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An interactive GUI for path tracing and extraction in 2D images. The inteded use is for 2D medical images of Amphisbaena sutures, but we have found that it extends well into other domains aswell.
Already a pro? Just edit this README.md and make it your own. Want to make it easy? [Use the template at the bottom](#editing-this-readme)!
The user places a start and end point between which the program automatically finds a viable path. The user can place multiple new guide points to help fit the path to their liking. The smoothness of the path can be adjusted aswell. Advanced settings are available.
## Add your files
The points making up the final path can be exported to a `.csv` file.
-[ ] [Create](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#create-a-file) or [upload](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#upload-a-file) files
-[ ] [Add files using the command line](https://docs.gitlab.com/ee/gitlab-basics/add-file.html#add-a-file-using-the-command-line) or push an existing Git repository with the following command:
-[ ] [Set up project integrations](https://lab.compute.dtu.dk/QIM/tools/tracing_sutures/-/settings/integrations)
## Collaborate with your team
-[ ] [Invite team members and collaborators](https://docs.gitlab.com/ee/user/project/members/)
-[ ] [Create a new merge request](https://docs.gitlab.com/ee/user/project/merge_requests/creating_merge_requests.html)
-[ ] [Automatically close issues from merge requests](https://docs.gitlab.com/ee/user/project/issues/managing_issues.html#closing-issues-automatically)
Use the built-in continuous integration in GitLab.
The program can be installed using pip:
-[ ] [Get started with GitLab CI/CD](https://docs.gitlab.com/ee/ci/quick_start/index.html)
-[ ] [Analyze your code for known vulnerabilities with Static Application Security Testing (SAST)](https://docs.gitlab.com/ee/user/application_security/sast/)
-[ ] [Deploy to Kubernetes, Amazon EC2, or Amazon ECS using Auto Deploy](https://docs.gitlab.com/ee/topics/autodevops/requirements.html)
-[ ] [Use pull-based deployments for improved Kubernetes management](https://docs.gitlab.com/ee/user/clusters/agent/)
-[ ] [Set up protected environments](https://docs.gitlab.com/ee/ci/environments/protected_environments.html)
***
# Editing this README
When you're ready to make this README your own, just edit this file and use the handy template below (or feel free to structure it however you want - this is just a starting point!). Thanks to [makeareadme.com](https://www.makeareadme.com/) for this template.
## Suggestions for a good README
Every project is different, so consider which of these sections apply to yours. The sections used in the template are suggestions for most open source projects. Also keep in mind that while a README can be too long and detailed, too long is better than too short. If you think your README is too long, consider utilizing another form of documentation rather than cutting out information.
```plaintext
pip install pt2d
```
## Name
Choose a self-explaining name for your project.
### Usage
## Description
Let people know what your project can do specifically. Provide context and add a link to any reference visitors might be unfamiliar with. A list of Features or a Background subsection can also be added here. If there are alternatives to your project, this is a good place to list differentiating factors.
To open the program type out `pt2d` in a terminal. The GUI looks the following:
## Badges
On some READMEs, you may see small images that convey metadata, such as whether or not all the tests are passing for the project. You can use Shields to add some to your README. Many services also have instructions for adding a badge.
Depending on what you are making, it can be a good idea to include screenshots or even a video (you'll frequently see GIFs rather than actual videos). Tools like ttygif can help, but check out Asciinema for a more sophisticated method.
The functionality of the program extends to the following:
## Installation
Within a particular ecosystem, there may be a common way of installing things, such as using Yarn, NuGet, or Homebrew. However, consider the possibility that whoever is reading your README is a novice and would like more guidance. Listing specific steps helps remove ambiguity and gets people to using your project as quickly as possible. If it only runs in a specific context like a particular programming language version or operating system or has dependencies that have to be installed manually, also add a Requirements subsection.
* Main window:S
* Start/end point of the path
* Add new points (left click)
* Drag points (hold left click on point and drag)S
* Drag image (hold left click and drag)
* Remove points (right click on point)
* Zoom (mouse wheel)
* Export as `.csv` file
* Advanced window:
* Rainbow toggle (displays a color gradient showing the order of points)
* Calibration of filter
* Resize dot (mouse wheel on dot)
* Line smoothing
* Contrast
* Displays contrasted blurred image
* Displays cost image
## Usage
Use examples liberally, and show the expected output if you can. It's helpful to have inline the smallest example of usage that you can demonstrate, while providing links to more sophisticated examples if they are too long to reasonably include in the README.
### Methodology
## Support
Tell people where they can go to for help. It can be any combination of an issue tracker, a chat room, an email address, etc.
The project follows a simple methodology somewhat similar to that of the livewire segmentation technique.
## Roadmap
If you have ideas for releases in the future, it is a good idea to list them in the README.
***Grayscaling:** The image is converted to grayscale for simpler processing.
***Contrasting:** The contrast in the image is enhanced to improve visibility of the path.
***Smoothing:** Gaussian blurring is applied to improve generalization.
***Edge detection:** The Canny edge detector is applied to generate an image highlighting the edges in the original image.
***Convolution:** A disk-shaped kernel, with values increasing radially from the center to the circumference, is convolved with the image to create a new image highlighting the centers of the paths.
***Cost image creation:** A cost image is generated by first identifying the maximum intensity value of the convolved image, `I_max`. The cost at each pixel is then computed as `(I_max - I(x,y))**4`, where `I(x,y)` represents the intensity at pixel `(x,y)`.
***Graph construction:** A graph is then constructed by connecting every pixel to it's 8 neighbouring pixels. The cost of going between two given pixels will simply be the average of the two pixel's values in the cost image.
***Pathfinding:** Djikstra's algorithm is then applied to find the cheapest path from the user placed start point to the user placed end point.
## Contributing
State if you are open to contributions and what your requirements are for accepting them.
### Known bugs & issues
For people who want to make changes to your project, it's helpful to have some documentation on how to get started. Perhaps there is a script that they should run or some environment variables that they need to set. Make these steps explicit. These instructions could also be useful to your future self.
* Guide points need to be placed in order from start to finish along the path for the extracted path not to overlap incorrectly.
* Dots don't currently scale with the image size, meaning the dots will appear small on large images.
You can also document commands to lint the code or run tests. These steps help to ensure high code quality and reduce the likelihood that the changes inadvertently break something. Having instructions for running tests is especially helpful if it requires external setup, such as starting a Selenium server for testing in a browser.
### Authors and acknowledgment
## Authors and acknowledgment
Show your appreciation to those who have contributed to the project.
This project is developed by Aske T. Rove, Christian L. Bjerregaard & Mikkel W. Breinstrup under the supervision of Hans M. Kjer & Felipe D. Matos at DTU Compute.
## License
For open source projects, say how it is licensed.
### License
## Project status
If you have run out of energy or time for your project, put a note at the top of the README saying that development has slowed down or stopped completely. Someone may choose to fork your project or volunteer to step in as a maintainer or owner, allowing your project to keep going. You can also make an explicit request for maintainers.
