# Engineering

**URL:** https://discourse.itk.org/c/engineering/6.md?page=8

[Latest](https://discourse.itk.org/latest.md) · [Categories](https://discourse.itk.org/categories.md) · [Tags](https://discourse.itk.org/tags.md)

**Page:** 9

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## [GetImageViewFromArray in SimpleITK](https://discourse.itk.org/t/getimageviewfromarray-in-simpleitk/4436)

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**Author:** [@rogertrullo](https://discourse.itk.org/u/rogertrullo)\
**Replies:** 7\
**Last updated:** [September 22, 2021, 2:03pm UTC](https://discourse.itk.org/t/getimageviewfromarray-in-simpleitk/4436 "2021-09-22T14:03:22Z")

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Hi all, I am using Simpleitk and it seems that there is no GetImageViewFromArray funciton. I have the GetArrayViewFromImage function though. Is there any reason on why is this function not available? When I do GetImageF…

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## [AffineGeometryFrame class is removed as part of migration from v4 to v5](https://discourse.itk.org/t/affinegeometryframe-class-is-removed-as-part-of-migration-from-v4-to-v5/4433)

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**Author:** [@Mahesh\_Timmanagoudar](https://discourse.itk.org/u/Mahesh_Timmanagoudar)\
**Replies:** 3\
**Last updated:** [September 20, 2021, 3:24pm UTC](https://discourse.itk.org/t/affinegeometryframe-class-is-removed-as-part-of-migration-from-v4-to-v5/4433 "2021-09-20T15:24:24Z")

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I need that transform on its own. How can i make use of AffineGeometryFrame class functionalities in new ITK version (v5). I have debugged below things. typedef itk::TubeSpatialObject\< Dimension \> TubeType; typename Tu…

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## [ITK not loading NRRD files any more](https://discourse.itk.org/t/itk-not-loading-nrrd-files-any-more/4224)

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**Author:** [@Fijoy\_Vadakkumpadan](https://discourse.itk.org/u/Fijoy_Vadakkumpadan)\
**Replies:** 12\
**Last updated:** [September 17, 2021, 2:54pm UTC](https://discourse.itk.org/t/itk-not-loading-nrrd-files-any-more/4224 "2021-09-17T14:54:29Z")

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Hello, Does ITK no longer fully support NRRD files? I’m trying to upgrade the ITK version in my application from 4.10.1 to 5.1.1. Unfortunately, the new ITK version is throwing a floating point exception when attemptin…

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## [ITKCudaCommon automatic linking error](https://discourse.itk.org/t/itkcudacommon-automatic-linking-error/4418)

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**Author:** [@Gabriele\_Belotti](https://discourse.itk.org/u/Gabriele_Belotti)\
**Replies:** 1\
**Last updated:** [September 14, 2021, 9:55am UTC](https://discourse.itk.org/t/itkcudacommon-automatic-linking-error/4418 "2021-09-14T09:55:16Z")

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Hi, I’m trying to update a script that was once linked to RTK module directly (around 1.4). I linked against my 5.2 build with only one issue: ITKCudaCommon seems to be referred to without relative path to build\\lib\\Re…

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## [Why to invert the order of the indices between numpy and SimpleITK?](https://discourse.itk.org/t/why-to-invert-the-order-of-the-indices-between-numpy-and-simpleitk/809)

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**Author:** [@Diego\_C](https://discourse.itk.org/u/Diego_C)\
**Replies:** 15\
**Last updated:** [May 31, 2020, 12:46pm UTC](https://discourse.itk.org/t/why-to-invert-the-order-of-the-indices-between-numpy-and-simpleitk/809 "2020-05-31T12:46:35Z")

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HI, Can anyone explain the logic between this: \[image\] This is taken from the SimpleITK Notebooks It states that the order of the indices is the opposite in numpy. But in fact this is an arbitrary choice. For instanc…

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## [Thread safety of itk::ObjectFactoryBase::Initialize()](https://discourse.itk.org/t/thread-safety-of-itk-initialize/4404)

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**Author:** [@seanm](https://discourse.itk.org/u/seanm)\
**Replies:** 7\
**Last updated:** [September 9, 2021, 8:38pm UTC](https://discourse.itk.org/t/thread-safety-of-itk-initialize/4404 "2021-09-09T20:38:38Z")

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Hi all, In testing my own app with clang thread sanitizer (TSan) I hit a race condition with ITK. I reduced it to many threads running this code: typedef itk::Image\<float, 2\> MyTypedef; MyTypedef::New(); The issue is…

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## [No such module: "MinimalPathExtraction"](https://discourse.itk.org/t/no-such-module-minimalpathextraction/4393)

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**Author:** [@Mahesh\_Timmanagoudar](https://discourse.itk.org/u/Mahesh_Timmanagoudar)\
**Replies:** 8\
**Last updated:** [September 3, 2021, 11:50am UTC](https://discourse.itk.org/t/no-such-module-minimalpathextraction/4393 "2021-09-03T11:50:50Z")

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– Configuring extension directory: TubeTK – Checking EXTENSION\_NAME variable – Checking EXTENSION\_NAME variable - TubeTK – Configuring Launcher script – Configuring Launcher script - ok \[windows\] – Configuring SEM C…

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## [Vector Image To Image of Vectors](https://discourse.itk.org/t/vector-image-to-image-of-vectors/4385)

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**Author:** [@Tom\_Birdsong](https://discourse.itk.org/u/Tom_Birdsong)\
**Replies:** 4\
**Last updated:** [August 30, 2021, 9:51pm UTC](https://discourse.itk.org/t/vector-image-to-image-of-vectors/4385 "2021-08-30T21:51:09Z")

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Hi all, In discussion on the ITKStrain remote module we recently encountered a question of handling vector-valued image data in the ITK Python wrapping. I’ve worked with itk.VectorImage and itk.Image\[itk.Vector\[t,d\],d\] …

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## [GetGDCMSeriesFileNames: ordering of the returned files](https://discourse.itk.org/t/getgdcmseriesfilenames-ordering-of-the-returned-files/4369)

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**Author:** [@KrisHan999](https://discourse.itk.org/u/KrisHan999)\
**Replies:** 3\
**Last updated:** [August 26, 2021, 11:49pm UTC](https://discourse.itk.org/t/getgdcmseriesfilenames-ordering-of-the-returned-files/4369 "2021-08-26T23:49:43Z")

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Same as the title, I had a CT series, after running the ‘GetGDCMSeriesFileNames’, the files were returned according to the file name, instead of the z coordinates. I just wonder, how the files are ordered in function ‘Ge…

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## [Upgrade from 413 to 512 and vnl](https://discourse.itk.org/t/upgrade-from-413-to-512-and-vnl/4370)

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**Author:** [@rfrank](https://discourse.itk.org/u/rfrank)\
**Replies:** 3\
**Last updated:** [August 26, 2021, 8:10pm UTC](https://discourse.itk.org/t/upgrade-from-413-to-512-and-vnl/4370 "2021-08-26T20:10:36Z")

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I’m trying to upgrade an existing project that uses vnl directly for some matrix computations. for instance vnl\_vector\_fixed\<float, 4\> temp; loat ctr4\[4\] = {(float) ctr\[0\],(float)ctr\[1\],(float)ctr\[2\],1.0f }; temp.set(c…

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## [BGFDG\_vtkMRMLModelNodeH.vtp does not contain coordinate system information. Assuming LPS](https://discourse.itk.org/t/bgfdg-vtkmrmlmodelnodeh-vtp-does-not-contain-coordinate-system-information-assuming-lps/4342)

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**Author:** [@Mahesh\_Timmanagoudar](https://discourse.itk.org/u/Mahesh_Timmanagoudar)\
**Replies:** 1\
**Last updated:** [August 19, 2021, 2:21pm UTC](https://discourse.itk.org/t/bgfdg-vtkmrmlmodelnodeh-vtp-does-not-contain-coordinate-system-information-assuming-lps/4342 "2021-08-19T14:21:00Z")

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Centerline.tre file created correctly. But there is no points in BranchCenterline\_0.fcsv file. We got message in log that is “BGFDG\_vtkMRMLModelNodeH.vtp does not contain coordinate system information” . I have atta…

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## [SimpleITK wrong Resampling](https://discourse.itk.org/t/simpleitk-wrong-resampling/4333)

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**Author:** [@machadoL](https://discourse.itk.org/u/machadoL)\
**Replies:** 1\
**Last updated:** [August 15, 2021, 5:48pm UTC](https://discourse.itk.org/t/simpleitk-wrong-resampling/4333 "2021-08-15T17:48:47Z")

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Guys, I need help reviewing this code. I am trying to resample a MRI FLAIR image in to a 1mm x 1mm x 1mm space, and then resample that image’s label according to the resampled image. Everything sound ok, BUT the result …

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## [How to delete points in a tube spatial object?](https://discourse.itk.org/t/how-to-delete-points-in-a-tube-spatial-object/4322)

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**Author:** [@Mahesh\_Timmanagoudar](https://discourse.itk.org/u/Mahesh_Timmanagoudar)\
**Replies:** 4\
**Last updated:** [August 11, 2021, 8:18pm UTC](https://discourse.itk.org/t/how-to-delete-points-in-a-tube-spatial-object/4322 "2021-08-11T20:18:30Z")

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Graft Plan Log.txt (12.6 KB) I have changed as per the following link. Spatial Objects Refactoring section of the ITK 5 Migration Guide. I got run time error while executing below code. /\*\* Remove duplicate points \*/…

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## ['SetSpacing': is not a member of 'itk::VesselTubeSpatialObject\<2\>'](https://discourse.itk.org/t/setspacing-is-not-a-member-of-itk-vesseltubespatialobject-2/4294)

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**Author:** [@Mahesh\_Timmanagoudar](https://discourse.itk.org/u/Mahesh_Timmanagoudar)\
**Replies:** 1\
**Last updated:** [August 2, 2021, 3:23pm UTC](https://discourse.itk.org/t/setspacing-is-not-a-member-of-itk-vesseltubespatialobject-2/4294 "2021-08-02T15:23:48Z")

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Error C2039 ‘SetSpacing’: is not a member of ‘itk::VesselTubeSpatialObject\<2\>’ \[D:\\W4-rel\\S-bld\\Slicer-build\\E\\TubeTK\\Applications\\SegmentTubeUsingMinimalPath\\SegmentTubeUsingMinimalPathLib.vcxproj\] Slicer D:\\W4\\S-rel\\S-…

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## [Possible to compile against a conda install ITK?](https://discourse.itk.org/t/possible-to-compile-against-a-conda-install-itk/4319)

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**Author:** [@imikejackson](https://discourse.itk.org/u/imikejackson)\
**Replies:** 4\
**Last updated:** [August 6, 2021, 6:18pm UTC](https://discourse.itk.org/t/possible-to-compile-against-a-conda-install-itk/4319 "2021-08-06T18:18:02Z")

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I have installed ITK 5.0 using conda install libitk libitk-devel I’m now trying to compile a c++ code against that version of ITK but I get: In file included from /opt/local/anaconda3/envs/dream3d/include/ITK-5.0/itkIm…

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## [GPU support in Python packages](https://discourse.itk.org/t/gpu-support-in-python-packages/4267)

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**Author:** [@zhuangming.shen](https://discourse.itk.org/u/zhuangming.shen)\
**Replies:** 1\
**Last updated:** [July 14, 2021, 2:21pm UTC](https://discourse.itk.org/t/gpu-support-in-python-packages/4267 "2021-07-14T14:21:49Z")

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Hi @matt.mccormick, is the python-supported ITK+GPU available in ITK 4.13.3 ? Thanks in advance.

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## [New at master branch: itk::MakePoint, itk::MakeVector, itk::MakeIndex, itk::MakeSize](https://discourse.itk.org/t/new-at-master-branch-itk-makepoint-itk-makevector-itk-makeindex-itk-makesize/4260)

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**Author:** [@Niels\_Dekker](https://discourse.itk.org/u/Niels_Dekker)\
**Replies:** 1\
**Last updated:** [July 13, 2021, 5:56pm UTC](https://discourse.itk.org/t/new-at-master-branch-itk-makepoint-itk-makevector-itk-makeindex-itk-makesize/4260 "2021-07-13T17:56:09Z")

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Four little convenience function templates are just added to the ITK “master” branch, to ease the creation of an itk::Point, an itk::Vector, an itk::Index, and an itk::Size, after review by @dzenanz, @blowekamp, and @Lee…

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## [External Module: bypass ITKData](https://discourse.itk.org/t/external-module-bypass-itkdata/4202)

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**Author:** [@LucasGandel](https://discourse.itk.org/u/LucasGandel)\
**Replies:** 7\
**Last updated:** [July 12, 2021, 10:28am UTC](https://discourse.itk.org/t/external-module-bypass-itkdata/4202 "2021-07-12T10:28:13Z")

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Hi all, I’d like to propose a patch to allow external modules to skip the creation of the ITKData target. We might want to discuss this here first. The use case is that RTK embeds another external module internally: IT…

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## [readImageFile - webworker generation](https://discourse.itk.org/t/readimagefile-webworker-generation/4249)

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**Author:** [@sam](https://discourse.itk.org/u/sam)\
**Replies:** 0\
**Last updated:** [July 7, 2021, 10:16am UTC](https://discourse.itk.org/t/readimagefile-webworker-generation/4249 "2021-07-07T10:16:11Z")

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Hello everyone, I work on an application that allows to read medical images (DICOM format) and I use a itk js (readImageFile) that allows to read these images but that returns a webworker to each image read the problem i…

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## [ITK in production](https://discourse.itk.org/t/itk-in-production/4226)

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**Author:** [@Stephan\_Hahn1](https://discourse.itk.org/u/Stephan_Hahn1)\
**Replies:** 4\
**Last updated:** [July 6, 2021, 4:38pm UTC](https://discourse.itk.org/t/itk-in-production/4226 "2021-07-06T16:38:45Z")

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Hi everyone I would like to start a discussion concerning deployment of a ITK pipeline in production. How do you deploy your ITK pipeline to scale, parallelize, automatize jobs/tasks? I am doing segmentation using a p…

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## [SimpleITK: Using TransformPoint() to Transform Mask Vertices](https://discourse.itk.org/t/simpleitk-using-transformpoint-to-transform-mask-vertices/4244)

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**Author:** [@bbikdash](https://discourse.itk.org/u/bbikdash)\
**Replies:** 2\
**Last updated:** [July 6, 2021, 3:23pm UTC](https://discourse.itk.org/t/simpleitk-using-transformpoint-to-transform-mask-vertices/4244 "2021-07-06T15:23:13Z")

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Hello, I have a similar problem as the OP here but I’m attempting to use the TransformPoint() function from SimpleITK with a DisplacementFieldTransform instead of an affine transform. Problem I have a moving image with…

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## [SimpleITK Transform.TransformPoint() does not accept variables by reference?](https://discourse.itk.org/t/simpleitk-transform-transformpoint-does-not-accept-variables-by-reference/4238)

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**Author:** [@bbikdash](https://discourse.itk.org/u/bbikdash)\
**Replies:** 1\
**Last updated:** [July 1, 2021, 8:06pm UTC](https://discourse.itk.org/t/simpleitk-transform-transformpoint-does-not-accept-variables-by-reference/4238 "2021-07-01T20:06:12Z")

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Hello, I’m trying to apply a Displacement Field Transform to a point using the Transform.TransformPoint(). I’ve been following the example on this webpage: 21\_Transforms\_and\_Resampling I currently have a M \\cdot 2 nump…

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## [May we start using C++14 at the master branch?](https://discourse.itk.org/t/may-we-start-using-c-14-at-the-master-branch/4172)

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**Author:** [@Niels\_Dekker](https://discourse.itk.org/u/Niels_Dekker)\
**Replies:** 24\
**Last updated:** [June 9, 2021, 3:34pm UTC](https://discourse.itk.org/t/may-we-start-using-c-14-at-the-master-branch/4172 "2021-06-09T15:34:27Z")

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Now that ITK 5.2 is released, may we start using C++14 features at the master branch of ITK? It is now more than three years ago that ITK (master) moved from C++98/ C++03 to C++11: Obviously it’s a much smaller step …

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## [Difficulties installing ITK4.10.0 as rusage be no longer used](https://discourse.itk.org/t/difficulties-installing-itk4-10-0-as-rusage-be-no-longer-used/4166)

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**Author:** [@mausam](https://discourse.itk.org/u/mausam)\
**Replies:** 1\
**Last updated:** [May 28, 2021, 2:43pm UTC](https://discourse.itk.org/t/difficulties-installing-itk4-10-0-as-rusage-be-no-longer-used/4166 "2021-05-28T14:43:25Z")

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I am trying to install itk4.10.0 version, However, I am getting the following error. I have attempted to google the answer but have not found anything. Any and all help would be very much appreciated! \*\*InsightToolkit-4…

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## [How to distribute both debug and release binaries (windows)](https://discourse.itk.org/t/how-to-distribute-both-debug-and-release-binaries-windows/4139)

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**Author:** [@sullivak](https://discourse.itk.org/u/sullivak)\
**Replies:** 4\
**Last updated:** [May 21, 2021, 2:52pm UTC](https://discourse.itk.org/t/how-to-distribute-both-debug-and-release-binaries-windows/4139 "2021-05-21T14:52:48Z")

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What I would like to do is build ITK once, and then each member of the team can just copy the built version for building our projects linking to ITK, rather than everyone building locally. However I have not been able to…

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## [error building v5.1.1 for Mac Big Sur 11.2.3](https://discourse.itk.org/t/error-building-v5-1-1-for-mac-big-sur-11-2-3/3959)

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**Author:** [@Christian](https://discourse.itk.org/u/Christian)\
**Replies:** 7\
**Last updated:** [May 19, 2021, 2:56pm UTC](https://discourse.itk.org/t/error-building-v5-1-1-for-mac-big-sur-11-2-3/3959 "2021-05-19T14:56:30Z")

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Hi Guys, I am getting this error when trying to build (I used the option Module\_ITKVtkGlue=ON) and make v5.1.1 for Mac Big Sur 11.2.3. \[ 40%\] Building CXX object Modules/Core/Common/src/CMakeFiles/ITKCommon.dir/itkFloa…

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## [How to slim down ITK install based on required functions?](https://discourse.itk.org/t/how-to-slim-down-itk-install-based-on-required-functions/4134)

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**Author:** [@AshishUthama](https://discourse.itk.org/u/AshishUthama)\
**Replies:** 10\
**Last updated:** [May 17, 2021, 6:12pm UTC](https://discourse.itk.org/t/how-to-slim-down-itk-install-based-on-required-functions/4134 "2021-05-17T18:12:19Z")

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Hi I am trying to build ITK WITHOUT any of the IO modules. I cant seem to figure out the required cmake switches to do this. Lets say I only need registration functions: -DITKGroup\_Registration:BOOL=ON -DITK\_BUILD\_D…

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## [ITK 5.2.0 with system HDF5 - condaforge](https://discourse.itk.org/t/itk-5-2-0-with-system-hdf5-condaforge/4130)

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**Author:** [@blowekamp](https://discourse.itk.org/u/blowekamp)\
**Replies:** 3\
**Last updated:** [May 14, 2021, 1:03pm UTC](https://discourse.itk.org/t/itk-5-2-0-with-system-hdf5-condaforge/4130 "2021-05-14T13:03:45Z")

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Hello, I am working on updating the conda-forge libitk package for ITK 5.2.0. The package uses the condo-forge hdf5 library instead of the ITK’s thirdparty HDF5 module. The compilation of ITK is fine. But when testing …

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## [File format for general-purpose medical image computing](https://discourse.itk.org/t/file-format-for-general-purpose-medical-image-computing/4067)

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**Author:** [@lassoan](https://discourse.itk.org/u/lassoan)\
**Replies:** 17\
**Last updated:** [May 7, 2021, 11:21am UTC](https://discourse.itk.org/t/file-format-for-general-purpose-medical-image-computing/4067 "2021-05-07T11:21:20Z")

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We encounter so many issues due to redundancies and inconsistencies within the nifti file format. Am I alone with being frustrated by this? I try to educate users one by one to not use nifti except for brain imaging, but…

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## [is gcc supported only](https://discourse.itk.org/t/is-gcc-supported-only/4098)

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**Author:** [@hfeng](https://discourse.itk.org/u/hfeng)\
**Replies:** 4\
**Last updated:** [May 5, 2021, 1:11pm UTC](https://discourse.itk.org/t/is-gcc-supported-only/4098 "2021-05-05T13:11:34Z")

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itk 5.1.2 is installed. In a generated file itk\_compiler\_detection.h, i saw a few lines: if ITK\_COMPILER\_IS\_GNU include “compilers/ITK\_COMPILER\_INFO\_GNU\_CXX.h” else error Unsupported compiler endif Does this mean only G…

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