extended fitting tests

fsl_mrs/tests/test_utils_fitting.py

 from fsl_mrs.utils.synthetic import syntheticFID
+from fsl_mrs.utils.synthetic.synthetic_from_basis import syntheticFromBasisFile  
 from fsl_mrs.core import MRS
 from fsl_mrs.utils.fitting import fit_FSLModel
+from fsl_mrs.utils import mrs_io
 from pytest import fixture
 import numpy as np
 
+from pathlib import Path
 
+testsPath = Path(__file__).parent
+basis_path = testsPath / 'testdata/fsl_mrs/steam_basis'
 
 @fixture
 def data():
@@ -55,6 +60,25 @@ def test_fit_FSLModel_Newton(data):
     assert np.allclose(fittedconcs,amplitudes,atol=1E-1)
     assert np.allclose(fittedRelconcs,amplitudes/(amplitudes[0]+amplitudes[1]),atol=1E-1)
 
+def test_fit_FSLModel_lorentzian_Newton(data):
+
+    mrs = data[0]
+    amplitudes = data[1]
+
+    metab_groups = [0]*mrs.numBasis
+    Fitargs = {'ppmlim': [0.2,4.2],
+               'method': 'Newton',
+               'baseline_order': -1,
+               'metab_groups': metab_groups,
+               'model': 'lorentzian'}
+    
+    res = fit_FSLModel(mrs,**Fitargs)
+
+    fittedconcs = res.getConc(metab = mrs.names)
+    fittedRelconcs = res.getConc(scaling='internal',metab = mrs.names)
+    assert np.allclose(fittedconcs,amplitudes,atol=1E-1)
+    assert np.allclose(fittedRelconcs,amplitudes/(amplitudes[0]+amplitudes[1]),atol=1E-1)
+
 def test_fit_FSLModel_MH(data):
 
     mrs = data[0]
@@ -72,4 +96,53 @@ def test_fit_FSLModel_MH(data):
     fittedRelconcs = res.getConc(scaling='internal',metab = mrs.names)
 
     assert np.allclose(fittedconcs,amplitudes,atol=1E-1)
-    assert np.allclose(fittedRelconcs,amplitudes/(amplitudes[0]+amplitudes[1]),atol=1E-1)
\ No newline at end of file
+    assert np.allclose(fittedRelconcs,amplitudes/(amplitudes[0]+amplitudes[1]),atol=1E-1)
+
+def test_fit_FSLModel_lorentzian_MH(data):
+
+    mrs = data[0]
+    amplitudes = data[1]
+
+    metab_groups = [0]*mrs.numBasis
+    Fitargs = {'ppmlim':[0.2,4.2],
+               'method':'MH',
+               'baseline_order':-1,
+               'metab_groups':metab_groups,
+               'MHSamples':100,
+               'model': 'lorentzian'}
+    
+    res = fit_FSLModel(mrs,**Fitargs)
+
+    fittedconcs = res.getConc(metab = mrs.names)
+    fittedRelconcs = res.getConc(scaling='internal',metab = mrs.names)
+
+    assert np.allclose(fittedconcs,amplitudes,atol=1E-1)
+    assert np.allclose(fittedRelconcs,amplitudes/(amplitudes[0]+amplitudes[1]),atol=1E-1)
+
+def test_fit_FSLModel_on_invivo_sim():
+
+    FIDs,hdr,trueconcs = syntheticFromBasisFile(basis_path,
+                                                noisecovariance=[[1E-3]],
+                                                broadening=(9.0, 9.0),
+                                                concentrations={'Mac':2.0})
+
+    basis,names,header = mrs_io.read_basis(basis_path)
+
+    mrs = MRS(FID=FIDs,header=hdr,basis=basis,basis_hdr=header[0],names=names)
+    mrs.processForFitting()
+
+    metab_groups = [0]*mrs.numBasis
+    Fitargs = {'ppmlim':[0.2,4.2],
+               'method':'MH',
+               'baseline_order':-1,
+               'metab_groups':metab_groups,
+               'MHSamples':100}
+    
+    res = fit_FSLModel(mrs,**Fitargs)
+
+    fittedRelconcs = res.getConc(scaling='internal',metab = mrs.names)
+
+    answers = np.asarray(trueconcs)
+    answers /= (answers[names.index('Cr')]+trueconcs[names.index('PCr')])
+
+    assert np.allclose(fittedRelconcs,answers,atol=5E-2)
\ No newline at end of file

fsl_mrs/utils/synthetic/synthetic_from_basis.py

@@ -74,7 +74,7 @@ def syntheticFromBasisFile(basisFile,
     Returns:
         FIDs: Numpy array of synthetic FIDs
         outHeader: Header suitable for loading FIDs into MRS object.
-        concentrations: Final concentration scalinfs
+        concentrations: Final concentration scalings
     """
     basis,names,header = mrs_io.read_basis(basisFile)