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Subject: | Re: hdf5 (h5py) anyone? |
From: | "Pete R. Jemian" <[email protected]> |
To: | [email protected] |
Date: | Thu, 22 Mar 2012 12:53:58 -0500 |
A single image is stored as one dataset. It is also possible to store a series of image frames as one dataset. It is possible to do even more advanced arrangements.
There is an international group of scientists (NeXus) that formed to define a standard of how to arrange scientific data in HDF files to make it easy (ok, easier) to use experiment data collected from various X-ray, neutron, and muon science user facilities. See the website for more details: http://www.nexusformat.org
I'm not sure the choice of data file format can help in the reconstruction. Rather, the data file format helps in the organization of data files, potentially reducing the number of data files related to a single experiment or other use case.
Pete On 3/22/2012 12:27 PM, Emmanuel Mayssat wrote:
Just out of curiosity, why would you store images in hdf5 files? How do you store them? 1 image = 1 huge table with pixel intensity? It must be because it is easier to get statistics, extract region of interest, work with several images (datasets), etc. Is that correct? For a project, I worked on some time ago (but dropped due to lack of funding), we were looking at CT-scan type of applications with 8 exposures per rotation angle, 180 deg rotation with 0.5 deg step, i.e. descent size data set. I am wondering if hdf5 could have helped in the reconstruction. Then and still today, we were/are using mar/crayonix software. MAR doesn't store image in hdf5 format, but can the areaDetector package convert those files on the fly? -- E ------------------------------------------------------------------------ *From:* Mark Rivers <[email protected]> *To:* 'Emmanuel Mayssat' <[email protected]>; epics <[email protected]> *Sent:* Thursday, March 22, 2012 7:32 AM *Subject:* RE: hdf5 (h5py) anyone? The EPICS areaDetector <http://cars9.uchicago.edu/software/epics/areaDetector.html> package currently has 2 file writers that produce HDF5 files: NDFileNexus <http://cars.uchicago.edu/software/epics/NDPluginFile.html#NeXus> creates NeXus compliant HDF5 files using the NeXus API. It was written by John Hammonds from the APS. NDFileHDF5 <http://cars.uchicago.edu/software/epics/NDPluginFile.html#HDF5> creates HDF5 files using the native HDF5 API. It was written by Ulrik Pedersen from Diamond Light Source Mark
-- ---------------------------------------------------------- Pete R. Jemian, Ph.D. <[email protected]> Beam line Controls and Data Acquisition, Group Leader Advanced Photon Source, Argonne National Laboratory Argonne, IL 60439 630 - 252 - 3189 ----------------------------------------------------------- Education is the one thing for which people are willing to pay yet not receive. -----------------------------------------------------------