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That's all there is to it! |
@@ -1,467 +1,24 @@ | |||
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@@ -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. |
@@ -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 ยฑ 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)) + "ยฑ" + | |||
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)) + "ยฑ" + | |||
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()) | |||
@@ -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 ยตs. | |||
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|MOโข | |||
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.") |
@@ -0,0 +1,6 @@ | |||
""" | |||
asd | |||
""" | |||
from .plate_sniffer import detect_wells as wells_id | |||