# Development

**URL:** https://discourse.slicer.org/c/dev/5.md?page=125

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

**Page:** 126

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## [Why is master-48 branch divergent from trunk history?](https://discourse.slicer.org/t/why-is-master-48-branch-divergent-from-trunk-history/1336)

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**Author:** [@ihnorton](https://discourse.slicer.org/u/ihnorton)\
**Replies:** 2\
**Last updated:** [October 31, 2017, 7:11pm UTC](https://discourse.slicer.org/t/why-is-master-48-branch-divergent-from-trunk-history/1336 "2017-10-31T19:11:34Z")

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I noticed this when pushing a branch that I had incidentally created from the master-48… This divergence makes tree downloads much larger than necessary, and will make cherry-picks difficult.

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## [Build error on linux](https://discourse.slicer.org/t/build-error-on-linux/1334)

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**Author:** [@gcsharp](https://discourse.slicer.org/u/gcsharp)\
**Replies:** 4\
**Last updated:** [October 31, 2017, 5:40pm UTC](https://discourse.slicer.org/t/build-error-on-linux/1334 "2017-10-31T17:40:02Z")

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Hi, I have a build failure on linux (debian stable, gcc 6.3.0). Fresh build directory, DCMTK fails. Excerpts below. Any idea? -Greg \[ 48%\] Performing configure step for ‘DCMTK’ – Info: C++11 features disabled …

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## [Slice view performance](https://discourse.slicer.org/t/slice-view-performance/1290)

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**Author:** [@adamrankin](https://discourse.slicer.org/u/adamrankin)\
**Replies:** 14\
**Last updated:** [October 27, 2017, 5:36pm UTC](https://discourse.slicer.org/t/slice-view-performance/1290 "2017-10-27T17:36:17Z")

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Hello all, I’m helping someone develop a Guidelet for her research, and I’m running into some very poor performance. We use SlicerIGT to connect to two Plus servers for a combined 2 images and 6 transforms. With some mo…

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## [How to manage and update Slicer dependency forks?](https://discourse.slicer.org/t/how-to-manage-and-update-slicer-dependency-forks/1308)

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**Author:** [@jcfr](https://discourse.slicer.org/u/jcfr)\
**Replies:** 1\
**Last updated:** [October 27, 2017, 4:48pm UTC](https://discourse.slicer.org/t/how-to-manage-and-update-slicer-dependency-forks/1308 "2017-10-27T16:48:01Z")

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It is convenient to have staging area to maintain and test patches that are being contributed back to official repositories. The following wiki page outlines the naming convention for branches pushed to such fork: https…

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## [Solved: Address build error related to overwritten 'setup.cfg'](https://discourse.slicer.org/t/solved-address-build-error-related-to-overwritten-setup-cfg/1231)

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**Author:** [@jcfr](https://discourse.slicer.org/u/jcfr)\
**Replies:** 5\
**Last updated:** [October 26, 2017, 8:46pm UTC](https://discourse.slicer.org/t/solved-address-build-error-related-to-overwritten-setup-cfg/1231 "2017-10-26T20:46:22Z")

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Following r26470, we update the version of setuptools used in Slicer, as a side effect you may get an error like the one reported below. To address the problem cd Slicer-Superbuild/python-setuptools git reset --hard H…

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## [Object address vs Python REPL output](https://discourse.slicer.org/t/object-address-vs-python-repl-output/1270)

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**Author:** [@ihnorton](https://discourse.slicer.org/u/ihnorton)\
**Replies:** 2\
**Last updated:** [October 23, 2017, 8:36pm UTC](https://discourse.slicer.org/t/object-address-vs-python-repl-output/1270 "2017-10-23T20:36:25Z")

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What is the address (0x1307bea10) printed next to the object type below for the “basic” REPL output? I guess it might be the PythonQt temporary for the string return, or maybe the constructor? (clearly the real object ad…

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## [3D Slicer Extension: Is it required to have an API key to contribute an extension?](https://discourse.slicer.org/t/3d-slicer-extension-is-it-required-to-have-an-api-key-to-contribute-an-extension/1256)

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**Author:** [@algohary](https://discourse.slicer.org/u/algohary)\
**Replies:** 1\
**Last updated:** [October 21, 2017, 1:09am UTC](https://discourse.slicer.org/t/3d-slicer-extension-is-it-required-to-have-an-api-key-to-contribute-an-extension/1256 "2017-10-21T01:09:02Z")

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Hi, I am trying to upload a Slicer plugin (Radiomics plugin, Collage, that I developed at Case Western Reserve University) to the Extension Serve. I am contacting you regarding gaining access. I use my email and API key…

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## [Integrating Sequences into Slicer core](https://discourse.slicer.org/t/integrating-sequences-into-slicer-core/744)

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**Author:** [@moselhy](https://discourse.slicer.org/u/moselhy)\
**Replies:** 10\
**Last updated:** [October 19, 2017, 2:47pm UTC](https://discourse.slicer.org/t/integrating-sequences-into-slicer-core/744 "2017-10-19T14:47:44Z")

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Seeing as that Sequences are going to be the new era of browsing through multiple volumes, transforms, etc… I think it would be appropriate to integrate sequences into the core of Slicer without being an optional extensi…

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## [Determining current file name](https://discourse.slicer.org/t/determining-current-file-name/1241)

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**Author:** [@stevenagl12](https://discourse.slicer.org/u/stevenagl12)\
**Replies:** 1\
**Last updated:** [October 18, 2017, 7:03pm UTC](https://discourse.slicer.org/t/determining-current-file-name/1241 "2017-10-18T19:03:46Z")

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I was wondering if someone can create some sort of interface to determine the file name of the image that is currently portrayed within the red scene view. This would help the viewer to determine which file might need to…

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## [Update existent extension on ExtensionManager - Nightly - Linux](https://discourse.slicer.org/t/update-existent-extension-on-extensionmanager-nightly-linux/1220)

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**Author:** [@acsenrafilho](https://discourse.slicer.org/u/acsenrafilho)\
**Replies:** 6\
**Last updated:** [October 13, 2017, 8:47pm UTC](https://discourse.slicer.org/t/update-existent-extension-on-extensionmanager-nightly-linux/1220 "2017-10-13T20:47:03Z")

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Hello, slicers! I am sorry if this a naive question, but I’ve got stuck with my own extension updates inside ExtensionManager. I have been developing new functionalities to my extension (AnomalousFilters https://gith…

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## [vtkSlicerTransformLogic access in CLI module](https://discourse.slicer.org/t/vtkslicertransformlogic-access-in-cli-module/1214)

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**Author:** [@danielbr](https://discourse.slicer.org/u/danielbr)\
**Replies:** 2\
**Last updated:** [October 12, 2017, 7:55pm UTC](https://discourse.slicer.org/t/vtkslicertransformlogic-access-in-cli-module/1214 "2017-10-12T19:55:22Z")

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Having a small issue that is driving me crazy and I can’t figure it out. It is such a simple problem, but I can’t seem to remedy the problem. I am writing a CLI module and need access to the transform module logic. I …

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## [Packaging Requirements for External Toolkit for Automatic Segmentation of Brain Tumor and Lesions in MR Images](https://discourse.slicer.org/t/packaging-requirements-for-external-toolkit-for-automatic-segmentation-of-brain-tumor-and-lesions-in-mr-images/1212)

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**Author:** [@ckuzi001](https://discourse.slicer.org/u/ckuzi001)\
**Replies:** 2\
**Last updated:** [October 12, 2017, 3:42pm UTC](https://discourse.slicer.org/t/packaging-requirements-for-external-toolkit-for-automatic-segmentation-of-brain-tumor-and-lesions-in-mr-images/1212 "2017-10-12T15:42:56Z")

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Hello Everyone, The Old Dominion University (ODU) Vision Lab has been working to develop an external toolkit, scripted with Python, for the purpose of automatic tumor segmentation with 3D-Slicer. Is there a preferred w…

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## [Simplified welcome module](https://discourse.slicer.org/t/simplified-welcome-module/1203)

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**Author:** [@jcfr](https://discourse.slicer.org/u/jcfr)\
**Replies:** 1\
**Last updated:** [October 11, 2017, 2:45am UTC](https://discourse.slicer.org/t/simplified-welcome-module/1203 "2017-10-11T02:45:12Z")

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As discussed during the last Slicer office hour, this commit simplifies the Welcome module. The associated documentation was out of date and a duplicate of what is already available on the wiki. After completing the tra…

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## [NUMPY build errors on mac and linux](https://discourse.slicer.org/t/numpy-build-errors-on-mac-and-linux/1187)

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**Author:** [@pieper](https://discourse.slicer.org/u/pieper)\
**Replies:** 0\
**Last updated:** [October 5, 2017, 8:44pm UTC](https://discourse.slicer.org/t/numpy-build-errors-on-mac-and-linux/1187 "2017-10-05T20:44:09Z")

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I’m seeing NUMPY build errors on both mac and linux. Is anyone else seeing these? https://issues.slicer.org/view.php?id=4452 https://issues.slicer.org/view.php?id=4453

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## [Modification of model's color in a vtkMRMLSequenceNode](https://discourse.slicer.org/t/modification-of-models-color-in-a-vtkmrmlsequencenode/1166)

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**Author:** [@laurapascal](https://discourse.slicer.org/u/laurapascal)\
**Replies:** 6\
**Last updated:** [October 5, 2017, 3:50pm UTC](https://discourse.slicer.org/t/modification-of-models-color-in-a-vtkmrmlsequencenode/1166 "2017-10-05T15:50:18Z")

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Hi everyone! I am trying to create a python scripted module using Sequences extension and I have an issue to modify the color of the models in a sequence: I would like to have different color for each model contained in…

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## [Access to a loadable module from the python console](https://discourse.slicer.org/t/access-to-a-loadable-module-from-the-python-console/1038)

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**Author:** [@laurapascal](https://discourse.slicer.org/u/laurapascal)\
**Replies:** 3\
**Last updated:** [October 3, 2017, 2:53pm UTC](https://discourse.slicer.org/t/access-to-a-loadable-module-from-the-python-console/1038 "2017-10-03T14:53:03Z")

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Hi everyone! I am trying to create a scripted module using Sequences extension. I was wondering if, from the python console, there is a way to use a loadable module in the same way than a CLI (slicer.cli.run(slicer.modu…

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## [Cannot compile Slicer on Mac - macOS Sierra + clang 9 + cmake 3.9.1](https://discourse.slicer.org/t/cannot-compile-slicer-on-mac-macos-sierra-clang-9-cmake-3-9-1/1104)

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**Author:** [@fedorov](https://discourse.slicer.org/u/fedorov)\
**Replies:** 21\
**Last updated:** [October 3, 2017, 4:29am UTC](https://discourse.slicer.org/t/cannot-compile-slicer-on-mac-macos-sierra-clang-9-cmake-3-9-1/1104 "2017-10-03T04:29:09Z")

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I recently had to reinstall the OS on my Mac, and since then I cannot compile Slicer due to this error: I installed Qt using the brew recipe, turned off TCL, and set deployment target to 10.11, following instructions…

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## [Call "Center Volume" button from python script](https://discourse.slicer.org/t/call-center-volume-button-from-python-script/1132)

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**Author:** [@mangotee](https://discourse.slicer.org/u/mangotee)\
**Replies:** 8\
**Last updated:** [September 29, 2017, 1:31pm UTC](https://discourse.slicer.org/t/call-center-volume-button-from-python-script/1132 "2017-09-29T13:31:01Z")

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Hi all, In the Volumes module, there is a “Center Volume” button. Unfortunately, I cannot find how to call this button from a python script… I know how to do this e.g. with an ITK workaround (using sitkUtils as sitku): …

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## [Matlab Bridge Extension](https://discourse.slicer.org/t/matlab-bridge-extension/314)

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**Author:** [@Alba\_Garcia\_de\_la\_Ca](https://discourse.slicer.org/u/Alba_Garcia_de_la_Ca)\
**Replies:** 28\
**Last updated:** [September 28, 2017, 6:25am UTC](https://discourse.slicer.org/t/matlab-bridge-extension/314 "2017-09-28T06:25:00Z")

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Operating system: ubuntu 16.04 Slicer version: 4.6 | 4.7 Expected behavior: Matlab bridge executes Matlab properly Actual behavior: There is an error calling Matlab Hi everyone! I am trying to call a script from Matl…

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## [Slicer extensions: Action required by maintainers](https://discourse.slicer.org/t/slicer-extensions-action-required-by-maintainers/1003)

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**Author:** [@jcfr](https://discourse.slicer.org/u/jcfr)\
**Replies:** 1\
**Last updated:** [September 27, 2017, 8:55pm UTC](https://discourse.slicer.org/t/slicer-extensions-action-required-by-maintainers/1003 "2017-09-27T20:55:15Z")

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During the past few days, while testing the recent updates associated with Slicer build system, I ended updating some extensions. List of extension that will be fixed shortly Eigen3 missing packageupload: We will pr…

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## [Failing Slicer Extension Test - ITK cannot load test image](https://discourse.slicer.org/t/failing-slicer-extension-test-itk-cannot-load-test-image/1115)

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**Author:** [@mschwier](https://discourse.slicer.org/u/mschwier)\
**Replies:** 6\
**Last updated:** [September 26, 2017, 1:44pm UTC](https://discourse.slicer.org/t/failing-slicer-extension-test-itk-cannot-load-test-image/1115 "2017-09-26T13:44:58Z")

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System: Win 10 64 Bit Visual Studio 2013 Dear all, I’m trying to debug a test executable of a Slicer Extension (PkModeling). The problem is that running the test, which processes an image, fails in itkImageFileReader.h…

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## [SlicerOpenCV MD5 hash mismatch](https://discourse.slicer.org/t/sliceropencv-md5-hash-mismatch/1051)

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**Author:** [@tdiprima](https://discourse.slicer.org/u/tdiprima)\
**Replies:** 10\
**Last updated:** [September 18, 2017, 5:35pm UTC](https://discourse.slicer.org/t/sliceropencv-md5-hash-mismatch/1051 "2017-09-18T17:35:50Z")

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Hello Folks :slight\_smile: I’m building SlicerOpenCV. And I’m getting an error that says that the MD5 hash of SlicerOpenCV-build/OpenCV-prefix/src/3.1.0.tar.gz does not match expected value. expected: '70e1dd07f0aa066…

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## [Writing labels out to file](https://discourse.slicer.org/t/writing-labels-out-to-file/1054)

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**Author:** [@ebremer](https://discourse.slicer.org/u/ebremer)\
**Replies:** 4\
**Last updated:** [September 15, 2017, 3:02pm UTC](https://discourse.slicer.org/t/writing-labels-out-to-file/1054 "2017-09-15T15:02:09Z")

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I’m trying to print out a single label image with the following in Slicer 4.7.9-2017-09-10 ================================================= labelNodes = slicer.util.getNodes(‘vtkMRMLLabelMapVolumeNode\*’) vs = labelNo…

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## [SlicerOpenCV nightly build failed](https://discourse.slicer.org/t/sliceropencv-nightly-build-failed/1058)

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**Author:** [@tdiprima](https://discourse.slicer.org/u/tdiprima)\
**Replies:** 0\
**Last updated:** [September 15, 2017, 2:05pm UTC](https://discourse.slicer.org/t/sliceropencv-nightly-build-failed/1058 "2017-09-15T14:05:53Z")

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Hi guys, SlicerPathology depends on SlicerOpenCV… I hope you can help me out. Here’s the build error. And it says: -- MD5 hash of /.../SlicerOpenCV-build/OpenCV-prefix/src/3.1.0.tar.gz does not match expected v…

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## [Requests: HTTP for Humans](https://discourse.slicer.org/t/requests-http-for-humans/994)

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**Author:** [@ebremer](https://discourse.slicer.org/u/ebremer)\
**Replies:** 5\
**Last updated:** [September 15, 2017, 12:45am UTC](https://discourse.slicer.org/t/requests-http-for-humans/994 "2017-09-15T00:45:40Z")

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Would it be possible to add: http://docs.python-requests.org/en/latest/ to the Slicer distribution. It has an Apache 2.0 license and is a lot easier to use than urllib or urllib2

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## [Building CLI Extension copies to wrong output directories (cmake issue)](https://discourse.slicer.org/t/building-cli-extension-copies-to-wrong-output-directories-cmake-issue/1024)

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**Author:** [@mschwier](https://discourse.slicer.org/u/mschwier)\
**Replies:** 3\
**Last updated:** [September 11, 2017, 8:03pm UTC](https://discourse.slicer.org/t/building-cli-extension-copies-to-wrong-output-directories-cmake-issue/1024 "2017-09-11T20:03:11Z")

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I hope I might find some help here. I recently started working on the PkModeling extension an I am trying to get it to build on various continuous integration platforms (Appveyor for Win and Travis CI for Linux and Mac). …

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## [macOS factory down until Monday](https://discourse.slicer.org/t/macos-factory-down-until-monday/1028)

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**Author:** [@fedorov](https://discourse.slicer.org/u/fedorov)\
**Replies:** 1\
**Last updated:** [September 11, 2017, 6:31pm UTC](https://discourse.slicer.org/t/macos-factory-down-until-monday/1028 "2017-09-11T18:31:43Z")

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Here is the message from @jcfr: The macOS factory needs to be physically restarted. Our sysadmins will do so on Monday.

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## [When I add module path, unexpected errors have occured - "No module named \*\*\*\*"](https://discourse.slicer.org/t/when-i-add-module-path-unexpected-errors-have-occured-no-module-named/999)

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**Author:** [@shenziheng](https://discourse.slicer.org/u/shenziheng)\
**Replies:** 11\
**Last updated:** [September 6, 2017, 4:06am UTC](https://discourse.slicer.org/t/when-i-add-module-path-unexpected-errors-have-occured-no-module-named/999 "2017-09-06T04:06:57Z")

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Hello, I use ExtensionWizard to create a loadable module, and then use Cmake & Visual Studio to build it. Lastly, I add its path to Additional module paths in Slicer Setting. But, when I restart 3DSlcier,there are som…

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## [Runtime warning on startup in numpy](https://discourse.slicer.org/t/runtime-warning-on-startup-in-numpy/757)

<div class="topic-metadata">

**Author:** [@fedorov](https://discourse.slicer.org/u/fedorov)\
**Replies:** 20\
**Last updated:** [September 5, 2017, 2:14pm UTC](https://discourse.slicer.org/t/runtime-warning-on-startup-in-numpy/757 "2017-09-05T14:14:15Z")

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I am getting this warning on startup: /Applications/Slicer.app/Contents/lib/Python/lib/python2.7/site-packages/numpy-1.13.1-py2.7-macosx-10.6-x86\_64.egg/numpy/core/getlimits.py:82: RuntimeWarning: invalid value encount…

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## [Build failure SITK](https://discourse.slicer.org/t/build-failure-sitk/1004)

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**Author:** [@gcsharp](https://discourse.slicer.org/u/gcsharp)\
**Replies:** 2\
**Last updated:** [September 5, 2017, 5:03am UTC](https://discourse.slicer.org/t/build-failure-sitk/1004 "2017-09-05T05:03:14Z")

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Hi, I get the following error from a fresh build from source. Linux, gcc 7.2, QT5. Any idea? Greg \[ 61%\] Building CXX object Code/Common/src/CMakeFiles/SimpleITKCommon.dir/sitkImage.cxx.o In file included from /home…

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