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SyneRBI / SyneRBI_VM

Virtual Machine with pre-installed SyneRBI software
http://www.ccpsynerbi.ac.uk
Apache License 2.0
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Gadgetron DICOM gadget not built on VM #173

Closed evgueni-ovtchinnikov closed 3 years ago

evgueni-ovtchinnikov commented 3 years ago

SIRF output in DICOM format not possible on VM because Gadgetron DICOM gadget is not built:

 Could NOT find DCMTK (missing: DCMTK_config_INCLUDE_DIR
 DCMTK_ofstd_INCLUDE_DIR DCMTK_ofstd_LIBRARY DCMTK_oflog_INCLUDE_DIR
 DCMTK_oflog_LIBRARY DCMTK_dcmdata_INCLUDE_DIR DCMTK_dcmdata_LIBRARY
 DCMTK_dcmimgle_INCLUDE_DIR DCMTK_dcmimgle_LIBRARY)
 DCMTK NOT found, not compiling DICOM gadget

I tried

sirfuser@vagrant:~$ sudo apt-get install dcmtk
Reading package lists... Done
Building dependency tree       
Reading state information... Done
The following additional packages will be installed:
  libcharls1 libdcmtk12
The following NEW packages will be installed:
  dcmtk libcharls1 libdcmtk12
0 upgraded, 3 newly installed, 0 to remove and 250 not upgraded.
Need to get 5,447 kB of archives.
After this operation, 25.5 MB of additional disk space will be used.
Do you want to continue? [Y/n] y
Get:1 http://archive.ubuntu.com/ubuntu bionic/universe amd64 libcharls1 amd64 1.1.0+dfsg-2 [56.1 kB]
Get:2 http://archive.ubuntu.com/ubuntu bionic/universe amd64 libdcmtk12 amd64 3.6.2-3build3 [4,499 kB]
Get:3 http://archive.ubuntu.com/ubuntu bionic/universe amd64 dcmtk amd64 3.6.2-3build3 [892 kB]
Fetched 5,447 kB in 21s (258 kB/s)                                             
Selecting previously unselected package libcharls1:amd64.
(Reading database ... 123424 files and directories currently installed.)
Preparing to unpack .../libcharls1_1.1.0+dfsg-2_amd64.deb ...
Unpacking libcharls1:amd64 (1.1.0+dfsg-2) ...
Selecting previously unselected package libdcmtk12.
Preparing to unpack .../libdcmtk12_3.6.2-3build3_amd64.deb ...
Unpacking libdcmtk12 (3.6.2-3build3) ...
Selecting previously unselected package dcmtk.
Preparing to unpack .../dcmtk_3.6.2-3build3_amd64.deb ...
Unpacking dcmtk (3.6.2-3build3) ...
Setting up libcharls1:amd64 (1.1.0+dfsg-2) ...
Setting up libdcmtk12 (3.6.2-3build3) ...
Setting up dcmtk (3.6.2-3build3) ...
Adding `dcmtk' group to system ...
Adding `dcmtk' user to system ...
adduser: Warning: The home directory `/var/lib/dcmtk/db' does not belong to the user you are currently creating.
Processing triggers for man-db (2.8.3-2ubuntu0.1) ...
Processing triggers for libc-bin (2.27-3ubuntu1) ...

but DCMTK is still not found by find_package(DCMTK).

evgueni-ovtchinnikov commented 3 years ago

turned out I needed libdcmtk-dev, not dcmtk.

@paskino: please build the next VM with libdcmtk-dev

KrisThielemans commented 3 years ago

you could easily add it to the relevant INSTALL file. Note that the same has to be done for the SIRF-Superbuild/docker file, as we still don't sync these.

paskino commented 3 years ago

This is fine for Ubuntu, but for other OS it may be useful to add to the SuperBuild external projects?

KrisThielemans commented 3 years ago

This is fine for Ubuntu, but for other OS it may be useful to add to the SuperBuild external projects?

it's true, but we've given up on other Gadgetron dependencies (libxml etc etc). Until we attempt to build it on Windows, I wouldn't put in the effort.