boost-corr

A high-performance correlation (multi-tau/two-time) package for X-ray Photon Correlation Spectroscopy (XPCS) running on GPU and CPU.

Features

High Performance: GPU-accelerated correlation computation using PyTorch
Flexible: Supports both multi-tau and two-time correlation analysis
Multiple Formats: Handles IMM, Rigaku, HDF5, and Timepix4 data formats
Timepix4 Support: Native support for Timepix4 detectors with configurable time binning
CPU Fallback: Automatic fallback to CPU when GPU is unavailable
Command-line Interface: Easy-to-use CLI for batch processing
Python API: Programmatic access for custom workflows

Installation

Prerequisites

Python 3.12 or higher
PyTorch (with CUDA support for GPU acceleration)

Step 1: Create Virtual Environment

Create a new virtual environment using conda (recommended):

# Create environment
conda create -n boost_corr python=3.12

# Activate environment
conda activate boost_corr

Alternatively, use venv:

python -m venv boost_corr_env
source boost_corr_env/bin/activate  # On Linux/Mac
# or
boost_corr_env\Scripts\activate  # On Windows

Step 2: Install boost-corr

From PyPI (Stable)

pip install boost-corr

From Source (Development)

# Clone repository
git clone https://github.com/AdvancedPhotonSource/boost_corr.git
cd boost_corr
pip install -e .

Using Docker or Podman

You can run boost-corr using Docker or Podman. Podman is generally a drop-in replacement for Docker.

Build the Image

docker build -t boost_corr .
# OR
podman build -t boost_corr .

Run the Container

You need to mount your data directory to the container. Run the following command (replace paths as needed):

docker run --rm -v /local/data/path:/data boost_corr -t Multitau \
  -r /data/sample.h5 \
  -q /data/qmap.h5 \
  -o /data/outputdir

Podman Notes:

Command: simply replace docker with podman.
Permissions (SELinux): If you are on an SELinux-enabled system (RHEL/CentOS/Fedora), you may need to append :z to the volume mount to allow the container to access the files: -v /local/data/path:/data:z

GPU Support:

Docker: Requires NVIDIA Container Toolkit.
```
docker run --gpus all ...
```

Podman: Requires NVIDIA Container Toolkit (CDI).

podman run --device nvidia.com/gpu=all --security-opt=label=disable ...

Real-world Examples (Podman):

Using CPU (mounting data to /app with SELinux relabeling):

podman run --rm --shm-size=64gb \
  -v /home/beams/MQICHU/Datasets/xpcs_edge_computing_datasets/eiger4m:/app:z \
  boost_corr \
  -r /app/D0131_US-Cup2_a0010_f005000_r00001/D0131_US-Cup2_a0010_f005000_r00001.h5 \
  -q /app/D0131_qmap_with_blemish.hdf \
  -o /app/cluster_results \
  -v

Note --shm-size is needed for large datasets. PyTorch’s DataLoader uses shared memory for multi-process data loading, and the default Docker limit (64MB) will cause your container to crash as soon as you start training

Using GPU (mounting data to /app with SELinux relabeling):

podman run --rm --shm-size=64gb --device nvidia.com/gpu=all \
  -v /home/beams/MQICHU/Datasets/xpcs_edge_computing_datasets/eiger4m:/app:z \
  boost_corr \
  -r /app/D0131_US-Cup2_a0010_f005000_r00001/D0131_US-Cup2_a0010_f005000_r00001.h5 \
  -q /app/D0131_qmap_with_blemish.hdf \
  -o /app/cluster_results \
  -v -i 0

Usage

Command-Line Interface

Multi-tau Correlation Example

Using GPU 0, with frame stride of 3 and averaging every 3 frames:

boost_corr -t Multitau -i 0 \
  -r /data/A005_Dragonite_25p_Quiescent_att0_Lq0_001_00001-20000.imm \
  -q /data/qmap/harden201912_qmap_Dragonite_Lq0_S270_D54.h5 \
  -o /output \
  -f 3 -a 3 \
  -v

Two-time Correlation Example

Using CPU with sqmap smoothing, averaging every 3 frames:

boost_corr -t Twotime -i -1 \
  -r /data/A056_Ludox15_att00_L2M_quiescent_001_001.h5 \
  -q /data/qmap/leheny202202_qmap_2M_Test_S360_D60_A009.h5 \
  -o /output \
  -s sqmap \
  -a 3 \
  -d "1-60" \
  -v

Using Configuration File

boost_corr -c config.json

Example config.json:

{
  "raw": "/data/sample_001.h5",
  "qmap": "/data/qmap.h5",
  "output": "/results",
  "type": "Multitau",
  "gpu_id": 0,
  "verbose": true
}

Command-Line Options

usage: boost_corr [-h] -r RAW_FILENAME [-q QMAP_FILENAME] [-o OUTPUT_DIR]
                  [-s SMOOTH] [-i GPU_ID] [-nf {0,1}] [-b BEGIN_FRAME]
                  [-e END_FRAME] [-f STRIDE_FRAME] [-a AVG_FRAME] [-t TYPE]
                  [-d DQ_SELECTION] [-v] [-G] [-n] [-np NUM_PARTIAL_G2]
                  [--crop-ratio-threshold CROP_RATIO_THRESHOLD] [-p PREFIX]
                  [-u SUFFIX] [--bin-time-s BIN_TIME_S]
                  [--run-config-path RUN_CONFIG_PATH] [-w] [-c CONFIG_JSON]

Options:
  -h, --help            Show this help message and exit
  -r, --raw             Raw data file (imm/rigaku/hdf) [REQUIRED]
  -q, --qmap            Q-map file (h5/hdf)
  -o, --output          Output directory [default: cluster_results]
  -s, --smooth          Smoothing method for two-time correlation [default: sqmap]
  -i, --gpu-id          GPU selection: -1=CPU, -2=auto, >=0=specific GPU [default: -1]
  -nf, --normalize-frame  Frame normalization: 0=disable, 1=enable [default: 1]
  -b, --begin-frame     Starting frame index (0-based) [default: 0]
  -e, --end-frame       Ending frame index (-1=all frames) [default: -1]
  -f, --stride-frame    Frame stride for processing [default: 1]
  -a, --avg-frame       Number of frames to average [default: 1]
  -t, --type            Analysis type: Multitau, Twotime, or Both [default: Multitau]
  -d, --dq-selection    DQ selection (e.g., "1,2,5-7" or "all") [default: all]
  -v, --verbose         Enable verbose output
  -G, --save-G2         Save G2, IP, and IF to file
  -n, --dry-run         Show arguments without executing
  -np, --num-partial-g2 Number of partial G2 to compute [default: 0]
  --crop-ratio-threshold Threshold for valid pixel ratio to trigger cropping [default: 0.5]
  -p, --prefix          Prefix for result filename
  -u, --suffix          Suffix for result filename
  --bin-time-s          Time bin size in seconds for Timepix4 data [default: 1e-6]
  --run-config-path     Path to the run configuration file for Timepix4 data
  -w, --overwrite       Overwrite existing result files
  -c, --config          Configuration JSON file path
  --max-memory          Max memory to use in GB [default: 36.0]

Python API

Basic Multi-tau Correlation

import torch
from boost_corr import MultitauCorrelator

# Check version
import boost_corr
print(f"boost-corr version: {boost_corr.__version__}")

# Setup
frame_num = 1024
det_size = (128, 128)
device = 'cuda:0'  # Use 'cpu' for CPU-only

# Create correlator
mc = MultitauCorrelator(frame_num=frame_num, det_size=det_size, device=device)

# Process frames
for n in range(frame_num):
    # Generate or load frame data
    frame = torch.rand(det_size, device=device).reshape(1, -1)
    mc.process(frame)

# Get results
mc.post_process()
result = mc.get_results()

print(f"Correlation shape: {result['g2'].shape}")

Two-time Correlation

from boost_corr import TwotimeCorrelator

# Create two-time correlator
tc = TwotimeCorrelator(frame_num=frame_num, det_size=det_size, device=device)

# Process frames
for n in range(frame_num):
    frame = torch.rand(det_size, device=device).reshape(1, -1)
    tc.process(frame)

# Get results
tc.post_process()
result = tc.get_results()

Using with Real XPCS Data

from boost_corr.xpcs_aps_8idi.gpu_corr_multitau import solve_multitau

result = solve_multitau(
    raw='/data/sample_001.h5',
    qmap='/data/qmap.h5',
    output='/results',
    gpu_id=0,
    begin_frame=0,
    end_frame=-1,
    stride_frame=1,
    avg_frame=1,
    verbose=True
)

Timepix4 Detector Support

boost-corr provides native support for Timepix4 detectors with advanced features:

Basic Timepix4 Usage

boost_corr -t Multitau -i 0 \
  -r /data/sample_001.tpx \
  -q /data/qmap.h5 \
  -o /output \
  -v

Multi-chip Timepix4 Configuration

For multi-chip setups (e.g., .tpx.000, .tpx.001, .tpx.002), provide a run configuration file:

boost_corr -t Multitau -i 0 \
  -r /data/sample_001.tpx.000 \
  -q /data/qmap.h5 \
  -o /output \
  --run-config-path /data/run_config.json \
  -v

The run configuration file specifies chip layout and time binning parameters. See the timepix_dataset package for configuration details.

Key Features

Sparse Data Handling: Efficient processing of photon-counting sparse data
Time Binning: Configurable time binning (default: 1 μs)
Memory Optimization: Automatic GPU/CPU memory management based on data size
bfloat16 Precision: Optimized data type for GPU performance

GPU Scheduling

For automatic GPU selection on multi-GPU systems:

boost_corr -i -2 -r data.h5 -q qmap.h5

This will automatically select an available GPU with sufficient memory.

Performance Tips

Use GPU: GPU acceleration provides 10-100x speedup over CPU
Batch Processing: Use frame averaging (-a) to reduce memory usage
Frame Stride: Use stride (-f) to skip frames for faster processing
Memory: Monitor GPU memory usage for large datasets

Supported Data Formats

HDF5: Standard XPCS HDF5 format (.h5, .hdf, .hdf5)
IMM: APS 8-ID-I IMM format (.imm)
Rigaku: Rigaku detector format (.bin, .bin.000)
Timepix4: Amsterdam Scientific Instruments Timepix4 detector (.tpx, .tpx.000, .tpx.001, .tpx.002)
- Supports single and multi-chip configurations
- Configurable time binning for photon-counting data
- Automatic sparse-to-dense conversion with bfloat16 optimization

Output Files

Results are saved in the specified output directory:

*_multitau.h5: Multi-tau correlation results
*_twotime.h5: Two-time correlation results

Citation

If you use boost-corr in your research, please cite:

@software{boost_corr,
  author = {Chu, Miaoqi},
  title = {boost-corr: High-performance XPCS correlation analysis},
  url = {https://github.com/AdvancedPhotonSource/boost_corr},
  year = {2022}
}

License

This software is distributed under a 3-clause BSD license. See LICENSE for details.

Credits

This package was developed at Argonne National Laboratory for the Advanced Photon Source.

Support

Issues: GitHub Issues
Documentation: Read the Docs (coming soon)
Contact: mqichu@anl.gov

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benchmark		benchmark
docs		docs
examples		examples
src/boost_corr		src/boost_corr
tests		tests
user-guide		user-guide
.dockerignore		.dockerignore
.editorconfig		.editorconfig
.gitignore		.gitignore
Dockerfile		Dockerfile
LICENSE		LICENSE
README.md		README.md
pyproject.toml		pyproject.toml

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boost-corr

Features

Installation

Prerequisites

Step 1: Create Virtual Environment

Step 2: Install boost-corr

From PyPI (Stable)

From Source (Development)

Using Docker or Podman

Build the Image

Run the Container

Usage

Command-Line Interface

Multi-tau Correlation Example

Two-time Correlation Example

Using Configuration File

Command-Line Options

Python API

Basic Multi-tau Correlation

Two-time Correlation

Using with Real XPCS Data

Timepix4 Detector Support

Basic Timepix4 Usage

Multi-chip Timepix4 Configuration

Key Features

GPU Scheduling

Performance Tips

Supported Data Formats

Output Files

Citation

License

Credits

Support

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