User Manual

There are many different Matlab commands within Libisis. These include basic commands, such as taking the exponential of a dataset, through to integration and plotting commands. The following is an online user manual for the matlab interface of the Libisis software.

Overview

There are many different object types within Libisis used to store experimental data. Once an object is created, functions exist to manipulate the data contained within. The most common objects for plotting and data manipulation are IXTdataset_1d, IXTdataset_2d and IXTdataset_3d objects. IXTrunfile objects contain all raw data from a run.

IXTdataset_1d objects store signal and error information against one dimension (the x axis). Label and titling information is also stored. IXTdataset_2d objects also contain a second dimension (the y axis). As would be expected IXTdataset_3d objects contain yet another (z) dimension. All relevant data pertaining to a run can be stored in an IXTrunfile object. The object can be thought of as an array of IXTdataset_2d objects with a lot of additional information. IXTdataset_1d, IXTdataset_2d and IXTrunfile have fully implemented and similar functions, IXTdataset_3d is a special case and does not have many of the data manipulation functions as of yet.

Data is read into these objects (using methods described below) and can then be manipulated using many different tools and functions described in this documentation.

General Behaviour

Most functions share a general behaviour outlined here

Data Manipulation Functions

Input and Output Functions

Below are just a few of the possible read and write functions, other formats can also be used.

• getspectra, getspectrum - Read in spectra from IXTraw_file objects or from RAW files

• read_ascii, write_ascii - Read or write to text files

• read_points, write_points - Read or write to text files, forcing data to be point data

• read_hist, write_hist - Read or write to text files, forcing data to be histogram data

• read_slice, read_cut, read_mask - Special functions to read from other formats

• read_nxs - Read from Nexus file format

• Homer - Information about using Homer to import data into Libisis

Binary Operators

Binary operators such as +, -, *, etc. are used to perform arithmetic operations between datasets and/or numbers

Elementary Functions

Elementary functions act on each signal element identically

• log, exp - logarithmic functions

• sin, cos, tan - trigonomic functions

• sinh, cosh, tanh - hyperbolic functions

Data Manipulation Functions

• shift, shift_x, shift_y, shift_xy - Shift data along an independent axis

• scale, scale_x, scale_y - Scale one of the independent axes

• flip, flip_x, flip_y - Reverse the data in a dataset

Rebin Functions

Three different methods exist for rebinning a function. Rebin will rebin the data into user defined bins. Rebunch will bunch together a user defined number of bins. Regroup rebins data using a minimum binwidth given by the user but insures that the new bins are coincident with the existing bins.

• rebin, rebin_x, rebin_y, rebin_xy

• rebunch, rebunch_x, rebunch_y, rebunch_xy

• regroup, regroup_x, regroup_y, regroup_xy

High Level Functions

• deriv1x, deriv2x, deriv1y, deriv2y, deriv1, deriv2 - Takes derivatives of a dataset

• integrate_x, integrate_y, integrate_xy, integrate - Integrates a dataset between user defined limits

• smooth - Smooths out signal data to avoid small, sharp deviations

• interp_x, interp_y, interp - Interpolates data onto a different set of points

• unspike - Removes any large spikes from the data

• fit - Fitting data to known functions and giving curves of best fit

• func_eval - Evaluate a function at the given x and y data points

Special Functions

Special functions are used to transform data between different types.

• contract - Turn an array of IXTdataset_2d objects into a single IXTdataset_2d object

• expand_d1d, expand_listd1d, expand_d2d, expand_listd2d - Expand single objects into many objects

• oned_to_twod - Convert an IXTdataset_1d into an IXTdataset_2d

• hist2point, hist2point_x, hist2point_y - Convert between histogram and point data

• noisify - Add noise to a dataset.

Graphics

Using Default Properties and Name Tags

Default properties and name tags are an integral part of Libisis graphics. They allow greater control of plots and it is particularly important to know about them when building applications on top of the Libisis structure. Names and tags can be used to easily identify and set properties for plots.

Plot Commands

• dh, dl, dm, de, dp, dd - One dimensional plotting commands

• ph, pl, pm, pe, pp, pd - over plotting commands

• ds, da, mp - Two dimensional plotting commands

• sm - Sliceomatic (three dimensional) plotting

Pre-Emptive Formatting

• acolor, aline, amark - Change default properties of plots before they are made

Retrospective Formatting

• lx, ly, lz - Changes the limits of the axes

• linlogbutton, linlogmenu, linx, liny, linz, logx ,logy ,logz - changes the axes scale to logarithmic or linear

• aspect - changes the aspect ratio

• dxyz - returns the co-ordinates of a clicked point on a plot, and/or marks the point with a label

• kf / keep_figure, rf / release_figure - hold or release a figure window

• set_plot, set_axes, set_figure - set advanced properties in the figure, axes or plot

• set_legend - adds a legend to the plot

Other Commands

• rename - rename a plot but keep default properties

• fromplot, get_all_name_tags, get_all_handles, get_handles, check_figure - get information from a plot

• set_user_preferences, set_default_properties, reset_default, reset_all - set (or reset) default properties for plot types

• undop - undo the last plot

• color_slider - add a color slider to a two dimensional plot

• alias - make an alias for a function

User Reference

Information for reference purposes, such as valid linestyles, marker styles etc.

Tutorial

A general tutorial. This is mainly from the graphics viewpoint but should provide a good overview of how to do things.

• Tutorial#Before You Begin
• Tutorial#Introduction To Libisis
• Tutorial#Reading In Data
• Tutorial#Setting Colours and Styles on 1d Plots
• Tutorial#Two Dimensional Plotting
• Tutorial#Reading from a slice
• Tutorial#Data Manipulation In Matlab
• Tutorial#Some Rebinning
• Tutorial#Some Binary Operations
• Tutorial#Integrating Data
• Tutorial#Fitting
• Tutorial#Using the Homer GUI
• Tutorial#Getting Help