The SciDAVis Handbook

Ion Vasilief

Roger Gadiou

Knut Franke

Copyright © 2001, 2002, 2003, 2004, 2005 Ion Vasilief

Copyright © 2006, 2007 Roger Gadiou, Knut Franke and Ion Vasilief

Copyright © 2008 Knut Franke

This document is a handbook for using SciDAVis, a program for two- and three-dimensional graphical presentation of data sets and for data analysis.

This manual is organized in several chapters:

-The first one describes the main concepts and terms which are used in SciDAVis.

- The second chapter is a tutorial on how to obtain plots from different data sets. It is the one you need to read first to understand the basics of SciDAVis and to be able to draw plots.

- The three following chapters are descriptions of all the commands, buttons and dialogs used in SciDAVis. These chapters are the reference manual of SciDAVis.

- The two following chapters describe more deeply some specific possibilities of SciDAVis, that is the statistical and mathematical analysis of data, and the scripting.

Legal notice: Permission is granted to copy, distribute and/or modify this document under the terms of the GNU Free Documentation License, Version 1.1 or any later version published by the Free Software Foundation; with no Invariant Sections, with no Front-Cover Texts, and with no Back-Cover Texts.

Table of Contents
1. Introduction
What is SciDAVis?
Command Line Parameters
Specify a File
Command Line Options
General Concepts and Terms
Tables
Matrix
Plot Window
Note
Log Window
The Project Explorer
2. Drawing plots with SciDAVis
2D plots
2D plot from data.
2D plot from function.
3D plots
Direct 3D plot from a function
3D plot from a matrix
Multilayer Plots
Building a multilayer plot panel
Building a multilayer plot step by step
3. Command Reference
The File Menu
The Edit Menu
The View Menu
The Graph Menu
The Plot Menu
The Plot 3D menu
The Data Menu
The Analysis Menu
Commands for the analysis of data in tables
Commands for the analysis of curves in plots
The Table Menu
The Matrix Menu
The Format Menu
The Window Menu
Customization of 3D plots
4. The Toolbars
The Edit Toolbar
The File Toolbar
The Plot Toolbar.
The Table Toolbar.
The Plot 3D Toolbar.
5. The Dialogs
Add Error bars
Add Function
Add Layer
Add/Remove curves.
Add Text
Arrange Layers
Add Arrow
Column Options
Contour Curves Options
Custom Curves
Custom curves for lines and scatter plots
Custom curves for pie plots
Custom curves for box plots
Custom curves for pie histogram
Define surface plot
Export ASCII
Fast Fourier Transform
Integrate dialog
Non linear curve fit
General Plot Options
Plot Wizard
Project Explorer
Preferences Dialog
Printer-setup
Set Column Values
Set Dimensions...
Set options for Importation of ASCII files.
Set Properties...
Set Values...
Surface plot options
Text options
6. Analysis of data and curves
Fast Fourier Transform
Correlation
Convolution
Deconvolution
Non Linear Curve Fit
Fitting to specific curves
Fitting to a line
Fitting to a polynome
Fitting to a Bolzmann function
Fitting to a Gauss function
Fitting to a Lorentz function
Multi-Peaks fitting
Filtering of data curves
FFT low pass filter
FFT high pass filter
FFT band pass filter
FFT block band filter
Interpolation
7. Mathematical Expressions and Scripting
muParser
Python
Getting Started
Python Basics
Evaluation Reloaded
Mathematical Functions
Accessing SciDAVis's functions from Python
The Initialization File
A. Appendix
Credits and License
GNU Free Documentation License
How to obtain SciDAVis
Requirements
Installation from binary packages
Compilation and Installation from sources
8. Frequently asked questions
index
List of Tables
4-1. Edit toolbar commands.
4-2. File toolbar commands.
4-3. Plot toolbar commands
4-4. Table toolbar commands.
4-5. 3D Plot toolbar commands.
7-1. Supported Mathematical Operators
7-2. Mathematical Functions
7-3. Non-Mathematical Functions
7-4. Supported Mathematical Functions
List of Figures
1-1. A typical SciDAVis session
1-2. The SciDAVis table
1-3. The SciDAVis matrix
1-4. An example of SciDAVis 2D graph
1-5. The SciDAVis Note Window
1-6. The SciDAVis Log window
1-7. The SciDAVis Project Explorer
2-1. A simple 2D plot: the table.
2-2. A simple 2D plot: the default plot.
2-3. A simple 2D plot: the plot finished.
2-4. A 2D plot with two Y axis.
2-5. Direct plot of a function.
2-6. Function plot: filling of the X column.
2-7. Function plot: filling of the Y column.
2-8. Example of a 3D Plots.
2-9. Definition of a new surface 3D plot
2-10. The 3D surface plot created by default
2-11. The 3D surface plot after customizations
3-1. The Smooth -> Moving Window Average... dialog.
3-2. The Smooth -> Moving Window Average... dialog.
3-3. The FFT Filter -> Low Pass... dialog.
3-4. The FFT Filter -> High Pass... dialog.
3-5. The FFT Filter -> Band Pass... dialog.
3-6. The FFT Filter -> Band Block... dialog.
3-7. The Interpolate... dialog.
4-1. The SciDAVis Edit Toolbar
4-2. The SciDAVis File Toolbar
4-3. The SciDAVis Plot Toolbar
4-4. The SciDAVis Table Toolbar
4-5. The SciDAVis Plot 3D Toolbar
5-1. The Add Error Bars... dialog.
5-2. A plot with X and Y Error Bars.
5-3. The Add Function... dialog box: cartesian coordinates.
5-4. The Add Function... dialog box: parametric coordinates.
5-5. The Add Function... dialog box: polar coordinates.
5-6. The Add Layer dialog box.
5-7. The Add/Remove Curves... dialog box.
5-8. The Add Text dialog box.
5-9. The Arrange Layers dialog
5-10. The Arrow options dialog: first tab
5-11. The Arrow options dialog: second tab
5-12. The Geometry dialog: third tab
5-13. The Column Options... dialog.
5-14. The Contour Options dialog.
5-15. The Custom Curves Dialog: Line formatting.
5-16. The Custom Curves Dialog: Plot Associations.
5-17. The Custom Curves Dialog: Line formatting.
5-18. The Custom Curves Dialog: Symbol formatting.
5-19. The Custom Curves Dialog for pies: pie segment formatting.
5-20. The Custom Curves Dialog for box: pattern formatting.
5-21. The Custom Curves Dialog for box: whiskers formatting.
5-22. The Custom Curves Dialog for box: percentile formatting.
5-23. The Custom Curves Dialog for histogram: pattern formatting.
5-24. The Custom Curves Dialog for histogram: spacing formatting.
5-25. The Custom Curves Dialog for histogram: data formatting.
5-26. The New -> New Surface 3D Plot dialog box.
5-27. Export of a selection in a table to an ASCII file.
5-28. The FFT... dialog box for a curve.
5-29. The FFT... dialog box for a table.
5-30. The Integrate... dialog box.
5-31. The first step of the Non Linear Curve Fit... dialog box.
5-32. The second step of the Non Linear Curve Fit... dialog box.
5-33. General plot options dialog: the scale tab.
5-34. General plot options dialog: the grid tab.
5-35. General plot options dialog: the axis tab.
5-36. General plot options dialog: General settings.
5-37. The plot wizard dialog box.
5-38. The project explorer panel.
5-39. The preferences dialog: general parameters for the application.
5-40. The preferences dialog: table options.
5-41. The preferences dialog: 2D plot options.
5-42. The preferences dialog: 3D plot options.
5-43. The preferences dialog: fitting options.
5-44. The Print dialog.
5-45. The Set Column Values... dialog.
5-46. The Set Dimensions... dialog for matrix.
5-47. The Set Import Options... dialog box.
5-48. The Set Properties... dialog for matrix.
5-49. The Set Values... dialog for matrix.
5-50. The surface plot options dialog box.
5-51. The surface plot options dialog box with tab 5: aspect ratio.
5-52. The text options dialog.
6-1. An example of a inverse FFT.
6-2. An example of a correlation between two sinus functions.
6-3. The results of the Non Linear Curve Fit....
6-4. The results of a Fit Linear.
6-5. The results of a Fit Polynomial..., showing the initial data, the curve added to the plot, and the results in the log panel.
6-6. The results of a Fit Bolzmann (sigmoidal).
6-7. The results of a Fit Gaussian.
6-8. The results of a Fit Lorentzian.
6-9. The results of a Fit Multi-peak ->Gaussian....
6-10. Signal after a FFT low pass filter
6-11. Signal after a FFT high pass filter
6-12. Signal after a FFT band pass filter
6-13. Signal after a FFT block band filter
6-14. Comparison of the three methods of interpolation
List of Equations
6-1. Fourier equation
6-2. Covariance function of two signals x(t) and y(t)
6-3. Bolzmann equation
6-4. Gauss equation
6-5. Lorentz equation
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