aghplctools package¶
Subpackages¶
aghplctools.batch module¶
aghplctools.config module¶
aghplctools.data_types module¶
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class
aghplctools.data_types.
DADSignal
(wavelength: Union[float, unithandler.base.UnitFloat], bandwidth: Union[float, unithandler.base.UnitFloat] = 1.0, reference: Union[DADSignal, aghplctools.data_types.DADSignalInfo, str] = None, name: str = None, spectrum: aghplctools.data_types.DADSpectrum = None)¶ Bases:
aghplctools.data_types.DADSignalInfo
Class describing a DAD signal and its data.
Parameters: - wavelength – wavelength for the signal
- bandwidth – band width for the wavelength (signal is centered on the wavelength with this width)
- reference – reference information for the signal
- name – convenience name for the signal
- spectrum – a DADSpectrum object which will be referenced for retrieving data.
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as_data_table
() → list¶ Returns the signal as a list-style data table with appropriate headers and data
Returns: data table
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as_iterable_data_table
()¶ Returns an iterable which yields a data table with appropriate headers and data
Returns: data table as iterable
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band_string
¶ A string representation of the band specified (e.g. “210 (4) nm”)
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bandwidth
¶ band width for the signal band
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classmethod
create_from_DADSignalInfo
(obj: aghplctools.data_types.DADSignalInfo, spectrum: aghplctools.data_types.DADSpectrum) → aghplctools.data_types.DADSignal¶ generates a DADSignal object from a DADSignalInfo object and a spectrum
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mean_referenced_intensities
¶ mean referenced band (mean unreferenced intensities minus the mean intensities of the reference)
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mean_unreferenced_intensities
¶ mean unreferenced intensities for the band
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reference
¶ reference band for the signal band
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retention_times
¶ retention times associated with the intensity array
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unreferenced_intensities
¶ unreferenced intensities for the band
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wavelength
¶ wavelength for the signal
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write_signal_to_csv
(filename: str) → str¶ Writes the signal intensities to the specified csv file.
Parameters: filename – file name to write to Returns: file path that was written
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class
aghplctools.data_types.
DADSignalInfo
(wavelength: Union[float, unithandler.base.UnitFloat], bandwidth: Union[float, unithandler.base.UnitFloat] = 1.0, reference: Union[DADSignalInfo, str] = None, name: str = None)¶ Bases:
object
Class describing a DAD signal and its parameters
Parameters: - wavelength – wavelength for the signal
- bandwidth – band width for the wavelength (signal is centered on the wavelength with this width)
- reference – reference information for the signal
- name – convenience name for the signal
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DEFAULT_TIME_UNIT
= 'min'¶
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DEFAULT_WAVELENGTH_UNIT
= 'nm'¶
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agilent_specification_string
¶ the specification string describing this instance (can be passed to create_from_string to reinstantiate)
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bandwidth
¶ bandwidth for the signal band
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classmethod
create_from_agilent_string
(string: str, name_override: str = None) → aghplctools.data_types.DADSignalInfo¶ Creates a class instance from a standard Agilent signal description string (e.g. ‘DAD1 A, Sig=210,4 Ref=360,100’)
Parameters: - string – signal description string
- name_override – override for name specification
Returns: DADSignal object
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classmethod
get_values_from_agilent_string
(string: str) → dict¶ Parses a standard Agilent signal description string (e.g. ‘DAD1 A, Sig=210,4 Ref=360,100’) and returns a dictionary of parsed values (can be used to instantiate a DADSignalInfo instance).
Parameters: string – signal description string Returns: dictionary of parameters
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reference
¶ Reference band for the signal band
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wavelength
¶ Wavelength for the signal
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class
aghplctools.data_types.
DADSpectrum
(filename=None, ftype=None, data=None)¶ Bases:
aston.tracefile.agilent_uv.AgilentCSDAD2
An object describing an Agilent DAD spectrum for a sample. Inherits Aston AgilentCSDAD2 and has additional methods for retrieving band information.
Parameters: - filename – target filetype
- ftype –
- data –
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classmethod
create_from_D_file
(file_path: Union[pathlib.Path, str]) → aghplctools.data_types.DADSpectrum¶ Creates a DADSpectrum instance from an Agilent .D file
Parameters: file_path – path to .D sample file Returns: interpreted .D file with metadata and loaded UV data
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get_band_intensities
(wavelength: float, bandwidth: float = 1.0) → numpy.ndarray¶ Retrieve array of values described by the wavelength and band width described. The returned array will have shape [wavelength, retention time]. The corresponding wavelengths are given by DADSpectrum.get_band_wavelengths and the retention times by DADSpectrum.retention_times.
Parameters: - wavelength – wavelength
- bandwidth – band width
Returns: array of band intensities
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get_band_mean_intensity
(wavelength: float, bandwidth: float = 1.0) → numpy.ndarray¶ Retrieve the intensity array described by the wavelength and bandwidth described. The returned array will be the mean of the intensities in the band (wavelength - bandwidth / 2, wavelength + bandwidth / 2).
Parameters: - wavelength – wavelength
- bandwidth – band width
Returns: array of mean intensities
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get_band_wavelengths
(wavelength: float, bandwidth: float = 1.0) → list¶ Returns a list of wavelengths corresponding to the band specified.
Parameters: - wavelength – wavelength
- bandwidth – band width
Returns:
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get_intensities_from_signal
(signal: aghplctools.data_types.DADSignalInfo) → numpy.ndarray¶ Retrieve the intensity array described by the DADSignalInfo object.
Parameters: signal – signal descriptor Returns: array of mean intensities
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maximum_wavelength_array
¶ Array of the wavelengths for the maximum intensity at each retention time
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retention_times
¶ retention times corresponding to the data array (min)
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total_absorbance_chromatogram
¶ The total absorbance chromatogram for the spectrum (sum of all intensities for each retention time)
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wavelengths
¶ list of wavelengths for the DAD
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write_to_allotrope
(filename: str)¶
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class
aghplctools.data_types.
HPLCSample
(sample_name: str, datetimestamp: Union[str, datetime.datetime], method_name: str, signals: Union[List[aghplctools.data_types.DADSignalInfo], List[aghplctools.data_types.DADSignal], List[str]], spectrum: aghplctools.data_types.DADSpectrum = None, directory: str = None)¶ Bases:
aghplctools.data_types.HPLCSampleInfo
Data class for describing an HPLC sample containing metadata and spectral data.
Parameters: - sample_name – name for sample
- datetimestamp – date and time stamp for when the sample was run
- method_name – name of method used to run the sample
- signals – list of signals associated with the run
- spectrum – DADSpectrum object with loaded data
- directory – directory path where the sample may be found
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add_signal
(new_signal: Union[aghplctools.data_types.DADSignalInfo, dict, str]) → aghplctools.data_types.DADSignal¶ Adds a new signal to the HPLCSample instance.
Parameters: new_signal – new signal to add. Supported inputs are Agilent specification strings (e.g. ‘DAD1 A, Sig=210,4 Ref=360,100’) DADSignalInfo objects or a dictionary of keyword arguments for instantiating the same. Returns: the created signal
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classmethod
create_from_D_file
(file_path: Union[pathlib.Path, str]) → aghplctools.data_types.HPLCSample¶ Creates an HPLCSample instance from a .D file.
Parameters: file_path – file path to Agilent .D folder Returns: instantiated HPLCSample with loaded data
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classmethod
create_from_acaml
(acaml: Union[str, xml.etree.ElementTree.ElementTree]) → aghplctools.data_types.HPLCSampleInfo¶ not supported for HPLCSample class
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write_signals_to_csv
(directory: Union[str, pathlib.Path] = None) → List[str]¶ Writes the signals to csv in the directory specified. If no directory is specified, the csv files will be written to the directory path specified in the directory attribute of the instance.
Parameters: directory – directory path
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write_signals_to_xlsx
(output_file: str = None) → str¶ Writes the signals to a single excel file.
Parameters: output_file – target file. If this is not specified Returns: path to the written file
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class
aghplctools.data_types.
HPLCSampleInfo
(sample_name: str, datetimestamp: Union[str, datetime.datetime], method_name: str, signals: Union[List[aghplctools.data_types.DADSignalInfo], List[str]])¶ Bases:
object
Data class for describing an HPLC sample.
Parameters: - sample_name – name for sample
- datetimestamp – date and time stamp for when the sample was run
- method_name – name of method used to run the sample
- signals – list of signals associated with the run
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as_dict
() → dict¶ Returns the sample data as a dictionary
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classmethod
create_from_acaml
(acaml: Union[str, xml.etree.ElementTree.ElementTree]) → aghplctools.data_types.HPLCSampleInfo¶ Creates sample structure from an acaml file. (use sequence.acam_ in the desired .D folder)
Parameters: acaml – path to acaml file or parsed element tree root Returns: parsed Sample instance
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date
¶ date which the sample was run on
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classmethod
get_values_from_acaml
(acaml: Union[str, pathlib.Path, xml.etree.ElementTree.ElementTree]) → dict¶ Gets relevant values from an acaml file. (use sequence.acam_ in the desired .D folder)
Parameters: acaml – path to acaml file or parsed element tree root Returns: dictionary of values of interest
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timestamp
¶ Time of the day when the sample was run
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aghplctools.data_types.
strptime_agilent_dt
(dt_string: str) → datetime.datetime¶ Performs strptime on Agilent datetime string
Parameters: dt_string – agilent datetime strings Returns: parsed datetime object