Image_operate_v31

!xmipp_image_operate (v3.1)

Usage

A simple Xmipp images calculator. Binary and unary operations

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.

Binary operations: $: Sums two images, volumes or adds a numerical value to an image $ or: Substracts two images, volumes or substracts a numerical value to an image $ or: Multiplies two images, volumes, or multiplies per a given number $ or: Divides two images, volumes, or divides per a given number $ or: Minimum of two images, volumes, or number (pixel-wise) $ or: Maximum of two images, volumes, or number (pixel-wise) $ or: Returns -1 if the left value is less, 0 if are equal or 1 if greater.(pixel-wise) $ or: Dot product between two images or volumes

Relational operations: $ or: Returns 1 if the pixels values are equal, 0 otherwise (pixel-wise) $ or: Returns 1 if the pixels values are equal less, 0 otherwise (pixel-wise) $ or: Returns 1 if the pixels values are equal less, 0 otherwise (pixel-wise) $ or: Returns 1 if the pixels values are equal less, 0 otherwise (pixel-wise) $ or: Returns 1 if the pixels values are equal less, 0 otherwise (pixel-wise) $ or: Returns 1 if the pixels values are equal less, 0 otherwise (pixel-wise)

Unary operations: $ or: Computes the natural logarithm of an image $ or: Computes the decimal logarithm of an image $ or: Computes the square root of an image $ or: Computes the absolute value of an image $ or--pow <value2> $ or: Extracts a given slice from a volume $ or: Extracts a given column from a image or volume $ or: Extracts a given row from a image or volume $ or: Compute the radial average of an image $ or``: Set the image to 0

Examples and notes

Sum two volumes and save result

xmipp_image_operate -i volume1.vol --plus volume2.vol -o result.vol

Calculate the log10 of an image called example.xmp and store the resulting one in example_log.xmp

xmipp_image_operate -i example.xmp --log10 -o example_log.xmp

Calculate the square root of a volume called example.vol and store it in expample_sq.vol

xmipp_image_operate -i example.vol --sqrt  -o expample_sq.vol

Extract the slice number 10 of a set of of volumes given in the sel file called volumes.sel. The names of the output images its supposed to be in the selfile images.sel

xmipp_image_operate -i volumes.sel --slice 10 -o images.sel

Sum 5 to every image in images.sel and rewrite the input images

xmipp_image_operate -i images.sel --plus 5

Substract two volumes:

xmipp_image_operate -i volume1.vol --minus volume2.vol -o volume3.vol

Multiply an image by 2 in every pixel:

xmipp_image_operate -i image.xmp --mult 2 -o image2.xmp

Divide 2 by the value of every pixel in the image:

xmipp_image_operate -i 2 -divide image.xmp -o image2.xmp

Rotational average

xmipp_image_operate -i image.xmp -radial_avg -o image.rad

where image.rad is an ascii file for plotting the radial_averaged profile, image.rad.img a radial_averaged image

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