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.
- PYME/Acquire/ActionManager.py +450 -0
- PYME/Acquire/ExecTools.py +235 -0
- PYME/Acquire/Hardware/AAOptoelectronics/MDS.py +175 -0
- PYME/Acquire/Hardware/AAOptoelectronics/__init__.py +0 -0
- PYME/Acquire/Hardware/ARCoptix/__init__.py +0 -0
- PYME/Acquire/Hardware/ARCoptix/lcdriver.py +149 -0
- PYME/Acquire/Hardware/ARCoptix/lcserver32.py +123 -0
- PYME/Acquire/Hardware/AndorIXon/AndorCam.py +1095 -0
- PYME/Acquire/Hardware/AndorIXon/AndorControlFrame.py +312 -0
- PYME/Acquire/Hardware/AndorIXon/AndorIXon.py +737 -0
- PYME/Acquire/Hardware/AndorIXon/__init__.py +27 -0
- PYME/Acquire/Hardware/AndorNeo/AndorNeo.py +644 -0
- PYME/Acquire/Hardware/AndorNeo/AndorNeoControlFrame.py +161 -0
- PYME/Acquire/Hardware/AndorNeo/AndorZyla.py +761 -0
- PYME/Acquire/Hardware/AndorNeo/SDK3.py +307 -0
- PYME/Acquire/Hardware/AndorNeo/SDK3Cam.py +171 -0
- PYME/Acquire/Hardware/AndorNeo/ZylaControlPanel.py +105 -0
- PYME/Acquire/Hardware/AndorNeo/__init__.py +22 -0
- PYME/Acquire/Hardware/AndorNeo/parseAtdebug.py +46 -0
- PYME/Acquire/Hardware/AndorNeo/plotTimings.py +73 -0
- PYME/Acquire/Hardware/AndorNeo/testNeo.py +62 -0
- PYME/Acquire/Hardware/Camera.py +1199 -0
- PYME/Acquire/Hardware/CameraSkeleton.py +642 -0
- PYME/Acquire/Hardware/Coherent/OBIS.py +147 -0
- PYME/Acquire/Hardware/Coherent/Sapphire.py +162 -0
- PYME/Acquire/Hardware/Coherent/__init__.py +0 -0
- PYME/Acquire/Hardware/DMDGui.py +198 -0
- PYME/Acquire/Hardware/DigiData/DigiData.py +95 -0
- PYME/Acquire/Hardware/DigiData/DigiDataClient.py +30 -0
- PYME/Acquire/Hardware/DigiData/RemoteDigiData.py +51 -0
- PYME/Acquire/Hardware/DigiData/__init__.py +24 -0
- PYME/Acquire/Hardware/DigiData/axDD132x.py +348 -0
- PYME/Acquire/Hardware/EMCCDTheory.py +41 -0
- PYME/Acquire/Hardware/ExciterWheel.py +167 -0
- PYME/Acquire/Hardware/FilterWheel.py +184 -0
- PYME/Acquire/Hardware/FocCorr.py +106 -0
- PYME/Acquire/Hardware/FocCorrR.py +196 -0
- PYME/Acquire/Hardware/FrFilter.py +51 -0
- PYME/Acquire/Hardware/GCS/GCS_DLL.py +370 -0
- PYME/Acquire/Hardware/GCS/__init__.py +0 -0
- PYME/Acquire/Hardware/GCS/gcs.py +210 -0
- PYME/Acquire/Hardware/HamamatsuDCAM/HamamatsuDCAM.py +662 -0
- PYME/Acquire/Hardware/HamamatsuDCAM/HamamatsuORCA.py +602 -0
- PYME/Acquire/Hardware/HamamatsuDCAM/Hamamatsu_control_panel.py +54 -0
- PYME/Acquire/Hardware/HamamatsuDCAM/__init__.py +23 -0
- PYME/Acquire/Hardware/LaserControlFrame.py +160 -0
- PYME/Acquire/Hardware/MPBCommunications/MPBCW.py +132 -0
- PYME/Acquire/Hardware/MPBCommunications/__init__.py +0 -0
- PYME/Acquire/Hardware/Mercury/Mercury.py +269 -0
- PYME/Acquire/Hardware/Mercury/PI_Mercury_GCS_DLL.py +857 -0
- PYME/Acquire/Hardware/Mercury/__init__.py +22 -0
- PYME/Acquire/Hardware/Mercury/mercuryStepper.py +203 -0
- PYME/Acquire/Hardware/Mercury/mercuryStepperGCS.py +281 -0
- PYME/Acquire/Hardware/NikonTE2000.py +68 -0
- PYME/Acquire/Hardware/NikonTi.py +214 -0
- PYME/Acquire/Hardware/NikonTiGUI.py +81 -0
- PYME/Acquire/Hardware/OrielCornerstone.py +125 -0
- PYME/Acquire/Hardware/PM100USB.py +51 -0
- PYME/Acquire/Hardware/Piezos/__init__.py +22 -0
- PYME/Acquire/Hardware/Piezos/base_piezo.py +108 -0
- PYME/Acquire/Hardware/Piezos/offsetPiezo.py +162 -0
- PYME/Acquire/Hardware/Piezos/offsetPiezoREST.py +308 -0
- PYME/Acquire/Hardware/Piezos/piezo_c867.py +486 -0
- PYME/Acquire/Hardware/Piezos/piezo_e255.py +68 -0
- PYME/Acquire/Hardware/Piezos/piezo_e662.py +61 -0
- PYME/Acquire/Hardware/Piezos/piezo_e709.py +434 -0
- PYME/Acquire/Hardware/Piezos/piezo_e816.py +452 -0
- PYME/Acquire/Hardware/Piezos/piezo_e816_corr.py +70 -0
- PYME/Acquire/Hardware/Piezos/piezo_e816_dll.py +518 -0
- PYME/Acquire/Hardware/Piezos/piezo_e816b.py +70 -0
- PYME/Acquire/Hardware/Piezos/piezo_pipython_gcs.py +560 -0
- PYME/Acquire/Hardware/Piezos/piezo_test.py +55 -0
- PYME/Acquire/Hardware/Simulator/EmpiricalHist.py +273 -0
- PYME/Acquire/Hardware/Simulator/__init__.py +22 -0
- PYME/Acquire/Hardware/Simulator/dSimControl.py +961 -0
- PYME/Acquire/Hardware/Simulator/fakeCam.py +651 -0
- PYME/Acquire/Hardware/Simulator/fakePiezo.py +95 -0
- PYME/Acquire/Hardware/Simulator/fluor.py +336 -0
- PYME/Acquire/Hardware/Simulator/illuminate.cp313-win_amd64.dll.a +0 -0
- PYME/Acquire/Hardware/Simulator/illuminate.cp313-win_amd64.pyd +0 -0
- PYME/Acquire/Hardware/Simulator/illuminate.pyx +93 -0
- PYME/Acquire/Hardware/Simulator/lasersliders.py +90 -0
- PYME/Acquire/Hardware/Simulator/rend_im.py +446 -0
- PYME/Acquire/Hardware/Simulator/setup.py +69 -0
- PYME/Acquire/Hardware/Simulator/simcontrol.py +348 -0
- PYME/Acquire/Hardware/Simulator/simui_wx.py +794 -0
- PYME/Acquire/Hardware/Tango/__init__.py +0 -0
- PYME/Acquire/Hardware/Tango/marzhauser_tango.py +583 -0
- PYME/Acquire/Hardware/TiLightCrafter.py +388 -0
- PYME/Acquire/Hardware/__init__.py +22 -0
- PYME/Acquire/Hardware/aotf.py +271 -0
- PYME/Acquire/Hardware/arclampshutterpanel.py +71 -0
- PYME/Acquire/Hardware/cameraSoftwareBuffer.py +215 -0
- PYME/Acquire/Hardware/camera_noise.py +270 -0
- PYME/Acquire/Hardware/ccdAdjPanel.py +188 -0
- PYME/Acquire/Hardware/ccdCalibrator.py +161 -0
- PYME/Acquire/Hardware/cobaltLaser.py +108 -0
- PYME/Acquire/Hardware/cobaltLaser561.py +94 -0
- PYME/Acquire/Hardware/comports.py +26 -0
- PYME/Acquire/Hardware/driftTrackGUI.py +488 -0
- PYME/Acquire/Hardware/driftTracking.py +595 -0
- PYME/Acquire/Hardware/fakeShutters.py +52 -0
- PYME/Acquire/Hardware/focusKeys.py +204 -0
- PYME/Acquire/Hardware/focus_locks/__init__.py +0 -0
- PYME/Acquire/Hardware/focus_locks/reflection_focus_lock.py +684 -0
- PYME/Acquire/Hardware/frZStage.py +117 -0
- PYME/Acquire/Hardware/fw102.py +38 -0
- PYME/Acquire/Hardware/ids_peak_cam.py +561 -0
- PYME/Acquire/Hardware/ioslave.py +305 -0
- PYME/Acquire/Hardware/lasers.py +292 -0
- PYME/Acquire/Hardware/matchboxLaser.py +58 -0
- PYME/Acquire/Hardware/microscope_adapter.py +104 -0
- PYME/Acquire/Hardware/mpd_picosecond_delayer.py +395 -0
- PYME/Acquire/Hardware/multiview.py +287 -0
- PYME/Acquire/Hardware/olympusix81.py +59 -0
- PYME/Acquire/Hardware/pco/__init__.py +0 -0
- PYME/Acquire/Hardware/pco/pco_cam.py +348 -0
- PYME/Acquire/Hardware/pco/pco_edge_42_lt.py +34 -0
- PYME/Acquire/Hardware/pco/pco_sdk.py +1645 -0
- PYME/Acquire/Hardware/pco/pco_sdk_cam.py +518 -0
- PYME/Acquire/Hardware/pco/pco_sdk_cam_control_panel.py +54 -0
- PYME/Acquire/Hardware/phoxxLaser.py +199 -0
- PYME/Acquire/Hardware/phoxxLaserOLD.py +242 -0
- PYME/Acquire/Hardware/priorLumen.py +102 -0
- PYME/Acquire/Hardware/priorarclampshutter.py +52 -0
- PYME/Acquire/Hardware/setup.py +50 -0
- PYME/Acquire/Hardware/spacenav.py +148 -0
- PYME/Acquire/Hardware/splitter.py +394 -0
- PYME/Acquire/Hardware/thorlabsPiezo.py +98 -0
- PYME/Acquire/Hardware/thorlabs_cam.py +136 -0
- PYME/Acquire/Hardware/thorlabs_mff_flipper.py +400 -0
- PYME/Acquire/Hardware/toptica_ibeam.py +51 -0
- PYME/Acquire/Hardware/uc480/AndorControlFrame.py +308 -0
- PYME/Acquire/Hardware/uc480/__init__.py +27 -0
- PYME/Acquire/Hardware/uc480/uCam480.py +695 -0
- PYME/Acquire/Hardware/uc480/uc480.py +189 -0
- PYME/Acquire/Hardware/uc480/uc480Deprecated.py +87 -0
- PYME/Acquire/Hardware/uc480/uc480_h.py +767 -0
- PYME/Acquire/Hardware/uc480/uc480_h_gen.py +62 -0
- PYME/Acquire/Hardware/uc480/ucCamControlFrame.py +83 -0
- PYME/Acquire/Hardware/ueye.py +702 -0
- PYME/Acquire/PYMEAcquire.py +186 -0
- PYME/Acquire/Protocols/DMDMFM.py +74 -0
- PYME/Acquire/Protocols/__init__.py +22 -0
- PYME/Acquire/Protocols/darkCalibrate.py +56 -0
- PYME/Acquire/Protocols/dual671_470.py +45 -0
- PYME/Acquire/Protocols/dual671_488.py +46 -0
- PYME/Acquire/Protocols/gainCal.py +53 -0
- PYME/Acquire/Protocols/htsms-cal-psf.py +32 -0
- PYME/Acquire/Protocols/htsms-cal-registration.py +52 -0
- PYME/Acquire/Protocols/htsms-flow.py +29 -0
- PYME/Acquire/Protocols/htsms-staggered.py +31 -0
- PYME/Acquire/Protocols/htsms-tile.py +68 -0
- PYME/Acquire/Protocols/htsms-two-color.py +29 -0
- PYME/Acquire/Protocols/htsms-widefield.py +32 -0
- PYME/Acquire/Protocols/paint671.py +61 -0
- PYME/Acquire/Protocols/photoconversion.py +52 -0
- PYME/Acquire/Protocols/photoconversion2.py +55 -0
- PYME/Acquire/Protocols/prebleach488.py +70 -0
- PYME/Acquire/Protocols/prebleach490.py +69 -0
- PYME/Acquire/Protocols/prebleach561.py +72 -0
- PYME/Acquire/Protocols/prebleach561NeomEos2.py +70 -0
- PYME/Acquire/Protocols/prebleach561NeomEos2ND1.py +70 -0
- PYME/Acquire/Protocols/prebleach642.py +70 -0
- PYME/Acquire/Protocols/prebleach671.py +69 -0
- PYME/Acquire/Protocols/prebleach671ND1.py +58 -0
- PYME/Acquire/Protocols/prebleach671ND2.py +57 -0
- PYME/Acquire/Protocols/prebleach671Neo.py +69 -0
- PYME/Acquire/Protocols/recover671.py +62 -0
- PYME/Acquire/Protocols/sequence642_488.py +85 -0
- PYME/Acquire/Protocols/sequence642_561.py +87 -0
- PYME/Acquire/Protocols/shiftfield.py +198 -0
- PYME/Acquire/Protocols/simul488.py +59 -0
- PYME/Acquire/Protocols/simul642.py +63 -0
- PYME/Acquire/Protocols/simul642HTSMS.py +63 -0
- PYME/Acquire/Protocols/simulPA.py +37 -0
- PYME/Acquire/Protocols/simulSIM.py +76 -0
- PYME/Acquire/Protocols/simulStep.py +62 -0
- PYME/Acquire/Protocols/spdscan.py +178 -0
- PYME/Acquire/Protocols/standard470.py +45 -0
- PYME/Acquire/Protocols/standard488.py +47 -0
- PYME/Acquire/Protocols/standard671.py +48 -0
- PYME/Acquire/Protocols/standard671_no532.py +47 -0
- PYME/Acquire/Protocols/standardArclamp.py +46 -0
- PYME/Acquire/Protocols/strip_tile.py +204 -0
- PYME/Acquire/Protocols/tile.py +204 -0
- PYME/Acquire/Protocols/tile3D.py +192 -0
- PYME/Acquire/Protocols/tile671.py +190 -0
- PYME/Acquire/Protocols/tile_triggered.py +189 -0
- PYME/Acquire/Scripts/init.py +232 -0
- PYME/Acquire/Scripts/init_N1_Ti_Exeter_ZIx.py +374 -0
- PYME/Acquire/Scripts/init_N2_Ti_Zyla_lasers.py +290 -0
- PYME/Acquire/Scripts/init_Neo.py +266 -0
- PYME/Acquire/Scripts/init_NeoSim.py +159 -0
- PYME/Acquire/Scripts/init_TIRF.py +232 -0
- PYME/Acquire/Scripts/init_TIRF_Neo.py +242 -0
- PYME/Acquire/Scripts/init_TIRF_NeoO.py +241 -0
- PYME/Acquire/Scripts/init_TIRF_onecam.py +233 -0
- PYME/Acquire/Scripts/init_Ti.py +257 -0
- PYME/Acquire/Scripts/init_UOA_n.py +256 -0
- PYME/Acquire/Scripts/init_UOA_n2.py +246 -0
- PYME/Acquire/Scripts/init_Y1.py +249 -0
- PYME/Acquire/Scripts/init_Zyla.py +260 -0
- PYME/Acquire/Scripts/init_drift_tracking.py +80 -0
- PYME/Acquire/Scripts/init_emccd_basic.py +277 -0
- PYME/Acquire/Scripts/init_htsms.py +277 -0
- PYME/Acquire/Scripts/init_htsms_focus_lock.py +132 -0
- PYME/Acquire/Scripts/init_micrpi.py +45 -0
- PYME/Acquire/Scripts/init_orca.py +70 -0
- PYME/Acquire/Scripts/init_pco.py +49 -0
- PYME/Acquire/Scripts/init_rev.py +74 -0
- PYME/Acquire/Scripts/init_sim100.py +169 -0
- PYME/Acquire/Scripts/init_sim103.py +169 -0
- PYME/Acquire/Scripts/init_sim2.py +211 -0
- PYME/Acquire/Scripts/init_sim50.py +169 -0
- PYME/Acquire/Scripts/init_sim75.py +169 -0
- PYME/Acquire/Scripts/init_sim_drift_tracking.py +166 -0
- PYME/Acquire/Scripts/init_sim_htsms.py +224 -0
- PYME/Acquire/Scripts/init_sim_htsms_n.py +233 -0
- PYME/Acquire/Scripts/init_sim_main.py +229 -0
- PYME/Acquire/Scripts/init_sim_min.py +197 -0
- PYME/Acquire/Scripts/init_sim_rem.py +176 -0
- PYME/Acquire/Scripts/init_smi1.py +110 -0
- PYME/Acquire/Scripts/init_spectro.py +78 -0
- PYME/Acquire/Scripts/init_spim.py +116 -0
- PYME/Acquire/Scripts/init_thorcam.py +62 -0
- PYME/Acquire/Scripts/init_twophoton.py +112 -0
- PYME/Acquire/Scripts/init_uc480.py +262 -0
- PYME/Acquire/Scripts/init_ueye.py +261 -0
- PYME/Acquire/SpoolController.py +958 -0
- PYME/Acquire/Utils/MultiPointScanner.py +80 -0
- PYME/Acquire/Utils/__init__.py +13 -0
- PYME/Acquire/Utils/failsafe.py +157 -0
- PYME/Acquire/Utils/fastTiler.py +153 -0
- PYME/Acquire/Utils/pointScanner.py +496 -0
- PYME/Acquire/Utils/sarcSpacing.py +86 -0
- PYME/Acquire/Utils/strip_tiler.py +93 -0
- PYME/Acquire/Utils/tiler.py +464 -0
- PYME/Acquire/Utils/vibrationAnalysis.py +65 -0
- PYME/Acquire/__init__.py +44 -0
- PYME/Acquire/acquire_client.py +90 -0
- PYME/Acquire/acquire_server.py +316 -0
- PYME/Acquire/acquirebase.py +139 -0
- PYME/Acquire/acquiremainframe.py +716 -0
- PYME/Acquire/acquirewx.py +61 -0
- PYME/Acquire/acquisition_base.py +148 -0
- PYME/Acquire/actions.py +209 -0
- PYME/Acquire/autofocus.py +54 -0
- PYME/Acquire/eventLog.py +95 -0
- PYME/Acquire/event_loop.py +119 -0
- PYME/Acquire/frameWrangler.py +530 -0
- PYME/Acquire/htsms/__init__.py +8 -0
- PYME/Acquire/htsms/rule_ui.py +970 -0
- PYME/Acquire/htsms/rule_ui_v2.py +573 -0
- PYME/Acquire/htsms/tweeter.py +222 -0
- PYME/Acquire/microscope.py +1050 -0
- PYME/Acquire/positionTracker.py +181 -0
- PYME/Acquire/protocol.py +299 -0
- PYME/Acquire/protocol_acquisition.py +404 -0
- PYME/Acquire/sampleInformation.py +591 -0
- PYME/Acquire/sampleInformationDjangoDirect.py +446 -0
- PYME/Acquire/setup.py +52 -0
- PYME/Acquire/stackSettings.py +295 -0
- PYME/Acquire/stage_leveling.py +285 -0
- PYME/Acquire/ui/AnalysisSettingsUI.py +184 -0
- PYME/Acquire/ui/HDFSpoolFrame.py +584 -0
- PYME/Acquire/ui/__init__.py +0 -0
- PYME/Acquire/ui/actionUI.py +892 -0
- PYME/Acquire/ui/focus_lock_gui.py +149 -0
- PYME/Acquire/ui/intensity_trace.py +143 -0
- PYME/Acquire/ui/intsliders.py +222 -0
- PYME/Acquire/ui/lasersliders.py +329 -0
- PYME/Acquire/ui/mpd_picosecond_delay_panel.py +69 -0
- PYME/Acquire/ui/multiview_select.py +77 -0
- PYME/Acquire/ui/positionUI.py +519 -0
- PYME/Acquire/ui/preflight.py +58 -0
- PYME/Acquire/ui/scanner_panel.py +41 -0
- PYME/Acquire/ui/selectCameraPanel.py +46 -0
- PYME/Acquire/ui/seqdialog.py +501 -0
- PYME/Acquire/ui/splashScreen.py +175 -0
- PYME/Acquire/ui/spool_panel.py +830 -0
- PYME/Acquire/ui/tile_panel.py +556 -0
- PYME/Acquire/ui/tilesettingsui.py +91 -0
- PYME/Acquire/ui/voxelSizeDialog.py +149 -0
- PYME/Acquire/webui/__init__.py +36 -0
- PYME/Acquire/webui/ipy.py +361 -0
- PYME/Acquire/webui/static/css/pyme-bootstrap.css +9908 -0
- PYME/Acquire/webui/static/css/pymeacquire.css +85 -0
- PYME/Acquire/webui/static/js/pymeacquire.js +375 -0
- PYME/Acquire/webui/static/js/pzf.js +95 -0
- PYME/Acquire/webui/templates/PYMEAcquire.html +232 -0
- PYME/Acquire/webui/templates/login.html +84 -0
- PYME/Acquire/webui/templates/xtermpage.html +106 -0
- PYME/Acquire/xyztc.py +418 -0
- PYME/Acquire/zScanner.py +287 -0
- PYME/Analysis/BleachProfile/__init__.py +26 -0
- PYME/Analysis/BleachProfile/deMod.py +91 -0
- PYME/Analysis/BleachProfile/fitRecover.py +90 -0
- PYME/Analysis/BleachProfile/intensProf.py +519 -0
- PYME/Analysis/BleachProfile/kinModels.py +507 -0
- PYME/Analysis/BleachProfile/rawIntensity.py +227 -0
- PYME/Analysis/BleachProfile/rollins.py +555 -0
- PYME/Analysis/Colocalisation/__init__.py +27 -0
- PYME/Analysis/Colocalisation/colocScaleDep.py +126 -0
- PYME/Analysis/Colocalisation/correlationCoeffs.py +198 -0
- PYME/Analysis/Colocalisation/distColoc.py +110 -0
- PYME/Analysis/Colocalisation/edtColoc.py +191 -0
- PYME/Analysis/MetaData.py +278 -0
- PYME/Analysis/PSFEst/__init__.py +27 -0
- PYME/Analysis/PSFEst/dec.py +283 -0
- PYME/Analysis/PSFEst/extractImages.py +316 -0
- PYME/Analysis/PSFEst/fit_psf_zernikes.py +194 -0
- PYME/Analysis/PSFEst/psfQuality.py +225 -0
- PYME/Analysis/PSFGen/__init__.py +40 -0
- PYME/Analysis/PSFGen/fourier.py +138 -0
- PYME/Analysis/PSFGen/fourierHNA.py +1108 -0
- PYME/Analysis/PSFGen/fourierHNA2.py +979 -0
- PYME/Analysis/PSFGen/genCRBcurves.py +185 -0
- PYME/Analysis/PSFGen/nijboer_zernike.py +79 -0
- PYME/Analysis/PSFGen/ps_app.cp313-win_amd64.dll.a +0 -0
- PYME/Analysis/PSFGen/ps_app.cp313-win_amd64.pyd +0 -0
- PYME/Analysis/PSFGen/test_ps_app.py +24 -0
- PYME/Analysis/Tracking/__init__.py +3 -0
- PYME/Analysis/Tracking/msd.py +57 -0
- PYME/Analysis/Tracking/trackUtils.py +528 -0
- PYME/Analysis/Tracking/tracking.py +152 -0
- PYME/Analysis/__init__.py +30 -0
- PYME/Analysis/_fithelpers.py +161 -0
- PYME/Analysis/angleFilter.py +287 -0
- PYME/Analysis/annealThresh.py +157 -0
- PYME/Analysis/autoencoder_classifier.py +45 -0
- PYME/Analysis/binAvg.py +144 -0
- PYME/Analysis/composite.py +183 -0
- PYME/Analysis/cramerRao.py +259 -0
- PYME/Analysis/deTile.py +441 -0
- PYME/Analysis/density_filter.py +45 -0
- PYME/Analysis/distributed_pyramid.py +426 -0
- PYME/Analysis/fiducial_matching.py +220 -0
- PYME/Analysis/gen_sCMOS_maps.py +355 -0
- PYME/Analysis/graphing_filters.py +311 -0
- PYME/Analysis/implicitFilter.py +359 -0
- PYME/Analysis/keep_pairs.py +69 -0
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- PYME/tileviewer/templates/roi_list.html +12 -0
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- PYME/util/shmarray/shmTest.py +74 -0
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- PYME/util/webframework.py +365 -0
- PYME/version.py +62 -0
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- python_microscopy-25.11.20.dist-info/RECORD +1278 -0
- python_microscopy-25.11.20.dist-info/WHEEL +4 -0
- python_microscopy-25.11.20.dist-info/entry_points.txt +18 -0
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'''
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Alternative bindings for IDS ueye cameras using the pyueye module.
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See also the uc480 module which talks directly to the ueye DLLs without an
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intermediate python shim. The uc480 implementation has been widely used with
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previous ueye driver versions (e.g. <4.93). At present, there might be issues
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using uc480 with the most recent versions of the ueye SDK, hence this module.
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This module works with ueye driver 4.96.1, and pyueye 4.96.952. Pyueye handles
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some boiler plate ctypes code for us, but in the future we may call the dll
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directly as in uc480.
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# NOTE to developers: pyueye typing is somewhat obnoxious. Some oddities with
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# ctypes pointers (testing for equality of a factory-produced class) makes it
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# safer to use their pointer cast method, and their 'extra functionality' ctypes
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Application notes for specific cameras from the SDK:
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327x:
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Triggering: The internal sensor delay is about 2-3 lines when triggering.
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The line period depends on the selected pixel clock. The higher the
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pixel clock, the smaller the line period is. In overlapping trigger
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mode, the camera timestamp may be overwritten if the maximum exposure
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time is used. In this case, reduce the exposure time by approx. 1%
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'''
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from PYME.Acquire.Hardware.Camera import Camera, MultiviewCameraMixin
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from pyueye import ueye
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import ctypes
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import threading
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import logging
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import queue
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import numpy as np
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import time
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from PYME.Acquire import eventLog as event_log
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logger = logging.getLogger(__name__)
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def GetError(camera_handle):
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error_message = ctypes.c_char_p()
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ueye.is_GetError(camera_handle, error, error_message)
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return error.value, error_message.value
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ROI_LIMITS = {
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'UI306x' : {
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'xmin' : 96,
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'xstep' : 8,
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'ymin' : 32,
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},
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'UI327x' : {
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'xmin' : 256,
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'xstep' : 8,
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},
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'UI324x' : {
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'xmin' : 16,
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'xstep' : 4,
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},
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'UI124x' : {
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'xmin' : 16,
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'xstep' : 4,
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'ymin' : 4,
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}
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}
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# this info is partly from the IDS datasheets that one can request for each camera model
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BaseProps = {
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'UI306x' : {
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# from Steve Hearn (IDS)
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# The default gain of that camera is the absolute minimum gain the camera can deliver.
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# All other gain factors are higher than that. This means, the system gain of 0.125 DN
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# per electron, as specified in the camera test sheet, is the smallest possible value.
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'ElectronsPerCount' : 7.97,
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'ReadNoise' : 6.0,
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'ADOffset' : 10
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},
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'UI327x' : { # calibrated by AESB 2022/04 on S/N 4103211322 running in 12 bit mode, 100 ms integration time.
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'ElectronsPerCount': 2.706, # fitted from Var [ADU^2] vs Mean [ADU] plot (1/slope)
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'ReadNoise' : 2.425, # median of 100 ms varmap from gen_sCMOS_maps.py is 5.883 e-^2. ReadNoise is sigma, i.e. sqrt of that
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'ADOffset' : 7.67, # median of 100 ms dark map from gen_sCMOS_maps.py
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},
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'default' : { # fairly arbitrary values
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'ElectronsPerCount' : 10,
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'ReadNoise' : 20,
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'ADOffset' : 10
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}
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}
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class UEyeCamera(Camera):
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def __init__(self, device_number=0, nbits=8):
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Camera.__init__(self)
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self.initialized = False
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if nbits not in (8, 10, 12):
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raise RuntimeError('Supporting only 8, 10 or 12 bit depth, requested %d bit' % (nbits))
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self.nbits = nbits
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self.h = ueye.HIDS(device_number)
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self.check_success(ueye.is_InitCamera(self.h, None))
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self.initialized = True
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# get serial number
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cam_info = ueye.CAMINFO()
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self.check_success(ueye.is_GetCameraInfo(self.h, cam_info))
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self._serno = cam_info.SerNo.decode()
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# get chip size
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sensor_info = ueye.SENSORINFO()
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self.check_success(ueye.is_GetSensorInfo(self.h, sensor_info))
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self._chip_size = (int(sensor_info.nMaxWidth), int(sensor_info.nMaxHeight)) # convert from c_uint, otherwise trips up JSON dumps
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self.sensor_type = sensor_info.strSensorName.decode().split('x')[0] + 'x'
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# work out the camera base parameters for this sensortype
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self.baseProps = BaseProps.get(self.sensor_type,BaseProps['default'])
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# note that some uEye cameras have a sensor size which exceeds the 'usable' ROI
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self.SetROI(0, 0, self._chip_size[0], self._chip_size[1])
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self.check_success(ueye.is_SetColorMode(self.h, getattr(ueye,
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'IS_CM_MONO%d' % self.nbits)))
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# turn off hardware gamma if supported.
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hw_gamma = ueye.is_SetHardwareGamma(self.h, ueye.int(ueye.IS_GET_HW_SUPPORTED_GAMMA))
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if hw_gamma == ueye.IS_SET_HW_GAMMA_ON: # SetHardwareGamma returns IS_SET_HW_GAMMA_ON (1) if supported
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logger.debug('model supports hardware gamma correction, turning it off')
|
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135
|
+
self.check_success(ueye.is_SetHardwareGamma(self.h, ueye.IS_SET_HW_GAMMA_OFF))
|
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136
|
+
|
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137
|
+
self.SetAcquisitionMode(self.MODE_CONTINUOUS)
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+
self._buffers = []
|
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139
|
+
self.full_buffers = queue.Queue()
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140
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+
self.free_buffers = None
|
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141
|
+
|
|
142
|
+
self.n_full = 0
|
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143
|
+
|
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144
|
+
self.n_accum = 1
|
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145
|
+
self.n_accum_current = 0
|
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146
|
+
|
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147
|
+
self.SetIntegTime(0.1)
|
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148
|
+
self.Init()
|
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149
|
+
|
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150
|
+
def check_success(self, function_return):
|
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151
|
+
if function_return != ueye.IS_SUCCESS:
|
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152
|
+
error, message = GetError(self.h)
|
|
153
|
+
raise RuntimeError('Error %d: %s' % (error, message))
|
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154
|
+
|
|
155
|
+
def Init(self):
|
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156
|
+
self._poll = False
|
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157
|
+
self.poll_loop_active = True
|
|
158
|
+
self.poll_thread = threading.Thread(target=self._poll_loop)
|
|
159
|
+
self.poll_thread.start()
|
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160
|
+
|
|
161
|
+
def GetCCDWidth(self):
|
|
162
|
+
return self._chip_size[0]
|
|
163
|
+
|
|
164
|
+
def GetCCDHeight(self):
|
|
165
|
+
return self._chip_size[1]
|
|
166
|
+
|
|
167
|
+
def InitBuffers(self, n_buffers=50, n_accum_buffers=50):
|
|
168
|
+
for ind in range(n_buffers):
|
|
169
|
+
data = ueye.c_mem_p()
|
|
170
|
+
buffer_id = ueye.int()
|
|
171
|
+
|
|
172
|
+
if self.nbits == 8:
|
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173
|
+
bitsperpix = 8
|
|
174
|
+
bufferdtype = np.uint8
|
|
175
|
+
else: # 10 & 12 bits
|
|
176
|
+
bitsperpix = 16
|
|
177
|
+
bufferdtype = np.uint16
|
|
178
|
+
|
|
179
|
+
self.check_success(ueye.is_AllocImageMem(self.h, self.GetPicWidth(), self.GetPicHeight(), bitsperpix, data, buffer_id))
|
|
180
|
+
self.check_success(ueye.is_AddToSequence(self.h, data, buffer_id))
|
|
181
|
+
|
|
182
|
+
self._buffers.append((buffer_id, data))
|
|
183
|
+
|
|
184
|
+
self.check_success(ueye.is_ImageQueue(self.h, ueye.IS_IMAGE_QUEUE_CMD_INIT, None, ctypes.c_int(0)))
|
|
185
|
+
|
|
186
|
+
self.curr_height, self.curr_width = self.GetPicHeight(), self.GetPicWidth()
|
|
187
|
+
self.transfer_buffer_size = self.curr_height * self.curr_width * bufferdtype().itemsize
|
|
188
|
+
self.transfer_buffer_dtype = bufferdtype
|
|
189
|
+
self.transfer_buffer = ctypes.create_string_buffer(self.transfer_buffer_size)
|
|
190
|
+
self.transfer_buffer_memory_v = ueye.char()
|
|
191
|
+
self.transfer_buffer_memory = ueye._pointer_cast(self.transfer_buffer_memory_v, ueye.char_p)
|
|
192
|
+
self.transfer_buffer_id = ueye.int()
|
|
193
|
+
self.wait_buffer = ueye.IMAGEQUEUEWAITBUFFER()
|
|
194
|
+
self.wait_buffer.timeout = ueye.uint(1000)
|
|
195
|
+
|
|
196
|
+
self.wait_buffer.pnMemId = ueye._pointer_cast(self.transfer_buffer_id, ctypes.POINTER(ueye.int))
|
|
197
|
+
self.wait_buffer.ppcMem = ueye._pointer_cast(self.transfer_buffer_memory, ctypes.POINTER(ueye.char_p))
|
|
198
|
+
|
|
199
|
+
self.free_buffers = queue.Queue()
|
|
200
|
+
# CS: we leave this as uint16 regardless of 8 or 12 bits for now as accumulation
|
|
201
|
+
# of the underlying 12 bit data should be ok (but maybe not?)
|
|
202
|
+
for ind in range(n_accum_buffers):
|
|
203
|
+
self.free_buffers.put(np.zeros([self.GetPicHeight(),
|
|
204
|
+
self.GetPicWidth()], np.uint16))
|
|
205
|
+
self.accum_buffer = self.free_buffers.get()
|
|
206
|
+
self.n_accum_current = 0
|
|
207
|
+
self._poll = True
|
|
208
|
+
|
|
209
|
+
def DestroyBuffers(self):
|
|
210
|
+
self._poll = False # already in StopAq, can probably remove
|
|
211
|
+
self.n_full = 0
|
|
212
|
+
# exit the image queue
|
|
213
|
+
self.check_success(ueye.is_ImageQueue(self.h, ueye.IS_IMAGE_QUEUE_CMD_EXIT, None, ueye.int(0)))
|
|
214
|
+
|
|
215
|
+
# remove all image memories from the sequence list we created
|
|
216
|
+
self.check_success(ueye.is_ClearSequence(self.h))
|
|
217
|
+
|
|
218
|
+
# free up each image memory we allocated on the device
|
|
219
|
+
while len(self._buffers) > 0:
|
|
220
|
+
buffer_id, data = self._buffers.pop()
|
|
221
|
+
self.check_success(ueye.is_FreeImageMem(self.h, data, buffer_id))
|
|
222
|
+
|
|
223
|
+
# destroy free buffers and remove queue of full ones
|
|
224
|
+
self.free_buffers = None
|
|
225
|
+
while not self.full_buffers.empty():
|
|
226
|
+
try:
|
|
227
|
+
self.full_buffers.get_nowait()
|
|
228
|
+
except queue.Empty:
|
|
229
|
+
pass
|
|
230
|
+
|
|
231
|
+
def StartExposure(self):
|
|
232
|
+
logger.debug('StartAq')
|
|
233
|
+
if self._poll:
|
|
234
|
+
# stop, we'll allocate buffers and restart
|
|
235
|
+
self.StopAq()
|
|
236
|
+
# allocate at least 2 seconds of buffers
|
|
237
|
+
buffer_size = int(max(2 * self.GetFPS(), 50))
|
|
238
|
+
self.InitBuffers(buffer_size, buffer_size)
|
|
239
|
+
|
|
240
|
+
self._log_exposure_start()
|
|
241
|
+
if self._cont_mode:
|
|
242
|
+
self.check_success(ueye.is_CaptureVideo(self.h, ueye.IS_DONT_WAIT))
|
|
243
|
+
else:
|
|
244
|
+
self.check_success(ueye.is_FreezeVideo(self.h, ueye.IS_DONT_WAIT))
|
|
245
|
+
return 0
|
|
246
|
+
|
|
247
|
+
def SetAcquisitionMode(self, mode):
|
|
248
|
+
if mode == self.MODE_SINGLE_SHOT:
|
|
249
|
+
self._cont_mode = False
|
|
250
|
+
else:
|
|
251
|
+
self._cont_mode = True
|
|
252
|
+
|
|
253
|
+
def GetAcquisitionMode(self):
|
|
254
|
+
if self._cont_mode:
|
|
255
|
+
return self.MODE_CONTINUOUS
|
|
256
|
+
else:
|
|
257
|
+
return self.MODE_SINGLE_SHOT
|
|
258
|
+
|
|
259
|
+
def ExpReady(self):
|
|
260
|
+
return (self.full_buffers is not None) and (self.n_full > 0)
|
|
261
|
+
|
|
262
|
+
def ExtractColor(self, ch_slice, mode):
|
|
263
|
+
# get nowait to hard-throw an Empty error if we've entered this method
|
|
264
|
+
# and we shouldn't have
|
|
265
|
+
buf = self.full_buffers.get_nowait()
|
|
266
|
+
ch_slice[:] = buf.T
|
|
267
|
+
if self.free_buffers is not None:
|
|
268
|
+
# recycle buffer
|
|
269
|
+
self.free_buffers.put(buf)
|
|
270
|
+
self.n_full -= 1
|
|
271
|
+
|
|
272
|
+
def StopAq(self):
|
|
273
|
+
self._poll = False
|
|
274
|
+
# cancel any ongoing waits (e.g. shutdown)
|
|
275
|
+
self.check_success(ueye.is_ImageQueue(self.h, ueye.IS_IMAGE_QUEUE_CMD_CANCEL_WAIT, None, ueye.int(0)))
|
|
276
|
+
self.check_success(ueye.is_StopLiveVideo(self.h, ueye.IS_WAIT))# ueye.IS_FORCE_VIDEO_STOP))
|
|
277
|
+
self.DestroyBuffers()
|
|
278
|
+
|
|
279
|
+
def _poll_buffer(self):
|
|
280
|
+
try:
|
|
281
|
+
# Query the ID/location of earlier frame in the ring buffer, or wait
|
|
282
|
+
# for the next one. Will fill wait_buffer.nMemId and pcMem
|
|
283
|
+
self.check_success(ueye.is_ImageQueue(self.h, ueye.IS_IMAGE_QUEUE_CMD_WAIT,
|
|
284
|
+
self.wait_buffer, ueye.sizeof(self.wait_buffer)))
|
|
285
|
+
# self.check_success(ueye.is_CopyImageMem(self.h, self.wait_buffer.ppcMem, self.transfer_buffer_id,
|
|
286
|
+
# self.transfer_buffer))#.ctypes.data_as(ctypes.POINTER(ueye.char_p))))
|
|
287
|
+
# self.transfer_buffer.ctypes.data_as(ctypes.POINTER(ctypes.c_uint16))))
|
|
288
|
+
ctypes.memmove(self.transfer_buffer, self.wait_buffer.ppcMem.contents, self.transfer_buffer_size)
|
|
289
|
+
arr = np.frombuffer(self.transfer_buffer, dtype=self.transfer_buffer_dtype)
|
|
290
|
+
arr = arr.reshape((self.curr_height, self.curr_width))
|
|
291
|
+
except RuntimeError as e:
|
|
292
|
+
if 'Error %d' % ueye.IS_OPERATION_ABORTED in str(e):
|
|
293
|
+
# we are shutting down the camera, let the other thread handle
|
|
294
|
+
# clean-up
|
|
295
|
+
logger.debug('ImageQueue wait canceled, returning')
|
|
296
|
+
return
|
|
297
|
+
logger.error(e)
|
|
298
|
+
try:
|
|
299
|
+
self.check_success(ueye.is_UnlockSeqBuf(self.h, self.transfer_buffer_id, None))
|
|
300
|
+
except Exception as e:
|
|
301
|
+
logger.error(e)
|
|
302
|
+
finally:
|
|
303
|
+
return
|
|
304
|
+
|
|
305
|
+
if self.n_accum_current == 0:
|
|
306
|
+
self.accum_buffer[:] = arr
|
|
307
|
+
else:
|
|
308
|
+
self.accum_buffer[:] = self.accum_buffer + arr
|
|
309
|
+
self.n_accum_current += 1
|
|
310
|
+
|
|
311
|
+
self.check_success(ueye.is_UnlockSeqBuf(self.h, self.transfer_buffer_id, None))
|
|
312
|
+
|
|
313
|
+
if self.n_accum_current >= self.n_accum:
|
|
314
|
+
self.full_buffers.put(self.accum_buffer)
|
|
315
|
+
self.accum_buffer = self.free_buffers.get()
|
|
316
|
+
self.n_accum_current = 0
|
|
317
|
+
self.n_full += 1
|
|
318
|
+
|
|
319
|
+
def _poll_loop(self):
|
|
320
|
+
while self.poll_loop_active:
|
|
321
|
+
if self._poll: # only poll if an acquisition is running
|
|
322
|
+
try:
|
|
323
|
+
self._poll_buffer()
|
|
324
|
+
except Exception as e:
|
|
325
|
+
logger.exception(str(e))
|
|
326
|
+
else:
|
|
327
|
+
time.sleep(.05)
|
|
328
|
+
|
|
329
|
+
def CamReady(self):
|
|
330
|
+
"""
|
|
331
|
+
Returns true if the camera is ready (initialized) not really used for
|
|
332
|
+
anything, but might still be checked.
|
|
333
|
+
|
|
334
|
+
Returns
|
|
335
|
+
-------
|
|
336
|
+
bool
|
|
337
|
+
Is the camera ready?
|
|
338
|
+
"""
|
|
339
|
+
|
|
340
|
+
return self.initialized
|
|
341
|
+
|
|
342
|
+
def SetIntegTime(self, integ_time):
|
|
343
|
+
"""
|
|
344
|
+
Sets the exposure time in s. Currently assumes that we will want to go as fast as possible at this exposure time
|
|
345
|
+
and also sets the frame rate to match.
|
|
346
|
+
|
|
347
|
+
Parameters
|
|
348
|
+
----------
|
|
349
|
+
iTime : float
|
|
350
|
+
Exposure time in s
|
|
351
|
+
|
|
352
|
+
Returns
|
|
353
|
+
-------
|
|
354
|
+
None
|
|
355
|
+
|
|
356
|
+
See Also
|
|
357
|
+
--------
|
|
358
|
+
GetIntegTime
|
|
359
|
+
"""
|
|
360
|
+
new_fps = ueye.double()
|
|
361
|
+
self.check_success(ueye.is_SetFrameRate(self.h, 1 / integ_time,
|
|
362
|
+
new_fps))
|
|
363
|
+
# by default, set exposure time to max for this frame rate
|
|
364
|
+
# "If 0 is passed, the exposure time is set to the maximum value of 1/frame rate."
|
|
365
|
+
exposure = ueye.double(0)
|
|
366
|
+
self.check_success(ueye.is_Exposure(self.h,
|
|
367
|
+
ueye.IS_EXPOSURE_CMD_SET_EXPOSURE,
|
|
368
|
+
exposure, ueye.sizeof(exposure)))
|
|
369
|
+
|
|
370
|
+
def GetIntegTime(self):
|
|
371
|
+
"""
|
|
372
|
+
Get Camera object integration time.
|
|
373
|
+
|
|
374
|
+
Returns
|
|
375
|
+
-------
|
|
376
|
+
float
|
|
377
|
+
The exposure time in s
|
|
378
|
+
|
|
379
|
+
See Also
|
|
380
|
+
--------
|
|
381
|
+
SetIntegTime
|
|
382
|
+
"""
|
|
383
|
+
exposure = ueye.double()
|
|
384
|
+
self.check_success(ueye.is_Exposure(self.h,
|
|
385
|
+
ueye.IS_EXPOSURE_CMD_GET_EXPOSURE,
|
|
386
|
+
exposure, ueye.sizeof(exposure)))
|
|
387
|
+
return exposure.value / 1e3
|
|
388
|
+
|
|
389
|
+
|
|
390
|
+
def GetCycleTime(self):
|
|
391
|
+
"""
|
|
392
|
+
Get camera cycle time (1/fps) in seconds (float)
|
|
393
|
+
|
|
394
|
+
Returns
|
|
395
|
+
-------
|
|
396
|
+
float
|
|
397
|
+
Camera cycle time (seconds)
|
|
398
|
+
"""
|
|
399
|
+
return 1 / self.GetFPS()
|
|
400
|
+
|
|
401
|
+
def GetPicWidth(self):
|
|
402
|
+
"""
|
|
403
|
+
Returns the width (in pixels) of the currently selected ROI.
|
|
404
|
+
|
|
405
|
+
Returns
|
|
406
|
+
-------
|
|
407
|
+
int
|
|
408
|
+
Width of ROI (pixels)
|
|
409
|
+
"""
|
|
410
|
+
x0, _, x1, _ = self.GetROI()
|
|
411
|
+
return x1 - x0
|
|
412
|
+
|
|
413
|
+
def GetPicHeight(self):
|
|
414
|
+
"""
|
|
415
|
+
Returns the height (in pixels) of the currently selected ROI
|
|
416
|
+
|
|
417
|
+
Returns
|
|
418
|
+
-------
|
|
419
|
+
int
|
|
420
|
+
Height of ROI (pixels)
|
|
421
|
+
"""
|
|
422
|
+
_, y0, _, y1 = self.GetROI()
|
|
423
|
+
return y1 - y0
|
|
424
|
+
|
|
425
|
+
def SetROI(self, x1, y1, x2, y2):
|
|
426
|
+
"""
|
|
427
|
+
Set the ROI via coordinates (as opposed to via an index).
|
|
428
|
+
|
|
429
|
+
Parameters
|
|
430
|
+
----------
|
|
431
|
+
x1 : int
|
|
432
|
+
Left x-coordinate, zero-indexed
|
|
433
|
+
y1 : int
|
|
434
|
+
Top y-coordinate, zero-indexed
|
|
435
|
+
x2 : int
|
|
436
|
+
Right x-coordinate, (excluded from ROI)
|
|
437
|
+
y2 : int
|
|
438
|
+
Bottom y-coordinate, (excluded from ROI)
|
|
439
|
+
|
|
440
|
+
Returns
|
|
441
|
+
-------
|
|
442
|
+
None
|
|
443
|
+
|
|
444
|
+
|
|
445
|
+
"""
|
|
446
|
+
logger.debug('setting ROI: %d, %d, %d, %d' % (x1, y1, x2, y2))
|
|
447
|
+
limits = ROI_LIMITS[self.sensor_type]
|
|
448
|
+
x1 = max(x1, limits['xmin'])
|
|
449
|
+
y1 = max(y1, limits['ymin'])
|
|
450
|
+
x2 = min(x2, self.GetCCDWidth())
|
|
451
|
+
y2 = min(y2, self.GetCCDHeight())
|
|
452
|
+
|
|
453
|
+
x_change = (x2 - x1) % limits['xstep']
|
|
454
|
+
y_change = (y2 - y1) % limits['ystep']
|
|
455
|
+
x2 -= x_change
|
|
456
|
+
y2 -= y_change
|
|
457
|
+
logger.debug('adjusted ROI: %d, %d, %d, %d' % (x1, y1, x2, y2))
|
|
458
|
+
|
|
459
|
+
aoi = ueye.IS_RECT()
|
|
460
|
+
aoi.s32X = ueye.int(x1)
|
|
461
|
+
aoi.s32Y = ueye.int(y1)
|
|
462
|
+
aoi.s32Width = ueye.int(x2 - x1)
|
|
463
|
+
aoi.s32Height = ueye.int(y2 - y1)
|
|
464
|
+
|
|
465
|
+
self.check_success(ueye.is_AOI(self.h, ueye.IS_AOI_IMAGE_SET_AOI, aoi,
|
|
466
|
+
ueye.sizeof(aoi)))
|
|
467
|
+
# have to set the integration time explicitly after changing AOI
|
|
468
|
+
self.SetIntegTime(self.GetIntegTime())
|
|
469
|
+
|
|
470
|
+
|
|
471
|
+
def GetROI(self):
|
|
472
|
+
"""
|
|
473
|
+
|
|
474
|
+
Returns
|
|
475
|
+
-------
|
|
476
|
+
|
|
477
|
+
The ROI, [x1, y1, x2, y2] in the numpy convention used by SetROI
|
|
478
|
+
|
|
479
|
+
"""
|
|
480
|
+
aoi = ueye.IS_RECT()
|
|
481
|
+
self.check_success(ueye.is_AOI(self.h, ueye.IS_AOI_IMAGE_GET_AOI, aoi,
|
|
482
|
+
ueye.sizeof(aoi)))
|
|
483
|
+
x0, y0 = aoi.s32X.value, aoi.s32Y.value
|
|
484
|
+
return x0, y0, x0 + aoi.s32Width.value, y0 + aoi.s32Height.value
|
|
485
|
+
|
|
486
|
+
|
|
487
|
+
def GetNumImsBuffered(self):
|
|
488
|
+
"""
|
|
489
|
+
Return the number of images in the buffer.
|
|
490
|
+
|
|
491
|
+
Returns
|
|
492
|
+
-------
|
|
493
|
+
int
|
|
494
|
+
Number of images in buffer
|
|
495
|
+
"""
|
|
496
|
+
return self.n_full
|
|
497
|
+
|
|
498
|
+
def GetBufferSize(self):
|
|
499
|
+
"""
|
|
500
|
+
Return the total size of the buffer (in images).
|
|
501
|
+
|
|
502
|
+
Returns
|
|
503
|
+
-------
|
|
504
|
+
int
|
|
505
|
+
Number of images that can be stored in the buffer.
|
|
506
|
+
"""
|
|
507
|
+
if self._poll:
|
|
508
|
+
return len(self._buffers)
|
|
509
|
+
else:
|
|
510
|
+
# if we aren't polling, spoof infinitely large buffer so we don't
|
|
511
|
+
# flag a buffer overflow while we e.g. rebuild the buffers. This
|
|
512
|
+
# makes no functional difference for us, but avoids a spurious
|
|
513
|
+
# warning from frameWrangler about the buffer overflowing.
|
|
514
|
+
return np.iinfo(np.int32).max
|
|
515
|
+
|
|
516
|
+
def GetCCDTemp(self):
|
|
517
|
+
di = self._GetDeviceInfo()
|
|
518
|
+
tword = di.infoDevHeartbeat.wTemperature.value
|
|
519
|
+
# from IDS docs:
|
|
520
|
+
# wTemperature
|
|
521
|
+
# Camera temperature in degrees Celsius
|
|
522
|
+
# Bits 15: algebraic sign
|
|
523
|
+
# Bits 14...11: filled according to algebraic sign
|
|
524
|
+
# Bits 10...4: temperature (places before the decimal point)
|
|
525
|
+
# Bits 3...0: temperature (places after the decimal point)
|
|
526
|
+
tempfloat = 1.0*(tword >> 4 & 0b1111111) + 0.1 * (tword & 0b1111)
|
|
527
|
+
if (tword >> 15):
|
|
528
|
+
tempfloat = -1.0 * tempfloat
|
|
529
|
+
return tempfloat
|
|
530
|
+
|
|
531
|
+
@property
|
|
532
|
+
def noise_properties(self):
|
|
533
|
+
try: # try and get noise properties following the current convention
|
|
534
|
+
return super().noise_properties
|
|
535
|
+
except RuntimeError: # fall back loudly on "base properties"
|
|
536
|
+
logger.exception('Noise properties not set up for this camera, falling back on values which are likely wrong')
|
|
537
|
+
return {'ElectronsPerCount': self.baseProps['ElectronsPerCount']/self.GetGainFactor(),
|
|
538
|
+
'ReadNoise': self.baseProps['ReadNoise'],
|
|
539
|
+
'ADOffset': self.baseProps['ADOffset'],
|
|
540
|
+
'SaturationThreshold': 2 ** self.nbits - 1}
|
|
541
|
+
|
|
542
|
+
@property
|
|
543
|
+
def _gain_mode(self):
|
|
544
|
+
return '%d-bit' % self.nbits
|
|
545
|
+
|
|
546
|
+
|
|
547
|
+
# @property
|
|
548
|
+
# def noise_properties(self):
|
|
549
|
+
# """
|
|
550
|
+
|
|
551
|
+
# Returns
|
|
552
|
+
# -------
|
|
553
|
+
|
|
554
|
+
# a dictionary with the following entries:
|
|
555
|
+
|
|
556
|
+
# 'ReadNoise' : camera read noise as a standard deviation in units of photoelectrons (e-)
|
|
557
|
+
# 'ElectronsPerCount' : AD conversion factor - how many electrons per ADU
|
|
558
|
+
# 'NoiseFactor' : excess (multiplicative) noise factor 1.44 for EMCCD, 1 for standard CCD/sCMOS. See
|
|
559
|
+
# doi: 10.1109/TED.2003.813462
|
|
560
|
+
|
|
561
|
+
# and optionally
|
|
562
|
+
# 'ADOffset' : the dark level (in ADU)
|
|
563
|
+
# 'DefaultEMGain' : a sensible EM gain setting to use for localization recording
|
|
564
|
+
# 'SaturationThreshold' : the full well capacity (in ADU)
|
|
565
|
+
|
|
566
|
+
# """
|
|
567
|
+
|
|
568
|
+
# return {
|
|
569
|
+
# 'ReadNoise': 1,
|
|
570
|
+
# 'ElectronsPerCount': 1,
|
|
571
|
+
# 'NoiseFactor': 1,
|
|
572
|
+
# 'ADOffset': 0,
|
|
573
|
+
# 'SaturationThreshold': 2 ** self.nbits - 1
|
|
574
|
+
# }
|
|
575
|
+
|
|
576
|
+
def GetFPS(self):
|
|
577
|
+
"""
|
|
578
|
+
Get the camera frame rate in frames per second (float).
|
|
579
|
+
|
|
580
|
+
Returns
|
|
581
|
+
-------
|
|
582
|
+
float
|
|
583
|
+
Camera frame rate (frames per second)
|
|
584
|
+
"""
|
|
585
|
+
fps = ueye.double()
|
|
586
|
+
self.check_success(ueye.is_GetFramesPerSecond(self.h, fps))
|
|
587
|
+
return fps.value
|
|
588
|
+
|
|
589
|
+
def GetSerialNumber(self):
|
|
590
|
+
return self._serno
|
|
591
|
+
|
|
592
|
+
def GetName(self):
|
|
593
|
+
return 'ueye-camera'
|
|
594
|
+
|
|
595
|
+
def GetHeadModel(self):
|
|
596
|
+
return self.sensor_type
|
|
597
|
+
|
|
598
|
+
def SetGain(self, gain=100):
|
|
599
|
+
self.check_success(ueye.is_SetHardwareGain(self.h, gain, ueye.IS_IGNORE_PARAMETER,
|
|
600
|
+
ueye.IS_IGNORE_PARAMETER, ueye.IS_IGNORE_PARAMETER))
|
|
601
|
+
|
|
602
|
+
def GetGain(self):
|
|
603
|
+
ret = ueye.is_SetHardwareGain(self.h, ueye.IS_GET_MASTER_GAIN,
|
|
604
|
+
ueye.IS_IGNORE_PARAMETER, ueye.IS_IGNORE_PARAMETER, ueye.IS_IGNORE_PARAMETER)
|
|
605
|
+
return ret
|
|
606
|
+
|
|
607
|
+
def GetGainFactor(self):
|
|
608
|
+
gain = self.GetGain()
|
|
609
|
+
ret = ueye.is_SetHWGainFactor(self.h, ueye.IS_INQUIRE_MASTER_GAIN_FACTOR, gain)
|
|
610
|
+
return 0.01*ret
|
|
611
|
+
|
|
612
|
+
def SetOutputTrigger(self, mode, delay=0, width=0.0001, positive=True):
|
|
613
|
+
"""
|
|
614
|
+
Set output trigger of the camera. Currently hard-coded to use GPIO1
|
|
615
|
+
|
|
616
|
+
Parameters
|
|
617
|
+
----------
|
|
618
|
+
mode : str
|
|
619
|
+
Currently supported modes include:
|
|
620
|
+
low: constant TTL low
|
|
621
|
+
high: constant TTL high
|
|
622
|
+
flash: goes TTL high during exposure. If 0 is passed, the flash
|
|
623
|
+
output will be active until the end of the exposure time.
|
|
624
|
+
With global start shutter this is the time until the end of
|
|
625
|
+
exposure for the first row.
|
|
626
|
+
delay : float, optional
|
|
627
|
+
delay after trigger event, in seconds, to emit TTL high (assuming
|
|
628
|
+
posiive polarity), by default 0 s.
|
|
629
|
+
width : float, optional
|
|
630
|
+
TTL high pulse width, in seconds, by default 0.0001 s, or 0.1 ms
|
|
631
|
+
positive : bool, optional
|
|
632
|
+
CURRENTLY IGNORED Sets polarity of the output trigger to positive
|
|
633
|
+
(True) or negative (False). True, by default.
|
|
634
|
+
|
|
635
|
+
"""
|
|
636
|
+
# set GPIO1 to be output flash
|
|
637
|
+
m = ueye.int(ueye.IO_FLASH_MODE_GPIO_1)
|
|
638
|
+
self.check_success(ueye.is_IO(self.h,
|
|
639
|
+
ueye.IS_IO_CMD_FLASH_SET_MODE,
|
|
640
|
+
m, ueye.sizeof(m)))
|
|
641
|
+
|
|
642
|
+
if mode == 'high':
|
|
643
|
+
mode = ueye.int(ueye.IO_FLASH_MODE_CONSTANT_HIGH)
|
|
644
|
+
self.check_success(ueye.is_IO(self.h,
|
|
645
|
+
ueye.IS_IO_CMD_FLASH_SET_MODE,
|
|
646
|
+
mode, ueye.sizeof(mode)))
|
|
647
|
+
return
|
|
648
|
+
elif mode == 'low':
|
|
649
|
+
mode = ueye.int(ueye.IO_FLASH_MODE_CONSTANT_LOW)
|
|
650
|
+
self.check_success(ueye.is_IO(self.h,
|
|
651
|
+
ueye.IS_IO_CMD_FLASH_SET_MODE,
|
|
652
|
+
mode, ueye.sizeof(mode)))
|
|
653
|
+
return
|
|
654
|
+
|
|
655
|
+
if mode =='flash':
|
|
656
|
+
mode = ueye.int(ueye.IO_FLASH_MODE_FREERUN_HI_ACTIVE)
|
|
657
|
+
self.check_success(ueye.is_IO(self.h,
|
|
658
|
+
ueye.IS_IO_CMD_FLASH_SET_MODE,
|
|
659
|
+
mode, ueye.sizeof(mode)))
|
|
660
|
+
else:
|
|
661
|
+
raise RuntimeError('Unsupported output trigger mode: %s' % mode)
|
|
662
|
+
|
|
663
|
+
fp = ueye.IO_FLASH_PARAMS()
|
|
664
|
+
fp.s32Delay = ueye.c_int(int(delay * 1e6)) # [s] -> [us]
|
|
665
|
+
fp.u32Duration = ueye.c_uint(int(width * 1e6)) # [s] -> [us]
|
|
666
|
+
self.check_success(ueye.is_IO(self.h,
|
|
667
|
+
ueye.IS_IO_CMD_FLASH_SET_PARAMS,
|
|
668
|
+
fp, ueye.sizeof(fp)))
|
|
669
|
+
|
|
670
|
+
#### Some extra functions for this camera
|
|
671
|
+
|
|
672
|
+
def _GetDeviceInfo(self):
|
|
673
|
+
dev_info = ueye.IS_DEVICE_INFO()
|
|
674
|
+
self.check_success(ueye.is_DeviceInfo(self.h,ueye.IS_DEVICE_INFO_CMD_GET_DEVICE_INFO,
|
|
675
|
+
dev_info,ueye.sizeof(dev_info)))
|
|
676
|
+
return dev_info
|
|
677
|
+
|
|
678
|
+
def GetGlobalFlashSettings(self):
|
|
679
|
+
"""Query current global 'flash', i.e. output trigger settings
|
|
680
|
+
|
|
681
|
+
Returns
|
|
682
|
+
-------
|
|
683
|
+
delay: float
|
|
684
|
+
[s]
|
|
685
|
+
width: float
|
|
686
|
+
duration of TTL in [s]
|
|
687
|
+
|
|
688
|
+
"""
|
|
689
|
+
fp = ueye.IO_FLASH_PARAMS()
|
|
690
|
+
self.check_success(ueye.is_IO(self.h,
|
|
691
|
+
ueye.IS_IO_CMD_FLASH_GET_GLOBAL_PARAMS,
|
|
692
|
+
fp, ueye.sizeof(fp)))
|
|
693
|
+
return fp.s32Delay.value / 1e6, fp.u32Duration.value / 1e6
|
|
694
|
+
|
|
695
|
+
|
|
696
|
+
#TODO - replace MultiviewCameraMixin with a Multiview wrapper so that we don't need to have explicit multiview versions of all cameras.
|
|
697
|
+
class MultiviewUEye(MultiviewCameraMixin, UEyeCamera):
|
|
698
|
+
def __init__(self, camNum, multiview_info, nbits=8):
|
|
699
|
+
UEyeCamera.__init__(self, camNum, nbits)
|
|
700
|
+
# default to the whole chip
|
|
701
|
+
default_roi = dict(xi=0, xf=int(self._chip_size[0]), yi=0, yf=int(self._chip_size[1]))
|
|
702
|
+
MultiviewCameraMixin.__init__(self, multiview_info, default_roi, UEyeCamera)
|