@chauffeur_afni colorbar parameter

AFNI Message Board
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AFNI version info (afni -ver): Precompiled binary macos_13_ARM: Jan 21 2025 (Version AFNI_25.0.00 'Severus Alexander')

Hi all,

I really like @chauffeur_afni and the options for multiple thresholds/overlays. Is there a way to define the lower limits of the colorbar too? Right now, I only managed to set the upper limits and defining e.g. only a positive bar. The lower limit always defaults to 0 (with posbar only). Can this be changed somehow?

Thanks for any hints!
-gregor

2

Hi, Gregor-

Glad you are enjoying @chauffeur_afni!

The colorbar only goes from [-X, X] or [0, X], where X>0.

However, there is a cheating way around this, by defining your own colorbar, and putting 'none' as a value >0. What I mean by that can be seen by comparing these examples (using AFNI Bootcamp data, in ~/AFNI_data6/FT/):

Case of discrete colorbar ranges:

# case AAA: colorbar is 'full' down to zero
@chauffeur_afni                                                              \
    -ulay             FT_anat+orig.                                          \
    -olay             FT_anat+orig.                                          \
    -func_range_perc  95                                                     \
    -prefix           AAA                                                    \
    -pbar_saveim      AAA.cbar.jpg                                           \
    -pbar_posonly                                                            \
    -cbar_ncolors     6                                                      \
    -cbar_topval      ""                                                     \
    -cbar             "1000=yellow 800=cyan 600=rbgyr20_10 400=rbgyr20_08 200=rbgyr20_05 100=rbgyr20_03 0=none"

# case BBB: same cbar as AAA, but clipping out values from <100
@chauffeur_afni                                                              \
    -ulay             FT_anat+orig.                                          \
    -olay             FT_anat+orig.                                          \
    -func_range_perc  95                                                     \
    -prefix           BBB                                                    \
    -pbar_saveim      BBB.cbar.jpg                                           \
    -pbar_posonly                                                            \
    -cbar_ncolors     6                                                      \
    -cbar_topval      ""                                                     \
    -cbar             "1000=yellow 800=cyan 600=rbgyr20_10 400=rbgyr20_08 200=rbgyr20_05 100=none"

The results of the image+cbar for each of those are (just using "sag" view and cbar):

Note that the black/white in the bottom of the "BBB" case is actually empty/void, and you don't see those colors.

Case of smooth/continuous colorbars, where new_cbar_CCC.pal is this short file:

Yellow-Lime-Red-Blue
  1.0 #ffff00
  0.7 limegreen
  0.5 #ff0000
  0.3 #aa00aa
  0.0 #0000ff

and new_cbar_DDD.pal is this short file (the break happens by having exact-zero-color starting as a duplicate of the bottom actual-color range):

Yellow-Lime-Red-Blue-stop
  1.0 #ffff00
  0.7 limegreen
  0.5 #ff0000
  0.3 #aa00aa
  0.2 #0000ff
  0.2 #000000
  0.0 #000000

And then these commands:

@chauffeur_afni                                                              \
    -ulay             FT_anat+orig.                                          \
    -olay             FT_anat+orig.                                          \
    -func_range_perc  95                                                     \
    -prefix           CCC                                                    \
    -pbar_saveim      CCC.cbar.jpg                                           \
    -pbar_posonly                                                            \
    -colorscale_idx_file 01 new_cbar_CCC.pal

@chauffeur_afni                                                              \
    -ulay             FT_anat+orig.                                          \
    -olay             FT_anat+orig.                                          \
    -func_range_perc  95                                                     \
    -prefix           DDD                                                    \
    -pbar_saveim      DDD.cbar.jpg                                           \
    -pbar_posonly                                                            \
    -colorscale_idx_file 02 new_cbar_DDD.pal

... produce:

So, those are a couple of ways you can "fake" having a nonzero lower bound to your cbar. The reason why it is "faking" it is that there still is a zero bound, but it is filled in with emptiness.

--pt

3

Hi paul,

wow, thanks for the quick reply! I thought that something like that should work, but that would've taken me way longer to figure out. Already implemented it, and it looks just as I hoped.

thanks again!
-gregor