Transform_geometry_v31

!xmipp_transform_geometry (v3.1)

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 files will be overwritten. When output param -o is a stack file, associated metadata file is also generated using same rootname. If geometrical transformation are applied, involved labels are reset in output metadata.

Parameters

$``: Input file: metadata, stack, volume or image. $--mode <modeoverwrite> where <mode> can be:

• • $--label <image_labelimage> $-o, --output <output_file> $--oroot <root> $--save_metadata_stack <output_md> $: Store the original image filename in the output metadata in column imageOriginal. $: Preserve the columns from the input metadata. Some of the column values can be changed by the program. $``: for 2D-images: do not apply transformation stored in metadata

Transformations $--rotate <ang0> $``: Rotation of volumes. where <rotation_type> can be:

• • $--scale, -s <factor1> $--shift <x0> <y=0> <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 and notes

Write a metadata with geometrical transformations keeping the reference to original images:

xmipp_transform_geometry -i mD1.xmd --shift 2 3 4 --scale 1.2 --rotate 23 -o newGeo.xmd

Write a metadata with geometrical transformations copying original images to new stack file:

xmipp_transform_geometry -i mD1.xmd --shift 2 3 4 --scale 1.2 --rotate 23 -o newGeo.stk

Apply geometrical transformations to images ,reset involved labels and save in new metadata and stack files:

xmipp_transform_geometry -i mD1.xmd --shift 2 3 4 --scale 1.2 --rotate 23 -o newGeo.xmd --apply_transform

To simply apply the transformations in a metadata to the images:

xmipp_transform_geometry -i mD1.xmd --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.xmd --scale 0.5 -o halvedOriginal.xmd

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