diff --git a/README.md b/README.md
index 70ab553..c01f1ff 100755
--- a/README.md
+++ b/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`
\ No newline at end of file
diff --git a/picamera_library_modified/picamera.egg-info/dependency_links.txt b/debug/__init__.py
old mode 100755
new mode 100644
similarity index 100%
rename from picamera_library_modified/picamera.egg-info/dependency_links.txt
rename to debug/__init__.py
diff --git a/calibrate.py b/debug/calibrate.py
similarity index 100%
rename from calibrate.py
rename to debug/calibrate.py
diff --git a/camera_test.py b/debug/camera_test.py
similarity index 100%
rename from camera_test.py
rename to debug/camera_test.py
diff --git a/control_preview.py b/debug/control_preview.py
similarity index 100%
rename from control_preview.py
rename to debug/control_preview.py
diff --git a/debug/generate_reward_trajectory.py b/debug/generate_reward_trajectory.py
new file mode 100644
index 0000000..4d2cbed
--- /dev/null
+++ b/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)
\ No newline at end of file
diff --git a/mounting_hard_drive.txt b/debug/mounting_hard_drive.txt
similarity index 100%
rename from mounting_hard_drive.txt
rename to debug/mounting_hard_drive.txt
diff --git a/press_button.py b/debug/press_button.py
similarity index 100%
rename from press_button.py
rename to debug/press_button.py
diff --git a/pump_debug.py b/debug/pump_debug.py
similarity index 70%
rename from pump_debug.py
rename to debug/pump_debug.py
index 946f369..dc0beda 100755
--- a/pump_debug.py
+++ b/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])
diff --git a/pygame_debug.py b/debug/pygame_debug.py
similarity index 100%
rename from pygame_debug.py
rename to debug/pygame_debug.py
diff --git a/record_treadmill.py b/debug/record_treadmill.py
similarity index 100%
rename from record_treadmill.py
rename to debug/record_treadmill.py
diff --git a/record_video.py b/debug/record_video.py
similarity index 100%
rename from record_video.py
rename to debug/record_video.py
diff --git a/debug/reward_distribution.py b/debug/reward_distribution.py
new file mode 100644
index 0000000..8a066b2
--- /dev/null
+++ b/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']
\ No newline at end of file
diff --git a/debug/syringe_pump_pygame_debug.py b/debug/syringe_pump_pygame_debug.py
new file mode 100644
index 0000000..14cfaed
--- /dev/null
+++ b/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)
\ No newline at end of file
diff --git a/treadmill_debug.py b/debug/treadmill_debug.py
similarity index 100%
rename from treadmill_debug.py
rename to debug/treadmill_debug.py
diff --git a/environment/__init__.py b/environment/__init__.py
new file mode 100644
index 0000000..8b13789
--- /dev/null
+++ b/environment/__init__.py
@@ -0,0 +1 @@
+
diff --git a/essential/ADC/__init__.py b/essential/ADC/__init__.py
new file mode 100644
index 0000000..8b13789
--- /dev/null
+++ b/essential/ADC/__init__.py
@@ -0,0 +1 @@
+
diff --git a/ADC/readme.md b/essential/ADC/readme.md
similarity index 100%
rename from ADC/readme.md
rename to essential/ADC/readme.md
diff --git a/ADS1x15.py b/essential/ADS1x15.py
similarity index 100%
rename from ADS1x15.py
rename to essential/ADS1x15.py
diff --git a/FlipperOutput.py b/essential/FlipperOutput.py
similarity index 100%
rename from FlipperOutput.py
rename to essential/FlipperOutput.py
diff --git a/essential/RTC/__init__.py b/essential/RTC/__init__.py
new file mode 100644
index 0000000..8b13789
--- /dev/null
+++ b/essential/RTC/__init__.py
@@ -0,0 +1 @@
+
diff --git a/RTC/readme.md b/essential/RTC/readme.md
similarity index 100%
rename from RTC/readme.md
rename to essential/RTC/readme.md
diff --git a/Treadmill.py b/essential/Treadmill.py
similarity index 100%
rename from Treadmill.py
rename to essential/Treadmill.py
diff --git a/essential/__init__.py b/essential/__init__.py
new file mode 100644
index 0000000..8b13789
--- /dev/null
+++ b/essential/__init__.py
@@ -0,0 +1 @@
+
diff --git a/behavbox.py b/essential/behavbox.py
similarity index 69%
rename from behavbox.py
rename to essential/behavbox.py
index caeb719..d8aebf2 100755
--- a/behavbox.py
+++ b/essential/behavbox.py
@@ -104,13 +104,33 @@ def __init__(self, session_info):
         # there is a DIO6, but that is the same pin as the camera strobe
 
         ###############################################################################################
-        # IR detection - for nosepoke detection
+        # IR detection - for nosepoke
+        ###############################################################################################
+        self.IR_rx1 = Button(5, None, True)  # None, True inverts the signal so poke=True, no-poke=False
+        self.IR_rx2 = Button(6, None, True)
+        self.IR_rx3 = Button(12, None, True)
+        self.IR_rx4 = Button(13, None, True)  # (optional, reserved for future use
+        self.IR_rx5 = Button(16, None, True)  # (optional, reserved for future use
+
+        # link nosepoke event detections to callbacks
+        self.IR_rx1.when_pressed = self.IR_1_entry
+        self.IR_rx2.when_pressed = self.IR_2_entry
+        self.IR_rx3.when_pressed = self.IR_3_entry
+        self.IR_rx4.when_pressed = self.IR_4_entry
+        self.IR_rx5.when_pressed = self.IR_5_entry
+        self.IR_rx1.when_released = self.IR_1_exit
+        self.IR_rx2.when_released = self.IR_2_exit
+        self.IR_rx3.when_released = self.IR_3_exit
+        self.IR_rx4.when_released = self.IR_4_exit
+        self.IR_rx5.when_released = self.IR_5_exit
+        ###############################################################################################
+        # close circuit detection - for ground pin circuit lick detection
         ###############################################################################################
         self.lick1 = Button(26, None, True)
         self.lick2 = Button(27, None, True)
         self.lick3 = Button(15, None, True)
-        self.reserved_rx1 = Button(13, None, True)  # for mitch
-        self.reserved_rx2 = Button(16, None, True)  # for mitch
+        #self.reserved_rx1 = Button(13, None, True)  # for mitch
+        #self.reserved_rx2 = Button(16, None, True)  # for mitch
         #
         # # link nosepoke event detections to callbacks
         self.lick1.when_pressed = self.left_exit
@@ -121,10 +141,10 @@ def __init__(self, session_info):
         self.lick2.when_released = self.right_entry
         self.lick3.when_released = self.center_entry
 
-        self.reserved_rx1.when_pressed = self.reserved_rx1_pressed
-        self.reserved_rx2.when_pressed = self.reserved_rx2_pressed
-        self.reserved_rx1.when_released = self.reserved_rx1_released
-        self.reserved_rx2.when_released = self.reserved_rx2_released
+        # self.reserved_rx1.when_pressed = self.reserved_rx1_pressed
+        # self.reserved_rx2.when_pressed = self.reserved_rx2_pressed
+        # self.reserved_rx1.when_released = self.reserved_rx1_released
+        # self.reserved_rx2.when_released = self.reserved_rx2_released
 
         ###############################################################################################
         # sound: audio board DIO - pins sending TTL to the Tsunami soundboard via SMA connectors
@@ -142,7 +162,7 @@ def __init__(self, session_info):
         ###############################################################################################
         # pump: trigger signal output to a driver board induce the solenoid valve to deliver reward
         ###############################################################################################
-        self.pump = Pump()
+        self.pump = Pump(self.session_info)
 
         ###############################################################################################
         # flipper strobe signal (previously called camera strobe signal)
@@ -260,39 +280,42 @@ def check_keybd(self):
                         self.keyboard_active = False
                     elif event.key == pygame.K_1:
                         self.left_entry()
+                        self.left_IR_entry()
                         logging.info(";" + str(time.time()) + ";[action];key_pressed_left_entry()")
                     elif event.key == pygame.K_2:
                         self.center_entry()
+                        self.center_IR_entry()
                         logging.info(";" + str(time.time()) + ";[action];key_pressed_center_entry()")
                     elif event.key == pygame.K_3:
                         self.right_entry()
+                        self.right_IR_entry()
                         logging.info(";" + str(time.time()) + ";[action];key_pressed_right_entry()")
-                    elif event.key == pygame.K_4:
-                        self.reserved_rx1_pressed()
-                        logging.info(";" + str(time.time()) + ";[action];key_pressed_reserved_rx1_pressed()")
-                    elif event.key == pygame.K_5:
-                        self.reserved_rx2_pressed()
-                        logging.info(";" + str(time.time()) + ";[action];key_pressed_reserved_rx2_pressed()")
+                    # elif event.key == pygame.K_4:
+                    #     self.reserved_rx1_pressed()
+                    #     logging.info(";" + str(time.time()) + ";[action];key_pressed_reserved_rx1_pressed()")
+                    # elif event.key == pygame.K_5:
+                    #     self.reserved_rx2_pressed()
+                    #     logging.info(";" + str(time.time()) + ";[action];key_pressed_reserved_rx2_pressed()")
                     elif event.key == pygame.K_q:
                         # print("Q down: syringe pump 1 moves")
-                        logging.info(";" + str(time.time()) + ";[reward];key_pressed_pump1")
-                        self.pump.reward("1", 5)
+                        # logging.info(";" + str(time.time()) + ";[reward];key_pressed_pump1")
+                        self.pump.reward("key_1", self.session_info["key_reward_amount"])
                     elif event.key == pygame.K_w:
                         # print("W down: syringe pump 2 moves")
-                        logging.info(";" + str(time.time()) + ";[reward];key_pressed_pump2")
-                        self.pump.reward("2", 5)
+                        # logging.info(";" + str(time.time()) + ";[reward];key_pressed_pump2")
+                        self.pump.reward("key_2", self.session_info["key_reward_amount"])
                     elif event.key == pygame.K_e:
                         # print("E down: syringe pump 3 moves")
-                        logging.info(";" + str(time.time()) + ";[reward];key_pressed_pump3")
-                        self.pump.reward("3", 5)
+                        # logging.info(";" + str(time.time()) + ";[reward];key_pressed_pump3")
+                        self.pump.reward("key_3", self.session_info["key_reward_amount"])
                     elif event.key == pygame.K_r:
                         # print("R down: syringe pump 4 moves")
-                        logging.info(";" + str(time.time()) + ";[reward];key_pressed_pump4")
-                        self.pump.reward("4", 5)
+                        # logging.info(";" + str(time.time()) + ";[reward];key_pressed_pump4")
+                        self.pump.reward("key_4", self.session_info["key_reward_amount"])
                     elif event.key == pygame.K_t:
                         # print("T down: vacuum on")
-                        logging.info(";" + str(time.time()) + ";[reward];key_pressed_pump_vacuum")
-                        self.pump.reward("vacuum", 1)
+                        # logging.info(";" + str(time.time()) + ";[reward];key_pressed_pump_vacuum")
+                        self.pump.reward("key_vacuum", 1)
                 elif event.type == pygame.KEYUP:
                     if event.key == pygame.K_1:
                         self.left_exit()
@@ -455,27 +478,65 @@ def right_exit(self):
         self.interact_list.append((time.time(), "right_exit"))
         logging.info(";" + str(time.time()) + ";[action];right_exit")
 
-    def reserved_rx1_pressed(self):
-        self.event_list.append("reserved_rx1_pressed")
-        self.interact_list.append((time.time(), "reserved_rx1_pressed"))
-        logging.info(";" + str(time.time()) + ";[action];reserved_rx1_pressed")
-
-    def reserved_rx2_pressed(self):
-        self.event_list.append("reserved_rx2_pressed")
-        self.interact_list.append((time.time(), "reserved_rx2_pressed"))
-        logging.info(";" + str(time.time()) + ";[action];reserved_rx2_pressed")
-
-    def reserved_rx1_released(self):
-        self.event_list.append("reserved_rx1_released")
-        self.interact_list.append((time.time(), "reserved_rx1_released"))
-        logging.info(";" + str(time.time()) + ";[action];reserved_rx1_released")
-
-    def reserved_rx2_released(self):
-        self.event_list.append("reserved_rx2_released")
-        self.interact_list.append((time.time(), "reserved_rx2_released"))
-        logging.info(";" + str(time.time()) + ";[action];reserved_rx2_released")
-
-
+    # def reserved_rx1_pressed(self):
+    #     self.event_list.append("reserved_rx1_pressed")
+    #     self.interact_list.append((time.time(), "reserved_rx1_pressed"))
+    #     logging.info(";" + str(time.time()) + ";[action];reserved_rx1_pressed")
+    #
+    # def reserved_rx2_pressed(self):
+    #     self.event_list.append("reserved_rx2_pressed")
+    #     self.interact_list.append((time.time(), "reserved_rx2_pressed"))
+    #     logging.info(";" + str(time.time()) + ";[action];reserved_rx2_pressed")
+    #
+    # def reserved_rx1_released(self):
+    #     self.event_list.append("reserved_rx1_released")
+    #     self.interact_list.append((time.time(), "reserved_rx1_released"))
+    #     logging.info(";" + str(time.time()) + ";[action];reserved_rx1_released")
+    #
+    # def reserved_rx2_released(self):
+    #     self.event_list.append("reserved_rx2_released")
+    #     self.interact_list.append((time.time(), "reserved_rx2_released"))
+    #     logging.info(";" + str(time.time()) + ";[action];reserved_rx2_released")
+    def IR_1_entry(self):
+        self.event_list.append("IR_1_entry")
+        logging.info(str(time.time()) + ", IR_1_entry")
+
+    def IR_2_entry(self):
+        self.event_list.append("IR_2_entry")
+        logging.info(str(time.time()) + ", IR_2_entry")
+
+    def IR_3_entry(self):
+        self.event_list.append("IR_3_entry")
+        logging.info(str(time.time()) + ", IR_3_entry")
+
+    def IR_4_entry(self):
+        self.event_list.append("IR_4_entry")
+        logging.info(str(time.time()) + ", IR_4_entry")
+
+    def IR_5_entry(self):
+        self.event_list.append("IR_5_entry")
+        logging.info(str(time.time()) + ", IR_5_entry")
+
+    def IR_1_exit(self):
+        self.event_list.append("IR_1_exit")
+        logging.info(str(time.time()) + ", IR_1_exit")
+
+    def IR_2_exit(self):
+        self.event_list.append("IR_2_exit")
+        # self.cueLED2.off()
+        logging.info(str(time.time()) + ", IR_2_exit")
+
+    def IR_3_exit(self):
+        self.event_list.append("IR_3_exit")
+        logging.info(str(time.time()) + ", IR_3_exit")
+
+    def IR_4_exit(self):
+        self.event_list.append("IR_4_exit")
+        logging.info(str(time.time()) + ", IR_4_exit")
+
+    def IR_5_exit(self):
+        self.event_list.append("IR_5_exit")
+        logging.info(str(time.time()) + ", IR_5_exit")
 
 # this is for the cue LEDs. BoxLED.value is the intensity value (PWM duty cycle, from 0 to 1)
 # currently. BoxLED.set_value is the saved intensity value that determines how bright the
@@ -491,7 +552,8 @@ def on(
 
 
 class Pump(object):
-    def __init__(self):
+    def __init__(self, session_info):
+        self.session_info = session_info
         self.pump1 = LED(19)
         self.pump2 = LED(20)
         self.pump3 = LED(21)
@@ -502,44 +564,73 @@ def __init__(self):
         # visualization
 
     def reward(self, which_pump, reward_size):
-        # coefficient_fit = np.array([8.78674242e-04, 7.33609848e-02, 1.47535000e+00]) # further calibration is needed
-        # coefficient_1 = coefficient_fit[-1]
-        # coefficient_2 = coefficient_fit[-2]
-        # coefficient_3 = coefficient_fit[-3] - reward_size
-        tube_fit = 0.11609 # ml/s
-        # discriminant = coefficient_2 ** 2 - 4 * coefficient_1 * coefficient_3
-        # # find solution, i.e. duration of pulse, by calculating the solution for the quadratic equation
-        # solution = np.array([(-coefficient_2 + np.sqrt(discriminant)) / (2 * coefficient_1),
-        #                      (-coefficient_2 - np.sqrt(discriminant)) / (2 * coefficient_1)])
-
-        # With two solution, get the positive value
-        # solution_positive = solution[(solution > 0).nonzero()[0][0]]
-        # round to the second decimal
-        # duration = round(solution_positive, 3) * (10**-3)
-
-        duration = round((reward_size/1000)/tube_fit, 3)
-        duration_vacuum = 0.5
+        # import coefficient from the session_information
+        coefficient_p1 = self.session_info["calibration_coefficient"]['1']
+        coefficient_p2 = self.session_info["calibration_coefficient"]['2']
+        coefficient_p3 = self.session_info["calibration_coefficient"]['3']
+        coefficient_p4 = self.session_info["calibration_coefficient"]['4']
+        duration_air = self.session_info['air_duration']
+        duration_vac = self.session_info["vacuum_duration"]
 
         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_" + str(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_" + str(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_" + str(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_" + str(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, 0.1, 1)
+            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_vacuum, 0.1, 1)
-            logging.info(";" + str(time.time()) + ";[reward];pump_vacuum")
\ No newline at end of file
+            self.pump_vacuum.blink(duration_vac, 0.1, 1)
+            logging.info(";" + str(time.time()) + ";[reward];pump_vacuum" + str(duration_vac))
+        elif which_pump == "key_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()) + ";[key];pump1_reward(reward_coeff: " + str(coefficient_p1) +
+                         ", reward_amount: " + str(reward_size) + "duration: " + str(duration) + ")")
+        elif which_pump == "key_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()) + ";[key];pump2_reward(reward_coeff: " + str(coefficient_p2) +
+                         ", reward_amount: " + str(reward_size) + "duration: " + str(duration) + ")")
+        elif which_pump == "key_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()) + ";[key];pump3_reward(reward_coeff: " + str(coefficient_p3) +
+                         ", reward_amount: " + str(reward_size) + "duration: " + str(duration) + ")")
+        elif which_pump == "key_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()) + ";[key];pump4_reward(reward_coeff: " + str(coefficient_p4) +
+                         ", reward_amount: " + str(reward_size) + "duration: " + str(duration) + ")")
+        elif which_pump == "key_air_puff":
+            self.pump_air.blink(duration_air, 0.1, 1)
+            self.reward_list.append(("air_puff", reward_size))
+            logging.info(";" + str(time.time()) + ";[key];pump4_reward_" + str(reward_size))
+        elif which_pump == "key_vacuum":
+            self.pump_vacuum.blink(duration_vac, 0.1, 1)
+            logging.info(";" + str(time.time()) + ";[key];pump_vacuum" + str(duration_vac))
\ No newline at end of file
diff --git a/camera/Video-Capture-Behavior.py b/essential/camera/Video-Capture-Behavior.py
similarity index 100%
rename from camera/Video-Capture-Behavior.py
rename to essential/camera/Video-Capture-Behavior.py
diff --git a/essential/camera/__init__.py b/essential/camera/__init__.py
new file mode 100644
index 0000000..8b13789
--- /dev/null
+++ b/essential/camera/__init__.py
@@ -0,0 +1 @@
+
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rename from picamera_library_modified/tests/conftest.py
rename to essential/picamera_library_modified/tests/conftest.py
diff --git a/picamera_library_modified/tests/test_array.py b/essential/picamera_library_modified/tests/test_array.py
similarity index 100%
rename from picamera_library_modified/tests/test_array.py
rename to essential/picamera_library_modified/tests/test_array.py
diff --git a/picamera_library_modified/tests/test_attr.py b/essential/picamera_library_modified/tests/test_attr.py
similarity index 100%
rename from picamera_library_modified/tests/test_attr.py
rename to essential/picamera_library_modified/tests/test_attr.py
diff --git a/picamera_library_modified/tests/test_capture.py b/essential/picamera_library_modified/tests/test_capture.py
similarity index 100%
rename from picamera_library_modified/tests/test_capture.py
rename to essential/picamera_library_modified/tests/test_capture.py
diff --git a/picamera_library_modified/tests/test_exc.py b/essential/picamera_library_modified/tests/test_exc.py
similarity index 100%
rename from picamera_library_modified/tests/test_exc.py
rename to essential/picamera_library_modified/tests/test_exc.py
diff --git a/picamera_library_modified/tests/test_misc.py b/essential/picamera_library_modified/tests/test_misc.py
similarity index 100%
rename from picamera_library_modified/tests/test_misc.py
rename to essential/picamera_library_modified/tests/test_misc.py
diff --git a/picamera_library_modified/tests/test_record.py b/essential/picamera_library_modified/tests/test_record.py
similarity index 100%
rename from picamera_library_modified/tests/test_record.py
rename to essential/picamera_library_modified/tests/test_record.py
diff --git a/picamera_library_modified/tests/test_streams.py b/essential/picamera_library_modified/tests/test_streams.py
similarity index 100%
rename from picamera_library_modified/tests/test_streams.py
rename to essential/picamera_library_modified/tests/test_streams.py
diff --git a/picamera_library_modified/tests/verify.py b/essential/picamera_library_modified/tests/verify.py
similarity index 100%
rename from picamera_library_modified/tests/verify.py
rename to essential/picamera_library_modified/tests/verify.py
diff --git a/pygame_matplotlib/__init__.py b/essential/pygame_matplotlib/__init__.py
similarity index 100%
rename from pygame_matplotlib/__init__.py
rename to essential/pygame_matplotlib/__init__.py
diff --git a/pygame_matplotlib/backend_pygame.py b/essential/pygame_matplotlib/backend_pygame.py
similarity index 100%
rename from pygame_matplotlib/backend_pygame.py
rename to essential/pygame_matplotlib/backend_pygame.py
diff --git a/pygame_matplotlib/gui_window.py b/essential/pygame_matplotlib/gui_window.py
similarity index 100%
rename from pygame_matplotlib/gui_window.py
rename to essential/pygame_matplotlib/gui_window.py
diff --git a/essential/scripts/__init__.py b/essential/scripts/__init__.py
new file mode 100644
index 0000000..8b13789
--- /dev/null
+++ b/essential/scripts/__init__.py
@@ -0,0 +1 @@
+
diff --git a/scripts/root_crontab.sh b/essential/scripts/root_crontab.sh
similarity index 100%
rename from scripts/root_crontab.sh
rename to essential/scripts/root_crontab.sh
diff --git a/scripts/user_crontab.sh b/essential/scripts/user_crontab.sh
similarity index 100%
rename from scripts/user_crontab.sh
rename to essential/scripts/user_crontab.sh
diff --git a/essential/sound/001-beep.wav b/essential/sound/001-beep.wav
new file mode 100644
index 0000000..4959964
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diff --git a/essential/sound/002-buzz.wav b/essential/sound/002-buzz.wav
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index 0000000..428916f
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diff --git a/essential/sound/003-buzz.wav b/essential/sound/003-buzz.wav
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diff --git a/essential/sound/004-white-noise-44-1-16bit.wav b/essential/sound/004-white-noise-44-1-16bit.wav
new file mode 100644
index 0000000..f0d50a8
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diff --git a/syringe_pump_c_code/main.c b/essential/syringe_pump_c_code/main.c
similarity index 100%
rename from syringe_pump_c_code/main.c
rename to essential/syringe_pump_c_code/main.c
diff --git a/syringe_pump_c_code/main.py b/essential/syringe_pump_c_code/main.py
similarity index 100%
rename from syringe_pump_c_code/main.py
rename to essential/syringe_pump_c_code/main.py
diff --git a/syringe_pump_c_code/main.so b/essential/syringe_pump_c_code/main.so
similarity index 100%
rename from syringe_pump_c_code/main.so
rename to essential/syringe_pump_c_code/main.so
diff --git a/syringe_pump_c_code/readme.md b/essential/syringe_pump_c_code/readme.md
similarity index 100%
rename from syringe_pump_c_code/readme.md
rename to essential/syringe_pump_c_code/readme.md
diff --git a/treadmill/Bounce2-master (1).zip b/essential/treadmill/Bounce2-master (1).zip
similarity index 100%
rename from treadmill/Bounce2-master (1).zip
rename to essential/treadmill/Bounce2-master (1).zip
diff --git a/treadmill/Treadmill.ino b/essential/treadmill/Treadmill.ino
similarity index 100%
rename from treadmill/Treadmill.ino
rename to essential/treadmill/Treadmill.ino
diff --git a/treadmill/Treadmill_20200302.ino b/essential/treadmill/Treadmill_20200302.ino
similarity index 100%
rename from treadmill/Treadmill_20200302.ino
rename to essential/treadmill/Treadmill_20200302.ino
diff --git a/treadmill/Treadmill_20211112.ino b/essential/treadmill/Treadmill_20211112.ino
similarity index 100%
rename from treadmill/Treadmill_20211112.ino
rename to essential/treadmill/Treadmill_20211112.ino
diff --git a/essential/treadmill/__init__.py b/essential/treadmill/__init__.py
new file mode 100644
index 0000000..8b13789
--- /dev/null
+++ b/essential/treadmill/__init__.py
@@ -0,0 +1 @@
+
diff --git a/treadmill/digitalWriteFast-master (1).zip b/essential/treadmill/digitalWriteFast-master (1).zip
similarity index 100%
rename from treadmill/digitalWriteFast-master (1).zip
rename to essential/treadmill/digitalWriteFast-master (1).zip
diff --git a/treadmill/readme.md b/essential/treadmill/readme.md
similarity index 100%
rename from treadmill/readme.md
rename to essential/treadmill/readme.md
diff --git a/treadmill/treadmill_current.ino b/essential/treadmill/treadmill_current.ino
similarity index 100%
rename from treadmill/treadmill_current.ino
rename to essential/treadmill/treadmill_current.ino
diff --git a/treadmill_distance.ino b/essential/treadmill/treadmill_distance.ino
similarity index 100%
rename from treadmill_distance.ino
rename to essential/treadmill/treadmill_distance.ino
diff --git a/treadmill_i2c.py b/essential/treadmill/treadmill_i2c.py
similarity index 100%
rename from treadmill_i2c.py
rename to essential/treadmill/treadmill_i2c.py
diff --git a/video_acquisition/README.md b/essential/video_acquisition/README.md
similarity index 100%
rename from video_acquisition/README.md
rename to essential/video_acquisition/README.md
diff --git a/video_acquisition/StartAcquisition_gpio.py b/essential/video_acquisition/StartAcquisition_gpio.py
similarity index 100%
rename from video_acquisition/StartAcquisition_gpio.py
rename to essential/video_acquisition/StartAcquisition_gpio.py
diff --git a/video_acquisition/VideoCapture.py b/essential/video_acquisition/VideoCapture.py
similarity index 100%
rename from video_acquisition/VideoCapture.py
rename to essential/video_acquisition/VideoCapture.py
diff --git a/essential/video_acquisition/__init__.py b/essential/video_acquisition/__init__.py
new file mode 100644
index 0000000..8b13789
--- /dev/null
+++ b/essential/video_acquisition/__init__.py
@@ -0,0 +1 @@
+
diff --git a/video_acquisition/control_acquisition.py b/essential/video_acquisition/control_acquisition.py
similarity index 100%
rename from video_acquisition/control_acquisition.py
rename to essential/video_acquisition/control_acquisition.py
diff --git a/video_acquisition/killrecording.py b/essential/video_acquisition/killrecording.py
similarity index 100%
rename from video_acquisition/killrecording.py
rename to essential/video_acquisition/killrecording.py
diff --git a/video_acquisition/start_acquisition.py b/essential/video_acquisition/start_acquisition.py
similarity index 100%
rename from video_acquisition/start_acquisition.py
rename to essential/video_acquisition/start_acquisition.py
diff --git a/video_acquisition/start_acquisition_old.py b/essential/video_acquisition/start_acquisition_old.py
similarity index 100%
rename from video_acquisition/start_acquisition_old.py
rename to essential/video_acquisition/start_acquisition_old.py
diff --git a/start_preview.py b/essential/video_acquisition/start_preview.py
similarity index 100%
rename from start_preview.py
rename to essential/video_acquisition/start_preview.py
diff --git a/video_acquisition/stop_acquisition.sh b/essential/video_acquisition/stop_acquisition.sh
similarity index 100%
rename from video_acquisition/stop_acquisition.sh
rename to essential/video_acquisition/stop_acquisition.sh
diff --git a/stop_preview.sh b/essential/video_acquisition/stop_preview.sh
similarity index 100%
rename from stop_preview.sh
rename to essential/video_acquisition/stop_preview.sh
diff --git a/stop_video b/essential/video_acquisition/stop_video
similarity index 100%
rename from stop_video
rename to essential/video_acquisition/stop_video
diff --git a/essential/visual_stimuli/__init__.py b/essential/visual_stimuli/__init__.py
new file mode 100644
index 0000000..8b13789
--- /dev/null
+++ b/essential/visual_stimuli/__init__.py
@@ -0,0 +1 @@
+
diff --git a/visual_stimuli/readme.md b/essential/visual_stimuli/readme.md
similarity index 100%
rename from visual_stimuli/readme.md
rename to essential/visual_stimuli/readme.md
diff --git a/visual_stimuli/vstest.py b/essential/visual_stimuli/vstest.py
similarity index 100%
rename from visual_stimuli/vstest.py
rename to essential/visual_stimuli/vstest.py
diff --git a/visualstim.py b/essential/visualstim.py
similarity index 100%
rename from visualstim.py
rename to essential/visualstim.py
diff --git a/behavbox_v2.py b/obsolete/behavbox_v2.py
similarity index 100%
rename from behavbox_v2.py
rename to obsolete/behavbox_v2.py
diff --git a/fake_session_info.py b/obsolete/fake_session_info.py
similarity index 100%
rename from fake_session_info.py
rename to obsolete/fake_session_info.py
diff --git a/headfixed2FC_task.py b/obsolete/headfixed2FC_task_old.py
similarity index 93%
rename from headfixed2FC_task.py
rename to obsolete/headfixed2FC_task_old.py
index 9b28b8a..996b29b 100644
--- a/headfixed2FC_task.py
+++ b/obsolete/headfixed2FC_task_old.py
@@ -123,8 +123,8 @@ def __init__(self, **kwargs):  # name and session_info should be provided as kwa
         self.wrong_choice_error = False
         self.multiple_choice_error = False
         self.error_repeat = False
-        self.reward_time_start = None # for reward_available state time keeping purpose
-        self.reward_time = 10 # sec. could be incorporate into the session_info; available time for reward
+        self.reward_time_start = None  # for reward_available state time keeping purpose
+        self.reward_time = 10  # sec. could be incorporate into the session_info; available time for reward
         self.reward_times_up = False
 
         self.block_count = 0
@@ -160,6 +160,7 @@ def __init__(self, **kwargs):  # name and session_info should be provided as kwa
         # session_statistics
         self.total_reward = 0
         self.correct_trial_in_block = 0
+
     ########################################################################
     # functions called when state transitions occur
     ########################################################################
@@ -205,7 +206,6 @@ def run(self):
                         self.restart()
             # first detect the lick signal:
             cue_state = self.current_card[0]
-            # side_choice = self.current_card[2]
             side_mice = None
             if self.event_name == "left_entry":
                 side_mice = 'left'
@@ -222,34 +222,35 @@ def run(self):
                 if cue_state == 'all':
                     side_choice = side_mice
                     if side_choice == 'left':
-                        reward_size = self.current_card[2][0]
+                        left_reward = self.session_info['reward_size'][self.current_card[2][0]]
+                        reward_size = random.uniform(left_reward - self.session_info['reward_deviation'],
+                                                     left_reward + self.session_info['reward_deviation'])
                         pump_num = self.current_card[3][0]
                     elif side_choice == 'right':
-                        reward_size = self.current_card[2][1]
+                        right_reward = self.session_info['reward_size'][self.current_card[2][1]]
+                        reward_size = random.uniform(right_reward - self.session_info['reward_deviation'],
+                                                     right_reward + self.session_info['reward_deviation'])
                         pump_num = self.current_card[3][1]
                 else:
                     side_choice = self.current_card[1]
-                    reward_size = self.current_card[2]
+                    forced_reward = self.session_info['reward_size'][self.current_card[2]]
+                    reward_size = random.uniform(forced_reward - self.session_info['reward_deviation'],
+                                                 forced_reward + self.session_info['reward_deviation'])
                     pump_num = self.current_card[3]
                 if side_mice == side_choice:  # if the animal chose correctly
                     print("Number of lick detected: " + str(self.lick_count))
                     if self.lick_count == 0:  # if this is the first lick
-                        # self.side_mice_buffer = side_mice
-                        self.pump.reward(pump_num, self.session_info["reward_size"][reward_size])
+                        self.pump.reward(pump_num, reward_size)
                         self.total_reward += 1
                         self.correct_trial_in_block += 1
                         self.reward_time_start = time.time()
                         print("Reward time start" + str(self.reward_time_start))
                     self.lick_count += 1
-
                 elif self.side_mice_buffer:
                     if self.lick_count == 0:
                         self.check_cue('sound2')
                         self.wrong_choice_error = True
                         self.restart()
-                    #else:  # wrong side - wrong_choice error
-                    #    self.multiple_choice_error = True
-                    #    self.restart()
 
         # look for keystrokes
         self.box.check_keybd()
@@ -331,11 +332,6 @@ def exit_reward_available(self):
             self.error_repeat = True
             self.error_list.append('wrong_choice_error')
             self.wrong_choice_error = False
-        #elif self.multiple_choice_error:
-        #    logging.info(";" + str(time.time()) + ";[error];multiple_choice_error;" + str(self.error_repeat))
-        #    self.error_repeat = False
-        #    self.error_list.append('multiple_choice_error')
-        #    self.multiple_choice_error = False
         elif self.lick_count == 0:
             logging.info(";" + str(time.time()) + ";[error];no_choice_error;" + str(self.error_repeat))
             self.error_repeat = True
@@ -360,16 +356,13 @@ def check_cue(self, cue):
             # self.LED_blink = True
             self.box.cueLED2.on()
             logging.info(";" + str(time.time()) + ";[cue];cueLED_R_on;" + str(self.error_repeat))
-        elif cue =='all':
-            #self.box.cueLED1.blink(0.2, 0.1)
+        elif cue == 'all':
             self.box.cueLED1.on()
             self.box.cueLED2.on()
             logging.info(";" + str(time.time()) + ";[cue];LED_L+R_on; " + str(self.error_repeat))
 
     def cue_off(self, cue):
         if cue == 'all':
-            #self.box.sound1.off()
-            #self.box.sound2.off()
             self.box.cueLED1.off()
             self.box.cueLED2.off()
         elif cue == 'sound1':
@@ -380,7 +373,6 @@ def cue_off(self, cue):
             logging.info(";" + str(time.time()) + ";[cue];cue_sound2_off;" + str(self.error_repeat))
         elif cue == 'LED_L':
             self.box.cueLED1.off()
-            #self.LED_blink = False
             logging.info(";" + str(time.time()) + ";[cue];cueLED1_off;" + str(self.error_repeat))
         elif cue == 'LED_R':
             self.box.cueLED2.off()
@@ -406,8 +398,6 @@ def update_plot_error(self):
         ticks = range(len(counts))
         fig, ax = plt.subplots(1, 1, )
         ax.bar(ticks, counts, align='center', tick_label=labels)
-        # plt.xticks(ticks, labels)
-        # plt.title(session_name)
         ax = plt.gca()
         ax.set_xticks(ticks, labels)
         ax.set_xticklabels(labels=labels, rotation=70)
diff --git a/headfixed_task.py b/obsolete/headfixed_task_old.py
similarity index 100%
rename from headfixed_task.py
rename to obsolete/headfixed_task_old.py
diff --git a/lick_task.py b/obsolete/lick_task.py
similarity index 100%
rename from lick_task.py
rename to obsolete/lick_task.py
diff --git a/pump_task.py b/obsolete/pump_task.py
similarity index 100%
rename from pump_task.py
rename to obsolete/pump_task.py
diff --git a/record_run_test.py b/obsolete/record_run_test.py
similarity index 100%
rename from record_run_test.py
rename to obsolete/record_run_test.py
diff --git a/run_flip_task.py b/obsolete/run_flip_task.py
similarity index 100%
rename from run_flip_task.py
rename to obsolete/run_flip_task.py
diff --git a/run_headfixed2FC_task.py b/obsolete/run_headfixed2FC_task.py
similarity index 100%
rename from run_headfixed2FC_task.py
rename to obsolete/run_headfixed2FC_task.py
diff --git a/run_headfixed_task.py b/obsolete/run_headfixed_task.py
similarity index 100%
rename from run_headfixed_task.py
rename to obsolete/run_headfixed_task.py
diff --git a/run_lick_task.py b/obsolete/run_lick_task.py
similarity index 100%
rename from run_lick_task.py
rename to obsolete/run_lick_task.py
diff --git a/run_season_task.py b/obsolete/run_season_task.py
similarity index 100%
rename from run_season_task.py
rename to obsolete/run_season_task.py
diff --git a/run_soyoun_task.py b/obsolete/run_soyoun_task.py
similarity index 100%
rename from run_soyoun_task.py
rename to obsolete/run_soyoun_task.py
diff --git a/run_visualization_task.py b/obsolete/run_visualization_task.py
similarity index 100%
rename from run_visualization_task.py
rename to obsolete/run_visualization_task.py
diff --git a/run_walk_task.py b/obsolete/run_walk_task.py
similarity index 100%
rename from run_walk_task.py
rename to obsolete/run_walk_task.py
diff --git a/session_info_headfixed.py b/obsolete/session_info_headfixed.py
similarity index 100%
rename from session_info_headfixed.py
rename to obsolete/session_info_headfixed.py
diff --git a/session_info_headfixed2FC.py b/obsolete/session_info_headfixed2FC.py
similarity index 85%
rename from session_info_headfixed2FC.py
rename to obsolete/session_info_headfixed2FC.py
index 54c165c..8136923 100644
--- a/session_info_headfixed2FC.py
+++ b/obsolete/session_info_headfixed2FC.py
@@ -55,6 +55,7 @@
 session_info['choice'] = ['right', 'left']  # lick port
 session_info['reward'] = ['small', 'large']  # reward size
 session_info['reward_size'] = {'small': 5, 'large': 10}
+session_info['reward_deviation'] = 1
 
 if session_info['phase'] == 1:
     session_info['reward_size'] = {'small': 10, 'large': 10}
@@ -74,3 +75,14 @@
 session_info['consecutive_control'] = False
 if session_info['consecutive_control']:
     session_info['consecutive_max'] = 3
+
+session_info["calibration_coefficient"] = {}
+
+session_info["calibration_coefficient"]['1'] = [0.13, 0]  # highest power first
+session_info["calibration_coefficient"]['2'] = [0.13, 0]
+session_info["calibration_coefficient"]['3'] = [0.13, 0.0]
+session_info["calibration_coefficient"]['4'] = [0.13, 0.0]
+
+session_info['air_duration'] = 0
+session_info["vacuum_duration"] = 1
+session_info["key_reward_amount"] = 5
\ No newline at end of file
diff --git a/session_info_walk.py b/obsolete/session_info_walk.py
similarity index 100%
rename from session_info_walk.py
rename to obsolete/session_info_walk.py
diff --git a/soyoun_task.py b/obsolete/soyoun_task.py
similarity index 100%
rename from soyoun_task.py
rename to obsolete/soyoun_task.py
diff --git a/task_information_headfixed.py b/obsolete/task_information_headfixed.py
similarity index 100%
rename from task_information_headfixed.py
rename to obsolete/task_information_headfixed.py
diff --git a/task_information_headfixed2FC.py b/obsolete/task_information_headfixed2FC.py
similarity index 100%
rename from task_information_headfixed2FC.py
rename to obsolete/task_information_headfixed2FC.py
diff --git a/task_information_lick.py b/obsolete/task_information_lick.py
similarity index 100%
rename from task_information_lick.py
rename to obsolete/task_information_lick.py
diff --git a/task_information_phase_1.py b/obsolete/task_information_phase_1.py
similarity index 100%
rename from task_information_phase_1.py
rename to obsolete/task_information_phase_1.py
diff --git a/test_session_info.py b/obsolete/test_session_info.py
similarity index 100%
rename from test_session_info.py
rename to obsolete/test_session_info.py
diff --git a/testing_visualstim.py b/obsolete/testing_visualstim.py
similarity index 100%
rename from testing_visualstim.py
rename to obsolete/testing_visualstim.py
diff --git a/visualization_task.py b/obsolete/visualization_task.py
similarity index 100%
rename from visualization_task.py
rename to obsolete/visualization_task.py
diff --git a/walk_task.py b/obsolete/walk_task.py
similarity index 100%
rename from walk_task.py
rename to obsolete/walk_task.py
diff --git a/syringe_pump_pygame_debug.py b/syringe_pump_pygame_debug.py
deleted file mode 100644
index a2dfbcc..0000000
--- a/syringe_pump_pygame_debug.py
+++ /dev/null
@@ -1,38 +0,0 @@
-import pygame
-from behavbox import Pump
-import numpy as np
-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)
\ No newline at end of file
diff --git a/EFO_task/EFO_task.py b/task_protocol/EFO_task/EFO_task.py
similarity index 98%
rename from EFO_task/EFO_task.py
rename to task_protocol/EFO_task/EFO_task.py
index 4eaddd7..5b86cde 100644
--- a/EFO_task/EFO_task.py
+++ b/task_protocol/EFO_task/EFO_task.py
@@ -26,7 +26,9 @@
     }
 )
 # all modules above this line will have logging disabled
-
+# updated with reorganization (on 7/11/2023)
+import sys
+sys.path.insert(0,'/home/pi/RPi4_behavior_boxes/essential')
 import behavbox
 
 # adding timing capability to the state machine
diff --git a/task_protocol/EFO_task/__init__.py b/task_protocol/EFO_task/__init__.py
new file mode 100644
index 0000000..8b13789
--- /dev/null
+++ b/task_protocol/EFO_task/__init__.py
@@ -0,0 +1 @@
+
diff --git a/task_protocol/__init__.py b/task_protocol/__init__.py
new file mode 100644
index 0000000..8b13789
--- /dev/null
+++ b/task_protocol/__init__.py
@@ -0,0 +1 @@
+
diff --git a/task_protocol/headfixed_task/__init__.py b/task_protocol/headfixed_task/__init__.py
new file mode 100644
index 0000000..8b13789
--- /dev/null
+++ b/task_protocol/headfixed_task/__init__.py
@@ -0,0 +1 @@
+
diff --git a/task_protocol/headfixed_task/headfixed_independent_reward_task.py b/task_protocol/headfixed_task/headfixed_independent_reward_task.py
new file mode 100644
index 0000000..9484671
--- /dev/null
+++ b/task_protocol/headfixed_task/headfixed_independent_reward_task.py
@@ -0,0 +1,471 @@
+# python3: headfixed_task.py
+"""
+author: tian qiu & Soyoun Kim
+date: 2023-02-16
+name: headfixed2FC_task.py
+goal: model_free reinforcement learning behavioral training task structure
+description:
+    an updated test version of headfixed_task.py & add foraging reward condition
+
+"""
+import importlib
+from transitions import Machine
+from transitions import State
+from transitions.extensions.states import add_state_features, Timeout
+import pysistence, collections
+from icecream import ic
+import logging
+import time
+from datetime import datetime
+import os
+from gpiozero import PWMLED, LED, Button
+from colorama import Fore, Style
+import logging.config
+from time import sleep
+import random
+import threading
+import matplotlib
+import matplotlib.pyplot as plt
+import matplotlib.figure as fg
+import numpy as np
+
+logging.config.dictConfig(
+    {
+        "version": 1,
+        "disable_existing_loggers": True,
+    }
+)
+# all modules above this line will have logging disabled
+
+import sys
+sys.path.insert(0,'/home/pi/RPi4_behavior_boxes/essential')
+import behavbox
+
+
+# adding timing capability to the state machine
+@add_state_features(Timeout)
+class TimedStateMachine(Machine):
+    pass
+
+
+class HeadfixedIndependentRewardTask(object):
+    # Define states. States where the animals is waited to make their decision
+
+    def __init__(self, **kwargs):  # name and session_info should be provided as kwargs
+
+        # if no name or session, make fake ones (for testing purposes)
+        if kwargs.get("name", None) is None:
+            self.name = "name"
+            print(
+                Fore.RED
+                + Style.BRIGHT
+                + "Warning: no name supplied; making fake one"
+                + Style.RESET_ALL
+            )
+        else:
+            self.name = kwargs.get("name", None)
+
+        if kwargs.get("session_info", None) is None:
+            print(
+                Fore.RED
+                + Style.BRIGHT
+                + "Warning: no session_info supplied; making fake one"
+                + Style.RESET_ALL
+            )
+            from fake_session_info import fake_session_info
+
+            self.session_info = fake_session_info
+        else:
+            self.session_info = kwargs.get("session_info", None)
+        ic(self.session_info)
+
+        # initialize the state machine
+        self.states = [
+            State(name='standby',
+                  on_enter=["enter_standby"],
+                  on_exit=["exit_standby"]),
+            Timeout(name="initiate",
+                    on_enter=["enter_initiate"],
+                    on_exit=["exit_initiate"],
+                    timeout=self.session_info["initiation_timeout"],
+                    on_timeout=["restart"]),
+            Timeout(name='cue_state',
+                    on_enter=["enter_cue_state"],
+                    on_exit=["exit_cue_state"],
+                    timeout=self.session_info["cue_timeout"],
+                    on_timeout=["restart"]),
+            Timeout(name='reward_available',
+                    on_enter=["enter_reward_available"],
+                    on_exit=["exit_reward_available"],
+                    timeout=self.session_info["wait_for_choice"],
+                    on_timeout=["restart"])
+        ]
+        self.transitions = [
+            ['start_trial', 'standby', 'initiate'],
+            ['start_cue', 'initiate', 'cue_state'],
+            ['evaluate_reward', 'cue_state', 'reward_available'],
+            ['restart', ['initiate', 'cue_state', 'reward_available'], 'standby']
+        ]
+
+        self.machine = TimedStateMachine(
+            model=self,
+            states=self.states,
+            transitions=self.transitions,
+            initial='standby'
+        )
+        self.trial_running = False
+
+        # trial statistics
+        self.correct_trial_number = 0
+        self.actual_trial_number = 0
+        self.error_count = 0
+        self.error_list = []
+        self.early_lick_error = False
+        self.initiate_error = False
+        self.cue_state_error = False
+        self.wrong_choice_error = True
+        self.multiple_choice_error = False
+        self.error_repeat = False
+
+        self.pump_num = None
+        self.reward_size = None
+        self.current_reward = None
+        self.reward_check = False
+        self.reward_size_offset = self.session_info['reward_size_offset']
+
+        self.block_count = 0
+        self.blocknumber = self.session_info["block_number"]
+        self.current_card = None
+        self.left_poke_count = 0
+        self.right_poke_count = 0
+        self.timeline_left_poke = []
+        self.left_poke_count_list = []
+        self.timeline_right_poke = []
+        self.right_poke_count_list = []
+        self.event_name = ""
+        # initialize behavior box
+        self.box = behavbox.BehavBox(self.session_info)
+        self.pump = self.box.pump
+
+        self.treadmill = self.box.treadmill
+
+        self.distance_initiation = self.session_info['treadmill_setup']['distance_initiation']
+        self.distance_cue = self.session_info['treadmill_setup']['distance_cue']
+        self.distance_buffer = None
+        self.distance_diff = 0
+
+        # for foragaing parameters
+        self.side_choice = None  # whether free choice is left or right
+        self.cue_state = None
+
+        # for refining the lick detection
+        self.lick_count = 0
+        self.side_mice_buffer = None
+        self.LED_blink = False
+        try:
+            self.lick_threshold = self.session_info["lick_threshold"]
+        except:
+            print("No lick_threshold defined in session_info. Therefore, default defined as 2 \n")
+            self.lick_threshold = 1
+
+        # session_statistics
+        self.total_reward = 0
+
+    ########################################################################
+    # functions called when state transitions occur
+    ########################################################################
+    def run(self):
+        if self.box.event_list:
+            self.event_name = self.box.event_list.popleft()
+        else:
+            self.event_name = ""
+        # there can only be lick during the reward available state
+        # if lick detected prior to reward available state
+        # the trial will restart and transition to standby
+        if self.event_name is "left_entry" or self.event_name == "right_entry":
+            # print("EVENT NAME !!!!!! " + self.event_name)
+            if self.state == "reward_available" or self.state == "standby" or self.state == "initiate":
+                pass
+            else:
+                self.early_lick_error = True
+                self.error_repeat = True
+                self.restart()
+        if self.state == "standby":
+            pass
+        elif self.state == "initiate":
+            self.distance_diff = self.get_distance() - self.distance_buffer
+            if self.distance_diff >= self.distance_initiation:
+                self.initiate_error = False
+                self.start_cue()
+            else:
+                self.initiate_error = True
+        elif self.state == "cue_state":
+            self.distance_diff = self.get_distance() - self.distance_buffer
+            if self.distance_diff >= self.distance_cue:
+                self.cue_state_error = False
+                self.evaluate_reward()
+            else:
+                self.cue_state_error = True
+        elif self.state == "reward_available":
+            cue_state = self.current_card[0]
+            side_mice = None
+            if self.event_name == "left_entry":
+                side_mice = 'left'
+                self.left_poke_count += 1
+                self.left_poke_count_list.append(self.left_poke_count)
+                self.timeline_left_poke.append(time.time())
+            elif self.event_name == "right_entry":
+                side_mice = 'right'
+                self.right_poke_count += 1
+                self.right_poke_count_list.append(self.right_poke_count)
+                self.timeline_right_poke.append(time.time())
+            if side_mice:
+                self.side_mice_buffer = side_mice
+                self.cue_state = cue_state # cue state for foraging
+                if cue_state == 'all':
+                    side_choice = side_mice
+                    if side_choice == 'left':
+                        self.pump_num = self.current_card[2][0]
+                        self.reward_size = self.current_reward[0]
+                        print("self.current_reward[0]: " + str(self.current_reward[0]))
+                    elif side_choice == 'right':
+                        self.pump_num = self.current_card[2][1]
+                        self.reward_size = self.current_reward[1]
+                        print("self.current_reward[0]: " + str(self.current_reward[1]))
+                elif cue_state == 'LED_L':
+                    side_choice = self.current_card[1]
+                    self.pump_num = self.current_card[2]
+                    self.reward_size = self.current_reward[0]
+                elif cue_state == 'LED_R':
+                    side_choice = self.current_card[1]
+                    self.pump_num = self.current_card[2]
+                    self.reward_size = self.current_reward[1]
+                print("!!!!!!!!CUE_STATE: " + str(cue_state))
+                if side_mice == side_choice:  # if the animal chose correctly
+                    self.side_mice_buffer = side_mice
+                    if side_mice == side_choice:  # if the animal chose correctly
+                        if self.lick_count == 0:  # if this is the first lick
+                            self.side_choice = side_choice # foraging task
+                            self.wrong_choice_error = False
+                            self.reward_check = True
+                            self.lick_count += 1
+                            self.restart()
+                elif self.side_mice_buffer:
+                    if self.lick_count == 0:
+                        self.wrong_choice_error = True
+                        self.lick_count += 1
+                        self.restart()
+
+        # look for keystrokes
+        self.box.check_keybd()
+
+    def enter_standby(self):
+        logging.info(";" + str(time.time()) + ";[transition];enter_standby;" + str(self.error_repeat))
+        self.update_plot_choice()
+        # self.update_plot_error()
+        self.trial_running = False
+        # self.reward_error = False
+        if self.early_lick_error:
+            self.error_list.append("early_lick_error")
+            logging.info(";" + str(time.time()) + ";[error];early_lick_error;" + str(self.error_repeat))
+            self.check_cue('sound2')
+            self.early_lick_error = False
+        print(str(time.time()) + ", Total reward up till current session: " + str(self.total_reward))
+        logging.info(";" + str(time.time()) + ";[trial];trial_" + str(self.actual_trial_number) + ";" + str(self.error_repeat))
+
+    def exit_standby(self):
+        logging.info(";" + str(time.time()) + ";[transition];exit_standby;" + str(self.error_repeat))
+        self.lick_count = 0
+        self.side_mice_buffer = None
+        self.box.event_list.clear()
+        pass
+
+    def enter_initiate(self):
+        # print("!!!!!!!!!!!event name is " + self.event_name) # for debugging purposes
+        # check error_repeat
+        logging.info(";" + str(time.time()) + ";[transition];enter_initiate;" + str(self.error_repeat))
+        self.check_cue('sound1')
+        self.trial_running = True
+        # wait for treadmill signal and process the treadmill signal
+        self.distance_buffer = self.get_distance()
+        logging.info(
+            ";" + str(time.time()) + ";[treadmill];" + str(self.distance_buffer) + ";" + str(self.error_repeat))
+
+    def exit_initiate(self):
+        # check the flag to see whether to shuffle or keep the original card
+        logging.info(";" + str(time.time()) + ";[transition];exit_initiate;" + str(self.error_repeat))
+        print("EVENT NAME: " + str(self.box.event_list))
+        self.cue_off('sound1')
+        if self.initiate_error:
+            self.error_list.append('initiate_error')
+            self.error_repeat = True
+            logging.info(";" + str(time.time()) + ";[error];initiate_error;" + str(self.error_repeat))
+            self.error_count += 1
+
+    def enter_cue_state(self):
+        logging.info(";" + str(time.time()) + ";[transition];enter_cue_state;" + str(self.error_repeat))
+        # turn on the cue according to the current card
+        self.check_cue(self.current_card[0])
+        # wait for treadmill signal and process the treadmill signal
+        self.distance_buffer = self.get_distance()
+        logging.info(
+            ";" + str(time.time()) + ";[treadmill];" + str(self.distance_buffer) + ";" + str(self.error_repeat))
+
+    def exit_cue_state(self):
+        logging.info(";" + str(time.time()) + ";[transition];exit_cue_state;" + str(self.error_repeat))
+        self.cue_off(self.current_card[0])
+        if not self.early_lick_error:
+            if self.cue_state_error:
+                self.check_cue("sound2")
+                self.error_list.append('cue_state_error')
+                self.error_repeat = True
+                logging.info(";" + str(time.time()) + ";[error];cue_state_error;" + str(self.error_repeat))
+                self.error_count += 1
+                self.cue_state_error = False
+
+    def enter_reward_available(self):
+        logging.info(";" + str(time.time()) + ";[transition];enter_reward_available;" + str(self.error_repeat))
+        print(str(time.time()) + ", " + str(self.actual_trial_number) + ", cue_state distance satisfied")
+
+    def exit_reward_available(self):
+        logging.info(";" + str(time.time()) + ";[transition];exit_reward_available;" + str(self.error_repeat))
+        if self.lick_count == 0:
+            logging.info(";" + str(time.time()) + ";[error];no_choice_error;" + str(self.error_repeat))
+            self.check_cue('sound2')
+            self.error_repeat = True
+            self.error_count += 1
+            self.error_list.append('no_choice_error')
+        elif self.wrong_choice_error:
+            logging.info(";" + str(time.time()) + ";[error];wrong_choice_error;" + str(self.error_repeat))
+            self.check_cue('sound2')
+            self.error_repeat = True
+            self.error_count += 1
+            self.error_list.append('wrong_choice_error')
+        elif self.reward_check:
+            logging.info(";" + str(time.time()) + ";[error];correct_trial;" + str(self.error_repeat))
+            self.pump.reward(self.pump_num, self.reward_size)
+            self.error_repeat = False
+            self.total_reward += 1
+            self.reward_check = False
+            self.error_list.append('correct_trial')
+        self.pump_num = None
+        self.reward_size = None
+        self.wrong_choice_error = False
+
+
+    def check_cue(self, cue):
+        if cue == 'sound1':
+            logging.info(";" + str(time.time()) + ";[cue];cue_sound1_on;" + str(self.error_repeat))
+            self.box.sound1.on()
+        if cue == 'sound2':
+            logging.info(";" + str(time.time()) + ";[cue];cue_sound2_on;" + str(self.error_repeat))
+            self.box.sound2.blink(1, 0.1, 1)
+        elif cue == 'LED_L':
+            self.box.cueLED1.on()
+            logging.info(";" + str(time.time()) + ";[cue];cueLED_L_on;" + str(self.error_repeat))
+        elif cue == 'LED_R':
+            self.box.cueLED2.on()
+            logging.info(";" + str(time.time()) + ";[cue];cueLED_R_on;" + str(self.error_repeat))
+        elif cue == 'all':
+            self.box.cueLED1.on()
+            self.box.cueLED2.on()
+            logging.info(";" + str(time.time()) + ";[cue];LED_L+R_on; " + str(self.error_repeat))
+
+    def cue_off(self, cue):
+        if cue == 'all':
+            self.box.cueLED1.off()
+            self.box.cueLED2.off()
+        elif cue == 'sound1':
+            self.box.sound1.off()
+            logging.info(";" + str(time.time()) + ";[cue];cue_sound1_off;" + str(self.error_repeat))
+        elif cue == 'sound2':
+            self.box.sound2.off()
+            logging.info(";" + str(time.time()) + ";[cue];cue_sound2_off;" + str(self.error_repeat))
+        elif cue == 'LED_L':
+            self.box.cueLED1.off()
+            logging.info(";" + str(time.time()) + ";[cue];cueLED1_off;" + str(self.error_repeat))
+        elif cue == 'LED_R':
+            self.box.cueLED2.off()
+            logging.info(";" + str(time.time()) + ";[cue];cueLED2_off;" + str(self.error_repeat))
+
+    def get_distance(self):
+        try:
+            distance = self.treadmill.distance_cm
+        except Exception as e:
+            logging.info(";" + str(time.time()) + ";[system_error];" + str(e) + ";" + str(self.error_repeat))
+            self.treadmill = self.box.treadmill
+            distance = self.treadmill.distance_cm
+        return distance
+
+    def update_plot(self):
+        fig, axes = plt.subplots(1, 1, )
+        axes.plot([1, 2], [1, 2], color='green', label='test')
+        self.box.check_plot(fig)
+
+    def update_plot_error(self):
+        error_event = self.error_list
+        labels, counts = np.unique(error_event, return_counts=True)
+        ticks = range(len(counts))
+        fig, ax = plt.subplots(1, 1, )
+        ax.bar(ticks, counts, align='center', tick_label=labels)
+        ax = plt.gca()
+        ax.set_xticks(ticks, labels)
+        ax.set_xticklabels(labels=labels, rotation=70)
+
+        self.box.check_plot(fig)
+
+    def update_plot_choice(self, save_fig=False):
+        trajectory_left = self.left_poke_count_list
+        time_left = self.timeline_left_poke
+        trajectory_right = self.right_poke_count_list
+        time_right = self.timeline_right_poke
+        fig, ax = plt.subplots(1, 1, )
+        print(type(fig))
+
+        ax.plot(time_left, trajectory_left, color='b', marker="o", label='left_lick_trajectory')
+        ax.plot(time_right, trajectory_right, color='r', marker="o", label='right_lick_trajectory')
+        if save_fig:
+            plt.savefig(self.session_info['basedir'] + "/" + self.session_info['basename'] + "/" + \
+                        self.session_info['basename'] + "_choice_plot" + '.png')
+        self.box.check_plot(fig)
+
+    def integrate_plot(self, save_fig=False):
+
+        fig, ax = plt.subplots(2, 1)
+
+        trajectory_left = self.left_poke_count_list
+        time_left = self.timeline_left_poke
+        trajectory_right = self.right_poke_count_list
+        time_right = self.timeline_right_poke
+        print(type(fig))
+
+        ax[0].plot(time_left, trajectory_left, color='b', marker="o", label='left_lick_trajectory')
+        ax[0].plot(time_right, trajectory_right, color='r', marker="o", label='right_lick_trajectory')
+
+        error_event = self.error_list
+        labels, counts = np.unique(error_event, return_counts=True)
+        ticks = range(len(counts))
+        ax[1].bar(ticks, counts, align='center', tick_label=labels)
+        # plt.xticks(ticks, labels)
+        # plt.title(session_name)
+        ax[1] = plt.gca()
+        ax[1].set_xticks(ticks, labels)
+        ax[1].set_xticklabels(labels=labels, rotation=70)
+
+        if save_fig:
+            plt.savefig(self.session_info['basedir'] + "/" + self.session_info['basename'] + "/" + \
+                        self.session_info['basename'] + "_summery" + '.png')
+        self.box.check_plot(fig)
+
+    ########################################################################
+    # methods to start and end the behavioral session
+    ########################################################################
+
+    def start_session(self):
+        ic("TODO: start video")
+        self.box.video_start()
+
+    def end_session(self):
+        ic("TODO: stop video")
+        self.update_plot_choice(save_fig=True)
+        self.box.video_stop()
\ No newline at end of file
diff --git a/task_protocol/headfixed_task/headfixed_task.py b/task_protocol/headfixed_task/headfixed_task.py
new file mode 100644
index 0000000..76c6da0
--- /dev/null
+++ b/task_protocol/headfixed_task/headfixed_task.py
@@ -0,0 +1,470 @@
+# python3: headfixed_task.py
+"""
+author: tian qiu & Soyoun Kim
+date: 2023-02-16
+name: headfixed2FC_task.py
+goal: model_free reinforcement learning behavioral training task structure
+description:
+    an updated test version of headfixed_task.py & add foraging reward condition
+
+"""
+import importlib
+from transitions import Machine
+from transitions import State
+from transitions.extensions.states import add_state_features, Timeout
+import pysistence, collections
+from icecream import ic
+import logging
+import time
+from datetime import datetime
+import os
+from gpiozero import PWMLED, LED, Button
+from colorama import Fore, Style
+import logging.config
+from time import sleep
+import random
+import threading
+import matplotlib
+import matplotlib.pyplot as plt
+import matplotlib.figure as fg
+import numpy as np
+
+logging.config.dictConfig(
+    {
+        "version": 1,
+        "disable_existing_loggers": True,
+    }
+)
+# all modules above this line will have logging disabled
+import sys
+sys.path.insert(0,'/home/pi/RPi4_behavior_boxes/essential')
+import behavbox
+
+
+# adding timing capability to the state machine
+@add_state_features(Timeout)
+class TimedStateMachine(Machine):
+    pass
+
+
+class HeadfixedTask(object):
+    # Define states. States where the animals is waited to make their decision
+
+    def __init__(self, **kwargs):  # name and session_info should be provided as kwargs
+
+        # if no name or session, make fake ones (for testing purposes)
+        if kwargs.get("name", None) is None:
+            self.name = "name"
+            print(
+                Fore.RED
+                + Style.BRIGHT
+                + "Warning: no name supplied; making fake one"
+                + Style.RESET_ALL
+            )
+        else:
+            self.name = kwargs.get("name", None)
+
+        if kwargs.get("session_info", None) is None:
+            print(
+                Fore.RED
+                + Style.BRIGHT
+                + "Warning: no session_info supplied; making fake one"
+                + Style.RESET_ALL
+            )
+            from fake_session_info import fake_session_info
+
+            self.session_info = fake_session_info
+        else:
+            self.session_info = kwargs.get("session_info", None)
+        ic(self.session_info)
+
+        # initialize the state machine
+        self.states = [
+            State(name='standby',
+                  on_enter=["enter_standby"],
+                  on_exit=["exit_standby"]),
+            Timeout(name="initiate",
+                    on_enter=["enter_initiate"],
+                    on_exit=["exit_initiate"],
+                    timeout=self.session_info["initiation_timeout"],
+                    on_timeout=["restart"]),
+            Timeout(name='cue_state',
+                    on_enter=["enter_cue_state"],
+                    on_exit=["exit_cue_state"],
+                    timeout=self.session_info["cue_timeout"],
+                    on_timeout=["restart"]),
+            Timeout(name='reward_available',
+                    on_enter=["enter_reward_available"],
+                    on_exit=["exit_reward_available"],
+                    timeout=self.session_info["wait_for_choice"],
+                    on_timeout=["restart"])
+        ]
+        self.transitions = [
+            ['start_trial', 'standby', 'initiate'],
+            ['start_cue', 'initiate', 'cue_state'],
+            ['evaluate_reward', 'cue_state', 'reward_available'],
+            ['restart', ['initiate', 'cue_state', 'reward_available'], 'standby']
+        ]
+
+        self.machine = TimedStateMachine(
+            model=self,
+            states=self.states,
+            transitions=self.transitions,
+            initial='standby'
+        )
+        self.trial_running = False
+
+        # trial statistics
+        self.correct_trial_number = 0
+        self.actual_trial_number = 0
+        self.error_count = 0
+        self.error_list = []
+        self.early_lick_error = False
+        self.initiate_error = False
+        self.cue_state_error = False
+        self.wrong_choice_error = True
+        self.multiple_choice_error = False
+        self.error_repeat = False
+
+        self.pump_num = None
+        self.reward_size = None
+        self.current_reward = None
+        self.reward_check = False
+        self.reward_size_offset = self.session_info['reward_size_offset']
+
+        self.block_count = 0
+        self.blocknumber = self.session_info["block_number"]
+        self.current_card = None
+        self.left_poke_count = 0
+        self.right_poke_count = 0
+        self.timeline_left_poke = []
+        self.left_poke_count_list = []
+        self.timeline_right_poke = []
+        self.right_poke_count_list = []
+        self.event_name = ""
+        # initialize behavior box
+        self.box = behavbox.BehavBox(self.session_info)
+        self.pump = self.box.pump
+
+        self.treadmill = self.box.treadmill
+
+        self.distance_initiation = self.session_info['treadmill_setup']['distance_initiation']
+        self.distance_cue = self.session_info['treadmill_setup']['distance_cue']
+        self.distance_buffer = None
+        self.distance_diff = 0
+
+        # for foragaing parameters
+        self.side_choice = None  # whether free choice is left or right
+        self.cue_state = None
+
+        # for refining the lick detection
+        self.lick_count = 0
+        self.side_mice_buffer = None
+        self.LED_blink = False
+        try:
+            self.lick_threshold = self.session_info["lick_threshold"]
+        except:
+            print("No lick_threshold defined in session_info. Therefore, default defined as 2 \n")
+            self.lick_threshold = 1
+
+        # session_statistics
+        self.total_reward = 0
+
+    ########################################################################
+    # functions called when state transitions occur
+    ########################################################################
+    def run(self):
+        if self.box.event_list:
+            self.event_name = self.box.event_list.popleft()
+        else:
+            self.event_name = ""
+        # there can only be lick during the reward available state
+        # if lick detected prior to reward available state
+        # the trial will restart and transition to standby
+        if self.event_name is "left_entry" or self.event_name == "right_entry":
+            # print("EVENT NAME !!!!!! " + self.event_name)
+            if self.state == "reward_available" or self.state == "standby" or self.state == "initiate":
+                pass
+            else:
+                self.early_lick_error = True
+                self.error_repeat = True
+                self.restart()
+        if self.state == "standby":
+            pass
+        elif self.state == "initiate":
+            self.distance_diff = self.get_distance() - self.distance_buffer
+            if self.distance_diff >= self.distance_initiation:
+                self.initiate_error = False
+                self.start_cue()
+            else:
+                self.initiate_error = True
+        elif self.state == "cue_state":
+            self.distance_diff = self.get_distance() - self.distance_buffer
+            if self.distance_diff >= self.distance_cue:
+                self.cue_state_error = False
+                self.evaluate_reward()
+            else:
+                self.cue_state_error = True
+        elif self.state == "reward_available":
+            cue_state = self.current_card[0]
+            side_mice = None
+            if self.event_name == "left_entry":
+                side_mice = 'left'
+                self.left_poke_count += 1
+                self.left_poke_count_list.append(self.left_poke_count)
+                self.timeline_left_poke.append(time.time())
+            elif self.event_name == "right_entry":
+                side_mice = 'right'
+                self.right_poke_count += 1
+                self.right_poke_count_list.append(self.right_poke_count)
+                self.timeline_right_poke.append(time.time())
+            if side_mice:
+                self.side_mice_buffer = side_mice
+                self.cue_state = cue_state # cue state for foraging
+                if cue_state == 'all':
+                    side_choice = side_mice
+                    if side_choice == 'left':
+                        self.pump_num = self.current_card[2][0]
+                        self.reward_size = self.current_reward[0]
+                        print("self.current_reward[0]: " + str(self.current_reward[0]))
+                    elif side_choice == 'right':
+                        self.pump_num = self.current_card[2][1]
+                        self.reward_size = self.current_reward[1]
+                        print("self.current_reward[0]: " + str(self.current_reward[1]))
+                elif cue_state == 'LED_L':
+                    side_choice = self.current_card[1]
+                    self.pump_num = self.current_card[2]
+                    self.reward_size = self.current_reward[0]
+                elif cue_state == 'LED_R':
+                    side_choice = self.current_card[1]
+                    self.pump_num = self.current_card[2]
+                    self.reward_size = self.current_reward[1]
+                print("!!!!!!!!CUE_STATE: " + str(cue_state))
+                if side_mice == side_choice:  # if the animal chose correctly
+                    self.side_mice_buffer = side_mice
+                    if side_mice == side_choice:  # if the animal chose correctly
+                        if self.lick_count == 0:  # if this is the first lick
+                            self.side_choice = side_choice # foraging task
+                            self.wrong_choice_error = False
+                            self.reward_check = True
+                            self.lick_count += 1
+                            self.restart()
+                elif self.side_mice_buffer:
+                    if self.lick_count == 0:
+                        self.wrong_choice_error = True
+                        self.lick_count += 1
+                        self.restart()
+
+        # look for keystrokes
+        self.box.check_keybd()
+
+    def enter_standby(self):
+        logging.info(";" + str(time.time()) + ";[transition];enter_standby;" + str(self.error_repeat))
+        self.update_plot_choice()
+        # self.update_plot_error()
+        self.trial_running = False
+        # self.reward_error = False
+        if self.early_lick_error:
+            self.error_list.append("early_lick_error")
+            logging.info(";" + str(time.time()) + ";[error];early_lick_error;" + str(self.error_repeat))
+            self.check_cue('sound2')
+            self.early_lick_error = False
+        print(str(time.time()) + ", Total reward up till current session: " + str(self.total_reward))
+        logging.info(";" + str(time.time()) + ";[trial];trial_" + str(self.actual_trial_number) + ";" + str(self.error_repeat))
+
+    def exit_standby(self):
+        logging.info(";" + str(time.time()) + ";[transition];exit_standby;" + str(self.error_repeat))
+        self.lick_count = 0
+        self.side_mice_buffer = None
+        self.box.event_list.clear()
+        pass
+
+    def enter_initiate(self):
+        # print("!!!!!!!!!!!event name is " + self.event_name) # for debugging purposes
+        # check error_repeat
+        logging.info(";" + str(time.time()) + ";[transition];enter_initiate;" + str(self.error_repeat))
+        self.check_cue('sound1')
+        self.trial_running = True
+        # wait for treadmill signal and process the treadmill signal
+        self.distance_buffer = self.get_distance()
+        logging.info(
+            ";" + str(time.time()) + ";[treadmill];" + str(self.distance_buffer) + ";" + str(self.error_repeat))
+
+    def exit_initiate(self):
+        # check the flag to see whether to shuffle or keep the original card
+        logging.info(";" + str(time.time()) + ";[transition];exit_initiate;" + str(self.error_repeat))
+        print("EVENT NAME: " + str(self.box.event_list))
+        self.cue_off('sound1')
+        if self.initiate_error:
+            self.error_list.append('initiate_error')
+            self.error_repeat = True
+            logging.info(";" + str(time.time()) + ";[error];initiate_error;" + str(self.error_repeat))
+            self.error_count += 1
+
+    def enter_cue_state(self):
+        logging.info(";" + str(time.time()) + ";[transition];enter_cue_state;" + str(self.error_repeat))
+        # turn on the cue according to the current card
+        self.check_cue(self.current_card[0])
+        # wait for treadmill signal and process the treadmill signal
+        self.distance_buffer = self.get_distance()
+        logging.info(
+            ";" + str(time.time()) + ";[treadmill];" + str(self.distance_buffer) + ";" + str(self.error_repeat))
+
+    def exit_cue_state(self):
+        logging.info(";" + str(time.time()) + ";[transition];exit_cue_state;" + str(self.error_repeat))
+        self.cue_off(self.current_card[0])
+        if not self.early_lick_error:
+            if self.cue_state_error:
+                self.check_cue("sound2")
+                self.error_list.append('cue_state_error')
+                self.error_repeat = True
+                logging.info(";" + str(time.time()) + ";[error];cue_state_error;" + str(self.error_repeat))
+                self.error_count += 1
+                self.cue_state_error = False
+
+    def enter_reward_available(self):
+        logging.info(";" + str(time.time()) + ";[transition];enter_reward_available;" + str(self.error_repeat))
+        print(str(time.time()) + ", " + str(self.actual_trial_number) + ", cue_state distance satisfied")
+
+    def exit_reward_available(self):
+        logging.info(";" + str(time.time()) + ";[transition];exit_reward_available;" + str(self.error_repeat))
+        if self.lick_count == 0:
+            logging.info(";" + str(time.time()) + ";[error];no_choice_error;" + str(self.error_repeat))
+            self.check_cue('sound2')
+            self.error_repeat = True
+            self.error_count += 1
+            self.error_list.append('no_choice_error')
+        elif self.wrong_choice_error:
+            logging.info(";" + str(time.time()) + ";[error];wrong_choice_error;" + str(self.error_repeat))
+            self.check_cue('sound2')
+            self.error_repeat = True
+            self.error_count += 1
+            self.error_list.append('wrong_choice_error')
+        elif self.reward_check:
+            logging.info(";" + str(time.time()) + ";[error];correct_trial;" + str(self.error_repeat))
+            self.pump.reward(self.pump_num, self.reward_size)
+            self.error_repeat = False
+            self.total_reward += 1
+            self.reward_check = False
+            self.error_list.append('correct_trial')
+        self.pump_num = None
+        self.reward_size = None
+        self.wrong_choice_error = False
+
+
+    def check_cue(self, cue):
+        if cue == 'sound1':
+            logging.info(";" + str(time.time()) + ";[cue];cue_sound1_on;" + str(self.error_repeat))
+            self.box.sound1.on()
+        if cue == 'sound2':
+            logging.info(";" + str(time.time()) + ";[cue];cue_sound2_on;" + str(self.error_repeat))
+            self.box.sound2.blink(1, 0.1, 1)
+        elif cue == 'LED_L':
+            self.box.cueLED1.on()
+            logging.info(";" + str(time.time()) + ";[cue];cueLED_L_on;" + str(self.error_repeat))
+        elif cue == 'LED_R':
+            self.box.cueLED2.on()
+            logging.info(";" + str(time.time()) + ";[cue];cueLED_R_on;" + str(self.error_repeat))
+        elif cue == 'all':
+            self.box.cueLED1.on()
+            self.box.cueLED2.on()
+            logging.info(";" + str(time.time()) + ";[cue];LED_L+R_on; " + str(self.error_repeat))
+
+    def cue_off(self, cue):
+        if cue == 'all':
+            self.box.cueLED1.off()
+            self.box.cueLED2.off()
+        elif cue == 'sound1':
+            self.box.sound1.off()
+            logging.info(";" + str(time.time()) + ";[cue];cue_sound1_off;" + str(self.error_repeat))
+        elif cue == 'sound2':
+            self.box.sound2.off()
+            logging.info(";" + str(time.time()) + ";[cue];cue_sound2_off;" + str(self.error_repeat))
+        elif cue == 'LED_L':
+            self.box.cueLED1.off()
+            logging.info(";" + str(time.time()) + ";[cue];cueLED1_off;" + str(self.error_repeat))
+        elif cue == 'LED_R':
+            self.box.cueLED2.off()
+            logging.info(";" + str(time.time()) + ";[cue];cueLED2_off;" + str(self.error_repeat))
+
+    def get_distance(self):
+        try:
+            distance = self.treadmill.distance_cm
+        except Exception as e:
+            logging.info(";" + str(time.time()) + ";[system_error];" + str(e) + ";" + str(self.error_repeat))
+            self.treadmill = self.box.treadmill
+            distance = self.treadmill.distance_cm
+        return distance
+
+    def update_plot(self):
+        fig, axes = plt.subplots(1, 1, )
+        axes.plot([1, 2], [1, 2], color='green', label='test')
+        self.box.check_plot(fig)
+
+    def update_plot_error(self):
+        error_event = self.error_list
+        labels, counts = np.unique(error_event, return_counts=True)
+        ticks = range(len(counts))
+        fig, ax = plt.subplots(1, 1, )
+        ax.bar(ticks, counts, align='center', tick_label=labels)
+        ax = plt.gca()
+        ax.set_xticks(ticks, labels)
+        ax.set_xticklabels(labels=labels, rotation=70)
+
+        self.box.check_plot(fig)
+
+    def update_plot_choice(self, save_fig=False):
+        trajectory_left = self.left_poke_count_list
+        time_left = self.timeline_left_poke
+        trajectory_right = self.right_poke_count_list
+        time_right = self.timeline_right_poke
+        fig, ax = plt.subplots(1, 1, )
+        print(type(fig))
+
+        ax.plot(time_left, trajectory_left, color='b', marker="o", label='left_lick_trajectory')
+        ax.plot(time_right, trajectory_right, color='r', marker="o", label='right_lick_trajectory')
+        if save_fig:
+            plt.savefig(self.session_info['basedir'] + "/" + self.session_info['basename'] + "/" + \
+                        self.session_info['basename'] + "_choice_plot" + '.png')
+        self.box.check_plot(fig)
+
+    def integrate_plot(self, save_fig=False):
+
+        fig, ax = plt.subplots(2, 1)
+
+        trajectory_left = self.left_poke_count_list
+        time_left = self.timeline_left_poke
+        trajectory_right = self.right_poke_count_list
+        time_right = self.timeline_right_poke
+        print(type(fig))
+
+        ax[0].plot(time_left, trajectory_left, color='b', marker="o", label='left_lick_trajectory')
+        ax[0].plot(time_right, trajectory_right, color='r', marker="o", label='right_lick_trajectory')
+
+        error_event = self.error_list
+        labels, counts = np.unique(error_event, return_counts=True)
+        ticks = range(len(counts))
+        ax[1].bar(ticks, counts, align='center', tick_label=labels)
+        # plt.xticks(ticks, labels)
+        # plt.title(session_name)
+        ax[1] = plt.gca()
+        ax[1].set_xticks(ticks, labels)
+        ax[1].set_xticklabels(labels=labels, rotation=70)
+
+        if save_fig:
+            plt.savefig(self.session_info['basedir'] + "/" + self.session_info['basename'] + "/" + \
+                        self.session_info['basename'] + "_summery" + '.png')
+        self.box.check_plot(fig)
+
+    ########################################################################
+    # methods to start and end the behavioral session
+    ########################################################################
+
+    def start_session(self):
+        ic("TODO: start video")
+        self.box.video_start()
+
+    def end_session(self):
+        ic("TODO: stop video")
+        self.update_plot_choice(save_fig=True)
+        self.box.video_stop()
\ No newline at end of file
diff --git a/task_protocol/headfixed_task/run_headfixed_independent_reward_task.py b/task_protocol/headfixed_task/run_headfixed_independent_reward_task.py
new file mode 100644
index 0000000..1957312
--- /dev/null
+++ b/task_protocol/headfixed_task/run_headfixed_independent_reward_task.py
@@ -0,0 +1,265 @@
+#!/usr/bin/env -S ipython3 -i
+# run_headfixed2FC_task.py
+"""
+author: tian qiu & Soyoun Kim
+date: 2023-02-16
+name: run_headfixed_independent_reward_task.py
+goal: model_free reinforcement learning behavioral training run task file
+description:
+    an updated test version of run_headfixed_task.py & add foraging task
+
+"""
+import random
+import numpy as np
+from transitions import Machine
+from transitions import State
+from icecream import ic
+import logging
+from datetime import datetime
+import os
+import logging.config
+import pysistence, collections
+import socket
+import importlib
+import colorama
+import warnings
+import scipy.io, pickle
+import pygame
+from colorama import Fore, Style
+import time
+from time import sleep
+
+debug_enable = False
+
+# all modules above this line will have logging disabled
+logging.config.dictConfig({
+    'version': 1,
+    'disable_existing_loggers': True,
+})
+
+if debug_enable:
+    # enabling debugger
+    from IPython import get_ipython
+
+    ipython = get_ipython()
+    ipython.magic("pdb on")
+    ipython.magic("xmode Verbose")
+
+# import your task class here
+from headfixed_independent_reward_task import HeadfixedIndependentRewardTask
+
+try:
+    # load in session_info file, check that dates are correct, put in automatic
+    # time and date stamps for when the experiment was run
+
+    datestr = datetime.now().strftime("%Y-%m-%d")
+    timestr = datetime.now().strftime('%H%M%S')
+    full_module_name = 'session_info_' + datestr
+
+    import sys
+
+    session_info_path = '/home/pi/experiment_info/headfixed_independent_reward_task/session_info'
+    sys.path.insert(0, session_info_path)
+    tempmod = importlib.import_module(full_module_name)
+    session_info = tempmod.session_info
+    mouse_info = tempmod.mouse_info
+
+    session_info['date'] = datestr
+    session_info['time'] = timestr
+    session_info['datetime'] = session_info['date'] + '_' + session_info['time']
+    session_info['basename'] = session_info['mouse_name'] + '_' + session_info['datetime']
+    session_info['dir_name'] = session_info['basedir'] + "/" + session_info['basename']
+
+    if session_info['manual_date'] != session_info['date']:  # check if file is updated
+        print('wrong date!!')
+        raise RuntimeError('manual_date field in session_info file is not updated')
+
+    # make data directory and initialize logfile
+    os.makedirs(session_info['dir_name'])
+    os.chdir(session_info['dir_name'])
+    session_info['file_basename'] = session_info['dir_name'] + '/' + session_info['basename']
+
+    logging.basicConfig(
+        level=logging.INFO,
+        format="%(asctime)s.%(msecs)03d,[%(levelname)s],%(message)s",
+        datefmt=('%H:%M:%S'),
+        handlers=[
+            logging.FileHandler(session_info['file_basename'] + '.log'),
+            logging.StreamHandler()  # sends copy of log output to screen
+        ]
+    )
+
+    from task_information_independent_reward import TaskInformation
+    task_information = TaskInformation()
+    # print("Imported task_information_headfixed: " + str(task_information.name))
+    task = HeadfixedIndependentRewardTask(name="headfixed_independent_reward_task", session_info=session_info)
+
+
+    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
+            rewards_L.append(cumsum_positive(temp) + offset)
+            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
+
+    def generate_sine_wave(increment, period_width, amplitude_offset, amplitude_scale, deviation, session_length): # for training purpose only
+        session_start = random.uniform(0, period_width)
+        session_end = session_start + session_length
+        value_input = np.arange(session_start, session_end, increment)
+
+        sine_output = (np.sin((np.pi / period_width) * value_input) + amplitude_offset) * amplitude_scale
+        negative_sine_output = (np.sin((np.pi / period_width) * -value_input) + amplitude_offset) * amplitude_scale
+        left_side_reward = np.random.normal(sine_output, deviation)
+        right_side_reward = np.random.normal(negative_sine_output, deviation)
+        reward_list = list(zip(left_side_reward, right_side_reward))
+        return reward_list
+
+    if session_info['phase'] == "independent_reward":
+        # from reward_distribution import generate_reward_trajectory
+        scale = session_info['independent_reward']['scale']
+        offset = session_info['independent_reward']['offset']
+        change_point = session_info['independent_reward']['change_point']
+        ntrials = session_info['independent_reward']['ntrials']
+        reward_distribution_list = generate_reward_trajectory(scale, offset, change_point, ntrials)
+    elif session_info['phase'] == "forced_choice":
+        reward_size = session_info['reward_size']
+    elif session_info['phase'] == "sine_reward":
+        session_length = session_info["sine_reward"]["session_length"]
+        increment = session_info["sine_reward"]["increment"]
+        period_width = session_info["sine_reward"]["period_width"]
+        amplitude_offset = session_info["sine_reward"]["amplitude_offset"]
+        amplitude_scale = session_info["sine_reward"]["amplitude_scale"]
+        deviation = session_info["sine_reward"]["deviation"]
+        reward_distribution_list = generate_sine_wave(increment, period_width, amplitude_offset,
+                                                      amplitude_scale, deviation, session_length)
+    elif session_info['phase'] == 'foraging_reward':
+        offset = session_info['foraging_reward']['offset']
+        max_reward = session_info['foraging_reward']['max_reward']
+        increment = session_info['foraging_reward']['increment']
+        reward_distribution = (3,3)
+
+
+    first_trial_of_the_session = True
+
+    # # you can change various parameters if you want
+    # task.machine.states['cue'].timeout = 2
+
+    # start session
+    task.start_session()
+    scipy.io.savemat(session_info['file_basename'] + '_session_info.mat', {'session_info': session_info})
+    pickle.dump(session_info, open(session_info['file_basename'] + '_session_info.pkl', "wb"))
+    sleep(10)
+    # loop over trials
+    # Set a timer
+    t_minute = int(input("Enter the time in minutes: ")) # wll add in the session info
+    t_end = time.time() + 60 * t_minute
+    while time.time() < t_end: # time check
+        if task.error_repeat:  # error repeat check
+            task.error_repeat = False
+            print("punishment_time_out: " + str(session_info["punishment_timeout"]))
+            sleep(session_info["punishment_timeout"])
+            print("Trial " + str(task.actual_trial_number) + " \n")
+            task.actual_trial_number += 1
+            print("*******************************\n")
+            print("*error_repeat trial* \n" +
+                  " - Current card condition: \n" +
+                  "*******************************\n" +
+                  "*reward_side: " + str(task.current_card[0]) + "\n" +
+                  "*reward_size: " + str(task.current_reward)[1:-1] + "\n")
+        else:
+            if not first_trial_of_the_session:
+                print("reward_time_out: " + str(session_info["reward_timeout"]))
+                sleep(session_info["reward_timeout"])
+            else:
+                first_trial_of_the_session = False
+            # setup the beginning of a new trial
+            task.error_count = 0 # reset the error count if previous trial is correct
+            print("Trial " + str(task.actual_trial_number) + " \n")
+            task.correct_trial_number += 1
+            task.actual_trial_number += 1
+            print("*******************************\n")
+            # acquire new reward contingency and cue association
+            #print("fraction " + str(session_info['fraction']) + " \n")
+            task.current_card = task_information.draw_card(session_info['phase'], session_info['fraction'])
+            if session_info['phase'] == "independent_reward":
+                task.current_reward = reward_distribution_list[task.correct_trial_number] + float(task.reward_size_offset)
+            elif session_info['phase'] == "forced_choice":
+                task.current_reward = session_info['reward_size']
+            elif session_info['phase'] == "sine_reward":
+                task.current_reward = reward_distribution_list[task.correct_trial_number]
+            elif session_info['phase'] == 'foraging_reward':
+                reward_L = reward_distribution[0]
+                reward_R = reward_distribution[1]
+                task.current_reward = reward_distribution
+                if task.cue_state == 'all':
+                    if task.side_choice == 'left':
+                        reward_L = reward_L - increment
+                        reward_R = reward_R + increment
+                        if reward_L < 0:
+                            reward_L = 0
+                        if reward_R > max_reward:
+                             reward_R = max_reward
+                    elif task.side_choice == 'right':
+                        reward_R = reward_R - increment
+                        reward_L = reward_L + increment
+                        if reward_R < 0:
+                            reward_R = 0
+                        if reward_L > max_reward:
+                            reward_L = max_reward
+                    reward_distribution = (reward_L, reward_R)
+                    task.current_reward = reward_distribution
+
+
+        logging.info(";" + str(time.time()) + ";[condition];current_card_" + str(task.current_card) +
+                         ";current_reward_" + str(task.current_reward)[1:-1])
+
+        print(" - Current card condition: \n" +
+                  "*******************************\n" +
+                  "*reward_side: " + str(task.current_card[0]) + "\n" +
+                  "*reward_size: " + str(task.current_reward)[1:-1] + "\n")
+        logging.info(";" + str(time.time()) + ";[transition];start_trial()")
+        task.start_trial()  # initiate the time state machine, start_trial() is a trigger
+        while task.trial_running:
+            task.run()  # run command trigger additional functions outside of the state machine
+        print("error_count: " + str(task.error_count))
+    raise SystemExit
+
+# graceful exit
+except (KeyboardInterrupt, SystemExit):
+    print(Fore.RED + Style.BRIGHT + 'Exiting now...' + Style.RESET_ALL)
+    ic('about to call end_session()')
+    task.end_session()
+    ic('just called end_session()')
+    # save dicts to disk
+    scipy.io.savemat(session_info['file_basename'] + '_session_info.mat', {'session_info': session_info})
+    pickle.dump(session_info, open(session_info['file_basename'] + '_session_info.pkl', "wb"))
+    pygame.quit()
+
+# exit because of error
+except RuntimeError as ex:
+    print(Fore.RED + Style.BRIGHT + 'ERROR: Exiting now' + Style.RESET_ALL)
+    # save dicts to disk
+    scipy.io.savemat(session_info['file_basename'] + '_session_info.mat', {'session_info': session_info})
+    pickle.dump(session_info, open(session_info['file_basename'] + '_session_info.pkl', "wb"))
+    task.end_session()
\ No newline at end of file
diff --git a/task_protocol/headfixed_task/run_headfixed_task.py b/task_protocol/headfixed_task/run_headfixed_task.py
new file mode 100644
index 0000000..be08437
--- /dev/null
+++ b/task_protocol/headfixed_task/run_headfixed_task.py
@@ -0,0 +1,265 @@
+#!/usr/bin/env -S ipython3 -i
+# run_headfixed2FC_task.py
+"""
+author: tian qiu & Soyoun Kim
+date: 2023-02-16
+name: run_headfixed_independent_reward_task.py
+goal: model_free reinforcement learning behavioral training run task file
+description:
+    an updated test version of run_headfixed_task.py & add foraging task
+
+"""
+import random
+import numpy as np
+from transitions import Machine
+from transitions import State
+from icecream import ic
+import logging
+from datetime import datetime
+import os
+import logging.config
+import pysistence, collections
+import socket
+import importlib
+import colorama
+import warnings
+import scipy.io, pickle
+import pygame
+from colorama import Fore, Style
+import time
+from time import sleep
+
+debug_enable = False
+
+# all modules above this line will have logging disabled
+logging.config.dictConfig({
+    'version': 1,
+    'disable_existing_loggers': True,
+})
+
+if debug_enable:
+    # enabling debugger
+    from IPython import get_ipython
+
+    ipython = get_ipython()
+    ipython.magic("pdb on")
+    ipython.magic("xmode Verbose")
+
+# import your task class here
+from headfixed_task import HeadfixedTask
+
+try:
+    # load in session_info file, check that dates are correct, put in automatic
+    # time and date stamps for when the experiment was run
+
+    datestr = datetime.now().strftime("%Y-%m-%d")
+    timestr = datetime.now().strftime('%H%M%S')
+    full_module_name = 'session_info_' + datestr
+
+    import sys
+
+    session_info_path = '/home/pi/experiment_info/headfixed_task/session_info'
+    sys.path.insert(0, session_info_path)
+    tempmod = importlib.import_module(full_module_name)
+    session_info = tempmod.session_info
+    mouse_info = tempmod.mouse_info
+
+    session_info['date'] = datestr
+    session_info['time'] = timestr
+    session_info['datetime'] = session_info['date'] + '_' + session_info['time']
+    session_info['basename'] = session_info['mouse_name'] + '_' + session_info['datetime']
+    session_info['dir_name'] = session_info['basedir'] + "/" + session_info['basename']
+
+    if session_info['manual_date'] != session_info['date']:  # check if file is updated
+        print('wrong date!!')
+        raise RuntimeError('manual_date field in session_info file is not updated')
+
+    # make data directory and initialize logfile
+    os.makedirs(session_info['dir_name'])
+    os.chdir(session_info['dir_name'])
+    session_info['file_basename'] = session_info['dir_name'] + '/' + session_info['basename']
+
+    logging.basicConfig(
+        level=logging.INFO,
+        format="%(asctime)s.%(msecs)03d,[%(levelname)s],%(message)s",
+        datefmt=('%H:%M:%S'),
+        handlers=[
+            logging.FileHandler(session_info['file_basename'] + '.log'),
+            logging.StreamHandler()  # sends copy of log output to screen
+        ]
+    )
+
+    from task_information_independent_reward import TaskInformation
+    task_information = TaskInformation()
+    # print("Imported task_information_headfixed: " + str(task_information.name))
+    task = HeadfixedTask(name="headfixed_task", session_info=session_info)
+
+
+    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
+            rewards_L.append(cumsum_positive(temp) + offset)
+            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
+
+    def generate_sine_wave(increment, period_width, amplitude_offset, amplitude_scale, deviation, session_length): # for training purpose only
+        session_start = random.uniform(0, period_width)
+        session_end = session_start + session_length
+        value_input = np.arange(session_start, session_end, increment)
+
+        sine_output = (np.sin((np.pi / period_width) * value_input) + amplitude_offset) * amplitude_scale
+        negative_sine_output = (np.sin((np.pi / period_width) * -value_input) + amplitude_offset) * amplitude_scale
+        left_side_reward = np.random.normal(sine_output, deviation)
+        right_side_reward = np.random.normal(negative_sine_output, deviation)
+        reward_list = list(zip(left_side_reward, right_side_reward))
+        return reward_list
+
+    if session_info['phase'] == "independent_reward":
+        # from reward_distribution import generate_reward_trajectory
+        scale = session_info['independent_reward']['scale']
+        offset = session_info['independent_reward']['offset']
+        change_point = session_info['independent_reward']['change_point']
+        ntrials = session_info['independent_reward']['ntrials']
+        reward_distribution_list = generate_reward_trajectory(scale, offset, change_point, ntrials)
+    elif session_info['phase'] == "forced_choice":
+        reward_size = session_info['reward_size']
+    elif session_info['phase'] == "sine_reward":
+        session_length = session_info["sine_reward"]["session_length"]
+        increment = session_info["sine_reward"]["increment"]
+        period_width = session_info["sine_reward"]["period_width"]
+        amplitude_offset = session_info["sine_reward"]["amplitude_offset"]
+        amplitude_scale = session_info["sine_reward"]["amplitude_scale"]
+        deviation = session_info["sine_reward"]["deviation"]
+        reward_distribution_list = generate_sine_wave(increment, period_width, amplitude_offset,
+                                                      amplitude_scale, deviation, session_length)
+    elif session_info['phase'] == 'foraging_reward':
+        offset = session_info['foraging_reward']['offset']
+        max_reward = session_info['foraging_reward']['max_reward']
+        increment = session_info['foraging_reward']['increment']
+        reward_distribution = (3,3)
+
+
+    first_trial_of_the_session = True
+
+    # # you can change various parameters if you want
+    # task.machine.states['cue'].timeout = 2
+
+    # start session
+    task.start_session()
+    scipy.io.savemat(session_info['file_basename'] + '_session_info.mat', {'session_info': session_info})
+    pickle.dump(session_info, open(session_info['file_basename'] + '_session_info.pkl', "wb"))
+    sleep(10)
+    # loop over trials
+    # Set a timer
+    t_minute = int(input("Enter the time in minutes: ")) # wll add in the session info
+    t_end = time.time() + 60 * t_minute
+    while time.time() < t_end: # time check
+        if task.error_repeat:  # error repeat check
+            task.error_repeat = False
+            print("punishment_time_out: " + str(session_info["punishment_timeout"]))
+            sleep(session_info["punishment_timeout"])
+            print("Trial " + str(task.actual_trial_number) + " \n")
+            task.actual_trial_number += 1
+            print("*******************************\n")
+            print("*error_repeat trial* \n" +
+                  " - Current card condition: \n" +
+                  "*******************************\n" +
+                  "*reward_side: " + str(task.current_card[0]) + "\n" +
+                  "*reward_size: " + str(task.current_reward)[1:-1] + "\n")
+        else:
+            if not first_trial_of_the_session:
+                print("reward_time_out: " + str(session_info["reward_timeout"]))
+                sleep(session_info["reward_timeout"])
+            else:
+                first_trial_of_the_session = False
+            # setup the beginning of a new trial
+            task.error_count = 0 # reset the error count if previous trial is correct
+            print("Trial " + str(task.actual_trial_number) + " \n")
+            task.correct_trial_number += 1
+            task.actual_trial_number += 1
+            print("*******************************\n")
+            # acquire new reward contingency and cue association
+            #print("fraction " + str(session_info['fraction']) + " \n")
+            task.current_card = task_information.draw_card(session_info['phase'], session_info['fraction'])
+            if session_info['phase'] == "independent_reward":
+                task.current_reward = reward_distribution_list[task.correct_trial_number] + float(task.reward_size_offset)
+            elif session_info['phase'] == "forced_choice":
+                task.current_reward = session_info['reward_size']
+            elif session_info['phase'] == "sine_reward":
+                task.current_reward = reward_distribution_list[task.correct_trial_number]
+            elif session_info['phase'] == 'foraging_reward':
+                reward_L = reward_distribution[0]
+                reward_R = reward_distribution[1]
+                task.current_reward = reward_distribution
+                if task.cue_state == 'all':
+                    if task.side_choice == 'left':
+                        reward_L = reward_L - increment
+                        reward_R = reward_R + increment
+                        if reward_L < 0:
+                            reward_L = 0
+                        if reward_R > max_reward:
+                             reward_R = max_reward
+                    elif task.side_choice == 'right':
+                        reward_R = reward_R - increment
+                        reward_L = reward_L + increment
+                        if reward_R < 0:
+                            reward_R = 0
+                        if reward_L > max_reward:
+                            reward_L = max_reward
+                    reward_distribution = (reward_L, reward_R)
+                    task.current_reward = reward_distribution
+
+
+        logging.info(";" + str(time.time()) + ";[condition];current_card_" + str(task.current_card) +
+                         ";current_reward_" + str(task.current_reward)[1:-1])
+
+        print(" - Current card condition: \n" +
+                  "*******************************\n" +
+                  "*reward_side: " + str(task.current_card[0]) + "\n" +
+                  "*reward_size: " + str(task.current_reward)[1:-1] + "\n")
+        logging.info(";" + str(time.time()) + ";[transition];start_trial()")
+        task.start_trial()  # initiate the time state machine, start_trial() is a trigger
+        while task.trial_running:
+            task.run()  # run command trigger additional functions outside of the state machine
+        print("error_count: " + str(task.error_count))
+    raise SystemExit
+
+# graceful exit
+except (KeyboardInterrupt, SystemExit):
+    print(Fore.RED + Style.BRIGHT + 'Exiting now...' + Style.RESET_ALL)
+    ic('about to call end_session()')
+    task.end_session()
+    ic('just called end_session()')
+    # save dicts to disk
+    scipy.io.savemat(session_info['file_basename'] + '_session_info.mat', {'session_info': session_info})
+    pickle.dump(session_info, open(session_info['file_basename'] + '_session_info.pkl', "wb"))
+    pygame.quit()
+
+# exit because of error
+except RuntimeError as ex:
+    print(Fore.RED + Style.BRIGHT + 'ERROR: Exiting now' + Style.RESET_ALL)
+    # save dicts to disk
+    scipy.io.savemat(session_info['file_basename'] + '_session_info.mat', {'session_info': session_info})
+    pickle.dump(session_info, open(session_info['file_basename'] + '_session_info.pkl', "wb"))
+    task.end_session()
\ No newline at end of file
diff --git a/task_protocol/headfixed_task/session_info_headfixed_independent_reward.py b/task_protocol/headfixed_task/session_info_headfixed_independent_reward.py
new file mode 100644
index 0000000..4c4bbf1
--- /dev/null
+++ b/task_protocol/headfixed_task/session_info_headfixed_independent_reward.py
@@ -0,0 +1,130 @@
+from datetime import datetime
+import os
+import pysistence, collections
+import socket
+import pandas as pd
+import numpy as np
+
+# defining immutable mouse dict (once defined for a mouse, NEVER EDIT IT)
+mouse_info = pysistence.make_dict({'mouse_name': 'test',
+                                   'fake_field': 'fake_info',
+                                   })
+
+# Information for this session (the user should edit this each session)
+session_info = collections.OrderedDict()
+session_info['mouse_info'] = mouse_info
+session_info['mouse_name'] = mouse_info['mouse_name']
+
+session_info['basedir'] = '/home/pi/buffer'
+session_info['external_storage'] = '/mnt/hd'
+session_info['flipper_filename'] = '/home/pi/buffer/flipper_timestamp'
+# for actual data save to this dir:
+# session_info['basedir']					  	= '/home/pi/video'
+session_info['weight'] = 0.0
+session_info['manual_date'] = '2023-07-13'
+session_info['box_name'] = socket.gethostname()
+session_info['block_number'] = 1  # 1 (left large) or 2 (right large) which block starts
+
+session_info['config'] = 'headfixed2FC'
+
+# behavior parameters
+session_info['timeout_length'] = 5  # in seconds
+session_info["lick_threshold"] = 1
+# visual stimulus
+session_info["visual_stimulus"] = False
+
+session_info['config'] = 'headfixed2FC'
+session_info['treadmill_setup'] = {}
+session_info['treadmill'] = True
+session_info['fraction'] = 0.3     # 0.3, 0.5,0.7,1 # free choice fraction 1 for all free choice
+session_info['phase'] = 'foraging_reward' # 'forced_choice', 'sine_reward'
+
+
+
+if session_info['treadmill']:
+    session_info['treadmill_setup']['distance_cue'] = 5  # cm
+    session_info['treadmill_setup']['distance_initiation'] = 10  # cm
+else:
+    session_info['treadmill_setup'] = None
+
+session_info['error_repeat'] = True
+if session_info['error_repeat']:
+    session_info['error_max'] = 3
+
+# condition setup
+session_info['cue'] = ['LED_L', 'LED_R', 'all']
+# session_info['state'] = ['block1', 'block2']  #
+session_info['choice'] = ['right', 'left']  # lick port
+session_info['air_duration'] = 0
+session_info["vacuum_duration"] = 1
+
+""" solenoid calibration information configuration """
+
+solenoid_coeff = None
+def get_coefficient():
+    df_calibration = pd.read_csv("~/experiment_info/calibration_info/calibration.csv")
+    pump_coefficient = {}
+
+    for pump_num in range(1, 5):
+        df_pump = df_calibration[df_calibration['pump_number'] == pump_num]
+        mg_per_pulse = df_pump['weight_fluid'].div(df_pump['iteration'])
+        on_time = df_pump['on_time']
+
+        fit_calibration = np.polyfit(mg_per_pulse, on_time, 1)  # output with highest power first
+        pump_coefficient[str(pump_num)] = fit_calibration
+    return pump_coefficient
+
+try:
+    solenoid_coeff = get_coefficient()
+except Exception as e:
+    print(e)
+
+session_info["calibration_coefficient"] = {}
+
+if solenoid_coeff:
+    session_info["calibration_coefficient"]['1'] = solenoid_coeff["1"]
+    session_info["calibration_coefficient"]['2'] = solenoid_coeff["2"]
+    session_info["calibration_coefficient"]['3'] = solenoid_coeff["3"]
+    session_info["calibration_coefficient"]['4'] = solenoid_coeff["4"]
+else:
+    print("No coefficients, generate the default")
+    # solenoid valve linear fit coefficient for each pump
+    session_info["calibration_coefficient"]['1'] = [0.13, 0]  # highest power first
+    session_info["calibration_coefficient"]['2'] = [0.13, 0]
+    session_info["calibration_coefficient"]['3'] = [0.13, 0.0]
+    session_info["calibration_coefficient"]['4'] = [0.13, 0.0]
+
+# define timeout during each condition
+session_info['initiation_timeout'] = 120  # s
+session_info['cue_timeout'] = 120
+session_info['wait_for_choice'] = 60
+session_info['reward_timeout'] = 1
+session_info["punishment_timeout"] = 3
+
+session_info["key_reward_amount"] = 2
+session_info['reward_size_offset'] = 2
+session_info['reward_size'] = (5, 5)
+
+if session_info["phase"] == 'independent_reward':
+    session_info['independent_reward'] = {}
+    session_info['independent_reward']['scale'] = 0.5
+    session_info['independent_reward']['offset'] = 3.0
+    session_info['independent_reward']['change_point'] = 20
+    session_info['independent_reward']['ntrials'] = 1000
+elif session_info["phase"] == 'sine_reward':
+    session_info["sine_reward"] = {}
+    session_info["sine_reward"]["increment"] = 1
+    session_info["sine_reward"]["period_width"] = 40
+    session_info["sine_reward"]["amplitude_offset"] = 2
+    session_info["sine_reward"]["amplitude_scale"] = 3
+    session_info["sine_reward"]["deviation"] = 0
+elif session_info['phase'] == 'foraging_reward':
+    session_info["foraging_reward"] = {}
+    session_info["foraging_reward"]["increment"] = 0.25
+    session_info["foraging_reward"]["offset"] = 3
+    session_info["foraging_reward"]["max_reward"] = 10
+
+
+session_info['consecutive_control'] = False
+if session_info['consecutive_control']:
+    session_info['consecutive_max'] = 3
\ No newline at end of file
diff --git a/task_protocol/headfixed_task/session_info_headfixed_task.py b/task_protocol/headfixed_task/session_info_headfixed_task.py
new file mode 100644
index 0000000..5b8795d
--- /dev/null
+++ b/task_protocol/headfixed_task/session_info_headfixed_task.py
@@ -0,0 +1,131 @@
+from datetime import datetime
+import os
+import pysistence, collections
+import socket
+import pandas as pd
+import numpy as np
+
+# defining immutable mouse dict (once defined for a mouse, NEVER EDIT IT)
+mouse_info = pysistence.make_dict({'mouse_name': 'test',
+                                   'fake_field': 'fake_info',
+                                   })
+
+# Information for this session (the user should edit this each session)
+session_info = collections.OrderedDict()
+session_info['mouse_info'] = mouse_info
+session_info['mouse_name'] = mouse_info['mouse_name']
+
+session_info['basedir'] = '/home/pi/buffer'
+session_info['external_storage'] = '/mnt/hd'
+session_info['flipper_filename'] = '/home/pi/buffer/flipper_timestamp'
+# for actual data save to this dir:
+# session_info['basedir']					  	= '/home/pi/video'
+session_info['weight'] = 0.0
+session_info['manual_date'] = '2023-07-13'
+session_info['box_name'] = socket.gethostname()
+session_info['block_number'] = 1  # 1 (left large) or 2 (right large) which block starts
+
+session_info['config'] = 'headfixed2FC'
+
+# behavior parameters
+session_info['timeout_length'] = 5  # in seconds
+session_info["lick_threshold"] = 1
+# visual stimulus
+session_info["visual_stimulus"] = False
+
+session_info['config'] = 'headfixed2FC'
+session_info['treadmill_setup'] = {}
+session_info['treadmill'] = True
+session_info['fraction'] = 0.3     # 0.3, 0.5,0.7,1 # free choice fraction 1 for all free choice
+session_info['phase'] = 'foraging_reward' # 'forced_choice', 'sine_reward'
+
+
+
+if session_info['treadmill']:
+    session_info['treadmill_setup']['distance_cue'] = 5  # cm
+    session_info['treadmill_setup']['distance_initiation'] = 10  # cm
+else:
+    session_info['treadmill_setup'] = None
+
+session_info['error_repeat'] = True
+if session_info['error_repeat']:
+    session_info['error_max'] = 3
+
+# condition setup
+session_info['cue'] = ['LED_L', 'LED_R', 'all']
+# session_info['state'] = ['block1', 'block2']  #
+session_info['choice'] = ['right', 'left']  # lick port
+session_info['air_duration'] = 0
+session_info["vacuum_duration"] = 1
+
+""" solenoid calibration information configuration """
+
+solenoid_coeff = None
+def get_coefficient():
+    df_calibration = pd.read_csv("~/experiment_info/calibration_info/calibration.csv")
+    pump_coefficient = {}
+
+    for pump_num in range(1, 5):
+        df_pump = df_calibration[df_calibration['pump_number'] == pump_num]
+        mg_per_pulse = df_pump['weight_fluid'].div(df_pump['iteration'])
+        on_time = df_pump['on_time']
+
+        fit_calibration = np.polyfit(mg_per_pulse, on_time, 1)  # output with highest power first
+        pump_coefficient[str(pump_num)] = fit_calibration
+    return pump_coefficient
+
+try:
+    solenoid_coeff = get_coefficient()
+except Exception as e:
+    print(e)
+
+session_info["calibration_coefficient"] = {}
+
+if solenoid_coeff:
+    session_info["calibration_coefficient"]['1'] = solenoid_coeff["1"]
+    session_info["calibration_coefficient"]['2'] = solenoid_coeff["2"]
+    session_info["calibration_coefficient"]['3'] = solenoid_coeff["3"]
+    session_info["calibration_coefficient"]['4'] = solenoid_coeff["4"]
+else:
+    print("No coefficients, generate the default")
+    # solenoid valve linear fit coefficient for each pump
+    session_info["calibration_coefficient"]['1'] = [0.13, 0]  # highest power first
+    session_info["calibration_coefficient"]['2'] = [0.13, 0]
+    session_info["calibration_coefficient"]['3'] = [0.13, 0.0]
+    session_info["calibration_coefficient"]['4'] = [0.13, 0.0]
+
+# define timeout during each condition
+session_info['initiation_timeout'] = 120  # s
+session_info['cue_timeout'] = 120
+session_info['wait_for_choice'] = 60
+session_info['reward_timeout'] = 1
+session_info["punishment_timeout"] = 3
+
+session_info["key_reward_amount"] = 2
+session_info['reward_size_offset'] = 2
+session_info['reward_size'] = (5, 5)
+
+if session_info["phase"] == 'independent_reward':
+    session_info['independent_reward'] = {}
+    session_info['independent_reward']['scale'] = 0.5
+    session_info['independent_reward']['offset'] = 3.0
+    session_info['independent_reward']['change_point'] = 20
+    session_info['independent_reward']['ntrials'] = 1000
+elif session_info["phase"] == 'sine_reward':
+    session_info["sine_reward"] = {}
+    session_info["sine_reward"]["increment"] = 1
+    session_info["sine_reward"]["period_width"] = 40
+    session_info["sine_reward"]["amplitude_offset"] = 2
+    session_info["sine_reward"]["amplitude_scale"] = 3
+    session_info["sine_reward"]["deviation"] = 0
+elif session_info['phase'] == 'foraging_reward':
+    session_info["foraging_reward"] = {}
+    session_info["foraging_reward"]["increment"] = 0.25
+    session_info["foraging_reward"]["offset"] = 3
+    session_info["foraging_reward"]["max_reward"] = 10
+
+
+session_info['consecutive_control'] = False
+if session_info['consecutive_control']:
+    session_info['consecutive_max'] = 3
+
diff --git a/task_protocol/headfixed_task/task_information_headfixed.py b/task_protocol/headfixed_task/task_information_headfixed.py
new file mode 100644
index 0000000..ddcf184
--- /dev/null
+++ b/task_protocol/headfixed_task/task_information_headfixed.py
@@ -0,0 +1,46 @@
+import random
+
+
+class TaskInformation(object):
+    def __init__(self, **kwargs):
+        self.name = "model_based_reinforcement_learning_task"
+        self.deck = [('LED_L', 'left', '1'), ('LED_R',  'right', '2'),
+                     ('LED_L', 'left', '1'), ('LED_R',  'right', '2'),
+                     ('LED_L', 'left', '1'), ('LED_R', 'right', '2'),
+                     ('LED_L', 'left', '1'), ('LED_R', 'right', '2'),
+                     ('LED_L', 'left', '1'), ('LED_R', 'right', '2'),
+                     ('all',  ('left', 'right'), ('1', '2')), ('all',  ('left', 'right'), ('1', '2')),
+                     ('all', ('left', 'right'), ('1', '2')), ('all', ('left', 'right'), ('1', '2')),
+                     ('all', ('left', 'right'), ('1', '2')), ('all', ('left', 'right'), ('1', '2')),
+                     ('all', ('left', 'right'), ('1', '2')), ('all', ('left', 'right'), ('1', '2')),
+                     ('all', ('left', 'right'), ('1', '2')), ('all', ('left', 'right'), ('1', '2')),
+                     ]
+
+    def draw_card(self, phase="independent_reward", fraction=0.5):
+        row_start = 0
+        row_end = len(self.deck)-1
+
+        if phase == 'forced_choice':
+            row_end = 1
+        elif phase == 'free_choice':
+            row_start = 9
+        elif phase == 'forced_choice_left':
+            row_end = 0
+        elif phase == 'forced_choice_right':
+            row_start = 1
+            row_end = 1
+        else:
+            if fraction == 0.5:
+                row_start = 8
+                row_end = 11
+            elif fraction == 0.7:
+                row_start = 6
+            elif fraction == 0.3:
+                row_end = 13
+            elif fraction == 1:
+                row_start = 11
+
+        card = self.deck[random.randint(row_start, row_end)]
+        return card
+
+# print(TaskInformation().draw_card())
diff --git a/task_protocol/headfixed_task/task_information_independent_reward.py b/task_protocol/headfixed_task/task_information_independent_reward.py
new file mode 100644
index 0000000..a423b6d
--- /dev/null
+++ b/task_protocol/headfixed_task/task_information_independent_reward.py
@@ -0,0 +1,46 @@
+import random
+
+
+class TaskInformation(object):
+    def __init__(self, **kwargs):
+        self.name = "model_based_reinforcement_learning_task"
+        self.deck = [('LED_L', 'left', '1'), ('LED_R',  'right', '2'),
+                     ('LED_L', 'left', '1'), ('LED_R',  'right', '2'),
+                     ('LED_L', 'left', '1'), ('LED_R', 'right', '2'),
+                     ('LED_L', 'left', '1'), ('LED_R', 'right', '2'),
+                     ('LED_L', 'left', '1'), ('LED_R', 'right', '2'),
+                     ('all',  ('left', 'right'), ('1', '2')), ('all',  ('left', 'right'), ('1', '2')),
+                     ('all', ('left', 'right'), ('1', '2')), ('all', ('left', 'right'), ('1', '2')),
+                     ('all', ('left', 'right'), ('1', '2')), ('all', ('left', 'right'), ('1', '2')),
+                     ('all', ('left', 'right'), ('1', '2')), ('all', ('left', 'right'), ('1', '2')),
+                     ('all', ('left', 'right'), ('1', '2')), ('all', ('left', 'right'), ('1', '2')),
+                     ]
+
+    def draw_card(self, phase="independent_reward", fraction=0.5):
+        row_start = 0
+        row_end = len(self.deck)-1
+
+        if phase == 'forced_choice':
+            row_end = 1
+        elif phase == 'free_choice':
+            row_start = 9
+        elif phase == 'forced_choice_left':
+            row_end = 0
+        elif phase == 'forced_choice_right':
+            row_start = 1
+            row_end = 1
+        else:
+            if fraction == 0.5:
+                row_start = 8
+                row_end = 11
+            elif fraction == 0.7:
+                row_start = 6
+            elif fraction == 0.3:
+                row_end = 13
+            elif fraction == 1:
+                row_start = 11
+
+        card = self.deck[random.randint(row_start, row_end)]
+        return card
+
+# print(TaskInformation().draw_card())
\ No newline at end of file
diff --git a/task_protocol/kelly_task/__init__.py b/task_protocol/kelly_task/__init__.py
new file mode 100644
index 0000000..8b13789
--- /dev/null
+++ b/task_protocol/kelly_task/__init__.py
@@ -0,0 +1 @@
+
diff --git a/kelly_record_task.py b/task_protocol/kelly_task/kelly_record_task.py
similarity index 93%
rename from kelly_record_task.py
rename to task_protocol/kelly_task/kelly_record_task.py
index 1440cce..a149eb8 100755
--- a/kelly_record_task.py
+++ b/task_protocol/kelly_task/kelly_record_task.py
@@ -15,7 +15,9 @@
 )
 # all modules above this line will have logging disabled
 
-# import behavbox_test
+# updated with reorganization (on 7/11/2023)
+import sys
+sys.path.insert(0,'/home/pi/RPi4_behavior_boxes/essential')
 import behavbox
 class KellyRecordTask(object):
     def __init__(self, **kwargs):  # name and session_info should be provided as kwargs
diff --git a/kelly_task.py b/task_protocol/kelly_task/kelly_task.py
similarity index 98%
rename from kelly_task.py
rename to task_protocol/kelly_task/kelly_task.py
index 73cae35..f3ce1f1 100755
--- a/kelly_task.py
+++ b/task_protocol/kelly_task/kelly_task.py
@@ -17,7 +17,9 @@
     }
 )
 # all modules above this line will have logging disabled
-
+# updated with reorganization (on 7/11/2023)
+import sys
+sys.path.insert(0,'/home/pi/RPi4_behavior_boxes/essential')
 import behavbox
 
 # adding timing capability to the state machine
diff --git a/run_kelly_task.py b/task_protocol/kelly_task/run_kelly_task.py
similarity index 100%
rename from run_kelly_task.py
rename to task_protocol/kelly_task/run_kelly_task.py
diff --git a/run_record_task.py b/task_protocol/kelly_task/run_record_task.py
similarity index 100%
rename from run_record_task.py
rename to task_protocol/kelly_task/run_record_task.py
diff --git a/session_info_year-month-date.py b/task_protocol/kelly_task/session_info_year-month-date.py
similarity index 100%
rename from session_info_year-month-date.py
rename to task_protocol/kelly_task/session_info_year-month-date.py
diff --git a/task_protocol/self_admin_task/__init__.py b/task_protocol/self_admin_task/__init__.py
new file mode 100644
index 0000000..8b13789
--- /dev/null
+++ b/task_protocol/self_admin_task/__init__.py
@@ -0,0 +1 @@
+
diff --git a/remi_self_admin_task.py b/task_protocol/self_admin_task/remi_self_admin_task.py
similarity index 99%
rename from remi_self_admin_task.py
rename to task_protocol/self_admin_task/remi_self_admin_task.py
index 5b28f8e..76db1a1 100644
--- a/remi_self_admin_task.py
+++ b/task_protocol/self_admin_task/remi_self_admin_task.py
@@ -46,7 +46,9 @@
     }
 )
 # all modules above this line will have logging disabled
-
+# updated with reorganization (on 7/11/2023)
+import sys
+sys.path.insert(0,'/home/pi/RPi4_behavior_boxes/essential')
 import behavbox
 # import ivsa_syringe_pump  # I will need to add the ivsa_syringe_pump class to the behavbox code
 
diff --git a/run_remi_self_admin_task.py b/task_protocol/self_admin_task/run_remi_self_admin_task.py
similarity index 100%
rename from run_remi_self_admin_task.py
rename to task_protocol/self_admin_task/run_remi_self_admin_task.py
diff --git a/run_self_admin_task.py b/task_protocol/self_admin_task/run_self_admin_task.py
similarity index 100%
rename from run_self_admin_task.py
rename to task_protocol/self_admin_task/run_self_admin_task.py
diff --git a/self_admin_task.py b/task_protocol/self_admin_task/self_admin_task.py
similarity index 99%
rename from self_admin_task.py
rename to task_protocol/self_admin_task/self_admin_task.py
index fec7a43..1f04a15 100644
--- a/self_admin_task.py
+++ b/task_protocol/self_admin_task/self_admin_task.py
@@ -36,7 +36,9 @@
     }
 )
 # all modules above this line will have logging disabled
-
+# updated with reorganization (on 7/11/2023)
+import sys
+sys.path.insert(0,'/home/pi/RPi4_behavior_boxes/essential')
 import behavbox
 
 
diff --git a/session_info_self_admin.py b/task_protocol/self_admin_task/session_info_self_admin.py
similarity index 100%
rename from session_info_self_admin.py
rename to task_protocol/self_admin_task/session_info_self_admin.py
diff --git a/treadmill_20211115.ino b/treadmill_20211115.ino
deleted file mode 100644
index 31e5267..0000000
--- a/treadmill_20211115.ino
+++ /dev/null
@@ -1,145 +0,0 @@
-// when the treadmil encoder is located in the front
-// include rev output for stablity
-//#include <digitalWriteFast.h>
-#include <Wire.h>
-#define VERSION "20211112"
-// ===== VERSIONS ======
-#define MAXSPEED    1000.0f  // maximum speed for dac out (mm/sec)
-#define MAXDACVOLTS 2.5f    // DAC ouput voltage at maximum speed
-#define MAXDACCNTS  4095.0f // maximum dac value
-//float maxDACval = MAXDACVOLTS * MAXDACCNTS / 3.3; // limit dac output to max allowed
-float maxDACval = MAXDACVOLTS * MAXDACCNTS / 3.3 / 2; // limit dac output to max allowed // JR edit 5/28/19 make in both directions
-#define encAPin 0
-#define encBPin 1
-#define dacPin  A14
-//#define idxPin  2  // not use d here
-
-// counts per rotation of treadmill encoder wheel
-// 200 counts per rev
-// 1.03" per rev
-// so - 1.03 * 25.4 * pi / 200 /1000 = microns/cnt
-#define MM_PER_COUNT 410950  // actually 1/10^6mm per count since we divide by usecs
-#define DIST_PER_COUNT ((float)MM_PER_COUNT/1000000.0)
-//(float)0.41095
-#define SPEED_TIMEOUT 50000  // if we don't move in this many microseconds assume we are stopped
-static float runSpeed = 0;
-static float lastSpeed = 0;
-volatile uint32_t lastUsecs;
-volatile uint32_t thisUsecs;
-volatile uint32_t encoderUsecs;
-volatile float distance = 0;
-int counts = 0; // net count
-
-int countAdj = 0; // 0-250 and 0-50 for negative 50-250 for positive
-//int rev = 0;//count revolution
-#define FW 1
-#define BW -1
-int dir = FW;
-// ------------------------------------------
-// interrupt routine for ENCODER_A rising edge
-// ---------------------------------------------
-void encoderInt()
-{
-  int ENCA = digitalRead(encAPin);  // always update output
-  int ENCB = digitalRead(encBPin);
-  if (ENCA == ENCB )    // figure out the direction
-  {
-    Serial.print('F');
-    dir = FW;
-    thisUsecs = micros();
-    encoderUsecs = thisUsecs - lastUsecs;
-    lastUsecs = thisUsecs;
-    runSpeed = (float)MM_PER_COUNT / encoderUsecs;
-    distance += DIST_PER_COUNT;
-    counts += 1;
-  }
-  else
-  {
-    Serial.print('B');
-    dir = BW;
-    thisUsecs = micros();
-    encoderUsecs = thisUsecs - lastUsecs;
-    lastUsecs = thisUsecs;
-    runSpeed = (float)MM_PER_COUNT / encoderUsecs* -1;
-    distance -= DIST_PER_COUNT;
-    counts -= 1;
-  }
-}
-void setup()
-{
-  //Serial.begin(115200);
-  //Serial2.begin(115200);
-  Serial.begin(19200);
-  Serial2.begin(19200);
-  //while ( !Serial);  // if no serial USB is connected, may need to comment this out
-  pinMode(encAPin, INPUT_PULLUP); // sets the digital pin as input
-  pinMode(encBPin, INPUT_PULLUP); // sets the digital pin as input
-  analogWriteResolution(12);
-
-  Serial.print("Treadmill Interface V: ");
-  Serial.println(VERSION);
-  Serial.println("distance,speed");
-  Serial.println(maxDACval);
-
-  Wire.begin(8);
-  Wire.setSDA(18);
-  Wire.setSCL(19);
-  Wire.onRequest(sendData);
-
-  lastUsecs = micros();
-  attachInterrupt(encAPin, encoderInt, RISING); // check encoder every A pin rising edge
-}
-void loop()
-{
-  noInterrupts();
-  uint32_t now = micros();
-  uint32_t lastU = lastUsecs;
-  if ( (now > lastU) && ((now - lastU) > SPEED_TIMEOUT)  )
-  { // now should never be < lastUsecs, but sometiems it is
-    // I question if noInterupts works
-    runSpeed = 0;
-  }
-  interrupts();
-  if ( runSpeed != lastSpeed )
-  {
-    lastSpeed = runSpeed;
-    //    float dacval = runSpeed / MAXSPEED * maxDACval;
-    float dacval = (.5 + runSpeed / MAXSPEED) * maxDACval;
-    if ( dacval < 0 ) dacval = 0;
-    if ( dacval > maxDACval) dacval = maxDACval;
-//    Serial.print(distance);
-    countAdj = counts+50;
-    if (countAdj>250)
-    {
-    counts=1;
-    countAdj = 51;
-    }
-    if (counts<-50){
-      counts = -50;
-      countAdj = 0;
-    }
-    Serial.print(countAdj);
-    Serial.print(",");
-    Serial.println(runSpeed);
-    int a=(uint16_t)dacval-730;
-    analogWrite(A14, (uint16_t) dacval);
-    Serial.println("iiiiiiiiiiiiiii");
-    Serial.println(a);
-//    Wire.onRequest(sendData); //for debug purpose
-//    Wire.write(counts); //for transmitting the count as data
-    Serial2.write(counts);//Serial2.write(a);
-  }
-//    Serial.println(distance);d
-}
-
-void sendData()
-{
-//  long Dst = distance;
-//  long Spd = runSpeed;
-//  long data = (Dst << 8) | Spd;
-//  Wire.write(data);
-//  Serial.println(data);
-  Wire.write(counts); //for transmitting the count as data
-//  Wire.write("iiiiiiiiiiiiiii");
-//  Wire.write(a);
-}
\ No newline at end of file