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sync_PZTcam.py
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sync_PZTcam.py
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# -*- coding: utf-8 -*-
"""
Created on Fri Sep 28 14:20:44 2018
@author: Evangelos Tzardis
"""
from time import sleep, time
import serial
import mylibrary as mlb
import rw_config as cfg
import numpy as np
import imageio
import os
#def init_camera():
# settings = ['acquisition mode','continuous',\
# 'pixel format','mono16',\
# 'exposure auto','off',\
# 'exposure time', '396',\
# 'width','84',\
# 'height','22',\
# 'offset x','508',\
# 'offset y','546',\
# 'trigger mode','on',\
# 'trigger source','software']
# cfg.write_config(settings)
# cam_num = 0
#
# # Init camera, set configurations
# cam_nodes = mlb.run_camera(cam_num)
#
# return cam_nodes
def init_camera():
# read config file
config_with = 'IMAGE SEQUENCE CONFIGURATION'
config_with_enum = 1
section = cfg.load_config(config_with)
section = section[0]
keys = ['height','width']
settings = [ section[key] for key in keys ]
# Init camera, set configurations
cam_num = 0
nodes = mlb.run_camera(cam_num, config_with_enum)
return [nodes, settings]
def encode_int2fixednumbytes(number):
max_num = 5
enc = str(number)+'\n'
while len(enc) < max_num:
enc = '0' + enc
return str.encode(enc)
cam_nodes, cam_settings = init_camera()
cam = cam_nodes[0]
mode = input('Enter \'c\' for calibration or \'m\' for measurement...')
while(mode != 'c' and mode != 'm'):
mode = input('Enter \'c\' for calibration or \'m\' for measurement...')
#input('Capture sample illuminance: Enter when ready...')
#Is = mlb.trigger_image_acquisition(cam_nodes)
#Is = gaussian_filter(Is, sigma=5)
#
#input('Capture reference illuminance: Enter when ready...')
#Ir = mlb.trigger_image_acquisition(cam_nodes)
#Ir = gaussian_filter(Ir, sigma=5)
#
#input('Capture background illuminance: Enter when ready...')
#Ib = mlb.trigger_image_acquisition(cam_nodes)
#Ib = gaussian_filter(Ib, sigma=5)
if mode == 'c':
subfolder = '\\images_calibration'
elif mode == 'm':
subfolder = '\\images_measurement'
folder = os.path.dirname(os.path.realpath(__file__)) + subfolder + '\\stack'
folder_srb = folder + '\\IsIrIb'
if not os.path.exists(folder):
os.makedirs(folder)
if not os.path.exists(folder_srb):
os.makedirs(folder_srb)
#imageio.imsave(folder_srb + '\\Is.tiff', Is)
#imageio.imsave(folder_srb + '\\Ir.tiff', Ir)
#imageio.imsave(folder_srb + '\\Ib.tiff', Ib)
input('Enter to continue...')
ser = serial.Serial('COM4', 9600) # Establish the connection on a specific port
sleep(4)
max_steps = 4096 # minimum step: 1 mV, maximum step: 4096 mV
steps = 600
increment = round(max_steps/steps)
ser.write(encode_int2fixednumbytes(steps)) # Send number of steps to arduino
ser.flush()
ser.write(encode_int2fixednumbytes(increment)) # Send voltage increment to arduino
ser.flush()
# rounding of increment may lead to extra steps
extra = (increment*steps - max_steps)//increment
extra = extra if extra > 0 else 0
# arbitrarily omit a few of the first images, since PZT is oscillating
# at the beginning
omit = 5
rows = mlb.correct_type(cam_settings[0]) # Look at init_camera() --> keys
cols = mlb.correct_type(cam_settings[1])
height = steps-extra-omit-1
image_stack = np.zeros([height, rows, cols])
#t1 = np.zeros(steps-extra)
#t2 = np.zeros(steps-extra)
#t3 = np.zeros(steps-extra)
#t4 = np.zeros(steps-extra)
#t5 = np.zeros(steps-extra)
ts = time()
mlb.begin_acquisition(cam)
for i in range(steps-extra):
# ts1 = time()
rvalue = ser.readline().split(b'\r')[0]
# t1[i] = time() - ts1
# ts2 = time()
print(rvalue)
# t2[i] = time() - ts2
# ts3 = time()
if i+1 > omit:
image_stack[i-omit-1] = mlb.grab_next_image_by_trigger(cam)
# image_stack[i] = mlb.trigger_image_acquisition(cam_nodes)
# t3[i] = time() - ts3
# ts4 = time()
ser.write(b'ok\n')
# t4[i] = time() - ts4
# ts5 = time()
ser.flush()
# t5[i] = time() - ts5
t = time() - ts
del cam
mlb.end_acquisition(cam_nodes)
ser.close()
# SAVE IMAGES TO DISK
for j in range(height):
fn = '\\' + str(j) + '.tiff'
imageio.imsave(folder + fn, image_stack[j])