3D TDS intensity distribution on sub Volume:ΒΆ

The script make_TDS_SubVolunme cuts a subvolumes out of 3D TDS intensity distribution calculation. It reqires the results of a make_TDS_intensityVolume calculation.

  • The usage is

    make_TDS_IntensityVolume intensityVolume_file.h5

    where the intensityVolume_file.h5 is the result of the make_TDS_intensityVolume calculation in .h5 format

  • The input_file must set the variables :

    • Mandatories

      • redCenter
      • DQ
      • Ngrid1
      • Ngrid2
      • Ngrid3
      • CuttingPlanes
      • outputname

    • Output

      The calculated intensities are written to a .ccp and .h5 file for visualization with chimera and pymca respectively.

make_TDS_SubVolume.redCenter = array([ 0., 0., 0.])

Center of sub volume, example redCenter=numpy.array([0.0,0.0,0.0])

make_TDS_SubVolume.DQ = 0.08

q-resolution in 1/Ang

make_TDS_SubVolume.Ngrid1 = 100

number of grid points along one axis

make_TDS_SubVolume.Ngrid2 = 100

number of grid points along one axis

make_TDS_SubVolume.Ngrid3 = 100

number of grid points along one axis

make_TDS_SubVolume.CuttingPlanes = [[[0, 0, 1.0], [1, 0, 1.0], [0, 1, 1.0]], [[0, 0, -1.0], [-1, 0, -1.0], [0, -1, -1.0]], [[1, 0, 0], [1, 0, 1], [0, 1, 0]], [[-1, 0, 0], [-1, 0, -1], [0, -1, 0]], [[1, 0, 0], [1, -1, 1], [1, -1, 0]], [[-1, 0, 0], [-1, 1, -1], [-1, 1, 0]], [[0, 1, 0], [-1, 1, 1], [-1, 1, 0]], [[0, -1, 0], [1, -1, 1], [1, -1, 0]]]

Cutting Planes, example Cutting

Planes= [
 [ [0,0,1.0 ], [1,0,1.0 ],    [0, 1, 1.0 ] ],
 [ [0,0,-1.0 ], [-1,0,-1.0 ], [0,-1,-1.0 ] ],

 [ [ 1,0,0 ], [ 1,0, 1 ], [ 0, 1,0 ] ],
 [ [-1,0,0 ], [-1,0,-1 ], [ 0,-1,0 ] ],

 [ [ 1,0,0 ], [  1,-1,  1 ], [ 1,-1,0 ] ],
 [ [-1,0,0 ], [ -1,+1, -1 ], [-1,+1,0 ] ],

 [ [0, 1,0 ], [ -1 ,+1 , 1 ], [ -1 , + 1 , 0 ] ],
 [ [0,-1,0 ], [  1 ,-1 , 1 ], [  1 , - 1 , 0 ] ],
 ]
make_TDS_SubVolume.outputname = 'subvolume_'

prefix of output file, example outputname=”subvolume_”