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Per wavelength shutter speeds implementation

master
Carlos Reding 1 year ago
parent
6ce65b6c7b
commit
fe2224697f
4 changed files with 68 additions and 46 deletions
Split View Show Diff Stats
  1. 2
    2
      puppeteer/__init__.py
  2. 60
    41
      puppeteer/_core.py
  3. 4
    1
      pupuicon/translator/_core.py
  4. 2
    2
      pupuicon/translator/handlers/hardwareVariables.py

+ 2
- 2
puppeteer/__init__.py View File

@@ -38,7 +38,7 @@ def Controller(USR_INSTRUCTIONS, Connection, cancel_switch, ConnectionStatus,
# Configure protocol. Additional field: notes='' as **kwarg
Protocol = SetProtocol(with_device=Box, filters=user_filters,
and_wavelenghts=USR_INSTRUCTIONS.user_wavelengths,
well_number=96, PREHEAT_TIME=15.0,
well_number=96, PREHEAT_TIME=10.0,
protocol_name='default_protocol')
if BoxQueue:
BoxQueue.put([Box, Protocol, USR_INSTRUCTIONS.QueueFile]) # Export `Protocol' before Run begins.
@@ -69,7 +69,7 @@ def ProtocolTest(Connection, cancel_switch, DoneFlag):
# 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,
PREHEAT_TIME=15.0, protocol_name='test_protocol')
PREHEAT_TIME=10.0, 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,),

+ 60
- 41
puppeteer/_core.py View File

@@ -34,17 +34,20 @@ if os.path.exists(Path + hw_fName):
__FILTER_PWM__ = hwSettings["filterSet"] # Filter locations
# Default camera settings
__SHUTTER_SPEED__ = hwSettings["SHUTTER_SPEED"] # Shutter speed time in SECONDS.
DEFAULT_ISO = hwSettings["DEFAULT_ISO"]
ISO_F1 = hwSettings["ISO_F1"]
ISO_F2 = hwSettings["ISO_F2"]
ISO_F3 = hwSettings["ISO_F3"]
__DEFAULT_SHUTTER_SPEED__ = hwSettings["DEFAULT_SHUTTER_SPEED"] # Shutter speed time in SECONDS.
__SHUTTER_SPEED_L1__ = hwSettings["SHUTTER_SPEED_L1"] # Shutter speed time in SECONDS.
__SHUTTER_SPEED_L2__ = hwSettings["SHUTTER_SPEED_L2"] # Shutter speed time in SECONDS.
__SHUTTER_SPEED_L3__ = hwSettings["SHUTTER_SPEED_L3"] # Shutter speed time in SECONDS.
__DEFAULT_ISO__ = hwSettings["DEFAULT_ISO"]
__ISO_F1__ = hwSettings["ISO_F1"]
__ISO_F2__ = hwSettings["ISO_F2"]
__ISO_F3__ = hwSettings["ISO_F3"]
# Light frequencies
DEFAULT_LIGHT_FREQ = hwSettings["DEFAULT_LIGHT_FREQ"]
LIGHT_FREQ_F1 = hwSettings["LIGHT_FREQ_F1"]
LIGHT_FREQ_F2 = hwSettings["LIGHT_FREQ_F2"]
LIGHT_FREQ_F3 = hwSettings["LIGHT_FREQ_F3"]
__DEFAULT_LIGHT_FREQ__ = hwSettings["DEFAULT_LIGHT_FREQ"]
__LIGHT_FREQ_F1__ = hwSettings["LIGHT_FREQ_F1"]
__LIGHT_FREQ_F2__ = hwSettings["LIGHT_FREQ_F2"]
__LIGHT_FREQ_F3__ = hwSettings["LIGHT_FREQ_F3"]
# Replicates
__REPLICATES__ = hwSettings["cameraRepetitions"]
@@ -64,22 +67,25 @@ else:
__FILTER_PWM__["No_Filter"] = 1460 # No filter (RGB image).
# Default camera settings
__SHUTTER_SPEED__ = 0.1 # Shutter speed time in SECONDS.
DEFAULT_ISO = 10
ISO_F1 = 100
ISO_F2 = 100
ISO_F3 = 400
__DEFAULT_SHUTTER_SPEED__ = 0.1 # Shutter speed time in SECONDS.
__SHUTTER_SPEED_L1__ = 0.1 # Shutter speed time in SECONDS.
__SHUTTER_SPEED_L2__ = 0.1 # Shutter speed time in SECONDS.
__SHUTTER_SPEED_L3__ = 0.1 # Shutter speed time in SECONDS.
__DEFAULT_ISO__ = 10
__ISO_F1__ = 100
__ISO_F2__ = 100
__ISO_F3__ = 400
# Light frequencies
DEFAULT_LIGHT_FREQ = 20000
LIGHT_FREQ_F1 = 200
LIGHT_FREQ_F2 = 200
LIGHT_FREQ_F3 = 200
__DEFAULT_LIGHT_FREQ__ = 20000
__LIGHT_FREQ_F1__ = 200
__LIGHT_FREQ_F2__ = 200
__LIGHT_FREQ_F3__ = 200
# Replicates
__REPLICATES__ = 3

def _img_settings(Camera, Filter=None):
def _img_settings(Camera, Filter=None, Wavelength=None):
"""
Private method. Define camera settings. Auto-exposure or
auto-white-balance result in aleatory camera settings depending upon
@@ -105,6 +111,9 @@ def _img_settings(Camera, Filter=None):
Filter : string or None, optional
Specify filter being used. Used in case there is a need to specify
camera settings for each filter installed in the light modulator.
Wavelength : int
Value between 0 and 3, where 0 means *Filter_1*, 1 means
*Filter_2*, 2 means *Filter_3* and 3 means *No_Filter*.
Returns
-------
@@ -117,18 +126,28 @@ def _img_settings(Camera, Filter=None):
Camera.hflip = True # Ensures well A1 is in the bottom-left.
Camera.awb_mode = 'off'
Camera.awb_gains = (1.45, 1.45)
SHUTTER_SPEED = __SHUTTER_SPEED__ # Shutter speed _IN SECONDS_.
# De-couple shutter speeds from filters used, link to LED.
# Set ISO for each Filter.
if Filter == "Filter_1":
Camera.iso = ISO_F1
Camera.iso = __ISO_F1__
elif Filter == "Filter_2":
# SHUTTER_SPEED = 5 # Uncomment after Rob/Kai tests
Camera.iso = ISO_F2
Camera.iso = __ISO_F2__
elif Filter == "Filter_3":
Camera.iso = ISO_F3
Camera.iso = __ISO_F3__
else: # NO_FILTER
Camera.iso = __DEFAULT_ISO__
# Set shutter speeds for each LED
if Wavelength == 0:
SHUTTER_SPEED = __SHUTTER_SPEED_L1__
elif Wavelength == 1:
SHUTTER_SPEED = __SHUTTER_SPEED_L2__
elif Wavelength == 2:
SHUTTER_SPEED = __SHUTTER_SPEED_L3__
else:
Camera.iso = DEFAULT_ISO
SHUTTER_SPEED = __DEFAULT_SHUTTER_SPEED__
Camera.framerate = 1/SHUTTER_SPEED # slowest SHUTTER_SPEED = 1/framerate. Autoadjust.
Camera.shutter_speed = int(SHUTTER_SPEED * 10**6) # Translate SHUTTER_SPEED to µS.
Camera.shutter_speed = int(SHUTTER_SPEED * 10**6) # Translate SHUTTER_SPEED to µs.
# 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).
@@ -238,7 +257,7 @@ def img_acquisition_routine_replicates(self, light_intensity, wavelength,
"""
for r in range(replicates):
self._device._modulate_LED_intensity(light_intensity, channel=wavelength)
t.sleep(__SHUTTER_SPEED__)
t.sleep(self._device._camera.shutter_speed / 10**6) # From µs to seconds.
yield photo_path + file_name + str(r) + self._pic_ext
if light_intensity == 255 or flag is True:
yield photo_path + "findWells" + self._pic_ext
@@ -503,12 +522,12 @@ class SetupDevice:
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], DEFAULT_LIGHT_FREQ) # Hz (20KHz max with -s 2).
light_panel.set_PWM_frequency(self._GPIO_PIN[0], __DEFAULT_LIGHT_FREQ__) # Hz (20KHz 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, DEFAULT_LIGHT_FREQ) # Hz (20KHz max with -s 2).
light_panel.set_PWM_frequency(pin, __DEFAULT_LIGHT_FREQ__) # Hz (20KHz max with -s 2).
# light_panel.write(pin, 0) # Init off state.
else:
raise ValueError("Channels must be 1 < chnl < 3, but ",
@@ -733,7 +752,7 @@ class SetupDevice:

self._FILTER_PIN = FILTER_PIN
self._HEATER_PIN = HEATER_PIN
self.__SHUTTER_SPEED__ = __SHUTTER_SPEED__
self.__SHUTTER_SPEED__ = __DEFAULT_SHUTTER_SPEED__
# Initialise hardware.
self._light_panel, self._heater,\
@@ -1090,39 +1109,39 @@ class SetProtocol:
# Check if `wavelenght' is WHITE, as it is produced by combining mutiple PIN
if wavelength == 3:
for PIN in range(len(self._device._GPIO_PIN)):
self._device._light_panel.set_PWM_frequency(self._device._GPIO_PIN[PIN], DEFAULT_LIGHT_FREQ)
self._device._light_panel.set_PWM_frequency(self._device._GPIO_PIN[PIN], __DEFAULT_LIGHT_FREQ__)
else:
self._device._light_panel.set_PWM_frequency(self._device._GPIO_PIN[wavelength], LIGHT_FREQ_F1)
self._device._light_panel.set_PWM_frequency(self._device._GPIO_PIN[wavelength], __LIGHT_FREQ_F1__)
elif flt == "Filter_2":
# Check if `wavelenght' is WHITE, as it is produced by combining mutiple PIN
if wavelength == 3:
for PIN in range(len(self._device._GPIO_PIN)):
self._device._light_panel.set_PWM_frequency(self._device._GPIO_PIN[PIN], DEFAULT_LIGHT_FREQ)
self._device._light_panel.set_PWM_frequency(self._device._GPIO_PIN[PIN], __DEFAULT_LIGHT_FREQ__)
else:
self._device._light_panel.set_PWM_frequency(self._device._GPIO_PIN[wavelength], LIGHT_FREQ_F2)
self._device._light_panel.set_PWM_frequency(self._device._GPIO_PIN[wavelength], __LIGHT_FREQ_F2__)
elif flt == "Filter_3":
# Check if `wavelenght' is WHITE, as it is produced by combining mutiple PIN
if wavelength == 3:
for PIN in range(len(self._device._GPIO_PIN)):
self._device._light_panel.set_PWM_frequency(self._device._GPIO_PIN[PIN], DEFAULT_LIGHT_FREQ)
self._device._light_panel.set_PWM_frequency(self._device._GPIO_PIN[PIN], __DEFAULT_LIGHT_FREQ__)
else:
self._device._light_panel.set_PWM_frequency(self._device._GPIO_PIN[wavelength], LIGHT_FREQ_F3)
self._device._light_panel.set_PWM_frequency(self._device._GPIO_PIN[wavelength], __LIGHT_FREQ_F3__)
elif flt == "No_Filter":
if wavelength == 0:
self._device._light_panel.set_PWM_frequency(self._device._GPIO_PIN[wavelength], LIGHT_FREQ_F1)
self._device._light_panel.set_PWM_frequency(self._device._GPIO_PIN[wavelength], __LIGHT_FREQ_F1__)
elif wavelength == 1:
self._device._light_panel.set_PWM_frequency(self._device._GPIO_PIN[wavelength], LIGHT_FREQ_F2)
self._device._light_panel.set_PWM_frequency(self._device._GPIO_PIN[wavelength], __LIGHT_FREQ_F2__)
elif wavelength == 2:
self._device._light_panel.set_PWM_frequency(self._device._GPIO_PIN[wavelength], LIGHT_FREQ_F3)
self._device._light_panel.set_PWM_frequency(self._device._GPIO_PIN[wavelength], __LIGHT_FREQ_F3__)
else:
for PIN in range(len(self._device._GPIO_PIN)):
self._device._light_panel.set_PWM_frequency(self._device._GPIO_PIN[PIN], DEFAULT_LIGHT_FREQ)
self._device._light_panel.set_PWM_frequency(self._device._GPIO_PIN[PIN], __DEFAULT_LIGHT_FREQ__)
# Set camera on-the-fly to adapt to different wavelenghts.
# Because this step happens with any filter, it does not require
# a post-read reset.
self._preheat_channel(wavelength) # Preheat LEDs. **DO NOT** move from here.
self._device._camera = _img_settings(self._device._camera,
Filter=flt)
Filter=flt, Wavelength=wavelength)
servo_state = self._device.set_filter(flt, current_pwm=servo_state)
self._data_acquisition(light_range, current_time, flt,
wavelength, referenceRead)

+ 4
- 1
pupuicon/translator/_core.py View File

@@ -203,7 +203,10 @@ class HardwareHandler():
hwSettings["ISO_F1"] = Settings.ISO_F1
hwSettings["ISO_F2"] = Settings.ISO_F2
hwSettings["ISO_F3"] = Settings.ISO_F3
hwSettings["SHUTTER_SPEED"] = Settings.SHUTTER_SPEED
hwSettings["DEFAULT_SHUTTER_SPEED"] = Settings.DEFAULT_SHUTTER_SPEED
hwSettings["SHUTTER_SPEED_L1"] = Settings.SHUTTER_SPEED_L1
hwSettings["SHUTTER_SPEED_L2"] = Settings.SHUTTER_SPEED_L2
hwSettings["SHUTTER_SPEED_L3"] = Settings.SHUTTER_SPEED_L3
# Light settings
hwSettings["DEFAULT_LIGHT_FREQ"] = Settings.DEFAULT_LIGHT_FREQ
hwSettings["LIGHT_FREQ_F1"] = Settings.LIGHT_FREQ_F1

+ 2
- 2
pupuicon/translator/handlers/hardwareVariables.py View File

@@ -45,9 +45,9 @@ class hardwareVariables():
self.ISO_MIN = 1
self.ISO_MAX = 800
self.SHUTTER_SPEED = 0.25 # Shutter speed time in SECONDS. Defaults to 0.25s
self.SHUTTER_SPEED_MIN = 0.1
self.SHUTTER_SPEED_MIN = 0.01
self.SHUTTER_SPEED_MAX = 2
self.SHUTTER_SPEED = self.SHUTTER_SPEED_MAX # Shutter speed time in SECONDS. Defaults to MAX
# Default light frequency (Hz)
self.DEFAULT_LIGHT_FREQ = 20000

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