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 +1,287 @@
1
+ import imp
2
+ from PYME.Acquire.Hardware import Camera
3
+ from PYME.Acquire.Hardware.Simulator import fakeCam
4
+ import numpy as np
5
+ import logging
6
+ logger = logging.getLogger(__name__)
7
+
8
+ class MultiviewWrapper(object):
9
+ def __init__(self, base_camera, multiview_info, default_roi=None):
10
+ """
11
+ Used principally for cutting horizontally spaced ROIs out of a vertical band of the sCMOS chip, where there
12
+ is dark space between the images and we want to avoid saving and transmitting this dark data.
13
+
14
+ This class supports the standard full chip and cropped ROI modes, as well as a new multiview mode. The
15
+ multiview mode makes the frames appear to the outside world as though they are just active multiview views
16
+ concatenated horizontally.
17
+
18
+ The class wraps around an existing camera class, redefining the methods associated
19
+ with getting and setting ROIs and image data, other camera methods are passed through to the
20
+ base camera class.
21
+
22
+ Usage is as follows:
23
+
24
+ ```
25
+ #initialise base camera as normal
26
+ base_camera = SomeCameraClass(...)
27
+ # wrap it
28
+ mvcam = MultiviewWrapper(base_camera, multiview_info, default_roi)
29
+ ```
30
+
31
+ Parameters
32
+ ----------
33
+ base_camera: Camera.Camera (or subclass) instance
34
+ the object representing the actual physical camera.
35
+ multiview_info : dict
36
+ Information about how to crop the image. Can either be a dictionary, or something which behaves like a
37
+ dictionary (e.g. a MetaDataHandler).
38
+ default_roi: dict, optional
39
+ contains the default ROI of the camera. This will usually be automatically read from the base camera
40
+
41
+
42
+ Notes
43
+ -----
44
+ For now, the 0th multiview ROI should be the upper-left most multiview ROI, in order to properly spoof the
45
+ position to match up with the stage. See PYME.IO.MetaDataHandler.get_camera_roi_origin.
46
+ """
47
+ self._camera = base_camera # type: Camera.Camera
48
+
49
+ if default_roi is None:
50
+
51
+ #full field of base camera
52
+ default_roi = {
53
+ 'xi' : 0,
54
+ 'yi' : 0,
55
+ 'xf' : self._camera.GetCCDWidth(),
56
+ 'yf' : self._camera.GetCCDHeight()
57
+ }
58
+
59
+ self.multiview_info = multiview_info
60
+ self._channel_color = multiview_info['Multiview.ChannelColor']
61
+
62
+ self.n_views = multiview_info['Multiview.NumROIs']
63
+ self.view_origins = [multiview_info['Multiview.ROI%dOrigin' % i] for i in range(self.n_views)]
64
+ self.size_x, self.size_y = multiview_info['Multiview.DefaultROISize']
65
+ self.multiview_roi_size_options = multiview_info['Multiview.ROISizeOptions']
66
+
67
+ self.view_centers = [(ox + int(0.5*self.size_x), oy + int(0.5*self.size_y)) for ox, oy in self.view_origins]
68
+
69
+ self.multiview_enabled = False
70
+ self.active_views = []
71
+
72
+ # set default width and height to return to when multiview is disabled
73
+ self._default_chip_width = default_roi['xf'] - default_roi['xi']
74
+ self._default_chip_height = default_roi['yf'] - default_roi['yi']
75
+ self.default_chip_roi = default_roi
76
+ self._current_pic_width = self._default_chip_width
77
+ self._current_pic_height = self._default_chip_height
78
+
79
+ #hack for simulator TODO - move this somewhere more sensible
80
+ if isinstance(self._camera, fakeCam.FakeCamera):
81
+ vx = self._camera.XVals[1] - self._camera.XVals[0]
82
+ self._camera._chan_x_offsets = [vx*x0 for x0, y0 in self.view_origins]
83
+
84
+ def ChangeMultiviewROISize(self, x_size, y_size):
85
+ """
86
+ Changes the ROI size of the views. Currently they are all the same size
87
+ Parameters
88
+ ----------
89
+ x_size: int
90
+ first dimension size
91
+ y_size: int
92
+ second dimension size
93
+
94
+ Returns
95
+ -------
96
+ None
97
+ """
98
+ # shift the origins
99
+ self.view_origins = [(xc - int(0.5*x_size), yc - int(0.5*y_size)) for xc, yc in self.view_centers]
100
+ # store the new sizes
101
+ self.size_x, self.size_y = x_size, y_size
102
+
103
+ if self.multiview_enabled:
104
+ # re-set the slices for frame cropping
105
+ self.enable_multiview(self.active_views)
106
+
107
+
108
+ def GetPicWidth(self):
109
+ """
110
+ This clobbers the inherited self.camera_class GetPicWidth method so that the outside world (FrameWrangler)
111
+ only allocates memory/thinks our camera frames are the final concatenated multiview width.
112
+ Returns
113
+ -------
114
+ pic_width: int
115
+ width of the concatenated multiview frame
116
+ """
117
+ if self.multiview_enabled:
118
+ return self._current_pic_width
119
+ else:
120
+ return self._camera.GetPicWidth()
121
+
122
+ def GetPicHeight(self):
123
+ """
124
+ This clobbers the inherited self.camera_class GetPicHeight method so that the outside world (FrameWrangler)
125
+ only allocates memory/thinks our camera frames are the final multiview frame height.
126
+ Returns
127
+ -------
128
+ pic_height: int
129
+ height of the multiview frame
130
+ """
131
+ if self.multiview_enabled:
132
+ return self._current_pic_height
133
+ else:
134
+ return self._camera.GetPicHeight()
135
+
136
+ def set_active_views(self, views):
137
+ if len(views) == 0:
138
+ self.disable_multiview()
139
+ elif sorted(views) == self.active_views:
140
+ pass
141
+ else:
142
+ self.enable_multiview(views)
143
+
144
+
145
+ def enable_multiview(self, views):
146
+ """
147
+
148
+ Parameters
149
+ ----------
150
+ views: list
151
+ views to activate. Should be integers which can be used to index self.multiview_info
152
+
153
+ Returns
154
+ -------
155
+
156
+ Notes
157
+ -----
158
+ FrameWrangler must be stopped before this function is called, and "prepared" afterwards before being started
159
+ again. This is not special to this function, but rather anytime SetROI gets called.
160
+
161
+ """
162
+ views = sorted(list(views)) # tuple(int) isn't iterable, make sure we avoid it
163
+ # set the camera FOV to be just large enough so we do most of the cropping where it is already optimized
164
+ self.x_origins, self.y_origins = zip(*[self.view_origins[view] for view in views])
165
+ chip_x_min, chip_x_max = min(self.x_origins), max(self.x_origins)
166
+ chip_y_min, chip_y_max = min(self.y_origins), max(self.y_origins)
167
+
168
+ chip_width = chip_x_max + self.size_x - chip_x_min
169
+ chip_height = chip_y_max + self.size_y - chip_y_min
170
+
171
+ self.chip_roi = [chip_x_min, chip_y_min, chip_x_min + chip_width, chip_y_min + chip_height]
172
+ logger.debug('setting chip ROI')
173
+ self._camera.SetROI(*self.chip_roi)
174
+ actual = self._camera.GetROI()
175
+ try:
176
+ assert actual == tuple(self.chip_roi)
177
+ except AssertionError:
178
+ raise(AssertionError('Error setting camera ROI. Check that ROI is feasible for camera, target: %s, actual: %s'
179
+ % (tuple(self.chip_roi), actual)))
180
+
181
+ # hold an array for temporarily writing the roughly cropped chip
182
+ self.chip_data = np.empty((chip_width, chip_height), dtype='uint16', order='F')
183
+
184
+ # precalculate slices for each view
185
+ self.view_slices, self.output_slices = [], []
186
+ for x_ind, view in enumerate(views):
187
+ ox, oy = self.view_origins[view]
188
+ # calculate the offset from the chip origin
189
+ oxp, oyp = ox - chip_x_min, oy - chip_y_min
190
+ # calculate the slices to pull out of roi on chip
191
+ self.view_slices.append(np.s_[oxp:oxp + self.size_x, oyp: oyp + self.size_y])
192
+ # calculate slices to write into out array
193
+ self.output_slices.append(np.s_[self.size_x * x_ind:self.size_x * (x_ind + 1), 0:self.size_y])
194
+
195
+ # update our apparent height and widths, concatenating along 'x' or the 0th dim
196
+ self._current_pic_width = len(views) * self.size_x
197
+ self._current_pic_height = self.size_y
198
+ # tell the world what we've accomplished here today
199
+ self.multiview_enabled = True
200
+ self.active_views = views
201
+
202
+ def disable_multiview(self):
203
+ """
204
+ Disables multiview mode and returns camera to the default ROI (e.g. full chip)
205
+ Returns
206
+ -------
207
+
208
+ """
209
+ self.multiview_enabled = False
210
+ self.active_views = []
211
+ self._camera.SetROI(self.default_chip_roi['xi'], self.default_chip_roi['yi'],
212
+ self.default_chip_roi['xf'], self.default_chip_roi['yf'],)
213
+
214
+
215
+ def ExtractColor(self, output_frame, mode):
216
+ """
217
+ Override camera get-frame function, but with multiview cropping.
218
+
219
+ Parameters
220
+ ----------
221
+ output_frame: np.array
222
+ array sized for the final multiview frame
223
+ mode: int
224
+ camera acquisition mode.
225
+
226
+ Returns
227
+ -------
228
+
229
+ """
230
+ if self.multiview_enabled:
231
+ # logger.debug('pulling frame')
232
+ # pull data off the roughly cropped frame
233
+ self._camera.ExtractColor(self.chip_data, mode)
234
+ # extract the multiview frames from the cropped chip into our output
235
+ for out_slice, view_slice in zip(self.output_slices, self.view_slices):
236
+ output_frame[out_slice] = self.chip_data[view_slice]
237
+
238
+ else:
239
+ # skip extra cropping, extract the full chip directly into the output frame
240
+ self._camera.ExtractColor(output_frame, mode)
241
+
242
+ def GenStartMetadata(self, mdh):
243
+ """
244
+ Light shim to record multiview metadata, when appropriate
245
+
246
+ Parameters
247
+ ----------
248
+ mdh : MetaDataHandler
249
+ MetaDataHandler object for Camera.
250
+
251
+ Returns
252
+ -------
253
+ None
254
+ """
255
+ self._camera.GenStartMetadata(mdh)
256
+ # add in multiview info
257
+ if self.multiview_enabled:
258
+ mdh.setEntry('Multiview.NumROIs', self.n_views)
259
+ mdh.setEntry('Multiview.ROISize', [self.size_x, self.size_y])
260
+ mdh.setEntry('Multiview.ChannelColor', self._channel_color)
261
+ mdh.setEntry('Multiview.ActiveViews', self.active_views)
262
+ for ind in range(self.n_views):
263
+ mdh.setEntry('Multiview.ROI%dOrigin' % ind, self.view_origins[ind])
264
+
265
+ def register_state_handlers(self, state_manager):
266
+ """ Allow key multiview settings to be updated easily through
267
+ the microscope state handler
268
+
269
+ Parameters
270
+ ----------
271
+ state_manager : PYME.Acquire.microscope.State
272
+ """
273
+ logger.debug('registering multiview camera state handlers')
274
+
275
+ state_manager.registerHandler('Multiview.ActiveViews',
276
+ lambda : self.active_views,
277
+ self.set_active_views, True)
278
+ state_manager.registerHandler('Multiview.ROISize',
279
+ lambda : [self.size_x, self.size_y],
280
+ lambda p : self.ChangeMultiviewROISize(p[0], p[1]),
281
+ True)
282
+
283
+ def __getattr__(self, key):
284
+ """
285
+ Proxy any methods we don't implement here by passing through to the base camera class
286
+ """
287
+ return getattr(self._camera, key)
@@ -0,0 +1,59 @@
1
+ """
2
+ Control the halogen lamp (transmitted light) on an Olympus IX81 stand.
3
+
4
+ Uses the serial command set described at https://madhadron.com/science/olympus_ix81_commands.html
5
+
6
+ TODO - move logic to an IX81 class which also allows control of other stand features and support more of the command set.
7
+ TODO - some form of error handling
8
+ TODO - consider re-writing the query function to try and match responses to commands (these are not guaranteed to be synchronous)
9
+
10
+ """
11
+ import serial
12
+ import time
13
+ import threading
14
+ from PYME.Acquire.Hardware.lasers import Laser
15
+
16
+ class OlympusIX81HalogenLamp(Laser):
17
+ def __init__(self, name, portname='COM17', turn_on=False, **kwargs):
18
+ self.ser_port = serial.Serial(portname, 19200, parity='E',
19
+ timeout=2, writeTimeout=2)
20
+ self.lock = threading.Lock()
21
+ self.name = name
22
+ self.powerControlable = False
23
+ self.isOn = False
24
+ #self.TurnOn()
25
+ Laser.__init__(self, name, turn_on, **kwargs)
26
+
27
+ def _query(self, command, lines_expected=1):
28
+ with self.lock:
29
+ self.ser_port.reset_input_buffer()
30
+ self.ser_port.write(command)
31
+ reply = [self.ser_port.readline() for line in range(lines_expected)]
32
+ self.ser_port.reset_input_buffer()
33
+ return reply
34
+
35
+ def IsOn(self):
36
+ return self.isOn
37
+
38
+ def TurnOn(self):
39
+ # make sure serial is open
40
+ try:
41
+ self.ser_port.open()
42
+ except serial.SerialException:
43
+ pass
44
+
45
+ self.isOn = True
46
+
47
+ # turn on the laser
48
+ self._query(b'1LOG IN\r\n', lines_expected=1)
49
+ self._query(b'1LMPSW ON\r\n', lines_expected=1)
50
+ self._query(b'1LOG OUT\r\n', lines_expected=1)
51
+ #self.ser_port.flush()
52
+
53
+ def TurnOff(self):
54
+ self._query(b'1LOG IN\r\n', lines_expected=1)
55
+ self._query(b'1LMPSW OFF\r\n', lines_expected=1)
56
+ self._query(b'1LOG OUT\r\n', lines_expected=1)
57
+ #self.ser_port.flush()
58
+ self.isOn = False
59
+
File without changes
@@ -0,0 +1,348 @@
1
+ # -*- coding: utf-8 -*-
2
+
3
+ """
4
+ Created on Mon August 10 2020
5
+
6
+ @author: zacsimile
7
+ """
8
+
9
+ from PYME.Acquire.Hardware.Camera import Camera
10
+ from PYME.Acquire import eventLog
11
+
12
+ import numpy as np
13
+ import logging
14
+ logger = logging.getLogger(__name__)
15
+
16
+ import ctypes
17
+ import platform
18
+ import time
19
+
20
+ sys = platform.system()
21
+ if sys != 'Windows':
22
+ raise Exception("Operating system is not supported.")
23
+
24
+ # We use https://pypi.org/project/pco/
25
+ # For API docs, see https://www.pco.de/fileadmin/user_upload/pco-manuals/pco.sdk_manual.pdf and
26
+ # https://www.pco.de/fileadmin/user_upload/pco-manuals/pco.recorder_manual.pdf
27
+ try:
28
+ import pco
29
+ except ModuleNotFoundError:
30
+ raise ModuleNotFoundError('Please install the pco package from https://pypi.org/project/pco/.')
31
+
32
+ timebase = {'ns': 1e-9, 'us': 1e-6, 'ms': 1e-3} # Conversions from a pco dictionary
33
+
34
+ class PcoCam(Camera):
35
+ numpy_frames = 1
36
+
37
+ def __init__(self, camNum, debuglevel='off'):
38
+ Camera.__init__(self)
39
+ self.camNum = camNum
40
+ self.initalized = False
41
+ self.noiseProps = None
42
+ self._debuglevel = debuglevel # ['off', 'error', 'verbose', 'extra verbose']
43
+
44
+ def Init(self):
45
+ self.cam = pco.Camera(debuglevel=self._debuglevel)
46
+ self.SetDescription()
47
+ self._mode = self.MODE_CONTINUOUS
48
+ self.SetHotPixelCorrectionMode('off')
49
+ self.buffer_size = 0
50
+ self.n_read = 0
51
+ self.initalized = True
52
+ self._roi = None
53
+ self.SetROI(1, 1, self.GetCCDWidth(), self.GetCCDHeight())
54
+ self._ccd_temp = 0
55
+ self._ccd_temp_set_point = 0
56
+ self._electr_temp = 0
57
+ self._cycle_time = 0
58
+ self._integ_time = 0
59
+ self._binning_x = 0
60
+ self._binning_y = 0
61
+ self.recording = False
62
+
63
+ @property
64
+ def noise_properties(self):
65
+ return self.noiseProps
66
+
67
+ def SetDescription(self):
68
+ self.desc = self.cam.sdk.get_camera_description()
69
+
70
+ def ExpReady(self):
71
+ return self.recording and (self.GetNumImsBuffered() >= 1)
72
+
73
+ def GetName(self):
74
+ return self.cam.sdk.get_camera_name()['camera name']
75
+
76
+ def CamReady(self):
77
+ # return self.cam.sdk.get_camera_busy_status()['busy status'] == 0
78
+ return self.initalized
79
+
80
+ def ExtractColor(self, chSlice, mode):
81
+ # Somehow this check matters... shouldn't this be taken care of by ExpReady???
82
+ if (not self.recording) or (self.GetNumImsBuffered() < 1):
83
+ raise RuntimeError('Trying to grab a frame when there is no frame to grab.')
84
+
85
+ if self.n_read < self.buffer_size:
86
+ curr_frame = self.n_read
87
+ else:
88
+ curr_frame = self.buffer_size-self.GetNumImsBuffered()
89
+
90
+ # Grab the image (unused metadata _)
91
+ image, _ = self.cam.image(curr_frame)
92
+
93
+ ctypes.cdll.msvcrt.memcpy(chSlice.ctypes.data_as(ctypes.POINTER(ctypes.c_uint16)),
94
+ image.ctypes.data_as(ctypes.POINTER(ctypes.c_uint16)),
95
+ chSlice.nbytes)
96
+
97
+ self.n_read += 1
98
+
99
+ def GetHeadModel(self):
100
+ return self.cam.sdk.get_camera_type()['camera type']
101
+
102
+ def GetSerialNumber(self):
103
+ return str(self.cam.sdk.get_camera_type()['serial number'])
104
+
105
+ def SetIntegTime(self, time):
106
+ lb = self.desc['Min Expos DESC']*1e-9 # ns
107
+ ub = self.desc['Max Expos DESC']*1e-3 # ms
108
+ step = self.desc['Min Expos Step DESC']*1e-9 # ns
109
+
110
+ # Round to a multiple of time step
111
+ time = np.floor(time/step)*step
112
+
113
+ # Don't let this go out of bounds
114
+ time = np.clip(time, lb, ub)
115
+
116
+ self.cam.set_exposure_time(time)
117
+ d = self.cam.sdk.get_delay_exposure_time()
118
+ self._integ_time = d['exposure']*timebase[d['exposure timebase']]
119
+
120
+ def GetIntegTime(self):
121
+ return self._integ_time
122
+
123
+ def GetCycleTime(self):
124
+ return self._cycle_time
125
+
126
+ def GetCCDWidth(self):
127
+ return int(self.desc['max. horizontal resolution standard'])
128
+
129
+ def GetCCDHeight(self):
130
+ return int(self.desc['max. vertical resolution standard'])
131
+
132
+ def GetPicWidth(self):
133
+ return self.GetROI()[2] - self.GetROI()[0] + 1
134
+
135
+ def GetPicHeight(self):
136
+ return self.GetROI()[3] - self.GetROI()[1] + 1
137
+
138
+ def SetHorizontalBin(self, value):
139
+ b_max, step_type = self.desc['max. binning horizontal'], self.desc['binning horizontal stepping']
140
+
141
+ if step_type == 0:
142
+ # binary binning, round to powers of two
143
+ value = 1<<(value-1).bit_length()
144
+ else:
145
+ value = int(np.round(value)) # integer
146
+
147
+ value = np.clip(value, 1, b_max)
148
+
149
+ self.cam.sdk.set_binning(value, self.GetVerticalBin())
150
+ self._binning_x = self.cam.sdk.get_binning()['binning x']
151
+
152
+ def GetHorizontalBin(self):
153
+ return self._binning_x
154
+
155
+ def SetVerticalBin(self, value):
156
+ b_max, step_type = self.desc['max. binning vert'], self.desc['binning vert stepping']
157
+
158
+ if step_type == 0:
159
+ # binary binning, round to powers of two
160
+ value = 1<<(value-1).bit_length()
161
+ else:
162
+ value = int(np.round(value))
163
+
164
+ value = np.clip(value, 1, b_max)
165
+
166
+ self.cam.sdk.set_binning(self.GetHorizontalBin(), value)
167
+ self._binning_y = self.cam.sdk.get_binning()['binning y']
168
+
169
+ def GetVerticalBin(self):
170
+ return self._binning_y
171
+
172
+ def GetSupportedBinning(self):
173
+ import itertools
174
+
175
+ bx_max, bx_step_type = self.desc['max. binning horizontal'], self.desc['binning horizontal stepping']
176
+ by_max, by_step_type = self.desc['max. binning vert'], self.desc['binning vert stepping']
177
+
178
+ if bx_step_type == 0:
179
+ # binary step type
180
+ x = [2**j for j in np.arange((bx_max).bit_length())]
181
+ else:
182
+ x = [j for j in np.arange(bx_max)]
183
+
184
+ if by_step_type == 0:
185
+ y = [2**j for j in np.arange((by_max).bit_length())]
186
+ else:
187
+ y = [j for j in np.arange(by_max)]
188
+
189
+ return list(itertools.product(x,y))
190
+
191
+ def SetROI(self, x0, y0, x1, y1):
192
+ # Stepping (n pixels)
193
+ dx = self.desc['roi hor steps']
194
+ dy = self.desc['roi vert steps']
195
+
196
+ # Chip size
197
+ lx_max = self.GetCCDWidth()
198
+ ly_max = self.GetCCDHeight()
199
+
200
+ # Minimum ROI size
201
+ lx_min = self.desc['min size horz']
202
+ ly_min = self.desc['min size vert']
203
+
204
+ # Make sure bounds are ordered
205
+ if x1 < x0:
206
+ x0, x1 = x1, x0
207
+ if y1 < y0:
208
+ y0, y1 = y1, y0
209
+
210
+ # Don't let the ROI go out of bounds
211
+ # See pco.sdk manual chapter 3: IMAGE AREA SELECTION (ROI)
212
+ x0 = np.clip(x0, 1, lx_max-dx+1)
213
+ y0 = np.clip(y0, 1, ly_max-dy+1)
214
+ x1 = np.clip(x1, 1+dx, lx_max)
215
+ y1 = np.clip(y1, 1+dy, ly_max)
216
+
217
+ # Don't let us choose too small an ROI
218
+ if (x1-x0+1) < lx_min:
219
+ logger.debug('Selected ROI width is too small, automatically adjusting to {}.'.format(lx_min))
220
+ guess_pos = x0+lx_min
221
+ # Deal with boundaries
222
+ if guess_pos <= lx_max:
223
+ x1 = guess_pos
224
+ else:
225
+ x0 = x1-lx_min-1
226
+ if (y1-y0+1) < ly_min:
227
+ logger.debug('Selected ROI height is too small, automatically adjusting to {}.'.format(ly_min))
228
+ guess_pos = y0+ly_min
229
+ if guess_pos <= ly_max:
230
+ y1 = guess_pos
231
+ else:
232
+ y0 = y1-ly_min-1
233
+
234
+ # Round to a multiple of dx, dy
235
+ # TODO: Why do I need the 1 correction only on x0, y0???
236
+ x0 = 1+int(np.floor((x0-1)/dx)*dx)
237
+ y0 = 1+int(np.floor((y0-1)/dy)*dy)
238
+ x1 = int(np.floor(x1/dx)*dx)
239
+ y1 = int(np.floor(y1/dy)*dy)
240
+
241
+ self.cam.sdk.set_roi(x0, y0, x1, y1)
242
+ self._roi = [x0, y0, x1, y1]
243
+
244
+ logger.debug('ROI set: x0 %3.1f, y0 %3.1f, w %3.1f, h %3.1f' % (x0, y0, x1-x0+1, y1-y0+1))
245
+
246
+ def GetROI(self):
247
+ return self._roi
248
+
249
+ def GetElectrTemp(self):
250
+ return self._electr_temp
251
+
252
+ def GetCCDTemp(self):
253
+ return self._ccd_temp
254
+
255
+ def GetCCDTempSetPoint(self):
256
+ return self._ccd_temp_set_point
257
+
258
+ def SetCCDTemp(self, temp):
259
+ lb = self.desc['Min Cool Set DESC']
260
+ ub = self.desc['Max Cool Set DESC']
261
+ temp = np.clip(temp, lb, ub)
262
+
263
+ self.cam.sdk.set_cooling_setpoint_temperature(temp)
264
+ self._ccd_temp_set_point = temp
265
+ self._get_temps()
266
+
267
+ def _get_temps(self):
268
+ # NOTE: temperature only gets probed when acquisition starts/stops (which can be fairly
269
+ # irregularly - to the point of not being useful).
270
+ # TODO - find a way to safely call this while the camera is running
271
+ d = self.cam.sdk.get_temperature()
272
+ self._ccd_temp = d['sensor temperature']
273
+ self._electr_temp = d['camera temperature'] # FIXME: should this be 'power temperature'?
274
+
275
+ def GetAcquisitionMode(self):
276
+ return self._mode
277
+
278
+ def SetAcquisitionMode(self, mode):
279
+ if mode in [self.MODE_CONTINUOUS, self.MODE_SINGLE_SHOT]:
280
+ self._mode = mode
281
+ else:
282
+ raise RuntimeError('Mode %d not supported' % mode)
283
+
284
+ def StartExposure(self):
285
+ self.StopAq()
286
+ self._get_temps()
287
+
288
+ d = self.cam.sdk.get_delay_exposure_time()
289
+ self._integ_time = d['exposure']*timebase[d['exposure timebase']]
290
+ self._cycle_time = self._integ_time \
291
+ + d['delay']*timebase[d['delay timebase']]
292
+ if self._mode == self.MODE_SINGLE_SHOT:
293
+ self.cam.record(number_of_images=1, mode='sequence')
294
+ elif self._mode == self.MODE_CONTINUOUS:
295
+ # Allocate buffer (2 seconds of buffer)
296
+ self.buffer_size = int(max(int(2.0*self.GetFPS()), 1))
297
+ self.cam.record(number_of_images=self.buffer_size, mode='ring buffer')
298
+ self.recording = True
299
+
300
+ self._log_exposure_start()
301
+
302
+ return 0
303
+
304
+ def StopAq(self):
305
+ self.recording = False
306
+ if self.cam.rec.recorder_handle.value is not None:
307
+ # NOTE: probably don't need this if statement thanks to the self.recording flag,
308
+ # but better to be safe
309
+ self.cam.rec.stop_record()
310
+ self.cam.rec.delete()
311
+
312
+ self._integ_time = 0
313
+ self._cycle_time = 0
314
+ self.buffer_size = 0
315
+ self.n_read = 0
316
+
317
+ # read the temp in StopAq too, as this has the side effect of making sure we have
318
+ # a reasonably correct temperature in acquisition metadata (as we
319
+ # stop acquisition, record metadata, and then restart)
320
+ self._get_temps()
321
+
322
+ def GetNumImsBuffered(self):
323
+ if self.recording:
324
+ # FIXME: dwProcImgCount is an unsigned 32-bit integer, so this will
325
+ # fail after 2**32 images
326
+ n_buf = self.cam.rec.get_status()['dwProcImgCount'] - self.n_read
327
+ else:
328
+ n_buf = 0
329
+ # print(n_buf+self.n_read, self.n_read)
330
+ return n_buf
331
+
332
+ def GetBufferSize(self):
333
+ # return self.cam.rec.get_settings()['maximum number of images']
334
+ return self.buffer_size
335
+
336
+ def GetFPS(self):
337
+ if self.GetCycleTime() == 0:
338
+ return 0
339
+ return 1.0/self.GetCycleTime()
340
+
341
+ def SetHotPixelCorrectionMode(self, mode):
342
+ if mode in ['on', 'off']:
343
+ self.cam.sdk.set_hot_pixel_correction_mode(mode)
344
+ else:
345
+ logger.debug('Hot Pixel Correction not set. Invalid mode {}. Choose "on" or "off".'.format(mode))
346
+
347
+ def Shutdown(self):
348
+ self.cam.close()