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Learning SciPy for Numerical and Scientific Computing Second Edition

Learning SciPy for Numerical and Scientific Computing Second Edition - Second Edition

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Learning SciPy for Numerical and Scientific Computing Second Edition

Learning SciPy for Numerical and Scientific Computing Second Edition

4.3 (10)
Buy this Book

Overview of this book

This book targets programmers and scientists who have basic Python knowledge and who are keen to perform scientific and numerical computations with SciPy.
Table of Contents (10 chapters)
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Preface
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Preface
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What this book covers
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What you need for this book
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Who this book is for
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Conventions
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Reader feedback
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Customer support
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1
1. Introduction to SciPy
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1. Introduction to SciPy
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What is SciPy?
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Installing SciPy
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SciPy organization
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How to find documentation
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Scientific visualization
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How to open IPython Notebooks
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Summary
2
2. Working with the NumPy Array As a First Step to SciPy
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2. Working with the NumPy Array As a First Step to SciPy
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Object essentials
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Using datatypes
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Indexing and slicing arrays
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The array object
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Array routines
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Summary
3
3. SciPy for Linear Algebra
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3. SciPy for Linear Algebra
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Vector creation
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Vector operations
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Creating a matrix
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Matrix methods
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Summary
4
4. SciPy for Numerical Analysis
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4. SciPy for Numerical Analysis
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The evaluation of special functions
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Convenience and test functions
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Univariate polynomials
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The gamma function
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The Riemann zeta function
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Airy and Bairy functions
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The Bessel and Struve functions
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Other special functions
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Interpolation
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Regression
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Optimization
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Integration
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Ordinary differential equations
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Lorenz attractors
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Summary
5
5. SciPy for Signal Processing
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5. SciPy for Signal Processing
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Discrete Fourier Transforms
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Signal construction
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Filters
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Summary
6
6. SciPy for Data Mining
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6. SciPy for Data Mining
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Descriptive statistics
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Distributions
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Interval estimation, correlation measures, and statistical tests
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Distribution fitting
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Distances
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Clustering
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Summary
7
7. SciPy for Computational Geometry
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7. SciPy for Computational Geometry
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The structural model of oxides
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A finite element solver for Laplace's equation
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Summary
8
8. Interaction with Other Languages
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8. Interaction with Other Languages
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Interaction with Fortran
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Interaction with C/C++
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Interaction with MATLAB/Octave
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Summary
9
Index
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Index

The structural model of oxides

In this example, we will cover the extraction of the structural model of a molecule of a bronze-type Niobium oxide, from HAADF-STEM micrographs (further background on this topic can be found in Chapter 5, High-Quality Image Formation by Nonlocal Means Applied to High-Angle Annular Dark-Field Scanning Transmission Electron Microscopy (HAADF--STEM) of the book Modeling Nanoscale Imaging in Electron Microscopy, Vogt T., Dahmen W., and Binev P., Springer Publishing.

The following diagram shows the HAADF-STEM micrograph of a bronze-type Niobium oxide (taken from http://www.microscopy.ethz.ch/BFDF-STEM.htm):

The structural model of oxides

Courtesy: ETH Zurich

For pedagogical purposes, we took the following approach to solving this problem:

  • Segmentation of the atoms by thresholding and morphological operations.
  • Connected component labeling to extract each single atom for posterior examination.
  • Computation of the centers of mass of each label identified as an atom. This presents us with a lattice of...
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