circadian experiment folder created

Author: ruthmoon

experiments/snail_circadian_experiment/.DS_Store

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+Title
+========
+
+Aim
+------------
+
+Protocol
+------------
+
+* a
+* b
+* c
+
+
+

experiments/snail_circadian_experiment/README.md

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+"""
+This a small python program to collect, save and visualise data from the serial port in real time.
+Each data point is a scalar number.
+Consecutive data points result in a time series that is assumed to be irregular (i.e. heterogeneous).
+"""
+
+__author__ = "Quentin Geissmann, [http://github.com/qgeissmann]"
+
+
+import os
+import time
+# In order to read from serial port
+import serial
+# Command line argument parsing
+import argparse
+# For basic linear algebra
+import numpy as np
+# To have a queue (FIFO) of values
+from collections import deque
+# Plotting the data
+import pygame
+
+import sys
+import glob
+
+
+_BAUD = 57600
+_N_POINTS = 200
+DISPLAY_WIDTH, DISPLAY_HEIGHT = 1200, 520
+
+
+def plot(screen, time_queue, value_queue, window_size):
+    """
+    The function to draw new data on a window.
+    Calling repetitively this function, with new data, will display a dynamic "scrolling" plot.
+    The y axis if for the values (value_queue) and the x axis is for time.
+    The most recent values are plotted on the right most part of the window, whilst the
+    oldest ones are on the left (until they eventually "leave" the screen)
+
+    :param screen: The display window to draw on
+    :param time_queue: A collection of time stamps
+    :param value_queue:  A collection of y values matching time stamps.
+    :param window_size:  The duration (in seconds) corresponding to the width of the window.
+
+    """
+    # time
+    t = np.array(list(time_queue))
+    # y values
+    values = np.array(list(value_queue), dtype=np.float32)
+    
+    # We scale the signal so that all values lie between 0 and 1
+
+    new_y =  values - np.min(values,0)
+    # the maximal value in y
+    mmax = np.max(new_y,0)
+    # we ensure no division by 0 can happen
+    if mmax == 0:
+        return
+    # after that new_y is between 0 and 1
+    new_y /= np.max(new_y,0)
+    
+    # Now, we scale new_y to the fit int the plotting window
+    new_y *= DISPLAY_HEIGHT
+    new_y = DISPLAY_HEIGHT - new_y
+    
+    #we express time as a proportion of the window size
+    new_t = t - t[0]
+    new_t *= (DISPLAY_WIDTH/float(window_size))
+
+    # Clear the window (filling with black)
+    screen.fill((0,0,0))
+
+    # Creating points (i.e. `x,y` tuples of int values)
+    pts = [(int(x),int(y)) for x,y in zip(new_t, new_y )]
+    # Then drawing in yellow
+    pygame.draw.lines(screen, (255, 255, 0),False, pts, 3)
+    pygame.display.flip()
+    
+
+
+def serial_ports():
+    """Lists serial ports, from:
+    http://stackoverflow.com/questions/12090503/listing-available-com-ports-with-python
+
+    :raises EnvironmentError:
+        On unsupported or unknown platforms
+    :returns:
+        A list of available serial ports
+    """
+    if sys.platform.startswith('win'):
+        ports = ['COM' + str(i + 1) for i in range(256)]
+
+    elif sys.platform.startswith('linux') or sys.platform.startswith('cygwin'):
+        # this is to exclude your current terminal "/dev/tty"
+        ports = glob.glob('/dev/tty[A-Za-z]*')
+
+    elif sys.platform.startswith('darwin'):
+        ports = glob.glob('/dev/tty.*')
+
+    else:
+        raise EnvironmentError('Unsupported platform')
+
+    result = []
+    for port in ports:
+        try:
+            s = serial.Serial(port)
+            s.close()
+            result.append(port)
+        except (OSError, serial.SerialException):
+            pass
+    return result
+
+
+if __name__ == "__main__":
+    
+    
+    # parsing command line arguments
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--port', help='port', type=str, default=None)
+    parser.add_argument('--vws', help='The duration of the viewing window (s)', type=int, default=20)
+    parser.add_argument('--out', help='An optional output file', type=str, default=os.devnull)
+
+    args = parser.parse_args()
+    arg_dict = vars(args)
+    window_size = arg_dict["vws"]
+    out_file = arg_dict["out"]
+    
+    # Here we open the serial port
+    port = arg_dict["port"]
+    if port is None:
+        print "Scanning serial ports..."
+        ports = serial_ports()
+        if len(ports) == 0:
+            raise Exception("No serial port found. Ensure your device is plugged. You ab also explicitly use the option `--port`")
+        elif len(ports) > 2:
+            print "%i serial ports found:\n %s" % (len(ports), "\n\t".join(ports))
+        port = ports[0]
+        print "Using %s " % port
+
+
+    serial_port = serial.Serial(port, _BAUD, timeout=2)
+    
+    # We start a timer using the real time from the operating system
+    start = time.time()
+    
+    # Then we make two queues (FIFO containers); one for the values and one for the time stamps
+    time_queue, value_queue = deque(), deque()
+
+    # We need to initialise pygame
+    pygame.init()
+
+    # We build the pygame window before we can start painting inside
+    display = pygame.display.set_mode((DISPLAY_WIDTH, DISPLAY_HEIGHT))
+    # Let us set the window name as well
+    pygame.display.set_caption('Snail Heart Rate Monitor')
+    
+    # The `with statement` will ensure the file is closed properly, should any exception happen
+    with open(out_file, "w") as f:
+        try:
+            # Header of a csv like file
+            f.write("t, y\n")
+
+            # Infinite loop
+            while True:
+                # we read a line from serial port and remove any `\r` and `\n` character
+                line = serial_port.readline().rstrip()
+                # Just after, we get a time stamp
+                now = time.time()
+                # we try to convert the line to an integer value
+                try:
+                    value =  float(line)
+
+                # If something goes wrong, we do not stop, but we print the error message
+                except ValueError as e:
+                    print e
+                    continue
+
+                # The relative time from the start of the program is `dt`
+                dt =  now - start
+
+                # We write a formatted line to the end of the result file
+                f.write("%f, %f\n" % (dt, value))
+
+                # We append relative time and value to their respective queues
+                time_queue.append(dt)
+                value_queue.append(value)
+
+                # We wait to have at least five points AND three seconds of data
+                if time_queue[-1] < 3 or len(time_queue) < 5:
+                    continue
+
+                # Now, we remove/forget from the queues any value older than the window size
+                # This way. we will only plot the last n (default 20) seconds of data
+                while time_queue[-1] - time_queue[0] > window_size:
+                    time_queue.popleft()
+                    value_queue.popleft()
+
+                # Now we plot the values
+                plot(display, time_queue, value_queue, window_size)
+
+                # So that the program stops if we close the window
+                for et in pygame.event.get():
+                    if et.type == pygame.QUIT:
+                        raise KeyboardInterrupt
+
+
+        except KeyboardInterrupt:
+            print "Interrupting program..."

experiments/snail_circadian_experiment/acquisition.py

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+library("data.table")
+df <- fread("20150313_johnDoe.txt") 
+
+#todo INTERPOLATION/RESAMPLING here
+
+df$min <- round(df$t /60)
+ldf <- split(df, df$min)
+
+pdf("visual.pdf",w=16,h=9)
+par(mfrow=c(2,1))
+for(d in ldf){
+	h <- round(d$t[1] / 3600,3)
+	title <- paste0("Starts at h = ", h)
+	print(title)
+	plot(y ~ t, d, type='l', main=title)
+	acf(d$y, lag.max=100)
+}
+dev.off()

experiments/snail_circadian_experiment/analysis.R

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+int time_on = 5000;//us
+int time_off = 200;
+int light_pin = 6;
+int sensor_pin = 4;
+int N = 64;
+
+
+void setup(){
+	// put your setup code here, to run once:
+	Serial.begin(57600);
+	pinMode(light_pin,OUTPUT);
+	pinMode(sensor_pin,INPUT);
+	digitalWrite(light_pin,HIGH);
+	analogReference(EXTERNAL);
+}
+
+void loop() {
+	unsigned long t0 = millis();
+
+	float accum = 0;
+	
+	digitalWrite(light_pin,HIGH);
+	delayMicroseconds(time_on);
+	
+	//sample as many times as N
+	for(int i = 0; i < N; i++) {
+		// We increment the accumulator by the value in the phototransistor pin
+		accum += analogRead(sensor_pin);
+	}
+
+	digitalWrite(light_pin, LOW);
+	
+	accum = accum / N;
+	Serial.println(accum);
+
+	unsigned long t1 = millis();
+	unsigned long dt = t1 - t0;
+	
+	delay(time_off - dt);
+}

experiments/snail_circadian_experiment/arduino.iso

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+Data units
+============
+time (seconds), light intensity (a.u.), temperature (C)

experiments/snail_circadian_experiment/results/.DS_Store

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+temperature_experiment,,,,,,,,,
+ID,temp_file,heart_file,date_begin_dd/mm/yy,date_end_dd/mm/yy,mass_g,size_cm,box_N,uploaded_Y/N,notes
+009,temp_009_010.csv,heart_009.csv,07/05/15,08/05/15,14.190,4.2,S5,Y,-
+010,temp_009_010.csv,heart_010.csv,07/05/15,08/05/15,15.188,4.5,S5,Y,-
+011,temp_011_012.csv,heart_011.csv,08/05/15,09/05/15,14.177,4.2,S5,Y,-
+012,temp_011_012.csv,heart_012.csv,08/05/15,09/05/15,10.181,4.0,S5,Y,weighed_when_(w.w.)_non_dormant
+013,temp_013_014.csv,heart_013.csv,11/05/15,12/05/15,10.870,4.0,S6,Y,-
+014,temp_013_014.csv,heart_014.csv,11/05/15,12/05/15,12.427,4.1,S6,Y,-
+015,temp_015_016.csv,heart_015.csv,12/05/15,13/05/15,12.652,4.1,S6,Y,-
+016,temp_015_016.csv,heart_016.csv,12/05/15,13/05/15,11.432,3.9,S7,Y,-
+017,temp_017_018.csv,heart_017.csv,13/05/15,14/05/15,10.632,4.0,S7,Y,protective_bubble_w.w.
+018,temp_017_018.csv,heart_018.csv,13/05/15,14/05/15,11.474,4.1,S8,Y,-
+019,temp_019_020.csv,heart_019.csv,14/05/15,15/05/15,11.523,4.1,S8,Y,foam_w.w.
+020,temp_019_020.csv,heart_020.csv,14/05/15,15/05/15,13.331,4.4,S8,Y,-
+021,temp_021_022.csv,heart_021.csv,15/05/15,16/05/15,12.325,4.1,S8,N,-
+022,temp_021_022.csv,heart_022.csv,15/05/15,16/05/15,11.401,4.0,S7,N,-
+,,,,,,,,,
+experiment_trials,,,,,,,,, 
+ID,file,,date_begin_dd/mm/yy,date_end_dd/mm/yy,mass_g,size_cm,box_N,uploaded_Y/N,notes
+001,temp_001.csv,,27/03/15,29/03/15,12.18,3.3,S12,Y,-
+002,temp_002.csv,,28/03/15,29/03/15,,,S12,Y,-
+003,temp_003.csv,,29/03/15,30/03/15,,,S12,Y,-
+004,temp_004.csv,,30/03/15,31/03/15,,,S12,Y,-
+005,temp_005.csv,,31/03/15,01/04/15,,,S12,Y,-
+006,temp_006.csv,,28/04/15,29/04/15,10.760,3.8,S9,Y,-
+007,temp_007.csv,,28/04/15,29/04/15,9.035,3.5,S9,Y,-
+007,temp_008.csv,,29/04/15,29/04/15,9.035,3.5,S9,Y,-
+007,temp_009.csv,,29/04/15,29/04/15,9.035,3.5,S9,Y,-
+007,temp_010.csv,,30/04/15,01/05/15,9.035,3.5,S9,Y,-
+008,temp_011.csv,,01/05/15,02/05/15,8.860,3.7,S9,Y,heart_rate
+008,tempC_011.csv,,01/05/15,02/05/15,8.860,3.7,S9,Y,temperature