Victor M. Vergara

41 papers C 1Misc 2Journal 11Unranked 27
YearRankTypeTitle / Venue / Authors
2025 conf
HPEC
Victor M. Vergara, Francisco Viramontes, Amanda E. Romero, Matthew E. Spear, Evan Kain, Windy S. Slater, Heather M. Quinn, Qing Wu
2024 conf
EMBC
Biozid Bostami, Noah Lewis, Victor M. Vergara, Vince D. Calhoun
2024 conf
SSIAI
Robyn L. Miller, Victor M. Vergara, Vince D. Calhoun
2023 conf
EMBC
Robyn L. Miller, Victor M. Vergara, Vince D. Calhoun
2023 conf
ICASSP Workshops
Robyn L. Miller, Victor M. Vergara, Helen Petropoulos, Vince D. Calhoun
2022 J jnl
Brain Connect.
Mustafa S. Salman, Tor D. Wager, Eswar Damaraju, Anees Abrol, Victor M. Vergara, Zening Fu, Vince D. Calhoun
2022 conf
EMBC
Biozid Bostami, Flor A. Espinoza, Harm J. van der Horn, Joukje van der Naalt, Vince D. Calhoun, Victor M. Vergara
2021 conf
ISBI
Shile Qi, Sergey M. Plis, Robyn L. Miller, Rogers F. Silva, Victor M. Vergara, Rongtao Jiang, Dongmei Zhi, Jing Sui, Vince D. Calhoun
2021 conf
EMBC
Robyn L. Miller, Victor M. Vergara, Vince D. Calhoun
2021 conf
EMBC
Victor M. Vergara, Farshad Rafiei, Martijn E. Wokke, Hakwan Lau, Dobromir Rahnev, Vince D. Calhoun
2021 C conf
BIBE
Biozid Bostami, Vince D. Calhoun, Harm J. van der Horn, Victor M. Vergara
2021 conf
EMBC
Robyn L. Miller, Victor M. Vergara, Vince D. Calhoun
2020 J jnl
IEEE Trans. Biomed. Eng.
Haleh Falakshahi, Victor M. Vergara, Jingyu Liu, Daniel H. Mathalon, Judith M. Ford, James Voyvodic, Bryon A. Mueller, Aysenil Belger, Sarah C. McEwen, Steven G. Potkin, Adrian Preda, Hooman Rokham, Jing Sui, Jessica A. Turner, Sergey M. Plis, Vince D. Calhoun
2020 J jnl
CoRR
Haleh Falakshahi, Victor M. Vergara, Jingyu Liu, Daniel H. Mathalon, Judith M. Ford, James Voyvodic, Bryon A. Mueller, Aysenil Belger, Sarah C. McEwen, Steven G. Potkin, Adrian Preda, Hooman Rokham, Jing Sui, Jessica A. Turner, Sergey M. Plis, Vince D. Calhoun
2020 conf
SSIAI
Victor M. Vergara, Vince D. Calhoun
2019 conf
EMBC
Victor M. Vergara, Anees Abrol, Flor A. Espinoza, Vince D. Calhoun
2018 conf
EMBC
Na Luo, Lin Tian, Vince D. Calhoun, Jiayu Chen, Dongdong Lin, Victor M. Vergara, Shuquan Rao, Fuquan Zhang, Jing Sui
2018 conf
SSIAI
Victor M. Vergara, Qingbao Yu, Vince D. Calhoun
2018 Misc conf
ACSSC
Mustafa S. Salman, Victor M. Vergara, Eswar Damaraju, Vince D. Calhoun
2018 J jnl
Brain Connect.
Flor A. Espinoza, Jessica A. Turner, Victor M. Vergara, Robyn L. Miller, Eva Mennigen, Jingyu Liu, Maria B. Misiura, Jennifer Ciarochi, Hans J. Johnson, Jeffrey D. Long, Henry Jeremy Bockholt, Vincent A. Magnotta, Jane S. Paulsen, Vince D. Calhoun
2017 J jnl
NeuroImage
Victor M. Vergara, Jingyu Liu, Eric D. Claus, Kent Hutchison, Vince D. Calhoun
2017 Misc conf
ACSSC
Victor M. Vergara, Vince D. Calhoun
2017 J jnl
NeuroImage
Victor M. Vergara, Andrew R. Mayer, Eswar Damaraju, Kent Hutchison, Vince D. Calhoun
2016 J jnl
IEEE Trans. Biomed. Eng.
Robyn L. Miller, Victor M. Vergara, David B. Keator, Vince D. Calhoun
2016 conf
EMBC
Victor M. Vergara, Vince D. Calhoun
2015 conf
EMBC
Robyn L. Miller, Victor M. Vergara, Vince D. Calhoun
2015 conf
EMBC
Mustafa S. Çetin, Jon M. Houck, Victor M. Vergara, Robyn L. Miller, Vince D. Calhoun
2015 conf
EMBC
Victor M. Vergara, Eswar Damaraju, Andrew B. Mayer, Robyn L. Miller, Mustafa S. Çetin, Vince D. Calhoun
2014 J jnl
NeuroImage
Victor M. Vergara, Alvaro Ulloa, Vince D. Calhoun, David Boutte, Jiayu Chen, Jingyu Liu
2014 conf
EMBC
Alvaro Ulloa, Jingyu Liu, Victor M. Vergara, Jiayu Chen, Vince D. Calhoun, Marios S. Pattichis
2012 conf
RWS
Victor M. Vergara, Silvio E. Barbin
2010 J jnl
Int. J. Intell. Syst.
Victor M. Vergara, Shan Xia
2009 conf
MMVR
Victor M. Vergara, Darra Kingsley, Dale C. Alverson, Timothy E. Goldsmith, Shan Xia, Thomas P. Caudell
2008 conf
MMVR
Jennifer Pierce, Fátima Gutiérrez, Victor M. Vergara, Dale C. Alverson, Clifford Qualls, Linda Saland, Timothy E. Goldsmith, Thomas Preston Caudell
2008 conf
VTC Fall
Victor M. Vergara, Silvio E. Barbin, Ramiro Jordan
2008 conf
MMVR
Laura Addison, Victor M. Vergara, Takeshi Hakamata, Dale C. Alverson, Stanley M. Saiki, Thomas Preston Caudell
2008 J jnl
J. Commun.
Victor M. Vergara, Silvio E. Barbin, Ramiro Jordan
2007 conf
VTC Fall
Victor M. Vergara, Ramiro Jordan, Silvio E. Barbin
2007 conf
MMVR
Fátima Gutiérrez, Jennifer Pierce, Victor M. Vergara, Robert Coulter, Linda Saland, Thomas P. Caudell, Timothy E. Goldsmith, Dale C. Alverson
2006 conf
VTC Fall
Victor M. Vergara, Silvio E. Barbin, Ramiro Jordan
2005 J jnl
ACM Trans. Appl. Percept.
Nadine E. Miner, Victor M. Vergara, Panaiotis, Thomas P. Caudell
redb/extractors/pe_extractors/pe_dotnet.py
← Index redb/extractors/pe_extractors/pe_dotnet.py python
import inspect
import pefile
from dotnetfile import DotNetPE

import base64
from hashlib import md5
from pprint import pprint

import magic
import pefile

from redb.extractors.enum import Tag
from redb.extractors.pe_extractor import PEExtractor
from redb.models.dataclasses import PEDotNet
from datetime import datetime, timezone
import json
from typing import Any


class PEDotNetExtractor(PEExtractor):

    def __init__(
        self,
        filepath,
        log,
        exporters=None,
        index_prefix=None,
        elastic_index=None,
        known_benign=False,
        known_malicious=False,
        pe=None,
    ):
        super().__init__(
            filepath,
            log,
            exporters,
            index_prefix,
            elastic_index,
            known_benign,
            known_malicious,
            pe,
        )
        # self.pe_features = None
        self.elastic_index = self.index_prefix + "-pe_dotnet"
        self.dotnet, self.error = self._generate_dotnetfile_object()
        self.log.debug(inspect.currentframe().f_code.co_name)

    def _decode_assembly_flags(self, flag_value):
        self.log.debug(inspect.currentframe().f_code.co_name)
        ASSEMBLY_FLAGS = {
            0x00000001: "COMIMAGE_FLAGS_ILONLY",
            0x00000002: "COMIMAGE_FLAGS_32BITREQUIRED",
            0x00000004: "COMIMAGE_FLAGS_IL_LIBRARY",
            0x00000008: "COMIMAGE_FLAGS_STRONGNAMESIGNED",
            0x00000010: "COMIMAGE_FLAGS_NATIVE_ENTRYPOINT",
            0x00010000: "COMIMAGE_FLAGS_TRACKDEBUGDATA",
            0x00020000: "COMIMAGE_FLAGS_32BITPREFERRED",
        }
        flags = []
        for bit, name in ASSEMBLY_FLAGS.items():
            if flag_value & bit:
                flags.append(name)
        return flags

    def _normalize_data(self, data):
        self.log.debug(inspect.currentframe().f_code.co_name)
        if isinstance(data, str):
            return {"value": data}
        return data

    def _compute_md5(self, data):
        self.log.debug(inspect.currentframe().f_code.co_name)
        if isinstance(data, str):
            # If it's a string, encode it to first
            return md5(data.encode("raw_unicode_escape")).hexdigest()
        elif not isinstance(data, bytes):
            # If it's neither string nor bytes, convert it to string and then to bytes
            return md5(str(data).encode("raw_unicode_escape")).hexdigest()
        else:
            return md5(data).hexdigest()

    def tag(self):
        return Tag.PE_DOTNET.value

    def extract(self):
        self.log.debug(inspect.currentframe().f_code.co_name)
        metadata = {}

        if self.error:
            metadata["Corrupted"] = self.error.args[0]
            dotnet = PEDotNet(metadata)
            self.dotnet = dotnet  # Store for later use in prepare_export_data
            return dotnet  # Return the extracted data instead of exporting directly

        metadata["info"] = {}
        try:
            available_tables = self.dotnet.existent_metadata_tables()
        except Exception as e:
            self.log.error(f"Error getting metadata tables for {self.hash.sha256}: {e}")
            available_tables = []
            metadata["info"]["PotentiallyCorrupted"] = True

        # GUID extraction
        try:
            input_string = self.dotnet.guid_stream_guids[0].string_representation
            
            formatted_uuid = (
                f"{input_string[6:8]}{input_string[4:6]}{input_string[2:4]}{input_string[0:2]}"
                f"-{input_string[10:12]}{input_string[8:10]}"
                f"-{input_string[14:16]}{input_string[12:14]}"
                f"-{input_string[16:20]}"
                f"-{input_string[20:]}"
            )
            metadata["info"]["ModuleVersionID"] = formatted_uuid
        except Exception as e:
            self.log.error(f"Error extracting GUID for {self.hash.sha256}: {e}")

        # CLR Version
        try:
            metadata["info"]["CLRversion"] = self.dotnet.get_runtime_target_version()
        except Exception as e:
            self.log.error(f"Error getting CLR version for {self.hash.sha256}: {e}")

        # Module information
        try:
            if self.dotnet.metadata_table_exists("Module"):
                metadata["info"]["AssemblyModuleName"] = self.dotnet.Module.get_module_name()
        except Exception as e:
            self.log.error(f"Error getting module info for {self.hash.sha256}: {e}")

        # Basic properties
        try:
            metadata["info"].update({
                "IsNativeNgenImage": self.dotnet.is_native_image(),
                "IsMixedAssembly": self.dotnet.is_mixed_assembly(),
                "IsWindowsFormsApp": self.dotnet.is_windows_forms_app(),
                "EntryPointToken": self.dotnet.clr_header.EntryPointToken.value,
                "HasNativeEntryPoint": self.dotnet.has_native_entry_point(),
            })
        except Exception as e:
            self.log.error(f"Error getting basic properties for {self.hash.sha256}: {e}")

        # Assembly flags
        try:
            metadata["info"]["AssemblyFlags"] = self._decode_assembly_flags(
                self.dotnet.clr_header.Flags.value
            )
        except Exception as e:
            self.log.error(f"Error getting assembly flags for {self.hash.sha256}: {e}")

        # More Metadata/Info CLR Header
        try:
            metadata["info"]["NumOfStreams"] = self.dotnet.get_number_of_streams()
            # [TODO] The following two on VT are "RVA entry point"
            #  and "Resources va" respectively. To verify.
            metadata["info"][
                "ResourcesDirectoryAddress"
            ] = self.dotnet.clr_header.ResourcesDirectoryAddress.value
            metadata["info"][
                "ResourcesDirectorySize"
            ] = self.dotnet.clr_header.ResourcesDirectorySize.value
            metadata["info"][
                "StrongNameSignatureAddress"
            ] = self.dotnet.clr_header.StrongNameSignatureAddress.value
            metadata["info"][
                "StrongNameSignatureSize"
            ] = self.dotnet.clr_header.StrongNameSignatureSize.value
            metadata["info"][
                "CodeManagerTableAddress"
            ] = self.dotnet.clr_header.CodeManagerTableAddress.value
            metadata["info"][
                "CodeManagerTableSize"
            ] = self.dotnet.clr_header.CodeManagerTableSize.value
            metadata["info"][
                "VTableFixupsAddress"
            ] = self.dotnet.clr_header.VTableFixupsAddress.value
            metadata["info"][
                "VTableFixupsSize"
            ] = self.dotnet.clr_header.VTableFixupsSize.value
            metadata["info"][
                "ExportAddressTableJumpsAddress"
            ] = self.dotnet.clr_header.ExportAddressTableJumpsAddress.value
            metadata["info"][
                "ExportAddressTableJumpsSize"
            ] = self.dotnet.clr_header.ExportAddressTableJumpsSize.value
            metadata["info"][
                "ManagedNativeHeaderAddress"
            ] = self.dotnet.clr_header.ManagedNativeHeaderAddress.value
            metadata["info"][
                "ManagedNativeHeaderSize"
            ] = self.dotnet.clr_header.ManagedNativeHeaderSize.value
        except Exception as e:
            self.log.error(f"Error getting more metadata/info clr header for {self.hash.sha256}: {e}")

        # Streams section
        try:
            metadata["Streams"] = {}
            stream_names = self.dotnet.get_stream_names()
            for name in stream_names:
                indx = stream_names.index(name)
                stream_header = self.dotnet.dotnet_stream_headers[indx]
                stream_address = self.dotnet.dotnet_streams[indx].address
                metadata["Streams"][name] = {}
                metadata["Streams"][name]["raw_name"] = base64.b64encode(
                    stream_header.Name.value
                ).decode()
                # metadata["Streams"][name]["raw_name"] = name
                metadata["Streams"][name]["size"] = stream_header.Size.value
                # Retrieve the stream data directly using the given address and size
                stream_data = self.pe.get_data(stream_address, stream_header.Size.value)
                metadata["Streams"][name]["entropy"] = (
                    "%.2f" % pefile.SectionStructure.entropy_H(self.pe, stream_data)
                )
                metadata["Streams"][name]["md5"] = md5(stream_data).hexdigest()
        except Exception as e:
            self.log.error(f"Error getting streams for {self.hash.sha256}: {e}")

        # ManifestResource
        try:
            metadata["ManifestResource"] = ()
            if "ManifestResource" in available_tables:
                metadata["info"]["HasManifestResource"] = True
                metadata["ManifestResource"] = (
                    self.dotnet.ManifestResource.get_resource_names()
                )
        except Exception as e:
            self.log.error(f"Error getting manifest resource for {self.hash.sha256}: {e}")

        # ExternalAssemblyRef
        try:
            metadata["ExternalAssemblyRef"] = {}
            if "AssemblyRef" in available_tables:
                metadata["ExternalAssemblyRef"][
                    "names"
                ] = self.dotnet.AssemblyRef.get_assemblyref_names()
                metadata["ExternalAssemblyRef"][
                    "cultures"
                ] = self.dotnet.AssemblyRef.get_assemblyref_cultures()
        except Exception as e:
            self.log.error(f"Error getting external assembly ref for {self.hash.sha256}: {e}")

        # AssemblyData
        try:
            metadata["AssemblyData"] = {}
            if "Assembly" in available_tables:
                metadata["AssemblyData"][
                    "name"
                ] = self.dotnet.Assembly.get_assembly_name()
                # It's officially a one-row table, but there are ITW files with more than one row.
                # It stores information about the current assembly. It is documented in ECMA-335.
                assembly_table = self.dotnet.metadata_tables_lookup[
                    "Assembly"
                ].table_rows[0]
                metadata["AssemblyData"][
                    "MajorVersion"
                ] = assembly_table.MajorVersion.value
                metadata["AssemblyData"][
                    "MinorVersion"
                ] = assembly_table.MinorVersion.value
                metadata["AssemblyData"]["hashalgid"] = assembly_table.HashAlgId.value
                metadata["AssemblyData"][
                    "BuildNumber"
                ] = assembly_table.BuildNumber.value
                metadata["AssemblyData"][
                    "RevisionNumber"
                ] = assembly_table.RevisionNumber.value
                metadata["AssemblyData"][
                    "culture"
                ] = self.dotnet.Assembly.get_assembly_culture()
        except Exception as e:
            self.log.error(f"Error getting assembly data for {self.hash.sha256}: {e}")

        # TypeDef handling
        try:
            metadata["TypeDef"] = {}
            if "TypeDef" in available_tables:
                metadata["info"]["HasTypeDef"] = True
                # Get basic type definitions
                try:
                    # Get all types (ANY visibility)
                    type_defs = self.dotnet.TypeDef.get_type_names()
                    metadata["TypeDef"]["names"] = type_defs if type_defs else []
                    
                    # Get detailed type information with methods
                    types_with_methods = self.dotnet.TypeDef.get_type_names_with_methods()
                    if types_with_methods:
                        metadata["TypeDef"]["detailed"] = []
                        for type_info in types_with_methods:
                            type_data = {
                                "type": type_info.Type,
                                "namespace": type_info.Namespace,
                                "flags": type_info.Flags,
                                "methods": []
                            }
                            for method in type_info.Methods:
                                method_data = {
                                    "name": method.Name,
                                    "flags": method.Flags
                                }
                                if method.Signature:
                                    method_data["signature"] = {
                                        "parameters": method.Signature.get("parameter", []),
                                        "return_type": method.Signature.get("return", ""),
                                        "has_this": method.Signature.get("hasthis", False)
                                    }
                                type_data["methods"].append(method_data)
                            metadata["TypeDef"]["detailed"].append(type_data)
                except AttributeError as e:
                    self.log.warning(f"TypeDef table exists but attributes missing for {self.hash.sha256}: {e}")
                    # metadata["info"]["TypeDefParsingError"] = f"Missing attributes: {str(e)}"
                except Exception as e:
                    self.log.error(f"Error parsing TypeDef table for {self.hash.sha256}: {e}")
                    # metadata["info"]["TypeDefParsingError"] = str(e)
        except Exception as e:
            self.log.error(f"Error handling TypeDef section for {self.hash.sha256}: {e}")
            metadata["TypeDef"] = {"names": [], "detailed": []}
            # metadata["info"]["TypeDefParsingError"] = str(e)

        # ExternalUnmanagedModules
        try:
            metadata["ExternalUnmanagedModules"] = ()
            if "ModuleRef" in available_tables:
                metadata["info"]["HasModuleRef"] = True
                metadata["ExternalUnmanagedModules"] = (
                    self.dotnet.ModuleRef.get_unmanaged_module_names(
                        self.dotnet.Type.UnmanagedModules.RAW
                    )
                )
        except Exception as e:
            self.log.error(f"Error getting external unmanaged modules for {self.hash.sha256}: {e}")

        # ExternalUnmanagedMethods
        try:
            metadata["ExternalUnmanagedMethods"] = ()
            if "ImplMap" in available_tables:
                metadata["info"]["HasImplMap"] = True
                metadata["ExternalUnmanagedMethods"] = (
                    self.dotnet.ImplMap.get_unmanaged_functions()
                )
        except Exception as e:
            self.log.error(f"Error getting external unmanaged methods for {self.hash.sha256}: {e}")

        # Event
        try:
            metadata["Event"] = ()
            if "Event" in available_tables:
                metadata["info"]["HasEvent"] = True
                metadata["Event"] = self.dotnet.Event.get_event_names()
        except Exception as e:
            self.log.error(f"Error getting event for {self.hash.sha256}: {e}")

        # Resources
        try:
            metadata["Resources"] = []
            if self.dotnet.has_resources():
                tmp_resources_list = []
                resource_data = self.dotnet.get_resources()
                for data in resource_data:
                    tmp_dict = {}
                    for resource_item in data.items():
                        if resource_item[0] == "SubResources":
                            if resource_item[1]:
                                tmp_dict["SubResources"] = {}
                                for sub_resource in resource_item[1]:
                                    for sub_resource_item in sub_resource.items():
                                        if sub_resource_item[0] == "Data":
                                            # Check if data is a sequence type that supports len()
                                            if hasattr(sub_resource_item[1], '__len__') and len(sub_resource_item[1]) > 100:
                                                tmp_dict["SubResources"]["Data"] = {}
                                                try:
                                                    # tmp_dict["SubResources"]["Data"][
                                                    #     "md5"
                                                    # ] = md5(
                                                    #     sub_resource_item[1].encode()
                                                    # ).hexdigest()
                                                    tmp_dict["SubResources"]["Data"][
                                                        "md5"
                                                    ] = self._compute_md5(
                                                        sub_resource_item[1]
                                                    )
                                                except Exception as e:
                                                    self.log.error(
                                                        f"Error in dotnet resources"
                                                        f" extraction {self.hash.sha256}: {e}"
                                                    )
                                                guess = magic.from_buffer(
                                                    sub_resource_item[1], mime=True
                                                )
                                                tmp_dict["SubResources"]["Data"][
                                                    "MimeType"
                                                ] = (guess if guess else None)
                                            else:
                                                normalized_data = self._normalize_data(
                                                    sub_resource_item[1].decode()
                                                    if isinstance(
                                                        sub_resource_item[1], bytes
                                                    )
                                                    else sub_resource_item[1]
                                                )
                                                tmp_dict["SubResources"][
                                                    sub_resource_item[0]
                                                ] = normalized_data
                                        else:
                                            tmp_dict["SubResources"][
                                                sub_resource_item[0]
                                            ] = (
                                                sub_resource_item[1].decode()
                                                if isinstance(
                                                    sub_resource_item[1], bytes
                                                )
                                                else sub_resource_item[1]
                                            )
                        elif resource_item[0] == "Data":
                            # Check if data is a sequence type that supports len()
                            if hasattr(resource_item[1], '__len__') and len(resource_item[1]) > 100:
                                tmp_dict["Data"] = {}
                                tmp_dict["Data"]["md5"] = self._compute_md5(
                                    resource_item[1]
                                )
                                guess = magic.from_buffer(resource_item[1], mime=True)
                                tmp_dict["Data"]["MimeType"] = guess if guess else None
                            else:
                                normalized_data = self._normalize_data(
                                    resource_item[1].decode()
                                    if isinstance(resource_item[1], bytes)
                                    else resource_item[1]
                                )
                                tmp_dict["Data"] = normalized_data
                        else:
                            tmp_dict[resource_item[0]] = (
                                resource_item[1].decode()
                                if isinstance(resource_item[1], bytes)
                                else resource_item[1]
                            )
                    tmp_resources_list.append(tmp_dict)
                metadata["Resources"] = tmp_resources_list
        except Exception as e:
            self.log.error(f"Error getting resources for {self.hash.sha256}: {e}")
            metadata["Resources"] = []  # Ensure we always have a valid list even on error

        dotnet = PEDotNet(metadata)
        self.dotnet = dotnet  # Store for later use in prepare_export_data
        return dotnet  # Return the extracted data instead of exporting directly


    def prepare_export_data(self, exporter_type: str) -> Any:
        if exporter_type == "ElasticsearchExporter":
            return self.dotnet
        elif exporter_type == "ClickHouseExporter":
            # Convert metadata to JSON string
            metadata_json = json.dumps(self.dotnet.dotnet)
            
            data = [[
                self.sha256,
                self.md5,
                self.sha1,
                metadata_json,
                datetime.now(timezone.utc)
            ]]
            
            column_names = [
                'sha256', 'md5', 'sha1', 'dotnet', 'analysis_date'
            ]
            
            if not data:
                return None

            column_type_names = [
                'String', 'String', 'String', 'JSON', 'DateTime64(3, \'UTC\')'
            ]

            return (data, column_names, column_type_names)

    def get_clickhouse_table(self) -> str:
        return "redb_pe_dotnet"