More efficient Matlab wrapping

Author: benfulcher

featureList.txt

@@ -1,7 +1,5 @@
 DN_HistogramMode_5
 DN_HistogramMode_10
-DN_Mean
-DN_Spread_Std
 CO_f1ecac
 CO_FirstMin_ac
 CO_HistogramAMI_even_2_5
@@ -21,4 +19,6 @@ SB_MotifThree_quantile_hh
 SC_FluctAnal_2_rsrangefit_50_1_logi_prop_r1
 SC_FluctAnal_2_dfa_50_1_2_logi_prop_r1
 SP_Summaries_welch_rect_centroid
-FC_LocalSimple_mean3_stderr
+FC_LocalSimple_mean3_stderr
+DN_Mean
+DN_Spread_Std

wrap_Matlab/GetAllFeatureNames.m

@@ -0,0 +1,33 @@
+function featureNames = GetAllFeatureNames(doCatch24)
+% Retrieve all feature names from featureList.txt
+
+if nargin < 1 || isempty(doCatch24)
+    doCatch24 = true;
+end
+%-------------------------------------------------------------------------------
+
+fid = fopen('../featureList.txt','r');
+i = 1;
+tline = fgetl(fid);
+featureNames{i} = tline;
+while ischar(tline)
+    i = i + 1;
+    tline = fgetl(fid);
+    if ischar(tline)
+        featureNames{i} = tline;
+    end
+end
+fclose(fid);
+
+%-------------------------------------------------------------------------------
+% Filter out the two extra features: 'DN_Mean' and 'DN_Spread_Std'
+isMeanStd = strcmp(featureNames,'DN_Mean') | strcmp(featureNames,'DN_Spread_Std');
+assert(sum(isMeanStd) == 2)
+if ~doCatch24
+    featureNames = featureNames(~isMeanStd);
+    fprintf(1,'Using catch22\n');
+else
+    fprintf(1,'Using catch24\n');
+end
+
+end

wrap_Matlab/catch22_all.m

@@ -12,48 +12,16 @@
 %% Check inputs and set defaults
 %-------------------------------------------------------------------------------
 if nargin < 2
-    doCatch24 = false;
+    doCatch24 = true;
 end
 
 %-------------------------------------------------------------------------------
 % Define the features:
 %-------------------------------------------------------------------------------
-
-% catch22:
-featureNames = ...
-{ ...
-'DN_HistogramMode_5', ...
-'DN_HistogramMode_10', ...
-'CO_f1ecac', ...
-'CO_FirstMin_ac', ...
-'CO_HistogramAMI_even_2_5', ...
-'CO_trev_1_num', ...
-'MD_hrv_classic_pnn40', ...
-'SB_BinaryStats_mean_longstretch1', ...
-'SB_TransitionMatrix_3ac_sumdiagcov', ...
-'PD_PeriodicityWang_th0_01', ...
-'CO_Embed2_Dist_tau_d_expfit_meandiff', ...
-'IN_AutoMutualInfoStats_40_gaussian_fmmi', ...
-'FC_LocalSimple_mean1_tauresrat', ...
-'DN_OutlierInclude_p_001_mdrmd', ...
-'DN_OutlierInclude_n_001_mdrmd', ...
-'SP_Summaries_welch_rect_area_5_1', ...
-'SB_BinaryStats_diff_longstretch0', ...
-'SB_MotifThree_quantile_hh', ...
-'SC_FluctAnal_2_rsrangefit_50_1_logi_prop_r1', ...
-'SC_FluctAnal_2_dfa_50_1_2_logi_prop_r1', ...
-'SP_Summaries_welch_rect_centroid', ...
-'FC_LocalSimple_mean3_stderr'
-};
-
-% Add basic properties of the distribution (mean and standard deviation) as catch24 if desired:
-if doCatch24
-    additionals = {'DN_Mean', 'DN_Spread_Std'};
-    featureNames = [featureNames, additionals];
-end
+featureNames = GetAllFeatureNames(doCatch24);
 
 %-------------------------------------------------------------------------------
-% Compute all features from their local catch22 (compiled) implementations
+% Compute all features from their local compiled implementations
 %-------------------------------------------------------------------------------
 numFeatures = length(featureNames);
 featureValues = zeros(numFeatures,1);

wrap_Matlab/mexAll.m

@@ -13,18 +13,7 @@
 includeFiles = cellfun(@(x) fullfile(basePath, x), CFileNames, 'UniformOutput', false);
 
 % Get function names
-fid = fopen('../featureList.txt','r');
-i = 1;
-tline = fgetl(fid);
-featureNames{i} = tline;
-while ischar(tline)
-    i = i + 1;
-    tline = fgetl(fid);
-    if ischar(tline)
-        featureNames{i} = tline;
-    end
-end
-fclose(fid);
+featureNames = GetAllFeatureNames(true);
 
 % mex all feature functions separately
 numFeatures = length(featureNames);

wrap_Matlab/testing.m

@@ -1,37 +1,34 @@
-% get function names
-fid = fopen('../featureList.txt','r');
-i = 1;
-tline = fgetl(fid);
-featureNames{i} = tline;
-while ischar(tline)
-    i = i+1;
-    tline = fgetl(fid);
-    featureNames{i} = tline;
-end
-fclose(fid);
+%-------------------------------------------------------------------------------
+% Get the function names
+featureNames = GetAllFeatureNames();
+numFeatures = length(featureNames);
 
-% get the data
+%-------------------------------------------------------------------------------
+% Get the data
 dataFileNames = {'../testData/test.txt', '../testData/test2.txt'};
-for j = 1:2
-    
+numTestFiles = length(dataFileNames);
+
+fprintf(1,'Testing %u compiled features on %u data files\n',numFeatures,numTestFiles);
+
+%-------------------------------------------------------------------------------
+% Test all functions on all the data files
+for j = 1:numTestFiles
+
     dataFileName = dataFileNames{j};
-    fprintf('\n%s\n', dataFileName)
-    
+    fprintf('\n%s\n\n', dataFileName)
+
     fileID = fopen(dataFileName,'r');
-    
     data = fscanf(fileID,'%f');
-    
-    for featureInd = 1:length(featureNames)-1
-    
-        featureName = featureNames{featureInd};
 
-        fh = str2func(['catch22_', featureName]);
+    for featureInd = 1:numFeatures
 
+        featureName = featureNames{featureInd};
+        fh = str2func(['catch22_', featureName]);
         out = fh(data');
-        
+
         fprintf("%s: %1.6f\n", featureName, out);
     end
-    
+
     fclose(fileID);
-    
+
 end