ITKResampleImage

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Group (Subgroup)

DREAM3D Review (Registration)

Description

This Filter resamples a single data array, series of images, or series of CTF files according to a transformation file provided by the user. The transformation file is an .hdf5 file that contains information about the transformation. More information can be found here. It is expected that the user will use this Filter after using the ITK Pairwise Registration Filter, although it is possible for the user to construct the transformation hdf5 file elsewhere and use it in this Filter. The transformation file should contain the information about the type of transformation (either rigid, affine or b-spline), along with the fixed parameters (TransformFixedParamters) and learned parameters (TransformParameters). Additionally, the file should contain information about the fixed image direction, origin, size and spacing (resolution).

If the user selects 'Single Data Array' as the Opeartion Mode, the user will be required to set the moving image as an Attribute Array that has somehow been already read in using another filer.

If the user selects 'Series of Images' the user will have to point to a folder on their file system where the moving images are located and where the resampled images should be output to. The images must be somehow numerically ordered, but the user can select a subset of images by selecting the start and end index of the image numbering. The total number of images must equal the total number of transforms (number of HDF5 groups) in the transform HDF5 file specified by the user.

If the user selects 'Series of CTFs' as the Operation mode, it will work similarly as above except instead of resampling images, the CTF files will be resampled and written out to the specified folder.

The transformation used by this filter is the inverse transformation. That is, for each grid point on the fixed image, the transformation indicates which moving image point to put in that location. If there isn't an exact moving point to put in that location, the value is determined by the type of interpolation selected. The transformation Points in the new resampled image that require a pixel outside the original moving image domain will be set to a value of 0.

Parameters

Name Type Description
Operation Mode int Whether to resample a Single Data Array, a Series of Images, or a Series of CTF files
Transform File Name Path Location of HDF5 Transform file that describes the transformation to apply
Interpolation Type int Choose either linear or or nearest-neighbor for the type of interpolation when resampling the image
Output Image File Name Prefix string Choose the prefix for the output file name if 'Series of Images' was selected
Output EBSD File Name Prefix string Chose the prefix for the output EBSD file name if 'Series of CTFs' was selected
Output Path for Resampled Images Path Choose the path for the output images if 'Series of Images' was selected
Output Path for Resampled Orientation Data Path Choose the path for the output images if 'Series of CTFs' was selected

Required Objects

Kind Default Name Type Component Dimensions Description
Moving Image Attribute Array Any The Attribute Array to be resampled if 'Single Data Array' was selected

Created Objects

Kind Default Name Type Component Dimensions Description
Data Container ResampledDataDC Data Container N/A The newly created data container for the resampled image if 'Single Data Array' was selected
Cell Attribute Matrix ResampledDataAM Attribute Matrix N/A The newly created cell attribute matrix for the resampled image if 'Single Data Array' was selected
Image Data ResampledData Attribute Array Same as Moving Image The resampled image data if 'Single Data Array' was selected

Example Pipelines

Please see the description file distributed with this plugin.

DREAM3D Mailing Lists

If you need more help with a filter, please consider asking your question on the DREAM3D Users mailing list: