mantidproject · thomashampson · Oct 16, 2024 · Oct 2, 2024 · Oct 2, 2024 · Oct 2, 2024
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diff --git a/docs/source/release/v6.11.0/diffraction.rst b/docs/source/release/v6.11.0/diffraction.rst
@@ -10,34 +10,80 @@ Powder Diffraction
 
 New features
 ############
-.. amalgamate:: Diffraction/Powder/New_features
+- Algorithm :ref:`AlignAndFocusPowder <algm-AlignAndFocusPowder>` now supports logarithmic compression.
+- Algorithm :ref:`AlignAndFocusPowderFromFiles <algm-AlignAndFocusPowderFromFiles>` now takes advantage of a new compression technique in :ref:`LoadEventNexus <algm-LoadEventNexus>` and :ref:`AlignAndFocusPowder <algm-AlignAndFocusPowder>`.
+- Algorithm :ref:`SNSPowderReduction <algm-SNSPowderReduction>` now takes advantage of a new compression technique in :ref:`AlignAndFocusPowderFromFiles <algm-AlignAndFocusPowderFromFiles>` and :ref:`AlignAndFocusPowder <algm-AlignAndFocusPowder>`.
+- Algorithm :ref:`LoadEventAndCompress <algm-LoadEventAndCompress>` now takes advantage of a new compression technique in :ref:`LoadEventNexus <algm-LoadEventNexus>`.
+- Algorithms :ref:`FitPeaks <algm-FitPeaks>` and :ref:`PDCalibration <algm-PDCalibration>` now do a check after the fit for the minimum signal-to-sigma ratio, where peaks with a signal below the provided threshold will be rejected.
+- :ref:`HRPD reduction scripts <isis-powder-diffraction-hrpd-ref>` now support the boolean option ``fit_prompt_pulse`` to fit and subtract prompt pulse (as opposed to the default method of masking of prompt pulse in TOF).
+  You can either specify this option in the configuration file or with ``hrpd.HRPD(fit_prompt_pulse=True)``.
 
 Bugfixes
 ############
-.. amalgamate:: Diffraction/Powder/Bugfixes
+- Algorithm :ref:`AlignAndFocusPowder <algm-AlignAndFocusPowder-v1>` now runs compression when ``logarithmic`` is selected.
+- Applying absorption correction with missing sample details in :ref:`powder diffraction scripts <isis-powder-diffraction-ref>` now displays a clearer error message:
+
+.. figure::  ../../images/6_11_release/improved_error_message.png
+   :width: 600px
+
+- Algorithm :ref:`DiffractionFocussing <algm-DiffractionFocussing-v2>` is now properly accumulating data when :ref:`CompressEvents <algm-CompressEvents-v1>` is run prior to it in ``PreserveEvents=False`` mode.
+- Algorithm :ref:`PPDCalibration <algm-PDCalibration-v1>` is once again masking input pixels with empty event lists (bug was present since 6.9.0).
+- :ref:`Calibration Diagnostics <Calibration Diagnostics>` plotting now successfully extracts the solid angle of detectors.
+- :ref:`Polaris diffraction <isis-powder-diffraction-polaris-ref>` routine ``create_total_scattering_pdf`` no longer causes an unhandled error when calculating cross-sections of multi-atom unit cells for pdf normalisation.
 
 
 Engineering Diffraction
 -----------------------
 
-New features
-############
-.. amalgamate:: Diffraction/Engineering/New_features
-
 Bugfixes
 ############
-.. amalgamate:: Diffraction/Engineering/Bugfixes
+- The :ref:`fitting tab <ui engineering fitting>` of the :ref:`Engineering Diffraction interface<Engineering_Diffraction-ref>` no longer crashes when a fit is re-run for a function like a ``PseudoVoigt`` that contains a ``FWHM`` parameter as the peak function.
 
 
 Single Crystal Diffraction
 --------------------------
 
 New features
 ############
-.. amalgamate:: Diffraction/Single_Crystal/New_features
+- :ref:`IntegratePeaksSkew <algm-IntegratePeaksSkew>` is better at determining background bins by minimising third-moment (skew).
+  This is achieved by forcing skew > 0 (minimum skew we would expect in background).
+  This change stops peak mask of :ref:`IntegratePeaksSkew <algm-IntegratePeaksSkew>` including too many pixels due to small diffuse scattering:
+
+.. figure::  ../../images/6_11_release/single-crystal-peak-background-edited.png
+   :width: 500px
+
+- New option not to integrate peaks that include a masked detector in the following algorithms:
+
+  - :ref:`IntegratePeaksSkew <algm-IntegratePeaksSkew>`
+  - :ref:`IntegratePeaksShoeboxTOF <algm-IntegratePeaksShoeboxTOF>`
+  - :ref:`IntegratePeaks1DProfile <algm-IntegratePeaks1DProfile>`
+
+- ISIS single-crystal reduction classes now have the method ``find_consistent_ub`` to find a UB that preserves indexing given a reference workspace (at different goniometer angle(s)).
+- ISIS single-crystal reduction classes now have the method ``optimize_goniometer_axis`` to optimise the goniometer axes and angles given a sequence of workspaces at different goniometer angle with consistent UBs.
+- ISIS single-crystal reduction classes now have the method ``calc_absorption_weighted_path_lengths`` that calculates tbar for each peak (saved in a column of the table) and optionally apply an attenuation correction to the integrated intensity of each peak.
+  By default the correction will be applied if the class has the property ``scale_integrated = True``.
+- Algorithm :ref:`AddAbsorptionWeightedPathLengths <algm-AddAbsorptionWeightedPathLengths>` now allows lean peaks to be used.
+  There is also an option to apply the correction.
+- New algorithm :ref:`FindMultipleUMatrices <algm-FindMultipleUMatrices>` to find multiple UB matrices (given lattice parameters) for samples with multiple domains or spurious peaks.
+
+  - This algorithm will use the lattice parameters and spacegroup provided to optimise a number (``NumberOfUBs``)
+    of UB matrices (B is hard-coded due to the lattice parameters provided) and return a group of peak workspaces
+    (one for each UB) containing the peaks that are indexed most accurately by that UB.
+    The algorithm is useful for finding a single UB in the presence of spurious peaks, or finding multiple UBs when there
+    are multiple domains.
+
+  .. figure::  ../../images/6_11_release/FindMultipleUMatrices.png
+     :width: 400px
+
+- Algorithm :ref:`ShowPossibleCells <algm-ShowPossibleCells>` now has a new output property, ``Cells``, that includes the cell information in a usable way.
+- New algorithm :ref:`SaveMDHistoToVTK <algm-SaveMDHistoToVTK>` that saves a :ref:`MDHistoWorkspace <MDHistoWorkspace>` as a ``VTK`` file so that it can be visualized by ``Paraview``.
+- :ref:`IntegratePeaksShoeboxTOF <algm-IntegratePeaksShoeboxTOF>` has improved optimisation for shoebox position - would previously be centred on nearby stronger peaks if present.
+- Execution time of :ref:`IntegratePeaks1DProfile <algm-IntegratePeaks1DProfile>` has been sped up by an order of magnitude.
+
 
 Bugfixes
 ############
-.. amalgamate:: Diffraction/Single_Crystal/Bugfixes
+- :ref:`LoadWANDSCD <algm-LoadWANDSCD>` now keeps the sgl/sgu angles set by the goniometer.
+- :ref:`ConverWANDSCDToQ <algm-ConvertWANDSCDToQ>` simplifies the underlying code by using histograms directly.
 
-:ref:`Release 6.11.0 <v6.11.0>`
+:ref:`Release 6.11.0 <v6.11.0>`
diff --git a/docs/source/release/v6.11.0/direct_geometry.rst b/docs/source/release/v6.11.0/direct_geometry.rst
@@ -10,35 +10,27 @@ General
 
 New features
 ############
-.. amalgamate:: Direct_Geometry/General/New_features
+- :ref:`SaveNXSPE <algm-SaveNXSPE-v1>` now stores the run number of the input workspace in the instrument section.
+
+  For Indirect instruments it also saves ``efixed``, taken from the detector's crystal analyzer properties.
+  If all crystal analyzers have the same energy, a single ``efixed`` is written into ``NXSPE_info->fixed_energy`` as before,
+  while if detectors have different analyzer energies, an array of the energies is written into the ``NXSPE_info->fixed_energy`` field of the ``.nxspe`` file.
+  Also for Indirect instruments, no ``fermi`` field is added to the ``instrument`` folder.
+  The algorithm has also been modified so if ``Ei`` is provided as the propery value it always overrides the values retrieved from the workspace.
 
 Bugfixes
 ############
-.. amalgamate:: Direct_Geometry/General/Bugfixes
+- :ref:`ALFView <ALFView-ref>` no longer crashs when moving the cursor over the Instrument View while loading data.
+- :ref:`PyChop` no longer uses random phase values on Merlin when instrument scientist mode disabled.
 
 
 CrystalField
 -------------
 
-New features
-############
-.. amalgamate:: Direct_Geometry/CrystalField/New_features
-
-Bugfixes
-############
-.. amalgamate:: Direct_Geometry/CrystalField/Bugfixes
-
-
-MSlice
-------
-
-New features
-############
-.. amalgamate:: Direct_Geometry/MSlice/New_features
-
 Bugfixes
 ############
-.. amalgamate:: Direct_Geometry/MSlice/Bugfixes
+- The method `cf.getMagneticMoment()` no longer ignores the `Hmag` field, which is now
+  correctly considered in the calculations of the magnetic moment.
 
 
-:ref:`Release 6.11.0 <v6.11.0>`
+:ref:`Release 6.11.0 <v6.11.0>`
diff --git a/docs/source/release/v6.11.0/framework.rst b/docs/source/release/v6.11.0/framework.rst
@@ -10,66 +10,101 @@ Algorithms
 
 New features
 ############
-.. amalgamate:: Framework/Algorithms/New_features
+- Errors due to H5 file exceptions are now caught with improved error reporting.
+- Algorithm :ref:`algm-Load` will now give a warning if the extension specified on the filename, eg. `MUSR15189.txt`, is not found.
+  Loading files from interfaces or other algorithms should also give this warning.
+  The algorithm will still load the file by looking for other extensions, as was the case before.
+- A new version of :ref:`GenerateGroupingPowder <algm-GenerateGroupingPowder>` (version 2) that will save the grouping file with groups starting at 1 instead of 0 to make them consisted with ``GroupingWorkspace``.
+  The ``FileFormat`` parameter has also been removed as it will now be determined from the extension of ``GroupingFilename``.
+- Algorithm :ref:`LoadEventNexus <algm-LoadEventNexus>` now has a new ``FilterBadPulsesLowerCutoff`` parameter that implements the functionality of :ref:`FilterBadPulses <algm-FilterBadPulses>`.
+- Algorithm :ref:`algm-PolarizationCorrectionWildes` and :ref:`algm-PolarizationEfficiencyCor` have a new ``SpinStates`` property to allow the order of the workspaces in the output workspace group to be set.
+- Algorithm :ref:`algm-CombineDiffCal` has improved time-scaling performance and new extra validations.
+- Algorithm :ref:`CompareWorkspaces <algm-CompareWorkspaces>` now supports :ref:`Ragged Workspaces <Ragged_Workspace>`.
+- Binary operations :ref:`Plus <algm-Plus>`, :ref:`Minus <algm-Minus>`, :ref:`Divide <algm-Divide>` and :ref:`Multiply <algm-Multiply>` now support :ref:`Ragged Workspaces <Ragged_Workspace>`.
+- Algorithm :ref:`CompressEvents <algm-CompressEvents>` a new ``SortFirst`` property that controls whether sorting happens before compressing events.
+  If ``SortFirst=False`` then a different method is used to compress events that will not sort first. This is faster when you have a large number of events per compress tolerance.
+- Algorithm :ref:`ISISIndirectEnergyTransfer <algm-ISISIndirectEnergyTransfer>` has the new property ``OutputSuffix`` that will append a suffix to the end of output workspace names.
+- Algorithms :ref:`AlignAndFocusPowderFromFiles <algm-AlignAndFocusPowderFromFiles>` and ref: :ref:`SNSPowderReduction <algm-SNSPowderReduction>` have new a property called ``MinSizeCompressOnLoad`` for specifying load compression.
+- Algorithm :ref:`NMoldyn4Interpolation <algm-NMoldyn4Interpolation>` now uses ``scipy.interpolate.RectBivariateSpline`` instead of ``scipy.interpolate.interp2d``, since ``interp2d`` has been removed in version 1.14 of ``scipy``.
+  See reference documentation here (https://docs.scipy.org/doc/scipy/reference/generated/scipy.interpolate.interp2d.html).
+- Algorithm :ref:`DiscusMultipleScatteringCorrection <algm-DiscusMultipleScatteringCorrection-v1>` now supports a radial collimator that restricts scatter points within a small region within the larger sample volume.
+  The algorithm was modified to assign zero weight to tracks where the final scatter is not in a position that allows the final track segment to pass through the collimator toward detectors.
+- Version 2 of the algorithm :ref:`LoadEventAsWorkspace2D <algm-LoadEventAsWorkspace2D>` that adds the property ``FilterByTime``.
+- New algorithm :ref:`ScaleInstrumentComponent <algm-ScaleInstrumentComponent>` to scale all detectors in an instrument component around the component's geometrical position.
+
+  .. figure::  ../../images/6_11_release/ScaleInstrumentComponent.png
+     :width: 400px
+
+- Algorithm :ref:`GenerateGroupingSNSInelastic <algm-GenerateGroupingSNSInelastic>` has the new input option :ref:`InstrumentDefinitionFile`.
+  Selecting the new ``InstrumentDefinitionFile`` option in the instrument drop down menu will create a new field allowing users to select older instrument definition files.
+- Algorithm :ref:`CompareWorkspaces <algm-CompareWorkspaces>` has a new ``CheckUncertainty`` property to turn off comparing the y-value uncertainties.
+- Algorithm :ref:`ScaleX <algm-ScaleX>` is now 95% faster when using the ``InstrumentParameter`` property.
 
 Bugfixes
 ############
-.. amalgamate:: Framework/Algorithms/Bugfixes
+- Algorithm :ref:`CompareWorkspaces <algm-CompareWorkspaces-v1>` is now fixed for relative differences of small values.
+- Algorithm :ref:`LoadEventNexus <algm-LoadEventNexus>` now has the minimum histogram bin edge equal to the lowest time-of-flight event rather than one less.
+  There are no longer negative bin edges unless there is actually a negative time-of-flight in the data.
+- Isotope densities have been updated, see https://pypi.org/project/periodictable/1.6.1/#history for notes about the updates from NIST.
+- All sample times are now allowed to be before 01/01/1991.
+- Algorithm :ref:`ExtractFFTSpectrum <algm-ExtractFFTSpectrum>` no longer causes an unreliable segmentation fault.
+- Algorithm :ref:`LoadIsawUB <algm-LoadIsawUB>` now correctly adds the UB to the first experiment info when the input workspace has more than one.
+- Algorithms :ref:`SaveNexusProcessed <algm-SaveNexusProcessed>` and :ref:`LoadNexusProcessed <algm-LoadNexusProcessed>` have been fixed to correctly work with :ref:`Ragged Workspaces <Ragged_Workspace>`.
 
 Removed
 #######
-.. amalgamate:: Framework/Algorithms/Removed
+- Algorithm ``SaveDiffFittingAscii`` was deprecated in :ref:`Release 3.13.0 <v3.13.0>` and has now been removed. Use :ref:`EnggSaveSinglePeakFitResultsToHDF5 <algm-EnggSaveSinglePeakFitResultsToHDF5>` instead.
+- Algorithm ``AddNote`` was deprecated in :ref:`Release 3.6.0 <v3.6.0>` and has now been removed. Please use :ref:`Comment <algm-Comment>` instead.
+- Algorithm ``FilterEventsByLogValuePreNexus`` was deprecated in 2014 and has now been removed.
+- Algorithm ``FindUBUsingMinMaxD`` was deprecated in 2013 and has now been removed. Use :ref:`FindUBUsingFFT<algm-FindUBUsingFFT>` instead.
+- Algorithm ``ConvertEmptyToTof`` was deprecated in :ref:`Release 3.9.0 <v3.9.0>` and has now been removed.
+- Algorithm ``RecordPythonScript`` was deprecated in :ref:`Release 5.1.0 <v5.1.0>` and has now been removed. Use :ref:`GeneratePythonScript<algm-generatepythonscript>` instead.
+- Algorithm ``CheckWorkspacesMatch`` was deprecated in :ref:`Release 3.9.0 <v3.9.0>` and has now been removed. Use :ref:`CompareWorkspaces<algm-compareworkspaces>` instead.
 
 Fit Functions
 -------------
 
 New features
 ############
-.. amalgamate:: Framework/Fit_Functions/New_features
-
-Bugfixes
-############
-.. amalgamate:: Framework/Fit_Functions/Bugfixes
+- Fit function :ref:`PearsonIV <func-PearsonIV>` now available to fit model prompt pulses.
+- Fit function :ref:`SpinDiffusion <func-SpinDiffusion>` now available in the Muon category.
 
 
 Data Objects
 ------------
 
-New features
-############
-.. amalgamate:: Framework/Data_Objects/New_features
-
 Bugfixes
 ############
-.. amalgamate:: Framework/Data_Objects/Bugfixes
+- Added a `+ 1` to `EventWorkspace::sortAll` to prevent grainsize from being 0.
+- Loading ``ENGIN-X`` data on IDAaaS from the instrument data cache no longer throws a ``path not found`` error.
 
 
 Python
 ------
 
 New features
 ############
-.. amalgamate:: Framework/Python/New_features
-
-Bugfixes
-############
-.. amalgamate:: Framework/Python/Bugfixes
+- Created documentation for :mod:`mantid.dataobjects` python bindings.
+- Fix python fuction ``assert_almost_equal`` to fail for non-equal workspaces.
+- The python function ``assert_almost_equal`` for testing if two modules are within a tolerance was reworked.
 
 
 Dependencies
 ------------------
 
 New features
 ############
-.. amalgamate:: Framework/Dependencies/New_features
+- Linux compiler has been updated to gcc version 12, which should improve performance in some circumstances.
 
 Bugfixes
 ############
-.. amalgamate:: Framework/Dependencies/Bugfixes
+- Introduced a run constraint to the mantid package to constrain the optional matplotlib dependency to v3.7.
+  Previously it was possible to install any version of matplotlib alongside mantid in a conda environment, but we cannot guarantee compatibility for any version other than 3.7.
+- Versions of `pycifrw` are now allowed to be greater than 4.4.1.
 
 
 MantidWorkbench
 ---------------
 
 See :doc:`mantidworkbench`.
-:ref:`Release 6.11.0 <v6.11.0>`
+:ref:`Release 6.11.0 <v6.11.0>`
diff --git a/docs/source/release/v6.11.0/index.rst b/docs/source/release/v6.11.0/index.rst
@@ -4,9 +4,9 @@
 Mantid 6.11.0 Release Notes
 ===========================
 
-.. figure:: ../../images/ImageNotFound.png
+.. figure::  ../../images/6_11_release/single-crystal-peak-background-edited.png
+   :width: 500px
    :class: screenshot
-   :width: 385px
    :align: right
 
 .. contents:: Table of Contents
@@ -16,7 +16,23 @@ Mantid 6.11.0 Release Notes
 
 We are proud to announce version 6.11.0 of Mantid.
 
-**TODO: Add paragraph summarizing big changes**
+In this release we gave extra attention to fixing bugs and improving algorithms (for example by making them run faster or use less memory).
+We also added several new algorithms. These are the highlights for this release:
+
+- For single crystal diffraction, we added a new algorithm :ref:`FindMultipleUMatrices <algm-FindMultipleUMatrices>`
+  to find multiple UB matrices when given lattice parameters for sample with multiple domains or spurious peaks.
+- Also for single crystal diffraction,  :ref:`IntegratePeaksSkew <algm-IntegratePeaksSkew>` is better at determining background bins by minimising third-moment (skew).
+  This is achieved by forcing skew > 0 (minimum skew we would expect in background).
+  This change stops peak mask of :ref:`IntegratePeaksSkew <algm-IntegratePeaksSkew>` including too many pixels due to small diffuse scattering (seen in the figure above).
+- For powder diffraction, the algorithms
+  :ref:`AlignAndFocusPowder <algm-AlignAndFocusPowder>`,
+  :ref:`AlignAndFocusPowderFromFiles <algm-AlignAndFocusPowderFromFiles>`,
+  :ref:`SNSPowderReduction <algm-SNSPowderReduction>` and
+  :ref:`LoadEventAndCompress <algm-LoadEventAndCompress>`
+  were updated to use logarithmic compression, which uses less memory.
+- For reflectometry, we added a new algorithm :ref:`algm-PolarizationEfficienciesWildes` has been added for calculating the efficiencies of the polarizing components of an instrument with two flippers.
+  This algorithm implements the approach from the A. R. Wildes 2006 paper.
+- For SANS, we added new algorithm :ref:`PolarizerEfficiency <algm-PolarizerEfficiency-v1>` for calculating the efficiency of a polariser.
 
 **TODO: Add a note about new mantid-developer metapackage**
 

diff --git a/docs/source/release/v6.11.0/indirect_geometry.rst b/docs/source/release/v6.11.0/indirect_geometry.rst
@@ -5,25 +5,12 @@ Indirect Geometry Changes
 .. contents:: Table of Contents
    :local:
 
-New Features
-------------
-.. amalgamate:: Indirect/New_features
-
 
 Bugfixes
 --------
-.. amalgamate:: Indirect/Bugfixes
-
-
-Algorithms
-----------
+- Fixed a bug on the Energy Transfer tab of the :ref:`Indirect Data Reduction <interface-indirect-data-reduction>` interface where the first raw file would be loaded into the ADS but never deleted.
+- Reduced files from the :ref:`Indirect Data Reduction <interface-indirect-data-reduction>` interface now have spectra numbering consistent for a summed file reduction compared to individual file reduction.
+- :ref:`interface-indirect-simulation` interface no longer crashes after clicking ``Run`` without loading data.
 
-New features
-############
-.. amalgamate:: Indirect/Algorithms/New_features
-
-Bugfixes
-############
-.. amalgamate:: Indirect/Algorithms/Bugfixes
 
-:ref:`Release 6.11.0 <v6.11.0>`
+:ref:`Release 6.11.0 <v6.11.0>`