User guide

Warning

This user guide is work in progress. It aims to provide a didactic, textbook-like introduction to pyGIMLi and is intended to eventually replace the Tutorials. The Examples will continue to exist in parallel.

• 1. Getting started
• 2. Fundamentals
  • 2.1. Software design
  • 2.2. Module/method overview
  • 2.3. Basic pyGIMLi classes
  • 2.4. Viewer interface
• 3. Data
  • 3.1. The DataContainer class
  • 3.2. Creating Sensors
  • 3.3. File export
  • 3.4. File format import
  • 3.5. Processing
  • 3.6. Visualization
• 4. Meshes
  • 4.1. Basics of the mesh class
  • 4.2. Mesh creation
    • 4.2.1. Creating a regular mesh / grid in 2D
    • 4.2.2. Creating an irregular mesh with pyGIMLi
  • 4.3. Utilizing markers
    • 4.3.1. Region markers
    • 4.3.2. Boundary markers
  • 4.4. Mesh import
    • 4.4.1. Import options for meshes in pyGIMLi
    • 4.4.2. Example: mesh generation using Gmsh
  • 4.5. Mesh modification
    • 4.5.1. Merging meshes
    • 4.5.2. Translating meshes
    • 4.5.3. Scaling meshes
    • 4.5.4. Rotating meshes
  • 4.6. Mesh export
• 5. Inversion
  • 5.1. Theory
    • 5.1.1. The objective function
    • 5.1.2. Regularization
    • 5.1.3. Minimization
      • 5.1.3.1. Gradient-based methods
    • 5.1.4. Newton-type methods
      • 5.1.4.1. Gauss-Newton method
    • 5.1.5. Transformations
    • 5.1.6. Running inversion
    • 5.1.7. Error model and misfit
    • 5.1.8. Model appraisal
    • 5.1.9. Frameworks
• 6. Modelling
  • 6.1. Finite Elements for Poisson equation
  • 6.2. Boundary conditions (BC)
  • 6.3. Modelling in the halfspace
• 7. Visualization
  • 7.1. Plotting in 2D
    • 7.1.1. Plotting meshes and models
  • 7.2. Plotting in 3D
    • 7.2.1. Plotting meshes and models in 3D
  • 7.3. External plotting
• 8. Advanced topics
  • 8.1. Setting up your own inversion with custom forward operator
  • 8.2. Matrices
    • 8.2.1. Dense matrix Matrix
    • 8.2.2. Index-based sparse matrix SparseMapMatrix
    • 8.2.3. Column-compressed matrix SparseMatrix
    • 8.2.4. Diagonal matrices
    • 8.2.5. Weighted matrices
    • 8.2.6. Combinations of matrices
    • 8.2.7. Block matrices
    • 8.2.8. Matrix combinations
    • 8.2.9. Matrix wrappers
    • 8.2.10. Matrix generators
    • 8.2.11. Geostatistical constraint matrix
  • 8.3. HPC & Parallel computing
  • 8.4. Caching