python-microscopy 25.11.20__cp313-cp313-win_amd64.whl

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 (1278) hide show
  1. PYME/Acquire/ActionManager.py +450 -0
  2. PYME/Acquire/ExecTools.py +235 -0
  3. PYME/Acquire/Hardware/AAOptoelectronics/MDS.py +175 -0
  4. PYME/Acquire/Hardware/AAOptoelectronics/__init__.py +0 -0
  5. PYME/Acquire/Hardware/ARCoptix/__init__.py +0 -0
  6. PYME/Acquire/Hardware/ARCoptix/lcdriver.py +149 -0
  7. PYME/Acquire/Hardware/ARCoptix/lcserver32.py +123 -0
  8. PYME/Acquire/Hardware/AndorIXon/AndorCam.py +1095 -0
  9. PYME/Acquire/Hardware/AndorIXon/AndorControlFrame.py +312 -0
  10. PYME/Acquire/Hardware/AndorIXon/AndorIXon.py +737 -0
  11. PYME/Acquire/Hardware/AndorIXon/__init__.py +27 -0
  12. PYME/Acquire/Hardware/AndorNeo/AndorNeo.py +644 -0
  13. PYME/Acquire/Hardware/AndorNeo/AndorNeoControlFrame.py +161 -0
  14. PYME/Acquire/Hardware/AndorNeo/AndorZyla.py +761 -0
  15. PYME/Acquire/Hardware/AndorNeo/SDK3.py +307 -0
  16. PYME/Acquire/Hardware/AndorNeo/SDK3Cam.py +171 -0
  17. PYME/Acquire/Hardware/AndorNeo/ZylaControlPanel.py +105 -0
  18. PYME/Acquire/Hardware/AndorNeo/__init__.py +22 -0
  19. PYME/Acquire/Hardware/AndorNeo/parseAtdebug.py +46 -0
  20. PYME/Acquire/Hardware/AndorNeo/plotTimings.py +73 -0
  21. PYME/Acquire/Hardware/AndorNeo/testNeo.py +62 -0
  22. PYME/Acquire/Hardware/Camera.py +1199 -0
  23. PYME/Acquire/Hardware/CameraSkeleton.py +642 -0
  24. PYME/Acquire/Hardware/Coherent/OBIS.py +147 -0
  25. PYME/Acquire/Hardware/Coherent/Sapphire.py +162 -0
  26. PYME/Acquire/Hardware/Coherent/__init__.py +0 -0
  27. PYME/Acquire/Hardware/DMDGui.py +198 -0
  28. PYME/Acquire/Hardware/DigiData/DigiData.py +95 -0
  29. PYME/Acquire/Hardware/DigiData/DigiDataClient.py +30 -0
  30. PYME/Acquire/Hardware/DigiData/RemoteDigiData.py +51 -0
  31. PYME/Acquire/Hardware/DigiData/__init__.py +24 -0
  32. PYME/Acquire/Hardware/DigiData/axDD132x.py +348 -0
  33. PYME/Acquire/Hardware/EMCCDTheory.py +41 -0
  34. PYME/Acquire/Hardware/ExciterWheel.py +167 -0
  35. PYME/Acquire/Hardware/FilterWheel.py +184 -0
  36. PYME/Acquire/Hardware/FocCorr.py +106 -0
  37. PYME/Acquire/Hardware/FocCorrR.py +196 -0
  38. PYME/Acquire/Hardware/FrFilter.py +51 -0
  39. PYME/Acquire/Hardware/GCS/GCS_DLL.py +370 -0
  40. PYME/Acquire/Hardware/GCS/__init__.py +0 -0
  41. PYME/Acquire/Hardware/GCS/gcs.py +210 -0
  42. PYME/Acquire/Hardware/HamamatsuDCAM/HamamatsuDCAM.py +662 -0
  43. PYME/Acquire/Hardware/HamamatsuDCAM/HamamatsuORCA.py +602 -0
  44. PYME/Acquire/Hardware/HamamatsuDCAM/Hamamatsu_control_panel.py +54 -0
  45. PYME/Acquire/Hardware/HamamatsuDCAM/__init__.py +23 -0
  46. PYME/Acquire/Hardware/LaserControlFrame.py +160 -0
  47. PYME/Acquire/Hardware/MPBCommunications/MPBCW.py +132 -0
  48. PYME/Acquire/Hardware/MPBCommunications/__init__.py +0 -0
  49. PYME/Acquire/Hardware/Mercury/Mercury.py +269 -0
  50. PYME/Acquire/Hardware/Mercury/PI_Mercury_GCS_DLL.py +857 -0
  51. PYME/Acquire/Hardware/Mercury/__init__.py +22 -0
  52. PYME/Acquire/Hardware/Mercury/mercuryStepper.py +203 -0
  53. PYME/Acquire/Hardware/Mercury/mercuryStepperGCS.py +281 -0
  54. PYME/Acquire/Hardware/NikonTE2000.py +68 -0
  55. PYME/Acquire/Hardware/NikonTi.py +214 -0
  56. PYME/Acquire/Hardware/NikonTiGUI.py +81 -0
  57. PYME/Acquire/Hardware/OrielCornerstone.py +125 -0
  58. PYME/Acquire/Hardware/PM100USB.py +51 -0
  59. PYME/Acquire/Hardware/Piezos/__init__.py +22 -0
  60. PYME/Acquire/Hardware/Piezos/base_piezo.py +108 -0
  61. PYME/Acquire/Hardware/Piezos/offsetPiezo.py +162 -0
  62. PYME/Acquire/Hardware/Piezos/offsetPiezoREST.py +308 -0
  63. PYME/Acquire/Hardware/Piezos/piezo_c867.py +486 -0
  64. PYME/Acquire/Hardware/Piezos/piezo_e255.py +68 -0
  65. PYME/Acquire/Hardware/Piezos/piezo_e662.py +61 -0
  66. PYME/Acquire/Hardware/Piezos/piezo_e709.py +434 -0
  67. PYME/Acquire/Hardware/Piezos/piezo_e816.py +452 -0
  68. PYME/Acquire/Hardware/Piezos/piezo_e816_corr.py +70 -0
  69. PYME/Acquire/Hardware/Piezos/piezo_e816_dll.py +518 -0
  70. PYME/Acquire/Hardware/Piezos/piezo_e816b.py +70 -0
  71. PYME/Acquire/Hardware/Piezos/piezo_pipython_gcs.py +560 -0
  72. PYME/Acquire/Hardware/Piezos/piezo_test.py +55 -0
  73. PYME/Acquire/Hardware/Simulator/EmpiricalHist.py +273 -0
  74. PYME/Acquire/Hardware/Simulator/__init__.py +22 -0
  75. PYME/Acquire/Hardware/Simulator/dSimControl.py +961 -0
  76. PYME/Acquire/Hardware/Simulator/fakeCam.py +651 -0
  77. PYME/Acquire/Hardware/Simulator/fakePiezo.py +95 -0
  78. PYME/Acquire/Hardware/Simulator/fluor.py +336 -0
  79. PYME/Acquire/Hardware/Simulator/illuminate.cp313-win_amd64.dll.a +0 -0
  80. PYME/Acquire/Hardware/Simulator/illuminate.cp313-win_amd64.pyd +0 -0
  81. PYME/Acquire/Hardware/Simulator/illuminate.pyx +93 -0
  82. PYME/Acquire/Hardware/Simulator/lasersliders.py +90 -0
  83. PYME/Acquire/Hardware/Simulator/rend_im.py +446 -0
  84. PYME/Acquire/Hardware/Simulator/setup.py +69 -0
  85. PYME/Acquire/Hardware/Simulator/simcontrol.py +348 -0
  86. PYME/Acquire/Hardware/Simulator/simui_wx.py +794 -0
  87. PYME/Acquire/Hardware/Tango/__init__.py +0 -0
  88. PYME/Acquire/Hardware/Tango/marzhauser_tango.py +583 -0
  89. PYME/Acquire/Hardware/TiLightCrafter.py +388 -0
  90. PYME/Acquire/Hardware/__init__.py +22 -0
  91. PYME/Acquire/Hardware/aotf.py +271 -0
  92. PYME/Acquire/Hardware/arclampshutterpanel.py +71 -0
  93. PYME/Acquire/Hardware/cameraSoftwareBuffer.py +215 -0
  94. PYME/Acquire/Hardware/camera_noise.py +270 -0
  95. PYME/Acquire/Hardware/ccdAdjPanel.py +188 -0
  96. PYME/Acquire/Hardware/ccdCalibrator.py +161 -0
  97. PYME/Acquire/Hardware/cobaltLaser.py +108 -0
  98. PYME/Acquire/Hardware/cobaltLaser561.py +94 -0
  99. PYME/Acquire/Hardware/comports.py +26 -0
  100. PYME/Acquire/Hardware/driftTrackGUI.py +488 -0
  101. PYME/Acquire/Hardware/driftTracking.py +595 -0
  102. PYME/Acquire/Hardware/fakeShutters.py +52 -0
  103. PYME/Acquire/Hardware/focusKeys.py +204 -0
  104. PYME/Acquire/Hardware/focus_locks/__init__.py +0 -0
  105. PYME/Acquire/Hardware/focus_locks/reflection_focus_lock.py +684 -0
  106. PYME/Acquire/Hardware/frZStage.py +117 -0
  107. PYME/Acquire/Hardware/fw102.py +38 -0
  108. PYME/Acquire/Hardware/ids_peak_cam.py +561 -0
  109. PYME/Acquire/Hardware/ioslave.py +305 -0
  110. PYME/Acquire/Hardware/lasers.py +292 -0
  111. PYME/Acquire/Hardware/matchboxLaser.py +58 -0
  112. PYME/Acquire/Hardware/microscope_adapter.py +104 -0
  113. PYME/Acquire/Hardware/mpd_picosecond_delayer.py +395 -0
  114. PYME/Acquire/Hardware/multiview.py +287 -0
  115. PYME/Acquire/Hardware/olympusix81.py +59 -0
  116. PYME/Acquire/Hardware/pco/__init__.py +0 -0
  117. PYME/Acquire/Hardware/pco/pco_cam.py +348 -0
  118. PYME/Acquire/Hardware/pco/pco_edge_42_lt.py +34 -0
  119. PYME/Acquire/Hardware/pco/pco_sdk.py +1645 -0
  120. PYME/Acquire/Hardware/pco/pco_sdk_cam.py +518 -0
  121. PYME/Acquire/Hardware/pco/pco_sdk_cam_control_panel.py +54 -0
  122. PYME/Acquire/Hardware/phoxxLaser.py +199 -0
  123. PYME/Acquire/Hardware/phoxxLaserOLD.py +242 -0
  124. PYME/Acquire/Hardware/priorLumen.py +102 -0
  125. PYME/Acquire/Hardware/priorarclampshutter.py +52 -0
  126. PYME/Acquire/Hardware/setup.py +50 -0
  127. PYME/Acquire/Hardware/spacenav.py +148 -0
  128. PYME/Acquire/Hardware/splitter.py +394 -0
  129. PYME/Acquire/Hardware/thorlabsPiezo.py +98 -0
  130. PYME/Acquire/Hardware/thorlabs_cam.py +136 -0
  131. PYME/Acquire/Hardware/thorlabs_mff_flipper.py +400 -0
  132. PYME/Acquire/Hardware/toptica_ibeam.py +51 -0
  133. PYME/Acquire/Hardware/uc480/AndorControlFrame.py +308 -0
  134. PYME/Acquire/Hardware/uc480/__init__.py +27 -0
  135. PYME/Acquire/Hardware/uc480/uCam480.py +695 -0
  136. PYME/Acquire/Hardware/uc480/uc480.py +189 -0
  137. PYME/Acquire/Hardware/uc480/uc480Deprecated.py +87 -0
  138. PYME/Acquire/Hardware/uc480/uc480_h.py +767 -0
  139. PYME/Acquire/Hardware/uc480/uc480_h_gen.py +62 -0
  140. PYME/Acquire/Hardware/uc480/ucCamControlFrame.py +83 -0
  141. PYME/Acquire/Hardware/ueye.py +702 -0
  142. PYME/Acquire/PYMEAcquire.py +186 -0
  143. PYME/Acquire/Protocols/DMDMFM.py +74 -0
  144. PYME/Acquire/Protocols/__init__.py +22 -0
  145. PYME/Acquire/Protocols/darkCalibrate.py +56 -0
  146. PYME/Acquire/Protocols/dual671_470.py +45 -0
  147. PYME/Acquire/Protocols/dual671_488.py +46 -0
  148. PYME/Acquire/Protocols/gainCal.py +53 -0
  149. PYME/Acquire/Protocols/htsms-cal-psf.py +32 -0
  150. PYME/Acquire/Protocols/htsms-cal-registration.py +52 -0
  151. PYME/Acquire/Protocols/htsms-flow.py +29 -0
  152. PYME/Acquire/Protocols/htsms-staggered.py +31 -0
  153. PYME/Acquire/Protocols/htsms-tile.py +68 -0
  154. PYME/Acquire/Protocols/htsms-two-color.py +29 -0
  155. PYME/Acquire/Protocols/htsms-widefield.py +32 -0
  156. PYME/Acquire/Protocols/paint671.py +61 -0
  157. PYME/Acquire/Protocols/photoconversion.py +52 -0
  158. PYME/Acquire/Protocols/photoconversion2.py +55 -0
  159. PYME/Acquire/Protocols/prebleach488.py +70 -0
  160. PYME/Acquire/Protocols/prebleach490.py +69 -0
  161. PYME/Acquire/Protocols/prebleach561.py +72 -0
  162. PYME/Acquire/Protocols/prebleach561NeomEos2.py +70 -0
  163. PYME/Acquire/Protocols/prebleach561NeomEos2ND1.py +70 -0
  164. PYME/Acquire/Protocols/prebleach642.py +70 -0
  165. PYME/Acquire/Protocols/prebleach671.py +69 -0
  166. PYME/Acquire/Protocols/prebleach671ND1.py +58 -0
  167. PYME/Acquire/Protocols/prebleach671ND2.py +57 -0
  168. PYME/Acquire/Protocols/prebleach671Neo.py +69 -0
  169. PYME/Acquire/Protocols/recover671.py +62 -0
  170. PYME/Acquire/Protocols/sequence642_488.py +85 -0
  171. PYME/Acquire/Protocols/sequence642_561.py +87 -0
  172. PYME/Acquire/Protocols/shiftfield.py +198 -0
  173. PYME/Acquire/Protocols/simul488.py +59 -0
  174. PYME/Acquire/Protocols/simul642.py +63 -0
  175. PYME/Acquire/Protocols/simul642HTSMS.py +63 -0
  176. PYME/Acquire/Protocols/simulPA.py +37 -0
  177. PYME/Acquire/Protocols/simulSIM.py +76 -0
  178. PYME/Acquire/Protocols/simulStep.py +62 -0
  179. PYME/Acquire/Protocols/spdscan.py +178 -0
  180. PYME/Acquire/Protocols/standard470.py +45 -0
  181. PYME/Acquire/Protocols/standard488.py +47 -0
  182. PYME/Acquire/Protocols/standard671.py +48 -0
  183. PYME/Acquire/Protocols/standard671_no532.py +47 -0
  184. PYME/Acquire/Protocols/standardArclamp.py +46 -0
  185. PYME/Acquire/Protocols/strip_tile.py +204 -0
  186. PYME/Acquire/Protocols/tile.py +204 -0
  187. PYME/Acquire/Protocols/tile3D.py +192 -0
  188. PYME/Acquire/Protocols/tile671.py +190 -0
  189. PYME/Acquire/Protocols/tile_triggered.py +189 -0
  190. PYME/Acquire/Scripts/init.py +232 -0
  191. PYME/Acquire/Scripts/init_N1_Ti_Exeter_ZIx.py +374 -0
  192. PYME/Acquire/Scripts/init_N2_Ti_Zyla_lasers.py +290 -0
  193. PYME/Acquire/Scripts/init_Neo.py +266 -0
  194. PYME/Acquire/Scripts/init_NeoSim.py +159 -0
  195. PYME/Acquire/Scripts/init_TIRF.py +232 -0
  196. PYME/Acquire/Scripts/init_TIRF_Neo.py +242 -0
  197. PYME/Acquire/Scripts/init_TIRF_NeoO.py +241 -0
  198. PYME/Acquire/Scripts/init_TIRF_onecam.py +233 -0
  199. PYME/Acquire/Scripts/init_Ti.py +257 -0
  200. PYME/Acquire/Scripts/init_UOA_n.py +256 -0
  201. PYME/Acquire/Scripts/init_UOA_n2.py +246 -0
  202. PYME/Acquire/Scripts/init_Y1.py +249 -0
  203. PYME/Acquire/Scripts/init_Zyla.py +260 -0
  204. PYME/Acquire/Scripts/init_drift_tracking.py +80 -0
  205. PYME/Acquire/Scripts/init_emccd_basic.py +277 -0
  206. PYME/Acquire/Scripts/init_htsms.py +277 -0
  207. PYME/Acquire/Scripts/init_htsms_focus_lock.py +132 -0
  208. PYME/Acquire/Scripts/init_micrpi.py +45 -0
  209. PYME/Acquire/Scripts/init_orca.py +70 -0
  210. PYME/Acquire/Scripts/init_pco.py +49 -0
  211. PYME/Acquire/Scripts/init_rev.py +74 -0
  212. PYME/Acquire/Scripts/init_sim100.py +169 -0
  213. PYME/Acquire/Scripts/init_sim103.py +169 -0
  214. PYME/Acquire/Scripts/init_sim2.py +211 -0
  215. PYME/Acquire/Scripts/init_sim50.py +169 -0
  216. PYME/Acquire/Scripts/init_sim75.py +169 -0
  217. PYME/Acquire/Scripts/init_sim_drift_tracking.py +166 -0
  218. PYME/Acquire/Scripts/init_sim_htsms.py +224 -0
  219. PYME/Acquire/Scripts/init_sim_htsms_n.py +233 -0
  220. PYME/Acquire/Scripts/init_sim_main.py +229 -0
  221. PYME/Acquire/Scripts/init_sim_min.py +197 -0
  222. PYME/Acquire/Scripts/init_sim_rem.py +176 -0
  223. PYME/Acquire/Scripts/init_smi1.py +110 -0
  224. PYME/Acquire/Scripts/init_spectro.py +78 -0
  225. PYME/Acquire/Scripts/init_spim.py +116 -0
  226. PYME/Acquire/Scripts/init_thorcam.py +62 -0
  227. PYME/Acquire/Scripts/init_twophoton.py +112 -0
  228. PYME/Acquire/Scripts/init_uc480.py +262 -0
  229. PYME/Acquire/Scripts/init_ueye.py +261 -0
  230. PYME/Acquire/SpoolController.py +958 -0
  231. PYME/Acquire/Utils/MultiPointScanner.py +80 -0
  232. PYME/Acquire/Utils/__init__.py +13 -0
  233. PYME/Acquire/Utils/failsafe.py +157 -0
  234. PYME/Acquire/Utils/fastTiler.py +153 -0
  235. PYME/Acquire/Utils/pointScanner.py +496 -0
  236. PYME/Acquire/Utils/sarcSpacing.py +86 -0
  237. PYME/Acquire/Utils/strip_tiler.py +93 -0
  238. PYME/Acquire/Utils/tiler.py +464 -0
  239. PYME/Acquire/Utils/vibrationAnalysis.py +65 -0
  240. PYME/Acquire/__init__.py +44 -0
  241. PYME/Acquire/acquire_client.py +90 -0
  242. PYME/Acquire/acquire_server.py +316 -0
  243. PYME/Acquire/acquirebase.py +139 -0
  244. PYME/Acquire/acquiremainframe.py +716 -0
  245. PYME/Acquire/acquirewx.py +61 -0
  246. PYME/Acquire/acquisition_base.py +148 -0
  247. PYME/Acquire/actions.py +209 -0
  248. PYME/Acquire/autofocus.py +54 -0
  249. PYME/Acquire/eventLog.py +95 -0
  250. PYME/Acquire/event_loop.py +119 -0
  251. PYME/Acquire/frameWrangler.py +530 -0
  252. PYME/Acquire/htsms/__init__.py +8 -0
  253. PYME/Acquire/htsms/rule_ui.py +970 -0
  254. PYME/Acquire/htsms/rule_ui_v2.py +573 -0
  255. PYME/Acquire/htsms/tweeter.py +222 -0
  256. PYME/Acquire/microscope.py +1050 -0
  257. PYME/Acquire/positionTracker.py +181 -0
  258. PYME/Acquire/protocol.py +299 -0
  259. PYME/Acquire/protocol_acquisition.py +404 -0
  260. PYME/Acquire/sampleInformation.py +591 -0
  261. PYME/Acquire/sampleInformationDjangoDirect.py +446 -0
  262. PYME/Acquire/setup.py +52 -0
  263. PYME/Acquire/stackSettings.py +295 -0
  264. PYME/Acquire/stage_leveling.py +285 -0
  265. PYME/Acquire/ui/AnalysisSettingsUI.py +184 -0
  266. PYME/Acquire/ui/HDFSpoolFrame.py +584 -0
  267. PYME/Acquire/ui/__init__.py +0 -0
  268. PYME/Acquire/ui/actionUI.py +892 -0
  269. PYME/Acquire/ui/focus_lock_gui.py +149 -0
  270. PYME/Acquire/ui/intensity_trace.py +143 -0
  271. PYME/Acquire/ui/intsliders.py +222 -0
  272. PYME/Acquire/ui/lasersliders.py +329 -0
  273. PYME/Acquire/ui/mpd_picosecond_delay_panel.py +69 -0
  274. PYME/Acquire/ui/multiview_select.py +77 -0
  275. PYME/Acquire/ui/positionUI.py +519 -0
  276. PYME/Acquire/ui/preflight.py +58 -0
  277. PYME/Acquire/ui/scanner_panel.py +41 -0
  278. PYME/Acquire/ui/selectCameraPanel.py +46 -0
  279. PYME/Acquire/ui/seqdialog.py +501 -0
  280. PYME/Acquire/ui/splashScreen.py +175 -0
  281. PYME/Acquire/ui/spool_panel.py +830 -0
  282. PYME/Acquire/ui/tile_panel.py +556 -0
  283. PYME/Acquire/ui/tilesettingsui.py +91 -0
  284. PYME/Acquire/ui/voxelSizeDialog.py +149 -0
  285. PYME/Acquire/webui/__init__.py +36 -0
  286. PYME/Acquire/webui/ipy.py +361 -0
  287. PYME/Acquire/webui/static/css/pyme-bootstrap.css +9908 -0
  288. PYME/Acquire/webui/static/css/pymeacquire.css +85 -0
  289. PYME/Acquire/webui/static/js/pymeacquire.js +375 -0
  290. PYME/Acquire/webui/static/js/pzf.js +95 -0
  291. PYME/Acquire/webui/templates/PYMEAcquire.html +232 -0
  292. PYME/Acquire/webui/templates/login.html +84 -0
  293. PYME/Acquire/webui/templates/xtermpage.html +106 -0
  294. PYME/Acquire/xyztc.py +418 -0
  295. PYME/Acquire/zScanner.py +287 -0
  296. PYME/Analysis/BleachProfile/__init__.py +26 -0
  297. PYME/Analysis/BleachProfile/deMod.py +91 -0
  298. PYME/Analysis/BleachProfile/fitRecover.py +90 -0
  299. PYME/Analysis/BleachProfile/intensProf.py +519 -0
  300. PYME/Analysis/BleachProfile/kinModels.py +507 -0
  301. PYME/Analysis/BleachProfile/rawIntensity.py +227 -0
  302. PYME/Analysis/BleachProfile/rollins.py +555 -0
  303. PYME/Analysis/Colocalisation/__init__.py +27 -0
  304. PYME/Analysis/Colocalisation/colocScaleDep.py +126 -0
  305. PYME/Analysis/Colocalisation/correlationCoeffs.py +198 -0
  306. PYME/Analysis/Colocalisation/distColoc.py +110 -0
  307. PYME/Analysis/Colocalisation/edtColoc.py +191 -0
  308. PYME/Analysis/MetaData.py +278 -0
  309. PYME/Analysis/PSFEst/__init__.py +27 -0
  310. PYME/Analysis/PSFEst/dec.py +283 -0
  311. PYME/Analysis/PSFEst/extractImages.py +316 -0
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@@ -0,0 +1,372 @@
1
+ from .base import BaseEngine, EngineLayer
2
+ from PYME.LMVis.shader_programs.DefaultShaderProgram import DefaultShaderProgram, OpaquePointShaderProgram, BigOpaquePointShaderProgram, TransparentPointShaderProgram, BigTransparentPointShaderProgram
3
+ from PYME.LMVis.shader_programs.PointSpriteShaderProgram import PointSpriteShaderProgram, BigPointSpriteShaderProgram
4
+ from PYME.LMVis.shader_programs.GouraudShaderProgram import GouraudShaderProgram, GouraudSphereShaderProgram, BigGouraudSphereShaderProgram, GouraudFlatpointsShaderProgram, BigGouraudFlatpointsShaderProgram
5
+
6
+ from PYME.recipes.traits import CStr, Float, Enum, ListFloat, List, Bool
7
+ # from pylab import cm
8
+ from PYME.misc.colormaps import cm
9
+ import numpy as np
10
+ from PYME.contrib import dispatch
11
+
12
+ import logging
13
+ logger = logging.getLogger(__name__)
14
+
15
+ from OpenGL.GL import *
16
+
17
+ class Points3DEngine(BaseEngine):
18
+ def __init__(self, *args, **kwargs):
19
+ BaseEngine.__init__(self, *args, **kwargs)
20
+ self.set_shader_program(OpaquePointShaderProgram)
21
+ self.point_scale_correction = 1.0
22
+
23
+ def point_size_px(self, gl_canvas, layer, sp):
24
+ point_scale_correction = self.point_scale_correction*getattr(sp, 'size_factor', 1.0)
25
+
26
+ if gl_canvas:
27
+ if layer.point_size == 0:
28
+ point_size = (1 / gl_canvas.pixelsize)
29
+ else:
30
+ point_size = (layer.point_size*point_scale_correction / gl_canvas.pixelsize)
31
+ else:
32
+ point_size(layer.point_size*point_scale_correction)
33
+
34
+ point_size = point_size*gl_canvas.content_scale_factor # scale for high DPI displays
35
+
36
+ return point_size
37
+
38
+ def render(self, gl_canvas, layer):
39
+ core_profile = gl_canvas.core_profile
40
+ max_ps = glGetFloatv(GL_POINT_SIZE_RANGE)[1]
41
+
42
+ sp = self.get_shader_program(gl_canvas)
43
+
44
+ point_size = self.point_size_px(gl_canvas, layer, sp)
45
+ bigpoints = False
46
+
47
+ if (point_size > max_ps) and core_profile:
48
+ #logger.debug(f'Point size ({point_size}) larger than OpenGL maximum ({max_ps}), size scaling might not work as expected')
49
+ try:
50
+ sp = self.get_specific_shader_program(gl_canvas, self._big_point_shader_cls)
51
+ bigpoints = True
52
+ except AttributeError:
53
+ logger.exception('error finding big point shader class')
54
+ logger.debug('No big point shader class defined, using default shader - points will appear smaller than expected')
55
+
56
+ vertices = layer.get_vertices()
57
+ n_vertices = vertices.shape[0]
58
+ if n_vertices == 0:
59
+ return False
60
+
61
+ normals = layer.get_normals()
62
+ colors = layer.get_colors()
63
+
64
+ with sp:
65
+ sp.set_clipping(gl_canvas.view.clipping.squeeze(), gl_canvas.view.clip_plane_matrix)
66
+
67
+ self._bind_data('points', vertices, normals, colors, sp, core_profile=core_profile)
68
+ if core_profile:
69
+ sp.set_modelviewprojectionmatrix(np.array(gl_canvas.mvp))
70
+ sp.set_point_size(point_size)
71
+ #glBindVertexArray(self._bound_data['points'][0])
72
+
73
+ if bigpoints:
74
+ vp = glGetIntegerv(GL_VIEWPORT)
75
+ sx = vp[2]
76
+ glUniform1f(sp.get_uniform_location('point_size_vp'), 2.0*point_size/float(sx))
77
+ glUniform2f(sp.get_uniform_location('viewport_size'), vp[2], vp[3])
78
+
79
+ else:
80
+ glPointSize(point_size)
81
+
82
+ glDrawArrays(GL_POINTS, 0, n_vertices)
83
+ #print(f'draw arrays called with {n_vertices} vertices')
84
+
85
+
86
+ if layer.display_normals:
87
+ normal_buffer = np.empty((vertices.shape[0]+normals.shape[0],3), dtype=vertices.dtype)
88
+ normal_buffer[0::2,:] = vertices
89
+ normal_buffer[1::2,:] = vertices
90
+ # assert(np.allclose(np.linalg.norm(normals,axis=1),1))
91
+ normal_buffer[1::2,:] += layer.normal_scaling*normals
92
+
93
+ sc = np.array([1, 1, 1, 1])
94
+ cols = (np.ones((normal_buffer.shape[0],4),dtype=colors.dtype)*sc[None,:]) # white normals
95
+ norms = (np.ones((normal_buffer.shape[0],3),dtype=normals.dtype))
96
+
97
+ self._bind_data('normals', normal_buffer, norms, cols, sp, core_profile=core_profile)
98
+
99
+ glLineWidth(3) # slightly thick
100
+ glDrawArrays(GL_LINES, 0, 2*n_vertices)
101
+
102
+
103
+ class OpaquePointsEngine(Points3DEngine):
104
+ def __init__(self, *args, **kwargs):
105
+ BaseEngine.__init__(self, *args, **kwargs)
106
+ self.set_shader_program(OpaquePointShaderProgram)
107
+ self._big_point_shader_cls = BigOpaquePointShaderProgram
108
+ self.point_scale_correction = 1.0
109
+
110
+ class PointSpritesEngine(Points3DEngine):
111
+ def __init__(self, *args, **kwargs):
112
+ BaseEngine.__init__(self, *args, **kwargs)
113
+ self.set_shader_program(PointSpriteShaderProgram)
114
+ self._big_point_shader_cls = BigPointSpriteShaderProgram
115
+ self.point_scale_correction = 1.0
116
+
117
+ class ShadedPointsEngine(Points3DEngine):
118
+ def __init__(self, *args, **kwargs):
119
+ BaseEngine.__init__(self, *args, **kwargs)
120
+ self.set_shader_program(GouraudFlatpointsShaderProgram)
121
+ self._big_point_shader_cls = BigGouraudFlatpointsShaderProgram
122
+ self.point_scale_correction = 1.0
123
+
124
+ class TransparentPointsEngine(Points3DEngine):
125
+ def __init__(self, *args, **kwargs):
126
+ BaseEngine.__init__(self, *args, **kwargs)
127
+ self.set_shader_program(TransparentPointShaderProgram)
128
+ self._big_point_shader_cls = BigTransparentPointShaderProgram
129
+ self.point_scale_correction = 1.0
130
+
131
+ class SpheresEngine(Points3DEngine):
132
+ def __init__(self, *args, **kwargs):
133
+ BaseEngine.__init__(self, *args, **kwargs)
134
+ self.set_shader_program(GouraudSphereShaderProgram)
135
+ self._big_point_shader_cls = BigGouraudSphereShaderProgram
136
+ self.point_scale_correction = 1.0
137
+
138
+
139
+ ENGINES = {
140
+ 'points' : OpaquePointsEngine,
141
+ 'transparent_points' : TransparentPointsEngine,
142
+ 'pointsprites' : PointSpritesEngine,
143
+ 'shaded_points' : ShadedPointsEngine,
144
+ 'spheres' : SpheresEngine,
145
+ }
146
+
147
+ class PointCloudRenderLayer(EngineLayer):
148
+ """
149
+ A layer for viewing point-cloud data, using one of 3 engines (indicated above)
150
+
151
+ """
152
+
153
+ # properties to show in the GUI. Note that we also inherit 'visible' from BaseLayer
154
+ vertexColour = CStr('', desc='Name of variable used to colour our points')
155
+ point_size = Float(30.0, desc='Rendered size of the points in nm')
156
+ cmap = Enum(*cm.cmapnames, default='gist_rainbow', desc='Name of colourmap used to colour points')
157
+ clim = ListFloat([0, 1], desc='How our variable should be scaled prior to colour mapping')
158
+ alpha = Float(1.0, desc='Point tranparency')
159
+ method = Enum(*ENGINES.keys(), desc='Method used to display points')
160
+ display_normals = Bool(False)
161
+ normal_scaling = Float(10.0)
162
+ dsname = CStr('output', desc='Name of the datasource within the pipeline to use as a source of points')
163
+ _datasource_keys = List()
164
+ _datasource_choices = List()
165
+
166
+ def __init__(self, pipeline, method='points', dsname='', **kwargs):
167
+ EngineLayer.__init__(self, **kwargs)
168
+ self._pipeline = pipeline
169
+ self.engine = None
170
+ self.cmap = 'gist_rainbow'
171
+
172
+ self.x_key = 'x' #TODO - make these traits?
173
+ self.y_key = 'y'
174
+ self.z_key = 'z'
175
+
176
+ self.xn_key = 'xn'
177
+ self.yn_key = 'yn'
178
+ self.zn_key = 'zn'
179
+
180
+ self._bbox = None
181
+
182
+ # define a signal so that people can be notified when we are updated (currently used to force a redraw when
183
+ # parameters change)
184
+ self.on_update = dispatch.Signal()
185
+
186
+ # signal for when the data is updated (used to, e.g., refresh histograms)
187
+ self.data_updated = dispatch.Signal()
188
+
189
+ # define responses to changes in various traits
190
+ self.on_trait_change(self._update, 'vertexColour')
191
+ self.on_trait_change(lambda: self.on_update.send(self), 'visible')
192
+ self.on_trait_change(self.update, 'cmap, clim, alpha, dsname, point_size')
193
+ self.on_trait_change(self._set_method, 'method')
194
+
195
+ # update any of our traits which were passed as command line arguments
196
+ self.trait_set(**kwargs)
197
+
198
+ # update datasource name and method
199
+ #logger.debug('Setting dsname and method')
200
+ self.dsname = dsname
201
+ self.method = method
202
+
203
+ self._set_method()
204
+
205
+ # if we were given a pipeline, connect ourselves to the onRebuild signal so that we can automatically update
206
+ # ourselves
207
+ if not self._pipeline is None:
208
+ self._pipeline.onRebuild.connect(self.update)
209
+
210
+
211
+ @property
212
+ def datasource(self):
213
+ """
214
+ Return the datasource we are connected to (through our dsname property).
215
+ """
216
+ return self._pipeline.get_layer_data(self.dsname)
217
+
218
+ def _set_method(self):
219
+ #logger.debug('Setting layer method to %s' % self.method)
220
+ old_engine = self.engine
221
+ self.engine = ENGINES[self.method]()
222
+ #self.update()
223
+ if old_engine is None:
224
+ self.update()
225
+ else:
226
+ self.on_update.send(self)
227
+
228
+ def _get_cdata(self):
229
+ try:
230
+ cdata = self.datasource[self.vertexColour]
231
+ except KeyError:
232
+ cdata = np.array([0, 1])
233
+
234
+ return cdata
235
+
236
+ def _update(self, *args, **kwargs):
237
+ cdata = self._get_cdata()
238
+ self.clim = [float(np.nanmin(cdata)), float(np.nanmax(cdata))+1e-9]
239
+ #self.update(*args, **kwargs)
240
+
241
+ def update(self, *args, **kwargs):
242
+ #print('lw update')
243
+ self._datasource_choices = self._pipeline.layer_data_source_names
244
+ if not self.datasource is None:
245
+ self._datasource_keys = sorted(self.datasource.keys())
246
+
247
+ if not (self.engine is None or self.datasource is None):
248
+ self.update_from_datasource(self.datasource)
249
+ self.on_update.send(self)
250
+
251
+
252
+
253
+ @property
254
+ def bbox(self):
255
+ return self._bbox
256
+
257
+
258
+ def update_from_datasource(self, ds):
259
+ print('pointcloud.update_from_datasource() - dsname=%s' % self.dsname)
260
+ x, y = ds[self.x_key], ds[self.y_key]
261
+
262
+ if not self.z_key is None:
263
+ try:
264
+ z = ds[self.z_key]
265
+ except KeyError:
266
+ z = 0*x
267
+ else:
268
+ z = 0 * x
269
+
270
+ if not self.vertexColour == '':
271
+ c = ds[self.vertexColour]
272
+ else:
273
+ c = 0*x
274
+
275
+ if self.xn_key in ds.keys():
276
+ xn, yn, zn = ds[self.xn_key], ds[self.yn_key], ds[self.zn_key]
277
+ self.update_data(x, y, z, c, cmap=cm[self.cmap], clim=self.clim, alpha=self.alpha, xn=xn, yn=yn, zn=zn)
278
+ else:
279
+ self.update_data(x, y, z, c, cmap=cm[self.cmap], clim=self.clim, alpha=self.alpha)
280
+
281
+ self.data_updated.send(self)
282
+
283
+
284
+ def update_data(self, x=None, y=None, z=None, colors=None, cmap=None, clim=None, alpha=1.0, xn=None, yn=None, zn=None):
285
+ self._vertices = None
286
+ self._normals = None
287
+ self._colors = None
288
+ self._color_map = None
289
+ self._color_limit = 0
290
+ self._alpha = 0
291
+
292
+ if x is not None and y is not None and z is not None and len(x) > 0:
293
+ vertices = np.vstack((x.ravel(), y.ravel(), z.ravel()))
294
+ vertices = vertices.T.ravel().reshape(len(x.ravel()), 3)
295
+
296
+ if not xn is None:
297
+ normals = np.vstack((xn.ravel(), yn.ravel(), zn.ravel())).T.ravel().reshape(len(x.ravel()), 3)
298
+ else:
299
+ normals = -0.69 * np.ones(vertices.shape)
300
+
301
+ self._bbox = np.array([x.min(), y.min(), z.min(), x.max(), y.max(), z.max()])
302
+ else:
303
+ vertices = None
304
+ normals = None
305
+ self._bbox = None
306
+
307
+ if clim is not None and colors is not None and clim is not None:
308
+ cs_ = ((colors - clim[0]) / (clim[1] - clim[0]))
309
+ cs = cmap(cs_)
310
+ cs[:, 3] = alpha
311
+
312
+ cs = cs.ravel().reshape(len(colors), 4)
313
+ else:
314
+ if not vertices is None:
315
+ cs = np.ones((vertices.shape[0], 4), 'f')
316
+ else:
317
+ cs = None
318
+
319
+ self.set_values(vertices, normals, cs, cmap, clim, alpha)
320
+
321
+ def set_values(self, vertices=None, normals=None, colors=None, color_map=None, color_limit=None, alpha=None):
322
+ if vertices is not None:
323
+ self._vertices = vertices
324
+ if normals is not None:
325
+ self._normals = normals
326
+ if color_map is not None:
327
+ self._color_map = color_map
328
+ if colors is not None:
329
+ self._colors = colors
330
+ if color_limit is not None:
331
+ self._color_limit = color_limit
332
+ if alpha is not None:
333
+ self._alpha = alpha
334
+
335
+ def get_vertices(self):
336
+ return self._vertices
337
+
338
+ def get_normals(self):
339
+ return self._normals
340
+
341
+ def get_colors(self):
342
+ return self._colors
343
+
344
+ def get_color_map(self):
345
+ return self._color_map
346
+
347
+ @property
348
+ def colour_map(self):
349
+ return self._color_map
350
+
351
+ def get_color_limit(self):
352
+ return self._color_limit
353
+
354
+ @property
355
+ def default_view(self):
356
+ from traitsui.api import View, Item, Group, InstanceEditor, EnumEditor, TextEditor
357
+ from PYME.ui.custom_traits_editors import HistLimitsEditor, CBEditor
358
+
359
+ vis_when = 'cmap not in %s' % cm.solid_cmaps
360
+
361
+ return View([Group([Item('dsname', label='Data', editor=EnumEditor(name='_datasource_choices')), ]),
362
+ Item('method'),
363
+ Item('vertexColour', editor=EnumEditor(name='_datasource_keys'), label='Colour', visible_when=vis_when),
364
+ Group([Item('clim', editor=HistLimitsEditor(data=self._get_cdata, update_signal=self.data_updated), show_label=False), ], visible_when=vis_when),
365
+ Group(Item('cmap', label='LUT'),
366
+ Item('alpha', visible_when="method in ['pointsprites', 'transparent_points']", editor=TextEditor(auto_set=False, enter_set=True, evaluate=float)),
367
+ Item('point_size', label=u'Point\u00A0size', editor=TextEditor(auto_set=False, enter_set=True, evaluate=float)))])
368
+ #buttons=['OK', 'Cancel'])
369
+
370
+ def default_traits_view(self):
371
+ return self.default_view
372
+
@@ -0,0 +1,271 @@
1
+ from .base import BaseEngine, EngineLayer
2
+ from PYME.LMVis.shader_programs.DefaultShaderProgram import DefaultShaderProgram, FatLineShaderProgram
3
+ from PYME.LMVis.shader_programs.WireFrameShaderProgram import WireFrameShaderProgram
4
+ from PYME.LMVis.shader_programs.GouraudShaderProgram import GouraudShaderProgram, OITGouraudShaderProgram #, OITCompositorProgram
5
+ from PYME.LMVis.shader_programs.TesselShaderProgram import TesselShaderProgram
6
+
7
+ from PYME.recipes.traits import CStr, Float, Enum, ListFloat, List, Bool
8
+ # from pylab import cm
9
+ from PYME.misc.colormaps import cm
10
+ import numpy as np
11
+ from PYME.contrib import dispatch
12
+
13
+ from OpenGL.GL import *
14
+
15
+
16
+ class QuiverEngine(BaseEngine):
17
+ _outlines = True
18
+ def __init__(self):
19
+ BaseEngine.__init__(self)
20
+ #self.set_shader_program(WireFrameShaderProgram)
21
+ self.set_shader_program(DefaultShaderProgram)
22
+
23
+
24
+ def render(self, gl_canvas, layer):
25
+ if gl_canvas.core_profile:
26
+ sp = self.get_specific_shader_program(gl_canvas, FatLineShaderProgram)
27
+ else:
28
+ sp = self.get_specific_shader_program(gl_canvas, DefaultShaderProgram)
29
+
30
+ with sp:
31
+ sp.set_clipping(gl_canvas.view.clipping.squeeze(), gl_canvas.view.clip_plane_matrix)
32
+
33
+ vertices = layer.get_vertices()
34
+ n_vertices = vertices.shape[0]
35
+ vecs = layer.get_vecs()
36
+
37
+ vec_buffer = np.empty((vertices.shape[0]+vecs.shape[0],3), dtype=vertices.dtype)
38
+ vec_buffer[0::2,:] = vertices
39
+ vec_buffer[1::2,:] = vertices
40
+
41
+ vec_buffer[1::2,:] += layer.scaling*vecs
42
+
43
+ sc = np.array([1, 1, 1, 1])
44
+ cols = np.ones((vec_buffer.shape[0],4),dtype='f4')*sc[None,:]
45
+
46
+ # glVertexPointerf(vec_buffer)
47
+ # glColorPointerf(cols) # white normals
48
+ # glNormalPointerf(np.ones((vec_buffer.shape[0],3),dtype='f4'))
49
+
50
+ if gl_canvas.core_profile:
51
+ sp.set_modelviewprojectionmatrix(gl_canvas.mvp)
52
+ glUniform1f(sp.get_uniform_location('line_width_px'), 3.0*gl_canvas.content_scale_factor)
53
+ vp = glGetIntegerv(GL_VIEWPORT)
54
+ glUniform2f(sp.get_uniform_location('viewport_size'), vp[2], vp[3])
55
+
56
+
57
+ self._bind_data('quiver', vec_buffer, cols, np.ones((vec_buffer.shape[0],3),dtype='f4'), sp, core_profile=gl_canvas.core_profile)
58
+
59
+ glLineWidth(min(3.0, glGetFloatv(GL_LINE_WIDTH_RANGE)[1])) # slightly thick
60
+
61
+ glDrawArrays(GL_LINES, 0, 2*n_vertices)
62
+
63
+
64
+
65
+
66
+
67
+ ENGINES = {
68
+ 'quiver' : QuiverEngine,
69
+ }
70
+
71
+
72
+ class QuiverRenderLayer(EngineLayer):
73
+ """
74
+ Layer for viewing 3D vectors (e.g. search directions).
75
+ """
76
+ # properties to show in the GUI. Note that we also inherit 'visible' from BaseLayer
77
+ vector_property = CStr('vertex_normals', desc='Name of variable used to colour our points')
78
+ #cmap = Enum(*cm.cmapnames, default='gist_rainbow', desc='Name of colourmap used to colour faces')
79
+ #clim = ListFloat([0, 1], desc='How our variable should be scaled prior to colour mapping')
80
+ #alpha = Float(1.0, desc='Face tranparency')
81
+ method = Enum(*ENGINES.keys(), desc='Method used to display vectors')
82
+ #normal_mode = Enum(['Per vertex', 'Per face'])
83
+ #display_normals = Bool(False)
84
+ scaling = Float(1.0)
85
+ dsname = CStr('output', desc='Name of the datasource within the pipeline to use as a source of triangles (should be a TriangularMesh object)')
86
+ _datasource_choices = List()
87
+ _datasource_keys = List()
88
+
89
+ def __init__(self, pipeline, method='quiver', dsname='', **kwargs):
90
+ EngineLayer.__init__(self, **kwargs)
91
+ self._pipeline = pipeline
92
+ self.engine = None
93
+ self.cmap = 'gist_rainbow'
94
+
95
+ self.x_key = 'x' # TODO - make these traits?
96
+ self.y_key = 'y'
97
+ self.z_key = 'z'
98
+
99
+ self._bbox = None
100
+
101
+ # define a signal so that people can be notified when we are updated (currently used to force a redraw when
102
+ # parameters change)
103
+ self.on_update = dispatch.Signal()
104
+
105
+ # define responses to changes in various traits
106
+ self.on_trait_change(self._update, 'vector_property')
107
+ self.on_trait_change(lambda: self.on_update.send(self), 'visible')
108
+ self.on_trait_change(self.update, 'dsname, scaling')
109
+ self.on_trait_change(self._set_method, 'method')
110
+
111
+ # update any of our traits which were passed as command line arguments
112
+ self.trait_set(**kwargs)
113
+
114
+ # update datasource and method
115
+ self.dsname = dsname
116
+ if self.method == method:
117
+ #make sure we still call _set_method even if we start with the default method
118
+ self._set_method()
119
+ else:
120
+ self.method = method
121
+
122
+ # if we were given a pipeline, connect ourselves to the onRebuild signal so that we can automatically update
123
+ # ourselves
124
+ if not self._pipeline is None:
125
+ try:
126
+ self._pipeline.onRebuild.connect(self.update)
127
+ except AttributeError:
128
+ pass
129
+
130
+ @property
131
+ def datasource(self):
132
+ """
133
+ Return the datasource we are connected to (does not go through the pipeline for triangles_mesh).
134
+ """
135
+ try:
136
+ return self._pipeline.get_layer_data(self.dsname)
137
+ except AttributeError:
138
+ try:
139
+ return self._pipeline[self.dsname]
140
+ except AttributeError:
141
+ return None
142
+ #return self.datasource
143
+
144
+ @property
145
+ def _ds_class(self):
146
+ # from PYME.experimental import triangle_mesh
147
+ from PYME.experimental import _triangle_mesh as triangle_mesh
148
+ return triangle_mesh.TrianglesBase
149
+
150
+ def _set_method(self):
151
+ self.engine = ENGINES[self.method]()
152
+ self.update()
153
+
154
+ #def _get_cdata(self):
155
+ # try:
156
+ # cdata = self.datasource[self.vertexColour]
157
+ # except (KeyError, TypeError):
158
+ # cdata = np.array([0, 1])
159
+ #
160
+ # return cdata
161
+
162
+ def _update(self, *args, **kwargs):
163
+ #pass
164
+ #cdata = self._get_cdata()
165
+ #self.clim = [float(np.nanmin(cdata)), float(np.nanmax(cdata))]
166
+ self.update(*args, **kwargs)
167
+
168
+ def update(self, *args, **kwargs):
169
+ try:
170
+ self._datasource_choices = [k for k, v in self._pipeline.dataSources.items() if isinstance(v, self._ds_class)]
171
+ except AttributeError:
172
+ pass
173
+
174
+ if not self.datasource is None:
175
+ dks = sorted(getattr(self.datasource, 'vertex_vector_properties', []))
176
+
177
+ self._datasource_keys = dks
178
+
179
+ if not (self.engine is None or self.datasource is None):
180
+ print('lw update')
181
+ self.update_from_datasource(self.datasource)
182
+ self.on_update.send(self)
183
+
184
+ @property
185
+ def bbox(self):
186
+ return self._bbox
187
+
188
+ @property
189
+ def colour_map(self):
190
+ return cm.gray
191
+
192
+ def update_from_datasource(self, ds):
193
+ """
194
+ Pulls vertices/normals from a binary STL file. See PYME.IO.FileUtils.stl for more info. Calls update_data on the input.
195
+
196
+ Parameters
197
+ ----------
198
+ ds :
199
+ PYME.experimental.triangular_mesh.TriangularMesh object
200
+
201
+ Returns
202
+ -------
203
+ None
204
+ """
205
+ #t = ds.vertices[ds.faces]
206
+ #n = ds.vertex_normals[ds.faces]
207
+
208
+ valid = ds._vertices['halfedge'] != -1
209
+ x, y, z = ds.vertices.reshape(-1, 3)[valid, :].T
210
+
211
+ vec_data = getattr(ds, self.vector_property).reshape(-1, 3)[valid,:].T
212
+ xv, yv, zv = vec_data
213
+
214
+ #if self.normal_mode == 'Per vertex':
215
+ # xn, yn, zn = ds.vertex_normals[ds.faces].reshape(-1, 3).T
216
+ #else:
217
+ # xn, yn, zn = np.repeat(ds.face_normals.T, 3, axis=1)
218
+
219
+ #if self.vertexColour in ['', 'constant']:
220
+ # c = np.ones(len(x))
221
+ # clim = [0, 1]
222
+ #elif self.vertexColour == 'vertex_index':
223
+ # c = np.arange(0, len(x))
224
+ #else:
225
+ # c = ds[self.vertexColour][ds.faces].ravel()
226
+ # clim = self.clim
227
+
228
+ #cmap = cm[self.cmap]
229
+ #alpha = float(self.alpha)
230
+
231
+ # Do we have coordinates? Concatenate into vertices.
232
+ if x is not None and y is not None and z is not None:
233
+ vertices = np.vstack((x.ravel(), y.ravel(), z.ravel()))
234
+ self._vertices = vertices.T.ravel().reshape(len(x.ravel()), 3)
235
+ self._vecs = np.vstack((xv.ravel(), yv.ravel(), zv.ravel())).T.ravel().reshape(len(x.ravel()), 3)
236
+
237
+ self._bbox = np.array([x.min(), y.min(), z.min(), x.max(), y.max(), z.max()])
238
+ else:
239
+ self._bbox = None
240
+
241
+ # TODO: This temporarily sets all triangles to the color red. User should be able to select color.
242
+ #if c is None:
243
+ # c = np.ones(self._vertices.shape[0]) * 255 # vector of pink
244
+
245
+
246
+
247
+ def get_vertices(self):
248
+ return self._vertices
249
+
250
+ def get_vecs(self):
251
+ return self._vecs
252
+
253
+ @property
254
+ def default_view(self):
255
+ from traitsui.api import View, Item, Group, InstanceEditor, EnumEditor
256
+ from PYME.ui.custom_traits_editors import HistLimitsEditor, CBEditor
257
+
258
+ return View([Group([Item('dsname', label='Data', editor=EnumEditor(name='_datasource_choices'), visible_when='_datasource_choices')]),
259
+ #Item('method'),
260
+ Item('scaling'),
261
+ #Item('normal_mode', visible_when='method=="shaded"'),
262
+ Item('vector_property', editor=EnumEditor(name='_datasource_keys'), label='Property'),
263
+ #Group([Item('clim', editor=HistLimitsEditor(data=self._get_cdata), show_label=False), ], visible_when='vertexColour != "constant"'),
264
+ #Group([Item('cmap', label='LUT'),
265
+ # Item('alpha', visible_when='method in ["flat", "tessel", "shaded"]')
266
+ # ])
267
+ ], )
268
+ # buttons=['OK', 'Cancel'])
269
+
270
+ def default_traits_view(self):
271
+ return self.default_view