def main():
assembly = collect_data()
assembly.name = ASSEMBLY_NAME
print('Packaging assembly')
package_data_assembly(xarray.DataArray(assembly), assembly_identifier=assembly.name,
stimulus_set_identifier=SPATIAL_FREQUENCY_STIM_NAME, assembly_class='PropertyAssembly',
bucket_name='brainio.contrib')
def repackage_assemblies():
for identifier in assemblies.list_assemblies():
print(f"Repackaging {identifier}")
assembly = brainio_collection.get_assembly(identifier)
stimulus_set_identifier = assembly.stimulus_set_name
# fix individual assemblies
assembly_class = assembly.__class__.__name__
if identifier == 'dicarlo.Kar2019': # change OST assembly
assembly_class = 'DataAssembly' # it's not actually a NeuronRecordingAssembly because it contains OSTs
if identifier == 'klab.Zhang2018search_obj_array':
assembly_class = 'BehavioralAssembly' # was incorrectly packaged as NeuronRecordingAssembly but is behavior
if identifier.startswith('dicarlo.Majaj2015'):
assembly.name = assembly.name.replace(
'Majaj2015', 'MajajHong2015') # joint first authors
# strip
assembly = _strip_presentation_coords(assembly)
del assembly.attrs['stimulus_set']
del assembly.attrs['stimulus_set_name']
# re-assign bucket
assembly_model = assemblies.lookup_assembly(identifier)
store = assembly_model.assembly_store_maps[0]
location = store.assembly_store_model.location
bucket = 'brainio-dicarlo' if 'brainio-dicarlo' in location else 'brainio-contrib'
bucket = bucket.replace('-', '.')
# package
package_data_assembly(assembly,
assembly_identifier=assembly.name,
stimulus_set_identifier=stimulus_set_identifier,
assembly_class=assembly_class,
bucket_name=bucket)
def main():
metric_bins_path = Path("/braintree/home/darren/work/metric_bins.npy")
csv_path = Path(
__file__).parents[2] / "notebooks" / "2020-11-22_hvm_from_dldata.csv"
stimuli = brainio_collection.get_stimulus_set('dicarlo.hvm')
assembly = load_responses(metric_bins_path, csv_path)
assembly.name = 'dicarlo.Seibert2019'
print('Packaging assembly')
package_data_assembly(assembly,
assembly_identifier=assembly.name,
stimulus_set_identifier=stimuli.identifier,
bucket_name='brainio.dicarlo')
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():
data_dir = Path(__file__).parents[
6] / 'data2' / 'active' / 'users' / 'sachis' / 'database'
assert os.path.isdir(data_dir)
stimuli = brainio_collection.get_stimulus_set('dicarlo.hvm')
assembly = load_responses(data_dir, stimuli)
assembly.name = 'dicarlo.Sanghavi2020'
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():
stimuli = brainio_collection.get_stimulus_set('dicarlo.Rust2012')
single_nc_path = Path("/Users/jjpr/dev/dldata/scripts/rust_single.nc")
da_single = xr.open_dataarray(single_nc_path)
da_single.name = 'dicarlo.Rust2012.single'
print('Packaging assembly for single-unit')
package_data_assembly(da_single, assembly_identifier=da_single.name, stimulus_set_identifier=stimuli.identifier,
bucket_name='brainio.dicarlo')
array_nc_path = Path("/Users/jjpr/dev/dldata/scripts/rust_array.nc")
da_array = xr.open_dataarray(array_nc_path)
da_array.name = 'dicarlo.Rust2012.array'
print('Packaging assembly for array')
package_data_assembly(da_array, assembly_identifier=da_array.name, stimulus_set_identifier=stimuli.identifier,
bucket_name='brainio.dicarlo')
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')
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")