def truncate(experiment, lifespan):
e = deepcopy(experiment)
if 'stimulus' in experiment:
e["spikes"] = e["spikes"][np.where(e["spikes"] < lifespan)]
e['lifespan'] = lifespan
else:
e['units'] = glia.f_map(lambda x: x[np.where(x < lifespan)])(
e['units'])
e['lifespan'] = lifespan
return e
def units_to_SpikeTrain(experiment):
t = experiment["lifespan"]
return glia.f_map(lambda x: SpikeTrain(x * quantities.s, t))(
experiment["units"])
def save_grating_npz(units,
stimulus_list,
name,
append,
group_by,
sinusoid=False):
"Psychophysics discrimination grating 0.2.0"
print("Saving grating NPZ file.")
if sinusoid:
stimulus_type = "SINUSOIDAL_GRATING"
else:
stimulus_type = 'GRATING'
get_gratings = glia.compose(
partial(glia.create_experiments,
stimulus_list=stimulus_list,
append_lifespan=append),
glia.f_filter(lambda x: x['stimulusType'] == stimulus_type),
partial(glia.group_by, key=group_by),
glia.f_map(partial(glia.group_by, key=lambda x: x["width"])),
glia.f_map(
glia.f_map(
partial(glia.group_by,
key=lambda x: x["metadata"]["cohort"]))))
gratings = get_gratings(units)
max_duration = 0.0
for condition, sizes in gratings.items():
for size, cohorts in sizes.items():
for cohort, experiments in cohorts.items():
max_duration = max(max_duration, experiments[0]['lifespan'])
max_duration += append
conditions = sorted(list(gratings.keys()))
print("Conditions:", name, conditions)
nconditions = len(conditions)
example_condition = glia.get_value(gratings)
sizes = sorted(list(example_condition.keys()))
print("Sizes:", sizes)
nsizes = len(sizes)
example_size = glia.get_value(example_condition)
ncohorts = len(example_size)
# print(list(gratings.values()))
d = int(np.ceil(max_duration * 1000)) # 1ms bins
tvt = glia.tvt_by_percentage(ncohorts, 60, 40, 0)
# 2 per cohort
training_data = np.full((nconditions, nsizes, tvt.training * 2, d,
Unit.nrow, Unit.ncol, Unit.nunit),
0,
dtype='int8')
training_target = np.full((nconditions, nsizes, tvt.training * 2),
0,
dtype='int8')
validation_data = np.full((nconditions, nsizes, tvt.validation * 2, d,
Unit.nrow, Unit.ncol, Unit.nunit),
0,
dtype='int8')
validation_target = np.full((nconditions, nsizes, tvt.validation * 2),
0,
dtype='int8')
condition_map = {c: i for i, c in enumerate(conditions)}
size_map = {s: i for i, s in enumerate(sizes)}
for condition, sizes in gratings.items():
for size, cohorts in sizes.items():
X = glia.f_split_dict(tvt)(cohorts)
td, tt = glia.experiments_to_ndarrays(glia.training_cohorts(X),
get_grating_class_from_stim,
append)
missing_duration = d - td.shape[1]
pad_td = np.pad(td, ((0, 0), (0, missing_duration), (0, 0), (0, 0),
(0, 0)),
mode='constant')
condition_index = condition_map[condition]
size_index = size_map[size]
training_data[condition_index, size_index] = pad_td
training_target[condition_index, size_index] = tt
td, tt = glia.experiments_to_ndarrays(glia.validation_cohorts(X),
get_grating_class_from_stim,
append)
pad_td = np.pad(td, ((0, 0), (0, missing_duration), (0, 0), (0, 0),
(0, 0)),
mode='constant')
validation_data[condition_index, size_index] = pad_td
validation_target[condition_index, size_index] = tt
print('saving to ', name)
np.savez(name,
training_data=training_data,
training_target=training_target,
validation_data=validation_data,
validation_target=validation_target)
def save_checkerboard_flicker_npz(units,
stimulus_list,
name,
append,
group_by,
quad=False):
"Psychophysics discrimination checkerboard 0.2.0"
print("Saving checkerboard NPZ file.")
get_checkers = glia.compose(
partial(
glia.create_experiments,
progress=True,
append_lifespan=append,
# stimulus_list=stimulus_list,append_lifespan=0.5),
stimulus_list=stimulus_list),
partial(glia.group_by, key=lambda x: x["metadata"]["group"]),
glia.group_dict_to_list,
glia.f_filter(group_contains_checkerboard),
glia.f_map(
glia.f_filter(lambda x: x['stimulusType'] == 'CHECKERBOARD')),
glia.f_map(glia.merge_experiments),
partial(glia.group_by, key=group_by),
glia.f_map(partial(glia.group_by, key=lambda x: x["size"])),
glia.f_map(
glia.f_map(
partial(glia.group_by,
key=lambda x: x["metadata"]["cohort"]))))
checkers = get_checkers(units)
max_duration = 0.0
for condition, sizes in checkers.items():
for size, cohorts in sizes.items():
for cohort, experiments in cohorts.items():
max_duration = max(max_duration, experiments[0]['lifespan'])
max_duration += append
print(f"max_duration: {max_duration}")
conditions = sorted(list(checkers.keys()))
print("Conditions:", name, conditions)
nconditions = len(conditions)
example_condition = glia.get_value(checkers)
sizes = sorted(list(example_condition.keys()))
nsizes = len(sizes)
# TODO remove
if max_duration < 9:
print(example_condition)
example_size = glia.get_value(example_condition)
ncohorts = len(example_size)
# print(list(checkers.values()))
d = int(np.ceil(max_duration * 1000)) # 1ms bins
tvt = glia.tvt_by_percentage(ncohorts, 60, 40, 0)
logger.info(f"{tvt}, {ncohorts}")
# (TODO?) 2 dims for first checkerboard and second checkerboard
# 4 per cohort
if quad:
ntraining = tvt.training * 4
nvalid = tvt.validation * 4
else:
ntraining = tvt.training * 2
nvalid = tvt.validation * 2
training_data = np.full(
(nconditions, nsizes, ntraining, d, Unit.nrow, Unit.ncol, Unit.nunit),
0,
dtype='int8')
training_target = np.full((nconditions, nsizes, ntraining),
0,
dtype='int8')
validation_data = np.full(
(nconditions, nsizes, nvalid, d, Unit.nrow, Unit.ncol, Unit.nunit),
0,
dtype='int8')
validation_target = np.full((nconditions, nsizes, nvalid), 0, dtype='int8')
# test_data = np.full((nsizes,tvt.test,d,nunits),0,dtype='int8')
# test_target = np.full((nsizes,tvt.test),0,dtype='int8')
if quad:
get_class = get_checker_quad_discrimination_class
else:
get_class = get_checker_discrimination_class
condition_map = {c: i for i, c in enumerate(conditions)}
size_map = {s: i for i, s in enumerate(sizes)}
for condition, sizes in checkers.items():
for size, cohorts in sizes.items():
X = glia.f_split_dict(tvt)(cohorts)
td, tt = glia.experiments_to_ndarrays(glia.training_cohorts(X),
get_class, append)
logger.info(td.shape)
missing_duration = d - td.shape[1]
pad_td = np.pad(td, ((0, 0), (0, missing_duration), (0, 0), (0, 0),
(0, 0)),
mode='constant')
condition_index = condition_map[condition]
size_index = size_map[size]
training_data[condition_index, size_index] = pad_td
training_target[condition_index, size_index] = tt
td, tt = glia.experiments_to_ndarrays(glia.validation_cohorts(X),
get_class, append)
pad_td = np.pad(td, ((0, 0), (0, missing_duration), (0, 0), (0, 0),
(0, 0)),
mode='constant')
validation_data[condition_index, size_index] = pad_td
validation_target[condition_index, size_index] = tt
print('saving to ', name)
np.savez(name,
training_data=training_data,
training_target=training_target,
validation_data=validation_data,
validation_target=validation_target)
def save_images_h5(units, stimulus_list, name, frame_log, video_file, append):
"""Assumes each group is three stimuli with image in second position.
Concatenate second stimuli with first 0.5s of third stimuli"""
# open first so if there's a problem we don't waste time
compression_level = 3
dset_filter = tables.filters.Filters(complevel=compression_level,
complib='blosc:zstd')
with tables.open_file(name + ".h5", 'w') as h5:
class_resolver = get_classes_from_stimulus_list(stimulus_list)
nclasses = len(class_resolver)
frames, image_classes = glia.get_images_from_vid(
stimulus_list, frame_log, video_file)
image_class_num = list(
map(lambda x: class_resolver[str(x)], image_classes))
idx_sorted_order = np.argsort(image_class_num)
# save mapping of class_num target to class metadata
# this way h5.root.image_classes[n] will give the class metadata string
logger.info("create class_resolver with max string of 256")
resolver = h5.create_carray(h5.root, "image_classes",
tables.StringAtom(itemsize=256),
(nclasses, ))
img_class_array = np.array(image_classes,
dtype="S256")[idx_sorted_order]
for i, image_class in enumerate(img_class_array):
resolver[i] = image_class
atom = tables.Atom.from_dtype(frames[0].dtype)
images = h5.create_carray(h5.root,
"images",
atom, (nclasses, *frames[0].shape),
filters=dset_filter)
frames = np.array(frames)
nFrames = len(frames)
for i, idx in enumerate(idx_sorted_order):
if idx >= nFrames:
logger.warn(
f"skipping class {image_classes[idx]} as no accompanying frame. This should only occur if experiment stopped early."
)
continue
images[i] = frames[idx]
print("finished saving images")
get_image_responses = glia.compose(
# returns a list
partial(glia.create_experiments,
stimulus_list=stimulus_list,
progress=True,
append_lifespan=append),
partial(glia.group_by, key=lambda x: x["metadata"]["group"]),
glia.group_dict_to_list,
glia.f_filter(partial(glia.group_contains, "IMAGE")),
# truncate to 0.5s
glia.f_map(lambda x: [x[1], truncate(x[2], 0.5)]),
glia.f_map(glia.merge_experiments),
partial(glia.group_by, key=lambda x: x["metadata"]["cohort"]),
# glia.f_map(f_flatten)
)
image_responses = get_image_responses(units)
ncohorts = len(image_responses)
ex_cohort = glia.get_value(image_responses)
images_per_cohort = len(ex_cohort)
print("images_per_cohort", images_per_cohort)
duration = ex_cohort[0]["lifespan"]
d = int(np.ceil(duration * 1000)) # 1ms bins
logger.info(f"ncohorts: {ncohorts}")
# import pdb; pdb.set_trace()
logger.info(f"nclasses: {nclasses}")
if nclasses < 256:
class_dtype = np.dtype('uint8')
else:
class_dtype = np.dtype('uint16')
class_resolver_func = lambda c: class_resolver[str(c)]
# determine shape
experiments = glia.flatten_group_dict(image_responses)
nE = len(experiments)
d = int(np.ceil(duration * 1000)) # 1ms bins
data_shape = (nE, d, Unit.nrow, Unit.ncol, Unit.nunit)
print(f"writing to {name}.h5 with zstd compression...")
data = h5.create_carray("/",
"data",
tables.Atom.from_dtype(np.dtype('uint8')),
shape=data_shape,
filters=dset_filter)
target = h5.create_carray("/",
"target",
tables.Atom.from_dtype(class_dtype),
shape=(nE, ),
filters=dset_filter)
glia.experiments_to_h5(experiments,
data,
target,
partial(get_image_class_from_stim,
class_resolver=class_resolver_func),
append,
class_dtype=class_dtype)
def save_acuity_image_npz(units, stimulus_list, name, append):
"Assumes metadata includes a parameter to group by, as well as a blank image"
get_letters = glia.compose(
partial(glia.create_experiments,
stimulus_list=stimulus_list,
progress=True,
append_lifespan=append),
partial(glia.group_by, key=lambda x: x["metadata"]["group"]),
glia.group_dict_to_list,
glia.f_filter(partial(glia.group_contains, "IMAGE")),
glia.f_map(lambda x: x[0:2]),
partial(glia.group_by, key=lambda x: x[1]["metadata"]["parameter"]),
glia.f_map(
partial(glia.group_by, key=lambda x: x[1]["metadata"]["cohort"])),
glia.f_map(glia.f_map(f_flatten)),
glia.f_map(glia.f_map(partial(balance_blanks, key='image'))))
letters = get_letters(units)
sizes = sorted(list(letters.keys()))
nsizes = len(sizes)
ncohorts = len(list(letters.values())[0])
ex_letters = glia.get_value(list(letters.values())[0])
nletters = len(ex_letters)
print("nletters", nletters)
duration = ex_letters[0]["lifespan"]
# small hack to fix bug in letters 0.2.0
letter_duration = ex_letters[1]['lifespan']
if duration != letter_duration:
new_letters = {}
for size, cohorts in letters.items():
new_letters[size] = {}
for cohort, stimuli in cohorts.items():
new_letters[size][cohort] = list(
map(lambda s: truncate(s, letter_duration), stimuli))
letters = new_letters
d = int(np.ceil(duration * 1000)) # 1ms bins
nunits = len(units.keys())
tvt = glia.tvt_by_percentage(ncohorts, 60, 40, 0)
logger.info(f"{tvt}, ncohorts: {ncohorts}")
experiments_per_cohort = 11
training_data = np.full((nsizes, tvt.training * experiments_per_cohort, d,
Unit.nrow, Unit.ncol, Unit.nunit),
0,
dtype='int8')
training_target = np.full((nsizes, tvt.training * experiments_per_cohort),
0,
dtype='int8')
validation_data = np.full((nsizes, tvt.validation * experiments_per_cohort,
d, Unit.nrow, Unit.ncol, Unit.nunit),
0,
dtype='int8')
validation_target = np.full(
(nsizes, tvt.validation * experiments_per_cohort), 0, dtype='int8')
size_map = {s: i for i, s in enumerate(sizes)}
for size, cohorts in letters.items():
X = glia.f_split_dict(tvt)(cohorts)
logger.info(f"ncohorts: {len(cohorts)}")
td, tt = glia.experiments_to_ndarrays(glia.training_cohorts(X),
acuity_image_class, append)
logger.info(td.shape)
missing_duration = d - td.shape[1]
pad_td = np.pad(td, ((0, 0), (0, missing_duration), (0, 0), (0, 0),
(0, 0)),
mode='constant')
size_index = size_map[size]
training_data[size_index] = pad_td
training_target[size_index] = tt
td, tt = glia.experiments_to_ndarrays(glia.validation_cohorts(X),
acuity_image_class, append)
pad_td = np.pad(td, ((0, 0), (0, missing_duration), (0, 0), (0, 0),
(0, 0)),
mode='constant')
validation_data[size_index] = pad_td
validation_target[size_index] = tt
np.savez(name,
training_data=training_data,
training_target=training_target,
validation_data=validation_data,
validation_target=validation_target)
def save_letter_npz(units, stimulus_list, name, append):
print(
"Saving letter NPZ file. Warning: not including Off response--performance can be improved!"
)
# TODO use merge_experiment
# TODO add TEST!!!
get_letters = glia.compose(
partial(glia.create_experiments,
stimulus_list=stimulus_list,
progress=True,
append_lifespan=append),
partial(glia.group_by, key=lambda x: x["metadata"]["group"]),
glia.group_dict_to_list, glia.f_filter(group_contains_letter),
glia.f_map(lambda x: x[0:2]),
partial(glia.group_by, key=lambda x: x[1]["size"]),
glia.f_map(
partial(glia.group_by, key=lambda x: x[1]["metadata"]["cohort"])),
glia.f_map(glia.f_map(f_flatten)),
glia.f_map(glia.f_map(balance_blanks)))
letters = get_letters(units)
sizes = sorted(list(letters.keys()))
nsizes = len(sizes)
ncohorts = len(list(letters.values())[0])
ex_letters = glia.get_value(list(letters.values())[0])
nletters = len(ex_letters)
print("nletters", nletters)
duration = ex_letters[0]["lifespan"]
d = int(np.ceil(duration * 1000)) # 1ms bins
nunits = len(units.keys())
tvt = glia.tvt_by_percentage(ncohorts, 60, 40, 0)
logger.info(f"{tvt}, ncohorts: {ncohorts}")
experiments_per_cohort = 11
training_data = np.full((nsizes, tvt.training * experiments_per_cohort, d,
Unit.nrow, Unit.ncol, Unit.nunit),
0,
dtype='int8')
training_target = np.full((nsizes, tvt.training * experiments_per_cohort),
0,
dtype='int8')
validation_data = np.full((nsizes, tvt.validation * experiments_per_cohort,
d, Unit.nrow, Unit.ncol, Unit.nunit),
0,
dtype='int8')
validation_target = np.full(
(nsizes, tvt.validation * experiments_per_cohort), 0, dtype='int8')
size_map = {s: i for i, s in enumerate(sizes)}
for size, cohorts in letters.items():
X = glia.f_split_dict(tvt)(cohorts)
logger.info(f"ncohorts: {len(cohorts)}")
td, tt = glia.experiments_to_ndarrays(glia.training_cohorts(X),
letter_class, append)
logger.info(td.shape)
missing_duration = d - td.shape[1]
pad_td = np.pad(td, ((0, 0), (0, missing_duration), (0, 0), (0, 0),
(0, 0)),
mode='constant')
size_index = size_map[size]
training_data[size_index] = pad_td
training_target[size_index] = tt
td, tt = glia.experiments_to_ndarrays(glia.validation_cohorts(X),
letter_class, append)
pad_td = np.pad(td, ((0, 0), (0, missing_duration), (0, 0), (0, 0),
(0, 0)),
mode='constant')
validation_data[size_index] = pad_td
validation_target[size_index] = tt
np.savez(name,
training_data=training_data,
training_target=training_target,
validation_data=validation_data,
validation_target=validation_target)
def save_eyechart_npz(units, stimulus_list, name, append=0.5):
print("Saving eyechart NPZ file.")
# TODO add blanks
get_letters = glia.compose(
partial(glia.create_experiments,
stimulus_list=stimulus_list,
append_lifespan=append),
partial(glia.group_by, key=lambda x: x["metadata"]["group"]),
glia.group_dict_to_list,
glia.f_filter(group_contains_letter),
glia.f_map(lambda x: adjust_lifespan(x[1])),
partial(glia.group_by, key=lambda x: x["size"]),
glia.f_map(
partial(glia.group_by,
key=lambda x: x[1]["stimulus"]["metadata"]["cohort"])),
glia.f_map(glia.f_map(f_flatten)),
)
letters = get_letters(units)
sizes = sorted(list(letters.keys()))
nsizes = len(sizes)
ncohorts = len(list(letters.values())[0])
ex_letters = glia.get_a_value(list(letters.values())[0])
nletters = len(ex_letters)
print("nletters", nletters)
duration = ex_letters[0]["lifespan"]
d = int(np.ceil(duration * 1000)) # 1ms bins
nunits = len(units.keys())
tvt = glia.tvt_by_percentage(ncohorts, 60, 40, 0)
logger.info(f"{tvt}, {ncohorts}")
training_data = np.full((nsizes, tvt.training, d, nunits), 0, dtype='int8')
training_target = np.full((nsizes, tvt.training), 0, dtype='int8')
validation_data = np.full((nsizes, tvt.validation, d, nunits),
0,
dtype='int8')
validation_target = np.full((nsizes, tvt.validation), 0, dtype='int8')
test_data = np.full((nsizes, tvt.test, d, nunits), 0, dtype='int8')
test_target = np.full((nsizes, tvt.test), 0, dtype='int8')
size_map = {s: i for i, s in enumerate(sizes)}
for size, experiments in letters.items():
split = glia.f_split_dict(tvt)
flatten_cohort = glia.compose(glia.group_dict_to_list, f_flatten)
X = glia.tvt_map(split(experiments), flatten_cohort)
td, tt = glia.experiments_to_ndarrays(X.training, letter_class, append)
size_index = size_map[size]
training_data[size_index] = td
training_target[size_index] = tt
td, tt = glia.experiments_to_ndarrays(X.validation, letter_class,
append)
validation_data[size_index] = td
validation_target[size_index] = tt
td, tt = glia.experiments_to_ndarrays(X.test, letter_class, append)
test_data[size_index] = td
test_target[size_index] = tt
np.savez(name,
training_data=training_data,
training_target=training_target,
validation_data=validation_data,
validation_target=validation_target)