deepcut works with pyGhida

codecut-gui/src/main/java/codecutguiv2/CodeCutGUIPlugin.java

@@ -84,6 +84,7 @@ import ghidra.program.model.listing.*;
 import ghidra.program.model.symbol.*;
 import ghidra.program.util.ChangeManager;
 import ghidra.program.util.DefinedDataIterator;
+import ghidra.program.util.DefinedStringIterator;
 import ghidra.program.util.GhidraProgramUtilities;
 import ghidra.program.util.ProgramChangeRecord;
 import ghidra.program.util.ProgramLocation;
@@ -1069,7 +1070,8 @@ public class CodeCutGUIPlugin extends ProgramPlugin implements DomainObjectListe
 			Accumulator<ProgramLocation> accumulator = new ListAccumulator<>();
 
 			Swing.allowSwingToProcessEvents();
-			for (Data stringInstance : DefinedDataIterator.definedStrings(currentProgram)) {
+			// 09032025 Vivian, changed to accommodate updated ghidra api
+			for (Data stringInstance : DefinedStringIterator.forProgram(currentProgram)) {
 				Address strAddr = stringInstance.getAddress();
 				ReferenceIterator refIterator = refManager.getReferencesTo(strAddr);
 				while (refIterator.hasNext()) {

codecut-gui/src/main/java/graphcut/GraphCutLayout.java

@@ -65,7 +65,6 @@ public class GraphCutLayout extends AbstractVisualGraphLayout<GraphCutVertex, Gr
 		return newLayout;
 	}
 	
-	@Override
 	protected Point2D getVertexLocation(GraphCutVertex v, Column col, Row<GraphCutVertex> row, Rectangle bounds) {
 		return getCenteredVertexLocation(v, col, row, bounds);
 	}

deepcut-ghidra/ghidra_scripts/DeepCutRun.py

@@ -0,0 +1,77 @@
+# @category CodeCut
+# @menupath CodeCut.DeepCut (Run)
+# @toolbar codecut.png
+# @runtime PyGhidra
+
+# (C) 2022 The Johns Hopkins University Applied Physics Laboratory LLC
+# (JHU/APL).  All Rights Reserved.
+#
+# This material may be only be used, modified, or reproduced by or for
+# the U.S. Government pursuant to the license rights granted under the
+# clauses at DFARS 252.227-7013/7014 or FAR 52.227-14. For any other
+# permission, please contact the Office of Technology Transfer at
+# JHU/APL.
+#
+# NO WARRANTY, NO LIABILITY. THIS MATERIAL IS PROVIDED "AS IS." JHU/APL
+# MAKES NO REPRESENTATION OR WARRANTY WITH RESPECT TO THE PERFORMANCE OF
+# THE MATERIALS, INCLUDING THEIR SAFETY, EFFECTIVENESS, OR COMMERCIAL
+# VIABILITY, AND DISCLAIMS ALL WARRANTIES IN THE MATERIAL, WHETHER
+# EXPRESS OR IMPLIED, INCLUDING (BUT NOT LIMITED TO) ANY AND ALL IMPLIED
+# WARRANTIES OF PERFORMANCE, MERCHANTABILITY, FITNESS FOR A PARTICULAR
+# PURPOSE, AND NON-INFRINGEMENT OF INTELLECTUAL PROPERTY OR OTHER THIRD
+# PARTY RIGHTS. ANY USER OF THE MATERIAL ASSUMES THE ENTIRE RISK AND
+# LIABILITY FOR USING THE MATERIAL. IN NO EVENT SHALL JHU/APL BE LIABLE
+# TO ANY USER OF THE MATERIAL FOR ANY ACTUAL, INDIRECT, CONSEQUENTIAL,
+# SPECIAL OR OTHER DAMAGES ARISING FROM THE USE OF, OR INABILITY TO USE,
+# THE MATERIAL, INCLUDING, BUT NOT LIMITED TO, ANY DAMAGES FOR LOST
+# PROFITS.
+#
+# HAVE A NICE DAY.
+
+# This material is based upon work supported by the Defense Advanced Research
+# Projects Agency (DARPA) and Naval Information Warfare Center Pacific (NIWC Pacific)
+# under Contract Number N66001-20-C-4024.
+
+import sys
+import json
+
+print("started DeepCutRun")
+
+
+from dependency_bootstrap import DependencyManager
+
+# list the packages you need
+# dictionary of "import name" : "pip name"
+# for when they differ, e.g. "sklearn": "scikit-learn"
+deps = DependencyManager(
+    {"networkx": "networkx",
+     "scipy": "scipy",
+     "torch": "torch",
+     "torch_geometric": "torch-geometric"})
+
+# make sure they're installed
+if not deps.ensure_or_prompt():
+    println("[DeepCut] Required Python packages not available, exiting.")
+    exit(1)
+    
+from deepcut import Deepcut
+
+# Pass Ghidra context + args into your package entry point
+# run(currentProgram, state, monitor, *args)
+
+def main():
+    args = list(getScriptArgs())
+        
+    with open(args[0], "r") as f:
+        fcg = json.load(f)
+
+    model_path = args[2]
+    d = Deepcut(fcg, model_path)
+    
+    with open(args[1], "w") as f:
+        json.dump(d.module_list(), f)
+        
+    print("Successfully exported module boundaries")
+
+if __name__ == "__main__":
+    main()

deepcut-ghidra/ghidra_scripts/GNN_Net.py

@@ -1,4 +1,4 @@
-# © 2021 The Johns Hopkins University Applied Physics Laboratory LLC
+# (C) 2022 The Johns Hopkins University Applied Physics Laboratory LLC
 # (JHU/APL).  All Rights Reserved.
 #
 # This material may be only be used, modified, or reproduced by or for
@@ -7,7 +7,7 @@
 # permission, please contact the Office of Technology Transfer at
 # JHU/APL.
 #
-# NO WARRANTY, NO LIABILITY. THIS MATERIAL IS PROVIDED “AS IS.” JHU/APL
+# NO WARRANTY, NO LIABILITY. THIS MATERIAL IS PROVIDED "AS IS." JHU/APL
 # MAKES NO REPRESENTATION OR WARRANTY WITH RESPECT TO THE PERFORMANCE OF
 # THE MATERIALS, INCLUDING THEIR SAFETY, EFFECTIVENESS, OR COMMERCIAL
 # VIABILITY, AND DISCLAIMS ALL WARRANTIES IN THE MATERIAL, WHETHER
@@ -88,12 +88,6 @@ class Net(torch.nn.Module):
         self.out2 = torch.nn.Linear(dim, 4)
 
     def forward(self, x, edge_attr, edge_index, batch):
-        # x, edge_attr, edge_index, batch = (
-        #     data.x,
-        #     data.edge_attr,
-        #     data.edge_index,
-        #     data.batch,
-        # )
 
         x = F.relu(self.init_mlp(x))
         x = self.init_bn(x)
@@ -118,20 +112,14 @@ class Net(torch.nn.Module):
         edge_attr = self.e_mlp3(edge_attr)
         edge_attr = self.ebn2(edge_attr)  # oops typo this should be a 3
 
-        #x = x[edge_index[0]] + x[edge_index[1]] + edge_attr
-        #x = F.softmax(x, dim=1)
-        #edge_attr = F.softmax(edge_attr, dim=1)
         x = torch.cat([x[edge_index[0]], x[edge_index[1]], edge_attr], dim=1)
 
         x = F.relu(self.out1(x))
         x = self.out_bn(x)
         x = self.out2(x)
 
-        #ret = torch.max(x, dim=1)[0]
         ret = torch.mean(x, dim=1)
 
-        #ret = torch.max(x[edge_index[0]] + x[edge_index[1]], dim=1)[0]
-        #ret = torch.mean(x[edge_index[0]] + x[edge_index[1]], dim=1)
         return ret
 
 def load_gnn(model_file):

deepcut-ghidra/ghidra_scripts/deepcut.py

@@ -1,6 +1,4 @@
-#!/usr/bin/env python
-#
-# © 2022 The Johns Hopkins University Applied Physics Laboratory LLC
+# (C) 2022 The Johns Hopkins University Applied Physics Laboratory LLC
 # (JHU/APL).  All Rights Reserved.
 #
 # This material may be only be used, modified, or reproduced by or for
@@ -9,7 +7,7 @@
 # permission, please contact the Office of Technology Transfer at
 # JHU/APL.
 #
-# NO WARRANTY, NO LIABILITY. THIS MATERIAL IS PROVIDED “AS IS.” JHU/APL
+# NO WARRANTY, NO LIABILITY. THIS MATERIAL IS PROVIDED "AS IS." JHU/APL
 # MAKES NO REPRESENTATION OR WARRANTY WITH RESPECT TO THE PERFORMANCE OF
 # THE MATERIALS, INCLUDING THEIR SAFETY, EFFECTIVENESS, OR COMMERCIAL
 # VIABILITY, AND DISCLAIMS ALL WARRANTIES IN THE MATERIAL, WHETHER
@@ -29,7 +27,6 @@
 # Projects Agency (DARPA) and Naval Information Warfare Center Pacific (NIWC Pacific)
 # under Contract Number N66001-20-C-4024.
 
-
 import json
 import sys
 import numpy as np
@@ -188,7 +185,7 @@ def main():
     if len(sys.argv) == 2:
         model_file = sys.argv[1]
     else:
-        model_file = "model_weights_1.p"
+        model_file = "model_weights.p"
 
     d = Deepcut(fcg, model_file)
 

deepcut-ghidra/ghidra_scripts/dependency_bootstrap.py

@@ -0,0 +1,96 @@
+from __future__ import annotations
+import sys, os, io, importlib, subprocess
+from typing import Dict, List, Tuple
+
+class DependencyManager:
+    """
+    Minimal dependency manager for Ghidra Python (PyGhidra/CPython).
+    - Takes a dict {import_name: pip_name}.
+    - Prompts the user to install missing ones via a Swing/Ghidra popup.
+    - Reloads site/import caches so new installs are importable immediately.
+    """
+
+    def __init__(self, packages: Dict[str, str], *, title: str = "Missing Python Packages"):
+        self.packages = packages
+        self.title = title
+
+    # -------- public API --------
+    def ensure_or_prompt(self) -> bool:
+        _, missing = self._try_imports(list(self.packages.keys()))
+        if not missing:
+            return True
+
+        if not self._ask_to_install(missing):
+            return False
+
+        pip_names = [self.packages[name] for name in missing]
+        if not self._pip_install(pip_names):
+            return False
+
+        self._reload_paths()
+        _, still = self._try_imports(missing)
+        if still:
+            print("[deps] Still missing after install:", still)
+            return False
+        return True
+
+    # -------- internals --------
+    def _try_imports(self, names: List[str]) -> Tuple[List[str], List[str]]:
+        ok, missing = [], []
+        for n in names:
+            try:
+                importlib.import_module(n)
+                ok.append(n)
+            except Exception:
+                missing.append(n)
+        return ok, missing
+
+    def _ask_to_install(self, missing: List[str]) -> bool:
+        # Prefer Ghidra OptionDialog (GUI-safe)
+        try:
+            from docking.widgets import OptionDialog
+            lines = ["The following Python packages are required and missing:\n"]
+            lines += [f"  • import '{name}'   (pip install {self.packages[name]})" for name in missing]
+            lines += ["", "Install them now with pip?"]
+            msg = "\n".join(lines)
+            return OptionDialog.showYesNoDialog(None, self.title, msg) == OptionDialog.YES_OPTION
+        except Exception:
+            # Headless fallback is unlikely in-tool, but just in case:
+            print(f"{self.title}: will install {', '.join(self.packages[n] for n in missing)}")
+            return True
+
+    def _pip_install(self, pip_names: List[str]) -> bool:
+        args = ["install", "--upgrade", "--no-input"] + pip_names
+        print(f"[deps] pip {' '.join(args)}")
+
+        # Suppress pip’s version check and ensure no interactive prompts
+        env = dict(os.environ)
+        env.setdefault("PIP_DISABLE_PIP_VERSION_CHECK", "1")
+        env.setdefault("PYTHONWARNINGS", "ignore")  # optional: quiet noisy warnings
+
+
+        # pip 20+: use cli.main
+        from pip._internal.cli.main import main as pip_main  # type: ignore
+
+        try:
+            code = pip_main(args)
+        except SystemExit as e:  # pip may call sys.exit()
+            code = int(e.code) if e.code is not None else 0
+
+        if int(code) == 0:
+            return True
+        print(f"[deps] pip (in-process) failed with code {code}")
+
+
+    def _reload_paths(self) -> None:
+        importlib.invalidate_caches()
+        try:
+            import site
+            importlib.reload(site)  # process site-packages & .pth files
+        except Exception:
+            pass
+        try:
+            import pkg_resources  # type: ignore
+            pkg_resources.working_set.__init__()  # rebuild dist cache
+        except Exception:
+            pass

deepcut-ghidra/ghidra_scripts/vivvy_test.py

@@ -0,0 +1,14 @@
+# @category Diagnostics
+# @menupath Diagnostics.Test askYesNo
+# @runtime PyGhidra
+
+def main():
+    try:
+        # Ghidra injects askYesNo into the script's globals
+        result = askYesNo("askYesNo Test", "Does askYesNo() work in this environment?")
+        println(f"[test] askYesNo returned: {result!r}")
+    except Exception as e:
+        println(f"[test] askYesNo failed: {e}")
+
+if __name__ == "__main__":
+    main()

deepcut-ghidra/src/main/java/deepcut/DeepCutAnalyzer.java

@@ -25,11 +25,16 @@
 
 package deepcut;
 
+import java.io.FileNotFoundException;
+
+import com.google.gson.Gson;
+import com.google.gson.GsonBuilder;
+
+import ghidra.app.script.GhidraScriptLoadException;
 import ghidra.app.services.AbstractAnalyzer;
 import ghidra.app.services.AnalysisPriority;
 import ghidra.app.services.AnalyzerType;
 import ghidra.app.util.importer.MessageLog;
-import ghidra.app.util.opinion.ElfLoader;
 import ghidra.framework.options.Options;
 import ghidra.program.model.address.Address;
 import ghidra.program.model.address.AddressFactory;
@@ -40,34 +45,32 @@ import ghidra.program.model.listing.Program;
 import ghidra.program.model.symbol.Namespace;
 import ghidra.program.model.symbol.SourceType;
 import ghidra.program.model.symbol.SymbolTable;
+import ghidra.util.Msg;
 import ghidra.util.exception.CancelledException;
 import ghidra.util.exception.DuplicateNameException;
 import ghidra.util.exception.InvalidInputException;
 import ghidra.util.task.TaskMonitor;
 
-import com.google.gson.GsonBuilder;
-
 /**
- * TODO: Provide class-level documentation that describes what this analyzer does.
+ * Uses the DeepCut algorithm to find module boundaries.
  */
 public class DeepCutAnalyzer extends AbstractAnalyzer {
-	private final static String NAME = "Deepcut";
-	private final static String DESCRIPTION = "Uses the deepcut algorithm to find module boundaries.";
-	
-	private final static String OPTION_NAME_PYTHON_EXEC = "Python Executable";
-	private final static String OPTION_DESCRIPTION_PYTHON_EXEC = "";
-	private final static String OPTION_DEFAULT_PYTHON_EXEC = "/usr/bin/python3";
-	private String pythonExec = OPTION_DEFAULT_PYTHON_EXEC;
+    private static final String NAME = "Deepcut";
+    private static final String DESCRIPTION = "Uses the deepcut algorithm to find module boundaries.";
 
-	public DeepCutAnalyzer() {
-		super(NAME, DESCRIPTION, AnalyzerType.FUNCTION_ANALYZER);
-		setDefaultEnablement(false);
-		setPriority(AnalysisPriority.REFERENCE_ANALYSIS.after());
-		setPrototype();
-		setSupportsOneTimeAnalysis();
-	}
+    private final Gson gson = new GsonBuilder().create();
 
-	@Override
+    public DeepCutAnalyzer() {
+        super(NAME, DESCRIPTION, AnalyzerType.FUNCTION_ANALYZER);
+        setDefaultEnablement(false);
+        setPriority(AnalysisPriority.REFERENCE_ANALYSIS.after());
+        setPrototype();
+        setSupportsOneTimeAnalysis();
+        
+        Msg.info(this, "DeepCutAnalyzer loaded");
+    }
+
+    @Override
 	public boolean getDefaultEnablement(Program program) {
 		// Only supports one-time analysis.
 		return false;
@@ -80,86 +83,79 @@ public class DeepCutAnalyzer extends AbstractAnalyzer {
 
 	@Override
 	public void registerOptions(Options options, Program program) {
-		options.registerOption(OPTION_NAME_PYTHON_EXEC, pythonExec,
-				null, OPTION_DESCRIPTION_PYTHON_EXEC);	
+		// no options
 	}
 	
     @Override
     public void optionsChanged(Options options, Program program) {
-            pythonExec = options.getString(OPTION_NAME_PYTHON_EXEC, pythonExec);
+            // no options
     }
 
-    private boolean checkError(DeepCutPython deepcut, MessageLog log)
-    {
-		String error = deepcut.readProcessError();			
-		if (!error.isEmpty()) {
-			log.appendMsg(error);
-			return true;			
-		}
-  
-		return false;
-    }
-    
-	@Override
-	public boolean added(Program program, AddressSetView set, TaskMonitor monitor, MessageLog log)
-			throws CancelledException {
-		
-		DeepCutPython deepcut = new DeepCutPython(pythonExec);
-		FunctionCallGraph fcg = new FunctionCallGraph(program, monitor);
-		
-		try {
-			deepcut.startProcess();
-		
-			if (checkError(deepcut, log)) {
-				return false;
+
+    @Override
+    public boolean added(Program program, AddressSetView set, TaskMonitor monitor, MessageLog log)
+            throws CancelledException {
+
+        
+            // 1) Build input JSON from the program
+            FunctionCallGraph fcg = new FunctionCallGraph(program, monitor);
+            String inputJson = fcg.toJson();
+
+            // 2) Run DeepCut via the launcher (blocking, file-IO args under the hood)
+            String cutsJson="";
+			try {
+				cutsJson = DeepCutLauncher.runDeepCutFileMode(program, set, inputJson, monitor);
+			} catch (IllegalAccessException e) {
+				// TODO Auto-generated catch block
+				e.printStackTrace();
+			} catch (FileNotFoundException e) {
+				// TODO Auto-generated catch block
+				e.printStackTrace();
+			} catch (GhidraScriptLoadException e) {
+				// TODO Auto-generated catch block
+				e.printStackTrace();
 			}
-			
-			deepcut.writeProcess(fcg.toJson() + "\n");
-			deepcut.waitFor();
+            if (cutsJson == null || cutsJson.isEmpty()) {
+                log.appendMsg("DeepCut returned no output.");
+                return false;
+            }
+            
+        try {
 
-			if (checkError(deepcut, log)) {
-				return false;
-			}			
-			
-			String cuts_json = deepcut.readProcessOutput();
+            // 3) Parse result and apply namespaces
+            Cut[] cuts = gson.fromJson(cutsJson, Cut[].class);
+            int i = 0;
 
-			
-			Cut[] cuts = new GsonBuilder().create().fromJson(cuts_json, Cut[].class);
+            for (FunctionInfo fi : fcg.getFunctionInfos()) {
+                AddressFactory af = program.getAddressFactory();
+                Address cutAddress = af.getAddress(cuts[i].address);
 
-			int i = 0;
-			for (FunctionInfo fi : fcg.getFunctionInfos()) {
-				AddressFactory af = program.getAddressFactory();
-				Address cutAddress = af.getAddress(cuts[i].address);
-				
-				if (fi.getAddress().compareTo(cutAddress) == -1) {
-					addNamespace(program, "object" + i, fi.getFunction());
-				} else {
-					i++;
-					addNamespace(program, "object" + i, fi.getFunction());
-				}				
-			}		
-		} catch (Exception e) {
-			log.appendException(e);
-			return false;
-		}
-		
-		return true;
-	}
-	
-
-
-	public void addNamespace(Program program, String name, Function function)
-			throws DuplicateNameException, InvalidInputException, CircularDependencyException {
-        SymbolTable symbolTable = program.getSymbolTable();
-        Namespace namespace = null;
-		
-        namespace = symbolTable.getNamespace(name, null);
-        if(namespace == null) {
-        	namespace = symbolTable.createNameSpace(null, name,
-                                                        SourceType.USER_DEFINED);
+                if (fi.getAddress().compareTo(cutAddress) < 0) {
+                    addNamespace(program, "object" + i, fi.getFunction());
+                } else {
+                    i++;
+                    addNamespace(program, "object" + i, fi.getFunction());
+                    if (i >= cuts.length) {
+                        // no more cuts; remaining functions go into the last bucket
+                        // (optional: break; if you prefer to stop assigning)
+                        i = cuts.length - 1;
+                    }
+                }
+            }
+            return true;
+        } catch (Exception e) {
+            log.appendException(e);
+            return false;
         }
-
-        function.setParentNamespace(namespace);
     }
 
-}
+    private void addNamespace(Program program, String name, Function function)
+            throws DuplicateNameException, InvalidInputException, CircularDependencyException {
+        SymbolTable symbolTable = program.getSymbolTable();
+        Namespace ns = symbolTable.getNamespace(name, null);
+        if (ns == null) {
+            ns = symbolTable.createNameSpace(null, name, SourceType.USER_DEFINED);
+        }
+        function.setParentNamespace(ns);
+    }
+}

deepcut-ghidra/src/main/java/deepcut/DeepCutLauncher.java

@@ -0,0 +1,178 @@
+/* ###
+* © 2022 The Johns Hopkins University Applied Physics Laboratory LLC
+* (JHU/APL).
+*
+* NO WARRANTY, NO LIABILITY. THIS MATERIAL IS PROVIDED “AS IS.” JHU/APL
+* MAKES NO REPRESENTATION OR WARRANTY WITH RESPECT TO THE PERFORMANCE OF
+* THE MATERIALS, INCLUDING THEIR SAFETY, EFFECTIVENESS, OR COMMERCIAL
+* VIABILITY, AND DISCLAIMS ALL WARRANTIES IN THE MATERIAL, WHETHER
+* EXPRESS OR IMPLIED, INCLUDING (BUT NOT LIMITED TO) ANY AND ALL IMPLIED
+* WARRANTIES OF PERFORMANCE, MERCHANTABILITY, FITNESS FOR A PARTICULAR
+* PURPOSE, AND NON-INFRINGEMENT OF INTELLECTUAL PROPERTY OR OTHER THIRD
+* PARTY RIGHTS. ANY USER OF THE MATERIAL ASSUMES THE ENTIRE RISK AND
+* LIABILITY FOR USING THE MATERIAL. IN NO EVENT SHALL JHU/APL BE LIABLE
+* TO ANY USER OF THE MATERIAL FOR ANY ACTUAL, INDIRECT, CONSEQUENTIAL,
+* SPECIAL OR OTHER DAMAGES ARISING FROM THE USE OF, OR INABILITY TO USE,
+* THE MATERIAL, INCLUDING, BUT NOT LIMITED TO, ANY DAMAGES FOR LOST
+* PROFITS.
+*
+* This material is based upon work supported by the Defense Advanced Research
+* Projects Agency (DARPA) and Naval Information Warfare Center Pacific (NIWC Pacific)
+* under Contract Number N66001-20-C-4024.
+*
+* HAVE A NICE DAY.
+*/
+
+package deepcut;
+
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.nio.charset.StandardCharsets;
+import java.nio.file.Files;
+import java.nio.file.Path;
+
+import ghidra.util.Msg;
+
+import generic.jar.ResourceFile;
+import ghidra.app.plugin.core.analysis.AutoAnalysisManager;
+import ghidra.app.script.GhidraScript;
+import ghidra.app.script.GhidraScriptLoadException;
+import ghidra.app.script.GhidraScriptProvider;
+import ghidra.app.script.GhidraScriptUtil;
+import ghidra.app.script.GhidraState;
+import ghidra.app.services.ConsoleService;
+import ghidra.framework.model.Project;
+import ghidra.framework.plugintool.PluginTool;
+import ghidra.program.model.address.AddressSetView;
+import ghidra.program.model.listing.Program;
+import ghidra.program.util.ProgramLocation;
+import ghidra.program.util.ProgramSelection;
+import ghidra.util.Msg;
+import ghidra.util.exception.CancelledException;
+import ghidra.util.task.TaskMonitor;
+import ghidra.framework.Application;
+
+public class DeepCutLauncher {
+
+    /**
+     * Runs DeepCutRun.py synchronously with two args: infile and outfile.
+     * Writes the provided JSON string to a temp infile, runs the script, reads the temp outfile,
+     * and returns its contents. Best-effort temp cleanup.
+     * @throws IllegalAccessException
+     * @throws FileNotFoundException 
+     */
+    public static String runDeepCutFileMode(Program program,
+                                            AddressSetView set,
+                                            String inputJson,
+                                            TaskMonitor monitor) throws IllegalAccessException, FileNotFoundException, GhidraScriptLoadException {
+        final String scriptName = "DeepCutRun.py"; // must be on Ghidra script path
+
+        AutoAnalysisManager aam = AutoAnalysisManager.getAnalysisManager(program);
+        PluginTool tool = aam.getAnalysisTool();
+        Project project = tool != null ? tool.getProject() : null;
+
+        GhidraState state = new GhidraState(
+                tool,
+                project,
+                program,
+                new ProgramLocation(program, set.getMinAddress()),
+                new ProgramSelection(set),
+                null
+        );
+
+        PrintWriter out = getOut(tool);
+        PrintWriter err = getErr(tool);
+
+        Path inFile = null, outFile = null;
+            // 1) Locate script
+            ResourceFile sourceFile = GhidraScriptUtil.findScriptByName(scriptName);
+            if (sourceFile == null) {
+                throw new IllegalAccessException("Couldn't find script: " + scriptName);
+            }
+            GhidraScriptProvider provider = GhidraScriptUtil.getProvider(sourceFile);
+            if (provider == null) {
+                throw new IllegalAccessException("Couldn't find script provider for: " + scriptName);
+            }
+            ResourceFile pythonFile = Application.getModuleDataFile("model_weights.p");
+            if (pythonFile == null) {
+                throw new IllegalAccessException("Couldn't find weights file for: " + scriptName);
+            }
+            
+
+            Msg.info(DeepCutLauncher.class, "Chosen provider: " + provider.getClass().getName() + "  (runtime=" + provider.getRuntimeEnvironmentName() + ")");
+            
+            GhidraScript script;
+            try {
+            	script = provider.getScriptInstance(sourceFile, err);
+            }
+            catch(GhidraScriptLoadException e) {
+            	Msg.showError(
+            	        null,                      // parent object (your plugin/analyzer/launcher)
+            	        null,                      // parent component (null = center on tool)
+            	        "PyGhidra Required",       // dialog title
+            	        "DeepCut requires the PyGhidra extension.\n\nDetails: " + e.getMessage()
+            	    );
+            	    throw new GhidraScriptLoadException("DeepCut requires PyGhidra", e);
+            }
+            
+             
+ 
+            try {
+
+            // 2) Prep temp files
+            inFile  = Files.createTempFile("deepcut_in_",  ".json");
+            outFile = Files.createTempFile("deepcut_out_", ".json");
+            // ensure delete on JVM exit as a fallback
+            inFile.toFile().deleteOnExit();
+            outFile.toFile().deleteOnExit();
+
+            // write input JSON
+            Files.writeString(inFile, (inputJson == null ? "" : inputJson) + "\n", StandardCharsets.UTF_8);
+
+            // 3) Pass args: [infile, outfile, modelfile]
+            script.setScriptArgs(new String[] {
+            		inFile.toString(),
+            		outFile.toString(),
+            		pythonFile.toString() });
+            
+            
+
+            // 4) Run blocking
+            script.execute(state, monitor, out);
+
+            // 5) Read result JSON
+            String result = Files.readString(outFile, StandardCharsets.UTF_8).trim();
+            return result;
+        }
+        catch (CancelledException e) {
+            // user cancelled; return null or empty to signal no result
+            return null;
+        }
+        catch (Exception e) {
+            Msg.warn(DeepCutLauncher.class, "Error running script " + scriptName + ": " + e.getMessage(), e);
+            return null;
+        }
+        finally {
+            // best-effort cleanup
+            try { if (inFile  != null) Files.deleteIfExists(inFile);  } catch (IOException ignored) {}
+            try { if (outFile != null) Files.deleteIfExists(outFile); } catch (IOException ignored) {}
+        }
+    }
+    
+    private static PrintWriter getOut(PluginTool tool) {
+        if (tool != null) {
+            ConsoleService console = tool.getService(ConsoleService.class);
+            if (console != null) return console.getStdOut();
+        }
+        return new PrintWriter(System.out);
+    }
+
+    private static PrintWriter getErr(PluginTool tool) {
+        if (tool != null) {
+            ConsoleService console = tool.getService(ConsoleService.class);
+            if (console != null) return console.getStdErr();
+        }
+        return new PrintWriter(System.err);
+    }
+}

deepcut-ghidra/src/main/java/deepcut/DeepCutPython.java

@@ -1,102 +0,0 @@
-/* ###
-* © 2022 The Johns Hopkins University Applied Physics Laboratory LLC
-* (JHU/APL).
-*
-* NO WARRANTY, NO LIABILITY. THIS MATERIAL IS PROVIDED “AS IS.” JHU/APL
-* MAKES NO REPRESENTATION OR WARRANTY WITH RESPECT TO THE PERFORMANCE OF
-* THE MATERIALS, INCLUDING THEIR SAFETY, EFFECTIVENESS, OR COMMERCIAL
-* VIABILITY, AND DISCLAIMS ALL WARRANTIES IN THE MATERIAL, WHETHER
-* EXPRESS OR IMPLIED, INCLUDING (BUT NOT LIMITED TO) ANY AND ALL IMPLIED
-* WARRANTIES OF PERFORMANCE, MERCHANTABILITY, FITNESS FOR A PARTICULAR
-* PURPOSE, AND NON-INFRINGEMENT OF INTELLECTUAL PROPERTY OR OTHER THIRD
-* PARTY RIGHTS. ANY USER OF THE MATERIAL ASSUMES THE ENTIRE RISK AND
-* LIABILITY FOR USING THE MATERIAL. IN NO EVENT SHALL JHU/APL BE LIABLE
-* TO ANY USER OF THE MATERIAL FOR ANY ACTUAL, INDIRECT, CONSEQUENTIAL,
-* SPECIAL OR OTHER DAMAGES ARISING FROM THE USE OF, OR INABILITY TO USE,
-* THE MATERIAL, INCLUDING, BUT NOT LIMITED TO, ANY DAMAGES FOR LOST
-* PROFITS.
-*
-* This material is based upon work supported by the Defense Advanced Research
-* Projects Agency (DARPA) and Naval Information Warfare Center Pacific (NIWC Pacific)
-* under Contract Number N66001-20-C-4024.
-*
-* HAVE A NICE DAY.
-*/
-
-package deepcut;
-
-import java.io.BufferedReader;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.io.OutputStream;
-import java.util.stream.Collectors;
-
-import ghidra.framework.Application;
-
-public class DeepCutPython {
-	public Runtime runtime;
-	public String pythonExec;
-	
-	public Process process;
-	public OutputStream stdin;
-	public InputStream stdout;
-	public InputStream stderr;
-
-	public DeepCutPython(String pythonExec) {
-		this.pythonExec = pythonExec;
-		this.runtime = Runtime.getRuntime();
-	}
-	
-	public void startProcess() throws IOException {
-		String pythonFile = Application.getModuleDataFile("deepcut.py").toString();
-		String modelFile = Application.getModuleDataFile("model_weights_1.p").toString(); 
-		
-		//pythonFile = "/Users/desteaj1/Programs/AMP/deepcut/src/deepcut";
-		String[] exec = {pythonExec, pythonFile, modelFile};
-		
-		process = runtime.exec(exec);
-
-		// Yes this is confusing. stdin is a Java OutputStream, stdout is an InputStream
-		stdin = process.getOutputStream();
-		stdout = process.getInputStream();
-		stderr = process.getErrorStream();		
-	}
-	
-	public void waitFor() throws InterruptedException {
-		process.waitFor();
-	}
-
-	public void writeProcess(String data) throws IOException {
-		writeProcess(data.getBytes());
-	}
-
-	public void writeProcess(byte[] data) throws IOException {
-		stdin.write(data);
-	}
-	
-	public String readProcessOutput() {
-		return readProcess(stdout);
-
-	}	
-	
-	public String readProcessError() {
-		return readProcess(stderr);
-
-	}
-
-	private String readProcess(InputStream stream) {
-		String result = "";
-		
-		try {
-			if (stream.available() > 0 ) {
-				result = new BufferedReader(new InputStreamReader(stream))
-						.lines().collect(Collectors.joining("\n"));
-			}
-		} catch (IOException e) {
-			return result;
-		}
-		
-		return result;
-	}
-}