Add acdc-data CLI for BioIO metadata, convert, and restructure.

cellacdc/_run.py

@@ -619,6 +619,50 @@ def run_cli(ini_filepath):
     logger.info('**********************************************')
     logger.info(f'Cell-ACDC command-line closed. {myutils.get_salute_string()}')
     logger.info('**********************************************')
+
+
+def run_data_metadata(parser_args):
+    from cellacdc import myutils, cli
+
+    logger, logs_path, log_path, log_filename = myutils.setupLogger(
+        module='data_metadata', logs_path=None
+    )
+    kernel = cli.DataMetadataKernel(logger, log_path, parser_args)
+    kernel.run()
+
+    logger.info('**********************************************')
+    logger.info(f'Cell-ACDC metadata CLI closed. {myutils.get_salute_string()}')
+    logger.info('**********************************************')
+
+
+def run_data_convert(parser_args):
+    from cellacdc import myutils, cli
+
+    logger, logs_path, log_path, log_filename = myutils.setupLogger(
+        module='data_convert', logs_path=None
+    )
+    kernel = cli.DataConvertKernel(logger, log_path, parser_args)
+    kernel.run()
+
+    logger.info('**********************************************')
+    logger.info(f'Cell-ACDC data convert closed. {myutils.get_salute_string()}')
+    logger.info('**********************************************')
+
+
+def run_data_restructure(parser_args):
+    from cellacdc import myutils, cli
+
+    logger, logs_path, log_path, log_filename = myutils.setupLogger(
+        module='data_restructure', logs_path=None
+    )
+    kernel = cli.DataRestructureKernel(logger, log_path, parser_args)
+    kernel.run()
+
+    logger.info('**********************************************')
+    logger.info(
+        f'Cell-ACDC data restructure closed. {myutils.get_salute_string()}'
+    )
+    logger.info('**********************************************')
 
 
 def _setup_numpy(caller_name='Cell-ACDC'):

cellacdc/cli.py

@@ -1995,3 +1995,46 @@ def _add_derived_cell_cycle_columns(self, all_frames_acdc_df):
             self.sigLog.emit(traceback.format_exc())
 
         return all_frames_acdc_df
+
+
+class DataMetadataKernel(_WorkflowKernel):
+    def __init__(self, logger, log_path, parser_args):
+        super().__init__(logger, log_path, is_cli=True)
+        self.parser_args = parser_args
+
+    @exception_handler_cli
+    def run(self):
+        from cellacdc import data_cli
+
+        self.logger.info('Extracting metadata from raw microscopy file...')
+        data_cli.run_metadata_cli(self.parser_args)
+
+
+class DataConvertKernel(_WorkflowKernel):
+    def __init__(self, logger, log_path, parser_args):
+        super().__init__(logger, log_path, is_cli=True)
+        self.parser_args = parser_args
+
+    @exception_handler_cli
+    def run(self):
+        from cellacdc import data_cli
+
+        self.logger.info('Starting BioIO data conversion...')
+        data_cli.run_convert_cli(
+            self.parser_args, logger_func=self.logger.info
+        )
+
+
+class DataRestructureKernel(_WorkflowKernel):
+    def __init__(self, logger, log_path, parser_args):
+        super().__init__(logger, log_path, is_cli=True)
+        self.parser_args = parser_args
+
+    @exception_handler_cli
+    def run(self):
+        from cellacdc import data_cli
+
+        self.logger.info('Starting data restructure...')
+        data_cli.run_restructure_cli(
+            self.parser_args, logger_func=self.logger.info
+        )