merge cli and maps json function

clinicadl/commandline/pipelines/interpret/cli.py

@@ -1,3 +1,5 @@
+from pathlib import Path
+
 import click
 
 from clinicadl.commandline import arguments
@@ -40,8 +42,12 @@ def cli(**kwargs):
     NAME is the name of the saliency map task.
     METHOD is the method used to extract an attribution map.
     """
+    from clinicadl.utils.iotools.train_utils import merge_cli_and_maps_json_options
 
-    interpret_config = InterpretConfig(**kwargs)
+    dict_ = merge_cli_and_maps_json_options(
+        Path(kwargs["input_maps"]) / "maps.json", **kwargs
+    )
+    interpret_config = InterpretConfig(**dict_)
     predict_manager = Predictor(interpret_config)
     predict_manager.interpret()
 

clinicadl/maps_manager/maps_manager.py

@@ -17,7 +17,7 @@
 from clinicadl.metrics.utils import (
     check_selection_metric,
 )
-from clinicadl.predictor.utils import get_prediction
+from clinicadl.predict.utils import get_prediction
 from clinicadl.splitter.config import SplitterConfig
 from clinicadl.splitter.splitter import Splitter
 from clinicadl.trainer.tasks_utils import (
@@ -139,6 +139,10 @@ def __getattr__(self, name):
         else:
             raise AttributeError(f"'MapsManager' object has no attribute '{name}'")
 
+    ###################################
+    # High-level functions templates  #
+    ###################################
+
     ###############################
     # Checks                      #
     ###############################

clinicadl/utils/iotools/train_utils.py

@@ -198,3 +198,36 @@ def merge_cli_and_config_file_options(task: Task, **kwargs) -> Dict[str, Any]:
         pass
     ###
     return options
+
+
+def merge_cli_and_maps_json_options(maps_json: Path, **kwargs) -> Dict[str, Any]:
+    """
+    Merges options from the CLI (passed by the user) and from the config file
+    (if it exists).
+
+    Priority is given to options passed by the user via the CLI. If it is not
+    provided, it will look for the option in the possible config file.
+    If an option is not passed by the user and not found in the config file, it will
+    not be in the output.
+
+    Parameters
+    ----------
+    task : Task
+        The task that is performed (e.g. classification).
+
+    Returns
+    -------
+    Dict[str, Any]
+        A dictionary with training options.
+    """
+    from clinicadl.caps_dataset.caps_dataset_utils import read_json
+
+    options = read_json(maps_json)
+    for arg in kwargs:
+        if (
+            click.get_current_context().get_parameter_source(arg)
+            == ParameterSource.COMMANDLINE
+        ):
+            options[arg] = kwargs[arg]
+
+    return options