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SANS TOML Files¶

General Notes¶

• Lengths are always specified in meters within TOML files, unlike previous legacy formats.

• Angles are specified in degrees.

Format Changes¶

V0 (Mantid 6.3+) to V1 (Mantid 6.4+)¶

• norm_monitor and trans_monitor in instrument.configuration now take a monitor name (e.g. “M1”) instead of a spectrum number

• selected_monitor in normalisation and transmission has been removed in favour of this change in instrument.configuration

• trans_monitor can now have the value “ROI”

V0 (Mantid 6.1.x) to V0 (Mantid 6.3+)¶

• normalisation and normalization are both accepted and equivalent

• detector.calibration was renamed to detector.correction

• normalisation.all_monitors was added to support BACK/MON/TIMES

• [gravity] and gravity.enabled were merged into instrument.configuration.gravity_enabled

• detector.configuration.selected_detector is now mandatory

• detector.configuration.selected_detector accepts front and rear instead of HAB and LAB respectively.

• detector.configuration.all_centre has been added to set the front and rear centre at the same time.

• reduction.merged.shift.distance was renamed from distance to factor

New Fields¶

toml_file_version¶

This is always the first line of the file and represents the TOML file version. Long-term this allows us to make changes in a backwards compatible way.

Available TOML Versions:

• 1

# First line of file
toml_file_version = 1

# Everything else


This is a free-form field, typically at the top of the file to enter any user attributes. They are ignored by the TOML parser.

[metadata]
created = "1980-12-31"
weather_that_day = "sunny"
this_is_toml = true


Instrument¶

This is a required entry to specify the instrument name and instrument.configuration, documented in the conversion guide below.

[instrument]
name = "LARMOR"  # or "LOQ" / "SANS2D" / "ZOOM"...etc.

[instrument.configuration]
# ...


Conversion From Legacy User Files¶

Layout¶

This section is designed like a reference that users can paste straight into existing TOML files, but means that the sections are listed alphabetically by the old command name!

Note: TOML files use SI units rather than a mix of unit prefixes. For example, you will need to convert any measurements in millimetres to meters.

The following is used to note optional qualifiers which were available in the existing user file format: [ ].

Examples are given in a way that they can be merged together where headers match, for example these three examples:

[binning]
wavelength = {start = 2.0, step=0.125, stop=14.0, type = "Lin"}

[binning]
[binning.1d_reduction]
binning = "0.02,0.05,0.5,-0.1,10.0"

[binning]
[binning.2d_reduction]
step = 0.002
stop = 0.1
type = "Lin"


Are combined into the following when writing the TOML file:

[binning]
wavelength = {start = 2.0, step=0.125, stop=14.0, type = "Lin"}

[binning.1d_reduction]
binning = "0.02,0.05,0.5,-0.1,10.0"

[binning.2d_reduction]
step = 0.002
stop = 0.1
type = "Lin"


Tips for converting¶

For converting existing files the following process is recommended:

• Make a copy of the existing (old-format) user file to work with

• Create a blank TOML file (file.toml instead of file.txt)

• Add the following to the start of the TOML file in the order shown:

toml_file_version = 1

[instrument]
name = "instrument"  # give name of instrument

[instrument.configuration]

• Copy any comments from the old user file that need to be preserved to [metadata] in the TOML user file and replace any leading ! with #

• Remove any commented out lines in the old user file (lines starting with !)

• Work down the old user file line-by-line using this guide to find the new replacement TOML commands

• Add the replacement TOML commands to the TOML user file

• Delete each line from the old user file as conversion proceeds

• When done, save the new TOML user file and delete the edited copy of the old user file; do not delete the reference copy of the old user file!!!

• Try the TOML user file in Mantid!

Legacy Command Set¶

BACK/MON/TIMES t1 t2¶

BACK was used to specify a time window over which to estimate the (time-independent) background on monitor spectra. This background is then subtracted from the specified monitor spectra before the data are rebinned into wavelength.

This particular command subtracts the same background level from all monitors. The continued use of this method of monitor correction is now deprecated. See also BACK/M[n]/TIMES t1 t2.

Times were specified in microseconds.

[normalisation]
[normalisation.all_monitors]
background = [t1, t2]
enabled = true


Existing Example

BACK/MON/TIMES 30000 40000


Replacement Example

[normalisation]
[normalisation.all_monitors]
background = [30000, 40000]
enabled = true


Note: if using this, set any instances of use_own_background to false.

BACK/M[n]/TIMES t1 t2¶

This command was used to estimate and subtract the (time-independent) background level on a specified monitor. See also BACK/MON/TIMES t1 t2.

Times were specified in microseconds.

# Note: both "normalisation" and "normalisation" are both accepted
[normalisation]
[normalisation.monitor.Mn]
spectrum_number = n
use_own_background = true
background = [t1, t2]


OR

[transmission]
[transmission.monitor.Mn]
spectrum_number = n
use_own_background = true
background = [t1, t2]


Existing Example

BACK/M1 30000 40000


Replacement Example

[normalisation]
[normalisation.monitor.M1]
spectrum_number = 1
use_own_background = true
background = [30000.0, 40000.0]


COMPATIBILITY ON¶

This command was used to allow event data to be reduced in a manner that, so far as was possible, emulated the reduction of histogram data. The primary use of this command was as a diagnostic. Omitting this command was equivalent to COMPATIBILITY OFF.

Existing Example

COMPATIBILITY ON


Replacement Example

Unsupported

DET/CORR [FRONT][REAR] [X][Y][Z] [XTILT][YTILT][ZTILT] [ROT] [SIDE] [RADIUS] n¶

This command was used to fine tune the position of a specified detector by applying a relative correction to the logged encoder value. The parameter n could be a distance or an angle depending on the specified context as shown below.

If specified, SIDE applies a translation to the rotation axis of the detector perpendicular to the plane of the detector. RADIUS increases the apparent radius from the rotation axis of the detector to the active plane.

XYZ applies a translation to in the specified direction to a given bank in the specified axis.

Tilt rotates a bank by the given number of degrees along the axis specified.

[detector]
[detector.correction.position]
# Note fields can be added or omitted as required
# This is the complete list of adjustments available
front_x = a
front_y = b
front_z = c

front_x_tilt = d
front_y_tilt = e
front_z_tilt = f

front_rot = g
front_side = h

rear_x = a
rear_y = b
rear_z = c

rear_x_tilt = d
rear_y_tilt = e
rear_z_tilt = f

rear_rot = g
rear_side = h


Existing Example

DET/CORR FRONT X -33
DET/CORR FRONT Y -20
DET/CORR FRONT Z -47
DET/CORR FRONT XTILT -0.0850
DET/CORR FRONT YTILT 0.1419
DET/CORR FRONT ROT 0.0
DET/CORR FRONT SIDE 0.19
DET/CORR REAR X 0.0
DET/CORR REAR Z 58


Replacement Example

[detector]
[detector.correction.position]
front_x = -0.033
front_y = -0.020
front_z = -0.047
front_x_tilt = -0.000085
front_y_tilt = 0.0001419
front_rot = 0.0
front_side = 0.00019
rear_x = 0.0
rear_z = 0.058


DET/[REAR][FRONT][MERGED][BOTH]¶

This command was used to specify which detector(s) were to be processed during data reduction.

On the LOQ instrument the qualifier /FRONT could be equivalently replaced by /HAB (for high-angle bank) in existing user files. Similarly, /MERGED and /MERGE were equivalent.

If an instrument only has one detector it is assumed to be equivalent to the rear detector.

In TOML the detectors must be specified in lower case, and /BOTH has been replaced by “all”.

[detector.configuration]
selected_detector = "rear"


Existing Example

DET/HAB


Replacement Example

[detector.configuration]
# Accepts "front", "rear", "merged", or "all".
selected_detector = "front"


DET/RESCALE n¶

This command specified the factor by which the reduced front detector data should be multiplied to allow it to overlap the reduced rear detector data. If omitted n was assumed to be 1.0 (no rescaling). See also DET/RESCALE/FIT [q1 q2] and DET/SHIFT y.

[reduction]
[reduction.merged.rescale]
factor = n
use_fit = false  # Must be false for single value


Existing Example

DET/RESCALE 0.123


Replacement Example

[reduction]
[reduction.merged.rescale]
factor = 0.123
use_fit = false


DET/RESCALE/FIT [q1 q2]¶

This command was used to automatically estimate the factor by which the reduced front detector data should be multiplied to allow it to overlap the reduced rear detector data. A specific Q-range over which to compare intensities could be optionally specified. If omitted, all overlapping Q values were used. See also DET/RESCALE/FIT [q1 q2].

Scattering vectors were specified in inverse Angstroms.

[reduction]
[reduction.merged.rescale]
min = q1
max = q2
use_fit = true  # Must be true for fitting


Existing Example

DET/RESCALE/FIT 0.14 0.24


Replacement Example

[reduction]
[reduction.merged.rescale]
min = 0.14
max = 0.24
use_fit = true


DET/SHIFT y¶

This command specified the relative amount (a constant) by which the reduced front detector data should be shifted in intensity to allow it to overlap the reduced rear detector data. If omitted n was assumed to be 0.0 (no shift). See also DET/RESCALE/FIT [q1 q2] and DET/SHIFT y.

[reduction]
[reduction.merged.shift]
factor = y
use_fit = false  # Must be false for single value


Existing Example

DET/SHIFT 0.123


Replacement Example

[reduction]
[reduction.merged.shift]
factor = 0.123
use_fit = false


DET/SHIFT/FIT [q1 q2]¶

This command was used to automatically estimate the relative amount (a constant) by which the reduced front detector data should be shifted to allow it to overlap the reduced rear detector data. A specific Q-range over which to compare intensities could be optionally specified. If omitted, all overlapping Q values were used. See also DET/SHIFT y.

Scattering vectors were specified in inverse Angstroms.

[reduction]
[reduction.merged.shift]
min = q1
max = q2
use_fit = true  # Must be true for fitting


Existing Example

DET/SHIFT/FIT 0.1 0.2


Replacement Example

[reduction]
[reduction.merged.shift]
min = 0.1
max = 0.2
use_fit = true


DET/OVERLAP q1 q2¶

This command was used to specify the Q-range over which merging of the rear and front detectors was to be done. If omitted, all overlapping Q values were used.

Scattering vectors were specified in inverse Angstroms.

[reduction]
[reduction.merged.merge_range]
min = q1
max = q2
use_fit = true


Existing Example

DET/OVERLAP 0.14 0.24


Replacement Example

[merged]
[reduction.merged.merge_range]
min = 0.14
max = 0.24
use_fit = true


FIT/CENTRE t1 t2¶

This command was used to specify a time window within which the ‘prompt spike’ could be found in detector spectra. This information was used to remove the spike by interpolating along the time-of-flight distribution. See also FIT/MONITOR t1 t2.

Times were specified in microseconds.

This command was never implemented in Mantid (but was in COLETTE)!

Existing Example

FIT/CENTRE 19900 20500


Replacement Example

Unsupported

FIT/MID[/HAB]/FILE=script.txt¶

This command was used to drive automatic determination of the coordinates of the centre of the scattering pattern on the specified detector using a script file. It has been superseded by the Beam Centre Finder tool in Mantid.

If /HAB (equivalent to the “front” detector) was omitted the command applied to the “rear” detector.

Existing Example

FIT/MID/FILE=FIND_CENTRE128SC.COM
FIT/MID/HAB/FILE=FIND_CENTRE_HAB2.COM


Replacement Example

Unsupported

FIT/MONITOR t1 t2¶

This command was used to specify a time window within which the ‘prompt spike’ could be found in monitor spectra. This information was used to remove the spike by interpolating along the time-of-flight distribution. See also FIT/CENTRE t1 t2.

Times were specified in microseconds.

Replacement

[mask]
prompt_peak = {start = t1, stop = t2}


Existing Example

FIT/MONITOR 19900 20500


Replacement Example

[mask]
prompt_peak = {start = 19900.0, stop = 20500.0}


FIT/TRANS[/CLEAR][/OFF]¶

This command was used to disable fitting of the calculated transmission data. See also FIT/TRANS[[/SAMPLE][/CAN]][/LINEAR][/YLOG][/POLYNOMIALn] [w1 w2].

Replacement

[transmission]
[transmission.fitting]
enabled = false
parameters = {lambda_min = w1, lambda_max = w2}
# Can be: "Linear" / "Logarithmic" / "Polynomial"
function = "Linear"
# Only used when set to "Polynomial"
polynomial_order = 3


Existing Example

FIT/TRANS/OFF


Replacement Example

[transmission]
[transmission.fitting]
enabled = false
parameters = {lambda_min = 3.0, lambda_max = 11.0}
function = "Linear"


FIT/TRANS[[/SAMPLE][/CAN]][/LINEAR][/YLOG][/POLYNOMIALn] [w1 w2]¶

This command was used to specify how the calculated transmission data should be fitted. Subsequent data processing would then use transmission values interpolated using the fit function. In some instances doing this could improve the statistical quality of the transmission data. See also FIT/TRANS[/CLEAR][/OFF].

Wavelengths were specified in Angstroms. If w1 and w2 were omitted then the fit was applied to the full wavelength range.

The SAMPLE qualifier only applied the specified fit to the sample transmission data. Similarly, the CAN qualifier only applied the specified fit to the can transmission data. If neither of these qualifiers was present then the same fit function was applied to both sets of transmission data.

The LINEAR (which could be abbreviated to LIN) qualifier implemented a fit function of the form Y=mX+C.

The YLOG (which could be abbreviated to LOG) qualifier implemented a fit function of the form Y=exp(aX)+C.

The POLYNOMIALn qualifier implemented a fit function of the form Y=C0+C1X+C2X^2+…CnX^n where n>2.

Replacement

[transmission]
[transmission.fitting]
enabled = true
parameters = {lambda_min = w1, lambda_max = w2}
# Can be: "Linear" / "Logarithmic" / "Polynomial"
function = "Linear"
# Only used when set to "Polynomial"
polynomial_order = 3


Existing Example

FIT/TRANS/LIN 3.0 11.0


Replacement Example

[transmission]
[transmission.fitting]
enabled = true
parameters = {lambda_min = 3.0, lambda_max = 11.0}
function = "Linear"


GRAVITY[/ON/OFF]¶

This command was used to specify whether the detector data should be corrected for the ballistic effects of gravity on the neutrons. This correction is particularly important at long sample-detector distances and/or when using long wavelengths. See also GRAVITY/LEXTRA x.

If Q-resolution estimation is enabled (see QRESOL[/ON][/OFF]) any gravity corrections will be included in that calculation too.

Replacement

[instrument.configuration]
gravity_enabled = true


Existing Example

GRAVITY/ON


Replacement Example

[instrument.configuration]
gravity_enabled = true


GRAVITY/LEXTRA x¶

This command was used to specify an extra length that can be added to the gravity correction. The extra length is only taken into account when the gravity correction is enabled and the default value is x=0.0. See also GRAVITY[/ON/OFF].

Unless there is a reason not too, set the value of gravity_extra_length equal to 0.5 * collimation_length. See also QRESOL/LCOLLIM=z.

Replacement

[instrument.configuration]
gravity_extra_length = x


Existing Example

GRAVITY/LEXTRA 2.0


Replacement Example

[instrument.configuration]
gravity_extra_length = 2.0


L/EVENTSTIME binning_string¶

L was an accepted abbreviation for LIMIT.

This command was used to specify a binning scheme to be applied to event mode data. The scheme comprised a comma-separated string of the form t1,tstep1,t2,tstep2,t3… where t1, t2, t3, etc specified event times and tstep1, tstep2, etc specified the binning interval between those event times.

A positive tstep would result in linear (ie, equally-spaced) bins, whilst a negative tstep would result in logarithmic (ie, geometrically-expanding) bins.

All times and linear tsteps were specified in microseconds. Logarithmic tsteps were specified as %/100.

Replacement

[reduction.events]
binning = "str"


Existing Example

L/EVENTSTIME 7000.0,500.0,60000.0


Replacement Example

[reduction.events]
# A negative step (middle val) indicates Log
# Therefore this is linear binning
binning = "7000.0,500.0,60000.0"


L/PHI[/NOMIRROR] a b¶

L was an accepted abbreviation for LIMIT.

This command specified the azimuthal range of 2D detector data to be included in data reduction. Viewed along the direction of travel of the neutrons 0 (or 360) degrees was at 3 O’clock, 90 degrees was at 12 O’clock, 180 (or -180) degrees was at 9 O’clock, and 270 (or -90) degrees was at 6 O’clock. By default the mirror sector was always included (ie, selecting a=-30 & b=+30 would also include the sector 150-210), but this could be overridden with the /NOMIRROR qualifier.

Angles were specified in degrees.

Replacement

[mask]
mirror = bool
start = a
stop = b


Existing Example

L/PHI/NOMIRROR -45 45


Replacement Example

[mask]
mirror = false
start = -45
stop = 45


L/Q binning_string¶

L was an accepted abbreviation for LIMIT.

This command was used to specify a Q-binning scheme to be applied during 1D data reduction. See also L/QXY binning_string.

For historical reasons, several variants of this command were implemented but they can be summarised thus:

L/Q q1 q2 qstep/LIN   same as   L/Q/LIN q1 q2 qstep
L/Q q1 q2 qstep/LOG   same as   L/Q/LOG q1 q2 qstep
L/Q q1,qstep1,q2,qstep2,q3...


In the first two cases the type of Q-binning is fixed by the choice of the LIN or LOG qualifier. But in the last case variable Q-binning is permitted if required.

A positive qstep would result in linear (ie, equally-spaced) bins, whilst a negative qstep would result in logarithmic (ie, geometrically-expanding) bins.

All Q-values and linear qsteps were specified in inverse Angstroms. Logarithmic qsteps were specified as %/100.

Replacement

[binning.1d_reduction]
# Negative indicates log
binning = "rebin_string"


Existing Example

L/Q .02,0.05,0.5,-0.1,10


Replacement Example

[binning]
[binning.1d_reduction]
# Negative indicates log
binning = "0.02,0.05,0.5,-0.1,10.0"


L/Q/RCUT r¶

L was an accepted abbreviation for LIMIT.

This command was used to specify the ‘radius cut’ value, a construct which could be used to improve the statistical uncertainty on Q bins suffering from poor instrumental resolution. This command would typically, but not exclusively, be used in conjunction with L/Q/WCUT w.

Replacement

[binning.1d_reduction]


Existing Example

L/Q/RCUT 100


Replacement Example

[binning]
[binning.1d_reduction]


L/Q/WCUT w¶

L was an accepted abbreviation for LIMIT.

This command was used to specify the ‘wavelength cut’ value, a construct which could be used to improve the statistical uncertainty on Q bins suffering from poor instrumental resolution. This command would typically, but not exclusively, be used in conjunction with L/Q/RCUT r.

The cut-off wavelength was specified in Angstroms.

Replacement

[binning.1d_reduction]
wavelength_cut = w


Existing Example

L/Q/WCUT 8


Replacement Example

[binning]
[binning.1d_reduction]
wavelength_cut = 8.0


L/QXY binning_string¶

L was an accepted abbreviation for LIMIT.

This command was used to specify a Q-binning scheme to be applied during 2D data reduction. See also L/Q binning_string.

For historical reasons, several variants of this command were implemented but they can be summarised thus:

L/QXY 0 q2 qstep/LIN   same as   L/QXY/LIN 0 q2 qstep
L/QXY 0 q2 qstep/LOG   same as   L/QXY/LOG 0 q2 qstep


The type of Q-binning is fixed by the choice of the LIN or LOG qualifier but variable binning is not permitted during 2D reductions. Also note that the Q-range must start at zero.

All Q-values and linear qsteps were specified in inverse Angstroms. Logarithmic qsteps were specified as %/100.

Replacement

[binning]
[binning.2d_reduction]
#binning MUST start at 0.0
step = step
stop = stop
#type can be "Lin" or "Log"
type = "Lin"


Existing Example

L/QXY 0 0.1 .002/lin


Replacement Example

[binning]
[binning.2d_reduction]
step = 0.002
stop = 0.1
type = "Lin"


L/R r1 r2 [rstep]¶

L was an accepted abbreviation for LIMIT.

This command was used to specify the radii on the detector between which the radial integration of the data was to be performed. Typically, r1 would be set to be just outside the radius of the beamstop in use.

On the LOQ instrument the maximum values of r2 on the rear and front detectors are 0.419 m and 0.750 m, respectively. But with the advent of the TS2 SANS instruments with moving detectors a convenience was introduced to make setting r2 easier and less prone to error: setting r2 = -0.001 m is equivalent to using the maximum radius. But note it is not clear how this is now achieved!

On LOQ the rstep parameter originally specified the width of the virtual rings used for the radial integration, a value of rstep = 0.003 m was typical. However, at some point this rstep seemed to become optional, and indeed was never used on some the TS2 instruments. How the virtual ring width was decided in such cases is also unclear!

[detector]
radius_limit = {min = 0.038, max = -0.001}


Existing Example

L/R 38 -1


Replacement Example

[detector]
radius_limit = {min = 0.038, max = -0.001}


L/SP¶

L was an accepted abbreviation for LIMIT.

This command was used to specify the detector spectra (ie, pixels) to be included in the data reduction. Historically this mitigated computation challenges. This command has effectively been superseded by the DET/[REAR][FRONT][MERGED][BOTH] command.

Existing Example

L/SP 3 16386


Replacement Example

Unsupported

L/WAV binning_string¶

L was an accepted abbreviation for LIMIT.

This command was used to specify a wavelength-binning scheme to be applied during data reduction.

For historical reasons, several variants of this command were implemented but they can be summarised thus:

L/WAV w1 w2 wstep/LIN   same as   L/WAV/LIN w1 w2 wstep
L/WAV w1 w2 wstep/LOG   same as   L/WAV/LOG w1 w2 wstep


The /LIN qualifier would result in linear (ie, equally-spaced) bins, whilst the /LOG qualifier would result in logarithmic (ie, geometrically-expanding) bins.

All wavelength-values and linear wsteps were specified in Angstroms. Logarithmic wsteps were specified as %/100.

Replacement

wavelength = {start = min, step = step, stop = max, type = "Lin"}
# Alternative for ranges
wavelength = {binning = "min,max", step = step, type = "RangeLin"}


Existing Example

L/WAV 2.0 14.0 0.125/LIN


Replacement Example

[binning]
# Only for "Lin", "Log"
wavelength = {start = 2.0, step=0.125, stop=14.0, type = "Lin"}
# Only for "RangeLin" or "RangeLog"
wavelength = {binning="2.0-7.0, 7.0-14.0", step=0.125, type = "RangeLin"}


This command was used to clear any detector masks in operation. Without the TIME qualifier only spatial masks were cleared; with the TIME qualifier only time masks were cleared.

Existing Example

MASK/CLEAR


Replacement Example

Unsupported

This command was used to specify one or more detector mask files to be applied during data reduction to omit individual detector pixels or regions of pixels from the calculation.

Replacement

[mask]


Existing Example

MASKFILE=a.xml,b.xml,c.xml


Replacement Example

[mask]


This command was used to specify a horizontal row of detector pixels to be omitted from the calculation during data reduction. See also MASK[/FRONT][/REAR] Hn.

The TOML replacement command actually permits several rows to be specified at once.

Replacement

[mask]
detector_rows = [h1, h2, h3, ...hn]


Existing Example

MASK/REAR H100


Replacement Example

[mask]
# Masks horizontal 100 and 200
detector_rows = [100, 200]


This command was used to specify several contiguous horizontal rows of detector pixels to be omitted from the calculation during data reduction. See also MASK[/FRONT][/REAR] Hn.

The TOML replacement command actually permits multiple ranges of rows to be specified at once.

Replacement

[mask]
detector_row_ranges = [[x, y]]


Existing Example

MASK/REAR H126>H127


Replacement Example

[mask]
# Masks horizontal 126 AND 127
# Also includes 130-135 to show multiple can be masked
detector_row_ranges = [[126, 127], [130, 135]]


This command was used to specify a vertical column of detector pixels to be omitted from the calculation during data reduction. See also MASK[/FRONT][/REAR] Vn.

The TOML replacement command actually permits several columns to be specified at once.

Replacement

[mask]
detector_rows = [v1, v2, v3, ...vn]


Existing Example

MASK/REAR V100


Replacement Example

[mask]
# Masks vertical 100 and 200
detector_columns = [100, 200]


This command was used to specify several contiguous vertical columns of detector pixels to be omitted from the calculation during data reduction. See also MASK[/FRONT][/REAR] Vn.

The TOML replacement command actually permits multiple ranges of columns to be specified at once.

Replacement

[mask]
detector_column_ranges = [[x, y]]


Existing Example

MASK/REAR V126>V127


Replacement Example

[mask]
# Masks vertical 126 AND 127
# Also includes 130-135 to show multiple can be masked
detector_column_ranges = [[126, 127], [130, 135]]


This command was used to specify a rectangular box of detector pixels to be omitted from the calculation during data reduction.

The parameters were specified in mm.

This command is not implemented in Mantid as there are other ways to achieve the same outcome (eg, using the Instrument View tools). Also, a combination of MASK[/FRONT][/REAR] Hn>Hm and MASK[/FRONT][/REAR] Vn>Vm could be used to replicate some of the same functionality.

Existing Example

MASK 0 40 0 40


Replacement Example

Unsupported

This command was used to specify a diagonal line of detector pixels to be omitted from the calculation during data reduction. See also MASK/LINE a b c d.

The line started at the centre of the scattering pattern (see SET CENTRE a b) and extended to the edge of the pattern at the specified angle b with the specified width a in mm. Only pixels wholly within the line were excluded. The angle was defined in the same way as for L/PHI.

An infinite cylinder (length 100m) with the angle and width set by the user is created in the plane of the detector from the point at which the transmitted beam is incident on the detector.

MaskDetectorsInShape v1 is subsequently used the apply the generated shape. The central point of each detector must lie within the shape to be masked, partially overlapping detectors (whose centre does not sit in the masked region) will not be masked.

The primary use of this command was to mask out the beamstop support arm on some instruments.

Replacement

beamstop_shadow = {width = a, angle = b}


Existing Example:

MASK/LINE 30 170


Replacement Example

[mask]
beamstop_shadow = {width = 0.03, angle = 170.0}


This command was used to specify a diagonal line of detector pixels to be omitted from the calculation during data reduction. See also MASK/LINE a b.

This command works identically to MASK/LINE a b. Instead of starting at (0, 0) the coordinates for x and y (represented by c and d) are given by the user.

Note that whilst parameter a was given in mm, c and d were specified in metres even in legacy files!

Replacement

beamstop_shadow = {width = a, angle = b, x_pos = c, y_pos = d}


Existing Example:

MASK/LINE 30 170 0.3 0.1


Replacement Example

[mask]
beamstop_shadow = {width = 0.03, angle = 170.0, x_pos=0.3, y_pos=0.1}


This command was used to specify individual detector spectra (ie, pixels) to be omitted from the calculation during data reduction.

The TOML replacement command actually permits several spectra to be specified at once.

Replacement

[mask]


Existing Example

MASK S123


Replacement Example

[mask]


This command was used to specify regions of the time-of-flight spectrum in all spectra to be omitted from the calculation during data reduction. Note that the action of this command differs from FIT/CENTRE and FIT/MONITOR.

Times were specified in microseconds.

The TOML replacement command actually permits multiple time ranges to be specified at once.

Replacement

[mask]
tof = [
{start = t1, stop = t2},
{start = t3, stop = t4},
# ...etc
]


Existing Example

# Note multiple lines can be collapsed into one section


Replacement Example

[mask]
tof = [
{start = 19711.5, stop = 21228.5},
{start = 39354.5, stop = 41348.5}
]


MON/DIRECT[/FRONT][/HAB]=filename¶

This command was used to specify the name of a file containing the ratio of the efficiency of the detector to that of the incident beam monitor as a function of wavelength.

If the /FRONT or /HAB qualifiers, which were equivalent (/HAB was retained for backward compatibility), are omitted then the command was assumed to refer to the rear detector.

The efficiency file was required to be in 1D RKH text format with data arranged as wavelength (in Angstroms), efficiency ratio, uncertainty on efficiency ratio.

Replacement

[detector]
[detector.correction.direct]
rear_file = "filename"
front_file = "filename"


Existing Example:

MON/DIRECT=DIRECT_RUN524.dat
MON/DIRECT/HAB=DIRECT_RUN524.dat


Replacement Example

[detector]
[detector.correction.direct]
rear_file = "DIRECT_RUN524.dat"
front_file = "DIRECT_RUN524.dat"


MON/FLAT[/FRONT][/REAR]=filename¶

This command was used to specify the name of a file containing the relative efficiency of the individual detector pixels, also known as the ‘flat cell’ or ‘flood source’ file.

If the /FRONT qualifier was omitted then the command was assumed to refer to the rear detector.

The relative efficiency file was required to be in 1D RKH text format with data arranged as spectrum number, relative efficiency, uncertainty on relative efficiency.

Replacement

[detector]
[detector.correction.flat]
rear_file = "str"


Existing Example:

MON/FLAT="flat_file.091"


Replacement Example

[detector]
[detector.correction.flat]
rear_file = "flat_file.091"


MON/HABEFF=a¶

This command was used to specify an approximate correction to the LOQ instrument high-angle detector efficiencies arising from the longer path length through the detection volume at high angles. See also MON/HABPATH[/ON][/OFF].

The correction assumed a value (parameter a) for the efficiency at 1 Angstrom, the default value of which was 0.2. Setting a=1.0 was akin to ignoring this correction.

This command was never (knowingly) implemented in Mantid (but was in COLETTE)!

Existing Example:

MON/HABEFF=0.2


Replacement Example

Unsupported

MON/HABPATH[/ON][/OFF]¶

This command was used to activate a correction to calculated transmissions on the LOQ instrument arising from the longer path length through the sample/can at high angles. See also MON/HABEFF=a.

This command was never implemented in Mantid (but was in COLETTE)! But see SAMPLE/PATH[/ON][/OFF].

Existing Example:

MON/HABPATH/ON


Replacement Example

Unsupported

MON/LENGTH=z s¶

This command was intended to override the default distance of the specified monitor s stored in the Mantid Instrument Definition File in instances where a very accurate time-of-flight calculation was required. The parameter z was the moderator-monitor distance.

This command was never (knowingly) implemented in Mantid! But see TRANS/TRANSPEC=s.

Replacement Example

Unsupported

MON/SPECTRUM=n¶

This command was used to specify which monitor spectrum (not number) was to be used for normalisation during data reduction.

[instrument.configuration]
norm_monitor = "Mn"

[normalisation]
#Normalisation monitor

[normalisation.monitor.Ma]
spectrum_number = n1

[normalisation.monitor.Mb]
spectrum_number = n2


Existing Example:

MON/SPECTRUM=1


Replacement Example

[instrument.configuration]
norm_monitor = "M1"

[normalisation]
[normalisation.monitor.M1]
spectrum_number = 1


MON [/INTERPOLATE]¶

The optional /INTERPOLATE qualifier could be used to apply an interpolating rebin of the specified monitor spectrum. This could be useful as a means of ‘smoothing’ noisy monitor spectra where the normal rebin command generated ‘stepped’ histograms.

This command has been been made obsolete by the switch to monitors running in Event mode.

Existing Example:

MON/SPECTRUM=1/INTERPOLATE


Replacement Example

Unsupported - Obsolete

MON/TRANS/SPECTRUM=n¶

This command could also be used to specify which monitor spectrum (not number) was to be used for normalisation during data reduction. As the /TRANS qualifier was present the command only applied to the normalisation of transmission spectra.

[instrument.configuration]
norm_monitor = "Ma"
trans_monitor = "Mb"

[normalisation]
#Normalisation monitor

[normalisation.monitor.Ma]
spectrum_number = n1

[normalisation.monitor.Mb]
spectrum_number = n2

[normalisation.monitor.Mc]
spectrum_number = n3

[transmission]
[transmission.monitor.Mb]
use_different_norm_monitor = true
trans_norm_monitor = "Mc"


Existing Example:

MON/SPECTRUM=1
TRANS/TRANSPEC=2
MON/TRANS/SPECTRUM=4


Replacement Example

[instrument.configuration]
norm_monitor = "M1"
trans_monitor = "M2"

[normalisation]
[normalisation.monitor.M1]
spectrum_number = 1

[normalisation.monitor.M4]
spectrum_number = 4

[transmission]
[transmission.monitor.M2]
spectrum_number = 2
use_different_norm_monitor = true
trans_norm_monitor = "M4"

# If interpolation is also required:
[binning]
[binning.2d_reduction]
interpolate = true


QRESOL[/ON][/OFF]¶

This command was used to specify whether data reduction should also calculate an estimate of the Q-resolution. If gravity corrections are also enabled (see GRAVITY[/ON/OFF]) these are included in the calculation.

Replacement

[q_resolution]
enabled = true  # Or false


Existing Example:

QRESOL/ON


Replacement Example

[q_resolution]
enabled = true  # Or false


QRESOL/MODERATOR=filename¶

This command was used to specify the name of a file containing the moderator time spread as a function of wavelength. At ISIS these data were produced from moderator performance simulations conducted by R Bewley & S Ansell. For sensible estimates of the Q-resolution it is imperative that the moderator file be for the moderator in use!

The moderator file was required to be in 1D RKH text format with data arranged as wavelength (in Angstroms), time spread (in microseconds), uncertainty on time spread (zero if unknown).

Replacement

[q_resolution]
moderator_file = "filename"


Existing Example:

QRESOL/MODERATOR=ModeratorStdDev_TS2_SANS_LETexptl_07Aug2015.txt


Replacement Example

[q_resolution]
moderator_file = "ModeratorStdDev_TS2_SANS_LETexptl_07Aug2015.txt"


QRESOL/DELTAR=dr¶

This command was used to specify the width of the virtual rings used for the radial integration. A value of 3 mm would be typical, otherwise it would be sensible to use the rstep value specified in the L/R r1 r2 [rstep] command if present.

The virtual ring width of the detector in meters. This is used to calculate the Q Resolution from TOF SANS Data on a per-pixel in TOFSANSResolutionByPixel v1.

Replacement

[q_resolution]
delta_r = dr


Existing Example:

QRESOL/DELTAR=3  # m


Replacement Example

[q_resolution]
delta_r = 0.003  # mm


QRESOL/A1=x¶

This command was used to specify the source aperture diameter to be used in the estimation of the Q-resolution. See also QRESOL/A2=x and QRESOL[/H1=x1][/W1=y1][/H2=x2][/W2=y2].

This command assumes that the data were collected on an instrument with pinhole collimation!

Replacement

[q_resolution]
source_aperture = x


Existing Example:

QRESOL/A1=30


Replacement Example

[q_resolution]
source_aperture = 0.03


QRESOL/A2=x¶

This command was used to specify the sample aperture diameter to be used in the estimation of the Q-resolution. See also QRESOL/A1=x and QRESOL[/H1=x1][/W1=y1][/H2=x2][/W2=y2].

This command assumes that the data were collected on an instrument with pinhole collimation!

The sample aperture will normally be smaller than the source aperture!

Note that because the source aperture size is frequently altered, the ISIS SANS Group decided to place the TOML replacement in the [instrument.configuration] block at the top of TOML User Files instead of the [q_resolution] block.

Replacement

[instrument.configuration]
sample_aperture_diameter = x


Existing Example:

QRESOL/A2=20


Replacement Example

[instrument.configuration]
sample_aperture_diameter = 0.02


QRESOL[/H1=x1][/W1=y1][/H2=x2][/W2=y2]¶

This command was used to specify the source and sample slit sizes to be used in the estimation of the Q-resolution. See also QRESOL/A1=x and QRESOL/A2=x.

This command assumes that the data were collected on an instrument with slit/jaw collimation!

The sample slit size will normally be smaller than the source slit size! But the heights and widths of a slit do not have to be the same.

Replacement

[q_resolution]
h1 = x1
w1 = y1
h2 = x2
w2 = y2


Existing Example:

QRESOL/H1=16.0
QRESOL/W1=16.0
QRESOL/H2=8.0
QRESOL/W2=8.0


Replacement Example

[q_resolution]
h1 = 0.016
w1 = 0.016
h2 = 0.008
w2 = 0.008


QRESOL/LCOLLIM=z¶

This command was used to specify the length of the collimation - the distance between the source and sample apertures/slits/jaws - to be used in the estimation of the Q-resolution.

Note that because the collimation length is frequently altered, the ISIS SANS Group decided to place the TOML replacement in the [instrument.configuration] block at the top of TOML User Files instead of the [q_resolution] block.

Also note that the collimation length was historically specified in metres too.

Replacement

[instrument.configuration]
collimation_length = z


Existing Example:

QRESOL/LCOLLIM=4.0


Replacement Example

[instrument.configuration]
collimation_length = 4.0


SAMPLE/OFFSET z¶

This command was used to specify any correction to the default Z coordinate in the Mantid Instrument Definition File defining the nominal position of the sample. The offset is a relative value with positive offsets translating the sample position towards the detector(s).

Replacement

[instrument.configuration]
sample_offset = z


Existing Example:

SAMPLE/OFFSET -60


Replacement Example

[instrument.configuration]
sample_offset = -0.06


SAMPLE/PATH[/ON][/OFF]¶

This command was used to activate a correction to calculated transmissions arising from the longer path length through the sample/can at high angles. Unlike MON/HABPATH[/ON][/OFF] this command was generic.

Existing Example:

SAMPLE/PATH/ON


Replacement Example

Unsupported, pending future discussion.

SET CENTRE a b¶

This command was used to specify the (x,y) coordinates (in real-space) of the centre of the scattering pattern on the rear (ie, main) detector. See also SET CENTRE[/MAIN][/HAB] a b [c d].

Warning: the TOML replacement for this command will apply the same centre coordinates to a front detector if present. In most instances this will not be sensible.

[detector]
[detector.configuration]
all_centre = {x=a, y=b}


Existing Example:

SET CENTRE 84.2 -196.5


Replacement Example

[detector]
[detector.configuration]
# This will set both front and rear to the same centre values.
all_centre = {x=0.0842, y=-0.1965}


SET CENTRE[/MAIN][/HAB] a b [c d]¶

This command was used to specify the (x,y) coordinates (in real-space) of the centre of the scattering pattern on a specific detector. Compare with SET CENTRE a b.

If the /MAIN qualifier was omitted the command was assumed to apply to the main (ie, rear) detector anyway. The /HAB qualifier was required to specify the beam centre coordinates for a high-angle (ie, front) detector.

The parameters c and d allowed the size of the detector pixels in x & y to be passed to the data reduction.

Approximate centre coordinates on the ISIS SANS instruments (which should be optimised using the beam centre finder tool!) are:

LARMOR: ( 0.020,  1.000)
LOQ:    ( 0.320,  0.320)
SANS2D: ( 0.100, -0.080)
ZOOM:   (-0.170, -0.050)

[detector]
[detector.configuration]
front_centre = {x=a, y=b}
rear_centre = {x=a, y=b}


Existing Example:

SET CENTRE 324.31 328.547 5.00 5.00
SET CENTRE/HAB 317.92 325.498


Replacement Example

[detector]
[detector.configuration]
# Note for identical results the values will
# only take a and b in the above example due to a bug
# with the legacy user file parser
front_centre = {x=0.31792, y=0.325498}
rear_centre = {x=0.32431, y=0.328547}


SET SCALES a b c d e¶

This command was used to specify the absolute intensity calibration scale factor (parameter a) to be applied to all intensity values at the end of the data reduction calculation.

In the case of the LOQ instrument, it also allowed the relative scaling of the four high-angle detector banks (parameters b, c, d & e) to be accounted for (as a*b, a*c, a*d & a*e). For all other ISIS SANS instruments these four parameters should be set to unity.

Note: In 2020 it was discovered that due to a forever bug in the legacy User File command parser the parameters b, c, d & e have never been implemented in Mantid. See this issue.

All workspaces are currently scaled by the value represented by a for all values, rather than on a per-bank basis.

The TOML replacement command allows separate but single scaling factors for both rear and front detectors to be specified. But to maintain compatibility front_scale is ignored by the parser and will not do anything.

[detector]
[detector.configuration]
front_scale = a
rear_scale = a


Existing Example:

SET SCALES 0.02938 1.0 1.0 1.0 1.0


Replacement Example

[detector]
[detector.configuration]
front_scale = 1.0
rear_scale = 0.02938


SET[/NOTABLES] BANK a b c d e¶

This command was used to specify the physical location and orientation of the four LOQ instrument high-angle detector modules.

The parameters were: an ISIS Detector ID Code, the distance from the moderator (in metres), an anticlockwise rotation angle, and the x & y coordinates (in mm) of the first pixel on the specified module. Viewed from the direction of travel of the neutrons, positive values of x & y corresponded to right and up, respectively.

The /NOTABLES (/NOTAB was also supported) qualifier could be used to stop a redundant call to the routine mapping detectors.

This command became redundant with improvements in the Mantid Instrument Definition File.

Existing Example:

SET/NOTAB BANK 305 11.582 0. 112.28 -245.19
SET/NOTAB BANK 304 11.582 90. 244.28 114.82
SET/NOTAB BANK 306 11.582 180. -115.72 246.82
SET/NOTAB BANK 307 11.582 270. -247.72 -113.19


Replacement Example

Unsupported

SET[/XCOR][/YCOR][/ON][/OFF][/CLEAR]¶

This command was used to specify if non-linear coordinate corrections to LOQ instrument detector data should be applied during data reduction. The /XCOR (/XC was also supported) qualifier specified that detector x coordinates were to be corrected. Similarly, the /YCOR (or /YC) qualifier specified that detector y coordinates were to be corrected. See also SET[/NOTABLES][/XCOR][/YCOR]=filename.

The /CLEAR qualifier was equivalent to /OFF.

Existing Example:

SET/XCOR/ON


Replacement Example

Unsupported

SET[/NOTABLES][/XCOR][/YCOR]=filename¶

This command was used to specify a file containing non-linear coordinate corrections to LOQ instrument detector data. Separate files were required for the x and y coordinates. See also SET[/XCOR][/YCOR][/ON][/OFF][/CLEAR].

The /NOTABLES (/NOTAB was also supported) qualifier could be used to stop a redundant call to the routine mapping detectors if both x and y1 coordinates were being corrected (see example below).

This command became redundant from Mantid 1.1.9556 and LOQ_Definition.xml valid from 2002-02-26.

Existing Example:

SET/NOTAB/XC=xcorr.991_994
SET/YC=ycorr.991_994


Replacement Example

Unsupported

This command was used in conjunction with TRANS/RADIUS=r or, more likely, TRANS/ROI=filename to exclude regions of the detector specified by those commands. See also TRANS/RADIUS=r and TRANS/ROI=filename.

filename was expected to be a Mantid mask file in XML format.

Note that if also present a TRANS/TRANSPEC=s command would always supersede a TRANS/MASK=filename command. See also TRANS/TRANSPEC=s.

Existing Example:

TRANS/ROI=select.xml


Replacement Example

Unsupported, see TRANS/ROI=filename.

This command was used to specify a circular region-of-interest (ROI) of radius r on the detector taking the transmitted beam which was to be used in place of a dedicated transmission monitor. The ROI was assumed to be centred on the beam centre coordinates (see SET CENTRE a b). See also TRANS/MASK=filename and TRANS/ROI=filename.

For this command to have had any sensible purpose, it would have been necessary for the detector beamstop to have been removed for transmission measurements.

The radius was specified in mm.

Note that if also present a TRANS/TRANSPEC=s command would always supersede a TRANS/RADIUS=r command. See also TRANS/TRANSPEC=s.

Existing Example:

TRANS/RADIUS=30


Replacement Example

Unsupported, pending future discussion.

TRANS/ROI=filename¶

This command was used to specify an arbitrary region-of-interest (ROI) on the detector taking the transmitted beam which was to be used in place of a dedicated transmission monitor. See also TRANS/MASK=filename and TRANS/RADIUS=r.

For this command to have had any sensible purpose, the ROI would have been needed to have been outside of any masked regions of the detector (eg, the beamstop and/or beamstop support arm shadows).

filename was expected to be a Mantid mask file in XML format.

Note that if also present a TRANS/TRANSPEC=s command would always supersede a TRANS/ROI=filename command. See also TRANS/TRANSPEC=s.

Replacement

[instrument.configuration]
trans_monitor = "ROI"

[transmission]
# This will be ignored:
[transmission.monitor.Mn]
spectrum_number = s

[transmission.ROI]
file = "roi_file.xml"


Existing Example:

TRANS/ROI=filename.xml


Replacement Example

[instrument.configuration]

trans_monitor = “ROI”

[transmission]

[transmission.ROI]

file = “filename.xml”

TRANS/TRANSPEC=s¶

This command was used to specify the spectrum (not monitor) number containing the transmission data. The spectrum number and the monitor* number may, or may not, be the same depending on the instrument!

Replacement

[instrument.configuration]
# Where Mn is arbitrary but must match the section label
trans_monitor = "Mn"

[transmission]
[transmission.monitor.Mn]
spectrum_number = s


Existing Example:

TRANS/TRANSPEC=3


Replacement Example

[instrument.configuration]
trans_monitor = "M3"

[transmission]
[transmission.monitor.M3]
spectrum_number = 3


TRANS/TRANSPEC=s/SHIFT=dz¶

This command was used to specify any correction to the default Z coordinate in the Mantid Instrument Definition File defining the nominal position of the transmission monitor represented by the specified spectrum number. The offset is a relative value with positive offsets translating the sample position towards the detector(s).

This command was typically used to fine tune the position of beamstop-mounted transmission monitors.

Replacement

[instrument.configuration]
# Where Mn is arbitrary but must match the section label
trans_monitor = "Mn"

[transmission]
[transmission.monitor.Mn]
spectrum_number = s
shift = dz


Existing Example:

TRANS/TRANSPEC=17788/SHIFT=-12


Replacement Example

[instrument.configuration]
trans_monitor = "M4"

[transmission]
[transmission.monitor.M4]
spectrum_number = 17788
shift = -0.012


TUBECALIBFILE=filename¶

This command was used to specify a spatial calibration file for tube array detectors. Only one file could be specified, and so if an instrument had more than one such detector the calibrations for each needed to be amalgamated.

Replacement

[detector]

[detector.correction.tube]
file = "filename"


Existing Example:

TUBECALIBFILE=TUBE_SANS2D_BOTH_64393_15Mar20.nxs


Replacement Example

[detector]

[detector.correction.tube]
file = "TUBE_SANS2D_BOTH_64393_15Mar20.nxs"


Category: Techniques