def tilepair_file(render, stack_from_json):
tile_pair_file = "pt_match_opts_tilepair.json"
tile_pairs = render_json_template(example_env, 'pt_match_opts_tilepairs.json',
owner=render.DEFAULT_OWNER,
project=render.DEFAULT_PROJECT,
stack=pt_match_input_stack)
with open(tile_pair_file, 'w') as f:
json.dump(tile_pairs, f, indent=4)
yield tile_pair_file
def tilepair_file(render, stack_from_json, tmpdir_factory):
output_dir = str(tmpdir_factory.mktemp('tpairdir'))
tile_pair_file = os.path.join(output_dir, "pt_match_opts_tilepair.json")
tile_pairs = render_json_template(example_env,
'pt_match_opts_tilepairs.json',
owner=render.DEFAULT_OWNER,
project=render.DEFAULT_PROJECT,
stack=pt_match_input_stack)
with open(tile_pair_file, 'w') as f:
json.dump(tile_pairs, f, indent=4)
yield tile_pair_file
"/allen/aibs/pipeline/image_processing/volume_assembly/render-jars/production/scripts",
'memGB': '2G'
},
"reference_stack": "reference_stack",
"moving_stack": "moving_stack",
"output_stack": "output_stack",
"match_collection": "rough_align_fixes",
"regsitration_model": "Affine",
"reference_z": 133,
"moving_z": 133,
"overwrite_output": True,
"consolidate_transforms": True
}
REF_STACK_TSPECS = render_json_template(
example_env,
'rough_registration_ref_stack_tspecs.json',
test_data_root=TEST_DATA_ROOT)
MOVING_STACK_TSPECS = render_json_template(
example_env,
'rough_registration_moving_stack_tspecs.json',
test_data_root=TEST_DATA_ROOT)
POINT_MATCHES = render_json_template(example_env,
'rough_registration_point_matches.json',
test_data_root=TEST_DATA_ROOT)
@pytest.fixture(scope='module')
def render():
render_params['project'] = 'rough_registration'
},
"url_options":{
"normalizeForMatching": "true",
"renderWithFilter": "true",
"renderWithoutMask": "true"
},
"outputDirectory": "/allen/programs/celltypes/workgroups/em-connectomics/gayathrim/scratch/ptmatch",
"tile_stack": "point_match_optimization_test",
"stack": "em_2d_montage_apply_mipmaps",
"tilepair_file": "/allen/programs/celltypes/workgroups/em-connectomics/gayathrim/scratch/17797_1R/tilepairs/temca4_tilepair_test.json",
"filter_tilepairs":True,
"no_tilepairs_to_test":4,
"max_tilepairs_with_matches":4
}
POINT_MATCH_OPTS_INPUT_STACK_TS = render_json_template(example_env, 'point_match_opts_tilespecs.json',
test_data_root=TEST_DATA_ROOT)
@pytest.fixture(scope='module')
def render():
render_params['project'] = 'point_match_optimization'
render = renderapi.connect(**render_params)
return render
@pytest.fixture(scope='module')
def stack_from_json():
tilespecs = [renderapi.tilespec.TileSpec(json=d)
for d in POINT_MATCH_OPTS_INPUT_STACK_TS]
return tilespecs
@pytest.fixture(scope='module')