Utilities

Isotherm interpolator

A class used for isotherm interpolation.

class pygaps.utilities.isotherm_interpolator.IsothermInterpolator(known_data, interp_data, interp_branch='ads', interp_kind='linear', interp_fill=None)

Class used to interpolate between isotherm points.

Call directly to use.

It is mainly a wrapper around scipy.interpolate.interp1d.

Parameters:

• interp_type (str) -- What variable the interpolator works on (pressure, loading etc).

• known_data (str) -- The values corresponding to the input variable.

• interp_data (str) -- The values corresponding to the variable to be interpolated.

• interp_branch (str, optional) -- Stores which isotherm branch the interpolator is based on.

• interp_kind (str, optional) -- Determine which kind of interpolation is done between the datapoints.

• interp_fill (str, optional) -- The parameter passed to the scipy.interpolate.interp1d function to determine what to do outside data bounds.

Thermodynamic backend utilities

Utilities for interacting with the CoolProp backend.

pygaps.utilities.coolprop_utilities.COOLPROP_BACKEND = 'HEOS'

The backend which CoolProp uses, normally either HEOS or REFPROP.

pygaps.utilities.coolprop_utilities.backend_use_refprop()

Switch the equation of state used to REFPROP. User should have REFPROP installed.

pygaps.utilities.coolprop_utilities.backend_use_coolprop()

Switch the equation of state used to HEOS (CoolProp).

Python utilities

Collections of various python utilities.

pygaps.utilities.python_utilities.zip_varlen(*iterables)

Variable length zip() function.

pygaps.utilities.python_utilities.grouped(iterable, n)

Divide an iterable in subgroups of max n elements.

pygaps.utilities.python_utilities.deep_merge(a, b, path=None, update=True)

Recursive updates of a dictionary.

class pygaps.utilities.python_utilities.SimpleWarning

Context manager overrides warning formatter to remove unneeded info.

Exceptions

Custom errors thrown by the program.

exception pygaps.utilities.exceptions.pgError

Base error raised by pyGAPS.

exception pygaps.utilities.exceptions.ParameterError

Raised when one of the parameters is unsuitable.

exception pygaps.utilities.exceptions.CalculationError

Raised when a calculation fails.

exception pygaps.utilities.exceptions.ParsingError

Raised when parsing fails.

exception pygaps.utilities.exceptions.GraphingError

Raised when graphing fails.

Math utilities

Function-independent mathematical calculations.

pygaps.utilities.math_utilities.split_ads_data(data, pressure_key)

Find the inflection in an adsorption dataset with adsorption/desorption.

pygaps.utilities.math_utilities.find_limit_indices(array: list, limits: tuple[float, float] = None, smallest_selection: int = 3)

Find the indices of an array limits

pygaps.utilities.math_utilities.find_linear_sections(xdata, ydata)

Find all sections of a curve which are linear.

pygaps.utilities.math_utilities.bspline(xs, ys, n=100, degree=2, periodic=False)

Calculate n samples on a b-spline.

Adapted from: https://stackoverflow.com/questions/24612626/b-spline-interpolation-with-python

Parameters:

• xs (array) -- X points of the curve to fit

• ys (array) -- Y points of the curve to fit

• n (int) -- Number of samples to return

• degree (int) -- Curve degree

• periodic (bool) -- True - Curve is closed False - Curve is open

pygaps.utilities.math_utilities.same_orders_of_maximum(vals)

Determines if the maximum of two lists are within one order of magnitude.

Parameters:

vals (list of list of floats) -- The lists to compare

Returns:

• True -- If within one order of magnitude

• False -- If not

String processing utilities

General functions for string transformations.

pygaps.utilities.string_utilities.convert_chemformula_ltx(string: str) → str

Convert a chemical formula string to a matplotlib parsable format (latex).

Parameters:

string or Adsorbate (str) -- String to process.

Returns:

str -- Processed string.

pygaps.utilities.string_utilities.convert_unit_ltx(string: str, negative: bool = False) → str

Convert a unit string to a nice matplotlib parsable format (latex).

Parameters:

• string (str) -- String to process.

• negative (bool) -- Whether the power is negative instead.

Returns:

str -- Processed string.

pygaps.utilities.string_utilities.cast_string(s)

Check and cast strings of various data types.

SQLite utilities

General functions for SQL query building.

pygaps.utilities.sqlite_utilities.db_execute_general(statement: str, pth: str, verbose: bool = False)

Execute general SQL statements.

Parameters:

• statement (str) -- SQL statement to execute.

• pth (str) -- Path where the database is located.

• verbose (bool) -- Print out extra information.

pygaps.utilities.sqlite_utilities.build_update(table: str, to_set: list, where: list, prefix: str = None)

Build an update request.

Parameters:

• table (str) -- Table where query will be directed.

• to_set (iterable) -- The list of columns to update.

• where (iterable) -- The list of conditions to constrain the query.

• prefix (str, optional) -- The prefix to introduce to the second part of the constraint.

Returns:

str -- Built query string.

pygaps.utilities.sqlite_utilities.build_insert(table: str, to_insert: list)

Build an insert request.

Parameters:

• table (str) -- Table where query will be directed.

• to_insert (iterable) -- The list of columns where the values will be inserted.

Returns:

str -- Built query string.

pygaps.utilities.sqlite_utilities.build_select(table: str, to_select: list, where: list = None)

Build a select request.

Parameters:

• table (str) -- Table where query will be directed.

• to_set (iterable) -- The list of columns to select.

• where (iterable) -- The list of conditions to constrain the query.

Returns:

str -- Built query string.

pygaps.utilities.sqlite_utilities.build_select_unnamed(table: str, to_select: list, where: list, join: str = 'AND')

Build an select request with multiple parameters.

Parameters:

• table (str) -- Table where query will be directed.

• to_set (iterable) -- The list of columns to select

• where (iterable) -- The list of conditions to constrain the query.

• join (str) -- The joining clause of the parameters.

Returns:

str -- Built query string.

pygaps.utilities.sqlite_utilities.build_delete(table: str, where: list)

Build a delete request.

Parameters:

• table (str) -- Table where query will be directed.

• where (iterable) -- The list of conditions to constrain the query.

Returns:

str -- Built query string.

pygaps.utilities.sqlite_utilities.check_SQL_bool(val)

Check if a value is a bool. Useful for storage.

pygaps.utilities.sqlite_utilities.check_SQL_python_type(val)

Convert between the database string dtype and a python data type.

pygaps.utilities.sqlite_utilities.find_SQL_python_type(val)

Convert between a python data type and a database string.

Generate the default sqlite database.

pygaps.utilities.sqlite_db_creator.db_create(path: str, verbose: bool = False)

Create the entire database.

Parameters:

• path (str) -- Path where the database is created.

• verbose (bool) -- Print out extra information.

All sql pragmas to generate the sqlite database.