Dan Porter DanPorter

## read_i16_nexus_file.py

import numpy as np
import h5py
import matplotlib.pyplot as plt

file = '1109527.nxs'

with h5py.File(file, 'r') as hdf:
    scan_command = hdf['/entry/scan_command'].asstr()[...]  # str
    crystal = hdf['/entry/sample/name'].asstr()[...]  # str

## run.py
#!/usr/bin/env python
# -*- coding: utf-8 -*-


def load_gist(gist_id):
    """read gist source code"""
    from json import load
    from urllib.request import urlopen

    gist_api = urlopen("https://api.github.com/gists/" + gist_id)

## jupyter_notebook_runner.py
"""
Example python code to adapt a jupyter notebook template and convert it to html

Uses nbformat and nbconvert
See also: papermill
"""

import os
import shutil
import nbformat

## element-edge-enums.py
"""
Create element-edge enum

X-Ray absorption edges are taken from the X-ray Data Booklet
https://xdb.lbl.gov/Section1/Sec_1-1.html

These are convieniently stored in Dans_Diffraction with other atomic data
$ pip install Dans_Diffraction

For refrences, see: https://github.com/DanPorter/Dans_Diffraction/tree/master/Dans_Diffraction/data

## pdnx_with_tests_i16_example.ipynb

      
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                pdnx_with_tests_i16_example
              
          
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## hdfmap_example.py
"""
Example of HdfMap code

GitHub repo: https://github.com/DiamondLightSource/hdfmap
Docs: https://diamondlightsource.github.io/hdfmap/

installation:
$ python -m pip install hdfmap

Dan Porter 2024

## find_ExternalLink_files.py
"""
Find ExternalLink files in NeXus file

By Dan Porter
9 / 10/ 2024
"""

import os
import h5py

## find_files_with_links.py
"""
Find NeXus files with external links

By Dan Porter
9 / 10/ 2024
"""

import os
import h5py

## oriented_reciprocal_lattice_vectors.py
import Dans_Diffraction as dif

xtl = Crystal('filename.cif')
# rotate the crystal basis
xtl.Cell.orientation.rotate_6circle(mu=5)  # rotate about x-axis, in degrees
# get return the lab-frame q-vector for a single reflection:
q = xtl.Cell.calculateQ([0, 0, 2])

# or, generate the entire reciprocal lattice
all_hkl = xtl.Scatter.get_hkl(energy_kev=8)  # there are lots of other arguments for this!

## i16_read_nxs_files_babelscan.py
# module load python/3
# or pip install babelscan

import sys
sys.path.insert(0, '/dls_sw/i16/software/python/babelscan')
from babelscan import file_loader, FolderMonitor

# Load scan object
scan = file_loader('/dls/i16/data/2021/mm29566-1/12345.nxs')
print(scan)

	import numpy as np
	import h5py
	import matplotlib.pyplot as plt

	file = '1109527.nxs'

	with h5py.File(file, 'r') as hdf:
	scan_command = hdf['/entry/scan_command'].asstr()[...] # str
	crystal = hdf['/entry/sample/name'].asstr()[...] # str
	#!/usr/bin/env python
	# -- coding: utf-8 --


	def load_gist(gist_id):
	"""read gist source code"""
	from json import load
	from urllib.request import urlopen

	gist_api = urlopen("https://api.github.com/gists/" + gist_id)
	"""
	Example python code to adapt a jupyter notebook template and convert it to html

	Uses nbformat and nbconvert
	See also: papermill
	"""

	import os
	import shutil
	import nbformat
	"""
	Create element-edge enum

	X-Ray absorption edges are taken from the X-ray Data Booklet
	https://xdb.lbl.gov/Section1/Sec_1-1.html

	These are convieniently stored in Dans_Diffraction with other atomic data
	$ pip install Dans_Diffraction

	For refrences, see: https://github.com/DanPorter/Dans_Diffraction/tree/master/Dans_Diffraction/data
	"""
	Example of HdfMap code

	GitHub repo: https://github.com/DiamondLightSource/hdfmap
	Docs: https://diamondlightsource.github.io/hdfmap/

	installation:
	$ python -m pip install hdfmap

	Dan Porter 2024
	"""
	Find ExternalLink files in NeXus file

	By Dan Porter
	9 / 10/ 2024
	"""

	import os
	import h5py
	"""
	Find NeXus files with external links

	By Dan Porter
	9 / 10/ 2024
	"""

	import os
	import h5py
	import Dans_Diffraction as dif

	xtl = Crystal('filename.cif')
	# rotate the crystal basis
	xtl.Cell.orientation.rotate_6circle(mu=5) # rotate about x-axis, in degrees
	# get return the lab-frame q-vector for a single reflection:
	q = xtl.Cell.calculateQ([0, 0, 2])

	# or, generate the entire reciprocal lattice
	all_hkl = xtl.Scatter.get_hkl(energy_kev=8) # there are lots of other arguments for this!
	# module load python/3
	# or pip install babelscan

	import sys
	sys.path.insert(0, '/dls_sw/i16/software/python/babelscan')
	from babelscan import file_loader, FolderMonitor

	# Load scan object
	scan = file_loader('/dls/i16/data/2021/mm29566-1/12345.nxs')
	print(scan)