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README.md

@@ -1,128 +1,110 @@
----
-license: apache-2.0
-datasets:
-- nikoloside/break4models
-language:
-- en
-pipeline_tag: other
-tags:
-- fracture
-- game
-- 3d
-- physical
-- animation
----
-# DeepFracture
+# DeepFracture: A Generative Approach for Predicting Brittle Fractures with Neural Discrete Representation Learning
 
-## Model Description
+This is a collection of pre-trained models for deepfracture: a conditional vq-vae model for predicting fracture pattern from impulse code, trained on the [Break4Models](https://huggingface.co/datasets/nikoloside/break4models) dataset created by [FractureRB](https://github.com/david-hahn/FractureRB).
 
-- **Model type**: 3D Fracture Pattern Prediction via impulse-code conditional VQ-VAE models
-- **Language(s)**: Python
-- **License**: Apache-2.0
-- **Finetuned from model**: Custom architecture
 
-### Model Sources
+📖 **For more details, please visit:**
+- [GitHub Repository](https://github.com/nikoloside/TEBP)
+- [Project Page](https://nikoloside.graphics/deepfracture/)
 
-- **Repository**: https://github.com/nikoloside/TEBP
-- **Paper**: https://doi.org/10.1111/cgf.70002
-- **Demo**: [WIP]
+## Overview
 
-## Uses
+These models are designed to predict fracture patterns based on impact conditions. Each model is trained on a specific target shape and can be used for real-time physics simulation and computer graphics applications.
 
-### Direct Use
+## Model Architecture
 
-These models are designed for:
-- Computer graphics applications
-- Game development
-- Virtual reality environments
-- Paper code release
+The models use an encoder-decoder architecture:
+- **Encoder**: Processes input impulse conditions and generates latent representations
+- **Decoder**: Reconstructs GS-SDF(Geometrically-Segmented Signed Distance Fields) from latent representations
+- **Training**: Supervised learning on physics simulation data
 
-### Out-of-Scope Use
+## Available Models
 
-- Medical applications
-- Safety-critical systems
-- High-precision engineering simulations
-
-## Bias, Risks, and Limitations
-
-### Bias
+```
+pre-trained-v2/
+├── base/           # Base object model
+├── pot/            # Pot object model
+├── squirrel/       # Squirrel object model
+├── bunny/          # Bunny object model
+├── lion/           # Lion object model
+├── objs/           # Different original mesh files
+├── csv/            # Initial collision scene
+└── README.md       # This file
+```
 
-The models are trained on synthetic simulation data and may not generalize well to real-world scenarios with different material properties or environmental conditions.
+Each model directory contains:
+- `{shape}-encoder.pt` - Encoder weights
+- `{shape}-decoder.pt` - Decoder weights
+- `{shape}-1000-encoder.pt` - Encoder weights (1000 epoch version)
+- `{shape}-1000-decoder.pt` - Decoder weights (1000 epoch version)
 
-### Risks
+Other folders:
+- `{shape}.obj` - Reference original 3D mesh file
+- `{shape}-{csv_num}.obj` - Reference initial collision scene. Containing pos, direct, impulse strength.
 
-- Models may produce unrealistic deformations under extreme conditions
-- Performance may significantly different from training data
-- No guarantees for physical accuracy in safety-critical applications
+## Usage
 
-### Limitations
+### Loading Models
 
-- Limited to the specific one target shape and object categories in the training dataset
-- Be able to reach real-time inference in network, but need resconstruction within 2-10 seconds
+```python
+import torch
+from your_model_architecture import Encoder, Decoder
 
-## Training Details
+# Load encoder
+encoder = Encoder()
+encoder.load_state_dict(torch.load('base/base-encoder.pt'))
+encoder.eval()
 
-### Training Data
+# Load decoder  
+decoder = Decoder()
+decoder.load_state_dict(torch.load('base/base-decoder.pt'))
+decoder.eval()
 
-- **Dataset**: Break4Model dataset
-- **Training samples**: Varies by model (277-433 samples per category)
-- **Validation samples**: 20% of training data
-- **Data preprocessing**: Normalized impact conditions and geometry of GS-SDF
+# Load reference mesh
+reference_mesh = 'objs/base.obj'
+init_collision = 'csv/base-261.txt'
+work_path = 'result/base-exp-1/
+```
 
-### Training Procedure
+### Inference
 
-- **Training regime**: Supervised learning
-- **Optimizer**: Adam
-- **Learning rate**: 1e-3 - 1e-5
-- **Batch size**: 1
-- **Training epochs**: 1000
-- **Hardware**: NVIDIA RTX 3090 GPU
-- **Training time**: ~24 hours per model
+- [Example](https://github.com/nikoloside/TEBP/blob/main/04.Run-time/predict-runtime.py)
 
-### Training Results
+- [Details](https://github.com/nikoloside/TEBP/blob/main/04.Run-time/MorphoImageJ.py#L34)
 
-(metrics and performance)[https://doi.org/10.1111/cgf.70002]
+```python
+# Prepare input conditions
+input_conditions = prepare_impact_conditions(impact_point, velocity, impulse_strength)
 
-## Evaluation
+# Encode
+with torch.no_grad():
+    latent = encoder(input_conditions)
+    
+# Decode
+latent = decoder.cook(latent)
+gssdf_voxel = deocoder.predict(latent)
 
-### Testing Data
+# Apply to reference mesh
+result_mesh = processCagedSDFSeg(gssdf_voxel, work_path, reference_mesh, isBig = False, maxValue = 1.0)
+```
 
-- **Dataset**: Break4Models
-- **Metrics**: Geometric accuracy, Fragment size, Inference time, Fragment distribution, Surface normals, MPCD (Multiple-Phase Charmfer Distance)
+## Model Performance
 
-### Results
+(metrics and performance)[https://doi.org/10.1111/cgf.70002]
 
-The models achieve high accuracy in predicting fracture patterns while maintaining nearly real-time performance suitable for interactive applications.
 
-## Environmental Impact
+## Training Details
 
-- **Hardware Type**: GPU
-- **Hours used**: ~24 hours per model
 - **Dataset**: Break4Model dataset
 - **Framework**: PyTorch
 - **Optimizer**: Adam
 - **Loss Function**: L2 Loss
 - **Training Time**: ~24 hours per model on NVIDIA RTX 3090
 
-## Technical Specifications
-
-### Model Architecture
-
-- **Encoder**: SIREN Layer
-- **Decoder**: CNN
-- **Parameters**: ~2M parameters per model
-- **Input**: Impact conditions (position, velocity, impulse strength) from Bullet3
-- **Output**: GS-SDF (Geometrically-Segmented Signed Distance Fields)
-
-### Compute Requirements
-
-- **Training**: NVIDIA RTX 3090 or equivalent
-- **Inference**: CPU or GPU
-- **Memory**: 8GB RAM minimum
-- **Storage**: ~200MB per model
-
 ## Citation
 
+If you use these models in your research, please cite:
+
 ```bibtex
 @article{huang2025deepfracture,
 author = {Huang, Yuhang and Kanai, Takashi},
@@ -137,10 +119,10 @@ eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1111/cgf.70002}
 }
 ```
 
-## Data Card Authors
+## License
 
-Huang Niko(nikoloside), Fang Chaowei(fangsunjian)
+APACHE 2.0
 
-## Data Card Contact
+## Contact
 
-https://github.com/nikoloside/TEBP
+For questions or issues, please open an issue on the Hugging Face model page.

csv/base-261.csv

@@ -0,0 +1,2 @@
+collisionObject2;base1;0;0;0;0;0;0;0;0;0;0;0;0;0;1; 0.1;0.01;3.10E+09;0.327;1000;7.60E+05;1.00E+03;6.0;1500;0;default;10;1
+collisionObject1;sphere1;-2.56583;1.53773;0.227859;0;0;0;42.7638;-25.6288;-3.79765;0;0;0;0;1; 0.6;0.1 ;3.10E+09;0.327;8900;7.60E+99;1.00E+03;3.0;  60;0;default;-1;1

csv/bunny-260.csv

@@ -0,0 +1,2 @@
+collisionObject2;bunny1;0;0;0;0;0;0;0;0;0;0;0;0;0;1; 0.1;0.01;3.10E+09;0.327;1000;7.60E+05;1.00E+03;6.0;1500;0;default;10;1
+collisionObject1;sphere1;0.10268;0.822366;2.88326;0;0;0;-2.33654;-18.7134;-65.6102;0;0;0;0;1; 0.6;0.1 ;3.10E+09;0.327;8900;7.60E+99;1.00E+03;3.0;  60;0;default;-1;1

csv/bunny-261.csv

@@ -0,0 +1,2 @@
+collisionObject2;base1;0;0;0;0;0;0;0;0;0;0;0;0;0;1; 0.1;0.01;3.10E+09;0.327;1000;7.60E+05;1.00E+03;6.0;1500;0;default;10;1
+collisionObject1;sphere1;-2.56583;1.53773;0.227859;0;0;0;42.7638;-25.6288;-3.79765;0;0;0;0;1; 0.6;0.1 ;3.10E+09;0.327;8900;7.60E+99;1.00E+03;3.0;  60;0;default;-1;1

csv/pot-79.csv

@@ -0,0 +1,2 @@
+collisionObject2;pot1;0;0;0;0;0;0;0;0;0;0;0;0;0;1; 0.1;0.01;3.10E+09;0.327;1000;7.60E+05;1.00E+03;6.0;1500;0;default;10;1
+collisionObject1;sphere1;1.26043;1.17937;-2.45365;0;0;0;-40.8424;-38.2156;79.5069;0;0;0;0;1; 0.6;0.1 ;3.10E+09;0.327;8900;7.60E+99;1.00E+03;3.0;  60;0;default;-1;1

csv/squirrel-260.csv

@@ -0,0 +1,2 @@
+collisionObject2;squirrel1;0;0;0;0;0;0;0;0;0;0;0;0;0;1; 0.1;0.01;3.10E+09;0.327;1000;7.60E+05;1.00E+03;6.0;1500;0;default;10;1
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fiji/fiji-linux64/Fiji.app/Contents/Info.plist

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+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "https://www.apple.com/DTDs/PropertyList-1.0.dtd">
+<plist version="1.0">
+	<dict>
+		<key>CFBundleAllowMixedLocalizations</key>
+		<true/>
+		<key>CFBundleDevelopmentRegion</key>
+		<string>English</string>
+		<!--
+		<key>CFBundleDocumentTypes</key>
+		<array>
+			<dict>
+				<key>CFBundleTypeExtensions</key>
+				<array>
+					<string>*</string>
+				</array>
+				<key>CFBundleTypeMIMETypes</key>
+				<array>
+					<string>*/*</string>
+				</array>
+				<key>CFBundleTypeName</key>
+				<string>any</string>
+				<key>CFBundleTypeRole</key>
+				<string>Viewer</string>
+				<key>LSTypeIsPackage</key>
+				<false/>
+			</dict>
+		</array>
+		-->
+		<key>CFBundleExecutable</key>
+		<string>ImageJ-macosx</string> <!-- <string>fiji-macos-universal</string> -->
+		<key>CFBundleGetInfoString</key>
+		<string>Fiji for macOS</string>
+		<key>CFBundleIconFile</key>
+		<string>Fiji.icns</string>
+		<key>CFBundleIdentifier</key>
+		<string>sc.fiji</string>
+		<key>CFBundleInfoDictionaryVersion</key>
+		<string>6.0</string>
+		<key>CFBundleName</key>
+		<string>Fiji</string>
+		<key>CFBundlePackageType</key>
+		<string>APPL</string>
+		<!-- See https://developer.apple.com/app-store/categories/ for list of AppStore categories -->
+		<key>LSApplicationCategoryType</key>
+		<string>public.app-category.utilities</string>
+		<key>CFBundleVersion</key>
+		<string>1</string>
+		<key>NSHumanReadableCopyright</key>
+		<string>Copyright (C) 2024</string>
+		<key>NSHighResolutionCapable</key>
+		<string>true</string>
+		<!--
+			<key>NSPrincipalClass</key>
+			<string>NSApplication</string>
+		-->
+		<key>fiji</key>
+		<dict>
+			<key>memory</key>
+			<string>auto</string>
+			<key>system</key>
+			<string>0</string>
+			<key>allowMultiple</key>
+			<string>false</string>
+			<key>JVMOptions</key>
+			<string></string>
+			<key>DefaultArguments</key>
+			<string></string>
+		</dict>
+	</dict>
+</plist>

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fiji/fiji-linux64/Fiji.app/ImageJ2.desktop

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+[Desktop Entry]
+Version=1.0
+Name=ImageJ
+GenericName=ImageJ
+X-GNOME-FullName=ImageJ
+Comment=Scientific Image Analysis
+Type=Application
+Categories=Education;Science;ImageProcessing;
+Exec=/home/nikoloside/Downloads/fiji-linux64/Fiji.app/ImageJ-linux64 %F
+TryExec=/home/nikoloside/Downloads/fiji-linux64/Fiji.app/ImageJ-linux64
+Terminal=false
+StartupNotify=true
+MimeType=image/*;
+Icon=/home/nikoloside/Downloads/fiji-linux64/Fiji.app/images/icon.png
+StartupWMClass=net-imagej-launcher-ClassLauncher

fiji/fiji-linux64/Fiji.app/README.md

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+ImageJ2 is a new version of [ImageJ](http://imagej.net/) seeking to strengthen
+both the software and its community. Internally, it is a total redesign of
+ImageJ, but it is backwards compatible with ImageJ 1.x via a "legacy layer" and
+features a user interface closely modeled after the original.
+
+Under the hood, ImageJ2 completely isolates the image processing logic from the
+graphical user interface (UI), allowing ImageJ2 commands to be used in many
+contexts, including headless in the cloud or on a server such as
+[OMERO](http://openmicroscopy.org/site/support/omero4), or from within another
+application such as [KNIME](http://knime.org/),
+[Icy](http://icy.bioimageanalysis.org/) or
+[CellProfiler](http://cellprofiler.org/) (a Python application).
+
+ImageJ2 has an N-dimensional data model driven by the powerful
+[ImgLib2](http://imglib2.net/) library, which supports image data expressed in
+an extensible set of numeric and non-numeric types, and accessed from an
+extensible set of data sources. ImageJ2 is driven by a state-of-the-art,
+collaborative development process, including version control, unit testing,
+automated builds via a continuous integration system, a bug tracker and more.
+
+We are collaborating closely with related projects including
+[Fiji](http://fiji.sc/), [SCIFIO](http://scif.io/) and
+[OME](http://openmicroscopy.org/), and are striving to deliver a coherent
+software stack reusable throughout the life sciences community and beyond. For
+more details, see the [SciJava web site](http://scijava.org/).
+
+ImageJ2 is currently in the "beta" stage, meaning the code is not finished. It
+is being released for early community feedback and testing. Comments, questions
+and bug reports are much appreciated!
+
+To maintain ImageJ's continuity of development, we have modeled the application
+after ImageJ v1.x as much as is reasonable. However, please be aware that
+ImageJ2 is essentially a total rewrite of ImageJ from the ground up. It
+provides backward compatibility with older versions of ImageJ by bundling the
+latest v1.x code and translating between "legacy" and "modern" image
+structures.
+
+For more details on the project, see the [ImageJ web site](http://imagej.net/).
+
+
+LICENSING
+---------
+
+ImageJ2 is distributed under a
+[Simplified BSD License](http://en.wikipedia.org/wiki/BSD_licenses);
+for the full text of the license, see
+[LICENSE.txt](https://github.com/imagej/imagej/blob/master/LICENSE.txt).
+
+For the list of developers and contributors, see
+[pom.xml](https://github.com/imagej/imagej/blob/master/pom.xml).
+
+
+IMAGEJ AS A LIBRARY
+-------------------
+
+This repository is the master ImageJ application, which brings together all of
+ImageJ under the artifact
+[net.imagej:imagej](http://maven.imagej.net/index.html#nexus-search;gav~net.imagej~imagej~~~~kw,versionexpand).
+It is the easiest entry point if you are looking to use ImageJ as a library from
+your own software. E.g., in your Maven `pom.xml`:
+
+```
+<parent>
+  <groupId>net.imagej</groupId>
+  <artifactId>pom-imagej</artifactId>
+  <version>2.35</version>
+</parent>
+...
+<dependency>
+  <groupId>net.imagej</groupId>
+  <artifactId>imagej</artifactId>
+</dependency>
+```
+
+We recommend inheriting from the
+[pom-imagej](https://github.com/imagej/pom-imagej) parent, although it is not
+required. (If you do not, you will need to include the `<version>` of ImageJ in
+your `<dependency>` declaration.)
+
+
+DEPENDENCIES
+------------
+
+This component depends on other, lower level components, each of which lives in
+its own repository:
+
+* [ImageJ Common](https://github.com/imagej/imagej-common)
+* [ImageJ Legacy](https://github.com/imagej/imagej-legacy)
+* [ImageJ OPS](https://github.com/imagej/imagej-ops)
+* [ImageJ Updater](https://github.com/imagej/imagej-updater)
+* [ImgLib2](https://github.com/imglib/imglib)
+* [SCIFIO](https://github.com/scifio/scifio)
+* [SciJava Common](https://github.com/scijava/scijava-common)
+
+It also includes uses various "plugin" components at runtime:
+
+* [Imagej Plugins: Commands](https://github.com/imagej/imagej-plugins-commands)
+* [Imagej Plugins: Tools](https://github.com/imagej/imagej-plugins-tools)
+* [Imagej Plugins: Uploader: SSH](https://github.com/imagej/imagej-plugins-uploader-ssh)
+* [Imagej Plugins: Uploader: WebDAV](https://github.com/imagej/imagej-plugins-uploader-webdav)
+* [SciJava Plugins: Platforms](https://github.com/scijava/scijava-plugins-platforms)
+* [SciJava Plugins: Text: Markdown](https://github.com/scijava/scijava-plugins-text-markdown)
+* [SciJava Plugins: Text: Plain](https://github.com/scijava/scijava-plugins-text-plain)
+* [Scripting: Beanshell](https://github.com/scijava/scripting-beanshell)
+* [Scripting: Clojure](https://github.com/scijava/scripting-clojure)
+* [Scripting: Java](https://github.com/scijava/scripting-java)
+* [Scripting: JavaScript](https://github.com/scijava/scripting-javascript)
+* [Scripting: JRuby](https://github.com/scijava/scripting-jruby)
+* [Scripting: Jython](https://github.com/scijava/scripting-jython)
+
+See the [pom.xml](pom.xml) for a complete list of dependencies.
+
+
+BUGS
+----
+
+For a list of known issues, see the
+[issue tracking system](http://trac.imagej.net/report/1).
+
+Please report any bugs by following the [instructions
+online](http://imagej.net/Bugs).

fiji/fiji-linux64/Fiji.app/WELCOME.md

@@ -0,0 +1,120 @@
+# Welcome to ImageJ2!
+
+[ImageJ2](http://developer.imagej.net/about) is an effort to broaden the
+functionality of ImageJ beyond the limitations of ImageJ 1.x, to support the
+next generation of multidimensional scientific imaging.
+
+To ensure backwards compatibility, we designed ImageJ2 to fully integrate into
+the existing ImageJ user interface. This allows you to keep using ImageJ in
+familiar ways, while providing the ability to migrate toward more powerful new
+features as needed.
+
+The [Fiji](http://fiji.sc/) distribution of ImageJ has shipped with beta
+versions of ImageJ2 for quite some time, so you may already be familiar with
+some of ImageJ2's features -- some of which, such as the
+[Updater](http://wiki.imagej.net/Updater) and
+[Launcher](http://wiki.imagej.net/Launcher), were originally developed as part
+of Fiji.
+
+## Features of ImageJ2
+
+ImageJ2 provides a wealth of new features and capabilities:
+
+* The ImageJ Updater makes it simple to keep your ImageJ up to date, and to
+  add new plugins by enabling additional
+  [Update Sites](http://wiki.imagej.net/Update_Sites).
+* New and enhanced file format support via the SCIFIO library (see below).
+* More powerful [Script Editor](http://wiki.imagej.net/Script_Editor) with
+  support for several scripting languages.
+* New commands:
+    * `Plugins > Debug > Dump Stack` for debugging when things
+      [hang](https://en.wikipedia.org/wiki/Hang_(computing)).
+    * `Plugins > Debug > System Information` for reporting on versions of
+      installed plugins and libraries.
+* Use ImageJ2's N-dimensional [ImgLib2](http://wiki.imagej.net/ImgLib2)-based
+  data structures (still in beta).
+* Write parameterized commands and scripts:
+    * Typed inputs and outputs with no dependence on AWT user interface.
+    * Mix and match ImageJ 1.x and ImageJ2 data structures.
+    * Plugins appear in the menu automatically without plugins.config files.
+    * Reusable in many contexts: KNIME, CellProfiler, OMERO, headless...
+
+## ImageJ2 is more than just an application
+
+ImageJ2 is also a collection of reusable software libraries built on the
+[SciJava](http://www.scijava.org/) software stack, using a powerful plugin
+framework to facilitate rapid development and painless user customization.
+
+The following software component libraries form the core of ImageJ2:
+
+* [ImageJ Common](https://github.com/imagej/imagej-common) -
+  The core image data model, using ImgLib2.
+* [ImageJ OPS](https://github.com/imagej/imagej-ops) -
+  An extensible framework for reusable image processing algorithms.
+* [ImageJ Updater](https://github.com/imagej/imagej-updater) -
+  A mechanism to update individual plugins and libraries within ImageJ.
+* [ImageJ Legacy](https://github.com/imagej/imagej-legacy) -
+  Provides complete backwards compatibility with ImageJ 1.x.
+* [SciJava Common](https://github.com/scijava/scijava-common) -
+  The core frameworks for plugins, modules and the application itself.
+
+## Improved image I/O with the SCIFIO library
+
+ImageJ2 uses the [SCIFIO](http://wiki.imagej.net/SCIFIO) library (SCientific
+Image Format Input and Output) by default for most image input tasks. You can
+change this behavior at any time by running `Edit > Options > ImageJ2` and
+modifying the `Use SCIFIO when opening files` option.
+
+### Benefits of using SCIFIO
+
+SCIFIO is focused on robust and extensible support for reading and writing
+image file formats. Using it with ImageJ provides many advantages:
+
+* There is no need to call a special SCIFIO plugin; it works with commands like
+  `File > Open` automatically.
+* There are additional import options available via the `File > Import >
+  Image...` command.
+* There is a [Bio-Formats](http://fiji.sc/Bio-Formats) plugin for SCIFIO,
+  included with the [Fiji](http://fiji.sc/) distribution of ImageJ, that adds
+  automatic support for over a hundred life sciences file formats.
+* Additional SCIFIO file format plugins can be dropped into ImageJ and will
+  also work automatically.
+* Unlike the ImageJ 1.x TIFF implementation, SCIFIO's support for TIFF adheres
+  to the specification, allowing to successfully read many more sorts of TIFFs.
+* Similarly, SCIFIO supports more sorts of JPEG files since it uses its own
+  JPEG decoder.
+* SCIFIO also ships with support for several QuickTime codecs, allowing ImageJ
+  to read QuickTime MOV files even in 64-bit mode without QuickTime for Java.
+* SCIFIO supports many additional open file formats out of the box:
+    * animated GIF
+    * animated PNG
+    * encapsulated postscript (EPS)
+    * JPEG-2000
+    * Micro-Manager datasets
+    * Multi-image Network Graphics (MNG)
+    * Nearly Raw Raster Data (NRRD)
+    * Imspector OBF
+    * OME-TIFF (multidimensional rich metadata TIFF)
+    * OME-XML
+    * PCX
+    * PICT (even in 64-bit mode and/or without QuickTime for Java installed)
+* If SCIFIO cannot handle the image file, it falls back to ImageJ 1.x.
+* You can save to SCIFIO-supported file formats using the `File > Export >
+  Image...` command. Supported formats for export include:
+    * APNG
+    * AVI
+    * EPS
+    * ICS
+    * JPEG
+    * JPEG2000
+    * QuickTime
+    * TIFF
+
+### Current limitations of SCIFIO
+
+* SCIFIO is still in beta, so there is likely to be a higher incidence of bugs.
+  Issues can be reported on the
+  [SCIFIO issue tracker](https://github.com/scifio/scifio/issues).
+* Although we strive for full backwards compatibility, some files may appear
+  slightly different when opened.
+* Opening files with SCIFIO is not fully macro recordable yet.

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