def server_record(N=10, camera_name='MicroscopeCamera'):
camera = Camera(camera_name)
camera.acquiring = True
# Offload the image saving to the camera server for performance
filenames = [template % i for i in range(N)]
frame_counts = [camera.frame_count + 1 + i for i in range(len(filenames))]
camera.send("camera.acquire_sequence(%r,%r)" % (frame_counts, filenames))
def save_images(buffer, t=10):
sys.path.append(
'z:\\all projects\\aps\\instrumentation\\software\\lauecollect\\')
from GigE_camera_client import Camera
camera = Camera('MicrofluidicsCamera')
camera.exposure_time = 0.001
camera.stream_bytes_per_second = 1392640
from ubcs_auxiliary.threading import new_thread
new_thread(save_image_loop, t, buffer, camera)
def record1(camera_name='MicroscopeCamera'):
template_NIH= "//femto/C/All Projects/Crystallization/2019/Lysozyme3/"\
"%s_%r.tiff"
camera1 = Camera('LabMicroscope')
camera1.acquiring = True
i = 0
while True:
filename = template % (time(), i)
print("%s" % basename(filename))
camera1.save_image(filename)
i += 1
def get_background():
from numpy import array
sys.path.append(
'z:\\all projects\\aps\\instrumentation\\software\\lauecollect\\')
from GigE_camera_client import Camera
camera = Camera('MicrofluidicsCamera')
data = camera.RGB_array
return array(data[:, :, 720:840])
def record(camera_name='MicroscopeCamera'):
camera1 = Camera('MicroscopeCamera')
camera1.acquiring = True
camera2 = Camera('WideFieldCamera')
#camera2.ip_address = '164.54.161.34:2001'
camera2.acquiring = True
try:
i = 0
while True:
ins = 0
filename = template % ("Microscope/", time(), i, int(ins),
temperature.value)
print("%s" % basename(filename))
camera1.save_image(filename)
filename = template % ("WideField/", time(), i, int(ins),
temperature.value)
print("%s" % basename(filename))
camera2.save_image(filename)
i += 1
sleep(delay)
except KeyboardInterrupt:
pass
logging.basicConfig(filename=gettempdir() + '/scripts.log',
level=logging.DEBUG,
format="%(asctime)s %(levelname)s: %(message)s")
from sys import platform
if platform == "linux" or platform == "linux2":
pass
elif platform == "darwin":
sys.path.append(
'/net/femto/C/All Projects/APS/Instrumentation/Software/Lauecollect/'
)
elif platform == "win32":
sys.path.append(
'z:\\all projects\\aps\\instrumentation\\software\\lauecollect\\')
from GigE_camera_client import Camera
camera = Camera('MicrofluidicsCamera')
data = camera.RGB_array
from matplotlib import pyplot as plt
anchors = [(0, 730), (1360, 830)]
import matplotlib.patches as patches
# Create figure and axes
fig, ax = plt.subplots(1)
# Display the image
ax.imshow(data[0].T)
# Create a Rectangle patch
rect = patches.Rectangle(anchors[0],
1360,
100,
linewidth=1,
edgecolor='r',
facecolor='none')
return (motorX.value, motorY.value, motorZ.value)
def get_DVH_position():
from numpy import sin, cos, pi
V = round(motorY.value * sin(pi / 6.0), 3)
H = motorZ.value
D = round(motorY.value * cos(pi / 6.0), 3)
return (D, V, H)
template = template_APS_MAC
delay = 0.0025 #in seconds
i = 0
camere_Microscope = Camera("MicroscopeCamera")
camere_Microscope.acquiring = True
camera_WideField = Camera('WideFieldCamera')
camera_WideField.acquiring = True
g_res = []
def analyze(g_res):
from PIL import Image
import numpy as np
import traceback
from time import time
list_of_files = os.listdir(template_APS_MAC_folder)
res = []
t1 = time()
for i in range(len(list_of_files)):
numpy.save(self.logFolder + filename, data, allow_pickle=True)
"""plotting functions"""
def plot_array(self, arr):
from numpy import float32
if arr.min() < 0: #for difference image to be plotted properly
plt.imshow(arr[:, :, 0:3] - arr.min())
else:
plt.imshow(arr[:, :, 0:3])
plt.colorbar()
plt.show()
from GigE_camera_client import Camera
camera = Camera("MicroscopeCamera")
laue_image_analyser = Camera_image_analyser(
name='LAUE_image_analyser',
camera_name='MicroscopeCamera') #for LAUE crystalography
if __name__ == "__main__":
import logging
from tempfile import gettempdir
import logging
logfile = gettempdir() + "/logging/camera_image_analyser.log"
logger = logging.getLogger('camera_image_analyser')
hdlr = logging.FileHandler(logfile)
formatter = logging.Formatter('%(asctime)s %(levelname)s %(message)s')
hdlr.setFormatter(formatter)
logger.addHandler(hdlr)
"%s_%00d_%r_%r_%r.tiff"
template = template_NIH
delay = 0.0025 #in seconds
i = 0
from EPICS_motor import motor
from instrumentation import temperature
from sample_frozen_optical import sample_frozen_optical as sfo
motorX = motor("NIH:SAMPLEX")
motorY = motor("NIH:SAMPLEY")
motorZ = motor("NIH:SAMPLEZ")
#camera = Camera("Microscope")
camera1 = Camera('MicroscopeCamera')
camera1.acquiring = True
#camera = Camera("MicroscopeCamera")
def record_T_once(l):
from numpy import zeros, flip
from SAXS_WAXS_control import SAXS_WAXS_control
ins = 0 #str(SAXS_WAXS_control.inserted)
filename = template % ("Microscope/", time(), l, int(ins),
temperature.value)
print("%s" % basename(filename))
img = camera1.RGB_array
gray = sum(img, 2)
arr = zeros((4, 1024, 1360))
for i in range(3):
def camera(self):
from GigE_camera_client import Camera
camera = Camera("MicroscopeCamera")
return camera