RascalSoftware
diff --git a/‎ratapi/project.py‎
Lines changed: 20 additions & 9 deletions b/‎ratapi/project.py‎
Lines changed: 20 additions & 9 deletions
diff --git a/‎ratapi/utils/matlab.py‎
Lines changed: 22 additions & 9 deletions b/‎ratapi/utils/matlab.py‎
Lines changed: 22 additions & 9 deletions
@@ -927,16 +927,14 @@ def classlist_script(name, classlist):
             + "\n)"
         )
 
-    def save(self, filepath: str | Path = "./project.json"):
-        """Save a project to a JSON file.
+    def model_dump(self):
+        """Generate a dictionary representation of the model.
 
-        Parameters
-        ----------
-        filepath : str or Path
-            The path to where the project file will be written.
+        Returns
+        -------
+        json_dict : dict
+            A dict containing the model information.
         """
-        filepath = Path(filepath).with_suffix(".json")
-
         json_dict = {}
         for field in self.model_fields:
             attr = getattr(self, field)
@@ -960,7 +958,7 @@ def make_custom_file_dict(item):
                         "name": item.name,
                         "filename": item.filename,
                         "language": item.language,
-                        "path": try_relative_to(item.path, filepath.parent),
+                        "path": item.path,
                     }
                     if item.name != item.function_name:
                         file_dict["function_name"] = item.function_name
@@ -973,7 +971,20 @@ def make_custom_file_dict(item):
                 json_dict[field] = [item.model_dump() for item in attr]
             else:
                 json_dict[field] = attr
+        return json_dict
 
+    def save(self, filepath: str | Path = "./project.json"):
+        """Save a project to a JSON file.
+
+        Parameters
+        ----------
+        filepath : str or Path
+            The path to where the project file will be written.
+        """
+        filepath = Path(filepath).with_suffix(".json")
+        json_dict = self.model_dump()
+        for file in json_dict["custom_files"]:
+            file["path"] = try_relative_to(file["path"], filepath.parent)
         filepath.write_text(json.dumps(json_dict))
 
     @classmethod
 
@@ -1,5 +1,6 @@
 """Runs RAT from the MATLAB API."""
 
+import json
 import tempfile
 import warnings
 from pathlib import Path
@@ -14,31 +15,40 @@
 cd('{rat_path}');
 addPaths;
 cd(cur_dir);
-        
+
 project = jsonToProject('{project}');
 controls = jsonToControls('{control}');
+if any(strcmpi(controls.procedure, {{procedures.DE.value, procedures.Simplex.value}}))
+    disp("hello")
+    useLivePlot(1);
+end
 for i=1:project.customFile.rowCount
     addpath(project.customFile.varTable{{i, 5}});
 end
 [project, results] = RAT(project, controls);
 
 projectToJson(project, '{project}');
 resultsToJson(results, '{result}');
+close all
 end
 """
 
 
-def run_matlab_directly(project, controls, matlab_rat_path):
+def run_matlab_directly(project, controls, matlab_rat_path, stdout=None, stderr=None):
     """Run User provided MATLAB RAT for the given project and controls inputs.
 
     Parameters
     ----------
-    project : RAT.Project
-        The project model, which defines the physical system under study.
-    controls : RAT.Controls
-        The controls model, which defines algorithmic properties.
+    project : RAT.Project or dict
+        The project model (or equivalent json dict), which defines the physical system under study.
+    controls : RAT.Controls or dict
+        The controls model (or equivalent json dict), which defines algorithmic properties.
     matlab_rat_path : str
         The path to MATLAB RAT folder.
+    stdout : io.TextIOBase, optional
+        Text stream for MATLAB console output
+    stderr : io.TextIOBase, optional
+        Text stream for MATLAB console error output
     """
     if MatlabWrapper.loader is None:
         raise ImportError(MatlabWrapper.loader_error_message) from None
@@ -56,13 +66,16 @@ def run_matlab_directly(project, controls, matlab_rat_path):
                 RUNNER.format(project=project_file, control=control_file, result=result_file, rat_path=matlab_rat_path)
             )
 
+        controls.save(control_file) if not isinstance(controls, dict) else control_file.write_text(json.dumps(controls))
+
         with warnings.catch_warnings():  # Avoid warning about relative paths
             warnings.simplefilter("ignore")
-            project.save(project_file)
-        controls.save(control_file)
+            project.save(project_file) if not isinstance(project, dict) else project_file.write_text(
+                json.dumps(project)
+            )
 
         engine.addpath(tmp, nargout=0)
-        engine.executeRAT(nargout=0)
+        engine.executeRAT(nargout=0, stdout=stdout, stderr=stderr)
         engine.rmpath(tmp, nargout=0)
 
         project = Project.load(project_file)