Transform_filter_v31

!xmipp_transform_filter (v3.1)

Usage

Apply different type of filters to images or volumes.

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.

Fourier $``: Filter in Fourier space where <filter_type> can be:

• • $`` ( requires --fourier ): If provided pass frequencies are taken in Ang $--save <filename>

Wavelet $--wavelet, -w <DWT_typeDAUB12> <mode=remove_scale> where <DWT_type> can be:

• • where <mode> can be:
  • $--scale <s0> $--output_scale <s0> $--th <th50> $-R <r-1> $``: Select if the noise is white. Used by Bayesian filter.

Bad pixels $``: Applied filters on bad pixels of the image. where <type> can be:

Anisotropic diffusion $``: Use anisotropic diffusion filter. $--shah_iter <outer10> <inner=1> <refinement=1> $`--shah_weight <w0`0> <w1=50> <w2=50> <w3=0.02> = ( requires --diffusion ): Diffusion weights w0` data matching w1 = 1st derivative smooth w2 = edge strength w3 = edge smoothness` ( requires --diffusion ): Produce the edge image of the diffusion

Mean shift $--mean_shift, -t <hr> <hs> <iter1> $--thr <n1> $: Use faster processing (avoid gaussian calculations) $: Save result image/volume for each iteration

Background removal $--background, -g <typeplane> where <type> can be:

Median $``: Use median filter.

Basis filter $--basis <file> <N-1>

Log filter (for scanners) uses equation fa-fb*log(x+fc) $: $: $: $:

Examples and notes

Filter a volume using a maskvolumeMask.volto remove bad pixels:

xmipp_transform_filter -i volume.vol -o volumeFiltered1.vol --bad_pixels mask volumeMask.vol

Remove extreme pixels:

xmipp_transform_filter -i volume.vol  -o volumeFiltered2.vol --bad_pixels outliers 0.5

Apply a Fourier filter on a volume:

xmipp_transform_filter -i volume.vol -o volumeFiltered.vol --fourier low_pass 0.05
xmipp_transform_filter  -i volume.vol -o volumeFiltered.vol -f band_pass 0.1 0.3
xmipp_transform_filter  -i image.ser  -o imageFiltered.xmp --background plane
xmipp_transform_filter  -i smallStack.stk -o smallFiltered.stk -w DAUB12 difussion

Filter a volume using a wedge mask rotated 10 degress

xmipp_transform_filter  --fourier wedge  -60 60 0 0 10 -i ico.spi -o kk0.spi --verbose

Save filtering mask (do not filter)

xmipp_transform_filter  --fourier wedge  -60 60 0 0 10 -i ico.spi -o kk0.spi --verbose --save mask.spi

Preprocess image optained in the nikon coolscan

xmipp_transform_filter  --log  -i ico.spi -o kk0.spi --fa 4.431 --fb 0.4018 --fc 336.6

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