import numpy as np
from src.wrappers.OsipiBase import OsipiBase
from src.original.ETP_SRI.LinearFitting import LinearFit
import warnings
warnings.simplefilter('once', UserWarning)
[docs]
class ETP_SRI_LinearFitting(OsipiBase):
"""WIP
Implementation and execution of the submitted algorithm
"""
# I'm thinking that we define default attributes for each submission like this
# And in __init__, we can call the OsipiBase control functions to check whether
# the user inputs fulfil the requirements
# Some basic stuff that identifies the algorithm
id_author = "Eric T. Peterson, SRI"
id_algorithm_type = "Linear fit"
id_return_parameters = "f, D*, D"
id_units = "seconds per milli metre squared"
# Algorithm requirements
required_bvalues = 3
required_thresholds = [0,1] # Interval from 1 to 1, in case submissions allow a custom number of thresholds
required_bounds = False
required_bounds_optional = True # Bounds may not be required but are optional
required_initial_guess = False
required_initial_guess_optional = False
# Not sure how to define this for the number of accepted dimensions. Perhaps like the thresholds, at least and at most?
# Supported inputs in the standardized class
supported_bounds = False
supported_initial_guess = False
supported_thresholds = True
supported_dimensions = 1
supported_priors = False
def __init__(self, bvalues=None, thresholds=None, bounds=None, initial_guess=None, weighting=None, stats=False):
"""
Everything this method requires should be implemented here.
Number of segmentation thresholds, bounds, etc.
Our OsipiBase object could contain functions that compare the inputs with
the requirements.
"""
super(ETP_SRI_LinearFitting, self).__init__(bvalues, thresholds, bounds, initial_guess)
if bounds is not None:
print('warning, bounds from wrapper are not (yet) used in this algorithm')
self.use_bounds = False
self.use_initial_guess = False
# Could be a good idea to have all the submission-specfic variable be
# defined with initials?
self.ETP_weighting = weighting
self.ETP_stats = stats
# Check the inputs
[docs]
def ivim_fit(self, signals, bvalues=None, linear_fit_option=False, **kwargs):
"""Perform the IVIM fit
Args:
signals (array-like)
bvalues (array-like, optional): b-values for the signals. If None, self.bvalues will be used. Default is None.
linear_fit_option (bool, optional): This fit has an option to only run a linear fit. Defaults to False.
Returns:
_type_: _description_
"""
signals[signals<0.0000001]=0.0000001
if bvalues is None:
bvalues = self.bvalues
if self.thresholds is None:
ETP_object = LinearFit()
else:
ETP_object = LinearFit(self.thresholds[0])
results = {}
if linear_fit_option:
f, Dstar = ETP_object.linear_fit(bvalues, signals, self.ETP_weighting, self.ETP_stats)
results["f"] = f
results["Dp"] = Dstar
return results
else:
f, D, Dstar = ETP_object.ivim_fit(bvalues, signals)
results["f"] = f
results["Dp"] = Dstar
results["D"] = D
results = self.D_and_Ds_swap(results)
return results