fractionationSlide also stores the time offset of the signals for usa…

…ge in graphing

graphing fractionation now writes out the time offset and if the signal is early or late
fixed a problem related to the tutorials
Separated generating graphs + 2D from 3D graphs in the command line interface so the default for --generate_graphs is no longer to also generate 3D graphs

CADETMatch.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: CADETMatch
-Version: 0.5.22
+Version: 0.5.23
 Summary: CADETMatch is a parameter estimation and error modeling library for CADET
 Home-page: https://github.com/modsim/CADET-Match
 Author: William Heymann

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\Example1\Dextran\NSGA3_dextran.json" 6</CommandLineArguments>
+    <CommandLineArguments>"F:\temp\TestDatasets\NSGA3_binding_PTD_mass_space.json" 1</CommandLineArguments>
     <EnableNativeCodeDebugging>False</EnableNativeCodeDebugging>
     <InterpreterArguments>
     </InterpreterArguments>

CADETMatch/__main__.py

@@ -23,7 +23,11 @@ def makeParser():
                         action='store_true')
 
     parser.add_argument('--generate_graphs',
-                        help="Generate general graphs",
+                        help="Generate general graphs excluding 3D",
+                        action='store_true')
+
+    parser.add_argument('--generate_graphs_all',
+                        help="Generate general graphs including 3D",
                         action='store_true')
 
     parser.add_argument('--generate_spearman',
@@ -73,6 +77,8 @@ def run_command(module, json, number_of_jobs, additional=None):
     if args.generate_corner:
         sys.exit(run_command('CADETMatch.generate_corner_graphs', args.json, args.n))
     if args.generate_graphs:
+        sys.exit(run_command('CADETMatch.generate_graphs', args.json, args.n, ['1']))
+    if args.generate_graphs_all:
         sys.exit(run_command('CADETMatch.generate_graphs', args.json, args.n, ['2']))
     if args.generate_spearman:
         sys.exit(run_command('CADETMatch.graph_spearman', args.json, args.n, ['end']))

CADETMatch/generate_graphs.py

@@ -276,7 +276,7 @@ def plotExperiments(args):
         exp_time = target[experimentName]['time']
         exp_value = target[experimentName]['value']
 
-        fig = figure.Figure(figsize=[15, 15*numPlots])
+        fig = figure.Figure(figsize=[24, 12*numPlots])
         canvas = FigureCanvas(fig)
 
         simulation = Cadet()
@@ -334,6 +334,7 @@ def plotExperiments(args):
 
                 graph_exp = results['graph_exp']
                 graph_sim = results['graph_sim']
+                graph_sim_offset = results.get('graph_sim_offset', {})
 
                 findMax = 0
                 max_comp = {}
@@ -359,7 +360,19 @@ def plotExperiments(args):
                         mult = findMax/(2 * max_comp[key])
                         values = values * mult
                     factors.append(mult)
-                    graph.plot(time, values, '--', color=get_color(idx, len(graph_sim), cm_plot), label='Simulation Comp: %s Mult:%.2f' % (key, mult))
+
+                    time_offset = graph_sim_offset.get(key, None)
+                    if time_offset is not None:
+                        if time_offset >0:
+                            time_str = "time early (s): %.3g" % abs(time_offset)
+                        else:
+                            time_str = "time late (s): %.3g" % abs(time_offset)
+                    else:
+                        time_str = ""
+
+                    label = 'Simulation Comp: %s Mult:%.2f %s' % (key, mult, time_str)
+
+                    graph.plot(time, values, '--', color=get_color(idx, len(graph_sim), cm_plot), label=label)
 
                 for idx, (key, value) in enumerate(graph_exp.items()):
                     (time, values) = zip(*value)
@@ -369,7 +382,7 @@ def plotExperiments(args):
                     graph.plot(time, values, ':', color=get_color(idx, len(graph_sim), cm_plot), label='Experiment Comp: %s Mult:%.2f' % (key, mult))
                 graphIdx += 1
             graph.legend()
-        fig.set_size_inches((12,6*numPlots))
+        fig.set_size_inches((24,12*numPlots))
         fig.savefig(str(dst))
 
 def graphSpace(fullGeneration, cache, map_function):
@@ -442,18 +455,18 @@ def plot_3d(arg):
 
     scoreName = header3
     if scoreName == 'SSE':
-        scores = -numpy.log(scores)
-        scoreName = '-log(%s)' % scoreName
+        scores = -numpy.log10(scores)
+        scoreName = '-log10(%s)' % scoreName
 
     x = data1
     y = data2
 
     fig = figure.Figure()
     canvas = FigureCanvas(fig)
     ax = fig.add_subplot(111, projection='3d')
-    ax.scatter(numpy.log(x), numpy.log(y), scores, c=scores, cmap=my_cmap)
-    ax.set_xlabel('log(%s)' % header1)
-    ax.set_ylabel('log(%s)' % header2)
+    ax.scatter(numpy.log10(x), numpy.log10(y), scores, c=scores, cmap=my_cmap)
+    ax.set_xlabel('log10(%s)' % header1)
+    ax.set_ylabel('log10(%s)' % header2)
     ax.set_zlabel(scoreName)
     filename = "%s_%s_%s.png" % (header1, header2, scoreName)
     filename = filename.replace(':', '_').replace('/', '_')
@@ -475,17 +488,17 @@ def plot_2d_single(directory_path, header_x, scoreName, data, scores):
     #score_scale = numpy.max(scores)/numpy.min(scores)
 
     if  scoreName.startswith('1-'):
-        scores = numpy.log(scores)
-        scoreName = 'log(%s)' % scoreName
+        scores = numpy.log10(scores)
+        scoreName = 'log10(%s)' % scoreName
 
     fig = figure.Figure(figsize=[10,10])
     canvas = FigureCanvas(fig)
     graph = fig.add_subplot(1, 1, 1)
 
     format = '%s'
     if numpy.max(data)/numpy.min(data) > 100.0:
-        data = numpy.log(data)
-        format = 'log(%s)'
+        data = numpy.log10(data)
+        format = 'log10(%s)'
 
     graph.scatter(data, scores, c=scores, cmap=my_cmap)
     graph.set_xlabel(format % header_x)
@@ -545,14 +558,14 @@ def singleGraphProgress(arg):
 
     graph = fig.add_subplot(1, 1, 1)
 
-    graph.plot(df[i],numpy.log(1-df[j]))
+    graph.plot(df[i],numpy.log10(1-df[j]))
     a = max(df[j])
     #graph.set_ylim((0,1.1*max(df[j])))
-    graph.set_title('%s vs log(1-%s)' % (i,j))
+    graph.set_title('%s vs log10(1-%s)' % (i,j))
     graph.set_xlabel(i)
-    graph.set_ylabel('log(1-%s)' % j)
+    graph.set_ylabel('log10(1-%s)' % j)
 
-    filename = "%s vs log(1-%s).png" % (i,j)
+    filename = "%s vs log10(1-%s).png" % (i,j)
     file_path = output / filename
     fig.savefig(str(file_path))
 

CADETMatch/jupyter.py

@@ -12,6 +12,7 @@ def __init__(self, json_path):
         self.json_path = json_path
         self.cache = Cache()
         self.cache.setup_dir(json_path)
+        CADETMatch.match.createDirectories(self.cache, json_path)
         self.cache.setup(json_path)
 
     def start_sim(self):

CADETMatch/scores/fractionationSlide.py

@@ -64,6 +64,7 @@ def run(sim_data, feature):
 
     graph_sim = {}
     graph_exp = {}
+    graph_sim_offset = {}
 
     searchIndexStart, searchIndexStop = searchRange(times, start, stop, CV_time)
 
@@ -106,9 +107,11 @@ def run(sim_data, feature):
 
         graph_sim[component] = list(zip(time_center, fracOffset))
         graph_exp[component] = list(zip(time_center, exp_values))
+        graph_sim_offset[component] = time_offset
 
     sim_data['graph_exp'] = graph_exp
     sim_data['graph_sim'] = graph_sim
+    sim_data['graph_sim_offset'] = graph_sim_offset
 
     return (scores, util.sse(numpy.array(sim_values_sse), numpy.array(exp_values_sse)), len(sim_values_sse), 
         time_center, numpy.array(sim_values_sse), numpy.array(exp_values_sse), [1.0 - i for i in scores])

setup.py

@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="CADETMatch",
-    version="0.5.22",
+    version="0.5.23",
     author="William Heymann",
     author_email="[email protected]",
     description="CADETMatch is a parameter estimation and error modeling library for CADET",