def get_gain(line,
imaging_dir,
last_field,
end_63x,
sock,
stop_com,
r_script,
initialgains_file,
gain_dict
):
# empty lists for keeping csv file base path names
# and corresponding well names
filebases = []
fin_wells = []
# Parse reply, check well (UV), field (XY).
# Get well path.
# Get all image paths in well.
# Make a max proj per channel and well.
# Save meta data and image max proj.
if 'image' in line:
root = parse_reply(line, imaging_dir)
img = File(root)
img_name = img.get_name('image--.*.tif')
field_name = img.get_name('X\d\d--Y\d\d')
channel = img.get_name('C\d\d')
field_path = img.get_dir()
well_path = Directory(field_path).get_dir()
if (field_name == last_field and channel == 'C31'):
if end_63x:
sock.send(stop_com)
ptime = time.time()
get_imgs(well_path,
well_path,
'E02',
img_save=False
)
print(str(time.time()-ptime) + ' secs')
# get all CSVs and wells
csv_result = get_csvs(well_path,
filebases,
fin_wells,
)
filebases = csv_result['bases']
fin_wells = csv_result['wells']
# For all experiment wells imaged so far, run R script
if filebases:
gain_dict = run_r(filebases,
fin_wells,
r_script,
imaging_dir,
initialgains_file,
gain_dict
)
return gain_dict
def send_com(com_list,
end_com_list,
sock,
start_com,
cstart,
stop_cam_com,
stop_com,
imaging_dir,
last_field,
end_63x,
r_script,
initialgains_file,
saved_gains,
template,
job_list,
pattern,
first_job,
coords,
stage1=None,
stage3=None,
stage4=None
):
for com, end_com in zip(com_list, end_com_list):
# Send CAM list for the gain job to the server (stage1).
# Send gain change command to server in the four channels (stage3/4).
# Send CAM list for the experiment jobs to server (stage3/4).
# Reset gain_dict for each iteration.
gain_dict = defaultdict(list)
com = '/cli:1 /app:matrix /cmd:deletelist\n' + com
print(com)
sock.send(com)
time.sleep(3)
# Start scan.
print(start_com)
sock.send(start_com)
time.sleep(7)
# Start CAM scan.
print(cstart)
sock.send(cstart)
time.sleep(3)
stage5 = True
while stage5:
print('Waiting for images...')
reply = sock.recv_timeout(120, ['image--'])
for line in reply.splitlines():
if stage1:
print('Stage1')
gain_dict = get_gain(line,
imaging_dir,
last_field,
end_63x,
sock,
stop_com,
r_script,
initialgains_file,
gain_dict
)
#print(gain_dict) #testing
if not saved_gains:
saved_gains = gain_dict
if saved_gains:
#print(saved_gains) #testing
saved_gains.update(gain_dict)
header = ['well', 'green', 'blue', 'yellow', 'red']
csv_name = 'output_gains.csv'
write_csv(os.path.normpath(os.path.join(imaging_dir,
csv_name
)
),
saved_gains,
header
)
com_result = gen_com(gain_dict,
template,
job_list,
pattern,
first_job,
end_63x,
coords=coords
)
late_com_list = com_result['com']
late_end_com_list = com_result['end_com']
else:
if stage3:
print('Stage3')
img_saving = False
if stage4:
print('Stage4')
img_saving = True
if 'image' in line:
error = True
count = 0
while error and count < 2:
try:
root = parse_reply(line, imaging_dir)
img = File(root)
img_name = img.get_name('image--.*.tif')
print(img_name)
job_order = img.get_name('E\d\d')
field_path = img.get_dir()
get_imgs(field_path,
imaging_dir,
job_order,
f_job=first_job,
img_save=img_saving,
csv_save=False
)
error = False
except TypeError as e:
error = True
count += 1
time.sleep(1)
print('No images yet... but maybe later?' , e)
if all(test in line for test in end_com):
stage5 = False
# Stop scan
#print(stop_cam_com)
#sock.send(stop_cam_com)
#time.sleep(5)
print(stop_com)
sock.send(stop_com)
time.sleep(6) # Wait for it to come to complete stop.
if gain_dict and stage1:
send_com(late_com_list,
late_end_com_list,
sock,
start_com,
cstart,
stop_cam_com,
stop_com,
imaging_dir,
last_field,
end_63x,
r_script,
initialgains_file,
saved_gains,
template,
job_list,
pattern,
first_job,
coords,
stage1=False,
stage3=stage3,
stage4=stage4
)
