Update test.

fsl_mrs/tests/test_utils_results.py

@@ -7,90 +7,101 @@ from fsl_mrs.utils.fitting import fit_FSLModel
 from pytest import fixture
 import numpy as np
 
-# Set up some synthetic data to use 
+
+# Set up some synthetic data to use
 @fixture(scope='module')
 def data():
     noiseCov = 0.01
-    amplitude = np.asarray([0.5,0.5,1.0])*10
-    chemshift = np.asarray([3.0,3.05,2.0])-4.65
-    lw = [10,10,10]
-    phases = [0,0,0]
-    g = [0,0,0]
-    basisNames = ['Cr','PCr','NAA']
+    amplitude = np.asarray([0.5, 0.5, 1.0])*10
+    chemshift = np.asarray([3.0, 3.05, 2.0])-4.65
+    lw = [10, 10, 10]
+    phases = [0, 0, 0]
+    g = [0, 0, 0]
+    basisNames = ['Cr', 'PCr', 'NAA']
     begintime = 0.00005
 
     basisFIDs = []
-    for idx,_ in enumerate(amplitude):
-        tmp,basisHdr = syntheticFID(noisecovariance=[[0.0]],
-                                        chemicalshift=[chemshift[idx]+0.1],
-                                        amplitude=[1.0],
-                                        linewidth=[lw[idx]/5],
-                                        phase=[phases[idx]],
-                                        g=[g[idx]],
-                                        begintime=0)
+    for idx, _ in enumerate(amplitude):
+        tmp, basisHdr = syntheticFID(noisecovariance=[[0.0]],
+                                     chemicalshift=[chemshift[idx]+0.1],
+                                     amplitude=[1.0],
+                                     linewidth=[lw[idx]/5],
+                                     phase=[phases[idx]],
+                                     g=[g[idx]],
+                                     begintime=0)
         basisFIDs.append(tmp[0])
     basisFIDs = np.asarray(basisFIDs)
 
-    synFID,synHdr =  syntheticFID(noisecovariance=[[noiseCov]],
-                                     chemicalshift=chemshift,
-                                     amplitude=amplitude,
-                                     linewidth=lw,
-                                     phase=phases,
-                                     g=g,
-                                     begintime=begintime)
+    synFID, synHdr = syntheticFID(noisecovariance=[[noiseCov]],
+                                  chemicalshift=chemshift,
+                                  amplitude=amplitude,
+                                  linewidth=lw,
+                                  phase=phases,
+                                  g=g,
+                                  begintime=begintime)
 
-    synMRS = MRS(FID =synFID[0],header=synHdr,basis =basisFIDs,basis_hdr=basisHdr,names=basisNames)
+    synMRS = MRS(FID=synFID[0],
+                 header=synHdr,
+                 basis=basisFIDs,
+                 basis_hdr=basisHdr,
+                 names=basisNames)
 
     metab_groups = [0]*synMRS.numBasis
-    Fitargs = {'ppmlim':[0.2,4.2],
-            'method':'MH','baseline_order':-1,
-            'metab_groups':metab_groups,
-            'MHSamples':100,
-            'disable_mh_priors':True}
-    
-    res = fit_FSLModel(synMRS,**Fitargs)
+    Fitargs = {'ppmlim': [0.2, 4.2],
+               'method': 'MH',
+               'baseline_order': -1,
+               'metab_groups': metab_groups,
+               'MHSamples': 100,
+               'disable_mh_priors': True}
+
+    res = fit_FSLModel(synMRS, **Fitargs)
+
+    return res, amplitude
 
-    return res,amplitude
 
 def test_peakcombination(data):
 
     res = data[0]
     amplitudes = data[1]
 
-    res.combine([['Cr','PCr']])    
+    res.combine([['Cr', 'PCr']])
 
     fittedconcs = res.getConc()
     fittedRelconcs = res.getConc(scaling='internal')
 
-    amplitudes = np.append(amplitudes,amplitudes[0]+amplitudes[1])
+    amplitudes = np.append(amplitudes, amplitudes[0]+amplitudes[1])
 
     assert 'Cr+PCr' in res.metabs
-    assert np.allclose(fittedconcs,amplitudes,atol=1E-1)
-    assert np.allclose(fittedRelconcs,amplitudes/(amplitudes[0]+amplitudes[1]),atol=2E-1)
+    assert np.allclose(fittedconcs, amplitudes, atol=2E-1)
+    assert np.allclose(fittedRelconcs,
+                       amplitudes/(amplitudes[0]+amplitudes[1]),
+                       atol=2E-1)
+
 
 def test_units(data):
     res = data[0]
 
     # Phase
-    p0,p1 = res.getPhaseParams(phi0='degrees',phi1='seconds')    
-    assert np.isclose(p0,0.0,atol=1E-1)
-    assert np.isclose(p1,0.00005,atol=3E-5)
+    p0, p1 = res.getPhaseParams(phi0='degrees', phi1='seconds')
+    assert np.isclose(p0, 0.0, atol=1E-1)
+    assert np.isclose(p1, 0.00005, atol=3E-5)
 
     # Shift
     shift = res.getShiftParams(units='ppm')
     shift_hz = res.getShiftParams(units='Hz')
-    assert np.isclose(shift,0.1,atol=1E-2)
-    assert np.isclose(shift_hz,0.1*123.0,atol=1E-1)
+    assert np.isclose(shift, 0.1, atol=1E-2)
+    assert np.isclose(shift_hz, 0.1*123.0, atol=1E-1)
 
     # Linewidth
     lw = res.getLineShapeParams(units='Hz')[0]
     lw_ppm = res.getLineShapeParams(units='ppm')[0]
-    assert np.isclose(lw,8.0,atol=1E-1) #10-2
-    assert np.isclose(lw_ppm,8.0/123.0,atol=1E-1)
+    assert np.isclose(lw, 8.0, atol=1E-1)  # 10-2
+    assert np.isclose(lw_ppm, 8.0/123.0, atol=1E-1)
+
 
 def test_qcOutput(data):
     res = data[0]
-    SNR,FWHM = res.getQCParams()
+    SNR, FWHM = res.getQCParams()
 
-    assert np.allclose(FWHM,10.0,atol=1E0)
+    assert np.allclose(FWHM, 10.0, atol=1E0)
     assert SNR.size == 3