Data access
Data from DanMAX is stored centrally at MAX IV and is available for further processing using MAX IV resources – or for download using either the Globus connect service or sftp. Detailed information about downloading the data can be found at the following link.
Data handling guides
Format
All scans at DanMAX results in a number of files written in the HDF5 format (*.h5). The files are written to be NeXuS compatible.
Destinations
The raw files are stored in:
/data/visitors/danmax/#Proposal/#Visit/raw/while reduced files are stored in:
/data/visitors/danmax/#Proposal/#Visit/process/Ipython notebookes for processing data will be placed in:
/data/visitors/danmax/#Proposal/#Visit/scripts/Separate experiments/samples may be stored in their own folder. The ‘raw’ folder is write protected to protect the raw data. The ‘process’, ‘scripts’ and other folders are not protected so it is possible to edit/overwrite files in these
Archiving
Each scan will be saved with the name scan-####.h5 where #### is a sequential number. It is important to keep track of this number and the corresponding sample/experiment, e.g. by using the Elogy logbook at elogy.maxiv.lu.se.
The scan-####.h5 file is a master file that contains the command issued to perform the scan, the scanned parameters (e.g. motor positions), experimental channels (e.g. beam intensity, position, temperature) a snapshot of the instrument at the beginning of the scan and links to the detector data files.
The data from the detectors are located in separate files, e.g. scan-####_pilatus.h5 and scan-####_falconx.h5. The link from the master file to the detector data is relative, and thus all files must be located in the same folder.
Additional information
To visualize the data and the file structure we recommend to use silx view which is available on the control computers. The Silx installation files can be found on silx.org
As the area detector data is compressed using a bit-shuffle algorithm, it is necessary to install hdf5plugin, which can be found on pypi.org
A description of the experimental snapshot parameters is given in the next tab.
Azimuthal integration pipeline
An automated azimuthal integration pipeline is available based on the MATFRAIA algorithm developed by the Birkedal group at Aarhus University (Publication: https://scripts.iucr.org/cgi-bin/paper?S1600577522008232, MATLAB source code). To prepare the pipeline a .poni file and a detector mask (.npy) is needed.
pyFAI-calib2 is installed on the control computers and is commonly used to generate these files. More information about the pipeline can be found on the beamline wiki, under Pilatus 2M CdTe
The integrated data will be available as saved in the following folder, mirroring the folder name and scan number in the /raw/ folder.
/data/visitors/danmax/#Proposal/#Visit/process/azint/Jupyter
It is also possible to process the data in Jupyter notebooks, using jupyterhub.maxiv.se, where you need to log in using your DUO credentials. To have access to the regular environment with HDF5, silx and pyFAI tools you should select the “HDF5 / Simple Analysis /GPU” kernel.
The experimental snapshot is a recording of the essential instrument parameters at the beginning of the scan. The snap shot is contained in the master file for each scan, and is located under
/entry/instrument/start_positioners/.| Name | Description |
| ea_ppm3_1 | Sample to detector distance (Pilatus 2M) – may not reflect the actual distance if calibration has not been performed after changing configuration. |
| ea_xrf_z | Sample to detector distance (Fluorescence detector) – may not reflect the actual distance if calibration has not been performed after changing configuration. |
| ea_slit1_* | This is the slit located on the BCU |
| ea_slit2_* | This is the slit located on the PXRD2D instrument |
| ea_mm_* | Is the location of the collimator/pinhole |
| ea_bst_* | Is the location of the beamstop |
| hex_* | Is the positions and angles of the hexapod |
| Spinner moving | Is indicating wheter or not the spinner is spinning at the beginning of the scan. |
| IVU_R3_304_GAP | Is the undulator gap |
| hdcm_energy | Energy of the Si111 hDCM based on encoder position |
| mlm_energy | Energy of the hMLM based on encoder position |
| Pilatus energy | Is the energy setting on the Pilatus responsible for setting the flatfield of the detector |
| Pilatus threshold | Is the threshold energy of the Pilatus responsible for energy discrimination |
Some names are self-explanatory and not listed here.