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/recipes/pointcloud.py +510 -0
- PYME/recipes/processing.py +2954 -0
- PYME/recipes/pyramid.py +206 -0
- PYME/recipes/recipe.py +965 -0
- PYME/recipes/recipeGui.py +1029 -0
- PYME/recipes/recipeLayout.py +499 -0
- PYME/recipes/runRecipe.py +140 -0
- PYME/recipes/setup.py +37 -0
- PYME/recipes/simulation.py +91 -0
- PYME/recipes/skfilters.py +143 -0
- PYME/recipes/surface_fitting.py +776 -0
- PYME/recipes/tablefilters.py +275 -0
- PYME/recipes/tracking.py +343 -0
- PYME/recipes/traits.py +157 -0
- PYME/recipes/vertical_recipe_display.py +373 -0
- PYME/resources/__init__.py +23 -0
- PYME/resources/config_template/distributor.yaml +14 -0
- PYME/resources/config_template/nodeserver.yaml +15 -0
- PYME/resources/icons/LUT.png +0 -0
- PYME/resources/icons/YSM_Shield.png +0 -0
- PYME/resources/icons/YSM_logo.png +0 -0
- PYME/resources/icons/arrow.png +0 -0
- PYME/resources/icons/crosshairs.png +0 -0
- PYME/resources/icons/line_select.png +0 -0
- PYME/resources/icons/logo_fmhs.png +0 -0
- PYME/resources/icons/media-playback-pause.png +0 -0
- PYME/resources/icons/media-playback-start.png +0 -0
- PYME/resources/icons/media-skip-backward.png +0 -0
- PYME/resources/icons/media-skip-forward.png +0 -0
- PYME/resources/icons/mesh.png +0 -0
- PYME/resources/icons/mesh.svg +28 -0
- PYME/resources/icons/pmacquire.icns +0 -0
- PYME/resources/icons/pmacquire.ico +0 -0
- PYME/resources/icons/pmanal.icns +0 -0
- PYME/resources/icons/pmanal.ico +0 -0
- PYME/resources/icons/pmvis.icns +0 -0
- PYME/resources/icons/pmvis.ico +0 -0
- PYME/resources/icons/points.png +0 -0
- PYME/resources/icons/points.svg +16 -0
- PYME/resources/icons/pymeLogo.png +0 -0
- PYME/resources/icons/rect_select.png +0 -0
- PYME/resources/icons/squiggle_select.png +0 -0
- PYME/resources/icons/text3800.icns +0 -0
- PYME/resources/icons/text3800.ico +0 -0
- PYME/resources/icons/text3800.png +0 -0
- PYME/resources/icons/text3800.tif +0 -0
- PYME/resources/icons/text5377.icns +0 -0
- PYME/resources/icons/text5377.ico +0 -0
- PYME/resources/icons/text5377.png +0 -0
- PYME/resources/icons/tracks.png +0 -0
- PYME/resources/icons/tracks.svg +19 -0
- PYME/resources/icons/view-front.png +0 -0
- PYME/resources/icons/view-home.png +0 -0
- PYME/resources/icons/view-right.png +0 -0
- PYME/resources/icons/view-top.png +0 -0
- PYME/resources/test_datasets/README.md +8 -0
- PYME/resources/test_datasets/t_im.tif +0 -0
- PYME/resources/test_datasets/test_csv.csv +4282 -0
- PYME/resources/test_datasets/test_hdf.hdf +0 -0
- PYME/resources/web/rule_inline.html +21 -0
- PYME/resources/web/ruleserver.html +75 -0
- PYME/resources/web/static/bootstrap.min.js +7 -0
- PYME/resources/web/static/cluster.css +137 -0
- PYME/resources/web/static/css/bootstrap-theme.css +587 -0
- PYME/resources/web/static/css/bootstrap-theme.min.css +6 -0
- PYME/resources/web/static/css/bootstrap.css +6757 -0
- PYME/resources/web/static/css/bootstrap.min.css +6 -0
- PYME/resources/web/static/css/flat_design_colors_full.css +306 -0
- PYME/resources/web/static/css/recipe_editor.css +106 -0
- PYME/resources/web/static/dashboard.css +106 -0
- PYME/resources/web/static/fileselector.js +77 -0
- PYME/resources/web/static/fonts/glyphicons-halflings-regular.eot +0 -0
- PYME/resources/web/static/fonts/glyphicons-halflings-regular.svg +288 -0
- PYME/resources/web/static/fonts/glyphicons-halflings-regular.ttf +0 -0
- PYME/resources/web/static/fonts/glyphicons-halflings-regular.woff +0 -0
- PYME/resources/web/static/fonts/glyphicons-halflings-regular.woff2 +0 -0
- PYME/resources/web/static/images/osd_flat/LICENSE.txt +116 -0
- PYME/resources/web/static/images/osd_flat/README.md +9 -0
- PYME/resources/web/static/images/osd_flat/fullpage_grouphover.png +0 -0
- PYME/resources/web/static/images/osd_flat/fullpage_hover.png +0 -0
- PYME/resources/web/static/images/osd_flat/fullpage_pressed.png +0 -0
- PYME/resources/web/static/images/osd_flat/fullpage_rest.png +0 -0
- PYME/resources/web/static/images/osd_flat/home_grouphover.png +0 -0
- PYME/resources/web/static/images/osd_flat/home_hover.png +0 -0
- PYME/resources/web/static/images/osd_flat/home_pressed.png +0 -0
- PYME/resources/web/static/images/osd_flat/home_rest.png +0 -0
- PYME/resources/web/static/images/osd_flat/next_grouphover.png +0 -0
- PYME/resources/web/static/images/osd_flat/next_hover.png +0 -0
- PYME/resources/web/static/images/osd_flat/next_pressed.png +0 -0
- PYME/resources/web/static/images/osd_flat/next_rest.png +0 -0
- PYME/resources/web/static/images/osd_flat/previous_grouphover.png +0 -0
- PYME/resources/web/static/images/osd_flat/previous_hover.png +0 -0
- PYME/resources/web/static/images/osd_flat/previous_pressed.png +0 -0
- PYME/resources/web/static/images/osd_flat/previous_rest.png +0 -0
- PYME/resources/web/static/images/osd_flat/rotateleft_grouphover.png +0 -0
- PYME/resources/web/static/images/osd_flat/rotateleft_hover.png +0 -0
- PYME/resources/web/static/images/osd_flat/rotateleft_pressed.png +0 -0
- PYME/resources/web/static/images/osd_flat/rotateleft_rest.png +0 -0
- PYME/resources/web/static/images/osd_flat/rotateright_grouphover.png +0 -0
- PYME/resources/web/static/images/osd_flat/rotateright_hover.png +0 -0
- PYME/resources/web/static/images/osd_flat/rotateright_pressed.png +0 -0
- PYME/resources/web/static/images/osd_flat/rotateright_rest.png +0 -0
- PYME/resources/web/static/images/osd_flat/zoomin_grouphover.png +0 -0
- PYME/resources/web/static/images/osd_flat/zoomin_hover.png +0 -0
- PYME/resources/web/static/images/osd_flat/zoomin_pressed.png +0 -0
- PYME/resources/web/static/images/osd_flat/zoomin_rest.png +0 -0
- PYME/resources/web/static/images/osd_flat/zoomout_grouphover.png +0 -0
- PYME/resources/web/static/images/osd_flat/zoomout_hover.png +0 -0
- PYME/resources/web/static/images/osd_flat/zoomout_pressed.png +0 -0
- PYME/resources/web/static/images/osd_flat/zoomout_rest.png +0 -0
- PYME/resources/web/static/jigna-vue-bare.js +1395 -0
- PYME/resources/web/static/jquery.min.js +2 -0
- PYME/resources/web/static/jstree.min.js +6 -0
- PYME/resources/web/static/openSeadragonGL.js +102 -0
- PYME/resources/web/static/openseadragon-svg-overlay.js +103 -0
- PYME/resources/web/static/openseadragon-viewerinputhook.min.js +6 -0
- PYME/resources/web/static/openseadragon.min.js +9 -0
- PYME/resources/web/static/recipe_editor.js +119 -0
- PYME/resources/web/static/shaders/fragment/lut.glsl +20 -0
- PYME/resources/web/static/shaders/fragment/none.glsl +17 -0
- PYME/resources/web/static/shaders/fragment/outline.glsl +43 -0
- PYME/resources/web/static/shaders/fragment/rect.glsl +7 -0
- PYME/resources/web/static/shaders/fragment/sobel3.glsl +71 -0
- PYME/resources/web/static/shaders/fragment/white.glsl +4 -0
- PYME/resources/web/static/shaders/vertex/rect.glsl +22 -0
- PYME/resources/web/static/shaders/vertex/square.glsl +9 -0
- PYME/resources/web/static/utils.js +3 -0
- PYME/resources/web/static/viaWebGL.js +217 -0
- PYME/setup.py +109 -0
- PYME/setup_exe.py +57 -0
- PYME/simulation/__init__.py +0 -0
- PYME/simulation/locify.py +319 -0
- PYME/simulation/pointsets.py +279 -0
- PYME/simulation/wormlike.py +99 -0
- PYME/simulation/wormlike2.py +198 -0
- PYME/simulation/wormlike3.py +197 -0
- PYME/simulation/wormlike_curled.py +104 -0
- PYME/tileviewer/__init__.py +0 -0
- PYME/tileviewer/templates/roi_list.html +12 -0
- PYME/tileviewer/templates/tileviewer.html +247 -0
- PYME/tileviewer/tileviewer.py +207 -0
- PYME/ui/AUIFrame.py +279 -0
- PYME/ui/MetadataTree.py +469 -0
- PYME/ui/__init__.py +4 -0
- PYME/ui/about_dlg.py +29 -0
- PYME/ui/autoFoldPanel.py +643 -0
- PYME/ui/cascading_layout.py +45 -0
- PYME/ui/crop_dialog.py +145 -0
- PYME/ui/custom_traits_editors.py +508 -0
- PYME/ui/editFilterDialog.py +80 -0
- PYME/ui/editList.py +40 -0
- PYME/ui/fastGraph.py +240 -0
- PYME/ui/filterPane.py +348 -0
- PYME/ui/histLimits.py +543 -0
- PYME/ui/layerFoldPanel.py +232 -0
- PYME/ui/manualFoldPanel.py +870 -0
- PYME/ui/mytimer.py +116 -0
- PYME/ui/patch_traitsui.py +151 -0
- PYME/ui/progress.py +160 -0
- PYME/ui/recArrayView.py +145 -0
- PYME/ui/selection.py +71 -0
- PYME/ui/shell.py +37 -0
- PYME/ui/traitsui_constants.py +91 -0
- PYME/ui/wx_compat.py +43 -0
- PYME/update_version.py +159 -0
- PYME/util/__init__.py +3 -0
- PYME/util/authenticate.py +164 -0
- PYME/util/execfile.py +21 -0
- PYME/util/fProfile/__init__.py +1 -0
- PYME/util/fProfile/convertProfile.py +117 -0
- PYME/util/fProfile/fProfile.py +162 -0
- PYME/util/fProfile/html/404.html +60 -0
- PYME/util/fProfile/html/css/main.css +258 -0
- PYME/util/fProfile/html/css/normalize.css +427 -0
- PYME/util/fProfile/html/css/normalize.min.css +1 -0
- PYME/util/fProfile/html/index.html +64 -0
- PYME/util/fProfile/html/js/main.js +492 -0
- PYME/util/fProfile/html/js/plugins.js +24 -0
- PYME/util/fProfile/html/js/vendor/crossfilter.min.js +1 -0
- PYME/util/fProfile/html/js/vendor/jquery-1.11.2.min.js +4 -0
- PYME/util/fProfile/html/js/vendor/modernizr-2.8.3.min.js +4 -0
- PYME/util/fProfile/html/js/vendor/tinycolor-min.js +4 -0
- PYME/util/fProfile/viewProfile.py +30 -0
- PYME/util/install_dependencies.py +95 -0
- PYME/util/log_verbosity.py +11 -0
- PYME/util/mProfile/__init__.py +1 -0
- PYME/util/mProfile/colorize_db_t.py +297 -0
- PYME/util/mProfile/mProfile.py +164 -0
- PYME/util/mProfile/p.py +101 -0
- PYME/util/mProfile/tProfile.py +165 -0
- PYME/util/pymelauncher.py +47 -0
- PYME/util/shmarray/__init__.py +0 -0
- PYME/util/shmarray/shmTest.py +74 -0
- PYME/util/shmarray/shmarray.py +165 -0
- PYME/util/webframework.py +365 -0
- PYME/version.py +62 -0
- python_microscopy-25.11.20.dist-info/METADATA +68 -0
- 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
PYME/recipes/traits.py
ADDED
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@@ -0,0 +1,157 @@
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""" Shim to give us a uniform way of importing traits (and replacing them if needed in the future)"""
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from __future__ import absolute_import
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import numpy as np
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import logging
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logger = logging.getLogger(__name__)
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try:
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from enthought.traits.api import *
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except ImportError:
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from traits.api import *
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# definitions below have been adapted based on https://docs.enthought.com/traits-futures/0.2/_modules/traits/trait_types.html
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# these Dict have been deprecated for a while and need to be defined here for newer traits.api modules
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# FIXME - change usage within code and remove aliases
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DictStrAny = Dict(str, Any)
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DictStrStr = Dict(str, str)
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DictStrList = Dict(str, list)
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DictStrFloat = Dict(str, float)
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DictStrBool = Dict(str, bool)
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# -- List Traits ------- same as dict traits; we define only a subset of all possible List traits here
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# FIXME - change usage within code and remove aliases
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ListInt = List(int)
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ListFloat = List(float)
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ListStr = List(str)
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ListUnicode = List(str)
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ListComplex = List(complex)
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ListBool = List(bool)
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#Monkey-patch traits so that editors need enter / focus change to update by default
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from traits import trait_types
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trait_types.TraitType.auto_set = False
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trait_types.TraitType.enter_set = True
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class Input(CStr):
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fast_validate = None
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def validate(self, object, name, value):
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value = CStr.validate(self, object, name, value)
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if getattr(object, '_initial_set', False):
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# defer validation when performed in constructor to avoid detection of spurious circular references with default values (see issue #695)
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# make sure we're not assigning to an output of this module
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mod_outputs = getattr(object, 'outputs', [])
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if value in mod_outputs:
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# trying to assign input to output
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raise TraitError('Assigning "%s" to input "%s" would result in a circular reference (value is in module outputs).' % (value, name))
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# make sure we are not assigning to any downstream outputs
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recipe = getattr(object, '_parent', None)
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if recipe is not None:
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if value in recipe.downstream_outputs(list(object.outputs)):
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# trying to assign input to output
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raise TraitError('Assigning "%s" to input "%s" would result in a circular reference (value is in downstream outputs).' % (value, name))
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return value
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# class InputList(ListStr):
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# fast_validate=None
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#
|
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63
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# def validate(self, object, name, value):
|
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# value = ListStr.validate(self, object, name, value)
|
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65
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#
|
|
66
|
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# if getattr(object, '_initial_set', False):
|
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# # defer validation when performed in constructor to avoid detection of spurious circular references with default values (see issue #695)
|
|
68
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#
|
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69
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# for v in value:
|
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70
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+
# # make sure we're not assigning to an output of this module
|
|
71
|
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# mod_outputs = getattr(object, 'outputs', [])
|
|
72
|
+
# if v in mod_outputs:
|
|
73
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# # trying to assign input to output
|
|
74
|
+
# raise TraitError(
|
|
75
|
+
# 'Assigning "%s" to input "%s" would result in a circular reference (value is in module outputs).' % (
|
|
76
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+
# v, name))
|
|
77
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#
|
|
78
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# # make sure we are not assigning to any downstream outputs
|
|
79
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+
# recipe = getattr(object, '_parent', None)
|
|
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|
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# if recipe is not None:
|
|
81
|
+
# if v in recipe.downstream_outputs(list(object.outputs)):
|
|
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# # trying to assign input to output
|
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83
|
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# raise TraitError(
|
|
84
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# 'Assigning "%s" to input "%s" would result in a circular reference (value is in downstream outputs).' % (
|
|
85
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+
# v, name))
|
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#
|
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87
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# return value
|
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88
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#
|
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89
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91
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class Output(CStr):
|
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fast_validate = None
|
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+
|
|
95
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def validate(self, object, name, value):
|
|
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value = CStr.validate(self, object, name, value)
|
|
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+
|
|
98
|
+
if getattr(object, '_initial_set', False):
|
|
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+
# defer validation when performed in constructor to avoid detection of spurious circular references with default values (see issue #695)
|
|
100
|
+
|
|
101
|
+
# make sure we're not assigning to an input of this module
|
|
102
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+
mod_inputs = getattr(object, 'inputs', [])
|
|
103
|
+
if value in mod_inputs:
|
|
104
|
+
# trying to assign input to output
|
|
105
|
+
raise TraitError(
|
|
106
|
+
'Assigning "%s" to output "%s" would result in a circular reference (value is in module inputs).' % (value, name))
|
|
107
|
+
|
|
108
|
+
|
|
109
|
+
# make sure we are not assigning to any downstream outputs
|
|
110
|
+
recipe = getattr(object, '_parent', None)
|
|
111
|
+
if recipe is not None:
|
|
112
|
+
if value in recipe.upstream_inputs(list(object.inputs)):
|
|
113
|
+
# trying to assign input to output
|
|
114
|
+
raise TraitError(
|
|
115
|
+
'Assigning "%s" to output "%s" would result in a circular reference (value is in upstream inputs).' % (
|
|
116
|
+
value, name))
|
|
117
|
+
|
|
118
|
+
|
|
119
|
+
return value
|
|
120
|
+
|
|
121
|
+
class FileOrURI(File):
|
|
122
|
+
'''Custom trait for files that can either be on disk or on the cluster
|
|
123
|
+
|
|
124
|
+
Used for calibration data such as PSFs and shiftmaps which are static across multiple invocations of a recipe.
|
|
125
|
+
|
|
126
|
+
Disables validation to work around traitsUI issues
|
|
127
|
+
'''
|
|
128
|
+
|
|
129
|
+
info_text = 'a local file name or pyme-cluster:// URI'
|
|
130
|
+
|
|
131
|
+
def __init__(self, *args, **kwargs):
|
|
132
|
+
kwargs['exists'] = True # file must exist
|
|
133
|
+
File.__init__(self, *args, **kwargs)
|
|
134
|
+
|
|
135
|
+
def validate(self, object, name, value):
|
|
136
|
+
# Traitsui hangs up if a file doesn't validate correctly and doesn't allow selecting a replacement - disable validation for now :(
|
|
137
|
+
# FIXME
|
|
138
|
+
return value
|
|
139
|
+
|
|
140
|
+
class _IntFloat(BaseFloat):
|
|
141
|
+
# WARNING: This is a fudge used in skimage wrapping. It should not be used unless absolutely necessary and might dissappear if and when we
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# find a better replacement. Has a 'private' (leading underscore) name to discourage use.
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# TODO - Can we inherit from Float instead to eliminate the `set()` method?
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default_value = 0.0
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info_text = 'Frankenstein to deal with automatic introspection'
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def set(self, obj, name, value):
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setattr(self, name, value)
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self.set_value(obj, name, value)
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def get(self, obj, name):
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val = self.get_value(obj, name)
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if val is None:
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val = self.default_value
|
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if val == np.round(val):
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val = int(val)
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return val
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@@ -0,0 +1,373 @@
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1
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from . import recipeLayout
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2
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+
import wx
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3
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+
import numpy as np
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4
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+
from PYME.IO import tabular
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5
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+
|
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6
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+
import logging
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7
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+
logger = logging.getLogger(__name__)
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8
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+
|
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9
|
+
# class RecipeDisplayPanel(wx.ScrolledWindow):
|
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10
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+
# def __init__(self, *args, **kwargs):
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11
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+
# wx.ScrolledWindow.__init__(self, *args, **kwargs)
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12
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+
|
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13
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+
class RecipeDisplayPanel(wx.Panel):
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14
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+
def __init__(self, *args, **kwargs):
|
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15
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+
wx.Panel.__init__(self, *args,**kwargs)
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16
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+
self.recipe = None
|
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17
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+
|
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18
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+
self.output_positions = {}
|
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19
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+
self.input_positions = {}
|
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20
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+
self.data_positions = {}
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21
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+
self.data_positions_in = {}
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22
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+
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23
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+
self.input_target_panes = {}
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24
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+
self.output_source_panes = {}
|
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25
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+
self.data_panes = {}
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26
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+
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27
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+
self.orderd = []
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28
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+
self.x0s = {}
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29
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+
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30
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+
self.cols = {}
|
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31
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self._pens = {}
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32
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+
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33
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+
self.fp = None
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34
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+
|
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35
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+
self._traits_views = []
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36
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+
|
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37
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+
self._layout_valid = False
|
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38
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+
|
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39
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+
#self.SetMinSize((200, 500))
|
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40
|
+
|
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41
|
+
#self.SetScrollRate(0, 20)
|
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42
|
+
#self.ShowScrollbars(wx.SHOW_SB_DEFAULT, wx.SHOW_SB_ALWAYS)
|
|
43
|
+
|
|
44
|
+
self.Bind(wx.EVT_PAINT, self.OnPaint)
|
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45
|
+
self.Bind(wx.EVT_IDLE, self.OnIdle)
|
|
46
|
+
|
|
47
|
+
def _col(self,node):
|
|
48
|
+
dark_mode = False
|
|
49
|
+
|
|
50
|
+
try:
|
|
51
|
+
dark_mode = wx.SystemSettings.GetAppearance().IsDark()
|
|
52
|
+
except AttributeError:
|
|
53
|
+
# wx < 4.1 doesn't have GetAppearance
|
|
54
|
+
pass
|
|
55
|
+
|
|
56
|
+
if dark_mode:
|
|
57
|
+
factor = 1.0
|
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58
|
+
else:
|
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59
|
+
factor = 0.7
|
|
60
|
+
|
|
61
|
+
import matplotlib.pyplot as plt
|
|
62
|
+
if not node in self.cols.keys():
|
|
63
|
+
self.cols[node] = factor*np.array(plt.cm.hsv(np.random.rand()))
|
|
64
|
+
#cols[node] = 0.7 * np.array(plt.cm.hsv((_col.n_col % len(data_nodes)) / float(len(data_nodes))))
|
|
65
|
+
#return self.cols[node]
|
|
66
|
+
|
|
67
|
+
c = self.cols[node]
|
|
68
|
+
if self.recipe.failed and not node in self.recipe.namespace.keys():
|
|
69
|
+
c = 0.2 * c + 0.8 * 0.5
|
|
70
|
+
return np.array([.9,.6,.6,1.])
|
|
71
|
+
|
|
72
|
+
return c
|
|
73
|
+
|
|
74
|
+
def SetRecipe(self, recipe):
|
|
75
|
+
self.recipe = recipe
|
|
76
|
+
self.recipe.recipe_changed.connect(self.invalidate_layout)
|
|
77
|
+
self.recipe.recipe_failed.connect(self.invalidate_layout)
|
|
78
|
+
self.invalidate_layout()
|
|
79
|
+
self.recipe.recipe_executed.connect(self._update_n_events)
|
|
80
|
+
|
|
81
|
+
def _refr(self, **kwargs):
|
|
82
|
+
#print 'p_'
|
|
83
|
+
#wx.CallLater(10, self.Refresh)
|
|
84
|
+
self.Layout()
|
|
85
|
+
#print self.GetSizer().GetSize()
|
|
86
|
+
#self.SetMinSize(self.GetSizer().GetSize())
|
|
87
|
+
self.GetParent().Layout()
|
|
88
|
+
self.GetParent().GetParent().Layout()
|
|
89
|
+
self.Refresh()
|
|
90
|
+
|
|
91
|
+
def _set_n_events(self, node, st):
|
|
92
|
+
node_col = tuple([int(v) for v in (255 * self._col(node)[:3])])
|
|
93
|
+
|
|
94
|
+
evts = ''
|
|
95
|
+
data = self.recipe.namespace.get(node, None)
|
|
96
|
+
if isinstance(data, tabular.TabularBase):
|
|
97
|
+
evts = ' [%d evts]' % len(data)
|
|
98
|
+
|
|
99
|
+
st.SetLabelMarkup("<span foreground='#%02x%02x%02x'>%s%s</span>" % (node_col + (node,evts)))
|
|
100
|
+
|
|
101
|
+
def _update_n_events(self, *args, **kwargs):
|
|
102
|
+
for node, t in self.data_panes.items():
|
|
103
|
+
self._set_n_events(node, t[1])
|
|
104
|
+
|
|
105
|
+
def OnIdle(self, evt=None):
|
|
106
|
+
if not self._layout_valid:
|
|
107
|
+
self._layout_valid = True
|
|
108
|
+
self._layout()
|
|
109
|
+
|
|
110
|
+
def invalidate_layout(self, *args, **kwargs):
|
|
111
|
+
# avoid re-doing the layout multiple times
|
|
112
|
+
# flag as invalid and let OnIdle do the layout
|
|
113
|
+
self._layout_valid = False
|
|
114
|
+
|
|
115
|
+
def _layout(self, *args, **kwargs):
|
|
116
|
+
#print('RecipeView._layout')
|
|
117
|
+
#import traceback
|
|
118
|
+
#traceback.print_stack()
|
|
119
|
+
|
|
120
|
+
# dispose of any current traits views
|
|
121
|
+
for tv in self._traits_views:
|
|
122
|
+
tv.dispose()
|
|
123
|
+
|
|
124
|
+
self._traits_views.clear()
|
|
125
|
+
|
|
126
|
+
wx.CallAfter(self._layout2)
|
|
127
|
+
#self._layout2()
|
|
128
|
+
|
|
129
|
+
def _layout2(self):
|
|
130
|
+
#print('RecipeView._layout2')
|
|
131
|
+
|
|
132
|
+
if self.fp:
|
|
133
|
+
_popEventHandlers(self.fp, handler_type=wx.EvtHandler)
|
|
134
|
+
self.fp.elements = []
|
|
135
|
+
# Wrap this in a try block to prevent an error when using OutputModules
|
|
136
|
+
# TODO: Figure out why this is necessary.
|
|
137
|
+
|
|
138
|
+
try:
|
|
139
|
+
self.fp.DestroyChildren()
|
|
140
|
+
except:
|
|
141
|
+
logger.exception('error destroying fold panel children')
|
|
142
|
+
pass
|
|
143
|
+
self.fp = None
|
|
144
|
+
#print('destroyed fold panel children')
|
|
145
|
+
|
|
146
|
+
self.DestroyChildren()
|
|
147
|
+
#print('destroyed children')
|
|
148
|
+
|
|
149
|
+
|
|
150
|
+
from matplotlib import pyplot as plt
|
|
151
|
+
from .base import ModuleBase, OutputModule
|
|
152
|
+
import textwrap
|
|
153
|
+
|
|
154
|
+
#from PYME.ui import autoFoldPanel as afp
|
|
155
|
+
import PYME.ui.manualFoldPanel as afp
|
|
156
|
+
|
|
157
|
+
dg = self.recipe.dependancyGraph()
|
|
158
|
+
rdg = self.recipe.reverseDependancyGraph()
|
|
159
|
+
|
|
160
|
+
self.ordered, self.x0s = recipeLayout.layout_vertical(dg, rdg)
|
|
161
|
+
|
|
162
|
+
x_vals = -.1 * (1 + np.arange(len(self.ordered)))
|
|
163
|
+
|
|
164
|
+
|
|
165
|
+
self.input_target_panes = {}
|
|
166
|
+
self.output_source_panes = {}
|
|
167
|
+
self.data_panes = {}
|
|
168
|
+
|
|
169
|
+
#what data do we already have in the namespace?
|
|
170
|
+
self.input_datasources = list(self.recipe.namespace.keys())
|
|
171
|
+
|
|
172
|
+
for node in self.ordered:
|
|
173
|
+
if isinstance(node, ModuleBase):
|
|
174
|
+
for op in node.outputs:
|
|
175
|
+
try:
|
|
176
|
+
#this is obviously not an input - remove from list of input data
|
|
177
|
+
self.input_datasources.remove(op)
|
|
178
|
+
except ValueError:
|
|
179
|
+
pass
|
|
180
|
+
|
|
181
|
+
hsizer = wx.BoxSizer(wx.HORIZONTAL)
|
|
182
|
+
hsizer.AddSpacer(20)
|
|
183
|
+
|
|
184
|
+
self.fp = afp.foldPanel(self)
|
|
185
|
+
hsizer.Add(self.fp, 1, wx.EXPAND, 0)
|
|
186
|
+
|
|
187
|
+
hsizer.AddSpacer(10)
|
|
188
|
+
|
|
189
|
+
for N, node in enumerate(self.ordered):
|
|
190
|
+
if isinstance(node, ModuleBase):
|
|
191
|
+
#This is a module - plot a box
|
|
192
|
+
s = node.__class__.__name__
|
|
193
|
+
|
|
194
|
+
item = afp.foldingPane(self.fp, -1, caption=s, pinned = False)
|
|
195
|
+
if getattr(node, '_has_buttons', False) or (getattr(node,'_get_actions', None) is not None):
|
|
196
|
+
kind = 'panel'
|
|
197
|
+
else:
|
|
198
|
+
kind = 'subpanel'
|
|
199
|
+
pan = node.edit_traits(parent=item, kind=kind, view='pipeline_view_min')
|
|
200
|
+
self._traits_views.append(pan)
|
|
201
|
+
pan.control.SetMinSize((150, -1))
|
|
202
|
+
item.AddNewElement(pan.control)
|
|
203
|
+
if getattr(node, '_last_error', None):
|
|
204
|
+
# error on this node, turn background red
|
|
205
|
+
# TODO - this is a rather hacky
|
|
206
|
+
item.stCaption.style.update({'BACKGROUND_COLOUR_1': (220, 198, 198), #default AUI caption colours
|
|
207
|
+
'BACKGROUND_COLOUR_2': (255, 226, 226)})
|
|
208
|
+
self.fp.AddPane(item)
|
|
209
|
+
|
|
210
|
+
#p = pan.control
|
|
211
|
+
#j += 1
|
|
212
|
+
|
|
213
|
+
#draw input lines
|
|
214
|
+
inputs = list(node.inputs)
|
|
215
|
+
ip_xs = [self._data_output_pos(ip)[0] for ip in inputs]
|
|
216
|
+
ip_ys = np.linspace(0, 1, 2 * len(inputs) + 1)[1::2]
|
|
217
|
+
ip_ys = ip_ys[np.argsort(ip_xs)[::-1]]
|
|
218
|
+
|
|
219
|
+
for ip_y, ip in zip(ip_ys, inputs):
|
|
220
|
+
self.input_target_panes[ip] = (item, ip_y)
|
|
221
|
+
#self.input_positions[ip] = lambda : (self.fp.panes[j].Position[0], self.fp.panes[j].Position[1] + ip_y*self.fp.panes[j].GetSize()[1])
|
|
222
|
+
#self.input_positions[ip] = lambda : _get_op(j)
|
|
223
|
+
#
|
|
224
|
+
# #draw the nodes outputs
|
|
225
|
+
outputs = list(node.outputs)[::-1]
|
|
226
|
+
if len(outputs) > 0:
|
|
227
|
+
op_y = np.linspace(0, 1, 2 * len(outputs) + 1)[1::2]
|
|
228
|
+
op_x = 5*np.arange(len(outputs))[::-1]
|
|
229
|
+
|
|
230
|
+
for yp, xp, op in zip(op_y, op_x, outputs):
|
|
231
|
+
self.output_source_panes[op] = (item, xp, yp)
|
|
232
|
+
|
|
233
|
+
#self.output_positions[op] = lambda : (item.GetPosition()[0] + item.GetSize()[0] + 5 + xp, item.GetPosition()[1] + yp*item.GetSize()[1])
|
|
234
|
+
|
|
235
|
+
else:
|
|
236
|
+
# we must be an input - route back to LHS
|
|
237
|
+
try:
|
|
238
|
+
#only map back if we are going to be used.
|
|
239
|
+
if True:#rdg.get(node, False):
|
|
240
|
+
xi, yi = self._output_position(node)
|
|
241
|
+
x_0 = x_vals[self.x0s[node]]
|
|
242
|
+
#ax.plot([2, xi, xi, x_0], [yi, yi, y, y], '-', color=_col(node), lw=2)
|
|
243
|
+
|
|
244
|
+
#print('Adding static text')
|
|
245
|
+
item = afp.foldingPane(self.fp, -1, caption=None, pinned=True, folded=False, padding=0, style=0)
|
|
246
|
+
st = wx.StaticText(item, -1, node)
|
|
247
|
+
|
|
248
|
+
self._set_n_events(node, st)
|
|
249
|
+
|
|
250
|
+
item.AddNewElement(st, foldable=False)
|
|
251
|
+
self.fp.AddPane(item)
|
|
252
|
+
|
|
253
|
+
self.data_panes[node] = (item, st)
|
|
254
|
+
|
|
255
|
+
#self.data_positions[node] = lambda : (item.GetPosition()[0] + x_0, item.GetPosition()[1] + 0.5 * item.GetSize()[1])
|
|
256
|
+
#self.data_positions_in[node] = lambda : (item.GetPosition()[0] + st.GetSize()[0], item.GetPosition()[1] + 0.5 * item.GetSize()[1])
|
|
257
|
+
|
|
258
|
+
|
|
259
|
+
except KeyError:
|
|
260
|
+
#dangling input
|
|
261
|
+
#print('dangling input')
|
|
262
|
+
|
|
263
|
+
x_0 = x_vals[self.x0s[node]]
|
|
264
|
+
|
|
265
|
+
item = afp.foldingPane(self.fp, -1, caption=None, pinned=True, folded=False, padding=0, style=0)
|
|
266
|
+
st = wx.StaticText(item, -1, node)
|
|
267
|
+
|
|
268
|
+
node_col = tuple([int(v) for v in (255 * self._col(node)[:3])])
|
|
269
|
+
|
|
270
|
+
|
|
271
|
+
bg = ''
|
|
272
|
+
evts = ''
|
|
273
|
+
|
|
274
|
+
if node in self.input_datasources:
|
|
275
|
+
bg = " background='#D0D0D0'"
|
|
276
|
+
|
|
277
|
+
data = self.recipe.namespace.get(node, None)
|
|
278
|
+
if isinstance(data, tabular.TabularBase):
|
|
279
|
+
evts = ' [%d evts]' % len(data)
|
|
280
|
+
|
|
281
|
+
st.SetLabelMarkup("<u><span foreground='#%02x%02x%02x' weight='bold'%s>%s%s</span></u>" % (node_col + (bg, node,evts)))
|
|
282
|
+
item.AddNewElement(st, foldable=False)
|
|
283
|
+
self.fp.AddPane(item)
|
|
284
|
+
|
|
285
|
+
self.data_panes[node] = (item, st)
|
|
286
|
+
#self.data_positions[node] = lambda : (item.GetPosition()[0] + x_0, item.GetPosition()[1] + 0.5 * item.GetSize()[1])
|
|
287
|
+
|
|
288
|
+
|
|
289
|
+
print('Input datasources: ', self.input_datasources)
|
|
290
|
+
|
|
291
|
+
self.fp.fold_signal.connect(self._refr)
|
|
292
|
+
self.SetSizerAndFit(hsizer)
|
|
293
|
+
self.Layout()
|
|
294
|
+
|
|
295
|
+
def _input_position(self, key):
|
|
296
|
+
item, ip_y = self.input_target_panes[key]
|
|
297
|
+
xp, yp = item.Position
|
|
298
|
+
sx, sy = item.Size
|
|
299
|
+
|
|
300
|
+
return xp, yp + ip_y*sy
|
|
301
|
+
|
|
302
|
+
def _output_position(self, key):
|
|
303
|
+
item, ip_x, ip_y = self.output_source_panes[key]
|
|
304
|
+
xp, yp = item.Position
|
|
305
|
+
sx, sy = item.Size
|
|
306
|
+
|
|
307
|
+
return xp + sx + 5 + ip_x, yp + ip_y * sy
|
|
308
|
+
|
|
309
|
+
def _data_input_pos(self, key):
|
|
310
|
+
item, st = self.data_panes[key]
|
|
311
|
+
xp, yp = item.Position
|
|
312
|
+
sx, sy = item.Size
|
|
313
|
+
|
|
314
|
+
return xp + st.GetTextExtent(st.GetLabel())[0] + 3, yp + 0.5*sy
|
|
315
|
+
|
|
316
|
+
def _data_output_pos(self, key):
|
|
317
|
+
item, st = self.data_panes[key]
|
|
318
|
+
xp, yp = item.Position
|
|
319
|
+
sx, sy = item.Size
|
|
320
|
+
|
|
321
|
+
return xp - 5*(1+self.x0s[key]), yp + 0.5 * sy
|
|
322
|
+
|
|
323
|
+
|
|
324
|
+
def OnPaint(self, dc):
|
|
325
|
+
#print 'p'
|
|
326
|
+
#if not self.IsShownOnScreen():
|
|
327
|
+
# return
|
|
328
|
+
if self.fp is None:
|
|
329
|
+
return
|
|
330
|
+
|
|
331
|
+
|
|
332
|
+
dc = wx.PaintDC(self)
|
|
333
|
+
#self.PrepareDC(dc)
|
|
334
|
+
#dc.BeginDrawing()
|
|
335
|
+
|
|
336
|
+
x_0 = self.fp.Position[0]
|
|
337
|
+
x_1 = x_0 + self.fp.Size[0]
|
|
338
|
+
|
|
339
|
+
dc.SetPen(wx.BLACK_PEN)
|
|
340
|
+
for nd in self.x0s.keys():
|
|
341
|
+
dc.SetPen(wx.Pen(wx.Colour(*((255*self._col(nd))[:3]).astype('i').tolist()), 2))
|
|
342
|
+
try:
|
|
343
|
+
x0, y0 = self._output_position(nd)
|
|
344
|
+
x1, y1 = self._data_input_pos(nd)
|
|
345
|
+
|
|
346
|
+
dc.DrawLines([(x_1, y0), (x0+x_0, y0), (x0+x_0, y1), (x1+x_0, y1)])
|
|
347
|
+
except KeyError:
|
|
348
|
+
pass
|
|
349
|
+
|
|
350
|
+
try:
|
|
351
|
+
x0, y0 = self._input_position(nd)
|
|
352
|
+
x1, y1 = self._data_output_pos(nd)
|
|
353
|
+
|
|
354
|
+
dc.DrawLines([(x_0, y0), (x1+x_0, y0), (x1+x_0, y1), (x_0, y1)])
|
|
355
|
+
except KeyError:
|
|
356
|
+
pass
|
|
357
|
+
|
|
358
|
+
#dc.EndDrawing()
|
|
359
|
+
|
|
360
|
+
def _popEventHandlers(ctrl, handler_type=wx.EvtHandler):
|
|
361
|
+
"""Pop any event handlers that have been pushed on to a window and its
|
|
362
|
+
children.
|
|
363
|
+
"""
|
|
364
|
+
# borrowed from traitsui.wx.toolkit
|
|
365
|
+
|
|
366
|
+
handler = ctrl.GetEventHandler()
|
|
367
|
+
while ctrl is not handler:
|
|
368
|
+
next_handler = handler.GetNextHandler()
|
|
369
|
+
if isinstance(handler, handler_type):
|
|
370
|
+
ctrl.PopEventHandler(True)
|
|
371
|
+
handler = next_handler
|
|
372
|
+
for child in ctrl.GetChildren():
|
|
373
|
+
_popEventHandlers(child, handler_type)
|
|
@@ -0,0 +1,23 @@
|
|
|
1
|
+
"""
|
|
2
|
+
PYME.resources
|
|
3
|
+
==============
|
|
4
|
+
|
|
5
|
+
A storage area for non-code based resources.
|
|
6
|
+
|
|
7
|
+
"""
|
|
8
|
+
import os
|
|
9
|
+
dirname = os.path.dirname(__file__)
|
|
10
|
+
|
|
11
|
+
def getIconPath(name):
|
|
12
|
+
"""Returns the full path to the icon with the given name"""
|
|
13
|
+
|
|
14
|
+
return os.path.join(dirname, 'icons', name)
|
|
15
|
+
|
|
16
|
+
def get_web_static_dir():
|
|
17
|
+
return os.path.join(dirname, 'web', 'static')
|
|
18
|
+
|
|
19
|
+
def get_web_dir():
|
|
20
|
+
return os.path.join(dirname, 'web')
|
|
21
|
+
|
|
22
|
+
def get_test_data_dir():
|
|
23
|
+
return os.path.join(dirname, 'test_datasets')
|
|
@@ -0,0 +1,14 @@
|
|
|
1
|
+
distributor:
|
|
2
|
+
http_endpoint: 0.0.0.0:1234
|
|
3
|
+
http_print_debug_logs: false
|
|
4
|
+
logic:
|
|
5
|
+
max_allowed_fails: 5
|
|
6
|
+
node_timeout: 10s
|
|
7
|
+
max_parallel_rate_requests: 10
|
|
8
|
+
rating_buffer_size: 50
|
|
9
|
+
rating_buffer_flush_interval: 1s
|
|
10
|
+
queue_stats_ttl: 24h0m0s
|
|
11
|
+
queue_stats_gc_interval: 2m0s
|
|
12
|
+
rate_request_timeout: 3s
|
|
13
|
+
http_client_timeout: 10s
|
|
14
|
+
default_num_want: 50
|
|
@@ -0,0 +1,15 @@
|
|
|
1
|
+
nodeserver:
|
|
2
|
+
http_endpoint: 0.0.0.0:1337
|
|
3
|
+
http_print_debug_logs: false
|
|
4
|
+
distributors:
|
|
5
|
+
- 10.150.7.1:1234
|
|
6
|
+
pyme_cluster_rater:
|
|
7
|
+
data_server_root_dir: /mnt/storage/pyme
|
|
8
|
+
logic:
|
|
9
|
+
gc_interval: 1m0s
|
|
10
|
+
gc_cutoff: 5m0s
|
|
11
|
+
announce_interval: 3s
|
|
12
|
+
hand_in_buffer_size: 50
|
|
13
|
+
hand_in_buffer_flush_interval: 3s
|
|
14
|
+
num_want_tasks: -1
|
|
15
|
+
get_tasks_long_polling_timeout: 10s
|
|
Binary file
|
|
Binary file
|
|
Binary file
|
|
Binary file
|
|
Binary file
|
|
Binary file
|
|
Binary file
|
|
Binary file
|
|
Binary file
|
|
Binary file
|
|
Binary file
|
|
Binary file
|
|
@@ -0,0 +1,28 @@
|
|
|
1
|
+
<?xml version="1.0" encoding="utf-8"?>
|
|
2
|
+
<!-- Generator: Adobe Illustrator 20.1.0, SVG Export Plug-In . SVG Version: 6.00 Build 0) -->
|
|
3
|
+
<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
|
|
4
|
+
viewBox="0 0 300 300" style="enable-background:new 0 0 300 300;" xml:space="preserve">
|
|
5
|
+
<style type="text/css">
|
|
6
|
+
.st0{fill:url(#SVGID_1_);stroke:#000000;stroke-width:7;stroke-miterlimit:10;}
|
|
7
|
+
.st1{fill:url(#SVGID_2_);stroke:#000000;stroke-width:7;stroke-miterlimit:10;}
|
|
8
|
+
.st2{fill:none;stroke:#000000;stroke-width:7;stroke-miterlimit:10;}
|
|
9
|
+
</style>
|
|
10
|
+
<g>
|
|
11
|
+
<radialGradient id="SVGID_1_" cx="150.6468" cy="146.0155" r="142.9088" gradientUnits="userSpaceOnUse">
|
|
12
|
+
<stop offset="0" style="stop-color:#FFFFFF"/>
|
|
13
|
+
<stop offset="0.8099" style="stop-color:#ED1C24"/>
|
|
14
|
+
<stop offset="1" style="stop-color:#780000"/>
|
|
15
|
+
</radialGradient>
|
|
16
|
+
<polygon class="st0" points="4.1,185.5 47.4,100.3 149.4,6.8 271.1,50.9 297.1,209.3 208,285.2 149.4,192.6 "/>
|
|
17
|
+
<radialGradient id="SVGID_2_" cx="101.6654" cy="234.4909" r="0" gradientUnits="userSpaceOnUse">
|
|
18
|
+
<stop offset="0" style="stop-color:#FFFFFF"/>
|
|
19
|
+
<stop offset="0.8099" style="stop-color:#ED1C24"/>
|
|
20
|
+
<stop offset="1" style="stop-color:#780000"/>
|
|
21
|
+
</radialGradient>
|
|
22
|
+
<path class="st1" d="M101.7,234.5"/>
|
|
23
|
+
<line class="st2" x1="47.4" y1="100.3" x2="149.4" y2="192.6"/>
|
|
24
|
+
<line class="st2" x1="149.4" y1="6.8" x2="149.4" y2="192.6"/>
|
|
25
|
+
<line class="st2" x1="271.1" y1="50.9" x2="149.4" y2="192.6"/>
|
|
26
|
+
<line class="st2" x1="297.1" y1="209.3" x2="149.4" y2="192.6"/>
|
|
27
|
+
</g>
|
|
28
|
+
</svg>
|
|
Binary file
|
|
Binary file
|
|
Binary file
|
|
Binary file
|
|
Binary file
|
|
Binary file
|
|
Binary file
|
|
@@ -0,0 +1,16 @@
|
|
|
1
|
+
<?xml version="1.0" encoding="utf-8"?>
|
|
2
|
+
<!-- Generator: Adobe Illustrator 20.1.0, SVG Export Plug-In . SVG Version: 6.00 Build 0) -->
|
|
3
|
+
<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
|
|
4
|
+
viewBox="0 0 300 300" style="enable-background:new 0 0 300 300;" xml:space="preserve">
|
|
5
|
+
<style type="text/css">
|
|
6
|
+
.st0{fill:#FF0000;stroke:#000000;stroke-width:2;}
|
|
7
|
+
.st1{fill:#00FFFF;stroke:#000000;stroke-width:2;}
|
|
8
|
+
.st2{fill:#FF00FF;stroke:#000000;stroke-width:2;}
|
|
9
|
+
</style>
|
|
10
|
+
<g>
|
|
11
|
+
<title>Layer 1</title>
|
|
12
|
+
<ellipse id="svg_6" class="st0" cx="84.5" cy="199.5" rx="49.5" ry="49.5"/>
|
|
13
|
+
<ellipse id="svg_7" class="st1" cx="168.5" cy="77.5" rx="49.5" ry="49.5"/>
|
|
14
|
+
<ellipse id="svg_8" class="st2" cx="197.8" cy="213.2" rx="47.8" ry="47.8"/>
|
|
15
|
+
</g>
|
|
16
|
+
</svg>
|
|
Binary file
|