| --- |
| license: other |
| license_name: sdrbench |
| license_link: https://sdrbench.github.io/ |
| pretty_name: "SDRBench: EXAFEL" |
| tags: |
| - scientific-data |
| - lossy-compression |
| - sdrbench |
| - hpc |
| - sz3 |
| configs: |
| - config_name: files |
| data_files: files.jsonl |
| default: true |
| --- |
| |
| # SDRBench — EXAFEL |
|
|
| X-ray free-electron laser images from the LCLS instrument (SLAC): events x detector panels x rows x columns. |
|
|
| > **Raw binary arrays, not an Arrow/Parquet dataset.** `datasets.load_dataset("sdrbench/exafel")` returns the table of files (`files.jsonl`: path, dtype, shape, sha256). Read the arrays with the `sdrbench` package or `hf_hub_download` + numpy as shown below. |
| |
| This repository is an **unmodified mirror** of the EXAFEL data of [SDRBench](https://sdrbench.github.io/datasets.html), the |
| Scientific Data Reduction Benchmark. The originals are hosted by Argonne National Laboratory on Globus; |
| every archive was unpacked and its files uploaded byte-for-byte (sha256 verified) (revision `484ab4c6a9`). `metadata/` holds |
| the original SDRBench property and template files. Kept in sync automatically by |
| [szcompressor/sdrbench](https://github.com/szcompressor/sdrbench). |
| |
| - **Data provider:** LCLS (SLAC) |
| - **Size:** 10.4 GB in 3 variant(s) |
| - **Format:** raw little-endian binary, C order (slowest dimension first); dtype and shape per field below |
| |
| ## Usage |
| |
| ```bash |
| pip install "sdrbench[sz3]" # sdrbench + pysz (SZ3) |
| ``` |
| |
| ```python |
| import numpy as np |
| import sdrbench |
| from pysz import sz, szConfig, szErrorBoundMode |
| |
| ds = sdrbench.dataset("exafel") # default variant "small" |
| print(ds.fields) |
| x = ds["dark"] # numpy array, dtype <u2, shape (10, 32, 185, 388) |
| |
| # compress with SZ3 (pysz) at a 1e-3 value-range-relative error bound |
| conf = szConfig() |
| conf.errorBoundMode = szErrorBoundMode.REL |
| conf.relErrorBound = 1e-3 |
| compressed, ratio = sz.compress(np.ascontiguousarray(x), conf) |
| y, _ = sz.decompress(compressed, x.dtype.type, x.shape) |
| max_err, psnr, nrmse = sz.verify(np.asarray(x), y) |
| print(f"ratio {ratio:.1f}x, PSNR {psnr:.1f} dB, max error {max_err:.3g}") |
| ``` |
| |
| Files are fetched on first use (in parallel with `ds.download("data/")`) and cached, pinned to the revision |
| of the installed `sdrbench` release; if Hugging Face is unreachable the package falls back to the original |
| archive on Globus. Existing local SDRBench copies can be used with `sdrbench.dataset("exafel", root="/path")`. |
| |
| Without the package, with `huggingface_hub` and numpy only: |
| |
| ```python |
| from huggingface_hub import hf_hub_download |
| import numpy as np |
| p = hf_hub_download("sdrbench/exafel", "10x32x185x388/smd-cxif5315-r129-dark.u16", repo_type="dataset", revision="484ab4c6a935c25c8f5ad09854d71c6c1316912c") |
| x = np.fromfile(p, dtype="<u2").reshape((10, 32, 185, 388)) |
| ``` |
| |
| ## Variants and fields |
| |
| |
| ### `small` (default) |
| |
| `sdrbench.dataset("exafel", "small")` — folder `10x32x185x388/` — 3 files, 137.8 MB, from [SDRBENCH-EXAFEL-10x32x185x388.tar.gz](https://g-d0cd3f.fd635.8443.data.globus.org/raw-data/EXAFEL/SDRBENCH-EXAFEL-10x32x185x388.tar.gz). |
| |
| 10 events of the 32-panel detector as raw counts: raw, dark (background) and calib-fde frames, unsigned 16-bit. |
| |
| | Field | dtype | Shape (C order) | File | |
| |---|---|---|---| |
| | `dark` | `<u2` | 10 x 32 x 185 x 388 | `10x32x185x388/smd-cxif5315-r129-dark.u16` | |
| | `calib-fde` | `<u2` | 10 x 32 x 185 x 388 | `10x32x185x388/smd-cxif5315-r169-calib-fde.u16` | |
| | `raw` | `<u2` | 10 x 32 x 185 x 388 | `10x32x185x388/smd-cxif5315-r169-raw.u16` | |
| |
| ### `large` |
| |
| `sdrbench.dataset("exafel", "large")` — folder `986x32x185x388/` — 1 files, 9.1 GB, from [SDRBENCH-EXAFEL-986x32x185x388.tar.gz](https://g-d0cd3f.fd635.8443.data.globus.org/raw-data/EXAFEL/SDRBENCH-EXAFEL-986x32x185x388.tar.gz). |
| |
| 986 calibrated events of the 32-panel detector, single precision. |
| |
| | Field | dtype | Shape (C order) | File | |
| |---|---|---|---| |
| | `data` | `<f4` | 986 x 32 x 185 x 388 | `986x32x185x388/EXAFEL-LCLS-986x32x185x388.f32` | |
| |
| ### `assembled` |
| |
| `sdrbench.dataset("exafel", "assembled")` — folder `130x1480x1552/` — 4 files, 1.2 GB, from [SDRBENCH-EXAFEL-130x1480x1552.tar.gz](https://g-d0cd3f.fd635.8443.data.globus.org/raw-data/EXAFEL/SDRBENCH-EXAFEL-130x1480x1552.tar.gz). |
| |
| 130 assembled 1480 x 1552 detector images with Bragg peak positions and counts per event. |
| |
| | Field | dtype | Shape (C order) | File | |
| |---|---|---|---| |
| | `data` | `<f4` | 130 x 1480 x 1552 | `130x1480x1552/SDRBENCH-EXAFEL-data-130x1480x1552.f32` | |
| | `nPeaks` | `<i8` | 130 | `130x1480x1552/SDRBENCH-EXAFEL-nPeaks.i64` | |
| | `peakXPosRaw` | `<f8` | 130 x 2048 | `130x1480x1552/SDRBENCH-EXAFEL-peakXPosRaw-130x2048.d64` | |
| | `peakYPosRaw` | `<f8` | 130 x 2048 | `130x1480x1552/SDRBENCH-EXAFEL-peakYPosRaw-130x2048.d64` | |
| |
| ## Citation |
| |
| Please cite SDRBench; `sdrbench cite exafel` prints it: |
| |
| ```bibtex |
| @inproceedings{zhao2020sdrbench, |
| title = {{SDRBench}: Scientific Data Reduction Benchmark for Lossy Compressors}, |
| author = {Zhao, Kai and Di, Sheng and Liang, Xin and Li, Sihuan and Tao, Dingwen and Chen, Zizhong and Cappello, Franck}, |
| booktitle = {2020 IEEE International Conference on Big Data (Big Data)}, |
| pages = {2716--2724}, |
| year = {2020} |
| } |
| ``` |
| |
| ## License and terms |
| |
| The data are distributed by the SDRBench team for research use under the terms of the original |
| data providers listed above (see the [SDRBench website](https://sdrbench.github.io/datasets.html)); please acknowledge them as |
| requested. Rights remain with the data providers. |
| |
