def get_csvs(path, fbs, wells):
"""Function to find the correct csv files and get their base names."""
search = Directory(path)
csvs = sorted(search.get_all_files('*.ome.csv'))
for csv_path in csvs:
csv_file = File(csv_path)
# Get the filebase from the csv path.
fbase = csv_file.cut_path('C\d\d.+$')
# Get the well from the csv path.
well_name = csv_file.get_name('U\d\d--V\d\d')
fbs.append(fbase)
wells.append(well_name)
return {'wells':wells, 'bases':fbs}
def make_proj(img_list):
"""Function to make a dict of max projections from a list of paths
to images. Each channel will make one max projection"""
channels = []
print('Making max projections')
ptime = time.time()
sorted_images = defaultdict(list)
max_imgs = {}
for path in img_list:
img = File(path)
channel = img.get_name('C\d\d')
sorted_images[channel].append(img.read_image())
max_imgs[channel] = np.maximum.reduce(sorted_images[channel])
print('Max proj:' + str(time.time()-ptime) + ' secs')
return max_imgs
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
)
def get_imgs(path, imdir, job_order, f_job=None, img_save=None, csv_save=None):
"""Function to handle the acquired images, do renaming,
max projections etc."""
if f_job is None:
f_job = 2
if img_save is None:
img_save = True
if csv_save is None:
csv_save = True
img_paths = Directory(path).get_all_files('*' + job_order + '*.tif')
new_paths = []
metadata_d = {}
for img_path in img_paths:
img = File(img_path)
img_array = img.read_image()
well = img.get_name('U\d\d--V\d\d')
job_order = img.get_name('E\d\d')
job_ord_int = int(re.sub("\D", "", job_order))
field = img.get_name('X\d\d--Y\d\d')
z_slice = img.get_name('Z\d\d')
channel = img.get_name('C\d\d')
if job_ord_int == f_job:
new_name = os.path.normpath(os.path.join(path, (well + '--' +
job_order + '--' +
field + '--' +
z_slice + '--' +
channel +
'.ome.tif'
)
)
)
elif job_ord_int == f_job + 1 and channel == 'C00':
new_name = os.path.normpath(os.path.join(path, (well + '--' +
job_order + '--' +
field + '--' +
z_slice +
'--C01.ome.tif'
)
)
)
channel = 'C01'
elif job_ord_int == f_job + 1 and channel == 'C01':
new_name = os.path.normpath(os.path.join(path, (well + '--' +
job_order + '--' +
field + '--' +
z_slice +
'--C02.ome.tif'
)
)
)
channel = 'C02'
elif job_ord_int == f_job + 2:
new_name = os.path.normpath(os.path.join(path, (well + '--' +
job_order + '--' +
field + '--' +
z_slice +
'--C03.ome.tif'
)
)
)
channel = 'C03'
else:
new_name = img_path
if not (len(img_array) == 16 or len(img_array) == 256):
new_paths.append(new_name)
metadata_d[well + '--' + field + '--' + channel] = img.meta_data()
os.rename(img_path, new_name)
max_projs = make_proj(new_paths)
new_dir = os.path.normpath(os.path.join(imdir, 'maxprojs'))
if not os.path.exists(new_dir):
os.makedirs(new_dir)
if img_save:
print('Saving images')
if csv_save:
print('Calculating histograms')
for channel, proj in max_projs.iteritems():
if img_save:
ptime = time.time()
p = os.path.normpath(os.path.join(new_dir, 'image--' + well + '--' +
field + '--' + channel + '.ome.tif'))
metadata = metadata_d[well + '--' + field + '--' + channel]
File(p).save_image(proj, metadata)
print('Save image:' + str(time.time()-ptime) + ' secs')
if csv_save:
ptime = time.time()
if proj.dtype.name == 'uint8':
max_int = 255
if proj.dtype.name == 'uint16':
max_int = 65535
histo = histogram(proj, 0, max_int, 256)
rows = defaultdict(list)
for b, count in enumerate(histo):
rows[b].append(count)
p = os.path.normpath(os.path.join(new_dir, well + '--' + channel +
'.ome.csv'))
write_csv(p, rows, ['bin', 'count'])
print('Save csv:' + str(time.time()-ptime) + ' secs')
return