Viewer 3D align
^^^^^^^^^^^^^^^
To generate a UB matirx, it is convinient to use the 3D Viewer. We recommend to use the alignToRefs function. By running 3D Viewer with rlu=False, you can read of the coordinates of two reflections in Q-space. These coordinates and the corresponding HKL will then be used for making a UB. You can change the orientation of the 3D Viewer by pressing 0, 1 and 2. When apropriate Q-coordinates are identified, they can be used to align and plot the data in HKL, as showed in the code below. 

.. code-block:: python
   :linenos:

   from DMCpy import DataSet,DataFile,_tools
   import numpy as np
   
   # Give file number and folder the file is stored in.
   scanNumbers = '12153-12154' 
   folder = 'data/SC'
   year = 2022
  
   filePath = _tools.fileListGenerator(scanNumbers,folder,year=year) 
   
   unitCell = np.array([ 7.218, 7.218, 18.183, 90.0, 90.0, 120.0])
   
   # # # load dataFiles
   dataFiles = [DataFile.loadDataFile(dFP,unitCell = unitCell) for dFP in filePath]
         
   # load data files and make data set
   ds = DataSet.DataSet(dataFiles)
      
   # Define Q coordinates and HKL for the coordinates. 
   q1 = [-0.447,-0.914,-0.003]
   q2 = [-1.02,-0.067,-0.02]
   HKL1 = [1,0,0]
   HKL2 = [0,1,0]
   
   # this function uses two coordinates in Q space and align them to corrdinates in HKL space
   ds.alignToRefs(q1=q1,q2=q2,HKL1=HKL1,HKL2=HKL2)
   
   Viewer = ds.Viewer3D(0.01,0.01,0.02,rlu=True)
   
   # Set the color bar limits to 0 and 0.001
   Viewer.set_clim(0,0.001)
   
   # Find the number of steps and set viewer to middel value
   # This can also be done interactively in the viewer by pressing up or down,
   # or by scrolling the mouse wheel or clicking the sliding bar.
   zSteps = Viewer.Z.shape[-1]
   Viewer.setPlane(int(zSteps/2)-1)
   
   fig = Viewer.ax.get_figure()
   fig.savefig('figure0.png',format='png')
   

The above code takes the data from the A3 scan files 12153-12154 from 2022 and generates the Viewer 3D utilizing a voxel size of 0.01 x 0.01 x 0.01 in Q-space, and plot the data in HKL space. By default, the viewer starts out in projection 2, i.e. with Qz being the axis stepped through. The end results are shown below:

First data overview the HK0-plane

.. figure:: CenterMiddel_aligned_hk0.png 
  :width: 50%
  :align: center