aghplctools package¶

Subpackages¶

aghplctools.ingestion package

aghplctools.batch module¶

aghplctools.batch.batch_convert_signals_to_csv(folder_path: str, *additional_signals, verbose: Union[bool, int] = True)¶

Iterates through all .D files in the target directory and writes the signals of those files to csv. Additional signals may be specified to “reprocess” the data.

Parameters:	folder_path – folder path to iterate through additional_signals – additional signals to process. Supported inputs are agilent specification strings (e.g. ‘DAD1 A, Sig=210,4 Ref=360,100’), DADSignalInfo objects, or dictionaries of keyword arguments for instantiation of DADSignalInfo objects verbose – logging flag or level for function (prints progress info to console)

aghplctools.batch.batch_report_text_to_xlsx(folder: str, watchfor: str = 'Report.TXT')¶

Batch converts all report text files in a directory to xlsx

Parameters:	folder – directory to search watchfor – file name to watch for

aghplctools.batch.pull_hplc_data_from_folder(folder, targets, wiggle=0.01, watchfor='Report.TXT')¶

Pulls the HPLC integrations for all report files within the specified directory. This function was designed to pull all data from a given day. This method only pulls data which exists in the reports, which can result in asymmetric data for timepoint analysis (i.e. it assumes that subsequent runs are unrelated to others). If the data in a folder are for time-course analysis, use pull_hplc_data_from_folder_timepoint().

Parameters:	folder – The folder to search for report files targets – target dictionary of the form {‘name’: [wavelength, retention time], …} wiggle – the wiggle time around retention times watchfor – the name of the report file to watch
Returns:	dictionary of HPLCTarget instances in the format {‘name’: HPLCTarget, …}
Return type:	dict

aghplctools.batch.pull_hplc_data_from_folder_timepoint(folder, wiggle=0.02, watchfor='Report.TXT')¶

Pulls all HPLC data from a folder assuming that the contents of a folder are from an ordered, time-course run (i.e. the contents of one report are related to the others in the folder). The method will automatically watch for new retention times and will prepopulate appearing values with zeros. The resulting targets will have a consistent number of values across the folder.

Parameters:	folder – The folder to search for report files wiggle – the wiggle time around retention times watchfor – the name of the report file to watch
Returns:	dictionary of HPLCTarget instances in the format {wavelength: {retention_time: HPLCTarget, …}, …}
Return type:	dict

aghplctools.config module¶

Common configuration variables which are consistent across the system

aghplctools.data_types module¶

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.

as_data_table() → list¶

Returns the signal as a list-style data table with appropriate headers and data

Returns:	data table

as_iterable_data_table()¶

Returns an iterable which yields a data table with appropriate headers and data

Returns:	data table as iterable

band_string¶: A string representation of the band specified (e.g. “210 (4) nm”)

bandwidth¶: band width for the signal band

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

mean_referenced_intensities¶: mean referenced band (mean unreferenced intensities minus the mean intensities of the reference)

mean_unreferenced_intensities¶: mean unreferenced intensities for the band

reference¶: reference band for the signal band

retention_times¶: retention times associated with the intensity array

unreferenced_intensities¶: unreferenced intensities for the band

wavelength¶: wavelength for the signal

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

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

DEFAULT_TIME_UNIT = 'min'¶

DEFAULT_WAVELENGTH_UNIT = 'nm'¶

agilent_specification_string¶: the specification string describing this instance (can be passed to create_from_string to reinstantiate)

bandwidth¶: bandwidth for the signal band

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

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

reference¶: Reference band for the signal band

wavelength¶: Wavelength for the signal

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 –

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

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

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

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:

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

maximum_wavelength_array¶: Array of the wavelengths for the maximum intensity at each retention time

retention_times¶: retention times corresponding to the data array (min)

total_absorbance_chromatogram¶: The total absorbance chromatogram for the spectrum (sum of all intensities for each retention time)

wavelengths¶: list of wavelengths for the DAD

write_to_allotrope(filename: str)¶

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

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

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

classmethod create_from_acaml(acaml: Union[str, xml.etree.ElementTree.ElementTree]) → aghplctools.data_types.HPLCSampleInfo¶: not supported for HPLCSample class

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

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

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

as_dict() → dict¶: Returns the sample data as a dictionary

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

date¶: date which the sample was run on

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

timestamp¶: Time of the day when the sample was run

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

aghplctools.hplc module¶

class aghplctools.hplc.HPLCTarget(wavelength: float, retention_time: float, name: str = None, wiggle: float = 0.2, zero_pad: int = 0)¶

Bases: object

A data storage class for tracking an HPLC retention target.

Parameters:

wavelength (float) – wavelength to track the target on
retention_time (float) – retention time to look for the target
name (str) – convenience name
wiggle (float) – wiggle value in minutes for finding the target around the retention_time (the window will be [retention_time-wiggle, retention_time+wiggle])
zero_pad – adds n zeros to the front of the value lists

add_from_pulled(signals, timepoint=None)¶

Retrieves values from the output of the pull_hplc_area function and stores them in the instance.

Parameters:	signals (dict) – output dictionary from pull_hplc_area timepoint (float) – timepoint to save (if None, the current time will be retrieved)
Returns:	area, height, width, timepoint
Return type:	tuple

add_value(area, width=0.0, height=0.0, timepoint=None)¶

Adds a value to the tracker lists.

Parameters:	area (float) – area to add (required) width (float) – width to add (optional) height (float) – height to add (optional) timepoint (float) – timepoint to use (if None, the current time will be called)

retrieve_index(index)¶

Retrieves the values of the provided index.

Parameters:	index – pythonic list index
Returns:	{area, width, height, timepoint}
Return type:	dict

retrieve_timepoint(timepoint)¶

Retrieves the values of the provided timepoint.

Parameters:	timepoint (float) – time point to retrieve
Returns:	{area, width, height, timepoint}
Return type:	dict

aghplctools.hplc.acquiring_filename()¶

Retrieves the path name of the next Agilent HPLC acquisition (from acquiring.txt)

Returns:	file being currently acquired
Return type:	str

aghplctools.hplc.find_max_area(signals)¶

Returns the wavelength and retention time corresponding to the maximum area in a set of HPLC peak data.

Parameters:	signals (dict) – dict[wavelength][retention time (float)][width/area/height]
Returns:

aghplctools.hplc.plot(yvalues, xvalues=None, xlabel='injection #', ylabel=None, hline=None)¶: plots one set of values :param yvalues: list of y values :param xvalues: list of x values (optional) :param xlabel: label for x :param ylabel: label for y :param hline: plot a horizontal line at this value if specified :return:

aghplctools.hplc.stackedplot(rets, xlabel='injection #')¶: Creates a stacked plot for the dictionary generated by pull_hplc_data_from_folder :param rets: dictionary of retetion times :param xlabel: optional changing of x label

aghplctools.indirect module¶

tools for indirect run control of ChemStation

aghplctools.indirect.current_file() → str¶

Returns the current data file name being acquired (next up in the sequence)

Returns:	data file name

aghplctools.indirect.current_file_path() → pathlib.Path¶

Returns the full path for the file name being acquired (next up in the sequence)

Returns:	full path to the data file

aghplctools.indirect.current_num_and_file() → Tuple[int, str]¶

Returns the current number in the sequence and the name of the data file being acquired.

Returns:	current file number, current file name

aghplctools.indirect.locate_acquiring_file(*search_path) → pathlib.Path¶

determines the path for ACQUIRING.TXT

Parameters:	search_path – search paths. If not specified, uses CHEMSTATION_DATA_PATH
Returns:	file path for ACQUIRING.TXT

aghplctools.indirect.sequence_is_running() → bool¶: returns whether a sequence is running