"""
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
