table-py.py

#!/usr/bin/python2
"""
    Todo: 
        make the nested ifs more human readable by moving them to functions
"""
# import all python 2.7 native modules
import serial
import sys
import os
import subprocess
import time
import atexit

# import SerialException class from non-native module: serial
from serial import SerialException


def exit_handler(serial_name):
    """In the event of the user interrupting the program using a 'ctrl + c' command
       or 'keyboard interrupt', this function will attempt to send the off command
       'N' to the arduino in order to switch off the motors and give feedback to the
       user if the off command was written to the USB serial port.

       Args:
                    serial_name (str): The name of the serial port as defined in main()

       Returns:
                    N/A
    """
    # define a serial object using serial_name and connect at the baud rate in use by the arduino
    ser = serial.Serial(serial_name, 9600)
    # write an 'N' character to the serial buffer
    ser.write('N')

    # print a message to the terminal telling the user the program is now closing
    print "\n\nApplication terminating, closing down motor, Goodbye!\n"


def main():
    # try until user uses a keyboard interrupt
    try:
        # register the exit_handler function to exit event
        atexit.register(exit_handler)

        # serial name will be different for a Mac or Linux/GNU
        serial_name = "/dev/cu.usbmodem1411"  # set for Mac

        # define working directory by grabbing the path of the current script
        # can be changed to something like '/home/user/Documents/subfolder' but currently just grabs the directory the python script is in!
        working_directory = sys.path[0]

        # try establishing a serial connection
        try:
            # define serial using name grabbed above
            ser = serial.Serial(serial_name, 9600)

            # look for flags passed as arguments in the system command line
            options = sys.argv

            # if there is an override '--o' flag then the user will be prompted for the custom number of steps they want the table to make, it's usually around 35 per turn.
            if "--o" in options:

                # loop until user gives correct answer
                while True:
                    # ask user to define how many pictures they need per 360 degs via the terminal
                    iterations = raw_input(
                        "\nHow many iterations do you need? ")

                    # try to convert the answer given by the user to a integer
                    try:
                        iterations = int(iterations)
                        break

                    # if variable isnt convertable to an integer ask again for correct input
                    except:
                        print "\nThis is not an integer (whole number), please type in an integer value!\n"

            # otherwise use the default value.
            else:
                iterations = 38

            # if there is an override '--c' flag then the user will be prompted for the number of seconds they want the delay to be between each step and photo.  The camera will turn off and the table will just turn with the object on.
            if "--c" in options:
                # do not use the camera
                camera_override = True

                # loop until user gives correct answer
                while True:
                    # ask user to define how many seconds they want to wait between each step (to simulate presence of a camera)
                    time_interval = raw_input("\nHow many seconds would you like inbetween each step? ")

                    # try to convert the answer given by the user to a integer
                    try:
                        time_interval = int(time_interval)
                        break

                    # if variable isnt convertable to an integer ask again for correct input
                    except:
                        print "\nThis is not an integer (whole number), please type in an integer value!\n"

            # otherwise assume a camera is attached!
            else:
                # loop until user gives correct answer re: institution ID
                while True:

                    # loop until user gives correct answer re: motor type
                    while True:

                        # ask for user to choose between a 5v or a 12v motor by typing a 1 or a 2
                        motor_type = raw_input("\nWhat type of motor are you using (e.g. 1 for 5v, 2 for 12v)? ")

                        # if answer isn't a 1 or a 2 ask again for correct input
                        if motor_type not in ['1', '2']:
                            print "\nPlease select only a '1' or a '2'"
                        else:
                            break

                    # terminal text spacer to make terminal more readable
                    print ""

                    # ask for user to define a unique sample code for each set of photos
                    institution_ID = raw_input("What is the institutional code and unique id for this specimen (e.g. NMBE_XXXX)? ")

                    # terminal text spacer to make terminal more readable
                    print ""

                    # ask user to confirm their choice of sample code
                    confirmation = raw_input("Are you sure you wish to use this ID#: " + institution_ID + "?  Type y/n: ")

                    # if the user confirms move on
                    if confirmation == "y":

                        # terminal text spacer to make terminal more readable
                        print ""
                        break

                    # if the user rejects ask for input again
                    elif confirmation == "n":

                        # terminal text spacer to make terminal more readable
                        print ""

                # loop until the user defines if the sample being photographed is the dorsal or ventral side
                while True:

                    # ask user to use a 'd' or a 'v' to select dorsal or ventral
                    position = raw_input("Dorsal or Ventral?  Type d/v: ")

                    # terminal text spacer to make terminal more readable
                    print ""

                    # ask user to confirm their choice of side
                    confirmation = raw_input("Are you sure you want to use this position: " + position + "?  Type y/n: ")

                    # if the user confirms move on
                    if confirmation == "y":

                        # if dorsal selected set position variable to "DORSAL"
                        if position == "d":
                            position = "DORSAL"
                            break

                        # if ventral selected set position variable to "VENTRAL"
                        elif position == "v":

                            position = "VENTRAL"
                            break

                        # if neither dorsal or ventral selected then ask user to reconfirm their input
                        else:
                            print "\n'd' or 'v' has not been selected, please specify ventral or dorsal by following the instructions!\n"

                    # if the user rejects ask for input again
                    elif confirmation == "n":

                        # terminal text spacer to make terminal more readable
                        print ""

                # flag camera as in user
                camera_override = False

                # adjust the timings if you need to here, default is 0 but if the camera is slow, user can set this higher
                time_interval = 0

            # warn the user of the default settings and the override options.
            if "--o" in options and "--c" in options:

                print "\nRunning program with user specified steps and camera overridden!\n"

            elif "--o" in options and "--c" not in options:

                print "\nRunning program with user specified steps and camera active!\n"

            elif "--o" not in options and "--c" in options:

                print "\nRunning program with default steps and camera overridden!\n"

            else:

                print "Running program in default mode: of 35 photos and steps.\n\nIf you require more per revolution include the flag '--o'.\n\nIf you want to turn off the camera include '--c'.\n"

            # define gphoto2 command to capture images
            cmd = ['gphoto2', '--auto-detect', '--capture-image', '--keep']

            # change to true to attempt test image capture at the start of capture
            check = False

            # here the for loop runs three times prompting the user to change camera positions
            for i in range(0, 3):
                for a in range(1, int(iterations)+1):
                    # code to execute in loop only if camera has been overidden using the --c flag
                    if camera_override == True:
                        if motor_type == '1':
                            ser.write('1')
                        elif motor_type == '2':
                            ser.write('2')

                        # pause program for time interval defined earlier
                        time.sleep(time_interval)

                    else:

                        # check for camera errors!  If it can't connect to the camera to take a picture it will
                        if check != True:

                            print "Taking a test image to see if the camera is working!"

                            # attempt to take a picture using gphoto to control the camera
                            try:
                                # use subprocess to run the gphoto2 terminal program shelless and pass it the command list defined above and the working directory
                                subprocess.check_output(
                                    cmd, cwd=working_directory)

                                # terminal text spacer to make terminal more readable
                                print ""

                                print "Camera works, runing through iterations now!\n"

                                # flag check as True once complete so that no more test photos get taken with each loop
                                check = True

                            # if the subprocess fails tell the user and exit the program
                            except:

                                print "/nThere seems to be an issue communicating with your camera, please check it is plugged in, the battery is charged, it is unmounted, and a supported model for gphoto2!\n"

                                break

                        # use subprocess to run the gphoto2 terminal program shelless and pass it the command list defined above and the working directory
                        process = subprocess.Popen(cmd, cwd=working_directory)

                        output = process.communicate()[0]

                        time.sleep(0.25)

                        print output

                        process.wait()

                        # reset proceed variable each iteration
                        proceed = ''

                        # write to the serial port which motor is in use
                        if motor_type == '1':
                            ser.write('1')
                            print str(a) + " Using motor 1"
                        elif motor_type == '2':
                            ser.write('2')
                            print str(a) + " Using motor 2"

                        # wait for the arduino to signal it is done turning by reading the serial port and looking for a 'D'
                        while (proceed != 'D'):
                            proceed = ser.read()
                            print proceed
                            pass

                        print ""

                    # define the last_int variable by grabbing last count of loop
                    last_int = a-1

                # wait for 3 seconds
                time.sleep(3)

                # write an 'N' to the USB serial port to instruct the arudino to turn off the motor
                ser.write('N')

                # wait for the user to confirm if they wish to keep taking photographs and finish 3 rounds at 3 camera angles?
                while True:

                    # if number of rounds is not equal to 3 (index 0) then keep asking user for input each round
                    if i != 2:
                        continue_run = raw_input("Run " + str(i+1) + " of 3 complete, please reposition the camera, type 'y' and enter to confirm or 'n' to cancel and stop the run. ")

                        # check if user has used a 'y' or an 'n'
                        if continue_run != 'y':

                            # if user rejects continue with an 'n' then break loop
                            if continue_run == 'n':
                                print "\nEnding run, continuing with image processing...\n"
                                break

                            # ask user again if answer was not a 'y' or a 'n'
                            else:
                                print "\nPlease type either 'y' or 'n'\n"

                        # if user confirms with a 'y' then break loop
                        elif continue_run == 'y':
                            break
                        else:
                            print "\nPlease type either 'y' or 'n'\n"

                    # if user rejects continue with an 'n' then break loop
                    if continue_run == 'n':
                        break

                    # if number of rounds is equal to 3 (index 0) then break loop
                    if i == 2:
                        print "Run 3 of 3 complete, moving on to image processing!"
                        break
                print ""

            # define gphoto2 command to list files on camera
            cmd = ['gphoto2', '--auto-detect', '--list-files']

            # use subprocess to run the gphoto2 terminal program shelless and pass it the command list defined above and the working directory
            process = subprocess.Popen(
                cmd, cwd=working_directory, stdout=subprocess.PIPE)

            process.wait()

            # define a variable to hold the list of photographs
            files = []

            # iterate through the output of subprocess and append the file names to the files variable
            for line in iter(process.stdout.readline, ''):

                if "#" in line.rstrip():

                    files.append(line.rstrip())

            # define the number of the last picture taken
            last_pic = int(files[-1].split(" ")[0].strip("#"))

            # loop in reverse using number of photos taken and last file number in order to calculate which files to rename and download
            for i in reversed(range(1, last_int+1)):

                # define the gphoto2 command to download a target image to the working directory
                cmd = ['gphoto2', '--auto-detect', "--filename=" + institution_ID +
                       "_" + position + "_" + str(i) + ".jpg", '--get-file', str(last_pic-i)]

                # use subprocess to run the gphoto2 terminal program shelless and pass it the command list defined above and the working directory
                process = subprocess.Popen(cmd, cwd=working_directory)

                process.wait()

            # tell the user that capture is done
            print "Done!"

        # if serial connection fails to initiate tell the user this is what the issue is
        except SerialException:

            print "Port not found, please make sure the arduino is plugged into the USB port!"

    # trigger keyboard interrupt function and shut down the arduino motors
    except KeyboardInterrupt:
        sys.tracebacklimit = 0


# if script is running from this file run main()
if __name__ == "__main__":
    main()