def main():
data_dir = Path('/braintree/home/msch/brain-score/brainscore/benchmarks')
assert os.path.isdir(data_dir)
stimuli = collect_stimuli(data_dir)
stimuli.identifier = 'fei-fei.Deng2009'
print('Packaging stimuli')
package_stimulus_set(stimuli, stimulus_set_identifier=stimuli.identifier, bucket_name='brainio.contrib')
def repackage_stimulus_sets():
for identifier in stimuli.list_stimulus_sets():
stimulus_set = brainio_collection.get_stimulus_set(identifier)
# re-assign bucket
stimulus_set_model = stimuli.StimulusSetModel.get(
stimuli.StimulusSetModel.name == identifier)
location = stimulus_set_model.stimulus_set_image_maps[
0].image.image_image_store_maps[0].image_store.location
bucket = 'brainio-dicarlo' if 'brainio-dicarlo' in location else 'brainio-contrib'
bucket = bucket.replace('-', '.')
# package
package_stimulus_set(stimulus_set,
stimulus_set_identifier=stimulus_set.name,
bucket_name=bucket)
def main():
data_dir = Path(__file__).parents[6] / 'data2' / 'active' / 'users' / 'sachis'
assert os.path.isdir(data_dir)
stimuli = collect_stimuli(data_dir)
stimuli.identifier = 'dicarlo.THINGS2'
assembly = load_responses(data_dir, stimuli)
assembly.name = 'dicarlo.SanghaviMurty2020THINGS2'
print('Packaging stimuli')
package_stimulus_set(stimuli, stimulus_set_identifier=stimuli.identifier, bucket_name='brainio.dicarlo')
print('Packaging assembly')
package_data_assembly(assembly, assembly_identifier=assembly.name, stimulus_set_identifier=stimuli.identifier,
bucket_name='brainio.dicarlo')
return
def main():
stimuli = collect_stimuli(storage_location)
stimuli.name = 'aru.Kuzovkin2018'
assembly = load_responses(storage_location, stimuli)
assembly.name = 'aru.Kuzovkin2018'
print("Packaging stimuli")
package_stimulus_set(stimuli,
stimulus_set_identifier=stimuli.name,
bucket_name="brainio.contrib")
print("Packaging assembly")
package_data_assembly(assembly,
assembly_identifier=assembly.name,
stimulus_set_identifier=stimuli.name,
bucket_name="brainio.contrib")
def main():
data_dir = Path(
"/Users/jjpr/dev/brainio_contrib/mkgu_packaging/dicarlo/BashivanKar2019"
)
assert os.path.isdir(data_dir)
h5_path = data_dir / "from_pouya" / "npc_v4_data.h5"
h5 = tables.open_file(h5_path)
stimuli_nat = collect_stimuli_nat(h5, data_dir)
stimuli_nat.identifier = "dicarlo.BashivanKar2019.naturalistic"
responses_nat_d = collect_responses_nat(h5, stimuli_nat)
stimuli_synth, responses_synth_d = collect_synth(h5, data_dir)
stimuli_synth.identifier = "dicarlo.BashivanKar2019.synthetic"
_logger.debug('Packaging naturalistic stimuli')
package_stimulus_set(stimuli_nat,
stimulus_set_identifier=stimuli_nat.identifier,
bucket_name='brainio.dicarlo')
_logger.debug('Packaging naturalistic assembly')
responses_nat_concat = xr.concat(responses_nat_d.values(), dim="neuroid")
assert responses_nat_concat.shape == (24320, 233, 1)
package_data_assembly(
responses_nat_concat,
assembly_identifier="dicarlo.BashivanKar2019.naturalistic",
stimulus_set_identifier=stimuli_nat.identifier,
bucket_name='brainio.dicarlo')
_logger.debug('Packaging synthetic stimuli')
package_stimulus_set(stimuli_synth,
stimulus_set_identifier=stimuli_synth.identifier,
bucket_name='brainio.dicarlo')
_logger.debug('Packaging synthetic assembly')
responses_synth_concat = xr.concat(responses_synth_d.values(),
dim="presentation")
assert responses_synth_concat.shape == (21360, 233, 1)
package_data_assembly(
responses_synth_concat,
assembly_identifier="dicarlo.BashivanKar2019.synthetic",
stimulus_set_identifier=stimuli_synth.identifier,
bucket_name='brainio.dicarlo')
def repackage_stimulus_sets():
for identifier in stimuli.list_stimulus_sets():
stimulus_set = brainio_collection.get_stimulus_set(identifier)
if identifier.startswith('movshon') or identifier.startswith(
'dicarlo.hvm'):
filenames = stimulus_set['image_file_name'].apply(
lambda s: s.replace('.png', ''))
stimulus_set['image_path_within_store'] = filenames
# re-assign bucket
stimulus_set_model = stimuli.StimulusSetModel.get(
stimuli.StimulusSetModel.name == identifier)
location = stimulus_set_model.stimulus_set_image_maps[
0].image.image_image_store_maps[0].image_store.location
bucket = 'brainio-dicarlo' if 'brainio-dicarlo' in location else 'brainio-contrib'
bucket = bucket.replace('-', '.')
# package
package_stimulus_set(stimulus_set,
stimulus_set_identifier=stimulus_set.name,
bucket_name=bucket)
def main():
blank_dir = DATA_DIR + os.sep + BLANK_STIM_NAME
if not (os.path.isdir(blank_dir)):
gen_blank_stim(degrees=DEGREES, size_px=448, save_dir=blank_dir)
stimuli = load_stim_info(BLANK_STIM_NAME, blank_dir)
print('Packaging stimuli:' + stimuli.identifier)
package_stimulus_set(stimuli,
stimulus_set_identifier=stimuli.identifier,
bucket_name='brainio.dicarlo')
for stim_name in STIM_NAMES:
stim_dir = DATA_DIR + os.sep + stim_name
if not (os.path.isdir(stim_dir)):
gen_grating_stim(degrees=DEGREES,
size_px=SIZE_PX,
stim_name=stim_name,
grat_params=GRAT_PARAMS[stim_name],
save_dir=stim_dir)
stimuli = load_stim_info(stim_name, stim_dir)
print('Packaging stimuli:' + stimuli.identifier)
package_stimulus_set(stimuli,
stimulus_set_identifier=stimuli.identifier,
bucket_name='brainio.dicarlo')
texture_dir = DATA_DIR + os.sep + TEXTURE_STIM_NAME
if not (os.path.isdir(texture_dir)):
gen_texture_stim(degrees=TEXTURE_DEGREES,
stim_pos=np.array([POS[0], POS[0]]),
save_dir=texture_dir)
stimuli = load_stim_info(TEXTURE_STIM_NAME, texture_dir)
print('Packaging stimuli:' + stimuli.identifier)
package_stimulus_set(stimuli,
stimulus_set_identifier=stimuli.identifier,
bucket_name='brainio.contrib')
return
def package(stimulus_set):
print("Packaging stimuli")
package_stimulus_set(stimulus_set,
stimulus_set_identifier=stimulus_set.identifier,
bucket_name='brainio.requested')
assembly = xr.DataArray(rdm_response,
coords={
'presentation': pres_coord,
'presentation': pres_coord,
"image_id": ('presentation', pres_coord),
'subject': list(range(rdm_response.shape[2])),
},
dims=['presentation', 'presentation', 'subject'])
assembly = DataAssembly(assembly)
#assembly = assembly.transpose('presentation', 'presentation', 'subject')
return assembly
if __name__ == "__main__":
stimuli = collect_stimuli(storage_location)
stimuli.name = 'aru.Cichy2019'
assembly = load_responses(storage_location + "RDM.npy", stimuli)
assembly.name = 'aru.Cichy2019'
print("Packaging stimuli")
package_stimulus_set(stimuli,
stimulus_set_identifier=stimuli.name,
bucket_name="brainio.contrib")
print("Packaging assembly")
package_data_assembly(assembly,
assembly_identifier=assembly.name,
stimulus_set_identifier=stimuli.name,
bucket_name="brainio.contrib",
assembly_class="DataAssembly")
