shinestacker 1.8.0__tar.gz → 1.9.0__tar.gz

{shinestacker-1.8.0 → shinestacker-1.9.0}/CHANGELOG.md

@@ -2,6 +2,45 @@
 
 This page reports the main releases only and the main changes therein.
 
+
+## [v1.9.0] - 2025-10-19
+** Added PNG format support and EXIF failure fix**
+
+### Added
+- support of images in PNG format, both in 8 bit and 16 bit depth. Note: EXIF data are not supported for 16 bit PNG because of limitations in the PIL and Open CV python libraries.
+
+### Fixed
+- if saving EXIF data fails, a warning is issued instead of stopping the run
+
+-----
+
+
+## [v1.8.1] - 2025-10-16
+** Alignment stability and performance improvements **
+
+### Added
+- optional alignment algorithm based on phase correlation as fallback when no feature match is found
+- retry limits in parallel alignment, determined by new configurable parameter delta_max
+- new configurable parameters in persistent default settings
+
+### Fixed
+- reference frame indexing if sequential processing is applied as fallback from multithread run
+- job configuration dialog failure if input is aready selected
+- preview thumbnail failure for very large images
+- minor inaccuracies in logger messages
+- minor GUI issues
+- computations for vignetting summary plot
+
+### Changed
+- improved robustness of alignment strategy for poorly focused images
+- better tuning of parallel frame alignment
+- consistent handling of noise map output folders
+- improved naming scheme for wizard-generated projects
+- more reliable default settings persistency
+- code refactoring and cleanup
+
+-----
+
 ## [v1.8.0] - 2025-10-08
 ** Minor improvements and accessibility fix **
 

{shinestacker-1.8.0/src/shinestacker.egg-info → shinestacker-1.9.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: shinestacker
-Version: 1.8.0
+Version: 1.9.0
 Summary: ShineStacker
 Author-email: Luca Lista <luka.lista@gmail.com>
 License-Expression: LGPL-3.0
@@ -30,11 +30,9 @@ Provides-Extra: dev
 Requires-Dist: pytest; extra == "dev"
 Dynamic: license-file
 
-<img src='https://raw.githubusercontent.com/lucalista/shinestacker/main/src/shinestacker/gui/ico/shinestacker.png' width="150" referrerpolicy="no-referrer" alt="Shine Stacker Logo">
-
 # Shine Stacker
 
-## Focus Stacking Processing Framework and GUI
+Focus Stacking Processing Framework and GUI designed for macro photographers, microscopists, and researchers who need precise control and reproducible stacking results.
 
 [![CI multiplatform](https://github.com/lucalista/shinestacker/actions/workflows/ci-multiplatform.yml/badge.svg)](https://github.com/lucalista/shinestacker/actions/workflows/ci-multiplatform.yml)
 [![PyPI version](https://img.shields.io/pypi/v/shinestacker?color=success)](https://pypi.org/project/shinestacker/)
@@ -45,60 +43,55 @@ Dynamic: license-file
 [![Documentation Status](https://readthedocs.org/projects/shinestacker/badge/?version=latest)](https://shinestacker.readthedocs.io/en/latest/?badge=latest)
  [![License: LGPL v3](https://img.shields.io/badge/License-LGPL_v3-blue.svg)](https://www.gnu.org/licenses/lgpl-3.0)
 [![PyPI Downloads](https://static.pepy.tech/badge/shinestacker)](https://pepy.tech/projects/shinestacker)
-
-<img src='https://raw.githubusercontent.com/lucalista/shinestacker/main/img/flies.gif' width="400" referrerpolicy="no-referrer">  <img src='https://raw.githubusercontent.com/lucalista/shinestacker/main/img/flies_stack.jpg' width="400" referrerpolicy="no-referrer">
-
-<img src='https://raw.githubusercontent.com/lucalista/shinestacker/main/img/coffee.gif' width="400" referrerpolicy="no-referrer">  <img src='https://raw.githubusercontent.com/lucalista/shinestacker/main/img/coffee_stack.jpg' width="400" referrerpolicy="no-referrer">
-
-> **Focus stacking** for microscopy, macro photography, and computational imaging
+<center><img src='https://raw.githubusercontent.com/lucalista/shinestacker/main/src/shinestacker/gui/ico/shinestacker.png' width="150" referrerpolicy="no-referrer" alt="Shine Stacker Logo"></center>
 
 ## Key Features
-- 🚀 **Batch Processing**: Align, balance, and stack hundreds of images
-- 🧩 **Modular Architecture**: Mix-and-match processing modules
-- 🖌️ **Retouch Editing**: Final interactive retouch of stacked image from individual frames
-- 📊 **Jupyter Integration**: Image processing python notebooks
+- 🪟 **Cross-Platform GUI**: Native app built with Qt6, available for Windows, macOS, and Linux.
+- 🚀 **Batch Processing**: Automatically align, balance, and stack hundreds of images — perfect for macro or microscopy datasets.
+- 🧩 **Modular Architecture**: Combine configurable modules for alignment, normalization, and blending to build custom workflows.
+- 🖌️ **Retouch Editor**: Interactively refine your stacked image by painting in details from individual frames.
+- 📊 **Jupyter & Python Integration**: Use Shine Stacker as a library inside your Python or Jupyter workflows.
+
+<img src='https://raw.githubusercontent.com/lucalista/shinestacker/main/img/flies.gif' width="400" referrerpolicy="no-referrer">  <img src='https://raw.githubusercontent.com/lucalista/shinestacker/main/img/flies_stack.jpg' width="400" referrerpolicy="no-referrer">
 
 ## Interactive GUI
 
-The GUI has two main working areas: 
+The graphical interface makes complex stacking tasks simple:
+- **Project View** – Configure, preview, and run stacking workflows with optional intermediate results.
+- **Retouch View** – Manually refine the final image by blending details from selected frames and applying filters.
 
-* *Project*: manage and run focus stacking workflows in a flexible and configurable way, with optional intermediate batch stacking.
+Ideal for users who want the power of scripting and the comfort of a modern UI.
 
-<img src='https://raw.githubusercontent.com/lucalista/shinestacker/main/img/gui-project-run.png' width="600" referrerpolicy="no-referrer">
+<img src='https://raw.githubusercontent.com/lucalista/shinestacker/main/img/coffee.gif' width="400" referrerpolicy="no-referrer">  <img src='https://raw.githubusercontent.com/lucalista/shinestacker/main/img/coffee_stack.jpg' width="400" referrerpolicy="no-referrer">
 
-* *Retouch*: select interactively details from individual frames and apply final filters to the blended image.
+## Get Started
 
-<img src='https://raw.githubusercontent.com/lucalista/shinestacker/main/img/gui-retouch.png' width="600" referrerpolicy="no-referrer">
+- 📦 [Install via PyPI](https://pypi.org/project/shinestacker/)
+- 💻 [Run the GUI app](https://shinestacker.readthedocs.io/en/latest/gui.html)
+- 🧠 [Reference](https://shinestacker.readthedocs.io/en/)
+- 🐛 [Report an issue](https://github.com/lucalista/shinestacker/issues)
 
 ## Resources
 
  🌍 [Website on WordPress](https://shinestacker.wordpress.com) • 📖 [Main documentation](https://shinestacker.readthedocs.io) • 📝 [Changelog](https://github.com/lucalista/shinestacker/blob/main/CHANGELOG.md) 
 
-## Note for macOS users
-
-**The following note is only relevant if you download the application as compressed archive from the [release page](https://github.com/lucalista/shinestacker/releases).**
+## Installation
 
-The macOS system security protection prevent to run applications downloaded from the web that come from developers that don't hold an Apple Developer Certificate. 
+See the [main documentation](https://github.com/lucalista/shinestacker/blob/main/docs/main.md) for detailed installation instructions.
 
-In order to prevent this, follow the instructions below:
+**Platform notes:**
+- **Windows:** If you download the installer or ZIP archive, you may need to whitelist the app in your antivirus software.
+- **macOS:** See the [installation note for macOS users](https://github.com/lucalista/shinestacker/blob/main/docs/macos-install.md).
 
-1. Download the compressed archive ```shinestacker-macos.tar.gz``` in your ```Download``` folder.
-2. Double-click the archive to uncompress it. You will find a new folder ```shinestacker```.
-3. Open a terminal (*Applications > Utilities > Terminal*)
-4. Type the folliwng command on the terminal (assuming you installed the app from the ```dmg``` image under ```Applications```):
-```bash
-xattr -cr /Applications/shinestacker/shinestacker.app
-```
-5. Now you can double-click the Sine Stacker icon app and it should run.
 
-macOS adds a quarantine flag to all files downloaded from the internet. The above command removes that flag while preserving all other application functionality.
+## Acknowledgements & References
 
-## Credits
-
-The first version of the core focus stack algorithm was initially inspired by the [Laplacian pyramids method](https://github.com/sjawhar/focus-stacking) implementation by Sami Jawhar that was used under permission of the author. The implementation in the latest releases was rewritten from the original code.
-
-## Resources
+The first version of the core focus stack algorithm was inspired by the 
+[Laplacian pyramids method](https://github.com/sjawhar/focus-stacking) implementation 
+by Sami Jawhar, used under permission. The implementation in the latest releases 
+was rewritten from the original code.
 
+Key references:
 * [Pyramid Methods in Image Processing](https://www.researchgate.net/publication/246727904_Pyramid_Methods_in_Image_Processing), E. H. Adelson, C. H. Anderson,  J. R. Bergen, P. J. Burt, J. M. Ogden, RCA Engineer, 29-6, Nov/Dec 1984
 Pyramid methods in image processing
 * [A Multi-focus Image Fusion Method Based on Laplacian Pyramid](http://www.jcomputers.us/vol6/jcp0612-07.pdf), Wencheng Wang, Faliang Chang, Journal of Computers 6 (12), 2559, December 2011
@@ -108,13 +101,18 @@ Pyramid methods in image processing
 <img src="https://www.gnu.org/graphics/lgplv3-147x51.png" alt="LGPL 3 logo">
 
 - **Code**: The software is provided as is under the [GNU Lesser General Public License v3.0](https://www.gnu.org/licenses/lgpl-3.0.en.html). See [LICENSE](https://github.com/lucalista/shinestacker/blob/main/LICENSE) for details.
-<img src='https://raw.githubusercontent.com/lucalista/shinestacker/main/src/shinestacker/gui/ico/shinestacker.png' width="150" referrerpolicy="no-referrer" alt="Shine Stacker Logo">
 
 - **Logo**: The Shine Stacker logo was designed by [Alessandro Lista](https://linktr.ee/alelista). Copyright © Alessandro Lista. All rights reserved. The logo is not covered by the LGPL-3.0 license of this project.
 
 ## Attribution request
+
 📸 If you publish images created with Shine Stacker, please consider adding a note such as:
 
 *Created with Shine Stacker – https://github.com/lucalista/shinestacker*
 
 This is not mandatory, but highly appreciated.
+
+---
+> Developed and maintained by [Luca Lista](https://github.com/lucalista).
+> 💡 Contributions, feedback, and feature suggestions are warmly welcome.
+> If you enjoy Shine Stacker, consider giving it a ⭐️ on GitHub — it really helps visibility!

{shinestacker-1.8.0 → shinestacker-1.9.0}/README.md

@@ -1,8 +1,6 @@
-<img src='https://raw.githubusercontent.com/lucalista/shinestacker/main/src/shinestacker/gui/ico/shinestacker.png' width="150" referrerpolicy="no-referrer" alt="Shine Stacker Logo">
-
 # Shine Stacker
 
-## Focus Stacking Processing Framework and GUI
+Focus Stacking Processing Framework and GUI designed for macro photographers, microscopists, and researchers who need precise control and reproducible stacking results.
 
 [![CI multiplatform](https://github.com/lucalista/shinestacker/actions/workflows/ci-multiplatform.yml/badge.svg)](https://github.com/lucalista/shinestacker/actions/workflows/ci-multiplatform.yml)
 [![PyPI version](https://img.shields.io/pypi/v/shinestacker?color=success)](https://pypi.org/project/shinestacker/)
@@ -13,60 +11,55 @@
 [![Documentation Status](https://readthedocs.org/projects/shinestacker/badge/?version=latest)](https://shinestacker.readthedocs.io/en/latest/?badge=latest)
  [![License: LGPL v3](https://img.shields.io/badge/License-LGPL_v3-blue.svg)](https://www.gnu.org/licenses/lgpl-3.0)
 [![PyPI Downloads](https://static.pepy.tech/badge/shinestacker)](https://pepy.tech/projects/shinestacker)
-
-<img src='https://raw.githubusercontent.com/lucalista/shinestacker/main/img/flies.gif' width="400" referrerpolicy="no-referrer">  <img src='https://raw.githubusercontent.com/lucalista/shinestacker/main/img/flies_stack.jpg' width="400" referrerpolicy="no-referrer">
-
-<img src='https://raw.githubusercontent.com/lucalista/shinestacker/main/img/coffee.gif' width="400" referrerpolicy="no-referrer">  <img src='https://raw.githubusercontent.com/lucalista/shinestacker/main/img/coffee_stack.jpg' width="400" referrerpolicy="no-referrer">
-
-> **Focus stacking** for microscopy, macro photography, and computational imaging
+<center><img src='https://raw.githubusercontent.com/lucalista/shinestacker/main/src/shinestacker/gui/ico/shinestacker.png' width="150" referrerpolicy="no-referrer" alt="Shine Stacker Logo"></center>
 
 ## Key Features
-- 🚀 **Batch Processing**: Align, balance, and stack hundreds of images
-- 🧩 **Modular Architecture**: Mix-and-match processing modules
-- 🖌️ **Retouch Editing**: Final interactive retouch of stacked image from individual frames
-- 📊 **Jupyter Integration**: Image processing python notebooks
+- 🪟 **Cross-Platform GUI**: Native app built with Qt6, available for Windows, macOS, and Linux.
+- 🚀 **Batch Processing**: Automatically align, balance, and stack hundreds of images — perfect for macro or microscopy datasets.
+- 🧩 **Modular Architecture**: Combine configurable modules for alignment, normalization, and blending to build custom workflows.
+- 🖌️ **Retouch Editor**: Interactively refine your stacked image by painting in details from individual frames.
+- 📊 **Jupyter & Python Integration**: Use Shine Stacker as a library inside your Python or Jupyter workflows.
+
+<img src='https://raw.githubusercontent.com/lucalista/shinestacker/main/img/flies.gif' width="400" referrerpolicy="no-referrer">  <img src='https://raw.githubusercontent.com/lucalista/shinestacker/main/img/flies_stack.jpg' width="400" referrerpolicy="no-referrer">
 
 ## Interactive GUI
 
-The GUI has two main working areas: 
+The graphical interface makes complex stacking tasks simple:
+- **Project View** – Configure, preview, and run stacking workflows with optional intermediate results.
+- **Retouch View** – Manually refine the final image by blending details from selected frames and applying filters.
 
-* *Project*: manage and run focus stacking workflows in a flexible and configurable way, with optional intermediate batch stacking.
+Ideal for users who want the power of scripting and the comfort of a modern UI.
 
-<img src='https://raw.githubusercontent.com/lucalista/shinestacker/main/img/gui-project-run.png' width="600" referrerpolicy="no-referrer">
+<img src='https://raw.githubusercontent.com/lucalista/shinestacker/main/img/coffee.gif' width="400" referrerpolicy="no-referrer">  <img src='https://raw.githubusercontent.com/lucalista/shinestacker/main/img/coffee_stack.jpg' width="400" referrerpolicy="no-referrer">
 
-* *Retouch*: select interactively details from individual frames and apply final filters to the blended image.
+## Get Started
 
-<img src='https://raw.githubusercontent.com/lucalista/shinestacker/main/img/gui-retouch.png' width="600" referrerpolicy="no-referrer">
+- 📦 [Install via PyPI](https://pypi.org/project/shinestacker/)
+- 💻 [Run the GUI app](https://shinestacker.readthedocs.io/en/latest/gui.html)
+- 🧠 [Reference](https://shinestacker.readthedocs.io/en/)
+- 🐛 [Report an issue](https://github.com/lucalista/shinestacker/issues)
 
 ## Resources
 
  🌍 [Website on WordPress](https://shinestacker.wordpress.com) • 📖 [Main documentation](https://shinestacker.readthedocs.io) • 📝 [Changelog](https://github.com/lucalista/shinestacker/blob/main/CHANGELOG.md) 
 
-## Note for macOS users
-
-**The following note is only relevant if you download the application as compressed archive from the [release page](https://github.com/lucalista/shinestacker/releases).**
+## Installation
 
-The macOS system security protection prevent to run applications downloaded from the web that come from developers that don't hold an Apple Developer Certificate. 
+See the [main documentation](https://github.com/lucalista/shinestacker/blob/main/docs/main.md) for detailed installation instructions.
 
-In order to prevent this, follow the instructions below:
+**Platform notes:**
+- **Windows:** If you download the installer or ZIP archive, you may need to whitelist the app in your antivirus software.
+- **macOS:** See the [installation note for macOS users](https://github.com/lucalista/shinestacker/blob/main/docs/macos-install.md).
 
-1. Download the compressed archive ```shinestacker-macos.tar.gz``` in your ```Download``` folder.
-2. Double-click the archive to uncompress it. You will find a new folder ```shinestacker```.
-3. Open a terminal (*Applications > Utilities > Terminal*)
-4. Type the folliwng command on the terminal (assuming you installed the app from the ```dmg``` image under ```Applications```):
-```bash
-xattr -cr /Applications/shinestacker/shinestacker.app
-```
-5. Now you can double-click the Sine Stacker icon app and it should run.
 
-macOS adds a quarantine flag to all files downloaded from the internet. The above command removes that flag while preserving all other application functionality.
+## Acknowledgements & References
 
-## Credits
-
-The first version of the core focus stack algorithm was initially inspired by the [Laplacian pyramids method](https://github.com/sjawhar/focus-stacking) implementation by Sami Jawhar that was used under permission of the author. The implementation in the latest releases was rewritten from the original code.
-
-## Resources
+The first version of the core focus stack algorithm was inspired by the 
+[Laplacian pyramids method](https://github.com/sjawhar/focus-stacking) implementation 
+by Sami Jawhar, used under permission. The implementation in the latest releases 
+was rewritten from the original code.
 
+Key references:
 * [Pyramid Methods in Image Processing](https://www.researchgate.net/publication/246727904_Pyramid_Methods_in_Image_Processing), E. H. Adelson, C. H. Anderson,  J. R. Bergen, P. J. Burt, J. M. Ogden, RCA Engineer, 29-6, Nov/Dec 1984
 Pyramid methods in image processing
 * [A Multi-focus Image Fusion Method Based on Laplacian Pyramid](http://www.jcomputers.us/vol6/jcp0612-07.pdf), Wencheng Wang, Faliang Chang, Journal of Computers 6 (12), 2559, December 2011
@@ -76,13 +69,18 @@ Pyramid methods in image processing
 <img src="https://www.gnu.org/graphics/lgplv3-147x51.png" alt="LGPL 3 logo">
 
 - **Code**: The software is provided as is under the [GNU Lesser General Public License v3.0](https://www.gnu.org/licenses/lgpl-3.0.en.html). See [LICENSE](https://github.com/lucalista/shinestacker/blob/main/LICENSE) for details.
-<img src='https://raw.githubusercontent.com/lucalista/shinestacker/main/src/shinestacker/gui/ico/shinestacker.png' width="150" referrerpolicy="no-referrer" alt="Shine Stacker Logo">
 
 - **Logo**: The Shine Stacker logo was designed by [Alessandro Lista](https://linktr.ee/alelista). Copyright © Alessandro Lista. All rights reserved. The logo is not covered by the LGPL-3.0 license of this project.
 
 ## Attribution request
+
 📸 If you publish images created with Shine Stacker, please consider adding a note such as:
 
 *Created with Shine Stacker – https://github.com/lucalista/shinestacker*
 
 This is not mandatory, but highly appreciated.
+
+---
+> Developed and maintained by [Luca Lista](https://github.com/lucalista).
+> 💡 Contributions, feedback, and feature suggestions are warmly welcome.
+> If you enjoy Shine Stacker, consider giving it a ⭐️ on GitHub — it really helps visibility!

{shinestacker-1.8.0 → shinestacker-1.9.0}/docs/alignment.md

@@ -67,7 +67,9 @@ alignment_config = {
     'border_blur': 50,
     'subsample': 0,
     'fast_subsampling': False,
-    'min_good_matches': 100
+    'min_good_matches': 100,
+    'phase_corr_fallback': False,
+    'abort_abnormal': False
 }
 ```
 * ```transform``` (optional, default: ```ALIGN_RIGID```): the transformation applied to register images. Possible values are:
@@ -83,6 +85,8 @@ alignment_config = {
 * ```subsample``` (optional, default: 0=automatic): subsample image for faster alignment. Faster, but alignment could be less accurate if only a small portion of the image is focused. It can save time, in particular for large images.
 * ```fast_subsampling``` (optional, default: ```False```): perform fast image subsampling without interpolation. Used if ```subsample``` is set to ```True```.
 * ```min_good_matches``` (optional, default: 100): if ```subsample```>1 and the number of good matches is below ```min_good_matches```, the alignment is retried without subsampling. This improbes robustness in case a too large subsampling factor is specified. 
+* ```phase_corr_fallback``` (optional, default: ```False```): use phase correlation alignment in case the number of matches is too low to allow to estimate the transformation. This algorithm is not very precise, and may help only in case of blurred images.
+* ```abort_abnormal``` (optional, default: ```False```): abort in case of anormal tansformation. By default, frames where abnormal transformation is found are skipped, and processing continunes to next frame.
 * ```border_mode``` (optional, default: ```BORDER_REPLICATE_BLUR```): border mode. See [Adding borders to your images](https://docs.opencv.org/3.4/dc/da3/tutorial_copyMakeBorder.html) for more details.  Possible values are:
   * ```BORDER_CONSTANT```: pad the image with a constant value. The border value is specified with the parameter ```border_value```.
   * ```BORDER_REPLICATE```: the rows and columns at the very edge of the original are replicated to the extra border.
@@ -101,6 +105,7 @@ This class has extra parameters, in addition to the above ones:
 * ```max_threads``` (optional, default: ```2```): number of parallel processes allowed. The number of actual threads will not be greater than the number of available CPU cores.
 * ```chunk_submit``` (optional, default: ```True```): submit at most ```max_threads``` parallel processes. If ```chunk_submit``` is greater than ```max_threads``` a moderate performance gain is achieved at the cost of a possibly large memory occupancy.
 * ```bw_matching``` (optional, default: ```False```): perform matches on black and white version of the images in order to save memory. Preliminary tests indicate that the gain with this option is marginal, and this option may be dropped in the future.
+* ```delta_max``` (optional, defaut: 2): maximum consecutive frames skipped in case of too few matches found.
 
 ## Automatic selection of processing strategy
 

{shinestacker-1.8.0 → shinestacker-1.9.0}/docs/focus_stacking.md

@@ -13,6 +13,8 @@ Arguments for the constructor of ```FocusStack``` are:
 * ```denoise_amount``` (optoinal): if specified, a denois algorithm is applied. A value of 0.75 to 1.00 does not reduce details in an appreciable way, and is suitable for modest noise reduction. denoise may be useful for 8-bit images, or for images taken at large ISO. 16-bits images at low ISO usually don't require denoise. See [Image Denoising](https://docs.opencv.org/3.4/d5/d69/tutorial_py_non_local_means.html) for more details.
 * ```prefix``` (optional): if specified, the specified string is pre-pended to the file name. May be useful if more algorithms are ran, and different file names are used for the output of different algorithms.
 * ```enabled``` (optional, default: ``True```): allows to switch on and off this module.
+* ```scratch_output_dir``` (optional, default: ```True```): scratch output directory before processing. This avoids that existing files pollute the output.
+* ```delete_output_at_end``` (optional, default: ```False```): delete output after processing. This cleans disk space in case of processing an intermediate step that is not part of the final output.
 
 ## Focus Stacking in bunches of frames
 
@@ -31,6 +33,8 @@ Arguments for the constructor of ```FocusStackBunch``` are:
 * ```denoise_amount``` (optoinal): if specified, a denois algorithm is applied. A value of 0.75 to 1.00 does not reduce details in an appreciable way, and is suitable for modest noise reduction. denoise may be useful for 8-bit images, or for images taken at large ISO. 16-bits images at low ISO usually don't require denoise. See [Image Denoising](https://docs.opencv.org/3.4/d5/d69/tutorial_py_non_local_means.html) for more details.
 * ```prefix``` (optional): if specified, the specified string is pre-pended to the file name. May be useful if more algorithms are ran, and different file names are used for the output of different algorithms.
 * ```enabled``` (optional, default: ```True```): allows to switch on and off this module.
+* ```scratch_output_dir``` (optional, default: ```True```): scratch output directory before processing. This avoids that existing files pollute the output.
+* ```delete_output_at_end``` (optional, default: ```False```): delete output after processing. This cleans disk space in case of processing an intermediate step that is not part of the final output.
 
 ## Stack algorithms
 

{shinestacker-1.8.0 → shinestacker-1.9.0}/docs/gui.md

@@ -12,24 +12,28 @@ noisy pixel masking.
 
 ## Starting
 
-* If the python package is donwloaded and installed, the GUI can start either from a console command line :
+* The python package can be installed from [PyPI](https://pypi.org/project/shinestacker/) using ```pip```:
 
 ```console
-> focusstack
+> pip install shinestacker
 ```
+ Onace installed, the GUI app can start either from a console command line :
 
-* If the app is dowloaded from the [releases page](https://github.com/lucalista/focusstack/releases), after the  ```zip``` archive is uncompressed, just double-click the app icon.
-
-<img src='https://raw.githubusercontent.com/lucalista/shinestacker/main/img/gui-finder.png' width="300" referrerpolicy="no-referrer">
+```console
+> shinestacker
+```
 
-**Platform Tip**: Windows apps are inside `/focusstack/`, macOS/Linux apps are directly in the uncompressed folder.
+* The app can be dowloaded from the [releases page](https://github.com/lucalista/shinestacker/releases):
+   - Windows: as installer or  ```zip``` archive for local installation
+   - macOS: as ```dmg``` disk image, where the app can be dragged to the Application folder
+   - Linux: as ```tar.gz``` archive
 
 The GUI has two main working areas: 
 
 * *Project* 
 * *Retouch*
 
-Switching from *Project* to *Retouch* can be done from the *FocusStack* main menu.
+Switching from *Project* to *Retouch* can be done from the *ShineStacker* main menu.
 
 ## Project area
 
@@ -48,17 +52,13 @@ When the app starts, it proposes to create a new project.
 
 > **Large Set Tip**: For 100+ images:
 > - Split into 10-15 image "bunches" 
-> - Set frame overlap (default: 2 frames)
+> - Set number of overlapping frame from consecutive bunches
 > - Combine intermediate results later
 
-> 💡 **RAM Warning**: >15 images of 20Mpx resolution may need 16GB+ RAM. Combine smaller bunches first, if needed, to stack up to hundreds of frames.
-
 The newly created project consists of a single job that contains more actions.
 Each action produces a folder as output that has, by default, the action's name.
 Some actions can be combined in order to produce a single intermediate output (alignment, balancing, etc.).
 
-**Action Outputs**: 📁 `aligned-balanced/` | 📁 `bunches/` | 📁 `stacked/`
-
 > **Pro Tip**: Duplicate jobs when processing similar image sets to save configuration time. You can run multiple jobs in sequence.
 
 It is possible to run a single job, or all jobs within a project.
@@ -67,7 +67,7 @@ It is possible to run a single job, or all jobs within a project.
 
 ### Project Run Tabs
 
-1. Job progress bar
+1. Job progress bar with CPU and RAM usage monitor
 2. Real-time log viewer
 3. Retouch button (enabled after processing)
 

{shinestacker-1.8.0 → shinestacker-1.9.0}/docs/job.md

@@ -43,6 +43,8 @@ Arguments for the constructor of ```CombinedActions``` are for the :
 * ```resample``` (optional, default: 1): take every *n*<sup>th</sup> frame in the selected directory. Default: take all frames.
 * ```reference_index``` (optional, default: 0): the index of the image used as reference. Images are numbered starting from one to N. -1 is interpreted as the last image, 0 as the median index.
 * ```step_process``` (optional): if equal to ```True``` (default), each image is processed with respect to the previous or next image, depending if its file is placed in alphabetic order after or befor the reference image.
-* ```enabled``` (optional, default: ```True```): allows to switch on and off this module. 
+* ```enabled``` (optional, default: ```True```): allows to switch on and off this module.
+* ```scratch_output_dir``` (optional, default: ```True```): scratch output directory before processing. This avoids that existing files pollute the output.
+* ```delete_output_at_end``` (optional, default: ```False```): delete output after processing. This cleans disk space in case of processing an intermediate step that is not part of the final output.
 * ```max_threads``` (optional, default: ```2```): number of parallel processes allowed. The number of actual threads will not be greater than the number of available CPU cores.
 * ```chunk_submit``` (optional, default: ```True```): submit at most ```max_threads``` parallel processes. If ```chunk_submit``` is greater than ```max_threads``` a moderate performance gain is achieved at the cost of a possibly large memory occupancy.

shinestacker-1.9.0/docs/macos-install.md

@@ -0,0 +1,19 @@
+# Installation Note for macOS Users
+
+**This note applies only if you downloaded Shine Stacker as a compressed archive from the [release page](https://github.com/lucalista/shinestacker/releases).**
+
+macOS system security (Gatekeeper) may prevent applications from running if they were downloaded from the Internet and are not signed with an official Apple Developer Certificate.
+
+To allow Shine Stacker to run safely, please follow these steps:
+
+1. Download the disk image file ```shinestacker-macos.dmg```.
+2. Double-click the ```.dmg``` file and drag the **Shine Stacker** app into your **Application** folder.
+3. Open the **Terminal** (found in *Applications > Utilities > Terminal*).
+4. Run the following command to remove the quarantine attribute:
+```bash
+xattr -cr /Applications/shinestacker/shinestacker.app
+```
+5. You can now launch Shine Stacker normally from your Applications folder.
+
+> 💡 Tip: macOS might still show a security warning the first time you open the app.
+> If that happens, right-click the app and choose Open, then confirm.

{shinestacker-1.8.0 → shinestacker-1.9.0}/docs/main.md

@@ -103,5 +103,6 @@ pip install ipywidgets
 
 | Issue    |  Workaround    |
 |----------|----------------|
-| PNG and RAW unsupported  | Convert to TIFF/JPEG first |
+| RAW format unsupported  | Convert to TIFF/JPEG first |
+| EXIF data not supported for 16-bit PNG files | convert to 16-bit TIFF first |
 | GUI tests limited     | Report any bugs as GitHub issuse |

{shinestacker-1.8.0 → shinestacker-1.9.0}/docs/noise.md

@@ -13,14 +13,14 @@ Usually, this job should be run first, enabling the option ```plot_histograms```
 Arguments for the constructor of ```NoiseDetection``` are:
 * ```name``` (optional, default: ```noise-map```): name of the action and default name of the subdirectory within ```working_path``` where aligned noise map is written. 
 * ```input_path``` (optional): one or more subdirectory within ```working_path``` that contains input images to be combined. If not specified, the last output path is used, or, if this is the first action, the ```input_path``` specified with the ```StackJob``` construction is used. If the ```StackJob``` specifies no ```input_path```, at least the first action must specify an  ```input_path```.
-* ```output_path``` (optional): unused
+* ```output_path``` (optional): the subdirectory within ```working_path``` where noise map is written. If not specified,  it is equal to  ```name```.
 * ```working_path``` (optional): the directory that contains input and output image subdirectories. If not specified, it is the same as ```job.working_path```.
 * ```max_frames``` (optional): if provided, at most ```max_frames``` images are analyzed to extract noisy pixel mask.
 * ```plot_path``` (optional, default: ```plots```): the directory within ```working_path``` that contains plots produced by the different actions
 * ```plot_histograms```  (optional, default: ```False```): if ```True```, plot a summary of the number of hot pixel by channel as a function of the applied threshold. It may be useful to set the optimal threshold values.
 * ```channel_thresholds``` (optional, default: ```(13, 13, 13)```): threshold values for noisy pixel detections in the color channels R, G, B, respectively.
 * ```blur_size``` (optional, default: 5): image blur amount for pixel detection.
-* ```file_name``` (optional, default: ```hot```): noise map filename. The noisy pixel map is stored bydefault in the file ```hot-rgb.png```. Noisy pixel maps individyally for the R, G and B channels are also stored in  ```hot-r.png```,  ```hot-g.png``` and  ```hot-b.png```, respectively.
+* ```file_name``` (optional, default: ```hot_pixels.png```): noise map filename.
 * ```plot_range``` (optiona, default: (5, 30)): range of the horizontal axis of the plot showing the number of hot pixel as a function of the intensity threshold.
 * ```enabled``` (optional, default: ```True```): allows to switch on and off this module. 
 
@@ -41,7 +41,7 @@ job.add_action(Actions("align", [MaskNoise(),
 Note that if the number of pixels contained in the mask file (```noise_mask``` option) is greater than 1000, the job is aborted.
 
 Arguments for the constructor of ```NoiseDetection``` are:
-* ```noise_mask``` (optional, default: ```noise-map/hot-rgb.png```): filename of the noise mask
+* ```noise_mask``` (optional, default: ```hot-rgb.png```): filename of the noise mask
 *  ```kernel_size``` (optional, default: 3): blur size use to extract noisy pixels
 *  ```method``` (optional, default: ```INTERPOLATE_MEAN```): possible values: ```INTERPOLATE_MEAN```, ```INTERPOLATE_MEDIAN```. Interpolate using mean or median of neighborhood pixels to replace a noisy pixel.
 * ```enabled``` (optional, default: ```True```): allows to switch on and off this module. 

shinestacker-1.9.0/src/shinestacker/_version.py

@@ -0,0 +1 @@
+__version__ = '1.9.0'