fixed a problem in linear bounds and added some tests for it

cadet · Mar 4, 2020 · 7bb7595 · 7bb7595
1 parent 1f32919
commit 7bb7595
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Showing 10 changed files with 1,694 additions and 3 deletions.
diff --git a/CADETMatch/CADETMatch.pyproj b/CADETMatch/CADETMatch.pyproj
@@ -14,7 +14,7 @@
     <IsWindowsApplication>False</IsWindowsApplication>
     <InterpreterId>CondaEnv|CondaEnv|CADETMatch</InterpreterId>
     <LaunchProvider>Standard Python launcher</LaunchProvider>
-    <CommandLineArguments>"C:\Users\kosh_000\Documents\Visual Studio 2017\Projects\CADETMatch\Examples\MCMC\Dextran\MCMC_dextran_nsga3.json" 6</CommandLineArguments>
+    <CommandLineArguments>"C:\Users\kosh_000\Documents\Visual Studio 2017\Projects\CADETMatch\Examples\TransformTest\linear\Linear_test.json" 6</CommandLineArguments>
     <EnableNativeCodeDebugging>False</EnableNativeCodeDebugging>
     <InterpreterArguments>
     </InterpreterArguments>

diff --git a/CADETMatch/transform/norm_linear.py b/CADETMatch/transform/norm_linear.py
@@ -104,8 +104,8 @@ def getBounds(self):
         minUpper = self.parameter['minUpper']
         maxUpper = self.parameter['maxUpper']
 
-        minValues = numpy.array([minLower, minUpper])
-        maxValues = numpy.array([maxLower, maxUpper])
+        minValues = [minLower, minUpper]
+        maxValues = [maxLower, maxUpper]
 
         return minValues, maxValues
 

diff --git a/Examples/TransformTest/linear/Linear_test.json b/Examples/TransformTest/linear/Linear_test.json
@@ -0,0 +1,94 @@
+{
+  "CADETPath": "C:/Users/kosh_000/cadet_build/CADET-dev/MS_SMKL_RELEASE/bin/cadet-cli.exe",
+  "baseDir": "C:/Users/kosh_000/Documents/Visual Studio 2017/Projects/CADETMatch/Examples/TransformTest/linear",
+    "tempDir": "L:/",
+  "resultsDir": "fit_linear",
+  "CSV": "dextran_NSGA3.csv",
+  "checkpointFile": "check",
+  "stopAverage": 1,
+  "stopBest": 1,
+  "gradCheck": 1.0,
+  "gradVector": 1,
+  "searchMethod": "NSGA3",
+  "mutationRate": 1.0,
+  "crossoverRate": 1.0,
+  "generations": 1000,
+  "population": 10,
+  "metaResultsOnly": 1,
+  "sobolGeneration":1,
+  "stallGenerations": 10,
+  "progressCorrect": 2,
+  "normalizeOutput":1,
+  "continueMCMC":0,
+  "graphMetaTime": 600,
+  "finalGradRefinement": 1,
+  "fullTrainingData": 0,
+  "progress_elapsed_time": 360,
+  "parameters": [
+    {
+      "transform": "log",
+      "component": -1,
+      "bound": -1,
+      "location": "/input/model/unit_001/COL_DISPERSION",
+      "min": 1e-12,
+      "max": 1e-3
+    },
+    {
+      "transform": "linear",
+      "component": -1,
+      "bound": -1,
+      "location": "/input/model/unit_001/COL_POROSITY",
+      "minX":0,
+      "maxX":2,
+      "x_name":"pH",
+      "minLower": 0.1,
+      "maxLower": 0.9,
+      "minUpper": 0.1,
+      "maxUpper": 0.9
+    }
+  ],
+  "experiments": [
+    {
+      "CSV": "dex_03.csv",
+      "isotherm": "/output/solution/unit_001/SOLUTION_OUTLET_COMP_000",
+      "HDF5": "dex_03.h5",
+      "name": "main1",
+      "timeout": 30.0,
+      "pH":0,
+      "features": [
+        {
+            "name": "Pulse",
+            "type": "DextranShape"
+        }
+      ]
+    },
+    {
+      "CSV": "dex_04.csv",
+      "isotherm": "/output/solution/unit_001/SOLUTION_OUTLET_COMP_000",
+      "HDF5": "dex_04.h5",
+      "name": "main2",
+      "timeout": 30.0,
+      "pH":1,
+      "features": [
+        {
+            "name": "Pulse",
+            "type": "DextranShape"
+        }
+      ]
+    },
+    {
+      "CSV": "dex_05.csv",
+      "isotherm": "/output/solution/unit_001/SOLUTION_OUTLET_COMP_000",
+      "HDF5": "dex_05.h5",
+      "name": "main3",
+      "timeout": 30.0,
+      "pH":2,
+      "features": [
+        {
+            "name": "Pulse",
+            "type": "DextranShape"
+        }
+      ]
+    }
+  ]
+}
diff --git a/Examples/TransformTest/linear/Linear_test_norm.json b/Examples/TransformTest/linear/Linear_test_norm.json
@@ -0,0 +1,94 @@
+{
+  "CADETPath": "C:/Users/kosh_000/cadet_build/CADET-dev/MS_SMKL_RELEASE/bin/cadet-cli.exe",
+  "baseDir": "C:/Users/kosh_000/Documents/Visual Studio 2017/Projects/CADETMatch/Examples/TransformTest/linear",
+    "tempDir": "L:/",
+  "resultsDir": "fit_linear_norm",
+  "CSV": "dextran_NSGA3.csv",
+  "checkpointFile": "check",
+  "stopAverage": 1,
+  "stopBest": 1,
+  "gradCheck": 1.0,
+  "gradVector": 1,
+  "searchMethod": "NSGA3",
+  "mutationRate": 1.0,
+  "crossoverRate": 1.0,
+  "generations": 1000,
+  "population": 10,
+  "metaResultsOnly": 1,
+  "sobolGeneration":1,
+  "stallGenerations": 10,
+  "progressCorrect": 2,
+  "normalizeOutput":1,
+  "continueMCMC":0,
+  "graphMetaTime": 600,
+  "finalGradRefinement": 1,
+  "fullTrainingData": 0,
+  "progress_elapsed_time": 360,
+  "parameters": [
+    {
+      "transform": "norm_log",
+      "component": -1,
+      "bound": -1,
+      "location": "/input/model/unit_001/COL_DISPERSION",
+      "min": 1e-12,
+      "max": 1e-3
+    },
+    {
+      "transform": "norm_linear",
+      "component": -1,
+      "bound": -1,
+      "location": "/input/model/unit_001/COL_POROSITY",
+      "minX":0,
+      "maxX":2,
+      "x_name":"pH",
+      "minLower": 0.1,
+      "maxLower": 0.9,
+      "minUpper": 0.1,
+      "maxUpper": 0.9
+    }
+  ],
+  "experiments": [
+    {
+      "CSV": "dex_03.csv",
+      "isotherm": "/output/solution/unit_001/SOLUTION_OUTLET_COMP_000",
+      "HDF5": "dex_03.h5",
+      "name": "main1",
+      "timeout": 30.0,
+      "pH":0,
+      "features": [
+        {
+            "name": "Pulse",
+            "type": "DextranShape"
+        }
+      ]
+    },
+    {
+      "CSV": "dex_04.csv",
+      "isotherm": "/output/solution/unit_001/SOLUTION_OUTLET_COMP_000",
+      "HDF5": "dex_04.h5",
+      "name": "main2",
+      "timeout": 30.0,
+      "pH":1,
+      "features": [
+        {
+            "name": "Pulse",
+            "type": "DextranShape"
+        }
+      ]
+    },
+    {
+      "CSV": "dex_05.csv",
+      "isotherm": "/output/solution/unit_001/SOLUTION_OUTLET_COMP_000",
+      "HDF5": "dex_05.h5",
+      "name": "main3",
+      "timeout": 30.0,
+      "pH":2,
+      "features": [
+        {
+            "name": "Pulse",
+            "type": "DextranShape"
+        }
+      ]
+    }
+  ]
+}