setup triexp testing step 1: adding algorithm to json and slightly changing the code to work with bounds

Author: DKuppens

src/original/PV_MUMC/triexp_fitting_algorithms.py

@@ -104,9 +104,9 @@ def monofit(bvalues, Dpar, Fp):
 
     else:
         if not fitS0:
-            bounds = ([bounds[0][1] , bounds[0][2] , bounds[0][3] , bounds[0][4] , bounds[0][5] ],
+            newbounds = ([bounds[0][1] , bounds[0][2] , bounds[0][3] , bounds[0][4] , bounds[0][5] ],
                         [Dpar1          , bounds[1][2] , bounds[1][3] , bounds[1][4] , bounds[1][5] ])      
-            params, _ = curve_fit(tri_expN_noS0, bvalues, dw_data, p0=[Dpar1, 0.0, (bounds[0][3]+bounds[1][3])/2, 0.05, (bounds[0][5]+bounds[1][5])/2], bounds=bounds)
+            params, _ = curve_fit(tri_expN_noS0, bvalues, dw_data, p0=[Dpar1, 0.0, (bounds[0][3]+bounds[1][3])/2, 0.05, (bounds[0][5]+bounds[1][5])/2], bounds=newbounds)
             Dpar, Fint, Dint, Fmv, Dmv = params[0], params[1], params[2], params[3], params[4]
             #when the fraction of a compartment equals zero (or very very small), the corresponding diffusivity is non-existing (=NaN)
 

src/standardized wip/PV_MUMC_triexp.py renamed to src/standardized/PV_MUMC_triexp.py

@@ -45,7 +45,6 @@ def ivim_fit(self, signals, bvalues=None):
         Returns:
             _type_: _description_
         """
-        
 
         fit_results = self.PV_algorithm(bvalues, signals)
         Dpar, Fint, Dint, Fmv, Dmv = fit_results

tests/IVIMmodels/unit_tests/algorithms.json

@@ -11,6 +11,7 @@
         "OGC_AmsterdamUMC_biexp_segmented",
         "OGC_AmsterdamUMC_biexp",
         "PV_MUMC_biexp",
+        "PV_MUMC_triexp",
         "PvH_KB_NKI_IVIMfit"
     ],
     "IAR_LU_biexp": {
@@ -162,5 +163,23 @@
                 "Dp": 1e-1
             }
         }
+    },
+    "PV_MUMC_triexp": {
+        "tolerances": {
+            "rtol": {
+                "Dpar": 5,
+                "Fint": 5,
+                "Dint": 25,
+                "Fmv": 25,
+                "Dmv": 25
+            },
+            "atol": {
+                "Dpar": 1e-2,
+                "Fint": 1e-2,
+                "Dint": 1e-1,
+                "Fmv": 1e-1,
+                "Dmv": 1e-1
+            }
+        }
     }
 }