Transform_window_v3

!xmipp_transform_window (v3.0)

Usage

This program takes a region from the input images

But... what is windowing? Let's suppose we have an image 32x32, and we window it to 16x16, then the central part which contains this 16x16 square is returned, but if we window to 64x64 then the image is kept in the center of the final image and it is padded with 0's until the new size is reached (the padding value may be modified using --pad_value, --corner_pad_value or --average_pad_value).

With this idea in mind of padding or cutting, if you define two logical corners in the input image (the most negative -the top left in an image- and the most positive -bottom right in an image-) you can store the new image or volume generated by windowing with a square box.

Parameters

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

• • $--label <image_labelimage> $-o, --output <output_file> $--oroot <root> $: for 2D-images: do not apply transformation stored in the header $: Windows corners (by default indexes are logical) 2D: 3D: $ or--size <sizeX> <sizeY0> <sizeZ=0> $ or--crop <sizeX> <sizeY0> <sizeZ=0> $`` ( requires --corners ): use physical instead of logical coordinates $--pad <padtypevalue> where <padtype> can be:

Examples and notes

Window a single image to 16x16, overwriting input image

xmipp_transform_window -i g0ta0001.xmp --size 16

Window a single volume to 32x64x64

xmipp_transform_window -i g0ta.vol --size 64 64 32

The same using logical indexes

xmipp_transform_window -i g0ta.vol --corners -32 -32 -16 31 31 15

Note that r0 and rF are not symmetric because the volume is of an even size, if we wanted to get a 33x65x65 volume, the right indexes would be

xmipp_transform_window -i g0ta.vol --corners -32 -32 -16 32 32 16

Reduce the volume by 10 pixels on each direction

xmipp_transform_window -i g0ta.vol --crop 10

Enlarge the volume by 10 pixels on each direction (negative crop)

xmipp_transform_window -i g0ta.vol --crop -10

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