Xmipp

xmipp_image_statistics (v3.0)

Usage

Display statistics of 2D/3Dimages. A mask can be applied. Average Images may be computed All images must have same size Mask is ignored for this operation
NOTE
Geometry will NOT be applied to volumes even if apply_geo flag is on

Parameters

-i, --input <input_file>
Input file: metadata, stack, volume or image.
--mode <mode=overwrite>
Metadata writing mode.
where <mode> can be:
  • overwrite Replace the content of the file with the Metadata
  • append Write the Metadata as a new block, removing the old one
--dont_apply_geo
for 2D-images: do not apply transformation stored in the header
-o <metadata>
Save the statistics in this metadata file.
--short_format
Do not show labels for statistics.
--show_angles
Also show angles in the image header.
--save_mask <maskFileName>
Save 2D and 3D masks.
--save_image_stats <statFilename>
Save average and standard deviation images
--mask <mask_type=circular>
Statistics restricted 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

User's comments

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