GUI images (#49)

* update

* util changes for gui plot figs, starting binding_polynomial c extension

* binding polynomial extension

* organization

* updates

* more changes to binding polynomial

* binding polynomial C extension

* gui image update

* bp.c clean up

pytc/indiv_models/binding_polynomial.py

@@ -93,4 +93,4 @@ def dQ(self):
             self._fit_beta_array, self._fit_dH_array, S_conc_corr, self._T_conc, self._T_conc_free, 
             final_array)
 
-        return final_array
+        return final_array

setup.py

@@ -29,4 +29,4 @@
       install_requires=["matplotlib","scipy","numpy","emcee","corner"],
       classifiers=['Programming Language :: Python'],
       ext_modules=[ext],
-      include_dirs=numpy.distutils.misc_util.get_numpy_include_dirs())
+      include_dirs=numpy.distutils.misc_util.get_numpy_include_dirs())

src/binding_polynomial.c

@@ -144,10 +144,17 @@ void *dQ(double *fit_beta_obj, double *fit_dH_obj, double *S_conc_corr, double *
 
     // num and denom arrays
     numerator = (double *)malloc(num_shots*sizeof(double));
+    if (numerator== NULL){
+        return NULL;
+    }
     for (i = 0; i < num_shots; i++){
         numerator[i] = 0.0;
     }
     denominator = (double *)malloc(num_shots*sizeof(double));
+    if (denominator == NULL){
+        return NULL;
+    }
+
     for (i = 0; i < num_shots; i++){
         denominator[i] = 1.0;
     }
@@ -211,47 +218,48 @@ void *dQ(double *fit_beta_obj, double *fit_dH_obj, double *S_conc_corr, double *
     if (avg_dH == NULL){
         return NULL;
     }
-    for (j = 0; j < num_shots; j++){
-        avg_dH[j] = numerator[j]/denominator[j];
+
+    for (i = 0; i < num_shots; i++){
+        avg_dH[i] = numerator[i]/denominator[i];
     }
     // avg_dh[1:]
     subset_first_dH = (double *)malloc(num_shots_reduced*sizeof(double));
     if (subset_first_dH == NULL){
         return NULL;
     }
-    for(j = 0; j < num_shots_reduced; j++){
-        subset_first_dH[j] = avg_dH[j+1];
+    for(i = 0; i < num_shots_reduced; i++){
+        subset_first_dH[i] = avg_dH[i+1];
     }
 
     // avg_dh[:-1]
     subset_last_dH = (double *)malloc(num_shots_reduced*sizeof(double));
     if (subset_last_dH == NULL){
         return NULL;
     }
-    for(j = 0; j < num_shots_reduced; j++){
-        subset_last_dH[j] = avg_dH[j];
+    for(i = 0; i < num_shots_reduced; i++){
+        subset_last_dH[i] = avg_dH[i];
     }
 
     // avg_dh[1:]-avg_dh[:-1];
     X = (double *)malloc(num_shots_reduced*sizeof(double));
     if (X == NULL){
         return NULL;
     }
-    for (j = 0; j < num_shots_reduced; j++){
-        X[j] = subset_first_dH[j] - subset_last_dH[j];
+    for (i = 0; i < num_shots_reduced; i++){
+        X[i] = subset_first_dH[i] - subset_last_dH[i];
     }
 
     // S_conc_corr[1:]
     subset_s_conc = (double *)malloc(num_shots_reduced*sizeof(double));
     if (subset_s_conc == NULL){
         return NULL;
     }
-    for(j = 0; j < num_shots_reduced; j++){
-        subset_s_conc[j] = S_conc_corr[j+1];
+    for(i = 0; i < num_shots_reduced; i++){
+        subset_s_conc[i] = S_conc_corr[i+1];
     }
 
-    for(j = 0; j < num_shots_reduced; j++){
-        final_array[j] = cell_volume*subset_s_conc[j]*X[j] + dilution_heats[j];
+    for(i = 0; i < num_shots_reduced; i++){
+        final_array[i] = cell_volume*subset_s_conc[i]*X[i] + dilution_heats[i];
     }
 
     // clean up
@@ -263,4 +271,4 @@ void *dQ(double *fit_beta_obj, double *fit_dH_obj, double *S_conc_corr, double *
     free(subset_s_conc);
     free(numerator);
     free(denominator);
-}
+}