Xmipp

xmipp_image_vectorize (v3.0)

Usage

Convert an image/volume to data and viceversa. Data is the file format used by KerDenSOM and other classification programs

Parameters

-i <file>
If Image->Vector: Input Single image/volume/stack or selfile If Vector->Image: Input Vector metadata
-o <file>
If Image->Vector: Output vector metadata If Vector->Image: Output stack
--mask <mask_type=circular>
Extract pixel values from a 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

Produce vectors from images or volumes
xmipp_image_vectorize -i projections.sel -o vectors.xmd
Produce images from vectors
xmipp_image_vectorize -i vectors.xmd -o images.stk
Produce vectors from images or volumes with a mask
xmipp_image_vectorize -i projections.sel -o vectors.xmd --mask circular -16
Produce images from vectors that were defined using a mask
xmipp_image_vectorize -i vectors.xmd -o images.stk --mask circular -16

User's comments

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