diff --git a/Framework/Properties/Mantid.properties.template b/Framework/Properties/Mantid.properties.template
index baec26b172e9d72f18b487f6d74432ab7b607e3d..aa98016f34e54182ce72ffdff53cd35db52ca658 100644
--- a/Framework/Properties/Mantid.properties.template
+++ b/Framework/Properties/Mantid.properties.template
@@ -21,7 +21,7 @@ Q.convention = Inelastic
# Set of PyQt interfaces to add to the Interfaces menu, separated by a space. Interfaces are seperated from their respective categories by a "/".
-mantidqt.python_interfaces = Direct/DGS_Reduction.py Direct/DGSPlanner.py Direct/PyChop.py Direct/MSlice.py SANS/ORNL_SANS.py Utility/TofConverter.py Diffraction/Engineering_Diffraction_2.py Diffraction/Powder_Diffraction_Reduction.py Utility/FilterEvents.py Diffraction/HFIR_4Circle_Reduction.py Utility/QECoverage.py SANS/ISIS_SANS.py Muon/Frequency_Domain_Analysis.py Muon/Elemental_Analysis.py Muon/Frequency_Domain_Analysis_Old.py Muon/Muon_Analysis.py
+mantidqt.python_interfaces = Direct/DGS_Reduction.py Direct/DGSPlanner.py Direct/PyChop.py Direct/MSlice.py SANS/ORNL_SANS.py Utility/TofConverter.py Diffraction/Engineering_Diffraction.py Diffraction/Powder_Diffraction_Reduction.py Utility/FilterEvents.py Diffraction/HFIR_4Circle_Reduction.py Utility/QECoverage.py SANS/ISIS_SANS.py Muon/Frequency_Domain_Analysis.py Muon/Elemental_Analysis.py Muon/Frequency_Domain_Analysis_Old.py Muon/Muon_Analysis.py
# Directory containing the above startup scripts
mantidqt.python_interfaces_directory = @MANTID_ROOT@/scripts
diff --git a/dev-docs/source/Testing/EngineeringDiffraction/EngineeringDiffraction2TestGuide.rst b/dev-docs/source/Testing/EngineeringDiffraction/EngineeringDiffractionTestGuide.rst
similarity index 94%
rename from dev-docs/source/Testing/EngineeringDiffraction/EngineeringDiffraction2TestGuide.rst
rename to dev-docs/source/Testing/EngineeringDiffraction/EngineeringDiffractionTestGuide.rst
index 2f53943d636acbff5b2e08de6ff5c058a61d5b1f..1093176dd6ae1896a48c8a4ba084cd9f93a953b0 100644
--- a/dev-docs/source/Testing/EngineeringDiffraction/EngineeringDiffraction2TestGuide.rst
+++ b/dev-docs/source/Testing/EngineeringDiffraction/EngineeringDiffractionTestGuide.rst
@@ -1,6 +1,6 @@
-.. _Engineering_Diffraction_2_TestGuide-ref:
+.. _Engineering_Diffraction_TestGuide-ref:
-Engineering Diffraction 2 Testing
+Engineering Diffraction Testing
=================================
.. contents:: Table of Contents
@@ -9,14 +9,14 @@ Engineering Diffraction 2 Testing
Preamble
^^^^^^^^^
This document is tailored towards developers intending to test the Engineering Diffraction
-interface 2.
+interface.
Runs can be loaded from the archive, however it is possible that different run numbers
will be needed as older runs may be deleted.
Overview
^^^^^^^^
-The Engineering Diffraction 2 interface allows scientists using the EnginX instrument to interactively
+The Engineering Diffraction interface allows scientists using the EnginX instrument to interactively
process their data. There are 3 tabs which are ordered according to the main steps performed.
These are:
diff --git a/docs/source/interfaces/Engineering Diffraction (Old).rst b/docs/source/interfaces/Engineering Diffraction (Old).rst
new file mode 100644
index 0000000000000000000000000000000000000000..d6d9b438abc1a904c318915b277690fb00c3f8e0
--- /dev/null
+++ b/docs/source/interfaces/Engineering Diffraction (Old).rst
@@ -0,0 +1,603 @@
+.. _Engineering_Diffraction_(Old)-ref:
+
+Engineering Diffraction (Old)
+=============================
+
+.. contents:: Table of Contents
+ :local:
+
+Overview
+--------
+This interface is hidden and will likely be removed from the next release of mantid.
+
+This custom interface integrates several tasks related to engineering
+diffraction. It provides functionality for calibration, focusing, and
+pre-processing of event mode data. Further extensions can be expected
+for future releases as it is under active development. Feedback is very
+much welcome. The following sections describe the different tabs or
+functionality areas of the interface.
+
+General options
+^^^^^^^^^^^^^^^
+RB Number
+ To enable the GUI specify a RB Number (where "RB Number" usually
+ denotes the experiment reference number at ISIS). This reference
+ will be used for the output paths, so that files from different
+ users and/or experiments can be kept separate.
+
+Instrument
+ Select the instrument. Only ENGIN-X (ISIS) is supported in this version.
+
+?
+ Shows this documentation page.
+
+Close
+ Close the interface
+
+Status at the bottom of the interface
+ A short message will be displayed which indicates whether the last
+ important calculations finished successfully, and when the interface
+ is busy calculating (calibrating, focusing, fitting, etc.).
+
+* Red Star Sign
+ If a red star sign is displayed next to the Browse Button, it is mostly
+ likely because the file specified has not been found. Error message
+ can be viewed by hovering over the red star sign.
+
+.. _ui engineering calibration:
+
+Calibration
+-----------
+
+This tab provides a graphical interface to calculate calibrations and
+visualize them.
+
+It is possible to:
+
+- Generate a new calibration file (which becomes the new current
+ calibration)
+- Load an existing calibration from a GSAS instrument
+ parameters file previously generated
+
+For the current calibration, the following parameters are displayed:
+
+- The vanadium run number
+- The calibration sample run number
+- The path to the output calibration file.
+
+This calibration file output is a GSAS instrument parameters file (IPARM/PAR/PRM). The interface
+produces a calibration file containing all banks and in addition a calibration
+file for every individual bank. All the calibration files are written
+in the same directory.
+
+With the help of Cropped Calibration user can also calibrate according
+to specific banks or by setting the Spectrum Numbers once the Cropped Calibration group
+box has been enabled.
+
+The plot Calibrated Workspace check-box will enable user to plot
+vanadium curves and Ceria peaks. For Ceria peaks there will be two
+workspaces generated and plotted, one for each bank, whereas for a
+cropped calibration there will only be one workspace generated
+and plotted, depending on the selected bank or provided Spectrum
+IDs. The workspace contains difa, difc and tzero data which is then
+utilised to plot the Ceria peaks per bank, the graph will plot Peaks
+Fitted and TOF Straight Line for comparison. More information
+regarding the fit peaks can be found on the
+:ref:`EnggFitPeaks<algm-EnggFitPeaks>` documentation.
+
+The calibration files are written into two different output
+directories. First, they are written to a user specific directory
+which for the ENGIN-X instrument on Windows systems is:
+
+`C:\\EnginX_Mantid\\<Username>\\<RBNumber>\\Calibration`
+
+On UNIX based platforms this path is:
+
+`~/EnginX_Mantid/<Username>/<RBNumber>/Calibration`
+
+They are also copied into a general (all) output directory:
+
+`C:\\EnginX_Mantid\\Calibration` on Windows or
+
+`~/EnginX_Mantid/Calibration` on UNIX platforms.
+
+The calibration parameters for each bank are made available for user
+inspection in a workspace named
+**engggui_calibration_banks_parameters** which is updated when new
+calibrations are loaded or calculated.
+
+Parameters
+^^^^^^^^^^
+
+These parameters are required to generate new calibrations:
+
+Vanadium #
+ Number of the vanadium run used to correct calibration and experiment
+ runs.
+
+Calibration sample #
+ Number of the calibration sample run (for example Ceria run) used to
+ calibrate experiment runs.
+
+Bank Name:
+ This parameter is only required when Cropped Calibration is being
+ carried out. The bank name can be selected from a drop down list with
+ option of "North" and "South", which are equivalent to 1 and 2
+ respectively.
+ Custom bank mappings can be created by setting the Bank Name option
+ to `Use spectrum numbers`. When the option *Use Spectrum Numbers* is
+ set a bank name must be specified in *Customise Bank Name*.
+
+Spectrum Numbers:
+ This parameter is only required when Cropped Calibration is being
+ carried out, the parameter will set the spectrum numbers of the
+ detectors, that should be considered in the calibration while all
+ others will be ignored. This option cannot be used together with
+ Bank Name, as they overlap. You may also give multiple ranges, for
+ example: "0-100", or "0-9", "150-750".
+
+Customise Bank Name:
+ This parameter is only required when Cropped Calibration is being
+ carried out with Spectrum Numbers, the parameter will set the workspace
+ and `.his` file name according to this Bank Name provided by the user.
+ However if the user does not provide a personalised name, the
+ interface will use "cropped" as a default bank name.
+
+The calibration process depends on several additional parameters and
+settings which can be modified in the *Settings* tab, see :ref:`setting-Engineering_Diffraction-ref` for details.
+
+.. _focus-Engineering_Diffraction-ref:
+
+Focus
+-----
+
+Here it is possible to focus run files, by providing a run number or a
+range of run number to enable multi-run focusing, along with that the
+user may also select the files with the help of Browse button.
+
+The focusing process uses the algorithm :ref:`EnggFocus
+<algm-EnggFocus>`. In the documentation of the algorithm you can find
+the details on how the input runs are focused.
+
+The interface will also create workspaces that can be inspected in the
+workspaces window:
+
+1. The *engggui_focusing_input_ws workspace* for the data being focused
+2. The *engggui_focusing_output_ws... workspace* for the corresponding
+ focused data (where the ... denotes a suffix explained below).
+
+Three focusing alternatives are provided:
+
+1. Normal focusing, which includes all the spectra from the input run.
+2. Cropped focusing, where several spectra or ranges of spectra can
+ be specified, as a list separated by commas.
+3. Texture focusing, where the *texture* group of detectors is given
+ in a Detector Grouping File.
+
+Depending on the alternative chosen, the focusing operation will
+include different banks and/or combinations of spectra (detectors).
+The behavior for each option is as follows:
+
+1. *Normal focusing* - All the selected banks and spectra present
+in the input runs are considered. The output focused workspace will
+be named with suffixes such as *_bank_1, _bank_2*, and so on
+
+2. *Cropped Focusing* - All the banks are considered in
+principle but only a list of spectra provided manually are
+processed. The output focused workspace will be named with
+the suffix *_cropped*.
+
+3. *Texture Focusing* - The banks are selected by a user-defined
+list of banks and corresponding spectrum numbers provided in a file.
+The output workspaces will be named with suffixes such as *_texture_bank_1,
+_texture_bank_2*, and so on. These suffixes are determined by the
+bank IDs given in the detector grouping file.
+
+Cropped focusing and Texture focusing have been disabled by default to
+declutter the interface, but each section can be enabled simply by
+ticking the check-box next to Focus Cropped and Focus Texture.
+
+For texture focusing, the detector grouping file is a text (csv) file
+with one line per bank. Each line must contain at least two numeric
+fields, where the first one specifies the bank ID, and the second and
+subsequent ones different spectrum numbers or ranges of spectrum
+numbers. For example::
+
+ # Bank ID, spectrum numbers
+ 1, 205-210
+ 2, 100, 102, 107
+ 3, 300, 310, 320-329, 350-370
+
+When a focus run process is being carried out, Focus Stop button will
+be enabled. Focus Stop button will allow the user to abort once the
+current focus run process has been completed. Inside the *Result Log*
+a warning message will be displayed with last successful run and total
+number of focus runs that could not be processed.
+
+The focused data files are saved in NeXus format into the user
+specific and general directories (as with the calibration output
+files). That is the files are written into
+`C:\\EnginX_Mantid\\User\\<RBNumber>\\Calibration` and
+`C:\\EnginX_Mantid\\Calibration` on Windows, or
+`~/EnginX_Mantid/User/<RBNumber>/Calibration` and
+`~/EnginX_Mantid/Calibration` on UNIX platforms. See below for
+additional, optional outputs.
+
+Run Number
+^^^^^^^^^^
+The run provided to focus can be for example 228061-228063, this will
+run all the files within the given range as long as the file
+directories are included in the
+`User Directories <http://www.mantidproject.org/ManageUserDirectories>`_.
+The user may also provide an input of 228061-3 or 228061, 228062,
+2280623 which should work the same way.
+
+If a red star sign is displayed next to the Browse Button, it is mostly
+likely because the file specified has not been found. Error message
+can be viewed by hovering over the red star sign.
+
+Checking the availability of all the files can take some time, for this
+reason it is also possible that a file may not have been found but the
+red star sign has not been displayed. If you manage to click Focus
+before red sign is displayed, the interface will process the last valid
+focus run instead.
+
+Output
+^^^^^^
+
+Under the output section, the user is provided with an option of
+plotting data in three different formats.
+
+- One Window - Replacing Plots: will replace the previous graph and plot a new graph on top.
+
+- One Window - Waterfall: will plot all the generated focused workspace graphs in one window
+ which can be useful while comparing various graphs.
+
+- Multiple Windows - will plot graph in separate windows.
+
+However, user may also change the Plot Data representation drop-down box while a run is being carried out. This
+will update the interface and plot workspace according to the new given input.
+For example, if a user has selected *One Window - Replacing Plots* and then decides to change it to *One Window -
+Waterfall* during a run, the interface will carry on by plotting
+Waterfall within the same window.
+
+The user also has an option of saving GSS, XYE and OpenGenie formatted
+files by clicking the Output Files checkbox. This will generate three
+different files for each focused output workspace in Mantid. These
+files can be found with appropriate name within:
+
+`C:\\EnginX_Mantid\\<User>\\<RBNumber>\\Focus` on Windows or
+
+`~/EnginX_Mantid/Foxus` on UNIX systems.
+
+The files are also copied to the general (all) output directory which is
+
+`C:\\EnginX_Mantid\\Focus` on Windows
+
+`~/EnginX_Mantid/Focus` under on UNIX systems
+
+`The Multiple Runs Focus Mode` combo-box enables two alternative
+focus modes. `Focus Individual Run Files Separately` is the default
+option set, which allows user to run focus with multi-run files.
+Whereas the `Focus Sum Of Files` option merges all the multi-run
+number files together and applies the Focus Process to the merged
+file.
+
+Pre-processing
+--------------
+
+.. warning:: This is a new capability that is currently in a very
+ early stage of definition and implementation. Not all
+ options may be supported and/or consistent at the moment.
+
+The focusing options can be applied directly to histogram data. For
+event mode experiments, the event data (which would be loaded as event
+workspaces in Mantid) need to be pre-processed.
+
+The simplest pre-processing option is "regular time binning" which
+will produce a histogram data workspace (as a :ref:`Workspace2D
+<Workspace2D>`). The only parameter required is the bin width. The
+workspace will be named with the following convention:
+
+- *engggui_preproc_time_ws*
+
+When the input run file contains multiple workspaces (it would be
+loaded by :ref:`Load <algm-Load>` as multiple :ref:`EventWorkspace
+<EventWorkspace>` workspaces) the output workspace will be a group
+with the corresponding number of histogram workspaces, binned
+separately. This is the case when the input run file comes from a
+multi-period experiment. Note that the time bin can be a multiple of
+the pulse time.
+
+A different way of pre-processing event data is by rebinning
+multi-period data by pulse times. In this case the input required is
+the time step for the binning (the x axis of the output will be time
+instead of time-of-flight). It is also possible to specify the number
+of periods that will be processed (starting from the first one). This
+type of pre-processing produces workspaces with the following naming
+convention:
+
+- *engggui_preproc_by_pulse_time_ws*
+
+Focussing uses the algorithms :ref:`Rebin <algm-Rebin>` and :ref:`RebinByPulseTimes
+<algm-RebinByPulseTimes>` to bin the data in different ways when
+converting event data into histogram data.
+
+Fitting
+-------
+
+.. warning:: This is a new capability that is currently in a very
+ early stage of definition and implementation. Not all
+ options may be supported and/or consistent at the moment.
+
+.. warning:: The input workspace must be converted into a focused file
+ first. The steps to complete this are found here: :ref:`focus-Engineering_Diffraction-ref`
+
+The Fitting tab provides a graphical interface which fits an expected
+diffraction pattern and visualises them. The pattern is specified by
+providing a list of peak centre values where Bragg peaks are expected.
+These values can have units of either TOF of dSpacing but **not** both.
+The algorithm :ref:`EnggFitPeaks<algm-EnggFitPeaks>` is used to
+background fit peaks in those areas using a peak fitting function.
+
+To use the Fitting tab, user is required to follow these steps:
+
+1. Load run(s) to perform fitting on by browsing for focused nexus
+ files *User may click Load button to load the focused file to the
+ canvas*
+2. List of expected peaks which can be either by browsing a (*CSV*) file,
+ manually selecting peaks from the canvas using peak picker tool and the "Add Peak to List" button after
+ loading the focused file or by entering the peaks list within the text-field
+3. Next click on the *Fit* button if you would like to fit single focused
+ file or you can click *Fit All* button which will enable user to
+ batch-process all the runs and banks when several files are loaded.
+ *Fit All* process may also be used when a single run number is given
+ or a file is browsed
+
+.. _ExpectedPeaks-Engineering_Diffraction-ref:
+
+Parameters
+^^^^^^^^^^
+
+These parameters are required to process Fitting successfully:
+
+Focused Run files:
+ .nxs files containing focused diffraction data. These should be the result
+ of focusing data with the :ref:`focus-Engineering_Diffraction-ref` tab.
+
+Peaks:
+ A list of dSpacing values to be translated into TOF to find expected
+ peaks. These peaks can be manually written or imported by selecting a
+ (*CSV*) file.
+
+Output
+^^^^^^
+
+Once the Fit button has been clicked Mantid will process the data. Please wait
+until the Fitting process has completed. Upon completion you should be able to
+view the Fitting tab which will contain:
+
+- The focused workspace plotted in the background in gray crosses.
+- The expected peaks plotted in various colours overlapping the
+ focused workspace peaks.
+
+Within the :ref:`Preview-Engineering_Diffraction-ref` section a user is
+able to zoom-in or zoom-out as well as select, add and save peaks.
+
+The interface will also generate workspaces that can be inspected in the
+workspaces window:
+
+1. The *engggui_fitting_fitpeaks_param* Table workspace
+ with the parameters of the peaks found and fitted.
+2. The *engggui_fitting_focused_ws* Focused workspace also loaded
+ so the fitted data can be compared with focused data
+3. The *engggui_fitting_single_peaks* workspace with each workspace
+ index representing individual expected peak.
+
+During the Fit process, :ref:`EnggSaveSinglePeakFitResultsToHDF5
+<algm-EnggSaveSinglePeakFitResultsToHDF5>` algorithm will be utilised
+to save *engggui_fitting_fitpeaks_param* TableWorkspace as a `hdf5`
+file. There will one file per run, indexed by bank ID, and the file
+will be found in the **Runs** directory of the user's output
+directory. If **Fit All** was run on multiple runs, then an additional
+file for all runs will be output, which is indexed first by run number
+and then by bank ID.
+
+In the plots, the x or abscissa axis is in d-spacing units, which are
+more convenient for peak fitting than time-of-flight. However the run
+files and the focus files are normally stored as time-of-flight
+data. For this reason a conversion from the time-of-flight data to
+d-spacing is required. The conversion is performed using the current
+calibration of banks. The interface handles this internally and adds
+special sample logs to the fitting workspaces
+(*engggui_fitting_single_peaks* and *engggui_fitting_focused_ws*). By
+inspecting the sample logs of these workspaces. The conversion is
+performed using the `GSAS
+<https://subversion.xray.aps.anl.gov/trac/pyGSAS>`__ equations, as
+calculated by the algorithm :ref:`AlignDetectors
+<algm-AlignDetectors>`
+
+.. _Preview-Engineering_Diffraction-ref:
+
+Preview
+^^^^^^^
+Once the fitting process has completed and you are able to view a
+focused workspace with listed expected peaks on the data plot, the *Select
+Peak* button should also be enabled. If the user choose to load the focus
+workspace or if fitting fails with the given peaks then the focused
+workspace will be plotted so that the user can select the peaks manually.
+
+If you've run a fit but you can't see the reconstructed peaks, make sure
+the checkbox **Plot fitted peaks** is checked - if the fit was successful,
+then clicking this should show the results. Equally, if you want to hide
+fitted peaks, just uncheck this box and they will disappear.
+
+By clicking Select Peak button the peak picker tool can be activated.
+To select a peak simply hold *Shift* key and left-click on the graph
+near the peak's center.
+
+To get help selecting the center of the peak, you may set the peak
+width by left-click and drag horizontally, while holding *Ctrl* key
+as well. Users may also zoom-in to the graph by holding left-click
+and dragging a box on the plot, and zoom-out by left-clicking on
+the plot.
+
+When user is happy with the center position of the peak, you may
+add the selected peak to :ref:`ExpectedPeaks-Engineering_Diffraction-ref`
+list by clicking Add Peak button. User may rerun Fit process by
+clearing peaks list using Clear button and manually selecting peaking
+using Select Peak button or instead Save the peaks list in *CSV* file
+by clicking Save button.
+
+User may plot single peak fitting workspace in separate window by using
+Plot To Separate Window button, if the *engggui_fitting_single_peaks*
+is available.
+
+.. _gsas-Engineering_Diffraction-ref:
+
+GSAS Fitting
+------------
+
+.. warning:: This is a new capability that is currently in a very
+ early stage of definition and implementation. Not all
+ options may be supported and/or consistent at the moment.
+
+The GSAS tab provides a graphical interface to the Mantid algorithm
+:ref:`GSASIIRefineFitPeaks <algm-GSASIIRefineFitPeaks>`. This allows
+users to perform GSAS-style fitting on their data from Mantid.
+
+The user must input the following files:
+
+- **Focused run file(s)** - these must have been generated either by
+ the **Fitting** tab or :ref:`EnggFocus <algm-EnggFocus>`.
+- **Instrument Parameter File** - contains DIFA and DIFC GSAS
+ constants, will probably be of ``.prm`` format
+- **Phase file(s)** - contain crystallographic information about the
+ sample in question. Currently only ``.cif`` files are supported
+
+The following parameters are also required:
+
+- **New GSAS-II Project** - GSASIIRefineFitPeaks creates a new
+ ``.gpx`` project here, which can be opened and inspected from the
+ GSAS-II GUI
+
+ - Note, if running **Refine All** on more than one run, the run
+ number and bank ID will be appended to the filename
+- **GSAS-II Installation Directory**
+
+ - This is the directory containing the GSAS-II executables and
+ Python libraries. In particular, it must contain
+ ``GSASIIscriptable.py``. This directory will normally be called
+ `GSASII`, if GSAS-II was installed normally
+ - You must have a version of GSAS-II from at least **February 2018**
+ to use the GUI. See :ref:`Installing_GSASII` for how to install a
+ compatible version
+- **Refinement method** - can either be **Pawley** or
+ **Rietveld**. Pawley refinement is currently under development, so
+ Rietveld is recommended.
+
+Optionally, you may also supply:
+
+- **XMin** and **XMax** - the limits (in TOF) to perform fitting
+ within
+- **DMin** - the minimum dSpacing to use for refinement when
+ performing Pawley refinement
+- **Negative weight** - The weight for a penalty function applied
+ during a Pawley refinement on resulting negative intensities.
+
+To do a refinement, take the following steps:
+
+1. Load a run by selecting the focused NeXuS file using the
+ corresponding **Browse** button, then clicking **Load**. The run
+ number and bank ID (for example ``123456_1``) should appear in the
+ **Run Number** list in the **Preview** section. Click the label,
+ and the run will be plotted
+2. Select your input files, and input any additional parameters in the
+ **GSASIIRefineFitPeaks Controls** section
+3. Click **Run Refinement**. Once complete, fitted peaks for the run
+ should be overplotted in the fitting area. In addition, Rwp
+ (goodness of fit index), Sigma and Gamma (peak broadening
+ coefficients) and lattice parameters should be displayed in the
+ **Fit Results** section.
+
+ - You can also click **Refine All** to run refinement on all runs
+ loaded into GSAS tab
+
+During the Fit process, :ref:`EnggSaveGSASIIFitResultsToHDF5
+<algm-EnggSaveGSASIIFitResultsToHDF5>` algorithm will be utilised to
+save the fit results, and also the parameters used, as a `hdf5`
+file. There will be one file per run, indexed by bank ID, and the file
+will be found in the **Runs** directory of the user's output
+directory.
+
+You can toggle the fitted peaks on and off with the **Plot Fitted
+Peaks** checkbox, remove runs from the list with the **Remove Run**
+button, and plot the run and fitted peaks to a larger, separate plot
+using **Plot to separate window**.
+
+.. _setting-Engineering_Diffraction-ref:
+
+Settings
+--------
+
+Controls several settings, including the input folders where the
+instrument run files can be found. Other advanced options can also be
+controlled to customize the way the underlying calculations are
+performed.
+
+Calibration Parameters
+^^^^^^^^^^^^^^^^^^^^^^
+
+The calibration settings are organized in three blocks:
+
+1. Input directories
+2. Pixel (full) calibration
+3. Advanced settings
+
+The input directories will be used when looking for run files
+(Vanadium and Ceria). They effectively become part of the search path
+of Mantid when using this interface.
+
+The pixel (full) calibration file contains the calibration details of
+every pixel of all banks, as produced by the algorithm
+:ref:`EnggCalibrateFull <algm-EnggCalibrateFull>`. A default pixel
+calibration file is provided with Mantid packages. This calibration
+has been produced for the Vanadium and calibration sample (Ceria) runs
+indicated in the name of the calibration file. Note that this
+calibration is currently subject to changes, as the fitting of peaks
+is being refined.
+
+The Following advanced settings are available to customize the
+behavior of this interface:
+
+Force recalculate all existing Vanadium files
+ If this is enabled, Vanadium corrections will be recalculated even
+ if previous correction results are available for the current Vanadium
+ run number. This is not required unless a modification is done to the
+ original Vanadium run file, or there is a change in the algorithms
+ that calculate the corrections
+
+Template .prm file
+ By changing this option you can Use a different template file for
+ the output GSAS IPAR/PAR/PRM that is generated in the Calibration
+ tab.
+
+Rebin for Calibrate
+ This sets a rebin width parameter that can be used by underlying
+ algorithms such as :ref:`EnggCalibrate <algm-EnggCalibrate>` and
+ :ref:`EnggFocus <algm-EnggFocus>`
+
+Algorithms
+----------
+
+Most of the functionality provided by this interface is based on the
+engineering diffraction Mantid algorithms (which are named with the
+prefix *Engg*). This includes :ref:`EnggCalibrate
+<algm-EnggCalibrate>`, :ref:`EnggCalibrateFull
+<algm-EnggCalibrateFull>`, :ref:`EnggVanadiumCorrections
+<algm-EnggVanadiumCorrections>`, :ref:`EnggFocus <algm-EnggFocus>`,
+:ref:`EnggFitPeaks<algm-EnggFitPeaks>`
+and several other algorithms, explained in detail in the following Mantid
+algorithms documentation pages.
+
+.. categories:: Interfaces Diffraction
diff --git a/docs/source/interfaces/Engineering Diffraction 2.rst b/docs/source/interfaces/Engineering Diffraction 2.rst
deleted file mode 100644
index abcd46ea6de7f44b6cc30a3b1cd46933990b991b..0000000000000000000000000000000000000000
--- a/docs/source/interfaces/Engineering Diffraction 2.rst
+++ /dev/null
@@ -1,171 +0,0 @@
-.. _Engineering_Diffraction_2-ref:
-
-Engineering Diffraction 2
-=========================
-
-.. contents:: Table of Contents
- :local:
-
-Interface Overview
-------------------
-
-This custom interface will integrate several tasks related to engineering
-diffraction. In its current state it provides functionality for creating
-and loading calibration files and focusing ENGINX run files.
-
-Functionality for performing single peak fitting on focused run files is currently in progress.
-
-This interface is under active development.
-
-General Options
-^^^^^^^^^^^^^^^
-RB Number
- The reference number for the output paths (usually an experiment reference
- number at ISIS). Leaving this field empty will result in no user directories
- being created, and only the general directory will be used for file storage.
-
-Instrument
- Select the instrument (ENGINX or IMAT). Currently only ENGINX is fully
- supported.
-
-?
- Show this documentation page.
-
-Settings
- Provides a range of options that apply across the entire interface, currently
- providing the option to change the default output directory and force the
- recalculation of the vanadium correction files.
-
-Close
- Close the interface.
-
-Red Stars
- Red stars next to browse boxes and other fields indicate that the file
- could not be found. Hover over the star to see more information.
-
-Calibration
------------
-
-This tab currently provides a graphical interface to create new calibrations, using the
-:ref:`EnggCalibrate<algm-EnggCalibrate>` algorithm, and visualise them.
-It also allows for the loading of GSAS parameter files created by the calibration process
-to load a previously created calibration into the interface.
-
-When loading an existing calibration, the fields for creating a new calibration will be
-automatically filled, allowing the recreation of the workspaces and plots generated by
-creating a new calibration.
-
-The "Plot Output" check-box will plot vanadium curves and ceria peaks for new calibrations.
-Four plots will be generated (for ENGINX), one of each plot for each of the detector banks.
-
-Creating a new calibration file generates 3 GSAS instrument parameter files,
-one covering all banks and separate ones for each individual bank. All 3 files are written
-to the same directory:
-
-`<CHOSEN_OUTPUT_DIRECTORY>/Calibration/`
-
-If an RB number has been specified the files will also be saved to a user directory
-in the base directory:
-
-`<CHOSEN_OUTPUT_DIRECTORY>/User/<RB_NUMBER>/Calibration/`
-
-Cropping
-^^^^^^^^
-
-The interface also provides the ability to restrict a new calibration to one of the two banks
-or to a custom list of spectra.
-
-Parameters
-^^^^^^^^^^
-
-Vanadium Number
- The run number or file path used to correct the calibration and experiment runs.
-
-Calibration Sample Number
- The run number for the calibration sample run (such as ceria) used to calibrate
- experiment runs.
-
-Path
- The path to the GSAS parameter file to be loaded.
-
-Bank/Spectra
- Select a bank to crop to or specify a custom spectra will be entered.
-
-Custom Spectra
- A comma separated list of spectra to restrict the calibration to. Can be provided as single spectrum numbers
- or ranges using hyphens (e.g. 14-150, 405, 500-600).
-
-Focus
------
-
-This tab allows for the focusing of data files by making use of the :ref:`EnggFocus<algm-EnggFocus>` algorithm.
-
-Files can be selected by providing run numbers or selecting the files manually using the browse button.
-
-In order to use the tab, a new or existing calibration must be created or loaded (see above).
-
-The interface allows for two kinds of focusing:
-
-- **Normal Focusing:**
- Run numbers can be entered and both banks will be focused for each workspace.
- The output workspaces will have a prefix for the run they are for and a suffix denoting which bank they are for.
-
-- **Cropped Focusing:**
- The entered workspace can be cropped to one of the two banks or to a user defined set of spectra.
- Workspaces cropped using custom spectra lists will have the suffix "cropped".
-
-Ticking the "Plot Focused Workspace" checkbox will create a plot of the focused workspace when the algorithm is
-complete. The number of plots that are generated is dependent on the type of focusing done. Normal focusing generates
-a plot for each bank and cropped focusing generates a plot for the single bank or one for the chosen spectra.
-
-Clicking the focus button will begin the focusing algorithm for the selected run files. The button and plotting checkbox
-will be disabled until the fitting algorithm is complete.
-
-The focused output files are saved in NeXus, GSS, and raw XYE format to:
-
-`<CHOSEN_OUTPUT_DIRECTORY>/Focus/`
-
-If an RB number has been specified the files will also be saved to a user directory:
-
-`<CHOSEN_OUTPUT_DIRECTORY>/User/<RB_NUMBER>/Focus/`
-
-Parameters
-^^^^^^^^^^
-
-Sample Run Number
- The run numbers of or file paths to the data files to be focused.
-
-Bank/Spectra
- Select which bank to restrict the focusing to or allow for the entry of custom spectra.
-
-Custom Spectra
- A comma separated list of spectra to restrict the calibration to. Can be provided as single spectrum numbers
- or ranges using hyphens (e.g. 14-150, 405, 500-600).
-
-Fitting
--------
-
-**This tab is currently a work in progress!**
-
-This tab will allow for single peak fitting of focused run files.
-
-Focused run files can be loaded from the file system into mantid from the interface, which will keep track of all the
-workspaces that it has created from these files.
-
-The plan for the rest of the functionality is to allow for loaded workspaces to be plotted in the interface. Peaks
-could then be selected by clicking on the plot or by using a text field to enter peak centres in d-spacing.
-Once the peaks have been selected, they would be fitted using the :ref:`Pseudo-Voigt <func-PseudoVoigt>` and
-:ref:`BackToBackExponential <func-BackToBackExponential>` fit functions.
-
-The output from the fitting functions will be stored in a multidimensional file format, along with the sample logs for
-the runs that have been fitted.
-
-Parameters
-^^^^^^^^^^
-
-Focused Run Files
- A comma separated list of files to load. Selecting files from the file system using the browse button will do this
- for you.
-
-Peak Positions
- A comma separated list of peak positions to be used when performing the fit.
diff --git a/docs/source/interfaces/Engineering Diffraction.rst b/docs/source/interfaces/Engineering Diffraction.rst
index ac36fe86cb58fccd8a772c72e4f28d5fd364ac7e..89477dfa73a00c494143c17a0cd66574c8f5cce2 100644
--- a/docs/source/interfaces/Engineering Diffraction.rst
+++ b/docs/source/interfaces/Engineering Diffraction.rst
@@ -1,605 +1,171 @@
.. _Engineering_Diffraction-ref:
Engineering Diffraction
-=======================
+=========================
.. contents:: Table of Contents
- :local:
-
-Overview
---------
-This custom interface integrates several tasks related to engineering
-diffraction. It provides functionality for calibration, focusing, and
-pre-processing of event mode data. Further extensions can be expected
-for future releases as it is under active development. Feedback is very
-much welcome. The following sections describe the different tabs or
-functionality areas of the interface.
-
-.. interface:: Engineering Diffraction
- :align: center
- :width: 400
-
-General options
+ :local:
+
+Interface Overview
+------------------
+
+This custom interface will integrate several tasks related to engineering
+diffraction. In its current state it provides functionality for creating
+and loading calibration files and focusing ENGINX run files.
+
+Functionality for performing single peak fitting on focused run files is currently in progress.
+
+This interface is under active development.
+
+General Options
^^^^^^^^^^^^^^^
RB Number
- To enable the GUI specify a RB Number (where "RB Number" usually
- denotes the experiment reference number at ISIS). This reference
- will be used for the output paths, so that files from different
- users and/or experiments can be kept separate.
+ The reference number for the output paths (usually an experiment reference
+ number at ISIS). Leaving this field empty will result in no user directories
+ being created, and only the general directory will be used for file storage.
Instrument
- Select the instrument. Only ENGIN-X (ISIS) is supported in this version.
+ Select the instrument (ENGINX or IMAT). Currently only ENGINX is fully
+ supported.
?
- Shows this documentation page.
-
-Close
- Close the interface
+ Show this documentation page.
-Status at the bottom of the interface
- A short message will be displayed which indicates whether the last
- important calculations finished successfully, and when the interface
- is busy calculating (calibrating, focusing, fitting, etc.).
+Settings
+ Provides a range of options that apply across the entire interface, currently
+ providing the option to change the default output directory and force the
+ recalculation of the vanadium correction files.
-* Red Star Sign
- If a red star sign is displayed next to the Browse Button, it is mostly
- likely because the file specified has not been found. Error message
- can be viewed by hovering over the red star sign.
+Close
+ Close the interface.
-.. _ui engineering calibration:
+Red Stars
+ Red stars next to browse boxes and other fields indicate that the file
+ could not be found. Hover over the star to see more information.
Calibration
-----------
-This tab provides a graphical interface to calculate calibrations and
-visualize them.
-
-It is possible to:
-
-- Generate a new calibration file (which becomes the new current
- calibration)
-- Load an existing calibration from a GSAS instrument
- parameters file previously generated
-
-For the current calibration, the following parameters are displayed:
-
-- The vanadium run number
-- The calibration sample run number
-- The path to the output calibration file.
-
-This calibration file output is a GSAS instrument parameters file (IPARM/PAR/PRM). The interface
-produces a calibration file containing all banks and in addition a calibration
-file for every individual bank. All the calibration files are written
-in the same directory.
-
-With the help of Cropped Calibration user can also calibrate according
-to specific banks or by setting the Spectrum Numbers once the Cropped Calibration group
-box has been enabled.
+This tab currently provides a graphical interface to create new calibrations, using the
+:ref:`EnggCalibrate<algm-EnggCalibrate>` algorithm, and visualise them.
+It also allows for the loading of GSAS parameter files created by the calibration process
+to load a previously created calibration into the interface.
-The plot Calibrated Workspace check-box will enable user to plot
-vanadium curves and Ceria peaks. For Ceria peaks there will be two
-workspaces generated and plotted, one for each bank, whereas for a
-cropped calibration there will only be one workspace generated
-and plotted, depending on the selected bank or provided Spectrum
-IDs. The workspace contains difa, difc and tzero data which is then
-utilised to plot the Ceria peaks per bank, the graph will plot Peaks
-Fitted and TOF Straight Line for comparison. More information
-regarding the fit peaks can be found on the
-:ref:`EnggFitPeaks<algm-EnggFitPeaks>` documentation.
+When loading an existing calibration, the fields for creating a new calibration will be
+automatically filled, allowing the recreation of the workspaces and plots generated by
+creating a new calibration.
-The calibration files are written into two different output
-directories. First, they are written to a user specific directory
-which for the ENGIN-X instrument on Windows systems is:
+The "Plot Output" check-box will plot vanadium curves and ceria peaks for new calibrations.
+Four plots will be generated (for ENGINX), one of each plot for each of the detector banks.
-`C:\\EnginX_Mantid\\<Username>\\<RBNumber>\\Calibration`
+Creating a new calibration file generates 3 GSAS instrument parameter files,
+one covering all banks and separate ones for each individual bank. All 3 files are written
+to the same directory:
-On UNIX based platforms this path is:
+`<CHOSEN_OUTPUT_DIRECTORY>/Calibration/`
-`~/EnginX_Mantid/<Username>/<RBNumber>/Calibration`
+If an RB number has been specified the files will also be saved to a user directory
+in the base directory:
-They are also copied into a general (all) output directory:
+`<CHOSEN_OUTPUT_DIRECTORY>/User/<RB_NUMBER>/Calibration/`
-`C:\\EnginX_Mantid\\Calibration` on Windows or
+Cropping
+^^^^^^^^
-`~/EnginX_Mantid/Calibration` on UNIX platforms.
-
-The calibration parameters for each bank are made available for user
-inspection in a workspace named
-**engggui_calibration_banks_parameters** which is updated when new
-calibrations are loaded or calculated.
+The interface also provides the ability to restrict a new calibration to one of the two banks
+or to a custom list of spectra.
Parameters
^^^^^^^^^^
-These parameters are required to generate new calibrations:
-
-Vanadium #
- Number of the vanadium run used to correct calibration and experiment
- runs.
-
-Calibration sample #
- Number of the calibration sample run (for example Ceria run) used to
- calibrate experiment runs.
-
-Bank Name:
- This parameter is only required when Cropped Calibration is being
- carried out. The bank name can be selected from a drop down list with
- option of "North" and "South", which are equivalent to 1 and 2
- respectively.
- Custom bank mappings can be created by setting the Bank Name option
- to `Use spectrum numbers`. When the option *Use Spectrum Numbers* is
- set a bank name must be specified in *Customise Bank Name*.
-
-Spectrum Numbers:
- This parameter is only required when Cropped Calibration is being
- carried out, the parameter will set the spectrum numbers of the
- detectors, that should be considered in the calibration while all
- others will be ignored. This option cannot be used together with
- Bank Name, as they overlap. You may also give multiple ranges, for
- example: "0-100", or "0-9", "150-750".
-
-Customise Bank Name:
- This parameter is only required when Cropped Calibration is being
- carried out with Spectrum Numbers, the parameter will set the workspace
- and `.his` file name according to this Bank Name provided by the user.
- However if the user does not provide a personalised name, the
- interface will use "cropped" as a default bank name.
-
-The calibration process depends on several additional parameters and
-settings which can be modified in the *Settings* tab, see :ref:`setting-Engineering_Diffraction-ref` for details.
-
-.. _focus-Engineering_Diffraction-ref:
-
-Focus
------
-
-Here it is possible to focus run files, by providing a run number or a
-range of run number to enable multi-run focusing, along with that the
-user may also select the files with the help of Browse button.
-
-The focusing process uses the algorithm :ref:`EnggFocus
-<algm-EnggFocus>`. In the documentation of the algorithm you can find
-the details on how the input runs are focused.
-
-The interface will also create workspaces that can be inspected in the
-workspaces window:
-
-1. The *engggui_focusing_input_ws workspace* for the data being focused
-2. The *engggui_focusing_output_ws... workspace* for the corresponding
- focused data (where the ... denotes a suffix explained below).
-
-Three focusing alternatives are provided:
-
-1. Normal focusing, which includes all the spectra from the input run.
-2. Cropped focusing, where several spectra or ranges of spectra can
- be specified, as a list separated by commas.
-3. Texture focusing, where the *texture* group of detectors is given
- in a Detector Grouping File.
-
-Depending on the alternative chosen, the focusing operation will
-include different banks and/or combinations of spectra (detectors).
-The behavior for each option is as follows:
-
-1. *Normal focusing* - All the selected banks and spectra present
-in the input runs are considered. The output focused workspace will
-be named with suffixes such as *_bank_1, _bank_2*, and so on
-
-2. *Cropped Focusing* - All the banks are considered in
-principle but only a list of spectra provided manually are
-processed. The output focused workspace will be named with
-the suffix *_cropped*.
-
-3. *Texture Focusing* - The banks are selected by a user-defined
-list of banks and corresponding spectrum numbers provided in a file.
-The output workspaces will be named with suffixes such as *_texture_bank_1,
-_texture_bank_2*, and so on. These suffixes are determined by the
-bank IDs given in the detector grouping file.
-
-Cropped focusing and Texture focusing have been disabled by default to
-declutter the interface, but each section can be enabled simply by
-ticking the check-box next to Focus Cropped and Focus Texture.
-
-For texture focusing, the detector grouping file is a text (csv) file
-with one line per bank. Each line must contain at least two numeric
-fields, where the first one specifies the bank ID, and the second and
-subsequent ones different spectrum numbers or ranges of spectrum
-numbers. For example::
-
- # Bank ID, spectrum numbers
- 1, 205-210
- 2, 100, 102, 107
- 3, 300, 310, 320-329, 350-370
-
-When a focus run process is being carried out, Focus Stop button will
-be enabled. Focus Stop button will allow the user to abort once the
-current focus run process has been completed. Inside the *Result Log*
-a warning message will be displayed with last successful run and total
-number of focus runs that could not be processed.
-
-The focused data files are saved in NeXus format into the user
-specific and general directories (as with the calibration output
-files). That is the files are written into
-`C:\\EnginX_Mantid\\User\\<RBNumber>\\Calibration` and
-`C:\\EnginX_Mantid\\Calibration` on Windows, or
-`~/EnginX_Mantid/User/<RBNumber>/Calibration` and
-`~/EnginX_Mantid/Calibration` on UNIX platforms. See below for
-additional, optional outputs.
-
-Run Number
-^^^^^^^^^^
-The run provided to focus can be for example 228061-228063, this will
-run all the files within the given range as long as the file
-directories are included in the
-`User Directories <http://www.mantidproject.org/ManageUserDirectories>`_.
-The user may also provide an input of 228061-3 or 228061, 228062,
-2280623 which should work the same way.
+Vanadium Number
+ The run number or file path used to correct the calibration and experiment runs.
-If a red star sign is displayed next to the Browse Button, it is mostly
-likely because the file specified has not been found. Error message
-can be viewed by hovering over the red star sign.
+Calibration Sample Number
+ The run number for the calibration sample run (such as ceria) used to calibrate
+ experiment runs.
-Checking the availability of all the files can take some time, for this
-reason it is also possible that a file may not have been found but the
-red star sign has not been displayed. If you manage to click Focus
-before red sign is displayed, the interface will process the last valid
-focus run instead.
+Path
+ The path to the GSAS parameter file to be loaded.
-Output
-^^^^^^
+Bank/Spectra
+ Select a bank to crop to or specify a custom spectra will be entered.
-Under the output section, the user is provided with an option of
-plotting data in three different formats.
+Custom Spectra
+ A comma separated list of spectra to restrict the calibration to. Can be provided as single spectrum numbers
+ or ranges using hyphens (e.g. 14-150, 405, 500-600).
-- One Window - Replacing Plots: will replace the previous graph and plot a new graph on top.
+Focus
+-----
-- One Window - Waterfall: will plot all the generated focused workspace graphs in one window
- which can be useful while comparing various graphs.
+This tab allows for the focusing of data files by making use of the :ref:`EnggFocus<algm-EnggFocus>` algorithm.
-- Multiple Windows - will plot graph in separate windows.
+Files can be selected by providing run numbers or selecting the files manually using the browse button.
-However, user may also change the Plot Data representation drop-down box while a run is being carried out. This
-will update the interface and plot workspace according to the new given input.
-For example, if a user has selected *One Window - Replacing Plots* and then decides to change it to *One Window -
-Waterfall* during a run, the interface will carry on by plotting
-Waterfall within the same window.
+In order to use the tab, a new or existing calibration must be created or loaded (see above).
-The user also has an option of saving GSS, XYE and OpenGenie formatted
-files by clicking the Output Files checkbox. This will generate three
-different files for each focused output workspace in Mantid. These
-files can be found with appropriate name within:
+The interface allows for two kinds of focusing:
-`C:\\EnginX_Mantid\\<User>\\<RBNumber>\\Focus` on Windows or
+- **Normal Focusing:**
+ Run numbers can be entered and both banks will be focused for each workspace.
+ The output workspaces will have a prefix for the run they are for and a suffix denoting which bank they are for.
-`~/EnginX_Mantid/Foxus` on UNIX systems.
+- **Cropped Focusing:**
+ The entered workspace can be cropped to one of the two banks or to a user defined set of spectra.
+ Workspaces cropped using custom spectra lists will have the suffix "cropped".
-The files are also copied to the general (all) output directory which is
+Ticking the "Plot Focused Workspace" checkbox will create a plot of the focused workspace when the algorithm is
+complete. The number of plots that are generated is dependent on the type of focusing done. Normal focusing generates
+a plot for each bank and cropped focusing generates a plot for the single bank or one for the chosen spectra.
-`C:\\EnginX_Mantid\\Focus` on Windows
+Clicking the focus button will begin the focusing algorithm for the selected run files. The button and plotting checkbox
+will be disabled until the fitting algorithm is complete.
-`~/EnginX_Mantid/Focus` under on UNIX systems
+The focused output files are saved in NeXus, GSS, and raw XYE format to:
-`The Multiple Runs Focus Mode` combo-box enables two alternative
-focus modes. `Focus Individual Run Files Separately` is the default
-option set, which allows user to run focus with multi-run files.
-Whereas the `Focus Sum Of Files` option merges all the multi-run
-number files together and applies the Focus Process to the merged
-file.
+`<CHOSEN_OUTPUT_DIRECTORY>/Focus/`
-Pre-processing
---------------
+If an RB number has been specified the files will also be saved to a user directory:
-.. warning:: This is a new capability that is currently in a very
- early stage of definition and implementation. Not all
- options may be supported and/or consistent at the moment.
+`<CHOSEN_OUTPUT_DIRECTORY>/User/<RB_NUMBER>/Focus/`
-The focusing options can be applied directly to histogram data. For
-event mode experiments, the event data (which would be loaded as event
-workspaces in Mantid) need to be pre-processed.
+Parameters
+^^^^^^^^^^
-The simplest pre-processing option is "regular time binning" which
-will produce a histogram data workspace (as a :ref:`Workspace2D
-<Workspace2D>`). The only parameter required is the bin width. The
-workspace will be named with the following convention:
+Sample Run Number
+ The run numbers of or file paths to the data files to be focused.
+
+Bank/Spectra
+ Select which bank to restrict the focusing to or allow for the entry of custom spectra.
-- *engggui_preproc_time_ws*
+Custom Spectra
+ A comma separated list of spectra to restrict the calibration to. Can be provided as single spectrum numbers
+ or ranges using hyphens (e.g. 14-150, 405, 500-600).
-When the input run file contains multiple workspaces (it would be
-loaded by :ref:`Load <algm-Load>` as multiple :ref:`EventWorkspace
-<EventWorkspace>` workspaces) the output workspace will be a group
-with the corresponding number of histogram workspaces, binned
-separately. This is the case when the input run file comes from a
-multi-period experiment. Note that the time bin can be a multiple of
-the pulse time.
+Fitting
+-------
-A different way of pre-processing event data is by rebinning
-multi-period data by pulse times. In this case the input required is
-the time step for the binning (the x axis of the output will be time
-instead of time-of-flight). It is also possible to specify the number
-of periods that will be processed (starting from the first one). This
-type of pre-processing produces workspaces with the following naming
-convention:
+**This tab is currently a work in progress!**
-- *engggui_preproc_by_pulse_time_ws*
+This tab will allow for single peak fitting of focused run files.
-Focussing uses the algorithms :ref:`Rebin <algm-Rebin>` and :ref:`RebinByPulseTimes
-<algm-RebinByPulseTimes>` to bin the data in different ways when
-converting event data into histogram data.
+Focused run files can be loaded from the file system into mantid from the interface, which will keep track of all the
+workspaces that it has created from these files.
-Fitting
--------
+The plan for the rest of the functionality is to allow for loaded workspaces to be plotted in the interface. Peaks
+could then be selected by clicking on the plot or by using a text field to enter peak centres in d-spacing.
+Once the peaks have been selected, they would be fitted using the :ref:`Pseudo-Voigt <func-PseudoVoigt>` and
+:ref:`BackToBackExponential <func-BackToBackExponential>` fit functions.
-.. warning:: This is a new capability that is currently in a very
- early stage of definition and implementation. Not all
- options may be supported and/or consistent at the moment.
-
-.. warning:: The input workspace must be converted into a focused file
- first. The steps to complete this are found here: :ref:`focus-Engineering_Diffraction-ref`
-
-The Fitting tab provides a graphical interface which fits an expected
-diffraction pattern and visualises them. The pattern is specified by
-providing a list of peak centre values where Bragg peaks are expected.
-These values can have units of either TOF of dSpacing but **not** both.
-The algorithm :ref:`EnggFitPeaks<algm-EnggFitPeaks>` is used to
-background fit peaks in those areas using a peak fitting function.
-
-To use the Fitting tab, user is required to follow these steps:
-
-1. Load run(s) to perform fitting on by browsing for focused nexus
- files *User may click Load button to load the focused file to the
- canvas*
-2. List of expected peaks which can be either by browsing a (*CSV*) file,
- manually selecting peaks from the canvas using peak picker tool and the "Add Peak to List" button after
- loading the focused file or by entering the peaks list within the text-field
-3. Next click on the *Fit* button if you would like to fit single focused
- file or you can click *Fit All* button which will enable user to
- batch-process all the runs and banks when several files are loaded.
- *Fit All* process may also be used when a single run number is given
- or a file is browsed
-
-.. _ExpectedPeaks-Engineering_Diffraction-ref:
+The output from the fitting functions will be stored in a multidimensional file format, along with the sample logs for
+the runs that have been fitted.
Parameters
^^^^^^^^^^
-These parameters are required to process Fitting successfully:
-
-Focused Run files:
- .nxs files containing focused diffraction data. These should be the result
- of focusing data with the :ref:`focus-Engineering_Diffraction-ref` tab.
-
-Peaks:
- A list of dSpacing values to be translated into TOF to find expected
- peaks. These peaks can be manually written or imported by selecting a
- (*CSV*) file.
-
-Output
-^^^^^^
-
-Once the Fit button has been clicked Mantid will process the data. Please wait
-until the Fitting process has completed. Upon completion you should be able to
-view the Fitting tab which will contain:
-
-- The focused workspace plotted in the background in gray crosses.
-- The expected peaks plotted in various colours overlapping the
- focused workspace peaks.
-
-Within the :ref:`Preview-Engineering_Diffraction-ref` section a user is
-able to zoom-in or zoom-out as well as select, add and save peaks.
-
-The interface will also generate workspaces that can be inspected in the
-workspaces window:
-
-1. The *engggui_fitting_fitpeaks_param* Table workspace
- with the parameters of the peaks found and fitted.
-2. The *engggui_fitting_focused_ws* Focused workspace also loaded
- so the fitted data can be compared with focused data
-3. The *engggui_fitting_single_peaks* workspace with each workspace
- index representing individual expected peak.
-
-During the Fit process, :ref:`EnggSaveSinglePeakFitResultsToHDF5
-<algm-EnggSaveSinglePeakFitResultsToHDF5>` algorithm will be utilised
-to save *engggui_fitting_fitpeaks_param* TableWorkspace as a `hdf5`
-file. There will one file per run, indexed by bank ID, and the file
-will be found in the **Runs** directory of the user's output
-directory. If **Fit All** was run on multiple runs, then an additional
-file for all runs will be output, which is indexed first by run number
-and then by bank ID.
-
-In the plots, the x or abscissa axis is in d-spacing units, which are
-more convenient for peak fitting than time-of-flight. However the run
-files and the focus files are normally stored as time-of-flight
-data. For this reason a conversion from the time-of-flight data to
-d-spacing is required. The conversion is performed using the current
-calibration of banks. The interface handles this internally and adds
-special sample logs to the fitting workspaces
-(*engggui_fitting_single_peaks* and *engggui_fitting_focused_ws*). By
-inspecting the sample logs of these workspaces. The conversion is
-performed using the `GSAS
-<https://subversion.xray.aps.anl.gov/trac/pyGSAS>`__ equations, as
-calculated by the algorithm :ref:`AlignDetectors
-<algm-AlignDetectors>`
-
-.. _Preview-Engineering_Diffraction-ref:
-
-Preview
-^^^^^^^
-Once the fitting process has completed and you are able to view a
-focused workspace with listed expected peaks on the data plot, the *Select
-Peak* button should also be enabled. If the user choose to load the focus
-workspace or if fitting fails with the given peaks then the focused
-workspace will be plotted so that the user can select the peaks manually.
-
-If you've run a fit but you can't see the reconstructed peaks, make sure
-the checkbox **Plot fitted peaks** is checked - if the fit was successful,
-then clicking this should show the results. Equally, if you want to hide
-fitted peaks, just uncheck this box and they will disappear.
-
-By clicking Select Peak button the peak picker tool can be activated.
-To select a peak simply hold *Shift* key and left-click on the graph
-near the peak's center.
-
-To get help selecting the center of the peak, you may set the peak
-width by left-click and drag horizontally, while holding *Ctrl* key
-as well. Users may also zoom-in to the graph by holding left-click
-and dragging a box on the plot, and zoom-out by left-clicking on
-the plot.
-
-When user is happy with the center position of the peak, you may
-add the selected peak to :ref:`ExpectedPeaks-Engineering_Diffraction-ref`
-list by clicking Add Peak button. User may rerun Fit process by
-clearing peaks list using Clear button and manually selecting peaking
-using Select Peak button or instead Save the peaks list in *CSV* file
-by clicking Save button.
-
-User may plot single peak fitting workspace in separate window by using
-Plot To Separate Window button, if the *engggui_fitting_single_peaks*
-is available.
-
-.. _gsas-Engineering_Diffraction-ref:
-
-GSAS Fitting
-------------
-
-.. warning:: This is a new capability that is currently in a very
- early stage of definition and implementation. Not all
- options may be supported and/or consistent at the moment.
-
-The GSAS tab provides a graphical interface to the Mantid algorithm
-:ref:`GSASIIRefineFitPeaks <algm-GSASIIRefineFitPeaks>`. This allows
-users to perform GSAS-style fitting on their data from Mantid.
-
-The user must input the following files:
-
-- **Focused run file(s)** - these must have been generated either by
- the **Fitting** tab or :ref:`EnggFocus <algm-EnggFocus>`.
-- **Instrument Parameter File** - contains DIFA and DIFC GSAS
- constants, will probably be of ``.prm`` format
-- **Phase file(s)** - contain crystallographic information about the
- sample in question. Currently only ``.cif`` files are supported
-
-The following parameters are also required:
-
-- **New GSAS-II Project** - GSASIIRefineFitPeaks creates a new
- ``.gpx`` project here, which can be opened and inspected from the
- GSAS-II GUI
-
- - Note, if running **Refine All** on more than one run, the run
- number and bank ID will be appended to the filename
-- **GSAS-II Installation Directory**
-
- - This is the directory containing the GSAS-II executables and
- Python libraries. In particular, it must contain
- ``GSASIIscriptable.py``. This directory will normally be called
- `GSASII`, if GSAS-II was installed normally
- - You must have a version of GSAS-II from at least **February 2018**
- to use the GUI. See :ref:`Installing_GSASII` for how to install a
- compatible version
-- **Refinement method** - can either be **Pawley** or
- **Rietveld**. Pawley refinement is currently under development, so
- Rietveld is recommended.
-
-Optionally, you may also supply:
-
-- **XMin** and **XMax** - the limits (in TOF) to perform fitting
- within
-- **DMin** - the minimum dSpacing to use for refinement when
- performing Pawley refinement
-- **Negative weight** - The weight for a penalty function applied
- during a Pawley refinement on resulting negative intensities.
-
-To do a refinement, take the following steps:
-
-1. Load a run by selecting the focused NeXuS file using the
- corresponding **Browse** button, then clicking **Load**. The run
- number and bank ID (for example ``123456_1``) should appear in the
- **Run Number** list in the **Preview** section. Click the label,
- and the run will be plotted
-2. Select your input files, and input any additional parameters in the
- **GSASIIRefineFitPeaks Controls** section
-3. Click **Run Refinement**. Once complete, fitted peaks for the run
- should be overplotted in the fitting area. In addition, Rwp
- (goodness of fit index), Sigma and Gamma (peak broadening
- coefficients) and lattice parameters should be displayed in the
- **Fit Results** section.
-
- - You can also click **Refine All** to run refinement on all runs
- loaded into GSAS tab
-
-During the Fit process, :ref:`EnggSaveGSASIIFitResultsToHDF5
-<algm-EnggSaveGSASIIFitResultsToHDF5>` algorithm will be utilised to
-save the fit results, and also the parameters used, as a `hdf5`
-file. There will be one file per run, indexed by bank ID, and the file
-will be found in the **Runs** directory of the user's output
-directory.
-
-You can toggle the fitted peaks on and off with the **Plot Fitted
-Peaks** checkbox, remove runs from the list with the **Remove Run**
-button, and plot the run and fitted peaks to a larger, separate plot
-using **Plot to separate window**.
-
-.. _setting-Engineering_Diffraction-ref:
+Focused Run Files
+ A comma separated list of files to load. Selecting files from the file system using the browse button will do this
+ for you.
-Settings
---------
-
-Controls several settings, including the input folders where the
-instrument run files can be found. Other advanced options can also be
-controlled to customize the way the underlying calculations are
-performed.
-
-Calibration Parameters
-^^^^^^^^^^^^^^^^^^^^^^
-
-The calibration settings are organized in three blocks:
-
-1. Input directories
-2. Pixel (full) calibration
-3. Advanced settings
-
-The input directories will be used when looking for run files
-(Vanadium and Ceria). They effectively become part of the search path
-of Mantid when using this interface.
-
-The pixel (full) calibration file contains the calibration details of
-every pixel of all banks, as produced by the algorithm
-:ref:`EnggCalibrateFull <algm-EnggCalibrateFull>`. A default pixel
-calibration file is provided with Mantid packages. This calibration
-has been produced for the Vanadium and calibration sample (Ceria) runs
-indicated in the name of the calibration file. Note that this
-calibration is currently subject to changes, as the fitting of peaks
-is being refined.
-
-The Following advanced settings are available to customize the
-behavior of this interface:
-
-Force recalculate all existing Vanadium files
- If this is enabled, Vanadium corrections will be recalculated even
- if previous correction results are available for the current Vanadium
- run number. This is not required unless a modification is done to the
- original Vanadium run file, or there is a change in the algorithms
- that calculate the corrections
-
-Template .prm file
- By changing this option you can Use a different template file for
- the output GSAS IPAR/PAR/PRM that is generated in the Calibration
- tab.
-
-Rebin for Calibrate
- This sets a rebin width parameter that can be used by underlying
- algorithms such as :ref:`EnggCalibrate <algm-EnggCalibrate>` and
- :ref:`EnggFocus <algm-EnggFocus>`
-
-Algorithms
-----------
-
-Most of the functionality provided by this interface is based on the
-engineering diffraction Mantid algorithms (which are named with the
-prefix *Engg*). This includes :ref:`EnggCalibrate
-<algm-EnggCalibrate>`, :ref:`EnggCalibrateFull
-<algm-EnggCalibrateFull>`, :ref:`EnggVanadiumCorrections
-<algm-EnggVanadiumCorrections>`, :ref:`EnggFocus <algm-EnggFocus>`,
-:ref:`EnggFitPeaks<algm-EnggFitPeaks>`
-and several other algorithms, explained in detail in the following Mantid
-algorithms documentation pages.
-
-.. categories:: Interfaces Diffraction
+Peak Positions
+ A comma separated list of peak positions to be used when performing the fit.
diff --git a/docs/source/release/v4.3.0/diffraction.rst b/docs/source/release/v4.3.0/diffraction.rst
index 56f6524240f745d2d2ee9b3d11f482f6b68c61e0..7331107f9f0b761719ffc0000dff23376904162f 100644
--- a/docs/source/release/v4.3.0/diffraction.rst
+++ b/docs/source/release/v4.3.0/diffraction.rst
@@ -14,7 +14,7 @@ New Features
Engineering Diffraction
-----------------------
-- Introduction of Engineering Diffraction 2 interface. Currently supports calibration and focusing for ENGINX.
+- Introduction of new Engineering Diffraction interface. Currently supports calibration and focusing for ENGINX.
Improvements
diff --git a/qt/scientific_interfaces/EnggDiffraction/EnggDiffractionViewQtGUI.cpp b/qt/scientific_interfaces/EnggDiffraction/EnggDiffractionViewQtGUI.cpp
index 5a5e210361df42860f3599012f3c5d622ecc97b9..4e7f9c954af3d60c33c028697d811475f93c80c4 100644
--- a/qt/scientific_interfaces/EnggDiffraction/EnggDiffractionViewQtGUI.cpp
+++ b/qt/scientific_interfaces/EnggDiffraction/EnggDiffractionViewQtGUI.cpp
@@ -28,7 +28,8 @@ namespace MantidQt {
namespace CustomInterfaces {
// Add this class to the list of specialised dialogs in this namespace
-DECLARE_SUBWINDOW(EnggDiffractionViewQtGUI)
+// Hidden for release of 5.0 to be removed as a maintainance issue.
+// DECLARE_SUBWINDOW(EnggDiffractionViewQtGUI)
const double EnggDiffractionViewQtGUI::g_defaultRebinWidth = -0.0005;
diff --git a/qt/scientific_interfaces/EnggDiffraction/EnggDiffractionViewQtGUI.h b/qt/scientific_interfaces/EnggDiffraction/EnggDiffractionViewQtGUI.h
index e9b0aeee81022ef6ccae356b92ca56f9f3d1d32b..53dc26e1855ce6bb3040aa639d6048e63105e784 100644
--- a/qt/scientific_interfaces/EnggDiffraction/EnggDiffractionViewQtGUI.h
+++ b/qt/scientific_interfaces/EnggDiffraction/EnggDiffractionViewQtGUI.h
@@ -49,7 +49,7 @@ public:
/// Default Constructor
EnggDiffractionViewQtGUI(QWidget *parent = nullptr);
/// Interface name
- static std::string name() { return "Engineering Diffraction"; }
+ static std::string name() { return "Engineering Diffraction (Old)"; }
/// This interface's categories.
static QString categoryInfo() { return "Diffraction"; }
diff --git a/scripts/Engineering/gui/engineering_diffraction/engineering_diffraction.py b/scripts/Engineering/gui/engineering_diffraction/engineering_diffraction.py
index 518b615fedbc06ea225f1f4804a3d223f5aed02d..4627ee476a7577b1f1256252fb8fb69afe71a63d 100644
--- a/scripts/Engineering/gui/engineering_diffraction/engineering_diffraction.py
+++ b/scripts/Engineering/gui/engineering_diffraction/engineering_diffraction.py
@@ -29,14 +29,14 @@ Ui_main_window, _ = load_ui(__file__, "main_window.ui")
class EngineeringDiffractionGui(QtWidgets.QMainWindow, Ui_main_window):
"""
- The engineering diffraction interface v2.0
+ The engineering diffraction interface
"""
def __init__(self, parent=None):
super(EngineeringDiffractionGui, self).__init__(parent)
# Main Window
self.setupUi(self)
- self.doc = "Engineering Diffraction 2"
+ self.doc = "Engineering Diffraction"
self.tabs = self.tab_main
self.setFocusPolicy(QtCore.Qt.StrongFocus)
self.calibration_presenter = None
diff --git a/scripts/Engineering_Diffraction_2.py b/scripts/Engineering_Diffraction.py
similarity index 100%
rename from scripts/Engineering_Diffraction_2.py
rename to scripts/Engineering_Diffraction.py