Difference between revisions of "User Manual"

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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.  
 
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.  
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== Overview ==
 
== Overview ==
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[[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.
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[[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. [[IXTpolygons]] contains a list of shapes with signal data that can be plotted. 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]] and [[IXTpolygons]] are a special case and do not have many of the data manipulation functions as of yet.
  
  
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=== [[Input and Output Functions]] ===
 
=== [[Input and Output Functions]] ===
  
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Below are just a few of the possible read and write functions, [[Input and Output Functions#Other Formats|other formats]] can also be used.
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* [[Input and Output Functions#Assigning a RAW File|set_path]], [[Input and Output Functions#Assigning a RAW File|set_inst]]. [[Input and Output Functions#Assigning a RAW File|set_ext]], [[Input and Output Functions#Assigning a RAW File|ass]].
  
 
*[[Input and Output Functions#RAW Files|getspectra]], [[Input and Output Functions#RAW Files|getspectrum]] - Read in spectra from IXTraw_file objects or from RAW files
 
*[[Input and Output Functions#RAW Files|getspectra]], [[Input and Output Functions#RAW Files|getspectrum]] - Read in spectra from IXTraw_file objects or from RAW files
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*[[Input and Output Functions#Histogram Data|read_hist]], [[Input and Output Functions#Histogram Data|write_hist]] - Read or write to text files, forcing data to be histogram data
 
*[[Input and Output Functions#Histogram Data|read_hist]], [[Input and Output Functions#Histogram Data|write_hist]] - Read or write to text files, forcing data to be histogram data
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*[[Input and Output Functions#Slices, Cuts and Masks|read_slice]], [[Input and Output Functions#Slices, Cuts and Masks|read_cut]], [[Input and Output Functions#Slices, Cuts and Masks|read_mask]] - Special functions to read from other formats
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* [[Input and Output Functions#Nexus Files|read_nxs]] [[Input and Output Functions#Nexus Files|write_nxs]]- Read and write from Nexus file format
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* [[Using Homer and Getting Started|Homer]] - Information about using Homer to import data into Libisis
  
  
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*[[Special Functions#Conversion Functions|hist2point]], [[Special Functions#Conversion Functions|hist2point_x]], [[Special Functions#Conversion Functions|hist2point_y]] - Convert between histogram and point data
 
*[[Special Functions#Conversion Functions|hist2point]], [[Special Functions#Conversion Functions|hist2point_x]], [[Special Functions#Conversion Functions|hist2point_y]] - Convert between histogram and point data
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*[[Special Functions#Noisify|noisify]] - Add noise to a dataset.
  
  
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*[[Plot Commands#Three Dimensional Plots|sm]] - Sliceomatic (three dimensional) plotting
 
*[[Plot Commands#Three Dimensional Plots|sm]] - Sliceomatic (three dimensional) plotting
 
  
 
===[[Pre-Emptive Formatting]]===
 
===[[Pre-Emptive Formatting]]===
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*[[Retrospective Formatting#Changing the Aspect Ratio|aspect]] - changes the aspect ratio
 
*[[Retrospective Formatting#Changing the Aspect Ratio|aspect]] - changes the aspect ratio
  
*[[Retrospective Formatting#Finding Points on a Plot|dxyz]] - returns the co-ordinates of a clicked point on a plot, and/or marks the point with a label
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*[[Retrospective Formatting#Finding Points on a Plot|dxy]],[[Retrospective Formatting#Finding Points on a Plot|dxyz]],[[Retrospective Formatting#Finding Points on a Plot|dxyc]] - returns the co-ordinates of a clicked point on a plot, and/or marks the point with a label
  
 
*[[Retrospective Formatting#Figure Control Functions|kf / keep_figure]], [[Retrospective Formatting#Figure Control Functions|rf / release_figure]] - hold or release a figure window
 
*[[Retrospective Formatting#Figure Control Functions|kf / keep_figure]], [[Retrospective Formatting#Figure Control Functions|rf / release_figure]] - hold or release a figure window
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Information for reference purposes, such as valid linestyles, marker styles etc.
 
Information for reference purposes, such as valid linestyles, marker styles etc.
  
==Redundant==
 
  
[[dean's test page]]
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==[[Tutorial]]==
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A general tutorial. This is mainly from the graphics viewpoint but should provide a good overview of how to do things.
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*[[Tutorial#Before You Begin]]
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*[[Tutorial#Introduction To Libisis]]
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*[[Tutorial#Reading In Data]]
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*[[Tutorial#Setting Colours and Styles on 1d Plots]]
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*[[Tutorial#Two Dimensional Plotting]]
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*[[Tutorial#Reading from a slice]]
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*[[Tutorial#Data Manipulation In Matlab]]
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*[[Tutorial#Some Rebinning]]
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*[[Tutorial#Some Binary Operations]]
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*[[Tutorial#Integrating Data]]
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*[[Tutorial#Fitting]]
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*[[Tutorial#Using the Homer GUI]]
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*[[Tutorial#Getting Help]]

Latest revision as of 10:29, 22 October 2009

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. IXTpolygons contains a list of shapes with signal data that can be plotted. 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 and IXTpolygons are a special case and do 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.

  • 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


Data Manipulation Functions


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.


High Level Functions

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


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

  • ds, da, mp - Two dimensional plotting commands
  • sm - Sliceomatic (three dimensional) plotting

Pre-Emptive Formatting


Retrospective Formatting

  • lx, ly, lz - Changes the limits of the axes
  • aspect - changes the aspect ratio
  • dxy,dxyz,dxyc - returns the co-ordinates of a clicked point on a plot, and/or marks the point with a label


Other Commands

  • rename - rename a plot but keep default properties
  • undop - undo the last 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.