1 year ago · 1b0824ac55
--- a/COPYING
+++ b/COPYING
@@ -0,0 +1,502 @@
                  GNU LESSER GENERAL PUBLIC LICENSE
                       Version 2.1, February 1999

 Copyright (C) 1991, 1999 Free Software Foundation, Inc.
 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 Everyone is permitted to copy and distribute verbatim copies
 of this license document, but changing it is not allowed.

 [This is the first released version of the Lesser GPL.  It also counts
 as the successor of the GNU Library Public License, version 2, hence
 the version number 2.1.]

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 That's all there is to it!
--- a/LICENSE
+++ b/LICENSE
@@ -1,467 +1,24 @@
 GNU LESSER GENERAL PUBLIC LICENSE

 Version 2.1, February 1999

 Copyright (C) 1991, 1999 Free Software Foundation, Inc.

 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA

 Everyone is permitted to copy and distribute verbatim copies of this license
 document, but changing it is not allowed.

 [This is the first released version of the Lesser GPL. It also counts as the
 successor of the GNU Library Public License, version 2, hence the version
 number 2.1.]

 Preamble

 The licenses for most software are designed to take away your freedom to share
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--- a/README.md
+++ b/README.md
@@ -1,2 +1,10 @@
 # limo-dev
 ### Folder content.
 - pupuicon and puppeteer are the `bespoke` python packages installed in the box.
 - box_test.py is the main program run by the box upon being turned on.

 - server_test.py is a mock script to test how a server is set from python. (In the box for testing purposes.)
 - client_test.py is a mock script to test how to established connection with a server from python. (In my laptop for testing purposes.)

 *Once* _upon_ a time---that is---

 Then our question is this.
--- a/puppeteer/__init__.py
+++ b/puppeteer/__init__.py
@@ -0,0 +1,167 @@
 """
    Puppeteer is the core library behind the light modulator, built to
    create a simple, low level interface with the device. It provides two 
    classes that will let any user program the light modulator: SetupDevice()
    and SetProtocol().\n

    SetupDevice(self, panel_type="rgb", default_filter="No_Filter")\n\t
        Initialise the light modulator and set the routines needed to control
        the hardware,ranging from light modulation, filte#r selection, 
        temperature control and or image acquisition. This library also provides
        the means to calibrate the device if needed, through the function 
        'calibrate()'. It defaults to multi-wavelength panel ('rgb') with no 
        filters. \n

    SetProtocol(with_device=None, filters=("No_Filter",), and_wavelenghts=(3,),
    well_number=96, protocol_name="default_protocol", **kwargs)\n\t
        Defines the core protocol in for the light modulator. It allows the
        selection of multiple settings, ranging from filters to microtitre plate
        type. These options are passed onto the function 'Run()', which lets the
        user run the protocol (for more info, see help(Run)). It defaults to a
        96-well microtitre plate using no filters.
 """

 from ._core import SetupDevice, SetProtocol
 from ._dataparser import export_img_data, export_queue
 import time

 def Controller(USR_INSTRUCTIONS, Connection, cancel_switch, ConnectionStatus,
               BoxQueue, ProtocolStatus):
    """
        Take user instructions and configure the instrument accordingly. If
        a connection is given, it will be used for synchronising reports and
        data transfer.
        
        Returns `Protocol', which is the protocol that has been programmed and
        carries the neccessary directory information to process and export all
        data.
    """
    # Initialise instrument.
    Box = SetupDevice(panel_type='rgb', default_filter='No_Filter')
    # Configure filters
    device_filters = tuple(Box._filter_set)
    user_filters = [device_filters[f] for f in USR_INSTRUCTIONS.user_filters]
    if len(user_filters) == 1:
        user_filters = tuple(user_filters)  # make singleton (iterable)
    # Configure protocol. Additional field: notes='' as **kwarg
    Protocol = SetProtocol(with_device=Box, filters=user_filters,
                           and_wavelenghts=USR_INSTRUCTIONS.user_wavelengths, 
                           well_number=96, protocol_name='default_protocol')
    BoxQueue.put([Protocol, USR_INSTRUCTIONS.QueueFile])  # Export `Protocol' before Run begins.
    # Run Protocol. `Connection' is no longer a dependency of this method as 
    # the log messages produced interfere with the GUI during a protocol run.
    Protocol.Run(assay_length=USR_INSTRUCTIONS.length,
                 read_every=USR_INSTRUCTIONS.frequency,
                 temperature=USR_INSTRUCTIONS.temperature,
                 light_range=USR_INSTRUCTIONS.light_intensities,
                 recalculate_wells=False,
                 process_data=USR_INSTRUCTIONS.process_data,
                 Queue=(USR_INSTRUCTIONS.Queue,
                        USR_INSTRUCTIONS.QueueInfo,
                        USR_INSTRUCTIONS.QueueFile),
                 event=cancel_switch)
    # Safely terminate instrument.
    Box.terminate_device(Connection, False)  # False to forcibly avoid reporting in.
    # Data must be exported _outside_ this function to allow GUI <-> Box 
    # communication during a protocol Run. 
    ProtocolStatus.set()

 def ProtocolTest(Connection, cancel_switch, DoneFlag):
    """
        Run a mock protocol using _all_ filters and wavelengths.
    """
    # Initialise instrument.
    Box = SetupDevice(panel_type='rgb', default_filter='No_Filter')
    # Configure protocol. Additional field: notes='' as **kwarg
    Protocol = SetProtocol(with_device=Box, filters=tuple(Box._filter_set),
                           and_wavelenghts=tuple(range(4)), well_number=96, 
                           protocol_name='test_protocol')
    # Run Protocol. `Connection' is no longer a dependency of this method as 
    # the log messages produced interfere with the GUI during a protocol run.
    Protocol.Run(light_range=(255,),
                 temperature=0,
                 recalculate_wells=True,
                 process_data=False,
                 event=cancel_switch)
    # Safely terminate instrument.
    Box.terminate_device(Connection, False)  # False to forcibly avoid reporting in.
    # Data must be exported _outside_ this function to allow GUI <-> Box 
    # communication during a protocol Run. 
    return Protocol

 def HardwareTest(Connection, ConnectionStatus):
    """
        Initialises the instrument, check for errors, and store the result in 
        a log. Once the log is generated, release the hardware to allow future 
        use.
    """
    Box = SetupDevice(panel_type='rgb', default_filter='No_Filter')
    Box.terminate_device(Connection, ConnectionStatus)

 def TemperatureTest(Connection, ConnectionStatus):
    """
        Routine to test whether the heating unit and temperature sensors operate
        correctly. By default, this routine will:\n
        1) Measure current temperature.
        2) Enable heater for a maximum of 10s.
        3) Measure the temperature once more.\n
        
        Both temperatures (mean ± standard deviation) are reported back to the 
        user, who will decide if the test past based on whether the clicky sound
        made by the heater can be heard and/or abnormalities in the temperature 
        reported (NaNs, abnormal standard deviations or means). 
    """
    # Initialise instrument.
    Box = SetupDevice(panel_type='rgb', default_filter='No_Filter')
    # Measure current temperature and store it in `Box' log.
    CurrentTemperature = Box.report_temperature()
    Box._status_list.append(tuple(["Current Temperature: ",
                                   str(CurrentTemperature.mean().round(decimals=2)) + "±" +
                                       str(CurrentTemperature.std().round(decimals=2))]))
    # Turn heater ON for 10.0 seconds to let `Box' warm up.
    Box._heater.write(Box._HEATER_PIN, 1)  # ON
    time.sleep(10.0)
    Box._heater.write(Box._HEATER_PIN, 0)  # OFF
    # Measure new temperature and store in `Box' log.
    NewTemperature = Box.report_temperature()  # Retrieve temperature after heater ON.
    Box._status_list.append(tuple(["New Temperature: ",
                                   str(NewTemperature.mean().round(decimals=2)) + "±" +
                                       str(NewTemperature.std().round(decimals=2))]))
    # Release hardware and report.
    Box.terminate_device(Connection, ConnectionStatus)

 def QueueStatus(QueueFile, Connection, BUFFER_SIZE=64):
    """ 
        Checks `QueueFile' to report the progress of an experimental protocol
        back to the user. 
    """
    export_queue(QueueFile, Connection, BUFFER_SIZE)  # TODO: change method name from export_queue to report_progress?

 def ExportData(Protocol, ProcessData, Connection, Status, BUFFER_SIZE=64,
               Test=False):
    """
        Export IMG or numerical information. Use variable `Status' to detect 
        wheter a user is connected through GUI or not.
    """
    # Is GUI connected? If so, send data. Otherwise, _WAIT_.
    if Status.is_set():
        log = str("GUI connected, proceeding.\n")
        print(log)
    elif not Status.is_set():
        log = str("No GUI connected. Waiting for one...\n")
        print(log)
        Status.wait()  # This will pause the code until user connects.
    # Export IMG data
    if ProcessData:
        pass
    else:
        for Filter in Protocol._filters:
            export_img_data(Protocol._dir_info, Filter, Connection, BUFFER_SIZE)
        # Export temperature record _ONLY IF_ running a normal protocol. 
        if Test is False:
            export_img_data(Protocol._dir_info, None, Connection, BUFFER_SIZE)
        # House keeping.
        # house_keeper(Protocol._dir_info)
        if Status.is_set:
            Connection.sendall("::Protocol run successfully::".encode())

--- a/puppeteer/__pycache__/__init__.cpython-34.pyc
+++ b/puppeteer/__pycache__/__init__.cpython-34.pyc
--- a/puppeteer/__pycache__/__init__.cpython-37.pyc
+++ b/puppeteer/__pycache__/__init__.cpython-37.pyc
--- a/puppeteer/__pycache__/_core.cpython-34.pyc
+++ b/puppeteer/__pycache__/_core.cpython-34.pyc
--- a/puppeteer/__pycache__/_core.cpython-37.pyc
+++ b/puppeteer/__pycache__/_core.cpython-37.pyc
--- a/puppeteer/__pycache__/_treeparser.cpython-34.pyc
+++ b/puppeteer/__pycache__/_treeparser.cpython-34.pyc
--- a/puppeteer/__pycache__/_treeparser.cpython-37.pyc
+++ b/puppeteer/__pycache__/_treeparser.cpython-37.pyc
--- a/puppeteer/_core.py
+++ b/puppeteer/_core.py
@@ -0,0 +1,844 @@
 import time as t
 import os, pickle
 import numpy as np
 import shutil as sh
 from pigpio import OUTPUT
 import threading, warnings
 from pigpio import pi as dev
 from w1thermsensor import W1ThermSensor as W1
 from picamera import PiCamera as imdev
 from ._treeparser import GenerateTree
 from . import _dataparser as dp
 import cv2

 # Set PINs (MODE == BCM).
 GPIO_PIN_RGB = [17, 27, 22]  # RGB mode, simulated white Ws = R + 0.6*G + B.
 GPIO_PIN_M = 17  # Monocolour mode (white).
 FILTER_PIN = 3  # Servo holding filters.
 HEATER_PIN = 10  # Heating unit.

 # Temperature sampling frequency in seconds.
 TEMPERATURE_SAMPLING_FREQ = 3.0
 TEMPERATURE_TOLERANCE = 1.0

 # Default buffer size in bytes
 BUFFER_SIZE = 64

 # Default camera settings
 DEFAULT_ISO = 10
 ISO_F1 = 100
 ISO_F3 = 400

 def img_acquisition_routine(self, light_range, wavelength, photo_path, 
                            file_name, flag=False, calibrate=False):
    """
        Main image acquisition routine.\n
        
        This method returns a generator that screens through `light_range` and 
        changes the LED intensity accordingly for each `wavelength`. A picture 
        is taken at every iteration. The resulting `file_name` is a composite 
        name, that includes metadata such as time, that here complemented by 
        adding the corresponding `light_intensity` value (i.e. `Read_0s_255`).
        This image is stored locally in `photo_path`.
        
        `flag=False`: 
        Additionaly, an extra picture is saved
        if the highest light intensity is used or else, `flag=True`. Defaults to 
        FALSE.\n
        
        The flag `calibrate' generates images at all intensities and filters
        that are stored locally in the device, used for blank correction in the 
        case data is processed locally. Defaults to FALSE.
    """
    for intensity in light_range:
        if calibrate is True:
            self._modulate_LED_intensity(intensity, channel=wavelength)
            t.sleep(0.5)  # Get's rid of French flag issue... why?
            yield photo_path + file_name +\
                str(intensity).zfill(3) + self._pic_ext
        else:
            self._device._modulate_LED_intensity(intensity, channel=wavelength)
            t.sleep(0.5)  # Get's rid of French flag issue... why?
            yield photo_path + file_name +\
                str(intensity).zfill(3) + self._pic_ext
            if intensity == 255 or flag is True:
                yield photo_path + 'findWells' + self._pic_ext
    # When finished, switch OFF
    if calibrate is True:
        self._modulate_LED_intensity(0, channel=wavelength)
    else:
        self._device._modulate_LED_intensity(0, channel=wavelength)

 def _get_response(Connection, BUFFER_SIZE):
    return Connection.recv(BUFFER_SIZE)

 class SetupDevice:
    """
        Initialise all components and allows the instrument to be programmed.
        and the components are initialised in an OFF state.\n

        'panel_type' defines the type of light panel depending on the
        availability of wavelengths. Possible values are 'rgb', if the light
        panel provides multiple (3) wavelengths, or 'white' if only one is
        available.\n

        'default_filter' defines the filter set during the instrument's set up.
        It defaults to 'No_Filter'.
    """
    def set_filter(self, selected_filter, current_pwm=0):
        """
            Rotate the servo to position defined by dictionary
            'selected_filter'. PWM's in `selected_filter' have been set to
            centre the filter with respect to the camera, facilitating the
            downstream pipeline.\n
            
            To avoid wear of the servo, the program remembers its last PWM 
            and only modulates the servo's locartion if the new PWM is 
            different from its past position.
        """
        # Define servo pulsewidth for each filter position.
        filter_pws = dict()
        if len(self._GPIO_PIN) == 1:
            filter_pws['No_Filter'] = 0  # Monowavelength contains no servo (yet?).
        elif len(self._GPIO_PIN) == 3:
            filter_pws['Filter_1'] = 1775  # 475nm band-pass.
            filter_pws['Filter_2'] = 1460   # 520nm band-pass (centre).
            filter_pws['Filter_3'] = 1130  # 590 long-pass + 610nm short-pass.
            filter_pws['No_Filter'] = 850  # No filter (RGB image).
        else:
            raise ValueError("Channels must be 1 < chnl < 3, but ",
                             str(len(self._GPIO_PIN)), " were specified.")
        # Set filter.
        if selected_filter != "expose_filters":  # Helps with calibration.
            new_pwm = filter_pws[selected_filter]
            if new_pwm != current_pwm:
                self._servo.set_servo_pulsewidth(self._FILTER_PIN, new_pwm)  # Adjust.
                t.sleep(1)  # Gives the servo time to move....
                self._servo.set_PWM_dutycycle(self._FILTER_PIN, 0)  # Turn back OFF.
                current_pwm = new_pwm
            return current_pwm
        elif selected_filter == "expose_filters":
            return sorted(filter_pws)
        return 0

    def _set_temperature(self, current_temperature, target_temperature,
                         TEMPERATURE_TOLERANCE, TEMPERATURE_SAMPLING_FREQ,
                         stop_flag):
        """
            Monitor temperature to make sure it remains as set by the target
            temperature. The method is run as a different thread and therefore 
            allows the rest of the program to carry on whilst monitoring the 
            temperature.\n
            
            The mechanism whereby temperature is regulate is simple: turn heater
            unit ON or OFF whenever the average temperature is below or above  
            `target_temperature'.\n
            
            TODO: Implement a more sophisticated algorithm. 
        """
        current_temperature = np.array(current_temperature)
        # Run forever (whilst the protocol is running).
        MAX_POWER = 255
        while True:
            if stop_flag.is_set():
                break
            
            # If current_temperature < target_temperature, heat up.
            if current_temperature.mean() < target_temperature - TEMPERATURE_TOLERANCE:
                self._heater.set_PWM_dutycycle(self._HEATER_PIN, MAX_POWER)
            elif  target_temperature - TEMPERATURE_TOLERANCE <= current_temperature.mean() < target_temperature:
                self._heater.set_PWM_dutycycle(self._HEATER_PIN, int(MAX_POWER*0.7))
            else:
                self._heater.set_PWM_dutycycle(self._HEATER_PIN, 0)
            temperature = self.report_temperature()
            current_temperature = np.array(temperature)
            t.sleep(1+TEMPERATURE_SAMPLING_FREQ)
        
        # If stop_flag.is_set()... stop heating.
        self._heater.write(self._HEATER_PIN, 0)
        return 0

    def _get_temperatures(self, sensor_id, report):
        """ Retrieve temperature information from sensor_id and include it in
            the report. """
        return report.append(self._sensors[sensor_id].get_temperature())

    def report_temperature(self):
        """ Read temperature from all sensors simultaneously (parallel) and
            report it in degrees Celsius. """
        report = list()
        thread_list = list()
        # Avoid 1s delay "per read" hardcoded in w1 library by running
        # a thread per sensor.
        for sensor_id in self._sensors.keys():
            process = threading.Thread(target=self._get_temperatures,
                                       args=(sensor_id, report))
            process.start()
            thread_list.append(process)
        # Once data retrieved, halt threads.
        for process in thread_list:
            process.join()
        return np.array(report)

    def _init_device(self, dev, OUTPUT, imdev, default_filter):
        """ 
            Initialise devices `dev' and `imdev'. GPIO_PIN is set up 
            automatically depending on panel_type. Servo defaults to PWM given 
            by `default_filter'.
        """
        err_list = list()
        status_list = list()
        # Light Panel
        try:
            light_panel = dev()
            if len(self._GPIO_PIN) == 1:
                light_panel.set_mode(self._GPIO_PIN[0], OUTPUT)
                light_panel.set_PWM_frequency(self._GPIO_PIN[0], 20000)  # Hz (20MHz max with -s 2).
                light_panel.write(self._GPIO_PIN[0], 0)  # Init off state.
            elif len(self._GPIO_PIN) == 3:
                for pin in self._GPIO_PIN:
                    light_panel.set_mode(pin, OUTPUT)
                    light_panel.set_PWM_frequency(pin, 20000)  # Hz (20MHz max with -s 2).
                    light_panel.write(pin, 0)  # Init off state.
            else:
                raise ValueError("Channels must be 1 < chnl < 3, but ",
                                 str(len(self._GPIO_PIN)), " were specified.")
            log = str("Panel... [OK]")
            status = str("OK")
        except:
            log = str("Panel... [FAILED]")
            status = str("FAILED")
            err_list.append(log)
        status_list.append(tuple(["Panel:", status]))
        print(log)

        # Heater
        try:
            heater = dev()
            heater.set_mode(self._HEATER_PIN, OUTPUT)
            heater.write(self._HEATER_PIN, 0)  # Init off state.
            log = str("Heater... [OK]")
            status = str("OK")
        except:
            log = str("Heater... [FAILED]")
            status = str("FAILED")
            err_list.append(log)
        status_list.append(tuple(["Heater:", status]))
        print(log)

        # Sensors
        try:
            w1_init = W1()
            w1_init.RETRY_DELAY_SECONDS = 0.0
            w1_init.RETRY_ATTEMPTS = 3
            n_sensors = len(w1_init.get_available_sensors())
            if n_sensors == 0:
                log = str("No sensors found.")
                status = str("None")
            else:
                # Report sensors.
                log = str(str(n_sensors) + " sensors " +
                            w1_init.type_name + " detected.")
                status = str("OK")
            # Aggregate into one dictionary.
            sensors = dict()
            for s in range(n_sensors):
                exec("sensors['sensor" + str(s) +
                     "'] = w1_init.get_available_sensors()[s]")
        except:
            log = str("Sensors... [FAILED]")
            status = str("FAILED")
            err_list.append(log)
            sensors = dict()
        # Report sensors found.
        status_list.append(tuple(["Sensors:", status]))
        print(log)

        # Camera
        try:
            camera = imdev()
            camera = self._img_settings(camera)
            log = str("Camera... [OK]")
            status = str("OK")
        except:
            log = str("Camera... [FAILED]")
            status = str("FAILED")
            err_list.append(log)
        status_list.append(tuple(["Camera:", status]))
        print(log)

        # Filters
        try:
            servo = dev()
            servo.set_mode(self._FILTER_PIN, OUTPUT)  # BCM mode!
            servo.set_PWM_frequency(self._FILTER_PIN, 50)  # Set servo at 50Hz (**hardware constrain**)
            servo.set_PWM_dutycycle(self._FILTER_PIN, 0)  # Init servo in an OFF state (**AVOID USING WRITE.(PIN, 0)**)
            log = str("Servo ready... [OK]")
            status = str("OK")
        except:
            log = str("Servo ready... [FAILED]")
            status = str("FAILED")
            err_list.append(log)
        status_list.append(tuple(["Servo:", status]))
        
        # Device status
        print("The device has been initialised with " +
              str(len(err_list)) + " errors.\n")
        return light_panel, heater, sensors,\
                camera, servo, err_list, status_list

    def terminate_device(self, Connection, ConnectionStatus):
        """
            Safe release of the hardware. Failure to do so will require the
            instrument to be restarted and release the resources needed to
            control it.
        """
        # Light Panel
        if len(self._GPIO_PIN) == 1:
            self._light_panel.write(self._GPIO_PIN[0], 0)
        elif len(self._GPIO_PIN) == 3:
            for PIN in self._GPIO_PIN:
                self._light_panel.write(PIN, 0)
        else:
            raise ValueError("Channels must be 1 < chnl < 3, but ",
                               str(len(self._GPIO_PIN)), " were specified.")
        self._light_panel.stop()
        # Heater
        self._heater.stop()
        # Sensors ? can they be stopped?
        # Camera
        self._camera.close()
        # Filters
        self._servo.stop()
        # Device status
        log = str("The device has been shut down with " +
                    str(len(self._err_list)) + " errors.\n")
        if len(self._err_list) == 0:
            status = "READY"
        else:
            status = "FAILED"
        # Updata status
        self._status_list.append(tuple(["Status:", status]))
        print(log)
        # Report to GUI
        if ConnectionStatus:
            t.sleep(0.1)  # Prevents mixing msg. TODO: Fix.
            pSize = len(pickle.dumps(self._status_list))
            Connection.sendall(str(pSize).encode())  # Send size of pickle.
            cli = _get_response(Connection, BUFFER_SIZE)
            if cli.decode() == "Acknowledged":
                Connection.sendall(pickle.dumps(self._status_list))

    def _img_settings(self, Camera):
        """
            Define camera settings. Auto-exposure or auto-white-balance result
            in aleatory camera settings depending upon light conditions. _WE DO
            NOT WANT THIS_. Turn them off and fix the camera values, making the
            images independent from light conditions.\n

            The default camera resolution in imdev V2 is HD720p (1280x720), but 
            it is not able to capture the plate (partial sensor area). The
            smallest resolution using full sensor area is 1640x922, which offers
            a good compromise between quality (data) and speed. HD1080p
            resolution takes longer to acquire and process, and it also is
            unable to capture a full microplate due to a different partial
            sensor area used. Information about these limitations can be found
            at https://imdev.readthedocs.io/en/release-1.13/fov.html#sensor-modes
        """
        Camera.hflip = True  # Ensures well A1 is in the bottom-left.
        Camera.awb_mode = 'off'
        Camera.awb_gains = (1.45, 1.45)
        SHUTTER_SPEED = 0.25  # Shutter speed time in SECONDS.
        Camera.shutter_speed = int(SHUTTER_SPEED * 10**6)  # Translate SHUTTER_SPEED to µs.
        Camera.iso = DEFAULT_ISO
        # max_res = Camera.MAX_RESOLUTION  # How big can the image be?
        # Camera.resolution = (int(max_res[0]), int(max_res[1]))
        Camera.resolution = (1640, 1232)  # Smallest resolution with full FoV (partial FoV results in plate not fully captured).
        # imdev v2 has issues with 'exposure_mode = off' causing black img.
        t.sleep(0.1)  # Solves those issues (WTF?) as long as it's _BEFORE_ exposure_mode.
        Camera.exposure_mode = 'off'
        return Camera

    # def _modulate_LED_intensity(self, light_intensity, channel=None):
    #     """ Change LED intensity for a given filter (channel). 'filter' is a
    #         function from python's core library, hence the use of 'channel'
    #         instead. Light panel is switched off prior to changing the filter
    #         to avoid the overlap of multiple wavelengths (LEDs). This step is
    #         fast enough to pass unnotices).\n

    #         In case of an RGB panel, the white light is emulated by reducing
    #         the green LED by 40% (visually checked).\n

    #         GPIO settings for 'rgb' plate_type : R (600nm, 0), G (GFP/YFP, 1)
    #         and B (CFP, 2).
    #     """
    #     available_filters = sorted(list(self._filter_set))
    #     if channel is None:
            # Single LED light panel, only one wavelength.
    #         self._light_panel.set_PWM_dutycycle(self._GPIO_PIN[0],
    #                                             light_intensity)
    #     else:
    #       # Turn off _ALL_ LEDs prior to change settings.
    #       # Otherwise, multiple wavelengths will overlap.
    #         for pin in self._GPIO_PIN:
    #             self._light_panel.write(pin, 0)

    #         if channel == available_filters[0]:  # CFP
    #             self._light_panel.set_PWM_dutycycle(self._GPIO_PIN[2],
    #                                                 light_intensity)
    #         elif channel == available_filters[1]:  # GFP/YFP
    #             self._light_panel.set_PWM_dutycycle(self._GPIO_PIN[1],
    #                                                 light_intensity)
    #         elif channel == available_filters[2]:  # OD
    #             self._light_panel.set_PWM_dutycycle(self._GPIO_PIN[0],
    #                                                 light_intensity)
    #         elif channel == available_filters[3]:
    #           # Simulated white light based on RGB LEDs
    #             self._light_panel.set_PWM_dutycycle(self._GPIO_PIN[0],
    #                                                 light_intensity)
    #             self._light_panel.set_PWM_dutycycle(self._GPIO_PIN[1],
    #                                                 int(light_intensity * 0.6))
    #             self._light_panel.set_PWM_dutycycle(self._GPIO_PIN[2],
    #                                                 light_intensity)

    def _modulate_LED_intensity(self, light_intensity, channel=None):
        """ 
            Change LED intensity for a given filter (channel). 'filter' is a
            function from python's core library, hence the use of 'channel'
            instead. Light panel is switched off prior to changing the filter
            to avoid the overlap of multiple wavelengths (LEDs). This step is
            fast enough to pass unnotices).\n

            In case of an RGB panel, the white light is emulated by reducing
            the green LED by 40% (visually checked).\n

            GPIO settings for 'rgb' plate_type : R (600nm, 0), G (GFP/YFP, 1)
            and B (CFP, 2).
        """
        if channel is None:
            # Single LED light panel, only one wavelength.
            self._light_panel.set_PWM_dutycycle(self._GPIO_PIN[0],
                                                light_intensity)
        else:
            # Turn off _ALL_ LEDs prior to change settings.
            # Otherwise, multiple wavelengths will overlap.
            for pin in self._GPIO_PIN:
                self._light_panel.write(pin, 0)

            if channel == 0:  # CFP
                self._light_panel.set_PWM_dutycycle(self._GPIO_PIN[2],
                                                    light_intensity)
            elif channel == 1:  # GFP/YFP
                self._light_panel.set_PWM_dutycycle(self._GPIO_PIN[1],
                                                    light_intensity)
            elif channel == 2:  # OD
                self._light_panel.set_PWM_dutycycle(self._GPIO_PIN[0],
                                                    light_intensity)
            elif channel == 3:
                # Simulated white light based on RGB LEDs
                self._light_panel.set_PWM_dutycycle(self._GPIO_PIN[0],
                                                    light_intensity)
                self._light_panel.set_PWM_dutycycle(self._GPIO_PIN[1],
                                                    light_intensity)
                self._light_panel.set_PWM_dutycycle(self._GPIO_PIN[2],
                                                    light_intensity)

 ###    def calibrate(self):  # TODO: include independent wavelengths.
 ###        """
 ###            Calibrate device (ABSENCE OF PLATE _REQUIRED_). Record the light
 ###            panel at different light intensities using all available filters.
 ###            This will generate an array of images that will later be use to
 ###            blank correct the data.
 ###        """
 ###        light_range = np.arange(0, 256, 1)
 ###        self._dir_info = GenerateTree(calibrate=True, filters=self._filter_set)  # TODO: change how calibration is detected.
 ###        if self._dir_info._argout == 0:  # 0 = tree created, 1 = already exists.
 ###            # Begin calibration routine
 ###            for flt in self._filter_set:
 ###                self._current_state = self.set_filter(flt)
 ###                photo_path = self._dir_info.root_path +\
 ###                    self._dir_info.ref_path + flt + "/"
 ###                # This method optimises photography time by 1) using JPEG
 ###                # hardware acceleration, 2) avoiding the overheads of
 ###                # initialising cameras' still pipeline (init still port + 
 ###                # encoder for every picture) and 3) eliminating overheads of 
 ###                # initialising preview port. use_video_port can accelerate this 
 ###                # further, but at the expense of a lower quality image.
 ###                self._camera.capture_sequence(img_acquisition_routine(self,
 ###                                                                      light_range,
 ###                                                                      flt,
 ###                                                                      photo_path,
 ###                                                                      self._pic_file_name,
 ###                                                                      flag=False,
 ###                                                                      calibrate=True),
 ###                                              format='jpeg', burst=True,
 ###                                              use_video_port=False, quality=90)
 ###        return self

    def __init__(self, panel_type="rgb", default_filter="No_Filter",
                 connection=None):
        """ 
            Initialise the class SetupDevice. """
        self._pic_file_name = 'Calibration_Int_'
        self._pic_ext = '.jpg'  # JPEG is lossy but hardware-accelerated.
        # Initialise box and filter wheel
        if panel_type.lower() == "white":
            self._GPIO_PIN = list([GPIO_PIN_M])  # `PIN = int' is not iterable.
        elif panel_type.lower() == "rgb":
            self._GPIO_PIN = GPIO_PIN_RGB
        else:
            raise ValueError("Panel type not recognised.")

        self._FILTER_PIN = FILTER_PIN
        self._HEATER_PIN = HEATER_PIN
        
        # Initialise hardware.
        self._light_panel, self._heater,\
        self._sensors, self._camera,\
        self._servo, self._err_list,\
        self._status_list = self._init_device(dev, OUTPUT, imdev,
                                              default_filter)
        # Default filter location.
        self._current_state = []  # Avoids moving the servo unnecessarily. PREV: self.set_filter(default_filter)
        # Available filters.
        self._filter_set = self.set_filter("expose_filters")


 class SetProtocol:
    """
        This class allows to define the steps needed to perform a complete
        laboratory assay. It requires a device, filter set, microtitre plate
        type and a protocol name. The information is channeled by the Run()
        program which is public, meaning the user will interface with Run() to
        initiate the assay.
    """
    def _data_acquisition(self, light_range, time, flt, wavelength, singleRead):
        """ Takes a picture at a given light_intensity. Files are named based
            on light intensity, time and filter used. """
        photo_path = self._dir_info.root_path + self._dir_info.protocol_path +\
                    self._dir_info.img_data_path + flt + "/"
        # If no custom names provided, use a preset name.
        if self._notes == '':
            file_name = self._pic_file_name + str(time) + "s_"
        else:
            file_name = self._pic_file_name + str(time) + "s_" + self._notes

        # This method optimises photography time by 1) using JPEG hardware
        # acceleration, 2) avoiding the overheads of initialising cameras'
        # still pipeline (init still port + encoder for every picture) and 3)
        # eliminating overheads of initialising preview port. use_video_port
        # can accelerate this further, but at the expense of a lower quality
        # image.
        self._device._camera.capture_sequence(img_acquisition_routine(self,
                                                                      light_range,
                                                                      wavelength,
                                                                      photo_path,
                                                                      file_name,
                                                                      flag=singleRead),
                                              format='jpeg', burst=True,
                                              use_video_port=False, quality=90)
        return 0

    def _detect_well_info(self, recalculate_wells,
                          plate_reference="findWells.jpg"):
        """
            Scan the microtitre plate to detect the wells and store their
            location for downstream processing. This can also be used to
            calibrate microtitre plates black plates and then use translucid
            plates (far more common in the laboratory). This routine simplifies
            the well detection algorithm and speed-up the program.
        """
        well_info_file = self._dir_info.root_path +\
                          "/.well_" + str(self._well_number) + "_info.npz"

        if recalculate_wells is True:
            os.remove(well_info_file)

        if not os.path.exists(well_info_file):
            # Detect well location only once, re-use afterwards.
            col_labels, row_labels,\
                img_limits, wells = dp.wells_id(self._dir_info,
                                                plate_reference,
                                                self._filters[0])
            # Store coordinates for future re-use. This command does not support
            # cv2, so 'wells' has to be manipulated so that it can be both
            # stored and loaded correctly by means of the variable
            # 'wells_temp_container'.
            wells_temp_container = list()  # cannot save cv2.KeyPoint, workaround.
            [wells_temp_container.append((well.pt, well.size))
            for well in wells]
            np.savez(well_info_file, col_labels, row_labels,
                     img_limits, wells_temp_container)
        else:
            # If microplate info exists, load well locations. Array order is
            # that used when saving the arrays with np.savez. This command does
            # not support cv2, so 'wells' has to be manipulated so that it can
            # be both stored and loaded correctly by means of the variable
            # 'wells_temp_container'.
            npzfile = np.load(well_info_file)
            col_labels = npzfile['arr_0']
            row_labels = npzfile['arr_1']
            img_limits = npzfile['arr_2']
            wells_temp_container = npzfile['arr_3']
            wells = list()
            [wells.append(cv2.KeyPoint(x=well[0][0], y=well[0][1],
                                       _size=well[1]))
             for well in wells_temp_container]
        return col_labels, row_labels, img_limits, wells

    def _update_queue(self, Queue, QueueInfo, QueueFile, Read):
        QueueInfo[Read].append(str(Queue[Read]))
        fIn = open(QueueFile).read().split('\n')
        fIn[Read+1] = ', '.join(QueueInfo[Read])
        with open(QueueFile, "w") as fOut:
            for line in fIn:
                fOut.writelines(line + "\n")
        print("QueueFile updated.")

    def _check_temperature_file(self):
        path = self._dir_info.root_path + self._dir_info.protocol_path + "/"
        filename = "temperature.csv"
        if os.path.exists(path + filename):
            os.remove(path + filename)

    def _update_temperature(self, current_time):
        # Create file to store temperature record.
        report_path = self._dir_info.root_path +\
                        self._dir_info.protocol_path + "/"
        report_fName = "temperature.csv"
        current_temperature = self._device.report_temperature()
        with open(report_path + report_fName, 'a+') as fOut:
            info = current_temperature.tolist()
            info.insert(0, current_time)
            fOut.writelines(','.join(str(entry) for entry in info) + "\n")

    def Run(self, assay_length="00:00:00", read_every="00:00:00",
            temperature=None, light_range=(0, 255), recalculate_wells=False,
            process_data=True, Queue=None, event=None):
        """
            Run assay. The routine will go through 'light_range' at aleatory
            intervals set by 'read_every' for the duration of the assay (set by
            the 'assay_length' variable). It will calculate well locations once,
            unless stated otherwise by 'recalculate_wells', and will let L|MO™
            process the data.\n\n
            
            `temperature' sets the temperature of the assay. Defaults to NONE 
            (runs at ambient temperature).\n\n
            
            `Queue' contains protocol data concerning the number of jobs to do,
            the waiting time between each job, and their status (queued, 
            completed). Used to keep track of progress from the GUI.\n\n
            
            `event' is a switch to cancel the current `Run' thread and is linked 
            to a button in the GUI. **This switch has a limitation:** once set 
            to TRUE, the thread will remain active until the following iteration
            when it is killed. When the following iteration occurs will depend 
            on the frequency set by the variable `read_every'.
            
            
        """
        # Initialise Queue. If no Queue provided, just read once.
        if Queue is not None:
            """ QueueInfo is a list of tuples: (init_time, status)"""
            [Queue, QueueInfo, QueueFile] = Queue
            ReadsNum = len(Queue)
        else:
            ReadsNum = 1
        
        StatusID = 2  # QueueFile field to modify (0=Date, 1=Time, 2=Status, 3=Inc. time)
        # Transform assay_length into seconds.
        HH, MM, SS = assay_length.split(sep=":")
        ASSAY_LENGTH = int(HH) * 3600 + int(MM) * 60 + int(SS)
        # Transform read_every into seconds.
        HH, MM, SS = read_every.split(sep=":")
        READ_FREQUENCY = int(HH) * 3600 + int(MM) * 60 + int(SS)
        # Run protocol. MAYBE USE A VIDEO INSTEAD OF 256 PICTURES? *NOPE*. Video
        # port uses soft-touch de-noise algorithm and red light stills looks
        # highly aliased.
        servo_state = self._device._current_state
        
        finished = False
        if ASSAY_LENGTH == 0:
            singleRead = True
        else:
            singleRead = False
        
        if ReadsNum > 1:
            self._check_temperature_file()
        
        # Set temperature.
        if "temperature_event" not in locals():
            temperature_event = threading.Event()
            if temperature is not 0:
                current_temperature = self._device.report_temperature()
                temperature_modulation =\
                    threading.Thread(target=self._device._set_temperature,
                                     args=(current_temperature, int(temperature),
                                           TEMPERATURE_TOLERANCE,
                                           TEMPERATURE_SAMPLING_FREQ,
                                           temperature_event))
                temperature_modulation.start()
        
        # Loop until protocol is finished.
        initiation_time = t.time()
        reading_time = 0.0  # Protocols with delay will fail without this. 
        for read in range(ReadsNum):  # Queue
            # Wait/Incubate
            if ReadsNum > 1:
                if Queue[read] == 0.0:
                    t.sleep(Queue[read])
                else:
                    t.sleep(Queue[read] - reading_time)
            
            current_time = int(t.time() - initiation_time)  # Makes t0 = ~0s.
            # Update temperature (even with `ambient', to keep track of it).
            self._update_temperature(current_time)
            
            # Handle cancel_protocol event.
            if event.is_set():
                # cancel_protocol.is_set() is now True. STOP.
                if temperature is not 0:
                    temperature_event.set()
                    temperature_modulation.join()
                log = str("Protocol cancelled.")
                print(log)
                # Retrieve data available until this point.
                # for flt in self._filters:
                    # Retrieve a reference IMG (highest light intensity by default).
                    # Use well location routine to crop images. Force `No_Filter'
                    # setting to ensure wells are detected correctly.
                   # if 'img_limits' not in locals():
                   #     _, _, _, _ = dp.wells_id(self._dir_info,
                   #                              'findWells.jpg',
                   #                              'No_Filter')
                    # TODO: CROP IMG HERE BEFORE SENDING TO MINIMISE DATA TRANSFERRED. [DONE]
                #     dp.export_img_data(self._dir_info, flt, connection, 
                #                         BUFFER_SIZE, status)
                    # export all data to client's GUI.
                    # DO NOT COMPRESS the data before sending. IT-TAKES-AGES.
                    # Send images over the network and delete them from the pi.
                return 1
            # Read plate
            init_time = t.time()  # Used to account for plate reading time.
            for flt, wavelength in zip(self._filters, self._wavelengths):
                # Re-set ISO value to brighten up these filters...
                if flt is "Filter_1":
                    self._device._camera.iso = ISO_F1
                elif flt is "Filter_3":
                    self._device._camera.iso = ISO_F3
                servo_state = self._device.set_filter(flt, current_pwm=servo_state)
                self._data_acquisition(light_range, current_time, flt,
                                       wavelength, singleRead)
                # Restore ISO value to DEFAULT_ISO to prevent overexposure
                # in other filters.
                if flt is "Filter_1" or flt is "Filter_3":
                    self._device._camera.iso = DEFAULT_ISO
                # Turn LED off
                self._device._modulate_LED_intensity(0, channel=wavelength)
            
            # Process data (inc. exporting data)
            if process_data is True:
                # TODO: Compare this to when flag is FALSE.
                log = str("Data acquisition at " + str(current_time) + 
                            "s completed. Exporting numeric data to client...")
                print(log)
                
                # Does well location info exists for microplate? Is it loaded?
                if 'col_labels' not in locals():
                    col_labels, row_labels,\
                          img_limits, wells = self._detect_well_info(recalculate_wells)

                for flt in self._filters:
                    raw_data = dp.read_plate(self._dir_info, wells, flt,
                                             row_labels, col_labels,
                                             img_limits, current_time)
                    dp.export_numeric_data(self._dir_info, raw_data, flt,
                                           current_time, connection,
                                           BUFFER_SIZE, status)
            else:
                pass
            # Wait for the next read. Queue waiting time _already_ in seconds.
            # Account for reading time, otherwise waits incrementally longer.
            if ReadsNum > 1:
                QueueInfo[read][StatusID] = "Completed"  # Update Queue
                self._update_queue(Queue, QueueInfo, QueueFile, read)
                reading_time = t.time() - init_time
        
 #         if process_data is False:
 #             for flt in self._filters:
                # Retrieve a reference IMG (highest light intensity by default).
                # Use well location routine to crop images. Force `No_Filter'
                # setting to ensure wells are detected correctly.
 #                if 'img_limits' not in locals():
 #                    _, _, _, _ = dp.wells_id(self._dir_info,
 #                                             'findWells.jpg',
 #                                             'No_Filter')
                # TODO: CROP IMG HERE BEFORE SENDING TO MINIMISE DATA TRANSFERRED. [DONE]
 #                 dp.export_img_data(self._dir_info, flt, connection,
 #                                    BUFFER_SIZE, status)
                # export all data to client's GUI.
                # DO NOT COMPRESS the data before sending. IT-TAKES-AGES.
                # Send images over the network and delete them from the pi.
        # PROTOCOL FINISHED:
        if temperature is not 0:
            temperature_event.set()  # Stop temperature control thread
            temperature_modulation.join()  
        # End msg.
        log = str("::Protocol run successfully::")
        print(log)
        return 0

    def __init__(self, with_device=None, filters=("No_Filter",), 
                 and_wavelenghts=(3,), well_number=96, 
                 protocol_name="default_protocol", **kwargs):
        """ Main program for SetProtocol(). Initiate class. """
        if with_device is not None:
            self._device = with_device
            self._filters = filters
            self._wavelengths = and_wavelenghts
            # Additional notes, if they exist.
            if 'notes' in kwargs.keys():
                self._notes = kwargs.get('notes')
            else:
                self._notes = ""
            # Set filename pattern
            self._pic_file_name = 'Read_'
            self._pic_ext = '.jpg'
            # Check directory does not exist. TODO: rewrite to remove try/except.
            try:
                self._dir_info = GenerateTree(label=protocol_name,
                                              filters=filters,
                                              annotations=self._notes)
            except FileExistsError as err:
                print("The directory already exists.")
                # possible_answers = ['o', 'r']
                # while True:
                #     answer = input("Do you want to [o]verwrite it or [r]ename it? (o/R): ")
                #     if answer in possible_answers:
                #         break
                #     else:
                #         print("Input not recognised, try again.")

                # Take action
                # if answer.lower() == 'o':  # If overwrite... overwrite.
                # Isolate protocol path (useful when multiple filters used)
                path_strings = err.filename.split(sep="/")
                idx = path_strings.index("data") + 2
                delete_path = "/".join(path_strings[:idx])
                # Regenerate.
                sh.rmtree(delete_path)
                self._dir_info = GenerateTree(label=protocol_name,
                                              filters=filters,
                                              annotations=self._notes)
                # else:
                #     annotations = input("Enter new name: ")
                #     annotations.replace(" ", "_").lower()  # No spaces.
                #     self._notes = annotations
                #     self._dir_info = GenerateTree(label=protocol_name,
                #                                   filters=and_filters,
                #                                   annotations=self._notes)
            self._well_number = int(well_number)
            self._resolution = self._device._camera.resolution
            self._cam_rev = str(self._device._camera.revision)
        else:
            raise ValueError("Instrument not specified.")
--- a/puppeteer/_dataparser/__init__.py
+++ b/puppeteer/_dataparser/__init__.py
@@ -0,0 +1,6 @@
 """
 asd
 """
 from .plate_sniffer import detect_wells as wells_id