Code

Modules:

• babelscan.babelscan
  • babelscan
  • Class: Scan
  • Class: MultiScan
• babelscan.folder_monitor
  • folder_monitor
  • Class: FolderMonitor
• babelscan.instrument
  • instrument
  • Class: Instrument
• babelscan.volume
  • volume
  • Class: Volume
  • Class: ArrayVolume
  • Class: ImageVolume
  • Class: DatasetVolume

babelscan

BabelScan A generic class for reading many types of scan data that you don’t need to put in your ear.

requirements: numpy, h5py, imageio, python-dateutil Optional requirements: matplotlib, lmfit

Installation:

pip install git+https://github.com/DanPorter/babelscan.git

Usage:

from babelscan import file_loader scan1 = file_loader(‘some/file.nxs’, **options) # creates Scan class scan2 = file_loader(‘another/file.dat’, **options) scans = scan1 + scan2 # creates MultiScan class

# Folder monitor: from babelscan import FolderMonitor mon = FolderMonitor(‘/some/folder’, **options) scan = mon.scan(0) # creates scan from latest file in folder

# intrument configuration file from babelscan import instrument_from_config i16 = instrument_from_config(‘config_files/i16.config’) experiment = i16.experiment(‘/data/folder’) scan = experiment.scan(0)

Scan class

Scan class contains an internal namespace where each dataset can contain multiple names. Calling the instantiated class searches the namespace (and then the file) for a dataset that matches the name given.

output = scan(‘name’)

Certain names are reserved and will automatically search the namespace and file for default values:

scan(‘axes’) # returns default scanned dataset (x-axis) scan(‘signal’) # returns default signal dataset (y-axis)

Operations will be evaluated*:

scan(‘name1 + name2’) # returns the result of the operation

For scans with detector images, regions of interest can be generated:

scan(‘nroi[127,127,31,31]’) # creates region of interest on image and returs array of sum of roi at each point

Functions

scan.title() # returns str title of scan scan.label() # returns short scan identifier scan.scan_command() # returns definition of the scan command (if available) scan.value(‘name’) # always returns a single value scan.string(‘name’) # returns ‘name = value’ string scan.array([‘name1’, ‘name2’], array_length) # returns square array of several datasets scan.image(idx) # if available, returns detector image scan.string_format(‘format {name:fmt}’) # returns string formated from namespace scan.get_plot_data(xname, yname) # return data for plotting with errors and labels scan.plot(xname, yname) # create plot** scan.fit(xname, yname) # fit data to peak***

MultiScan class

MultiScan class is a holder for multiple scans, allowing operations to be performed on all scans in the class.

scans = MultiScan([scan1, scan2], **options) scans = scan1 + scan2 scans = babelscan.load_files([‘file1’, ‘file2’], **options)

Works in the same way as underlying scan class - calling the class will return a list of datasets from the scans.

[output1, output2] = scans(‘name’)

Functions

scans.add_variable(‘name’) # add default parameter that changes between scans, displayed in print(scans) scans.array(‘name’) # return 2D array of scan data scans.griddata(‘name’) # generate 2D square grid of single values for each scan

FolderMonitor class

FolderMonitor watches a folder (or several) and allows easy loading of files by scan number:

fm = FolderMonitor(‘/some/folder’, filename_format=’%d.nxs’) scan = fm.scan(12345) # loads ‘/some/folder/12345.nxs’ scan = fm.scan(0) # loads most recent file scans = fm.scans(range(12340, 12345)) # MultiScan of several files

Functions:

fm.allscanfiles() # return list of all scan files in folder(s) fm.allscannumbers() # list of all scan numbers in folder(s) fm.updating_scan(12345) # the resulting Scan class will reload on each operation

Instrument class

An instrument is a generator of Scans and FolderMonitors (experiements) with specific default settings

beamline = Instrument(‘name’, default_names, functions, filename_format) or beamline = instrument_from_config(‘../config_files/i16.config’) scan = beamline.scan(‘/some/folder/12345.nxs’) fm = beamline.experiment(‘/some/folder’)

*functions using eval only available when the “EVAL_MODE” setting is active. **functions using plot only available if “MATPLOTLIB_PLOTTING” setting is active and matplotlib installed ***functions using fitting only available if lmfit installed

By Dan Porter, PhD Diamond Light Source Ltd. 2021

Version 0.8.4 Last updated: 18/01/23

Version History: 13/04/21 0.1.0 Version History started. 16/04/21 0.2.0 Added instrument and other additions to Scan, changed container.py to folder_monitor.py 22/04/21 0.3.0 Changed _get_data search path and added _default_values dict, added volume.py, settings.py 26/04/21 0.4.0 Various changes and fixes after testing with i06, i10 files 04/05/21 0.4.1 Added names dict to axes/signal from cmd functions 28/05/21 0.5.0 Tidied up code, various fixes 01/06/21 0.5.1 Added additional hdf functions 04/06/21 0.5.2 Added plot and fit functions for MultiScan 05/08/21 0.5.3 Added __main__.py 22/10/21 0.6.0 Various updates, included plotting in volume, removed automatic search any in scan(‘name’) 29/10/21 0.6.1 Major update to lmfitting, general purpous multi-peak fitting 31/10/21 0.6.2 Refactored fitting, added new functions, added plotly & html output options to plotting 27/01/22 0.7.0 Added _set_volume and allowed manual settting of volume location 21/02/22 0.8.0 Added plot.scananddetector, other various improvements 04/04/22 0.8.1 Added extra hdf methods load_all and hdf_addresses 26/04/22 0.8.2 Updated FolderMonitor with more plotting and printing functionality 28/04/22 0.8.3 corrected volume for multi-dimensional scans, dat file error corrected, unit tests updated 18/01/23 0.8.4 changed scan.hdf_structure to show NX_class attribute 12/04/23 0.8.5 caught a couple of errors in hdf tree and axes for scan length 1

ToDo

• Speed up very slow initial file_loader time

• Add SRS file generator, function nexus2srs

• allow address names such as ‘h-axis’

Licensed under the Apache License, Version 2.0 (the “License”); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an “AS IS” BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

Dr Daniel G Porter, dan.porter@diamond.ac.uk www.diamond.ac.uk Diamond Light Source, Chilton, Didcot, Oxon, OX11 0DE, U.K.