plot maps in three panels

[zaharko]

• [x] 1. plot data panel
  • [x] a. Increase the area for plotting maps for both hdf and ccl (increase horizontal and vertical axes by about 25%)
  • [x] b. ccl data:
  • [x] b1. skip labeling, axes for the orthogonal coordinate system
  • [x] b2. introduce hkl labels when mouse is clicked at(near) the hkl position from measured ccl or calculated hkl/mhkl files
  • [x] b3. switch off/on legend with displayed ccl files, k-vectors
  • [x] c. hdf data:
  • [ ] c1. ~adopt the change of the 'in-plane X' and 'normal' directions to the user defined ones~ ~For this three value should be changed in teh cell 3 of Camilla's code~ ~##x_dir should be changed to 'in-plane X'~ ~x_dir = [1,1,0]~ ~##orth_dir should be changed to 'normal'~ ~orth_dir = [-1,1,0]~ ~##and orth_cut should be changed to 'cut'~ ~orth_cut = 0.0~
  • [x] c2. add colorbar
  • [x] c3. add log scale intensity option
  • [x] c4. correct plot of the hkl/mhkl positions
• [x] 2. ccl prepare panel
  • [x] a. Increase the area for plotting maps for ccl (increase horizontal and vertical axes by about 25%)
  • [x] b. skip labeling, axes for the orthogonal coordinate system
  • [x] c. introduce hkl labels when mouse is clicked at(near) the hkl position from calculated hkl/mhkl files
• [x] 3. hdf viewer panel
  • [x] a. Increase the area for plotting maps for hdf (increase horizontal and vertical axes by about 20%)
  • [x] b. add log scale intensity option (the option would apply log scale generally on the panel, i.e. to both projections and frame plots)

[ivan-usov]

There is a problem with the logarithmic color mapping, namely, it can't include 0 values in data as it refers to -infinity on the axis. Unfortunately, the 2D detector data almost always includes 0 values (as background). Thus, we can't include it as it is.

There are a few workaround possibilities, but none of them are perfect. In fact, many argue that count data should not be log-transformed: https://www.nature.com/articles/npre.2010.4136.1

I'll hold this change for now.

[zaharko]

Hi Ivan,

Could we change zeroes into the small number C for which log can be taken and plot the data shifted by C? This might be strictly speaking not the correct solution, but it will serve the purpose to see a weak signal on top of a significant background.

Thank you Oksana

On 15 Feb 2023, at 16:07, Ivan Usov @.**@.>> wrote:

There is a problem with the logarithmic color mapping, namely, it can't include 0 values in data as it refers to -infinity on the axis. Unfortunately, the 2D detector data almost always includes 0 values (as background). Thus, we can't include it as it is.

There are a few workaround possibilities, but none of them are perfect. In fact, many argue that count data should not be log-transformed: https://www.nature.com/articles/npre.2010.4136.1

I'll hold this change for now.

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