piegy 2.2.3__cp37-cp37m-win32.whl → 2.3.1__cp37-cp37m-win32.whl

piegy/C_core/patch.h

@@ -23,14 +23,14 @@ typedef struct patch_t {
     double V_pi;
 
     struct patch_t* nb[4];
-    long double U_weight[4];  // stores migration weight of each of the 4 neighbors
-    long double V_weight[4];
-    long double sum_U_weight; // sum of U_weight
-    long double sum_V_weight;
+    double U_weight[4];  // stores migration weight of each of the 4 neighbors
+    double V_weight[4];
+    double sum_U_weight; // sum of U_weight
+    double sum_V_weight;
     double pi_death_rates[4];
-    long double mig_rates[8];
+    double mig_rates[8];
     double sum_pi_death_rates;
-    long double sum_mig_rates;
+    double sum_mig_rates;
 } patch_t;
 
 // in .c

piegy/C_core/sim_funcs.c

@@ -69,7 +69,7 @@ static void find_nb_periodical(size_t* restrict nb, size_t i, size_t j, size_t N
 
 // single_init function: initializes world, runs 1 event, returns updated variables
 static double single_init(const model_t* mod, patch_t* world, size_t* nb_indices, 
-                    long double* patch_rates, long double* sum_rates_by_row, long double* sum_rates_p, signal_t* sig_p, patch_picked_t* picked_p) {
+                    double* patch_rates, double* sum_rates_by_row, double* sum_rates_p, signal_t* sig_p, patch_picked_t* picked_p) {
 
     size_t N = mod->N;
     size_t M = mod->M;
@@ -141,7 +141,7 @@ static double single_init(const model_t* mod, patch_t* world, size_t* nb_indices
     }
 
     // pick the first random event
-    long double expected_sum = random01() * *sum_rates_p;
+    double expected_sum = random01() * *sum_rates_p;
     find_patch(picked_p, expected_sum, patch_rates, sum_rates_by_row, *sum_rates_p, N, M);
     size_t picked_idx = picked_p->i * M + picked_p->j;
     size_t e0 = find_event(&world[picked_idx], expected_sum - picked_p->current_sum);
@@ -223,9 +223,9 @@ static uint8_t single_test(model_t* restrict mod, uint32_t update_sum_freq, char
     patch_t* world = (patch_t*) calloc(NM, sizeof(patch_t));
     size_t* nb_indices = (size_t*) calloc(NM * 4, sizeof(size_t));
 
-    long double* patch_rates = (long double*) calloc(NM, sizeof(long double));
-    long double* sum_rates_by_row = (long double*) calloc(N, sizeof(long double));
-    long double sum_rates = 0;
+    double* patch_rates = (double*) calloc(NM, sizeof(double));
+    double* sum_rates_by_row = (double*) calloc(N, sizeof(double));
+    double sum_rates = 0;
 
     signal_t signal;
     patch_picked_t picked;
@@ -399,7 +399,7 @@ static uint8_t single_test(model_t* restrict mod, uint32_t update_sum_freq, char
 
 
         // pick a random event
-        long double expected_sum = random01() * sum_rates;
+        double expected_sum = random01() * sum_rates;
         find_patch(&picked, expected_sum, patch_rates, sum_rates_by_row, sum_rates, N, M);
         size_t picked_idx = picked.i * M + picked.j;
         uint8_t e0 = find_event(&world[picked_idx], expected_sum - picked.current_sum);
@@ -477,7 +477,7 @@ static uint8_t single_test(model_t* restrict mod, uint32_t update_sum_freq, char
 
 
 
-static void single_test_free(patch_t** world, size_t** nb_indices, long double** patch_rates, long double** sum_rates_by_row) {
+static void single_test_free(patch_t** world, size_t** nb_indices, double** patch_rates, double** sum_rates_by_row) {
     free(*world);
     free(*nb_indices);
     free(*patch_rates);

piegy/C_core/sim_funcs.h

@@ -37,7 +37,7 @@
 
 // where exp(x) is considered overflow
 // below the actual bound (709) because the large numbers will be computed with close-to-0 ones (payoff rates), so higher accuracy is needed
-#define EXP_OVERFLOW_BOUND 600
+#define EXP_OVERFLOW_BOUND 500
 
 
 static uint64_t pcg_state = 0;
@@ -83,9 +83,9 @@ typedef struct signal_t {
 static void find_nb_zero_flux(size_t* restrict nb, size_t i, size_t j, size_t N, size_t M, size_t NM);
 static void find_nb_periodical(size_t* restrict nb, size_t i, size_t j, size_t N, size_t M, size_t NM);
 static double single_init(const model_t* mod, patch_t* world, size_t* nb_indices, 
-                    long double* patch_rates, long double* sum_rates_by_row, long double* sum_rates, signal_t* sig_p, patch_picked_t* picked_p) ;
+                    double* patch_rates, double* sum_rates_by_row, double* sum_rates, signal_t* sig_p, patch_picked_t* picked_p) ;
 static uint8_t single_test(model_t* restrict mod, uint32_t update_sum_frequency, char* message);
-static void single_test_free(patch_t** world, size_t** nb_indices, long double** patch_rates, long double** sum_rates_by_row);
+static void single_test_free(patch_t** world, size_t** nb_indices, double** patch_rates, double** sum_rates_by_row);
 uint8_t run(model_t* mod, char* message, size_t msg_len, uint32_t update_sum_freq);
 
 
@@ -94,12 +94,12 @@ uint8_t run(model_t* mod, char* message, size_t msg_len, uint32_t update_sum_fre
  * Inline Functions
 */
 
-static inline long double random01() {
+static inline double random01() {
     // generate a 24 bit random int, then convert to a (0, 1) ranged double
     uint32_t r1 = rand() & 0x7fff;  // RAND_MAX is different across machines, ensure 15 bits
     uint32_t r2 = rand() & 0x7fff;
 
-    long double r_combined = (r1 << 15) + r2;  // discard the lower 3 bits, which are unstable
+    double r_combined = (r1  << 15) + r2;  // discard the lower 3 bits, which are unstable
     return (r_combined + 1) / RAND_UPPER_PLUS_2;
 }
 
@@ -155,8 +155,8 @@ static inline uint8_t update_mig_one(patch_t* restrict p, const double* restrict
 
     double mu1_U = P_start[0] * (double)p->U;
     double mu2_V = P_start[1] * (double)p->V;
-    long double* p_U_weight = p->U_weight;
-    long double* p_V_weight = p->V_weight;
+    double* p_U_weight = p->U_weight;
+    double* p_V_weight = p->V_weight;
 
     patch_t* nbi = p->nb[nb_loc];
     p->sum_U_weight -= p_U_weight[nb_loc];
@@ -210,8 +210,8 @@ static inline uint8_t update_mig_all(patch_t* restrict p, const double* restrict
     double mu1_U = P_start[0] * (double)p->U;
     double mu2_V = P_start[1] * (double)p->V;
 
-    long double* p_U_weight = p->U_weight;
-    long double* p_V_weight = p->V_weight;
+    double* p_U_weight = p->U_weight;
+    double* p_V_weight = p->V_weight;
 
     p->sum_U_weight = 0.0;
     p->sum_V_weight = 0.0;
@@ -255,7 +255,7 @@ static inline uint8_t update_mig_all(patch_t* restrict p, const double* restrict
 
 
 
-static inline uint8_t find_event(const patch_t* restrict p, long double expected_sum) {
+static inline uint8_t find_event(const patch_t* restrict p, double expected_sum) {
     size_t event = 0;
     double current_sum;
 
@@ -330,8 +330,8 @@ static inline void change_popu(patch_t* restrict p, uint8_t s) {
  * Main Simulation Functions
 */
 
-static inline void find_patch(patch_picked_t* restrict picked, long double expected_sum, 
-                                const long double* restrict patch_rates, const long double* restrict sum_rates_by_row, long double sum_rates, size_t N, size_t M) {
+static inline void find_patch(patch_picked_t* restrict picked, double expected_sum, 
+                                const double* restrict patch_rates, const double* restrict sum_rates_by_row, double sum_rates, size_t N, size_t M) {
     double current_sum = 0;
     size_t row = 0;
     size_t col = 0;

piegy/__init__.py

@@ -28,7 +28,7 @@ from .data_tools import save_data, read_data
 from .analysis import rounds_expected, scale_maxtime, check_convergence, combine_sim
 
 from .figures import (UV_hmap, UV_bar, UV_dyna, UV_hist, UV_std, UV_expected, 
-                      pi_hmap, pi_bar, pi_dyna, pi_hist, pi_std, UV_pi)
+                      pi_hmap, pi_bar, pi_dyna, pi_hist, pi_std, UV_pi, video_fig)
 
 from .test_var import (test_var1, var_UV1, var_pi1, var_convergence1, get_dirs1, 
                        test_var2, var_UV2, var_pi2, var_convergence2, get_dirs2)
@@ -43,7 +43,7 @@ data_members = ['save_data', 'read_data']
 analysis_members = ['expected_rounds', 'scale_maxtime', 'check_convergence', 'combine_mod']
 
 figures_members = ['UV_hmap', 'UV_bar', 'UV_dyna', 'UV_hist', 'UV_std', 'UV_expected_val', 'UV_expected', 
-                   'pi_hmap', 'pi_bar', 'pi_dyna', 'pi_hist', 'pi_std', 'UV_pi']
+                   'pi_hmap', 'pi_bar', 'pi_dyna', 'pi_hist', 'pi_std', 'UV_pi', 'video_fig']
 
 test_var_members = ['test_var1', 'var_UV1', 'var_pi1', 'var_convergence1', 'get_dirs1', 
                     'test_var2', 'var_UV2', 'var_pi2', 'var_convergence2', 'get_dirs2']

piegy/__version__.py

@@ -1,4 +1,4 @@
-__version__ = '2.2.3'
+__version__ = '2.3.1'
 
 '''
 version history:
@@ -35,4 +35,5 @@ version history:
 2.2.1: change heatmap plotting tool from Seaborn to Matplotlib. Change video maker to cv2 (opencv-python).
 2.2.2: impose stricter overflow error check. Used update_mig_one function (already written before, didn't use). This gives 30% speed improvement.
 2.2.3: raised rate calculation to higher accuracy (long double), and switched to 30-bit random number generator.
+2.3.1: roll back accuracy update. Decrease toleratable bound for exponent of exp() to 500. Add video_fig function to figures module, which plots change of patch popu/payoff overtime in a 2D figure.
 '''

piegy/build_info.py

@@ -4,8 +4,8 @@ Auto-generated at compile time.
 """
 
 build_info = {
-    "version": "2.2.3",
-    "build date": "2025-07-01 20:49:26",
+    "version": "2.3.1",
+    "build date": "2025-07-02 07:55:23",
     "python used": "3.7.9",
     "platform": "win32"
 }

piegy/figures.py

@@ -306,9 +306,9 @@ def pi_hmap(mod, ax_U = None, ax_V = None, U_color = 'BuPu', V_color = 'YlGn', s
     Upi_ave = figure_t.ave_interval(mod.Upi, start_index, end_index)
     V_pi_ave = figure_t.ave_interval(mod.Vpi, start_index, end_index)
     
-    U_title = figure_t.gen_title('Payoff ' + r'$p_U$', start, end)
+    U_title = figure_t.gen_title('Payoff ' + r'$p_H$', start, end)
     U_text = figure_t.gen_text(np.mean(Upi_ave), np.std(Upi_ave))
-    V_title = figure_t.gen_title('Payoff ' + r'$p_V$', start, end)
+    V_title = figure_t.gen_title('Payoff ' + r'$p_D$', start, end)
     V_text = figure_t.gen_text(np.mean(V_pi_ave), np.std(V_pi_ave))
     
     figure_t.hmap(Upi_ave, ax_U, U_color, U_title, U_text, vmin = vrange_U[0], vmax = vrange_U[1])
@@ -334,13 +334,13 @@ def pi_bar(mod, ax_U = None, ax_V = None, U_color = 'violet', V_color = 'yellowg
     Upi_ave = figure_t.ave_interval_1D(mod.Upi, start_index, end_index)
     V_pi_ave = figure_t.ave_interval_1D(mod.Vpi, start_index, end_index)
     
-    U_title = figure_t.gen_title(r'$p_U$', start, end)
+    U_title = figure_t.gen_title(r'$p_H$', start, end)
     U_text = figure_t.gen_text(np.mean(Upi_ave), np.std(Upi_ave))
-    V_title = figure_t.gen_title(r'$p_V$', start, end)
+    V_title = figure_t.gen_title(r'$p_D$', start, end)
     V_text = figure_t.gen_text(np.mean(V_pi_ave), np.std(V_pi_ave))
     
-    ax_U = figure_t.bar(Upi_ave, ax_U, U_color, 'Patches', 'Payoff ' + r'$p_U$', U_title, U_text)
-    ax_V = figure_t.bar(V_pi_ave, ax_V, V_color, 'Patches', 'Payoff ' + r'$p_V$', V_title, V_text)
+    ax_U = figure_t.bar(Upi_ave, ax_U, U_color, 'Patches', 'Payoff ' + r'$p_H$', U_title, U_text)
+    ax_V = figure_t.bar(V_pi_ave, ax_V, V_color, 'Patches', 'Payoff ' + r'$p_D$', V_title, V_text)
 
     return ax_U, ax_V
 
@@ -376,12 +376,12 @@ def pi_dyna(mod, ax = None, interval = 20, grid = True):
     if ax == None:
         _, ax = plt.subplots()
     ax.grid(grid)
-    ax.plot(xaxis, U_curve, CURVE_TYPE, label = r'$p_U$')
-    ax.plot(xaxis, V_curve, CURVE_TYPE, label = r'$p_V$')
+    ax.plot(xaxis, U_curve, CURVE_TYPE, label = r'$p_H$')
+    ax.plot(xaxis, V_curve, CURVE_TYPE, label = r'$p_D$')
     ax.plot(xaxis, total_curve, CURVE_TYPE, label = 'total')
     ax.set_xlabel('Time')
     ax.set_ylabel('Payoff')
-    ax.set_title('Payoff ' + r'$p_U$' + ' & ' + r'$p_V$' + ' over time')
+    ax.set_title('Payoff ' + r'$p_H$' + ' & ' + r'$p_D$' + ' over time')
     ax.legend()
 
     return ax
@@ -408,17 +408,17 @@ def pi_hist(mod, ax_U = None, ax_V = None, U_color = 'violet', V_color = 'yellow
     
     if ax_U == None:
         _, ax_U = plt.subplots()
-    ax_U.set_xlabel('Payoff ' + r'$p_U$')
+    ax_U.set_xlabel('Payoff ' + r'$p_H$')
     ax_U.set_ylabel('Density')
     ax_U.hist(Upi_ave, color = U_color, density = True)
-    ax_U.set_title(figure_t.gen_title('Payoff ' + r'$p_U$' + ' Hist', start, end))
+    ax_U.set_title(figure_t.gen_title('Payoff ' + r'$p_H$' + ' Hist', start, end))
     
     if ax_V == None:
         _, ax_V = plt.subplots()
-    ax_V.set_xlabel('Payoff ' + r'$p_V$')
+    ax_V.set_xlabel('Payoff ' + r'$p_D$')
     ax_V.set_ylabel('Density')
     ax_V.hist(V_pi_ave, color = V_color, density = True)
-    ax_V.set_title(figure_t.gen_title('Payoff ' + r'$p_V$' + ' Hist', start, end))
+    ax_V.set_title(figure_t.gen_title('Payoff ' + r'$p_D$' + ' Hist', start, end))
 
     return ax_U, ax_V
 
@@ -453,8 +453,8 @@ def pi_std(mod, ax = None, interval = 20, grid = True):
     if ax == None:
         _, ax = plt.subplots()
     ax.grid(grid)
-    ax.plot(xaxis, Upi_std, CURVE_TYPE, label = r'$p_U$' + ' std')
-    ax.plot(xaxis, V_pi_std, CURVE_TYPE, label = r'$p_V$' + ' std')
+    ax.plot(xaxis, Upi_std, CURVE_TYPE, label = r'$p_H$' + ' std')
+    ax.plot(xaxis, V_pi_std, CURVE_TYPE, label = r'$p_D$' + ' std')
     ax.legend()
     ax.set_xlabel('Time')
     ax.set_ylabel('Std Dev')
@@ -484,9 +484,66 @@ def UV_pi(mod, ax_U = None, ax_V = None, U_color = 'violet', V_color = 'yellowgr
     V_pi_ave = figure_t.ave_interval(mod.Vpi, start_index, end_index)
     
     
-    ax_U = figure_t.scatter(U_ave, Upi_ave, ax_U, U_color, alpha, xlabel = 'U', ylabel = 'Payoff ' + r'$p_U$', title = 'U - ' + r'$p_U$')
-    ax_V = figure_t.scatter(V_ave, V_pi_ave, ax_V, V_color, alpha, xlabel = 'V', ylabel = 'Payoff ' + r'$p_V$', title = 'V - ' + r'$p_V$')
+    ax_U = figure_t.scatter(U_ave, Upi_ave, ax_U, U_color, alpha, xlabel = 'U', ylabel = 'Payoff ' + r'$p_H$', title = 'U - ' + r'$p_H$')
+    ax_V = figure_t.scatter(V_ave, V_pi_ave, ax_V, V_color, alpha, xlabel = 'V', ylabel = 'Payoff ' + r'$p_D$', title = 'V - ' + r'$p_D$')
     
     return ax_U, ax_V
 
 
+
+def video_fig(mod, ax_list = None, num_itv = 100, U_color = 'Purples', V_color = 'Greens'):
+    '''
+    Plot distribution dynamics over time, of U, V population and payoff.
+
+    mod: simulation.model object
+    ax_list: a 2*2 list of ax, or None (a new 2*2 ax_list will be created)
+    num_itv: how many time intervals to plot
+    U_color & V_color: matplotlib color map, color for U, V population and payoff.
+    '''
+
+    if num_itv > mod.max_record:
+        raise ValueError('num_itv too large, larger than mod.max_record')
+    idx_step = int(mod.max_record / num_itv)
+    ave_U = []
+    ave_V = []
+    ave_Upi = []
+    ave_Vpi = []
+
+    for lower_idx in range(0, mod.max_record, idx_step):
+        ave_U.append(figure_t.ave_interval_1D(mod.U, lower_idx, lower_idx + idx_step))
+        ave_V.append(figure_t.ave_interval_1D(mod.V, lower_idx, lower_idx + idx_step))
+        ave_Upi.append(figure_t.ave_interval_1D(mod.Upi, lower_idx, lower_idx + idx_step))
+        ave_Vpi.append(figure_t.ave_interval_1D(mod.Vpi, lower_idx, lower_idx + idx_step))
+
+    if ax_list == None:
+
+        _, ax_list = plt.subplots(2, 2, figsize = (9.6, 12.8), dpi = 300)
+
+    for i in range(2):
+        for j in range(2):
+            ax_list[i, j].spines['top'].set_visible(False)
+            ax_list[i, j].spines['right'].set_visible(False)
+            ax_list[i, j].set_xlabel('Patches')
+            ax_list[i, j].set_ylabel('Time')
+            ax_list[i, j].set_xlim([0, mod.M - 1])
+            ax_list[i, j].set_ylim([0, mod.maxtime])
+    
+
+    im = ax_list[0, 0].imshow(ave_U, cmap = U_color)
+    ax_list[0, 0].get_figure().colorbar(im, ax = ax_list[0, 0])
+    ax_list[0, 0].set_title('Population U over time')
+        
+    im = ax_list[0, 1].imshow(ave_V, cmap = V_color)
+    ax_list[0, 1].get_figure().colorbar(im, ax = ax_list[0, 1])
+    ax_list[0, 1].set_title('Population V over time')
+
+    im = ax_list[1, 0].imshow(ave_Upi, cmap = U_color)
+    ax_list[1, 0].get_figure().colorbar(im, ax = ax_list[1, 0])
+    ax_list[1, 0].set_title('Payoff ' + r'$p_H$' + ' over time')
+
+    im = ax_list[1, 1].imshow(ave_Vpi, cmap = V_color)
+    ax_list[1, 1].get_figure().colorbar(im, ax = ax_list[1, 1])
+    ax_list[1, 1].set_title('Payoff ' + r'$p_D$' + ' over time')
+
+    return ax_list
+

piegy/test_var.py

@@ -347,12 +347,12 @@ def var_pi1(var, values, var_dirs, ax_U = None, ax_V = None, start = 0.95, end =
     var_disp = PATCH_VAR_DISP[var]
     
     ax_U.set_xlabel(var_disp)
-    ax_U.set_ylabel('Payoff ' + r'$p_U$')
+    ax_U.set_ylabel('Payoff ' + r'$p_H$')
     ax_U.plot(values, U_ave, DOTTED_CURVE_TYPE, color = U_color)
     ax_U.set_title(figure_t.gen_title(var_disp + r'$\,-\,p_U$', start, end))
     
     ax_V.set_xlabel(var_disp)
-    ax_V.set_ylabel('Payoff ' + r'$p_V$')
+    ax_V.set_ylabel('Payoff ' + r'$p_D$')
     ax_V.plot(values, V_ave, DOTTED_CURVE_TYPE, color = V_color)
     ax_V.set_title(figure_t.gen_title(var_disp  + r'$\,-\,p_V$', start, end))
 

piegy/tools/figure_tools.py

@@ -172,7 +172,7 @@ def ave_interval(data, start_index, end_index):
 def ave_interval_1D(data, start_index, end_index):
     '''
     Calculate average value of data over an interval. Return a 1D np.array.
-    Assume data is 3D and has shape (1 x M x K) or (N x 1 x K). Then implicitly 'compress' that 1 and takes average on the 3rd axis.
+    Assume data is 3D and has shape (N x M x K). Then implicitly 'compress' that N x M to 1D (NM) and takes average on the 3rd axis K.
 
     Input:
         data:       3D np.array or list. One of its dimensions must have size 1. Will take average on the 3rd axis.

{piegy-2.2.3.dist-info → piegy-2.3.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: piegy
-Version: 2.2.3
+Version: 2.3.1
 Summary: Payoff-Driven Stochastic Spatial Model for Evolutionary Game Theory
 Author-email: Chenning Xu <cxu7@caltech.edu>
 License: BSD 3-Clause License

piegy-2.3.1.dist-info/RECORD

@@ -0,0 +1,28 @@
+piegy/__init__.py,sha256=uFhdK4VLKN1e-JgW2h20RuDOhtm_sFPfjcCqPXbJ45w,2186
+piegy/__version__.py,sha256=kC8lX83uoch7LTyBS7ioArc9f-JC5ZQTLcsYdQkWb-g,2298
+piegy/analysis.py,sha256=tJhJTSFJsK_Zr34s78Cy7Im1NtONctkdNmg0R0teTeU,8941
+piegy/build_info.py,sha256=685DQ_5NO_TNkJpqg6Jlh3i4E__GxiWzvA2UdQuUgn0,258
+piegy/data_tools.py,sha256=uYEoCYO7ZVtKBsNDgco7kERvBlOFFK7wpTuqcCwCBEU,3573
+piegy/figures.py,sha256=UdY0A-zGmuGiUIuez87qYImiVLGRWxuI9jzS-YsTJNc,20811
+piegy/simulation.py,sha256=VRm4x8RnfmsBKzARoWJcATaibc8D7Z21JIZ3ElJlLQ4,21505
+piegy/simulation_py.py,sha256=BC87ONd3-OG9e8ri_8EP83QagEPPp-dMJ5pJJTa1pcw,30319
+piegy/test_var.py,sha256=18aMebUdh_lA34mGFbpAbWUfzvEiFWL0GLBCNegneAk,24096
+piegy/videos.py,sha256=L-FadrD4mRaamwvlpkukL2wI_2ECYBdLkpGC675X1SQ,10996
+piegy/C_core/Makefile,sha256=18sxm2A2kBP1H1_kW2nDFrQrzrpmjf1xmPaZZcQh9XQ,2189
+piegy/C_core/model.c,sha256=v4vOs7HGcyOpIKWQPoT8uqLaA4NRSkaUuShowlrbjeM,2962
+piegy/C_core/model.h,sha256=WijCKKxdHn4Zz_F5NDmCy9lBA5KonWuHR0kfUxcB5b0,1234
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