Transform_geometry_v3

!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

$``: Input file: metadata, stack, volume or image. $-o, --output <output_file> $`--oroot <root`>

Transformations $``: Perform rotation where <rotation_type> can be:

• • $``: Perform scaling All types of scaling produces a resize of images, exceptfactor where <scale_type> can be:
  • $--shift <x> <y0> <z=0> $``: Flip images, only valid for 2D

Other options $--interp <interpolation_typespline> where <interpolation_type> can be:

• • $: Apply inverse transformations $: By default, the original images are preserved and the alignment information is stored in metadata $: By default, the image/volume is wrapped $: 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

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