xpcs-correlator 0.1.0__tar.gz

xpcs_correlator-0.1.0/.gitignore

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+# Ignore Python bytecode and cache files
+__pycache__/
+*.py[cod]
+*.pyo
+*.pyd
+
+# Ignore virtual environment directories
+venv/
+env/
+*.egg-info/
+.eggs/
+
+# Ignore Jupyter Notebook checkpoints
+.ipynb_checkpoints/
+
+# Ignore temporary or backup files
+*.swp
+*.swo
+*.bak
+*.tmp
+*.log
+
+# Ignore compiled Cython files
+*.so
+*.c
+*.cpp
+
+# Ignore test coverage and profiling files
+.coverage
+*.prof
+*.profraw
+
+# Ignore build artifacts
+build/
+dist/
+*.egg
+
+# Ignore vscode settings
+.vscode/

xpcs_correlator-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2025 Maciej Jankowski
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

xpcs_correlator-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: xpcs-correlator
+Version: 0.1.0
+Summary: XPCS correlation calculations for synchrotron experiments
+Author-email: Maciej Jankowski <maciej.jankowski@esrf.fr>
+License-Expression: MIT
+Project-URL: Repository, https://gitlab.esrf.fr/mj/xpcs_developments/xpcscorr
+Classifier: Development Status :: 3 - Alpha
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: dask
+Requires-Dist: dask_jobqueue
+Requires-Dist: h5py
+Requires-Dist: hdf5plugin
+Requires-Dist: threadpoolctl
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: memory_profiler; extra == "dev"
+Requires-Dist: line_profiler; extra == "dev"
+Requires-Dist: ruff; extra == "dev"
+Dynamic: license-file
+
+# xpcs-correlator
+
+[![License: MIT](https://img.shields.io/badge/License-MIT-blue.svg)](LICENSE) [![Repository](https://img.shields.io/badge/Repo-GitLab-ff69b4.svg)](https://gitlab.esrf.fr/mj/xpcs_developments/xpcscorr)
+
+## Table of contents
+- About
+- Features
+- Requirements
+- Installation
+- Quickstart
+- Configuration / Logging
+- Tests
+- Contributing
+- License
+- Contact
+
+## About
+This package consolidates ongoing development of correlators for XPCS data analysis at ESRF, with a focus on the ID02 and ID10-coh beamlines.
+
+## Features
+- Dense frames data reference and chunked correlator implementations.
+- Calculates g2, g2 errors, and ttcf (2-time correlation function).
+- The ttcf calculations support linear binning for t1,t2 format and hybrid linear log binning for age,lag format.
+- Designed to handle large frame stacks via chunked (partitioned) processing.
+- Supports Dask for both cluster (SLURM) and local parallel execution
+
+## Requirements
+- Python 3.10+ (recommended: 3.10, 3.11, 3.12)
+- numpy
+- dask
+- dask_jobqueue
+- h5py
+- hdf5plugin
+- threadpoolctl
+
+## Installation
+Install in editable/develop mode (recommended during development):
+
+```bash
+pip install -e .
+```
+
+Install with development extras (for running tests and linters):
+
+```bash
+pip install -e .[dev]
+```
+
+When published to PyPI the package can be installed with:
+
+```bash
+pip install xpcs-correlator
+```
+
+## Quickstart
+Basic usage example — adapt to your data shape and correlator options:
+
+```python
+import numpy as np
+from xpcscorr import correlator_dense_reference, correlator_dense_chunked
+
+# Replace with your frames array; shape here is (n_frames, nx_pixels, ny_pixels)
+frames = np.random.random((100,512, 512))
+roimask= np.ones((512,512), dtype=bool)
+
+# Run reference  correlator
+result_ref = correlator_dense_reference(frames, roimask)
+
+# Run chunked correlator (handles large data in chunks)
+extra_options = {'chunks_N': 3}
+result_chunked = correlator_dense_chunked(frames, roimask, extra_options=extra_options)
+
+print(type(result_ref), type(result_chunked))
+```
+
+Notes:
+- Replace the synthetic `frames` with your real dataset (HDF5 dataset or numpy array).
+- Check correlator function docstrings for exact argument names and options.
+
+## Configuration / Logging
+Control logging with environment variables used by the package (see `src/xpcscorr/__init__.py`):
+
+- `XPCSCORR_LOG_TO_CLI` — set to `1` to enable logging to stdout (default in development)
+- `XPCSCORR_LOG_TO_FILE` — set to `1` to enable logging to a file named `xpcscorr.log`
+
+Example:
+
+```bash
+export XPCSCORR_LOG_TO_CLI=1
+export XPCSCORR_LOG_TO_FILE=0
+```
+
+## Tests
+Run tests with pytest:
+
+```bash
+pip install -e .[dev]
+pytest -q
+```
+
+There are unit tests under `tests/` that exercise correlator behavior and core utilities.
+
+## Contributing
+- Open issues for bugs or feature requests.
+- Fork the repo, create a feature branch, add tests, and submit a pull request.
+- Keep changes small, document API changes, and add tests for new behavior.
+
+## License
+This project is licensed under the MIT License — see the `LICENSE` file for details.
+
+## Contact
+Maintainer: Maciej Jankowski — maciej.jankowski@esrf.fr
+
+
+<!-- EOF -->
+

xpcs_correlator-0.1.0/README.md

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+# xpcs-correlator
+
+[![License: MIT](https://img.shields.io/badge/License-MIT-blue.svg)](LICENSE) [![Repository](https://img.shields.io/badge/Repo-GitLab-ff69b4.svg)](https://gitlab.esrf.fr/mj/xpcs_developments/xpcscorr)
+
+## Table of contents
+- About
+- Features
+- Requirements
+- Installation
+- Quickstart
+- Configuration / Logging
+- Tests
+- Contributing
+- License
+- Contact
+
+## About
+This package consolidates ongoing development of correlators for XPCS data analysis at ESRF, with a focus on the ID02 and ID10-coh beamlines.
+
+## Features
+- Dense frames data reference and chunked correlator implementations.
+- Calculates g2, g2 errors, and ttcf (2-time correlation function).
+- The ttcf calculations support linear binning for t1,t2 format and hybrid linear log binning for age,lag format.
+- Designed to handle large frame stacks via chunked (partitioned) processing.
+- Supports Dask for both cluster (SLURM) and local parallel execution
+
+## Requirements
+- Python 3.10+ (recommended: 3.10, 3.11, 3.12)
+- numpy
+- dask
+- dask_jobqueue
+- h5py
+- hdf5plugin
+- threadpoolctl
+
+## Installation
+Install in editable/develop mode (recommended during development):
+
+```bash
+pip install -e .
+```
+
+Install with development extras (for running tests and linters):
+
+```bash
+pip install -e .[dev]
+```
+
+When published to PyPI the package can be installed with:
+
+```bash
+pip install xpcs-correlator
+```
+
+## Quickstart
+Basic usage example — adapt to your data shape and correlator options:
+
+```python
+import numpy as np
+from xpcscorr import correlator_dense_reference, correlator_dense_chunked
+
+# Replace with your frames array; shape here is (n_frames, nx_pixels, ny_pixels)
+frames = np.random.random((100,512, 512))
+roimask= np.ones((512,512), dtype=bool)
+
+# Run reference  correlator
+result_ref = correlator_dense_reference(frames, roimask)
+
+# Run chunked correlator (handles large data in chunks)
+extra_options = {'chunks_N': 3}
+result_chunked = correlator_dense_chunked(frames, roimask, extra_options=extra_options)
+
+print(type(result_ref), type(result_chunked))
+```
+
+Notes:
+- Replace the synthetic `frames` with your real dataset (HDF5 dataset or numpy array).
+- Check correlator function docstrings for exact argument names and options.
+
+## Configuration / Logging
+Control logging with environment variables used by the package (see `src/xpcscorr/__init__.py`):
+
+- `XPCSCORR_LOG_TO_CLI` — set to `1` to enable logging to stdout (default in development)
+- `XPCSCORR_LOG_TO_FILE` — set to `1` to enable logging to a file named `xpcscorr.log`
+
+Example:
+
+```bash
+export XPCSCORR_LOG_TO_CLI=1
+export XPCSCORR_LOG_TO_FILE=0
+```
+
+## Tests
+Run tests with pytest:
+
+```bash
+pip install -e .[dev]
+pytest -q
+```
+
+There are unit tests under `tests/` that exercise correlator behavior and core utilities.
+
+## Contributing
+- Open issues for bugs or feature requests.
+- Fork the repo, create a feature branch, add tests, and submit a pull request.
+- Keep changes small, document API changes, and add tests for new behavior.
+
+## License
+This project is licensed under the MIT License — see the `LICENSE` file for details.
+
+## Contact
+Maintainer: Maciej Jankowski — maciej.jankowski@esrf.fr
+
+
+<!-- EOF -->
+

xpcs_correlator-0.1.0/pyproject.toml

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+[build-system]
+requires = ["setuptools", "setuptools-scm", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "xpcs-correlator"
+version = "0.1.0"
+authors = [
+    { name = "Maciej Jankowski", email = "maciej.jankowski@esrf.fr" }
+]
+description = "XPCS correlation calculations for synchrotron experiments"
+readme = { file = "README.md", content-type = "text/markdown" }
+requires-python = ">=3.10"
+
+license = "MIT"
+license-files = ["LICENSE"]
+
+urls = { "Repository" = "https://gitlab.esrf.fr/mj/xpcs_developments/xpcscorr" }
+
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering"
+]
+
+dependencies = [
+    "numpy",
+    "dask",
+    "dask_jobqueue",
+    "h5py",
+    "hdf5plugin",
+    "threadpoolctl",
+]
+
+[project.optional-dependencies]
+dev = ["pytest",
+       "memory_profiler",
+       "line_profiler",
+       "ruff"
+       ]
+
+[tool.setuptools]
+packages = ["xpcscorr"]
+package-dir = {"" = "src"}

xpcs_correlator-0.1.0/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

xpcs_correlator-0.1.0/src/xpcs_correlator.egg-info/PKG-INFO

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+Metadata-Version: 2.4
+Name: xpcs-correlator
+Version: 0.1.0
+Summary: XPCS correlation calculations for synchrotron experiments
+Author-email: Maciej Jankowski <maciej.jankowski@esrf.fr>
+License-Expression: MIT
+Project-URL: Repository, https://gitlab.esrf.fr/mj/xpcs_developments/xpcscorr
+Classifier: Development Status :: 3 - Alpha
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: dask
+Requires-Dist: dask_jobqueue
+Requires-Dist: h5py
+Requires-Dist: hdf5plugin
+Requires-Dist: threadpoolctl
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: memory_profiler; extra == "dev"
+Requires-Dist: line_profiler; extra == "dev"
+Requires-Dist: ruff; extra == "dev"
+Dynamic: license-file
+
+# xpcs-correlator
+
+[![License: MIT](https://img.shields.io/badge/License-MIT-blue.svg)](LICENSE) [![Repository](https://img.shields.io/badge/Repo-GitLab-ff69b4.svg)](https://gitlab.esrf.fr/mj/xpcs_developments/xpcscorr)
+
+## Table of contents
+- About
+- Features
+- Requirements
+- Installation
+- Quickstart
+- Configuration / Logging
+- Tests
+- Contributing
+- License
+- Contact
+
+## About
+This package consolidates ongoing development of correlators for XPCS data analysis at ESRF, with a focus on the ID02 and ID10-coh beamlines.
+
+## Features
+- Dense frames data reference and chunked correlator implementations.
+- Calculates g2, g2 errors, and ttcf (2-time correlation function).
+- The ttcf calculations support linear binning for t1,t2 format and hybrid linear log binning for age,lag format.
+- Designed to handle large frame stacks via chunked (partitioned) processing.
+- Supports Dask for both cluster (SLURM) and local parallel execution
+
+## Requirements
+- Python 3.10+ (recommended: 3.10, 3.11, 3.12)
+- numpy
+- dask
+- dask_jobqueue
+- h5py
+- hdf5plugin
+- threadpoolctl
+
+## Installation
+Install in editable/develop mode (recommended during development):
+
+```bash
+pip install -e .
+```
+
+Install with development extras (for running tests and linters):
+
+```bash
+pip install -e .[dev]
+```
+
+When published to PyPI the package can be installed with:
+
+```bash
+pip install xpcs-correlator
+```
+
+## Quickstart
+Basic usage example — adapt to your data shape and correlator options:
+
+```python
+import numpy as np
+from xpcscorr import correlator_dense_reference, correlator_dense_chunked
+
+# Replace with your frames array; shape here is (n_frames, nx_pixels, ny_pixels)
+frames = np.random.random((100,512, 512))
+roimask= np.ones((512,512), dtype=bool)
+
+# Run reference  correlator
+result_ref = correlator_dense_reference(frames, roimask)
+
+# Run chunked correlator (handles large data in chunks)
+extra_options = {'chunks_N': 3}
+result_chunked = correlator_dense_chunked(frames, roimask, extra_options=extra_options)
+
+print(type(result_ref), type(result_chunked))
+```
+
+Notes:
+- Replace the synthetic `frames` with your real dataset (HDF5 dataset or numpy array).
+- Check correlator function docstrings for exact argument names and options.
+
+## Configuration / Logging
+Control logging with environment variables used by the package (see `src/xpcscorr/__init__.py`):
+
+- `XPCSCORR_LOG_TO_CLI` — set to `1` to enable logging to stdout (default in development)
+- `XPCSCORR_LOG_TO_FILE` — set to `1` to enable logging to a file named `xpcscorr.log`
+
+Example:
+
+```bash
+export XPCSCORR_LOG_TO_CLI=1
+export XPCSCORR_LOG_TO_FILE=0
+```
+
+## Tests
+Run tests with pytest:
+
+```bash
+pip install -e .[dev]
+pytest -q
+```
+
+There are unit tests under `tests/` that exercise correlator behavior and core utilities.
+
+## Contributing
+- Open issues for bugs or feature requests.
+- Fork the repo, create a feature branch, add tests, and submit a pull request.
+- Keep changes small, document API changes, and add tests for new behavior.
+
+## License
+This project is licensed under the MIT License — see the `LICENSE` file for details.
+
+## Contact
+Maintainer: Maciej Jankowski — maciej.jankowski@esrf.fr
+
+
+<!-- EOF -->
+

xpcs_correlator-0.1.0/src/xpcs_correlator.egg-info/SOURCES.txt

@@ -0,0 +1,29 @@
+.gitignore
+LICENSE
+README.md
+pyproject.toml
+src/xpcs_correlator.egg-info/PKG-INFO
+src/xpcs_correlator.egg-info/SOURCES.txt
+src/xpcs_correlator.egg-info/dependency_links.txt
+src/xpcs_correlator.egg-info/requires.txt
+src/xpcs_correlator.egg-info/top_level.txt
+src/xpcscorr/__init__.py
+src/xpcscorr/benchmark/chunking/__init__.py
+src/xpcscorr/benchmark/chunking/chunking.py
+src/xpcscorr/benchmark/chunking/utils.py
+src/xpcscorr/benchmark/utils/mkl.py
+src/xpcscorr/core/__init__.py
+src/xpcscorr/core/base.py
+src/xpcscorr/core/utils.py
+src/xpcscorr/correlators/dense/__init__.py
+src/xpcscorr/correlators/dense/base.py
+src/xpcscorr/correlators/dense/chunked.py
+src/xpcscorr/correlators/dense/reference.py
+src/xpcscorr/correlators/sparse/__init__.py
+tests/conftest.py
+tests/test_core_utils.py
+tests/test_correlator_dens_chunk.py
+tests/test_correlator_dens_ref.py
+tests/old/test_chunking.py
+tests/old/test_mkl.py
+tests/old/test_reference.py

xpcs_correlator-0.1.0/src/xpcs_correlator.egg-info/dependency_links.txt

@@ -0,0 +1 @@
+

xpcs_correlator-0.1.0/src/xpcs_correlator.egg-info/requires.txt

@@ -0,0 +1,12 @@
+numpy
+dask
+dask_jobqueue
+h5py
+hdf5plugin
+threadpoolctl
+
+[dev]
+pytest
+memory_profiler
+line_profiler
+ruff

xpcs_correlator-0.1.0/src/xpcs_correlator.egg-info/top_level.txt

@@ -0,0 +1 @@
+xpcscorr

xpcs_correlator-0.1.0/src/xpcscorr/__init__.py

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+import logging
+import sys, os
+
+# Configure logging based on environment variables
+os.environ["XPCSCORR_LOG_TO_CLI"] = "1"
+
+logger = logging.getLogger("xpcscorr")
+logger.propagate = False           # <--- Set propagate to False immediately after getting the logger
+logger.setLevel(logging.INFO)
+
+if logger.hasHandlers():
+    logger.handlers.clear()
+
+if os.environ.get("XPCSCORR_LOG_TO_FILE", "0") == "1":
+    file_handler = logging.FileHandler("xpcscorr.log")
+    file_formatter = logging.Formatter('%(asctime)s %(levelname)s: %(message)s')
+    file_handler.setFormatter(file_formatter)
+    logger.addHandler(file_handler)
+
+if os.environ.get("XPCSCORR_LOG_TO_CLI", "0") == "1":
+    stream_handler = logging.StreamHandler(sys.stdout)
+    stream_formatter = logging.Formatter('%(asctime)s %(levelname)s: %(message)s')
+    stream_handler.setFormatter(stream_formatter)
+    logger.addHandler(stream_handler)
+
+# Easy access to main correlator functions
+from .correlators.dense.base import _create_correlator_function
+from .correlators.dense.reference import CorrelatorDenseReference
+from .correlators.dense.chunked import CorrelatorDenseChunked
+
+correlator_dense_reference = _create_correlator_function(CorrelatorDenseReference)
+correlator_dense_chunked = _create_correlator_function(CorrelatorDenseChunked)