Xmipp

xmipp_transform_geometry (v3.0)

Usage

Apply geometric transformations to images. You can shift, rotate and scale a group of images/volumes. By default the geometric transformations will be read from a metadata, if provided. Also, the original images will be preserved if possible, trying to write out transformations to the output metadata. If output is not specified, the original images will be overwritten.

Parameters

-i, --input <input_file>
Input file: metadata, stack, volume or image.
-o, --output <output_file=>
Output file: metadata, stack, volume or image.
--oroot <root=>
Rootname of output individual images. Output image format can be set adding extension after rootname as ":ext".

Transformations

--rotate <rotation_type>
Perform rotation
where <rotation_type> can be:
  • ang <angle> Rotate an image (positive angle values is a clockwise rotation)
  • euler <rot> <tilt> <psi> Rotate with these Euler angles
  • alignZ <x> <y> <z> Align (x,y,z) with Z axis
  • axis <ang> <x=0> <y=0> <z=1> Rotate degrees around (x,y,z)
--scale, -s <scale_type>
Perform scaling All types of scaling produces a resize of images, except factor
where <scale_type> can be:
  • factor <n=1> Scaling factor, 0.5 halves and 2 doubles
  • dim <x> <y=x> <z=x> New x,y and z dimensions
  • fourier <x> <y=x> <thr=1> Use padding/windowing in Fourier Space
  • pyramid <levels=1> Use positive value to expand and negative to reduce
--shift <x> <y=0> <z=0>
Shift by x, y and z
--flip
Flip images, only valid for 2D

Other options

--interp <interpolation_type=spline>
Interpolation type to be used.
where <interpolation_type> can be:
  • spline Use spline interpolation
  • linear Use bilinear/trilinear interpolation
--inverse
Apply inverse transformations
--apply_transform
By default, the original images are preserved and the alignment information is stored in metadata
--dont_wrap
By default, the image/volume is wrapped
--write_matrix
Print transformation matrix to screen

Examples

To simply apply the transformations in a metadata to the images:
   xmipp_transform_geometry -i mD1.doc --apply_transform
Shift a volume by 10, 5 and -10 in x,y and z and dont wrapping
   xmipp_transform_geometry -i a.vol --shift 10 5 -10 -o b.vol --dont_wrap
Scale a group of images to half size, not modifying image dimensions neither original image files
   xmipp_transform_geometry -i images.doc --scale factor 0.5 --oroot halvedOriginal
Scaling (from 128 to 64) using Fourier (this will apply tranformations)
   xmipp_transform_geometry -i images.doc --scale dim 128 --oroot halvedFourierDim
For pyramid scaling(reducing image size 4 times):
   xmipp_transform_geometry -i images.doc --scale pyramid -2 --oroot halvedPyramidDim

User's comments

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