def create_ephyspc_params(force=False):
if Path(params.getfile('ephyspc_params')).exists() and not force:
print(f"{params.getfile('ephyspc_params')} exists already, exiting...")
print(Path(params.getfile('ephyspc_params')).exists())
return
data_folder_path = cli_ask_default(
r"Where's your LOCAL 'Subjects' data folder?",
r"D:\iblrig_data\Subjects")
remote_data_folder_path = cli_ask_default(
r"Where's your REMOTE 'Subjects' data folder?",
r"\\iblserver.champalimaud.pt\ibldata\Subjects")
probe_type_00 = cli_ask_options("What's the type of PROBE 00?",
['3A', '3B'])
probe_type_01 = cli_ask_options("What's the type of PROBE 01?",
['3A', '3B'])
param_dict = {
'DATA_FOLDER_PATH': data_folder_path,
'REMOTE_DATA_FOLDER_PATH': remote_data_folder_path,
'PROBE_TYPE_00': probe_type_00,
'PROBE_TYPE_01': probe_type_01,
}
params.write('ephyspc_params', param_dict)
print(f"Created {params.getfile('ephyspc_params')}")
print(param_dict)
return param_dict
def create_ephyspc_params(force=False, silent=False):
if Path(params.getfile("ephyspc_params")).exists() and not force:
print(f"{params.getfile('ephyspc_params')} exists already, exiting...")
print(Path(params.getfile("ephyspc_params")).exists())
return
if silent:
data_folder_path = r"D:\iblrig_data\Subjects"
remote_data_folder_path = r"\\iblserver.champalimaud.pt\ibldata\Subjects"
probe_type_00 = "3A"
probe_type_01 = "3B"
else:
data_folder_path = cli_ask_default(
r"Where's your LOCAL 'Subjects' data folder?",
r"D:\iblrig_data\Subjects")
remote_data_folder_path = cli_ask_default(
r"Where's your REMOTE 'Subjects' data folder?",
r"\\iblserver.champalimaud.pt\ibldata\Subjects",
)
probe_type_00 = cli_ask_options("What's the type of PROBE 00?",
["3A", "3B"])
probe_type_01 = cli_ask_options("What's the type of PROBE 01?",
["3A", "3B"])
param_dict = {
"DATA_FOLDER_PATH": data_folder_path,
"REMOTE_DATA_FOLDER_PATH": remote_data_folder_path,
"PROBE_TYPE_00": probe_type_00,
"PROBE_TYPE_01": probe_type_01,
}
params.write("ephyspc_params", param_dict)
print(f"Created {params.getfile('ephyspc_params')}")
print(param_dict)
return param_dict
def create_videopc_params(force=False):
if Path(params.getfile('videopc_params')).exists() and not force:
print(f"{params.getfile('videopc_params')} exists already, exiting...")
print(Path(params.getfile('videopc_params')).exists())
return
data_folder_path = cli_ask_default(
r"Where's your LOCAL 'Subjects' data folder?",
r"D:\iblrig_data\Subjects")
remote_data_folder_path = cli_ask_default(
r"Where's your REMOTE 'Subjects' data folder?",
r"\\iblserver.champalimaud.pt\ibldata\Subjects")
body_cam_idx = cli_ask_default(
"Please select the index of the BODY camera", '0')
left_cam_idx = cli_ask_default(
"Please select the index of the LEFT camera", '1')
right_cam_idx = cli_ask_default(
"Please select the index of the RIGHT camera", '2')
param_dict = {
'DATA_FOLDER_PATH': data_folder_path,
'REMOTE_DATA_FOLDER_PATH': remote_data_folder_path,
'BODY_CAM_IDX': body_cam_idx,
'LEFT_CAM_IDX': left_cam_idx,
'RIGHT_CAM_IDX': right_cam_idx,
}
params.write('videopc_params', param_dict)
print(f"Created {params.getfile('videopc_params')}")
print(param_dict)
return param_dict
def create_videopc_params():
if VIDEOPC_PARAMS_FILE.exists():
print(f"{VIDEOPC_PARAMS_FILE} exists already, exiting...")
return
else:
default = " [default: {}]: "
data_folder_path = input(r"Where's your 'Subjects' data folder?" +
default.format(r"C:\iblrig_data\Subjects")
) or r"C:\iblrig_data\Subjects"
body_cam_idx = input("Please select the index of the BODY camera" +
default.format(0)) or 0
left_cam_idx = input("Please select the index of the LEFT camera" +
default.format(1)) or 1
right_cam_idx = input("Please select the index of the RIGHT camera" +
default.format(2)) or 2
param_dict = {
'DATA_FOLDER_PATH': data_folder_path,
'BODY_CAM_IDX': body_cam_idx,
'LEFT_CAM_IDX': left_cam_idx,
'RIGHT_CAM_IDX': right_cam_idx,
}
params.write('videopc_params', param_dict)
print(f"Created {VIDEOPC_PARAMS_FILE}")
return
def setup():
par_default = default()
par_current = iopar.read(_PAR_ID_STR, par_default)
par = iopar.as_dict(par_default)
for k in par.keys():
cpar = _get_current_par(k, par_current)
if "PWD" not in k:
par[k] = input("Param " + k + ", current value is [" + str(cpar) +
"]:") or cpar
cpar = _get_current_par("ALYX_PWD", par_current)
prompt = "Enter the Alyx password for " + par[
"ALYX_LOGIN"] + '(leave empty to keep current):'
par["ALYX_PWD"] = getpass(prompt) or cpar
cpar = _get_current_par("HTTP_DATA_SERVER_PWD", par_current)
prompt = "Enter the FlatIron HTTP password for " + par["HTTP_DATA_SERVER_LOGIN"] +\
'(leave empty to keep current): '
par["HTTP_DATA_SERVER_PWD"] = getpass(prompt) or cpar
# default to home dir if empty dir somehow made it here
if len(par['CACHE_DIR']) == 0:
par['CACHE_DIR'] = str(Path.home() / "Downloads" / "FlatIron")
par = iopar.from_dict(par)
# create directory if needed
if par.CACHE_DIR and not os.path.isdir(par.CACHE_DIR):
os.mkdir(par.CACHE_DIR)
iopar.write(_PAR_ID_STR, par)
print('ONE Parameter file location: ' + iopar.getfile(_PAR_ID_STR))
def setup_alyx_params():
setup_silent()
par = iopar.read(_PAR_ID_STR).as_dict()
[usr, pwd] = login(title='Alyx credentials')
par['ALYX_LOGIN'] = usr
par['ALYX_PWD'] = pwd
iopar.write(_PAR_ID_STR, par)
def setUp(self):
self.par_dict = {'A': 'tata',
'O': 'toto',
'I': 'titi',
'num': 15,
'liste': [1, 'turlu']}
params.write('toto', self.par_dict)
params.write('toto', params.from_dict(self.par_dict))
def test_setup_silent(self):
self.assertIsNone(iopar.read(params._PAR_ID_STR))
params.setup_silent()
par = iopar.read(params._PAR_ID_STR)
self.assertIsNotNone(par)
# now do another test to see if it preserves current values
par = par.as_dict()
par['ALYX_LOGIN'] = '******'
iopar.write(params._PAR_ID_STR, par)
params.setup_silent()
par2 = iopar.read(params._PAR_ID_STR)
self.assertEqual(par, par2.as_dict())
def AllenAtlas(res_um=25, par=None):
"""
Instantiates an atlas.BrainAtlas corresponding to the Allen CCF at the given resolution
using the IBL Bregma and coordinate system
:param res_um: 25 or 50 um
:return: atlas.BrainAtlas
"""
if par is None:
# Bregma indices for the 10um Allen Brain Atlas, mlapdv
pdefault = {
'PATH_ATLAS':
'/datadisk/BrainAtlas/ATLASES/Allen/',
'FILE_REGIONS':
str(Path(__file__).parent.joinpath('allen_structure_tree.csv')),
'INDICES_BREGMA':
list(np.array([1140 - (570 + 3.9), 540, 0 + 33.2]))
}
par = params.read('ibl_histology', default=pdefault)
if not Path(par.PATH_ATLAS).exists():
raise NotImplementedError(
"Atlas doesn't exist ! Mock option not implemented yet")
# TODO: mock atlas to get only the coordinate framework
pass
params.write('ibl_histology', par)
else:
par = Bunch(par)
# file_image = Path(path_atlas).joinpath(f'ara_nissl_{res_um}.nrrd')
file_image = Path(
par.PATH_ATLAS).joinpath(f'average_template_{res_um}.nrrd')
file_label = Path(par.PATH_ATLAS).joinpath(f'annotation_{res_um}.nrrd')
image, header = nrrd.read(file_image, index_order='C') # dv, ml, ap
image = np.swapaxes(np.swapaxes(image, 2, 0), 1, 2) # image[iap, iml, idv]
label, header = nrrd.read(file_label, index_order='C') # dv, ml, ap
label = np.swapaxes(np.swapaxes(label, 2, 0), 1, 2) # label[iap, iml, idv]
# resulting volumes origin: x right, y front, z top
df_regions = pd.read_csv(par.FILE_REGIONS)
regions = BrainRegions(id=df_regions.id.values,
name=df_regions.name.values,
acronym=df_regions.acronym.values)
xyz2dims = np.array([1, 0, 2])
dims2xyz = np.array([1, 0, 2])
dxyz = res_um * 1e-6 * np.array([-1, -1, -1])
ibregma = (np.array(par.INDICES_BREGMA) * 10 / res_um)
return BrainAtlas(image,
label,
regions,
dxyz,
ibregma,
dims2xyz=dims2xyz,
xyz2dims=xyz2dims)
def setup_silent():
par_current = iopar.read(_PAR_ID_STR)
par_default = default()
if par_current is None:
par = par_default
else:
par = iopar.as_dict(par_default)
for k in par.keys():
cpar = _get_current_par(k, par_current)
par[k] = cpar
par = iopar.from_dict(par)
if par.CACHE_DIR:
Path(par.CACHE_DIR).mkdir(parents=True, exist_ok=True)
iopar.write(_PAR_ID_STR, par)
def create_ephyspc_params():
if EPHYSPC_PARAMS_FILE.exists():
print(f"{EPHYSPC_PARAMS_FILE} exists already, exiting...")
return
else:
default = " [default: {}]: "
data_folder_path = input(r"Where's your 'Subjects' data folder?" +
default.format(r"C:\iblrig_data\Subjects")
) or r"C:\iblrig_data\Subjects"
param_dict = {
'DATA_FOLDER_PATH': data_folder_path,
}
params.write('ephyspc_params', param_dict)
print(f"Created {EPHYSPC_PARAMS_FILE}")
return
def create_videopc_params(force=False, silent=False):
if Path(params.getfile("videopc_params")).exists() and not force:
print(f"{params.getfile('videopc_params')} exists already, exiting...")
print(Path(params.getfile("videopc_params")).exists())
return
if silent:
data_folder_path = r"D:\iblrig_data\Subjects"
remote_data_folder_path = r"\\iblserver.champalimaud.pt\ibldata\Subjects"
body_cam_idx = 0
left_cam_idx = 1
right_cam_idx = 2
else:
data_folder_path = cli_ask_default(
r"Where's your LOCAL 'Subjects' data folder?",
r"D:\iblrig_data\Subjects")
remote_data_folder_path = cli_ask_default(
r"Where's your REMOTE 'Subjects' data folder?",
r"\\iblserver.champalimaud.pt\ibldata\Subjects",
)
body_cam_idx = cli_ask_default(
"Please select the index of the BODY camera", "0")
left_cam_idx = cli_ask_default(
"Please select the index of the LEFT camera", "1")
right_cam_idx = cli_ask_default(
"Please select the index of the RIGHT camera", "2")
param_dict = {
"DATA_FOLDER_PATH": data_folder_path,
"REMOTE_DATA_FOLDER_PATH": remote_data_folder_path,
"BODY_CAM_IDX": body_cam_idx,
"LEFT_CAM_IDX": left_cam_idx,
"RIGHT_CAM_IDX": right_cam_idx,
}
params.write("videopc_params", param_dict)
print(f"Created {params.getfile('videopc_params')}")
print(param_dict)
return param_dict
def setup(globus_client_id, str_app='globus/default'):
# Lookup and manage consents there
# https://auth.globus.org/v2/web/consents
gtok = _login(globus_client_id, refresh_tokens=True)
params.write(str_app, gtok)
print("""Setting up Globus
1. Login to the Globus Website (ask devs for the login credentials)
2. Go to Endpoints and create a new endpoint for the local device (the one that will run this
script).
3. In the new endpoint's overview page, copy the 'Endpoint UUID' field. This is the LOCAL_REPO_ID.
4. Go to the 'IBL Top Level' endpoint overview page and copy the 'Endpoint UUID' field. This is
the REMOTE_REPO_ID.
5. Copy your GLOBUS_CLIENT_ID (ask the software devs for this).
""")
params_id = 'globus/admin'
pars = params.read(params_id, DEFAULT_PAR)
default = pars.local_endpoint
local_endpoint = input(f'Enter your LOCAL_REPO_ID ({default}):')
pars = pars.set('local_endpoint', local_endpoint.strip() or default)
params.write(params_id, pars)
default = pars.remote_endpoint
remote_endpoint = input(f'Enter your REMOTE_REPO_ID ({default}):')
pars = pars.set('remote_endpoint', remote_endpoint.strip() or default)
params.write(params_id, pars)
default = pars.GLOBUS_CLIENT_ID
globus_client_id = input(f'Enter your GLOBUS_CLIENT_ID ({default}):').strip()
pars = pars.set('GLOBUS_CLIENT_ID', globus_client_id or default)
params.write(params_id, pars)
print("""Setting up fixtures
You will now need to define a directory to which you will download the integration test data.
""")
params_id = 'ibl_ci'