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Pole figure calculation adopts rotation matrix with Bunge Euler angles, i.e., in an opposite direction to the linear algebra rotation matrix. Correct it from the current definition.

Reference:
[1] http://engineering.snu.ac.kr/lecture/texture&anisotrop/Texture%20&%20Anisotropy%2010(Representation).pdf
[2] https://en.wikipedia.org/wiki/Rotation_matrix

This will following issue #30.

1. Move Grid-Setup to 3D slicing suite
2. Remove Reset button for different type of strain and stress
3. Slice view with interpolating strain/stress from matched (and only) calculated grids.

Ullich format.

1. Free format separated by tab
2. File posfix is ".jul"
3. Header:

Sample Name
alpha\tbeta\tintensity
1.23\t5.64\t2.49\n
... ...

4. alpha and beta shall be in degree but not radius

Enable PyRS to fit peak with scipy optimizer as an option upon users' request.

As one of the Requests form demo on May 8, 2018:
5) Option to compare the center of mass of the diffraction data to the peak center determined via peak fitting.

1. Save to /reduced/[sub-run]/2theta/ or /reduced/[sub-run]/dspacing/
2. Project file may contain the meta data such as min, max, step (no necessary)
3. reduce_HB2B/reduce_engine can reduce all the sub-runs, i.e.,

   _reduced_data_dict 
   

   considers all the sun-runs in the structure
4. Implement a one-time script to convert testing data (old HB2B runs in h5) to new project file for pole figure, peak fitting and strain/stress tests.

Refactor and enhance StrainStressCalculator

Tasks
1. Add a process progress tracker including ‘load’, ‘align’, ‘calculate’ and etc
2. Well organize the data structure for load data, grid alignment, calculated strain/stress
3. A better copy from one strain/stress type to strain type
4. Find a list of grids that are matched among E11/E22/E33

Use cases to support

1. New use case 1
   1. Load data to E11/E22/E33
   2. Check alignment and realize it shall be plane stress
   3. Reset to plane stress
   4. Calculate strain/stress

2. New use case 2
   1. Load data to E11/E22 (plane strain or stress)
   2. Check alignment and realize it shall be plane stress
   3. Reset to unconstrained strain/stress
   4. Load data to E33
   5. Align and calculate

Regardless of pause/resume, if VX, VY and VZ are not changed, the counts before pause and after resume shall be split to same output workspace.

1. use the finest grid as the default plot grid.

2. bug found in use case: change model from plane strain/stress to unconstrained (solved in #30)

3. make 1D slice working in 2D slice plot

Initialize pole figure matrix/array with all NaNs. It is because that as matplotlib interpolate data points for contour plot, those NaNs will be ignored. Thus, NaN is a good representation for not-measured data points.

This is a request from users during meeting on Nov 1st.

1. After pole figure is calculated, it shall plot pole figure automatically;

2. MTEX file's postfix shall be .jul

3. MTEX file format
   L 1 |NRSF2
   L 2 |alpha beta intensity

1. Bug fix: default working directory for Browse is problematic. (It is very likely hard coded to be under wzz)
2. Move strain/stress type selection to the top the window

File: LaB6_10kev_35deg-00004.tif ....

Traceback (most recent call last):
  File "./tests/Quick_Calibration_v2.py", line 167, in <module>
    engine, pyrs_reducer, mantid_reducer = create_instrument(hb2b_file_name, False, 2048)
  File "./tests/Quick_Calibration_v2.py", line 128, in create_instrument
    target_dimension=pixel_number, load_to_workspace=True)
  File "/home/wzz/Projects/PyRS/build/lib.linux-x86_64-2.7/pyrs/core/reductionengine.py", line 91, in load_data
    load_to_workspace=load_to_workspace)
  File "/home/wzz/Projects/PyRS/build/lib.linux-x86_64-2.7/pyrs/core/reductionengine.py", line 184, in _load_tif_image
    ''.format(image_2d_data.shape))
RuntimeError: Current algorithm can only handle 2048 x 2048 TIFF but not of size (4, 2048, 2048)

Add a new peak profile Asymmetric Pearson VII or split. A good example is LD_Log_Data…nxs

Develop a new widget that contains 2 canvas in vertical. The upper one is for data and model, while the lower one is for residual (Data - Model)

Requests form demo on May 8, 2018:

1. Auto-load data from index 1 when HDF5 data are loaded

2. Add difference plot between fitted and experimental data when displaying fit results

3. Add functionality to trim the 2theta range for the data fit
   a. Option to pull the data range from the view range of the data display

Extra:

• Fix the issue about plotting log vs log

• Show contour plot on loaded data

As title. And adapt the change to strain/stress module.

According to the demo on 09.07, the following modification shall be made:

1. Plot button on the main UI shall be removed. Instead, a new figure shall be plot atomically with the change of parameters.
2. Save strain/stress to csv file
3. Save strain/stress to ParaView format
4. Experiment VTK with strain/stress module
5. Keep aspect ratio between delta X and delta Y to 1:1 in slice view (2D)
6. Make colour space stable

Find out an approach and cost function to calibrate HZB diffractometer including all the data.

After calibration, by given a range on chi (out of plane angle), bin the selected pixels to 2theta-intensity.

Disjoint the pyrscore objects used by Fit Peak, Pole Figure and Strain & Stress.

It can reduce the interference among different interfaces that are used simultaneously.

In strain and stress module, not all the sample logs can be used for grid sample position. There are very limited possibilities. Filter the sample log names and add to combo box. Possible names are

vx, vy, vz, Delta Weld, Delta Thickness, Delta Length, Cuboid *

As title. Required by beam line scientist.

Note
This is the first in a series issues for developing algorithms and UI for HB2B's calibration.

Tasks

• 1. Generate and verify detector masks files at 7 solid angles: 0, +/- 10, +/- 20 and +/- 30.
• 2. Calibration GUI (test)
  • loads 7 masks
  • reduce with masks
  • optionally but as default normalize reduced data by vanadium
  • optionally convert to dspacing
  • compare the convert to dspacing: from a virtual single pixel detector or from 2D detector
• 3. Calibration algorithm prototype
  • fit peaks and present the result
  • evaluate the calibration result
  • refactor Chris' prototype (Quick..v2.py) by using PyRS-reducer
• 4. Implement an algorithm to mask detectors (ROI in fact) by solid angle.

Calibration algorithms

• GSAS: GSASIIimage.py.ImageCalibrate: decided not to use.
• Adopted: Separate detector into N zones by solid angle, reduce data and align peaks.

And thus there is no need to do it in Strain/stress calculation.

1. Save strain/stress to ParaView format
2. Experiment VTK with strain/stress module
3. Make colour space stable

In peak fitting module, it is required to show the fitting error of each individual peak parameter.

This will require the additional support from Mantid::FitPeaks.

Tag:

1. run start time;
2. monochormator setup;

Location:
/HFIR/HB2B/shared/CALIBRATION/Si422

Including: (same as from DAS log)

• Si422
• Si220
• Si311
• Si331AF
• Si511
• Si400

For every 5 degree,

1. calculate solid angles for each pixels
2. group pixels together by their solid angles (0, +/-10, ...)
3. check the change of ROI's boundaries along with 2theta to determine whether resolution of 5 degree in 2theta for ROI is not too coarse.
4. create an HDF file to contain a set of solid angle ROI/mask for future usage.

There are a series of issues that shall be resolved to test the calibration algorithm and workflow by neutron data.

• 1. #54
• 2. #55
• 3. #56
• 4. #57

1. Make the test cases work!
   • testing: all the previously reduced data
2. Make file loading UI exactly same as Peak-Fit module

According to meeting on Nov. 1st:

1. Need more buttons for saving fitting result
2. New use case: if user loads a HDF5 and entry ‘peak fit’ is found, user will be prompted whether he wants to fit the peaks again
3. Peak fitting result shall be saved to HDF5 (input file) automatically (with flag)

Design the skeleton codes for stress/strain module.
Design UI for stress/strain calculation.

Demo must include

1. HB2B project file
   • convert old HB2B data to new project file format
2. Re-reduction data (HZB) - #58, #60.
3. Peak fitting (Old HB2B) - #47.
4. Pole figure calculation (old HB2B + Chris's contribution)
5. Strain/stress calculation and mapping (old HB2B)

Tasks coming from demo

During demo, a list of issues that are exposed including

• PyQt4 and PyQt5 conflict: #63.

• Fails to fit PseudoVoigt:

• HB2B project file shall be completed:

As one of the Requests form demo on May 8, 2018:
4) Option for
a. NRSF2 team will supply data with 2 well resolved peaks

PyRS shall import and compile UI files dynamically but not relies on pyuicX.

1. Add a pole figure plot with scattered points on polar plot other than contour plot.

1. Inside mantidproject.geometry, complete the branch to create IDF for HB2B (HZB), HB3A and Zebra.
2. Generate the IDF (Mantid and PyRS) for HZB.
3. Load TIFF, convert to standard HDF
4. Verify by Mantid (oritientation)
5. Compare geometry from Mantid and PyRS

Implement GUI and its associated interface modules for texture analysis.

This issue will make sure the UI can have the correct response.

Reduce HZB data from 40 degree to 90 degree.

By visualization of all the reduced data, a decision will be made whether the prototyped calibration approach working with X-ray data can work with neutron data due to the difference in resolution.

Prototype the manual reduction module, including reduction engine and UI.

Design GUI for re-reduction, calibration and peak fitting and beyond.

1. Browse and load data

   • Move push button Load to first line with IPTS
   • Add a checkbox to load data automatically if push button Browse is clicked

2. Bug fix: if data is reloaded, upper-right corner plot shall be cleared and reset to original status

3. Bug fix: upper right corner plot’s parameter selection list gets new parameters added to the combobox while the old ones are still remained there.

4. Remove Lorentzian from the supported peak list because it is not a peak shape for HB2B

5. (previous 6) Bug fix: handle the case if user input a scan log index out of range to plot

== Note ==
Item 5 is taken out and will be resolved in an individual issue.
5. Output peak parameter ‘mixing’ in the fitted peak parameters

For all the peak fitting related plot, plot peak (data and model) and their residual (error/difference) in different plots.

It will be applied to both peak fitting and texture analysis UI.

From meeting 9/21:
5. Output peak parameter ‘mixing’ in the fitted peak parameters.

Also from meeting Nov 1st:

1. Need fitting error for effective peak parameters

It is identified as a Mantid issue.

1. Advanced fitting setup allowing to fit with a set of peak profiles instead one;
2. Fit result can be exported to a movie and PNGs with previous setup;
3. A report can be made (in table) to nail down the bad fits