LIBISIS - User contributions [en]

Main Page

2010-08-02T15:25:54Z

Toby Perring: /* Libisis: software for manipulating neutron scattering data */

==Libisis: software for manipulating and visualising neutron scattering data==

Libisis is a suite of tools for analyzing neutron scattering data developed at the [http://www.isis.rl.ac.uk ISIS pulsed neutron source].

Libisis takes raw signals obtained from number of the neutron scattering instruments and transforms these data into neutron scattering data in the form of <math>S_N (detector_n ,\tau _f )</math> where <math>S_N</math> is the number of neutron counted by the detector, <math>detector_n</math> -- number of the detector and <math>\tau _f</math> -- the time of the neutron's flight to this detector.

These data then have to be processed by the Homer application, which transforms these data into the data in the form <math>S(detector_n,\epsilon)</math>, where <math>S</math> is now in a physical units (e.g. '''mb'''/Sr/Unit_cell or relative units, related to a white beam vanadium run) and the <math>\epsilon</math> is the energy, lost by neutrons in collisions.

In addition to raw neutron scattering data, LIBISIS and HOMER use number of instrument and experiment description and calibration data files to do their job properly. Technical description of these files and what these programs are doing can be found [[Libisis_and_Homer_algorithms|here.]]

LIBISIS has a Fortran core with a Matlab interface. Some applications, such as Homer, can be run as standalone applications. Libisis was primarily developed by [[User:Dickon Champion|Dickon Champion]], [[User:Freddie Akeroyd|Freddie Akeroyd]], [[User:Pranav Amin|Pranav Amin]], [[User:Toby Perring|Toby Perring]] and [[User:Dean Whittaker|Dean Whittaker]].

==For Users==
* [[Download and setup LIBISIS]] - here are the download and setup instructions
* [[Using Homer and Getting Started| Using Homer]] - Information for the Homer application
* [[User Manual]] - a helpful user guide for the matlab components of Libisis
* [[Tutorial]] - a quick start tutorial including Homer and libisis

*[[Quick Start For Mgenie Users]] - a very brief look at the differences between mgenie and Libisis
*[[What's New]]
*[[FAQ]]

==For Developers==
* Getting Started: [[Installation Instructions]] for LIBISIS developers
* [[Developer Notes]]
* [[Subroutine Documentation]] - The Fortran components of Libisis
* Dean's [[Wiki Editing Tips]]
* '''MSLICE''' [[mex options]] to compile distributed mslice fortran files on linux
* [http://download.libisis.org/ Code documentation produced by Doxygen]
* [[Coding Conventions]]
* Browse the latest source code online via the [http://svn.libisis.org/viewvc/LIBISISCode/trunk ViewVC] or [http://trac.libisis.org/code/browser/trunk TRAC] browsers
* Information about accessing the latest source code directly from the [[SubversionServer]]

==Reporting and Tracking Bugs==
* [http://trac.libisis.org/code/timeline Timeline] (recent changes to the task list and source code)
* [http://trac.libisis.org/code/roadmap Roadmap] (progress and milestones)]
* '''List or Submit bugs via the [[IssueReporting]] system'''
* [http://lists.libisis.org/ Mailing lists]
* Archive of [http://lists.libisis.org/pipermail/libisis-code-tickets/ ticket change/update] and [http://lists.libisis.org/pipermail/libisis-code-svn/ subversion commit] emails
* '''OLD''' PHP wiki [http://web2.isis.rl.ac.uk/libisiswiki Library usage documentation]

Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

Wiki content primarily created by [[User:Dean Whittaker|Dean Whittaker]] and [[User:Dickon Champion|Dickon Champion]]

Main Page

2010-08-02T15:25:21Z

Toby Perring: /* Hello */

==Libisis: software for manipulating neutron scattering data==

Libisis is a suite of tools for analyzing neutron scattering data developed at the [http://www.isis.rl.ac.uk ISIS pulsed neutron source].

Libisis takes raw signals obtained from number of the neutron scattering instruments and transforms these data into neutron scattering data in the form of <math>S_N (detector_n ,\tau _f )</math> where <math>S_N</math> is the number of neutron counted by the detector, <math>detector_n</math> -- number of the detector and <math>\tau _f</math> -- the time of the neutron's flight to this detector.

These data then have to be processed by the Homer application, which transforms these data into the data in the form <math>S(detector_n,\epsilon)</math>, where <math>S</math> is now in a physical units (e.g. '''mb'''/Sr/Unit_cell or relative units, related to a white beam vanadium run) and the <math>\epsilon</math> is the energy, lost by neutrons in collisions.

In addition to raw neutron scattering data, LIBISIS and HOMER use number of instrument and experiment description and calibration data files to do their job properly. Technical description of these files and what these programs are doing can be found [[Libisis_and_Homer_algorithms|here.]]

LIBISIS has a Fortran core with a Matlab interface. Some applications, such as Homer, can be run as standalone applications. Libisis was primarily developed by [[User:Dickon Champion|Dickon Champion]], [[User:Freddie Akeroyd|Freddie Akeroyd]], [[User:Pranav Amin|Pranav Amin]], [[User:Toby Perring|Toby Perring]] and [[User:Dean Whittaker|Dean Whittaker]].

==For Users==
* [[Download and setup LIBISIS]] - here are the download and setup instructions
* [[Using Homer and Getting Started| Using Homer]] - Information for the Homer application
* [[User Manual]] - a helpful user guide for the matlab components of Libisis
* [[Tutorial]] - a quick start tutorial including Homer and libisis

*[[Quick Start For Mgenie Users]] - a very brief look at the differences between mgenie and Libisis
*[[What's New]]
*[[FAQ]]

==For Developers==
* Getting Started: [[Installation Instructions]] for LIBISIS developers
* [[Developer Notes]]
* [[Subroutine Documentation]] - The Fortran components of Libisis
* Dean's [[Wiki Editing Tips]]
* '''MSLICE''' [[mex options]] to compile distributed mslice fortran files on linux
* [http://download.libisis.org/ Code documentation produced by Doxygen]
* [[Coding Conventions]]
* Browse the latest source code online via the [http://svn.libisis.org/viewvc/LIBISISCode/trunk ViewVC] or [http://trac.libisis.org/code/browser/trunk TRAC] browsers
* Information about accessing the latest source code directly from the [[SubversionServer]]

==Reporting and Tracking Bugs==
* [http://trac.libisis.org/code/timeline Timeline] (recent changes to the task list and source code)
* [http://trac.libisis.org/code/roadmap Roadmap] (progress and milestones)]
* '''List or Submit bugs via the [[IssueReporting]] system'''
* [http://lists.libisis.org/ Mailing lists]
* Archive of [http://lists.libisis.org/pipermail/libisis-code-tickets/ ticket change/update] and [http://lists.libisis.org/pipermail/libisis-code-svn/ subversion commit] emails
* '''OLD''' PHP wiki [http://web2.isis.rl.ac.uk/libisiswiki Library usage documentation]

Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

Wiki content primarily created by [[User:Dean Whittaker|Dean Whittaker]] and [[User:Dickon Champion|Dickon Champion]]

Main Page

2010-08-02T15:24:41Z

Toby Perring: /* What Is Libisis? */

==Hello==

Libisis is a suite of tools for analyzing neutron scattering data developed at the [http://www.isis.rl.ac.uk ISIS pulsed neutron source].

Libisis takes raw signals obtained from number of the neutron scattering instruments and transforms these data into neutron scattering data in the form of <math>S_N (detector_n ,\tau _f )</math> where <math>S_N</math> is the number of neutron counted by the detector, <math>detector_n</math> -- number of the detector and <math>\tau _f</math> -- the time of the neutron's flight to this detector.

These data then have to be processed by the Homer application, which transforms these data into the data in the form <math>S(detector_n,\epsilon)</math>, where <math>S</math> is now in a physical units (e.g. '''mb'''/Sr/Unit_cell or relative units, related to a white beam vanadium run) and the <math>\epsilon</math> is the energy, lost by neutrons in collisions.

In addition to raw neutron scattering data, LIBISIS and HOMER use number of instrument and experiment description and calibration data files to do their job properly. Technical description of these files and what these programs are doing can be found [[Libisis_and_Homer_algorithms|here.]]

LIBISIS has a Fortran core with a Matlab interface. Some applications, such as Homer, can be run as standalone applications. Libisis was primarily developed by [[User:Dickon Champion|Dickon Champion]], [[User:Freddie Akeroyd|Freddie Akeroyd]], [[User:Pranav Amin|Pranav Amin]], [[User:Toby Perring|Toby Perring]] and [[User:Dean Whittaker|Dean Whittaker]].

==For Users==
* [[Download and setup LIBISIS]] - here are the download and setup instructions
* [[Using Homer and Getting Started| Using Homer]] - Information for the Homer application
* [[User Manual]] - a helpful user guide for the matlab components of Libisis
* [[Tutorial]] - a quick start tutorial including Homer and libisis

*[[Quick Start For Mgenie Users]] - a very brief look at the differences between mgenie and Libisis
*[[What's New]]
*[[FAQ]]

==For Developers==
* Getting Started: [[Installation Instructions]] for LIBISIS developers
* [[Developer Notes]]
* [[Subroutine Documentation]] - The Fortran components of Libisis
* Dean's [[Wiki Editing Tips]]
* '''MSLICE''' [[mex options]] to compile distributed mslice fortran files on linux
* [http://download.libisis.org/ Code documentation produced by Doxygen]
* [[Coding Conventions]]
* Browse the latest source code online via the [http://svn.libisis.org/viewvc/LIBISISCode/trunk ViewVC] or [http://trac.libisis.org/code/browser/trunk TRAC] browsers
* Information about accessing the latest source code directly from the [[SubversionServer]]

==Reporting and Tracking Bugs==
* [http://trac.libisis.org/code/timeline Timeline] (recent changes to the task list and source code)
* [http://trac.libisis.org/code/roadmap Roadmap] (progress and milestones)]
* '''List or Submit bugs via the [[IssueReporting]] system'''
* [http://lists.libisis.org/ Mailing lists]
* Archive of [http://lists.libisis.org/pipermail/libisis-code-tickets/ ticket change/update] and [http://lists.libisis.org/pipermail/libisis-code-svn/ subversion commit] emails
* '''OLD''' PHP wiki [http://web2.isis.rl.ac.uk/libisiswiki Library usage documentation]

Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

Wiki content primarily created by [[User:Dean Whittaker|Dean Whittaker]] and [[User:Dickon Champion|Dickon Champion]]

Main Page

2010-08-02T15:24:07Z

Toby Perring: /* For Users */

==What Is Libisis?==

Libisis is a suite of tools for analyzing neutron scattering data developed at the [http://www.isis.rl.ac.uk ISIS pulsed neutron source].

Libisis takes raw signals obtained from number of the neutron scattering instruments and transforms these data into neutron scattering data in the form of <math>S_N (detector_n ,\tau _f )</math> where <math>S_N</math> is the number of neutron counted by the detector, <math>detector_n</math> -- number of the detector and <math>\tau _f</math> -- the time of the neutron's flight to this detector.

These data then have to be processed by the Homer application, which transforms these data into the data in the form <math>S(detector_n,\epsilon)</math>, where <math>S</math> is now in a physical units (e.g. '''mb'''/Sr/Unit_cell or relative units, related to a white beam vanadium run) and the <math>\epsilon</math> is the energy, lost by neutrons in collisions.

In addition to raw neutron scattering data, LIBISIS and HOMER use number of instrument and experiment description and calibration data files to do their job properly. Technical description of these files and what these programs are doing can be found [[Libisis_and_Homer_algorithms|here.]]

LIBISIS has a Fortran core with a Matlab interface. Some applications, such as Homer, can be run as standalone applications. Libisis was primarily developed by [[User:Dickon Champion|Dickon Champion]], [[User:Freddie Akeroyd|Freddie Akeroyd]], [[User:Pranav Amin|Pranav Amin]], [[User:Toby Perring|Toby Perring]] and [[User:Dean Whittaker|Dean Whittaker]].

==For Users==
* [[Download and setup LIBISIS]] - here are the download and setup instructions
* [[Using Homer and Getting Started| Using Homer]] - Information for the Homer application
* [[User Manual]] - a helpful user guide for the matlab components of Libisis
* [[Tutorial]] - a quick start tutorial including Homer and libisis

*[[Quick Start For Mgenie Users]] - a very brief look at the differences between mgenie and Libisis
*[[What's New]]
*[[FAQ]]

==For Developers==
* Getting Started: [[Installation Instructions]] for LIBISIS developers
* [[Developer Notes]]
* [[Subroutine Documentation]] - The Fortran components of Libisis
* Dean's [[Wiki Editing Tips]]
* '''MSLICE''' [[mex options]] to compile distributed mslice fortran files on linux
* [http://download.libisis.org/ Code documentation produced by Doxygen]
* [[Coding Conventions]]
* Browse the latest source code online via the [http://svn.libisis.org/viewvc/LIBISISCode/trunk ViewVC] or [http://trac.libisis.org/code/browser/trunk TRAC] browsers
* Information about accessing the latest source code directly from the [[SubversionServer]]

==Reporting and Tracking Bugs==
* [http://trac.libisis.org/code/timeline Timeline] (recent changes to the task list and source code)
* [http://trac.libisis.org/code/roadmap Roadmap] (progress and milestones)]
* '''List or Submit bugs via the [[IssueReporting]] system'''
* [http://lists.libisis.org/ Mailing lists]
* Archive of [http://lists.libisis.org/pipermail/libisis-code-tickets/ ticket change/update] and [http://lists.libisis.org/pipermail/libisis-code-svn/ subversion commit] emails
* '''OLD''' PHP wiki [http://web2.isis.rl.ac.uk/libisiswiki Library usage documentation]

Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

Wiki content primarily created by [[User:Dean Whittaker|Dean Whittaker]] and [[User:Dickon Champion|Dickon Champion]]

IXTgeometry

2010-02-05T09:08:05Z

Toby Perring:

Describes geometrical items. The geometry object is built up of segments of shapes. Each segment has a position and orientation. The shape field may contain many different shapes in an array. Indexes describe which shape in the shape field the segment is.

==Structure==

{| {{Tablestyle}}
|-
! {{Headcellstyle}} | Field
!{{Headcellstyle}} | Type
! {{Headcellstyle}} | Description
|-
|'''base'''
| [[IXTbase]]
| Used internally
|-
|'''translation'''
| [[IXTtranslation]]
| positions of the geometrical items
|-
|'''orientation'''
| [[IXTorientation]]
| orientations of each of the geometrical items
|-
|'''elmt_to_shape'''
| int
| element of shape for a given geometrical item
|-
|'''elmt_to_index'''
| int
| index within that element of shape for a given geometrical item
|-
| '''shape'''
| [[IXTshape]](allocatable)
| array containing shapes that the geometrical item may be built up of.
|}

Homer Utilities

2010-02-02T19:43:53Z

Toby Perring:

== gget ==
generic raw file access

it is possible at the matlab comand line to extract any variable from the rawfile by making a call to a populated [[IXTraw_file]] object.

<pre>
>> rawfile=IXTraw_file('/path/to/my/file.raw')
>> value=gget(rawfile,'FIELD')
</pre>

== dae access ==

It is possible to access the data in the DAE by populating an [[IXTraw_file]] with a special string argument. We prefix <tt>DAE:</tt> to the name of the instrument control computer. Once this has been successfully populated all data access and get functions can be called.

<pre>
>> rawf=IXTraw_file('DAE:ndxmerlin')
>> w1=getspectrum(rawf,1)
>> title=gget(rawf,'TITL')
</pre>

This process is not possible with all instruments and requires the newest ICP to be installed. Full homer processes are possible but take a very long time, it is best used to access single spectra.

== head ==

head() returns the header information for the raw file defined by the run_number, or the path to a defined raw file. Multiple run numbers can be combined together with limited practical use.

<pre>
>> head(run_number)
>> head(path_to_raw_file)
</pre>

* <tt>run_number</tt> can be defined in the following ways
# a numerical array of numbers <tt> [12345 45673 34436]</tt> or a single numeric
# an array of strings <tt>char('12345' '45673' '34436')</tt> or a single string
# a cell array of strings <tt>{'12345' '45673' '34436'}</tt>
# a cell array of numerics <tt>{12345 45673 34436}</tt>

* <tt>path_to_raw_file</tt> is defined as a string or a cell array of strings of the form <tt>'C:\data\myfile.raw'</tt>, relative paths are also possible as well as using the [[Global IXTpath objects]] <tt>'inst_data:::myfile.raw'</tt> provided they have been set properly in the [[Instrument setup]]

mhead() returns the header information for each raw file defined by an '''array''' of run numbers, or an '''array''' of paths to a raw file.

<pre>
>> mhead(run_numbers)
>> mhead(paths_to_raw_files)
</pre>

* <tt>run_numbers</tt> can be defined in the following ways
# a numerical array of numbers <tt> [12345 45673 34436]</tt>
# an array of strings <tt>char('12345' '45673' '34436')</tt>
# a cell array of strings <tt>{'12345' '45673' '34436'}</tt>
# a cell array of numerics <tt>{12345 45673 34436}</tt>
* <tt>paths_to_raw_files</tt> is defined as a cell or string array of the form <tt>'C:\data\myfile.raw'</tt>, relative paths are also possible as well as using the [[Global IXTpath objects]] <tt>'inst_data:::myfile.raw'</tt> provided they have been set properly in the [[Instrument setup]]

== get_ei ==
get_ei() returns the energy of given a monochromatic run number, a guide energy can optionally be provided to focus the search for a monitor peak. It also optionally returns a structure containing the peak position, area and normalised area of the two monitors used to determine the energy. Multiple run numbers may be combined.

<pre>
>> [ei,props]=get_ei(run_number,ei_guess)
>> [ei,props]=get_ei(path_to_raw_file,ei_guess)
</pre>

* <tt>run_number</tt> can be defined in the following ways
# a numerical array of numbers <tt> [12345 45673 34436]</tt> or a single numeric
# an array of strings <tt>char('12345' '45673' '34436')</tt> or a single string
# a cell array of strings <tt>{'12345' '45673' '34436'}</tt>
# a cell array of numerics <tt>{12345 45673 34436}</tt>
* <tt>path_to_raw_file</tt> is defined as a string or a cell array of strings of the form <tt>'C:\data\myfile.raw'</tt>, relative paths are also possible as well as using the [[Global IXTpath objects]] <tt>'inst_data:::myfile.raw'</tt> provided they have been set properly in the [[Instrument setup]]
* ei_guess is a single numeric value containing the starting ei for get_ei to use in its calculation

mget_ei()

<pre>
>> [ei,props]=mget_ei(run_numbers,ei_guesses)
>> [ei,props]=mget_ei(path_to_raw_file,ei_guesses)
</pre>

* <tt>run_numbers</tt> can be defined in the following ways
# a numerical array of numbers <tt> [12345 45673 34436]</tt>
# an array of strings <tt>char('12345' '45673' '34436')</tt>
# a cell array of strings <tt>{'12345' '45673' '34436'}</tt>
# a cell array of numerics <tt>{12345 45673 34436}</tt>
* <tt>paths_to_raw_files</tt> is defined as a cell or string array of the form <tt>'C:\data\myfile.raw'</tt>, relative paths are also possible as well as using the [[Global IXTpath objects]] <tt>'inst_data:::myfile.raw'</tt> provided they have been set properly in the [[Instrument setup]]
*ei_guesses must be a numerical array equal to the number of run_numbers, containing the starting ei for mget_ei to use in the energy calculation for each run

Add monmap

2010-01-29T20:57:25Z

Toby Perring:

<pre>
>> dso = add_monmap(dso,monitor_map_file)
</pre>
This will add a monitor map file location to a data_source object:
* dso is a data_source object (class: [[IXTdata_source]])
* monitor_map_file is a string defining the location of the monitor map file to be loaded, eg. <tt>'X:\mapfiles\inst.map'</tt>, or <tt>'inst_maps:::myfile.map'</tt> (where inst_maps is a global path)

User:Freddie Akeroyd

2010-01-29T17:24:05Z

Toby Perring:

==Freddie Akeroyd==

;Phone:+44 1235 445457
;Fax: +44 1235 445720
;Email: [mailto:freddie.akeroyd@stfc.ac.uk freddie.akeroyd@stfc.ac.uk]

User:Toby Perring

2010-01-29T17:22:45Z

Toby Perring:

==Toby Perring==

;Phone:+44 1235 445428
;Fax: +44 1235 445720
;Email: [mailto:toby.perring@stfc.ac.uk toby.perring@stfc.ac.uk]

Getting Started

2010-01-29T17:18:52Z

Toby Perring:

* [[Download and setup LIBISIS]]

Before you can run the Homer GUI, you must set up the GUI

* [[Homer Gui setup]]

Before you can run any of the [[Homer and mgenie style functions]] you must setup your instrument details
* [[Instrument setup]]

Using Homer and Getting Started

2010-01-29T17:16:34Z

Toby Perring:

* [[Getting Started]] '''VERY IMPORTANT''' setup details defined

* [[Homer GUI]] - mini tutorial with screenshots

* [[Scripting Homer Functions]] are easy to use functions which call homer related functions underneath, as well as setting up the [[IXTdata_source]] object for use by homer

* [[Overriding and setting default values for homer processes]]

* [[Building a reference detector file]]

* [[Homer and mgenie style functions]] Direct calls to homer and some mgenie style functions

* [[Homer Utilities]] extra functions and utilities

* [[IXTrunfile operations]] including algebra, elementary functions and other manipulations

* [[diagnose]] diagnostic function for homer input

* [[Example Scripts]]

Input and Output Functions

2009-04-26T16:10:45Z

Toby Perring: /* Slices, Cuts and Masks */

== ASCII Files ==

* [[IXTdataset_1d]] objects may be stored in ASCII files.
* These files may contain x and y data ''or'' x, s, error data in a 2 or 3 column format.
* Column 1 will be x values, column 2 will be s values and if available column 3 will be error values, if not available then error is assumed to be 0.
* Any information at the start or end of the file that is not in a 2 or 3 column format is '''ignored''' (for instance, ''header information'' may be stored here).
* Columns may be separated by commas, tabs, or spaces.
* ASCII files may contain point or histogram data, the x column in histogram data will have one more value than the s and e columns.

* The following files would all be acceptable ASCII files

<pre>title = plots1 xaxis = wavelength yaxis = signal
490.2 30000
491.2 31923
492.2 40000</pre>

Represents a three point dataset with 0 error.

<pre>title = plots1 xaxis = wavelength yaxis = signal
490.2 30000 300
491.2 31923 300
492.2 40000 250
493.2</pre>

Represents a 3 column histogram dataset with error data.

<pre>490.2,30000,300
491.2,31923,300
492.2,40000,250
493.2
</pre>

Will represent the same 3 column histogram dataset with error data.

* When files are '''written''' by libisis a header is written at the top of the file with the following information

<pre>name = dataset name
title = dataset title
signal_units = dataset s axis label
x_units = dataset x axis label
x_distribution = 1

x1 s1 e1
x2 s2 e2
...</pre>

where the header information is taken from the dataset being written.

* To read and write ASCII files in the format (point or histogram) specified by the file or dataset use

<pre>>> read_ascii('filename')
>> write_ascii(dataset,'filename')</pre>

if no filename is given then the user will be prompted to locate the file.

=== Point Data ===
One can force the written or read ASCII file to be in the form of point data by using the commands

<pre>>>read_points('filename')
write_points(dataset, 'filename')</pre>

=== Histogram Data ===
One can force the written or read ASCII file to be in the form of histogram data by using the commands

<pre>>> read_hist('filename')
>> write_hist(dataset, 'filename')</pre>

== RAW Files ==

RAW files come directly from instruments and can also be read into Libisis. Data can then be extracted from the RAW file to form an [[IXTdataset_1d]] or an [[IXTdataset_2d]] object. One can do this in two different ways

=== Using RAW File Objects ===

* To read in a rawfile (in the form of an [[IXTraw_file]] object) use the command

<pre>>> rawfile1 = IXTraw_file('filename')</pre>

* To read data into an [[IXTdataset_1d]] object use the command

<pre>>> dataset = getspectrum(rawfile1, spectrum_number)</pre>

where '''spectrum_number''' is the spectrum which is required.

* to read multiple runs into an [[IXTdataset_2d]] object use the command

<pre>>> dataset_2d = getspectra(rawfile1, [start:end])</pre>

where start and end are the initial and final spectrum to include in the dataset_2d.

''''' EXAMPLE: '''''

<pre>>> rawfile1 = IXTraw_file('c:/RAWfiles/HET15958');
>> nsp = geti(rawfile1,'nsp1');
>> d2a = getspectra(rawfile1, [1:nsp]);
>> d1a = getspectrum(rawfile1, 25); </pre>

this will load all spectra from the HET15958 raw file contained in the folder c:/RAWfiles into an [[IXTdataset_2d]] object called d2a and load spectrum 25 into an [[IXTdataset_1d]] object name d1a.

* Other information is contained in the rawfile, see [[IXTraw_file]] documentation for more information.

=== Assigning a RAW File ===

Rawfiles can also be assigned in the matlab environment. Once assigned, the rawfile will be used in any commands (such as getspectrum and getspectra) that are not given a rawfile object. All actions that can be performed on a rawfile object may be performed on the assigned runfile by simply omitting the rawfile object in the call to the function.

* Assigning RAW files makes routine operations quicker by omitting the need to enter an object name each time an operation is to be performed
* Once a directory has been assigned, different file numbers (run numbers) can be chosen in a single command - making the process efficient.
* Only one RAW file may be assigned at any one time

To assign a runfile use the commands

<pre> >> set_path(path)
>> set_inst(inst)
>> set_ext('RAW')
>> ass(number)
</pre>

* path is the path where the RAW file is stored
* inst is the three letter abreviation of the instrument used to generate the raw file (e.g. MAP, MAR, MER, HET)
* number is the raw file number (run number) that you wish to assign.

'''''Example:'''''

<pre> >> set_path('c:/maps_files/raw_files')
>> set_inst('MAP')
>> set_ext('RAW')
>> ass(6404)
</pre>

* A file must exist called C:/maps_files/raw_files/MAP06404.RAW

=== Plotting Spectra From Assigned RAW Files ===

One can plot spectra from assigned raw files using the following commands:

<pre> >> dl(spectrum)
>> da(spectra)
</pre>

* dl is any [[Plot Commands#One Dimensional Plots|one dimensional plot ]] command
* da is any [[Plot Commands#Two Dimensional Plots|two dimensional plot]] command
* spectrum is an array of numbers indicating which spectra of the currently assigned RAW file to plot
* spectra is an array of numbers indicating which spectra of the currently assigned RAW file to plot in two dimensions.

==Slices, Cuts and Masks==

Some other programs can generate a slice, cut or mask object. Two such programs are mslice and Horace.

A slice can be read into a Libisis [[IXTdataset_2d]] object using the command

<pre>>>w = read_slice(filename)
w = read_slice</pre>

* '''filename''' is a string containing the location of the .slc file
* If filename is not given then a prompt will ask the user to locate the file
* Output is an [[IXTdataset_2d]], with as much information taken from the slice as possible, otherwise fields are blank.

Similarly, a Mask or a cut from Horace / mslice can be read into Libisis [[IXTdataset_1d]] objects using the commands

<pre> >> w = read_cut(filename)
>> w = read_mask(filename)</pre>

* '''filename''' is a string containing the location of the .cut or .msk file
* If filename is not given then a prompt will ask the user to locate the file
* Output is an [[IXTdataset_1d]], with as much information taken from the cut / mask as possible, otherwise fields are blank.

== Nexus Files==

Objects can be written to file in hdf format using the nexus API, using the write_nxs function. These files can also be read in using the read_nxs command.

<pre>>> write_nxs(IXTobject,'filename', entry)</pre>

*'''IXTobject''' is the object that is being written out (i.e. [[IXTrunfile]], [[IXTdataset_2d]])
*'''filename''' is a string showing the location of the .nxs file which is being written
*'''entry''' is a string, the top level directory to write the object to (i.e. 'runfile'), by ''default'' it is 'object' (optional)

'''''Example:'''''

<tt> write_nxs(IXTrunfile,'C:/nexusfiles/maps1020.nxs')</tt>

writes the data from the IXTrunfile object into the top-level directory 'runfile' of the maps1020.nxs file

<pre>>>w = read_nxs(filename, IXTobject, entry)</pre>

*'''filename''' is a string showing the location of the .nxs file
*'''IXTobject''' is the type of object that the data is being read into (i.e. [[IXTrunfile]], [[IXTdataset_2d]])
*'''entry''' is a string, the top level directory to read the object from (i.e. 'runfile'), by ''default'' it is 'object' (optional)
* '''w''' is the actual object which will hold the data being read, it will be of the same object type as IXTobject (i.e. [[IXTrunfile]])

'''''Example:'''''

<tt>wout = read_nxs('C:/nexusfiles/maps1020.nxs', IXTrunfile, 'runfile')</tt>

reads the data from the runfile top directory into the wout object that will be an [[IXTrunfile]] object.

== Other Formats ==

Data can be read from other formats or in other ways, such as using [[Homer_and_mgenie_style_functions| Homer]] to populate an [[IXTrunfile]] object.

Input and Output Functions

2009-04-26T16:10:33Z

Toby Perring: /* Slices, Cuts and Masks */

== ASCII Files ==

* [[IXTdataset_1d]] objects may be stored in ASCII files.
* These files may contain x and y data ''or'' x, s, error data in a 2 or 3 column format.
* Column 1 will be x values, column 2 will be s values and if available column 3 will be error values, if not available then error is assumed to be 0.
* Any information at the start or end of the file that is not in a 2 or 3 column format is '''ignored''' (for instance, ''header information'' may be stored here).
* Columns may be separated by commas, tabs, or spaces.
* ASCII files may contain point or histogram data, the x column in histogram data will have one more value than the s and e columns.

* The following files would all be acceptable ASCII files

<pre>title = plots1 xaxis = wavelength yaxis = signal
490.2 30000
491.2 31923
492.2 40000</pre>

Represents a three point dataset with 0 error.

<pre>title = plots1 xaxis = wavelength yaxis = signal
490.2 30000 300
491.2 31923 300
492.2 40000 250
493.2</pre>

Represents a 3 column histogram dataset with error data.

<pre>490.2,30000,300
491.2,31923,300
492.2,40000,250
493.2
</pre>

Will represent the same 3 column histogram dataset with error data.

* When files are '''written''' by libisis a header is written at the top of the file with the following information

<pre>name = dataset name
title = dataset title
signal_units = dataset s axis label
x_units = dataset x axis label
x_distribution = 1

x1 s1 e1
x2 s2 e2
...</pre>

where the header information is taken from the dataset being written.

* To read and write ASCII files in the format (point or histogram) specified by the file or dataset use

<pre>>> read_ascii('filename')
>> write_ascii(dataset,'filename')</pre>

if no filename is given then the user will be prompted to locate the file.

=== Point Data ===
One can force the written or read ASCII file to be in the form of point data by using the commands

<pre>>>read_points('filename')
write_points(dataset, 'filename')</pre>

=== Histogram Data ===
One can force the written or read ASCII file to be in the form of histogram data by using the commands

<pre>>> read_hist('filename')
>> write_hist(dataset, 'filename')</pre>

== RAW Files ==

RAW files come directly from instruments and can also be read into Libisis. Data can then be extracted from the RAW file to form an [[IXTdataset_1d]] or an [[IXTdataset_2d]] object. One can do this in two different ways

=== Using RAW File Objects ===

* To read in a rawfile (in the form of an [[IXTraw_file]] object) use the command

<pre>>> rawfile1 = IXTraw_file('filename')</pre>

* To read data into an [[IXTdataset_1d]] object use the command

<pre>>> dataset = getspectrum(rawfile1, spectrum_number)</pre>

where '''spectrum_number''' is the spectrum which is required.

* to read multiple runs into an [[IXTdataset_2d]] object use the command

<pre>>> dataset_2d = getspectra(rawfile1, [start:end])</pre>

where start and end are the initial and final spectrum to include in the dataset_2d.

''''' EXAMPLE: '''''

<pre>>> rawfile1 = IXTraw_file('c:/RAWfiles/HET15958');
>> nsp = geti(rawfile1,'nsp1');
>> d2a = getspectra(rawfile1, [1:nsp]);
>> d1a = getspectrum(rawfile1, 25); </pre>

this will load all spectra from the HET15958 raw file contained in the folder c:/RAWfiles into an [[IXTdataset_2d]] object called d2a and load spectrum 25 into an [[IXTdataset_1d]] object name d1a.

* Other information is contained in the rawfile, see [[IXTraw_file]] documentation for more information.

=== Assigning a RAW File ===

Rawfiles can also be assigned in the matlab environment. Once assigned, the rawfile will be used in any commands (such as getspectrum and getspectra) that are not given a rawfile object. All actions that can be performed on a rawfile object may be performed on the assigned runfile by simply omitting the rawfile object in the call to the function.

* Assigning RAW files makes routine operations quicker by omitting the need to enter an object name each time an operation is to be performed
* Once a directory has been assigned, different file numbers (run numbers) can be chosen in a single command - making the process efficient.
* Only one RAW file may be assigned at any one time

To assign a runfile use the commands

<pre> >> set_path(path)
>> set_inst(inst)
>> set_ext('RAW')
>> ass(number)
</pre>

* path is the path where the RAW file is stored
* inst is the three letter abreviation of the instrument used to generate the raw file (e.g. MAP, MAR, MER, HET)
* number is the raw file number (run number) that you wish to assign.

'''''Example:'''''

<pre> >> set_path('c:/maps_files/raw_files')
>> set_inst('MAP')
>> set_ext('RAW')
>> ass(6404)
</pre>

* A file must exist called C:/maps_files/raw_files/MAP06404.RAW

=== Plotting Spectra From Assigned RAW Files ===

One can plot spectra from assigned raw files using the following commands:

<pre> >> dl(spectrum)
>> da(spectra)
</pre>

* dl is any [[Plot Commands#One Dimensional Plots|one dimensional plot ]] command
* da is any [[Plot Commands#Two Dimensional Plots|two dimensional plot]] command
* spectrum is an array of numbers indicating which spectra of the currently assigned RAW file to plot
* spectra is an array of numbers indicating which spectra of the currently assigned RAW file to plot in two dimensions.

==Slices, Cuts and Masks==

Some other programs can generate a slice, cut or mask object. Two such programs are mslice and Horace.

A slice can be read into a Libisis [[IXTdataset_2d]] object using the command

<pre>>>w = read_slice(filename)
w = read_slice</pre>

* '''filename''' is a string containing the location of the .slc file
* If filename is not given then a prompt will ask the user to locate the file
* Output is an [[IXTdataset_2d]], with as much information taken from the slice as possible, otherwise fields are blank.

Similarly, a Mask or a cut from Horace / mslice can be read into Libisis [[IXTdataset_1d]] objects using the commands

<pre> >>w = read_cut(filename)
>> w = read_mask(filename)</pre>

* '''filename''' is a string containing the location of the .cut or .msk file
* If filename is not given then a prompt will ask the user to locate the file
* Output is an [[IXTdataset_1d]], with as much information taken from the cut / mask as possible, otherwise fields are blank.

== Nexus Files==

Objects can be written to file in hdf format using the nexus API, using the write_nxs function. These files can also be read in using the read_nxs command.

<pre>>> write_nxs(IXTobject,'filename', entry)</pre>

*'''IXTobject''' is the object that is being written out (i.e. [[IXTrunfile]], [[IXTdataset_2d]])
*'''filename''' is a string showing the location of the .nxs file which is being written
*'''entry''' is a string, the top level directory to write the object to (i.e. 'runfile'), by ''default'' it is 'object' (optional)

'''''Example:'''''

<tt> write_nxs(IXTrunfile,'C:/nexusfiles/maps1020.nxs')</tt>

writes the data from the IXTrunfile object into the top-level directory 'runfile' of the maps1020.nxs file

<pre>>>w = read_nxs(filename, IXTobject, entry)</pre>

*'''filename''' is a string showing the location of the .nxs file
*'''IXTobject''' is the type of object that the data is being read into (i.e. [[IXTrunfile]], [[IXTdataset_2d]])
*'''entry''' is a string, the top level directory to read the object from (i.e. 'runfile'), by ''default'' it is 'object' (optional)
* '''w''' is the actual object which will hold the data being read, it will be of the same object type as IXTobject (i.e. [[IXTrunfile]])

'''''Example:'''''

<tt>wout = read_nxs('C:/nexusfiles/maps1020.nxs', IXTrunfile, 'runfile')</tt>

reads the data from the runfile top directory into the wout object that will be an [[IXTrunfile]] object.

== Other Formats ==

Data can be read from other formats or in other ways, such as using [[Homer_and_mgenie_style_functions| Homer]] to populate an [[IXTrunfile]] object.

Input and Output Functions

2009-04-26T16:03:24Z

Toby Perring: /* Assigning a RAW File */

== ASCII Files ==

* [[IXTdataset_1d]] objects may be stored in ASCII files.
* These files may contain x and y data ''or'' x, s, error data in a 2 or 3 column format.
* Column 1 will be x values, column 2 will be s values and if available column 3 will be error values, if not available then error is assumed to be 0.
* Any information at the start or end of the file that is not in a 2 or 3 column format is '''ignored''' (for instance, ''header information'' may be stored here).
* Columns may be separated by commas, tabs, or spaces.
* ASCII files may contain point or histogram data, the x column in histogram data will have one more value than the s and e columns.

* The following files would all be acceptable ASCII files

<pre>title = plots1 xaxis = wavelength yaxis = signal
490.2 30000
491.2 31923
492.2 40000</pre>

Represents a three point dataset with 0 error.

<pre>title = plots1 xaxis = wavelength yaxis = signal
490.2 30000 300
491.2 31923 300
492.2 40000 250
493.2</pre>

Represents a 3 column histogram dataset with error data.

<pre>490.2,30000,300
491.2,31923,300
492.2,40000,250
493.2
</pre>

Will represent the same 3 column histogram dataset with error data.

* When files are '''written''' by libisis a header is written at the top of the file with the following information

<pre>name = dataset name
title = dataset title
signal_units = dataset s axis label
x_units = dataset x axis label
x_distribution = 1

x1 s1 e1
x2 s2 e2
...</pre>

where the header information is taken from the dataset being written.

* To read and write ASCII files in the format (point or histogram) specified by the file or dataset use

<pre>>> read_ascii('filename')
>> write_ascii(dataset,'filename')</pre>

if no filename is given then the user will be prompted to locate the file.

=== Point Data ===
One can force the written or read ASCII file to be in the form of point data by using the commands

<pre>>>read_points('filename')
write_points(dataset, 'filename')</pre>

=== Histogram Data ===
One can force the written or read ASCII file to be in the form of histogram data by using the commands

<pre>>> read_hist('filename')
>> write_hist(dataset, 'filename')</pre>

== RAW Files ==

RAW files come directly from instruments and can also be read into Libisis. Data can then be extracted from the RAW file to form an [[IXTdataset_1d]] or an [[IXTdataset_2d]] object. One can do this in two different ways

=== Using RAW File Objects ===

* To read in a rawfile (in the form of an [[IXTraw_file]] object) use the command

<pre>>> rawfile1 = IXTraw_file('filename')</pre>

* To read data into an [[IXTdataset_1d]] object use the command

<pre>>> dataset = getspectrum(rawfile1, spectrum_number)</pre>

where '''spectrum_number''' is the spectrum which is required.

* to read multiple runs into an [[IXTdataset_2d]] object use the command

<pre>>> dataset_2d = getspectra(rawfile1, [start:end])</pre>

where start and end are the initial and final spectrum to include in the dataset_2d.

''''' EXAMPLE: '''''

<pre>>> rawfile1 = IXTraw_file('c:/RAWfiles/HET15958');
>> nsp = geti(rawfile1,'nsp1');
>> d2a = getspectra(rawfile1, [1:nsp]);
>> d1a = getspectrum(rawfile1, 25); </pre>

this will load all spectra from the HET15958 raw file contained in the folder c:/RAWfiles into an [[IXTdataset_2d]] object called d2a and load spectrum 25 into an [[IXTdataset_1d]] object name d1a.

* Other information is contained in the rawfile, see [[IXTraw_file]] documentation for more information.

=== Assigning a RAW File ===

Rawfiles can also be assigned in the matlab environment. Once assigned, the rawfile will be used in any commands (such as getspectrum and getspectra) that are not given a rawfile object. All actions that can be performed on a rawfile object may be performed on the assigned runfile by simply omitting the rawfile object in the call to the function.

* Assigning RAW files makes routine operations quicker by omitting the need to enter an object name each time an operation is to be performed
* Once a directory has been assigned, different file numbers (run numbers) can be chosen in a single command - making the process efficient.
* Only one RAW file may be assigned at any one time

To assign a runfile use the commands

<pre> >> set_path(path)
>> set_inst(inst)
>> set_ext('RAW')
>> ass(number)
</pre>

* path is the path where the RAW file is stored
* inst is the three letter abreviation of the instrument used to generate the raw file (e.g. MAP, MAR, MER, HET)
* number is the raw file number (run number) that you wish to assign.

'''''Example:'''''

<pre> >> set_path('c:/maps_files/raw_files')
>> set_inst('MAP')
>> set_ext('RAW')
>> ass(6404)
</pre>

* A file must exist called C:/maps_files/raw_files/MAP06404.RAW

=== Plotting Spectra From Assigned RAW Files ===

One can plot spectra from assigned raw files using the following commands:

<pre> >> dl(spectrum)
>> da(spectra)
</pre>

* dl is any [[Plot Commands#One Dimensional Plots|one dimensional plot ]] command
* da is any [[Plot Commands#Two Dimensional Plots|two dimensional plot]] command
* spectrum is an array of numbers indicating which spectra of the currently assigned RAW file to plot
* spectra is an array of numbers indicating which spectra of the currently assigned RAW file to plot in two dimensions.

==Slices, Cuts and Masks==

Some other programs can generate a slice, cut or mask object. Two such programs are mslice and Horace.

A slice can be read into a Libisis [[IXTdataset_2d]] object using the command

<pre>>>w = read_slice(filename)
w = read_slice</pre>

* '''filename''' is a string containing the location of the .slc file
* If filename is not given then a prompt will ask the user to locate the file
* Output is an [[IXTdataset_2d]], with as much information taken from the slice as possible, otherwise fields are blank.

Similarly, a Mask or a cut from Horace / mslice can be read into Libisis [[IXTdataset_1d]] objects using the commands

<pre>>>w = read_cut(filename)
>> w = read_mask(filename)</pre>

* '''filename''' is a string containing the location of the .cut or .msk file
* If filename is not given then a prompt will ask the user to locate the file
* Output is an [[IXTdataset_1d]], with as much information taken from the cut / mask as possible, otherwise fields are blank.

== Nexus Files==

Objects can be written to file in hdf format using the nexus API, using the write_nxs function. These files can also be read in using the read_nxs command.

<pre>>> write_nxs(IXTobject,'filename', entry)</pre>

*'''IXTobject''' is the object that is being written out (i.e. [[IXTrunfile]], [[IXTdataset_2d]])
*'''filename''' is a string showing the location of the .nxs file which is being written
*'''entry''' is a string, the top level directory to write the object to (i.e. 'runfile'), by ''default'' it is 'object' (optional)

'''''Example:'''''

<tt> write_nxs(IXTrunfile,'C:/nexusfiles/maps1020.nxs')</tt>

writes the data from the IXTrunfile object into the top-level directory 'runfile' of the maps1020.nxs file

<pre>>>w = read_nxs(filename, IXTobject, entry)</pre>

*'''filename''' is a string showing the location of the .nxs file
*'''IXTobject''' is the type of object that the data is being read into (i.e. [[IXTrunfile]], [[IXTdataset_2d]])
*'''entry''' is a string, the top level directory to read the object from (i.e. 'runfile'), by ''default'' it is 'object' (optional)
* '''w''' is the actual object which will hold the data being read, it will be of the same object type as IXTobject (i.e. [[IXTrunfile]])

'''''Example:'''''

<tt>wout = read_nxs('C:/nexusfiles/maps1020.nxs', IXTrunfile, 'runfile')</tt>

reads the data from the runfile top directory into the wout object that will be an [[IXTrunfile]] object.

== Other Formats ==

Data can be read from other formats or in other ways, such as using [[Homer_and_mgenie_style_functions| Homer]] to populate an [[IXTrunfile]] object.

Input and Output Functions

2009-04-26T16:02:53Z

Toby Perring: /* Assigning a RAW File */

== ASCII Files ==

* [[IXTdataset_1d]] objects may be stored in ASCII files.
* These files may contain x and y data ''or'' x, s, error data in a 2 or 3 column format.
* Column 1 will be x values, column 2 will be s values and if available column 3 will be error values, if not available then error is assumed to be 0.
* Any information at the start or end of the file that is not in a 2 or 3 column format is '''ignored''' (for instance, ''header information'' may be stored here).
* Columns may be separated by commas, tabs, or spaces.
* ASCII files may contain point or histogram data, the x column in histogram data will have one more value than the s and e columns.

* The following files would all be acceptable ASCII files

<pre>title = plots1 xaxis = wavelength yaxis = signal
490.2 30000
491.2 31923
492.2 40000</pre>

Represents a three point dataset with 0 error.

<pre>title = plots1 xaxis = wavelength yaxis = signal
490.2 30000 300
491.2 31923 300
492.2 40000 250
493.2</pre>

Represents a 3 column histogram dataset with error data.

<pre>490.2,30000,300
491.2,31923,300
492.2,40000,250
493.2
</pre>

Will represent the same 3 column histogram dataset with error data.

* When files are '''written''' by libisis a header is written at the top of the file with the following information

<pre>name = dataset name
title = dataset title
signal_units = dataset s axis label
x_units = dataset x axis label
x_distribution = 1

x1 s1 e1
x2 s2 e2
...</pre>

where the header information is taken from the dataset being written.

* To read and write ASCII files in the format (point or histogram) specified by the file or dataset use

<pre>>> read_ascii('filename')
>> write_ascii(dataset,'filename')</pre>

if no filename is given then the user will be prompted to locate the file.

=== Point Data ===
One can force the written or read ASCII file to be in the form of point data by using the commands

<pre>>>read_points('filename')
write_points(dataset, 'filename')</pre>

=== Histogram Data ===
One can force the written or read ASCII file to be in the form of histogram data by using the commands

<pre>>> read_hist('filename')
>> write_hist(dataset, 'filename')</pre>

== RAW Files ==

RAW files come directly from instruments and can also be read into Libisis. Data can then be extracted from the RAW file to form an [[IXTdataset_1d]] or an [[IXTdataset_2d]] object. One can do this in two different ways

=== Using RAW File Objects ===

* To read in a rawfile (in the form of an [[IXTraw_file]] object) use the command

<pre>>> rawfile1 = IXTraw_file('filename')</pre>

* To read data into an [[IXTdataset_1d]] object use the command

<pre>>> dataset = getspectrum(rawfile1, spectrum_number)</pre>

where '''spectrum_number''' is the spectrum which is required.

* to read multiple runs into an [[IXTdataset_2d]] object use the command

<pre>>> dataset_2d = getspectra(rawfile1, [start:end])</pre>

where start and end are the initial and final spectrum to include in the dataset_2d.

''''' EXAMPLE: '''''

<pre>>> rawfile1 = IXTraw_file('c:/RAWfiles/HET15958');
>> nsp = geti(rawfile1,'nsp1');
>> d2a = getspectra(rawfile1, [1:nsp]);
>> d1a = getspectrum(rawfile1, 25); </pre>

this will load all spectra from the HET15958 raw file contained in the folder c:/RAWfiles into an [[IXTdataset_2d]] object called d2a and load spectrum 25 into an [[IXTdataset_1d]] object name d1a.

* Other information is contained in the rawfile, see [[IXTraw_file]] documentation for more information.

=== Assigning a RAW File ===

Rawfiles can also be assigned in the matlab environment. Once assigned, the rawfile will be used in any commands (such as getspectrum and getspectra) that are not given a rawfile object. All actions that can be performed on a rawfile object may be performed on the assigned runfile by simply omitting the rawfile object in the call to the function.

* Assigning RAW files makes routine operations quicker by omitting the need to enter an object name each time an operation is to be performed
* Once a directory has been assigned, different file numbers (run numbers) can be chosen in a single command - making the process efficient.
* Only one RAW file may be assigned at any one time

To assign a runfile use the commands

<pre> >> set_path(path)
>> set_inst(inst)
>> set_ext('RAW')
>> ass(number)
</pre>

* path is the path where the RAW file is stored
* inst is the three letter abreviation of the instrument used to generate the raw file (e.g. MAP, MAR, MER, HET)
* number is the raw file number (run number) that you wish to assign.

'''''Example:'''''

<pre> >> set_path('c:/maps_files/raw_files')
>> set_inst('MAP')
>> set_ext('RAW')
>> ass(6404)
</pre>

* A file must exist called C:/maps_files/raw_files/MAP06404.RAW

=== Plotting Spectra From Assigned RAW Files ===

One can plot spectra from assigned raw files using the following commands:

<pre> >> dl(spectrum)
>> da(spectra)
</pre>

* dl is any [[Plot Commands#One Dimensional Plots|one dimensional plot ]] command
* da is any [[Plot Commands#Two Dimensional Plots|two dimensional plot]] command
* spectrum is an array of numbers indicating which spectra of the currently assigned RAW file to plot
* spectra is an array of numbers indicating which spectra of the currently assigned RAW file to plot in two dimensions.

==Slices, Cuts and Masks==

Some other programs can generate a slice, cut or mask object. Two such programs are mslice and Horace.

A slice can be read into a Libisis [[IXTdataset_2d]] object using the command

<pre>>>w = read_slice(filename)
w = read_slice</pre>

* '''filename''' is a string containing the location of the .slc file
* If filename is not given then a prompt will ask the user to locate the file
* Output is an [[IXTdataset_2d]], with as much information taken from the slice as possible, otherwise fields are blank.

Similarly, a Mask or a cut from Horace / mslice can be read into Libisis [[IXTdataset_1d]] objects using the commands

<pre>>>w = read_cut(filename)
>> w = read_mask(filename)</pre>

* '''filename''' is a string containing the location of the .cut or .msk file
* If filename is not given then a prompt will ask the user to locate the file
* Output is an [[IXTdataset_1d]], with as much information taken from the cut / mask as possible, otherwise fields are blank.

== Nexus Files==

Objects can be written to file in hdf format using the nexus API, using the write_nxs function. These files can also be read in using the read_nxs command.

<pre>>> write_nxs(IXTobject,'filename', entry)</pre>

*'''IXTobject''' is the object that is being written out (i.e. [[IXTrunfile]], [[IXTdataset_2d]])
*'''filename''' is a string showing the location of the .nxs file which is being written
*'''entry''' is a string, the top level directory to write the object to (i.e. 'runfile'), by ''default'' it is 'object' (optional)

'''''Example:'''''

<tt> write_nxs(IXTrunfile,'C:/nexusfiles/maps1020.nxs')</tt>

writes the data from the IXTrunfile object into the top-level directory 'runfile' of the maps1020.nxs file

<pre>>>w = read_nxs(filename, IXTobject, entry)</pre>

*'''filename''' is a string showing the location of the .nxs file
*'''IXTobject''' is the type of object that the data is being read into (i.e. [[IXTrunfile]], [[IXTdataset_2d]])
*'''entry''' is a string, the top level directory to read the object from (i.e. 'runfile'), by ''default'' it is 'object' (optional)
* '''w''' is the actual object which will hold the data being read, it will be of the same object type as IXTobject (i.e. [[IXTrunfile]])

'''''Example:'''''

<tt>wout = read_nxs('C:/nexusfiles/maps1020.nxs', IXTrunfile, 'runfile')</tt>

reads the data from the runfile top directory into the wout object that will be an [[IXTrunfile]] object.

== Other Formats ==

Data can be read from other formats or in other ways, such as using [[Homer_and_mgenie_style_functions| Homer]] to populate an [[IXTrunfile]] object.

Installation Instructions

2009-04-26T13:59:24Z

Toby Perring:

'''Windows Systems'''

Installation for '''developers'''

* Install [http://download.nexusformat.org/kits/windows/ Nexus Library ]
* Install MS Visual Studio .NET 2003 and Intel Fortran with MS visual studio extensions
* Install Matlab
* Set Environment Variables IFORTDIR and MATLABDIR to your Intel Fortran and Matlab directories respectively eg..
IFORTDIR=C:\Program Files\Intel\Compiler\Fortran\9.1\IA32
MATLABDIR=c:\MATLAB\R2007a</pre>
* Download source code from the [[SubversionServer]] by:
** Downloading [http://tortoisesvn.tigris.org/ TortoiseSVN] and installing it.
** On windows - right click an empty folder you want to put the files (e.g. c:/libisis) and click on "SVN Checkout"
** In the "URL of repository" box, enter the web address http://svn.libisis.org/code/trunk and click ok.
* Open the libisisexc.sln file in MS Visual Studio .NET 2003 and 'Build Solution'

For advanced options (i.e. how to submit work back to the SVN server) see [[SubversionServer|here]]

Look at the [[Developer Notes]] for information about how to develop for Libisis

* If Intel 11 installed: follow the above instructions, and then
** Copy libisiscfig.h-windows to libisisconfig.h in the top level libisis folder
** Open the libisis.sln, and when prompted to convert the solution, accept
** Right-click on the libisisexc project, and in the project settings select Linker-General-Additional Library Directories and edit "$(IFORTDIR)\lib" to ""(IFORT_COMPILER11)\lib\ia32"

==Mslice==

* Download [http://tortoisesvn.tigris.org/ TortoiseSVN] and instal tortoise SVN.
* On windows - right click an empty folder you want to put the files (e.g. c:/mslice) and click on "SVN Checkout"
* In the "URL of repository" box, enter the web address http://svn.isis.rl.ac.uk/mslice/trunk and click ok.

IXTworkspace

2008-05-20T15:25:02Z

Toby Perring: /* Structure */

==Structure==

The elements of the object are as follows:

{| {{Tablestyle}}
|-
! {{Headcellstyle}} | Field
!{{Headcellstyle}} | Type
! {{Headcellstyle}} | Description
|-
|work_no (:) || real (ptr) || workspace number
|-
|effdet_index || IXTeffdet_index || Index of good detector parameters for the workspace
|-
|eff_det || IXTdetector || effective detector information
|}

==F90 syntax==

<pre>use IXMworkspace

type(IXTworkspace):: workspace
type(IXTstatus):: status</pre>

==Operations==

The following operations may be performed on this data type:

*[[General Operations]]
*[[Special Subroutines]]

Class Specific Operations:
* [[IXFpopulate_workspace]]