from intern.remote.boss import BossRemote from intern.remote.dvid import DVIDRemote from intern.resource.boss.resource import * import matplotlib.pyplot as plt import numpy as np # Define the BOSS remote rmt = BossRemote({"protocol": "https", "host": "api.bossdb.io", "token": "public"}) ANN_COLL_NAME = "allan_johnson" ANN_EXP_NAME = "gaj_17_40" experiment = rmt.get_experiment(ANN_COLL_NAME, ANN_EXP_NAME) print("Boss experiment extents: {}".format(rmt.get_extents(experiment))) # Define the DVID remote dvid = DVIDRemote({"protocol": "https", "host": "emdata.janelia.org",}) uuid = "822524777d3048b8bd520043f90c1d28" name = "grayscale" annos_name = "groundtruth" print( "DVID data instance extents: {}".format( dvid.get_extents(dvid.get_instance(uuid, name, datatype="uint8")) ) )
from intern.remote.boss import BossRemote from intern.resource.boss.resource import * # admin token needed to list all projects rmt = BossRemote("/home/ben/Documents/travis_user_neurodata.cfg") with open("public_datasets.csv", "w") as f: f.write( "coll,exp,ch,exp_description,num_hierarchy_levels,dtype,x_start,x_stop,y_start,y_stop,z_start,z_stop\n" ) colls = rmt.list_collections() colls.remove("ben_dev") colls.remove("ZBrain") for coll in colls: exps = rmt.list_experiments(coll) for exp in exps: exp_res = rmt.get_experiment(coll, exp) coord_frame_res = rmt.get_coordinate_frame(exp_res.coord_frame) chs = rmt.list_channels(coll, exp) for ch in chs: ch_res = rmt.get_channel(ch, coll, exp) with open("public_datasets.csv", "a") as f: f.write( f"{coll},{exp},{ch},{exp_res.description},{exp_res.num_hierarchy_levels},{ch_res.datatype},{coord_frame_res.x_start},{coord_frame_res.x_stop},{coord_frame_res.y_start},{coord_frame_res.y_stop},{coord_frame_res.z_start},{coord_frame_res.z_stop}\n" )