PyPI - cdi-stools - Versions diffs - 0.2.1__tar.gz → 0.2.2__tar.gz - Mend

cdi-stools 0.2.1tar.gz → 0.2.2tar.gz

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{cdi_stools-0.2.1 → cdi_stools-0.2.2}/CHANGELOG.md RENAMED Viewed

@@ -1,9 +1,25 @@
 # 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
@@ -67,42 +83,6 @@ All notable changes to CDI-ST are documented here.
   files and `[OK]` / `[MISSING]` markers. The empty-looking `/entry/data/`
   group on Eiger masters is no longer misleading.
-## [0.1.3] — 2026-05-20
-### Fixed
-- Fixed exporting VTI to Paraview
-### Added
-- SPEC+EDF converter: Added option to convert multiple scans
-## [0.1.2] — 2026-05-20
-### Fixed
-- SPEC+EDF converter: scan listing, frame range display, clear errors when EDFs fail to load
-- silx data column indexing
-- `find_bragg_peak_box` slice/int crash on empty volumes
-### Added
-- "Browse scans…" button in SPEC+EDF dialog
-## [0.1.1] — 2026-05-20
-### Fixed
-- SPEC+EDF converter crash with "slice - int" error when EDF files could not be loaded (`find_bragg_peak_box` now returns coordinates instead of slices in the zero-volume fallback)
-- silx data column indexing was wrong — modern silx returns `data.shape == (nlines, ncolumns)`, so `data[i]` was the i-th measurement row, not the i-th column. Now uses `scan.data_column_by_name(label)` with shape-aware fallback
-- Clear error message when no EDF frames can be loaded (lists likely causes instead of crashing later)
-- SPEC+EDF converter now prints the frame range of the chosen scan before loading
-### Added
-- New "Browse scans…" button in SPEC+EDF dialog: lists every scan in the SPEC file with its CCD frame range, so users can pick the scan matching their downloaded EDF files
-- New `list_spec_scans()` helper in `nn_experimental_loader.py`
-### Changed
-- Renamed output field "Output .npz:" to "Output file (.npz):" with clarifying placeholder and tooltip
 ## [0.1.0] — Alpha — 2026-05-08
 ### Added

{cdi_stools-0.2.1 → cdi_stools-0.2.2}/PKG-INFO RENAMED Viewed

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cdi-stools
-Version: 0.2.1
+Version: 0.2.2
 Summary: Coherent Diffraction Imaging Simulation Tools — BCDI simulation and NN-based phase retrieval
 Project-URL: Homepage, https://github.com/SAIDIsoufiane/CDI-St
 Project-URL: Documentation, https://github.com/SAIDIsoufiane/CDI-St#readme

{cdi_stools-0.2.1 → cdi_stools-0.2.2}/README.md RENAMED Viewed

@@ -1,279 +1,279 @@
-<div align="center">
-<img src="docs/screenshots/CDI_ST_logo.png" alt="CDI-ST" width="600"/>
-# CDI-ST
-**Coherent Diffraction Imaging — Simulation Tools**
-An end-to-end Bragg Coherent Diffraction Imaging (BCDI) Python application using low computational resources with an easy to learn GUI:
-crystal lattice construction, X-ray scattering simulation, neural-network phase retrieval,
-and 3D visualization, in a single GUI.
-[![PyPI version](https://img.shields.io/pypi/v/cdi-stools.svg)](https://pypi.org/project/cdi-stools/)
-[![Python](https://img.shields.io/pypi/pyversions/cdi-stools.svg)](https://pypi.org/project/cdi-stools/)
-[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
-[![Status](https://img.shields.io/badge/status-alpha-orange.svg)]()
-</div>
-## Screenshots
-<table>
-  <tr>
-    <td><img src="docs/screenshots/launcher.png" width="280"/></td>
-    <td><img src="docs/screenshots/material_tab.png" width="280"/></td>
-	<td><img src="docs/screenshots/results.png" width="280"/></td>
-  </tr>
-  <tr>
-    <td align="center"><sub>Launcher</sub></td>
-    <td align="center"><sub>Material — crystal builder</sub></td>
-	<td align="center"><sub>Results — simulated Bragg peak</sub></td>
-  </tr>
-  <tr>
-	<td><img src="docs/screenshots/3d_viewer.png" width="280"/></td>
-    <td><img src="docs/screenshots/strain.png" width="280"/></td>
-    <td><img src="docs/screenshots/reconstruction.png" width="280"/></td>
-  </tr>
-  <tr>
-	<td align="center"><sub>3D Viewer — diffraction simulation</sub></td>
-    <td align="center"><sub>2D reconstruction</sub></td>
-    <td align="center"><sub>3D Viewer — reconstruction</sub></td>
-  </tr>
-</table>
----
-## Installation
-```bash
-pip install cdi-stools
-```
-After installation, launch the GUI from any terminal:
-```bash
-cdi-st or cdi-stools
-```
-**Support for other beamlines files is coming in future updates...**
-> **Note**: `cdi-st` ships a Qt-based GUI. On Linux, you may need system Qt
-> dependencies (`sudo apt install libxcb-cursor0 libxkbcommon-x11-0` on Ubuntu/Debian).
-> On Windows and macOS the wheel includes everything.
----
-## What is BCDI?
-Bragg Coherent Diffraction Imaging is a synchrotron technique that reconstructs the
-3D shape and atomic-displacement field of nanocrystals by inverting the diffraction
-intensity around a Bragg peak. The intensity gives only |F(q)|², so reconstruction
-must recover the missing phase by iterative algorithms (HIO, RAAR, ER),
-more recently by neural networks.
-**CDI-ST integrates the entire workflow into one tool:**
-| Step | What you do | Where in the GUI |
-|---|---|---|
-| 1. Build a crystal | Define material, shape, orientation, optional defects | **BCDI Simulation → Material** |
-| 2. Set the X-ray geometry | Beam energy, detector geometry, oversampling | **BCDI Simulation → Beam** |
-| 3. Simulate diffraction | Compute the 3D Bragg peak | **BCDI Simulation → Results** |
-| 4. Generate training data | Build a labeled dataset of (object, diffraction) pairs | **BCDI Data Analysis → Generate Data** |
-| 5. Train an unsupervised NN | AutoPhase_NN: physics-driven, no ground truth | **BCDI Data Analysis → AutoPhase_NN** |
-| 6. Train a supervised NN | CDI_NN: PhaseUNet3D learning the phase mapping | **BCDI Data Analysis → CDI_NN** |
-| 7. Reconstruct | NN → optionally refine with HIO/RAAR/ER | **BCDI Data Analysis → Reconstruction** |
-| 8. Visualize and export | Interactive 3D viewer, ParaView VTI export | **BCDI Data Analysis → 3D Viewer** |
----
-## The simulation pipeline
-### 1. Material — build the crystal
-Choose from preset materials (Si, Ge, Pt, Au, SiC, GaAs, ...) or import a custom
-CIF file. The crystal is built atom-by-atom from the unit cell, replicated to the
-requested supercell size.
-You can:
-- Select the **particle shape**: cube, sphere, cylinder, hexagonal prism, octahedron, dodecahedron
-- Set the **target oversampling ratio** (controls how much of the diffraction
-  volume the object occupies)
-- Add **strain fields**: radial gradient, edge dislocation, random
-- Add **dislocations**: edge / screw / mixed, at a configurable position with
-  an arbitrary Burgers vector
-The 3D lattice view (powered by Plotly) shows every atom in the supercell.
-### 2. Beam — define the X-ray geometry
-Select a reflection (h k l) from the auto-computed list of allowed peaks.
-The Beam tab also lets you set:
-- **Beam energy** (and the resulting wavelength)
-- **Detector geometry**: pixel pitch, sample-to-detector distance, detector size
-- **Beam size** in microns
-- **Detector preset**: Maxipix (516×516), Eiger 2M...etc, custom rectangular
-Detector preset auto-fills the geometry parameters.
-### 3. Results — run the simulation
-CDI-ST computes the diffraction in **two paths**:
-- **Analytical path** (cube/rectangular shapes, no strain): closed-form Fourier transform of the support
-- **FFT path** (any shape, any strain field): full 3D FFT of the complex object
-Output: 3D diffraction volume `|F(q)|²`, displayed as 2D slices (qx-qy, qx-qz)
-and in an interactive 3D Plotly viewer with iso-surface controls.
-You can export the simulation as a `.npz` file ready for the data-analysis side,
-or for use as ground truth when training NNs.
----
-## The data-analysis pipeline
-### 4. Generate Data — create training samples
-Generates a dataset of synthetic BCDI samples for NN training. Each sample
-contains the ground-truth phase, support, and the simulated diffraction
-intensity. You control:
-- **Number of samples** (typically 2,000–10,000)
-- **Grid size** (64³ recommended for training, 128³ for production inference)
-- **Materials** (random or fixed)
-- **Particle size variation** (random supercell multiplier)
-- **Random dislocations** adds occasional edge/screw/mixed dislocations
-- **Random strain** adds occasional radial/edge/random strain fields
-Samples save as `sample_XXXXX.npz` and a `manifest.json`. Generation is
-parallelizable and resumable.
-### 5. AutoPhase_NN — unsupervised physics-driven NN
-AutoPhase_NN is a 3D dual-decoder convolutional network that learns to invert the
-Fourier modulus constraint **without ground truth**. It predicts the object's
-amplitude and phase such that `|FFT(amp · exp(iφ))|` matches the measured
-magnitude. The loss is a normalized-magnitude error plus optional regularizers
-on phase smoothness and support compactness. This is the network from (Yao, Yudong,
-et al. npj Computational Materials 8.1 (2022) ) reimplemented for this codebase.
-Training is GPU-accelerated (CUDA preferred) and converges in a few dozen
-epochs on 2,000+ samples. The best checkpoint is saved automatically.
-### 6. CDI_NN — supervised PhaseUNet3D
-A 3D U-Net that predicts the phase field from the diffraction magnitude, trained
-against the ground-truth phase from the data generator.
-Use AutoPhase_NN when you don't trust your simulator's ground truth (or have
-none). Use CDI_NN when you have a high-fidelity simulator and want a direct
-mapping. Use both via the **ensemble** mode in the Reconstruction tab.
-### 7. Reconstruction — invert experimental or simulated data
-Load any `.npz` (simulated) or `.h5` (experimental) BCDI file, or convert a
-SPEC + EDF scan from ID01 directly via the dialog. Choose:
-- **NN-only (Autophase_NN)**: forward pass, twin-image suppression, COM centering
-- **Refined**: NN seed → HIO + RAAR + ER iterative phase retrieval
-- **Ensemble**: AutoPhase_NN + CDI_NN combined, optionally refined
-- **Compare**: runs both modes side-by-side
-The output is a complex object (amplitude + phase), a binary support, the
-R-factor convergence curve, and 2D slices at the COM of the reconstruction.
-For experimental data, the loader handles:
-- Detector chip-gap masking (Maxipix, Eiger)
-- Hot-pixel removal
-- Beamstop / direct-beam streak removal
-- Bragg-peak-centered cropping
-- Optional q-space orthogonalization via xrayutilities (with `[id01]` extra)
-### 8. 3D Viewer — interactive visualization
-The viewer renders the reconstruction in three modes:
-- **Point cloud**: every voxel above threshold, colored by amplitude / phase / strain,
-  with per-voxel opacity weighted by intensity
-- **Isosurface**: smoothed iso-shell with internal data points showing through
-- **Surface only**: bare iso-mesh with edges visible
-Controls:
-- Threshold (% of peak amplitude), voxel size, opacity, colormap
-- Color scale auto / manual (`vmin` / `vmax`)
-- Clip plane on any axis
-- Mouse: left-drag rotate, right-drag pan, wheel zoom, double-click reset
-- Export PNG snapshot or VTI (ParaView)
----
-## Project structure
-```
-cdi-st/
-├── src/cdi_st/
-│   ├── __init__.py
-│   ├── __main__.py              # python -m cdi_st
-│   ├── bcdi_gui.py              # main entry point + launcher + splash
-│   ├── bcdi_core.py             # crystal builder, simulator, reflection calculator
-│   ├── nn_gui_tabs.py           # all NN-related GUI tabs
-│   ├── nn_data_generator.py     # training-data generator
-│   ├── nn_dataset.py            # PyTorch Dataset wrapper
-│   ├── nn_phase_model.py        # PhaseUNet3D (supervised)
-│   ├── nn_autophase_model.py    # AutoPhaseNet3D (unsupervised)
-│   ├── nn_train.py              # supervised training CLI
-│   ├── nn_autophase_train.py    # unsupervised training CLI
-│   ├── nn_phase_retrieval.py    # HIO / RAAR / ER iterative algorithms
-│   ├── nn_autophase_infer.py    # inference: nn_only / refined / ensemble
-│   ├── nn_experimental_loader.py # h5/spec/edf loading + preprocessing
-│   ├── nn_demo.py
-│   ├── nn_visualize.py
-│   └── CDI_ST_logo.png
-├── tests/
-├── docs/
-├── pyproject.toml
-├── README.md
-├── LICENSE
-└── CHANGELOG.md
-```
----
-## Citing
-If you use CDI-ST in published research, please cite:
-```bibtex
-@software{saidi_cdi_st_2026,
-  author       = {Saidi, Soufiane},
-  title        = {CDI-ST: Coherent Diffraction Imaging — Simulation Tools},
-  year         = {2026},
-  publisher    = {GitHub},
-  url          = {https://github.com/Refze/CDI-St}
-}
-```
----
-## License
-MIT — see [LICENSE](LICENSE).
-## Author
-**Soufiane SAIDI** — saidisoufiane@hotmail.com
-We heavily encourage you to use the in-app **Reports & Suggestions** button to send any type of feedback.
----
-## Acknowledgments
-Built on the shoulders of the BCDI and python community:
-[PyNX](https://pynx.esrf.fr/), [BCDI-Utilities](https://github.com/carnisj/bcdi),
-[cdiutils](https://github.com/clatlan/cdiutils), [Atomsk](https://atomsk.univ-lille.fr/) , [xrayutilities](https://xrayutilities.sourceforge.io/),
-[scikit-image](https://scikit-image.org/), [PyQt6](https://www.riverbankcomputing.com/software/pyqt/),
-and the AutoPhaseNN paper by Yao et al. (2022).
+<div align="center">
+<img src="docs/screenshots/CDI_ST_logo.png" alt="CDI-ST" width="600"/>
+# CDI-ST
+**Coherent Diffraction Imaging — Simulation Tools**
+An end-to-end Bragg Coherent Diffraction Imaging (BCDI) Python application using low computational resources with an easy to learn GUI:
+crystal lattice construction, X-ray scattering simulation, neural-network phase retrieval,
+and 3D visualization, in a single GUI.
+[![PyPI version](https://img.shields.io/pypi/v/cdi-stools.svg)](https://pypi.org/project/cdi-stools/)
+[![Python](https://img.shields.io/pypi/pyversions/cdi-stools.svg)](https://pypi.org/project/cdi-stools/)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+[![Status](https://img.shields.io/badge/status-alpha-orange.svg)]()
+</div>
+## Screenshots
+<table>
+  <tr>
+    <td><img src="docs/screenshots/launcher.png" width="280"/></td>
+    <td><img src="docs/screenshots/material_tab.png" width="280"/></td>
+	<td><img src="docs/screenshots/results.png" width="280"/></td>
+  </tr>
+  <tr>
+    <td align="center"><sub>Launcher</sub></td>
+    <td align="center"><sub>Material — crystal builder</sub></td>
+	<td align="center"><sub>Results — simulated Bragg peak</sub></td>
+  </tr>
+  <tr>
+	<td><img src="docs/screenshots/3d_viewer.png" width="280"/></td>
+    <td><img src="docs/screenshots/strain.png" width="280"/></td>
+    <td><img src="docs/screenshots/reconstruction.png" width="280"/></td>
+  </tr>
+  <tr>
+	<td align="center"><sub>3D Viewer — diffraction simulation</sub></td>
+    <td align="center"><sub>2D reconstruction</sub></td>
+    <td align="center"><sub>3D Viewer — reconstruction</sub></td>
+  </tr>
+</table>
+---
+## Installation
+```bash
+pip install cdi-stools
+```
+After installation, launch the GUI from any terminal:
+```bash
+cdi-st or cdi-stools
+```
+**Support for other beamlines files is coming in future updates...**
+> **Note**: `cdi-st` ships a Qt-based GUI. On Linux, you may need system Qt
+> dependencies (`sudo apt install libxcb-cursor0 libxkbcommon-x11-0` on Ubuntu/Debian).
+> On Windows and macOS the wheel includes everything.
+---
+## What is BCDI?
+Bragg Coherent Diffraction Imaging is a synchrotron technique that reconstructs the
+3D shape and atomic-displacement field of nanocrystals by inverting the diffraction
+intensity around a Bragg peak. The intensity gives only |F(q)|², so reconstruction
+must recover the missing phase by iterative algorithms (HIO, RAAR, ER),
+more recently by neural networks.
+**CDI-ST integrates the entire workflow into one tool:**
+| Step | What you do | Where in the GUI |
+|---|---|---|
+| 1. Build a crystal | Define material, shape, orientation, optional defects | **BCDI Simulation → Material** |
+| 2. Set the X-ray geometry | Beam energy, detector geometry, oversampling | **BCDI Simulation → Beam** |
+| 3. Simulate diffraction | Compute the 3D Bragg peak | **BCDI Simulation → Results** |
+| 4. Generate training data | Build a labeled dataset of (object, diffraction) pairs | **BCDI Data Analysis → Generate Data** |
+| 5. Train an unsupervised NN | AutoPhase_NN: physics-driven, no ground truth | **BCDI Data Analysis → AutoPhase_NN** |
+| 6. Train a supervised NN | CDI_NN: PhaseUNet3D learning the phase mapping | **BCDI Data Analysis → CDI_NN** |
+| 7. Reconstruct | NN → optionally refine with HIO/RAAR/ER | **BCDI Data Analysis → Reconstruction** |
+| 8. Visualize and export | Interactive 3D viewer, ParaView VTI export | **BCDI Data Analysis → 3D Viewer** |
+---
+## The simulation pipeline
+### 1. Material — build the crystal
+Choose from preset materials (Si, Ge, Pt, Au, SiC, GaAs, ...) or import a custom
+CIF file. The crystal is built atom-by-atom from the unit cell, replicated to the
+requested supercell size.
+You can:
+- Select the **particle shape**: cube, sphere, cylinder, hexagonal prism, octahedron, dodecahedron
+- Set the **target oversampling ratio** (controls how much of the diffraction
+  volume the object occupies)
+- Add **strain fields**: radial gradient, edge dislocation, random
+- Add **dislocations**: edge / screw / mixed, at a configurable position with
+  an arbitrary Burgers vector
+The 3D lattice view (powered by Plotly) shows every atom in the supercell.
+### 2. Beam — define the X-ray geometry
+Select a reflection (h k l) from the auto-computed list of allowed peaks.
+The Beam tab also lets you set:
+- **Beam energy** (and the resulting wavelength)
+- **Detector geometry**: pixel pitch, sample-to-detector distance, detector size
+- **Beam size** in microns
+- **Detector preset**: Maxipix (516×516), Eiger 2M...etc, custom rectangular
+Detector preset auto-fills the geometry parameters.
+### 3. Results — run the simulation
+CDI-ST computes the diffraction in **two paths**:
+- **Analytical path** (cube/rectangular shapes, no strain): closed-form Fourier transform of the support
+- **FFT path** (any shape, any strain field): full 3D FFT of the complex object
+Output: 3D diffraction volume `|F(q)|²`, displayed as 2D slices (qx-qy, qx-qz)
+and in an interactive 3D Plotly viewer with iso-surface controls.
+You can export the simulation as a `.npz` file ready for the data-analysis side,
+or for use as ground truth when training NNs.
+---
+## The data-analysis pipeline
+### 4. Generate Data — create training samples
+Generates a dataset of synthetic BCDI samples for NN training. Each sample
+contains the ground-truth phase, support, and the simulated diffraction
+intensity. You control:
+- **Number of samples** (typically 2,000–10,000)
+- **Grid size** (64³ recommended for training, 128³ for production inference)
+- **Materials** (random or fixed)
+- **Particle size variation** (random supercell multiplier)
+- **Random dislocations** adds occasional edge/screw/mixed dislocations
+- **Random strain** adds occasional radial/edge/random strain fields
+Samples save as `sample_XXXXX.npz` and a `manifest.json`. Generation is
+parallelizable and resumable.
+### 5. AutoPhase_NN — unsupervised physics-driven NN
+AutoPhase_NN is a 3D dual-decoder convolutional network that learns to invert the
+Fourier modulus constraint **without ground truth**. It predicts the object's
+amplitude and phase such that `|FFT(amp · exp(iφ))|` matches the measured
+magnitude. The loss is a normalized-magnitude error plus optional regularizers
+on phase smoothness and support compactness. This is the network from (Yao, Yudong,
+et al. npj Computational Materials 8.1 (2022) ) reimplemented for this codebase.
+Training is GPU-accelerated (CUDA preferred) and converges in a few dozen
+epochs on 2,000+ samples. The best checkpoint is saved automatically.
+### 6. CDI_NN — supervised PhaseUNet3D
+A 3D U-Net that predicts the phase field from the diffraction magnitude, trained
+against the ground-truth phase from the data generator.
+Use AutoPhase_NN when you don't trust your simulator's ground truth (or have
+none). Use CDI_NN when you have a high-fidelity simulator and want a direct
+mapping. Use both via the **ensemble** mode in the Reconstruction tab.
+### 7. Reconstruction — invert experimental or simulated data
+Load any `.npz` (simulated) or `.h5` (experimental) BCDI file, or convert a
+SPEC + EDF scan from ID01 directly via the dialog. Choose:
+- **NN-only (Autophase_NN)**: forward pass, twin-image suppression, COM centering
+- **Refined**: NN seed → HIO + RAAR + ER iterative phase retrieval
+- **Ensemble**: AutoPhase_NN + CDI_NN combined, optionally refined
+- **Compare**: runs both modes side-by-side
+The output is a complex object (amplitude + phase), a binary support, the
+R-factor convergence curve, and 2D slices at the COM of the reconstruction.
+For experimental data, the loader handles:
+- Detector chip-gap masking (Maxipix, Eiger)
+- Hot-pixel removal
+- Beamstop / direct-beam streak removal
+- Bragg-peak-centered cropping
+- Optional q-space orthogonalization via xrayutilities (with `[id01]` extra)
+### 8. 3D Viewer — interactive visualization
+The viewer renders the reconstruction in three modes:
+- **Point cloud**: every voxel above threshold, colored by amplitude / phase / strain,
+  with per-voxel opacity weighted by intensity
+- **Isosurface**: smoothed iso-shell with internal data points showing through
+- **Surface only**: bare iso-mesh with edges visible
+Controls:
+- Threshold (% of peak amplitude), voxel size, opacity, colormap
+- Color scale auto / manual (`vmin` / `vmax`)
+- Clip plane on any axis
+- Mouse: left-drag rotate, right-drag pan, wheel zoom, double-click reset
+- Export PNG snapshot or VTI (ParaView)
+---
+## Project structure
+```
+cdi-st/
+├── src/cdi_st/
+│   ├── __init__.py
+│   ├── __main__.py              # python -m cdi_st
+│   ├── bcdi_gui.py              # main entry point + launcher + splash
+│   ├── bcdi_core.py             # crystal builder, simulator, reflection calculator
+│   ├── nn_gui_tabs.py           # all NN-related GUI tabs
+│   ├── nn_data_generator.py     # training-data generator
+│   ├── nn_dataset.py            # PyTorch Dataset wrapper
+│   ├── nn_phase_model.py        # PhaseUNet3D (supervised)
+│   ├── nn_autophase_model.py    # AutoPhaseNet3D (unsupervised)
+│   ├── nn_train.py              # supervised training CLI
+│   ├── nn_autophase_train.py    # unsupervised training CLI
+│   ├── nn_phase_retrieval.py    # HIO / RAAR / ER iterative algorithms
+│   ├── nn_autophase_infer.py    # inference: nn_only / refined / ensemble
+│   ├── nn_experimental_loader.py # h5/spec/edf loading + preprocessing
+│   ├── nn_demo.py
+│   ├── nn_visualize.py
+│   └── CDI_ST_logo.png
+├── tests/
+├── docs/
+├── pyproject.toml
+├── README.md
+├── LICENSE
+└── CHANGELOG.md
+```
+---
+## Citing
+If you use CDI-ST in published research, please cite:
+```bibtex
+@software{saidi_cdi_st_2026,
+  author       = {Saidi, Soufiane},
+  title        = {CDI-ST: Coherent Diffraction Imaging — Simulation Tools},
+  year         = {2026},
+  publisher    = {GitHub},
+  url          = {https://github.com/Refze/CDI-St}
+}
+```
+---
+## License
+MIT — see [LICENSE](LICENSE).
+## Author
+**Soufiane SAIDI** — saidisoufiane@hotmail.com
+We heavily encourage you to use the in-app **Reports & Suggestions** button to send any type of feedback.
+---
+## Acknowledgments
+Built on the shoulders of the BCDI and python community:
+[PyNX](https://pynx.esrf.fr/), [BCDI-Utilities](https://github.com/carnisj/bcdi),
+[cdiutils](https://github.com/clatlan/cdiutils), [Atomsk](https://atomsk.univ-lille.fr/) , [xrayutilities](https://xrayutilities.sourceforge.io/),
+[scikit-image](https://scikit-image.org/), [PyQt6](https://www.riverbankcomputing.com/software/pyqt/),
+and the AutoPhaseNN paper by Yao et al. (2022).

{cdi_stools-0.2.1 → cdi_stools-0.2.2}/pyproject.toml RENAMED Viewed

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 [project]
 name = "cdi-stools"
-version = "0.2.1"
+version = "0.2.2"
 description = "Coherent Diffraction Imaging Simulation Tools — BCDI simulation and NN-based phase retrieval"
 readme = "README.md"
 requires-python = ">=3.9"

{cdi_stools-0.2.1 → cdi_stools-0.2.2}/src/cdi_st/__init__.py RENAMED Viewed

@@ -5,7 +5,7 @@ A Python application for end-to-end Bragg Coherent Diffraction Imaging (BCDI):
 crystal lattice construction, X-ray scattering simulation, neural-network
 phase retrieval, and 3D visualization.
 """
-__version__ = "0.2.1"
+__version__ = "0.2.2"
 __author__ = "Soufiane SAIDI"
 __email__ = "saidisoufiane@hotmail.com"
 __license__ = "MIT"

cdi-stools 0.2.1__tar.gz → 0.2.2__tar.gz

cdi-stools 0.2.1tar.gz → 0.2.2tar.gz