From dbf2720505daf31fa33c1decb25be8d5dc7effb3 Mon Sep 17 00:00:00 2001
From: DiffuseDevelopers <158596382+DiffuseDevelopers@users.noreply.github.com>
Date: Wed, 10 Apr 2024 13:25:24 +0200
Subject: [PATCH] Create README.md for Data format

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+Proposal for a common 3D-Diffuse / 3D PDF data structure
+ 
+The intensity/3D-PDF is essentially
+- A 3D voxel of real valued data points
+- It is based on a non-cartesian metric
+- Usually, it is based on an even spaced grid (different steps sizes along a/b/c are possible)
+ 
+For the Nexus file format:
+The only required field is a NXentry “These contain all the data that is required to describe an experimental run or scan” → This would be useful if we have several structures/datasets that are afterwards averaged. The default would only be one entry. 
+
+NXdata is one level below the NXentry. “contain the experimental results in a self-contained way, i.e., it should be possible to generate a sensible plot of the data from the information contained in each NXdata group.”
+
+NXsample and NXinstrument are likely not necessary in our case. We could think about making a NXProgram that dumps important program information.
+
+Necessary entries:
+
+NXentry/title:
+Content: title of the data
+Type: H5T_STRING
+
+NXentry/NXdata/type: 
+Content type of data, options could be, e.g.  experimental data, intensity, real part, imaginary part, structure factor,  …)
+Type: H5T_STRING
+
+NXentry/NXdata/space: 
+Content: real space or reciprocal space data 
+Type: boolean?  
+
+NXentry/NXdata/dimension: 
+Content: contains the dimension of the data: 1d, 2d, 3d 
+Type: integer
+
+NXentry/NXdata/data: 
+Content:The actual data array nd array of  
+Type: H5T_NATIVE_DOUBLE
+
+NXentry/NXdata/lower_limits:  
+Content: the lower left bottom corner in terms of a*/b*/c*  or a/b/c
+Type: 3 H5T_NATIVE_DOUBLE
+
+NXentry/NXdata/step_sizes:  
+Content: increment along the n axis in terms of  a*/b*/c*  or a/b/c
+Type: n*3 H5T_NATIVE_DOUBLE
+
+NXentry/NXdata/unit_cell:  
+Content: Metric tensor, alternatively a,b,c, alpha, beta, gramma
+Type: 6 H5T_NATIVE_DOUBLE
+
+NXentry/NXdata/radiation:  
+Content: radiation type used: x-ray, electron, neutron
+Type: H5T_STRING
+
+NXentry/NXdata/wavelength:  
+Content: Wavelength
+Type:  H5T_NATIVE_DOUBLE
+
+NXentry/NXprogram/program_version:
+Content: program used to generate the data with version number
+Type: H5T_STRING
+
+Optional entries:
+NXentry/NXdata/symmetry:  
+Content: Symmetry that has been applied to the data, specified as Laue symmetry
+Type:  H5T_STRING
+
+NXentry/NXdata/adp:  
+Content: Specifies if adp have been used in the calculation, possible value: non, isotropic, anisotropic
+Type:  H5T_STRING
+
+NXentry/NXdata/dispersion:  
+Content: Specifies if dispersion correction was applied
+Type:  Boolean
+
+NXentry/NXprogram/formfactors: 
+Content: Specifies a link to the form factors that have been used, e.g. which gaussian approximation
+Type:  H5T_STRING
+
+NXentry/NXprogram/averaging: 
+Content: Specifies the type of averaging used, e.g. Lots or Lanczos filter or similar
+Type:  H5T_STRING
+
+NXentry/NXprogram/approximation: 
+Content: Specifies approximations used in the calculation, e.g. fft, level of approximation in nufft….
+Type:  H5T_STRING
+ 
+NXentry/NXdata/structurefactor: 
+Content: complex structure factor
+Type: Is there a complex pre-defined h5 type?
+
+NXentry/NXdata/mask: 
+Content: mask applied to the data
+Type: H5T_NATIVE_DOUBLE
+
+NXentry/NXdata/kinematic: 
+Content: Kinematic or dynamical scattering intensity
+Type: Boolean
+
+NXentry/NXdata/elastic: 
+Content: Elastic or integral scattering intensity
+Type: Boolean
+