scikit-surgery / scikit-surgeryfredmatplotlib Goto Github PK

1.0 1.0 1.0 434 KB

This is the legacy Matplotlib frontend for SciKIt-SurgeryFRED. You should try this instead: https://github.com/UCL/scikit-surgeryfred

License: Other

Python 100.00%

scikit-surgeryfredmatplotlib's Introduction

scikit-surgery

SciKit-Surgery is a collection of compact libraries developed for surgical navigation. Individual libraries can be combined using Python to create clinical applications for translational research. However because each application's requirements are unique the individual SciKit-Surgery libraries are kept independent, enabling them to be maintained, modified and combined in new ways to create new clinical applications. Keeping the libraries independent enables researchers to implement novel algorithms within a small library that can be readily reused and built on by the research community.

A typical clinical application might consist of an imaging source (e.g. SciKit-SurgeryBK to stream ultrasound images), a tracking source (e.g. SciKitSurgery-NDITracker) to locate the images in space, an image processor (e.g. SciKit-SurgeryTorch) to segment anatomy from the image, and a visualisation layer (e.g. SciKit-SurgeryVTK)

SciKit-Surgery is developed at the Wellcome EPSRC Centre for Interventional and Surgical Sciences, part of University College London (UCL).

Packages

scikit-surgerycore - Algorithms/tools common to all scikit-surgery packages
scikit-surgeryimage - Image processing algorithms using OpenCV
scikit-surgeryvtk - Implements VTK functionality for IGS applications
scikit-surgeryutils - Example applications/utilities
scikit-surgerycalibration - Calibration algorithms (camera/pointer/ultrasound etc)
scikit-surgerysurfacematch - Stereo reconstruction and point cloud matching
scikit-surgerytf - IGS models implemented in TensorFlow
scikit-surgerytorch - IGS models implemented in PyTorch
scikit-surgerynditracker - Interface for Northern Digital (NDI) trackers. Vicra, Spectra, Vega, Aurora.
scikit-surgeryarucotracker - Interface for OpenCV ARuCo.
scikit-surgeryspeech - Speech/Wakeword detection

Please see Documentation for further module details.

Tutorials

Tutorials are split into three groups, those that show how to assemble SciKit-Surgery libraries into an application, those that concentrate on the workings a single application, and those that are aimed at general education in image guided interventions using SciKit-Surgery.

General Tutorials

Use SciKit-SurgeryUtils and SciKit-SurgeryArUcoTracker to build an AR application using your webcam.

* ROS Integration scikit-surgeryvtk

scikit-surgeryimage

Point/Chessboard detectors

scikit-surgerycalibration

* Camera Calibration

Educational Tutorials

Encountering Problems?

Please check list of common issues.

Contributing

Please see the contributing guidelines.

Useful links

Licensing and copyright

Acknowledgements

Supported by Wellcome and EPSRC.

scikit-surgeryfredmatplotlib's People

Contributors

Stargazers

Watchers

Forkers

mianasbat

scikit-surgeryfredmatplotlib's Issues

Tidy GUI and add reset button

Move to sksorg

Tidy up plotter

Formatting issue where the text labels is non response

So the app is working and in full screen or full window mode everything looks fine. However A minor issue is that when the GUI window is made smaller the text labels stays the same. The images become smaller but the labels stays the same as shown in the screen capture.

Re-implement without Matplotlib

I've had problems with matplotlib on windows. Would it make more sense to reimplement the main two widgets just with QT. That would help fix problems with layout too.

Game?

Make a separate entry point for a game. You get four fiducials and a random FLE. Mouse click puts the treatment point, then needle trajectory is done by finding the closest point on a subset of the countour. You can mdodify the treatment volume. Then score is some function of the percentage of tumour successfully hit and the amount of non tumourous tissue hit.
The user can configure what information they are given out of FRE, estimated FLE, expected TRE or FLE?

Replace unkown brain

Pylint output seems a bit suspecious

According to the readme file, I tried to run pylint command on the repo and while it run fine it is giving some erronous output too. Screenshot attached for the start of output.
Steps to reproduce

git clone https://github.com/UCL/scikit-surgeryfred
cd scikit-surgeryfred
pip install pylint
pylint --rcfile=tests/pylintrc sksurgeryfred

Error when executing the library

I believe I got another error related to logging module when executing the sksurgeryfred.py. The steps to reproduce on MAC are

git clone https://github.com/UCL/scikit-surgeryfred
cd scikit-surgeryfred
python sksurgeryfred

The error screenshot is

Error when executing pytests

According to the readme file, I cloned the repo and run the pytest and I got the following error (screenshots attached). I am on Mac and Python version is 3.7.3 and pytest library is installed.
To reproduce the error

git clone https://github.com/UCL/scikit-surgeryfred
cd scikit-surgeryfred
python -m pytest

Pytest version

$ pip list | grep pytest
pytest                             4.3.1   
pytest-arraydiff                   0.3     
pytest-astropy                     0.5.0   
pytest-doctestplus                 0.3.0   
pytest-openfiles                   0.3.2   
pytest-remotedata                  0.3.1

It would be nice to have a sample image in tests directory.

I was able to clone the repo and run it fine. But I got the error message to supply the image argument, which is not an error basically. Wouldn't it be nice to provide a sample image in the scikit-surgeryfred/tests directory so that users could run it for testing.
To reproduce

git clone https://github.com/UCL/scikit-surgeryfred
cd scikit-surgeryfred
python sksurgeryfred.py

The screenshot of missing argument error is

So if we have an image in tests then users could do

python sksurgeryfred.py -image tests/image

git clone https://github.com/UCL/scikit-surgeryfred
cd scikit-surgeryfred
python sksurgeryfred.py

the screenshot is

Open terminal on mac
$ pip install git+https://github.com/UCL/FiducialRegistrationEducationalDemonstration

Here is the screenshot and error details.

pylint: disable=too-many-instance-attributes

in registration_game.py