def get_iblrig_version():
ph.get_iblrig_folder()
# Find version number from `__init__.py` without executing it.
file_path = Path(ph.get_iblrig_folder()) / "setup.py"
with open(file_path, "r") as f:
version = re.search(r"version=\"([^\"]+)\"", f.read()).group(1)
return version
def make_stims_for_passiveCW_pcs(seed_num=None, save=False):
if seed_num is not None:
np.random.seed(seed_num)
iblrig_path = Path(ph.get_iblrig_folder())
# Generate the position and contrast for the replayed stims
contrasts = [1.0, 0.25, 0.125, 0.0625]
zero_contrasts = [0.0]
positions = [-35, 35]
pc_repeats = 20
# zero % contrast is added with half the amount of pc_repeats
zero_repeats = len(positions) * pc_repeats / 2
pos = sorted(positions * len(contrasts) * pc_repeats)
cont = contrasts * pc_repeats * len(positions)
pos.extend(positions * int(zero_repeats / len(positions)))
cont.extend(zero_contrasts * int(zero_repeats))
sphase = [np.random.uniform(0, 2 * math.pi) for x in cont]
gabors = np.array([[int(p), c, s] for p, c, s in zip(pos, cont, sphase)])
np.random.shuffle(gabors)
# Make into strings for saving
if save:
fpath = iblrig_path / "visual_stim" / "passiveChoiceWorld"
fpath = fpath / "Extensions" / "passiveCW_stims.csv"
np.savetxt(fpath, gabors, delimiter=" ", fmt=["%d", "%f", "%f"])
return gabors
def start_passive_visual_stim(save2folder):
here = os.getcwd()
bns = ph.get_bonsai_path()
stim_folder = str(
Path(ph.get_iblrig_folder()) / "visual_stim" / "passiveChoiceWorld"
)
wkfl = os.path.join(stim_folder, "passiveChoiceWorld_passive.bonsai")
os.chdir(stim_folder)
# Flags
noedit = "--no-editor" # implies start and no-debug?
noboot = "--no-boot"
# Properties
SA0_DueTime = "-p:Stim.SpontaneousActivity0.DueTime=00:10:00"
RFM_FileName = "-p:Stim.ReceptiveFieldMappingStim.FileNameRFMapStim=" + str(
Path(save2folder) / "_iblrig_RFMapStim.raw.bin"
)
RFM_MappingTime = "-p:Stim.ReceptiveFieldMappingStim.MappingTime=00:05:00"
cmd = [bns, wkfl, noboot, noedit, SA0_DueTime, RFM_FileName, RFM_MappingTime]
log.info("Starting spontaneous activity and RF mapping stims")
os.chdir(stim_folder)
s = subprocess.run(cmd, stdout=subprocess.PIPE) # locking call
os.chdir(here)
log.info("Done")
sys.stdout.flush()
return s
def start_frame2ttl_test(data_file, lengths_file, harp=False):
here = os.getcwd()
bns = ph.get_bonsai_path()
stim_folder = str(
Path(ph.get_iblrig_folder()) / 'visual_stim' / 'f2ttl_calibration'
)
wkfl = os.path.join(stim_folder, 'screen_60Hz.bonsai')
# Flags
noedit = '--no-editor' # implies start and no-debug?
noboot = '--no-boot'
data_file_name = "-p:FileNameData=" + str(data_file)
lengths_file_name = "-p:FileNameDataLengths=" + str(lengths_file)
if harp:
harp_file_name = "-p:FileName=" + str(data_file.parent / 'harp_ts_data.csv')
# Properties
log.info('Starting pulses @ 60Hz')
sys.stdout.flush()
os.chdir(stim_folder)
if harp:
s = subprocess.Popen(
[bns, wkfl, noboot, noedit, data_file_name, lengths_file_name, harp_file_name]
)
else:
s = subprocess.Popen(
[bns, wkfl, noboot, noedit, data_file_name, lengths_file_name])
os.chdir(here)
return s
def test_get_iblrig_params_folder(self):
f = ph.get_iblrig_params_folder()
self.assertTrue(isinstance(f, str))
self.assertTrue("iblrig_params" in f)
fp = Path(f)
self.assertTrue(
str(fp.parent) == str(Path(ph.get_iblrig_folder()).parent))
def test_get_commit_hash(self):
import subprocess
out = subprocess.check_output(["git", "rev-parse",
"HEAD"]).decode().strip()
# Run it
ch = ph.get_commit_hash(ph.get_iblrig_folder())
self.assertTrue(out == ch)
def plot_pcqs(session_num,
folder="./tasks/_iblrig_tasks_ephysChoiceWorld/sessions"):
iblrig_path = Path(ph.get_iblrig_folder())
folder_path = Path(folder)
folder = str(iblrig_path / folder_path)
num = session_num
pcqs = np.load(folder + f"/pcqs_session_{num}.npy")
len_block = np.load(folder + f"/pcqs_session_{num}_len_blocks.npy")
with plt.xkcd(scale=1, length=100, randomness=2):
f = plt.figure(figsize=(16, 12), dpi=80)
f.suptitle(f"Session number: {num}")
ax_position = plt.subplot2grid([2, 2], [0, 0],
rowspan=1,
colspan=1,
fig=f)
ax_contrast = plt.subplot2grid([2, 2], [0, 1],
rowspan=1,
colspan=1,
fig=f,
sharex=ax_position)
ax_qperiod = plt.subplot2grid([2, 2], [1, 0],
rowspan=1,
colspan=1,
fig=f,
sharex=ax_position)
ax_sphase = plt.subplot2grid([2, 2], [1, 1],
rowspan=1,
colspan=1,
fig=f,
sharex=ax_position)
ax_position.plot(pcqs[:, 0], ".", label="Position", color="b")
ax_position.plot(smooth(pcqs[:, 0], window_len=20, window="blackman"),
alpha=0.5,
color="k")
ax_contrast.plot(pcqs[:, 1] * 100, ".", label="Contrasts")
ax_qperiod.plot(pcqs[:, 2], ".", label="Quiescent period")
ax_sphase.plot(pcqs[:, 3], ".", label="Stimulus phase")
[
ax.set_ylabel(l) for ax, l in zip(
f.axes,
[
"Position (º)",
"Contrasts (%)",
"Quiescent period (s)",
"Stimulus phase (rad)",
],
)
]
[ax.axvline(x, alpha=0.5) for x in np.cumsum(len_block) for ax in f.axes]
f.show()
return pcqs, len_block
def pre_generate_ephysCW_session_files(
nsessions, path="./tasks/_iblrig_tasks_ephysChoiceWorld/sessions"):
iblrig_path = Path(ph.get_iblrig_folder())
path = iblrig_path / Path(path)
path.mkdir(parents=True, exist_ok=True)
for i in range(nsessions):
pc, len_block = make_ephysCW_pc()
pcqs = make_ephysCW_pcqs(pc)
np.save(path / f"session_{i}_ephys_pcqs.npy", pcqs)
np.save(path / f"session_{i}_ephys_len_blocks.npy", len_block)
def alyx_ok() -> bool:
out = False
try:
python = envs.get_env_python(env_name="ibllib")
here = os.getcwd()
os.chdir(os.path.join(ph.get_iblrig_folder(), "scripts"))
os.system(f'{python} -c "from one.api import ONE; ONE()"')
os.chdir(here)
out = True
except BaseException as e:
log.warning(f"{e}\nCan't connect to Alyx.")
return out
def plot_pcqs(session_num,
folder='./tasks/_iblrig_tasks_ephysChoiceWorld/sessions'):
iblrig_path = Path(ph.get_iblrig_folder())
folder_path = Path(folder)
folder = str(iblrig_path / folder_path)
num = session_num
pcqs = np.load(folder + f'/pcqs_session_{num}.npy')
len_block = np.load(folder + f'/pcqs_session_{num}_len_blocks.npy')
with plt.xkcd(scale=1, length=100, randomness=2):
f = plt.figure(figsize=(16, 12), dpi=80)
f.suptitle(f'Session number: {num}')
ax_position = plt.subplot2grid([2, 2], [0, 0],
rowspan=1,
colspan=1,
fig=f)
ax_contrast = plt.subplot2grid([2, 2], [0, 1],
rowspan=1,
colspan=1,
fig=f,
sharex=ax_position)
ax_qperiod = plt.subplot2grid([2, 2], [1, 0],
rowspan=1,
colspan=1,
fig=f,
sharex=ax_position)
ax_sphase = plt.subplot2grid([2, 2], [1, 1],
rowspan=1,
colspan=1,
fig=f,
sharex=ax_position)
ax_position.plot(pcqs[:, 0], '.', label='Position', color='b')
ax_position.plot(smooth(pcqs[:, 0], window_len=20, window='blackman'),
alpha=0.5,
color='k')
ax_contrast.plot(pcqs[:, 1] * 100, '.', label='Contrasts')
ax_qperiod.plot(pcqs[:, 2], '.', label='Quiescent period')
ax_sphase.plot(pcqs[:, 3], '.', label='Stimulus phase')
[
ax.set_ylabel(l) for ax, l in zip(f.axes, [
'Position (º)', 'Contrasts (%)', 'Quiescent period (s)',
'Stimulus phase (rad)'
])
]
[ax.axvline(x, alpha=0.5) for x in np.cumsum(len_block) for ax in f.axes]
f.show()
return pcqs, len_block
def pre_generate_stim_phase(
nsessions, path="./tasks/_iblrig_tasks_ephysChoiceWorld/sessions"):
iblrig_path = Path(ph.get_iblrig_folder())
path = iblrig_path / Path(path)
path.mkdir(parents=True, exist_ok=True)
for i in range(nsessions):
length = len(np.load(path.joinpath(f"session_{i}_ephys_pcqs.npy")))
sphase = np.array(
[np.random.uniform(0, 2 * math.pi) for x in range(length)])
np.save(path / f"session_{i}_stim_phase.npy", sphase)
else:
length = len(np.load(path.joinpath("session_mock_ephys_pcqs.npy")))
sphase = np.array(
[np.random.uniform(0, 2 * math.pi) for x in range(length)])
np.save(path / "session_mock_stim_phase.npy", sphase)
def start_screen_color():
here = os.getcwd()
iblrig_folder_path = Path(ph.get_iblrig_folder())
os.chdir(str(iblrig_folder_path / "visual_stim" / "f2ttl_calibration"))
bns = ph.get_bonsai_path()
wrkfl = str(iblrig_folder_path / "visual_stim" / "f2ttl_calibration" /
"screen_color.bonsai")
noedit = "--no-editor" # implies start
# nodebug = '--start-no-debug'
# start = '--start'
noboot = "--no-boot"
editor = noedit
subprocess.Popen([bns, wrkfl, editor, noboot])
time.sleep(3)
os.chdir(here)
def pre_generate_passiveCW_session_files(
nsessions, path="./tasks/_iblrig_tasks_ephysChoiceWorld/sessions"):
iblrig_path = Path(ph.get_iblrig_folder())
path = iblrig_path / Path(path)
path.mkdir(parents=True, exist_ok=True)
for i in range(nsessions):
delays, ids, = make_passiveCW_session_delays_ids()
pcs = make_stims_for_passiveCW_pcs()
np.save(path / f"session_{i}_passive_stimIDs.npy", ids)
np.save(path / f"session_{i}_passive_stimDelays.npy", delays)
np.save(path / f"session_{i}_passive_pcs.npy", pcs)
else:
delays, ids, = make_passiveCW_session_delays_ids()
pcs = make_stims_for_passiveCW_pcs()
np.save(path / "session_mock_passive_stimIDs.npy", ids)
np.save(path / "session_mock_passive_stimDelays.npy", delays)
np.save(path / "session_mock_passive_pcs.npy", pcs)
def make_stims_for_certification_pcs(seed_num=None, save=False):
if seed_num is not None:
np.random.seed(seed_num)
iblrig_path = Path(ph.get_iblrig_folder())
# Generate the position and contrast for the replayed stims
contrasts = [1.0, 0.5, 0.25, 0.125, 0.0625]
positions = [-35, 35]
pc_repeats = 20
pos = sorted(positions * len(contrasts) * pc_repeats)
cont = contrasts * pc_repeats * len(positions)
sphase = [np.random.uniform(0, 2 * math.pi) for x in cont]
gabors = np.array([[int(p), c, s] for p, c, s in zip(pos, cont, sphase)])
np.random.shuffle(gabors)
# Make into strings for saving
if save:
fpath = iblrig_path / "visual_stim" / "ephys_certification"
fpath = fpath / "Extensions" / "certification_stims.csv"
np.savetxt(fpath, gabors, delimiter=" ", fmt=["%d", "%f", "%f"])
return gabors
def test_get_iblrig_folder(self):
f = ph.get_iblrig_folder()
self.assertTrue(isinstance(f, str))
self.assertTrue("iblrig" in f)
create_ONE_alyx_user
create_local_subjects_from_alyx
Return: None or json dict
"""
import json
from pathlib import Path
from one.api import ONE
from pybpodgui_api.models.project import Project
import iblrig.path_helper as ph
IBLRIG_PARAMS_FOLDER = Path(ph.get_iblrig_params_folder())
print(ph.get_iblrig_folder(), "\n", IBLRIG_PARAMS_FOLDER)
local2alyx_names = {"IBL": "ibl_neuropixel_brainwide_01"}
alyx2local_names = {"ibl_neuropixel_brainwide_01": "IBL"}
# UTILS
def _load_pybpod_obj_json(obj):
objpath = Path(obj.path).joinpath(obj.name + ".json")
with open(objpath, "r") as f:
out = json.load(f)
return out
def _save_pybpod_obj_json(obj, data):
