This is a file structure validator for files that are exported targeting the NEXUS NXstxm application definition http://download.nexusformat.org/sphinx/classes/applications/NXstxm.html This validator depends on nexpy to provide the base class and application definitions which are found in:
<python dist>/Lib/site-packages/nexpy/definitions/base_classes
<python dist>/Lib/site-packages/nexpy/definitions/applications
Tested with:
- Python 3.7
The pyStxm software is dependent on the following python modules (note that their individual dependencies are not listed):
- h5py (2.6.0)
- NeXpy (0.9.3)
- nexusformat (0.4.5)
- numpy (1.11.3)
- simplejson (3.10.0)
- xmltodict (0.12.0)
Start by creating a clone of the repo:
- Create a directory to clone the repo
C:\tmp\Feb21>git clone https://github.com/RussBerg/nxstxm_validator.git
- From that directory type
pip install .
This will create a nxstxm_validator directory with all of the software in it and also place the script
nxstxm_validator in the python distributions Scripts directory if Windows and the bin directory
if linux.
To validate a single file:
nxstxm_validate -f C:/data/2019/0710/C190710197.hdf5
To validate all files within a directory:
nxstxm_validate -d C:/data/2019/0710
The structure of each entry found in the file will be traversed and a quick check done to make sure that fields and attributes that are required by the nxstxm definition exist in the file. Typical output for a single file looks like this, however the console output will contain some colorization to assist in finding issues in a file.
Validating nxstxm file [C:\tmp\aph_jul10\C190710197\C190710197.hdf5]:
####################################################################
### checking for nxentry group called <entry0>:
####################################################################
> it exists and type=NXentry
### checking <entry0> fields:
field[title] exists and type=NX_CHAR is correct
field[start_time] exists and type=NX_DATE_TIME is correct
field[end_time] exists and type=NX_DATE_TIME is correct
field[definition] exists and type=NX_CHAR is correct
### checking <entry0> groups:
NX_class[NXcollection] > EXISTS but it is OPTIONAL
NX_class[NXmonitor] > it exists
NX_class[NXdata] > it exists
NX_class[NXinstrument] > it exists
NX_class[NXsample] > it exists
### checking for NXcollection group
found NXcollection group called <collection>
> it exists and type=NXcollection
### checking <collection> fields:
field[scan_request] exists and type=NXscanDefinition is correct
### checking OPTIONAL NXmonitor group called <control>:
> it exists and type=NXmonitor
### checking <control> attributes:
attr[axes] > it exists
attr[energy] has a corresponding datagroup in this group
attr[sample_y] has a corresponding datagroup in this group
attr[sample_x] has a corresponding datagroup in this group
attr[signal] > it exists
attr[data] has a corresponding datagroup in this group
### checking <control> fields:
field[data] exists and type=NX_NUMBER is correct
field[energy] exists and type=NX_FLOAT is correct
field[epu_offset] exists and type=NX_FLOAT is correct
field[epu_polarization] exists and type=NX_FLOAT is correct
field[sample_x] exists and type=NX_FLOAT is correct
field[sample_y] exists and type=NX_FLOAT is correct
### checking for NXdata group called <counter0>:
> it exists and type=NXdata
### checking <counter0> attributes:
attr[axes] > it exists
attr[energy] has a corresponding datagroup in this group
attr[sample_y] has a corresponding datagroup in this group
attr[sample_x] has a corresponding datagroup in this group
attr[axes] > it exists
attr[energy] has a corresponding datagroup in this group
attr[sample_y] has a corresponding datagroup in this group
attr[sample_x] has a corresponding datagroup in this group
attr[signal] > it exists
attr[data] has a corresponding datagroup in this group
### checking <counter0> fields:
field[stxm_scan_type] exists and type=NX_CHAR is correct
field[data] exists and type=NX_NUMBER is correct
field[energy] exists and type=NX_FLOAT is correct
field[sample_y] exists and type=NX_FLOAT is correct
field[sample_x] exists and type=NX_FLOAT is correct
### checking <counter0> stxm_scan_type:
stxm_scan_type = <sample image stack> is a valid type
### checking for NXinstrument group called <instrument>:
> it exists and type=NXinstrument
### checking <instrument> fields:
field[monochromator] exists and type=NXmonochromator is correct
field[sample_x] exists and type=NXdetector is correct
field[sample_y] exists and type=NXdetector is correct
field[sample_z] > DOES NOT EXIST but it is optional
field[source] exists and type=NXsource is correct
### checking for NXsource group called <source>:
> it exists and type=NXsource
### checking <source> fields:
field[type] exists and type=NX_CHAR is correct
field[name] exists and type=NX_CHAR is correct
field[probe] exists and type=NX_CHAR is correct
### checking for NXsample group called <sample>:
> it exists and type=NXsample
### checking <sample> fields:
field[rotation_angle] exists and type=NX_FLOAT is correct
File: C:\tmp\aph_jul10\C190710197\C190710197.hdf5 contains a valid nxstxm structure
Done
In the event that there are errors they will be displayed as they are found as well as the offending file(s) will be listed at the completion of the validation process, similar to this:
[S:\STXM-data\Cryo-STXM\2019\guest\0622\C190622005.hdf5] FAILED nxstxm validation
[S:\STXM-data\Cryo-STXM\2019\guest\0622\C190622003.hdf5] FAILED nxstxm validation
[S:\STXM-data\Cryo-STXM\2019\guest\0622\C190622004.hdf5] FAILED nxstxm validation
[S:\STXM-data\Cryo-STXM\2019\guest\0622\C190622002.hdf5] FAILED nxstxm validation
- Russ Berg - [email protected]
This project is licensed under the GPL2 License - see the LICENSE.md file for details
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