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[WIP] Implemented estimation of particle size, peak picking and migra…
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…ted functionality from 'xrd' package (#7)

* chore: migrated functionality of xrd package

- parsers for brml and xy included together with the corresponding tests
- they could still need some more refactoring

* chore: added docstrings

* feat: Scherrer Analysis, Peak picking, fromXY

- we parse now the anode metal from BRML to be able to automatically do the Scherrer analysis 
- for this, there is also a constant object that tabulates wavelengths of common anodes 
- for this, we now also support peak picking 
- and there is also a function to create the annotation, potentially also with assignment 
- additionally, there is now also a fromXY function
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@kjappelbaum
kjappelbaum authored Jul 3, 2020
1 parent 21b4126 commit 8d5e7e0
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Showing 21 changed files with 8,861 additions and 4 deletions.
8 changes: 6 additions & 2 deletions package.json
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Original file line number Diff line number Diff line change
Expand Up @@ -52,7 +52,11 @@
"rollup": "^2.18.0"
},
"dependencies": {
"common-spectrum": "0.3.0",
"xrd": "0.2.1"
"common-spectrum": "^0.3.0",
"convert-to-jcamp": "^3.1.1",
"fast-xml-parser": "^3.17.4",
"jcampconverter": "^7.3.1",
"jszip": "^3.5.0",
"ml-gsd": "^5.0.1"
}
}
186 changes: 186 additions & 0 deletions src/analysis/__tests__/addPeak.test.js
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@@ -0,0 +1,186 @@
import { Analysis } from '../..';
import { addPeak } from '../addPeak';

test('addPeak', () => {
let analysis = new Analysis();

analysis.pushSpectrum(
{
x: {
data: [
10,
10.87014232,
11.74028464,
12.61042695,
13.48056927,
14.35071159,
15.22085391,
16.09099623,
16.96113855,
17.83128086,
18.70142318,
19.5715655,
20.44170782,
21.31185014,
22.18199246,
23.05213477,
23.92227709,
24.79241941,
25.66256173,
26.53270405,
27.40284637,
28.27298868,
29.143131,
30.01327332,
30.88341564,
31.75355796,
32.62370028,
33.49384259,
34.36398491,
35.23412723,
36.10426955,
36.97441187,
37.84455419,
38.7146965,
39.58483882,
40.45498114,
41.32512346,
42.19526578,
43.0654081,
43.93555041,
44.80569273,
45.67583505,
46.54597737,
47.41611969,
48.28626201,
49.15640432,
50.02654664,
50.89668896,
51.76683128,
52.6369736,
53.50711592,
54.37725823,
55.24740055,
56.11754287,
56.98768519,
57.85782751,
58.72796983,
59.59811214,
60.46825446,
61.33839678,
62.2085391,
63.07868142,
63.94882374,
64.81896605,
65.68910837,
66.55925069,
67.42939301,
68.29953533,
69.16967764,
],
units: 'xUnits',
label: 'X axis [xUnits]',
},
y: {
data: [
0.0,
2.81944455e-1,
-1.76789118e-1,
-2.61612632e-1,
-2.13420693e-1,
7.70339438e-1,
1.76926027e-1,
-6.15719808e-2,
-1.52426047e-2,
1.34201582e-1,
-3.21258697e-1,
8.91666765e-2,
9.81981592e-2,
5.38614167e-1,
-1.22550072e-1,
1.74433215e-1,
1.79804788e-1,
-3.28079254e-1,
-5.09646976e-2,
9.961077e-2,
2.17736107e-1,
-1.29382215e-1,
7.7247087e-1,
9.54841237e-1,
4.17728884e-1,
-6.33157697e-1,
4.16611111e-1,
-6.30172049e-1,
9.11546241e-1,
6.21294848,
5.51802847e1,
1.19177215e1,
3.63359221,
5.64039691,
5.52718888e-1,
3.03098156e-1,
1.73733837,
3.64738026e1,
2.36578407,
8.18592954e-1,
7.72784579e-1,
1.11845869e-1,
-2.7079057e-1,
6.17881315e-1,
6.42247963e-1,
1.65546523,
3.60457562e-1,
7.88020263e-2,
-2.94264172e-2,
1.03134295,
7.89296257e-1,
1.92793644e-1,
-3.58884917e-1,
-1.53114319e-1,
-5.190557e-1,
-3.43872664e-1,
-2.11089013e-1,
1.87279872,
4.18782812,
3.79396248e1,
4.58652209,
3.57686663e-1,
1.59368518e-1,
-3.93749997e-1,
7.90297702e-1,
6.35900771e-1,
1.89104455e-1,
-5.00912467e-2,
-1.17836305e-1,
],
units: 'yUnits',
label: 'Y axis [yUnits]',
},
},
{
title: 'My testpattern',
dataType: 'XRD',
},
);

let spectrum = analysis.getSpectrum();
const peak = {
x: 5,
y: 10,
fwhm: 1,
};
addPeak(spectrum, peak);

expect(spectrum).toHaveProperty('peaks');
expect(spectrum.peaks).toHaveLength(1);
expect(spectrum.peaks[0]).toStrictEqual(peak);

const peak2 = {
x: 5.9,
y: 1000.1,
fwhm: 0.5,
};
addPeak(spectrum, peak2);
expect(spectrum.peaks).toHaveLength(2);
expect(spectrum.peaks[1]).toStrictEqual(peak2);
});
169 changes: 169 additions & 0 deletions src/analysis/__tests__/autoPeakPicking.test.js
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@@ -0,0 +1,169 @@
import { Analysis } from '../..';
import { autoPeakPicking } from '../autoPeakPicking';

test('autoPeakPicking', () => {
let analysis = new Analysis();

analysis.pushSpectrum(
{
x: {
data: [
10,
10.87014232,
11.74028464,
12.61042695,
13.48056927,
14.35071159,
15.22085391,
16.09099623,
16.96113855,
17.83128086,
18.70142318,
19.5715655,
20.44170782,
21.31185014,
22.18199246,
23.05213477,
23.92227709,
24.79241941,
25.66256173,
26.53270405,
27.40284637,
28.27298868,
29.143131,
30.01327332,
30.88341564,
31.75355796,
32.62370028,
33.49384259,
34.36398491,
35.23412723,
36.10426955,
36.97441187,
37.84455419,
38.7146965,
39.58483882,
40.45498114,
41.32512346,
42.19526578,
43.0654081,
43.93555041,
44.80569273,
45.67583505,
46.54597737,
47.41611969,
48.28626201,
49.15640432,
50.02654664,
50.89668896,
51.76683128,
52.6369736,
53.50711592,
54.37725823,
55.24740055,
56.11754287,
56.98768519,
57.85782751,
58.72796983,
59.59811214,
60.46825446,
61.33839678,
62.2085391,
63.07868142,
63.94882374,
64.81896605,
65.68910837,
66.55925069,
67.42939301,
68.29953533,
69.16967764,
],
units: 'xUnits',
label: 'X axis [xUnits]',
},
y: {
data: [
0.0,
2.81944455e-1,
-1.76789118e-1,
-2.61612632e-1,
-2.13420693e-1,
7.70339438e-1,
1.76926027e-1,
-6.15719808e-2,
-1.52426047e-2,
1.34201582e-1,
-3.21258697e-1,
8.91666765e-2,
9.81981592e-2,
5.38614167e-1,
-1.22550072e-1,
1.74433215e-1,
1.79804788e-1,
-3.28079254e-1,
-5.09646976e-2,
9.961077e-2,
2.17736107e-1,
-1.29382215e-1,
7.7247087e-1,
9.54841237e-1,
4.17728884e-1,
-6.33157697e-1,
4.16611111e-1,
-6.30172049e-1,
9.11546241e-1,
6.21294848,
5.51802847e1,
1.19177215e1,
3.63359221,
5.64039691,
5.52718888e-1,
3.03098156e-1,
1.73733837,
3.64738026e1,
2.36578407,
8.18592954e-1,
7.72784579e-1,
1.11845869e-1,
-2.7079057e-1,
6.17881315e-1,
6.42247963e-1,
1.65546523,
3.60457562e-1,
7.88020263e-2,
-2.94264172e-2,
1.03134295,
7.89296257e-1,
1.92793644e-1,
-3.58884917e-1,
-1.53114319e-1,
-5.190557e-1,
-3.43872664e-1,
-2.11089013e-1,
1.87279872,
4.18782812,
3.79396248e1,
4.58652209,
3.57686663e-1,
1.59368518e-1,
-3.93749997e-1,
7.90297702e-1,
6.35900771e-1,
1.89104455e-1,
-5.00912467e-2,
-1.17836305e-1,
],
units: 'yUnits',
label: 'Y axis [yUnits]',
},
},
{
title: 'My testpattern',
dataType: 'XRD',
},
);

let spectrum = analysis.getSpectrum();
autoPeakPicking(spectrum);
expect(spectrum.peaks).toHaveLength(3);
});
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