3 d>@sdZddlmZmZmZmZmZmZmZm Z m Z m Z ddl Z GdddeZ GdddeZGdd d eZGd d d eZGd d d eZGdddeZdS)zuAutogenerated file - DO NOT EDIT If you spot a bug, please report it on the mailing list and/or change the generator.) CommandLineCommandLineInputSpecSEMLikeCommandLine TraitedSpecFile Directorytraits isdefinedInputMultiPathOutputMultiPathNc@sxeZdZeddddZejejeddddZej d d d Z ej d d d Z ejddd Z ejddd Zejddd ZdS)DicomToNrrdConverterInputSpeczDirectory holding Dicom seriesTz--inputDicomDirectory %s)descexistsargstrFz(Directory holding the output NRRD formatz--outputDirectory %s) hash_filesr rz Output filename (.nhdr or .nrrd)z--outputVolume %s)r rzIf a gradient magnitude is greater than 0 and less than smallGradientThreshold, then DicomToNrrdConverter will display an error message and quit, unless the useBMatrixGradientDirections option is set.z--smallGradientThreshold %fa4Write the protocol gradients to a file suffixed by '.txt' as they were specified in the procol by multiplying each diffusion gradient direction by the measurement frame. This file is for debugging purposes only, the format is not fixed, and will likely change as debugging of new dicom formats is necessary.z--writeProtocolGradientsFile zMAdjust all the gradients so that the measurement frame is an identity matrix.z--useIdentityMeaseurementFrame zFill the nhdr header with the gradient directions and bvalues computed out of the BMatrix. Only changes behavior for Siemens data.z--useBMatrixGradientDirections N)__name__ __module__ __qualname__rZinputDicomDirectoryrEitherBooloutputDirectoryStr outputVolumeZFloatZsmallGradientThresholdZwriteProtocolGradientsFileZuseIdentityMeaseurementFrameZuseBMatrixGradientDirectionsrrE/tmp/pip-build-7vycvbft/nipype/nipype/interfaces/slicer/converters.pyr s0 r c@seZdZedddZdS)DicomToNrrdConverterOutputSpecz(Directory holding the output NRRD formatT)r rN)rrrrrrrrrr7src@s$eZdZdZeZeZdZddiZ dS)DicomToNrrdConvertera.title: DICOM to NRRD Converter category: Converters description: Converts diffusion weighted MR images in dicom series into Nrrd format for analysis in Slicer. This program has been tested on only a limited subset of DTI dicom formats available from Siemens, GE, and Phillips scanners. Work in progress to support dicom multi-frame data. The program parses dicom header to extract necessary information about measurement frame, diffusion weighting directions, b-values, etc, and write out a nrrd image. For non-diffusion weighted dicom images, it loads in an entire dicom series and writes out a single dicom volume in a .nhdr/.raw pair. version: 0.2.0.$Revision: 916 $(alpha) documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/DicomToNrrdConverter license: https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt contributor: Xiaodong Tao (GE), Vince Magnotta (UIowa), Hans Johnson (UIowa) acknowledgements: This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Additional support for DTI data produced on Philips scanners was contributed by Vincent Magnotta and Hans Johnson at the University of Iowa. zDicomToNrrdConverter rN) rrr__doc__r input_specr output_spec_cmd_outputs_filenamesrrrrr=s rc7@seZdZedAddddZejejedBdddd Zej d d d d ddddddddddddddddddd d!d"d#d$d%d&d'd(d)d*d+d,d-d.d/d0d1d2d3d4d5d6d7d8d9d:d;dd?5Z d@S)COrientScalarVolumeInputSpeczInput volume 1Tz%s)positionr rrFzThe oriented volume)r$rr rZAxialZCoronalZSagittalZRIPZLIPZRSPZLSPZRIAZLIAZRSAZLSAZIRPZILPZSRPZSLPZIRAZILAZSRAZSLAZRPIZLPIZRAIZLAIZRPSZLPSZRASZLASZPRIZPLIZARIZALIZPRSZPLSZARSZALSZIPRZSPRZIARZSARZIPLZSPLZIALZSALZPIRZPSRZAIRZASRZPILZPSLZAILZASLzOrientation choicesz--orientation %s)r rN) rrrrZ inputVolume1rrrrEnumZ orientationrrrrr"Us|r"c@seZdZeddddZdS)OrientScalarVolumeOutputSpecr%zThe oriented volumeT)r$r rNr')rrrrrrrrrr)sr)c@s$eZdZdZeZeZdZddiZ dS)OrientScalarVolumeatitle: Orient Scalar Volume category: Converters description: Orients an output volume. Rearranges the slices in a volume according to the selected orientation. The slices are not interpolated. They are just reordered and/or permuted. The resulting volume will cover the original volume. NOTE: since Slicer takes into account the orientation of a volume, the re-oriented volume will not show any difference from the original volume, To see the difference, save the volume and display it with a system that either ignores the orientation of the image (e.g. Paraview) or displays individual images. version: 0.1.0.$Revision: 19608 $(alpha) documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/OrientImage 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. zOrientScalarVolume rzoutputVolume.niiN) rrrrr"rr)rr r!rrrrr*s r*)rZnipype.interfaces.baserrrrrrrr r r osr rrr"r)r*rrrrs0 "C