XRD-TAF

X Ray Diffraction - Theoretical Absorption Factors

A GUI app to compute theoretical xray absorption factors (for xray diffracted in a capillary) efficiently on the device's GPU. Made with C#/Unity.

Collaborators

AcediaKleea	d8xa	zzfab

Installation

Download the latest release here. Extract the zip file and put the folder wherever you want to run the app.

How to use

GUI

Main screen

Presets

The app uses presets to store all configurable parameters of the experiment setup. The main screen has input fields for all those parameters.
To save or overwrite a preset, enter a name into the field preset name and hit the save button.
To load an existing preset, enter the name and click load.

All presets are stored under XRD-TAF/Presets, in .json format and can be copied to other installations of the app.

Modes

There are three experiment modes available:

• Point: Computes a single averaged absorption factor for a single path of the xray (diffracted horizontally by angle 2theta).
• Area: Computes pointwise averaged absorption factors for all xray paths to the points on a detector screen.
• Integrated: For each horizontal diffraction angle 2theta, a ring segment is projected onto a detector screen, starting from the intersection point of xray and detector. A sequence of k points is distributed uniformly over that ring segment. The averaged absorption factors for each point are then combined into an average over the whole ring segment.

Parameters

The GUI only displays the parameters relevant to the currently selected mode.
Here's an overview of all parameters:

Parameter	Mode	Input type	Unit	Description
Experiment style	All	Dropdown	-	The experiment setup mode to use for computation.
Grid resolution	All	int	px	The number of points along each axis of the rectangle representing the capillary cross section.
Total diameter	All	float	mm	The total diameter of the capillary.
Cell thickness	All	float	mm	The thickness of the capillary glass.
µ (cell)	All	float	1/mm	Mass attenuation coefficient of the cell material.
µ (sample)	All	float	1/mm	Mass attenuation coefficient of the sample material.
Detector/sample distance	All	float	mm	The orthogonal distance from probe center to detector.
Pixel size (X,Y)	1	float,float	mm,mm	The size of pixels on the detector (width, height).
Resolution	1	float,float	px,px	The number of pixels along each axis of the detector (x,y).
Offset	All	float,float	mm,mm	The capillary's offset from the south-east detector corner.
Ray dimensions (X,Y)	All	float,float	mm,mm	The width and height of the xray beam.
Ray offset (X,Y)	All	float,float	mm,mm	The offset of the xray beam from the probe center (x,y).
Ray profile	All	Dropdown	-	The shape of the xray beam profile. Currently only rectangle is supported.
Filename of angle list	0,2	string	-	The filename (without extension) of a list of angles in XRD-TAF/Input.
Ring parameters	2	float,float,int		Controls the range of the ring segment, and the number of points along it. In order: Start angle, stop angle, number of points.

Settings screen

Contains global settings such as flags and default values. All settings have a description text.

Folder structure

Inside the XRD-TA folder containing the app, this is the folder/file structure:

├── Benchmark 
│   ├── benchmark.csv
│   └── config.csv
├── Input
│   ├── angle-list1.txt
│   ├── angle-list2.txt
│   ├── angle-list3.txt
│   └── ...
├── Logs
│   └── mode{mode}_debug.txt
├── Output
│   ├── group
│   │   ├── preset1
│   │   │   ├── [mode=<mode>][dim=(<res>,<n>,<m>,<k>)] Output.txt
│   │   │   └── ...
│   ├── preset2
│   │   └── [mode=<mode>][dim=(<res>,<n>,<m>,<k>)] Output.txt
│   ├── preset3
│   │   └── [mode=<mode>][dim=(<res>,<n>,<m>,<k>)] Output.txt
│   └── ...
├── Presets
│   ├── preset1.json
│   ├── preset2.json
│   ├── preset3.json
│   └── ...
└── Settings
    └── settings.json

All output directories will be created when needed, if not present.

Benchmark

Stores benchmark config and results.

config.csv is a user-generated table containing parameters for each iteration of the benchmark.
<timestamp> benchmark.csv contains a table of benchmark results for config.csv, generated at the timestamp.

Benchmark parameters are as follows:

mode is a value in (0,1,2), which stand for 0=point, 1=area, 2=integrated.
res is the grid resolution of the capillary cross-section.
n: The number of angles to use in the benchmark. In mode 1, n this is equivalent to the number of pixels on the horizontal axis of the detector.
m: The number of pixels on the vertical axis of the detector. (Ignored in mode 0 and 2).
k: Amount of angles in the projected ring segment of mode 2. (Ignored in mode 0 and 1).

Input

The directory where the app searches for angle lists. Lists are expected to have one value per line and no header.

Logs

If enabled in the settings, log files will be saved in this folder. The log filename will be <timestamp> log.txt.

Output

Calculated absorption factors will be saved in this folder. They will be grouped in folders by preset name -- and if a parent folder is specified in the preset, the whole preset folder will be put in a parent folder see section [Folder structure](### Folder structure).

The filename for each output is of the format [mode=<mode>][dim=(<res>,<n>,<m>,<k>)] Output.txt.

Presets

The directory where are stored, in the format <preset name>.json. The name specified in the preset is identical to the filename (without extension).

Settings

Stores global user settings in settings.json.

Benchmark

Preset

The pre-defined preset benchmark.json will be used for benchmarks. Changes to this preset do not influence the benchmark, since the app takes all time-complexity-relevant parameters from config.csv. Angle files will be ignored, since angle lists will be generated from the parameter n, i.e. n values evenly distributed between 0 and 180°.

Config

To add a benchmark iteration to the config, add a line containing the parameters mode, res, n, m k in the exact same order to Benchmark/config.csv.

Example:

mode	res	n	m	k
0	100	500	0	0
0	200	500	0	0
1	80	128	128	0
1	80	256	256	0
2	100	500	0	20
2	200	500	0	20

Parameter m will be ignored by modes 0 and 2, k will be ignored by mode 0 and 1.

The app expects tabs as value separators for the csv.

Value format

All float input values, in the GUI and in input files, are expectd in invariant culture style, i.e. with . as decimal separator.

All .csv files have to use tabs as separators.