Alexander
commited on
Commit
·
36bf2f6
1
Parent(s):
5e1b1b7
initial test
Browse files- Dockerfile +1 -1
- requirements.txt +4 -1
- src/app.py +256 -0
- src/utils/__init__.py +3 -0
- src/utils/__pycache__/__init__.cpython-311.pyc +0 -0
- src/utils/__pycache__/utils.cpython-311.pyc +0 -0
- src/utils/old_plots.py +1157 -0
- src/utils/utils.py +820 -0
Dockerfile
CHANGED
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@@ -17,4 +17,4 @@ EXPOSE 8501
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HEALTHCHECK CMD curl --fail http://localhost:8501/_stcore/health
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ENTRYPOINT ["streamlit", "run", "src/
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HEALTHCHECK CMD curl --fail http://localhost:8501/_stcore/health
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ENTRYPOINT ["streamlit", "run", "src/app.py", "--server.port=8501", "--server.address=0.0.0.0"]
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requirements.txt
CHANGED
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@@ -1,3 +1,6 @@
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altair
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pandas
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-
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altair
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pandas
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ssm-simulators
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streamlit>1.30.0
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matplotlib
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seaborn
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src/app.py
ADDED
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@@ -0,0 +1,256 @@
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| 1 |
+
import matplotlib.pyplot as plt
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import numpy as np
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import seaborn as sns
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import streamlit as st
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# from hssm import simulate_data
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from ssms.config import model_config
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| 8 |
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from ssms.basic_simulators.simulator import simulator
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| 9 |
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import pandas as pd
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import utils
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# Function to create input select widgets
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def create_param_selectors(model_name: str, model_num: int = 1):
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d_config = model_config[model_name]
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params = d_config["params"]
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param_bounds_low = d_config["param_bounds"][0]
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param_bounds_high = d_config["param_bounds"][1]
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param_defaults = d_config["default_params"]
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d_param_slider = {}
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for i, (name, low, high, default) in enumerate(
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zip(
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params,
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param_bounds_low,
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param_bounds_high,
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param_defaults,
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)
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):
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d_param_slider[i] = st.slider(
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label=name,
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min_value=float(low),
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max_value=float(high),
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value=float(default),
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key=f"param{i}"
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f"_{model_name}"
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f"_{model_num}"
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f'_{st.session_state["slider_version"]}',
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)
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return d_param_slider
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+
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def add_model():
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pass
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def reset_sliders():
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st.session_state["slider_version"] += 1
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# Initialize a slider version attribute state. Is used for resetting values
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if "slider_version" not in st.session_state:
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st.session_state["slider_version"] = 1
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+
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def draw_model_configurator(model_num=1):
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# Create widgets for the sidebar
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# st.markdown("<h2 style='text-align: center; color: black;'>Model Configurator</h1>",
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# unsafe_allow_html=True)
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# Dropdown selection of model name
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model_select = st.selectbox(
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"Model " + str(model_num), l_model_names, key="modelname" + str(model_num)
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)
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# Sliders for param values
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d_slider = create_param_selectors(model_select, model_num=model_num)
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# Number of data points to simulate
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nsamples = st.number_input("NSamples", value=5000, key="size" + str(model_num))
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# Number of trajectories to show
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ntrajectories = st.number_input(
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"NTrajectories", value=0, key="ntraj" + str(model_num)
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)
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return model_select, d_slider, nsamples, ntrajectories
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+
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+
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st.set_page_config(layout="wide")
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# Get list of model names
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l_model_names = list(model_config.keys())
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with st.sidebar:
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col1, col2 = st.columns(2)
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with col1:
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model_select_1, d_slider_1, nsamples_1, ntrajectories_1 = (
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draw_model_configurator(model_num=1)
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)
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with col2:
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model_select_2, d_slider_2, nsamples_2, ntrajectories_2 = (
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draw_model_configurator(model_num=2)
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)
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# Button to reset sliders to default values
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randomseed = st.number_input("RandomSeed", value=0, key="seed")
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st.button(
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| 94 |
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"Reset",
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| 95 |
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help="Reset parameters to defaults",
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key="reset",
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on_click=reset_sliders,
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)
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| 99 |
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| 100 |
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# st.title("SSM Model Plots", )
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st.markdown(
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| 102 |
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"<h1 style='text-align: center; color: black;'>SSM Model Plots</h1>",
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| 103 |
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unsafe_allow_html=True,
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| 104 |
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)
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| 105 |
+
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| 106 |
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# Display components for main panel
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| 107 |
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fig1, ax1 = plt.subplots()
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| 108 |
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if model_config[model_select_1]["nchoices"] == 2 and not ("race" in model_select_1):
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| 109 |
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ax1 = utils.utils.plot_func_model(
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| 110 |
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model_name=model_select_1,
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| 111 |
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theta=[list(d_slider_1.values())],
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| 112 |
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axis=ax1,
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| 113 |
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value_range=[-0.1, 5],
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| 114 |
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n_samples=nsamples_1,
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ylim=5,
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| 116 |
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data_color="blue",
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| 117 |
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add_trajectories=True,
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| 118 |
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n_trajectories=ntrajectories_1,
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| 119 |
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linewidth_model=1,
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linewidth_histogram=1,
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| 121 |
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random_state=randomseed,
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| 122 |
+
)
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| 123 |
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else:
|
| 124 |
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ax1 = utils.utils.plot_func_model_n(
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| 125 |
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model_name=model_select_1,
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| 126 |
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theta=[list(d_slider_1.values())],
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| 127 |
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axis=ax1,
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| 128 |
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value_range=[-0.1, 5],
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| 129 |
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n_samples=nsamples_1,
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data_color="blue",
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| 131 |
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add_trajectories=True,
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| 132 |
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n_trajectories=ntrajectories_1,
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| 133 |
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linewidth_model=1,
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| 134 |
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linewidth_histogram=1,
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| 135 |
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random_state=randomseed,
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| 136 |
+
)
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| 137 |
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ax1.set_title("Model 1")
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| 138 |
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ax1.set_xlabel("RT in seconds")
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| 139 |
+
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| 140 |
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fig2, ax2 = plt.subplots()
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| 141 |
+
if model_config[model_select_2]["nchoices"] == 2 and not ("race" in model_select_2):
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| 142 |
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ax2 = utils.utils.plot_func_model(
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| 143 |
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model_name=model_select_2,
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| 144 |
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theta=[list(d_slider_2.values())],
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| 145 |
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axis=ax2,
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| 146 |
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value_range=[-0.1, 5],
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| 147 |
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n_samples=nsamples_2,
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| 148 |
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ylim=5,
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| 149 |
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data_color="red",
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| 150 |
+
add_trajectories=True,
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| 151 |
+
n_trajectories=ntrajectories_2,
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| 152 |
+
linewidth_model=1,
|
| 153 |
+
linewidth_histogram=1,
|
| 154 |
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random_state=randomseed,
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| 155 |
+
)
|
| 156 |
+
else:
|
| 157 |
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ax2 = utils.utils.plot_func_model_n(
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| 158 |
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model_name=model_select_2,
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| 159 |
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theta=[list(d_slider_2.values())],
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| 160 |
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axis=ax2,
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| 161 |
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value_range=[-0.1, 5],
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| 162 |
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n_samples=nsamples_2,
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| 163 |
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data_color="red",
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| 164 |
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add_trajectories=True,
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| 165 |
+
n_trajectories=ntrajectories_2,
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| 166 |
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linewidth_model=1,
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| 167 |
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linewidth_histogram=1,
|
| 168 |
+
random_state=randomseed,
|
| 169 |
+
)
|
| 170 |
+
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| 171 |
+
ax2.set_title("Model 2")
|
| 172 |
+
ax2.set_xlabel("RT in seconds")
|
| 173 |
+
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| 174 |
+
# Place figure in placeholder
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| 175 |
+
col1, col2 = st.columns(2)
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| 176 |
+
with col1:
|
| 177 |
+
figure_placeholder_1 = st.empty() # Placeholder for figure render
|
| 178 |
+
figure_placeholder_1.pyplot(fig1)
|
| 179 |
+
with col2:
|
| 180 |
+
figure_placeholder_2 = st.empty() # Placeholder for figure render
|
| 181 |
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figure_placeholder_2.pyplot(fig2)
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| 182 |
+
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| 183 |
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# Simulate two datasets:
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| 184 |
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sim_output_1 = simulator(
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| 185 |
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model=model_select_1,
|
| 186 |
+
theta=[list(d_slider_1.values())],
|
| 187 |
+
n_samples=nsamples_1,
|
| 188 |
+
random_state=randomseed,
|
| 189 |
+
)
|
| 190 |
+
sim_output_2 = simulator(
|
| 191 |
+
model=model_select_2,
|
| 192 |
+
theta=[list(d_slider_2.values())],
|
| 193 |
+
n_samples=nsamples_2,
|
| 194 |
+
random_state=randomseed,
|
| 195 |
+
)
|
| 196 |
+
|
| 197 |
+
# Make metadata dataframe
|
| 198 |
+
metadata = pd.DataFrame(
|
| 199 |
+
{
|
| 200 |
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"Model 1": [
|
| 201 |
+
sim_output_1["metadata"]["model"],
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| 202 |
+
sim_output_1["choice_p"][0, 0],
|
| 203 |
+
sim_output_1["rts"].mean(),
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| 204 |
+
sim_output_1["metadata"]["s"],
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| 205 |
+
],
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| 206 |
+
"Model 2": [
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| 207 |
+
sim_output_2["metadata"]["model"],
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| 208 |
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sim_output_2["choice_p"][0, 0],
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| 209 |
+
sim_output_2["rts"].mean(),
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| 210 |
+
sim_output_2["metadata"]["s"],
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| 211 |
+
],
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| 212 |
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},
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| 213 |
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index=["Model", "Choice Probability", "Mean RT", "Noise SD"],
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| 214 |
+
)
|
| 215 |
+
|
| 216 |
+
col3, col4 = st.columns(2)
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| 217 |
+
with col3:
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| 218 |
+
if (
|
| 219 |
+
len(sim_output_1["metadata"]["possible_choices"])
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| 220 |
+
== 2 | len(sim_output_2["metadata"]["possible_choices"])
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| 221 |
+
== 2
|
| 222 |
+
):
|
| 223 |
+
figure_placeholder_3 = st.empty()
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| 224 |
+
|
| 225 |
+
# Plot the simulated data
|
| 226 |
+
fig3, ax3 = plt.subplots()
|
| 227 |
+
ax3.hist(
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| 228 |
+
sim_output_1["rts"][np.abs(sim_output_1["rts"]) != 999]
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| 229 |
+
* sim_output_1["choices"][np.abs(sim_output_1["rts"] != 999)],
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| 230 |
+
histtype="step",
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| 231 |
+
bins=50,
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| 232 |
+
density=True,
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| 233 |
+
color="blue",
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| 234 |
+
fill=None,
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| 235 |
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label="Model 1",
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| 236 |
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)
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| 237 |
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ax3.hist(
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| 238 |
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sim_output_2["rts"][np.abs(sim_output_2["rts"]) != 999]
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| 239 |
+
* sim_output_2["choices"][np.abs(sim_output_2["rts"] != 999)],
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| 240 |
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histtype="step",
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| 241 |
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bins=50,
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| 242 |
+
density=True,
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| 243 |
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color="red",
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| 244 |
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fill=None,
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| 245 |
+
label="Model 2",
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| 246 |
+
)
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| 247 |
+
ax3.legend()
|
| 248 |
+
ax3.set_xlabel("RT")
|
| 249 |
+
ax3.set_xlim(-5, 5)
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| 250 |
+
figure_placeholder_3.pyplot(fig3)
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| 251 |
+
else:
|
| 252 |
+
# TODO: Implement better comparison plot
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| 253 |
+
# for models with more than 2 choice options
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| 254 |
+
pass
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| 255 |
+
with col4:
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| 256 |
+
st.dataframe(metadata)
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src/utils/__init__.py
ADDED
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@@ -0,0 +1,3 @@
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+
from . import utils
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__all__ = ["utils"]
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src/utils/__pycache__/__init__.cpython-311.pyc
ADDED
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Binary file (276 Bytes). View file
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src/utils/__pycache__/utils.cpython-311.pyc
ADDED
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Binary file (26 kB). View file
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src/utils/old_plots.py
ADDED
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@@ -0,0 +1,1157 @@
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|
| 1 |
+
def _plot_func_model(
|
| 2 |
+
bottom_node,
|
| 3 |
+
axis,
|
| 4 |
+
value_range=None,
|
| 5 |
+
samples=10,
|
| 6 |
+
bin_size=0.05,
|
| 7 |
+
add_data_rts=True,
|
| 8 |
+
add_data_model=True,
|
| 9 |
+
add_data_model_keep_slope=True,
|
| 10 |
+
add_data_model_keep_boundary=True,
|
| 11 |
+
add_data_model_keep_ndt=True,
|
| 12 |
+
add_data_model_keep_starting_point=True,
|
| 13 |
+
add_data_model_markersize_starting_point=50,
|
| 14 |
+
add_data_model_markertype_starting_point=0,
|
| 15 |
+
add_data_model_markershift_starting_point=0,
|
| 16 |
+
add_posterior_uncertainty_model=False,
|
| 17 |
+
add_posterior_uncertainty_rts=False,
|
| 18 |
+
add_posterior_mean_model=True,
|
| 19 |
+
add_posterior_mean_rts=True,
|
| 20 |
+
add_trajectories=False,
|
| 21 |
+
data_label="Data",
|
| 22 |
+
secondary_data=None,
|
| 23 |
+
secondary_data_label=None,
|
| 24 |
+
secondary_data_color="blue",
|
| 25 |
+
linewidth_histogram=0.5,
|
| 26 |
+
linewidth_model=0.5,
|
| 27 |
+
legend_fontsize=12,
|
| 28 |
+
legend_shadow=True,
|
| 29 |
+
legend_location="upper right",
|
| 30 |
+
data_color="blue",
|
| 31 |
+
posterior_mean_color="red",
|
| 32 |
+
posterior_uncertainty_color="black",
|
| 33 |
+
alpha=0.05,
|
| 34 |
+
delta_t_model=0.01,
|
| 35 |
+
add_legend=True, # keep_frame=False,
|
| 36 |
+
**kwargs,
|
| 37 |
+
):
|
| 38 |
+
"""Calculate posterior predictive for a certain bottom node.
|
| 39 |
+
|
| 40 |
+
Arguments:
|
| 41 |
+
bottom_node: pymc.stochastic
|
| 42 |
+
Bottom node to compute posterior over.
|
| 43 |
+
|
| 44 |
+
axis: matplotlib.axis
|
| 45 |
+
Axis to plot into.
|
| 46 |
+
|
| 47 |
+
value_range: numpy.ndarray
|
| 48 |
+
Range over which to evaluate the likelihood.
|
| 49 |
+
|
| 50 |
+
Optional:
|
| 51 |
+
samples: int <default=10>
|
| 52 |
+
Number of posterior samples to use.
|
| 53 |
+
|
| 54 |
+
bin_size: float <default=0.05>
|
| 55 |
+
Size of bins used for histograms
|
| 56 |
+
|
| 57 |
+
alpha: float <default=0.05>
|
| 58 |
+
alpha (transparency) level for the sample-wise elements of the plot
|
| 59 |
+
|
| 60 |
+
add_data_rts: bool <default=True>
|
| 61 |
+
Add data histogram of rts ?
|
| 62 |
+
|
| 63 |
+
add_data_model: bool <default=True>
|
| 64 |
+
Add model cartoon for data
|
| 65 |
+
|
| 66 |
+
add_posterior_uncertainty_rts: bool <default=True>
|
| 67 |
+
Add sample by sample histograms?
|
| 68 |
+
|
| 69 |
+
add_posterior_mean_rts: bool <default=True>
|
| 70 |
+
Add a mean posterior?
|
| 71 |
+
|
| 72 |
+
add_model: bool <default=True>
|
| 73 |
+
Whether to add model cartoons to the plot.
|
| 74 |
+
|
| 75 |
+
linewidth_histogram: float <default=0.5>
|
| 76 |
+
linewdith of histrogram plot elements.
|
| 77 |
+
|
| 78 |
+
linewidth_model: float <default=0.5>
|
| 79 |
+
linewidth of plot elements concerning the model cartoons.
|
| 80 |
+
|
| 81 |
+
legend_location: str <default='upper right'>
|
| 82 |
+
string defining legend position. Find the rest of the options in the matplotlib documentation.
|
| 83 |
+
|
| 84 |
+
legend_shadow: bool <default=True>
|
| 85 |
+
Add shadow to legend box?
|
| 86 |
+
|
| 87 |
+
legend_fontsize: float <default=12>
|
| 88 |
+
Fontsize of legend.
|
| 89 |
+
|
| 90 |
+
data_color : str <default="blue">
|
| 91 |
+
Color for the data part of the plot.
|
| 92 |
+
|
| 93 |
+
posterior_mean_color : str <default="red">
|
| 94 |
+
Color for the posterior mean part of the plot.
|
| 95 |
+
|
| 96 |
+
posterior_uncertainty_color : str <default="black">
|
| 97 |
+
Color for the posterior uncertainty part of the plot.
|
| 98 |
+
|
| 99 |
+
delta_t_model:
|
| 100 |
+
specifies plotting intervals for model cartoon elements of the graphs.
|
| 101 |
+
"""
|
| 102 |
+
|
| 103 |
+
# AF-TODO: Add a mean version of this!
|
| 104 |
+
if value_range is None:
|
| 105 |
+
# Infer from data by finding the min and max from the nodes
|
| 106 |
+
raise NotImplementedError("value_range keyword argument must be supplied.")
|
| 107 |
+
|
| 108 |
+
if len(value_range) > 2:
|
| 109 |
+
value_range = (value_range[0], value_range[-1])
|
| 110 |
+
|
| 111 |
+
# Extract some parameters from kwargs
|
| 112 |
+
bins = np.arange(value_range[0], value_range[-1], bin_size)
|
| 113 |
+
|
| 114 |
+
# If bottom_node is a DataFrame we know that we are just plotting real data
|
| 115 |
+
if type(bottom_node) == pd.DataFrame:
|
| 116 |
+
samples_tmp = [bottom_node]
|
| 117 |
+
data_tmp = None
|
| 118 |
+
else:
|
| 119 |
+
samples_tmp = _post_pred_generate(
|
| 120 |
+
bottom_node,
|
| 121 |
+
samples=samples,
|
| 122 |
+
data=None,
|
| 123 |
+
append_data=False,
|
| 124 |
+
add_model_parameters=True,
|
| 125 |
+
)
|
| 126 |
+
data_tmp = bottom_node.value.copy()
|
| 127 |
+
|
| 128 |
+
# Relevant for recovery mode
|
| 129 |
+
node_data_full = kwargs.pop("node_data", None)
|
| 130 |
+
|
| 131 |
+
tmp_model = kwargs.pop("model_", "angle")
|
| 132 |
+
if len(model_config[tmp_model]["choices"]) > 2:
|
| 133 |
+
raise ValueError("The model plot works only for 2 choice models at the moment")
|
| 134 |
+
|
| 135 |
+
# ---------------------------
|
| 136 |
+
|
| 137 |
+
ylim = kwargs.pop("ylim", 3)
|
| 138 |
+
hist_bottom = kwargs.pop("hist_bottom", 2)
|
| 139 |
+
hist_histtype = kwargs.pop("hist_histtype", "step")
|
| 140 |
+
|
| 141 |
+
if ("ylim_high" in kwargs) and ("ylim_low" in kwargs):
|
| 142 |
+
ylim_high = kwargs["ylim_high"]
|
| 143 |
+
ylim_low = kwargs["ylim_low"]
|
| 144 |
+
else:
|
| 145 |
+
ylim_high = ylim
|
| 146 |
+
ylim_low = -ylim
|
| 147 |
+
|
| 148 |
+
if ("hist_bottom_high" in kwargs) and ("hist_bottom_low" in kwargs):
|
| 149 |
+
hist_bottom_high = kwargs["hist_bottom_high"]
|
| 150 |
+
hist_bottom_low = kwargs["hist_bottom_low"]
|
| 151 |
+
else:
|
| 152 |
+
hist_bottom_high = hist_bottom
|
| 153 |
+
hist_bottom_low = hist_bottom
|
| 154 |
+
|
| 155 |
+
axis.set_xlim(value_range[0], value_range[-1])
|
| 156 |
+
axis.set_ylim(ylim_low, ylim_high)
|
| 157 |
+
axis_twin_up = axis.twinx()
|
| 158 |
+
axis_twin_down = axis.twinx()
|
| 159 |
+
axis_twin_up.set_ylim(ylim_low, ylim_high)
|
| 160 |
+
axis_twin_up.set_yticks([])
|
| 161 |
+
axis_twin_down.set_ylim(ylim_high, ylim_low)
|
| 162 |
+
axis_twin_down.set_yticks([])
|
| 163 |
+
axis_twin_down.set_axis_off()
|
| 164 |
+
axis_twin_up.set_axis_off()
|
| 165 |
+
|
| 166 |
+
# ADD HISTOGRAMS
|
| 167 |
+
# -------------------------------
|
| 168 |
+
# POSTERIOR BASED HISTOGRAM
|
| 169 |
+
if add_posterior_uncertainty_rts: # add_uc_rts:
|
| 170 |
+
j = 0
|
| 171 |
+
for sample in samples_tmp:
|
| 172 |
+
tmp_label = None
|
| 173 |
+
|
| 174 |
+
if add_legend and j == 0:
|
| 175 |
+
tmp_label = "PostPred"
|
| 176 |
+
|
| 177 |
+
weights_up = np.tile(
|
| 178 |
+
(1 / bin_size) / sample.shape[0],
|
| 179 |
+
reps=sample.loc[sample.response == 1, :].shape[0],
|
| 180 |
+
)
|
| 181 |
+
weights_down = np.tile(
|
| 182 |
+
(1 / bin_size) / sample.shape[0],
|
| 183 |
+
reps=sample.loc[(sample.response != 1), :].shape[0],
|
| 184 |
+
)
|
| 185 |
+
|
| 186 |
+
axis_twin_up.hist(
|
| 187 |
+
np.abs(sample.rt[sample.response == 1]),
|
| 188 |
+
bins=bins,
|
| 189 |
+
weights=weights_up,
|
| 190 |
+
histtype=hist_histtype,
|
| 191 |
+
bottom=hist_bottom_high,
|
| 192 |
+
alpha=alpha,
|
| 193 |
+
color=posterior_uncertainty_color,
|
| 194 |
+
edgecolor=posterior_uncertainty_color,
|
| 195 |
+
zorder=-1,
|
| 196 |
+
label=tmp_label,
|
| 197 |
+
linewidth=linewidth_histogram,
|
| 198 |
+
)
|
| 199 |
+
|
| 200 |
+
axis_twin_down.hist(
|
| 201 |
+
np.abs(sample.loc[(sample.response != 1), :].rt),
|
| 202 |
+
bins=bins,
|
| 203 |
+
weights=weights_down,
|
| 204 |
+
histtype=hist_histtype,
|
| 205 |
+
bottom=hist_bottom_low,
|
| 206 |
+
alpha=alpha,
|
| 207 |
+
color=posterior_uncertainty_color,
|
| 208 |
+
edgecolor=posterior_uncertainty_color,
|
| 209 |
+
linewidth=linewidth_histogram,
|
| 210 |
+
zorder=-1,
|
| 211 |
+
)
|
| 212 |
+
j += 1
|
| 213 |
+
|
| 214 |
+
if add_posterior_mean_rts: # add_mean_rts:
|
| 215 |
+
concat_data = pd.concat(samples_tmp)
|
| 216 |
+
tmp_label = None
|
| 217 |
+
|
| 218 |
+
if add_legend:
|
| 219 |
+
tmp_label = "PostPred Mean"
|
| 220 |
+
|
| 221 |
+
weights_up = np.tile(
|
| 222 |
+
(1 / bin_size) / concat_data.shape[0],
|
| 223 |
+
reps=concat_data.loc[concat_data.response == 1, :].shape[0],
|
| 224 |
+
)
|
| 225 |
+
weights_down = np.tile(
|
| 226 |
+
(1 / bin_size) / concat_data.shape[0],
|
| 227 |
+
reps=concat_data.loc[(concat_data.response != 1), :].shape[0],
|
| 228 |
+
)
|
| 229 |
+
|
| 230 |
+
axis_twin_up.hist(
|
| 231 |
+
np.abs(concat_data.rt[concat_data.response == 1]),
|
| 232 |
+
bins=bins,
|
| 233 |
+
weights=weights_up,
|
| 234 |
+
histtype=hist_histtype,
|
| 235 |
+
bottom=hist_bottom_high,
|
| 236 |
+
alpha=1.0,
|
| 237 |
+
color=posterior_mean_color,
|
| 238 |
+
edgecolor=posterior_mean_color,
|
| 239 |
+
zorder=-1,
|
| 240 |
+
label=tmp_label,
|
| 241 |
+
linewidth=linewidth_histogram,
|
| 242 |
+
)
|
| 243 |
+
|
| 244 |
+
axis_twin_down.hist(
|
| 245 |
+
np.abs(concat_data.loc[(concat_data.response != 1), :].rt),
|
| 246 |
+
bins=bins,
|
| 247 |
+
weights=weights_down,
|
| 248 |
+
histtype=hist_histtype,
|
| 249 |
+
bottom=hist_bottom_low,
|
| 250 |
+
alpha=1.0,
|
| 251 |
+
color=posterior_mean_color,
|
| 252 |
+
edgecolor=posterior_mean_color,
|
| 253 |
+
linewidth=linewidth_histogram,
|
| 254 |
+
zorder=-1,
|
| 255 |
+
)
|
| 256 |
+
|
| 257 |
+
# DATA HISTOGRAM
|
| 258 |
+
if (data_tmp is not None) and add_data_rts:
|
| 259 |
+
tmp_label = None
|
| 260 |
+
if add_legend:
|
| 261 |
+
tmp_label = data_label
|
| 262 |
+
|
| 263 |
+
weights_up = np.tile(
|
| 264 |
+
(1 / bin_size) / data_tmp.shape[0],
|
| 265 |
+
reps=data_tmp[data_tmp.response == 1].shape[0],
|
| 266 |
+
)
|
| 267 |
+
weights_down = np.tile(
|
| 268 |
+
(1 / bin_size) / data_tmp.shape[0],
|
| 269 |
+
reps=data_tmp[(data_tmp.response != 1)].shape[0],
|
| 270 |
+
)
|
| 271 |
+
|
| 272 |
+
axis_twin_up.hist(
|
| 273 |
+
np.abs(data_tmp[data_tmp.response == 1].rt),
|
| 274 |
+
bins=bins,
|
| 275 |
+
weights=weights_up,
|
| 276 |
+
histtype=hist_histtype,
|
| 277 |
+
bottom=hist_bottom_high,
|
| 278 |
+
alpha=1,
|
| 279 |
+
color=data_color,
|
| 280 |
+
edgecolor=data_color,
|
| 281 |
+
label=tmp_label,
|
| 282 |
+
zorder=-1,
|
| 283 |
+
linewidth=linewidth_histogram,
|
| 284 |
+
)
|
| 285 |
+
|
| 286 |
+
axis_twin_down.hist(
|
| 287 |
+
np.abs(data_tmp[(data_tmp.response != 1)].rt),
|
| 288 |
+
bins=bins,
|
| 289 |
+
weights=weights_down,
|
| 290 |
+
histtype=hist_histtype,
|
| 291 |
+
bottom=hist_bottom_low,
|
| 292 |
+
alpha=1,
|
| 293 |
+
color=data_color,
|
| 294 |
+
edgecolor=data_color,
|
| 295 |
+
linewidth=linewidth_histogram,
|
| 296 |
+
zorder=-1,
|
| 297 |
+
)
|
| 298 |
+
|
| 299 |
+
# SECONDARY DATA HISTOGRAM
|
| 300 |
+
if secondary_data is not None:
|
| 301 |
+
tmp_label = None
|
| 302 |
+
if add_legend:
|
| 303 |
+
if secondary_data_label is not None:
|
| 304 |
+
tmp_label = secondary_data_label
|
| 305 |
+
|
| 306 |
+
weights_up = np.tile(
|
| 307 |
+
(1 / bin_size) / secondary_data.shape[0],
|
| 308 |
+
reps=secondary_data[secondary_data.response == 1].shape[0],
|
| 309 |
+
)
|
| 310 |
+
weights_down = np.tile(
|
| 311 |
+
(1 / bin_size) / secondary_data.shape[0],
|
| 312 |
+
reps=secondary_data[(secondary_data.response != 1)].shape[0],
|
| 313 |
+
)
|
| 314 |
+
|
| 315 |
+
axis_twin_up.hist(
|
| 316 |
+
np.abs(secondary_data[secondary_data.response == 1].rt),
|
| 317 |
+
bins=bins,
|
| 318 |
+
weights=weights_up,
|
| 319 |
+
histtype=hist_histtype,
|
| 320 |
+
bottom=hist_bottom_high,
|
| 321 |
+
alpha=1,
|
| 322 |
+
color=secondary_data_color,
|
| 323 |
+
edgecolor=secondary_data_color,
|
| 324 |
+
label=tmp_label,
|
| 325 |
+
zorder=-100,
|
| 326 |
+
linewidth=linewidth_histogram,
|
| 327 |
+
)
|
| 328 |
+
|
| 329 |
+
axis_twin_down.hist(
|
| 330 |
+
np.abs(secondary_data[(secondary_data.response != 1)].rt),
|
| 331 |
+
bins=bins,
|
| 332 |
+
weights=weights_down,
|
| 333 |
+
histtype=hist_histtype,
|
| 334 |
+
bottom=hist_bottom_low,
|
| 335 |
+
alpha=1,
|
| 336 |
+
color=secondary_data_color,
|
| 337 |
+
edgecolor=secondary_data_color,
|
| 338 |
+
linewidth=linewidth_histogram,
|
| 339 |
+
zorder=-100,
|
| 340 |
+
)
|
| 341 |
+
# -------------------------------
|
| 342 |
+
|
| 343 |
+
if add_legend:
|
| 344 |
+
if data_tmp is not None:
|
| 345 |
+
axis_twin_up.legend(
|
| 346 |
+
fontsize=legend_fontsize, shadow=legend_shadow, loc=legend_location
|
| 347 |
+
)
|
| 348 |
+
|
| 349 |
+
# ADD MODEL:
|
| 350 |
+
j = 0
|
| 351 |
+
t_s = np.arange(0, value_range[-1], delta_t_model)
|
| 352 |
+
|
| 353 |
+
# MAKE BOUNDS (FROM MODEL CONFIG) !
|
| 354 |
+
if add_posterior_uncertainty_model: # add_uc_model:
|
| 355 |
+
for sample in samples_tmp:
|
| 356 |
+
_add_model_cartoon_to_ax(
|
| 357 |
+
sample=sample,
|
| 358 |
+
axis=axis,
|
| 359 |
+
tmp_model=tmp_model,
|
| 360 |
+
keep_slope=add_data_model_keep_slope,
|
| 361 |
+
keep_boundary=add_data_model_keep_boundary,
|
| 362 |
+
keep_ndt=add_data_model_keep_ndt,
|
| 363 |
+
keep_starting_point=add_data_model_keep_starting_point,
|
| 364 |
+
markersize_starting_point=add_data_model_markersize_starting_point,
|
| 365 |
+
markertype_starting_point=add_data_model_markertype_starting_point,
|
| 366 |
+
markershift_starting_point=add_data_model_markershift_starting_point,
|
| 367 |
+
delta_t_graph=delta_t_model,
|
| 368 |
+
sample_hist_alpha=alpha,
|
| 369 |
+
lw_m=linewidth_model,
|
| 370 |
+
tmp_label=tmp_label,
|
| 371 |
+
ylim_low=ylim_low,
|
| 372 |
+
ylim_high=ylim_high,
|
| 373 |
+
t_s=t_s,
|
| 374 |
+
color=posterior_uncertainty_color,
|
| 375 |
+
zorder_cnt=j,
|
| 376 |
+
)
|
| 377 |
+
|
| 378 |
+
if (node_data_full is not None) and add_data_model:
|
| 379 |
+
_add_model_cartoon_to_ax(
|
| 380 |
+
sample=node_data_full,
|
| 381 |
+
axis=axis,
|
| 382 |
+
tmp_model=tmp_model,
|
| 383 |
+
keep_slope=add_data_model_keep_slope,
|
| 384 |
+
keep_boundary=add_data_model_keep_boundary,
|
| 385 |
+
keep_ndt=add_data_model_keep_ndt,
|
| 386 |
+
keep_starting_point=add_data_model_keep_starting_point,
|
| 387 |
+
markersize_starting_point=add_data_model_markersize_starting_point,
|
| 388 |
+
markertype_starting_point=add_data_model_markertype_starting_point,
|
| 389 |
+
markershift_starting_point=add_data_model_markershift_starting_point,
|
| 390 |
+
delta_t_graph=delta_t_model,
|
| 391 |
+
sample_hist_alpha=1.0,
|
| 392 |
+
lw_m=linewidth_model + 0.5,
|
| 393 |
+
tmp_label=None,
|
| 394 |
+
ylim_low=ylim_low,
|
| 395 |
+
ylim_high=ylim_high,
|
| 396 |
+
t_s=t_s,
|
| 397 |
+
color=data_color,
|
| 398 |
+
zorder_cnt=j + 1,
|
| 399 |
+
)
|
| 400 |
+
|
| 401 |
+
if add_posterior_mean_model: # add_mean_model:
|
| 402 |
+
tmp_label = None
|
| 403 |
+
if add_legend:
|
| 404 |
+
tmp_label = "PostPred Mean"
|
| 405 |
+
|
| 406 |
+
_add_model_cartoon_to_ax(
|
| 407 |
+
sample=pd.DataFrame(pd.concat(samples_tmp).mean().astype(np.float32)).T,
|
| 408 |
+
axis=axis,
|
| 409 |
+
tmp_model=tmp_model,
|
| 410 |
+
keep_slope=add_data_model_keep_slope,
|
| 411 |
+
keep_boundary=add_data_model_keep_boundary,
|
| 412 |
+
keep_ndt=add_data_model_keep_ndt,
|
| 413 |
+
keep_starting_point=add_data_model_keep_starting_point,
|
| 414 |
+
markersize_starting_point=add_data_model_markersize_starting_point,
|
| 415 |
+
markertype_starting_point=add_data_model_markertype_starting_point,
|
| 416 |
+
markershift_starting_point=add_data_model_markershift_starting_point,
|
| 417 |
+
delta_t_graph=delta_t_model,
|
| 418 |
+
sample_hist_alpha=1.0,
|
| 419 |
+
lw_m=linewidth_model + 0.5,
|
| 420 |
+
tmp_label=None,
|
| 421 |
+
ylim_low=ylim_low,
|
| 422 |
+
ylim_high=ylim_high,
|
| 423 |
+
t_s=t_s,
|
| 424 |
+
color=posterior_mean_color,
|
| 425 |
+
zorder_cnt=j + 2,
|
| 426 |
+
)
|
| 427 |
+
|
| 428 |
+
if add_trajectories:
|
| 429 |
+
_add_trajectories(
|
| 430 |
+
axis=axis,
|
| 431 |
+
sample=samples_tmp[0],
|
| 432 |
+
tmp_model=tmp_model,
|
| 433 |
+
t_s=t_s,
|
| 434 |
+
delta_t_graph=delta_t_model,
|
| 435 |
+
**kwargs,
|
| 436 |
+
)
|
| 437 |
+
|
| 438 |
+
|
| 439 |
+
# AF-TODO: Add documentation for this function
|
| 440 |
+
def _add_trajectories(
|
| 441 |
+
axis=None,
|
| 442 |
+
sample=None,
|
| 443 |
+
t_s=None,
|
| 444 |
+
delta_t_graph=0.01,
|
| 445 |
+
tmp_model=None,
|
| 446 |
+
n_trajectories=10,
|
| 447 |
+
supplied_trajectory=None,
|
| 448 |
+
maxid_supplied_trajectory=1, # useful for gifs
|
| 449 |
+
highlight_trajectory_rt_choice=True,
|
| 450 |
+
markersize_trajectory_rt_choice=50,
|
| 451 |
+
markertype_trajectory_rt_choice="*",
|
| 452 |
+
markercolor_trajectory_rt_choice="red",
|
| 453 |
+
linewidth_trajectories=1,
|
| 454 |
+
alpha_trajectories=0.5,
|
| 455 |
+
color_trajectories="black",
|
| 456 |
+
**kwargs,
|
| 457 |
+
):
|
| 458 |
+
# Check markercolor type
|
| 459 |
+
if type(markercolor_trajectory_rt_choice) == str:
|
| 460 |
+
markercolor_trajectory_rt_choice_dict = {}
|
| 461 |
+
for value_ in model_config[tmp_model]["choices"]:
|
| 462 |
+
markercolor_trajectory_rt_choice_dict[
|
| 463 |
+
value_
|
| 464 |
+
] = markercolor_trajectory_rt_choice
|
| 465 |
+
elif type(markercolor_trajectory_rt_choice) == list:
|
| 466 |
+
cnt = 0
|
| 467 |
+
for value_ in model_config[tmp_model]["choices"]:
|
| 468 |
+
markercolor_trajectory_rt_choice_dict[
|
| 469 |
+
value_
|
| 470 |
+
] = markercolor_trajectory_rt_choice[cnt]
|
| 471 |
+
cnt += 1
|
| 472 |
+
elif type(markercolor_trajectory_rt_choice) == dict:
|
| 473 |
+
markercolor_trajectory_rt_choice_dict = markercolor_trajectory_rt_choice
|
| 474 |
+
else:
|
| 475 |
+
pass
|
| 476 |
+
|
| 477 |
+
# Check trajectory color type
|
| 478 |
+
if type(color_trajectories) == str:
|
| 479 |
+
color_trajectories_dict = {}
|
| 480 |
+
for value_ in model_config[tmp_model]["choices"]:
|
| 481 |
+
color_trajectories_dict[value_] = color_trajectories
|
| 482 |
+
elif type(color_trajectories) == list:
|
| 483 |
+
cnt = 0
|
| 484 |
+
for value_ in model_config[tmp_model]["choices"]:
|
| 485 |
+
color_trajectories_dict[value_] = color_trajectories[cnt]
|
| 486 |
+
cnt += 1
|
| 487 |
+
elif type(color_trajectories) == dict:
|
| 488 |
+
color_trajectories_dict = color_trajectories
|
| 489 |
+
else:
|
| 490 |
+
pass
|
| 491 |
+
|
| 492 |
+
# Make bounds
|
| 493 |
+
(b_low, b_high) = _make_bounds(
|
| 494 |
+
tmp_model=tmp_model,
|
| 495 |
+
sample=sample,
|
| 496 |
+
delta_t_graph=delta_t_graph,
|
| 497 |
+
t_s=t_s,
|
| 498 |
+
return_shifted_by_ndt=False,
|
| 499 |
+
)
|
| 500 |
+
|
| 501 |
+
# Trajectories
|
| 502 |
+
if supplied_trajectory is None:
|
| 503 |
+
for i in range(n_trajectories):
|
| 504 |
+
rand_int = np.random.choice(400000000)
|
| 505 |
+
out_traj = simulator(
|
| 506 |
+
theta=sample[model_config[tmp_model]["params"]].values[0],
|
| 507 |
+
model=tmp_model,
|
| 508 |
+
n_samples=1,
|
| 509 |
+
no_noise=False,
|
| 510 |
+
delta_t=delta_t_graph,
|
| 511 |
+
bin_dim=None,
|
| 512 |
+
random_state=rand_int,
|
| 513 |
+
)
|
| 514 |
+
|
| 515 |
+
tmp_traj = out_traj[2]["trajectory"]
|
| 516 |
+
tmp_traj_choice = float(out_traj[1].flatten())
|
| 517 |
+
maxid = np.minimum(np.argmax(np.where(tmp_traj > -999)), t_s.shape[0])
|
| 518 |
+
|
| 519 |
+
# Identify boundary value at timepoint of crossing
|
| 520 |
+
b_tmp = b_high[maxid] if tmp_traj_choice > 0 else b_low[maxid]
|
| 521 |
+
|
| 522 |
+
axis.plot(
|
| 523 |
+
t_s[:maxid] + sample.t.values[0],
|
| 524 |
+
tmp_traj[:maxid],
|
| 525 |
+
color=color_trajectories_dict[tmp_traj_choice],
|
| 526 |
+
alpha=alpha_trajectories,
|
| 527 |
+
linewidth=linewidth_trajectories,
|
| 528 |
+
zorder=2000 + i,
|
| 529 |
+
)
|
| 530 |
+
|
| 531 |
+
if highlight_trajectory_rt_choice:
|
| 532 |
+
axis.scatter(
|
| 533 |
+
t_s[maxid] + sample.t.values[0],
|
| 534 |
+
b_tmp,
|
| 535 |
+
# tmp_traj[maxid],
|
| 536 |
+
markersize_trajectory_rt_choice,
|
| 537 |
+
color=markercolor_trajectory_rt_choice_dict[tmp_traj_choice],
|
| 538 |
+
alpha=1,
|
| 539 |
+
marker=markertype_trajectory_rt_choice,
|
| 540 |
+
zorder=2000 + i,
|
| 541 |
+
)
|
| 542 |
+
|
| 543 |
+
else:
|
| 544 |
+
if len(supplied_trajectory["trajectories"].shape) == 1:
|
| 545 |
+
supplied_trajectory["trajectories"] = np.expand_dims(
|
| 546 |
+
supplied_trajectory["trajectories"], axis=0
|
| 547 |
+
)
|
| 548 |
+
|
| 549 |
+
for j in range(supplied_trajectory["trajectories"].shape[0]):
|
| 550 |
+
maxid = np.minimum(
|
| 551 |
+
np.argmax(np.where(supplied_trajectory["trajectories"][j, :] > -999)),
|
| 552 |
+
t_s.shape[0],
|
| 553 |
+
)
|
| 554 |
+
if j == (supplied_trajectory["trajectories"].shape[0] - 1):
|
| 555 |
+
maxid_traj = min(maxid, maxid_supplied_trajectory)
|
| 556 |
+
else:
|
| 557 |
+
maxid_traj = maxid
|
| 558 |
+
|
| 559 |
+
axis.plot(
|
| 560 |
+
t_s[:maxid_traj] + sample.t.values[0],
|
| 561 |
+
supplied_trajectory["trajectories"][j, :maxid_traj],
|
| 562 |
+
color=color_trajectories_dict[
|
| 563 |
+
supplied_trajectory["trajectory_choices"][j]
|
| 564 |
+
], # color_trajectories,
|
| 565 |
+
alpha=alpha_trajectories,
|
| 566 |
+
linewidth=linewidth_trajectories,
|
| 567 |
+
zorder=2000 + j,
|
| 568 |
+
)
|
| 569 |
+
|
| 570 |
+
# Identify boundary value at timepoint of crossing
|
| 571 |
+
b_tmp = (
|
| 572 |
+
b_high[maxid_traj]
|
| 573 |
+
if supplied_trajectory["trajectory_choices"][j] > 0
|
| 574 |
+
else b_low[maxid_traj]
|
| 575 |
+
)
|
| 576 |
+
|
| 577 |
+
if maxid_traj == maxid:
|
| 578 |
+
if highlight_trajectory_rt_choice:
|
| 579 |
+
axis.scatter(
|
| 580 |
+
t_s[maxid_traj] + sample.t.values[0],
|
| 581 |
+
b_tmp,
|
| 582 |
+
# supplied_trajectory['trajectories'][j, maxid_traj],
|
| 583 |
+
markersize_trajectory_rt_choice,
|
| 584 |
+
color=markercolor_trajectory_rt_choice_dict[
|
| 585 |
+
supplied_trajectory["trajectory_choices"][j]
|
| 586 |
+
], # markercolor_trajectory_rt_choice,
|
| 587 |
+
alpha=1,
|
| 588 |
+
marker=markertype_trajectory_rt_choice,
|
| 589 |
+
zorder=2000 + j,
|
| 590 |
+
)
|
| 591 |
+
|
| 592 |
+
|
| 593 |
+
# AF-TODO: Add documentation to this function
|
| 594 |
+
def _add_model_cartoon_to_ax(
|
| 595 |
+
sample=None,
|
| 596 |
+
axis=None,
|
| 597 |
+
tmp_model=None,
|
| 598 |
+
keep_slope=True,
|
| 599 |
+
keep_boundary=True,
|
| 600 |
+
keep_ndt=True,
|
| 601 |
+
keep_starting_point=True,
|
| 602 |
+
markersize_starting_point=80,
|
| 603 |
+
markertype_starting_point=1,
|
| 604 |
+
markershift_starting_point=-0.05,
|
| 605 |
+
delta_t_graph=None,
|
| 606 |
+
sample_hist_alpha=None,
|
| 607 |
+
lw_m=None,
|
| 608 |
+
tmp_label=None,
|
| 609 |
+
ylim_low=None,
|
| 610 |
+
ylim_high=None,
|
| 611 |
+
t_s=None,
|
| 612 |
+
zorder_cnt=1,
|
| 613 |
+
color="black",
|
| 614 |
+
):
|
| 615 |
+
# Make bounds
|
| 616 |
+
b_low, b_high = _make_bounds(
|
| 617 |
+
tmp_model=tmp_model,
|
| 618 |
+
sample=sample,
|
| 619 |
+
delta_t_graph=delta_t_graph,
|
| 620 |
+
t_s=t_s,
|
| 621 |
+
return_shifted_by_ndt=True,
|
| 622 |
+
)
|
| 623 |
+
|
| 624 |
+
# MAKE SLOPES (VIA TRAJECTORIES HERE --> RUN NOISE FREE SIMULATIONS)!
|
| 625 |
+
out = simulator(
|
| 626 |
+
theta=sample[model_config[tmp_model]["params"]].values[0],
|
| 627 |
+
model=tmp_model,
|
| 628 |
+
n_samples=1,
|
| 629 |
+
no_noise=True,
|
| 630 |
+
delta_t=delta_t_graph,
|
| 631 |
+
bin_dim=None,
|
| 632 |
+
)
|
| 633 |
+
|
| 634 |
+
tmp_traj = out[2]["trajectory"]
|
| 635 |
+
maxid = np.minimum(np.argmax(np.where(tmp_traj > -999)), t_s.shape[0])
|
| 636 |
+
|
| 637 |
+
if "hddm_base" in tmp_model:
|
| 638 |
+
a_tmp = sample.a.values[0] / 2
|
| 639 |
+
tmp_traj = tmp_traj - a_tmp
|
| 640 |
+
|
| 641 |
+
if keep_boundary:
|
| 642 |
+
# Upper bound
|
| 643 |
+
axis.plot(
|
| 644 |
+
t_s, # + sample.t.values[0],
|
| 645 |
+
b_high,
|
| 646 |
+
color=color,
|
| 647 |
+
alpha=sample_hist_alpha,
|
| 648 |
+
zorder=1000 + zorder_cnt,
|
| 649 |
+
linewidth=lw_m,
|
| 650 |
+
label=tmp_label,
|
| 651 |
+
)
|
| 652 |
+
|
| 653 |
+
# Lower bound
|
| 654 |
+
axis.plot(
|
| 655 |
+
t_s, # + sample.t.values[0],
|
| 656 |
+
b_low,
|
| 657 |
+
color=color,
|
| 658 |
+
alpha=sample_hist_alpha,
|
| 659 |
+
zorder=1000 + zorder_cnt,
|
| 660 |
+
linewidth=lw_m,
|
| 661 |
+
)
|
| 662 |
+
|
| 663 |
+
# Slope
|
| 664 |
+
if keep_slope:
|
| 665 |
+
axis.plot(
|
| 666 |
+
t_s[:maxid] + sample.t.values[0],
|
| 667 |
+
tmp_traj[:maxid],
|
| 668 |
+
color=color,
|
| 669 |
+
alpha=sample_hist_alpha,
|
| 670 |
+
zorder=1000 + zorder_cnt,
|
| 671 |
+
linewidth=lw_m,
|
| 672 |
+
) # TOOK AWAY LABEL
|
| 673 |
+
|
| 674 |
+
# Non-decision time
|
| 675 |
+
if keep_ndt:
|
| 676 |
+
axis.axvline(
|
| 677 |
+
x=sample.t.values[0],
|
| 678 |
+
ymin=ylim_low,
|
| 679 |
+
ymax=ylim_high,
|
| 680 |
+
color=color,
|
| 681 |
+
linestyle="--",
|
| 682 |
+
linewidth=lw_m,
|
| 683 |
+
zorder=1000 + zorder_cnt,
|
| 684 |
+
alpha=sample_hist_alpha,
|
| 685 |
+
)
|
| 686 |
+
# Starting point
|
| 687 |
+
if keep_starting_point:
|
| 688 |
+
axis.scatter(
|
| 689 |
+
sample.t.values[0] + markershift_starting_point,
|
| 690 |
+
b_low[0] + (sample.z.values[0] * (b_high[0] - b_low[0])),
|
| 691 |
+
markersize_starting_point,
|
| 692 |
+
marker=markertype_starting_point,
|
| 693 |
+
color=color,
|
| 694 |
+
alpha=sample_hist_alpha,
|
| 695 |
+
zorder=1000 + zorder_cnt,
|
| 696 |
+
)
|
| 697 |
+
|
| 698 |
+
|
| 699 |
+
def _make_bounds(
|
| 700 |
+
tmp_model=None,
|
| 701 |
+
sample=None,
|
| 702 |
+
delta_t_graph=None,
|
| 703 |
+
t_s=None,
|
| 704 |
+
return_shifted_by_ndt=True,
|
| 705 |
+
):
|
| 706 |
+
# MULTIPLICATIVE BOUND
|
| 707 |
+
if tmp_model == "weibull" or tmp_model == "weibull_cdf":
|
| 708 |
+
b = np.maximum(
|
| 709 |
+
sample.a.values[0]
|
| 710 |
+
* model_config[tmp_model]["boundary"](
|
| 711 |
+
t=t_s, alpha=sample.alpha.values[0], beta=sample.beta.values[0]
|
| 712 |
+
),
|
| 713 |
+
0,
|
| 714 |
+
)
|
| 715 |
+
|
| 716 |
+
# Move boundary forward by the non-decision time
|
| 717 |
+
b_raw_high = deepcopy(b)
|
| 718 |
+
b_raw_low = deepcopy(-b)
|
| 719 |
+
b_init_val = b[0]
|
| 720 |
+
t_shift = np.arange(0, sample.t.values[0], delta_t_graph).shape[0]
|
| 721 |
+
b = np.roll(b, t_shift)
|
| 722 |
+
b[:t_shift] = b_init_val
|
| 723 |
+
|
| 724 |
+
# ADDITIVE BOUND
|
| 725 |
+
elif tmp_model == "angle":
|
| 726 |
+
b = np.maximum(
|
| 727 |
+
sample.a.values[0]
|
| 728 |
+
+ model_config[tmp_model]["boundary"](t=t_s, theta=sample.theta.values[0]),
|
| 729 |
+
0,
|
| 730 |
+
)
|
| 731 |
+
|
| 732 |
+
b_raw_high = deepcopy(b)
|
| 733 |
+
b_raw_low = deepcopy(-b)
|
| 734 |
+
# Move boundary forward by the non-decision time
|
| 735 |
+
b_init_val = b[0]
|
| 736 |
+
t_shift = np.arange(0, sample.t.values[0], delta_t_graph).shape[0]
|
| 737 |
+
b = np.roll(b, t_shift)
|
| 738 |
+
b[:t_shift] = b_init_val
|
| 739 |
+
|
| 740 |
+
# CONSTANT BOUND
|
| 741 |
+
elif (
|
| 742 |
+
tmp_model == "ddm"
|
| 743 |
+
or tmp_model == "ornstein"
|
| 744 |
+
or tmp_model == "levy"
|
| 745 |
+
or tmp_model == "full_ddm"
|
| 746 |
+
or tmp_model == "ddm_hddm_base"
|
| 747 |
+
or tmp_model == "full_ddm_hddm_base"
|
| 748 |
+
):
|
| 749 |
+
b = sample.a.values[0] * np.ones(t_s.shape[0])
|
| 750 |
+
|
| 751 |
+
if "hddm_base" in tmp_model:
|
| 752 |
+
b = (sample.a.values[0] / 2) * np.ones(t_s.shape[0])
|
| 753 |
+
|
| 754 |
+
b_raw_high = b
|
| 755 |
+
b_raw_low = -b
|
| 756 |
+
|
| 757 |
+
# Separate out upper and lower bound:
|
| 758 |
+
b_high = b
|
| 759 |
+
b_low = -b
|
| 760 |
+
|
| 761 |
+
if return_shifted_by_ndt:
|
| 762 |
+
return (b_low, b_high)
|
| 763 |
+
else:
|
| 764 |
+
return (b_raw_low, b_raw_high)
|
| 765 |
+
|
| 766 |
+
|
| 767 |
+
def _plot_func_model_n(
|
| 768 |
+
bottom_node,
|
| 769 |
+
axis,
|
| 770 |
+
value_range=None,
|
| 771 |
+
samples=10,
|
| 772 |
+
bin_size=0.05,
|
| 773 |
+
add_posterior_uncertainty_model=False,
|
| 774 |
+
add_posterior_uncertainty_rts=False,
|
| 775 |
+
add_posterior_mean_model=True,
|
| 776 |
+
add_posterior_mean_rts=True,
|
| 777 |
+
linewidth_histogram=0.5,
|
| 778 |
+
linewidth_model=0.5,
|
| 779 |
+
legend_fontsize=7,
|
| 780 |
+
legend_shadow=True,
|
| 781 |
+
legend_location="upper right",
|
| 782 |
+
delta_t_model=0.01,
|
| 783 |
+
add_legend=True,
|
| 784 |
+
alpha=0.01,
|
| 785 |
+
keep_frame=False,
|
| 786 |
+
**kwargs,
|
| 787 |
+
):
|
| 788 |
+
"""Calculate posterior predictive for a certain bottom node.
|
| 789 |
+
|
| 790 |
+
Arguments:
|
| 791 |
+
bottom_node: pymc.stochastic
|
| 792 |
+
Bottom node to compute posterior over.
|
| 793 |
+
|
| 794 |
+
axis: matplotlib.axis
|
| 795 |
+
Axis to plot into.
|
| 796 |
+
|
| 797 |
+
value_range: numpy.ndarray
|
| 798 |
+
Range over which to evaluate the likelihood.
|
| 799 |
+
|
| 800 |
+
Optional:
|
| 801 |
+
samples: int <default=10>
|
| 802 |
+
Number of posterior samples to use.
|
| 803 |
+
|
| 804 |
+
bin_size: float <default=0.05>
|
| 805 |
+
Size of bins used for histograms
|
| 806 |
+
|
| 807 |
+
alpha: float <default=0.05>
|
| 808 |
+
alpha (transparency) level for the sample-wise elements of the plot
|
| 809 |
+
|
| 810 |
+
add_posterior_uncertainty_rts: bool <default=True>
|
| 811 |
+
Add sample by sample histograms?
|
| 812 |
+
|
| 813 |
+
add_posterior_mean_rts: bool <default=True>
|
| 814 |
+
Add a mean posterior?
|
| 815 |
+
|
| 816 |
+
add_model: bool <default=True>
|
| 817 |
+
Whether to add model cartoons to the plot.
|
| 818 |
+
|
| 819 |
+
linewidth_histogram: float <default=0.5>
|
| 820 |
+
linewdith of histrogram plot elements.
|
| 821 |
+
|
| 822 |
+
linewidth_model: float <default=0.5>
|
| 823 |
+
linewidth of plot elements concerning the model cartoons.
|
| 824 |
+
|
| 825 |
+
legend_loc: str <default='upper right'>
|
| 826 |
+
string defining legend position. Find the rest of the options in the matplotlib documentation.
|
| 827 |
+
|
| 828 |
+
legend_shadow: bool <default=True>
|
| 829 |
+
Add shadow to legend box?
|
| 830 |
+
|
| 831 |
+
legend_fontsize: float <default=12>
|
| 832 |
+
Fontsize of legend.
|
| 833 |
+
|
| 834 |
+
data_color : str <default="blue">
|
| 835 |
+
Color for the data part of the plot.
|
| 836 |
+
|
| 837 |
+
posterior_mean_color : str <default="red">
|
| 838 |
+
Color for the posterior mean part of the plot.
|
| 839 |
+
|
| 840 |
+
posterior_uncertainty_color : str <default="black">
|
| 841 |
+
Color for the posterior uncertainty part of the plot.
|
| 842 |
+
|
| 843 |
+
|
| 844 |
+
delta_t_model:
|
| 845 |
+
specifies plotting intervals for model cartoon elements of the graphs.
|
| 846 |
+
"""
|
| 847 |
+
|
| 848 |
+
color_dict = {
|
| 849 |
+
-1: "black",
|
| 850 |
+
0: "black",
|
| 851 |
+
1: "green",
|
| 852 |
+
2: "blue",
|
| 853 |
+
3: "red",
|
| 854 |
+
4: "orange",
|
| 855 |
+
5: "purple",
|
| 856 |
+
6: "brown",
|
| 857 |
+
}
|
| 858 |
+
|
| 859 |
+
# AF-TODO: Add a mean version of this !
|
| 860 |
+
if value_range is None:
|
| 861 |
+
# Infer from data by finding the min and max from the nodes
|
| 862 |
+
raise NotImplementedError("value_range keyword argument must be supplied.")
|
| 863 |
+
|
| 864 |
+
if len(value_range) > 2:
|
| 865 |
+
value_range = (value_range[0], value_range[-1])
|
| 866 |
+
|
| 867 |
+
# Extract some parameters from kwargs
|
| 868 |
+
bins = np.arange(value_range[0], value_range[-1], bin_size)
|
| 869 |
+
|
| 870 |
+
# Relevant for recovery mode
|
| 871 |
+
node_data_full = kwargs.pop("node_data", None)
|
| 872 |
+
tmp_model = kwargs.pop("model_", "angle")
|
| 873 |
+
|
| 874 |
+
bottom = 0
|
| 875 |
+
# ------------
|
| 876 |
+
ylim = kwargs.pop("ylim", 3)
|
| 877 |
+
|
| 878 |
+
choices = model_config[tmp_model]["choices"]
|
| 879 |
+
|
| 880 |
+
# If bottom_node is a DataFrame we know that we are just plotting real data
|
| 881 |
+
if type(bottom_node) == pd.DataFrame:
|
| 882 |
+
samples_tmp = [bottom_node]
|
| 883 |
+
data_tmp = None
|
| 884 |
+
else:
|
| 885 |
+
samples_tmp = _post_pred_generate(
|
| 886 |
+
bottom_node,
|
| 887 |
+
samples=samples,
|
| 888 |
+
data=None,
|
| 889 |
+
append_data=False,
|
| 890 |
+
add_model_parameters=True,
|
| 891 |
+
)
|
| 892 |
+
data_tmp = bottom_node.value.copy()
|
| 893 |
+
|
| 894 |
+
axis.set_xlim(value_range[0], value_range[-1])
|
| 895 |
+
axis.set_ylim(0, ylim)
|
| 896 |
+
|
| 897 |
+
# ADD MODEL:
|
| 898 |
+
j = 0
|
| 899 |
+
t_s = np.arange(0, value_range[-1], delta_t_model)
|
| 900 |
+
|
| 901 |
+
# # MAKE BOUNDS (FROM MODEL CONFIG) !
|
| 902 |
+
if add_posterior_uncertainty_model: # add_uc_model:
|
| 903 |
+
for sample in samples_tmp:
|
| 904 |
+
tmp_label = None
|
| 905 |
+
|
| 906 |
+
if add_legend and (j == 0):
|
| 907 |
+
tmp_label = "PostPred"
|
| 908 |
+
|
| 909 |
+
_add_model_n_cartoon_to_ax(
|
| 910 |
+
sample=sample,
|
| 911 |
+
axis=axis,
|
| 912 |
+
tmp_model=tmp_model,
|
| 913 |
+
delta_t_graph=delta_t_model,
|
| 914 |
+
sample_hist_alpha=alpha,
|
| 915 |
+
lw_m=linewidth_model,
|
| 916 |
+
tmp_label=tmp_label,
|
| 917 |
+
linestyle="-",
|
| 918 |
+
ylim=ylim,
|
| 919 |
+
t_s=t_s,
|
| 920 |
+
color_dict=color_dict,
|
| 921 |
+
zorder_cnt=j,
|
| 922 |
+
)
|
| 923 |
+
|
| 924 |
+
j += 1
|
| 925 |
+
|
| 926 |
+
if add_posterior_mean_model: # add_mean_model:
|
| 927 |
+
tmp_label = None
|
| 928 |
+
if add_legend:
|
| 929 |
+
tmp_label = "PostPred Mean"
|
| 930 |
+
|
| 931 |
+
bottom = _add_model_n_cartoon_to_ax(
|
| 932 |
+
sample=pd.DataFrame(pd.concat(samples_tmp).mean().astype(np.float32)).T,
|
| 933 |
+
axis=axis,
|
| 934 |
+
tmp_model=tmp_model,
|
| 935 |
+
delta_t_graph=delta_t_model,
|
| 936 |
+
sample_hist_alpha=1.0,
|
| 937 |
+
lw_m=linewidth_model + 0.5,
|
| 938 |
+
linestyle="-",
|
| 939 |
+
tmp_label=None,
|
| 940 |
+
ylim=ylim,
|
| 941 |
+
t_s=t_s,
|
| 942 |
+
color_dict=color_dict,
|
| 943 |
+
zorder_cnt=j + 2,
|
| 944 |
+
)
|
| 945 |
+
|
| 946 |
+
if node_data_full is not None:
|
| 947 |
+
_add_model_n_cartoon_to_ax(
|
| 948 |
+
sample=node_data_full,
|
| 949 |
+
axis=axis,
|
| 950 |
+
tmp_model=tmp_model,
|
| 951 |
+
delta_t_graph=delta_t_model,
|
| 952 |
+
sample_hist_alpha=1.0,
|
| 953 |
+
lw_m=linewidth_model + 0.5,
|
| 954 |
+
linestyle="dashed",
|
| 955 |
+
tmp_label=None,
|
| 956 |
+
ylim=ylim,
|
| 957 |
+
t_s=t_s,
|
| 958 |
+
color_dict=color_dict,
|
| 959 |
+
zorder_cnt=j + 1,
|
| 960 |
+
)
|
| 961 |
+
|
| 962 |
+
# ADD HISTOGRAMS
|
| 963 |
+
# -------------------------------
|
| 964 |
+
|
| 965 |
+
# POSTERIOR BASED HISTOGRAM
|
| 966 |
+
if add_posterior_uncertainty_rts: # add_uc_rts:
|
| 967 |
+
j = 0
|
| 968 |
+
for sample in samples_tmp:
|
| 969 |
+
for choice in choices:
|
| 970 |
+
tmp_label = None
|
| 971 |
+
|
| 972 |
+
if add_legend and j == 0:
|
| 973 |
+
tmp_label = "PostPred"
|
| 974 |
+
|
| 975 |
+
weights = np.tile(
|
| 976 |
+
(1 / bin_size) / sample.shape[0],
|
| 977 |
+
reps=sample.loc[sample.response == choice, :].shape[0],
|
| 978 |
+
)
|
| 979 |
+
|
| 980 |
+
axis.hist(
|
| 981 |
+
np.abs(sample.rt[sample.response == choice]),
|
| 982 |
+
bins=bins,
|
| 983 |
+
bottom=bottom,
|
| 984 |
+
weights=weights,
|
| 985 |
+
histtype="step",
|
| 986 |
+
alpha=alpha,
|
| 987 |
+
color=color_dict[choice],
|
| 988 |
+
zorder=-1,
|
| 989 |
+
label=tmp_label,
|
| 990 |
+
linewidth=linewidth_histogram,
|
| 991 |
+
)
|
| 992 |
+
j += 1
|
| 993 |
+
|
| 994 |
+
if add_posterior_mean_rts:
|
| 995 |
+
concat_data = pd.concat(samples_tmp)
|
| 996 |
+
for choice in choices:
|
| 997 |
+
tmp_label = None
|
| 998 |
+
if add_legend and (choice == choices[0]):
|
| 999 |
+
tmp_label = "PostPred Mean"
|
| 1000 |
+
|
| 1001 |
+
weights = np.tile(
|
| 1002 |
+
(1 / bin_size) / concat_data.shape[0],
|
| 1003 |
+
reps=concat_data.loc[concat_data.response == choice, :].shape[0],
|
| 1004 |
+
)
|
| 1005 |
+
|
| 1006 |
+
axis.hist(
|
| 1007 |
+
np.abs(concat_data.rt[concat_data.response == choice]),
|
| 1008 |
+
bins=bins,
|
| 1009 |
+
bottom=bottom,
|
| 1010 |
+
weights=weights,
|
| 1011 |
+
histtype="step",
|
| 1012 |
+
alpha=1.0,
|
| 1013 |
+
color=color_dict[choice],
|
| 1014 |
+
zorder=-1,
|
| 1015 |
+
label=tmp_label,
|
| 1016 |
+
linewidth=linewidth_histogram,
|
| 1017 |
+
)
|
| 1018 |
+
|
| 1019 |
+
# DATA HISTOGRAM
|
| 1020 |
+
if data_tmp is not None:
|
| 1021 |
+
for choice in choices:
|
| 1022 |
+
tmp_label = None
|
| 1023 |
+
if add_legend and (choice == choices[0]):
|
| 1024 |
+
tmp_label = "Data"
|
| 1025 |
+
|
| 1026 |
+
weights = np.tile(
|
| 1027 |
+
(1 / bin_size) / data_tmp.shape[0],
|
| 1028 |
+
reps=data_tmp.loc[data_tmp.response == choice, :].shape[0],
|
| 1029 |
+
)
|
| 1030 |
+
|
| 1031 |
+
axis.hist(
|
| 1032 |
+
np.abs(data_tmp.rt[data_tmp.response == choice]),
|
| 1033 |
+
bins=bins,
|
| 1034 |
+
bottom=bottom,
|
| 1035 |
+
weights=weights,
|
| 1036 |
+
histtype="step",
|
| 1037 |
+
linestyle="dashed",
|
| 1038 |
+
alpha=1.0,
|
| 1039 |
+
color=color_dict[choice],
|
| 1040 |
+
edgecolor=color_dict[choice],
|
| 1041 |
+
zorder=-1,
|
| 1042 |
+
label=tmp_label,
|
| 1043 |
+
linewidth=linewidth_histogram,
|
| 1044 |
+
)
|
| 1045 |
+
# -------------------------------
|
| 1046 |
+
|
| 1047 |
+
if add_legend:
|
| 1048 |
+
if data_tmp is not None:
|
| 1049 |
+
custom_elems = [
|
| 1050 |
+
Line2D([0], [0], color=color_dict[choice], lw=1) for choice in choices
|
| 1051 |
+
]
|
| 1052 |
+
custom_titles = ["response: " + str(choice) for choice in choices]
|
| 1053 |
+
|
| 1054 |
+
custom_elems.append(
|
| 1055 |
+
Line2D([0], [0], color="black", lw=1.0, linestyle="dashed")
|
| 1056 |
+
)
|
| 1057 |
+
custom_elems.append(Line2D([0], [0], color="black", lw=1.0, linestyle="-"))
|
| 1058 |
+
custom_titles.append("Data")
|
| 1059 |
+
custom_titles.append("Posterior")
|
| 1060 |
+
|
| 1061 |
+
axis.legend(
|
| 1062 |
+
custom_elems,
|
| 1063 |
+
custom_titles,
|
| 1064 |
+
fontsize=legend_fontsize,
|
| 1065 |
+
shadow=legend_shadow,
|
| 1066 |
+
loc=legend_location,
|
| 1067 |
+
)
|
| 1068 |
+
|
| 1069 |
+
# FRAME
|
| 1070 |
+
if not keep_frame:
|
| 1071 |
+
axis.set_frame_on(False)
|
| 1072 |
+
|
| 1073 |
+
|
| 1074 |
+
def _add_model_n_cartoon_to_ax(
|
| 1075 |
+
sample=None,
|
| 1076 |
+
axis=None,
|
| 1077 |
+
tmp_model=None,
|
| 1078 |
+
delta_t_graph=None,
|
| 1079 |
+
sample_hist_alpha=None,
|
| 1080 |
+
lw_m=None,
|
| 1081 |
+
linestyle="-",
|
| 1082 |
+
tmp_label=None,
|
| 1083 |
+
ylim=None,
|
| 1084 |
+
t_s=None,
|
| 1085 |
+
zorder_cnt=1,
|
| 1086 |
+
color_dict=None,
|
| 1087 |
+
):
|
| 1088 |
+
if "weibull" in tmp_model:
|
| 1089 |
+
b = np.maximum(
|
| 1090 |
+
sample.a.values[0]
|
| 1091 |
+
* model_config[tmp_model]["boundary"](
|
| 1092 |
+
t=t_s, alpha=sample.alpha.values[0], beta=sample.beta.values[0]
|
| 1093 |
+
),
|
| 1094 |
+
0,
|
| 1095 |
+
)
|
| 1096 |
+
|
| 1097 |
+
elif "angle" in tmp_model:
|
| 1098 |
+
b = np.maximum(
|
| 1099 |
+
sample.a.values[0]
|
| 1100 |
+
+ model_config[tmp_model]["boundary"](t=t_s, theta=sample.theta.values[0]),
|
| 1101 |
+
0,
|
| 1102 |
+
)
|
| 1103 |
+
|
| 1104 |
+
else:
|
| 1105 |
+
b = sample.a.values[0] * np.ones(t_s.shape[0])
|
| 1106 |
+
|
| 1107 |
+
# Upper bound
|
| 1108 |
+
axis.plot(
|
| 1109 |
+
t_s + sample.t.values[0],
|
| 1110 |
+
b,
|
| 1111 |
+
color="black",
|
| 1112 |
+
alpha=sample_hist_alpha,
|
| 1113 |
+
zorder=1000 + zorder_cnt,
|
| 1114 |
+
linewidth=lw_m,
|
| 1115 |
+
linestyle=linestyle,
|
| 1116 |
+
label=tmp_label,
|
| 1117 |
+
)
|
| 1118 |
+
|
| 1119 |
+
# Starting point
|
| 1120 |
+
axis.axvline(
|
| 1121 |
+
x=sample.t.values[0],
|
| 1122 |
+
ymin=-ylim,
|
| 1123 |
+
ymax=ylim,
|
| 1124 |
+
color="black",
|
| 1125 |
+
linestyle=linestyle,
|
| 1126 |
+
linewidth=lw_m,
|
| 1127 |
+
alpha=sample_hist_alpha,
|
| 1128 |
+
)
|
| 1129 |
+
|
| 1130 |
+
# # MAKE SLOPES (VIA TRAJECTORIES HERE --> RUN NOISE FREE SIMULATIONS)!
|
| 1131 |
+
out = simulator(
|
| 1132 |
+
theta=sample[model_config[tmp_model]["params"]].values[0],
|
| 1133 |
+
model=tmp_model,
|
| 1134 |
+
n_samples=1,
|
| 1135 |
+
no_noise=True,
|
| 1136 |
+
delta_t=delta_t_graph,
|
| 1137 |
+
bin_dim=None,
|
| 1138 |
+
)
|
| 1139 |
+
|
| 1140 |
+
# # AF-TODO: Add trajectories
|
| 1141 |
+
tmp_traj = out[2]["trajectory"]
|
| 1142 |
+
|
| 1143 |
+
for i in range(len(model_config[tmp_model]["choices"])):
|
| 1144 |
+
tmp_maxid = np.minimum(np.argmax(np.where(tmp_traj[:, i] > -999)), t_s.shape[0])
|
| 1145 |
+
|
| 1146 |
+
# Slope
|
| 1147 |
+
axis.plot(
|
| 1148 |
+
t_s[:tmp_maxid] + sample.t.values[0],
|
| 1149 |
+
tmp_traj[:tmp_maxid, i],
|
| 1150 |
+
color=color_dict[i],
|
| 1151 |
+
linestyle=linestyle,
|
| 1152 |
+
alpha=sample_hist_alpha,
|
| 1153 |
+
zorder=1000 + zorder_cnt,
|
| 1154 |
+
linewidth=lw_m,
|
| 1155 |
+
) # TOOK AWAY LABEL
|
| 1156 |
+
|
| 1157 |
+
return b[0]
|
src/utils/utils.py
ADDED
|
@@ -0,0 +1,820 @@
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|
| 1 |
+
import numpy as np
|
| 2 |
+
import pandas as pd
|
| 3 |
+
import matplotlib.pyplot as plt
|
| 4 |
+
from ssms.config import model_config
|
| 5 |
+
from ssms.basic_simulators.simulator import simulator
|
| 6 |
+
from matplotlib.lines import Line2D
|
| 7 |
+
|
| 8 |
+
|
| 9 |
+
def plot_func_model(
|
| 10 |
+
model_name,
|
| 11 |
+
theta,
|
| 12 |
+
axis,
|
| 13 |
+
value_range=None,
|
| 14 |
+
n_samples=10,
|
| 15 |
+
bin_size=0.05,
|
| 16 |
+
add_data_rts=True,
|
| 17 |
+
add_data_model_keep_slope=True,
|
| 18 |
+
add_data_model_keep_boundary=True,
|
| 19 |
+
add_data_model_keep_ndt=True,
|
| 20 |
+
add_data_model_keep_starting_point=True,
|
| 21 |
+
add_data_model_markersize_starting_point=50,
|
| 22 |
+
add_data_model_markertype_starting_point=0,
|
| 23 |
+
add_data_model_markershift_starting_point=0,
|
| 24 |
+
n_trajectories = 0,
|
| 25 |
+
linewidth_histogram=0.5,
|
| 26 |
+
linewidth_model=0.5,
|
| 27 |
+
legend_fontsize=12,
|
| 28 |
+
legend_shadow=True,
|
| 29 |
+
legend_location="upper right",
|
| 30 |
+
data_color="blue",
|
| 31 |
+
posterior_uncertainty_color="black",
|
| 32 |
+
alpha=0.05,
|
| 33 |
+
delta_t_model=0.001,
|
| 34 |
+
random_state=None,
|
| 35 |
+
add_legend=True, # keep_frame=False,
|
| 36 |
+
**kwargs,
|
| 37 |
+
):
|
| 38 |
+
"""Calculate posterior predictive for a certain bottom node.
|
| 39 |
+
|
| 40 |
+
Arguments:
|
| 41 |
+
bottom_node: pymc.stochastic
|
| 42 |
+
Bottom node to compute posterior over.
|
| 43 |
+
|
| 44 |
+
axis: matplotlib.axis
|
| 45 |
+
Axis to plot into.
|
| 46 |
+
|
| 47 |
+
value_range: numpy.ndarray
|
| 48 |
+
Range over which to evaluate the likelihood.
|
| 49 |
+
|
| 50 |
+
Optional:
|
| 51 |
+
samples: int <default=10>
|
| 52 |
+
Number of posterior samples to use.
|
| 53 |
+
|
| 54 |
+
bin_size: float <default=0.05>
|
| 55 |
+
Size of bins used for histograms
|
| 56 |
+
|
| 57 |
+
alpha: float <default=0.05>
|
| 58 |
+
alpha (transparency) level for the sample-wise elements of the plot
|
| 59 |
+
|
| 60 |
+
add_data_rts: bool <default=True>
|
| 61 |
+
Add data histogram of rts ?
|
| 62 |
+
|
| 63 |
+
add_data_model: bool <default=True>
|
| 64 |
+
Add model cartoon for data
|
| 65 |
+
|
| 66 |
+
add_posterior_uncertainty_rts: bool <default=True>
|
| 67 |
+
Add sample by sample histograms?
|
| 68 |
+
|
| 69 |
+
add_posterior_mean_rts: bool <default=True>
|
| 70 |
+
Add a mean posterior?
|
| 71 |
+
|
| 72 |
+
add_model: bool <default=True>
|
| 73 |
+
Whether to add model cartoons to the plot.
|
| 74 |
+
|
| 75 |
+
linewidth_histogram: float <default=0.5>
|
| 76 |
+
linewdith of histrogram plot elements.
|
| 77 |
+
|
| 78 |
+
linewidth_model: float <default=0.5>
|
| 79 |
+
linewidth of plot elements concerning the model cartoons.
|
| 80 |
+
|
| 81 |
+
legend_location: str <default='upper right'>
|
| 82 |
+
string defining legend position. Find the rest of the options in the matplotlib documentation.
|
| 83 |
+
|
| 84 |
+
legend_shadow: bool <default=True>
|
| 85 |
+
Add shadow to legend box?
|
| 86 |
+
|
| 87 |
+
legend_fontsize: float <default=12>
|
| 88 |
+
Fontsize of legend.
|
| 89 |
+
|
| 90 |
+
data_color : str <default="blue">
|
| 91 |
+
Color for the data part of the plot.
|
| 92 |
+
|
| 93 |
+
posterior_mean_color : str <default="red">
|
| 94 |
+
Color for the posterior mean part of the plot.
|
| 95 |
+
|
| 96 |
+
posterior_uncertainty_color : str <default="black">
|
| 97 |
+
Color for the posterior uncertainty part of the plot.
|
| 98 |
+
|
| 99 |
+
delta_t_model:
|
| 100 |
+
specifies plotting intervals for model cartoon elements of the graphs.
|
| 101 |
+
"""
|
| 102 |
+
|
| 103 |
+
if value_range is None:
|
| 104 |
+
# Infer from data by finding the min and max from the nodes
|
| 105 |
+
raise NotImplementedError("value_range keyword argument must be supplied.")
|
| 106 |
+
|
| 107 |
+
if len(value_range) > 2:
|
| 108 |
+
value_range = (value_range[0], value_range[-1])
|
| 109 |
+
|
| 110 |
+
# Extract some parameters from kwargs
|
| 111 |
+
bins = np.arange(value_range[0], value_range[-1], bin_size)
|
| 112 |
+
|
| 113 |
+
if model_config[model_name]["nchoices"] > 2:
|
| 114 |
+
raise ValueError("The model plot works only for 2 choice models at the moment")
|
| 115 |
+
|
| 116 |
+
# RUN SIMULATIONS
|
| 117 |
+
# -------------------------------
|
| 118 |
+
|
| 119 |
+
# Simulator Data
|
| 120 |
+
if random_state is not None:
|
| 121 |
+
np.random.seed(random_state)
|
| 122 |
+
|
| 123 |
+
rand_int = np.random.choice(400000000)
|
| 124 |
+
sim_out = simulator(model = model_name, theta = theta, n_samples = n_samples,
|
| 125 |
+
no_noise = False, delta_t = 0.001,
|
| 126 |
+
bin_dim = None, random_state = rand_int)
|
| 127 |
+
|
| 128 |
+
sim_out_traj = {}
|
| 129 |
+
for i in range(n_trajectories):
|
| 130 |
+
rand_int = np.random.choice(400000000)
|
| 131 |
+
sim_out_traj[i] = simulator(model = model_name, theta = theta, n_samples = 1,
|
| 132 |
+
no_noise = False, delta_t = 0.001,
|
| 133 |
+
bin_dim = None, random_state = rand_int, smooth_unif = False)
|
| 134 |
+
|
| 135 |
+
sim_out_no_noise = simulator(model = model_name, theta = theta, n_samples = 1,
|
| 136 |
+
no_noise = True, delta_t = 0.001,
|
| 137 |
+
bin_dim = None, smooth_unif = False)
|
| 138 |
+
|
| 139 |
+
# ADD DATA HISTOGRAMS
|
| 140 |
+
weights_up = np.tile(
|
| 141 |
+
(1 / bin_size) / sim_out['rts'][(sim_out['rts'] != -999)].shape[0],
|
| 142 |
+
reps=sim_out['rts'][(sim_out['rts'] != -999) & (sim_out['choices'] == 1)].shape[0],
|
| 143 |
+
)
|
| 144 |
+
weights_down = np.tile(
|
| 145 |
+
(1 / bin_size) / sim_out['rts'][(sim_out['rts'] != -999)].shape[0],
|
| 146 |
+
reps=sim_out['rts'][(sim_out['rts'] != -999) & (sim_out['choices'] != 1)].shape[0],
|
| 147 |
+
)
|
| 148 |
+
|
| 149 |
+
(b_high, b_low) = (np.maximum(sim_out['metadata']['boundary'], 0),
|
| 150 |
+
np.minimum((-1) * sim_out['metadata']['boundary'], 0))
|
| 151 |
+
|
| 152 |
+
# ADD HISTOGRAMS
|
| 153 |
+
# -------------------------------
|
| 154 |
+
|
| 155 |
+
ylim = kwargs.pop("ylim", 3)
|
| 156 |
+
#hist_bottom = kwargs.pop("hist_bottom", 2)
|
| 157 |
+
hist_histtype = kwargs.pop("hist_histtype", "step")
|
| 158 |
+
|
| 159 |
+
if ("ylim_high" in kwargs) and ("ylim_low" in kwargs):
|
| 160 |
+
ylim_high = kwargs["ylim_high"]
|
| 161 |
+
ylim_low = kwargs["ylim_low"]
|
| 162 |
+
else:
|
| 163 |
+
ylim_high = ylim
|
| 164 |
+
ylim_low = -ylim
|
| 165 |
+
|
| 166 |
+
if ("hist_bottom_high" in kwargs) and ("hist_bottom_low" in kwargs):
|
| 167 |
+
hist_bottom_high = kwargs["hist_bottom_high"]
|
| 168 |
+
hist_bottom_low = kwargs["hist_bottom_low"]
|
| 169 |
+
else:
|
| 170 |
+
hist_bottom_high = b_high[0] #hist_bottom
|
| 171 |
+
hist_bottom_low = -b_low[0] #hist_bottom
|
| 172 |
+
|
| 173 |
+
axis.set_xlim(value_range[0], value_range[-1])
|
| 174 |
+
axis.set_ylim(ylim_low, ylim_high)
|
| 175 |
+
axis_twin_up = axis.twinx()
|
| 176 |
+
axis_twin_down = axis.twinx()
|
| 177 |
+
axis_twin_up.set_ylim(ylim_low, ylim_high)
|
| 178 |
+
axis_twin_up.set_yticks([])
|
| 179 |
+
axis_twin_down.set_ylim(ylim_high, ylim_low)
|
| 180 |
+
axis_twin_down.set_yticks([])
|
| 181 |
+
axis_twin_down.set_axis_off()
|
| 182 |
+
axis_twin_up.set_axis_off()
|
| 183 |
+
|
| 184 |
+
axis_twin_up.hist(
|
| 185 |
+
np.abs(sim_out['rts'][(sim_out['rts'] != -999) & (sim_out['choices'] == 1)]),
|
| 186 |
+
bins=bins,
|
| 187 |
+
weights=weights_up,
|
| 188 |
+
histtype=hist_histtype,
|
| 189 |
+
bottom=hist_bottom_high,
|
| 190 |
+
alpha=1,
|
| 191 |
+
color=data_color,
|
| 192 |
+
edgecolor=data_color,
|
| 193 |
+
linewidth=linewidth_histogram,
|
| 194 |
+
zorder=-1,
|
| 195 |
+
)
|
| 196 |
+
|
| 197 |
+
axis_twin_down.hist(
|
| 198 |
+
np.abs(sim_out['rts'][(sim_out['rts'] != -999) & (sim_out['choices'] != 1)]),
|
| 199 |
+
bins=bins,
|
| 200 |
+
weights=weights_down,
|
| 201 |
+
histtype=hist_histtype,
|
| 202 |
+
bottom=hist_bottom_low,
|
| 203 |
+
alpha=1,
|
| 204 |
+
color=data_color,
|
| 205 |
+
edgecolor=data_color,
|
| 206 |
+
linewidth=linewidth_histogram,
|
| 207 |
+
zorder=-1,
|
| 208 |
+
)
|
| 209 |
+
|
| 210 |
+
# ADD MODEL:
|
| 211 |
+
j = 0
|
| 212 |
+
t_s = np.arange(0, sim_out['metadata']['max_t'], delta_t_model) #value_range[-1], delta_t_model)
|
| 213 |
+
|
| 214 |
+
_add_model_cartoon_to_ax(
|
| 215 |
+
sample=sim_out_no_noise,
|
| 216 |
+
axis=axis,
|
| 217 |
+
keep_slope=add_data_model_keep_slope,
|
| 218 |
+
keep_boundary=add_data_model_keep_boundary,
|
| 219 |
+
keep_ndt=add_data_model_keep_ndt,
|
| 220 |
+
keep_starting_point=add_data_model_keep_starting_point,
|
| 221 |
+
markersize_starting_point=add_data_model_markersize_starting_point,
|
| 222 |
+
markertype_starting_point=add_data_model_markertype_starting_point,
|
| 223 |
+
markershift_starting_point=add_data_model_markershift_starting_point,
|
| 224 |
+
delta_t_graph=delta_t_model,
|
| 225 |
+
sample_hist_alpha=alpha,
|
| 226 |
+
lw_m=linewidth_model,
|
| 227 |
+
ylim_low=ylim_low,
|
| 228 |
+
ylim_high=ylim_high,
|
| 229 |
+
t_s=t_s,
|
| 230 |
+
color=posterior_uncertainty_color,
|
| 231 |
+
zorder_cnt=j,
|
| 232 |
+
)
|
| 233 |
+
|
| 234 |
+
if n_trajectories > 0:
|
| 235 |
+
_add_trajectories(
|
| 236 |
+
axis=axis,
|
| 237 |
+
sample=sim_out_traj,
|
| 238 |
+
t_s=t_s,
|
| 239 |
+
delta_t_graph=delta_t_model,
|
| 240 |
+
n_trajectories=n_trajectories,
|
| 241 |
+
**kwargs,
|
| 242 |
+
)
|
| 243 |
+
|
| 244 |
+
return axis
|
| 245 |
+
|
| 246 |
+
# AF-TODO: Add documentation for this function
|
| 247 |
+
def _add_trajectories(
|
| 248 |
+
axis=None,
|
| 249 |
+
sample=None,
|
| 250 |
+
t_s=None,
|
| 251 |
+
delta_t_graph=0.01,
|
| 252 |
+
n_trajectories=10,
|
| 253 |
+
supplied_trajectory=None,
|
| 254 |
+
maxid_supplied_trajectory=1, # useful for gifs
|
| 255 |
+
highlight_trajectory_rt_choice=True,
|
| 256 |
+
markersize_trajectory_rt_choice=50,
|
| 257 |
+
markertype_trajectory_rt_choice="*",
|
| 258 |
+
markercolor_trajectory_rt_choice="red",
|
| 259 |
+
linewidth_trajectories=1,
|
| 260 |
+
alpha_trajectories=0.5,
|
| 261 |
+
color_trajectories="black",
|
| 262 |
+
**kwargs,
|
| 263 |
+
):
|
| 264 |
+
"""Add trajectories to a given axis."""
|
| 265 |
+
# Check markercolor type
|
| 266 |
+
if isinstance(markercolor_trajectory_rt_choice, str):
|
| 267 |
+
markercolor_trajectory_rt_choice_dict = {}
|
| 268 |
+
for value_ in sample[0]['metadata']['possible_choices']:
|
| 269 |
+
markercolor_trajectory_rt_choice_dict[
|
| 270 |
+
value_
|
| 271 |
+
] = markercolor_trajectory_rt_choice
|
| 272 |
+
elif isinstance(markercolor_trajectory_rt_choice, list):
|
| 273 |
+
cnt = 0
|
| 274 |
+
for value_ in sample[0]['metadata']['possible_choices']:
|
| 275 |
+
markercolor_trajectory_rt_choice_dict[
|
| 276 |
+
value_
|
| 277 |
+
] = markercolor_trajectory_rt_choice[cnt]
|
| 278 |
+
cnt += 1
|
| 279 |
+
elif isinstance(markercolor_trajectory_rt_choice, dict):
|
| 280 |
+
markercolor_trajectory_rt_choice_dict = markercolor_trajectory_rt_choice
|
| 281 |
+
else:
|
| 282 |
+
pass
|
| 283 |
+
|
| 284 |
+
# Check trajectory color type
|
| 285 |
+
if isinstance(color_trajectories, str):
|
| 286 |
+
color_trajectories_dict = {}
|
| 287 |
+
for value_ in sample[0]['metadata']['possible_choices']:
|
| 288 |
+
color_trajectories_dict[value_] = color_trajectories
|
| 289 |
+
elif isinstance(color_trajectories, list):
|
| 290 |
+
cnt = 0
|
| 291 |
+
for value_ in sample[0]['metadata']['possible_choices']:
|
| 292 |
+
color_trajectories_dict[value_] = color_trajectories[cnt]
|
| 293 |
+
cnt += 1
|
| 294 |
+
elif isinstance(color_trajectories, dict):
|
| 295 |
+
color_trajectories_dict = color_trajectories
|
| 296 |
+
else:
|
| 297 |
+
pass
|
| 298 |
+
|
| 299 |
+
# Make bounds
|
| 300 |
+
(b_high, b_low) = (np.maximum(sample[0]['metadata']['boundary'], 0),
|
| 301 |
+
np.minimum((-1) * sample[0]['metadata']['boundary'], 0))
|
| 302 |
+
|
| 303 |
+
b_h_init = b_high[0]
|
| 304 |
+
b_l_init = b_low[0]
|
| 305 |
+
n_roll = int((sample[0]['metadata']['t'][0] / delta_t_graph) + 1)
|
| 306 |
+
b_high = np.roll(b_high, n_roll)
|
| 307 |
+
b_high[:n_roll] = b_h_init
|
| 308 |
+
b_low = np.roll(b_low, n_roll)
|
| 309 |
+
b_low[:n_roll] = b_l_init
|
| 310 |
+
|
| 311 |
+
print(n_trajectories)
|
| 312 |
+
# Trajectories
|
| 313 |
+
for i in range(n_trajectories):
|
| 314 |
+
tmp_traj = sample[i]['metadata']['trajectory']
|
| 315 |
+
tmp_traj_choice = float(sample[i]['choices'].flatten())
|
| 316 |
+
maxid = np.minimum(np.argmax(np.where(tmp_traj > -999)), t_s.shape[0])
|
| 317 |
+
|
| 318 |
+
# Identify boundary value at timepoint of crossing
|
| 319 |
+
b_tmp = b_high[maxid + n_roll] if tmp_traj_choice > 0 else b_low[maxid + n_roll]
|
| 320 |
+
|
| 321 |
+
axis.plot(
|
| 322 |
+
t_s[:maxid] + sample[i]['metadata']['t'][0], #sample.t.values[0],
|
| 323 |
+
tmp_traj[:maxid],
|
| 324 |
+
color=color_trajectories_dict[tmp_traj_choice],
|
| 325 |
+
alpha=alpha_trajectories,
|
| 326 |
+
linewidth=linewidth_trajectories,
|
| 327 |
+
zorder=2000 + i,
|
| 328 |
+
)
|
| 329 |
+
|
| 330 |
+
if highlight_trajectory_rt_choice:
|
| 331 |
+
axis.scatter(
|
| 332 |
+
t_s[maxid] + sample[i]['metadata']['t'][0], #sample.t.values[0],
|
| 333 |
+
b_tmp,
|
| 334 |
+
# tmp_traj[maxid],
|
| 335 |
+
markersize_trajectory_rt_choice,
|
| 336 |
+
color=markercolor_trajectory_rt_choice_dict[tmp_traj_choice],
|
| 337 |
+
alpha=1,
|
| 338 |
+
marker=markertype_trajectory_rt_choice,
|
| 339 |
+
zorder=2000 + i,
|
| 340 |
+
)
|
| 341 |
+
|
| 342 |
+
# AF-TODO: Add documentation to this function
|
| 343 |
+
def _add_model_cartoon_to_ax(
|
| 344 |
+
sample=None,
|
| 345 |
+
axis=None,
|
| 346 |
+
keep_slope=True,
|
| 347 |
+
keep_boundary=True,
|
| 348 |
+
keep_ndt=True,
|
| 349 |
+
keep_starting_point=True,
|
| 350 |
+
markersize_starting_point=80,
|
| 351 |
+
markertype_starting_point=1,
|
| 352 |
+
markershift_starting_point=-0.05,
|
| 353 |
+
delta_t_graph=None,
|
| 354 |
+
sample_hist_alpha=None,
|
| 355 |
+
lw_m=None,
|
| 356 |
+
tmp_label=None,
|
| 357 |
+
ylim_low=None,
|
| 358 |
+
ylim_high=None,
|
| 359 |
+
t_s=None,
|
| 360 |
+
zorder_cnt=1,
|
| 361 |
+
color="black",
|
| 362 |
+
):
|
| 363 |
+
# Make bounds
|
| 364 |
+
(b_high, b_low) = (np.maximum(sample['metadata']['boundary'], 0),
|
| 365 |
+
np.minimum((-1) * sample['metadata']['boundary'], 0))
|
| 366 |
+
|
| 367 |
+
b_h_init = b_high[0]
|
| 368 |
+
b_l_init = b_low[0]
|
| 369 |
+
n_roll = int((sample['metadata']['t'][0] / delta_t_graph) + 1)
|
| 370 |
+
b_high = np.roll(b_high, n_roll)
|
| 371 |
+
b_high[:n_roll] = b_h_init
|
| 372 |
+
b_low = np.roll(b_low, n_roll)
|
| 373 |
+
b_low[:n_roll] = b_l_init
|
| 374 |
+
|
| 375 |
+
tmp_traj = sample["metadata"]["trajectory"]
|
| 376 |
+
maxid = np.minimum(np.argmax(np.where(tmp_traj > -999)),
|
| 377 |
+
t_s.shape[0])
|
| 378 |
+
|
| 379 |
+
if keep_boundary:
|
| 380 |
+
# Upper bound
|
| 381 |
+
axis.plot(
|
| 382 |
+
t_s, # + sample.t.values[0],
|
| 383 |
+
b_high[:t_s.shape[0]],
|
| 384 |
+
color=color,
|
| 385 |
+
alpha=1,
|
| 386 |
+
zorder=1000 + zorder_cnt,
|
| 387 |
+
linewidth=lw_m,
|
| 388 |
+
label=tmp_label,
|
| 389 |
+
)
|
| 390 |
+
|
| 391 |
+
# Lower bound
|
| 392 |
+
axis.plot(
|
| 393 |
+
t_s, # + sample.t.values[0],
|
| 394 |
+
b_low[:t_s.shape[0]],
|
| 395 |
+
color=color,
|
| 396 |
+
alpha=1,
|
| 397 |
+
zorder=1000 + zorder_cnt,
|
| 398 |
+
linewidth=lw_m,
|
| 399 |
+
)
|
| 400 |
+
|
| 401 |
+
# Slope
|
| 402 |
+
if keep_slope:
|
| 403 |
+
axis.plot(
|
| 404 |
+
t_s[:maxid] + sample['metadata']['t'][0],
|
| 405 |
+
tmp_traj[:maxid],
|
| 406 |
+
color=color,
|
| 407 |
+
alpha=1,
|
| 408 |
+
zorder=1000 + zorder_cnt,
|
| 409 |
+
linewidth=lw_m,
|
| 410 |
+
) # TOOK AWAY LABEL
|
| 411 |
+
|
| 412 |
+
# Non-decision time
|
| 413 |
+
if keep_ndt:
|
| 414 |
+
axis.axvline(
|
| 415 |
+
x=sample['metadata']['t'][0],
|
| 416 |
+
ymin=ylim_low,
|
| 417 |
+
ymax=ylim_high,
|
| 418 |
+
color=color,
|
| 419 |
+
linestyle="--",
|
| 420 |
+
linewidth=lw_m,
|
| 421 |
+
zorder=1000 + zorder_cnt,
|
| 422 |
+
alpha=1,
|
| 423 |
+
)
|
| 424 |
+
# Starting point
|
| 425 |
+
if keep_starting_point:
|
| 426 |
+
axis.scatter(
|
| 427 |
+
sample['metadata']['t'][0] + markershift_starting_point,
|
| 428 |
+
b_low[0] + (sample['metadata']['z'][0] * (b_high[0] - b_low[0])),
|
| 429 |
+
markersize_starting_point,
|
| 430 |
+
marker=markertype_starting_point,
|
| 431 |
+
color=color,
|
| 432 |
+
alpha=1,
|
| 433 |
+
zorder=1000 + zorder_cnt,
|
| 434 |
+
)
|
| 435 |
+
|
| 436 |
+
def plot_func_model_n(
|
| 437 |
+
model_name,
|
| 438 |
+
theta,
|
| 439 |
+
axis,
|
| 440 |
+
n_trajectories=10,
|
| 441 |
+
value_range=None,
|
| 442 |
+
bin_size=0.05,
|
| 443 |
+
n_samples=10,
|
| 444 |
+
linewidth_histogram=0.5,
|
| 445 |
+
linewidth_model=0.5,
|
| 446 |
+
legend_fontsize=7,
|
| 447 |
+
legend_shadow=True,
|
| 448 |
+
legend_location="upper right",
|
| 449 |
+
delta_t_model=0.001,
|
| 450 |
+
add_legend=True,
|
| 451 |
+
alpha=1.0,
|
| 452 |
+
keep_frame=False,
|
| 453 |
+
random_state=None,
|
| 454 |
+
**kwargs,
|
| 455 |
+
):
|
| 456 |
+
"""Calculate posterior predictive for a certain bottom node.
|
| 457 |
+
|
| 458 |
+
Arguments:
|
| 459 |
+
bottom_node: pymc.stochastic
|
| 460 |
+
Bottom node to compute posterior over.
|
| 461 |
+
|
| 462 |
+
axis: matplotlib.axis
|
| 463 |
+
Axis to plot into.
|
| 464 |
+
|
| 465 |
+
value_range: numpy.ndarray
|
| 466 |
+
Range over which to evaluate the likelihood.
|
| 467 |
+
|
| 468 |
+
Optional:
|
| 469 |
+
samples: int <default=10>
|
| 470 |
+
Number of posterior samples to use.
|
| 471 |
+
|
| 472 |
+
bin_size: float <default=0.05>
|
| 473 |
+
Size of bins used for histograms
|
| 474 |
+
|
| 475 |
+
alpha: float <default=0.05>
|
| 476 |
+
alpha (transparency) level for the sample-wise elements of the plot
|
| 477 |
+
|
| 478 |
+
add_posterior_uncertainty_rts: bool <default=True>
|
| 479 |
+
Add sample by sample histograms?
|
| 480 |
+
|
| 481 |
+
add_posterior_mean_rts: bool <default=True>
|
| 482 |
+
Add a mean posterior?
|
| 483 |
+
|
| 484 |
+
add_model: bool <default=True>
|
| 485 |
+
Whether to add model cartoons to the plot.
|
| 486 |
+
|
| 487 |
+
linewidth_histogram: float <default=0.5>
|
| 488 |
+
linewdith of histrogram plot elements.
|
| 489 |
+
|
| 490 |
+
linewidth_model: float <default=0.5>
|
| 491 |
+
linewidth of plot elements concerning the model cartoons.
|
| 492 |
+
|
| 493 |
+
legend_loc: str <default='upper right'>
|
| 494 |
+
string defining legend position. Find the rest of the options in the matplotlib documentation.
|
| 495 |
+
|
| 496 |
+
legend_shadow: bool <default=True>
|
| 497 |
+
Add shadow to legend box?
|
| 498 |
+
|
| 499 |
+
legend_fontsize: float <default=12>
|
| 500 |
+
Fontsize of legend.
|
| 501 |
+
|
| 502 |
+
data_color : str <default="blue">
|
| 503 |
+
Color for the data part of the plot.
|
| 504 |
+
|
| 505 |
+
posterior_mean_color : str <default="red">
|
| 506 |
+
Color for the posterior mean part of the plot.
|
| 507 |
+
|
| 508 |
+
posterior_uncertainty_color : str <default="black">
|
| 509 |
+
Color for the posterior uncertainty part of the plot.
|
| 510 |
+
|
| 511 |
+
|
| 512 |
+
delta_t_model:
|
| 513 |
+
specifies plotting intervals for model cartoon elements of the graphs.
|
| 514 |
+
"""
|
| 515 |
+
|
| 516 |
+
color_dict = {
|
| 517 |
+
-1: "black",
|
| 518 |
+
0: "black",
|
| 519 |
+
1: "green",
|
| 520 |
+
2: "blue",
|
| 521 |
+
3: "red",
|
| 522 |
+
4: "orange",
|
| 523 |
+
5: "purple",
|
| 524 |
+
6: "brown",
|
| 525 |
+
}
|
| 526 |
+
|
| 527 |
+
# AF-TODO: Add a mean version of this !
|
| 528 |
+
if value_range is None:
|
| 529 |
+
# Infer from data by finding the min and max from the nodes
|
| 530 |
+
raise NotImplementedError("value_range keyword argument must be supplied.")
|
| 531 |
+
|
| 532 |
+
if len(value_range) > 2:
|
| 533 |
+
value_range = (value_range[0], value_range[-1])
|
| 534 |
+
|
| 535 |
+
# Extract some parameters from kwargs
|
| 536 |
+
bins = np.arange(value_range[0], value_range[-1], bin_size)
|
| 537 |
+
# ------------
|
| 538 |
+
ylim = kwargs.pop("ylim", 4)
|
| 539 |
+
|
| 540 |
+
axis.set_xlim(value_range[0], value_range[-1])
|
| 541 |
+
axis.set_ylim(0, ylim)
|
| 542 |
+
|
| 543 |
+
# ADD MODEL:
|
| 544 |
+
|
| 545 |
+
# RUN SIMULATIONS
|
| 546 |
+
# -------------------------------
|
| 547 |
+
|
| 548 |
+
# Simulator Data
|
| 549 |
+
if random_state is not None:
|
| 550 |
+
np.random.seed(random_state)
|
| 551 |
+
|
| 552 |
+
rand_int = np.random.choice(400000000)
|
| 553 |
+
sim_out = simulator(model = model_name, theta = theta, n_samples = n_samples,
|
| 554 |
+
no_noise = False, delta_t = 0.001,
|
| 555 |
+
bin_dim = None, random_state = rand_int)
|
| 556 |
+
|
| 557 |
+
choices = sim_out['metadata']['possible_choices']
|
| 558 |
+
|
| 559 |
+
sim_out_traj = {}
|
| 560 |
+
for i in range(n_trajectories):
|
| 561 |
+
rand_int = np.random.choice(400000000)
|
| 562 |
+
sim_out_traj[i] = simulator(model = model_name, theta = theta, n_samples = 1,
|
| 563 |
+
no_noise = False, delta_t = 0.001,
|
| 564 |
+
bin_dim = None, random_state = rand_int, smooth_unif = False)
|
| 565 |
+
|
| 566 |
+
sim_out_no_noise = simulator(model = model_name, theta = theta, n_samples = 1,
|
| 567 |
+
no_noise = True, delta_t = 0.001,
|
| 568 |
+
bin_dim = None, smooth_unif = False)
|
| 569 |
+
|
| 570 |
+
# ADD HISTOGRAMS
|
| 571 |
+
# -------------------------------
|
| 572 |
+
|
| 573 |
+
# POSTERIOR BASED HISTOGRAM
|
| 574 |
+
j = 0
|
| 575 |
+
b = np.maximum(sim_out['metadata']['boundary'], 0)
|
| 576 |
+
bottom = b[0]
|
| 577 |
+
for choice in choices:
|
| 578 |
+
tmp_label = None
|
| 579 |
+
|
| 580 |
+
if add_legend and j == 0:
|
| 581 |
+
tmp_label = "PostPred"
|
| 582 |
+
|
| 583 |
+
weights = np.tile(
|
| 584 |
+
(1 / bin_size) / sim_out['rts'].shape[0],
|
| 585 |
+
reps=sim_out['rts'][(sim_out['choices'] == choice) & (sim_out['rts'] != -999)].shape[0],
|
| 586 |
+
)
|
| 587 |
+
|
| 588 |
+
axis.hist(
|
| 589 |
+
np.abs(sim_out['rts'][(sim_out['choices'] == choice) & (sim_out['rts'] != -999)]),
|
| 590 |
+
bins=bins,
|
| 591 |
+
bottom=bottom,
|
| 592 |
+
weights=weights,
|
| 593 |
+
histtype="step",
|
| 594 |
+
alpha=alpha,
|
| 595 |
+
color=color_dict[choice],
|
| 596 |
+
zorder=-1,
|
| 597 |
+
label=tmp_label,
|
| 598 |
+
linewidth=linewidth_histogram,
|
| 599 |
+
)
|
| 600 |
+
j += 1
|
| 601 |
+
|
| 602 |
+
# ADD MODEL:
|
| 603 |
+
tmp_label = None
|
| 604 |
+
j = 0
|
| 605 |
+
t_s = np.arange(0, sim_out['metadata']['max_t'], delta_t_model)
|
| 606 |
+
|
| 607 |
+
if add_legend and (j == 0):
|
| 608 |
+
tmp_label = "PostPred"
|
| 609 |
+
|
| 610 |
+
_add_model_n_cartoon_to_ax(
|
| 611 |
+
sample=sim_out_no_noise,
|
| 612 |
+
axis=axis,
|
| 613 |
+
delta_t_graph=delta_t_model,
|
| 614 |
+
sample_hist_alpha=alpha,
|
| 615 |
+
lw_m=linewidth_model,
|
| 616 |
+
tmp_label=tmp_label,
|
| 617 |
+
linestyle="-",
|
| 618 |
+
ylim=ylim,
|
| 619 |
+
t_s=t_s,
|
| 620 |
+
color_dict=color_dict,
|
| 621 |
+
zorder_cnt=j,
|
| 622 |
+
)
|
| 623 |
+
|
| 624 |
+
if n_trajectories > 0:
|
| 625 |
+
_add_trajectories_n(
|
| 626 |
+
axis=axis,
|
| 627 |
+
sample=sim_out_traj,
|
| 628 |
+
t_s=t_s,
|
| 629 |
+
delta_t_graph=delta_t_model,
|
| 630 |
+
n_trajectories=n_trajectories,
|
| 631 |
+
**kwargs,
|
| 632 |
+
)
|
| 633 |
+
|
| 634 |
+
if add_legend:
|
| 635 |
+
custom_elems = [
|
| 636 |
+
Line2D([0], [0], color=color_dict[choice], lw=1) for choice in choices
|
| 637 |
+
]
|
| 638 |
+
custom_titles = ["response: " + str(choice) for choice in choices]
|
| 639 |
+
|
| 640 |
+
custom_elems.append(
|
| 641 |
+
Line2D([0], [0], color="black", lw=1.0, linestyle="dashed")
|
| 642 |
+
)
|
| 643 |
+
# custom_elems.append(Line2D([0], [0], color="black", lw=1.0, linestyle="-"))
|
| 644 |
+
# custom_titles.append("Data")
|
| 645 |
+
# custom_titles.append("Posterior")
|
| 646 |
+
|
| 647 |
+
axis.legend(
|
| 648 |
+
custom_elems,
|
| 649 |
+
custom_titles,
|
| 650 |
+
fontsize=legend_fontsize,
|
| 651 |
+
shadow=legend_shadow,
|
| 652 |
+
loc=legend_location,
|
| 653 |
+
)
|
| 654 |
+
|
| 655 |
+
# FRAME
|
| 656 |
+
if not keep_frame:
|
| 657 |
+
axis.set_frame_on(False)
|
| 658 |
+
|
| 659 |
+
return axis
|
| 660 |
+
|
| 661 |
+
def _add_trajectories_n(axis=None,
|
| 662 |
+
sample=None,
|
| 663 |
+
t_s=None,
|
| 664 |
+
delta_t_graph=0.01,
|
| 665 |
+
n_trajectories=10,
|
| 666 |
+
highlight_trajectory_rt_choice=True,
|
| 667 |
+
markersize_trajectory_rt_choice=50,
|
| 668 |
+
markertype_trajectory_rt_choice="*",
|
| 669 |
+
markercolor_trajectory_rt_choice="black",
|
| 670 |
+
linewidth_trajectories=1,
|
| 671 |
+
alpha_trajectories=0.5,
|
| 672 |
+
color_trajectories="black",
|
| 673 |
+
**kwargs,
|
| 674 |
+
):
|
| 675 |
+
|
| 676 |
+
"""Add trajectories to a given axis."""
|
| 677 |
+
color_dict = {
|
| 678 |
+
-1: "black",
|
| 679 |
+
0: "black",
|
| 680 |
+
1: "green",
|
| 681 |
+
2: "blue",
|
| 682 |
+
3: "red",
|
| 683 |
+
4: "orange",
|
| 684 |
+
5: "purple",
|
| 685 |
+
6: "brown",
|
| 686 |
+
}
|
| 687 |
+
|
| 688 |
+
# Check trajectory color type
|
| 689 |
+
if isinstance(color_trajectories, str):
|
| 690 |
+
color_trajectories_dict = {}
|
| 691 |
+
for value_ in sample[0]['metadata']['possible_choices']:
|
| 692 |
+
color_trajectories_dict[value_] = color_trajectories
|
| 693 |
+
elif isinstance(color_trajectories, list):
|
| 694 |
+
cnt = 0
|
| 695 |
+
for value_ in sample[0]['metadata']['possible_choices']:
|
| 696 |
+
color_trajectories_dict[value_] = color_trajectories[cnt]
|
| 697 |
+
cnt += 1
|
| 698 |
+
elif isinstance(color_trajectories, dict):
|
| 699 |
+
color_trajectories_dict = color_trajectories
|
| 700 |
+
else:
|
| 701 |
+
pass
|
| 702 |
+
|
| 703 |
+
# Make bounds
|
| 704 |
+
b = np.maximum(sample[0]['metadata']['boundary'], 0)
|
| 705 |
+
b_init = b[0]
|
| 706 |
+
n_roll = int((sample[0]['metadata']['t'][0] / delta_t_graph) + 1)
|
| 707 |
+
b = np.roll(b, n_roll)
|
| 708 |
+
b[:n_roll] = b_init
|
| 709 |
+
|
| 710 |
+
# Trajectories
|
| 711 |
+
for i in range(n_trajectories):
|
| 712 |
+
tmp_traj = sample[i]['metadata']['trajectory']
|
| 713 |
+
tmp_traj_choice = float(sample[i]['choices'].flatten())
|
| 714 |
+
|
| 715 |
+
for j in range(len(sample[i]['metadata']['possible_choices'])):
|
| 716 |
+
tmp_maxid = np.minimum(np.argmax(np.where(tmp_traj[:, j] > -999)), t_s.shape[0])
|
| 717 |
+
|
| 718 |
+
# Identify boundary value at timepoint of crossing
|
| 719 |
+
b_tmp = b[tmp_maxid + n_roll]
|
| 720 |
+
|
| 721 |
+
axis.plot(
|
| 722 |
+
t_s[:tmp_maxid] + sample[i]['metadata']['t'][0], #sample.t.values[0],
|
| 723 |
+
tmp_traj[:tmp_maxid, j],
|
| 724 |
+
color=color_dict[j],
|
| 725 |
+
alpha=alpha_trajectories,
|
| 726 |
+
linewidth=linewidth_trajectories,
|
| 727 |
+
zorder=2000 + i,
|
| 728 |
+
)
|
| 729 |
+
|
| 730 |
+
if highlight_trajectory_rt_choice and tmp_traj_choice == j:
|
| 731 |
+
axis.scatter(
|
| 732 |
+
t_s[tmp_maxid] + sample[i]['metadata']['t'][0], #sample.t.values[0],
|
| 733 |
+
b_tmp,
|
| 734 |
+
# tmp_traj[maxid],
|
| 735 |
+
markersize_trajectory_rt_choice,
|
| 736 |
+
color=color_dict[tmp_traj_choice],
|
| 737 |
+
alpha=1,
|
| 738 |
+
marker=markertype_trajectory_rt_choice,
|
| 739 |
+
zorder=2000 + i,
|
| 740 |
+
)
|
| 741 |
+
elif highlight_trajectory_rt_choice and tmp_traj_choice != j:
|
| 742 |
+
axis.scatter(
|
| 743 |
+
t_s[tmp_maxid] + sample[i]['metadata']['t'][0] + 0.05, #sample.t.values[0],
|
| 744 |
+
tmp_traj[tmp_maxid, j],
|
| 745 |
+
# tmp_traj[maxid],
|
| 746 |
+
markersize_trajectory_rt_choice,
|
| 747 |
+
color=color_dict[j],
|
| 748 |
+
alpha=1,
|
| 749 |
+
marker=5,
|
| 750 |
+
zorder=2000 + i,
|
| 751 |
+
)
|
| 752 |
+
|
| 753 |
+
def _add_model_n_cartoon_to_ax(
|
| 754 |
+
sample=None,
|
| 755 |
+
axis=None,
|
| 756 |
+
delta_t_graph=None,
|
| 757 |
+
sample_hist_alpha=None,
|
| 758 |
+
keep_boundary=True,
|
| 759 |
+
keep_ndt=True,
|
| 760 |
+
keep_slope=True,
|
| 761 |
+
keep_starting_point=True,
|
| 762 |
+
lw_m=None,
|
| 763 |
+
linestyle="-",
|
| 764 |
+
tmp_label=None,
|
| 765 |
+
ylim=None,
|
| 766 |
+
t_s=None,
|
| 767 |
+
zorder_cnt=1,
|
| 768 |
+
color_dict=None,
|
| 769 |
+
):
|
| 770 |
+
|
| 771 |
+
b = np.maximum(sample['metadata']['boundary'], 0)
|
| 772 |
+
b_init = b[0]
|
| 773 |
+
n_roll = int((sample['metadata']['t'][0] / delta_t_graph) + 1)
|
| 774 |
+
b = np.roll(b, n_roll)
|
| 775 |
+
b[:n_roll] = b_init
|
| 776 |
+
|
| 777 |
+
# Upper bound
|
| 778 |
+
if keep_boundary:
|
| 779 |
+
axis.plot(
|
| 780 |
+
t_s,
|
| 781 |
+
b[:t_s.shape[0]],
|
| 782 |
+
color="black",
|
| 783 |
+
alpha=sample_hist_alpha,
|
| 784 |
+
zorder=1000 + zorder_cnt,
|
| 785 |
+
linewidth=lw_m,
|
| 786 |
+
linestyle=linestyle,
|
| 787 |
+
label=tmp_label,
|
| 788 |
+
)
|
| 789 |
+
|
| 790 |
+
# Starting point
|
| 791 |
+
if keep_starting_point:
|
| 792 |
+
axis.axvline(
|
| 793 |
+
x=sample['metadata']['t'][0],
|
| 794 |
+
ymin=-ylim,
|
| 795 |
+
ymax=ylim,
|
| 796 |
+
color="black",
|
| 797 |
+
linestyle=linestyle,
|
| 798 |
+
linewidth=lw_m,
|
| 799 |
+
alpha=sample_hist_alpha,
|
| 800 |
+
)
|
| 801 |
+
|
| 802 |
+
# # MAKE SLOPES (VIA TRAJECTORIES HERE --> RUN NOISE FREE SIMULATIONS)!
|
| 803 |
+
if keep_slope:
|
| 804 |
+
tmp_traj = sample["metadata"]["trajectory"]
|
| 805 |
+
|
| 806 |
+
for i in range(len(sample["metadata"]["possible_choices"])):
|
| 807 |
+
tmp_maxid = np.minimum(np.argmax(np.where(tmp_traj[:, i] > -999)), t_s.shape[0])
|
| 808 |
+
|
| 809 |
+
# Slope
|
| 810 |
+
axis.plot(
|
| 811 |
+
t_s[:tmp_maxid] + sample['metadata']['t'][0],
|
| 812 |
+
tmp_traj[:tmp_maxid, i],
|
| 813 |
+
color=color_dict[i],
|
| 814 |
+
linestyle=linestyle,
|
| 815 |
+
alpha=sample_hist_alpha,
|
| 816 |
+
zorder=1000 + zorder_cnt,
|
| 817 |
+
linewidth=lw_m,
|
| 818 |
+
) # TOOK AWAY LABEL
|
| 819 |
+
|
| 820 |
+
return b[0]
|