v2.8.1

Author: fbordignon

BUILD.md

@@ -55,8 +55,8 @@ GeoSlicer is built on top of a modified version of 3D Slicer called **GeoSlicerB
 
 -   **Download the pre-built binaries (Recommended)**: This is the easiest and fastest way to get started. You can download the pre-built binaries for your operating system from the links below:
 
-    *   [Windows amd64](https://objectstorage.sa-saopaulo-1.oraclecloud.com/p/j3-M11OKFLGFcWJGYr4hUQnW8u4sFruUATaH2IcaoSp4f8PcRCisaQH6mH2rtGv0/n/grrjnyzvhu1t/b/General_ltrace_files/o/GeoSlicer/base/release/win32/GeoSlicer-2.2.2-2024-11-21-win-amd64.zip)
-    *   [Linux amd64](https://objectstorage.sa-saopaulo-1.oraclecloud.com/p/jy3VVQsDEJb9lVRLUz-6Iu_FBwPpw8ooCPdHP9aXKfEJPvWrFPt2Gy2hxwSy3mnq/n/grrjnyzvhu1t/b/General_ltrace_files/o/GeoSlicer/base/release/linux/GeoSlicer-2.2.2-2024-11-21-linux-amd64.tar.gz)
+    *   [Windows amd64](https://objectstorage.sa-saopaulo-1.oraclecloud.com/p/fTj1fha337JiQkTHVSJZzN1tNVvz7VFJ9mcfFlNpy6csjwIgIgy-KtH_h_PZoHhJ/n/grrjnyzvhu1t/b/General_ltrace_files/o/GeoSlicer/base/release/win32/GeoSlicer-2.7.1-2025-08-07-win-amd64.zip)
+    *   [Linux amd64](https://objectstorage.sa-saopaulo-1.oraclecloud.com/p/wxxSabOwh2b69CV3EodNcWF3srseT-R6D-5aUFTlv-KBqGNhKyF_eeV86WWhTR3O/n/grrjnyzvhu1t/b/General_ltrace_files/o/GeoSlicer/base/release/linux/GeoSlicer-2.7.1-2025-08-07-linux-amd64.tar.gz)
 -   **Build from source**: If you need to make changes to the base application, you can build GeoSlicerBase from the source by cloning the [geoslicerbase](https://github.com/ltracegeo/geoslicerbase) and [slicer](https://github.com/ltracegeo/Slicer) repositories.
 
 ## 3. Deployment

CITATION.cff

@@ -1,82 +1,82 @@
-cff-version: 1.2.0
-message: "If you use any resource published in this repository, please cite it as below."
-authors:
-- family-names: "Passos de Figueiredo"
-  given-names: "Leandro"
-  email: leandro@ltrace.com.br
-  affiliation: "LTrace Geociências"
-  orcid: ""
-- family-names: "Bordignon"
-  given-names: "Fernando Luis"
-  email: fernando@ltrace.com.br
-  affiliation: "LTrace Geociências"
-  orcid: "https://orcid.org/0000-0001-5205-8042"
-- family-names: "Surmas"
-  given-names: "Rodrigo"
-  email: surmas@petrobras.com.br
-  affiliation: "Petróleo Brasileiro S.A."
-  orcid: ""
-- family-names: "Weck Pereira"
-  given-names: "Marcio Valerio"
-  email: marcio.weck@ltrace.com.br
-  affiliation: "LTrace Geociências"
-  orcid: ""
-- family-names: "Damian"
-  given-names: "Frederico"
-  email: frederico.damian@ltrace.com.br
-  affiliation: "LTrace Geociências"
-  orcid: ""
-- family-names: "Arenhart"
-  given-names: "Rafael"
-  email: rafael.arenhart@ltrace.com.br
-  affiliation: "LTrace Geociências"
-  orcid: ""
-- family-names: "Exterkoetter"
-  given-names: "Rodrigo"
-  email: rodrigo@ltrace.com.br
-  affiliation: "LTrace Geociências"
-  orcid: ""
-- family-names: "Müller"
-  given-names: "Gabriel"
-  email: gabriel.muller@ltrace.com.br
-  affiliation: "LTrace Geociências"
-  orcid: ""
-- family-names: "Formighieri"
-  given-names: "Giovanni"
-  email: giovanni@ltrace.com.br
-  affiliation: "LTrace Geociências"
-  orcid: ""
-- family-names: "Schwedersky"
-  given-names: "Rodrigo"
-  email: rodrigo.schwedersky@ltrace.com.br
-  affiliation: "LTrace Geociências"
-  orcid: ""
-- family-names: "Costa"
-  given-names: "Fernando"
-  email: fernando.costa@ltrace.com.br
-  affiliation: "LTrace Geociências"
-  orcid: ""
-- family-names: "Mello"
-  given-names: "Jean"
-  email: jean.mello@ltrace.com.br
-  affiliation: "LTrace Geociências"
-  orcid: ""
-- family-names: "Cenci"
-  given-names: "Rômulo"
-  email: romulo.cenci@ltrace.com.br
-  affiliation: "LTrace Geociências"
-  orcid: ""
-- family-names: "Boing de Souza"
-  given-names: "José Vinícius"
-  email: jose.boing@ltrace.com.br
-  affiliation: "LTrace Geociências"
-  orcid: ""
-- family-names: "Pacheco"
-  given-names: "Robim"
-  email: robim.pacheco@ltrace.com.br
-  affiliation: "LTrace Geociências"
-  orcid: ""
-title: "GeoSlicer - Integrated Open-Source Digital Rocks Platform"
-version: 2.8.0
-date-released: "2025-09-30"
+cff-version: 1.2.0
+message: "If you use any resource published in this repository, please cite it as below."
+authors:
+- family-names: "Passos de Figueiredo"
+  given-names: "Leandro"
+  email: leandro@ltrace.com.br
+  affiliation: "LTrace Geociências"
+  orcid: ""
+- family-names: "Bordignon"
+  given-names: "Fernando Luis"
+  email: fernando@ltrace.com.br
+  affiliation: "LTrace Geociências"
+  orcid: "https://orcid.org/0000-0001-5205-8042"
+- family-names: "Surmas"
+  given-names: "Rodrigo"
+  email: surmas@petrobras.com.br
+  affiliation: "Petróleo Brasileiro S.A."
+  orcid: ""
+- family-names: "Weck Pereira"
+  given-names: "Marcio Valerio"
+  email: marcio.weck@ltrace.com.br
+  affiliation: "LTrace Geociências"
+  orcid: ""
+- family-names: "Damian"
+  given-names: "Frederico"
+  email: frederico.damian@ltrace.com.br
+  affiliation: "LTrace Geociências"
+  orcid: ""
+- family-names: "Arenhart"
+  given-names: "Rafael"
+  email: rafael.arenhart@ltrace.com.br
+  affiliation: "LTrace Geociências"
+  orcid: ""
+- family-names: "Exterkoetter"
+  given-names: "Rodrigo"
+  email: rodrigo@ltrace.com.br
+  affiliation: "LTrace Geociências"
+  orcid: ""
+- family-names: "Müller"
+  given-names: "Gabriel"
+  email: gabriel.muller@ltrace.com.br
+  affiliation: "LTrace Geociências"
+  orcid: ""
+- family-names: "Formighieri"
+  given-names: "Giovanni"
+  email: giovanni@ltrace.com.br
+  affiliation: "LTrace Geociências"
+  orcid: ""
+- family-names: "Schwedersky"
+  given-names: "Rodrigo"
+  email: rodrigo.schwedersky@ltrace.com.br
+  affiliation: "LTrace Geociências"
+  orcid: ""
+- family-names: "Costa"
+  given-names: "Fernando"
+  email: fernando.costa@ltrace.com.br
+  affiliation: "LTrace Geociências"
+  orcid: ""
+- family-names: "Mello"
+  given-names: "Jean"
+  email: jean.mello@ltrace.com.br
+  affiliation: "LTrace Geociências"
+  orcid: ""
+- family-names: "Cenci"
+  given-names: "Rômulo"
+  email: romulo.cenci@ltrace.com.br
+  affiliation: "LTrace Geociências"
+  orcid: ""
+- family-names: "Boing de Souza"
+  given-names: "José Vinícius"
+  email: jose.boing@ltrace.com.br
+  affiliation: "LTrace Geociências"
+  orcid: ""
+- family-names: "Pacheco"
+  given-names: "Robim"
+  email: robim.pacheco@ltrace.com.br
+  affiliation: "LTrace Geociências"
+  orcid: ""
+title: "GeoSlicer - Integrated Open-Source Digital Rocks Platform"
+version: 2.8.1
+date-released: "2025-11-05"
 url: "https://github.com/petrobras/GeoSlicer"

changelog

@@ -1,44 +1,51 @@
-# Highlights:
-- Added a supervised MicroCT (MCT) segmentation module with real-time preview capabilities (PL-2843)
-- Introduced the CLAHE (Contrast Limited Adaptive Histogram Equalization) tool for image processing (MUSA-122)
-- Enhanced the Image Log Export Widget to support exporting proportions labelmap with segmentation (MUSA-130)
-- Improved ROI visibility and usability by simplifying the UI and refining range sliders for Image Log cropping (MUSA-125)
-
-# New features:
-- Added a supervised MicroCT (MCT) segmentation module with real-time preview capabilities (PL-2843)
-- Added new visualizations for Kabs (PL-2898)
-- Added the CLAHE (Contrast Limited Adaptive Histogram Equalization) tool (MUSA-122)
-- Added a bug report upload feature to the service desk for closed-source versions (PL-2857)
-
-# Improvements:
-- Enhanced the Image Log Export Widget to support exporting proportions labelmap with segmentation and improved identification of proportions labelmaps (MUSA-130)
-- Improved the clone action for nodes to preserve properties and reference nodes, including role references for tables (PL-2914)
-- Failed remote jobs can now be restarted when attempting to collect results, with retries occurring in the same directory (PL-2864)
-- Adjusted shape factor calculation (PL-2910)
-- Reset masking section when effects change (PL-2913)
-- Implemented a new parameters architecture for local simulations and enabled parameter node creation after collecting remote execution results. Parameters are now saved after simulation, and the load button in subscale parameters was reintroduced (PL-2904)
-- Added the option to load NetCDF files in the data source panel (PL-2901)
-- Improved handling of failed extractor jobs and partially failed simulation jobs. Enhanced method and prefix display for Pore Network Model (PNM) remote jobs (PL-2892)
-- Centered the modal progress bar (PL-2857)
-- Updated the node custom behavior feature (PL-2850)
-- Renamed the 'Volumes Crop' module to 'Crop' (PL-2868)
-- Improved ROI visibility and usability by simplifying the UI with `ctkRangeSlider` for Image Log cropping (MUSA-125)
-- Improved modeling by adding new labels, handling numbers greater than int32_max, and increasing processing speed
-- Adjusted segmentation visualization to show segment colors directly
-
-# Bug fixes:
-- Fixed an issue with member access during module panel updates (PL-2920)
-- Fixed bugs related to Kabs, Krel, and MICP calculations (PL-2918)
-- Fixed missing parameter, log step, two-phase cancel, and number of simulations bugs in the simulation workflow (PL-2904)
-- Fixed an issue with importing LabelMapVolume from CSV files (MUSA-134)
-- Fixed issues with `keep_temporary` and `timeout_enabled` checkboxes, and corrected snapshot selection visibility and behavior (PL-2895)
-- Fixed an error during DLIS export caused by a variable with an incorrect name (MUSA-133)
-- Addressed several bugs found during integration tests (PL-2850)
-- Addressed issues related to memory leaks, stability, and errors during scene closing or segmentation restarts (PL-2843)
-- Fixed buggy behavior in spinboxes and UI glitches related to range slider and ROI interaction (MUSA-125)
-
-# Removed:
-- Removed the 'Color smudge' option (PL-2913)
-- Removed Tesseract from the repository for open-source versions (PL-2868)
-- Removed the "Grow from seeds" option from the Thin Section environment (PL-1972)
-- Removed deprecated functionalities from the saturation module
+# Highlights:
+- Pore Network Model (PNM) simulation can now be executed on the cluster. (PL-2866)
+- A new module was added to the ImageLog environment for creating KDE (Kernel Density Estimation) tables and grouping instance segmenter results by depth and attribute for analysis. (MUSA-143)
+- MicroCT Loader now supports loading NetCDF files directly from a directory. (PL-2921)
+
+# New features:
+- A new module for calculating Euclidean Distance Transform (EDT) from segmentations was added. (PL-2946)
+- New capability to measure segment coordination in watershed algorithms, including an interface checkbox. (PL-2968)
+
+# Improvements:
+- Bug Report widget now handles missing exceptions and provides a fallback message, with a description length limit for JIRA compatibility and placeholder instructions. (PL-2942)
+- Segmentation effect highlight updated for improved visibility when active. (PL-2972)
+- Improved user feedback and error logging when project loading fails. (PL-2950)
+- Subscale widget now supports SIRR import, with updated interface and instructions. (PL-2966)
+- Users can now resume annotation after changing the layout. (PL-2964)
+- Added a 'do_preprocessing' parameter to SegmentInspectorCLI and a 'Include Preprocessing' checkbox to SegmentInspector, Islands, and Snow widgets in InstanceSegmenter, allowing control over morphological operations. (PL-2953)
+- Added support for float pore maps with values between 0 and 1, and changed the warning color from red to yellow. (PL-2951)
+- Pore Network Model (PNM) Simulation manual updated with cluster execution information and figure numbering adjustments. (PL-2949)
+- Jobs can now be collected while in progress if configured to allow it. (PL-2866)
+- GeoSlicer manual updated to support internationalization (i18n), along with updated installation and development articles, translated Virtual Segmentation Flow charts, and updated ImageLogExport documentation translation. (PL-2883)
+- Implemented a simple query to check the connection with BIAEP. (PL-2930)
+- ImageLog dimensions are now always visible, with interface improvements in spacing and labels.
+- Thin Section environment help URL and category were set.
+- Documentation for Euclidean Distance Transform was added. (PL-2946)
+- Variogram Analysis documentation added and improved. (PL-2990)
+- Manual page for Interactive Segmenter added. (PL-2964)
+- Manual pages updated with information about coordination calculation. (PL-2968)
+- MicroCT Filters documentation improved. (PL-2965)
+- Improved object orientation of subres model classes and unified node creation with `ExtractionNodesCreator`. (PL-2925)
+
+# Bug fixes:
+- Addressed an application crash that occurred when running SegmentInspector tests. (PL-2987)
+- Re-enabled the Pore Network Model (PNM) extract apply button. (PL-2988)
+- Restored the `throat.volume` property for use with OpenPNM. (PL-2986)
+- Improved plotting behavior for KDE module, including handling of single-line tables and single unique values. (MUSA-143)
+- Enhanced error and warning handling for the KDE module, with user-facing error messages for empty or single-depth report tables. (MUSA-143)
+- Addressed an issue where volumes sometimes did not fit the view. (PL-2964)
+- Corrected the subres parameter parser. (PL-2970)
+- Corrected the behavior of the MicroCT Export button. (PL-2948)
+- Addressed a traceback issue in the Pore Network Model (PNM) visualization module. (PL-2960)
+- Addressed tracebacks in KabsREV when the network is unavailable. (PL-2955)
+- Corrected an issue where parallelization was inadvertently disabled. (PL-2910)
+- Fixed one-phase simulations failing when no throats are resolved. (PL-2925)
+- KabsREV was updated to use the current `set_subres_model` parameters structure. (PL-2925)
+- Helper buttons now correctly use the provided help URL links. (PL-2883)
+- Addressed an invalid node reference issue during segment editor destruction. (PL-2927)
+- Fixed an issue related to module updates when interacting with original 3DSlicer modules. (PL-2927)
+- Corrected an issue where the AI Models widget failed to load models when a directory was selected. (PL-2912)
+- Fixed the order of remote protocol options. (PL-2930)
+- Addressed an issue preventing the loading of EuclideanDistanceTransform.py on Windows due to case-insensitivity. (PL-2946)
+- Fixed a bug during Volume loading environment caused by specific imports.