Hi
Our understanding is that ` STIR_BUILD_EXECUTABLES:BOOL=ON` will set a cached variable. In any case, you don’t need -U for a variable that you do set. In our normal recommendation we use -U\*_URL -U\*_TAG such that it’ll pick up defaults again (which might have changed due to an update or changing the value of DEVEL_BUILD:BOOL).
Kris
From: CCP-PETMR Developers list <[log in to unmask]> On Behalf Of Edoardo Pasca - UKRI STFC
Sent: 12 December 2019 14:12
To: [log in to unmask]
Subject: Re: Using your Brainweb code of exercises of the training school
Would you not need at cmake issuing time?
-UBUILD_STIR_EXECUTABLES -DBUILD_STIR_EXECUTABLES=ON \
I suppose that the VM build has cached that variable as OFF?
Edo
From: CCP-PETMR Developers list <[log in to unmask]<mailto:[log in to unmask]>> On Behalf Of Brown, Richard
Sent: 12 December 2019 12:57
To: [log in to unmask]<mailto:[log in to unmask]>
Subject: Re: Using your Brainweb code of exercises of the training school
Hi Congying Chu,
I’m copying in the mailing list as it may be of interest to them.
It’s strange that having built the STIR executables, you still can’t use “zoom_image”. It makes me think something went wrong with the installation.
A couple of things to think about:
1. Is zoom_image available in your install location? I think this is "~devel/install/bin” on the VM.
2. If zoom_image isn’t in that folder, make sure it’s being built:
* Confirm you confirm that in buildVM/CMakeCache.txt there is the following: STIR_BUILD_EXECUTABLES:BOOL=ON
* If this is the case, run “make STIR”
3. Still no “zoom_image” in the install folder?
* cd ~/devel/buildVM/builds/STIR/build
* Confirm that ~/devel/buildVM/builds/STIR/build/CMakeCache.txt contains the following: BUILD_EXECUTABLES:BOOL=ON.
* If this is not the case: “cmake . -DBUILD_EXECUTABLES=ON”
* Make install
If you still don’t have zoom_image in ~devel/install/bin then you’ll have to send across some of your log files.
Let me know if any of these solves the problem.
Best Regards,
Richard
Research Associate in Medical Imaging Physics at University College London,
Institute of Nuclear Medicine, UCL Hospital, Tower 5,
235 Euston Road, London NW1 2BU, UK
On 12 Dec 2019, at 09:45, Chu, Congying <[log in to unmask]<mailto:[log in to unmask]>> wrote:
Dear Dr. Brown,
I am Congying Chu, from Institute of Neuroscience and Medicine-2, Forschungszentrum Jülich, Germany. I tried to follow the exercises in http://www.ccppetmr.ac.uk/node/200<https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.ccppetmr.ac.uk%2Fnode%2F200&data=02%7C01%7C%7Ca79d45132dde49d3766c08d77f0d34f4%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C637117567011172184&sdata=8eUwmudhHbN3Zai020ypa%2FTEZRv9y3NoJUdIAPA3g8U%3D&reserved=0> by using Oracle VM VirtualBox. However, when I tried to use your Brainweb code (Jupyter notebook, notebooks/SIRF-Exercises/notebooks/Synergistic/BrainWeb.ipynb), I met the issue of using the zoom_imgae command. As you have mentioned that we could remedy this with STIR_BUILD_EXECUTABLES=ON, I tried to add this option in the UPDATE.sh at the path ~/devel/CCPPETMR_VM/scripts as the following command:
git checkout $SB_TAG
cd ..
mkdir -p buildVM
cd buildVM
cmake ../SIRF-SuperBuild \
-DCMAKE_INSTALL_PREFIX=${SIRF_INSTALL_PATH} \
-U\*_URL -U\*_TAG \
-DUSE_SYSTEM_SWIG=On \
-DUSE_SYSTEM_Boost=On \
-DUSE_SYSTEM_Armadillo=On \
-DUSE_SYSTEM_FFTW3=On \
-DUSE_SYSTEM_HDF5=ON \
-DBUILD_siemens_to_ismrmrd=On \
-DUSE_ITK=ON \
-DDEVEL_BUILD=OFF \
-DBUILD_CIL=ON \
-DBUILD_STIR_EXECUTABLES=ON \
-DNIFTYREG_USE_CUDA=OFF
make -j${num_parallel}
I can run this changed script smoothly. But, after opening a new terminal, I still can’t use zoom_image. Could you please let me know whether I set a wrong paratemer?
Thank you for your help!!! Looking forward to your reply!
Best regards,
Congying
P.S. the error message from Jupyter
/bin/sh: 1: zoom_image: not found
sed: can't read FDG_small.hv: No such file or directory
File: /home/sirfuser/devel/install/python/sirf/STIR.py
Line: 216
check_status found the following message sent from the engine:
---------------------------------------------------------------------------
error Traceback (most recent call last)
<ipython-input-7-722e9a6d12dd> in <module>()
24 return pet.ImageData(small_fname)
25
---> 26 FDG = save_as_interfile(templ_sino, FDG, "FDG" )
27 amyl = save_as_interfile(templ_sino, amyl, "Amyloid")
28 uMap = save_as_interfile(templ_sino, uMap, "uMap" )
<ipython-input-7-722e9a6d12dd> in save_as_interfile(templ_sino, vol, fname)
22 get_ipython().system(u"sed -r -i 's/.*first pixel offset \\(mm\\).*//<file://(mm/).*/>' {small_fname}")
23 # Read back in and return
---> 24 return pet.ImageData(small_fname)
25
26 FDG = save_as_interfile(templ_sino, FDG, "FDG" )
/home/sirfuser/devel/install/python/sirf/STIR.pyc in __init__(self, arg)
214 if isinstance(arg, str):
215 self.handle = pystir.cSTIR_objectFromFile('Image', arg)
--> 216 check_status(self.handle)
217 elif isinstance(arg, AcquisitionData):
218 assert arg.handle is not None
/home/sirfuser/devel/install/python/sirf/Utilities.pyc in check_status(handle, stack)
372 repr(line) + ' of ' + file + '; ' + \
373 'the reconstruction engine output may provide more information'
--> 374 raise error(errorMsg)
375
376
error: ??? "'Error opening file FDG_small.hv\\n' exception caught at line 239 of /home/sirfuser/devel/buildVM/sources/SIRF/src/xSTIR/cSTIR/cstir.cpp; the reconstruction engine output may provide more information"
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Volker Rieke
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
________________________________
To unsubscribe from the CCP-PETMR-DEVEL list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP-PETMR-DEVEL&A=1<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2Fwebadmin%3FSUBED1%3DCCP-PETMR-DEVEL%26A%3D1&data=02%7C01%7C%7Ca79d45132dde49d3766c08d77f0d34f4%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C637117567011182178&sdata=g%2B6DAPZYE7u4GherBXsAm4nFEw%2FS08LPq8SY%2BzaHvJ0%3D&reserved=0>
________________________________
To unsubscribe from the CCP-PETMR-DEVEL list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP-PETMR-DEVEL&A=1<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2Fwebadmin%3FSUBED1%3DCCP-PETMR-DEVEL%26A%3D1&data=02%7C01%7C%7Ca79d45132dde49d3766c08d77f0d34f4%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C637117567011192174&sdata=JY3EoXpRdC%2FUmO%2BEbjSe6Ld4sOPN5XkNB9HNxuSZTFo%3D&reserved=0>
########################################################################
To unsubscribe from the CCP-PETMR-DEVEL list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP-PETMR-DEVEL&A=1
