type=str,
required=False,
help='Path to data directory. Overrides what is in param 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'
if namespace.path:
p = mm3.init_mm3_helpers(
param_file_path,
datapath=namespace.path) # initialized the helper library
else:
p = mm3.init_mm3_helpers(param_file_path, datapath=None)
# define variables here
source_dir = p['experiment_directory']
dest_dir = os.path.join(source_dir, 'TIFF')
file_prefix = p['experiment_name'] # prefix for output images
file_name_filters = p['metamorphToTIFF']['file_name_filters']
if not os.path.exists(dest_dir):
os.makedirs(dest_dir)
pat = re.compile(r'.+s(\d+)_t(\d+)\.TIF')
time_between_frames = p['metamorphToTIFF']['seconds_between_frames']
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 = []
if not os.path.exists(p['seg_dir']):
sys.exit("Exiting: Segmentation directory, {}, not found.".format(p['seg_dir']))
if not os.path.exists(p['chnl_dir']):
sys.exit("Exiting: Channel directory, {}, not found.".format(p['chnl_dir']))
specs = mm3.load_specs()
# make list of FOVs to process (keys of channel_mask file)
fov_id_list = sorted([fov_id for fov_id in specs.keys()])
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.')
p = mm3.init_mm3_helpers(param_file_path) # loads and returns
# load specs file
with open(os.path.join(p['ana_dir'], 'specs.yaml'), 'r') as specs_file:
specs = yaml.safe_load(specs_file)
# load cell data dict.
if pklfile == None:
pklfile = os.path.join(p['cell_dir'], 'complete_cells.pkl')
with open(pklfile, 'rb') as cell_file:
Cells = pickle.load(cell_file)
### Filters you may want to apply
if True:
# Filter based on birth_label. mother cells : label_num=1
Cells = mm3_plots.find_cells_of_birth_label(Cells, label_num=[1, 2])
