Merge pull request #765 from callumgassner/polar_new

[ENH] 4+ Angle Polarisation widget and Hyper Spectra vector plot

MANIFEST.in

@@ -8,6 +8,7 @@ recursive-include orangecontrib/spectroscopy/datasets NeaReaderGSF_test/*
 recursive-include orangecontrib/spectroscopy/datasets renishaw_test_files/*
 recursive-include orangecontrib/spectroscopy/datasets photothermal/*
 recursive-include orangecontrib/spectroscopy/datasets perkinelmer/*
+recursive-include orangecontrib/spectroscopy/datasets polar/*
 
 global-exclude __pycache__
 

doc/index.rst

@@ -36,6 +36,7 @@ Widgets
    widgets/pls
    widgets/peakfit
    widgets/snr
+   widgets/polar
 
 Indices and tables
 ------------------

doc/widgets.json

@@ -128,7 +128,14 @@
     "icon": "../orangecontrib/spectroscopy/widgets/icons/stackalign.svg",
     "background": "light-blue",
     "keywords": []
+   },
+   {
+    "text": "4+ Angle Polarisation",
+    "doc": "widgets/polar.md",
+    "icon": "../orangecontrib/spectroscopy/widgets/icons/unknown.svg",
+    "background": "light-blue",
+    "keywords": []
    }
   ]
  ]
-]
+]

doc/widgets/polar.md

@@ -0,0 +1,50 @@
+4+ Angle Polarization
+============
+
+Calculates vibrational mode orientation from polarized infrared spectroscopy datasets
+
+**Inputs**
+
+- Data: input dataset(s)
+
+**Outputs**
+
+- Polar Data: dataset with selected feature(s) orientation information
+- Curve Fit Model Data: dataset with the optimal parameters of the curve fit model
+
+The **4+ Angle Polarization** widget allows you to calculate orientation information of selected features using polarized spectroscopy data collected at 4 or more polarization angles. The implemented algorithm is the same as that outlined by Hikima et al. (2013)<sup>1</sup>
+
+If you use this widget for your data analysis, please cite the articles in which the <a href="https://doi.org/10.1021/ma302560q">method (Hikima et al. (2013)<sup>1</sup>)</a> and <a href="#references">widget (Gassner et al. (2025)<sup>2</sup>)</a> are introduced.
+
+![](images/Polar-stamped.png)
+
+1. Inputs: Define the polarization angles of the input dataset. Data can be passed to widget with two methods:
+    - *Multifile Input*: A single input with data from all polarization angles in a single dataset. (Each polarization angle must be separated with a categorical variable).
+    - *Multiple Inputs*: 1 input per polarization angle.
+2. Features: Select the features to calculate the orientation of. Features are selected by clicking on the desired feature(s) and assigning a TDM value (see point 5). A default value is assigned using the current value in the "TDM Tilt (°)" box, changing this value will change the associated value of the selected feature(s). Deselecting features will not remove them from the list to be calculated, only features with ("Not used") will not be calculated (see point 8).
+3. Data XY Selection: Define the attributes for the x and y axes for 2D datasets.
+4. Spectra Type: The type of spectra on the input. A conversion to *Absorptance* is performed before calculating orientation information when *Absorbance* or *Transmittance* is selected (this does not affect meta and class variables).
+5. TDM Tilt (°): The angle of the Transition Dipole Moment with respect to the molecular axis. Used in calculation of the value of Herman's orientation function.
+6. Invert Angles: Invert the calculated Azimuth Angles about the 0 degree axis (i.e. so that 90 degrees is output as -90 degrees).
+7. Average Spectra: Average all output variables across polarization angles.
+8. Don't use selected features: Remove the selected features from the list to be used in calculations
+
+Input Examples
+-------
+MultiFile Input
+
+![](images/Polar-Example1.PNG)
+
+Multiple Inputs
+
+![](images/Polar-Example2.PNG)
+
+
+
+
+References
+-------
+
+
+1. Hikima, Y.;  Morikawa, J.; Hashimoto, T., Wavenumber Dependence of FT-IR Image of Molecular Orientation in Banded Spherulites of Poly(3-hydroxybutyrate) and Poly(L-lactic acid). Macromolecules 2013, 46, 1582-1590.
+2. Gassner, C.; Vongsvivut, J.; Ryu, M.; Ng, S.H.; Toplak, M.; Takkalkar, P.; Fac, M.L.; Sims, N.A.; Wood, B.R.; Tobin, M.J.; Juodkazis, S.; Morikawa, J., 4+ Angle Polarization: New Multiple-Angle FTIR Polarization Widget for Molecular Orientation Analysis in the Open-Source Quasar Platform.

orangecontrib/spectroscopy/datasets/polar/4-angle-ftir_multiin1.tab

@@ -0,0 +1,7 @@
+1697.131066748047	1693.2739506872558	1689.416834626465	1685.5597185656738	1681.702602504883	1677.8454864440919	1673.9883703833011	1670.13125432251	1666.2741382617191	1662.417022200928	1658.5599061401367	1654.702790079346	1650.8456740185547	1646.988557957764	1643.1314418969728	1639.274325836182	1635.4172097753908	1631.5600937145996	1627.7029776538088	1623.8458615930176	1619.9887455322269	1616.1316294714356	1612.2745134106449	1608.4173973498537	1604.5602812890625	1600.7031652282717	1596.8460491674805	1592.9889331066897	1589.1318170458985	1585.2747009851078	1581.4175849243165	1577.5604688635258	1573.7033528027346	1569.8462367419434	1565.9891206811526	1562.1320046203614	1558.2748885595706	1554.4177724987794	1550.5606564379887	1546.7035403771974	1542.8464243164062	1538.9893082556155	1535.1321921948243	1531.2750761340335	1527.4179600732423	1523.5608440124515	1519.7037279516603	1515.846611890869	1511.9894958300783	1508.1323797692871	1504.2752637084964	1500.4181476477052	1496.5610315869144	1492.7039155261232	1488.8467994653324	1484.9896834045412	1481.13256734375	1477.2754512829592	1473.418335222168	1469.5612191613773	1465.704103100586	1461.8469870397953	1457.989870979004	1454.1327549182129	1450.275638857422	1446.418522796631	1442.5614067358401	1438.704290675049	1434.8471746142582	1430.990058553467	1427.1329424926757	1423.275826431885	1419.4187103710938	1415.561594310303	1411.7044782495118	1407.847362188721	1403.9902461279298	1400.133130067139	1396.2760140063479	1392.4188979455566	1388.5617818847659	1384.7046658239747	1380.847549763184	1376.9904337023927	1373.133317641602	1369.2762015808107	1365.4190855200195	1361.5619694592287	1357.7048533984375	1353.8477373376468	1349.9906212768556	1346.1335052160648	1342.2763891552736	1338.4192730944824	1334.5621570336916	1330.7050409729004	1326.8479249121096	1322.9908088513184	1319.1336927905277	1315.2765767297365	1311.4194606689457	1307.5623446081545	1303.7052285473633	1299.8481124865725	1295.9909964257813	1292.1338803649905	1288.2767643041993	1284.4196482434086	1280.5625321826174	1276.7054161218261	1272.8483000610354	1268.9911840002442	1265.1340679394534	1261.2769518786622	1257.4198358178714	1253.5627197570802	1249.705603696289	1245.8484876354983	1241.991371574707	1238.1342555139163	1234.277139453125	1230.4200233923343	1226.562907331543	1222.7057912707523	1218.8486752099611	1214.99155914917	1211.1344430883792	1207.277327027588	1203.4202109667972	map_x	map_y	1214.0 - 1258.0	1500.0 - 1580.0
+continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous	continuous
+																																																																																																																																	meta	meta	meta	meta
+0.3711118698120117	0.43782272934913635	0.49062955379486084	0.5547452569007874	0.6374028921127319	0.711500346660614	0.7876919507980347	0.8770861625671387	0.9559172987937927	1.0098530054092407	1.0404753684997559	1.0543735027313232	1.0619465112686157	1.0437582731246948	1.0013220310211182	0.9536964297294617	0.897933840751648	0.8533709645271301	0.8181004524230957	0.7584443688392639	0.6689296364784241	0.5782220363616943	0.513115644454956	0.46961721777915955	0.43171659111976624	0.3991532325744629	0.3810955286026001	0.37965840101242065	0.386007159948349	0.3947145342826843	0.4098324477672577	0.4343760311603546	0.46137940883636475	0.49168214201927185	0.528336226940155	0.5667646527290344	0.6178287267684937	0.6604256629943848	0.6766932010650635	0.6885275840759277	0.6986993551254272	0.6930281519889832	0.6724157929420471	0.6501829028129578	0.6263569593429565	0.5885990858078003	0.5376056432723999	0.5005533695220947	0.4779326319694519	0.4443279504776001	0.39699268341064453	0.36137861013412476	0.33436083793640137	0.30747178196907043	0.2803654670715332	0.2625480592250824	0.2592535614967346	0.27015992999076843	0.29309216141700745	0.31150364875793457	0.3194276988506317	0.328142374753952	0.3443129062652588	0.35353028774261475	0.3476772606372833	0.33774372935295105	0.32855379581451416	0.3200712502002716	0.31163617968559265	0.3032289445400238	0.2943628430366516	0.28816357254981995	0.2909632623195648	0.29872336983680725	0.3025616407394409	0.3057458698749542	0.3115512728691101	0.31618112325668335	0.3176253139972687	0.3175846040248871	0.3153497576713562	0.3088831901550293	0.3000914454460144	0.29377707839012146	0.2888909578323364	0.28027477860450745	0.270122230052948	0.26286780834198	0.2575746774673462	0.2533765435218811	0.2540722191333771	0.26083439588546753	0.2694004774093628	0.27414125204086304	0.2728372812271118	0.26937466859817505	0.2672775387763977	0.2684006989002228	0.2723020315170288	0.27508431673049927	0.2749064266681671	0.274681955575943	0.2775912284851074	0.28367695212364197	0.2893185019493103	0.290900319814682	0.2906703054904938	0.2926110625267029	0.2950325608253479	0.2977401614189148	0.3037301301956177	0.3114270567893982	0.318378210067749	0.32530495524406433	0.3349395990371704	0.3490666151046753	0.3638021945953369	0.3744945526123047	0.3803212642669678	0.3803481459617615	0.37394478917121887	0.3625723719596863	0.34696418046951294	0.3287803828716278	0.31259098649024963	0.3022864758968353	0.2975075840950012	0.2938818633556366	0.2872605323791504	30442.5687	41538.7379	15.009961445779307	43.87936019111817
+0.388348788022995	0.44867801666259766	0.502106249332428	0.5762503743171692	0.6664558053016663	0.739630937576294	0.8222108483314514	0.9173783659934998	0.9785887002944946	1.0107851028442383	1.0361779928207397	1.0637257099151611	1.0711760520935059	1.0423812866210938	1.025393009185791	0.9986843466758728	0.9373337626457214	0.8785869479179382	0.8271448612213135	0.7655133605003357	0.6908860802650452	0.6117749810218811	0.5471857190132141	0.4971246123313904	0.45541316270828247	0.42525458335876465	0.4062337279319763	0.39754077792167664	0.39981767535209656	0.41045162081718445	0.42612242698669434	0.4495392143726349	0.48013657331466675	0.509360134601593	0.5352477431297302	0.5706249475479126	0.6430520415306091	0.7104148864746094	0.7287077903747559	0.7300795912742615	0.7207353115081787	0.6928030848503113	0.6642997860908508	0.6465807557106018	0.6357985734939575	0.6169293522834778	0.5714240670204163	0.5247028470039368	0.49503496289253235	0.4588204622268677	0.41067439317703247	0.37448638677597046	0.34704023599624634	0.32218214869499207	0.29583585262298584	0.27490201592445374	0.26934197545051575	0.28096309304237366	0.3069058060646057	0.3270772397518158	0.33470597863197327	0.34152284264564514	0.35194724798202515	0.3573232889175415	0.3541431128978729	0.34866204857826233	0.3427005112171173	0.3312859833240509	0.3122206926345825	0.2955722510814667	0.2872144877910614	0.2867285907268524	0.2918354272842407	0.2956002652645111	0.2986833155155182	0.3060479462146759	0.31676867604255676	0.3262639045715332	0.330106645822525	0.32593291997909546	0.31699928641319275	0.30795541405677795	0.3018266558647156	0.29686442017555237	0.28721868991851807	0.2752007842063904	0.2667289972305298	0.2609139084815979	0.25778260827064514	0.2584190368652344	0.2610763907432556	0.2639258801937103	0.26595649123191833	0.26701226830482483	0.2679225206375122	0.2679891288280487	0.2669326663017273	0.2678163945674896	0.2720436155796051	0.2770630121231079	0.28001782298088074	0.27851158380508423	0.2751752436161041	0.276258647441864	0.2823660373687744	0.2899717390537262	0.29827389121055603	0.30697736144065857	0.3102128207683563	0.30654236674308777	0.30582261085510254	0.3128655254840851	0.3222534656524658	0.32939496636390686	0.33602944016456604	0.34821176528930664	0.3637096881866455	0.37178686261177063	0.3715791702270508	0.37046146392822266	0.36934414505958557	0.36342424154281616	0.350017786026001	0.33207470178604126	0.3140036165714264	0.2998875081539154	0.29220956563949585	0.2874009907245636	0.2815419137477875	30445.38885	41538.7379	14.936959331411803	45.349811063094954
+0.366887629032135	0.43671754002571106	0.49220016598701477	0.5703327059745789	0.6657547950744629	0.731933057308197	0.7937033176422119	0.8747525215148926	0.9398021697998047	0.9730452299118042	1.0031681060791016	1.0538406372070312	1.0965853929519653	1.0494016408920288	0.9825043678283691	0.9511120319366455	0.9302560687065125	0.8842418789863586	0.8129315972328186	0.7183979153633118	0.6205475330352783	0.5415375232696533	0.48775240778923035	0.44761666655540466	0.41458284854888916	0.39335882663726807	0.3796997666358948	0.36864838004112244	0.36498430371284485	0.3680277466773987	0.3732655644416809	0.38918817043304443	0.42386338114738464	0.46311137080192566	0.4917769134044647	0.5237820148468018	0.5971131920814514	0.6691277027130127	0.6892750859260559	0.7003340125083923	0.7168111801147461	0.6999649405479431	0.6541981101036072	0.6189929246902466	0.5926592946052551	0.5696735382080078	0.5413363575935364	0.5053853988647461	0.465243935585022	0.41113007068634033	0.36086025834083557	0.32808783650398254	0.3003191649913788	0.2793380916118622	0.26471295952796936	0.2541550099849701	0.24993854761123657	0.25305330753326416	0.2655698359012604	0.27899375557899475	0.2841063439846039	0.28888702392578125	0.30285078287124634	0.3161625862121582	0.3197145164012909	0.3178388774394989	0.31100529432296753	0.29754751920700073	0.28191861510276794	0.2750825583934784	0.27559351921081543	0.27823397517204285	0.2830919921398163	0.2850538194179535	0.2825995981693268	0.28359857201576233	0.2883332371711731	0.289949893951416	0.2929544150829315	0.30135759711265564	0.30265331268310547	0.2906714677810669	0.2753030061721802	0.2651992440223694	0.25924843549728394	0.25318726897239685	0.24550479650497437	0.23828820884227753	0.23315896093845367	0.23029816150665283	0.2334306240081787	0.24293583631515503	0.2510787546634674	0.25073981285095215	0.24615781009197235	0.2464907467365265	0.2522513270378113	0.2587389051914215	0.262591689825058	0.263126403093338	0.26156532764434814	0.2589862048625946	0.2572213411331177	0.2594248950481415	0.2655974328517914	0.27193424105644226	0.27772676944732666	0.28423818945884705	0.28888431191444397	0.29118603467941284	0.2921951413154602	0.29164180159568787	0.2948339283466339	0.3066503405570984	0.32164159417152405	0.333238422870636	0.34339842200279236	0.355623722076416	0.36564287543296814	0.36494630575180054	0.35201695561408997	0.3341171145439148	0.3175579309463501	0.30399125814437866	0.2928829789161682	0.28347793221473694	0.2780621647834778	0.276618093252182	0.27352389693260193	30442.5687	41541.616519999996	14.140093941838566	42.63377488797279
+0.36428871750831604	0.43003931641578674	0.47958770394325256	0.5450240969657898	0.634536862373352	0.7099695801734924	0.7796786427497864	0.8637834787368774	0.942089855670929	0.9903811812400818	1.0105667114257812	1.0208871364593506	1.005222201347351	0.963545024394989	0.9371297359466553	0.9139838814735413	0.8946059942245483	0.8827653527259827	0.840722918510437	0.7564958333969116	0.6611053943634033	0.5774503946304321	0.5202354192733765	0.48433250188827515	0.45376747846603394	0.4260224401950836	0.4059300422668457	0.3930695950984955	0.38632991909980774	0.3889123797416687	0.4001465141773224	0.4183931052684784	0.4428093135356903	0.47215187549591064	0.5050704479217529	0.5453080534934998	0.6085248589515686	0.658994734287262	0.668915331363678	0.6675289869308472	0.6717699766159058	0.6808158755302429	0.6681414842605591	0.6372467875480652	0.6000738739967346	0.5683797597885132	0.544323742389679	0.516345202922821	0.48224183917045593	0.4387160539627075	0.39499184489250183	0.3595888912677765	0.3304763436317444	0.3092094361782074	0.28860795497894287	0.26972246170043945	0.2605076730251312	0.26343077421188354	0.28140151500701904	0.29994896054267883	0.30823972821235657	0.31485551595687866	0.32437241077423096	0.33080095052719116	0.3303925395011902	0.3248642385005951	0.3165438175201416	0.3061983585357666	0.2946605384349823	0.2872968912124634	0.2868692874908447	0.2896806299686432	0.2909656763076782	0.2920180857181549	0.2945660948753357	0.2972028851509094	0.29964983463287354	0.3004482090473175	0.29766783118247986	0.2939799129962921	0.2927486002445221	0.2923987805843353	0.2889113426208496	0.2816716730594635	0.27281782031059265	0.2626931965351105	0.2514967918395996	0.24271203577518463	0.23827271163463593	0.23637256026268005	0.2380509227514267	0.24506837129592896	0.25348952412605286	0.25623422861099243	0.25412917137145996	0.2532842457294464	0.2547925114631653	0.2577175199985504	0.26068350672721863	0.2616606056690216	0.2597542703151703	0.2559884488582611	0.2536808252334595	0.256541907787323	0.2641761898994446	0.271513968706131	0.2755036950111389	0.27728980779647827	0.27779620885849	0.27858373522758484	0.28195881843566895	0.28836870193481445	0.29790475964546204	0.3091188371181488	0.317819207906723	0.3241935074329376	0.33264613151550293	0.3433806300163269	0.3505949378013611	0.35062962770462036	0.34647127985954285	0.3387751281261444	0.32535696029663086	0.3086860477924347	0.2940033972263336	0.2858646810054779	0.2827148139476776	0.2769644856452942	0.26818761229515076	30445.38885	41541.616519999996	13.949567230311496	43.05058779046659