Transform_mask_v31

!xmipp_transform_mask (v3.1)

Usage

Create or Apply a mask. Count pixels/voxels within a mask

You do not need to give the dimensions of the mask but you simply provide an example of image/volume you are going to apply the mask to, then the dimensions are taken from this file and the mask is created. In the creation of the mask, a file with the mask is written to disk but it is not applied to the input file.

You can generate blank images/volumes with the size of the sample one if you do not supply any mask type.You may also apply masks without having to generate the corresponding files (but you also can save them)

This utility also allows you to count the number of pixels/voxels in an image/volume which are inside a given mask and whose value is below|above or both some threshold.

See here for more information about the program.

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. $--mask <mask_typecircular>

    where <mask_type> can be:

• • 2D or 3D sincs if w > 0> outside sinc if w < 0 => inside sinc -m &lt;blob_order2> $-a <blob_alpha10.4> $--center <x00> <y0=0> <z0=0> $: Don't apply and save mask $: Voxels within mask >= th $``: Voxels within mask &lt;= th $--substitute <val0>

Examples and notes

Sample at circular mask inside radius 72:

xmipp_transform_mask  -i reference.vol -o output_volume.vol --mask circular -72

As above but save mask:

xmipp_transform_mask  -i reference.vol --create_mask  output_mask.vol --mask circular -25

Mask and overwrite a selection file:

xmipp_transform_mask  -i t7_10.sel --mask circular -72

Mask using rectangular mask:

xmipp_transform_mask -i singleImage.spi -o salida20.spi --mask rectangular -10 -10

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