Upload new file

IBD-Simulations/main.py

+'''
+Created on 17.10.2014
+This is the main file, controlling the other parts of the Spatial Block simulator
+@author: Harald Ringbauer
+'''
+
+from grid import factory_Grid  # Factory method to create Grid Object
+from analysis import Analysis
+import cProfile  # @UnusedImport
+# import cPickle as pickle
+
+growing = 1  # Wether to use growing model or not
+        
+def main():
+    '''Main loop of the Block-Simulator'''
+    grid = 0
+    data = 0
+    print("Welcome back!")
+    
+    while True:
+        print("\nWhat do you want to do?")
+        inp = int(input(" (1) Set Blocks \n (2) Update Generation \n (3) Data Analysis \n (4) Reset Grid \n"
+        " (5) Full MLE-Analysis\n (6) End program \n"))    
+            
+        if inp == 1:
+            print("Initiating Blocks...")
+            if grid == 0:  # Make new grid if not existing
+                grid = factory_Grid(growing)
+                
+            #position_list = [(50 + i * 2, 50 + j * 2, 0) for i 
+            #                 in range(12) for j in range(5)]    # Introduced this for grant
+            #grid.set_samples(position_list)
+            
+            grid.set_random_samples(500)    # Sets random samples
+                
+        if inp == 2:     
+            if grid == 0:  # Make new grid if not existing
+                grid = factory_Grid(growing)  # Factory method to produce Grid or Growing_grid class         
+            grid.plot_distribution()  # Plot the Grid
+            t = int(input("\nHow many generations?\n"))
+            grid.update_t(t)   
+                     
+        if inp == 3:
+            if grid == 0:
+                print("\n Error: No grid to analyze detected, generate one")
+                grid = factory_Grid(growing)
+            if data == 0:
+                print("Load data...")
+                data = Analysis(grid)  # Generate Data Analysis Object
+            print("\nData loaded: " + str(len(grid.IBD_blocks)) + " IBD Blocks\n")
+            
+            # Inner loop for this menu
+            while True:    
+                inp1 = int(input(" (1) Block-Statistics \n (2) MLE-estimation \n (3) Plot exponential decay\n"
+                            " (4) Show IBD-List\n (5) Exponential Fit \n" 
+                            " (6) Fit specific length \n (7) Plot blocks \n (8) Exit to main menu\n"))
+        
+                if inp1 == 1:
+                    # print(grid.IBD_blocks)
+                    data.which_blocks()
+                    data.which_times()
+                elif inp1 == 2:
+                    data.mle_estimate_error()
+                elif inp1 == 3:
+                    data.plot_expdecay(logy=False)
+                elif inp1 == 4:
+                    print(data.IBD_blocks) 
+                elif inp1 == 5:
+                    data.fit_expdecay()
+                elif inp1 == 6:
+                    interval1 = input("Interval start: \n")
+                    interval2 = input("Interval end: \n")
+                    interval = [interval1, interval2]
+                    data.fit_specific_length(interval)
+                elif inp1 == 7:
+                    data.plot_blocks()
+                elif inp1 == 8:
+                    break
+                else: print("Input invalid!")                     
+            
+        if inp == 4:
+            if grid == 0:
+                grid = factory_Grid(growing)
+            grid.reset_grid()
+        
+        elif inp == 5:
+            if grid == 0:
+                print("\n Error: No grid to analyze detected, generate one")
+                grid = factory_Grid(growing)
+            analysis = grid.create_MLE_object(bin_pairs=True)  # Create the POPRES-MLE-Object
+                
+            while True:
+                inp2 = input("\n(1) Choose MLE-model \n(2) Run Fit\n(3) Bin-plot fitted data \n(4) Log-Likelihood surface"
+                            "\n(5) Jack-Knive Countries \n(7) Boots-Trap (Country Pairs) \n(8) Boots-Trap (Blocks)" 
+                            "\n(9) Which times? \n(10) Analyze Residuals \n(0) Exit\n")
+                if inp2 == 1:
+                    inp3 = input("Which Model?\n(1) Constant \n(2) Doomsday"
+                    "\n(3) Power growth \n(4) Power-Const\n(0) Back\n")
+                    if inp3 == 1: analysis.create_mle_model("constant", grid.chrom_l, [1.0, 2.0])
+                    elif inp3 == 2: analysis.create_mle_model("doomsday", grid.chrom_l , [200, 2.0])
+                    elif inp3 == 3: analysis.create_mle_model("power_growth", grid.chrom_l, [200, 2.0, 1.0])
+                    elif inp3 == 4: analysis.create_mle_model("ddd")
+                    else: print("Invalid Input!! Please do again")
+
+                elif inp2 == 2: analysis.mle_analysis_error()
+                elif inp2 == 3: analysis.plot_fitted_data_error()    
+                elif inp2 == 4: analysis.plot_loglike_surface() 
+                elif inp2 == 5: analysis.jack_knife_ctries() 
+                elif inp2 == 7: 
+                    bts_nr = input("How many boots traps?\n")
+                    analysis.boots_trap_ctry(bts_nr)
+                elif inp2 == 8:
+                    bts_nr = input("How many boots traps?\n")
+                    analysis.boot_trap_blocks(bts_nr)
+                elif inp2 == 9:
+                    analysis.which_times()
+                elif inp2 == 10:
+                    analysis.calculate_pw_residuals()
+                elif inp2 == 0: break    
+               
+        if inp == 6:
+            print("Thanks for your patience future-Harald. See you later alligator!")
+            break
+    
+    pass
+
+def profiling_main():
+    '''Short script for profiling where the program spends time.'''
+    grid = factory_Grid()
+    grid.set_samples()
+    grid.update_t(40)
+    
+if __name__ == '__main__':
+    main()
+    # cProfile.run('profiling_main()')