nipype.interfaces.slicer.filtering.arithmetic module

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AddScalarVolumes

Link to code

Bases: SEMLikeCommandLine

Wrapped executable: AddScalarVolumes.

title: Add Scalar Volumes

category: Filtering.Arithmetic

description: Adds two images. Although all image types are supported on input, only signed types are produced. The two images do not have to have the same dimensions.

version: 0.1.0.$Revision: 19608 $(alpha)

documentation-url: http://slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/Add

contributor: Bill Lorensen (GE)

acknowledgements: This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149.

Optional Inputs:

  • args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

  • environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value: {})

  • inputVolume1 (a pathlike object or string representing an existing file) – Input volume 1. Maps to a command-line argument: %s (position: -3).

  • inputVolume2 (a pathlike object or string representing an existing file) – Input volume 2. Maps to a command-line argument: %s (position: -2).

  • order (‘0’ or ‘1’ or ‘2’ or ‘3’) – Interpolation order if two images are in different coordinate frames or have different sampling. Maps to a command-line argument: --order %s.

  • outputVolume (a boolean or a pathlike object or string representing a file) – Volume1 + Volume2. Maps to a command-line argument: %s (position: -1).

Outputs:

outputVolume (a pathlike object or string representing an existing file) – Volume1 + Volume2.

CastScalarVolume

Link to code

Bases: SEMLikeCommandLine

Wrapped executable: CastScalarVolume.

title: Cast Scalar Volume

category: Filtering.Arithmetic

description: Cast a volume to a given data type. Use at your own risk when casting an input volume into a lower precision type! Allows casting to the same type as the input volume.

version: 0.1.0.$Revision: 2104 $(alpha)

documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/Cast

contributor: Nicole Aucoin (SPL, BWH), Ron Kikinis (SPL, BWH)

acknowledgements: This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149.

Optional Inputs:

  • InputVolume (a pathlike object or string representing an existing file) – Input volume, the volume to cast. Maps to a command-line argument: %s (position: -2).

  • OutputVolume (a boolean or a pathlike object or string representing a file) – Output volume, cast to the new type. Maps to a command-line argument: %s (position: -1).

  • args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

  • environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value: {})

  • type (‘Char’ or ‘UnsignedChar’ or ‘Short’ or ‘UnsignedShort’ or ‘Int’ or ‘UnsignedInt’ or ‘Float’ or ‘Double’) – Type for the new output volume. Maps to a command-line argument: --type %s.

Outputs:

OutputVolume (a pathlike object or string representing an existing file) – Output volume, cast to the new type.

MaskScalarVolume

Link to code

Bases: SEMLikeCommandLine

Wrapped executable: MaskScalarVolume.

title: Mask Scalar Volume

category: Filtering.Arithmetic

description: Masks two images. The output image is set to 0 everywhere except where the chosen label from the mask volume is present, at which point it will retain it’s original values. Although all image types are supported on input, only signed types are produced. The two images do not have to have the same dimensions.

version: 0.1.0.$Revision: 8595 $(alpha)

documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/Mask

contributor: Nicole Aucoin (SPL, BWH), Ron Kikinis (SPL, BWH)

acknowledgements: This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149.

Optional Inputs:

  • InputVolume (a pathlike object or string representing an existing file) – Input volume to be masked. Maps to a command-line argument: %s (position: -3).

  • MaskVolume (a pathlike object or string representing an existing file) – Label volume containing the mask. Maps to a command-line argument: %s (position: -2).

  • OutputVolume (a boolean or a pathlike object or string representing a file) – Output volume: Input Volume masked by label value from Mask Volume. Maps to a command-line argument: %s (position: -1).

  • args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

  • environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value: {})

  • label (an integer) – Label value in the Mask Volume to use as the mask. Maps to a command-line argument: --label %d.

  • replace (an integer) – Value to use for the output volume outside of the mask. Maps to a command-line argument: --replace %d.

Outputs:

OutputVolume (a pathlike object or string representing an existing file) – Output volume: Input Volume masked by label value from Mask Volume.

MultiplyScalarVolumes

Link to code

Bases: SEMLikeCommandLine

Wrapped executable: MultiplyScalarVolumes.

title: Multiply Scalar Volumes

category: Filtering.Arithmetic

description: Multiplies two images. Although all image types are supported on input, only signed types are produced. The two images do not have to have the same dimensions.

version: 0.1.0.$Revision: 8595 $(alpha)

documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/Multiply

contributor: Bill Lorensen (GE)

acknowledgements: This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149.

Optional Inputs:

  • args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

  • environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value: {})

  • inputVolume1 (a pathlike object or string representing an existing file) – Input volume 1. Maps to a command-line argument: %s (position: -3).

  • inputVolume2 (a pathlike object or string representing an existing file) – Input volume 2. Maps to a command-line argument: %s (position: -2).

  • order (‘0’ or ‘1’ or ‘2’ or ‘3’) – Interpolation order if two images are in different coordinate frames or have different sampling. Maps to a command-line argument: --order %s.

  • outputVolume (a boolean or a pathlike object or string representing a file) – Volume1 * Volume2. Maps to a command-line argument: %s (position: -1).

Outputs:

outputVolume (a pathlike object or string representing an existing file) – Volume1 * Volume2.

SubtractScalarVolumes

Link to code

Bases: SEMLikeCommandLine

Wrapped executable: SubtractScalarVolumes.

title: Subtract Scalar Volumes

category: Filtering.Arithmetic

description: Subtracts two images. Although all image types are supported on input, only signed types are produced. The two images do not have to have the same dimensions.

version: 0.1.0.$Revision: 19608 $(alpha)

documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/Subtract

contributor: Bill Lorensen (GE)

acknowledgements: This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149.

Optional Inputs:

  • args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

  • environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value: {})

  • inputVolume1 (a pathlike object or string representing an existing file) – Input volume 1. Maps to a command-line argument: %s (position: -3).

  • inputVolume2 (a pathlike object or string representing an existing file) – Input volume 2. Maps to a command-line argument: %s (position: -2).

  • order (‘0’ or ‘1’ or ‘2’ or ‘3’) – Interpolation order if two images are in different coordinate frames or have different sampling. Maps to a command-line argument: --order %s.

  • outputVolume (a boolean or a pathlike object or string representing a file) – Volume1 - Volume2. Maps to a command-line argument: %s (position: -1).

Outputs:

outputVolume (a pathlike object or string representing an existing file) – Volume1 - Volume2.