Re: hawk

[Filipe Maia]

On Wed, Mar 9, 2011 at 14:38, Dritan Siliqi <dritan...@ic.cnr.it> wrote:

On 03/09/2011 09:32 PM, Filipe Maia wrote:

1) From what file are you trying to obtain the phases? Some files do not contain phase information. You can check the "phased" flag to see if there should be phase information. You do "h5dump -d phased <file>" to see only the phased flag (1 meaning phases should be there 0 otherwise). If you want to import the information to matlab or mathematica there are function in both programs to read hdf5 files directly (http://www.mathworks.com/help/techdoc/ref/hdf5read.html http://reference.wolfram.com/mathematica/ref/format/HDF5.html).

from the real-space-xxx.h5 create from Hawk.

h5dump -d phased real_space-0019999.h5   gave:
HDF5 "real_space-0019999.h5" {
DATASET "phased" {
  DATATYPE  H5T_IEEE_F32LE
  DATASPACE  SIMPLE { ( 1 ) / ( 1 ) }
  DATA {
  (0): 1
  }
so it seems that it' a "phased" file.


From h5dump real_space-0019999.h5  I got:

HDF5 "real_space-0019999.h5" {
GROUP "/" {
  DATASET "detector_distance" {
     DATATYPE  H5T_IEEE_F32LE
     DATASPACE  SIMPLE { ( 1 ) / ( 1 ) }
     DATA {
     (0): 6.33708e-10
     }
  }
  DATASET "imag" {
     DATATYPE  H5T_IEEE_F32LE
     DATASPACE  SIMPLE { ( 2048, 2048, 1 ) / ( 2048, 2048, 1 ) }
     DATA {
     (0,0,0): -2.89403e-05,
     (0,1,0): 6.23399e-05,
     (0,2,0): 0.000188466,
     (0,3,0): 0.000311784,
     (0,4,0): 0.000403239,
     (0,5,0): 0.000459086,
     (0,6,0): 0.000496623,
     (0,7,0): 0.000533712,
     (0,8,0): 0.000570532,
     (0,9,0): 0.000588564,
     (0,10,0): 0.000565864,
     (0,11,0): 0.000494439,
     (0,12,0): 0.000386535,
so, it's seems there are only real and not complex number! I don't know if I'm missing smth

The "imag" entry corresponds to the imaginary part of the complex number (and the "real" entry corresponds to the real part).

HDF5 does not natively support complex numbers so that's why I split it into 2 entries.

------
Great I didn't know that with mathematica it's possible to read them. thks

2) First it would be best if you could use the git version of the source file. Just go to https://github.com/FilipeMaia/libspimage and click on the Downloads button. You can also use git directly to clone the repository. It might be that the problem has already been fixed in the latest version. If not just send me the output you get.

I got a clone. At the moment I solved the problem for HDF5 (the problem was with HDF5_LIBRARY, but not for fftw . Looking in  CMakeCache.txt:
-----------------------------------------
//Path to a library.
FFTW3_FFTWF_LIBRARY:FILEPATH=FFTW3_FFTWF_LIBRARY-NOTFOUND

//Path to a library.
FFTW3_FFTWF_SSE_LIBRARY:FILEPATH=FFTW3_FFTWF_SSE_LIBRARY-NOTFOUND

//Path to a library.
FFTW3_FFTWF_THREADS_LIBRARY:FILEPATH=FFTW3_FFTWF_THREADS_LIBRARY-NOTFOUND

//Path to a library.
FFTW3_FFTWL_LIBRARY:FILEPATH=FFTW3_FFTWL_LIBRARY-NOTFOUND

//Path to a library.
FFTW3_FFTWL_THREADS_LIBRARY:FILEPATH=FFTW3_FFTWL_THREADS_LIBRARY-NOTFOUND

//Path to a library.
FFTW3_FFTW_LIBRARY:FILEPATH=/usr/local/lib/libfftw3.a

//Path to a library.
FFTW3_FFTW_SSE2_LIBRARY:FILEPATH=FFTW3_FFTW_SSE2_LIBRARY-NOTFOUND

//Path to a library.
FFTW3_FFTW_THREADS_LIBRARY:FILEPATH=FFTW3_FFTW_THREADS_LIBRARY-NOTFOUND
//Path to a file.
FFTW3_INCLUDE_DIR:PATH=/usr/local/include
----------------------------------------------------------
the /usr/local/lib/libfftw3.a it is correct and
in the /usr/local/include I have fftw3.f and fftw3.h files

The fact that the others libraries are not found is not necessarily an error. There are many ways(too many) to build fftw3 and some generate one library while others generate many libraries. You just have to make sure you compiled it with floating point (single precision) and threads support. Try running make and see how it goes. If there are symbols missing you should see it during the linking stage.

[dritan-IC]

thks Filipe,
now I understand better how it works. So, to dump the real dataset I
used:
h5dump -d real real_space-0059999.h5
and for "imag" dataset:
h5dump -d real real_space-0059999.h5

great.


On Mar 10, 12:14 am, Filipe Maia <filipe.c.m...@gmail.com> wrote:

> >> file. Just go tohttps://github.com/FilipeMaia/libspimageand click on

[dritan-IC]

at the end I succeed to compile libspimage and hawk (the libspimage
tests program and uwrapc works !).. but without HawkGUI.
To finish to compilation I used the option "USE_QT4:BOOL=OFF"

with the option ON I got the error:

[ 34%] Building CXX object src/HawkGUI/CMakeFiles/HawkGUI.dir/
hawkgui.cpp.o
/usr/local/filipe/hawk/src/HawkGUI/hawkgui.cpp: In member function
‘void HawkGUI::createGUI()’:
/usr/local/filipe/hawk/src/HawkGUI/hawkgui.cpp:39: error: ‘class
QStackedLayout’ has no member named ‘setStackingMode’
/usr/local/filipe/hawk/src/HawkGUI/hawkgui.cpp:39: error: ‘StackOne’
is not a member of ‘QStackedLayout

cheers
Dritan

On Mar 10, 12:14 am, Filipe Maia <filipe.c.m...@gmail.com> wrote:

> >> file. Just go tohttps://github.com/FilipeMaia/libspimageand click on

[Filipe Maia]

Great! You need Qt 4.4 or later to be able to build the GUI.

[dritan-IC]

ah .. ok.. my version is 4.3. I will update it
thks

> > > >> file. Just go tohttps://github.com/FilipeMaia/libspimageandclick on