updated wrapper of NKI, simple test run works

Author: petravanhoudt

src/standardized/PVH_KB_NKI_IVIMfit.py

@@ -49,10 +49,10 @@ def ivim_fit(self, signals, bvalues=None):
         Returns:
             _type_: _description_
         """
-        bvalues=np.array(bvalues)
-        # reshape signal as the function expects a 4D array
-        signals = np.reshape(signals, (1, 1, 1, len(signals)))  # Question = signals always a 1D array in the tests?
-        # to do reshape signals into a 4D array as this is what the function expects as input
+        #bvalues = np.array(bvalues)
+        bvalues = bvalues.tolist() #NKI code expects a list instead of nparray
+        # reshape signal as the NKI code expects a 4D array
+        signals = np.reshape(signals, (1, 1, 1, len(signals)))  # assuming that in this test the signals are always single voxel
         fit_results = self.NKI_algorithm(signals,bvalues)
 
         D = fit_results[0]/1000

tests/IVIMmodels/unit_tests/simple_test_run_of_algorithm.py

@@ -3,7 +3,8 @@
 from pathlib import Path
 #from src.standardized.ETP_SRI_LinearFitting import ETP_SRI_LinearFitting
 from src.standardized.IAR_LU_biexp import IAR_LU_biexp
-from src.standardized.IAR_LU_segmented_2step import IAR_LU_segmented_2step
+#from src.standardized.IAR_LU_segmented_2step import IAR_LU_segmented_2step
+from src.standardized.PVH_KB_NKI_IVIMfit import PVH_KB_NKI_IVIMfit
 #from src.standardized.PV_MUMC_biexp import PV_MUMC_biexp
 
 ## Simple test code... 
@@ -26,7 +27,7 @@ def ivim_model(b, S0=1, f=0.1, Dstar=0.01, D=0.001):
 
 #model1 = ETP_SRI_LinearFitting(thresholds=[200])
 #model2 = IAR_LU_biexp()
-model2 = IAR_LU_segmented_2step()
+model2 = PVH_KB_NKI_IVIMfit()
 
 #dev_test_run(model1, linear_fit_option=True)
-dev_test_run(model2, thresholds="Arbitrary kwarg for ivim_fit")
+dev_test_run(model2)