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')