James V. Miller

28 papers A* 4A 3B 2Journal 4Unranked 15
YearRankTypeTitle / Venue / Authors
2019 J jnl
CoRR
Y. Ye, Richard D. Boyce, M. K. Davis, Keith O. Elliston, Christos Davatzikos, Andrey Fedorov, Jean-Christophe Fillion-Robin, Ian T. Foster, John R. Gilbertson, Mervi Heiskanen, Juli D. Klemm, Andras Lasso, James V. Miller, M. Morgan, Steve Pieper, Brigitte Raumann, B. Sarachan, G. Savova, Jonathan C. Silverstein, D. Taylor, J. Zelnis, G. Q. Zhang, Michael J. Becich
2014 J jnl
Neuroinformatics
Harini Veeraraghavan, James V. Miller
2013 conf
ISBI
Anthony C. Bianchi, James V. Miller, Ek Tsoon Tan, Albert Montillo
2013 J jnl
CoRR
Jan Egger, Tina Kapur, Andriy Fedorov, Steve Pieper, James V. Miller, Harini Veeraraghavan, Bernd Freisleben, Alexandra J. Golby, Christopher Nimsky, Ron Kikinis
2013 B conf
Image Processing
Albert Montillo, Qi Song, Xiaoming Liu, James V. Miller
2011 conf
ISBI
Harini Veeraraghavan, James V. Miller
2011 conf
MICCAI (2)
Mahnaz Maddah, James V. Miller, Edith V. Sullivan, Adolf Pfefferbaum, Torsten Rohlfing
2010 conf
ISBI
Fei Zhao, Rahul Bhotika, Paulo R. S. Mendonça, Nils Krahnstoever, James V. Miller
2010 conf
ISBI
Roshni R. Bhagalia, James V. Miller, Arunabha Roy
2010 B conf
Image Processing
Roshni R. Bhagalia, James V. Miller, Arunabha Roy
2009 conf
MICCAI (1)
Sokratis Makrogiannis, Rahul Bhotika, James V. Miller, John Skinner, Melissa Vass
2008 conf
ISBI
James V. Miller, Girish Gopalakrishnan, Manasi Datar, Paulo R. S. Mendonça, Rakesh Mullick
2007 J jnl
Medical Image Anal.
Daniel J. Blezek, James V. Miller
2007 A* conf
ICCV
John Melonakos, Marc Niethammer, Vandana Mohan, Marek Kubicki, James V. Miller, Allen R. Tannenbaum
2007 conf
IPMI
Paulo R. S. Mendonça, Rahul Bhotika, Fei Zhao, James V. Miller
2007 conf
ISBI
Fei Zhao, Paulo R. S. Mendonça, Rahul Bhotika, James V. Miller
2006 conf
MICCAI (2)
Xiaodong Tao, James V. Miller
2006 conf
MICCAI (2)
Wesley D. Turner, Timothy P. Kelliher, James C. Ross, James V. Miller
2006 conf
MICCAI (1)
Daniel J. Blezek, James V. Miller
2006 conf
MICCAI (2)
Thomas B. Sebastian, Ravindra M. Manjeshwar, Timothy J. Akhurst, James V. Miller
2006 conf
MICCAI (2)
Rahul Bhotika, Paulo R. S. Mendonça, Saad A. Sirohey, Wesley D. Turner, Ying-Lin Lee, Julie M. McCoy, Rebecca E. B. Brown, James V. Miller
2005 A conf
MICCAI
Paulo R. S. Mendonça, Rahul Bhotika, Saad A. Sirohey, Wesley D. Turner, James V. Miller, Ricardo S. Avila
2005 A conf
MICCAI
Paulo R. S. Mendonça, Dirk Ryan Padfield, James C. Ross, James V. Miller, Sandeep Dutta, Sardar Mal Gautham
2004 conf
ECCV (2)
Paulo R. S. Mendonça, Dirk Ryan Padfield, James V. Miller, Matt Turek
1997 A* conf
CVPR
James V. Miller, Charles V. Stewart
1996 A* conf
CVPR
James V. Miller, Charles V. Stewart
1991 A* conf
SIGGRAPH
James V. Miller, David E. Breen, William E. Lorensen, Robert M. O'Bara, Michael J. Wozny
1990 A conf
IEEE Visualization
James V. Miller, David E. Breen, Michael J. Wozny
redb/s3_utils.py
← Index redb/s3_utils.py python
"""
S3 and file utility functions for REDB.

Contains MinIO/S3 client creation, S3 key generation,
file download, and archive extraction helpers.
"""
import os
import tempfile
from typing import Optional, List

from minio import Minio
from minio.error import S3Error


def get_minio_client():
    """Create and return a Minio client using credentials from .env file"""
    return Minio(
        endpoint=os.getenv("S3_ENDPOINT"),
        access_key=os.getenv("S3_ACCESS_KEY"),
        secret_key=os.getenv("S3_SECRET_KEY"),
        secure=os.getenv("S3_SECURE", "false").lower() == "true"
    )


def generate_s3_key_from_hash(sample_hash: str) -> str:
    """
    Generate S3 key from hash using sharding structure.
    Example: 09f7d02a3c2382199458c98a62b045145ee54ab6aba86166aecf3d10c3c1444c
    becomes: 09/f7/09f7d02a3c2382199458c98a62b045145ee54ab6aba86166aecf3d10c3c1444c.zip
    """
    if len(sample_hash) < 4:
        raise ValueError(f"Hash too short for sharding: {sample_hash}")

    # Create sharded path: first 2 chars / next 2 chars / full_hash.zip
    return f"{sample_hash[:2]}/{sample_hash[2:4]}/{sample_hash}.zip"


def download_s3_object(s3_bucket: str, s3_key: str, temp_dir: str, logger=None) -> Optional[str]:
    """
    Download an object from S3 to a local temporary directory and return the local path.
    If the .zip file is not found, automatically tries .7z as a fallback for legacy uploads.
    """
    try:
        minio_client = get_minio_client()
        local_path = os.path.join(temp_dir, os.path.basename(s3_key))

        # Download the file
        minio_client.fget_object(s3_bucket, s3_key, local_path)

        return local_path
    except S3Error as e:
        # If .zip not found and error is NoSuchKey, try .7z fallback
        if e.code == 'NoSuchKey' and s3_key.endswith('.zip'):
            s3_key_7z = s3_key[:-4] + '.7z'  # Replace .zip with .7z
            if logger:
                logger.info(f".zip not found, trying .7z fallback: {s3_key_7z}")
            try:
                local_path_7z = os.path.join(temp_dir, os.path.basename(s3_key_7z))
                minio_client.fget_object(s3_bucket, s3_key_7z, local_path_7z)
                if logger:
                    logger.info(f"Successfully downloaded .7z fallback: {s3_key_7z}")
                return local_path_7z
            except S3Error as e2:
                if logger:
                    logger.error(f"Failed to download S3 object {s3_key} (tried both .zip and .7z): {e2}")
                else:
                    print(f"[ERROR] Failed to download S3 object {s3_key} (tried both .zip and .7z): {e2}")
                return None
        else:
            if logger:
                logger.error(f"Failed to download S3 object {s3_key}: {e}")
            else:
                print(f"[ERROR] Failed to download S3 object {s3_key}: {e}")
            return None


def extract_fat_slices(macho, output_dir: str, logger) -> List[tuple]:
    """
    Extract slices from FAT Mach-O binary using machofile's dump_slices() API.

    Args:
        macho: Parsed machofile.UniversalMachO object
        output_dir: Directory to write slice files
        logger: Logger instance

    Returns:
        List of (arch_name, slice_path, slice_sha256, slice_md5, slice_sha1) tuples
    """
    result = []
    try:
        # Use machofile's dump_slices API (v2026.2.5+)
        slices = macho.dump_slices(output_dir=output_dir)
        logger.debug(f"Extracted {len(slices)} slices from FAT binary")

        for arch_name, slice_path in slices:
            # Get hash info for this slice from machofile
            general_info = macho.get_general_info(arch=arch_name)
            slice_sha256 = general_info.get('SHA256')
            slice_md5 = general_info.get('MD5')
            slice_sha1 = general_info.get('SHA1')
            result.append((arch_name, slice_path, slice_sha256, slice_md5, slice_sha1))
            logger.debug(f"Slice {arch_name}: {slice_sha256}")

    except Exception as e:
        logger.error(f"Error extracting FAT slices: {e}")

    return result