nmr-processing 9.5.1 → 9.5.2-pre.1685982544

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (543) hide show
  1. package/lib/apodization/apodization.d.ts +11 -5
  2. package/lib/apodization/apodization.js +7 -4
  3. package/lib/apodization/apodization.js.map +1 -1
  4. package/lib/apodization/applyWindow.js.map +1 -1
  5. package/lib/apodization/compose.js.map +1 -1
  6. package/lib/apodization/getFunction.js +3 -0
  7. package/lib/apodization/getFunction.js.map +1 -1
  8. package/lib/apodization/shapes/WindowFunctions.d.ts +6 -1
  9. package/lib/apodization/shapes/sineBell.d.ts +27 -0
  10. package/lib/apodization/shapes/sineBell.js +17 -0
  11. package/lib/apodization/shapes/sineBell.js.map +1 -0
  12. package/lib/apodization/utils/getData.js.map +1 -1
  13. package/lib/assignment/utils/getAssignment/buildAssignments.js +2 -3
  14. package/lib/assignment/utils/getAssignment/buildAssignments.js.map +1 -1
  15. package/lib/constants/SignalsKinds.d.ts +9 -0
  16. package/lib/constants/SignalsKinds.js +40 -0
  17. package/lib/constants/SignalsKinds.js.map +1 -0
  18. package/lib/datum/ExclusionZone.d.ts +5 -0
  19. package/lib/datum/ExclusionZone.js +3 -0
  20. package/lib/datum/ExclusionZone.js.map +1 -0
  21. package/lib/datum/Filters.d.ts +14 -0
  22. package/lib/datum/Filters.js +55 -0
  23. package/lib/datum/Filters.js.map +1 -0
  24. package/lib/datum/FiltersManager.d.ts +31 -0
  25. package/lib/datum/FiltersManager.js +184 -0
  26. package/lib/datum/FiltersManager.js.map +1 -0
  27. package/lib/datum/MatrixFilter.d.ts +39 -0
  28. package/lib/datum/MatrixFilter.js +3 -0
  29. package/lib/datum/MatrixFilter.js.map +1 -0
  30. package/lib/datum/MatrixOptions.d.ts +28 -0
  31. package/lib/datum/MatrixOptions.js +3 -0
  32. package/lib/datum/MatrixOptions.js.map +1 -0
  33. package/lib/datum/data1d/Entry1D.d.ts +17 -0
  34. package/lib/datum/data1d/Entry1D.js +3 -0
  35. package/lib/datum/data1d/Entry1D.js.map +1 -0
  36. package/lib/datum/data1d/filter1d/apodization/apodization.d.ts +25 -0
  37. package/lib/datum/data1d/filter1d/apodization/apodization.js +36 -0
  38. package/lib/datum/data1d/filter1d/apodization/apodization.js.map +1 -0
  39. package/lib/datum/data1d/filter1d/apodization/apodizationFilter.d.ts +14 -0
  40. package/lib/datum/data1d/filter1d/apodization/apodizationFilter.js +37 -0
  41. package/lib/datum/data1d/filter1d/apodization/apodizationFilter.js.map +1 -0
  42. package/lib/datum/data1d/filter1d/baselineCorrection.d.ts +32 -0
  43. package/lib/datum/data1d/filter1d/baselineCorrection.js +61 -0
  44. package/lib/datum/data1d/filter1d/baselineCorrection.js.map +1 -0
  45. package/lib/datum/data1d/filter1d/digitalFilter.d.ts +23 -0
  46. package/lib/datum/data1d/filter1d/digitalFilter.js +54 -0
  47. package/lib/datum/data1d/filter1d/digitalFilter.js.map +1 -0
  48. package/lib/datum/data1d/filter1d/equallySpaced.d.ts +31 -0
  49. package/lib/datum/data1d/filter1d/equallySpaced.js +59 -0
  50. package/lib/datum/data1d/filter1d/equallySpaced.js.map +1 -0
  51. package/lib/datum/data1d/filter1d/exclusionZones.d.ts +11 -0
  52. package/lib/datum/data1d/filter1d/exclusionZones.js +35 -0
  53. package/lib/datum/data1d/filter1d/exclusionZones.js.map +1 -0
  54. package/lib/datum/data1d/filter1d/fft.d.ts +19 -0
  55. package/lib/datum/data1d/filter1d/fft.js +93 -0
  56. package/lib/datum/data1d/filter1d/fft.js.map +1 -0
  57. package/lib/datum/data1d/filter1d/phaseCorrection.d.ts +33 -0
  58. package/lib/datum/data1d/filter1d/phaseCorrection.js +83 -0
  59. package/lib/datum/data1d/filter1d/phaseCorrection.js.map +1 -0
  60. package/lib/datum/data1d/filter1d/shiftX.d.ts +22 -0
  61. package/lib/datum/data1d/filter1d/shiftX.js +33 -0
  62. package/lib/datum/data1d/filter1d/shiftX.js.map +1 -0
  63. package/lib/datum/data1d/filter1d/signalProcessing.d.ts +17 -0
  64. package/lib/datum/data1d/filter1d/signalProcessing.js +87 -0
  65. package/lib/datum/data1d/filter1d/signalProcessing.js.map +1 -0
  66. package/lib/datum/data1d/filter1d/utils/padDataToNextPowerOfTwo.d.ts +7 -0
  67. package/lib/datum/data1d/filter1d/utils/padDataToNextPowerOfTwo.js +37 -0
  68. package/lib/datum/data1d/filter1d/utils/padDataToNextPowerOfTwo.js.map +1 -0
  69. package/lib/datum/data1d/filter1d/zeroFilling.d.ts +23 -0
  70. package/lib/datum/data1d/filter1d/zeroFilling.js +61 -0
  71. package/lib/datum/data1d/filter1d/zeroFilling.js.map +1 -0
  72. package/lib/datum/data1d/utils/RangeUtilities.d.ts +22 -0
  73. package/lib/datum/data1d/utils/RangeUtilities.js +83 -0
  74. package/lib/datum/data1d/utils/RangeUtilities.js.map +1 -0
  75. package/lib/datum/data1d/utils/checkIntegralKind.d.ts +7 -0
  76. package/lib/datum/data1d/utils/checkIntegralKind.js +14 -0
  77. package/lib/datum/data1d/utils/checkIntegralKind.js.map +1 -0
  78. package/lib/datum/data1d/utils/checkRangeKind.d.ts +2 -0
  79. package/lib/datum/data1d/utils/checkRangeKind.js +10 -0
  80. package/lib/datum/data1d/utils/checkRangeKind.js.map +1 -0
  81. package/lib/datum/data1d/utils/getShiftX.d.ts +2 -0
  82. package/lib/datum/data1d/utils/getShiftX.js +11 -0
  83. package/lib/datum/data1d/utils/getShiftX.js.map +1 -0
  84. package/lib/datum/data1d/utils/getSpectrumErrorValue.d.ts +2 -0
  85. package/lib/datum/data1d/utils/getSpectrumErrorValue.js +9 -0
  86. package/lib/datum/data1d/utils/getSpectrumErrorValue.js.map +1 -0
  87. package/lib/datum/data1d/utils/mapIntegrals.d.ts +13 -0
  88. package/lib/datum/data1d/utils/mapIntegrals.js +41 -0
  89. package/lib/datum/data1d/utils/mapIntegrals.js.map +1 -0
  90. package/lib/datum/data1d/utils/mapPeaks.d.ts +4 -0
  91. package/lib/datum/data1d/utils/mapPeaks.js +50 -0
  92. package/lib/datum/data1d/utils/mapPeaks.js.map +1 -0
  93. package/lib/datum/data1d/utils/mapRanges.d.ts +38 -0
  94. package/lib/datum/data1d/utils/mapRanges.js +83 -0
  95. package/lib/datum/data1d/utils/mapRanges.js.map +1 -0
  96. package/lib/datum/data1d/utils/mapValues.d.ts +26 -0
  97. package/lib/datum/data1d/utils/mapValues.js +15 -0
  98. package/lib/datum/data1d/utils/mapValues.js.map +1 -0
  99. package/lib/datum/data1d/utils/updateIntegrals.d.ts +2 -0
  100. package/lib/datum/data1d/utils/updateIntegrals.js +11 -0
  101. package/lib/datum/data1d/utils/updateIntegrals.js.map +1 -0
  102. package/lib/datum/data1d/utils/updateIntegralsRelativeValues.d.ts +2 -0
  103. package/lib/datum/data1d/utils/updateIntegralsRelativeValues.js +26 -0
  104. package/lib/datum/data1d/utils/updateIntegralsRelativeValues.js.map +1 -0
  105. package/lib/datum/data1d/utils/updatePeaks.d.ts +2 -0
  106. package/lib/datum/data1d/utils/updatePeaks.js +12 -0
  107. package/lib/datum/data1d/utils/updatePeaks.js.map +1 -0
  108. package/lib/datum/data1d/utils/updateRanges.d.ts +2 -0
  109. package/lib/datum/data1d/utils/updateRanges.js +14 -0
  110. package/lib/datum/data1d/utils/updateRanges.js.map +1 -0
  111. package/lib/datum/data1d/utils/updateRangesRelativeValues.d.ts +2 -0
  112. package/lib/datum/data1d/utils/updateRangesRelativeValues.js +26 -0
  113. package/lib/datum/data1d/utils/updateRangesRelativeValues.js.map +1 -0
  114. package/lib/datum/data2d/Entry2D.d.ts +12 -0
  115. package/lib/datum/data2d/Entry2D.js +3 -0
  116. package/lib/datum/data2d/Entry2D.js.map +1 -0
  117. package/lib/datum/data2d/filter2d/shiftX.d.ts +16 -0
  118. package/lib/datum/data2d/filter2d/shiftX.js +34 -0
  119. package/lib/datum/data2d/filter2d/shiftX.js.map +1 -0
  120. package/lib/datum/data2d/filter2d/shiftY.d.ts +16 -0
  121. package/lib/datum/data2d/filter2d/shiftY.js +34 -0
  122. package/lib/datum/data2d/filter2d/shiftY.js.map +1 -0
  123. package/lib/datum/data2d/utils/get2DSpectrumErrorValue.d.ts +6 -0
  124. package/lib/datum/data2d/utils/get2DSpectrumErrorValue.js +14 -0
  125. package/lib/datum/data2d/utils/get2DSpectrumErrorValue.js.map +1 -0
  126. package/lib/datum/data2d/utils/getShift.d.ts +6 -0
  127. package/lib/datum/data2d/utils/getShift.js +20 -0
  128. package/lib/datum/data2d/utils/getShift.js.map +1 -0
  129. package/lib/datum/data2d/utils/isZoneExists.d.ts +4 -0
  130. package/lib/datum/data2d/utils/isZoneExists.js +20 -0
  131. package/lib/datum/data2d/utils/isZoneExists.js.map +1 -0
  132. package/lib/datum/data2d/utils/mapZones.d.ts +34 -0
  133. package/lib/datum/data2d/utils/mapZones.js +68 -0
  134. package/lib/datum/data2d/utils/mapZones.js.map +1 -0
  135. package/lib/datum/data2d/utils/updateZones.d.ts +2 -0
  136. package/lib/datum/data2d/utils/updateZones.js +12 -0
  137. package/lib/datum/data2d/utils/updateZones.js.map +1 -0
  138. package/lib/index.d.ts +29 -0
  139. package/lib/index.js +26 -0
  140. package/lib/index.js.map +1 -1
  141. package/lib/multiplicity/joinPatterns.js +1 -1
  142. package/lib/multiplicity/joinPatterns.js.map +1 -1
  143. package/lib/prediction/utils/getPredictions.js +1 -1
  144. package/lib/prediction/utils/getPredictions.js.map +1 -1
  145. package/lib/signal/signalJoinCouplings.js +2 -5
  146. package/lib/signal/signalJoinCouplings.js.map +1 -1
  147. package/lib/signal/signalMultiplicityPattern.js +1 -1
  148. package/lib/signal/signalMultiplicityPattern.js.map +1 -1
  149. package/lib/signals/optimization/getInternalSignals.js +3 -5
  150. package/lib/signals/optimization/getInternalSignals.js.map +1 -1
  151. package/lib/signals/signalsJoin.js +4 -8
  152. package/lib/signals/signalsJoin.js.map +1 -1
  153. package/lib/signals/signalsToRanges.js.map +1 -1
  154. package/lib/signals/signalsToXY.js +1 -2
  155. package/lib/signals/signalsToXY.js.map +1 -1
  156. package/lib/signals/simulation/simulateXYPeaks.js.map +1 -1
  157. package/lib/signals/utils/jAnalyzer.d.ts +11 -8
  158. package/lib/signals/utils/jAnalyzer.js.map +1 -1
  159. package/lib/types/Data1D.d.ts +5 -0
  160. package/lib/types/Data1D.js +3 -0
  161. package/lib/types/Data1D.js.map +1 -0
  162. package/lib/types/Data2D.d.ts +5 -0
  163. package/{lib-esm/xyz → lib/types}/Data2D.js.map +1 -1
  164. package/lib/types/Filter.d.ts +11 -0
  165. package/lib/types/Filter.js +3 -0
  166. package/lib/types/Filter.js.map +1 -0
  167. package/lib/types/Info/Info.d.ts +15 -0
  168. package/lib/types/Info/Info.js +3 -0
  169. package/lib/types/Info/Info.js.map +1 -0
  170. package/lib/types/Info/Info1D.d.ts +13 -0
  171. package/lib/types/Info/Info1D.js +3 -0
  172. package/lib/types/Info/Info1D.js.map +1 -0
  173. package/lib/types/Info/Info2D.d.ts +10 -0
  174. package/lib/types/Info/Info2D.js +3 -0
  175. package/lib/types/Info/Info2D.js.map +1 -0
  176. package/lib/types/Integral.d.ts +10 -0
  177. package/lib/types/Integral.js +3 -0
  178. package/lib/types/Integral.js.map +1 -0
  179. package/lib/types/Integrals.d.ts +6 -0
  180. package/lib/types/Integrals.js +3 -0
  181. package/lib/types/Integrals.js.map +1 -0
  182. package/lib/types/Options/SumOptions.d.ts +24 -0
  183. package/lib/types/Options/SumOptions.js +3 -0
  184. package/lib/types/Options/SumOptions.js.map +1 -0
  185. package/lib/types/Peaks/BasePeak.d.ts +3 -0
  186. package/lib/types/Peaks/BasePeak.js +3 -0
  187. package/lib/types/Peaks/BasePeak.js.map +1 -0
  188. package/lib/types/Peaks/Peak1D.d.ts +5 -0
  189. package/lib/types/Peaks/Peak1D.js +3 -0
  190. package/lib/types/Peaks/Peak1D.js.map +1 -0
  191. package/lib/types/Peaks/Peak2D.d.ts +13 -0
  192. package/lib/types/Peaks/Peak2D.js +3 -0
  193. package/lib/types/Peaks/Peak2D.js.map +1 -0
  194. package/lib/types/Peaks/Peaks.d.ts +5 -0
  195. package/lib/types/Peaks/Peaks.js +3 -0
  196. package/lib/types/Peaks/Peaks.js.map +1 -0
  197. package/lib/types/Ranges/Ranges.d.ts +16 -0
  198. package/lib/types/Ranges/Ranges.js +3 -0
  199. package/lib/types/Ranges/Ranges.js.map +1 -0
  200. package/lib/types/Signals/Signal.d.ts +4 -0
  201. package/lib/types/Signals/Signal.js +3 -0
  202. package/lib/types/Signals/Signal.js.map +1 -0
  203. package/lib/types/Signals/Signal1D.d.ts +6 -0
  204. package/lib/types/Signals/Signal1D.js +3 -0
  205. package/lib/types/Signals/Signal1D.js.map +1 -0
  206. package/lib/types/Signals/Signal2D.d.ts +18 -0
  207. package/lib/types/Signals/Signal2D.js +3 -0
  208. package/lib/types/Signals/Signal2D.js.map +1 -0
  209. package/lib/types/Zones/Zone.d.ts +13 -0
  210. package/lib/types/Zones/Zone.js +3 -0
  211. package/lib/types/Zones/Zone.js.map +1 -0
  212. package/lib/types/Zones/Zones.d.ts +5 -0
  213. package/lib/types/Zones/Zones.js +3 -0
  214. package/lib/types/Zones/Zones.js.map +1 -0
  215. package/lib/types/common/MapOptions.d.ts +5 -0
  216. package/lib/types/common/MapOptions.js +3 -0
  217. package/lib/types/common/MapOptions.js.map +1 -0
  218. package/lib/utilities/checkData2DFid.d.ts +3 -0
  219. package/lib/utilities/checkData2DFid.js +10 -0
  220. package/lib/utilities/checkData2DFid.js.map +1 -0
  221. package/lib/utilities/cloneData1D.d.ts +6 -0
  222. package/lib/utilities/cloneData1D.js +9 -0
  223. package/lib/utilities/cloneData1D.js.map +1 -0
  224. package/lib/utilities/cloneData2D.d.ts +2 -0
  225. package/lib/utilities/cloneData2D.js +28 -0
  226. package/lib/utilities/cloneData2D.js.map +1 -0
  227. package/lib/utilities/getSum.d.ts +8 -0
  228. package/lib/utilities/getSum.js +24 -0
  229. package/lib/utilities/getSum.js.map +1 -0
  230. package/lib/xyz/quadrature.d.ts +7 -0
  231. package/lib/xyz/quadrature.js +54 -0
  232. package/lib/xyz/quadrature.js.map +1 -0
  233. package/lib/xyz/util/fft2d/digitalFilter.d.ts +7 -0
  234. package/lib/xyz/util/fft2d/digitalFilter.js +20 -0
  235. package/lib/xyz/util/fft2d/digitalFilter.js.map +1 -0
  236. package/lib/xyz/util/fft2d/fftDirectDimension.d.ts +24 -0
  237. package/lib/xyz/util/fft2d/fftDirectDimension.js +57 -0
  238. package/lib/xyz/util/fft2d/fftDirectDimension.js.map +1 -0
  239. package/lib/xyz/util/fft2d/fftIndirectDimension.d.ts +23 -0
  240. package/lib/xyz/util/fft2d/fftIndirectDimension.js +71 -0
  241. package/lib/xyz/util/fft2d/fftIndirectDimension.js.map +1 -0
  242. package/lib/xyz/util/fft2d/removeDCOffset.d.ts +5 -0
  243. package/lib/xyz/util/fft2d/removeDCOffset.js +19 -0
  244. package/lib/xyz/util/fft2d/removeDCOffset.js.map +1 -0
  245. package/lib/xyz/util/fft2d/zeroFilling.d.ts +10 -0
  246. package/lib/xyz/util/fft2d/zeroFilling.js +29 -0
  247. package/lib/xyz/util/fft2d/zeroFilling.js.map +1 -0
  248. package/lib/xyz/util/padData.d.ts +5 -3
  249. package/lib/xyz/util/padData.js +7 -7
  250. package/lib/xyz/util/padData.js.map +1 -1
  251. package/lib/xyz/xyzAutoSignalsPicking.d.ts +2 -2
  252. package/lib/xyz/xyzAutoSignalsPicking.js.map +1 -1
  253. package/lib/xyz/xyzAutoZonesPicking.d.ts +2 -8
  254. package/lib/xyz/xyzAutoZonesPicking.js.map +1 -1
  255. package/lib/xyz/xyzBidimensionalFFT.d.ts +40 -0
  256. package/lib/xyz/xyzBidimensionalFFT.js +79 -0
  257. package/lib/xyz/xyzBidimensionalFFT.js.map +1 -0
  258. package/lib/xyz/xyzJResAnalyzer.d.ts +1 -4
  259. package/lib/xyz/xyzJResAnalyzer.js +34 -26
  260. package/lib/xyz/xyzJResAnalyzer.js.map +1 -1
  261. package/lib-esm/apodization/apodization.js +7 -4
  262. package/lib-esm/apodization/apodization.js.map +1 -1
  263. package/lib-esm/apodization/applyWindow.js.map +1 -1
  264. package/lib-esm/apodization/compose.js.map +1 -1
  265. package/lib-esm/apodization/getFunction.js +3 -0
  266. package/lib-esm/apodization/getFunction.js.map +1 -1
  267. package/lib-esm/apodization/shapes/sineBell.js +13 -0
  268. package/lib-esm/apodization/shapes/sineBell.js.map +1 -0
  269. package/lib-esm/apodization/utils/getData.js.map +1 -1
  270. package/lib-esm/assignment/utils/getAssignment/buildAssignments.js +2 -3
  271. package/lib-esm/assignment/utils/getAssignment/buildAssignments.js.map +1 -1
  272. package/lib-esm/constants/SignalsKinds.js +37 -0
  273. package/lib-esm/constants/SignalsKinds.js.map +1 -0
  274. package/lib-esm/datum/ExclusionZone.js +2 -0
  275. package/lib-esm/datum/ExclusionZone.js.map +1 -0
  276. package/lib-esm/datum/Filters.js +28 -0
  277. package/lib-esm/datum/Filters.js.map +1 -0
  278. package/lib-esm/datum/FiltersManager.js +175 -0
  279. package/lib-esm/datum/FiltersManager.js.map +1 -0
  280. package/lib-esm/datum/MatrixFilter.js +2 -0
  281. package/lib-esm/datum/MatrixFilter.js.map +1 -0
  282. package/lib-esm/datum/MatrixOptions.js +2 -0
  283. package/lib-esm/datum/MatrixOptions.js.map +1 -0
  284. package/lib-esm/datum/data1d/Entry1D.js +2 -0
  285. package/lib-esm/datum/data1d/Entry1D.js.map +1 -0
  286. package/lib-esm/datum/data1d/filter1d/apodization/apodization.js +30 -0
  287. package/lib-esm/datum/data1d/filter1d/apodization/apodization.js.map +1 -0
  288. package/lib-esm/datum/data1d/filter1d/apodization/apodizationFilter.js +33 -0
  289. package/lib-esm/datum/data1d/filter1d/apodization/apodizationFilter.js.map +1 -0
  290. package/lib-esm/datum/data1d/filter1d/baselineCorrection.js +52 -0
  291. package/lib-esm/datum/data1d/filter1d/baselineCorrection.js.map +1 -0
  292. package/lib-esm/datum/data1d/filter1d/digitalFilter.js +48 -0
  293. package/lib-esm/datum/data1d/filter1d/digitalFilter.js.map +1 -0
  294. package/lib-esm/datum/data1d/filter1d/equallySpaced.js +53 -0
  295. package/lib-esm/datum/data1d/filter1d/equallySpaced.js.map +1 -0
  296. package/lib-esm/datum/data1d/filter1d/exclusionZones.js +29 -0
  297. package/lib-esm/datum/data1d/filter1d/exclusionZones.js.map +1 -0
  298. package/lib-esm/datum/data1d/filter1d/fft.js +87 -0
  299. package/lib-esm/datum/data1d/filter1d/fft.js.map +1 -0
  300. package/lib-esm/datum/data1d/filter1d/phaseCorrection.js +77 -0
  301. package/lib-esm/datum/data1d/filter1d/phaseCorrection.js.map +1 -0
  302. package/lib-esm/datum/data1d/filter1d/shiftX.js +27 -0
  303. package/lib-esm/datum/data1d/filter1d/shiftX.js.map +1 -0
  304. package/lib-esm/datum/data1d/filter1d/signalProcessing.js +57 -0
  305. package/lib-esm/datum/data1d/filter1d/signalProcessing.js.map +1 -0
  306. package/lib-esm/datum/data1d/filter1d/utils/padDataToNextPowerOfTwo.js +33 -0
  307. package/lib-esm/datum/data1d/filter1d/utils/padDataToNextPowerOfTwo.js.map +1 -0
  308. package/lib-esm/datum/data1d/filter1d/zeroFilling.js +55 -0
  309. package/lib-esm/datum/data1d/filter1d/zeroFilling.js.map +1 -0
  310. package/lib-esm/datum/data1d/utils/RangeUtilities.js +69 -0
  311. package/lib-esm/datum/data1d/utils/RangeUtilities.js.map +1 -0
  312. package/lib-esm/datum/data1d/utils/checkIntegralKind.js +10 -0
  313. package/lib-esm/datum/data1d/utils/checkIntegralKind.js.map +1 -0
  314. package/lib-esm/datum/data1d/utils/checkRangeKind.js +6 -0
  315. package/lib-esm/datum/data1d/utils/checkRangeKind.js.map +1 -0
  316. package/lib-esm/datum/data1d/utils/getShiftX.js +7 -0
  317. package/lib-esm/datum/data1d/utils/getShiftX.js.map +1 -0
  318. package/lib-esm/datum/data1d/utils/getSpectrumErrorValue.js +5 -0
  319. package/lib-esm/datum/data1d/utils/getSpectrumErrorValue.js.map +1 -0
  320. package/lib-esm/datum/data1d/utils/mapIntegrals.js +37 -0
  321. package/lib-esm/datum/data1d/utils/mapIntegrals.js.map +1 -0
  322. package/lib-esm/datum/data1d/utils/mapPeaks.js +46 -0
  323. package/lib-esm/datum/data1d/utils/mapPeaks.js.map +1 -0
  324. package/lib-esm/datum/data1d/utils/mapRanges.js +79 -0
  325. package/lib-esm/datum/data1d/utils/mapRanges.js.map +1 -0
  326. package/lib-esm/datum/data1d/utils/mapValues.js +11 -0
  327. package/lib-esm/datum/data1d/utils/mapValues.js.map +1 -0
  328. package/lib-esm/datum/data1d/utils/updateIntegrals.js +7 -0
  329. package/lib-esm/datum/data1d/utils/updateIntegrals.js.map +1 -0
  330. package/lib-esm/datum/data1d/utils/updateIntegralsRelativeValues.js +22 -0
  331. package/lib-esm/datum/data1d/utils/updateIntegralsRelativeValues.js.map +1 -0
  332. package/lib-esm/datum/data1d/utils/updatePeaks.js +8 -0
  333. package/lib-esm/datum/data1d/utils/updatePeaks.js.map +1 -0
  334. package/lib-esm/datum/data1d/utils/updateRanges.js +10 -0
  335. package/lib-esm/datum/data1d/utils/updateRanges.js.map +1 -0
  336. package/lib-esm/datum/data1d/utils/updateRangesRelativeValues.js +22 -0
  337. package/lib-esm/datum/data1d/utils/updateRangesRelativeValues.js.map +1 -0
  338. package/lib-esm/datum/data2d/Entry2D.js +2 -0
  339. package/lib-esm/datum/data2d/Entry2D.js.map +1 -0
  340. package/lib-esm/datum/data2d/filter2d/shiftX.js +28 -0
  341. package/lib-esm/datum/data2d/filter2d/shiftX.js.map +1 -0
  342. package/lib-esm/datum/data2d/filter2d/shiftY.js +28 -0
  343. package/lib-esm/datum/data2d/filter2d/shiftY.js.map +1 -0
  344. package/lib-esm/datum/data2d/utils/get2DSpectrumErrorValue.js +10 -0
  345. package/lib-esm/datum/data2d/utils/get2DSpectrumErrorValue.js.map +1 -0
  346. package/lib-esm/datum/data2d/utils/getShift.js +16 -0
  347. package/lib-esm/datum/data2d/utils/getShift.js.map +1 -0
  348. package/lib-esm/datum/data2d/utils/isZoneExists.js +16 -0
  349. package/lib-esm/datum/data2d/utils/isZoneExists.js.map +1 -0
  350. package/lib-esm/datum/data2d/utils/mapZones.js +64 -0
  351. package/lib-esm/datum/data2d/utils/mapZones.js.map +1 -0
  352. package/lib-esm/datum/data2d/utils/updateZones.js +8 -0
  353. package/lib-esm/datum/data2d/utils/updateZones.js.map +1 -0
  354. package/lib-esm/index.js +13 -0
  355. package/lib-esm/index.js.map +1 -1
  356. package/lib-esm/multiplicity/joinPatterns.js +1 -1
  357. package/lib-esm/multiplicity/joinPatterns.js.map +1 -1
  358. package/lib-esm/prediction/utils/getPredictions.js +1 -1
  359. package/lib-esm/prediction/utils/getPredictions.js.map +1 -1
  360. package/lib-esm/signal/signalJoinCouplings.js +2 -2
  361. package/lib-esm/signal/signalJoinCouplings.js.map +1 -1
  362. package/lib-esm/signal/signalMultiplicityPattern.js +1 -1
  363. package/lib-esm/signal/signalMultiplicityPattern.js.map +1 -1
  364. package/lib-esm/signals/optimization/getInternalSignals.js +3 -5
  365. package/lib-esm/signals/optimization/getInternalSignals.js.map +1 -1
  366. package/lib-esm/signals/signalsJoin.js +4 -5
  367. package/lib-esm/signals/signalsJoin.js.map +1 -1
  368. package/lib-esm/signals/signalsToRanges.js.map +1 -1
  369. package/lib-esm/signals/signalsToXY.js +2 -3
  370. package/lib-esm/signals/signalsToXY.js.map +1 -1
  371. package/lib-esm/signals/simulation/simulateXYPeaks.js.map +1 -1
  372. package/lib-esm/signals/utils/jAnalyzer.js.map +1 -1
  373. package/lib-esm/types/Data1D.js +2 -0
  374. package/lib-esm/types/Data1D.js.map +1 -0
  375. package/{lib/xyz → lib-esm/types}/Data2D.js.map +1 -1
  376. package/lib-esm/types/Filter.js +2 -0
  377. package/lib-esm/types/Filter.js.map +1 -0
  378. package/lib-esm/types/Info/Info.js +2 -0
  379. package/lib-esm/types/Info/Info.js.map +1 -0
  380. package/lib-esm/types/Info/Info1D.js +2 -0
  381. package/lib-esm/types/Info/Info1D.js.map +1 -0
  382. package/lib-esm/types/Info/Info2D.js +2 -0
  383. package/lib-esm/types/Info/Info2D.js.map +1 -0
  384. package/lib-esm/types/Integral.js +2 -0
  385. package/lib-esm/types/Integral.js.map +1 -0
  386. package/lib-esm/types/Integrals.js +2 -0
  387. package/lib-esm/types/Integrals.js.map +1 -0
  388. package/lib-esm/types/Options/SumOptions.js +2 -0
  389. package/lib-esm/types/Options/SumOptions.js.map +1 -0
  390. package/lib-esm/types/Peaks/BasePeak.js +2 -0
  391. package/lib-esm/types/Peaks/BasePeak.js.map +1 -0
  392. package/lib-esm/types/Peaks/Peak1D.js +2 -0
  393. package/lib-esm/types/Peaks/Peak1D.js.map +1 -0
  394. package/lib-esm/types/Peaks/Peak2D.js +2 -0
  395. package/lib-esm/types/Peaks/Peak2D.js.map +1 -0
  396. package/lib-esm/types/Peaks/Peaks.js +2 -0
  397. package/lib-esm/types/Peaks/Peaks.js.map +1 -0
  398. package/lib-esm/types/Ranges/Ranges.js +2 -0
  399. package/lib-esm/types/Ranges/Ranges.js.map +1 -0
  400. package/lib-esm/types/Signals/Signal.js +2 -0
  401. package/lib-esm/types/Signals/Signal.js.map +1 -0
  402. package/lib-esm/types/Signals/Signal1D.js +2 -0
  403. package/lib-esm/types/Signals/Signal1D.js.map +1 -0
  404. package/lib-esm/types/Signals/Signal2D.js +2 -0
  405. package/lib-esm/types/Signals/Signal2D.js.map +1 -0
  406. package/lib-esm/types/Zones/Zone.js +2 -0
  407. package/lib-esm/types/Zones/Zone.js.map +1 -0
  408. package/lib-esm/types/Zones/Zones.js +2 -0
  409. package/lib-esm/types/Zones/Zones.js.map +1 -0
  410. package/lib-esm/types/common/MapOptions.js +2 -0
  411. package/lib-esm/types/common/MapOptions.js.map +1 -0
  412. package/lib-esm/utilities/checkData2DFid.js +6 -0
  413. package/lib-esm/utilities/checkData2DFid.js.map +1 -0
  414. package/lib-esm/utilities/cloneData1D.js +5 -0
  415. package/lib-esm/utilities/cloneData1D.js.map +1 -0
  416. package/lib-esm/utilities/cloneData2D.js +24 -0
  417. package/lib-esm/utilities/cloneData2D.js.map +1 -0
  418. package/lib-esm/utilities/getSum.js +20 -0
  419. package/lib-esm/utilities/getSum.js.map +1 -0
  420. package/lib-esm/xyz/quadrature.js +50 -0
  421. package/lib-esm/xyz/quadrature.js.map +1 -0
  422. package/lib-esm/xyz/util/fft2d/digitalFilter.js +16 -0
  423. package/lib-esm/xyz/util/fft2d/digitalFilter.js.map +1 -0
  424. package/lib-esm/xyz/util/fft2d/fftDirectDimension.js +50 -0
  425. package/lib-esm/xyz/util/fft2d/fftDirectDimension.js.map +1 -0
  426. package/lib-esm/xyz/util/fft2d/fftIndirectDimension.js +64 -0
  427. package/lib-esm/xyz/util/fft2d/fftIndirectDimension.js.map +1 -0
  428. package/lib-esm/xyz/util/fft2d/removeDCOffset.js +15 -0
  429. package/lib-esm/xyz/util/fft2d/removeDCOffset.js.map +1 -0
  430. package/lib-esm/xyz/util/fft2d/zeroFilling.js +25 -0
  431. package/lib-esm/xyz/util/fft2d/zeroFilling.js.map +1 -0
  432. package/lib-esm/xyz/util/padData.js +7 -4
  433. package/lib-esm/xyz/util/padData.js.map +1 -1
  434. package/lib-esm/xyz/xyzAutoSignalsPicking.js.map +1 -1
  435. package/lib-esm/xyz/xyzAutoZonesPicking.js.map +1 -1
  436. package/lib-esm/xyz/xyzBidimensionalFFT.js +75 -0
  437. package/lib-esm/xyz/xyzBidimensionalFFT.js.map +1 -0
  438. package/lib-esm/xyz/xyzJResAnalyzer.js +34 -26
  439. package/lib-esm/xyz/xyzJResAnalyzer.js.map +1 -1
  440. package/package.json +8 -5
  441. package/src/apodization/apodization.ts +19 -6
  442. package/src/apodization/applyWindow.ts +0 -1
  443. package/src/apodization/compose.ts +1 -0
  444. package/src/apodization/getFunction.ts +3 -0
  445. package/src/apodization/shapes/WindowFunctions.ts +7 -1
  446. package/src/apodization/shapes/sineBell.ts +41 -0
  447. package/src/apodization/utils/getData.ts +0 -1
  448. package/src/constants/SignalsKinds.ts +37 -0
  449. package/src/datum/ExclusionZone.ts +5 -0
  450. package/src/datum/Filters.ts +53 -0
  451. package/src/datum/FiltersManager.ts +229 -0
  452. package/src/datum/MatrixFilter.ts +58 -0
  453. package/src/datum/MatrixOptions.ts +25 -0
  454. package/src/datum/data1d/Entry1D.ts +18 -0
  455. package/src/datum/data1d/filter1d/apodization/apodization.ts +53 -0
  456. package/src/datum/data1d/filter1d/apodization/apodizationFilter.ts +54 -0
  457. package/src/datum/data1d/filter1d/baselineCorrection.ts +83 -0
  458. package/src/datum/data1d/filter1d/digitalFilter.ts +66 -0
  459. package/src/datum/data1d/filter1d/equallySpaced.ts +66 -0
  460. package/src/datum/data1d/filter1d/exclusionZones.ts +34 -0
  461. package/src/datum/data1d/filter1d/fft.ts +143 -0
  462. package/src/datum/data1d/filter1d/phaseCorrection.ts +127 -0
  463. package/src/datum/data1d/filter1d/shiftX.ts +37 -0
  464. package/src/datum/data1d/filter1d/signalProcessing.ts +79 -0
  465. package/src/datum/data1d/filter1d/utils/padDataToNextPowerOfTwo.ts +49 -0
  466. package/src/datum/data1d/filter1d/zeroFilling.ts +93 -0
  467. package/src/datum/data1d/utils/RangeUtilities.ts +102 -0
  468. package/src/datum/data1d/utils/checkIntegralKind.ts +11 -0
  469. package/src/datum/data1d/utils/checkRangeKind.ts +8 -0
  470. package/src/datum/data1d/utils/getShiftX.ts +10 -0
  471. package/src/datum/data1d/utils/getSpectrumErrorValue.ts +6 -0
  472. package/src/datum/data1d/utils/mapIntegrals.ts +52 -0
  473. package/src/datum/data1d/utils/mapPeaks.ts +62 -0
  474. package/src/datum/data1d/utils/mapRanges.ts +107 -0
  475. package/src/datum/data1d/utils/mapValues.ts +18 -0
  476. package/src/datum/data1d/utils/updateIntegrals.ts +13 -0
  477. package/src/datum/data1d/utils/updateIntegralsRelativeValues.ts +36 -0
  478. package/src/datum/data1d/utils/updatePeaks.ts +10 -0
  479. package/src/datum/data1d/utils/updateRanges.ts +12 -0
  480. package/src/datum/data1d/utils/updateRangesRelativeValues.ts +36 -0
  481. package/src/datum/data2d/Entry2D.ts +14 -0
  482. package/src/datum/data2d/filter2d/shiftX.ts +37 -0
  483. package/src/datum/data2d/filter2d/shiftY.ts +36 -0
  484. package/src/datum/data2d/utils/get2DSpectrumErrorValue.ts +18 -0
  485. package/src/datum/data2d/utils/getShift.ts +23 -0
  486. package/src/datum/data2d/utils/isZoneExists.ts +27 -0
  487. package/src/datum/data2d/utils/mapZones.ts +80 -0
  488. package/src/datum/data2d/utils/updateZones.ts +10 -0
  489. package/src/index.ts +32 -0
  490. package/src/signal/signalJoinCouplings.ts +2 -2
  491. package/src/signals/signalsJoin.ts +4 -5
  492. package/src/signals/signalsToRanges.ts +1 -1
  493. package/src/signals/signalsToXY.ts +2 -3
  494. package/src/signals/simulation/simulateXYPeaks.ts +1 -1
  495. package/src/signals/utils/jAnalyzer.ts +20 -10
  496. package/src/types/Data1D.ts +5 -0
  497. package/src/types/Data2D.ts +7 -0
  498. package/src/types/Filter.ts +12 -0
  499. package/src/types/Info/Info.ts +15 -0
  500. package/src/types/Info/Info1D.ts +14 -0
  501. package/src/types/Info/Info2D.ts +11 -0
  502. package/src/types/Integral.ts +10 -0
  503. package/src/types/Integrals.ts +7 -0
  504. package/src/types/Options/SumOptions.ts +24 -0
  505. package/src/types/Peaks/BasePeak.ts +3 -0
  506. package/src/types/Peaks/Peak1D.ts +7 -0
  507. package/src/types/Peaks/Peak2D.ts +11 -0
  508. package/src/types/Peaks/Peaks.ts +6 -0
  509. package/src/types/Ranges/Ranges.ts +18 -0
  510. package/src/types/Signals/Signal.ts +4 -0
  511. package/src/types/Signals/Signal1D.ts +8 -0
  512. package/src/types/Signals/Signal2D.ts +21 -0
  513. package/src/types/Zones/Zone.ts +15 -0
  514. package/src/types/Zones/Zones.ts +6 -0
  515. package/src/types/common/MapOptions.ts +6 -0
  516. package/src/utilities/checkData2DFid.ts +10 -0
  517. package/src/utilities/cloneData1D.ts +6 -0
  518. package/src/utilities/cloneData2D.ts +27 -0
  519. package/src/utilities/getSum.ts +23 -0
  520. package/src/xyz/quadrature.ts +68 -0
  521. package/src/xyz/util/fft2d/digitalFilter.ts +24 -0
  522. package/src/xyz/util/fft2d/fftDirectDimension.ts +111 -0
  523. package/src/xyz/util/fft2d/fftIndirectDimension.ts +123 -0
  524. package/src/xyz/util/fft2d/removeDCOffset.ts +19 -0
  525. package/src/xyz/util/fft2d/zeroFilling.ts +39 -0
  526. package/src/xyz/util/padData.ts +13 -7
  527. package/src/xyz/xyzAutoSignalsPicking.ts +2 -2
  528. package/src/xyz/xyzAutoZonesPicking.ts +3 -9
  529. package/src/xyz/xyzBidimensionalFFT.ts +122 -0
  530. package/src/xyz/xyzJResAnalyzer.ts +51 -42
  531. package/lib/prediction/utils/flatGroupedDiaIDs.d.ts +0 -2
  532. package/lib/prediction/utils/flatGroupedDiaIDs.js +0 -14
  533. package/lib/prediction/utils/flatGroupedDiaIDs.js.map +0 -1
  534. package/lib/xyz/Data2D.d.ts +0 -7
  535. package/lib-esm/prediction/utils/flatGroupedDiaIDs.js +0 -10
  536. package/lib-esm/prediction/utils/flatGroupedDiaIDs.js.map +0 -1
  537. package/src/assignment/utils/getAssignment/data/correlations.js +0 -713
  538. package/src/assignment/utils/getAssignment/data/predictions.js +0 -34
  539. package/src/nmr-parser.d.ts +0 -17
  540. package/src/prediction/utils/flatGroupedDiaIDs.ts +0 -11
  541. package/src/xyz/Data2D.ts +0 -7
  542. /package/lib/{xyz → types}/Data2D.js +0 -0
  543. /package/lib-esm/{xyz → types}/Data2D.js +0 -0
@@ -0,0 +1,123 @@
1
+ import { DoubleArray } from 'cheminfo-types';
2
+ import Matrix from 'ml-matrix';
3
+ import {
4
+ reimAbsolute,
5
+ reimAutoPhaseCorrection,
6
+ reimFFT,
7
+ reimPhaseCorrection,
8
+ } from 'ml-spectra-processing';
9
+
10
+ import {
11
+ apodization,
12
+ ApodizationFilterOptions,
13
+ } from '../../../apodization/apodization';
14
+
15
+ import { zeroFilling, ZeroFillingOptions } from './zeroFilling';
16
+
17
+ interface PhaseCorrection {
18
+ mode?: string;
19
+ ph0?: number;
20
+ ph1?: number;
21
+ }
22
+
23
+ export interface IndirectDimensionOptions {
24
+ fnMode?: string;
25
+ zeroFilling?: ZeroFillingOptions;
26
+ apodization?: ApodizationFilterOptions;
27
+ phaseCorrection?: PhaseCorrection;
28
+ }
29
+
30
+ export function fftIndirectDimension(
31
+ data: { re: DoubleArray[] | Matrix; im: DoubleArray[] | Matrix },
32
+ options: IndirectDimensionOptions,
33
+ ) {
34
+ const reData = Matrix.checkMatrix(data.re);
35
+ const imData = Matrix.checkMatrix(data.im);
36
+
37
+ const nbRows = reData.rows;
38
+ const nbColumns = reData.columns;
39
+
40
+ const { zeroFilling: zeroFillingF1 } = options;
41
+ const { factor: f1Factor = 2 } = zeroFillingF1 || {};
42
+ const nbPointsF1 =
43
+ zeroFillingF1?.nbPoints || 2 ** Math.round(Math.log2(nbRows * f1Factor));
44
+ const { apodization: apodizationF1 } = options;
45
+ let {
46
+ ph0: ph0F1,
47
+ ph1: ph1F1,
48
+ mode: pcModeF1,
49
+ } = options.phaseCorrection || {};
50
+
51
+ const reResult = new Matrix(nbPointsF1, nbColumns);
52
+ const imResult = new Matrix(nbPointsF1, nbColumns);
53
+ for (let i = 0; i < nbColumns; i++) {
54
+ const { re: aRe, im: aIm } = apodization(
55
+ {
56
+ re: reData.getColumn(i),
57
+ im: imData.getColumn(i),
58
+ },
59
+ apodizationF1,
60
+ );
61
+
62
+ const newRe = [];
63
+ const newIm = [];
64
+ if (options.fnMode === 'echo') {
65
+ for (let j = 0; j < aRe.length; j += 2) {
66
+ newRe.push(aRe[j]);
67
+ newIm.push(aRe[j + 1]);
68
+ }
69
+ } else {
70
+ for (let j = 0; j < aRe.length; j++) {
71
+ newRe.push(aRe[j]);
72
+ newIm.push(-aIm[j]);
73
+ }
74
+ }
75
+
76
+ let transformed = reimFFT(
77
+ zeroFilling(
78
+ {
79
+ re: newRe,
80
+ im: newIm,
81
+ },
82
+ { digitalFilterValue: 0, nbPoints: nbPointsF1 },
83
+ ),
84
+ { applyZeroShift: true },
85
+ );
86
+ let { re, im } = transformed;
87
+
88
+ if (options.phaseCorrection?.mode === 'mc') {
89
+ re = reimAbsolute({ re, im });
90
+ im = new Float64Array(im.length);
91
+ }
92
+
93
+ if (pcModeF1 === 'pk') {
94
+ if (i === 0 && ph0F1 === undefined && ph1F1 === undefined) {
95
+ //here we can improve it by checking if the experiment is phase sensitive.
96
+ const phased = reimAutoPhaseCorrection(
97
+ { re, im },
98
+ { magnitudeMode: false },
99
+ );
100
+ ph0F1 = phased.ph0;
101
+ ph1F1 = phased.ph1;
102
+ }
103
+ if (ph0F1 !== undefined && ph1F1 !== undefined) {
104
+ Object.assign(
105
+ transformed,
106
+ reimPhaseCorrection(
107
+ transformed,
108
+ (ph0F1 * Math.PI) / 180,
109
+ (ph1F1 * Math.PI) / 180,
110
+ ),
111
+ );
112
+ }
113
+ }
114
+
115
+ reResult.setColumn(i, re);
116
+ imResult.setColumn(i, im);
117
+ }
118
+
119
+ return {
120
+ re: reResult,
121
+ im: imResult,
122
+ };
123
+ }
@@ -0,0 +1,19 @@
1
+ import { DataReIm, xMean } from 'ml-spectra-processing';
2
+
3
+ export function removeDCOffset(data: DataReIm, options: any) {
4
+ let { digitalFilterValue = 0 } = options;
5
+ const nbPoints = data.re.length;
6
+ const newRe = new Float64Array(data.re);
7
+ const newIm = new Float64Array(data.im);
8
+ const averageRe = xMean(
9
+ data.re.slice((nbPoints * 0.75) >> 0, nbPoints - digitalFilterValue),
10
+ );
11
+ const averageIm = xMean(
12
+ data.im.slice((nbPoints * 0.75) >> 0, nbPoints - digitalFilterValue),
13
+ );
14
+ for (let i = digitalFilterValue; i < nbPoints - digitalFilterValue; i++) {
15
+ newRe[i] -= averageRe;
16
+ newIm[i] -= averageIm;
17
+ }
18
+ return { re: newRe, im: newIm };
19
+ }
@@ -0,0 +1,39 @@
1
+ import { DataReIm } from 'ml-spectra-processing';
2
+
3
+ export interface ZeroFillingOptions {
4
+ nbPoints?: number;
5
+ factor?: number;
6
+ digitalFilterValue?: number;
7
+ }
8
+
9
+ export function zeroFilling(data: DataReIm, options: ZeroFillingOptions) {
10
+ let { nbPoints, factor = 2, digitalFilterValue: grpdly = 0 } = options;
11
+
12
+ if (!nbPoints) {
13
+ nbPoints = 2 ** Math.round(Math.log2(data.re.length * factor));
14
+ }
15
+
16
+ let pointsToShift;
17
+ if (grpdly > 0) {
18
+ pointsToShift = Math.floor(grpdly);
19
+ } else {
20
+ pointsToShift = 0;
21
+ }
22
+
23
+ const { re, im } = data;
24
+
25
+ let newRE = new Float64Array(nbPoints);
26
+ let newIM = new Float64Array(nbPoints);
27
+
28
+ const length = Math.min(nbPoints, re.length);
29
+
30
+ newRE.set(re.slice(0, length - pointsToShift));
31
+ newIM.set(im.slice(0, length - pointsToShift));
32
+
33
+ if (pointsToShift > 0 && pointsToShift < nbPoints) {
34
+ newRE.set(re.slice(re.length - pointsToShift), nbPoints - pointsToShift);
35
+ newIM.set(im.slice(re.length - pointsToShift), nbPoints - pointsToShift);
36
+ }
37
+
38
+ return { re: newRE, im: newIM };
39
+ }
@@ -1,8 +1,9 @@
1
- import Matrix from 'ml-matrix';
1
+ import { MinMaxContent } from 'cheminfo-types';
2
2
 
3
- import { Data2D } from '../Data2D';
4
-
5
- export function padData(spectraData: Data2D, options: { width: number }) {
3
+ export function padData(
4
+ spectraData: MinMaxContent,
5
+ options: { width: number },
6
+ ) {
6
7
  let { minX, maxX, minY, maxY } = spectraData;
7
8
 
8
9
  const width = options.width;
@@ -20,15 +21,20 @@ export function padData(spectraData: Data2D, options: { width: number }) {
20
21
 
21
22
  let xOffset = xDiff / 2;
22
23
  let yOffset = yDiff / 2;
23
- let newMatrix = Matrix.zeros(nbSubSpectra + yDiff, nbPoints + xDiff);
24
+
25
+ const newMatrix: Float64Array[] = [];
26
+ for (let i = 0; i < nbSubSpectra + yDiff; i++) {
27
+ newMatrix.push(new Float64Array(nbPoints + xDiff));
28
+ }
24
29
  for (let i = 0; i < nbSubSpectra; i++) {
25
30
  for (let j = 0; j < nbPoints; j++) {
26
- newMatrix.set(i + yOffset, j + xOffset, spectraData.z[i][j]);
31
+ newMatrix[i + yOffset].set(spectraData.z[i], xOffset);
27
32
  }
28
33
  }
29
34
 
30
35
  return {
31
- z: newMatrix.to2DArray(),
36
+ ...spectraData,
37
+ z: newMatrix,
32
38
  minX: minX - xOffset * xInterval,
33
39
  maxX: maxX + xOffset * xInterval,
34
40
  minY: minY - yOffset * yInterval,
@@ -1,4 +1,5 @@
1
1
  import { v4 as generateID } from '@lukeed/uuid';
2
+ import { MinMaxContent } from 'cheminfo-types';
2
3
  import * as convolution from 'ml-matrix-convolution';
3
4
  import * as matrixPeakFinders from 'ml-matrix-peaks-finder';
4
5
  import type { Peak2D } from 'ml-matrix-peaks-finder';
@@ -11,7 +12,6 @@ import type { GetKernelOptions } from '../peaks/util/getKernel';
11
12
  import * as PeakOptimizer from '../peaks/util/peakOptimizer';
12
13
  import { MakeMandatory } from '../utilities/MakeMandatory';
13
14
 
14
- import { Data2D } from './Data2D';
15
15
  import type { NMRSignal2D } from './NMRSignal2D';
16
16
  import { padData } from './util/padData';
17
17
 
@@ -89,7 +89,7 @@ export type NMRSignal2DWithID<T extends Peak2D = Peak2D> = MakeMandatory<
89
89
  >;
90
90
 
91
91
  export function xyzAutoSignalsPicking(
92
- spectraData: Data2D,
92
+ spectraData: MinMaxContent,
93
93
  options: XYZAutoSignalsPickingOptions,
94
94
  ) {
95
95
  let {
@@ -1,3 +1,5 @@
1
+ import { MinMaxContent } from 'cheminfo-types';
2
+
1
3
  import { xyzAutoSignalsPicking } from '..';
2
4
  import type { GetKernelOptions } from '../peaks/util/getKernel';
3
5
  import { MakeMandatory } from '../utilities/MakeMandatory';
@@ -5,14 +7,6 @@ import { MakeMandatory } from '../utilities/MakeMandatory';
5
7
  import { NMRZone } from './NMRZone';
6
8
  import { formatZones } from './util/formatZone';
7
9
 
8
- export interface Data2D {
9
- z: number[][] | Float64Array[];
10
- minX: number;
11
- maxX: number;
12
- minY: number;
13
- maxY: number;
14
- }
15
-
16
10
  export interface XYZAutoZonesPickingOptions {
17
11
  /**
18
12
  * max number of points in any dimension to pad the input data, this is needed to avoid lost peaks when the input matrix is too small.
@@ -71,7 +65,7 @@ export interface XYZAutoZonesPickingOptions {
71
65
  export type NMRZoneWithID = MakeMandatory<NMRZone, 'id'>;
72
66
 
73
67
  export function xyzAutoZonesPicking(
74
- spectraData: Data2D,
68
+ spectraData: MinMaxContent,
75
69
  options: XYZAutoZonesPickingOptions,
76
70
  ): NMRZoneWithID[] {
77
71
  const signals = xyzAutoSignalsPicking(spectraData, options);
@@ -0,0 +1,122 @@
1
+ import { Data2D, DoubleArray, Data2DFid } from 'cheminfo-types';
2
+ import Matrix from 'ml-matrix';
3
+
4
+ import { ApodizationFilterOptions } from '../apodization/apodization';
5
+
6
+ import { quadrature } from './quadrature';
7
+ import {
8
+ DirectDimensionOptions,
9
+ fftDirectDimension,
10
+ } from './util/fft2d/fftDirectDimension';
11
+ import {
12
+ fftIndirectDimension,
13
+ IndirectDimensionOptions,
14
+ } from './util/fft2d/fftIndirectDimension';
15
+ import { ZeroFillingOptions } from './util/fft2d/zeroFilling';
16
+
17
+ type Info2D = any;
18
+
19
+ interface BidimensionalFFTOptions {
20
+ fnMode: string;
21
+ info: Info2D;
22
+ zeroFilling?: ZeroFillingOptions;
23
+ phaseCorrection?: { ph0: number; ph1: number };
24
+ digitalFilterValue?: number;
25
+ apodization?: ApodizationFilterOptions;
26
+ indirect?: IndirectDimensionOptions;
27
+ direct?: DirectDimensionOptions;
28
+ }
29
+
30
+ export function xyzBidimensionalFFT(
31
+ data: Data2D,
32
+ options: BidimensionalFFTOptions,
33
+ ) {
34
+ ensureData2DFid(data);
35
+
36
+ const {
37
+ info,
38
+ fnMode,
39
+ digitalFilterValue = 0,
40
+ zeroFilling: zeroFillingGeneral,
41
+ } = options;
42
+
43
+ const orderedData = quadrature(data, { fnMode });
44
+
45
+ const { re: reData } = orderedData;
46
+ const nbRows = reData.length;
47
+ const nbColumns = reData[0].length;
48
+ const { direct = {}, indirect = {} } = options;
49
+
50
+ const { zeroFilling: zeroFillingF2 = zeroFillingGeneral } = direct;
51
+
52
+ const { factor: f2Factor = 2 } = zeroFillingF2 || {};
53
+ const nbPointsF2 =
54
+ zeroFillingF2?.nbPoints || 2 ** Math.round(Math.log2(nbColumns * f2Factor));
55
+
56
+ const transformed = fftDirectDimension(orderedData, {
57
+ ...direct,
58
+ fnMode,
59
+ digitalFilterValue,
60
+ zeroFilling: { nbPoints: nbPointsF2 },
61
+ });
62
+
63
+ const { zeroFilling: zeroFillingF1 } = options;
64
+ const { factor: f1Factor = 2 } = zeroFillingF1 || {};
65
+ const nbPointsF1 =
66
+ zeroFillingF1?.nbPoints || 2 ** Math.round(Math.log2(nbRows * f1Factor));
67
+ const { re: reResult, im: imResult } = fftIndirectDimension(transformed, {
68
+ ...indirect,
69
+ fnMode,
70
+ zeroFilling: { nbPoints: nbPointsF1 },
71
+ });
72
+
73
+ const minMaxXY = getMinMaxXY(info);
74
+ return {
75
+ re: {
76
+ z: convertToDoubleArray(reResult),
77
+ maxZ: reResult.max(),
78
+ minZ: reResult.min(),
79
+ ...minMaxXY,
80
+ },
81
+ im: {
82
+ z: convertToDoubleArray(imResult),
83
+ maxZ: imResult.max(),
84
+ minZ: imResult.min(),
85
+ ...minMaxXY,
86
+ },
87
+ };
88
+ }
89
+
90
+ function ensureData2DFid(data: Data2D): asserts data is Data2DFid {
91
+ if (!('re' in data)) {
92
+ throw new Error('bidimensional FFT only can be applied to raw data');
93
+ }
94
+ }
95
+
96
+ function convertToDoubleArray(data: Matrix) {
97
+ const result: DoubleArray[] = new Array(data.rows);
98
+ for (let i = 0; i < data.rows; i++) {
99
+ result[i] = new Float64Array(data.getRow(i));
100
+ }
101
+ return result;
102
+ }
103
+
104
+ function getMinMaxXY(info: Info2D) {
105
+ const min: number[] = [];
106
+ const max: number[] = [];
107
+ for (let i = 0; i < info.baseFrequency.length; i++) {
108
+ const baseFrequency = Number.parseFloat(info.baseFrequency[i]);
109
+ const frequencyOffset = Number.parseFloat(info.frequencyOffset[i]);
110
+ const spectralWidth = Number.parseFloat(info.spectralWidth[i]);
111
+ const offset = frequencyOffset / baseFrequency;
112
+ min.push(offset - spectralWidth * 0.5);
113
+ max.push(offset + spectralWidth * 0.5);
114
+ }
115
+
116
+ return {
117
+ minX: min[0],
118
+ maxX: max[0],
119
+ minY: min[1],
120
+ maxY: max[1],
121
+ };
122
+ }
@@ -1,9 +1,15 @@
1
1
  import { v4 as generateID } from '@lukeed/uuid';
2
+ import { PeakXYWidth } from 'cheminfo-types';
2
3
  import type { Peak2D } from 'ml-matrix-peaks-finder';
3
4
  import simpleClustering from 'ml-simple-clustering';
4
5
 
5
6
  import { addMissingIDs } from '../peaks/util/addMissingIDs';
6
- import type { JAxisKeys } from '../signals/utils/jAnalyzer';
7
+ import type {
8
+ JAxisKeys,
9
+ Peak1DIntern,
10
+ SignalFlexiblePeaks,
11
+ SignalIntern,
12
+ } from '../signals/utils/jAnalyzer';
7
13
  import jAnalyzer from '../signals/utils/jAnalyzer';
8
14
  import type { MakeMandatory } from '../utilities/MakeMandatory';
9
15
 
@@ -40,20 +46,14 @@ interface XYZJResAnalyzerOptions extends CompilePatternOptions {
40
46
  interface Peak2DInternalCompiler extends Peak2D {
41
47
  width?: number;
42
48
  }
43
- type Signal2DInternalCompiler = Omit<NMRSignal2D, 'peaks'> & {
44
- peaks: Peak2DInternalCompiler[];
45
- integralData: { from: number; to: number };
46
- nbPeaks: number;
47
- multiplicity: string;
48
- pattern: string;
49
- observe: number;
50
- };
51
49
 
52
50
  type CompilePatternOptionsMandatory = MakeMandatory<
53
51
  CompilePatternOptions,
54
52
  'observedFrequencies' | 'tolerances' | 'nuclei' | 'jAnalyzer'
55
53
  >;
56
54
 
55
+ type Peak2DWidth = PeakXYWidth & { z: number };
56
+
57
57
  export function xyzJResAnalyzer(
58
58
  signals: NMRSignal2D[],
59
59
  options: XYZJResAnalyzerOptions = {},
@@ -76,7 +76,7 @@ export function xyzJResAnalyzer(
76
76
  jAnalyzer,
77
77
  });
78
78
  //check if the signal are symmetric around the reference
79
- let signals2D = [];
79
+ let signals2D: any[] = [];
80
80
  for (const tempSignal of temporalSignals) {
81
81
  let delta = tempSignal.y.delta;
82
82
  if (Math.abs(delta - reference) > referenceMaxShiftError) continue;
@@ -108,43 +108,52 @@ function compilePattern(
108
108
  };
109
109
 
110
110
  const defaultWidth = 0.02 * observedFrequencies[0];
111
- const newSignals = parse(stringify(signals));
111
+ const newSignals: SignalFlexiblePeaks[] = [];
112
112
  //adapt to 1D jAnalyzer
113
- for (const signal of newSignals) {
114
- let peaks = signal.peaks;
115
- signal.nbPeaks = signal.peaks.length;
116
- signal.multiplicity = '';
117
- signal.pattern = '';
118
- signal.delta1 = signal.shiftY;
119
- signal.observe = observedFrequencies[1];
120
- signal.integralData = {
121
- from: Number.MAX_SAFE_INTEGER,
122
- to: Number.MIN_SAFE_INTEGER,
123
- };
124
- for (const peak of peaks) {
125
- if (!peak.width) peak.width = defaultWidth;
113
+ for (const signal of signals) {
114
+ let peaks: Peak2DWidth[] = [];
115
+ for (const peak of signal.peaks || []) {
116
+ peaks.push({
117
+ ...peak,
118
+ width: defaultWidth,
119
+ });
126
120
  }
127
- peaks.sort((a: Peak2D, b: Peak2D) => a.y - b.y);
121
+ peaks.sort((a, b) => a.y - b.y);
122
+ newSignals.push({
123
+ nbPeaks: peaks.length,
124
+ multiplicity: '',
125
+ pattern: '',
126
+ startX: peaks[0].y - defaultWidth,
127
+ stopX: peaks[peaks.length - 1].y + defaultWidth,
128
+ delta: signal.y.delta,
129
+ observe: observedFrequencies[1],
130
+ integralData: {
131
+ value: -1,
132
+ from: Number.MAX_SAFE_INTEGER,
133
+ to: Number.MIN_SAFE_INTEGER,
134
+ },
135
+ peaks,
136
+ });
128
137
  }
129
138
 
130
139
  for (let i = 0; i < signals.length; i++) {
131
- jAnalyzer.compilePattern(newSignals[i], jAnalyzerOptions);
140
+ const signal = jAnalyzer.compilePattern(newSignals[i], jAnalyzerOptions);
132
141
 
133
142
  if (
134
- newSignals[i].maskPattern &&
135
- newSignals[i].multiplicity !== 'm' &&
136
- newSignals[i].multiplicity !== ''
143
+ signal.maskPattern &&
144
+ signal.multiplicity !== 'm' &&
145
+ signal.multiplicity !== ''
137
146
  ) {
138
147
  // Create a new signal with the removed peaks
139
- let peaksO = [];
140
- for (let j = newSignals[i].maskPattern.length - 1; j >= 0; j--) {
141
- if (newSignals[i].maskPattern[j] === false) {
142
- let peakR = newSignals[i].peaks.splice(j, 1)[0];
148
+ let peaksO: Peak1DIntern[] = [];
149
+ for (let j = signal.maskPattern.length - 1; j >= 0; j--) {
150
+ if (!signal.maskPattern[j]) {
151
+ let peakR = signal.peaks.splice(j, 1)[0];
143
152
  peaksO.push(peakR);
144
- newSignals[i].mask.splice(j, 1);
145
- newSignals[i].mask2.splice(j, 1);
146
- newSignals[i].maskPattern.splice(j, 1);
147
- newSignals[i].nbPeaks--;
153
+ signal.mask.splice(j, 1);
154
+ signal.mask2?.splice(j, 1);
155
+ signal.maskPattern.splice(j, 1);
156
+ signal.nbPeaks--;
148
157
  }
149
158
  }
150
159
  if (peaksO.length > 0) {
@@ -165,7 +174,7 @@ function compilePattern(
165
174
  return signals;
166
175
  }
167
176
 
168
- function createSignals2D(peaksInput: Peak2D[], options: any) {
177
+ function createSignals2D(peaksInput: Peak1DIntern[], options: any) {
169
178
  let { observedFrequencies, tolerances, nuclei, dx, dy } = options;
170
179
 
171
180
  const peaks: Peak2DInternalCompiler[] = parse(stringify(peaksInput));
@@ -176,7 +185,7 @@ function createSignals2D(peaksInput: Peak2D[], options: any) {
176
185
 
177
186
  // The connectivity matrix is an square and symmetric matrix, so we'll only store the upper diagonal in an
178
187
  // array like form
179
- let connectivity = [];
188
+ let connectivity: Array<0 | 1> = [];
180
189
  for (let i = 0; i < peaks.length; i++) {
181
190
  for (let j = i; j < peaks.length; j++) {
182
191
  if (
@@ -192,7 +201,7 @@ function createSignals2D(peaksInput: Peak2D[], options: any) {
192
201
  }
193
202
  let clusters = simpleClustering(connectivity);
194
203
 
195
- let signals = [];
204
+ let signals: SignalIntern[] = [];
196
205
  if (clusters) {
197
206
  for (let cluster of clusters) {
198
207
  let signal: any = {
@@ -212,7 +221,7 @@ function createSignals2D(peaksInput: Peak2D[], options: any) {
212
221
  shiftX: 0,
213
222
  shiftY: 0,
214
223
  };
215
- let peaks2D = [];
224
+ let peaks2D: Peak2DInternalCompiler[] = [];
216
225
  let minMax1 = [Number.MAX_VALUE, 0];
217
226
  let minMax2 = [Number.MAX_VALUE, 0];
218
227
  let sumZ = 0;
@@ -247,7 +256,7 @@ function createSignals2D(peaksInput: Peak2D[], options: any) {
247
256
  signal.shiftY /= sumZ;
248
257
  signal.delta1 = signal.shiftY;
249
258
  signal.peaks = peaks2D;
250
- signals.push(signal as Signal2DInternalCompiler);
259
+ signals.push(signal);
251
260
  }
252
261
  }
253
262
  return signals;
@@ -1,2 +0,0 @@
1
- import type { GroupedDiastereotopicAtomIDs } from 'openchemlib-utils';
2
- export declare function flatGroupedDiaIDs(groups: GroupedDiastereotopicAtomIDs): string[];
@@ -1,14 +0,0 @@
1
- "use strict";
2
- Object.defineProperty(exports, "__esModule", { value: true });
3
- exports.flatGroupedDiaIDs = void 0;
4
- function flatGroupedDiaIDs(groups) {
5
- let diaIDs = [];
6
- for (let group of groups) {
7
- for (let atom of group.atoms) {
8
- diaIDs[atom] = group.oclID;
9
- }
10
- }
11
- return diaIDs;
12
- }
13
- exports.flatGroupedDiaIDs = flatGroupedDiaIDs;
14
- //# sourceMappingURL=flatGroupedDiaIDs.js.map
@@ -1 +0,0 @@
1
- {"version":3,"file":"flatGroupedDiaIDs.js","sourceRoot":"","sources":["../../../src/prediction/utils/flatGroupedDiaIDs.ts"],"names":[],"mappings":";;;AAEA,SAAgB,iBAAiB,CAAC,MAAoC;IACpE,IAAI,MAAM,GAAG,EAAE,CAAC;IAChB,KAAK,IAAI,KAAK,IAAI,MAAM,EAAE;QACxB,KAAK,IAAI,IAAI,IAAI,KAAK,CAAC,KAAK,EAAE;YAC5B,MAAM,CAAC,IAAI,CAAC,GAAG,KAAK,CAAC,KAAK,CAAC;SAC5B;KACF;IACD,OAAO,MAAM,CAAC;AAChB,CAAC;AARD,8CAQC"}
@@ -1,7 +0,0 @@
1
- export interface Data2D {
2
- z: number[][] | Float64Array[];
3
- minX: number;
4
- maxX: number;
5
- minY: number;
6
- maxY: number;
7
- }
@@ -1,10 +0,0 @@
1
- export function flatGroupedDiaIDs(groups) {
2
- let diaIDs = [];
3
- for (let group of groups) {
4
- for (let atom of group.atoms) {
5
- diaIDs[atom] = group.oclID;
6
- }
7
- }
8
- return diaIDs;
9
- }
10
- //# sourceMappingURL=flatGroupedDiaIDs.js.map
@@ -1 +0,0 @@
1
- {"version":3,"file":"flatGroupedDiaIDs.js","sourceRoot":"","sources":["../../../src/prediction/utils/flatGroupedDiaIDs.ts"],"names":[],"mappings":"AAEA,MAAM,UAAU,iBAAiB,CAAC,MAAoC;IACpE,IAAI,MAAM,GAAG,EAAE,CAAC;IAChB,KAAK,IAAI,KAAK,IAAI,MAAM,EAAE;QACxB,KAAK,IAAI,IAAI,IAAI,KAAK,CAAC,KAAK,EAAE;YAC5B,MAAM,CAAC,IAAI,CAAC,GAAG,KAAK,CAAC,KAAK,CAAC;SAC5B;KACF;IACD,OAAO,MAAM,CAAC;AAChB,CAAC"}