Program using ISMRMRD

[Yishi Wang]

Hi all,

    I'm try to program an application to write philips data to ISMRMRD, is it enough to just include the header files for ISMRMRD(dataset.h, export.h, ismrmrd.h, meta.h, xml.h) into my project in Visual Studio 2012 or I need to follow all the installation steps to make things work?

Thanks!

Yishi

[Souheil Inati]

No you need to install it and then you need to compile and link against it. 

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[Michael Hansen]

You need to compile and install the ISMRMRD library. As pointed out by Souheil, your application will need to link against the library. The header files just describe the functions that the library provides, your application will need to find the actual library when linking. 

If you want to see a "simple" example of setting up a CMake configuration for an application that links against ISMRMRD, you could checkout the gadgetron_ismrmrd_client:

https://github.com/gadgetron/gadgetron/blob/master/apps/clients/gadgetron_ismrmrd_client/CMakeLists.txt

Hope this helps,

Michael

PS. We would be interested in hearing about any progress you make on converting Philips data. I know of some efforts here and there, but not sure how far along it is. 

[Yishi Wang]

Thank you Michael, I'll keep you updated.

Yishi

在 2015年3月24日星期二 UTC+8下午7:53:52，Michael Hansen写道：

[Yishi Wang]

Thank you Souheil.

在 2015年3月24日星期二 UTC+8下午5:35:37，Souheil Inati写道：

[Yishi Wang]

During installing, the cmake could not find boost. I've tried a few versions of boost. I added the boost root folder to path:D:\Program Files\boost_1_57_0 and a few more such as:D:\Program Files\boost_1_55_0\lib64-msvc-11.0;D:\Program Files\boost_1_55_0_32\boost_1_55_0\lib32-msvc-11.0; 

But cmake still can't find boost.

在 2015年3月24日星期二 UTC+8下午5:16:24，Yishi Wang写道：

[Michael Hansen]

You don't need boost to build the ISMRMRD library. As it says it just means it cannot build some utilities. However, it looks like it cannot find HDF5 and that is an absolute requirement. Did you install HDF5?

On Tuesday, March 24, 2015 at 5:16:24 AM UTC-4, Yishi Wang wrote:

[Yishi Wang]

Yes, I installed HDF5. And added "C:\Program Files\HDF_Group\HDF5\1.8.14\bin" to the path. Did I miss something?

在 2015年3月25日星期三 UTC+8上午10:23:52，Michael Hansen写道：

[Michael Hansen]

Well if you look at your output it says that the HDF5_C_INCLUDE_DIR was NOTFOUND, so something is not quite right. It is unable to find the include files for HDF5 and so it fails. 

[Yishi Wang]

I added all of these to path:C:\Program Files\HDF_Group\HDF5\1.8.14\bin;C:\Program Files\HDF_Group\HDF5\1.8.14;C:\Program Files\HDF_Group\HDF5\1.8.14\lib;C:\Program Files\HDF_Group\HDF5\1.8.14\include;C:\Program Files\HDF_Group\HDF5\1.8.14\cmake\hdf5;

Still not working.

在 2015年3月25日星期三 UTC+8上午10:50:15，Michael Hansen写道：

[Yishi Wang]

Windows will drive me mad.

在 2015年3月25日星期三 UTC+8上午11:01:12，Yishi Wang写道：

[Yishi Wang]

Is it possible I skip cmake and go directly to visual studio 2012?

在 2015年3月25日星期三 UTC+8上午11:36:07，Yishi Wang写道：

[Yishi Wang]

Dear Michael, 

I don't know how but cmake is not giving the errors now.

But When I launched the generated vs project in vs 2012, it still can't find hdf5.h.

When I tried to include the folder containing hdf5.h into the project, more errors occurred.

在 2015年3月25日星期三 UTC+8上午11:44:20，Yishi Wang写道：

[Yishi Wang]

I just converted my language set from Chinese to English for vs 2012. 

The errors are shown below.

2>E:\ismrmrd\libsrc\ismrmrd.c(531): warning C4334: '<<' : result of 32-bit shift implicitly converted to 64 bits (was 64-bit shift intended?)

2>E:\ismrmrd\libsrc\ismrmrd.c(543): warning C4334: '<<' : result of 32-bit shift implicitly converted to 64 bits (was 64-bit shift intended?)

2>  ismrmrd.cpp

2>  dataset.c

2>E:\ismrmrd\libsrc\dataset.c(540): warning C4244: '=' : conversion from 'hsize_t' to 'uint32_t', possible loss of data

2>E:\ismrmrd\libsrc\dataset.c(1030): error C2143: syntax error : missing ';' before 'type'

2>E:\ismrmrd\libsrc\dataset.c(1034): error C2065: 'buff' : undeclared identifier

2>E:\ismrmrd\libsrc\dataset.c(1034): warning C4022: 'H5Dread' : pointer mismatch for actual parameter 6

2>E:\ismrmrd\libsrc\dataset.c(1035): error C2065: 'buff' : undeclared identifier

2>E:\ismrmrd\libsrc\dataset.c(1035): error C2109: subscript requires array or pointer type

2>E:\ismrmrd\libsrc\dataset.c(1042): error C2065: 'buff' : undeclared identifier

2>E:\ismrmrd\libsrc\dataset.c(1042): error C2109: subscript requires array or pointer type

2>E:\ismrmrd\libsrc\dataset.c(1042): error C2168: 'strlen' : too few actual parameters for intrinsic function

2>E:\ismrmrd\libsrc\dataset.c(1047): error C2065: 'buff' : undeclared identifier

2>E:\ismrmrd\libsrc\dataset.c(1047): error C2109: subscript requires array or pointer type

2>E:\ismrmrd\libsrc\dataset.c(1047): error C2168: 'strlen' : too few actual parameters for intrinsic function

2>E:\ismrmrd\libsrc\dataset.c(1047): warning C4022: 'memcpy' : pointer mismatch for actual parameter 2

2>E:\ismrmrd\libsrc\dataset.c(1047): error C2168: 'memcpy' : too few actual parameters for intrinsic function

2>E:\ismrmrd\libsrc\dataset.c(1074): error C2061: syntax error : identifier 'ismrmrd_get_number_of_acquisitions'

2>E:\ismrmrd\libsrc\dataset.c(1074): error C2059: syntax error : ';'

2>E:\ismrmrd\libsrc\dataset.c(1074): error C2059: syntax error : 'type'

========== Rebuild All: 1 succeeded, 1 failed, 0 skipped ==========

在 2015年3月25日星期三 UTC+8下午8:11:47，Yishi Wang写道：

[Yishi Wang]

At the same time, I am trying to do this job on Ubuntu 14.10 with codeblocks. ISMRMRD has already been installed on that machine. I included the 5 header files for ISMRMRD and the linked the library file found in /usr/local/lib. Is that enough for me to do my project? If not, what did I miss?

Thanks.

在 2015年3月25日星期三 UTC+8下午8:48:55，Yishi Wang写道：

[Joseph Naegele]

This problem:

2>E:\ismrmrd\libsrc\dataset.c(1030): error C2143: syntax error : missing ';' before 'type'

is due to VS2012 only supporting C89. We intend for ISMRMRD to compile with VS2012 but we didn't catch that one.
For now, I will fix it in the master branch.

[Yishi Wang]

Wow, thank you for pointing out the problem, then I can't use vs 2012 now.

So, should I switch to vs 2010 and do all the installation again or just wait for your fixing? How soon will it be fixed?

If I switch to vs2010, will vs 2010 conflict with 2012?

在 2015年3月25日星期三 UTC+8下午9:34:39，Joseph Naegele写道：

[Yishi Wang]

Or do you suggest VS 2013 or higher? As long as it works now, I'll take it.

Yishi

在 2015年3月25日星期三 UTC+8下午9:45:58，Yishi Wang写道：

[Michael Hansen]

VS2013 is what we use at the moment on our build systems. 

[Yishi Wang]

Thanks Michael and Joseph, I'll try 2013 then.

在 2015年3月25日星期三 UTC+8下午9:57:21，Michael Hansen写道：

[Yishi Wang]

Hi Michael and Joseph, I got this new error in VS 2013.

2>C:\Program Files\HDF_Group\HDF5\1.8.14\bin\hdf5.dll : fatal error LNK1107: invalid or corrupt file: cannot read at 0x330

I reinstalled HDF5 a few times, don't know why this file is invalid or corrupted.

Regards!

Yishi

在 2015年3月25日星期三 UTC+8下午10:37:11，Yishi Wang写道：

[Michael Hansen]

Try to gran HDF5 from here:

https://s3.amazonaws.com/install-gadgetron-vs2013/Dependencies/HDF5/hdf5-1.8.14-win64-vs2013-shared.zip

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[Michael Hansen]

There is obviously something wrong with your installation, but it is very hard for us to debug your specific Windows setup.

[Yishi Wang]

Thank you Michael, this is exactly the same version of HDF5 I used. The error is still there.

在 2015年3月27日星期五 UTC+8下午8:54:52，Michael Hansen写道：

[Michael Hansen]

You must have some other problem. We use it all the time. A complete build (ISMRMRD, Gadgetron, etc.) just ran on Windows VS2013. It finished 20 minutes ago:

http://174.129.2.39/builders/gadgetron_windows_master_builder/builds/157

So you must have some other configuration that is wrong. But is is basically impossibly for us to debug all the strangeness of windows installations. Sorry.

Michael

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[Michael Hansen]

Looks at the commands here to run CMake on the Windows machine. Take a note of the environment variables:

http://174.129.2.39/builders/gadgetron_windows_master_builder/builds/158/steps/shell/logs/stdio