fix(AutoML): added more config parsing for CLI (3D shape, input and o…

…utput path)

aucmedi/automl/parser_cli.py

@@ -0,0 +1,47 @@
+#==============================================================================#
+#  Author:       Dominik Müller                                                #
+#  Copyright:    2022 IT-Infrastructure for Translational Medical Research,    #
+#                University of Augsburg                                        #
+#                                                                              #
+#  This program is free software: you can redistribute it and/or modify        #
+#  it under the terms of the GNU General Public License as published by        #
+#  the Free Software Foundation, either version 3 of the License, or           #
+#  (at your option) any later version.                                         #
+#                                                                              #
+#  This program is distributed in the hope that it will be useful,             #
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of              #
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the               #
+#  GNU General Public License for more details.                                #
+#                                                                              #
+#  You should have received a copy of the GNU General Public License           #
+#  along with this program.  If not, see <http://www.gnu.org/licenses/>.       #
+#==============================================================================#
+#-----------------------------------------------------#
+#                   Library imports                   #
+#-----------------------------------------------------#
+# External libraries
+# Internal libraries
+#-----------------------------------------------------#
+#                     Parser - CLI                    #
+#-----------------------------------------------------#
+def parse_cli(args):
+    """ Internal function for parsing CLI arguments to a valid configuration
+    dictionary.
+    """
+    # Parse argument namespace to config dict
+    config = vars(args)
+
+    # Convert variables
+    if config["hub"] == "training":
+        # Handle 3D shape - from str to tuple
+        config["shape_3D"] = tuple(map(int, config["shape_3D"].split("x")))
+    else:
+        # Handle input path
+        config["input"] = config["path_input"]
+        del config["path_input"]
+    # Handle output path
+    config["output"] = config["path_output"]
+    del config["path_output"]
+
+    # Return valid configs
+    return config