Fixed a syntax error with fractionations related to the unit change

Renamed scoop_match.py to __main__.py to make it easier to run Now you can use python -m CADETMatch --match -j /path/to/file.json
cadet · Sep 24, 2019 · 901e089 · 901e089
1 parent 5ee3f95
commit 901e089
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Showing 8 changed files with 15 additions and 10 deletions.
diff --git a/CADETMatch.egg-info/SOURCES.txt b/CADETMatch.egg-info/SOURCES.txt
@@ -2,6 +2,7 @@ README.md
 setup.cfg
 setup.py
 CADETMatch/__init__.py
+CADETMatch/__main__.py
 CADETMatch/autocorr.py
 CADETMatch/cache.py
 CADETMatch/calc_coeff.py
@@ -25,7 +26,6 @@ CADETMatch/nsga2_simple.py
 CADETMatch/nsga3_selection.py
 CADETMatch/pareto.py
 CADETMatch/plugins.py
-CADETMatch/scoop_match.py
 CADETMatch/score.py
 CADETMatch/similarityDecay.py
 CADETMatch/synthetic_error.py

diff --git a/CADETMatch/CADETMatch.pyproj b/CADETMatch/CADETMatch.pyproj
@@ -16,7 +16,8 @@
     <LaunchProvider>Standard Python launcher</LaunchProvider>
     <CommandLineArguments>"F:\temp\example\fit\example.json"  2</CommandLineArguments>
     <EnableNativeCodeDebugging>False</EnableNativeCodeDebugging>
-    <InterpreterArguments>-m scoop -n 6</InterpreterArguments>
+    <InterpreterArguments>
+    </InterpreterArguments>
   </PropertyGroup>
   <PropertyGroup Condition=" '$(Configuration)' == 'Debug' ">
     <DebugSymbols>true</DebugSymbols>
@@ -95,7 +96,7 @@
     <Compile Include="plugins.py">
       <SubType>Code</SubType>
     </Compile>
-    <Compile Include="scoop_match.py">
+    <Compile Include="__main__.py">
       <SubType>Code</SubType>
     </Compile>
     <Compile Include="score.py">

diff --git a/CADETMatch/scoop_match.py → CADETMatch/__main__.py b/CADETMatch/scoop_match.py → CADETMatch/__main__.py
@@ -43,13 +43,17 @@ def makeParser():
                         action='store_true')
 
     parser.add_argument('-n',
-                        help="Number of scoop processes to use. Use 1 for debugging")
+                        help="Number of scoop processes to use. Use 1 for debugging",
+                        default=0)
 
     return parser
 
 
 def run_command(module, json, number_of_jobs, additional=None):
-    command = [sys.executable, '-m', 'scoop', '-n', str(number_of_jobs), module.__file__, str(json)]
+    command = [sys.executable, '-m', 'scoop']
+    if int(number_of_jobs) > 0:
+        command.extend(['-n', str(number_of_jobs)])
+    command.extend([module.__file__, str(json)])
     if additional is not None:
         command.extend(additional)
 

diff --git a/CADETMatch/scores/fractionation.py b/CADETMatch/scores/fractionation.py
@@ -32,7 +32,7 @@ def run(sim_data, feature):
         selected = (times >= start) & (times <= stop)
 
         local_times = times[selected]
-        local_values = simulation.root.output.solution[feature['unit']["solution_outlet_comp_%03d" % component][selected]
+        local_values = simulation.root.output.solution[feature['unit']]["solution_outlet_comp_%03d" % component][selected]
 
         sim_value = numpy.trapz(local_values, local_times)
 

diff --git a/CADETMatch/scores/fractionationCombine.py b/CADETMatch/scores/fractionationCombine.py
@@ -40,7 +40,7 @@ def run(sim_data, feature):
         selected = (times >= start) & (times <= stop)
 
         local_times = times[selected]
-        local_values = simulation.root.output.solution[feature['unit']["solution_outlet_comp_%03d" % component][selected]
+        local_values = simulation.root.output.solution[feature['unit']]["solution_outlet_comp_%03d" % component][selected]
 
         sim_value = numpy.trapz(local_values, local_times)
 

diff --git a/CADETMatch/scores/fractionationMeanVariance.py b/CADETMatch/scores/fractionationMeanVariance.py
@@ -35,7 +35,7 @@ def run(sim_data, feature):
     for (start, stop, component, values, func_mean_time, func_variance_time, func_mean_value, func_variance_value) in funcs:
         time_center = (start + stop)/2.0
 
-        sim_values = util.fractionate(start, stop, times, simulation.root.output.solution[feature['unit']["solution_outlet_comp_%03d" % component])
+        sim_values = util.fractionate(start, stop, times, simulation.root.output.solution[feature['unit']]["solution_outlet_comp_%03d" % component])
 
         mean_sim_time, variance_sim_time, skew_sim_time, mean_sim_value, variance_sim_value, skew_sim_value = util.fracStat(time_center, sim_values)
 

diff --git a/CADETMatch/scores/fractionationMoment.py b/CADETMatch/scores/fractionationMoment.py
@@ -35,7 +35,7 @@ def run(sim_data, feature):
     for (start, stop, component, values, func_mean_time, func_variance_time, func_skew_time, func_mean_value, func_variance_value, func_skew_value) in funcs:
         time_center = (start + stop)/2.0
 
-        sim_values = util.fractionate(start, stop, times, simulation.root.output.solution[feature['unit']["solution_outlet_comp_%03d" % component])
+        sim_values = util.fractionate(start, stop, times, simulation.root.output.solution[feature['unit']]["solution_outlet_comp_%03d" % component])
 
         mean_sim_time, variance_sim_time, skew_sim_time, mean_sim_value, variance_sim_value, skew_sim_value = util.fracStat(time_center, sim_values)
 

diff --git a/CADETMatch/scores/fractionationSlide.py b/CADETMatch/scores/fractionationSlide.py
@@ -75,7 +75,7 @@ def run(sim_data, feature):
 
     for component, value_func in funcs:
         exp_values = numpy.array(data[str(component)])
-        sim_value = simulation.root.output.solution[feature['unit']["solution_outlet_comp_%03d" % component]
+        sim_value = simulation.root.output.solution[feature['unit']]["solution_outlet_comp_%03d" % component]
 
         rollLeft, rollRight, searchMax = rollRange(times, sim_value, searchIndexStart, searchIndexStop)