from src.wrappers.OsipiBase import OsipiBase
from super_ivim_dc.source.Classsic_ivim_fit import IVIM_fit_sls_trf
import numpy as np
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class TCML_TechnionIIT_lsq_sls_trf(OsipiBase):
"""
TCML_TechnionIIT_lsqlm fitting algorithm by Angeleene Ang, Moti Freiman and Noam Korngut, TechnionIIT
"""
# 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 = "Angeleene Ang, Moti Freiman and Noam Korngut, TechnIIT"
id_algorithm_type = "Bi-exponential fit, SLS fit followed by Trust Region Reflective algorithm"
id_return_parameters = "f, D*, D, S0"
id_units = "seconds per milli metre squared or milliseconds per micro metre squared"
# Algorithm requirements
required_bvalues = 4
required_thresholds = [0,
1] # Interval from "at least" to "at most", 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
accepted_dimensions = 1 # 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 = True
supported_initial_guess = False
supported_thresholds = True
def __init__(self, bvalues=None, thresholds=None, bounds=None, initial_guess=None, fitS0=True):
"""
Everything this algorithm 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(TCML_TechnionIIT_lsq_sls_trf, self).__init__(bvalues=bvalues, bounds=bounds)
self.fit_least_squares = IVIM_fit_sls_trf
self.fitS0=fitS0
self.initialize(bounds, fitS0, thresholds)
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def initialize(self, bounds, fitS0, thresholds):
if bounds is None:
print('warning, no bounds were defined, so default bounds are used of ([0.0003, 0.001, 0.009, 0],[0.008, 1.0,0.04, 3])')
self.bounds = ([0.0003, 0.001, 0.009, 0],[0.008, 1.0,0.04, 3])
else:
bounds=bounds
self.bounds = bounds
if thresholds is None:
self.thresholds = 200
print('warning, no thresholds were defined, so default bounds are used of 200')
else:
self.thresholds = thresholds
self.fitS0=fitS0
self.use_bounds = False
self.use_initial_guess = False
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def ivim_fit(self, signals, bvalues, **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.
Returns:
_type_: _description_
"""
signals[signals<0]=0
bvalues=np.array(bvalues)
bounds=np.array(self.bounds)
bounds=[bounds[0][[0, 2, 1, 3]], bounds[1][[0, 2, 1, 3]]]
fit_results = self.fit_least_squares(np.array(signals)[:,np.newaxis],bvalues, bounds,min_bval_high=self.thresholds)
results = {}
results["D"] = fit_results[0]
results["f"] = fit_results[2]
results["Dp"] = fit_results[1]
return results