ImageJ

This page provides user documentation for the Format category of the CIP scripting package.

One can found additionnal information on the function parameters (type, optionnal/required, positionnal/named) on the parameters documentation page.

to acess another category of CIP functions: Format, Filter, Math, Segment, Assess, Experimental.

create

Description
this function allows to create image specifying their size, value, pixel type and name.

Signatures

    outputImage = cip.create( size*, value, type, name)
    will create an image of size extent initialized with the specified value, pixel type and name.

    outputImage = cip.create( inputImage*, value, type, name)
    will create an image of the same size as inputImage, initialized with the specified value, pixel type and name.

Input
    inputImage* : an image which size will be used to create an the image process
    size* : a list of scalars specifying the dimensions of the image to create
    value : value a scalar which value is used to initialize the new image
    type : a string in {'bit', 'uint8', 'int8', 'uint16', 'int16', 'uint32', 'int32', 'uint64', 'int64', 'float', 'double'} defining the pixel type of the output. denomination such as 'short' or 'ushort' or 'unsignedshort' can also be used.
    name : a string used for the new image name.

Output
    outputImage : an image with the specified size, value, pixel type and name.

Implementation
the function wraps the ops img function in the namespace create

duplicate

Description
The function duplicate an input image or a crop if the input image

Signature
    outputImage = cip.duplicate( inputImage*, origin, size, method)
    will duplicate the input image within the specified boundary.

Input
    inputImage* : the image to duplicate
    origin : a list of scalar specifying the origin of the region to duplicate. if not provided the input image origin is used
    size : a list of scalar specifying the extent of the region to duplicate. if not provided the max minus the origin is choosen for each dimension
    method : a string in {'deep', 'shallow'} specifying whether the output will copy the data or have a reference to the input data.

Output
    outputImage* : the duplicated image

Example
    img2 = cip.duplicate( img1 , 'origin', [300,200], 'size', [150,150] )

Implementation
the shallow copy is done with Views.offsetInterval in ImgLib2 and the deep copy is done with the ops function copy().rai().

slice

Description
This function reduce input image dimensionality by duplicating a region of the same size as the input except along a selected dimension where the input is duplicated only at a particular position.

Signature
    outputImage = cip.slice( inputImage*, dimension, position, method)
    will duplicate the input at the specified position along the specified dimension(s).

Input
    inputImage* : the image to process
    dimension : a scalar or a list of scalars specifying the dimension(s) to slice
    position : a scalar or list of scalars the same size as dimensions indicating the position to duplicate along the specified dimension(s).
    method : a string in {'deep', 'shallow'} specifying whether the output will copy the data or have a reference to the input data.

Output
    outputImage* : the duplicated image. The singleton dimension(s) are dropped so the image dimensionnality is effectively smaller than the input dimensionnality.

Example
    img2 = cip.slice( img1 , 'dimension', 2, 'position', 0 )

Implementation
The shallow copy is done with Views.offsetInterval in ImgLib2 and the deep copy also apply the ops function copy().rai().

project

Description
This function reduce input image dimensionality by applying an operation to all the pixel along user specified dimension(s). sum, max and ,min operation are currently implemented.

Signature
    valMap, argMap = cip.project( inputImage*, dimension, method, output)
    create a projected image along the specified dimension(s) with the specified method.

Input
    inputImage* : the image to process
    dimensions : a scalar or a list of scalars specifying the dimension(s) to slice
    position : a scalar or list of scalars the same size as dimensions indicating the position to duplicate along the specified dimension(s).
    output : a string in {'projection', 'argument', 'both'} specifying whether the output should be the projected image, the argument of the projection or both. if the argument construction is not applicable the argument has the value of the number of slice.

Output
    valMap : the projected image. The singleton dimension(s) are dropped so the image dimensionnality is effectively smaller than the input dimensionnality.
    argMap : the argument of the projection. that is for a max projection for instance the postions at the pixel value was maximum along the projection dimension.

Example
    img2 = cip.project( img1 , 'dimension',2 )

Implementation
The projection is implemented as part of CIP.

concatenate

To be implemented