def parse_args(parser: argparse.ArgumentParser):
"""
Parses arguments and returns ops with parameters filled in.
"""
args = parser.parse_args()
dargs = vars(args)
ops0 = default_ops()
ops = np.load(args.ops, allow_pickle=True).item() if args.ops else {}
set_param_msg = '->> Setting {0} to {1}'
# options defined in the cli take precedence over the ones in the ops file
for k in ops0:
default_key = ops0[k]
args_key = dargs[k]
if k in ['fast_disk', 'save_folder', 'save_path0']:
if args_key:
ops[k] = args_key
print(set_param_msg.format(k, ops[k]))
elif type(default_key) in [np.ndarray, list]:
n = np.array(args_key)
if np.any(n != np.array(default_key)):
ops[k] = n.astype(type(default_key))
print(set_param_msg.format(k, ops[k]))
elif isinstance(default_key, bool):
args_key = bool(
int(args_key)) # bool('0') is true, must convert to int
if default_key != args_key:
ops[k] = args_key
print(set_param_msg.format(k, ops[k]))
# checks default param to args param by converting args to same type
elif not (default_key == type(default_key)(args_key)):
ops[k] = type(default_key)(args_key)
print(set_param_msg.format(k, ops[k]))
return args, ops
def test_ops(tmpdir, data_dir):
"""Initializes ops to be used for test. Also, uses tmpdir fixture to create a unique temporary dir for each test."""
ops = suite2p.default_ops()
ops.update({
'use_builtin_classifier': True,
'data_path': [data_dir],
'save_path0': str(tmpdir)
})
return ops
def setup_and_teardown(tmpdir):
"""
Initializes ops to be used for test. Also, uses tmpdir fixture to create a unique temporary dir for
each test. Then, removes temporary directory after test is completed.
"""
ops = suite2p.default_ops()
ops['data_path'] = [test_data_dir]
ops['save_path0'] = str(tmpdir)
yield ops, str(tmpdir)
tmpdir_path = Path(str(tmpdir))
if tmpdir_path.is_dir():
shutil.rmtree(tmpdir)
print('Successful removal of tmp_path {}.'.format(tmpdir))
def parse_arguments():
parser = argparse.ArgumentParser(description='Suite2p parameters')
parser.add_argument('--ops', default=[], type=str, help='options')
parser.add_argument('--db', default=[], type=str, help='options')
ops0 = suite2p.default_ops()
for k in ops0.keys():
v = dict(default=ops0[k], help='{0}: {1}'.format(k, ops0[k]))
if k in ['fast_disk', 'save_folder', 'save_path0']:
v['default'] = None
v['type'] = str
if type(v['default']) in [np.ndarray, list]:
if len(v['default']):
v['nargs'] = '+'
v['type'] = type(v['default'][0])
parser.add_argument('--' + k, **v)
args = parser.parse_args()
dargs = vars(args)
ops = {}
db = {}
if len(args.ops) > 0:
ops = np.load(args.ops, allow_pickle=True).item()
# options defined in the cli take precedence over the ones in the ops file
for k in ops0:
v = ops0[k]
n = dargs[k]
if k in ['fast_disk', 'save_folder', 'save_path0']:
if not n is None:
ops[k] = n
print('->> Setting {0} to {1}'.format(k, ops[k]))
elif type(v) in [np.ndarray, list]:
if len(n):
n = np.array(n)
if np.any(n != np.array(v)):
ops[k] = n.astype(type(v))
print('->> Setting {0} to {1}'.format(k, ops[k]))
else:
if not v == type(v)(n):
ops[k] = type(v)(n)
print('->> Setting {0} to {1}'.format(k, ops[k]))
if len(args.db) > 0:
db = np.load(args.db, allow_pickle=True).item()
suite2p.run_s2p(ops, db)
else:
suite2p.run_gui()
def add_args(parser: argparse.ArgumentParser):
"""
Adds suite2p ops arguments to parser.
"""
parser.add_argument('--single_plane',
action='store_true',
help='run single plane ops')
parser.add_argument('--ops', default=[], type=str, help='options')
parser.add_argument('--db', default=[], type=str, help='options')
ops0 = default_ops()
for k in ops0.keys():
v = dict(default=ops0[k], help='{0} : {1}'.format(k, ops0[k]))
if k in ['fast_disk', 'save_folder', 'save_path0']:
v['default'] = None
v['type'] = str
if (type(v['default']) in [np.ndarray, list]) and len(v['default']):
v['nargs'] = '+'
v['type'] = type(v['default'][0])
parser.add_argument('--' + k, **v)
return parser
import numpy as np
import sys
import os
from suite2p import run_s2p, default_ops
import shutil
import glob
fnames = [os.path.normpath(sys.argv[1])]
# set your options for running
data_path = os.path.dirname(fnames[0])
range2 = int(fnames[0].split('range')[-1].split('_')[0])
step = int(fnames[0].split('step')[-1].split('_')[0])
nplanes = int((range2 / step) + 1)
ops = default_ops()
ops['fs'] = 2
ops['tau'] = 1.6
ops['save_mat'] = 1
ops['1Preg'] = True
ops['denoise'] = True
ops['diameter'] = [3, 4, 5]
ops['threshold_scaling'] = 0.5
ops['max_iterations'] = 100
ops['smooth_sigma'] = 4
ops['high_pass'] = 30
ops['nchannels'] = 1
ops['spatial_taper'] = 5
ops['pre_smooth'] = 2
ops['max_iterations'] = 100
ops['inner_neuropil_radius'] = 1
ops['neuropil_extract'] = 0
from pathlib import Path
import suite2p
from tempfile import TemporaryDirectory
ops = suite2p.default_ops()
ops['nplanes'] = 2
ops['nchannels'] = 2
data_path = Path(__file__).joinpath('../../../data/test_data')
ops['data_path'] = [str(data_path)]
ops['save_path0'] = TemporaryDirectory().name
suite2p.run_s2p(ops)
def test_ops(tmpdir, data_dir):
"""Initializes ops to be used for test. Also, uses tmpdir fixture to create a unique temporary dir for each test."""
ops = suite2p.default_ops()
ops['data_path'] = [data_dir]
ops['save_path0'] = str(tmpdir)
return ops
'input_format':
"h5",
'h5py_key':
'data',
'sparse_mode':
True,
'threshold_scaling':
1.,
'nchannels':
2,
'nframes':
data_bin.n_frames,
'Ly':
data_bin.shape[1],
'Lx':
data_bin.shape[2],
'xrange': [50, 462],
'yrange': [50, 745],
'nbinned':
10000,
'meanImg':
data_bin.sampled_mean(),
'meanImag_chan2':
data2_bin.sampled_mean(),
}
ops = {**s2p.default_ops(), **combined_ops}
np.save(ops['ops_path'], ops)
ops = s2p.run_s2p(ops=ops)
def run(self):
self.logger.name = type(self).__name__
self.logger.setLevel(self.args.pop('log_level'))
# explicitly set default Suite2P args that are not
# already specified in self.args
self.args = {**copy.deepcopy(suite2p.default_ops()), **self.args}
# Should always exist as either a valid SHA or "unknown build"
# if running in docker container.
ophys_etl_commit_sha = os.environ.get("OPHYS_ETL_COMMIT_SHA",
"local build")
self.logger.info(f"OPHYS_ETL_COMMIT_SHA: {ophys_etl_commit_sha}")
# determine nbinned from bin_duration and movie_frame_rate_hz
if self.args['nbinned'] is None:
with h5py.File(self.args['h5py'], 'r') as f:
nframes = f['data'].shape[0]
bin_size = (self.args['bin_duration'] *
self.args['movie_frame_rate_hz'])
if bin_size > nframes:
raise utils.Suite2PWrapperException(
f"The desired frame bin duration "
f"({self.args['bin_duration']} "
f"seconds) and movie frame rate "
f"({self.args['movie_frame_rate_hz']} Hz) "
"results in a bin "
f"size ({bin_size} frames) larger than the number of "
f"actual frames in the movie ({nframes})!")
self.args['nbinned'] = int(nframes / bin_size)
self.logger.info(f"Movie has {nframes} frames collected at "
f"{self.args['movie_frame_rate_hz']} Hz. "
"To get a bin duration of "
f"{self.args['bin_duration']} "
f"seconds, setting nbinned to "
f"{self.args['nbinned']}.")
# make a tempdir for Suite2P's output
with tempfile.TemporaryDirectory(dir=self.args['tmp_dir']) as tdir:
self.args['save_path0'] = tdir
self.logger.info(f"Running Suite2P with output going to {tdir}")
if self.args['movie_frame_rate_hz'] is not None:
self.args['fs'] = self.args['movie_frame_rate_hz']
# Make a copy of the args to remove the NumpyArray, refImg, as
# numpy.ndarray can't be serialized with json. Converting to list
# and writing to the logger causes the output to be unreadable.
copy_of_args = copy.deepcopy(self.args)
copy_of_args.pop('refImg')
msg = f'running Suite2P v{suite2p.version} with args\n'
msg += f'{json.dumps(copy_of_args, indent=2, sort_keys=True)}\n'
self.logger.info(msg)
# If we are using a external reference image (including our own
# produced by compute_referece) communicate this in the log.
if self.args['force_refImg']:
self.logger.info('\tUsing custom reference image: '
f'{self.args["refImg"]}')
try:
suite2p.run_s2p(self.args)
except ValueError as e:
if 'no ROIs were found' in str(e):
# Save an empty list of ROIs instead of failing
np.save(file=str(pathlib.Path(tdir) / 'stat.npy'), arr=[])
else:
raise
self.logger.info(f"Suite2P complete. Copying output from {tdir} "
f"to {self.args['output_dir']}")
# copy over specified retained files to the output dir
odir = pathlib.Path(self.args['output_dir'])
odir.mkdir(parents=True, exist_ok=True)
self.now = None
if self.args['timestamp']:
self.now = datetime.datetime.now().strftime('%Y%m%d%H%M%S%f')
output_files = utils.copy_and_add_uid(
srcdir=pathlib.Path(tdir),
dstdir=odir,
basenames=self.args['retain_files'],
uid=self.now,
use_mv=True)
for k, v in output_files.items():
self.logger.info(f"wrote {k} to {v}")
outdict = {'output_files': output_files}
self.output(outdict, indent=2)
def test_ops_suite2p_version_matches_cli_version_number(capfd):
os.system('suite2p --version')
captured = capfd.readouterr()
ops_version = suite2p.default_ops()['suite2p_version']
assert ops_version in captured.out