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Today's topic summary
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- [CCPPETMR/SIRF] matlab libload_*.m better errors (#304) [2 Updates]
http://groups.google.com/group/ccp-petmr-codebot/t/1d580562f170ee77
- [CCPPETMR/SIRF] NiftiImageData3DTensor construtor from array not accessible (#303) [5 Updates]
http://groups.google.com/group/ccp-petmr-codebot/t/cbba959c809ed3d7
- [CCPPETMR/SIRF] matlab: error catching in libload_*.m (#302) [3 Updates]
http://groups.google.com/group/ccp-petmr-codebot/t/442009d55f083485
- [CCPPETMR/SIRF-SuperBuild] Gadgetron tests fail but Travis stays green (#192) [4 Updates]
http://groups.google.com/group/ccp-petmr-codebot/t/ceff2cb9c533b386
- [CCPPETMR/SIRF] Travis failing for linux (#300) [1 Update]
http://groups.google.com/group/ccp-petmr-codebot/t/c5109ed8e472ad3f
- [CCPPETMR/SIRF-SuperBuild] added missing CMake FFTW variables to External_SIRF.cmake, fixes #197 (together with installing boost_1_65_1) (5b8cb89) [1 Update]
http://groups.google.com/group/ccp-petmr-codebot/t/c85e86567f89e791
- [CCPPETMR/SIRF] Travis use conda itk on OSX (#295) [3 Updates]
http://groups.google.com/group/ccp-petmr-codebot/t/65e721956e918868
- [CCPPETMR/SIRF] Add getter for number of total voxels to NiftiImageData (#301) [6 Updates]
http://groups.google.com/group/ccp-petmr-codebot/t/b7e60cc0d7761f55
- [CCPPETMR/SIRF] NiftiImageData template arguments other than float don't compile (#299) [1 Update]
http://groups.google.com/group/ccp-petmr-codebot/t/41dfa80d14f8c8a0
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Topic: [CCPPETMR/SIRF] matlab libload_*.m better errors (#304)
URL: http://groups.google.com/group/ccp-petmr-codebot/t/1d580562f170ee77
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---------- 1 of 2 ----------
From: Richard Brown <[log in to unmask]>
Date: Feb 05 04:26PM
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/172a374c283942
You can view, comment on, or merge this pull request online at:
https://github.com/CCPPETMR/SIRF/pull/304
-- Commit Summary --
* matlab libload_*.m better errors
-- File Changes --
---------- 2 of 2 ----------
From: Richard Brown <[log in to unmask]>
Date: Feb 05 06:02PM
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/183c4d3bc29341
Merged #304 into master.
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Topic: [CCPPETMR/SIRF] NiftiImageData3DTensor construtor from array not accessible (#303)
URL: http://groups.google.com/group/ccp-petmr-codebot/t/cbba959c809ed3d7
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---------- 1 of 5 ----------
From: Johannes Mayer <[log in to unmask]>
Date: Feb 05 08:10AM -0800
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/172952ff3123a4
@rijobro
The constructor
```
template<class inputType>
NiftiImageData3DDisplacement(const inputType * const data, const VoxelisedGeometricalInfo3D &geom)
---------- 2 of 5 ----------
From: Richard Brown <[log in to unmask]>
Date: Feb 05 08:32AM -0800
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/172a8bbec30403
Yes, I though about this the other day. When creating an image from geometrical info, we actually call this method: `create_from_geom_info`. We could add an argument (`bool is_tensor=false`).
---------- 3 of 5 ----------
From: Johannes Mayer <[log in to unmask]>
Date: Feb 05 08:33AM -0800
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/172a99bb2a9891
I'm very happy with it!
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---------- 4 of 5 ----------
From: Richard Brown <[log in to unmask]>
Date: Feb 05 05:24PM
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/172d60318406ad
Ok, pushed to master.
I also added `ctests` for `NiftiImageData3DTensor`, `NiftiImageData3DDisplacement` and `NiftiImageData3DDeformation` (as I'd already done for `NiftiImageData` and
---------- 5 of 5 ----------
From: Richard Brown <[log in to unmask]>
Date: Feb 05 10:02AM -0800
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/183c44535326e6
Ignore bottom comment, managed to do resampling of tensor images too.
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Topic: [CCPPETMR/SIRF] matlab: error catching in libload_*.m (#302)
URL: http://groups.google.com/group/ccp-petmr-codebot/t/442009d55f083485
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---------- 1 of 3 ----------
From: Richard Brown <[log in to unmask]>
Date: Feb 05 06:40AM -0800
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/172474df05c30f
loading libraries in matlab currently looks like this:
```
try
[notfound, warnings] = loadlibrary('miutilities');
catch
error('mutilities library failed to load\n')
---------- 2 of 3 ----------
From: Kris Thielemans <[log in to unmask]>
Date: Feb 05 08:19AM -0800
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/1729d74a45319c
yes. let's remove `try/catch`. It will error out just like the current code, but at least we'll see why.
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---------- 3 of 3 ----------
From: Richard Brown <[log in to unmask]>
Date: Feb 05 08:26AM -0800
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/172a3babe2d6c1
ok, see PR #304.
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Topic: [CCPPETMR/SIRF-SuperBuild] Gadgetron tests fail but Travis stays green (#192)
URL: http://groups.google.com/group/ccp-petmr-codebot/t/ceff2cb9c533b386
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---------- 1 of 4 ----------
From: Richard Brown <[log in to unmask]>
Date: Feb 05 06:54AM -0800
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/17252cae24805e
Reopened #192.
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From: Richard Brown <[log in to unmask]>
Date: Feb 05 06:55AM -0800
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/17254533303bde
This has started happening again. Most recent error that should be causing it to be red happened during the `cmake` of SIRF:
```
CMake Error at
---------- 3 of 4 ----------
From: Edoardo Pasca <[log in to unmask]>
Date: Feb 05 03:51PM
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/172854664f6497
on what OS?
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---------- 4 of 4 ----------
From: Richard Brown <[log in to unmask]>
Date: Feb 05 04:19PM
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/1729d92f7c6d7f
both unfortunately...
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Topic: [CCPPETMR/SIRF] Travis failing for linux (#300)
URL: http://groups.google.com/group/ccp-petmr-codebot/t/c5109ed8e472ad3f
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---------- 1 of 1 ----------
From: Richard Brown <[log in to unmask]>
Date: Feb 05 06:52AM -0800
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/1725197cc193c2
Due to https://github.com/CCPPETMR/SIRF-SuperBuild/commit/5b8cb8961a8db4376c67528abc98fc6442aad6b2
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Topic: [CCPPETMR/SIRF-SuperBuild] added missing CMake FFTW variables to External_SIRF.cmake, fixes #197 (together with installing boost_1_65_1) (5b8cb89)
URL: http://groups.google.com/group/ccp-petmr-codebot/t/c85e86567f89e791
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---------- 1 of 1 ----------
From: Richard Brown <[log in to unmask]>
Date: Feb 05 06:51AM -0800
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/17250d8f0f791e
I think this commit has broken SIRF's Travis (https://travis-ci.org/CCPPETMR/SIRF). The superbuild is also failing but returning green (a probem in itself).
I'm not sure what the problem is with
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Topic: [CCPPETMR/SIRF] Travis use conda itk on OSX (#295)
URL: http://groups.google.com/group/ccp-petmr-codebot/t/65e721956e918868
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---------- 1 of 3 ----------
From: Kris Thielemans <[log in to unmask]>
Date: Feb 05 02:17AM -0800
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/17161560889484
@rijobro, try doing
```sh
DYLD_PRINT_LIBRARIES=YES ctest -VV
```
[see here](https://apple.stackexchange.com/questions/247227/how-to-find-which-shared-library-is-loaded-by-a-process-on-osx)
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---------- 2 of 3 ----------
From: Richard Brown <[log in to unmask]>
Date: Feb 05 10:23AM
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/1716628c3bef37
@rijobro pushed 1 commit.
6b051fb547f9fe4858a98f67ec5369558cf19537 print library dependencies for debugging
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---------- 3 of 3 ----------
From: Richard Brown <[log in to unmask]>
Date: Feb 05 02:43PM
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/17249e0b0ac241
Gave this a go, but currently blocked by #300.
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Topic: [CCPPETMR/SIRF] Add getter for number of total voxels to NiftiImageData (#301)
URL: http://groups.google.com/group/ccp-petmr-codebot/t/b7e60cc0d7761f55
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---------- 1 of 6 ----------
From: Johannes Mayer <[log in to unmask]>
Date: Feb 05 12:33AM -0800
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/171067c64151c9
This function is useful to loop over the elements.
You can view, comment on, or merge this pull request online at:
https://github.com/CCPPETMR/SIRF/pull/301
-- Commit Summary --
---------- 2 of 6 ----------
From: Richard Brown <[log in to unmask]>
Date: Feb 05 02:09AM -0800
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/1715a9b3905c8f
Merged #301 into master.
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---------- 3 of 6 ----------
From: Richard Brown <[log in to unmask]>
Date: Feb 05 10:12AM
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/1715c9d8831fb5
Merged. Just for interest, I was using `get_raw_nifti_sptr()->nvox` before.
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---------- 4 of 6 ----------
From: Kris Thielemans <[log in to unmask]>
Date: Feb 05 02:12AM -0800
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/1715ceb484ca9f
can I ask how you're using this?
If we need it, we should have a virtual function higher up (which could just get it from the geo_info)
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---------- 5 of 6 ----------
From: Richard Brown <[log in to unmask]>
Date: Feb 05 02:20AM -0800
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/171642ae94f44b
Apologies for merging, do you want me to revert?
Although we should be using geom_info, I don't fully trust it quite yet (e.g., varying slice distances for MR images). Should we make this an issue
---------- 6 of 6 ----------
From: Johannes Mayer <[log in to unmask]>
Date: Feb 05 02:22AM -0800
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/1716533e5a5189
I decided to load the segmentation input of my simulation into a 'NiftiImageData3D' (no modality attached, just geometry and image information).
At some points I want to loop over all the pixels in
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Topic: [CCPPETMR/SIRF] NiftiImageData template arguments other than float don't compile (#299)
URL: http://groups.google.com/group/ccp-petmr-codebot/t/41dfa80d14f8c8a0
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---------- 1 of 1 ----------
From: Richard Brown <[log in to unmask]>
Date: Feb 05 02:08AM -0800
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/171590ed3472be
Can I close this?
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