midas-zipper 0.1.1__tar.gz

midas_zipper-0.1.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: midas-zipper
+Version: 0.1.1
+Summary: Standalone zarr-zip generation for MIDAS FF/PF workflows (no C-binary or source-tree dependency).
+Author-email: Hemant Sharma <hsharma@anl.gov>
+License: BSD-3-Clause
+Project-URL: Homepage, https://github.com/marinerhemant/MIDAS
+Project-URL: Issues, https://github.com/marinerhemant/MIDAS/issues
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3
+Classifier: Operating System :: OS Independent
+Classifier: Topic :: Scientific/Engineering :: Physics
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+Requires-Dist: numpy>=1.22
+Requires-Dist: h5py>=3.0
+Requires-Dist: zarr<3,>=2.13
+Requires-Dist: numcodecs>=0.11
+Requires-Dist: numba>=0.57
+Requires-Dist: pillow>=9.0
+Provides-Extra: dev
+Requires-Dist: pytest>=7; extra == "dev"
+
+# midas-zipper
+
+Standalone zarr-zip generation for MIDAS FF/PF workflows.
+
+`pip install midas-zipper` works with **no MIDAS source tree and no compiled C
+binaries** — it depends only on `numpy`, `h5py`, `zarr`, `numcodecs`, `numba`,
+and `pillow`, plus the system `zip`/`bzip2` tools.
+
+It packages the zarr ingest that the FF and PF pipelines need to turn raw
+detector data (HDF5/GE/TIFF) into the `*.MIDAS.zip` files the rest of MIDAS
+consumes — previously the source-tree script `utils/ffGenerateZipRefactor.py`,
+which broke `pip`-only installs because it lived outside any package.
+
+## CLI
+
+```bash
+# FF zarr-zip generation (formerly ffGenerateZipRefactor.py)
+midas-ff-zip -resultFolder <dir> -paramFN <params.txt> -LayerNr <n>
+
+# Update a key inside an existing Zarr.zip
+midas-update-zarr -fn <file.MIDAS.zip> -keyToUpdate <key> -updatedValue <...>
+```
+
+Both are also runnable as modules:
+
+```bash
+python -m midas_zipper.ff_zip   -resultFolder ... -paramFN ... -LayerNr ...
+python -m midas_zipper.update_zarr -fn ... -keyToUpdate ... -updatedValue ...
+```
+
+## Python API
+
+```python
+from midas_zipper import generate_ff_zip
+
+generate_ff_zip(
+    result_folder="/path/to/scan",
+    param_file="/path/to/Parameters.txt",
+    layer_nr=1,
+)
+```
+
+## Scope
+
+This package intentionally **excludes** `AutoCalibrateZarr.py`: that tool drives
+the C/OpenMP calibration binaries (`CalibrantPanelShiftsOMP`,
+`CalibrantIntegratorOMP`, `GetHKLList`) and so cannot be pip-portable. It stays
+with the calibration workflow.

midas_zipper-0.1.1/README.md

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+# midas-zipper
+
+Standalone zarr-zip generation for MIDAS FF/PF workflows.
+
+`pip install midas-zipper` works with **no MIDAS source tree and no compiled C
+binaries** — it depends only on `numpy`, `h5py`, `zarr`, `numcodecs`, `numba`,
+and `pillow`, plus the system `zip`/`bzip2` tools.
+
+It packages the zarr ingest that the FF and PF pipelines need to turn raw
+detector data (HDF5/GE/TIFF) into the `*.MIDAS.zip` files the rest of MIDAS
+consumes — previously the source-tree script `utils/ffGenerateZipRefactor.py`,
+which broke `pip`-only installs because it lived outside any package.
+
+## CLI
+
+```bash
+# FF zarr-zip generation (formerly ffGenerateZipRefactor.py)
+midas-ff-zip -resultFolder <dir> -paramFN <params.txt> -LayerNr <n>
+
+# Update a key inside an existing Zarr.zip
+midas-update-zarr -fn <file.MIDAS.zip> -keyToUpdate <key> -updatedValue <...>
+```
+
+Both are also runnable as modules:
+
+```bash
+python -m midas_zipper.ff_zip   -resultFolder ... -paramFN ... -LayerNr ...
+python -m midas_zipper.update_zarr -fn ... -keyToUpdate ... -updatedValue ...
+```
+
+## Python API
+
+```python
+from midas_zipper import generate_ff_zip
+
+generate_ff_zip(
+    result_folder="/path/to/scan",
+    param_file="/path/to/Parameters.txt",
+    layer_nr=1,
+)
+```
+
+## Scope
+
+This package intentionally **excludes** `AutoCalibrateZarr.py`: that tool drives
+the C/OpenMP calibration binaries (`CalibrantPanelShiftsOMP`,
+`CalibrantIntegratorOMP`, `GetHKLList`) and so cannot be pip-portable. It stays
+with the calibration workflow.

midas_zipper-0.1.1/midas_zipper/__init__.py

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+"""midas_zipper — standalone zarr-zip generation for MIDAS workflows.
+
+Pip-installable with no MIDAS source-tree or C-binary dependency. Wraps the
+zarr/HDF5 ingest that the FF and PF pipelines need to turn raw detector data
+into the ``*.MIDAS.zip`` files the rest of MIDAS consumes.
+
+Public API
+----------
+- :func:`generate_ff_zip` — programmatic entry to FF zarr-zip generation
+  (mirrors the ``ffGenerateZipRefactor`` CLI).
+- ``python -m midas_zipper.ff_zip`` / ``midas-ff-zip`` — CLI.
+- ``python -m midas_zipper.update_zarr`` / ``midas-update-zarr`` — CLI.
+"""
+
+from __future__ import annotations
+
+__version__ = "0.1.1"
+
+__all__ = ["generate_ff_zip", "__version__"]
+
+
+def generate_ff_zip(
+    *,
+    result_folder: str,
+    param_file: str,
+    layer_nr: int = 1,
+    data_fn: str = "",
+    dark_fn: str = "",
+    num_frame_chunks: int = -1,
+    preproc_thresh: int = -1,
+    num_files_per_scan: int = 1,
+    extra_args: list[str] | None = None,
+) -> int:
+    """Generate a ``*.MIDAS.zip`` by invoking the ported ff_zip ``main()``.
+
+    Runs in-process by populating ``sys.argv`` then calling
+    :func:`midas_zipper.ff_zip.main`. Returns 0 on success; raises on error.
+    Kept argv-driven so behavior is bit-identical to the legacy
+    ``ffGenerateZipRefactor.py`` CLI the pipelines used to shell out to.
+    """
+    import sys
+    from . import ff_zip
+
+    argv = [
+        "midas-ff-zip",
+        "-resultFolder", str(result_folder),
+        "-paramFN", str(param_file),
+        "-LayerNr", str(layer_nr),
+    ]
+    if data_fn:
+        argv += ["-dataFN", str(data_fn)]
+    if dark_fn:
+        argv += ["-darkFN", str(dark_fn)]
+    if num_frame_chunks and num_frame_chunks > 0:
+        argv += ["-numFrameChunks", str(num_frame_chunks)]
+    if preproc_thresh and preproc_thresh > 0:
+        argv += ["-preProcThresh", str(preproc_thresh)]
+    if num_files_per_scan and num_files_per_scan > 1:
+        argv += ["-numFilesPerScan", str(num_files_per_scan)]
+    if extra_args:
+        argv += [str(a) for a in extra_args]
+
+    saved = sys.argv
+    try:
+        sys.argv = argv
+        ff_zip.main()
+    finally:
+        sys.argv = saved
+    return 0