def liveview_acquire(datapath, config_filename, writeToDisk=False):
'''Aquire images from the SilCam
Args:
datapath (str) : Path to the image storage
config_filename=None (str) : Camera config file
writeToDisk=True (Bool) : True will enable writing of raw data to disc
False will disable writing of raw data to disc
gui=None (Class object) : Queue used to pass information between process thread and GUI
initialised in ProcThread within guicals.py
'''
#Load the configuration, create settings object
settings = PySilcamSettings(config_filename)
#Print configuration to screen
print('---- CONFIGURATION ----\n')
settings.config.write(sys.stdout)
print('-----------------------\n')
if (writeToDisk):
# Copy config file
configFile2Copy = datetime.datetime.now().strftime(
'D%Y%m%dT%H%M%S.%f') + os.path.basename(config_filename)
copyfile(config_filename, os.path.join(datapath, configFile2Copy))
configure_logger(settings.General)
# update path_length
updatePathLength(settings, logger)
acq = Acquire(USE_PYMBA=True) # ini class
t1 = time.time()
aqgen = acq.get_generator(datapath,
camera_config_file=config_filename,
writeToDisk=writeToDisk)
for i, (timestamp, imraw) in enumerate(aqgen):
t2 = time.time()
aq_freq = np.round(1.0 / (t2 - t1), 1)
requested_freq = settings.Camera.acquisitionframerateabs
rest_time = (1 / requested_freq) - (1 / aq_freq)
rest_time = np.max([rest_time, 0.])
actual_aq_freq = 1 / (1 / aq_freq + rest_time)
logger.info('Image {0} acquired at frequency {1:.1f} Hz'.format(
i, actual_aq_freq))
t1 = time.time()
yield timestamp, imraw
def silcam_process(config_filename,
datapath,
multiProcess=True,
realtime=False,
discWrite=False,
nbImages=None,
gui=None,
overwriteSTATS=True):
'''Run processing of SilCam images
Args:
config_filename (str) : The filename (including path) of the config.ini file
datapath (str) : Path to the data directory
multiProcess=True (bool) : If True, multiprocessing is used
realtime=False (bool) : If True, a faster but less accurate methods is used for segmentation and rts stats become active
discWrite=False (bool) : True will enable writing of raw data to disc
False will disable writing of raw data to disc
nbImages=None (int) : Number of images to skip
gui=None (Class object) : Queue used to pass information between process thread and GUI
initialised in ProcThread within guicals.py
'''
print(config_filename)
print('')
# ---- SETUP ----
# Load the configuration, create settings object
settings = PySilcamSettings(config_filename)
# Print configuration to screen
print('---- CONFIGURATION ----\n')
settings.config.write(sys.stdout)
print('-----------------------\n')
# Configure logging
configure_logger(settings.General)
logger = logging.getLogger(__name__ + '.silcam_process')
logger.info('Processing path: ' + datapath)
if realtime:
if discWrite:
# copy config file into data path
configFile2Copy = datetime.datetime.now().strftime(
'D%Y%m%dT%H%M%S.%f') + os.path.basename(config_filename)
copyfile(config_filename, os.path.join(datapath, configFile2Copy))
# update path_length
updatePathLength(settings, logger)
# make datafilename autogenerated for easier batch processing
if (not os.path.isdir(settings.General.datafile)):
logger.info('Folder ' + settings.General.datafile +
' was not found and is created')
os.mkdir(settings.General.datafile)
procfoldername = os.path.split(datapath)[-1]
datafilename = os.path.join(settings.General.datafile, procfoldername)
logger.info('output stats to: ' + datafilename)
adminSTATS(logger, settings, overwriteSTATS, datafilename, datapath)
# Initialize the image acquisition generator
if 'REALTIME_DISC' in os.environ.keys():
print('acq = Acquire(USE_PYMBA=False)')
aq = Acquire(USE_PYMBA=False)
else:
aq = Acquire(USE_PYMBA=realtime)
aqgen = aq.get_generator(datapath,
writeToDisk=discWrite,
camera_config_file=config_filename)
# Get number of images to use for background correction from config
print('* Initializing background image handler')
bggen = backgrounder(
settings.Background.num_images,
aqgen,
bad_lighting_limit=settings.Process.bad_lighting_limit,
real_time_stats=settings.Process.real_time_stats)
# Create export directory if needed
if settings.ExportParticles.export_images:
if (not os.path.isdir(settings.ExportParticles.outputpath)):
logger.info('Export folder ' +
settings.ExportParticles.outputpath +
' was not found and is created')
os.mkdir(settings.ExportParticles.outputpath)
# ---- END SETUP ----
# ---- RUN PROCESSING ----
# If only one core is available, no multiprocessing will be done
multiProcess = multiProcess and (multiprocessing.cpu_count() > 1)
print('* Commencing image acquisition and processing')
# initialise realtime stats class regardless of whether it is used later
rts = scog.rt_stats(settings)
if (multiProcess):
proc_list = []
mem = psutil.virtual_memory()
memAvailableMb = mem.available >> 20
distributor_q_size = np.min([
int(memAvailableMb / 2 * 1 / 15),
np.copy(multiprocessing.cpu_count() * 4)
])
logger.debug('setting up processing queues')
inputQueue, outputQueue = defineQueues(realtime, distributor_q_size)
logger.debug('setting up processing distributor')
distributor(inputQueue, outputQueue, config_filename, proc_list, gui)
# iterate on the bggen generator to obtain images
logger.debug('Starting acquisition loop')
t2 = time.time()
for i, (timestamp, imc, imraw) in enumerate(bggen):
t1 = np.copy(t2)
t2 = time.time()
print(t2 - t1, 'Acquisition loop time')
logger.debug('Corrected image ' + str(timestamp) +
' acquired from backgrounder')
# handle errors if the loop function fails for any reason
if (nbImages != None):
if (nbImages <= i):
break
logger.debug('Adding image to processing queue: ' + str(timestamp))
addToQueue(
realtime, inputQueue, i, timestamp, imc
) # the tuple (i, timestamp, imc) is added to the inputQueue
logger.debug('Processing queue updated')
# write the images that are available for the moment into the csv file
logger.debug('Running collector')
collector(inputQueue,
outputQueue,
datafilename,
proc_list,
False,
settings,
rts=rts)
logger.debug('Data collected')
if not gui == None:
logger.debug('Putting data on GUI Queue')
while (gui.qsize() > 0):
try:
gui.get_nowait()
time.sleep(0.001)
except:
continue
# try:
rtdict = dict()
rtdict = {
'dias': rts.dias,
'vd_oil': rts.vd_oil,
'vd_gas': rts.vd_gas,
'oil_d50': rts.oil_d50,
'gas_d50': rts.gas_d50,
'saturation': rts.saturation
}
gui.put_nowait((timestamp, imc, imraw, rtdict))
logger.debug('GUI queue updated')
if 'REALTIME_DISC' in os.environ.keys():
scog.realtime_summary(datafilename + '-STATS.csv',
config_filename)
logger.debug('Acquisition loop completed')
if (not realtime):
logger.debug('Halting processes')
for p in proc_list:
inputQueue.put(None)
# some images might still be waiting to be written to the csv file
logger.debug('Running collector on left over data')
collector(inputQueue,
outputQueue,
datafilename,
proc_list,
True,
settings,
rts=rts)
logger.debug('All data collected')
for p in proc_list:
p.join()
logger.info('%s.exitcode = %s' % (p.name, p.exitcode))
else: # no multiprocessing
# load the model for particle classification and keep it for later
nnmodel = []
nnmodel, class_labels = sccl.load_model(
model_path=settings.NNClassify.model_path)
# iterate on the bggen generator to obtain images
for i, (timestamp, imc, imraw) in enumerate(bggen):
# handle errors if the loop function fails for any reason
if (nbImages != None):
if (nbImages <= i):
break
image = (i, timestamp, imc)
# one single image is processed at a time
stats_all = processImage(nnmodel, class_labels, image, settings,
logger, gui)
if (not stats_all is None): # if frame processed
# write the image into the csv file
writeCSV(datafilename, stats_all)
if 'REALTIME_DISC' in os.environ.keys():
scog.realtime_summary(datafilename + '-STATS.csv',
config_filename)
if not gui == None:
collect_rts(settings, rts, stats_all)
logger.debug('Putting data on GUI Queue')
while (gui.qsize() > 0):
try:
gui.get_nowait()
time.sleep(0.001)
except:
continue
# try:
rtdict = dict()
rtdict = {
'dias': rts.dias,
'vd_oil': rts.vd_oil,
'vd_gas': rts.vd_gas,
'oil_d50': rts.oil_d50,
'gas_d50': rts.gas_d50,
'saturation': rts.saturation
}
gui.put_nowait((timestamp, imc, imraw, rtdict))
logger.debug('GUI queue updated')
print('PROCESSING COMPLETE.')
def silcam_acquire(datapath, config_filename, writeToDisk=True, gui=None):
'''Aquire images from the SilCam
Args:
datapath (str) : Path to the image storage
config_filename=None (str) : Camera config file
writeToDisk=True (Bool) : True will enable writing of raw data to disc
False will disable writing of raw data to disc
gui=None (Class object) : Queue used to pass information between process thread and GUI
initialised in ProcThread within guicals.py
'''
# Load the configuration, create settings object
settings = PySilcamSettings(config_filename)
# Print configuration to screen
print('---- CONFIGURATION ----\n')
settings.config.write(sys.stdout)
print('-----------------------\n')
if (writeToDisk):
# Copy config file
configFile2Copy = datetime.datetime.now().strftime(
'D%Y%m%dT%H%M%S.%f') + os.path.basename(config_filename)
copyfile(config_filename, os.path.join(datapath, configFile2Copy))
configure_logger(settings.General)
logger = logging.getLogger(__name__ + '.silcam_acquire')
# update path_length
updatePathLength(settings, logger)
acq = Acquire(USE_PYMBA=True) # ini class
t1 = time.time()
aqgen = acq.get_generator(datapath,
camera_config_file=config_filename,
writeToDisk=writeToDisk)
for i, (timestamp, imraw) in enumerate(aqgen):
t2 = time.time()
aq_freq = np.round(1.0 / (t2 - t1), 1)
requested_freq = settings.Camera.acquisitionframerateabs
rest_time = (1 / requested_freq) - (1 / aq_freq)
rest_time = np.max([rest_time, 0.])
time.sleep(rest_time)
actual_aq_freq = 1 / (1 / aq_freq + rest_time)
print('Image {0} acquired at frequency {1:.1f} Hz'.format(
i, actual_aq_freq))
t1 = time.time()
if not gui == None:
while (gui.qsize() > 0):
try:
gui.get_nowait()
time.sleep(0.001)
except:
continue
# try:
rtdict = dict()
rtdict = {
'dias': 0,
'vd_oil': 0,
'vd_gas': 0,
'oil_d50': 0,
'gas_d50': 0,
'saturation': 0
}
gui.put_nowait((timestamp, imraw, imraw, rtdict))