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23 """The monte_carlo user function definitions for Monte Carlo simulations."""
24
25
26 from graphics import WIZARD_IMAGE_PATH
27 from pipe_control import monte_carlo
28 from user_functions.data import Uf_info; uf_info = Uf_info()
29 from user_functions.objects import Desc_container
30
31
32
33 monte_carlo_desc = Desc_container("Monte Carlo Simulation Overview")
34 monte_carlo_desc.add_paragraph("For proper error analysis using Monte Carlo simulations, a sequence of function calls is required for running the various simulation components. The steps necessary for implementing Monte Carlo simulations are:")
35 monte_carlo_desc.add_item_list_element("1", "The measured data set together with the corresponding error set should be loaded into relax.")
36 monte_carlo_desc.add_item_list_element("2", "Either minimisation is used to optimise the parameters of the chosen model, or a calculation is run.")
37 monte_carlo_desc.add_item_list_element("3", "To initialise and turn on Monte Carlo simulations, the number of simulations, n, needs to be set.")
38 monte_carlo_desc.add_item_list_element("4", "The simulation data needs to be created either by back calculation from the fully minimised model parameters from step 2 or by direct calculation when values are calculated rather than minimised. The error set is used to randomise each simulation data set by assuming Gaussian errors. This creates a synthetic data set for each Monte Carlo simulation.")
39 monte_carlo_desc.add_item_list_element("5", "Prior to minimisation of the parameters of each simulation, initial parameter estimates are required. These are taken as the optimised model parameters. An alternative is to use a grid search for each simulation to generate initial estimates, however this is extremely computationally expensive. For the case where values are calculated rather than minimised, this step should be skipped (although the results will be unaffected if this is accidentally run).")
40 monte_carlo_desc.add_item_list_element("6", "Each simulation requires minimisation or calculation. The same techniques as used in step 2, excluding the grid search when minimising, should be used for the simulations.")
41 monte_carlo_desc.add_item_list_element("7", "Failed simulations are removed using the techniques of model elimination.")
42 monte_carlo_desc.add_item_list_element("8", "The model parameter errors are calculated from the distribution of simulation parameters.")
43 monte_carlo_desc.add_paragraph("Monte Carlo simulations can be turned on or off using functions within this class. Once the function for setting up simulations has been called, simulations will be turned on. The effect of having simulations turned on is that the functions used for minimisation (grid search, minimise, etc) or calculation will only affect the simulation parameters and not the model parameters. By subsequently turning simulations off using the appropriate function, the functions used in minimisation will affect the model parameters and not the simulation parameters.")
44 monte_carlo_desc.add_paragraph("An example for model-free analysis using the prompt UI mode which includes only the functions required for implementing the above steps is:")
45 monte_carlo_desc.add_prompt("relax> grid_search(inc=11) # Step 2.")
46 monte_carlo_desc.add_prompt("relax> minimise('newton') # Step 2.")
47 monte_carlo_desc.add_prompt("relax> monte_carlo.setup(number=500) # Step 3.")
48 monte_carlo_desc.add_prompt("relax> monte_carlo.create_data(method='back_calc') # Step 4.")
49 monte_carlo_desc.add_prompt("relax> monte_carlo.initial_values() # Step 5.")
50 monte_carlo_desc.add_prompt("relax> minimise('newton') # Step 6.")
51 monte_carlo_desc.add_prompt("relax> eliminate() # Step 7.")
52 monte_carlo_desc.add_prompt("relax> monte_carlo.error_analysis() # Step 8.")
53 monte_carlo_desc.add_paragraph("An example for reduced spectral density mapping is:")
54 monte_carlo_desc.add_prompt("relax> calc() # Step 2.")
55 monte_carlo_desc.add_prompt("relax> monte_carlo.setup(number=500) # Step 3.")
56 monte_carlo_desc.add_prompt("relax> monte_carlo.create_data(method='back_calc') # Step 4.")
57 monte_carlo_desc.add_prompt("relax> calc() # Step 6.")
58 monte_carlo_desc.add_prompt("relax> monte_carlo.error_analysis() # Step 8.")
59
60
61
62 uf_class = uf_info.add_class('monte_carlo')
63 uf_class.title = "Class containing the functions for Monte Carlo and related simulations."
64 uf_class.menu_text = "&monte_carlo"
65 uf_class.gui_icon = "oxygen.actions.roll-relax-blue"
66
67
68
69 uf = uf_info.add_uf('monte_carlo.create_data')
70 uf.title = "Create the Monte Carlo simulation data."
71 uf.title_short = "Data creation."
72 uf.add_keyarg(
73 name = "method",
74 default = "back_calc",
75 py_type = "str",
76 desc_short = "method",
77 desc = "The simulation method.",
78 wiz_element_type = "combo",
79 wiz_combo_choices = ["Monte Carlo", "Bootstrapping"],
80 wiz_combo_data = ["back_calc", "direct"],
81 wiz_read_only = True
82 )
83
84 uf.desc.append(Desc_container())
85 uf.desc[-1].add_paragraph("The method can either be set to back calculation (Monte Carlo) or direct (bootstrapping), the choice of which determines the simulation type. If the values or parameters are calculated rather than minimised, this option will have no effect. Errors should only be propagated via Monte Carlo simulations if errors have been measured. ")
86 uf.desc[-1].add_paragraph("For error analysis, the method should be set to back calculation which will result in proper Monte Carlo simulations. The data used for each simulation is back calculated from the minimised model parameters and is randomised using Gaussian noise where the standard deviation is from the original error set. When the method is set to back calculation, this function should only be called after the model is fully minimised.")
87 uf.desc[-1].add_paragraph("The simulation type can be changed by setting the method to direct. This will result in bootstrapping simulations which cannot be used in error analysis (and which are no longer Monte Carlo simulations). However, these simulations are required for certain model selection techniques (see the documentation for the model selection user function for details), and can be used for other purposes. Rather than the data being back calculated from the fitted model parameters, the data is generated by taking the original data and randomising using Gaussian noise with the standard deviations set to the original error set.")
88 uf.desc.append(monte_carlo_desc)
89 uf.backend = monte_carlo.create_data
90 uf.menu_text = "&create_data"
91 uf.gui_icon = "oxygen.actions.list-add-relax-blue"
92 uf.wizard_height_desc = 500
93 uf.wizard_size = (1000, 750)
94 uf.wizard_apply_button = False
95 uf.wizard_image = WIZARD_IMAGE_PATH + 'monte_carlo.png'
96
97
98
99 uf = uf_info.add_uf('monte_carlo.error_analysis')
100 uf.title = "Calculate parameter errors from the Monte Carlo simulations."
101 uf.title_short = "Error calculation."
102
103 uf.desc.append(Desc_container())
104 uf.desc[-1].add_paragraph("Parameter errors are calculated as the standard deviation of the distribution of parameter values. This function should never be used if parameter values are obtained by minimisation and the simulation data are generated using the method 'direct'. The reason is because only true Monte Carlo simulations can give the true parameter errors.")
105 uf.desc.append(monte_carlo_desc)
106 uf.backend = monte_carlo.error_analysis
107 uf.menu_text = "&error_analysis"
108 uf.gui_icon = "oxygen.actions.roll-relax-blue"
109 uf.wizard_height_desc = 620
110 uf.wizard_size = (1000, 750)
111 uf.wizard_apply_button = False
112 uf.wizard_image = WIZARD_IMAGE_PATH + 'monte_carlo.png'
113
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115
116 uf = uf_info.add_uf('monte_carlo.initial_values')
117 uf.title = "Set the initial simulation parameter values."
118 uf.title_short = "Initial value setting."
119
120 uf.desc.append(Desc_container())
121 uf.desc[-1].add_paragraph("This only effects where minimisation occurs and can therefore be skipped if the values or parameters are calculated rather than minimised. However, if accidentally run in this case, the results will be unaffected. It should only be called after the model or run is fully minimised. Once called, the functions 'grid_search' and 'minimise' will only effect the simulations and not the model parameters.")
122 uf.desc[-1].add_paragraph("The initial values of the parameters for each simulation is set to the minimised parameters of the model. A grid search can be undertaken for each simulation instead, although this is computationally expensive and unnecessary. The minimisation function should be executed for a second time after running this function.")
123 uf.desc.append(monte_carlo_desc)
124 uf.backend = monte_carlo.initial_values
125 uf.menu_text = "&initial_values"
126 uf.gui_icon = "oxygen.actions.list-add-relax-blue"
127 uf.wizard_height_desc = 620
128 uf.wizard_size = (1000, 750)
129 uf.wizard_apply_button = False
130 uf.wizard_image = WIZARD_IMAGE_PATH + 'monte_carlo.png'
131
132
133
134 uf = uf_info.add_uf('monte_carlo.off')
135 uf.title = "Turn the Monte Carlo simulations off."""
136 uf.title_short = "Simulations off."""
137
138 uf.desc.append(Desc_container())
139 uf.desc[-1].add_paragraph("This will turn off the Monte Carlo simulations so that subsequent optimisation will operate directly on the model parameters and not on the simulations.")
140 uf.desc.append(monte_carlo_desc)
141 uf.backend = monte_carlo.off
142 uf.menu_text = "o&ff"
143 uf.gui_icon = "oxygen.actions.dialog-cancel"
144 uf.wizard_height_desc = 620
145 uf.wizard_size = (1000, 750)
146 uf.wizard_apply_button = False
147 uf.wizard_image = WIZARD_IMAGE_PATH + 'monte_carlo.png'
148
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150
151 uf = uf_info.add_uf('monte_carlo.on')
152 uf.title = "Turn the Monte Carlo simulations on."""
153 uf.title_short = "Simulations on."""
154
155 uf.desc.append(Desc_container())
156 uf.desc[-1].add_paragraph("This will turn on the Monte Carlo simulations so that subsequent optimisation will operate on the simulations rather than on the real model parameters.")
157 uf.desc.append(monte_carlo_desc)
158 uf.backend = monte_carlo.on
159 uf.menu_text = "o&n"
160 uf.gui_icon = "oxygen.actions.dialog-ok"
161 uf.wizard_height_desc = 620
162 uf.wizard_size = (1000, 750)
163 uf.wizard_apply_button = False
164 uf.wizard_image = WIZARD_IMAGE_PATH + 'monte_carlo.png'
165
166
167
168 uf = uf_info.add_uf('monte_carlo.setup')
169 uf.title = "Set up the Monte Carlo simulations."
170 uf.title_short = "Simulation setup."
171 uf.add_keyarg(
172 name = "number",
173 default = 500,
174 py_type = "int",
175 min = 3,
176 max = 100000,
177 desc_short = "number of Monte Carlo simulations",
178 desc = "The number of Monte Carlo simulations."
179 )
180
181 uf.desc.append(Desc_container())
182 uf.desc[-1].add_paragraph("This must be called prior to any of the other Monte Carlo functions. The effect is that the number of simulations will be set and that simulations will be turned on.")
183 uf.desc.append(monte_carlo_desc)
184 uf.backend = monte_carlo.setup
185 uf.menu_text = "&setup"
186 uf.gui_icon = "oxygen.actions.document-edit"
187 uf.wizard_height_desc = 570
188 uf.wizard_size = (1000, 750)
189 uf.wizard_apply_button = False
190 uf.wizard_image = WIZARD_IMAGE_PATH + 'monte_carlo.png'
191