python-microscopy 25.6.5__cp39-cp39-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 (1277) 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.cp39-win_amd64.dll.a +0 -0
  80. PYME/Acquire/Hardware/Simulator/illuminate.cp39-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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PYME/util/mProfile/colorize_db_t.py ADDED
@@ -0,0 +1,297 @@
1
+ #!/usr/bin/python
2
+ # -*- coding: iso-8859-1 -*-
3
+ """
4
+ mProfile syntax highlighting and profile results display
5
+ """
6
+ # Based on the MoinMoin python source coloriser
7
+ #
8
+ # which is in turn based on the code from J�rgen Herman, to which the following changes where made:
9
+ #
10
+ # Mike Brown <http://skew.org/~mike/>:
11
+ # - make script callable as a CGI and a Apache handler for .py files.
12
+ #
13
+ # Christopher Arndt <http://chrisarndt.de>:
14
+ # - make script usable as a module
15
+ # - use class tags and style sheet instead of <style> tags
16
+ # - when called as a script, add HTML header and footer
17
+ #
18
+ # #
19
+ #
20
+ # David Baddeley david_baddeley <at> yahoo.com.au
21
+ # converted to display mProfile output:
22
+ # - added code to display line times, line numbers, and to highlight the expensive lines
23
+ # - may have broken some of the original features
24
+
25
+ __version__ = '0.1'
26
+ __date__ = '2009-01-22'
27
+ __license__ = 'GPL'
28
+ __author__ = 'J�rgen Hermann, Mike Brown, Christopher Arndt, David Baddeley'
29
+
30
+
31
+ # Imports
32
+ import cgi, string, sys
33
+ from io import StringIO
34
+ import keyword, token, tokenize
35
+
36
+ try:
37
+ from cgi import escape
38
+ except ImportError:
39
+ from html import escape
40
+
41
+ #############################################################################
42
+ ### Python Source Parser (does Highlighting)
43
+ #############################################################################
44
+
45
+ _KEYWORD = token.NT_OFFSET + 1
46
+ _TEXT = token.NT_OFFSET + 2
47
+
48
+ _css_classes = {
49
+ token.NUMBER: 'number',
50
+ token.OP: 'operator',
51
+ token.STRING: 'string',
52
+ tokenize.COMMENT: 'comment',
53
+ token.NAME: 'name',
54
+ token.ERRORTOKEN: 'error',
55
+ _KEYWORD: 'keyword',
56
+ _TEXT: 'text',
57
+ }
58
+
59
+ _HTML_HEADER = """\
60
+ <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
61
+ "http://www.w3.org/TR/html4/loose.dtd">
62
+ <html>
63
+ <head>
64
+ <title>%%(title)s</title>
65
+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
66
+ <meta name="Generator" content="colorize.py (version %s)">
67
+ </head>
68
+ <body>
69
+ """ % __version__
70
+
71
+ _HTML_FOOTER = """\
72
+ </body>
73
+ </html>
74
+ """
75
+
76
+ _STYLESHEET = """\
77
+ <style type="text/css">
78
+ pre.code {
79
+ font-style: Lucida,"Courier New";
80
+ }
81
+
82
+ .number {
83
+ color: #0080C0;
84
+ }
85
+ .operator {
86
+ color: #000000;
87
+ }
88
+ .string {
89
+ color: #008000;
90
+ }
91
+ .comment {
92
+ color: #808080;
93
+ }
94
+ .name {
95
+ color: #000000;
96
+ }
97
+ .error {
98
+ color: #FF8080;
99
+ border: solid 1.5pt #FF0000;
100
+ }
101
+ .keyword {
102
+ color: #0000FF;
103
+ font-weight: bold;
104
+ }
105
+ .text {
106
+ color: #000000;
107
+ }
108
+
109
+ }
110
+
111
+
112
+ </style>
113
+
114
+ """
115
+
116
+ class Parser:
117
+ """ Send colored python source.
118
+ """
119
+
120
+ stylesheet = _STYLESHEET
121
+
122
+ def __init__(self, raw, times, counts, thresholdT = 0.01, out=sys.stdout):
123
+ """ Store the source text.
124
+ """
125
+ self.raw = raw.expandtabs().strip()
126
+ self.out = out
127
+ self.times = times
128
+ self.counts = counts
129
+
130
+ self.totTime = sum(times.values())
131
+ self.maxTime = max(max(times.values()), 1e-3)
132
+ self.cover_flag = False
133
+ self.line_flag = False
134
+ self.thresholdT = thresholdT
135
+
136
+
137
+ def format(self):
138
+ """ Parse and send the colored source.
139
+ """
140
+ # store line offsets in self.lines
141
+ self.lines = [0, 0]
142
+ pos = 0
143
+
144
+ while 1:
145
+ pos = self.raw.find('\n', pos) + 1
146
+ if not pos: break
147
+ self.lines.append(pos)
148
+ self.lines.append(len(self.raw))
149
+
150
+ # parse the source and write it
151
+ self.pos = 0
152
+ text = StringIO(u'' + self.raw)
153
+ self.out.write(self.stylesheet)
154
+ self.out.write('<pre class="code">\n')
155
+ try:
156
+ #tokenize.tokenize(text.readline, self)
157
+ for tokens in tokenize.generate_tokens(text.readline):
158
+ self(*tokens)
159
+ except tokenize.TokenError as ex:
160
+ msg = ex[0]
161
+ line = ex[1][0]
162
+ self.out.write("<h3>ERROR: %s</h3>%s\n" % (
163
+ msg, self.raw[self.lines[line]:]))
164
+ if self.cover_flag:
165
+ self.out.write('</span>')
166
+ self.cover_flag = False
167
+ self.out.write('\n</pre>')
168
+
169
+ def __call__(self, toktype, toktext, start, end, line):
170
+ """ Token handler.
171
+ """
172
+ srow, scol = start
173
+ erow, ecol = end
174
+ if 0:
175
+ print("type", toktype, token.tok_name[toktype], "text", toktext,)
176
+ print("start", srow,scol, "end", erow,ecol, "<br>")
177
+
178
+ # calculate new positions
179
+ oldpos = self.pos
180
+ newpos = self.lines[srow] + scol
181
+ self.pos = newpos + len(toktext)
182
+
183
+
184
+ if (not self.line_flag):
185
+ #tspec = 'XXX.YYs'
186
+ tspec = ' ' + ' '
187
+ if (srow in self.times.keys()):
188
+ #print srow
189
+ t = self.times[srow]
190
+ gb = int(250*(1 - t/self.maxTime))
191
+ self.out.write('<span style="background-color :#FF%02X%02X; ">' %(gb, gb))
192
+ self.cover_flag = True
193
+
194
+ if (t/self.maxTime > self.thresholdT):
195
+ tspec = '%6.2fs n=%04d' % (t, self.counts[srow])
196
+
197
+
198
+ self.out.write('%s %03d ' % (tspec,srow ))
199
+ self.line_flag = True
200
+
201
+
202
+ #if scol == 0 and srow == 1:
203
+ # self.out.write('%03d ' % srow)
204
+
205
+
206
+ # handle newlines
207
+ if toktype in [token.NEWLINE, tokenize.NL]:
208
+ if self.cover_flag:
209
+ self.out.write('</span>')
210
+ self.cover_flag = False
211
+ self.out.write('\n')
212
+ self.line_flag = False
213
+ #self.out.write('%03d ' % (srow + 1))
214
+ return
215
+
216
+
217
+
218
+ # send the original whitespace, if needed
219
+ if newpos > oldpos:
220
+ self.out.write(self.raw[oldpos:newpos])
221
+ #ws = self.raw[oldpos:newpos].split('\n')
222
+ #ws1 = ws[0]
223
+ #for i in range(len(ws[1:])):
224
+ # ws1 += '\n%03d %s' % ((srow - len(ws) + i), ws[1+i])
225
+ #self.out.write(ws1)
226
+
227
+ # skip indenting tokens
228
+ if toktype in [token.INDENT, token.DEDENT]:
229
+ self.pos = newpos
230
+ return
231
+
232
+ # map token type to a color group
233
+ if token.LPAR <= toktype and toktype <= token.OP:
234
+ toktype = token.OP
235
+ elif toktype == token.NAME and keyword.iskeyword(toktext):
236
+ toktype = _KEYWORD
237
+ css_class = _css_classes.get(toktype, 'text')
238
+
239
+ # send text
240
+ self.out.write('<span class="%s">' % (css_class,))
241
+ self.out.write(escape(toktext))
242
+ self.out.write('</span>')
243
+
244
+ if toktype == tokenize.COMMENT and toktext[-1] == '\n':
245
+ #self.out.write('%03d ' % (srow + 1))
246
+ self.line_flag = False
247
+
248
+
249
+ def colorize_file(times, counts, file=None, outstream=sys.stdout, standalone=True):
250
+ """Convert a python source file into colorized HTML.
251
+
252
+ Reads file and writes to outstream (default sys.stdout). file can be a
253
+ filename or a file-like object (only the read method is used). If file is
254
+ None, act as a filter and read from sys.stdin. If standalone is True
255
+ (default), send a complete HTML document with header and footer. Otherwise
256
+ only a stylesheet and a <pre> section are written.
257
+ """
258
+
259
+ from os.path import basename
260
+ if hasattr(file, 'read'):
261
+ sourcefile = file
262
+ file = None
263
+ try:
264
+ filename = basename(file.name)
265
+ except:
266
+ filename = 'STREAM'
267
+ elif file is not None:
268
+ try:
269
+ sourcefile = open(file)
270
+ filename = basename(file)
271
+ except IOError:
272
+ raise "File %s unknown." % file
273
+ else:
274
+ sourcefile = sys.stdin
275
+ filename = 'STDIN'
276
+ source = sourcefile.read()
277
+
278
+ if standalone:
279
+ outstream.write(_HTML_HEADER % {'title': filename})
280
+ Parser(source, times, counts, out=outstream).format()
281
+ if standalone:
282
+ outstream.write(_HTML_FOOTER)
283
+
284
+ if file:
285
+ sourcefile.close()
286
+
287
+ #if __name__ == "__main__":
288
+ # import os
289
+ # if os.environ.get('PATH_TRANSLATED'):
290
+ # filepath = os.environ.get('PATH_TRANSLATED')
291
+ # print 'Content-Type: text/html; charset="iso-8859-1"\n'
292
+ # colorize_file(filepath)
293
+ # elif len(sys.argv) > 1:
294
+ # filepath = sys.argv[1]
295
+ # colorize_file(filepath)
296
+ # else:
297
+ # colorize_file()
PYME/util/mProfile/mProfile.py ADDED
@@ -0,0 +1,164 @@
1
+ #!/usr/bin/python
2
+
3
+ ###############
4
+ # mProfile.py
5
+ #
6
+ # Copyright David Baddeley, 2012
7
+ # d.baddeley@auckland.ac.nz
8
+ #
9
+ # This program is free software: you can redistribute it and/or modify
10
+ # it under the terms of the GNU General Public License as published by
11
+ # the Free Software Foundation, either version 3 of the License, or
12
+ # (at your option) any later version.
13
+ #
14
+ # This program is distributed in the hope that it will be useful,
15
+ # but WITHOUT ANY WARRANTY; without even the implied warranty of
16
+ # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
17
+ # GNU General Public License for more details.
18
+ #
19
+ # You should have received a copy of the GNU General Public License
20
+ # along with this program. If not, see <http://www.gnu.org/licenses/>.
21
+ #
22
+ ################
23
+ #!/usr/bin/python
24
+ """ mProfile.py - Matlab(TM) style line based profiling for Python
25
+
26
+ Copyright: David Baddeley 2008
27
+ david_baddeley <at> yahoo.com.au
28
+
29
+ useage is similar to profiling in matlab (profile on, profile off, report),
30
+ with the major difference being that you have to specify the filenames in which
31
+ you want to do the profiling (to improve performance & to save wading through
32
+ lots of standard library code etc ...).
33
+
34
+ e.g.
35
+
36
+ mProfile.profileOn(['onefile.py', 'anotherfile.py'])
37
+
38
+ stuff to be profiled ....
39
+
40
+ mProfile.profileOff()
41
+ mProfile.report()
42
+
43
+ Due to the fact that we're doing this in python, and hooking every line,
44
+ there is a substantial performance hit, although for the numeric code I wrote it
45
+ for (lots of vectorised numpy/scipy stuff) it's only on the order of ~30%.
46
+
47
+ Licensing: Take your pick of BSD or GPL
48
+ """
49
+
50
+ import sys
51
+ import time
52
+ import os
53
+ from . import colorize_db_t
54
+ import webbrowser
55
+ import tempfile
56
+ import threading
57
+
58
+ if sys.version_info[0] >= 3:
59
+ time_fcn = time.perf_counter
60
+ else:
61
+ time_fcn = time.clock
62
+
63
+ #lStore.tPrev = time.time()
64
+
65
+ #lStore.lPrev = None
66
+ class mydictn(dict):
67
+ def __init__(self, *args):
68
+ dict.__init__(self, *args)
69
+
70
+ def __getitem__(self,key):
71
+ return self.get(key, None)
72
+ # if self.has_key(key):
73
+ # return dict.__getitem__(self, key)
74
+ # else:
75
+ # return None
76
+
77
+
78
+ lStore = threading.local()
79
+ #lStore.tPrev = {}
80
+ #lStore.lPrev = mydictn()
81
+
82
+ global filenames, files, linecounts
83
+ filenames = []
84
+ files = {}
85
+ linecounts = {}
86
+ fullfilenames = {}
87
+
88
+ class mydict(dict):
89
+ def __init__(self, *args):
90
+ dict.__init__(self, *args)
91
+
92
+ def __getitem__(self,key):
93
+ return self.get(key, 0)
94
+ # if self.has_key(key):
95
+ # return dict.__getitem__(self, key)
96
+ # else:
97
+ # return 0
98
+
99
+ def profileOn(fnames):
100
+ global filenames, files, linecounts
101
+
102
+ filenames = fnames
103
+
104
+ files = {}
105
+ linecounts = {}
106
+ for f in fnames:
107
+ files[f] = mydict()
108
+ linecounts[f] = mydict()
109
+
110
+
111
+ #lStore.tPrev = time.time()
112
+ sys.settrace(te)
113
+ threading.settrace(te)
114
+
115
+ def profileOff():
116
+ sys.settrace(None)
117
+ threading.settrace(None)
118
+
119
+ def te(frame, event, arg):
120
+ #global filenames, files
121
+ if not hasattr(lStore, 'tPrev'):
122
+ lStore.tPrev = {}
123
+ if not hasattr(lStore, 'lPrev'):
124
+ lStore.lPrev = mydictn()
125
+
126
+ fn = frame.f_code.co_filename.split(os.sep)[-1]
127
+ funcName = fn + ' ' + frame.f_code.co_name
128
+ #print fn
129
+ if fn in filenames and not lStore.lPrev[funcName] is None:
130
+ t = time_fcn()
131
+ files[lStore.lPrev[funcName][0]][lStore.lPrev[funcName][1]] += (t - lStore.tPrev[funcName])
132
+ lStore.lPrev[funcName] = None
133
+
134
+ if event == 'call':
135
+ return te
136
+
137
+ if event == 'line':
138
+ if fn in filenames:
139
+ linecounts[fn][frame.f_lineno] += 1
140
+ fullfilenames[fn] = frame.f_code.co_filename
141
+ lStore.lPrev[funcName] = (fn,frame.f_lineno)
142
+ lStore.tPrev[funcName] = time_fcn()
143
+
144
+
145
+
146
+ def report(display=True, profiledir=None):
147
+ if profiledir is None:
148
+ tpath = os.path.join(tempfile.gettempdir(), 'mProf')
149
+ else:
150
+ tpath = profiledir
151
+
152
+ if not os.path.exists(tpath):
153
+ os.makedirs(tpath)
154
+
155
+ for f in filenames:
156
+ try:
157
+ tfn = os.path.join(tpath, f + '.html')
158
+ colorize_db_t.colorize_file(files[f], linecounts[f], fullfilenames[f],open(tfn, 'w'))
159
+
160
+ if display:
161
+ webbrowser.open('file://' + tfn, 2)
162
+ except KeyError:
163
+ pass
164
+
PYME/util/mProfile/p.py ADDED
@@ -0,0 +1,101 @@
1
+ #!/usr/bin/python
2
+
3
+ ##################
4
+ # p.py
5
+ #
6
+ # Copyright David Baddeley, 2009
7
+ # d.baddeley@auckland.ac.nz
8
+ #
9
+ # This program is free software: you can redistribute it and/or modify
10
+ # it under the terms of the GNU General Public License as published by
11
+ # the Free Software Foundation, either version 3 of the License, or
12
+ # (at your option) any later version.
13
+ #
14
+ # This program is distributed in the hope that it will be useful,
15
+ # but WITHOUT ANY WARRANTY; without even the implied warranty of
16
+ # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
17
+ # GNU General Public License for more details.
18
+ #
19
+ # You should have received a copy of the GNU General Public License
20
+ # along with this program. If not, see <http://www.gnu.org/licenses/>.
21
+ #
22
+ ##################
23
+
24
+ import sys
25
+ import time
26
+ import os
27
+ from . import colorize_db_t
28
+ import webbrowser
29
+
30
+ #tPrev = time.time()
31
+
32
+ #lPrev = None
33
+ class mydictn(dict):
34
+ def __init__(self, *args):
35
+ dict.__init__(self, *args)
36
+
37
+ def __getitem__(self,key):
38
+ if key in self:
39
+ return dict.__getitem__(self, key)
40
+ else:
41
+ return None
42
+
43
+ tPrev = {}
44
+ lPrev = mydictn()
45
+
46
+ filenames = []
47
+ files = {}
48
+ fullfilenames = {}
49
+
50
+ class mydict(dict):
51
+ def __init__(self, *args):
52
+ dict.__init__(self, *args)
53
+
54
+ def __getitem__(self,key):
55
+ if key in self:
56
+ return dict.__getitem__(self, key)
57
+ else:
58
+ return 0
59
+
60
+ def profOn(fnames):
61
+ global filenames, files, tPrev
62
+
63
+ filenames = fnames
64
+
65
+ files = {}
66
+ for f in fnames:
67
+ files[f] = mydict()
68
+
69
+ #tPrev = time.time()
70
+ sys.settrace(te)
71
+
72
+ def profOff():
73
+ sys.settrace(None)
74
+
75
+ def te(frame, event, arg):
76
+ global tPrev, filenames, files, lPrev
77
+ fn = frame.f_code.co_filename.split(os.sep)[-1]
78
+ funcName = fn + ' ' + frame.f_code.co_name
79
+ #print funcName
80
+ if fn in filenames and not lPrev[funcName] is None:
81
+ t = time.time()
82
+ files[lPrev[funcName][0]][lPrev[funcName][1]] += (t - tPrev[funcName])
83
+ lPrev[funcName] = None
84
+ if event == 'call':
85
+ return te
86
+ if event == 'line':
87
+ if fn in filenames:
88
+ fullfilenames[fn] = frame.f_code.co_filename
89
+ lPrev[funcName] = (fn,frame.f_lineno)
90
+ tPrev[funcName] = time.time()
91
+
92
+
93
+
94
+ def report():
95
+ if not os.path.exists('/tmp/mProf'):
96
+ os.makedirs('/tmp/mProf')
97
+
98
+ for f in filenames:
99
+ colorize_db_t.colorize_file(files[f], fullfilenames[f],open('/tmp/mProf/' + f + '.html', 'w'))
100
+ webbrowser.open('/tmp/mProf/' + f + '.html', 2)
101
+