tapsap.structures package

Submodules

tapsap.structures.Experiment module

class tapsap.structures.Experiment.Experiment

Bases: object

This class contains all of the experiment information. It mainly acts as a container for all of the species data / methods as well as a container for meta data.

Attributes:

file_name (str): The name of the read file or experiment.

collection_time (str): The collection time of the experiment.

pulse_spacing (float): The pulse spacing within the experiment.

time_start (float): The start time of each flux.

time_end (float): The end time of the experiment.

num_samples_per_pulse (int): The number of samples per pulse.

species_data (dict): A collection of Transient objects.

reactor (class Reactor): The reactor information.

calibrate_all_species(inert: Optional[str] = None, reference_index=10, enforce_max: bool = False) → None

This method calibrates all other flux to the inert species.

Args:

inert (str): The name of the inert species as found in the species_data keys. If none, then will use species_class contained in the experiment.

reference_index (optional int): The index in which to calibrate the inert values. Be sure to examine prior to application in case of outgassing.

enforce_max (bool): Enforce the maximum of the X values must be less than y.

make_copy(name_to_copy: str, new_species_name: str) → None

This method makes a deep copy of a species such that it may be transformed without removing the original flux.

Args:

name_to_copy (str): A name contained in the species_data attribute

new_species_name (str): The new name of the copy.

rate_reactivity_data(inert: Optional[str] = None, reactants: Optional[ndarray] = None, products: Optional[ndarray] = None, calibrate_data: bool = True, reference_index: int = 10, enforce_max: bool = False) → None

This method calculates the rate, concentration, and the accumulation for each different species.

Args:

inert (str): The name of the inert species as found in the species_data keys. If none, then will use species_class contained in the experiment.

reactants (ndarray or str): The name(s) of the reactant species. If none, then will use species_class contained in the experiment.

products (ndarray or str): The name(s) of the product species. If none, then will use species_class contained in the experiment.

calibrate_data (bool): To calibrate the data prior to measuring the rate_reactivity_data.

reference_index (optional int): The index in which to calibrate the inert values. Be sure to examine prior to application in case of outgassing.

enforce_max (bool): Enforce the maximum of the X values must be less than y.

remove_delay_time() → None

This method removes the delay time ranges from all gas species. This may need to be done if the experiment delays a pulse to determine the baseline at the front of the flux.

set_reactor_params() → None

This method sets the reactor parameters for each species in species_data based on the experiments reactor information.

tapsap.structures.Reactor module

class tapsap.structures.Reactor.Reactor

Bases: object

This class acts as a container for all of the reactor parameters.

Attributes:

zone_lengths (dict): The zone lengths for the reactor.

zone_porosity (dict): The bed porosity within each zone.

zone_diffusion (dict): The diffusion coefficient for each zone.

zone_residence_time (dict): The residence time within each zone.

reactor_radius (float): The radius of the reactor.

catalyst_weight (float): The catalyst weight.

mol_per_pulse (float): The mol per pulse.

tapsap.structures.Transient module

class tapsap.structures.Transient.Transient

Bases: object

This class contains all of the transient information per pulse for a single gas species. Most of the computation for preprocessing and transformations should take place in this class.

Attributes:

name (str): The name of the gas species.

pulse_id (str): The pulse index for the parent gas species.

mass (float): The mass of the gas species.

gain (float): The gain of the mass spectrometer for measuring the gas species.

delay_time (float): The delay time of the gas species.

flux (dataframe): The measured flux of the gas species.

times (float ndarray): An array of time.

amount_pulsed (float): The amount pulsed for each pulse.

initial_concentration (float): The initial concentration within the reaction.

num_pulse (int): The number of pulses injected.

df_moments (dataframe): A dataframe containing all of the summary information of the experiment.

reactor (Reactor): A Reactor class containing all of the reactor information.

reference_gas (Transient): The reference flux (inert flux) when measuring kinetic information.

integration_times (list): The integration times for the moments.

num_cores (int): The total number of cores to use in processing the data. Initially set to the total number of cores available - 1.

baseline_correct(baseline_time_range: Optional[list] = None, baseline_amount: Optional[float] = None, smooth_flux: bool = True) → None

A method for traditional baseline correction by either a baseline amount or baseline time range. If baseline_time_range and baseline_amount is None, then the baseline_gamma will be used.

Args:

baseline_time_range (float list): The points in time in which to take the baseline.

baseline_amount (float): The amount of baseline correction to apply.

smooth_flux (bool): Smoothing the flux prior to optimization.

See also:

tapsap.preprocess.baseline_correction

tapsap.preprocess.baseline_gamma

calibrate_flux(calibration_amount: Optional[float] = None, reference_index: Optional[ndarray] = None, smooth_flux: bool = True, huber_loss: bool = False, constraints: bool = True, fit_intercept: bool = True, enforce_max: bool = False) → None

A method for applying a calibration coefficient to the flux (multiplied). This method has the option to do traditional calibration via a calibration amount or if None, then will perform transient calibration. When the reference_index is not None, then this will loop over all flux and calibrate to a specific flux. The reference flux is usefull when accounting for drift in the inert flux.

Args:

calibration_amount (float): The amount to scale the flux.

reference_index (int): The index in which to calibrate all other flux.

smooth_flux (bool): Smoothing the flux prior to optimization.

huber_loss (bool): Use a robust loss function rather than the standard square error loss.

constraints (bool): This controls whether contrained regression is performed.

fit_intercept (bool): Fit the intercept within the convex optimization.

enforce_max (bool): Enforce the maximum of the X values must be less than y.

See also:

tapsap.preprocess.calibration_coef

tapsap.preprocess.tap_mix

tapsap.preprocess.calibration_teak

grahams_law(new_mass: float) → None

This method applies grahams_law to each flux.

Args:

new_mass (float): The mass to scale the flux to.

See also:

tapsap.diffusion.grahams_law

remove_delay_time() → None

This method removes the delay time ranges from the flux. This may need to be done if the experiment delays a pulse to determine the baseline at the front of the flux.

set_accumulation() → None

This method applies a cumulative intergral to the flux (preferably the rate to get the accumulation).

set_concentration(y_smoothing: Optional[float] = None, post_smoothing: bool = True) → None

A method calculates the gas concentration from the available flux. Note that by doing this method, the original flux will be overwritten. It is preferable to make a deepcopy of the original species information where the concentration will another object. If y_smoothing is left as None, then G-Procedure is used.

Args:

y_smoothing (float): This value controls the amount of smoothing placed on the gas concentration when the Y-Procedure is used. If None, then the G-Procedure is used.

post_smoothing (boolean): Smooth the concentration, placed in smoothed_flux, after calculating the concentration.

See also:

tapsap.transient_analysis.concentration_g

tapsap.transient_analysis.concentration_y

tapsap.transient_analysis.smooth_flux_gam

set_gas_diffusion() → None

A method for setting the gas diffusion based on the inert or reference flux diffusion. This method requires a reference gas and that the moments have been calculated.

set_min_mean_max() → None

A method for setting the summary information (min, mean, max) for each flux.

set_moments(smooth_flux: bool = False, find_integration_times: list = False) → None

A method for setting the moments.

Args:

smooth_flux (bool): Smoothing the flux prior to optimization.

See also:

tapsap.moments_analysis.moments

set_rate(y_smoothing: Optional[float] = None, isreactant: bool = False, post_smoothing: bool = True) → None

A method calculates the rate from the available flux. Note that by doing this method, the original flux will be overwritten. It is preferable to make a deepcopy of the original species information where the rate will another object. If y_smoothing is left as None, then G-Procedure is used.

Args:

y_smoothing (float): This value controls the amount of smoothing placed on the gas concentration when the Y-Procedure is used. If None, then the G-Procedure is used.

isreactant (bool): This controls whether the difference between the inert and the reactant is used when measuring the rate.

post_smoothing (boolean): Smooth the rate, placed in smoothed_flux, after calculating the rate.

See also:

tapsap.transient_analysis.rate_g

tapsap.transient_analysis.rate_y

tapsap.transient_analysis.smooth_flux_gam

set_reactivities(reactant_obj=None) → None

A method for setting the reactivites. The method requires that the reference_gas be set to the inert species using moments_analysis.diffusion_moments.

Args:

reactant_obj (Transient): If none, then it is assumed that the gas species is a reactant. If used, then the gas species is a product and the additional moments are the reactant moments.

See also:

tapsap.moments_analysis.diffusion_moments

tapsap.moments_analysis.reactivities_product

tapsap.moments_analysis.reactivities_reactant

set_rtd_parameters() → None

A method for setting the residence time distribution parameters. This requires calculating the moments.

See also:

tapsap.moments_analysis.rtd_parameters

smooth_flux() → None

This method applies smooth_flux_gam to each flux.

See also:

tapsap.transient_analysis.smooth_flux_gam

Module contents