# conditioned imports
if os.name == 'nt':
import yaml
else:
from ruamel import yaml
if not fg.my_dev_flag and fg.i2c:
from I2CDevice import I2CDevice
elif not fg.my_dev_flag and fg.is_serial:
# Quick hack to switch to USB
from SerialDevice import SerialDevice as I2CDevice
# %% Code
# activate logging
logger = logger_createChild('io', 'UC2')
def load_config(config_file):
try:
if not os.path.isfile(config_file):
raise fluidException('File "{0}" not found.'.format(config_file))
tmp_dict = {}
config_load = fluid_load(config_file)
for sub in config_load:
sub_file = uni.Path(config_file.parent, config_load[sub])
if not os.path.isfile(sub_file):
raise fluidException('File "{0}" not found.'.format(sub_file))
tmp_dict[sub] = {}
import tifffile as tif
# math
import numpy as np
from PIL import Image
try:
from scipy.ndimage import gaussian_filter
except Exception as e:
print(str(e))
if not fg.my_dev_flag:
from picamera.array import PiRGBArray
else:
import imageio as imo
# %% parameters and pre starts
logger = logger_createChild('autofocus', 'UC2')
#
# %%
# ----------------------------------- #
# @ interface toolbox @ #
# ----------------------------------- #
def autofocus_callback(self, instance, key, *rargs):
'''
Tests whether autofocus is already running or anything else is blocking. If not: blocks all measurements (and further autofocus-calls) and resets autofocus-count if scheduled.
To block running autofocus, click "AF now" as implemented in Toolbox.run_autofocus-function.
'''
# skip if AF already running
if fg.config['experiment']['autofocus_busy']:
pass
def __init__(self, setup, device):
self.setup = setup
self.device = device
self.topic_base = "/" + self.setup + "/" + self.device + "/"
self.mqtt_subscribe()
self.logger = logger_createChild(self.topic_base, 'UC2')
from I2CBus import I2CBus
elif fg.is_serial:
# Quick hack to switch to USB
from SerialDevice import SerialDevice as I2CDevice
elif fg.is_gpio:
# Quick hack to switch to GPIO
from GPIODevice import GPIODevice as I2CDevice
else:
from MQTTDevice import MQTTDevice
import paho.mqtt.client as mqtt
if not fg.my_dev_flag:
import picamera
# logging Functions ------------------------------------------------------------------------------
logger = logger_createChild('init', 'UC2')
# General Init ------------------------------------------------------------------------------
def controller_init():
if fg.i2c:
arduino_init()
elif fg.is_serial:
serial_init()
elif fg.is_gpio:
gpio_init()
else: # case of e.g. ESP32
mqtt_init()
camera_init()
import fluidiscopeInit
import fluidiscopeToolbox as toolbox
import fluidiscopeIO
import fluidiscopeLogging as fl
if fg.is_use_picamera:
import picamera
# Initialization
fl.logging_init()
fluidiscopeInit.load_config()
fluidiscopeInit.controller_init()
fluidiscopeInit.GUI_define_sizes()
# activate main-logger
logger = fl.logger_createChild('main', 'UC2')
# GUI classes
class Fluidiscope(BoxLayout):
init_var = ListProperty([
fg.config['light']['intensity_expt'],
str(fg.config['motor']['stepsize_z']),
fg.config['light_patterns']['active_p1'],
fg.config['light_patterns']['active_p2'],
fg.config['light_patterns']['active_p3'],
fg.config['light_patterns']['active_p4']
])
meas_var = ListProperty([
toolbox.imaging_set_time_write(fg.config['experiment']['interval']),
'''
Module that contains the tomography code.
'''
from fluidiscopeLogging import logger_createChild
import fluidiscopeGlobVar as fg
import fluidiscopeToolbox as toolbox
import fluidiscopeIO as fio
logger = logger_createChild('tomography','UC2')
# ----------------------------------------------------------------
# Tomographic-Functions
def tomography_callback(self):
'''
Real image acquisition-routine for tomographd mode.
'''
# parameters
nbr_steps = fg.config['tomo']['steps']+1
fg.config['tomo']['done'] = False
# get update (motor-movement direction)
fg.config['tomo']['direction'] = -1 if fg.config['tomo']['posSTART'] >= fg.config['tomo']['posEND'] else 1
if fg.config['tomo']['posSTART'] == fg.config['tomo']['posEND']:
logger.warning("Start and END-Pos are the same hence the system will take {} images at the same position.".format(nbr_steps))
# iterate through tomography stack
for imnbr in range(fg.config['tomo']['steps']+1):