Update the organization branch with the new deviation variable

README.md

@@ -1,2 +1,25 @@
 # RPi4_behavior_boxes
 BehavBox is a system with Raspberry Pi computers that is sufficient to provide a foundation of constructing animal behavior training and experiment.
+
+# Quick Start
+in task_protocol, you could find all the task examples. Each task has its run file, task file, task information file and an example of session_information file.
+
+To start running a task file, you need to first create a session_information pathway and session_information file in a path (suggested) in the home directory and outside of the git repo since you would have to configure and changes the file everyday for training purposes.
+
+After configure the session_information path and input the appropriate path leading to the exact session_information of the date, you could do python3 run_x_task.py to start running the task.
+
+# Example
+To start running the task `headfixed_task.py`
+1. Setup and configure the 'session_information_year-month-date.py' file:
+first, create the experimental_data directory in the home directory path: <br />
+`$ mkdir ~/experimental_data`<br />
+second, create all the necessary subdirectories for the specific task: <br />
+`$ mkdir ~/experimental_data/headfixed_task`<br />
+`$ mkdir ~/experimental_data/headfixed_task/session_info`<br />
+then, copy the session_information example file corresponding to the specific task: <br />
+`$ cp ~/RPi4_behavbior_boxes/task_protocol/headfixed_task/session_info_headfixed_independent_reward.py ~/experimental_data/headfixed_task/session_info` <br />
+2. Modify the newly created session_info file: <br />
+`$ sudo nano ~/experimental_data/headfixed_task/session_info_headfixed_independent_reward.py` <br />
+**KEEP IN MIND** after configuring the session_information to manually change the field manual date to the day of the experiment session (the day of the experiment), and the name of the session_info file from `session_info_headfixed_independent_reward.py` to `session_info_year-month-date.py`. Otherwise, an error would occur when running the task file.
+3. After setting up the session_info file, run the task: <br />
+`$ python3 ~/RPi4_behavior_boxes/task_protocol/headfixed_task/run_headfixed_task.py`

debug/generate_reward_trajectory.py

@@ -0,0 +1,45 @@
+def cumsum_positive(input_list):
+  for index in range(len(input_list)):
+    if index == 0 and input_list[index]<0:
+      input_list[index] = -input_list[index]
+    elif input_list[index]+input_list[index-1]<0:
+      input_list[index] = input_list[index] - input_list[index-1]
+    else:
+      input_list[index] = input_list[index] + input_list[index-1]
+  return input_list
+
+def generate_reward_trajectory(scale=0.5, offset=3.0, change_point=20, ntrials=200):
+    # initial reward (need to be random)
+    rewards_L = [1]
+    rewards_R = [1]
+    for a in np.arange(np.round(ntrials / change_point)):
+        temp = np.random.randn(change_point) * scale
+        # temp = np.random.uniform(low=0.0, high=10, size=(change_point,))
+
+        # print("ay o" + str(temp))
+        # while temp < 0:
+        #     temp = np.random.randn(change_point) * scale
+        rewards_L.append(cumsum_positive(temp) + offset)
+        temp = np.random.randn(change_point) * scale
+        # temp = np.random.uniform(low=0.0, high=10, size=(change_point,))
+        # while temp < 0:
+        #     temp = np.random.randn(change_point) * scale
+        rewards_R.append(cumsum_positive(temp) + offset)
+    rewards_L = np.hstack(rewards_L)
+    rewards_R = np.hstack(rewards_R)
+    # plt.plot(rewards_L,'b');plt.plot(rewards_R,'r--')
+    reward_LR = [rewards_L, rewards_R]
+    reward_LR = np.transpose(np.array(reward_LR))
+    reward_LR = reward_LR[0:ntrials, :]
+    # print(reward_LR)
+    return reward_LR
+
+# from reward_distribution import generate_reward_trajectory
+scale = 0.5
+offset = 3.0
+change_point = 20
+ntrials = 100
+
+reward_distribution_list = generate_reward_trajectory(scale, offset, change_point, ntrials)
+
+print(reward_distribution_list)

pump_debug.py → debug/pump_debug.py

@@ -1,6 +1,9 @@
 # pump_debug.py: it's for testing the pump class and the pump itself
 import sys
 import time
+# updated with reorganization (on 7/11/2023)
+import sys
+sys.path.insert(0,'/home/pi/RPi4_behavior_boxes/essential')
 from behavbox import Pump
 # from fake_session_info import fake_session_info
 side = str(sys.argv[1])

debug/reward_distribution.py

@@ -0,0 +1,24 @@
+import numpy as np
+
+def generate_reward_trajectory(scale=0.5, offset=3.0, change_point=20, ntrials=200):
+        # initial reward (need to be random)
+        rewards_L = [1]
+        rewards_R = [1]
+        for a in np.arange(np.round(ntrials/change_point)):
+                temp = np.random.randn(change_point)*scale
+                rewards_L.append(np.cumsum(temp, axis=-1) + offset)
+                temp = np.random.randn(change_point)*scale
+                rewards_R.append(np.cumsum(temp, axis=-1) + offset)
+        rewards_L=np.hstack(rewards_L)
+        rewards_R=np.hstack(rewards_R)
+        #plt.plot(rewards_L,'b');plt.plot(rewards_R,'r--')
+        reward_LR = [rewards_L, rewards_R]
+        reward_LR  = np.transpose(np.array(reward_LR))
+        reward_LR = reward_LR[0:ntrials,:]
+        print(reward_LR)
+        return reward_LR
+# generate_reward_trajectory()
+# session_information['reward']['scale']
+# session_information['reward']['offset']
+# session_information['reward']['change_point']
+# session_information['reward']['ntrials']

debug/syringe_pump_pygame_debug.py

@@ -0,0 +1,93 @@
+import pygame
+# updated with reorganization (on 7/11/2023)
+import sys
+sys.path.insert(0,'/home/pi/RPi4_behavior_boxes/essential')
+from behavbox import Pump
+import numpy as np
+
+class Pump(object):
+    def __init__(self, session_info):
+        self.pump1 = LED(19)
+        self.pump2 = LED(20)
+        self.pump3 = LED(21)
+        self.pump4 = LED(7)
+        self.pump_air = LED(8)
+        self.pump_vacuum = LED(25)
+        self.reward_list = [] # a list of tuple (pump_x, reward_amount) with information of reward history for data
+        # visualization
+
+    def reward(self, which_pump, reward_size):
+        # import coefficient from the session_information
+        coefficient_p1 = [0.13, 0]
+        coefficient_p2 = [0.13, 0]
+        coefficient_p3 = [0.13, 0]
+        coefficient_p4 = [0.13, 0]
+        duration_air = 1
+        duration_vac = 1
+
+        if which_pump == "1":
+            duration = round((coefficient_p1[0] * (reward_size / 1000) + coefficient_p1[1]), 5)  # linear function
+            self.pump1.blink(duration, 0.1, 1)
+            self.reward_list.append(("pump1_reward", reward_size))
+            logging.info(";" + str(time.time()) + ";[reward];pump1_reward(reward_coeff: " + str(coefficient_p1) +
+                         ", reward_amount: " + str(reward_size) + "duration: " + str(duration) + ")")
+        elif which_pump == "2":
+            duration = round((coefficient_p2[0] * (reward_size / 1000) + coefficient_p2[1]), 5)  # linear function
+            self.pump2.blink(duration, 0.1, 1)
+            self.reward_list.append(("pump2_reward", reward_size))
+            logging.info(";" + str(time.time()) + ";[reward];pump2_reward(reward_coeff: " + str(coefficient_p2) +
+                         ", reward_amount: " + str(reward_size) + "duration: " + str(duration) + ")")
+        elif which_pump == "3":
+            duration = round((coefficient_p3[0] * (reward_size / 1000) + coefficient_p3[1]), 5)  # linear function
+            self.pump3.blink(duration, 0.1, 1)
+            self.reward_list.append(("pump3_reward", reward_size))
+            logging.info(";" + str(time.time()) + ";[reward];pump3_reward(reward_coeff: " + str(coefficient_p3) +
+                         ", reward_amount: " + str(reward_size) + "duration: " + str(duration) + ")")
+        elif which_pump == "4":
+            duration = round((coefficient_p4[0] * (reward_size / 1000) + coefficient_p4[1]), 5)  # linear function
+            self.pump4.blink(duration, 0.1, 1)
+            self.reward_list.append(("pump4_reward", reward_size))
+            logging.info(";" + str(time.time()) + ";[reward];pump4_reward(reward_coeff: " + str(coefficient_p4) +
+                         ", reward_amount: " + str(reward_size) + "duration: " + str(duration) + ")")
+        elif which_pump == "air_puff":
+            self.pump_air.blink(duration_air, 0.1, 1)
+            self.reward_list.append(("air_puff", reward_size))
+            logging.info(";" + str(time.time()) + ";[reward];pump4_reward_" + str(reward_size))
+        elif which_pump == "vacuum":
+            self.pump_vacuum.blink(duration_vac, 0.1, 1)
+            logging.info(";" + str(time.time()) + ";[reward];pump_vacuum" + str(duration_vac))
+try:
+    pump = Pump()
+    pygame.init()
+    DISPLAYSURF = pygame.display.set_mode((200, 200))
+    pygame.display.set_caption("pygame debugging")
+except Exception as error_message:
+    print(str(error_message))
+
+run = True
+reward_size = float(input("Input reward_size: "))
+
+while run:
+    for event in pygame.event.get():
+        if event.type == pygame.KEYDOWN and event.key == pygame.K_ESCAPE:
+            run = False
+        if event.type == pygame.KEYDOWN:
+            # print("KeyDown: " + str(event.type) + "\n")
+            if event.key == pygame.K_q:
+                print("Q down: syringe pump 1")
+                pump.reward("1", reward_size)
+            if event.key == pygame.K_w:
+                print("W down: syringe pump 2")
+                pump.reward("2", reward_size)
+            if event.key == pygame.K_e:
+                print("E down: syringe pump 3")
+                pump.reward("3", reward_size)
+            if event.key == pygame.K_r:
+                print("R down: syringe pump 4")
+                pump.reward("4", reward_size)
+            if event.key == pygame.K_a:
+                print("A down: air puff on")
+                pump.reward("air_puff", reward_size)
+            if event.key == pygame.K_s:
+                print("S down: vacuum on")
+                pump.reward("vacuum", 1)

environment/__init__.py

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+

essential/ADC/__init__.py

@@ -0,0 +1 @@
+

essential/RTC/__init__.py

@@ -0,0 +1 @@
+

essential/__init__.py

@@ -0,0 +1 @@
+