data-exchange / dxfile

Subclasses the h5py module for interacting with Data Exchange files.

DXchange

DXchange provides an interface with TomoPy and raw tomographic data collected at different synchrotron facilities including the Data Exchange file format (DXfile), currently in use at the Advanced Photon Source beamline 2-BM and 32-ID, at the Swiss Light Source Tomcat beamline and at the Elettra SYRMEP beamline.

Warning

DXchange will drop support for Python 2 before 1 January 2020. For more information, visit https://python3statement.org/.

Documentation

• http://dxchange.readthedocs.io

Features

• Scientific Data Exchange file format.
• Readers for tomographic data files collected at different facilities.
• Writers for different file formats.

Highlights

• Based on Hierarchical Data Format 5 (HDF5).
• Focuses on technique rather than instrument descriptions.
• Provenance tracking for understanding analysis steps and results.
• Ease of readability.

Contribute

• Documentation: https://github.com/data-exchange/dxchange/tree/master/doc
• Issue Tracker: https://github.com/data-exchange/dxchange/issues
• Source Code: https://github.com/data-exchange/dxchange

dxfile's Issues

Tag for dxfile?

I'm in the process of writing a recipe for tomopy (cc @dgursoy @licode ) to add it and its dependencies to conda-forge at conda-forge/staged-recipes#681 and need to package this as part of that process. Would it be possible to get a tag on this project so I can point at a tag instead of a git hash?

Thanks!

store time as ISO8601

Currently we save time in the hdf data generated by areadetector using S:IOC:timeOfDayForm2SI:

caget S:IOC:timeOfDayForm2SI
S:IOC:timeOfDayForm2SI         06/08/20 16:07:14

but we should use ISO 8601 standard instead (see dxfile definition).

The change affects all Attribulte.xml files, replacing:

    <Attribute name="DateTimeStart"                 type="EPICS_PV"     source="S:IOC:timeOfDayForm1SI"                  dbrtype="DBR_STRING"  description="Date and time at start"/>
    <Attribute name="DateTimeEnd"                   type="EPICS_PV"     source="S:IOC:timeOfDayForm1SI"                  dbrtype="DBR_STRING"  description="Date and time at end"/>

with

    <Attribute name="DateTimeStart"                 type="EPICS_PV"     source="S:IOC:timeOfDayISO8601"                  dbrtype="DBR_STRING"  description="Date and time at start"/>
    <Attribute name="DateTimeEnd"                   type="EPICS_PV"     source="S:IOC:timeOfDayISO8601"                  dbrtype="DBR_STRING"  description="Date and time at end"/>

After this change the time will be saved as:

caget S:IOC:timeOfDayISO8601
S:IOC:timeOfDayISO8601         2020-06-08T15:59:06-0500

which is easier to manipulate and do math with.

Let me know if you agree with the change as it might break some tool using this tag.

change exposure time PV in the areadetector attribute xml file

Propagate #21 to 2-BM and 32-ID

update 13-BM xml files

@MarkRivers when stable please update the 13-BM xml files.