def compute(file, yaml_file, stack, section, client, bucket, key):
t0 = time()
img_fn = os.path.join(os.environ['ROOT_DIR'], file)
setup_download_from_s3(file, recursive=False)
run('python {0}/extractPatches.py {1} {2}'.format(os.environ['REPO_DIR'],
img_fn, yaml_file))
params = configuration(yaml_file).getParams()
size_thresholds = params['normalization']['size_thresholds']
dot = img_fn.rfind('.')
slash = img_fn.rfind('/')
local_dir = 'cells/' + img_fn[slash + 1:dot] + '_cells/'
for size in size_thresholds:
key_item = 'size_of_' + str(size)
local_fp = local_dir + str(size) + '.bin'
s3_fp = stack + '/cells/' + str(section) + '_cells/' + str(
size) + '.bin'
def s3_exist(s3_fp):
try:
report = client.stat_object(bucket, s3_fp)
return True
except:
return False
while not s3_exist(s3_fp):
setup_upload_from_s3(s3_fp, local_fp, recursive=False)
report = client.stat_object(bucket, s3_fp)
key[key_item] = int(report.size / 1000)
os.remove(os.path.join(os.environ['ROOT_DIR'], local_fp))
print(file, 'finished in', time() - t0, 'seconds')
os.remove(img_fn)
return key
def main(argv):
args = parse_cmd_args(argv[1:])
config = configuration(args)
dictConfig(config.LOGGING)
logger.info(
u'Run main loop. Worker pool size={}. Sleep time is {}.'.format(
config.WORKER_POOL_SIZE, config.SLEEP
))
parent_pid = os.getpid()
while keep_running:
main_loop_function(config, parent_pid)
sleep(config.SLEEP)
return config.EXIT_CODE
from time import time
parser = argparse.ArgumentParser()
parser.add_argument(
"filestem",
type=str,
help="Process <filestem>.tif into <filestem>_extracted.pkl")
parser.add_argument("yaml",
type=str,
help="Path to Yaml file with parameters")
# Add parameters for size of mexican hat and size of cell, threshold, percentile
# Define file name based on size. Use this name for log file and for countours image.
# save parameters in a log file ,
args = parser.parse_args()
config = configuration(args.yaml)
params = config.getParams()
_dir = params['paths']['data_dir'] + '/tiles/'
stem = args.filestem
infile = _dir + stem + '.tif'
out_stem = stem + '.' + params['name']
pkl_dir = params['paths']['pickle_subdir']
pkl_out_file = _dir + 'pickles/' + out_stem + '.pkl'
annotated_infile = _dir + out_stem + '_contours.jpg'
extractor = patch_extractor(infile, params)
tile = cv2.imread(infile)
gray = cv2.cvtColor(tile, cv2.COLOR_BGR2GRAY)
self.count.append(0)
for i in range(self.K):
self.fp = open(self.saveDir + '/permuted-' + str(i) + '.bin', 'bw')
for choice in np.random.choice(len(files), 100000, p=prob):
fn = files[choice]
V = np.fromfile(fn, np.float16)
V = V.reshape([-1, self.size**2])
self.fp.write(V[self.count[choice], :])
self.count[choice] += 1
clock(str(i) + ' files finished')
if __name__ == '__main__':
yamlfile = os.environ['REPO_DIR'] + 'shape_params-aws.yaml'
params = configuration(yamlfile).getParams()
stack = 'DK39'
root_dir = os.environ['ROOT_DIR']
clock('Process Begin')
t0 = time()
setup_download_from_s3(stack + '/cells/')
clock('Download From S3')
sorter = Sorter(src_root=root_dir + stack + '/cells/')
size_thresholds = params['normalization']['size_thresholds']
for size in size_thresholds:
sorter.sort_file(size, stem=root_dir + 'permute/permuted')
clock('Complete files of size ' + str(size))
print('Complete files of size ' + str(size), time() - t0, 'seconds')
log_fp = 'TimeLog/'
if not os.path.exists(log_fp):
#!/usr/bin/env python3
from os.path import isfile, getmtime
from glob import glob
from time import sleep, time
from os import system
from subprocess import Popen, PIPE
from lib.utils import configuration
config = configuration('shape_params.yaml')
params = config.getParams()
scripts_dir = params['paths']['scripts_dir']
local_data = params['paths']['data_dir']
script = 'process_file.py'
yaml_file = 'shape_params.yaml'
stack = 's3://mousebraindata-open/MD657'
exec_dir = params['paths']['scripts_dir']
def runPipe(command):
print('cmd=', command)
p = Popen(command.split(), stdout=PIPE, stderr=PIPE)
L = p.communicate()
stdout = L[0].decode("utf-8").split('\n')
stderr = L[1].decode("utf-8").split('\n')
return stdout, stderr
def run(command, out):
