required=False, help='List of fields of view to analyze. Input "1", "1,2,3", etc. ')
parser.add_argument('-t', '--traindir', type=str,
required=True, help='Absolute path to the directory where you want your "images" and "masks" training data directories to be created and images to be saved.')
parser.add_argument('-c', '--channel', type=int,
required=False, default=1,
help='Which channel, e.g. phase or some fluorescence image, should be used for creating masks. \
Accepts integers. Default is 1, which is usually your phase contrast images.')
parser.add_argument('-n', '--no_prior_mask', action='store_true',
help='Apply this argument is you are making masks de novo, i.e., if no masks exist yet for your images.')
namespace = parser.parse_args()
# Load the project parameters file
mm3.information('Loading experiment parameters.')
training_dir = namespace.traindir
if not os.path.exists(training_dir):
mm3.warning('Training directory not found, making directory.')
os.makedirs(training_dir)
if namespace.paramfile:
param_file_path = namespace.paramfile
else:
mm3.warning('No param file specified. Using 100X template.')
param_file_path = 'yaml_templates/params_SJ110_100X.yaml'
p = mm3.init_mm3_helpers(param_file_path) # initialized the helper library
GUI.init_params(param_file_path)
if namespace.fov:
user_spec_fovs = [int(val) for val in namespace.fov.split(",")]
else:
user_spec_fovs = []
parser.add_argument('-f', '--paramfile', type=str,
required=True, help='Yaml file containing parameters.')
parser.add_argument('-o', '--fov', type=str,
required=False, help='List of fields of view to analyze. Input "1", "1,2,3", or "1-10", etc.')
parser.add_argument('-j', '--nproc', type=int,
required=False, help='Number of processors to use.')
parser.add_argument('-c', '--color', type=str,
required=False, help='Color plane to subtract. "c1", "c2", etc.')
namespace = parser.parse_args()
# Load the project parameters file
mm3.information('Loading experiment parameters.')
if namespace.paramfile:
param_file_path = namespace.paramfile
else:
mm3.warning('No param file specified. Using 100X template.')
param_file_path = 'yaml_templates/params_SJ110_100X.yaml'
p = mm3.init_mm3_helpers(param_file_path) # initialized the helper library
if namespace.fov:
if '-' in namespace.fov:
user_spec_fovs = range(int(namespace.fov.split("-")[0]),
int(namespace.fov.split("-")[1])+1)
else:
user_spec_fovs = [int(val) for val in namespace.fov.split(",")]
else:
user_spec_fovs = []
# number of threads for multiprocessing
if namespace.nproc:
p['num_analyzers'] = namespace.nproc
gnuoptions = ["paramfile=", "fov=", "picklefile="]
opts, args = getopt.getopt(sys.argv[1:], unixoptions, gnuoptions)
# switches which may be overwritten
param_file_path = ''
except getopt.GetoptError:
warning('No arguments detected (-f -o).')
for opt, arg in opts:
if opt in ['-f', "--paramfile"]:
param_file_path = arg # parameter file path
if opt in ['-o', "--fov"]:
try:
for fov_to_proc in arg.split(","):
user_spec_fovs.append(int(fov_to_proc))
except:
mm3.warning("Couldn't convert -o argument to an integer:", arg)
raise ValueError
if opt in ['-p', "--picklefile"]:
pklfile = arg # parameter file path
# Load the project parameters file
if len(param_file_path) == 0:
raise ValueError("A parameter file must be specified (-f <filename>).")
mm3.information('Loading experiment parameters and cell data.')
with open(param_file_path, 'r') as param_file:
allparams = yaml.safe_load(param_file) # loads and returns
pklfile = os.path.join(allparams['cell_dir'], 'complete_cells_mothers.pkl')
print('using complete_cells.pkl')
with open(pklfile, 'rb') as cell_file:
# set switches and parameters
parser = argparse.ArgumentParser(prog='python mm3_Foci.py',
description='Finds foci.')
parser.add_argument('-f', '--paramfile', type=str,
required=True, help='Yaml file containing parameters.')
parser.add_argument('-c', '--cellfile', type=str,
required=False, help='Path to Cell object dicionary to analyze. Defaults to complete_cells.pkl.')
namespace = parser.parse_args()
# Load the project parameters file
mm3.information('Loading experiment parameters.')
if namespace.paramfile:
param_file_path = namespace.paramfile
else:
mm3.warning('No param file specified. Using 100X template.')
param_file_path = 'yaml_templates/params_SJ110_100X.yaml'
p = mm3.init_mm3_helpers(param_file_path) # initialized the helper library
# load cell file
mm3.information('Loading cell data.')
if namespace.cellfile:
cell_file_path = namespace.cellfile
else:
mm3.warning('No cell file specified. Using complete_cells.pkl.')
cell_file_path = os.path.join(p['cell_dir'], 'complete_cells.pkl')
with open(cell_file_path, 'rb') as cell_file:
Cells = pickle.load(cell_file)
# load specs file
action='store_true',
required=False,
help='Load cross correlation data instead of computing.')
parser.add_argument('-s',
'--specfile',
type=str,
required=False,
help='Path to spec.yaml file.')
namespace = parser.parse_args()
# Load the project parameters file
mm3.information('Loading experiment parameters.')
if namespace.paramfile:
param_file_path = namespace.paramfile
else:
mm3.warning('No param file specified. Using 100X template.')
param_file_path = 'yaml_templates/params_SJ110_100X.yaml'
p = mm3.init_mm3_helpers(param_file_path) # initialized the helper library
if namespace.fov:
if '-' in namespace.fov:
user_spec_fovs = range(int(namespace.fov.split("-")[0]),
int(namespace.fov.split("-")[1]) + 1)
else:
user_spec_fovs = [int(val) for val in namespace.fov.split(",")]
else:
user_spec_fovs = []
# number of threads for multiprocessing
if namespace.nproc:
p['num_analyzers'] = namespace.nproc
