/comvi

Comparative Visualization of Molecular Surfaces using Similarity-based Clustering

Primary LanguageC++BSD 3-Clause "New" or "Revised" LicenseBSD-3-Clause

comvi

Comparative Visualization of Molecular Surfaces using Similarity-based Clustering

Megamol-specific terms/keywords:

  • *.mmprj: MegaMol Project files These xml-based files can be invoked (with specific parameters given by the Configurator) with the megamol-console.

  • Configurator: C#/Mono Project files creator, with visual drag and drop interface for project generation. MM-Creator creates a xml-file (the *.mmprj files from above) which the megamol can understand.

  • StateFile: generated by the configurator upon first startup, holds all kinds of information about the mm-binary. is nessecary if you want to configure your project with the interface

Dependencies:

  • python:
    • everything was written in python 3.6
    • not tested in python<3.6 (or 2.7 for that matter)
    • dependencies:
      • numpy
      • tensorflow
      • sklearn
      • skimage
      • scipy
      • cv2
      • matplotlib for 2d plot-viz
  • comvi C++:
    • not sure
    • probably only vanilla c++11/14 (?) apart from:
      • glfw
      • glew
      • glad
      • glm
      • std_image
      • stdlib
      • KHR
      • opengl

Folder Structure:

  • papers:

    • contains all relevant papers for:
      • clustering
      • viz
      • feature extraction etc.

  • comvi Ausarbeitung:

    • contains .tex sourcecode for the comvi paper

  • programming:

    • contains:
      • PCA (python):
        • using dimensionality of extracted feature vector to cluster images
        • should be ported to C++ for the final project
      • SSIM (python):
        • uses similarity measure wihout relying on feature vector to cluster images
        • should be ported to C++ for the final project
      • image-generation (python):
        • will be used to generate images for the clustering
        • performs: pdb aggregation, pdb generation, image generation
      • comvi:
        • C++ project that will be used as a 2D rendered as a plugin in Megamol

  • Images:

    • Contains Images to sample
    • Delete when image-generation is up and functional for arbitraty pdb datasets

Already Implemented:

  • feature extraction

  • similarity measure (SSIM, cosine (with feature vector))

  • clustering with DBSCAN

  • dim. reduction

  • image generation

  • image exploration in clusterview