Karen C. Nanji

18 papers Misc 8Journal 8Unranked 2
YearRankTypeTitle / Venue / Authors
2022 Misc conf
AMIA
Marin E. Langlieb, Aziz A. Boxwala, Theo Nguyen-Cao, David W. Bates, Karen C. Nanji
2022 J jnl
J. Am. Medical Informatics Assoc.
Karen C. Nanji, Pamela M. Garabedian, Marin E. Langlieb, Angela Rui, Leo L. Tabayoyong, Michael Sampson, Hao Deng, Aziz A. Boxwala, Rebecca Minehart, David W. Bates
2021 J jnl
Appl. Clin. Inform.
Karen C. Nanji, Pamela M. Garabedian, Sofia D. Shaikh, Marin E. Langlieb, Aziz A. Boxwala, William J. Gordon, David W. Bates
2018 J jnl
J. Am. Medical Informatics Assoc.
Karen C. Nanji, Diane L. Seger, Sarah P. Slight, Mary G. Amato, Patrick E. Beeler, Qoua L. Her, Olivia Dalleur, Tewodros Eguale, Adrian Wong, Elizabeth R. Silvers, Michael Swerdloff, Salman T. Hussain, Nivethietha Maniam, Julie M. Fiskio, Patricia C. Dykes, David W. Bates
2017 Misc conf
AMIA
Diane L. Seger, Adrian Wong, Mary G. Amato, Sarah P. Slight, Patrick E. Beeler, Olivia Dalleur, Tewodros Eguale, Christine A. Rehr, Julie M. Fiskio, Karen C. Nanji, David W. Bates
2015 Misc conf
AMIA
InSook Cho, Diane L. Seger, Sarah P. Slight, Karen C. Nanji, Patricia C. Dykes, Olivia Dalleur, Mary G. Amato, David W. Bates
2015 Misc conf
AMIA
Diane L. Seger, Sarah P. Slight, Patrick E. Beeler, Olivia Dalleur, Mary G. Amato, Tewodros Eguale, Karen C. Nanji, Patricia C. Dykes, Michael Swerdloff, Julie M. Fiskio, David W. Bates
2015 Misc conf
AMIA
Karen C. Nanji, Sofia D. Shaikh, Amit Patel, Diane L. Seger, David W. Bates
2015 J jnl
Int. J. Medical Informatics
InSook Cho, Sarah P. Slight, Karen C. Nanji, Diane L. Seger, Nivethietha Maniam, Julie M. Fiskio, Patricia C. Dykes, David W. Bates
2014 Misc conf
AMIA
Nivethietha Maniam, Sarah P. Slight, Diane L. Seger, Mary G. Amato, Julie M. Fiskio, Dustin McEvoy, Karen C. Nanji, Patricia C. Dykes, David W. Bates
2014 Misc conf
AMIA
Olivia Dalleur, Diane L. Seger, Sarah P. Slight, Mary G. Amato, Tewodros Eguale, Karen C. Nanji, Nivethietha Maniam, Patricia C. Dykes, Julie M. Fiskio, David W. Bates
2014 J jnl
J. Am. Medical Informatics Assoc.
Karen C. Nanji, Sarah P. Slight, Diane L. Seger, InSook Cho, Julie M. Fiskio, Lisa M. Redden, Lynn A. Volk, David W. Bates
2014 J jnl
J. Am. Medical Informatics Assoc.
Karen C. Nanji, Jeffrey M. Rothschild, Jennifer J. Boehne, Carol A. Keohane, Joan S. Ash, Eric G. Poon
2013 Misc conf
AMIA
Sarah P. Slight, Diane L. Seger, Karen C. Nanji, InSook Cho, Nivethietha Maniam, Patricia C. Dykes, David W. Bates
2013 conf
MedInfo
Sarah P. Slight, Karen C. Nanji, Diane L. Seger, InSook Cho, Lynn A. Volk, David W. Bates
2013 conf
MedInfo
InSook Cho, Sarah P. Slight, Karen C. Nanji, Diane L. Seger, Patricia C. Dykes, David W. Bates
2011 J jnl
J. Am. Medical Informatics Assoc.
Karen C. Nanji, Jeffrey M. Rothschild, Claudia A. Salzberg, Carol A. Keohane, Katherine Zigmont, Jim Devita, Tejal K. Gandhi, Anuj K. Dalal, David W. Bates, Eric G. Poon
2009 J jnl
J. Am. Medical Informatics Assoc.
Karen C. Nanji, Jennifer L. Cina, Nirali Patel, William W. Churchill, Tejal K. Gandhi, Eric G. Poon
redb/extractors/decompiler/_archive/GhidraDecompilerScript-latest.java
← Index redb/extractors/decompiler/_archive/GhidraDecompilerScript-latest.java java
import ghidra.app.script.GhidraScript;
import ghidra.program.model.listing.*;
import ghidra.app.decompiler.*;
import ghidra.program.model.block.*;
import ghidra.program.model.symbol.*;
import ghidra.program.model.pcode.*;
import ghidra.program.model.address.*;
import org.json.JSONObject;
import org.json.JSONArray;
import java.security.MessageDigest;
import java.nio.charset.StandardCharsets;

public class GhidraDecompilerScript extends GhidraScript {
    private DecompInterface decompInterface;
    private BasicBlockModel basicBlockModel;
    
    @Override
    public void run() throws Exception {
        // Get binary hash and filepath from arguments
        String[] args = getScriptArgs();
        if (args.length < 2) {
            System.err.println("{\"error\": \"Both SHA256 and filepath arguments are required\"}");
            return;
        }
        String sha256 = args[0];
        String filepath = args[1];

        // Initialize analysis components
        setupDecompiler();
        basicBlockModel = new BasicBlockModel(currentProgram);

        // Create the main JSON object for output
        JSONObject output = new JSONObject();
        output.put("sha256", sha256);
        output.put("decompiled", new JSONArray());
        output.put("disassembled", new JSONArray());
        output.put("cfg", new JSONArray());

        // Process all functions
        FunctionIterator functions = currentProgram.getFunctionManager().getFunctions(true);
        for (Function function : functions) {
            processFunction(function, output);
        }

        // Output the final JSON to stdout
        System.out.println(output.toString());
    }

    private void setupDecompiler() {
        decompInterface = new DecompInterface();
        DecompileOptions options = new DecompileOptions();
        decompInterface.setOptions(options);
        decompInterface.openProgram(currentProgram);
    }

    private void processFunction(Function function, JSONObject output) {
        Address entry = function.getEntryPoint();
        String functionName = function.getName();
        String functionAddress = entry.toString();

        // Process decompiled code
        processDecompiledCode(function, output.getJSONArray("decompiled"), 
                            functionName, functionAddress);

        // Process disassembled code
        processDisassembledCode(function, output.getJSONArray("disassembled"), 
                              functionName, functionAddress);

        // Process CFG
        processCFG(function, output.getJSONArray("cfg"), functionAddress);
    }

    private void processDecompiledCode(Function function, JSONArray decompArray, 
                                     String functionName, String functionAddress) {
        DecompileResults results = decompInterface.decompileFunction(function, 30, monitor);
        if (results.decompileCompleted()) {
            String decompiledCode = results.getDecompiledFunction().getC();
            String contentHash = calculateHash(decompiledCode);

            JSONObject functionObj = new JSONObject();
            functionObj.put("decompiled_content_hash", contentHash);
            functionObj.put("decompiled_function_name", functionName);
            functionObj.put("decompiled_function_address", functionAddress);
            functionObj.put("decompiled_function", decompiledCode);
            
            decompArray.put(functionObj);
        }
    }

    private void processDisassembledCode(Function function, JSONArray disasmArray, 
                                       String functionName, String functionAddress) {
        try {
            StringBuilder disassembly = new StringBuilder();
            StringBuilder normalized = new StringBuilder();
            int instructionCount = 0;

            Listing listing = currentProgram.getListing();
            AddressSetView functionBody = function.getBody();
            InstructionIterator instructions = listing.getInstructions(functionBody, true);

            while (instructions.hasNext()) {
                try {
                    Instruction instr = instructions.next();
                    String disasmLine = instr.toString();
                    disassembly.append(disasmLine).append("\n");
                    normalized.append(normalizeInstruction(disasmLine)).append("\n");
                    instructionCount++;
                } catch (Exception e) {
                    System.err.println("Error processing instruction in " + functionName + ": " + e.getMessage());
                }
            }

            String disassembledCode = disassembly.toString();
            String contentHash = calculateHash(disassembledCode);

            JSONObject functionObj = new JSONObject();
            functionObj.put("disassembled_content_hash", contentHash);
            functionObj.put("disassembled_function_name", functionName);
            functionObj.put("disassembled_function_address", functionAddress);
            functionObj.put("disassembled_function", disassembledCode);
            functionObj.put("normalized_disassembly", normalized.toString());
            functionObj.put("instruction_count", instructionCount);

            // Set similarity-related fields to null for now
            functionObj.put("minhash_signature", JSONObject.NULL);
            functionObj.put("opcode_frequency_vector", JSONObject.NULL);
            functionObj.put("api_calls_vector", JSONObject.NULL);
            functionObj.put("instruction_embedding", JSONObject.NULL);

            disasmArray.put(functionObj);
        } catch (Exception e) {
            System.err.println("Error processing disassembly for " + functionName + ": " + e.getMessage());
        }
    }

    private void processCFG(Function function, JSONArray cfgArray, String functionAddress) {
        try {
            CodeBlockIterator blocks = basicBlockModel.getCodeBlocksContaining(
                function.getBody(), monitor);

            while (blocks.hasNext()) {
                CodeBlock block = blocks.next();
                String blockInstructions = getBlockInstructions(block);
                String blockId = calculateHash(blockInstructions);

                JSONObject blockObj = new JSONObject();
                blockObj.put("block_id", blockId);
                blockObj.put("function_address", functionAddress);
                blockObj.put("block_instructions", blockInstructions);

                // Get successor blocks
                CodeBlockReferenceIterator successors = block.getDestinations(monitor);
                JSONArray successorAddresses = new JSONArray();
                while (successors.hasNext()) {
                    CodeBlockReference ref = successors.next();
                    successorAddresses.put(ref.getDestinationAddress().toString());
                }
                blockObj.put("successor_blocks", successorAddresses);

                cfgArray.put(blockObj);
            }
        } catch (Exception e) {
            System.err.println("{\"error\": \"Error processing CFG: " + 
                             e.getMessage().replace("\"", "'") + "\"}");
        }
    }

    private String normalizeInstruction(String instruction) {
        return instruction.replaceAll("0x[0-9a-fA-F]+", "IMM")
                        .replaceAll("\\b\\d+\\b", "NUM");
    }

    private String getBlockInstructions(CodeBlock block) {
        StringBuilder instructions = new StringBuilder();
        AddressIterator addresses = block.getAddresses(true);
        while (addresses.hasNext()) {
            Address addr = addresses.next();
            Instruction instr = currentProgram.getListing().getInstructionAt(addr);
            if (instr != null) {
                instructions.append(instr.toString()).append("\n");
            }
        }
        return instructions.toString();
    }

    private String calculateHash(String content) {
        try {
            MessageDigest digest = MessageDigest.getInstance("SHA-256");
            byte[] hash = digest.digest(content.getBytes(StandardCharsets.UTF_8));
            StringBuilder hexString = new StringBuilder();
            for (byte b : hash) {
                hexString.append(String.format("%02x", b));
            }
            return hexString.toString();
        } catch (Exception e) {
            System.err.println("{\"error\": \"Error calculating hash\"}");
            return "";
        }
    }
}