Instrument Definition File ¶

Contents

The documentation on this wiki page is the full detailed description of the syntax you can use in an IDF to describe an instrument (note parameters of instrument components may optionally be stored in parameter file).

To get started creating an IDF follow the instructions on the Create an IDF page, then return here for more detailed explanations of syntax and structures.

Introduction ¶

An instrument definition file (IDF) aims to describe an instrument, in particular providing details about those components of the instruments that are critically affecting the observed signal from an experiment. Parameter values of components may also be specified such as information about the opening height of a slit, the final energy of a detector and so on. The value of such parameters can optionally be linked to values stored in log-files.

In summary an IDF may be used to describe any or all of the following:

Instrument components defined using a hierarchical structure. Take, for example, a detector bank containing 100 identical tubes each containing 100 detector pixels. One option is to describe this setup using a flat structure of 100*100=10000 pixel components. Although this is a valid approach it #. create unnecessarily large files #. but most importantly it does not capture the layout of the instrument. The preferred option is to describe this example by first defining a “pixel” type, then a “tube” type containing 100 “pixels” and finally a “bank” component containing 100 “tubes”. This latter approach requires the specification of 1(the bank)+100(tubes)+100(pixels)=201 components as compared to specifying 10000 components using the former approach. The other benefit of organising the IDF according to the layout of the instrument is that users can subsequently refer to the structure of the instrument as it is laid out. For example can then subsequently easily move entire ‘bank’ or associate parameters which relevant for a specific say ‘tube’ or ‘bank’.
The geometric shape and position of any component including: slits, mirrors, detectors etc.
A number of specialised component types are defined including:
- detector and monitor components: required to be associated with unique detector or monitor ID numbers. The importance of these IDs are described further in 1
- SamplePos component: Purpose to store the sample position. Needed e.g. to calculate sample-to-detector distances
- Source component: Purpose to store the source position or a position along the beamline but before the sample. Needed e.g. for spallation source instruments to calculate neutron flightpaths including the source-to-sample (primary path) distance. Also, used to define a point along the beam located before the sample. The direction from this position to the SamplePos is currently used to calculate the beam direction in some calculates (for example two-theta scattering angles).
Handling of log-files. Values specified in log-files can be used to modify parameters of components, such as a detector position coordinate or a slit opening height, in addition to assign values to such parameters directly
Specifying ‘fitting’ parameters of instrument profile functions and other function to be used when data from the instrument are analysed.
Choice of preferred coordinate system. For example the default is to define the beam along the z-axis and the y-axis to point up.

An IDF is structured as an XML document. For the purpose here it is enough to know that an XML document follows a tree-based structure of elements with attributes. For example:

<type name="main-detector-bank">
  <component type="main-detector-pixel" >
    <location x="-0.31" y="0.1" z="0.0" />
    <location x="-0.32" y="0.1" z="0.0" />
    <location x="-0.33" y="0.1" z="0.0" />
  </component>
</type>

defines an XML element with has the attribute name=”main-detector-bank”. This element contains one sub-element , which again contains 3 elements. In plain English the above XML code aims to describe a “main-detector-bank” that contains 3 detector pixels and their locations within the bank.

If a component is a cylindrical tube where slices of this types are treated as detector pixels the tube detector performance enhancement can optionally be used, which will e.g. make the display of this tube in the instrument viewer faster. This can be done by adding ‘outline’ attribute to the tag and setting its value to “yes”.

<type name="standard-tube" outline="yes">
  <component type="standard-pixel" >
    <location y="-1.4635693359375"/>
    <location y="-1.4607080078125"/>
    <location y="-1.4578466796875"/>
  </component>
</type>

The ‘outline attribute’ only affects the 3D view of the instrument, which appears by default. It may lead to a less accurate placing of the detector pixels and in particular may not show the effects of tube calibration. However a 2D view of the instrument will still place pixel detectors accurately.

IDF filename convention ¶

An IDF can be loaded manually from any file with extension .xml or .XML using LoadInstrument or LoadEmptyInstrument.

When loading a data file if the file has an embedded mantid instrument definition (as in some nexus files) then this one will be used, otherwise we will attempt to determine a matching file from the IDFs located in the MantidInstall instrument directory.

To be found automatically Instrument definition files are required to have the format INSTRUMENTNAME_DefinitionANYTHING.xml, where INSTRUMENTNAME is the name of the instrument and ANYTHING can be any string including an empty string. Where more than one IDF is defined for an instrument the appropriate IDF is loaded based on its valid-from date. Note for this to work the Workspace for which an IDF is loaded into must contain a record of when the data were collected. This information is taken from the workspace’s Run object, more specifically the run_start property of this object.

You can determine which file would be selected for an instrument and date using the following python:

Example: Getting the right instrument filename

# if no date is given it will default to returning the IDF filename that is currently valid.
from mantid.api import ExperimentInfo
currentIDF = ExperimentInfo.getInstrumentFilename("ARCS")
otherIDF = ExperimentInfo.getInstrumentFilename("ARCS", "2012-10-30T00:00:00")

Instrument Definition Directories ¶

Mantid ships with many instrument definition files within the installation but also has the capability of fetching new instrument definitions by running the DownloadInstrument algorithm (this is run automatically on startup). Downloaded definitions are written to a different directory to the shipped versions so that they do not overwrite them. The default list of directories searched (in the this order) for an IDF for a given instrument are:

For Windows:

%APPDATA%\mantidproject\instrument: location of downloaded files
[INSTALLDIR]\instrument: location of shipped files

For Linux/OSX:

$HOME/.mantid/instrument: location of downloaded files
/etc/mantid/instrument: system-wide location for all users of a machine
[INSTALLDIR]/instrument: location of shipped files

Editing Downloaded Definitions¶

You should not edit files in the downloaded location, or add new ones as the may be deleted or overwritten. If you have a change to an instrument definition you wish to use then edit a copy in the [INSTALLDIR] instrument directory, but update the valid-from date so mantid will pick that one up in preference. Or if you just wish to force a particular instrument definition for a particular workspace just run LoadInstrument for that workspace.

More detailed descriptions of various parts of the IDF ¶

Geometry shapes ¶

For information on how to define geometric shapes see HowToDefineGeometricShape.

Top level <instrument>¶

<instrument> is the top level XML element of an IDF. It takes attributes, three of which must be included. An example is

<instrument xmlns="http://www.mantidproject.org/IDF/1.0"
            xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
            xsi:schemaLocation="http://www.mantidproject.org/IDF/1.0 http://schema.mantidproject.org/IDF/1.0/IDFSchema.xsd"
            name="ARCS"
            valid-from="1900-01-31 23:59:59"
            valid-to="2100-01-31 23:59:59">

Of the attributes in the example above

xmlns, xmlns:xsi, xsi:schemaLocation are required attributes that can be copied verbatim as above
name is (at present) optional, although it is recommended to specify something sensible
valid-from is compulsory and is the date from which the IDF is valid from (+). This date must be larger than or equal to 1900-01-31 23:59:01
valid-to may optionally be added to indicate the date to which the IDF is valid to. If not used, the file is permanently valid. (+)

(+) Both valid-from and valid-to are required to be set using the ISO 8601 date-time format, i.e. as YYYY-MM-DD HH:MM:SS or YYYY-MM-DDTHH:MM:SS 2. Valid ranges may overlap, provided the valid-from times are all different. If several files are currently valid, the one with the most recent valid-from time is selected.

Using <component> and <type>¶

Use the element to define a physical part of the instrument. A requires two things

It must have a type=”some type” attribute. This specify the ‘type’ of the component and this type must be specified somewhere in the IDF using: .
It must contain at least one <location> element. If multiple <location> are specified then this is essentially a shorthand notation for defining multiple components of the same type at different locations.

Here is an example

<component type="slit" name="bob">
  <location x="10.651"/>
  <location x="11.983"/>
</component>

<type name="slit"></type>

Which defined two slits at two difference locations. Optionally a <component> can be given a ‘name’, in the above example this name is “bob”. If no ‘name’ attribute is specified the name of the <component> defaults to the ‘type’ string, in the above this is “slit”. Giving sensible names to components is recommended for a number of reasons including #. The ‘Instrument Tree’ view of an instrument in MantidPlot uses these names #. when specifying <parameter>s through <component-link>s these names are used.

Special <type>s¶

Within Mantid certain <type>s have special meaning. A special <type> is specified by including an ‘is’ attribute as demonstrated below

<type name="pixel" is="detector">
  <cuboid id="app-shape">
    <left-front-bottom-point x="0.0025" y="-0.1" z="0.0"  />
    <left-front-top-point  x="0.0025" y="-0.1" z="0.0002"  />
    <left-back-bottom-point  x="-0.0025" y="-0.1" z="0.0"  />
    <right-front-bottom-point  x="0.0025" y="0.1" z="0.0"  />
  </cuboid>
</type>

where the ‘is’ attribute of is used to say this is a detector-<type> (note this particular detector-<type> has been assigned a geometric shape, in this case a cuboid, see HowToDefineGeometricShape). Special types recognised are:

Detector (or detector)
Monitor (or monitor)
RectangularDetector (or rectangularDetector, rectangulardetector, or rectangular_detector)
StructuredDetector (or structuredDetector, structureddetector, or structured_detector)
Source (or source)
SamplePos (or samplePos)
ChopperPos (or chopperPos)

For example it is important to specify the location of one Source-<type> and one SamplePos-<type> in order for Mantid to be able to calculate L1 and L2 distances and convert time-of-flight to, for instance, d-spacing. An example of specifying a Source and SamplePos is shown below

<component type="neutron moderator"> <location z="-10.0"/> </component>
<type name="neutron moderator" is="Source"/>

<component type="some sample holder"> <location /> </component>
<type name="some sample holder" is="SamplePos" />

Using detector/monitor IDs ¶

Any component that is either a detector or monitor must be assigned a unique detector/monitor ID numbers (note this is not spectrum numbers but detector/monitor ID numbers). There are at least two important reason to insist on this.

Data stored in files need to have a way to be linked to detectors/monitors defined in the IDF. For example, at the ISIS facility, data are recorded together with unique detector ID numbers. Hence the job here to match the IDs in the data file with the IDs of the IDF. Where unique IDs are not stored with the data the creator of an IDF have some flexibility to chose these ID numbers since the data themselves does not contain such number. However a link between the IDs and spectra in a workspace still needs to be made. By default the LoadInstrument algorithm, see in particular the RewriteSpectraMap parameter of this algorithm, will map the detector/monitor IDs with spectrum numbers as follows: the detector/monitor IDs in the IDF are ordered from smallest to largest number and then assigned in that order to the spectra in the workspace used to hold the data in Mantid.
Mantid needs to have a way to associate data which the detectors/monitors of the instrument, which is do this using the detector IDs. Although not mandatory it is recommended to give memorisable names to collection of detectors/monitors or individual detectors/monitors that a user is likely to want to refer. This allow a user to refer to a collection of detectors by name rather than trying to remember a sequence of IDs. Note the counts in a histogram spectrum may be the sum of counts from a number of detectors and Mantid, behind the scene, use the IDs to keep track of this.

The <idlist> element and the idlist attribute of the elements is used to assign detector IDs. The notation for using idlist is

<component type="monitor" idlist="monitor-id-list">
  <location r="5.15800" t="180.0" p="0.0" /> <!-- set to ID=500 in list below -->
  <location r="5.20400" t="180.0" p="0.0" /> <!-- set to ID=510 -->
  <location r="5.30400" t="180.0" p="0.0" /> <!-- set to ID=520 -->
  <location r="5.40400" t="180.0" p="0.0" /> <!-- set to ID=531 -->
  <location r="6.10400" t="180.0" p="0.0" /> <!-- set to ID=611 -->
  <location r="6.24700" t="0.000" p="0.0" /> <!-- set to ID=612 -->
  <location r="6.34700" t="0.000" p="0.0" /> <!-- set to ID=613 -->
  <location r="6.50000" t="0.000" p="0.0" /> <!-- set to ID=650 -->
</component>

<type name="monitor" is="monitor"/>

<idlist idname="monitor-id-list">
  <id start="500" step="10" end="530" />  <!-- specifies IDs: 500, 510, 520, 530 -->
  <id start="611" end="613" />            <!-- specifies IDs: 611, 612 and 613 -->
  <id val="650" />                        <!-- specifies ID: 650 -->
</idlist>

As can be seen to specify a sequence of IDs use the notation <id start=”500” step=”10” end=”530” />, where if the step attribute defaults to step=”1” if it is left out. Just specify just a single ID number you may alternatively use the notation <id val=”650” />. Please note the number of ID specified must match the number of detectors/monitors defined.

Creating Rectangular Area Detectors ¶

There is a shortcut way to create 2D arrays of detector pixels. Here is an example of how to do it:

<component type="panel"  idstart="1000" idfillbyfirst="y" idstepbyrow="300">
  <location r="0" t="0" name="bank1">
  </location>
</component>

<component type="panel"  idstart="100000" idfillbyfirst="y" idstepbyrow="300">
  <location r="45.0" t="0" name="bank2">
  </location>
</component>

<!-- Rectangular Detector Panel. Position 100 "pixel" along x from -0.1 to 0.1
     and 200 "pixel" along y from -0.2 to 0.2 (relative to the coordinate system of the bank) -->
<type name="panel" is="RectangularDetector" type="pixel"
    xpixels="100" xstart="-0.100" xstep="+0.002"
    ypixels="200" ystart="-0.200" ystep="+0.002" >
</type>

<!-- Pixel for Detectors. Shape defined to be a (0.001m)^2 square in XY-plane with tickness 0.0001m -->
<type is="detector" name="pixel">
  <cuboid id="pixel-shape">
    <left-front-bottom-point y="-0.001" x="-0.001" z="0.0"/>
    <left-front-top-point y="0.001" x="-0.001" z="0.0"/>
    <left-back-bottom-point y="-0.001" x="-0.001" z="-0.0001"/>
    <right-front-bottom-point y="-0.001" x="0.001" z="0.0"/>
  </cuboid>
  <algebra val="pixel-shape"/>
</type>

The “panel” type defined above has the special “is” tag of “RectangularDetector”. The same type definition then needs these attributes specified:
- type: point to another type defining your pixel shape and size.
- xpixels: number of pixels in X
- xstart: x-position of the 0-th pixel (in length units, normally meters)
- xstep: step size between pixels in the horizontal direction (in length units, normally meters)
- ypixels: number of pixels in Y
- ystart: y-position of the 0-th pixel (in length units, normally meters)
- ystep: step size between pixels in the vertical direction (in length units, normally meters)
Detectors of the type specified (“pixel” in the example) will be replicated at the X Y coordinates given. The usual rotation and translation of the panel will rotate the pixels as needed.
Each instance of a “panel” needs to set these attributes, at the <component> tag, in order to specify the Pixel IDs of the 2D array.
- idstart: detector ID of the first pixel
- idfillbyfirst: set to true if ID numbers increase with Y indices first. That is: (0,0)=0; (0,1)=1, (0,2)=2 and so on. Default is idfillbyfirst=”y”.
- idstepbyrow: amount to increase the ID number on each row. e.g, if you fill by Y first,and set idstepbyrow = 100, and have 50 Y pixels, you would get: (0,0)=0; (0,1)=1; ... (0,49)=49; (1,0)=100; (1,1)=101; etc.
- idstep. Default to 1. Set the ID increment within a row.
DO NOT also specify an “idlist” attribute for rectangular detectors, as it will not be used.
Advantages of using a Rectangular Detector tag instead of defining every single pixel:
- The data will be displayed as a bitmap in the instrument 3D view, making rendering much faster.
- Smaller IDF and faster instrument loading times.
- No need to make a script to generate the pixel positions.
Disadvantages/Limitations:
- Must have constant pixel spacing in each direction.
- Must be rectangular shape.

Creating Structured (Irregular Geometry) Detectors ¶

In the previous example, we saw that Rectangular Detectors provide a simple way of producing detectors with regular topology and geometry. The StructuredDetector provides a way of producing detectors with regular topology and irregular geometry. It can be thought of as a warped RectangularDetector:

<component name="DetectorBank" type="fan" idstart="0" idfillfirst="y" idstepbyrow="100" idstep="1">
  <location />
</component>

<type name="fan" is="StructuredDetector" xpixels="4" ypixels="5" type="pixel">
   <vertex x="-0.0" y="0.0" z="0.0" />
   <vertex x="-0.0" y="0.0" z="0.0" />
   <vertex x="0.0" y="0.0" z="0.0" />
   <vertex x="0.0" y="0.0" z="0.0" />
   <vertex x="0.0" y="0.0" z="0.0" />
   <vertex x="-0.00138071187457" y="0.00333333333333" z="0.0" />
   <vertex x="-0.000663041224598" y="0.00333333333333" z="0.0" />
   <vertex x="0.0" y="0.00333333333333" z="0.0" />
   <vertex x="0.000663041224597" y="0.00333333333333" z="0.0" />
   <vertex x="0.00138071187457" y="0.00333333333333" z="0.0" />
   <vertex x="-0.00276142374915" y="0.00666666666667" z="0.0" />
   <vertex x="-0.0013260824492" y="0.00666666666667" z="0.0" />
   <vertex x="0.0" y="0.00666666666667" z="0.0" />
   <vertex x="0.00132608244919" y="0.00666666666667" z="0.0" />
   <vertex x="0.00276142374915" y="0.00666666666667" z="0.0" />
   <vertex x="-0.00414213562372" y="0.01" z="0.0" />
   <vertex x="-0.00198912367379" y="0.01" z="0.0" />
   <vertex x="0.0" y="0.01" z="0.0" />
   <vertex x="0.00198912367379" y="0.01" z="0.0" />
   <vertex x="0.00414213562372" y="0.01" z="0.0" />
   <vertex x="-0.0055228474983" y="0.0133333333333" z="0.0" />
   <vertex x="-0.00265216489839" y="0.0133333333333" z="0.0" />
   <vertex x="0.0" y="0.0133333333333" z="0.0" />
   <vertex x="0.00265216489839" y="0.0133333333333" z="0.0" />
   <vertex x="0.00552284749829" y="0.0133333333333" z="0.0" />
   <vertex x="-0.00690355937287" y="0.0166666666667" z="0.0" />
   <vertex x="-0.00331520612299" y="0.0166666666667" z="0.0" />
   <vertex x="0.0" y="0.0166666666667" z="0.0" />
   <vertex x="0.00331520612299" y="0.0166666666667" z="0.0" />
   <vertex x="0.00690355937287" y="0.0166666666667" z="0.0" />
</type>

<type is="detector" name="pixel"/>

The “DetectorBank” type defined above has the special “is” tag of “StructuredDetector”. The same type definition then needs these attributes specified:
- type: point to another type defining your pixel shape and size.
- xpixels: number of pixels in X.
- ypixels: number of pixels in Y.
The StrucuredDetector type contains special <vertex> tags enclosed by this type. There are some useful points to note about this type of definition:
- All vertices for a single detector panel must be defined.
- Detector panels can be duplicated and repositioned using <component> and <location> tags.
- Vertices appear in a particular winding order increasing in x then y then z e.g (1, 0, 0) (2, 0, 0) / (1, 1, 0) (2, 1, 0)/ (1, 2, 0) (2, 2, 0) etc. Z is assumed to be fixed.
- The total number of vertices are strictly (xpixels + 1) * (ypixels + 1)
Detectors of the type specified (“pixel” in the example) will be replicated at the X Y coordinates given. Shapes do not need to be provided for the structured detector, hexahedra are assumed. Any shape provided will be ignored.
Each instance of a “DetectorBank” needs to set these attributes, at the <component> tag, in order to specify the Pixel IDs of the 2D array.
- idstart: detector ID of the first pixel
- idfillbyfirst: set to true if ID numbers increase with Y indices first. That is: (0,0)=0; (0,1)=1, (0,2)=2 and so on. Default is idfillbyfirst=”y”.
- idstepbyrow: amount to increase the ID number on each row. e.g, if you fill by Y first,and set idstepbyrow = 100, and have 50 Y pixels, you would get: (0,0)=0; (0,1)=1; ... (0,49)=49; (1,0)=100; (1,1)=101; etc.
- idstep. Default to 1. Set the ID increment within a row.
DO NOT also specify an “idlist” attribute for structured detectors, as it will not be used.
Advantages of using a Structured Detector tag instead of defining every single pixel:
- Smaller IDF and faster instrument loading times.
- Can be used to produced any desired irregular shape once the winding order is correct.
Disadvantages/Limitations:
- Must define every vertex in one panel although significantly simpler than defining every detector in the IDF.
- Mistakes in the vertex winding order can lead to unpredictable geometries.
- Vertices will most likely need to be generated using a script for complex geometries.

Using <location>¶

The <location> element allows the specification of both the position of a component and a rotation or the component’s coordinate system. The position part can be specified either using standard x, y and z coordinates or using spherical coordinates: r, t and p, which stands for radius, theta and phi, t is the angle from the z-axis towards the x-axis and p is the azimuth angle in the xy-plane 3. Examples of translations include

<component type="something" name="bob">
  <location x="1.0" y="0.0" z="0.0" name="benny" />
  <location r="1.0" t="90.0" p="0.0"/>
</component>

The above two translations have identical effect. They both translate a component along the x-axis by “1.0”. Note that optionally a <location> can be given a name similarly to how a <location> can optionally be given a name. If a ‘name’ attribute is not specified for a <location> element it defaults to the name of the <component>.

The rotation part is specified using the attributes ‘rot’, ‘axis-x’, ‘axis-y’, ‘axis-z’ and these result in a rotation about the axis defined by the latter three attributes. As an example the effect of

<location rot="45.0" axis-x="0.0" axis-y="0.0" axis-z="1.0"/>

is to set the coordinate frame of the this component equal to that of the parent component rotated by 45 degrees around the z-axis.

Both a translation and rotation can be defined within one <location> element. For example

<location x="1.0" y="0.0" z="0.0" rot="45.0" axis-x="0.0" axis-y="0.0" axis-z="1.0"/>

will cause this component to be translation along the x-axis by “1.0” relative to the coordinate frame of the parent component followed by a rotation of the coordinate frame by 45 degrees around the z-axis as demonstrated in the figure below.

Location-element-transformation.png

Any rotation of a coordinate system can be performed by a rotation about some axis, however, sometime it may be advantageous to think of such a rotation as a composite of two or more rotations. For this reason a <location> element is allowed to have sub-rotation-elements, and an example of a composite rotation is

<location r="4.8" t="5.3" p="102.8" rot="-20.6" axis-x="0" axis-y="1" axis-z="0">
  <rot val="102.8">
    <rot val="50" axis-x="0" axis-y="1" axis-z="0" />
  </rot>
</location>

The outermost is applied first followed by the 2nd outermost operation and so on. In the above example this results in a -20.6 degree rotation about the y-axis followed by a 102.8 degree rotation about the z-axis (of the frame which has just be rotated by -20.6 degrees) and finally followed by another rotation about the y-axis, this time by 50 degrees. The ISIS NIMROD instrument (NIM_Definition.xml) uses this feature.

The translation part of a <location> element can like the rotation part also be split up into a nested set of translations. This is demonstrated below

<location  r="10" t="90" >
  <trans r="8" t="-90" />
</location>

This combination of two translations: one moving 10 along the x-axis in the positive direction and the other in the opposite direction by 8 adds up to a total translation of 2 in the positive x-direction. This feature, for example, is useful when the positions of detectors are best described in spherical coordinates with respect to an origin different from the origin of the parent component. For example, say you have defined a <type name=”bank”> with contains 3 pixels. The centre of the bank is at the location r=”1” with respect to the sample and the positions of the 3 pixels are known with respect to the sample to be at r=”1” and with t=”-1”, t=”0” and t=”1”. One option is to describe this bank/pixels structure as

<component type="bank">
  <location />
</component>

<type name="bank">
  <component type="pixel">
    <location r="1" t="-1" />
    <location r="1" t="0" />
    <location r="1" t="1" />
  </component>
</type>

However a better option for this case is to use nested translations as demonstrated below

<component type="bank">
  <location r="1"/>
</component>

<type name="bank">
  <component type="pixel">
    <location r="1" t="180"> <trans r="1" t="-1" /> </location>
    <location r="1" t="180"> <trans r="1" t="0" /> </location>
    <location r="1" t="180"> <trans r="1" t="1" /> </location>
  </component>
</type>

since this means the bank is actually specified at the right location, and not artificially at the sample position.

Finally a combination of <trans> and <rot> sub-elements of a <location> element can be used as demonstrated below

<location x="10" >
  <rot val="90" >
    <trans x="-8" />
  </rot>
</location>

which put something at the location (x,y,z)=(10,-8,0) relative to the parent component and with a 90 rotation around the z-axis, which causes the x-axis to be rotated onto the y-axis.

Most of the attributes of have default values. These are: x=”0” y=”0” z=”0” rot=”0” axis-x=”0” axis-y=”0” axis-z=”1”

Using <facing>¶

The <facing> element is an element you can use together with a <location>. Its purpose is to be able, with one line of IDF code, to make a given component face a point in space. For example many detectors on ISIS instruments are setup to face the sample. A <facing>element must be specified as a sub-element of a <location> element, and the facing operation is applied after the translation and/or rotation operation as specified by the location element. An example of a <facing> element is

<facing x="0.0" y="0.0" z="0.0"/>
or
<facing r="0.0" t="0.0" p="0.0"/>

In addition if the <components-are-facing> is set under <defaults>, i.e. by default any component in the IDF will be rotated to face a default position then

<facing val="none"/>

can be used to overwrite this default to say you don’t want to apply ‘facing’ to given component.

The process of facing is to make the xy-plane of the geometric shape of the component face the position specified in the <facing> element. The z-axis is normal to the xy-plan, and the operation of facing is to change the direction of the z-axis so that it points in the direction from the position specified in the facing <facing> towards the position of the component.

<facing> supports a rot attribute, which allow rotation of the z-axis around it own axis before changing its direction. The effect of rot here is identical to the effect of using rot in a <location> where axis-x=”0.0” axis-y=”0.0” axis-z=”1.0”. Allowing rot here perhaps make it slightly clearly that such a rot is as part of facing a component towards another component.

which rotate the is a convenient element for adjusting the orientation of the z-axis. The base rotation is to take the direction the z-axis points and change it to point from the position specified by the <facing> element to the position of the component.

Using <exclude>¶

A <location> specifies the location of a <type>. If this type consists of a number of sub-parts <exclude> can be used to exclude certain parts of a type. For example say the type below is defined in an IDF

<type name="door">
  <component type="standard-tube">
    <location r="2.5" t="19.163020" name="tube1"/>
    <location r="2.5" t="19.793250" name="tube2"/>
    <location r="2.5" t="20.423470" name="tube3"/>
    <location r="2.5" t="21.053700" name="tube4"/>
    <location r="2.5" t="21.683930" name="tube5"/>
  </component>
</type>

and the instrument consists of a number of these doors but where some of the doors are different in the sense that for example the 1st and/or the 2nd tube is missing from some of these. Using <exclude> this can be succinctly described as follows:

<component type="door">
  <location x="0">
    <exclude sub-part="tube1"/>
    <exclude sub-part="tube3"/>
  </location>
  <location x="1" />
  <location x="2" />
  <location x="3">
    <exclude sub-part="tube3"/>
  </location>
</component>

where the sub-part of refers to the ‘name’ of a part of the type ‘door’.

Extra options for indirect geometry instruments¶

Optionally, both physical and ‘neutronic’ detector positions can be specified for indirect geometry instrument. This is described here.

Using <locations>¶

Most instruments have detectors which are ordered in some way. For a rectangular array of detectors we have a shorthand notation. The <locations> tag is a shorthand notation to use for a linear/spherical sequence of detectors, as any of the position coordinates or the coordinate rotation angles of a <location> tag are changing.

For example a <locations> element may be used to describe the position of equally distanced pixels along a tube, in the example below along the y variable

<locations y="1.0" y-end="10.0" n-elements="10" name="det"/>

The above one line of XML is shorthand notation for

<location y="1.0" name="det0"/>
<location y="2.0" name="det1" />
<location y="3.0" name="det2" />
<location y="4.0" name="det3" />
<location y="5.0" name="det4" />
<location y="6.0" name="det5" />
<location y="7.0" name="det6" />
<location y="8.0" name="det7" />
<location y="9.0" name="det8" />
<location y="10.0" name="det9" />

As is seen n-elements is the number of <location> elements this <locations> element is shorthand for. y-end specifies the y end position, and the equal distance in y between the pixels is calculated in the code as (‘y’-‘y-end’)/(‘n-elements’-1). Multiple ‘variable’-end attributes can be specified for the <locations> tag, where ‘variable’ here is any of the <location> attributes: x, y, z, r, t, p and rot. The example below describes a list of detectors aligned in a semi-circle:

<locations n-elements="7" r="0.5" t="0.0" t-end="180.0" rot="0.0" rot-end="180.0" axis-x="0.0" axis-y="1.0" axis-z="0.0"/>

The above one line of XML is shorthand notation for

<location r="0.5" t="0"   rot="0"   axis-x="0.0" axis-y="1.0" axis-z="0.0"/>
<location r="0.5" t="30"  rot="30"  axis-x="0.0" axis-y="1.0" axis-z="0.0"/>
<location r="0.5" t="60"  rot="60"  axis-x="0.0" axis-y="1.0" axis-z="0.0"/>
<location r="0.5" t="90"  rot="90"  axis-x="0.0" axis-y="1.0" axis-z="0.0"/>
<location r="0.5" t="120" rot="120" axis-x="0.0" axis-y="1.0" axis-z="0.0"/>
<location r="0.5" t="150" rot="150" axis-x="0.0" axis-y="1.0" axis-z="0.0"/>
<location r="0.5" t="180" rot="180" axis-x="0.0" axis-y="1.0" axis-z="0.0"/>

If name is specified, e.g. as name=”det” in the first example, then as seen the <location> elements are given the ‘name’ plus a counter, where by default this counter starts from zero. This counter can optionally be changed by using attribute name-count-start, e.g. setting name-count-start=”1” in the above example would have named the 10 <location> elements det1, det2, ..., det10.

When one <locations> tag was used in ISIS LET_Definition.xml the number of lines of this file reduced from 1590 to 567.

Using <parameter>¶

Parameters which do not change or are changed via <logfile> should be stored using this element inside the IDF, however parameters which may need to be accessed and changed manually on a regular basis should be stored in a separate parameter file.

<parameter> is used to specify a value to a parameter which can then be extracted from Mantid. One usage of <parameter> is to link values stored in log-files to parameter names. For example

<parameter name="x">
  <logfile id="trolley2_x_displacement" extract-single-value-as="position 1" />
</parameter>

reads: “take the first value in the “trolley2_x_displacement” log-file and use this value to set the parameter named ‘x’.

The name of the <parameter> is specified using the ‘name’ tag. You may specify any name for a parameter except for name=”pos” and name=”rot”. These are reserved keywords. Further a few names have a special effect when processed by Mantid

“x”, “y”, and “z” overwrite the x, y and z coordinate respectively of the element of the component the is a sub-element of.
“r-position”, “t-position” and “p-position” like “x”, “y” and “z” overwrite the x, y, z coordinates but specified using spherical coordinates (as defined ). Note that the parameters “t-position” and “p-position” are ignored if the parameter “r-position” is not also set for the same component. If only “r-position” is set, say to r-position=”10.0”, than the component will be set to (x,y,z)=(0,0,10.0) i.e. theta and phi default to zero where not specified.
“rotx”, “roty” and “rotz” rotate the component’s coordinate system around the x-axis, y-axis and z-axis respectively in units of degrees. If any of these are specified they re-define the rotation for the component. You can specify two or three of these to create any rotation. Regardless of what order rotx, roty and rotz is specified in the IDF the combined rotation is equals that obtained by applying rotx, then roty and finally rotz.
“Efixed”. If specified the ConvertUnits algorithm uses this value in unit conversion
“SplitInto”. How many MD boxes to split into when converting to MD.
“SplitThreshold”. The threshold number of MDEvents in an MDBox before splitting into a new MDBox. Concerns convert to MD.
“MaxRecursionDepth”. The maximum depth of the MDBox tree when converting to MD.
“offset-phi”. Effective boolean for turning on/off Phi offsets by PI. Set to Always to apply.

The value of the parameter is in the above example specified using a log-file as specified with the element <logfile>. The required attribute of <logfile> is

id - the logfile name minus the file extension and the ISIS raw file name. For example the id for the logfile ‘CSP78173_height.txt’ is ‘height’.

Optional attributes of <logfile> are:

extract-single-value-as - specify which value (or values) from the logfile should be used to. This attribute takes any of the following strings
- mean (default)
- position n where n is an integer
- first_value The first value in the run
- last_value The last value in the run
- median The median value in the run
- minimum The minimum value in the run
- maximum The maximum value in the run
eq - the values in the log-file may not directly specify the parameter you want to set in the IDF. A simple example is where the values in the logfile are in units of mm, whereas the unit of length in the IDF is meters. Hence for this case by setting eq=”0.001*value” the values in the logfile are automatically converted to meters. A more complicated example is where the height of a detector is recorded in a log-file as the angle between from the horizontal plane to the detector in unit of degrees. Say the distance between the sample (which is assumed to be in the horizontal plane) and the detector is 1.863m then by specifying eq=”1.863*sin(value*0.0174533)” the values in the log-file are automatically converted into the height of the detector from the horizontal plane in units of meters. Note pi/180=0.0174533 in “sin(value*0.0174533)” above is to transform degrees to radians.

Another option for specifying a value for a parameter is to use the notation:

<parameter name="x">
  <value val="7.2"/>
</parameter>

Here a value for the parameter with name “x” is set directly to 7.2. The only and required attribute of the <value> element is ‘val’.

For a given <parameter> you should specify its value only once. If by mistake you specify a value twice as demonstrated in the example below then the first encountered <value> element is used, and if no <value> element is present then the first encountered <logfile> element is used.

<parameter name="x">
  <value val="7.2"/>
  <logfile id="trolley2_x_displacement" extract-single-value-as="position 1" />
</parameter>

In the above example <value val=”7.2”/> is used.

Accessing <parameter>¶

Parameters are by default accessed recursively. Demonstrated with an example:

<component type="dummy">
  <location/>
  <parameter name="something"> <value val="35.0"/> </parameter>
</component>

<type name="dummy">
  <component type="pixel" name="pixel1">
    <location y="0.0" x="0.707" z="0.707"/>
    <parameter name="something1"> <value val="25.0"/> </parameter>
  </component>

  <component type="pixel" name="pixel2">
    <location y="0.0" x="1.0" z="0.0"/>
    <parameter name="something2"> <value val="15.0"/> </parameter>
  </component>
</type>

this implies that if you for instance ask the component with name=”pixel1” what parameters it has then the answer is two: something1=25.5 and something=35.0. If you ask the component name=”dummy” the same question the answer is one: something=35.0 and so on.

Using string <parameter>¶

This is a special category of parameters where the value specified for the parameter is string rather than a double. The syntax is

<parameter name="instrument-status" type="string">
  <value val="closed"/>
</parameter>

Using fitting <parameter>¶

This is a special category of parameters, which follows the same syntax as other but allows a few extra features. Fitting parameters are meant to be used when raw data are fitted against models that contain parameters, where some of these parameters are instrument specific. If such parameters are specified these will be pulled in before the fitting process starts, where optionally these may, for instance, be specified to be treated as fixed by default. To specify a fitting parameter use the additional tag type=”fitting” as shown in the example below

<parameter name="IkedaCarpenterPV:Alpha0" type="fitting">
  <value val="7.2"/>
</parameter>

It is required that the parameter name uses the syntax NameOfFunction:Parameter, where NameOfFunction is the name of the fitting function the parameter is associated with. In the example above the fitting function name is IkedaCarpenterPV and the parameter name is Alpha0.

To specify that a parameter should be treated as fixed in the fitting process use the element as demonstrated in the example below

<parameter name="IkedaCarpenterPV:Alpha0" type="fitting">
  <value val="7.2"/>
  <fixed />
</parameter>

A parameter can be specified to have a min/max value, which results in a constraint being applied to this parameter. An example of this is shown below

<parameter name="IkedaCarpenterPV:Alpha0" type="fitting">
  <value val="7.2"/>
  <min val="4"/> <max val="12"/>
</parameter>

The min/max values may also be specified as percentage values. For example:

<parameter name="IkedaCarpenterPV:Alpha0" type="fitting">
  <value val="250"/>
  <min val="80%"/> <max val="120%"/>
  <penalty-factor val="2000"/>
</parameter>

results in Alpha0 being constrained to sit between 250*0.8=200 and 250*1.20=300. Further this example also demonstrates how a can be specified to tell how strongly the min/max constraints should be enforced. The default value for the penalty-factor is 1000. For more information about this factor see FitConstraint.

A value for a parameter may alternatively be set using a look-up-table or a formula. An example demonstrating a formula is

<parameter name="IkedaCarpenterPV:Alpha0" type="fitting">
  <formula eq="100.0+10*centre+centre^2" unit="TOF" result-unit="1/dSpacing^2"/>
</parameter>

‘centre’ in the formula is substituted with the centre-value of the peak shape function as known prior to the start of the fitting process. The attributes ‘unit’ is optional. If it is not set then the peak centre-value is directly substituted for the centre variable in the formula. If it is set then it must be set to no one of the units defined in Unit Factory, and what happens is that the peak centre-value is converted to this unit before assigned to the centre variable in the formula.

The optional ‘result-unit’ attribute tells what the unit is of the output of the formula. In the example above this unit is “1/dSpacing^2” (for the ‘result-unit’ this attribute can be set to an algebraic expression of the units defined in Unit Factory). If the x-axis unit of the data you are trying to fit is dSpacing then the output of the formula is left as it is. But for example if the x-axis unit of the data is TOF then the formula output is converted into, it in this case, the unit “1/TOF^2”. Examples where ‘unit’ and ‘result-unit’ are used include: CreateBackToBackParameters and CreateIkedaCarpenterParameters.

An example which demonstrate using a look-up-table is

<parameter name="IkedaCarpenterPV:Alpha0" type="fitting">
  <lookuptable interpolation="linear" x-unit="TOF" y-unit="dSpacing">
    <point x="1" y="1" />
    <point x="3" y="100" />
    <point x="5" y="1120" />
    <point x="10" y="1140" />
  </lookuptable>
</parameter>

As with a formula the look-up is done for the ‘x’-value that corresponds to the centre of the peak as known prior to the start of the fitting process. The only interpolation option currently supported is ‘linear’. The optional ‘x-unit’ and ‘y-unit’ attributes must be set to one of the units defined in Unit Factory. The ‘x-unit’ and ‘y-unit’ have very similar effect to the ‘unit’ and ‘result-unit’ attributes for described above. ‘x-unit’ converts the unit of the centre before lookup against the x-values. ‘y-axis’ is the unit of the y values listed, which for the example above correspond to Alpha0.

Using <component-link>¶

Allow <parameter>s to be linked to components without needing <parameter>s to be defined inside, as sub-elements, of the components they belong to. The standard approach for defining a parameter is

<component type="bank" name="bank_90degnew">
  <location />
  <parameter name="test"> <value val="50.0" /> </parameter>
</component>

where a parameter ‘test’ is defined to belong to the component with the name ‘bank_90degnew’. However, alternatively the parameter can be defined using the notation in the an example below. Note that if more than one component e.g. have the name ‘bank_90degnew’ then the specified parameters are applied to all such components.

<component type="bank" name="bank_90degnew">
  <location />
</component>

<component-link name="bank_90degnew" >
  <parameter name="test"> <value val="50.0" /> </parameter>
</component-link>

<component-link> is the only way parameters can be defined in a parameter file used by the LoadParameterFile algorithm.

If there are several components with name ‘bank_90degnew’ but you want specified paramentes to apply to only one of them, then you can specify the name by a path name.

<component-link name="HRPD/leftside/bank_90degnew" >
  <parameter name="test"> <value val="50.0" /> </parameter>
</component-link>

The path name need not be complete provided it specifies a unique component. Here we drop the instrument name HRPD.

<component-link name="leftside/bank_90degnew" >
  <parameter name="test"> <value val="50.0" /> </parameter>
</component-link>

Using <combine-components-into-one-shape>¶

The standard way of making up geometric shapes as a collection of parts is described here: HowToDefineGeometricShape. However, <combine-components-into-one-shape> offers in some circumstances a more convenient way of defining more complicated shapes, as for example is the case for the ISIS POLARIS instrument. This tag combining components into one shape as demonstrated below:

<component type="adjusted cuboid">
  <location />
</component>

<type name="adjusted cuboid" is="detector">
  <combine-components-into-one-shape />
  <component type="cuboid1">
    <location name="A"/>
    <!-- "A" translated by y=10 and rotated around x-axis by 90 degrees -->
    <location name="B" y="10" rot="90" axis-x="1" axis-y="0" axis-z="0" />
  </component>
  <algebra val="A : B" />

  <!-- this bounding box is used for this combined into one shape-->
  <bounding-box>
    <x-min val="-0.5"/>
    <x-max val="0.5"/>
    <y-min val="-5.0"/>
    <y-max val="10.5"/>
    <z-min val="-5.0"/>
    <z-max val="5.0"/>
  </bounding-box>

</type>

<type name="cuboid1" is="detector">
  <cuboid id="bob">
    <left-front-bottom-point x="0.5" y="-5.0" z="-0.5"  />
    <left-front-top-point  x="0.5" y="-5.0" z="0.5"  />
    <left-back-bottom-point  x="-0.5" y="-5.0" z="-0.5"  />
    <right-front-bottom-point  x="0.5" y="5.0" z="-0.5"  />
  </cuboid>

  <!-- this bounding box is not used in the combined shape -->
  <!-- Note you would not normally need to add a bounding box
       for a single cuboid shape. The reason for adding one
       here is just to illustrate that a bounding added here
       will not be used in created a combined shape as in
       "adjusted cuboid" above -->
  <bounding-box>
    <x-min val="-0.5"/>
    <x-max val="0.5"/>
    <y-min val="-5.0"/>
    <y-max val="5.0"/>
    <z-min val="-0.5"/>
    <z-max val="0.5"/>
  </bounding-box>
</type>

which combines two components “A” and “B” into one shape. The resulting shape is shape is shown here:

CombineIntoOneShapeExample.png

Note for this to work, a unique name for each component must be provided and these names must be used in the algebra sting (here “A : B”, see HowToDefineGeometricShape). Further a bounding-box may optionally be added to the to the type. Note the above geometric shape can alternatively be defined with the XML (Mantid behind the scene translates the above XML to the XML below before proceeding):

<component type="adjusted cuboid">
  <location />
</component>

<type name="adjusted cuboid" is="detector">
  <cuboid id="A">
    <left-front-bottom-point x="0.5" y="-5.0" z="-0.5"  />
    <left-front-top-point  x="0.5" y="-5.0" z="0.5"  />
    <left-back-bottom-point  x="-0.5" y="-5.0" z="-0.5"  />
    <right-front-bottom-point  x="0.5" y="5.0" z="-0.5"  />
  </cuboid>
  <!-- cuboid "A" translated along y by 10 and rotated around x by 90 degrees -->
  <cuboid id="B">
    <left-front-bottom-point x="0.5" y="10.5" z="-5.0"  />
    <left-front-top-point  x="0.5" y="9.5" z="-5.0"  />
    <left-back-bottom-point  x="-0.5" y="9.5" z="-5.0"  />
    <right-front-bottom-point  x="0.5" y="10.5" z="5.0"  />
  </cuboid>
  <algebra val="A : B" />
</type>

<combine-components-into-one-shape> for now works only for combining cuboids. Please do not hesitate to contact the Mantid team if you would like to extend this.

This applies when defining any geometric shape, but perhaps something which a user has to be in particular aware of when defining more complicated geometry shapes, for example, using the <combine-components-into-one-shape> tag: the coordinate system in which a shape is defined can be chosen arbitrary, and the origin of this coordinate system is the position returned when a user asked for its position. It is therefore highly recommended that when a user define a detector geometric shape, this could be simple cuboid, that it is defined with the origin at the centre of the front of the detector. For detector shapes build up of for example multiple cuboids the origin should be chosen perhaps for the center of the front face of the ‘middle’ cuboid. When Mantid as for the position of such a shape it will be with reference to coordinate system origin of the shape. However, sometimes it may simply be inconvenient to build up a geometry shape with an coordinate system as explained above. For this case, and for now only when using <combine-components-into-one-shape> it possible to get around this by using the element <translate-rotate-combined-shape-to>, which takes the same attributes as a <location> element. The effect of this element is basically to redefine the shape coordinate system origin (in fact also rotate it if requested).

Using <defaults>¶

Used for setting various defaults.

<components-are-facing>¶

Used to make the xy-plane of the geometric shape of any component by default face a given location. For example

<components-are-facing x="0.0" y="0.0" z="0.0" />

If this element is not specified the default is to not attempt to apply facing.

<offsets>¶

Originally introduced to handle detector position coordinates as defined by the Ariel software.

<offsets spherical="delta" />

When this is set all components which have coordinates specified using spherical coordinates (i.e. using the r, t, p attributes, see description of <location>) are then treated as offsets to the spherical position of the parent, i.e. the value given for $r$ are added to the parent’s $r$ to give the total radial coordinate, and the same for $\theta$ and $\phi$ . Note using this option breaks the symmetry that the <location> element of a child component equals the position of this component relative to its parent component.

<reference-frame>¶

Reference frame in which instrument is described. The author/reader of an IDF can chose the reference coordinate system in which the instrument is described. The default reference system is the one shown below. The direction here means the direction of the beam if it was not modified by any mirrors etc.

<reference-frame>
  <!-- The z-axis is set parallel to and in the direction of the beam. the
       y-axis points up and the coordinate system is right handed. -->
  <along-beam axis="z"/>
  <pointing-up axis="y"/>
  <handedness val="right"/>
</reference-frame>

This reference frame is e.g. used when a signed theta detector values are calculated where it is needed to know which direction is defined as up. By default, the axis defining the sign of the scattering angle is the one pointing up. Optionally this can be customized by inserting the following line into the reference-frame node:

<theta-sign axis="x"/>

In this case, negative x will correspond to negative theta. Note that both the pointing-up and theta-sign axes cannot be the same as the along-beam axis.

<default-view>¶

This tag is used to control how the instrument first appears in the Instrument View. Attribute view defines the type of the view that opens by default. It can have the following values: “3D”, “cylindrical_x”, “cylindrical_y”, “cylindrical_z”, “spherical_x”, “spherical_y”, “spherical_z”. If the attribute is omitted value “3D” is assumed. Opening the 3D view on start-up is also conditioned on the value of the MantidOptions.InstrumentView.UseOpenGL property in the Properties File. If set to “Off” this property prevents the Instrument View to start in 3D mode and “cylindrical_y” is used instead. The user can change to 3D later.

Another attribute, axis-view governs on which axis the instrument is initially viewed from in 3D and can be set equal to one of “Z-”, “Z+”, “X-”, etc. If “Z-” were selected then the view point would be on the z-axis on the negative of the origin looking in the +z direction.

<angle unit=”radian”>¶

<angle unit="radian"/>

is set then all angles specified in <location> elements and <parameter>’s with names “rotx”, “roty”, “rotz”, “t-position” and “p-position” are assumed to in radians. The default is to assume all angles are specified in degrees.

Other defaults¶

<length unit="meter"/>

This default, for now, does not do anything, but is the default unit for length used by Mantid. If it would be useful for you to specify user defined units do not hesitate to request this.

Parameter Files ¶

To prevent an IDF file from getting too long and complicated, information not related to the geometry of the instrument may be put into a separate file, whose content is automatically included into the IDF file.

For more information see the parameter file page.

Deprecated Features ¶

The following features are now deprecated and should no longer be used.

mark-as=”monitor”

The following notation to mark a detector as a monitor is now deprecated:

<component type="monitor" idlist="monitor">
    <location r="3.25800" t="180.0" p="0.0" mark-as="monitor"/>
</component>

<type name="monitor" is="detector"/>

<idlist idname="monitor">
  <id val="11" />
</idlist>

The above XML should be replaced with

<component type="monitor" idlist="monitor">
    <location r="3.25800" t="180.0" p="0.0"/>
</component>

<type name="monitor" is="monitor"/>

<idlist idname="monitor">
  <id val="11" />
</idlist>

Category: Concepts