the mass spectrum. Default is True. 112 load_settings : bool, optional 113 Whether to load the settings into the mass spectrum object. Default is True. 114 load_raw : bool, optional 115 Whether to load the raw data into the mass spectrum object. Default is True. 116 load_molecular_formula : bool, optional 117 Whether to load the molecular formula into the mass spectrum object. 118 Default is True. 119 120 Returns 121 ------- 122 MassSpecCentroid 123 The mass spectrum object. 124 125 Raises 126 ------ 127 ValueError 128 If the CoreMS file is not valid. 129 If the mass spectrum has not been processed and load_molecular_formula is True. 130 """ 131 if "mass_spectra" in self.scans[0]: 132 scan_index = self.scans.index("mass_spectra/" + str(scan_number)) 133 else: 134 scan_index = self.scans.index(str(scan_number)) 135 dataframe = self.get_dataframe(scan_index, time_index=time_index) 136 if dataframe["Molecular Formula"].any() and not dataframe["C"].any(): 137 cols = dataframe.columns.tolist() 138 cols = cols[cols.index("Molecular Formula") + 1 :] 139 for index, row in dataframe.iterrows(): 140 if row["Molecular Formula"] is not None: 141 og_formula = row["Molecular Formula"] 142 for col in cols: 143 if "col" in og_formula: 144 # get the digit after the element ("col") in the molecular formula and set it to the dataframe 145 row[col] = int(og_formula.split(col)[1].split(" ")[0]) 146 147 if not set( 148 ["H/C", "O/C", "Heteroatom Class", "Ion Type", "Is Isotopologue"] 149 ).issubset(dataframe.columns): 150 raise ValueError( 151 "%s it is not a valid CoreMS file" % str(self.file_location) 152 ) 153 154 dataframe.rename(columns=self.parameters.header_translate, inplace=True) 155 156 # Cast m/z, and 'Peak Height' to float 157 dataframe["m/z"] = dataframe["m/z"].astype(float) 158 dataframe["Peak Height"] = dataframe["Peak Height"].astype(float) 159 160 polarity = dataframe["Ion Charge"].values[0] 161 162 output_parameters = self.get_output_parameters(polarity, scan_index=scan_index) 163 164 mass_spec_obj = MassSpecCentroid( 165 dataframe.to_dict(orient="list"), output_parameters, auto_process=False 166 ) 167 168 if auto_process: 169 # Set the settings on the mass spectrum object to relative abuncance of 0 so all peaks get added 170 mass_spec_obj.settings.noise_threshold_method = "absolute_abundance" 171 mass_spec_obj.settings.noise_threshold_absolute_abundance = 0 172 mass_spec_obj.process_mass_spec() 173 174 if load_settings: 175 # Load settings into the mass spectrum object 176 self.load_settings( 177 mass_spec_obj, scan_index=scan_index, time_index=time_index 178 ) 179 180 if load_raw: 181 self.load_raw_data(mass_spec_obj, scan_index=scan_index) 182 183 if load_molecular_formula: 184 if not auto_process: 185 raise ValueError( 186 "Can only add molecular formula if the mass spectrum has been processed" 187 ) 188 else: 189 self.add_molecular_formula(mass_spec_obj, dataframe) 190 191 return mass_spec_obj 192 193 def load_settings(self, mass_spectrum, scan_index=0, time_index=-1): 194 """ 195 Load settings into the mass spectrum object. 196 197 Parameters 198 ---------- 199 mass_spectrum : MassSpecCentroid 200 The mass spectrum object to load the settings into. 201 scan_index : int, optional 202 The index of the scan to load the settings from. Default is 0. 203 time_index : int, optional 204 The index of the time point to load the settings from. Default is -1. 205 """ 206 207 loaded_settings = {} 208 loaded_settings["MoleculaSearch"] = self.get_scan_group_attr_data( 209 scan_index, time_index, "MoleculaSearchSetting" 210 ) 211 loaded_settings["MassSpecPeak"] = self.get_scan_group_attr_data( 212 scan_index, time_index, "MassSpecPeakSetting" 213 ) 214 loaded_settings["MassSpectrum"] = self.get_scan_group_attr_data( 215 scan_index, time_index, "MassSpectrumSetting" 216 ) 217 loaded_settings["Transient"] = self.get_scan_group_attr_data( 218 scan_index, time_index, "TransientSetting" 219 ) 220 221 _set_dict_data_ms(loaded_settings, mass_spectrum) 222 223 def get_dataframe(self, scan_index=0, time_index=-1): 224 """ 225 Get a pandas DataFrame representing the mass spectrum. 226 227 Parameters 228 ---------- 229 scan_index : int, optional 230 The index of the scan to retrieve the DataFrame from. Default is 0. 231 time_index : int, optional 232 The index of the time point to retrieve the DataFrame from. Default is -1. 233 234 Returns 235 ------- 236 DataFrame 237 The pandas DataFrame representing the mass spectrum. 238 """ 239 240 columnsLabels = self.get_scan_group_attr_data( 241 scan_index, time_index, "ColumnsLabels" 242 ) 243 244 scan_label = self.scans[scan_index] 245 246 index_to_pull = self.get_time_index_to_pull(scan_label, time_index) 247 248 corems_table_data = self.h5pydata[scan_label][index_to_pull] 249 250 list_dict = [] 251 for row in corems_table_data: 252 data_dict = {} 253 for data_index, data in enumerate(row): 254 label = columnsLabels[data_index] 255 # if data starts with a b' it is a byte string, so decode it 256 if isinstance(data, bytes): 257 data = data.decode("utf-8") 258 if data == "nan": 259 data = None 260 data_dict[label] = data 261 262 list_dict.append(data_dict) 263 264 # Reorder the columns from low to high "Index" to match the order of the dataframe 265 df = DataFrame(list_dict) 266 # set the "Index" column to int so it sorts correctly 267 df["Index"] = df["Index"].astype(int) 268 df = df.sort_values(by="Index") 269 # Reset index to match the "Index" column 270 df = df.set_index("Index", drop=False) 271 272 return df 273 274 def get_time_index_to_pull(self, scan_label, time_index): 275 """ 276 Get the time index to pull from the HDF5 file. 277 278 Parameters 279 ---------- 280 scan_label : str 281 The label of the scan. 282 time_index : int 283 The index of the time point. 284 285 Returns 286 ------- 287 str 288 The time index to pull. 289 """ 290 291 time_data = sorted( 292 [(i, int(i)) for i in self.h5pydata[scan_label].keys() if i != "raw_ms"], 293 key=lambda m: m[1], 294 ) 295 296 index_to_pull = time_data[time_index][0] 297 298 return index_to_pull 299 300 def get_high_level_attr_data(self, attr_str): 301 """ 302 Get high-level attribute data from the HDF5 file. 303 304 Parameters 305 ---------- 306 attr_str : str 307 The attribute string. 308 309 Returns 310 ------- 311 dict 312 The attribute data. 313 314 Raises 315 ------ 316 KeyError 317 If the attribute string is not found in the HDF5 file. 318 """ 319 320 return self.h5pydata.attrs[attr_str] 321 322 def get_scan_group_attr_data( 323 self, scan_index, time_index, attr_group, attr_srt=None 324 ): 325 """ 326 Get scan group attribute data from the HDF5 file. 327 328 Parameters 329 ---------- 330 scan_index : int 331 The index of the scan. 332 time_index : int 333 The index of the time point. 334 attr_group : str 335 The attribute group. 336 attr_srt : str, optional 337 The attribute string. Default is None. 338 339 Returns 340 ------- 341 dict 342 The attribute data. 343 344 Notes 345 ----- 346 This method retrieves attribute data from the HDF5 file for a specific scan and time point. 347 The attribute data is stored in the specified attribute group. 348 If an attribute string is provided, only the corresponding attribute value is returned. 349 If no attribute string is provided, all attribute data in the group is returned as a dictionary. 350 """ 351 # Get index of self.scans where scan_index_str is found 352 scan_label = self.scans[scan_index] 353 354 index_to_pull = self.get_time_index_to_pull(scan_label, time_index) 355 356 if attr_srt: 357 return json.loads( 358 self.h5pydata[scan_label][index_to_pull].attrs[attr_group] 359 )[attr_srt] 360 361 else: 362 data = self.h5pydata[scan_label][index_to_pull].attrs.get(attr_group) 363 if data: 364 return json.loads(data) 365 else: 366 return {} 367 368 def get_raw_data_attr_data(self, scan_index, attr_group, attr_str): 369 """ 370 Get raw data attribute data from the HDF5 file. 371 372 Parameters 373 ---------- 374 scan_index : int 375 The index of the scan. 376 attr_group : str 377 The attribute group. 378 attr_str : str 379 The attribute string. 380 381 Returns 382 ------- 383 dict 384 The attribute data. 385 386 Raises 387 ------ 388 KeyError 389 If the attribute string is not found in the attribute group. 390 391 Notes 392 ----- 393 This method retrieves the attribute data associated with a specific scan, attribute group, and attribute string 394 from the HDF5 file. It returns the attribute data as a dictionary. 395 396 Example usage: 397 >>> data = get_raw_data_attr_data(0, "group1", "attribute1") 398 >>> print(data) 399 {'key1': 'value1', 'key2': 'value2'} 400 """ 401 scan_label = self.scans[scan_index] 402 403 # First try to get from raw_ms dataset attributes (backward compatibility) 404 if "raw_ms" in self.h5pydata[scan_label] and attr_group in self.h5pydata[scan_label]["raw_ms"].attrs: 405 try: 406 return json.loads(self.h5pydata[scan_label]["raw_ms"].attrs[attr_group])[attr_str] 407 except KeyError: 408 attr_str = attr_str.replace("baseline", "baselise") 409 return json.loads(self.h5pydata[scan_label]["raw_ms"].attrs[attr_group])[attr_str] 410 411 # If not found in raw_ms, try to get from scan group attributes (new format) 412 elif attr_group in self.h5pydata[scan_label].attrs: 413 try: 414 return json.loads(self.h5pydata[scan_label].attrs[attr_group])[attr_str] 415 except KeyError: 416 attr_str = attr_str.replace("baseline", "baselise") 417 return json.loads(self.h5pydata[scan_label].attrs[attr_group])[attr_str] 418 419 else: 420 raise KeyError(f"Attribute group '{attr_group}' not found in either raw_ms dataset or scan group for scan {scan_label}") 421 422 def get_output_parameters(self, polarity, scan_index=0): 423 """ 424 Get the output parameters for the mass spectrum. 425 426 Parameters 427 ---------- 428 polarity : str 429 The polarity of the mass spectrum. 430 scan_index : int, optional 431 The index of the scan. Default is 0. 432 433 Returns 434 ------- 435 dict 436 The output parameters. 437 """ 438 439 d_params = default_parameters(self.file_location) 440 d_params["filename_path"] = self.file_location 441 d_params["polarity"] = self.get_raw_data_attr_data( 442 scan_index, "MassSpecAttrs", "polarity" 443 ) 444 d_params["rt"] = self.get_raw_data_attr_data(scan_index, "MassSpecAttrs", "rt") 445 446 d_params["tic"] = self.get_raw_data_attr_data( 447 scan_index, "MassSpecAttrs", "tic" 448 ) 449 450 d_params["mobility_scan"] = self.get_raw_data_attr_data( 451 scan_index, "MassSpecAttrs", "mobility_scan" 452 ) 453 d_params["mobility_rt"] = self.get_raw_data_attr_data( 454 scan_index, "MassSpecAttrs", "mobility_rt" 455 ) 456 d_params["Aterm"] = self.get_raw_data_attr_data( 457 scan_index, "MassSpecAttrs", "Aterm" 458 ) 459 d_params["Bterm"] = self.get_raw_data_attr_data( 460 scan_index, "MassSpecAttrs", "Bterm" 461 ) 462 d_params["Cterm"] = self.get_raw_data_attr_data( 463 scan_index, "MassSpecAttrs", "Cterm" 464 ) 465 d_params["baseline_noise"] = self.get_raw_data_attr_data( 466 scan_index, "MassSpecAttrs", "baseline_noise" 467 ) 468 d_params["baseline_noise_std"] = self.get_raw_data_attr_data( 469 scan_index, "MassSpecAttrs", "baseline_noise_std" 470 ) 471 472 d_params["analyzer"] = self.get_high_level_attr_data("analyzer") 473 d_params["instrument_label"] = self.get_high_level_attr_data("instrument_label") 474 d_params["sample_name"] = self.get_high_level_attr_data("sample_name") 475 476 return d_params
Class for reading mass spectrum data from a CoreMS HDF5 file.
Attributes
- h5pydata (h5py.File): The HDF5 file object.
- scans (list): List of scan labels in the HDF5 file.
Parameters
- file_location (str or S3Path): The path to the CoreMS HDF5 file.
Methods
- load_raw_data(mass_spectrum, scan_index=0) Load raw data into the mass spectrum object.
- get_mass_spectrum(scan_number=0, time_index=-1, auto_process=True, load_settings=True, load_raw=True).Get a mass spectrum object.
- load_settings(mass_spectrum, scan_index=0, time_index=-1). Load settings into the mass spectrum object.
- get_dataframe(scan_index=0, time_index=-1). Get a pandas DataFrame representing the mass spectrum.
- get_time_index_to_pull(scan_label, time_index). Get the time index to pull from the HDF5 file.
- get_high_level_attr_data(attr_str). Get high-level attribute data from the HDF5 file.
- get_scan_group_attr_data(scan_index, time_index, attr_group, attr_srt=None). Get scan group attribute data from the HDF5 file.
- get_raw_data_attr_data(scan_index, attr_group, attr_str). Get raw data attribute data from the HDF5 file.
- get_output_parameters(polarity, scan_index=0). Get the output parameters for the mass spectrum.
ReadCoreMSHDF_MassSpectrum(file_location)
43 def __init__(self, file_location): 44 super().__init__(file_location) 45 46 if isinstance(self.file_location, S3Path): 47 data = BytesIO(self.file_location.open("rb").read()) 48 else: 49 data = self.file_location 50 51 self.h5pydata = h5py.File(data, "r") 52 53 self.scans = list(self.h5pydata.keys())
def
close(self):
55 def close(self): 56 """Close the underlying HDF5 file handle.""" 57 if self.h5pydata and self.h5pydata.id.valid: 58 self.h5pydata.close()
Close the underlying HDF5 file handle.
def
load_raw_data(self, mass_spectrum, scan_index=0):
66 def load_raw_data(self, mass_spectrum, scan_index=0): 67 """ 68 Load raw data into the mass spectrum object. 69 70 Parameters 71 ---------- 72 mass_spectrum : MassSpecCentroid 73 The mass spectrum object to load the raw data into. 74 scan_index : int, optional 75 The index of the scan to load the raw data from. Default is 0. 76 """ 77 78 scan_label = self.scans[scan_index] 79 80 # Check if the "raw_ms" dataset exists and has data 81 if "raw_ms" in self.h5pydata[scan_label] and self.h5pydata[scan_label]["raw_ms"].shape is not None: 82 mz_profile = self.h5pydata[scan_label]["raw_ms"][0] 83 84 abundance_profile = self.h5pydata[scan_label]["raw_ms"][1] 85 86 mass_spectrum.mz_exp_profile = mz_profile 87 88 mass_spectrum.abundance_profile = abundance_profile
Load raw data into the mass spectrum object.
Parameters
- mass_spectrum (MassSpecCentroid): The mass spectrum object to load the raw data into.
- scan_index (int, optional): The index of the scan to load the raw data from. Default is 0.
def
get_mass_spectrum( self, scan_number=0, time_index=-1, auto_process=True, load_settings=True, load_raw=True, load_molecular_formula=True):
90 def get_mass_spectrum( 91 self, 92 scan_number=0, 93 time_index=-1, 94 auto_process=True, 95 load_settings=True, 96 load_raw=True, 97 load_molecular_formula=True, 98 ): 99 """ 100 Instantiate a mass spectrum object from the CoreMS HDF5 file. 101 Note that this always returns a centroid mass spectrum object; functionality for profile and 102 frequency mass spectra is not yet implemented. 103 104 Parameters 105 ---------- 106 scan_number : int, optional 107 The index of the scan to retrieve the mass spectrum from. Default is 0. 108 time_index : int, optional 109 The index of the time point to retrieve the mass spectrum from. Default is -1. 110 auto_process : bool, optional 111 Whether to automatically process the mass spectrum. Default is True. 112 load_settings : bool, optional 113 Whether to load the settings into the mass spectrum object. Default is True. 114 load_raw : bool, optional 115 Whether to load the raw data into the mass spectrum object. Default is True. 116 load_molecular_formula : bool, optional 117 Whether to load the molecular formula into the mass spectrum object. 118 Default is True. 119 120 Returns 121 ------- 122 MassSpecCentroid 123 The mass spectrum object. 124 125 Raises 126 ------ 127 ValueError 128 If the CoreMS file is not valid. 129 If the mass spectrum has not been processed and load_molecular_formula is True. 130 """ 131 if "mass_spectra" in self.scans[0]: 132 scan_index = self.scans.index("mass_spectra/" + str(scan_number)) 133 else: 134 scan_index = self.scans.index(str(scan_number)) 135 dataframe = self.get_dataframe(scan_index, time_index=time_index) 136 if dataframe["Molecular Formula"].any() and not dataframe["C"].any(): 137 cols = dataframe.columns.tolist() 138 cols = cols[cols.index("Molecular Formula") + 1 :] 139 for index, row in dataframe.iterrows(): 140 if row["Molecular Formula"] is not None: 141 og_formula = row["Molecular Formula"] 142 for col in cols: 143 if "col" in og_formula: 144 # get the digit after the element ("col") in the molecular formula and set it to the dataframe 145 row[col] = int(og_formula.split(col)[1].split(" ")[0]) 146 147 if not set( 148 ["H/C", "O/C", "Heteroatom Class", "Ion Type", "Is Isotopologue"] 149 ).issubset(dataframe.columns): 150 raise ValueError( 151 "%s it is not a valid CoreMS file" % str(self.file_location) 152 ) 153 154 dataframe.rename(columns=self.parameters.header_translate, inplace=True) 155 156 # Cast m/z, and 'Peak Height' to float 157 dataframe["m/z"] = dataframe["m/z"].astype(float) 158 dataframe["Peak Height"] = dataframe["Peak Height"].astype(float) 159 160 polarity = dataframe["Ion Charge"].values[0] 161 162 output_parameters = self.get_output_parameters(polarity, scan_index=scan_index) 163 164 mass_spec_obj = MassSpecCentroid( 165 dataframe.to_dict(orient="list"), output_parameters, auto_process=False 166 ) 167 168 if auto_process: 169 # Set the settings on the mass spectrum object to relative abuncance of 0 so all peaks get added 170 mass_spec_obj.settings.noise_threshold_method = "absolute_abundance" 171 mass_spec_obj.settings.noise_threshold_absolute_abundance = 0 172 mass_spec_obj.process_mass_spec() 173 174 if load_settings: 175 # Load settings into the mass spectrum object 176 self.load_settings( 177 mass_spec_obj, scan_index=scan_index, time_index=time_index 178 ) 179 180 if load_raw: 181 self.load_raw_data(mass_spec_obj, scan_index=scan_index) 182 183 if load_molecular_formula: 184 if not auto_process: 185 raise ValueError( 186 "Can only add molecular formula if the mass spectrum has been processed" 187 ) 188 else: 189 self.add_molecular_formula(mass_spec_obj, dataframe) 190 191 return mass_spec_obj
Instantiate a mass spectrum object from the CoreMS HDF5 file. Note that this always returns a centroid mass spectrum object; functionality for profile and frequency mass spectra is not yet implemented.
Parameters
- scan_number (int, optional): The index of the scan to retrieve the mass spectrum from. Default is 0.
- time_index (int, optional): The index of the time point to retrieve the mass spectrum from. Default is -1.
- auto_process (bool, optional): Whether to automatically process the mass spectrum. Default is True.
- load_settings (bool, optional): Whether to load the settings into the mass spectrum object. Default is True.
- load_raw (bool, optional): Whether to load the raw data into the mass spectrum object. Default is True.
- load_molecular_formula (bool, optional): Whether to load the molecular formula into the mass spectrum object. Default is True.
Returns
- MassSpecCentroid: The mass spectrum object.
Raises
- ValueError: If the CoreMS file is not valid. If the mass spectrum has not been processed and load_molecular_formula is True.
def
load_settings(self, mass_spectrum, scan_index=0, time_index=-1):
193 def load_settings(self, mass_spectrum, scan_index=0, time_index=-1): 194 """ 195 Load settings into the mass spectrum object. 196 197 Parameters 198 ---------- 199 mass_spectrum : MassSpecCentroid 200 The mass spectrum object to load the settings into. 201 scan_index : int, optional 202 The index of the scan to load the settings from. Default is 0. 203 time_index : int, optional 204 The index of the time point to load the settings from. Default is -1. 205 """ 206 207 loaded_settings = {} 208 loaded_settings["MoleculaSearch"] = self.get_scan_group_attr_data( 209 scan_index, time_index, "MoleculaSearchSetting" 210 ) 211 loaded_settings["MassSpecPeak"] = self.get_scan_group_attr_data( 212 scan_index, time_index, "MassSpecPeakSetting" 213 ) 214 loaded_settings["MassSpectrum"] = self.get_scan_group_attr_data( 215 scan_index, time_index, "MassSpectrumSetting" 216 ) 217 loaded_settings["Transient"] = self.get_scan_group_attr_data( 218 scan_index, time_index, "TransientSetting" 219 ) 220 221 _set_dict_data_ms(loaded_settings, mass_spectrum)
Load settings into the mass spectrum object.
Parameters
- mass_spectrum (MassSpecCentroid): The mass spectrum object to load the settings into.
- scan_index (int, optional): The index of the scan to load the settings from. Default is 0.
- time_index (int, optional): The index of the time point to load the settings from. Default is -1.
def
get_dataframe(self, scan_index=0, time_index=-1):
223 def get_dataframe(self, scan_index=0, time_index=-1): 224 """ 225 Get a pandas DataFrame representing the mass spectrum. 226 227 Parameters 228 ---------- 229 scan_index : int, optional 230 The index of the scan to retrieve the DataFrame from. Default is 0. 231 time_index : int, optional 232 The index of the time point to retrieve the DataFrame from. Default is -1. 233 234 Returns 235 ------- 236 DataFrame 237 The pandas DataFrame representing the mass spectrum. 238 """ 239 240 columnsLabels = self.get_scan_group_attr_data( 241 scan_index, time_index, "ColumnsLabels" 242 ) 243 244 scan_label = self.scans[scan_index] 245 246 index_to_pull = self.get_time_index_to_pull(scan_label, time_index) 247 248 corems_table_data = self.h5pydata[scan_label][index_to_pull] 249 250 list_dict = [] 251 for row in corems_table_data: 252 data_dict = {} 253 for data_index, data in enumerate(row): 254 label = columnsLabels[data_index] 255 # if data starts with a b' it is a byte string, so decode it 256 if isinstance(data, bytes): 257 data = data.decode("utf-8") 258 if data == "nan": 259 data = None 260 data_dict[label] = data 261 262 list_dict.append(data_dict) 263 264 # Reorder the columns from low to high "Index" to match the order of the dataframe 265 df = DataFrame(list_dict) 266 # set the "Index" column to int so it sorts correctly 267 df["Index"] = df["Index"].astype(int) 268 df = df.sort_values(by="Index") 269 # Reset index to match the "Index" column 270 df = df.set_index("Index", drop=False) 271 272 return df
Get a pandas DataFrame representing the mass spectrum.
Parameters
- scan_index (int, optional): The index of the scan to retrieve the DataFrame from. Default is 0.
- time_index (int, optional): The index of the time point to retrieve the DataFrame from. Default is -1.
Returns
- DataFrame: The pandas DataFrame representing the mass spectrum.
def
get_time_index_to_pull(self, scan_label, time_index):
274 def get_time_index_to_pull(self, scan_label, time_index): 275 """ 276 Get the time index to pull from the HDF5 file. 277 278 Parameters 279 ---------- 280 scan_label : str 281 The label of the scan. 282 time_index : int 283 The index of the time point. 284 285 Returns 286 ------- 287 str 288 The time index to pull. 289 """ 290 291 time_data = sorted( 292 [(i, int(i)) for i in self.h5pydata[scan_label].keys() if i != "raw_ms"], 293 key=lambda m: m[1], 294 ) 295 296 index_to_pull = time_data[time_index][0] 297 298 return index_to_pull
Get the time index to pull from the HDF5 file.
Parameters
- scan_label (str): The label of the scan.
- time_index (int): The index of the time point.
Returns
- str: The time index to pull.
def
get_high_level_attr_data(self, attr_str):
300 def get_high_level_attr_data(self, attr_str): 301 """ 302 Get high-level attribute data from the HDF5 file. 303 304 Parameters 305 ---------- 306 attr_str : str 307 The attribute string. 308 309 Returns 310 ------- 311 dict 312 The attribute data. 313 314 Raises 315 ------ 316 KeyError 317 If the attribute string is not found in the HDF5 file. 318 """ 319 320 return self.h5pydata.attrs[attr_str]
Get high-level attribute data from the HDF5 file.
Parameters
- attr_str (str): The attribute string.
Returns
- dict: The attribute data.
Raises
- KeyError: If the attribute string is not found in the HDF5 file.
def
get_scan_group_attr_data(self, scan_index, time_index, attr_group, attr_srt=None):
322 def get_scan_group_attr_data( 323 self, scan_index, time_index, attr_group, attr_srt=None 324 ): 325 """ 326 Get scan group attribute data from the HDF5 file. 327 328 Parameters 329 ---------- 330 scan_index : int 331 The index of the scan. 332 time_index : int 333 The index of the time point. 334 attr_group : str 335 The attribute group. 336 attr_srt : str, optional 337 The attribute string. Default is None. 338 339 Returns 340 ------- 341 dict 342 The attribute data. 343 344 Notes 345 ----- 346 This method retrieves attribute data from the HDF5 file for a specific scan and time point. 347 The attribute data is stored in the specified attribute group. 348 If an attribute string is provided, only the corresponding attribute value is returned. 349 If no attribute string is provided, all attribute data in the group is returned as a dictionary. 350 """ 351 # Get index of self.scans where scan_index_str is found 352 scan_label = self.scans[scan_index] 353 354 index_to_pull = self.get_time_index_to_pull(scan_label, time_index) 355 356 if attr_srt: 357 return json.loads( 358 self.h5pydata[scan_label][index_to_pull].attrs[attr_group] 359 )[attr_srt] 360 361 else: 362 data = self.h5pydata[scan_label][index_to_pull].attrs.get(attr_group) 363 if data: 364 return json.loads(data) 365 else: 366 return {}
Get scan group attribute data from the HDF5 file.
Parameters
- scan_index (int): The index of the scan.
- time_index (int): The index of the time point.
- attr_group (str): The attribute group.
- attr_srt (str, optional): The attribute string. Default is None.
Returns
- dict: The attribute data.
Notes
This method retrieves attribute data from the HDF5 file for a specific scan and time point. The attribute data is stored in the specified attribute group. If an attribute string is provided, only the corresponding attribute value is returned. If no attribute string is provided, all attribute data in the group is returned as a dictionary.
def
get_raw_data_attr_data(self, scan_index, attr_group, attr_str):
368 def get_raw_data_attr_data(self, scan_index, attr_group, attr_str): 369 """ 370 Get raw data attribute data from the HDF5 file. 371 372 Parameters 373 ---------- 374 scan_index : int 375 The index of the scan. 376 attr_group : str 377 The attribute group. 378 attr_str : str 379 The attribute string. 380 381 Returns 382 ------- 383 dict 384 The attribute data. 385 386 Raises 387 ------ 388 KeyError 389 If the attribute string is not found in the attribute group. 390 391 Notes 392 ----- 393 This method retrieves the attribute data associated with a specific scan, attribute group, and attribute string 394 from the HDF5 file. It returns the attribute data as a dictionary. 395 396 Example usage: 397 >>> data = get_raw_data_attr_data(0, "group1", "attribute1") 398 >>> print(data) 399 {'key1': 'value1', 'key2': 'value2'} 400 """ 401 scan_label = self.scans[scan_index] 402 403 # First try to get from raw_ms dataset attributes (backward compatibility) 404 if "raw_ms" in self.h5pydata[scan_label] and attr_group in self.h5pydata[scan_label]["raw_ms"].attrs: 405 try: 406 return json.loads(self.h5pydata[scan_label]["raw_ms"].attrs[attr_group])[attr_str] 407 except KeyError: 408 attr_str = attr_str.replace("baseline", "baselise") 409 return json.loads(self.h5pydata[scan_label]["raw_ms"].attrs[attr_group])[attr_str] 410 411 # If not found in raw_ms, try to get from scan group attributes (new format) 412 elif attr_group in self.h5pydata[scan_label].attrs: 413 try: 414 return json.loads(self.h5pydata[scan_label].attrs[attr_group])[attr_str] 415 except KeyError: 416 attr_str = attr_str.replace("baseline", "baselise") 417 return json.loads(self.h5pydata[scan_label].attrs[attr_group])[attr_str] 418 419 else: 420 raise KeyError(f"Attribute group '{attr_group}' not found in either raw_ms dataset or scan group for scan {scan_label}")
Get raw data attribute data from the HDF5 file.
Parameters
- scan_index (int): The index of the scan.
- attr_group (str): The attribute group.
- attr_str (str): The attribute string.
Returns
- dict: The attribute data.
Raises
- KeyError: If the attribute string is not found in the attribute group.
Notes
This method retrieves the attribute data associated with a specific scan, attribute group, and attribute string from the HDF5 file. It returns the attribute data as a dictionary.
Example usage:
>>> data = get_raw_data_attr_data(0, "group1", "attribute1")
>>> print(data)
{'key1': 'value1', 'key2': 'value2'}
def
get_output_parameters(self, polarity, scan_index=0):
422 def get_output_parameters(self, polarity, scan_index=0): 423 """ 424 Get the output parameters for the mass spectrum. 425 426 Parameters 427 ---------- 428 polarity : str 429 The polarity of the mass spectrum. 430 scan_index : int, optional 431 The index of the scan. Default is 0. 432 433 Returns 434 ------- 435 dict 436 The output parameters. 437 """ 438 439 d_params = default_parameters(self.file_location) 440 d_params["filename_path"] = self.file_location 441 d_params["polarity"] = self.get_raw_data_attr_data( 442 scan_index, "MassSpecAttrs", "polarity" 443 ) 444 d_params["rt"] = self.get_raw_data_attr_data(scan_index, "MassSpecAttrs", "rt") 445 446 d_params["tic"] = self.get_raw_data_attr_data( 447 scan_index, "MassSpecAttrs", "tic" 448 ) 449 450 d_params["mobility_scan"] = self.get_raw_data_attr_data( 451 scan_index, "MassSpecAttrs", "mobility_scan" 452 ) 453 d_params["mobility_rt"] = self.get_raw_data_attr_data( 454 scan_index, "MassSpecAttrs", "mobility_rt" 455 ) 456 d_params["Aterm"] = self.get_raw_data_attr_data( 457 scan_index, "MassSpecAttrs", "Aterm" 458 ) 459 d_params["Bterm"] = self.get_raw_data_attr_data( 460 scan_index, "MassSpecAttrs", "Bterm" 461 ) 462 d_params["Cterm"] = self.get_raw_data_attr_data( 463 scan_index, "MassSpecAttrs", "Cterm" 464 ) 465 d_params["baseline_noise"] = self.get_raw_data_attr_data( 466 scan_index, "MassSpecAttrs", "baseline_noise" 467 ) 468 d_params["baseline_noise_std"] = self.get_raw_data_attr_data( 469 scan_index, "MassSpecAttrs", "baseline_noise_std" 470 ) 471 472 d_params["analyzer"] = self.get_high_level_attr_data("analyzer") 473 d_params["instrument_label"] = self.get_high_level_attr_data("instrument_label") 474 d_params["sample_name"] = self.get_high_level_attr_data("sample_name") 475 476 return d_params
Get the output parameters for the mass spectrum.
Parameters
- polarity (str): The polarity of the mass spectrum.
- scan_index (int, optional): The index of the scan. Default is 0.
Returns
- dict: The output parameters.
Inherited Members
- corems.mass_spectrum.input.baseClass.MassListBaseClass
- file_location
- header_lines
- isCentroid
- isThermoProfile
- headerless
- analyzer
- instrument_label
- sample_name
- parameters
- set_parameter_from_toml
- set_parameter_from_json
- data_type
- delimiter
- encoding_detector
- set_data_type
- clean_data_frame
- check_columns
- read_xml_peaks
- get_xml_polarity