3.8

Framework Changes

Supported Operating Systems

  • We now support Ubuntu Xenial Xerus (16.04) and this will be the final release to support Trusty Tahr (14.04).
  • We now support OS X Yosemite (10.10) and support for OS X Mavericks (10.9) has been dropped.

HistogramData

A new module for dealing with histogram data has been added, it is now being used internally in Mantid to store data in various workspace types.

  • For C++ users, details can be found in the transition documentation.
  • For Python users, the interface is so far unchanged. However, to ensure data consistency and to reduce the risk of bugs, histograms now enforce length limitations. For example, there must be one bin edge more than data (Y and E) values. If you experience trouble, in particular exceptions about size mismatch, please refer to the section Dealing with problems.

Concepts

  • MatrixWorkspace : When masking bins or detectors with non-zero weights, undefined and infinite values and errors will be zeroed.
  • Lattice : Allow setting a UB matrix with negative determinant (improper rotation)

Algorithms

New

  • ClearCache an algorithm to simplify the clearance of several in memory or disk caches used in Mantid.
  • LoadPreNexusLive will load “live” data from file on legacy SNS DAS instruments.
  • CropToComponent allows for cropping a workspace to a list of component names.
  • CreateUserDefinedBackground takes a set of points that the user has chosen and creates a background workspace out of them. It interpolates the points so the resulting background can be subtracted from the original data.
  • SaveDiffFittingAscii an algorithm which saves a TableWorkspace containing diffraction fitting results as an ASCII file
  • UnwrapMonitorsInTOF handles the data which was collected beyond the end of a frame.
  • ExtractMonitors an algorithm to extract the monitor spectra into a new workspace. Can also be used to create a workspace with just the detectors, or two workspaces, one with the monitors and one with the detectors.

Improved

  • FlatPlatePaalmanPingsCorrection & CylinderPaalmanPingsCorrection now accept ‘Direct’ as a possible EMode parameter.
  • FilterEvents now produces output workspaces with the same workspace numbers as specified by the SplittersWorkspace.
  • ConvertAxisByFormula now supports instrument geometry vairables and several constants within the formula. Axes are now reversed if the need to be to maintain increasing axis values.
  • SavePlot1D has options for writing out plotly html files.
  • SofQW has option to replace any NaNs in output workspace with zeroes.
  • ConvertTableToMatrixWorkspace had a bug where the table columns were in a reversed order in the dialogue’s combo boxes. This is now fixed and the order is correct.
  • ConvertUnits and ConvertUnitsUsingDetectorTable <algm-ConvertUnitsUsingDetectorTable> will no longer corrupt a workspace used as input and output if the algorithm fails.
  • SetSample: Fixed a bug with interpreting the Center attribute for cylinders/annuli
  • MonteCarloAbsorption had a bug in cases where the beam was larger than the sample, which lead to the attenuation factor being too high. This has been fixed.
  • ConvertUnits now has the option to take a workspace with Points as input. A property has been added that will make the algorithm convert the workspace to Bins automatically. The output space will be converted back to Points.
  • RenameWorkspace and RenameWorkspaces <algm-RenameWorkspaces> now check if a Workspace with that name already exists in the ADS and gives the option to override it.
  • FindSXPeaks: Fixed a bug where peaks with an incorrect TOF would stored for some intrument geometries.
  • LoadILL was renamed to LoadILLTOF <algm-LoadILLTOF> to better reflect what it does. The new algorithm can also handle cases where the monitor IDs are greater than the detector IDs.
  • FFT deals correctly with histogram input data. Internally, it converts to point data, and the output is always a point data workspace. (It can be converted to histogram data using ConvertToHistogram if required).
  • StartLiveData has additional properties for specifying scripts to run for processing and post-processing.
  • LoadEmptyInstrument now also accepts a workspace name as input, as an alternative to an instrument definition xml file.
  • Mergeruns can now also deal with non-time series sample logs when merging. Behaviour can be to create a time series, a list of values and warn or fail if different.

MD Algorithms (VATES CLI)

  • MergeMD now preserves the display normalization from the first workspace in the list
  • BinMD fixed bug where algorithm would default to using orthogonal basis vectors when supplied with 4 bases and 4 dimensions

Performance

  • An internal change that is a preliminary step for “Instrument-2.0” can yield slight to moderate performance improvements of the following algorithms (and other algorithms that use one of these): AppendSpectra, ApplyTransmissionCorrection, CalculateEfficiency, CalculateFlatBackground, ConjoinSpectra, ConvertAxesToRealSpace, ConvertAxisByFormula, ConvertEmptyToTof, ConvertSpectrumAxis2, ConvertUnitsUsingDetectorTable, CorelliCrossCorrelate, DetectorEfficiencyVariation, EQSANSTofStructure, FilterEvents, FindCenterOfMassPosition, FindCenterOfMassPosition2, FindDetectorsOutsideLimits, GetEi, IntegrateByComponent, LorentzCorrection, MultipleScatteringCylinderAbsorption, NormaliseToMonitor, Q1D2, Q1DWeighted, RadiusSum, RemoveBackground, RemoveBins, RemoveMaskedSpectra, RingProfile, SANSDirectBeamScaling, SumSpectra, TOFSANSResolution, UnwrapMonitor, UnwrapSNS, VesuvioCalculateMS, and WeightedMeanOfWorkspace.

  • The introduction of the HistogramData module may have influenced the performance of some algorithms and many workflows. Some algorithms (listed below) experience a speedup and reduced memory consumption. If you experience unusual slowdowns, please contact the developer team.

    The following algorithms were adapted and show a noticeable speedup:

    In most of these cases memory consumption has also reduced. The performance improvements will vary from machine to machine, and will be different or even non-existent depending on the type and size of the input workspace and algorithm parameters.

    The following algorithms were adapted and do not show any speedup, however the memory consumption may have reduced slightly:

    AbsorptionCorrection, CalculateEfficiency, CalculateFlatBackground, CalculateZscore, ConvertEmptyToTof, ConvertToMatrixWorkspace, CrossCorrelate, ExtractFFTSpectrum, FindPeaks, GeneratePeaks, PolarizationCorrection, Rebin2D, RebinByTimeAtSample, ReflectometryTransform, StripPeaks

    Algorithms that are run after one of those listed above may also benefit from the improved data sharing that lead to speedup and reduced memory consumption. In some cases, however, follow-up algorithms may run slower (typically this can happen for algorithms that do in-place modification of data). However, the total runtime (sum of the runtimes of the improved and the degraded algorithm) should be unchanged in the worst case.

  • A race condition when accessing a singleton from multiple threads was fixed.

  • Log file buffers are no longer flushed by default for each newline received, increasing the speed of some system tests on Windows by 4.5x.

CurveFitting

  • Added a new minimizer belonging to the trust region family of algorithms developped for Mantid by the SCD Numerical Analysis Group at RAL. It has better performance characteristics compared to the existing minimizers especially when applied to the most difficult fitting problems.
  • Added new property EvaluationType to Fit algorithm. If set to “Histogram” and the input dataset is a histogram with large bins it can improve accuracy of the fit.
  • The concept page for Comparing fit minimizers has been updated to include the new minimizer and a comparison against neutron data examples.

Others

  • Facilities.xml was updated for changes to the SNS live data servers.
  • A cmake parameter ENABLE_MANTIDPLOT (default True) was added to facilitate framework only builds.
  • The case search in DataService has been replaced with a case-insensitive comparison function. Behavior is almost identical, but a small number of cases (such as adding the workspaces Z and z) will work in a more predictable manner.

Python

  • mantid.kernel.MaterialBuilder has been exposed to python and mantid.kernel.Material has been modified to expose the individual atoms.
  • mantid.geometry.OrientedLattice set U with determinant -1 exposed to python
  • The setDisplayNormalization and setDisplayNormalizationHisto methods for MDEventWorkspaces are now exposed to Python
  • Tube calibration now has saveCalibration and readCalibrationFile functions similar to savePeak and readPeakFile.

Python Algorithms

Bug Fixes

  • Scripts generated from history including algorithms that added dynamic properties at run time (for example Fit, and Load) will not not include those dynamic properties in their script. This means they will execute without warnings.
  • Cloning a MultiDomainFunction, or serializing to a string and recreating it, now preserves the domains.
  • EvaluateFunction now works from its dialog in the GUI as well as from a script
  • ConvertToMD ConvertToMD will now work on powder diffraction samples stored .nxspe files. This is because if a Goniometer contains a NaN value it will report itself as undefined.

Full list of Framework and Python changes on GitHub