Xmipp

xmipp_image_histogram (v3.0)

Usage

Calculate histogram from a list of images/volumes

See also
metadata_histogram

Parameters

-i <input_file>
input metadata, image, volume or stack
-o <text_file>
output text file with histogram
--range <m> <M>
range for the histogram, automatic calculated if not provided
--steps <N=100>
number of subdivisions
--norm
normalize histogram
--mask <mask_type=circular>
Histogram constrained to the mask area.
where <mask_type> can be:
  • circular <R> circle/sphere mask if R>0 => outside R if R<0 => inside R
  • DWT_circular <R> <smin> <smax> circle/sphere mask smin and smax define the scales to be kept
  • rectangular <Xrect> <Yrect> <Zrect=-1> 2D or 3D rectangle if X,Y,Z > 0 => outside rectangle if X,Y,Z < 0 => inside rectangle
  • crown <R1> <R2> 2D or 3D crown if R1,R2 > 0 => outside crown if R1,R2 < 0 => inside crown
  • cylinder <R> <H> 2D circle or 3D cylinder if R,H > 0 => outside cylinder if R,H < 0 => inside cylinder
  • cone <theta> 3D cone (parallel to Z) if theta > 0 => outside cone if theta < 0 => inside cone
  • wedge <th0> <thF> 3D missing-wedge mask for data collected between tilting angles th0 and thF (around the Y-axis)
  • binary_file <binary_file> Read from file
--center <x0=0> <y0=0> <z0=0>
mask center

Examples and notes

Create the histogram from an stack setting number of steps to 20
xmipp_histogram -i input/images_some.stk -o hist.txt --steps 20
You can use the hist.txt file with gnuplot to produce graphical histogram After you enter gnuplot terminal you can use:
gnuplot> plot "kk.txt" using 1:2 title "Histogram" with steps

User's comments

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