cdi-stools 0.2.0__tar.gz → 0.2.2__tar.gz

cdi_stools-0.2.2/CHANGELOG.md

@@ -0,0 +1,122 @@
+# Changelog
+
+All notable changes to CDI-ST are documented here.
+The format follows [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
+and the project adheres to [Semantic Versioning](https://semver.org/).
+
+## [Unreleased]
+
+## [0.2.2] — 2026-06-18
+
+### Fixed
+- **ID01 SPEC+EDF conversion now tolerates missing edge frames.**
+  Acquisitions are sometimes started a frame late or stopped a frame
+  early, so a SPEC scan can list frames 262–662 (401 points) while the
+  EDF directory only has 263–661 (399 files). The converter now probes
+  the disk first, loads only the EDF files that actually exist, and
+  trims the per-frame motor arrays (`eta`, `phi`, `nu`, `delta`,
+  `mpx4inr`) to stay in lock-step with the loaded data. A clear note
+  identifies which leading / trailing / interior frames were skipped.
+  New helper `_filter_existing_edf_frames()` exposes this filtering for
+  programmatic use.
+
+## [0.2.1] — 2026-06-15
+
+### Added
+- **PETRA III P10 / DESY Eiger compressed-data support.** Auto-imports
+  `hdf5plugin` at module load so bitshuffle + LZ4 compressed datasets
+  (the Eiger default at DESY P10 and many other beamlines) read
+  transparently. `hdf5plugin>=4.0` is now a runtime dependency.
+- **HDF5 external-link resolution.** The P10 loader now enumerates and
+  resolves external links in master files instead of relying on h5py's
+  default link-following, which was unreliable on Windows. Each chunk is
+  opened directly to bypass any path-mangling. Master files with hundreds
+  of external links to chunk files (the standard Eiger layout) work out
+  of the box.
+- **Scan range selection for P10** (new in the P10 converter dialog) —
+  similar to the ID01 SPEC+EDF scan browser. Avoids loading 49 GB of
+  detector frames into RAM when you only need the rocking-curve maximum:
+  - **Probe scan** button reads chunk metadata only (no decompression),
+    instantly reporting total frame count, detector shape, and estimated
+    full-load memory footprint.
+  - **Frame range** (`from`, `to`) reads only the requested global frame
+    range across all chunks. Loaded chunk-by-chunk so memory scales with
+    the chosen range, not the total dataset size.
+  - **Detector ROI** reads a centered square ROI from each frame instead
+    of the full detector. For BCDI you typically only need ~256×256
+    around the Bragg peak — cuts memory by `(2167*2070)/(roi²)` for
+    Eiger 4M data.
+  - **Memory budget** (default 8 GB) — the loader refuses reads that
+    would exceed this and tells you which `frame_range` would fit,
+    instead of crashing the Python process with an OOM error.
+- **Programmatic API additions** to `nn_experimental_loader`:
+  `p10_scan_info()` for cheap metadata previews, plus new
+  `frame_range`, `detector_roi`, `memory_budget_gb` parameters on
+  `load_p10_from_external_links()` and `p10_h5_to_npz()`.
+
+### Fixed
+- Cryptic "Can't synchronously read data (can't open directory)" error
+  on P10 / Eiger files. The message was HDF5 looking for the compression
+  plugin DLL in a non-existent directory — now caught and converted to
+  a clear "install hdf5plugin" instruction.
+- AutoPhase_NN tab missing `_on_epoch` slot (introduced in 0.2.0 during
+  the live-curve refactor; AutoPhase_NN's `epoch_done` signal had no
+  receiver and emitted unhandled errors). Restored.
+- CDI_NN `KeyError: 'phase_true'` — `BCDIDataset.__getitem__` now exposes
+  the GUI's expected keys (`phase_true`, `amplitude`) alongside the legacy
+  ones (`target_phase`, `input`).
+- `BCDIPhaseLoss` accepts both the GUI's descriptive kwargs (`alpha_amp`,
+  `beta_phase`, `gamma_diff`, `diff_amp`) and the original short ones
+  (`alpha`, `beta`, `gamma`, `amplitude`). Either spelling now works.
+- Training Stop button no longer crashes the program. `QThread.terminate()`
+  was killing PyTorch mid-`backward()` and corrupting CUDA / autograd
+  state — replaced with a cooperative `request_stop()` flag that the
+  training loop checks at batch / epoch boundaries, then exits cleanly
+  with a saved checkpoint.
+
+### Changed
+- Live training curve in AutoPhase_NN and CDI_NN — the dashed "running"
+  line updates every ~2 s during training so users can see progress
+  immediately on slow CPU runs (rather than staring at a blank plot
+  for an entire epoch).
+- `inspect_h5()` now properly shows external links with their target
+  files and `[OK]` / `[MISSING]` markers. The empty-looking `/entry/data/`
+  group on Eiger masters is no longer misleading.
+
+## [0.1.0] — Alpha — 2026-05-08
+
+### Added
+- **Initial public release** of CDI-ST as a packaged Python application.
+- BCDI Simulation module (Material → Beam → Results)
+  - Material presets: Si, Ge, Pt, Au, SiC, GaAs, and more
+  - CIF import for arbitrary crystals
+  - Particle shapes: cube, sphere, cylinder, hexagonal prism, octahedron, dodecahedron
+  - Strain fields: radial gradient, edge dislocation, random
+  - Configurable line dislocations: edge / screw / mixed with arbitrary Burgers vector
+  - 3D atomic lattice viewer (Plotly)
+  - Detector presets: Maxipix 2×2, Eiger 2M, custom rectangular
+  - Analytical and FFT simulation paths
+- BCDI Data Analysis module (Generate Data → AutoPhase_NN → CDI_NN → Reconstruction → 3D Viewer)
+  - Training-data generator with random material/shape/size/strain/dislocation
+  - Toggles for randomized strain and dislocations
+  - AutoPhaseNet3D (unsupervised, dual-decoder, physics-driven loss)
+  - PhaseUNet3D (supervised, BCDI loss with α/β/γ weights)
+  - Inference: NN-only, refined (HIO+RAAR+ER), ensemble, compare
+  - Iterative phase retrieval: HIO (β=0.9), RAAR (β=0.9), ER, with shrink-wrap
+  - Experimental data loader: HDF5, ID01 SPEC+EDF, q-space orthogonalization
+  - Detector chip-gap masking, hot pixel removal, beamstop streak removal
+  - 3D viewer with point cloud / isosurface / surface-only modes
+  - Per-voxel opacity weighted by intensity
+  - VTI export for ParaView
+- Splash screen and theme-matched launcher
+- In-app Reports & Suggestions feature
+- Cross-platform support (Linux, macOS, Windows) via PyQt6
+- MIT license, full source on GitHub
+
+### Known limitations (alpha)
+- Q-space orthogonalization is ID01-specific (can be extended)
+- Some checkpoints from earlier prototypes lack `grid_size` metadata
+- Mask-aware modulus constraint not yet implemented (gaps are filled instead)
+
+[Unreleased]: https://github.com/SAIDIsoufiane/CDI-St/compare/v0.1.0...HEAD
+[0.1.0]: https://github.com/SAIDIsoufiane/CDI-St/releases/tag/v0.1.0

{cdi_stools-0.2.0 → cdi_stools-0.2.2}/PKG-INFO

@@ -1,12 +1,12 @@
 Metadata-Version: 2.4
 Name: cdi-stools
-Version: 0.2.0
+Version: 0.2.2
 Summary: Coherent Diffraction Imaging Simulation Tools — BCDI simulation and NN-based phase retrieval
-Project-URL: Homepage, https://github.com/Refze/CDI-St
-Project-URL: Documentation, https://github.com/Refze/CDI-St#readme
-Project-URL: Repository, https://github.com/Refze/CDI-St
-Project-URL: Issues, https://github.com/Refze/CDI-St/issues
-Project-URL: Changelog, https://github.com/Refze/CDI-St/blob/main/CHANGELOG.md
+Project-URL: Homepage, https://github.com/SAIDIsoufiane/CDI-St
+Project-URL: Documentation, https://github.com/SAIDIsoufiane/CDI-St#readme
+Project-URL: Repository, https://github.com/SAIDIsoufiane/CDI-St
+Project-URL: Issues, https://github.com/SAIDIsoufiane/CDI-St/issues
+Project-URL: Changelog, https://github.com/SAIDIsoufiane/CDI-St/blob/main/CHANGELOG.md
 Author-email: Soufiane SAIDI <saidisoufiane@hotmail.com>
 License-Expression: MIT
 License-File: LICENSE
@@ -21,13 +21,12 @@ Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
-Classifier: Programming Language :: Python :: 3.13
-Classifier: Programming Language :: Python :: 3.14
 Classifier: Topic :: Scientific/Engineering :: Image Processing
 Classifier: Topic :: Scientific/Engineering :: Physics
 Requires-Python: >=3.9
 Requires-Dist: diffpy-structure>=3.1
 Requires-Dist: h5py>=3.7
+Requires-Dist: hdf5plugin>=4.0
 Requires-Dist: matplotlib>=3.6
 Requires-Dist: numpy>=1.22
 Requires-Dist: pandas>=1.5