""" from intern.remote.boss import BossRemote from intern.resource.boss.resource import * rmt = BossRemote('example.cfg') # First, create resource objects that identify the objects of interest in the # data model. Notice, that only the minimal information needed to identify # the objects of interest is given to the resources' constructors. coll = CollectionResource('gray') alpha_exp = ExperimentResource('alpha', 'gray', 'StdFrame') omega_chan = ChannelResource('omega', 'gray', 'alpha', 'image') # Add new metadata using create_metadata(). rmt.create_metadata(coll, {'mark': 'two', 'ten': 'four'}) rmt.create_metadata(alpha_exp, {'date': '04May2016', 'time': '13:00'}) rmt.create_metadata(omega_chan, {'channel_prep': '342', 'microscope': 'sem4'}) # Retrieve metadata with get_metadata(). # Use a list with a single string if you only want a single value. mark = rmt.get_metadata(coll, ['mark']) print(mark['mark']) omega_metadata = rmt.get_metadata(omega_chan, ['channel_prep', 'microscope']) print('omega\'s key-values:') for pair in omega_metadata.items(): print('\t{}: {}'.format(pair[0], pair[1])) # List existing metadata keys using list_metadata(). alpha_list = rmt.list_metadata(alpha_exp) print('alpha\'s keys:')
class BossResParams: def __init__(self, ingest_job, get_only=True): self.ingest_job = ingest_job self.coord_frame_name = '_'.join( (ingest_job.coll_name, ingest_job.exp_name)) self.rmt = BossRemote(self.ingest_job.boss_config_file) self.coll_resource = self.setup_boss_collection(get_only=get_only) self.coord_frame_resource = self.setup_boss_coord_frame( get_only=get_only) self.exp_resource = self.setup_boss_experiment(get_only=get_only) self.ch_resource = self.setup_boss_channel(get_only=get_only) def get_boss_project(self, proj_setup, get_only): try: proj_actual = self.rmt.get_project(proj_setup) except HTTPError as e: if get_only is False: try: proj_actual = self.rmt.create_project(proj_setup) except Exception as e: print(type(e), e) raise (e) else: print(type(e), e) raise e except Exception as e: print(type(e), e) raise (e) return proj_actual def setup_boss_collection(self, get_only=True): coll_setup = CollectionResource(self.ingest_job.coll_name) return self.get_boss_project(coll_setup, get_only) def setup_boss_coord_frame(self, get_only=True): # if we don't know the coordinate frame parameters, get the one with the same name if get_only: coord_setup = CoordinateFrameResource(self.coord_frame_name) else: coord_setup = CoordinateFrameResource( self.coord_frame_name, '', self.ingest_job.coord_frame_x_extent[0], self.ingest_job.coord_frame_x_extent[1], self.ingest_job.coord_frame_y_extent[0], self.ingest_job.coord_frame_y_extent[1], self.ingest_job.coord_frame_z_extent[0], self.ingest_job.coord_frame_z_extent[1], self.ingest_job.voxel_size[0], self.ingest_job.voxel_size[1], self.ingest_job.voxel_size[2], self.ingest_job.voxel_unit) coord_frame_resource = self.get_boss_project(coord_setup, get_only) if get_only: # matching ingest_job values to coordinate frame values (if they weren't specified, they are now populated) self.ingest_job.voxel_size = [ coord_frame_resource.x_voxel_size, coord_frame_resource.y_voxel_size, coord_frame_resource.z_voxel_size ] self.ingest_job.voxel_unit = coord_frame_resource.voxel_unit return coord_frame_resource def setup_boss_experiment(self, get_only=True): # if we don't know the coordinate frame parameters, get the one with the same name if get_only: exp_setup = ExperimentResource(self.ingest_job.exp_name, self.ingest_job.coll_name, self.coord_frame_name) else: # if all elements are the same, isotropic, otherwise anisotropic if len(set(self.ingest_job.voxel_size)) <= 1: hierarchy_method = 'isotropic' else: hierarchy_method = 'anisotropic' num_hierarchy_levels = self.calc_hierarchy_levels() exp_setup = ExperimentResource(self.ingest_job.exp_name, self.ingest_job.coll_name, self.coord_frame_name, '', num_hierarchy_levels, hierarchy_method) exp_resource = self.get_boss_project(exp_setup, get_only) # record the offset (if there is any) into BOSS metadata field for experiment self.record_offsets(exp_resource) return exp_resource def record_offsets(self, exp_resource): if any([a > 0 for a in self.ingest_job.offsets]): offsets_dict = {'offsets': self.ingest_job.offsets} try: self.rmt.create_metadata(exp_resource, offsets_dict) except HTTPErrorList: # keys already exist self.rmt.update_metadata(exp_resource, offsets_dict) def setup_boss_channel(self, ch_description='', get_only=True): ch_args = [ self.ingest_job.ch_name, self.ingest_job.coll_name, self.ingest_job.exp_name ] if not get_only: ch_args.extend( (self.ingest_job.ch_type, ch_description, 0, self.ingest_job.boss_datatype, self.ingest_job.res)) # annotation data if self.ingest_job.source_channel is not None: ch_args.append([self.ingest_job.source_channel]) # checking to make sure source channel exists (creating if needed) try: source_args = [ self.ingest_job.source_channel, self.ingest_job.coll_name, self.ingest_job.exp_name ] source_setup = ChannelResource(*source_args) self.get_boss_project(source_setup, True) except: self.ingest_job.send_msg( 'Creating a dummy source channel for this annotation because none exists yet' ) source_args.extend(('image', '', 0, 'uint8', 0)) source_setup = ChannelResource(*source_args) self.get_boss_project(source_setup, False) ch_setup = ChannelResource(*ch_args) ch_resource = self.get_boss_project(ch_setup, get_only) if get_only: self.ingest_job.boss_datatype = ch_resource.datatype if self.ingest_job.datatype is None: self.ingest_job.datatype = ch_resource.datatype self.ingest_job.res = ch_resource.base_resolution return ch_resource def calc_hierarchy_levels(self, lowest_res=512): img_size = [ self.coord_frame_resource.x_stop - self.coord_frame_resource.x_start, self.coord_frame_resource.y_stop - self.coord_frame_resource.y_start, self.coord_frame_resource.z_stop - self.coord_frame_resource.z_start ] max_xy = max(img_size[0:1]) # we add one because 0 is included in the number of downsampling levels num_levels = max(1, math.ceil(math.log(max_xy / lowest_res, 2)) + 1) return num_levels