object_file_postfixes.append(object_file_postfix)
pdc = import_cp2_csv_results(cp2_csv_path, image_file_postfix, object_file_postfixes, csv_delimiter, csv_extension)
Importer().set_pdc(pdc)
utils.update_state(importer.__name__, 'imported')
print 'Finished importing data from CellProfiler'
return 'Finished importing data from CellProfiler'
__dict__ = sys.modules[__name__].__dict__
utils.register_module(__name__, 'CellProfiler import', __dict__, utils.DEFAULT_STATE)
utils.register_parameter(__name__, 'image_cp2_file', utils.PARAM_INPUT_FILE, 'Image CSV file from CellProfiler 2', optional=True)
utils.set_parameter_hook(__name__, 'image_cp2_file', importer.filename_hook)
utils.register_parameter(__name__, 'object_cp2_csv_files', utils.PARAM_INPUT_FILES, 'Object CSV files from CellProfiler 2', optional=True)
utils.set_parameter_hook(__name__, 'object_cp2_csv_files', importer.filename_hook)
utils.register_parameter(__name__, 'cp2_csv_path', utils.PARAM_PATH, 'Path to CellProfiler 2 CSV files', optional=True)
utils.set_parameter_hook(__name__, 'cp2_csv_path', importer.filename_hook)
utils.register_parameter(__name__, 'csv_delimiter', utils.PARAM_STR, 'Delimiter for the CSV files', ',')
utils.register_parameter(__name__, 'csv_extension', utils.PARAM_STR, 'Extension for the CSV files', '.csv')
utils.register_action(__name__, 'import_cp', 'Import data from CellProfiler CSV files', import_data_from_cp)
def connect_to_database():
from sqlalchemy import create_engine, MetaData, Table
try:
database_url
except:
raise utils.ParameterException(
'You need to specify the url of the database!')
try:
print 'Connecting to database: {}'.format(database_url)
engine = create_engine(database_url)
metadata = MetaData(bind=engine)
metadata.create_all()
images_table = Table('images', metadata, autoload=True,
autoload_with=engine)
objects_table = Table('objects', metadata, autoload=True,
autoload_with=engine)
DBConnection(engine, metadata, images_table, objects_table)
utils.register_action(__name__, 'reload_db_schema',
'Reload database schema', reload_db_schema)
utils.register_parameter(
__name__, 'use_plate_filter', utils.PARAM_BOOL,
'Select plates to import?', False, hook=use_filter_hook)
utils.register_parameter(
__name__, 'use_well_filter', utils.PARAM_BOOL,
'Select wells to import?', False, hook=use_filter_hook)
utils.register_parameter(
__name__, 'use_replicate_filter', utils.PARAM_BOOL,
'Select replicates to import?', False, hook=use_filter_hook)
utils.register_parameter(
__name__, 'use_position_filter', utils.PARAM_BOOL,
'Select positions to import?', False, hook=use_filter_hook)
utils.register_parameter(
__name__, 'use_treatment_filter', utils.PARAM_BOOL,
'Filter treatments to import?', False, hook=use_filter_hook)
utils.register_parameter(
__name__, 'image_id_db_column', utils.PARAM_STR,
'Image id column in the image table', items=[])
utils.register_parameter(
__name__, 'object_img_id_db_column',
utils.PARAM_STR, 'Image id column in the object table', items=[])
utils.register_parameter(
__name__, 'position_x_db_column', utils.PARAM_STR,
'Position X column in the image table', items=[])
utils.register_parameter(
__name__, 'position_y_db_column', utils.PARAM_STR,
'Position Y column in the image table', items=[])
utils.register_parameter(
__name__, 'plate_db_column', utils.PARAM_STR,
'Plate column in the image table',
items=[], hook=db_column_hook)
utils.register_parameter(
__name__, 'well_db_column', utils.PARAM_STR,
'Well column in the image table',
items=[], hook=db_column_hook)
utils.register_parameter(
__name__, 'replicate_db_column', utils.PARAM_STR,
'Replicate column in the image table',
items=[], hook=db_column_hook)
utils.register_parameter(
__name__, 'position_db_column', utils.PARAM_STR,
'Position column in the image table',
items=[], hook=db_column_hook)
utils.register_parameter(
__name__, 'treatment_db_column', utils.PARAM_STR,
'Treatment column in the image table', items=[])
utils.register_parameter(
__name__, 'images_db_columns', utils.PARAM_STRS,
'Columns to extract from the image table', items=[])
utils.register_parameter(
__name__, 'objects_db_columns', utils.PARAM_STRS,
'Columns to extract from the objects table', items=[])
utils.register_parameter(
__name__, 'image_files_db_columns', utils.PARAM_STRS,
'File and Path columns in the image table', items=[])
utils.register_action(__name__, 'import_db',
'Import data from database', import_data_from_db)
reload_db_schema()
except:
logger.error('Unable to connect to the database')
raise
return 'Successfully connected to database'
else:
values = param_value
for i, value in enumerate(values):
if not os.path.isabs(value):
values[i] = os.path.join(os.path.dirname(yaml_filename), value)
if type(param_value) == str:
return values[0]
else:
return values
__dict__ = sys.modules[__name__].__dict__
utils.register_module(__name__, 'Data import', __dict__, utils.DEFAULT_STATE)
utils.register_parameter(__name__, 'hdf5_input_file', utils.PARAM_INPUT_FILE, 'YACA HDF5 input file', optional=True)
utils.set_parameter_hook(__name__, 'hdf5_input_file', filename_hook)
utils.register_parameter(__name__, 'optional_hdf5_input_files', utils.PARAM_INPUT_FILES, 'Further YACA HDF5 input files', optional=True)
utils.set_parameter_hook(__name__, 'optional_hdf5_input_files', filename_hook)
utils.register_parameter(__name__, 'hdf5_output_file', utils.PARAM_OUTPUT_FILE, 'YACA HDF5 output file', optional=True)
utils.set_parameter_hook(__name__, 'hdf5_output_file', filename_hook)
utils.register_action(__name__, 'load_hdf5', 'Load data from a YACA HDF5 file', load_hdf5)
utils.register_action(__name__, 'save_hdf5', 'Save data as YACA HDF5 file', save_hdf5)
utils.register_action(__name__, 'normalize_intensities', 'Normalize intensity features to mean control cell intensity', normalize_intensities)
utils.set_module_state_callback(__name__, set_state)
utils.update_state(importer.__name__, 'imported')
print 'Finished importing data from database'
return 'Finished importing data from database'
__dict__ = sys.modules[__name__].__dict__
utils.register_module(__name__, 'Database import', __dict__,
utils.DEFAULT_STATE)
utils.register_parameter(__name__, 'database_url', utils.PARAM_STR,
'URL specifying a database', 'mysql://localhost/YACA')
utils.register_action(__name__, 'connect_to_database', 'Connect to database',
connect_to_database)
utils.register_parameter(
__name__, 'use_plate_filter', utils.PARAM_BOOL,
'Select plates to import?', False, hidden=True)
utils.register_parameter(
__name__, 'plate_filter', utils.PARAM_STRS,
'Plates to import from the database',
optional=True, hidden=True, items=[])
utils.register_parameter(
__name__, 'use_well_filter', utils.PARAM_BOOL,
'Select wells to import?', False, hidden=True)
utils.register_parameter(
__name__, 'well_filter', utils.PARAM_STRS,
'Wells to import from the database',
optional=True, hidden=True, items=[])
