python-microscopy 26.7.9__cp313-cp313-macosx_26_0_arm64.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 +1249 -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.cpython-313-darwin.so +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_elliptec.py +109 -0
- PYME/Acquire/Hardware/thorlabs_elliptec_serial.py +166 -0
- PYME/Acquire/Hardware/thorlabs_mff_flipper.py +396 -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 +967 -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_app.py +14 -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 +223 -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.cpython-313-darwin.so +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
- PYME/Analysis/optic_flow.py +108 -0
- PYME/Analysis/piecewise.py +36 -0
- PYME/Analysis/piecewiseMapping.py +304 -0
- PYME/Analysis/piezo_movement_correction.py +153 -0
- PYME/Analysis/points/DeClump/__init__.py +78 -0
- PYME/Analysis/points/DeClump/deClump.cpython-313-darwin.so +0 -0
- PYME/Analysis/points/DeClump/deClumpGUI.py +87 -0
- PYME/Analysis/points/DeClump/pyDeClump.py +284 -0
- PYME/Analysis/points/DeClump/testClump.py +40 -0
- PYME/Analysis/points/DistHist/__init__.py +25 -0
- PYME/Analysis/points/DistHist/distHist.cpython-313-darwin.so +0 -0
- PYME/Analysis/points/DistHist/distHistThreaded.py +71 -0
- PYME/Analysis/points/DistHist/setup.py +54 -0
- PYME/Analysis/points/EdgeDB/__init__.py +24 -0
- PYME/Analysis/points/EdgeDB/edgeDB.cpython-313-darwin.so +0 -0
- PYME/Analysis/points/EdgeDB/edgeTest.py +66 -0
- PYME/Analysis/points/EdgeDB/edges.py +102 -0
- PYME/Analysis/points/EdgeDB/segment.py +75 -0
- PYME/Analysis/points/EdgeDB/setup.py +54 -0
- PYME/Analysis/points/QuadTree/QTrend.py +232 -0
- PYME/Analysis/points/QuadTree/__init__.py +25 -0
- PYME/Analysis/points/QuadTree/pointQT.py +227 -0
- PYME/Analysis/points/QuadTree/pointQTF.py +254 -0
- PYME/Analysis/points/QuadTree/qtUtils.py +36 -0
- PYME/Analysis/points/QuadTree/rendQT.py +118 -0
- PYME/Analysis/points/SoftRend/__init__.py +24 -0
- PYME/Analysis/points/SoftRend/setup.py +61 -0
- PYME/Analysis/points/SoftRend/testTetrahedra.py +41 -0
- PYME/Analysis/points/SoftRend/triRend.cpython-313-darwin.so +0 -0
- PYME/Analysis/points/__init__.py +3 -0
- PYME/Analysis/points/arcfit/__init__.py +1 -0
- PYME/Analysis/points/arcfit/arcmf.cpython-313-darwin.so +0 -0
- PYME/Analysis/points/arcfit/setup.py +51 -0
- PYME/Analysis/points/astigmatism/__init__.py +0 -0
- PYME/Analysis/points/astigmatism/astigTools.py +338 -0
- PYME/Analysis/points/astigmatism/astiglookup.cpython-313-darwin.so +0 -0
- PYME/Analysis/points/astigmatism/setup.py +54 -0
- PYME/Analysis/points/cluster_morphology.py +199 -0
- PYME/Analysis/points/coordinate_tools.py +278 -0
- PYME/Analysis/points/features/__init__.py +0 -0
- PYME/Analysis/points/features/metal.py +54 -0
- PYME/Analysis/points/features/shaders/vect_feat_3d.metal +49 -0
- PYME/Analysis/points/fiducials.py +142 -0
- PYME/Analysis/points/gen3DTriangs.py +796 -0
- PYME/Analysis/points/moments.py +143 -0
- PYME/Analysis/points/multiview.py +458 -0
- PYME/Analysis/points/objectMeasure.py +206 -0
- PYME/Analysis/points/qpaint.py +97 -0
- PYME/Analysis/points/rings.py +372 -0
- PYME/Analysis/points/ripleys.py +427 -0
- PYME/Analysis/points/segmentLL.py +134 -0
- PYME/Analysis/points/setup.py +56 -0
- PYME/Analysis/points/spherical_harmonics.py +918 -0
- PYME/Analysis/points/surfit.py +829 -0
- PYME/Analysis/points/tCluster.py +75 -0
- PYME/Analysis/points/traveling_salesperson/__init__.py +0 -0
- PYME/Analysis/points/traveling_salesperson/queue_opt.py +117 -0
- PYME/Analysis/points/traveling_salesperson/sectioned_two_opt.py +327 -0
- PYME/Analysis/points/traveling_salesperson/setup.py +40 -0
- PYME/Analysis/points/traveling_salesperson/sort.py +78 -0
- PYME/Analysis/points/traveling_salesperson/two_opt.py +189 -0
- PYME/Analysis/points/traveling_salesperson/two_opt_utils.cpython-313-darwin.so +0 -0
- PYME/Analysis/points/traveling_salesperson/two_opt_utils.pyx +41 -0
- PYME/Analysis/points/twoColour.py +572 -0
- PYME/Analysis/points/twoColourPlot.py +107 -0
- PYME/Analysis/processLogger.py +129 -0
- PYME/Analysis/profile_extraction.py +72 -0
- PYME/Analysis/setup.py +60 -0
- PYME/Analysis/splitting.py +372 -0
- PYME/Analysis/svmSegment.py +214 -0
- PYME/Analysis/thresholding.py +192 -0
- PYME/Analysis/tile_pyramid.py +938 -0
- PYME/Analysis/widefieldify.py +54 -0
- PYME/DSView/DisplayOptionsPanel.py +503 -0
- PYME/DSView/LUT/__init__.py +33 -0
- PYME/DSView/LUT/lut.cpython-313-darwin.so +0 -0
- PYME/DSView/LUT/setup.py +54 -0
- PYME/DSView/OpenSequenceDialog.py +83 -0
- PYME/DSView/OverlaysPanel.py +111 -0
- PYME/DSView/PYMEImage.py +18 -0
- PYME/DSView/__init__.py +32 -0
- PYME/DSView/arrayViewPanel.py +1036 -0
- PYME/DSView/displayOptions.py +453 -0
- PYME/DSView/displaySettingsPanel.py +276 -0
- PYME/DSView/dsviewer.py +542 -0
- PYME/DSView/eventLogViewer.py +805 -0
- PYME/DSView/fitInfo.py +486 -0
- PYME/DSView/htmlServe.py +72 -0
- PYME/DSView/logparser.py +100 -0
- PYME/DSView/modules/LMAnalysis.py +1057 -0
- PYME/DSView/modules/LMDisplay.py +194 -0
- PYME/DSView/modules/__init__.py +167 -0
- PYME/DSView/modules/_base.py +39 -0
- PYME/DSView/modules/annotation.py +725 -0
- PYME/DSView/modules/arrayView.py +71 -0
- PYME/DSView/modules/blobFinding.py +455 -0
- PYME/DSView/modules/blobMeasure.py +1093 -0
- PYME/DSView/modules/camera_maps.py +38 -0
- PYME/DSView/modules/coloc.py +414 -0
- PYME/DSView/modules/composite.py +715 -0
- PYME/DSView/modules/convnet.py +24 -0
- PYME/DSView/modules/cropping.py +133 -0
- PYME/DSView/modules/dark_and_flatfield.py +31 -0
- PYME/DSView/modules/deconvolution.py +499 -0
- PYME/DSView/modules/eventView.py +80 -0
- PYME/DSView/modules/extractBlobs.py +46 -0
- PYME/DSView/modules/fastGraphPanel.py +85 -0
- PYME/DSView/modules/filtering.py +335 -0
- PYME/DSView/modules/flowView.py +268 -0
- PYME/DSView/modules/fourierRingCorrelation.py +172 -0
- PYME/DSView/modules/gl_image_view.py +12 -0
- PYME/DSView/modules/graphViewPanel.py +272 -0
- PYME/DSView/modules/measure/__init__.py +1 -0
- PYME/DSView/modules/measure/filterPan.py +235 -0
- PYME/DSView/modules/metadataView.py +28 -0
- PYME/DSView/modules/multithreshold.py +98 -0
- PYME/DSView/modules/neuroglancer.py +129 -0
- PYME/DSView/modules/object_tagging.py +157 -0
- PYME/DSView/modules/particleTracking.py +463 -0
- PYME/DSView/modules/playback.py +256 -0
- PYME/DSView/modules/prebleachExtraction.py +75 -0
- PYME/DSView/modules/profileFitting.py +137 -0
- PYME/DSView/modules/profilePlotting.py +408 -0
- PYME/DSView/modules/projections.py +48 -0
- PYME/DSView/modules/psfExtraction.py +570 -0
- PYME/DSView/modules/psfGeneration.py +138 -0
- PYME/DSView/modules/psfTools.py +661 -0
- PYME/DSView/modules/pupilTools.py +204 -0
- PYME/DSView/modules/pupilView.py +139 -0
- PYME/DSView/modules/recipes.py +266 -0
- PYME/DSView/modules/redimension.py +75 -0
- PYME/DSView/modules/segmentation.py +192 -0
- PYME/DSView/modules/sheetView.py +24 -0
- PYME/DSView/modules/shell.py +39 -0
- PYME/DSView/modules/shiftfield_estimation.py +433 -0
- PYME/DSView/modules/sparkprepare.py +94 -0
- PYME/DSView/modules/splitter.py +148 -0
- PYME/DSView/modules/synchronise.py +64 -0
- PYME/DSView/modules/templates/astigCal.html +42 -0
- PYME/DSView/modules/templates/measureView.html +69 -0
- PYME/DSView/modules/templates/measureView2.html +48 -0
- PYME/DSView/modules/templates/measureView3.html +98 -0
- PYME/DSView/modules/templates/trackView.html +139 -0
- PYME/DSView/modules/templates/tracksOverview.html +21 -0
- PYME/DSView/modules/tiling.py +147 -0
- PYME/DSView/modules/unmixing.py +148 -0
- PYME/DSView/modules/vis3D.py +320 -0
- PYME/DSView/modules/visgui.py +163 -0
- PYME/DSView/modules/webview.py +14 -0
- PYME/DSView/overlays.py +295 -0
- PYME/DSView/scrolledImagePanel.py +188 -0
- PYME/DSView/setup.py +53 -0
- PYME/DSView/splashScreen.py +158 -0
- PYME/DSView/voxSizeDialog.py +84 -0
- PYME/Deconv/__init__.py +35 -0
- PYME/Deconv/beadGen.py +55 -0
- PYME/Deconv/dec.py +659 -0
- PYME/Deconv/decTask.py +65 -0
- PYME/Deconv/decThread.py +113 -0
- PYME/Deconv/dec_test.py +47 -0
- PYME/Deconv/deconvDialogs.py +417 -0
- PYME/Deconv/fftwWisdom.py +62 -0
- PYME/Deconv/richardsonLucy.py +141 -0
- PYME/Deconv/richardsonLucyMV.py +151 -0
- PYME/Deconv/richardsonLucyMVM.py +218 -0
- PYME/Deconv/test_block_dec.py +46 -0
- PYME/Deconv/tq_block_dec.py +331 -0
- PYME/Deconv/wiener.py +163 -0
- PYME/IO/DataSources/AlignDataSource.py +91 -0
- PYME/IO/DataSources/ArrayDataSource.py +260 -0
- PYME/IO/DataSources/BGSDataSource.py +354 -0
- PYME/IO/DataSources/BaseDataSource.py +457 -0
- PYME/IO/DataSources/BioformatsBFFDataSource.py +75 -0
- PYME/IO/DataSources/BioformatsDataSource.py +178 -0
- PYME/IO/DataSources/BufferedDataSource.py +101 -0
- PYME/IO/DataSources/ClusterPZFDataSource.py +124 -0
- PYME/IO/DataSources/ConcatenatedDataSource.py +56 -0
- PYME/IO/DataSources/CropDataSource.py +246 -0
- PYME/IO/DataSources/DcimgDataSource.py +54 -0
- PYME/IO/DataSources/ElectronsPerSecondDataSource.py +61 -0
- PYME/IO/DataSources/FlatFieldDataSource.py +87 -0
- PYME/IO/DataSources/HDFDataSource.py +160 -0
- PYME/IO/DataSources/HTTPDataSource.py +80 -0
- PYME/IO/DataSources/ImageSeriesDataSource.py +123 -0
- PYME/IO/DataSources/MultiviewDataSource.py +99 -0
- PYME/IO/DataSources/OBFDataSource.py +74 -0
- PYME/IO/DataSources/RandomDataSource.py +23 -0
- PYME/IO/DataSources/SupertileDatasource.py +148 -0
- PYME/IO/DataSources/TQDataSource.py +41 -0
- PYME/IO/DataSources/TiffDataSource.py +193 -0
- PYME/IO/DataSources/TileDataSource.py +91 -0
- PYME/IO/DataSources/UnsplitDataSource.py +92 -0
- PYME/IO/DataSources/__init__.py +59 -0
- PYME/IO/FileUtils/IJLut.py +43 -0
- PYME/IO/FileUtils/RawToHdf5.py +105 -0
- PYME/IO/FileUtils/SPAD.py +54 -0
- PYME/IO/FileUtils/TiffSeqToHdf5.py +87 -0
- PYME/IO/FileUtils/__init__.py +24 -0
- PYME/IO/FileUtils/compHdf.py +39 -0
- PYME/IO/FileUtils/fileID.py +246 -0
- PYME/IO/FileUtils/fnlGen.py +40 -0
- PYME/IO/FileUtils/freeSpace.py +59 -0
- PYME/IO/FileUtils/h5-thumbnailer.py +85 -0
- PYME/IO/FileUtils/h5ExFrames.py +98 -0
- PYME/IO/FileUtils/h5ToTiffSeries.py +50 -0
- PYME/IO/FileUtils/h5r-thumbnailer.py +118 -0
- PYME/IO/FileUtils/h5rFormatDef.py +99 -0
- PYME/IO/FileUtils/h5rToTxt.py +77 -0
- PYME/IO/FileUtils/nameUtils.py +300 -0
- PYME/IO/FileUtils/obf_support.py +538 -0
- PYME/IO/FileUtils/ply.py +147 -0
- PYME/IO/FileUtils/readSpeckle.py +78 -0
- PYME/IO/FileUtils/readTiff.py +64 -0
- PYME/IO/FileUtils/saveTiffStack.py +137 -0
- PYME/IO/FileUtils/setup.py +36 -0
- PYME/IO/FileUtils/sf-thumbnailer.py +76 -0
- PYME/IO/FileUtils/stl.py +44 -0
- PYME/IO/FileUtils/thumbnailDatabase.py +104 -0
- PYME/IO/HTTPSpooler_v2.py +141 -0
- PYME/IO/MetaDataHandler.py +1078 -0
- PYME/IO/PZFFormat.py +381 -0
- PYME/IO/Spooler.py +279 -0
- PYME/IO/__init__.py +12 -0
- PYME/IO/acquisition_backends.py +372 -0
- PYME/IO/buffer_helpers.cpython-313-darwin.so +0 -0
- PYME/IO/buffer_helpers.pyx +190 -0
- PYME/IO/buffers.py +291 -0
- PYME/IO/clusterDuplication.py +204 -0
- PYME/IO/clusterExport.py +152 -0
- PYME/IO/clusterGlob.py +108 -0
- PYME/IO/clusterIO.py +1076 -0
- PYME/IO/clusterListing.py +232 -0
- PYME/IO/clusterResults.py +206 -0
- PYME/IO/clusterUpload.py +49 -0
- PYME/IO/cluster_directory.py +419 -0
- PYME/IO/cluster_streaming.py +216 -0
- PYME/IO/compatibility.py +12 -0
- PYME/IO/countdir/__init__.py +5 -0
- PYME/IO/countdir/countdir.cpython-313-darwin.so +0 -0
- PYME/IO/countdir/setup.py +58 -0
- PYME/IO/csv_flavours.py +263 -0
- PYME/IO/dataExporter.py +470 -0
- PYME/IO/dataWrap.py +108 -0
- PYME/IO/dcimg.py +167 -0
- PYME/IO/events.py +161 -0
- PYME/IO/h5File.py +148 -0
- PYME/IO/h5rFile.py +323 -0
- PYME/IO/image.py +1546 -0
- PYME/IO/load_psf.py +26 -0
- PYME/IO/pyme_h5ls.py +58 -0
- PYME/IO/ragged.py +138 -0
- PYME/IO/rgb_image.py +94 -0
- PYME/IO/tabular.py +1343 -0
- PYME/IO/testClusterSpooling.py +199 -0
- PYME/IO/unifiedIO.py +301 -0
- PYME/LMVis/Extras/QPobjectSegment.py +220 -0
- PYME/LMVis/Extras/__init__.py +58 -0
- PYME/LMVis/Extras/animation.py +359 -0
- PYME/LMVis/Extras/annotation.py +78 -0
- PYME/LMVis/Extras/clusterAnalysis.py +460 -0
- PYME/LMVis/Extras/dockedPanel.py +69 -0
- PYME/LMVis/Extras/extra_layers.py +373 -0
- PYME/LMVis/Extras/fiducial.py +230 -0
- PYME/LMVis/Extras/flagZMotionArtifacts.py +60 -0
- PYME/LMVis/Extras/fusionUtils.py +9 -0
- PYME/LMVis/Extras/multiColourAnalysis.py +103 -0
- PYME/LMVis/Extras/multiviewMapping.py +489 -0
- PYME/LMVis/Extras/objectMeasurements.py +246 -0
- PYME/LMVis/Extras/particleTracking.py +272 -0
- PYME/LMVis/Extras/perFrameVariable.py +77 -0
- PYME/LMVis/Extras/photophysics.py +72 -0
- PYME/LMVis/Extras/pointSetGeneration.py +232 -0
- PYME/LMVis/Extras/pointwiseColoc.py +54 -0
- PYME/LMVis/Extras/saved_views.py +125 -0
- PYME/LMVis/Extras/scaleBox.py +115 -0
- PYME/LMVis/Extras/sequentialSpecies.py +125 -0
- PYME/LMVis/Extras/setBGImage.py +74 -0
- PYME/LMVis/Extras/shiftmapGenerator.py +138 -0
- PYME/LMVis/Extras/showShortcuts.py +69 -0
- PYME/LMVis/Extras/snapshot.py +135 -0
- PYME/LMVis/Extras/spherical_harmonics.py +98 -0
- PYME/LMVis/Extras/subsets.py +15 -0
- PYME/LMVis/Extras/surface_fitting.py +52 -0
- PYME/LMVis/Extras/temperaturePlot.py +53 -0
- PYME/LMVis/Extras/vibration.py +112 -0
- PYME/LMVis/PYMEVisualise.py +16 -0
- PYME/LMVis/VisGUI.py +506 -0
- PYME/LMVis/__init__.py +39 -0
- PYME/LMVis/colourFilterGUI.py +77 -0
- PYME/LMVis/colourPanel.py +491 -0
- PYME/LMVis/displayPane.py +475 -0
- PYME/LMVis/dyeRatios.py +116 -0
- PYME/LMVis/genImageDialog.py +298 -0
- PYME/LMVis/gl_offScreenHandler.py +134 -0
- PYME/LMVis/gl_render.py +1302 -0
- PYME/LMVis/gl_render3D.py +1453 -0
- PYME/LMVis/gl_render3D_shaders.py +1213 -0
- PYME/LMVis/glcanvas_core.py +1157 -0
- PYME/LMVis/imageView.py +752 -0
- PYME/LMVis/imageView2.py +372 -0
- PYME/LMVis/importTextDialog.py +342 -0
- PYME/LMVis/layer_panel.py +231 -0
- PYME/LMVis/layers/AxesOverlayLayer.py +126 -0
- PYME/LMVis/layers/LUTOverlayLayer.py +346 -0
- PYME/LMVis/layers/OverlayLayer.py +46 -0
- PYME/LMVis/layers/ScaleBarOverlayLayer.py +99 -0
- PYME/LMVis/layers/ScaleBoxOverlayLayer.py +181 -0
- PYME/LMVis/layers/SelectionOverlayLayer.py +124 -0
- PYME/LMVis/layers/__init__.py +53 -0
- PYME/LMVis/layers/base.py +319 -0
- PYME/LMVis/layers/image_layer.py +363 -0
- PYME/LMVis/layers/labels.py +186 -0
- PYME/LMVis/layers/layer_defaults.py +97 -0
- PYME/LMVis/layers/mesh.py +378 -0
- PYME/LMVis/layers/octree.py +194 -0
- PYME/LMVis/layers/pointcloud.py +372 -0
- PYME/LMVis/layers/quiver.py +271 -0
- PYME/LMVis/layers/text.py +250 -0
- PYME/LMVis/layers/tracks.py +309 -0
- PYME/LMVis/mv_math.py +78 -0
- PYME/LMVis/objectDarkMeasure.py +120 -0
- PYME/LMVis/pipeline.py +1227 -0
- PYME/LMVis/pipelineView.py +115 -0
- PYME/LMVis/pointSettingsPanel.py +135 -0
- PYME/LMVis/progGraph.py +59 -0
- PYME/LMVis/quadTreeSettings.py +90 -0
- PYME/LMVis/rendGauss.py +158 -0
- PYME/LMVis/renderers.py +576 -0
- PYME/LMVis/sessionpaths.py +136 -0
- PYME/LMVis/setup.py +39 -0
- PYME/LMVis/setup_exe.py +71 -0
- PYME/LMVis/shader_programs/DefaultShaderProgram.py +149 -0
- PYME/LMVis/shader_programs/GLProgram.py +119 -0
- PYME/LMVis/shader_programs/GouraudShaderProgram.py +157 -0
- PYME/LMVis/shader_programs/PointSpriteShaderProgram.py +163 -0
- PYME/LMVis/shader_programs/ShaderProgramFactory.py +54 -0
- PYME/LMVis/shader_programs/TesselShaderProgram.py +47 -0
- PYME/LMVis/shader_programs/WireFrameShaderProgram.py +50 -0
- PYME/LMVis/shader_programs/__init__.py +20 -0
- PYME/LMVis/shader_programs/oit_compositor.py +23 -0
- PYME/LMVis/shader_programs/shader_loader.py +84 -0
- PYME/LMVis/shader_programs/shader_program.py +168 -0
- PYME/LMVis/shader_programs/shaders/bigflatpoints_fs.glsl +16 -0
- PYME/LMVis/shader_programs/shaders/bigpoints_gs.glsl +40 -0
- PYME/LMVis/shader_programs/shaders/bigpointsprites_fs.glsl +20 -0
- PYME/LMVis/shader_programs/shaders/bigspheres_fs.glsl +53 -0
- PYME/LMVis/shader_programs/shaders/compose_fs.glsl +41 -0
- PYME/LMVis/shader_programs/shaders/compose_vs.glsl +25 -0
- PYME/LMVis/shader_programs/shaders/default_fs.glsl +27 -0
- PYME/LMVis/shader_programs/shaders/default_vs.glsl +88 -0
- PYME/LMVis/shader_programs/shaders/flatpoints_fs.glsl +27 -0
- PYME/LMVis/shader_programs/shaders/gouraud_flatpoints_fs.glsl +30 -0
- PYME/LMVis/shader_programs/shaders/gouraud_fs.glsl +26 -0
- PYME/LMVis/shader_programs/shaders/gouraud_oit_fs.glsl +68 -0
- PYME/LMVis/shader_programs/shaders/gouraud_vs.glsl +135 -0
- PYME/LMVis/shader_programs/shaders/image_fs.glsl +60 -0
- PYME/LMVis/shader_programs/shaders/image_vs.glsl +79 -0
- PYME/LMVis/shader_programs/shaders/phong_fs.glsl +43 -0
- PYME/LMVis/shader_programs/shaders/phong_vs.glsl +45 -0
- PYME/LMVis/shader_programs/shaders/pointsprites_fs.glsl +33 -0
- PYME/LMVis/shader_programs/shaders/pointsprites_vs.glsl +77 -0
- PYME/LMVis/shader_programs/shaders/spheres_fs.glsl +102 -0
- PYME/LMVis/shader_programs/shaders/tessel_fs.glsl +23 -0
- PYME/LMVis/shader_programs/shaders/tessel_vs.glsl +37 -0
- PYME/LMVis/shader_programs/shaders/text_fs.glsl +42 -0
- PYME/LMVis/shader_programs/shaders/text_vs.glsl +84 -0
- PYME/LMVis/shader_programs/shaders/widelines_fs.glsl +19 -0
- PYME/LMVis/shader_programs/shaders/widelines_gs.glsl +56 -0
- PYME/LMVis/shader_programs/shaders/widelines_vs.glsl +51 -0
- PYME/LMVis/statusLog.py +57 -0
- PYME/LMVis/triBlobs.py +142 -0
- PYME/LMVis/view_clipping_pane.py +429 -0
- PYME/LMVis/views.py +275 -0
- PYME/LMVis/visCore.py +1006 -0
- PYME/LMVis/visHelpers.py +880 -0
- PYME/LMVis/visHelpersMin.py +230 -0
- PYME/LMVis/workspaceTree.py +238 -0
- PYME/__init__.py +24 -0
- PYME/cluster/HTTPDataServer.py +1063 -0
- PYME/cluster/HTTPRulePusher.py +382 -0
- PYME/cluster/HTTPTaskPusher.py +377 -0
- PYME/cluster/PYMERuleNodeServer.py +192 -0
- PYME/cluster/PYMERuleServer.py +109 -0
- PYME/cluster/__init__.py +0 -0
- PYME/cluster/clusterUI/accounts/__init__.py +0 -0
- PYME/cluster/clusterUI/accounts/admin.py +85 -0
- PYME/cluster/clusterUI/accounts/forms.py +8 -0
- PYME/cluster/clusterUI/accounts/migrations/0001_initial.py +31 -0
- PYME/cluster/clusterUI/accounts/migrations/__init__.py +0 -0
- PYME/cluster/clusterUI/accounts/models.py +44 -0
- PYME/cluster/clusterUI/accounts/templates/accounts/user_form.html +13 -0
- PYME/cluster/clusterUI/accounts/templates/registration/initial_complete.html +6 -0
- PYME/cluster/clusterUI/accounts/templates/registration/initial_confirm.html +13 -0
- PYME/cluster/clusterUI/accounts/templates/registration/initial_done.html +7 -0
- PYME/cluster/clusterUI/accounts/templates/registration/verification.html +2 -0
- PYME/cluster/clusterUI/accounts/templates/registration/verification_subject.txt +1 -0
- PYME/cluster/clusterUI/accounts/urls.py +19 -0
- PYME/cluster/clusterUI/accounts/views.py +36 -0
- PYME/cluster/clusterUI/clusterUI/__init__.py +0 -0
- PYME/cluster/clusterUI/clusterUI/settings.py +147 -0
- PYME/cluster/clusterUI/clusterUI/urls.py +31 -0
- PYME/cluster/clusterUI/clusterUI/wsgi.py +16 -0
- PYME/cluster/clusterUI/clusterbrowser/__init__.py +0 -0
- PYME/cluster/clusterUI/clusterbrowser/admin.py +3 -0
- PYME/cluster/clusterUI/clusterbrowser/apps.py +7 -0
- PYME/cluster/clusterUI/clusterbrowser/migrations/__init__.py +0 -0
- PYME/cluster/clusterUI/clusterbrowser/models.py +5 -0
- PYME/cluster/clusterUI/clusterbrowser/templates/base.html +129 -0
- PYME/cluster/clusterUI/clusterbrowser/templates/clusterbrowser/dirlisting.html +231 -0
- PYME/cluster/clusterUI/clusterbrowser/templates/clusterbrowser/form_new_folder.html +18 -0
- PYME/cluster/clusterUI/clusterbrowser/templates/clusterbrowser/form_upload_file.html +17 -0
- PYME/cluster/clusterUI/clusterbrowser/templates/clusterbrowser/lightlisting.html +25 -0
- PYME/cluster/clusterUI/clusterbrowser/templates/registration/login.html +38 -0
- PYME/cluster/clusterUI/clusterbrowser/urls.py +10 -0
- PYME/cluster/clusterUI/clusterbrowser/views.py +148 -0
- PYME/cluster/clusterUI/clusterstatus/__init__.py +0 -0
- PYME/cluster/clusterUI/clusterstatus/admin.py +3 -0
- PYME/cluster/clusterUI/clusterstatus/apps.py +7 -0
- PYME/cluster/clusterUI/clusterstatus/migrations/__init__.py +0 -0
- PYME/cluster/clusterUI/clusterstatus/models.py +5 -0
- PYME/cluster/clusterUI/clusterstatus/templates/clusterstatus/load_content.html +29 -0
- PYME/cluster/clusterUI/clusterstatus/templates/clusterstatus/queue_info.html +28 -0
- PYME/cluster/clusterUI/clusterstatus/templates/clusterstatus/queue_info_content.html +50 -0
- PYME/cluster/clusterUI/clusterstatus/templates/clusterstatus/status_dash.html +29 -0
- PYME/cluster/clusterUI/clusterstatus/templates/clusterstatus/status_dash_content.html +90 -0
- PYME/cluster/clusterUI/clusterstatus/urls.py +9 -0
- PYME/cluster/clusterUI/clusterstatus/views.py +69 -0
- PYME/cluster/clusterUI/clusterui_tornado.py +117 -0
- PYME/cluster/clusterUI/deploy.py +62 -0
- PYME/cluster/clusterUI/localization/__init__.py +0 -0
- PYME/cluster/clusterUI/localization/admin.py +3 -0
- PYME/cluster/clusterUI/localization/apps.py +7 -0
- PYME/cluster/clusterUI/localization/migrations/__init__.py +0 -0
- PYME/cluster/clusterUI/localization/models.py +5 -0
- PYME/cluster/clusterUI/localization/templates/localization/settings_form.html +67 -0
- PYME/cluster/clusterUI/localization/urls.py +10 -0
- PYME/cluster/clusterUI/localization/views.py +170 -0
- PYME/cluster/clusterUI/manage.py +17 -0
- PYME/cluster/clusterUI/recipes/__init__.py +0 -0
- PYME/cluster/clusterUI/recipes/admin.py +3 -0
- PYME/cluster/clusterUI/recipes/migrations/__init__.py +0 -0
- PYME/cluster/clusterUI/recipes/models.py +3 -0
- PYME/cluster/clusterUI/recipes/templates/recipes/extra_inputs.html +35 -0
- PYME/cluster/clusterUI/recipes/templates/recipes/form_recipe.html +82 -0
- PYME/cluster/clusterUI/recipes/templates/recipes/input_list.html +7 -0
- PYME/cluster/clusterUI/recipes/templates/recipes/recipe_editor.html +28 -0
- PYME/cluster/clusterUI/recipes/templates/recipes/recipe_editor_common.html +46 -0
- PYME/cluster/clusterUI/recipes/templates/recipes/recipe_editrun.html +93 -0
- PYME/cluster/clusterUI/recipes/templates/recipes/recipe_standalone.html +100 -0
- PYME/cluster/clusterUI/recipes/templates/recipes/recipe_template.html +109 -0
- PYME/cluster/clusterUI/recipes/urls.py +17 -0
- PYME/cluster/clusterUI/recipes/views.py +109 -0
- PYME/cluster/cluster_of_one.py +204 -0
- PYME/cluster/dataserver_wsgi.py +615 -0
- PYME/cluster/distribution.py +71 -0
- PYME/cluster/rulenodeserver.py +487 -0
- PYME/cluster/rules.py +979 -0
- PYME/cluster/ruleserver.py +1106 -0
- PYME/cluster/status.py +101 -0
- PYME/cluster/taskWorkerHTTP.py +522 -0
- PYME/cluster/webdav.py +1102 -0
- PYME/config.py +673 -0
- PYME/contrib/TextCtrlAutoComplete.py +582 -0
- PYME/contrib/__init__.py +7 -0
- PYME/contrib/aniso/__init__.py +2 -0
- PYME/contrib/aniso/aniso.py +268 -0
- PYME/contrib/auiFloatBook.py +94 -0
- PYME/contrib/congrid.py +127 -0
- PYME/contrib/dispatch/__init__.py +19 -0
- PYME/contrib/dispatch/dispatcher.py +289 -0
- PYME/contrib/gohlke/__init__.py +1 -0
- PYME/contrib/gohlke/_tifffile.cpython-313-darwin.so +0 -0
- PYME/contrib/gohlke/czifile.py +1289 -0
- PYME/contrib/gohlke/fcsfiles.py +514 -0
- PYME/contrib/gohlke/setup.py +54 -0
- PYME/contrib/gohlke/tifffile.py +3095 -0
- PYME/contrib/listctrlMixins.py +896 -0
- PYME/contrib/lzw.py +838 -0
- PYME/contrib/pad/__init__.py +13 -0
- PYME/contrib/pad/info_pad.py +18 -0
- PYME/contrib/pad/pad.py +670 -0
- PYME/contrib/setup.py +38 -0
- PYME/contrib/wxPlotPanel.py +157 -0
- PYME/experimental/SimReconstruction.py +49 -0
- PYME/experimental/__init__.pxd +0 -0
- PYME/experimental/__init__.py +4 -0
- PYME/experimental/_octree.cpython-313-darwin.so +0 -0
- PYME/experimental/_octree.pyx +477 -0
- PYME/experimental/_treap.cpython-313-darwin.so +0 -0
- PYME/experimental/_treap.pyx +267 -0
- PYME/experimental/_triangle_mesh.cpython-313-darwin.so +0 -0
- PYME/experimental/_triangle_mesh.pxd +149 -0
- PYME/experimental/_triangle_mesh.pyx +2787 -0
- PYME/experimental/aqavg.py +40 -0
- PYME/experimental/dcimgFileChucker.py +375 -0
- PYME/experimental/dcimgSpoolShim.py +174 -0
- PYME/experimental/dcimg_chuck_test.py +78 -0
- PYME/experimental/dual_marching_cubes.py +801 -0
- PYME/experimental/dual_marching_cubes_v2.py +645 -0
- PYME/experimental/expectationMaximisation.py +298 -0
- PYME/experimental/func_octree.cpython-313-darwin.so +0 -0
- PYME/experimental/func_octree.pyx +381 -0
- PYME/experimental/fusionRadial.py +520 -0
- PYME/experimental/fusionUtils.py +522 -0
- PYME/experimental/isosurface.py +147 -0
- PYME/experimental/labview_spooling_hacks.py +48 -0
- PYME/experimental/marching_cubes.py +811 -0
- PYME/experimental/marching_tetrahedra.py +343 -0
- PYME/experimental/modified_marching_cubes.py +1245 -0
- PYME/experimental/music.py +25 -0
- PYME/experimental/octree.py +188 -0
- PYME/experimental/pSpaceMap.py +34 -0
- PYME/experimental/pointFitConfoc.py +112 -0
- PYME/experimental/scanner_control.py +107 -0
- PYME/experimental/setup.py +109 -0
- PYME/experimental/spark.py +31 -0
- PYME/experimental/tcHist.py +71 -0
- PYME/experimental/treap.py +262 -0
- PYME/experimental/triangle_mesh.py +2287 -0
- PYME/experimental/triangle_mesh_utils.cpython-313-darwin.so +0 -0
- PYME/experimental/triangle_utils.py +87 -0
- PYME/experimental/triangular_mesh.py +2255 -0
- PYME/experimental/zMotionArtifactUtils.py +55 -0
- PYME/localization/FitFactories/AstigGaussFitFR.py +175 -0
- PYME/localization/FitFactories/AstigGaussGPUFitFR.py +326 -0
- PYME/localization/FitFactories/BeadConvolvedAstigGaussFit.py +206 -0
- PYME/localization/FitFactories/ChecksumFR.py +82 -0
- PYME/localization/FitFactories/ChecksumGPUFR.py +213 -0
- PYME/localization/FitFactories/ChecksumMultifitSR.py +86 -0
- PYME/localization/FitFactories/ConfocCOIR.py +93 -0
- PYME/localization/FitFactories/Dumbell3DFitR.py +193 -0
- PYME/localization/FitFactories/DumbellFitR.py +163 -0
- PYME/localization/FitFactories/FFBase.py +403 -0
- PYME/localization/FitFactories/Gauss3DFitR.py +213 -0
- PYME/localization/FitFactories/GaussFitConstrR.py +177 -0
- PYME/localization/FitFactories/GaussMultifitLinesR.py +351 -0
- PYME/localization/FitFactories/GaussMultifitR.py +326 -0
- PYME/localization/FitFactories/GaussMultifitSR.py +373 -0
- PYME/localization/FitFactories/InterpFitR.py +236 -0
- PYME/localization/FitFactories/InterpFitWFR.py +111 -0
- PYME/localization/FitFactories/Interpolators/CSInterpolator.py +148 -0
- PYME/localization/FitFactories/Interpolators/CubeSInterpolatorP.py +121 -0
- PYME/localization/FitFactories/Interpolators/CubicSplineInterpolator.py +69 -0
- PYME/localization/FitFactories/Interpolators/LinearInterpolator.py +135 -0
- PYME/localization/FitFactories/Interpolators/LinearPInterpolatorP.py +95 -0
- PYME/localization/FitFactories/Interpolators/__init__.py +35 -0
- PYME/localization/FitFactories/Interpolators/baseInterpolator.py +202 -0
- PYME/localization/FitFactories/LatFitCOIR.py +82 -0
- PYME/localization/FitFactories/LatGaussFitFR.py +220 -0
- PYME/localization/FitFactories/LatObjFindFR.py +85 -0
- PYME/localization/FitFactories/LatPSFFitR.py +142 -0
- PYME/localization/FitFactories/MultiviewFitInterpNR.py +400 -0
- PYME/localization/FitFactories/PRInterpFitQR.py +192 -0
- PYME/localization/FitFactories/PRInterpFitR.py +223 -0
- PYME/localization/FitFactories/ROIExtractNR.py +93 -0
- PYME/localization/FitFactories/SpecGaussFitFR.py +174 -0
- PYME/localization/FitFactories/SplitterFitCOIR.py +142 -0
- PYME/localization/FitFactories/SplitterFitFNR.py +312 -0
- PYME/localization/FitFactories/SplitterFitFusionR.py +318 -0
- PYME/localization/FitFactories/SplitterFitInterpBNR.py +357 -0
- PYME/localization/FitFactories/SplitterFitInterpNR.py +343 -0
- PYME/localization/FitFactories/SplitterFitScavNR.py +352 -0
- PYME/localization/FitFactories/SplitterMultifitSR.py +410 -0
- PYME/localization/FitFactories/SplitterObjFindR.py +194 -0
- PYME/localization/FitFactories/SplitterROIExtractNR.py +91 -0
- PYME/localization/FitFactories/SplitterShiftEstFR.py +230 -0
- PYME/localization/FitFactories/__init__.py +105 -0
- PYME/localization/FitFactories/fitCommon.py +195 -0
- PYME/localization/FitFactories/zEstimators/__init__.py +31 -0
- PYME/localization/FitFactories/zEstimators/astigEstimator.py +173 -0
- PYME/localization/FitFactories/zEstimators/biplaneEstimator.py +209 -0
- PYME/localization/FitFactories/zEstimators/genericDualEstimator.py +232 -0
- PYME/localization/FitFactories/zEstimators/genericEstimator.py +224 -0
- PYME/localization/FitFactories/zEstimators/priEstimator.py +255 -0
- PYME/localization/MetaDataEdit.py +543 -0
- PYME/localization/Test/30_9_series_A_1.sf +0 -0
- PYME/localization/Test/PRI.md +45 -0
- PYME/localization/Test/PRI_qr.md +52 -0
- PYME/localization/Test/PRI_r.md +52 -0
- PYME/localization/Test/__init__.py +22 -0
- PYME/localization/Test/astig.md +50 -0
- PYME/localization/Test/astigCOI.md +50 -0
- PYME/localization/Test/astig_gauss.md +52 -0
- PYME/localization/Test/astig_pe.md +50 -0
- PYME/localization/Test/astig_splitter.md +66 -0
- PYME/localization/Test/astig_splitterCOI.md +67 -0
- PYME/localization/Test/astig_splitterQ.md +66 -0
- PYME/localization/Test/astig_theory.md +50 -0
- PYME/localization/Test/astig_theory.psf +0 -0
- PYME/localization/Test/astig_theory.tif +0 -0
- PYME/localization/Test/beads1.psf +0 -0
- PYME/localization/Test/beads1.tif +0 -0
- PYME/localization/Test/biplane_splitter.md +75 -0
- PYME/localization/Test/biplane_splitter2.md +103 -0
- PYME/localization/Test/biplane_splitter3.md +115 -0
- PYME/localization/Test/defoc.md +48 -0
- PYME/localization/Test/dumbell_3d.md +52 -0
- PYME/localization/Test/fitTestJig.py +172 -0
- PYME/localization/Test/fitTestJigSCMOS.py +487 -0
- PYME/localization/Test/fitTestJigWC.py +225 -0
- PYME/localization/Test/gauss.md +50 -0
- PYME/localization/Test/gaussCOI.md +50 -0
- PYME/localization/Test/pri_pe.md +50 -0
- PYME/localization/Test/pri_theory.md +51 -0
- PYME/localization/Test/pri_theory.psf +0 -0
- PYME/localization/Test/pri_theory.tif +0 -0
- PYME/localization/Test/psf_astig.psf +0 -0
- PYME/localization/Test/psf_astig.tif +0 -0
- PYME/localization/Test/psf_astig_bg_d.psf +0 -0
- PYME/localization/Test/psf_astig_bg_d.tif +0 -0
- PYME/localization/Test/psf_astig_pe.psf +0 -0
- PYME/localization/Test/psf_astig_pe.tif +0 -0
- PYME/localization/Test/psf_decon.psf +0 -0
- PYME/localization/Test/psf_decon.tif +0 -0
- PYME/localization/Test/psf_decon_pe.psf +0 -0
- PYME/localization/Test/psf_decon_pe.tif +0 -0
- PYME/localization/Test/psf_guess.psf +0 -0
- PYME/localization/Test/splitter.md +63 -0
- PYME/localization/Test/splitter_scav.md +63 -0
- PYME/localization/Test/test.psf +0 -0
- PYME/localization/Test/test.tif +0 -0
- PYME/localization/Test/test_decon.psf +0 -0
- PYME/localization/Test/test_decon.tif +0 -0
- PYME/localization/Test/test_pe.psf +0 -0
- PYME/localization/Test/test_pe.tif +0 -0
- PYME/localization/Test/wf_theory.psf +0 -0
- PYME/localization/Test/wf_theory2.psf +0 -0
- PYME/localization/__init__.py +17 -0
- PYME/localization/autopsf/__init__.py +1 -0
- PYME/localization/autopsf/autopsf.py +486 -0
- PYME/localization/autopsf/roifit.py +310 -0
- PYME/localization/cInterp/__init__.py +24 -0
- PYME/localization/cInterp/cInterp.cpython-313-darwin.so +0 -0
- PYME/localization/cInterp/setup.py +54 -0
- PYME/localization/cModels/__init__.py +24 -0
- PYME/localization/cModels/gauss_app.cpython-313-darwin.so +0 -0
- PYME/localization/ofind.py +444 -0
- PYME/localization/ofind3d.py +306 -0
- PYME/localization/ofind_nofilt.py +128 -0
- PYME/localization/ofind_pri.py +478 -0
- PYME/localization/ofind_split.py +399 -0
- PYME/localization/ofind_xcorr.py +351 -0
- PYME/localization/ofind_xcorr_fw.py +441 -0
- PYME/localization/remFitBuf.py +657 -0
- PYME/localization/setup.py +56 -0
- PYME/localization/splitting.py +240 -0
- PYME/localization/twist.py +60 -0
- PYME/misc/TiSettings.py +36 -0
- PYME/misc/TiffImagePlugin.py +838 -0
- PYME/misc/VolProj.py +144 -0
- PYME/misc/__init__.py +25 -0
- PYME/misc/aligned_array.py +10 -0
- PYME/misc/aniso.py +29 -0
- PYME/misc/big_sur_fix.py +20 -0
- PYME/misc/check_for_updates.py +146 -0
- PYME/misc/colormaps.py +199 -0
- PYME/misc/colorsys.py +201 -0
- PYME/misc/computerName.py +33 -0
- PYME/misc/coverslipGeometries.py +60 -0
- PYME/misc/cython_numpy_monkey.py +40 -0
- PYME/misc/depGraph.py +406 -0
- PYME/misc/dirSize.py +31 -0
- PYME/misc/diskCleanup.py +64 -0
- PYME/misc/djangoRecarray.py +57 -0
- PYME/misc/django_widgets.py +27 -0
- PYME/misc/editgrid.py +101 -0
- PYME/misc/eventSpy.py +122 -0
- PYME/misc/exceptions.py +30 -0
- PYME/misc/facsPlot.py +89 -0
- PYME/misc/fbpIcons.py +90 -0
- PYME/misc/fftw_compat.py +28 -0
- PYME/misc/findCycles.py +91 -0
- PYME/misc/fortran_interrupt_defeat.py +43 -0
- PYME/misc/glassModel.py +64 -0
- PYME/misc/hash32.py +41 -0
- PYME/misc/hillcurve.py +88 -0
- PYME/misc/hybrid_ns.py +84 -0
- PYME/misc/kdFit.py +72 -0
- PYME/misc/locate.py +10 -0
- PYME/misc/memUsage.py +65 -0
- PYME/misc/memmap.py +52 -0
- PYME/misc/mock_ctypes.py +28 -0
- PYME/misc/mock_traits.py +59 -0
- PYME/misc/mock_traitsui.py +29 -0
- PYME/misc/pyme_zeroconf.py +287 -0
- PYME/misc/pyro_tracebacks.py +32 -0
- PYME/misc/read_agf.py +605 -0
- PYME/misc/sffake.py +16 -0
- PYME/misc/snells.py +71 -0
- PYME/misc/sqlite_ns.py +132 -0
- PYME/misc/sqlitendarray.py +56 -0
- PYME/misc/taskDef.py +44 -0
- PYME/misc/tempDB.py +56 -0
- PYME/misc/wxThread.py +33 -0
- PYME/misc/zemax.py +259 -0
- PYME/misc/zernike.py +151 -0
- PYME/pyme_warnings.py +70 -0
- PYME/recipes/Recipes/STEDDeconvolution.yaml +14 -0
- PYME/recipes/Recipes/STEDMinistacks.yaml +15 -0
- PYME/recipes/Recipes/STED_COP3.yaml +25 -0
- PYME/recipes/Recipes/blobMeas.yaml +19 -0
- PYME/recipes/Recipes/blobMeas2.yaml +37 -0
- PYME/recipes/Recipes/blobMeasSR.yaml +66 -0
- PYME/recipes/Recipes/coloc.yaml +43 -0
- PYME/recipes/Recipes/coloc_roi_masked.yaml +46 -0
- PYME/recipes/Recipes/multiblob.yaml +38 -0
- PYME/recipes/Recipes/pre_particleTracking.yaml +30 -0
- PYME/recipes/Recipes/segmentAndMeasureLoci.yaml +41 -0
- PYME/recipes/__init__.py +6 -0
- PYME/recipes/acquisition.py +158 -0
- PYME/recipes/bakeshop.py +32 -0
- PYME/recipes/bakeshop_app.py +16 -0
- PYME/recipes/base.py +1389 -0
- PYME/recipes/batchProcess.py +147 -0
- PYME/recipes/filters.py +394 -0
- PYME/recipes/fudges.py +41 -0
- PYME/recipes/graphing.py +108 -0
- PYME/recipes/html_recipe_editor.py +90 -0
- PYME/recipes/localisations.py +1386 -0
- PYME/recipes/machine_learning.py +286 -0
- PYME/recipes/measurement.py +1063 -0
- PYME/recipes/modules.py +50 -0
- PYME/recipes/multiview.py +435 -0
- PYME/recipes/output.py +667 -0
- 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 +504 -0
- PYME/ui/editFilterDialog.py +80 -0
- PYME/ui/editList.py +40 -0
- PYME/ui/fastGraph.py +240 -0
- PYME/ui/filterPane.py +344 -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/packageutils.py +34 -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/uilaunch.py +39 -0
- PYME/util/webframework.py +365 -0
- PYME/version.py +62 -0
- python_microscopy-26.7.9.dist-info/METADATA +68 -0
- python_microscopy-26.7.9.dist-info/RECORD +1269 -0
- python_microscopy-26.7.9.dist-info/WHEEL +4 -0
- python_microscopy-26.7.9.dist-info/entry_points.txt +18 -0
PYME/cluster/webdav.py
ADDED
|
@@ -0,0 +1,1102 @@
|
|
|
1
|
+
# _*_ coding:utf-8 _*_
|
|
2
|
+
|
|
3
|
+
# Tiny WebDav Server for Pythonista - IOS. (Base on pandav WebDav server )
|
|
4
|
+
#
|
|
5
|
+
# (C)2013/11 By: Lai ChuJiang
|
|
6
|
+
#
|
|
7
|
+
# this code can run not just Pythonista on IOS ,also run on OSX python.
|
|
8
|
+
# Support Client: Windows / OSX / other Webdav client for IOS,etc : goodreader / iWorks for ios
|
|
9
|
+
#
|
|
10
|
+
# 20170907 Change Log:
|
|
11
|
+
# 1. Fix Coda WebDav access problem.(because Coda WebDav all xml item add xmlns="DAV:".)
|
|
12
|
+
#
|
|
13
|
+
# 2013/11 Change Log:
|
|
14
|
+
# 1. Combind all files to one file,so can using for Pythonista easy.
|
|
15
|
+
# 2. Add MKCOL(Create dir); MOVE(rename file); DELETE(delete file or dir); COPY (Copy file)
|
|
16
|
+
# 3. Change some decode, Now it's can support Chinese.
|
|
17
|
+
# 4. Pythonista(For IOS) not dircache module ,so change code,don't using this module.
|
|
18
|
+
# 5. change DAV version from 1 to 2, so the OSX finder can write.
|
|
19
|
+
# 6. for DAV version 2 support , add LOCK / UNLOCK fake support. (not real lock file)
|
|
20
|
+
# *** !!!! So Don't using > 1 client sametime write or delete same file. maybe lost files.
|
|
21
|
+
# 7. Change the do_PROPFIND module, now it's simply & right for OSX
|
|
22
|
+
# 8. Change the do_GET module, now support RANGE
|
|
23
|
+
# 9. Change the do_PUB module, add Content-Length=0 support (create empty file) ,so the OSX Finder support.
|
|
24
|
+
# *if not add empty file,the Finder copy files and then delete all this.
|
|
25
|
+
#10. Add WebDav Basic Auth function,now you can set user & passwd
|
|
26
|
+
# **using wdusers.conf file (just user:passwd), if not this file ,the Auth disable.
|
|
27
|
+
#11. Fix the broken pipe error message
|
|
28
|
+
#
|
|
29
|
+
# WebDav RFC: http://www.ics.uci.edu/~ejw/authoring/protocol/rfc2518.html
|
|
30
|
+
# http://restpatterns.org/HTTP_Methods
|
|
31
|
+
#
|
|
32
|
+
# Base : pandav v0.2
|
|
33
|
+
# Copyright (c) 2005.-2006. Ivan Voras <ivoras@gmail.com>
|
|
34
|
+
# Released under the Artistic License
|
|
35
|
+
#
|
|
36
|
+
|
|
37
|
+
#modified by D. Baddeley to use PYME Cluster IO as a backend, 2018
|
|
38
|
+
|
|
39
|
+
from http.server import HTTPServer, BaseHTTPRequestHandler
|
|
40
|
+
from socketserver import ThreadingMixIn
|
|
41
|
+
from io import StringIO
|
|
42
|
+
import sys,urllib,re
|
|
43
|
+
from urllib.parse import urlparse
|
|
44
|
+
from time import time, timezone, strftime, localtime, gmtime
|
|
45
|
+
import os, shutil, uuid, mimetypes, base64
|
|
46
|
+
from hashlib import md5
|
|
47
|
+
import socket
|
|
48
|
+
import ssl
|
|
49
|
+
|
|
50
|
+
import logging
|
|
51
|
+
logging.basicConfig(level=logging.DEBUG)
|
|
52
|
+
logger = logging.getLogger(__name__)
|
|
53
|
+
|
|
54
|
+
from PYME.IO import clusterIO
|
|
55
|
+
from PYME.IO import clusterListing
|
|
56
|
+
|
|
57
|
+
from io import BytesIO
|
|
58
|
+
|
|
59
|
+
def makedirs_safe(dir):
|
|
60
|
+
"""
|
|
61
|
+
A safe wrapper for makedirs, which won't throw an error if the directory already exists. This replicates the functionality
|
|
62
|
+
of the exists_ok flag in the python 3 version of os.makedirs, but should work with both pytion 2 and python 3.
|
|
63
|
+
|
|
64
|
+
Parameters
|
|
65
|
+
----------
|
|
66
|
+
dir : str, directory to be created
|
|
67
|
+
|
|
68
|
+
Returns
|
|
69
|
+
-------
|
|
70
|
+
|
|
71
|
+
"""
|
|
72
|
+
import errno
|
|
73
|
+
try:
|
|
74
|
+
os.makedirs(dir)
|
|
75
|
+
except OSError as e:
|
|
76
|
+
if e.errno != errno.EEXIST:
|
|
77
|
+
raise
|
|
78
|
+
|
|
79
|
+
# 获取本机IP地址
|
|
80
|
+
def get_localip():
|
|
81
|
+
try:
|
|
82
|
+
gAdd = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
|
|
83
|
+
gAdd.connect(('www.bing.com', 80))
|
|
84
|
+
return gAdd.getsockname()[0]
|
|
85
|
+
except:
|
|
86
|
+
return '127.0.0.1'
|
|
87
|
+
|
|
88
|
+
class Member:
|
|
89
|
+
M_MEMBER = 1
|
|
90
|
+
M_COLLECTION = 2
|
|
91
|
+
def getProperties(self):
|
|
92
|
+
return {}
|
|
93
|
+
|
|
94
|
+
class Collection(Member):
|
|
95
|
+
def __init__(self, name):
|
|
96
|
+
self.name = name
|
|
97
|
+
def getMembers(self):
|
|
98
|
+
return []
|
|
99
|
+
|
|
100
|
+
class FileMember(Member):
|
|
101
|
+
def __init__(self, name, parent):
|
|
102
|
+
self.name = name
|
|
103
|
+
self.parent = parent
|
|
104
|
+
self.name = name
|
|
105
|
+
self.fsname = parent.fsname + name # e.g. '/var/www/mysite/some.txt'
|
|
106
|
+
self.virname = parent.virname + name # e.g. '/mysite/some.txt'
|
|
107
|
+
self.type = Member.M_MEMBER
|
|
108
|
+
|
|
109
|
+
def __str__(self):
|
|
110
|
+
return "%s -> %s" % (self.virname, self.fsname)
|
|
111
|
+
|
|
112
|
+
def getProperties(self):
|
|
113
|
+
"""Return dictionary with WebDAV properties. Values shold be
|
|
114
|
+
formatted according to the WebDAV specs."""
|
|
115
|
+
st = clusterIO.stat(self.fsname)
|
|
116
|
+
p = {}
|
|
117
|
+
p['creationdate'] = unixdate2iso8601(st.st_ctime)
|
|
118
|
+
p['getlastmodified'] = unixdate2httpdate(st.st_mtime)
|
|
119
|
+
p['displayname'] = self.name
|
|
120
|
+
p['getetag'] = md5.new(self.fsname).hexdigest()
|
|
121
|
+
if self.type == Member.M_MEMBER:
|
|
122
|
+
p['getcontentlength'] = st.st_size
|
|
123
|
+
p['getcontenttype'], z = mimetypes.guess_type(self.name)
|
|
124
|
+
p['getcontentlanguage'] = None
|
|
125
|
+
else: # Member.M_COLLECTION
|
|
126
|
+
p['resourcetype'] = '<D:collection/>'
|
|
127
|
+
if self.name[0] == ".":
|
|
128
|
+
p['ishidden'] = 1
|
|
129
|
+
if True:# not os.access(self.fsname, os.W_OK):
|
|
130
|
+
p['isreadonly'] = 1
|
|
131
|
+
if self.name == '/':
|
|
132
|
+
p['isroot'] = 1
|
|
133
|
+
return p
|
|
134
|
+
|
|
135
|
+
def sendData(self, wfile,bpoint=0,epoint=0):
|
|
136
|
+
"""Send the file to the client. Literally."""
|
|
137
|
+
data = clusterIO.get_file(self.fsname)
|
|
138
|
+
f_size = len(data)
|
|
139
|
+
#st = clusterIO.stat(self.fsname)
|
|
140
|
+
#with open(self.fsname, 'rb') as f:
|
|
141
|
+
f = BytesIO(data) #TODO - does this make sense?
|
|
142
|
+
writ = 0
|
|
143
|
+
# for send Range xxx-xxx
|
|
144
|
+
if bpoint>0 and bpoint<f_size:
|
|
145
|
+
f.seek(bpoint)
|
|
146
|
+
|
|
147
|
+
if epoint>bpoint:
|
|
148
|
+
if epoint<=f_size:
|
|
149
|
+
rsize = epoint - bpoint + 1
|
|
150
|
+
else:
|
|
151
|
+
rsize = f_size - bpoint
|
|
152
|
+
else:
|
|
153
|
+
rsize = f_size
|
|
154
|
+
|
|
155
|
+
|
|
156
|
+
while writ < rsize:
|
|
157
|
+
if (rsize - writ) < 65536:
|
|
158
|
+
buf = f.read(rsize)
|
|
159
|
+
else:
|
|
160
|
+
buf = f.read(65536)
|
|
161
|
+
if not buf:
|
|
162
|
+
break
|
|
163
|
+
writ += len(buf)
|
|
164
|
+
wfile.write(buf)
|
|
165
|
+
|
|
166
|
+
class DummyFileMember(FileMember):
|
|
167
|
+
def getProperties(self):
|
|
168
|
+
p = {}
|
|
169
|
+
p['creationdate'] = unixdate2iso8601(time())
|
|
170
|
+
p['getlastmodified'] = unixdate2httpdate(time())
|
|
171
|
+
p['displayname'] = self.name
|
|
172
|
+
p['getetag'] = md5.new(self.fsname).hexdigest()
|
|
173
|
+
if self.type == Member.M_MEMBER:
|
|
174
|
+
p['getcontentlength'] = 0
|
|
175
|
+
p['getcontenttype'], z = mimetypes.guess_type(self.name)
|
|
176
|
+
p['getcontentlanguage'] = None
|
|
177
|
+
else: # Member.M_COLLECTION
|
|
178
|
+
p['resourcetype'] = '<D:collection/>'
|
|
179
|
+
if self.name[0] == ".":
|
|
180
|
+
p['ishidden'] = 1
|
|
181
|
+
if True:# not os.access(self.fsname, os.W_OK):
|
|
182
|
+
p['isreadonly'] = 1
|
|
183
|
+
if self.name == '/':
|
|
184
|
+
p['isroot'] = 1
|
|
185
|
+
return p
|
|
186
|
+
|
|
187
|
+
|
|
188
|
+
class DirCollection(FileMember, Collection):
|
|
189
|
+
COLLECTION_MIME_TYPE = 'httpd/unix-directory' # application/x-collection ?
|
|
190
|
+
def __init__(self, fsdir, virdir, parent=None):
|
|
191
|
+
if not clusterIO.exists(fsdir):
|
|
192
|
+
raise RuntimeError("Local directory (fsdir) not found: " + fsdir)
|
|
193
|
+
self.fsname = fsdir
|
|
194
|
+
self.name = virdir
|
|
195
|
+
if self.fsname[-1] != os.sep:
|
|
196
|
+
if self.fsname[-1] == '/': # fixup win/dos/mac separators
|
|
197
|
+
self.fsname = self.fsname[:-1] + os.sep
|
|
198
|
+
else:
|
|
199
|
+
self.fsname += os.sep
|
|
200
|
+
self.virname = virdir
|
|
201
|
+
if self.virname[-1] != '/':
|
|
202
|
+
self.virname += '/'
|
|
203
|
+
self.parent = parent
|
|
204
|
+
self.type = Member.M_COLLECTION
|
|
205
|
+
|
|
206
|
+
def getProperties(self):
|
|
207
|
+
p = FileMember.getProperties(self) # inherit file properties
|
|
208
|
+
p['iscollection'] = 1
|
|
209
|
+
p['getcontenttype'] = DirCollection.COLLECTION_MIME_TYPE
|
|
210
|
+
p['getcontentlength'] = 0
|
|
211
|
+
return p
|
|
212
|
+
|
|
213
|
+
def getMembers(self):
|
|
214
|
+
"""Get immediate members of this collection."""
|
|
215
|
+
l = clusterIO.listdirectory(self.fsname) # obtain a copy of dirlist
|
|
216
|
+
#tcount=0
|
|
217
|
+
#for tmpi in l:
|
|
218
|
+
# if os.path.isfile(self.fsname+tmpi) == False:
|
|
219
|
+
# l[tcount]=l[tcount]+'/'
|
|
220
|
+
# tcount += 1
|
|
221
|
+
|
|
222
|
+
|
|
223
|
+
r = []
|
|
224
|
+
for fn, f_info in l.items():
|
|
225
|
+
if f_info.type == clusterListing.FILETYPE_NORMAL:
|
|
226
|
+
m = FileMember(fn, self) # Member is a file
|
|
227
|
+
else:
|
|
228
|
+
m = DirCollection(self.fsname + fn, self.virname + fn, self) # Member is a collection
|
|
229
|
+
r.append(m)
|
|
230
|
+
|
|
231
|
+
for d_ in _temporary_directories:
|
|
232
|
+
real_dirs = l.keys()
|
|
233
|
+
if d_ in real_dirs or (d_ + '/') in real_dirs:
|
|
234
|
+
_temporary_directories.remove(d_)
|
|
235
|
+
|
|
236
|
+
if d_.startswith(self.fsname):
|
|
237
|
+
d__ = d_[len(self.fsname):]
|
|
238
|
+
if len(d__.lstrip('/').rstrip('/').split('/')) == 1:
|
|
239
|
+
#temporary directory is at this level
|
|
240
|
+
r.append(TempDirCollection(d_, self.virname + d__))
|
|
241
|
+
|
|
242
|
+
for f_ in _dummy_files:
|
|
243
|
+
if f_.startswith(self.fsname):
|
|
244
|
+
f__ = f_[len(self.fsname):]
|
|
245
|
+
if len(f__.lstrip('/').rstrip('/').split('/')) == 1:
|
|
246
|
+
#temporary directory is at this level
|
|
247
|
+
r.append(DummyFileMember(f__.lstrip('/'), self))
|
|
248
|
+
|
|
249
|
+
#print _temporary_directories
|
|
250
|
+
#print [str(r_) for r_ in r]
|
|
251
|
+
|
|
252
|
+
return r
|
|
253
|
+
|
|
254
|
+
# Return WebDav Root Dir info
|
|
255
|
+
def rootdir(self):
|
|
256
|
+
return self.fsname
|
|
257
|
+
|
|
258
|
+
def findMember(self, name):
|
|
259
|
+
"""Search for a particular member."""
|
|
260
|
+
#l = os.listdir(self.fsname) # obtain a copy of dirlist
|
|
261
|
+
l = clusterIO.listdirectory(self.fsname)
|
|
262
|
+
# tcount=0
|
|
263
|
+
# for tmpi in l:
|
|
264
|
+
# if os.path.isfile(self.fsname+tmpi) == False:
|
|
265
|
+
# l[tcount]=l[tcount]+'/'
|
|
266
|
+
# tcount += 1
|
|
267
|
+
|
|
268
|
+
|
|
269
|
+
# if name in l:
|
|
270
|
+
# if name[-1] != '/':
|
|
271
|
+
# return FileMember(name, self)
|
|
272
|
+
# else:
|
|
273
|
+
# return DirCollection(self.fsname + name, self.virname + name, self)
|
|
274
|
+
|
|
275
|
+
try:
|
|
276
|
+
info = l[name]
|
|
277
|
+
if info.type == clusterListing.FILETYPE_NORMAL:
|
|
278
|
+
return FileMember(name, self)
|
|
279
|
+
else:
|
|
280
|
+
return DirCollection(self.fsname + name, self.virname + name, self)
|
|
281
|
+
except KeyError:
|
|
282
|
+
pass
|
|
283
|
+
|
|
284
|
+
fname = (self.fsname.rstrip('/') + '/' + name.lstrip('/'))
|
|
285
|
+
if fname in _dummy_files:
|
|
286
|
+
return DummyFileMember(name, self)
|
|
287
|
+
|
|
288
|
+
name += '/'
|
|
289
|
+
#print (self.fsname + name), _temporary_directories
|
|
290
|
+
if name in l.keys():
|
|
291
|
+
return DirCollection(self.fsname + name, self.virname + name, self)
|
|
292
|
+
elif (self.fsname + name).rstrip('/') in _temporary_directories:
|
|
293
|
+
return TempDirCollection(self.fsname + name, self.virname + name, self)
|
|
294
|
+
|
|
295
|
+
def sendData(self, wfile):
|
|
296
|
+
"""Send "file" to the client. Since this is a directory, build some arbitrary HTML."""
|
|
297
|
+
memb = self.getMembers()
|
|
298
|
+
data = '<html><head><title>%s</title></head><body>' % self.virname
|
|
299
|
+
data += '<table><tr><th>Name</th><th>Size</th><th>Timestamp</th></tr>'
|
|
300
|
+
for m in memb:
|
|
301
|
+
p = m.getProperties()
|
|
302
|
+
if 'getcontentlength' in p:
|
|
303
|
+
p['size'] = int(p['getcontentlength'])
|
|
304
|
+
p['timestamp'] = p['getlastmodified']
|
|
305
|
+
else:
|
|
306
|
+
p['size'] = 0
|
|
307
|
+
p['timestamp'] = '-DIR-'
|
|
308
|
+
data += '<tr><td>%s</td><td>%d</td><td>%s</td></tr>' % (p['displayname'], p['size'], p['timestamp'])
|
|
309
|
+
data += '</table></body></html>'
|
|
310
|
+
wfile.write(data)
|
|
311
|
+
|
|
312
|
+
def recvMember(self, rfile, name, size, req):
|
|
313
|
+
"""Receive (save) a member file"""
|
|
314
|
+
|
|
315
|
+
fname = os.path.join(self.fsname, urllib.unquote(name))
|
|
316
|
+
|
|
317
|
+
if size==0:
|
|
318
|
+
_dummy_files.append(fname)
|
|
319
|
+
return
|
|
320
|
+
else:
|
|
321
|
+
try:
|
|
322
|
+
_dummy_files.remove(fname)
|
|
323
|
+
except ValueError:
|
|
324
|
+
pass
|
|
325
|
+
|
|
326
|
+
#f = file(fname, 'wb')
|
|
327
|
+
f = BytesIO()
|
|
328
|
+
# if size=-1 it's Transfer-Encoding: Chunked mode, like OSX finder using this mode put data
|
|
329
|
+
# so the file size need get here.
|
|
330
|
+
if size == -2:
|
|
331
|
+
l = int(rfile.readline(), 16)
|
|
332
|
+
ltotal = 0
|
|
333
|
+
while l > 0:
|
|
334
|
+
buf = rfile.read(l)
|
|
335
|
+
f.write(buf) #yield buf
|
|
336
|
+
rfile.readline()
|
|
337
|
+
ltotal += l
|
|
338
|
+
l = int(rfile.readline(), 16)
|
|
339
|
+
elif size > 0: # if size=0 ,just save a empty file.
|
|
340
|
+
writ = 0
|
|
341
|
+
bs = 65536
|
|
342
|
+
while True:
|
|
343
|
+
if size != -1 and (bs > size-writ):
|
|
344
|
+
bs = size-writ
|
|
345
|
+
buf = rfile.read(bs)
|
|
346
|
+
if len(buf) == 0:
|
|
347
|
+
break
|
|
348
|
+
f.write(buf)
|
|
349
|
+
writ += len(buf)
|
|
350
|
+
if size != -1 and writ >= size:
|
|
351
|
+
break
|
|
352
|
+
|
|
353
|
+
logger.debug('ClusterIO put: %s' % fname)
|
|
354
|
+
clusterIO.put_file(fname, f.getvalue())
|
|
355
|
+
|
|
356
|
+
f.close()
|
|
357
|
+
|
|
358
|
+
class TempDirCollection(DirCollection):
|
|
359
|
+
"""Temporary directories do not exist on disk. They are held in
|
|
360
|
+
memory on the server to provide a mechanism for creating new
|
|
361
|
+
directories with the create + rename/move mechanism used by most OSs"""
|
|
362
|
+
|
|
363
|
+
def __init__(self, fsdir, virdir, parent=None):
|
|
364
|
+
self.fsname = fsdir
|
|
365
|
+
self.name = virdir
|
|
366
|
+
if self.fsname[-1] != os.sep:
|
|
367
|
+
if self.fsname[-1] == '/': # fixup win/dos/mac separators
|
|
368
|
+
self.fsname = self.fsname[:-1] + os.sep
|
|
369
|
+
else:
|
|
370
|
+
self.fsname += os.sep
|
|
371
|
+
self.virname = virdir
|
|
372
|
+
if self.virname[-1] != '/':
|
|
373
|
+
self.virname += '/'
|
|
374
|
+
self.parent = parent
|
|
375
|
+
self.type = Member.M_COLLECTION
|
|
376
|
+
self.ctime = time()
|
|
377
|
+
|
|
378
|
+
def getProperties(self):
|
|
379
|
+
"""Return dictionary with WebDAV properties. Values shold be
|
|
380
|
+
formatted according to the WebDAV specs."""
|
|
381
|
+
#st = os.stat(self.fsname)
|
|
382
|
+
p = {}
|
|
383
|
+
p['creationdate'] = unixdate2iso8601(self.ctime)
|
|
384
|
+
p['getlastmodified'] = unixdate2httpdate(self.ctime)
|
|
385
|
+
p['displayname'] = self.name
|
|
386
|
+
p['getetag'] = md5.new(self.fsname).hexdigest()
|
|
387
|
+
|
|
388
|
+
# Member.M_COLLECTION
|
|
389
|
+
p['resourcetype'] = '<D:collection/>'
|
|
390
|
+
p['iscollection'] = 1
|
|
391
|
+
p['getcontenttype'] = DirCollection.COLLECTION_MIME_TYPE
|
|
392
|
+
|
|
393
|
+
if self.name[0] == ".":
|
|
394
|
+
p['ishidden'] = 1
|
|
395
|
+
if True:# not os.access(self.fsname, os.W_OK):
|
|
396
|
+
p['isreadonly'] = 1
|
|
397
|
+
if self.name == '/':
|
|
398
|
+
p['isroot'] = 1
|
|
399
|
+
return p
|
|
400
|
+
|
|
401
|
+
def getMembers(self):
|
|
402
|
+
r = []
|
|
403
|
+
|
|
404
|
+
for d_ in _temporary_directories:
|
|
405
|
+
if d_.startswith(self.fsname):
|
|
406
|
+
d__ = d_[len(self.fsname):]
|
|
407
|
+
if len(d__.lstrip('/').rstrip('/').split('/')) == 1:
|
|
408
|
+
#temporary directory is at this level
|
|
409
|
+
r.append(TempDirCollection(d_, self.virname + d__))
|
|
410
|
+
|
|
411
|
+
return r
|
|
412
|
+
|
|
413
|
+
|
|
414
|
+
def findMember(self, name):
|
|
415
|
+
if (self.fsname + name).rstrip('/') in _temporary_directories:
|
|
416
|
+
return TempDirCollection(self.fsname + name, self.virname + name, self)
|
|
417
|
+
|
|
418
|
+
def recvMember(self, rfile, name, size, req):
|
|
419
|
+
#actually create the directory
|
|
420
|
+
#makedirs_safe(self.fsname)
|
|
421
|
+
#_temporary_directories.remove(self.fsname.rstrip('/'))
|
|
422
|
+
|
|
423
|
+
DirCollection.recvMember(self, rfile, name, size, req)
|
|
424
|
+
|
|
425
|
+
def unixdate2iso8601(d):
|
|
426
|
+
tz = timezone / 3600 # can it be fractional?
|
|
427
|
+
tz = '%+03d' % tz
|
|
428
|
+
return strftime('%Y-%m-%dT%H:%M:%S', localtime(d)) + tz + ':00'
|
|
429
|
+
|
|
430
|
+
def unixdate2httpdate(d):
|
|
431
|
+
return strftime('%a, %d %b %Y %H:%M:%S GMT', gmtime(d))
|
|
432
|
+
|
|
433
|
+
class Tag:
|
|
434
|
+
def __init__(self, name, attrs, data='', parser=None):
|
|
435
|
+
self.d = {}
|
|
436
|
+
self.name = name
|
|
437
|
+
self.attrs = attrs
|
|
438
|
+
if type(self.attrs) == type(''):
|
|
439
|
+
self.attrs = splitattrs(self.attrs)
|
|
440
|
+
for a in self.attrs:
|
|
441
|
+
if a.startswith('xmlns'):
|
|
442
|
+
nsname = a[6:]
|
|
443
|
+
parser.namespaces[nsname] = self.attrs[a]
|
|
444
|
+
self.rawname = self.name
|
|
445
|
+
|
|
446
|
+
p = name.find(':')
|
|
447
|
+
if p > 0:
|
|
448
|
+
nsname = name[0:p]
|
|
449
|
+
if nsname in parser.namespaces:
|
|
450
|
+
self.ns = parser.namespaces[nsname]
|
|
451
|
+
self.name = self.rawname[p+1:]
|
|
452
|
+
else:
|
|
453
|
+
self.ns = ''
|
|
454
|
+
self.data = data
|
|
455
|
+
|
|
456
|
+
# Emulate dictionary d
|
|
457
|
+
def __len__(self):
|
|
458
|
+
return len(self.d)
|
|
459
|
+
|
|
460
|
+
def __getitem__(self, key):
|
|
461
|
+
return self.d[key]
|
|
462
|
+
|
|
463
|
+
def __setitem__(self, key, value):
|
|
464
|
+
self.d[key] = value
|
|
465
|
+
|
|
466
|
+
def __delitem__(self, key):
|
|
467
|
+
del self.d[key]
|
|
468
|
+
|
|
469
|
+
def __iter__(self):
|
|
470
|
+
return self.d.iterkeys()
|
|
471
|
+
|
|
472
|
+
def __contains__(self, key):
|
|
473
|
+
return key in self.d
|
|
474
|
+
|
|
475
|
+
def __str__(self):
|
|
476
|
+
"""Returns unicode semi human-readable representation of the structure"""
|
|
477
|
+
if self.attrs:
|
|
478
|
+
s = u'<%s %s> %s ' % (self.name, self.attrs, self.data)
|
|
479
|
+
else:
|
|
480
|
+
s = u'<%s> %s ' % (self.name, self.data)
|
|
481
|
+
|
|
482
|
+
for k in self.d:
|
|
483
|
+
if type(self.d[k]) == type(self):
|
|
484
|
+
s += u'|%s: %s|' % (k, str(self.d[k]))
|
|
485
|
+
else:
|
|
486
|
+
s += u'|' + u','.join([str(x) for x in self.d[k]]) + u'|'
|
|
487
|
+
return s
|
|
488
|
+
|
|
489
|
+
def addChild(self, tag):
|
|
490
|
+
"""Adds a child to self. tag must be instance of Tag"""
|
|
491
|
+
if tag.name in self.d:
|
|
492
|
+
if type(self.d[tag.name]) == type(self): # If there are multiple sibiling tags with same name, form a list :)
|
|
493
|
+
self.d[tag.name] = [self.d[tag.name]]
|
|
494
|
+
self.d[tag.name].append(tag)
|
|
495
|
+
else:
|
|
496
|
+
self.d[tag.name] = tag
|
|
497
|
+
return tag
|
|
498
|
+
|
|
499
|
+
class XMLDict_Parser:
|
|
500
|
+
def __init__(self, xml):
|
|
501
|
+
self.xml = xml
|
|
502
|
+
self.p = 0
|
|
503
|
+
self.encoding = sys.getdefaultencoding()
|
|
504
|
+
self.namespaces = {}
|
|
505
|
+
|
|
506
|
+
def getnexttag(self):
|
|
507
|
+
ptag = self.xml.find('<', self.p)
|
|
508
|
+
if ptag < 0:
|
|
509
|
+
return None, None, self.xml[self.p:].strip()
|
|
510
|
+
data = self.xml[self.p:ptag].strip()
|
|
511
|
+
self.p = ptag
|
|
512
|
+
self.tagbegin = ptag
|
|
513
|
+
p2 = self.xml.find('>', self.p+1)
|
|
514
|
+
if p2 < 0:
|
|
515
|
+
raise "Malformed XML - unclosed tag?"
|
|
516
|
+
tag = self.xml[ptag+1:p2]
|
|
517
|
+
self.p = p2+1
|
|
518
|
+
self.tagend = p2+1
|
|
519
|
+
ps = tag.find(' ')
|
|
520
|
+
### Change By LCJ @ 2017/9/7 from [ if ps > 0: ] ###
|
|
521
|
+
### for IOS Coda Webdav support ###
|
|
522
|
+
if ps > 0 and tag[-1] != '/':
|
|
523
|
+
tag, attrs = tag.split(' ', 1)
|
|
524
|
+
else:
|
|
525
|
+
attrs = ''
|
|
526
|
+
return tag, attrs, data
|
|
527
|
+
|
|
528
|
+
def builddict(self):
|
|
529
|
+
"""Builds a nested-dictionary-like structure from the xml. This method
|
|
530
|
+
picks up tags on the main level and calls processTag() for nested tags."""
|
|
531
|
+
d = Tag('<root>', '')
|
|
532
|
+
while True:
|
|
533
|
+
tag, attrs, data = self.getnexttag()
|
|
534
|
+
if data != '': # data is actually that between the last tag and this one
|
|
535
|
+
sys.stderr.write("Warning: inline data between tags?!\n")
|
|
536
|
+
if not tag:
|
|
537
|
+
break
|
|
538
|
+
if tag[-1] == '/': # an 'empty' tag (e.g. <empty/>)
|
|
539
|
+
d.addChild(Tag(tag[:-1], attrs, parser=self))
|
|
540
|
+
continue
|
|
541
|
+
elif tag[0] == '?': # special tag
|
|
542
|
+
t = d.addChild(Tag(tag, attrs, parser=self))
|
|
543
|
+
if tag == '?xml' and 'encoding' in t.attrs:
|
|
544
|
+
self.encoding = t.attrs['encoding']
|
|
545
|
+
else:
|
|
546
|
+
try:
|
|
547
|
+
self.processTag(d.addChild(Tag(tag, attrs, parser=self)))
|
|
548
|
+
except:
|
|
549
|
+
sys.stderr.write("Error processing tag %s\n" % tag)
|
|
550
|
+
d.encoding = self.encoding
|
|
551
|
+
return d
|
|
552
|
+
|
|
553
|
+
def processTag(self, dtag):
|
|
554
|
+
"""Process single tag's data"""
|
|
555
|
+
until = '/'+dtag.rawname
|
|
556
|
+
while True:
|
|
557
|
+
tag, attrs, data = self.getnexttag()
|
|
558
|
+
if data:
|
|
559
|
+
dtag.data += data
|
|
560
|
+
if tag == None:
|
|
561
|
+
sys.stderr.write("Unterminated tag '"+dtag.rawname+"'?\n")
|
|
562
|
+
break
|
|
563
|
+
if tag == until:
|
|
564
|
+
break
|
|
565
|
+
if tag[-1] == '/':
|
|
566
|
+
dtag.addChild(Tag(tag[:-1], attrs, parser=self))
|
|
567
|
+
continue
|
|
568
|
+
self.processTag(dtag.addChild(Tag(tag, attrs, parser=self)))
|
|
569
|
+
|
|
570
|
+
def splitattrs(att):
|
|
571
|
+
"""Extracts name="value" pairs from string; returns them as dictionary"""
|
|
572
|
+
d = {}
|
|
573
|
+
for m in re.findall('([a-zA-Z_][a-zA-Z_:0-9]*?)="(.+?)"', att):
|
|
574
|
+
d[m[0]] = m[1]
|
|
575
|
+
return d
|
|
576
|
+
|
|
577
|
+
def builddict(xml):
|
|
578
|
+
"""Wrapper function for straightforward parsing"""
|
|
579
|
+
p = XMLDict_Parser(xml)
|
|
580
|
+
return p.builddict()
|
|
581
|
+
|
|
582
|
+
#hold new directories in memory (not on disk) so they can be renamed
|
|
583
|
+
_temporary_directories = []
|
|
584
|
+
#similarly, for OSX 0-sized files
|
|
585
|
+
_dummy_files = []
|
|
586
|
+
|
|
587
|
+
|
|
588
|
+
class DAVRequestHandler(BaseHTTPRequestHandler):
|
|
589
|
+
server_version = "Pythonista_dav"
|
|
590
|
+
all_props = ['name', 'parentname', 'href', 'ishidden', 'isreadonly', 'getcontenttype',
|
|
591
|
+
'contentclass', 'getcontentlanguage', 'creationdate', 'lastaccessed', 'getlastmodified',
|
|
592
|
+
'getcontentlength', 'iscollection', 'isstructureddocument', 'defaultdocument',
|
|
593
|
+
'displayname', 'isroot', 'resourcetype']
|
|
594
|
+
basic_props = ['name', 'getcontenttype', 'getcontentlength', 'creationdate', 'iscollection']
|
|
595
|
+
auth_file = False
|
|
596
|
+
auth_enable = False
|
|
597
|
+
Auserlist = []
|
|
598
|
+
|
|
599
|
+
# User Auth
|
|
600
|
+
# if success ,return False;
|
|
601
|
+
# Get WebDav User/Pass file : wdusers.conf
|
|
602
|
+
# file formate: user:pass\n user:pass\n
|
|
603
|
+
def WebAuth(self):
|
|
604
|
+
if self.server.auth_enable:
|
|
605
|
+
if 'Authorization' in self.headers:
|
|
606
|
+
try:
|
|
607
|
+
AuthInfo = self.headers['Authorization'][6:]
|
|
608
|
+
except:
|
|
609
|
+
AuthInfo = ''
|
|
610
|
+
if AuthInfo in self.server.userpwd:
|
|
611
|
+
return False # Auth success
|
|
612
|
+
self.send_response(401,'Authorization Required')
|
|
613
|
+
self.send_header('WWW-Authenticate', 'Basic realm="WebDav Auth"')
|
|
614
|
+
self.send_header('Content-type', 'text/html')
|
|
615
|
+
self.end_headers()
|
|
616
|
+
return True
|
|
617
|
+
else:
|
|
618
|
+
return False
|
|
619
|
+
|
|
620
|
+
def do_OPTIONS(self):
|
|
621
|
+
if self.WebAuth():
|
|
622
|
+
return
|
|
623
|
+
self.send_response(200, DAVRequestHandler.server_version)
|
|
624
|
+
#self.send_header('Allow', 'GET, HEAD, POST, PUT, DELETE, OPTIONS, PROPFIND, PROPPATCH, MKCOL, LOCK, UNLOCK, MOVE, COPY')
|
|
625
|
+
self.send_header('Allow',
|
|
626
|
+
'GET, HEAD, POST, PUT, OPTIONS, PROPFIND, PROPPATCH, MKCOL')#, LOCK, UNLOCK')
|
|
627
|
+
self.send_header('Content-length', '0')
|
|
628
|
+
self.send_header('X-Server-Copyright', DAVRequestHandler.server_version)
|
|
629
|
+
self.send_header('DAV', '1, 2') #OSX Finder need Ver 2, if Ver 1 -- read only
|
|
630
|
+
self.send_header('MS-Author-Via', 'DAV')
|
|
631
|
+
self.end_headers()
|
|
632
|
+
|
|
633
|
+
def do_DELETE(self):
|
|
634
|
+
if self.WebAuth():
|
|
635
|
+
return
|
|
636
|
+
|
|
637
|
+
logger.debug('Attempting to delete %s' % self.path)
|
|
638
|
+
|
|
639
|
+
self.send_error(403, 'Forbidden')
|
|
640
|
+
self.send_header('Content-length', '0')
|
|
641
|
+
self.end_headers()
|
|
642
|
+
return
|
|
643
|
+
|
|
644
|
+
# path = urllib.unquote(self.path)
|
|
645
|
+
# if path == '':
|
|
646
|
+
# self.send_error(404, 'Object not found')
|
|
647
|
+
# self.send_header('Content-length', '0')
|
|
648
|
+
# self.end_headers()
|
|
649
|
+
# return
|
|
650
|
+
# path = self.server.root.rootdir() + path
|
|
651
|
+
# if os.path.isfile(path):
|
|
652
|
+
# os.remove(path) #delete file
|
|
653
|
+
# elif os.path.isdir(path):
|
|
654
|
+
# shutil.rmtree(path) #delete dir
|
|
655
|
+
# else:
|
|
656
|
+
# self.send_response(404,'Not Found')
|
|
657
|
+
# self.send_header('Content-length', '0')
|
|
658
|
+
# self.end_headers()
|
|
659
|
+
# return
|
|
660
|
+
# self.send_response(204, 'No Content')
|
|
661
|
+
# self.send_header('Content-length', '0')
|
|
662
|
+
# self.end_headers()
|
|
663
|
+
|
|
664
|
+
def do_MKCOL(self):
|
|
665
|
+
if self.WebAuth():
|
|
666
|
+
return
|
|
667
|
+
path = urllib.unquote(self.path)
|
|
668
|
+
|
|
669
|
+
logger.debug('MKCOL: %s' % path)
|
|
670
|
+
|
|
671
|
+
if path != '':
|
|
672
|
+
path = self.server.root.rootdir().rstrip('/') + '/' + path.lstrip('/')
|
|
673
|
+
if os.path.exists(path) == False:
|
|
674
|
+
#os.mkdir(path)
|
|
675
|
+
_temporary_directories.append(path)
|
|
676
|
+
self.send_response(201, "Created")
|
|
677
|
+
self.send_header('Content-length', '0')
|
|
678
|
+
self.end_headers()
|
|
679
|
+
return
|
|
680
|
+
|
|
681
|
+
self.send_response(403, "OK")
|
|
682
|
+
self.send_header('Content-length', '0')
|
|
683
|
+
self.end_headers()
|
|
684
|
+
|
|
685
|
+
def do_MOVE(self):
|
|
686
|
+
if self.WebAuth():
|
|
687
|
+
return
|
|
688
|
+
oldfile = self.server.root.rootdir().rstrip('/') + '/' + urllib.unquote(self.path).lstrip('/').rstrip('/')
|
|
689
|
+
newfile = self.server.root.rootdir().rstrip('/') + '/' + urlparse.urlparse(urllib.unquote(self.headers['Destination'])).path.lstrip('/').rstrip('/')
|
|
690
|
+
|
|
691
|
+
print('MOVE: %s -> %s' % (oldfile, newfile))
|
|
692
|
+
#print _temporary_directories
|
|
693
|
+
|
|
694
|
+
if oldfile in _temporary_directories:
|
|
695
|
+
_temporary_directories.remove(oldfile)
|
|
696
|
+
_temporary_directories.append(newfile)
|
|
697
|
+
|
|
698
|
+
#if (os.path.isfile(oldfile)==True and os.path.isfile(newfile)==False):
|
|
699
|
+
# shutil.move(oldfile,newfile)
|
|
700
|
+
#if (os.path.isdir(oldfile)==True and os.path.isdir(newfile)==False):
|
|
701
|
+
# os.rename(oldfile,newfile)
|
|
702
|
+
self.send_response(201, "Created")
|
|
703
|
+
self.send_header('Content-length', '0')
|
|
704
|
+
self.end_headers()
|
|
705
|
+
return
|
|
706
|
+
else:
|
|
707
|
+
self.send_error(403, 'Forbidden')
|
|
708
|
+
self.send_header('Content-length', '0')
|
|
709
|
+
self.end_headers()
|
|
710
|
+
return
|
|
711
|
+
|
|
712
|
+
|
|
713
|
+
def do_COPY(self):
|
|
714
|
+
if self.WebAuth():
|
|
715
|
+
return
|
|
716
|
+
|
|
717
|
+
logger.debug('Attempting to copy %s' % self.path)
|
|
718
|
+
|
|
719
|
+
self.send_error(403, 'Forbidden')
|
|
720
|
+
self.send_header('Content-length', '0')
|
|
721
|
+
self.end_headers()
|
|
722
|
+
return
|
|
723
|
+
# oldfile = self.server.root.rootdir() + urllib.unquote(self.path)
|
|
724
|
+
# newfile = self.server.root.rootdir() + urlparse.urlparse(urllib.unquote(self.headers['Destination'])).path
|
|
725
|
+
# if (os.path.isfile(oldfile)==True): # and os.path.isfile(newfile)==False): copy can rewrite.
|
|
726
|
+
# shutil.copyfile(oldfile,newfile)
|
|
727
|
+
# self.send_response(201, "Created")
|
|
728
|
+
# self.send_header('Content-length', '0')
|
|
729
|
+
# self.end_headers()
|
|
730
|
+
|
|
731
|
+
def do_LOCK(self):
|
|
732
|
+
if 'Content-length' in self.headers:
|
|
733
|
+
req = self.rfile.read(int(self.headers['Content-length']))
|
|
734
|
+
else:
|
|
735
|
+
req = self.rfile.read()
|
|
736
|
+
d = builddict(req)
|
|
737
|
+
#logger.debug('do_LOCK: path = ' + self.path)
|
|
738
|
+
#logger.debug('do_LOCK: headers = ' + str(self.headers))
|
|
739
|
+
#logger.debug('do_LOCK: req = ' + req)
|
|
740
|
+
#logger.debug('do_LOCK: d = ' + str(d))
|
|
741
|
+
|
|
742
|
+
if req == '':
|
|
743
|
+
#refreshing lock (windows)
|
|
744
|
+
locktoken = self.headers['If']
|
|
745
|
+
logger.debug(locktoken)
|
|
746
|
+
lockid = locktoken[18:-2]
|
|
747
|
+
logger.debug(lockid)
|
|
748
|
+
|
|
749
|
+
clientid = 'foo'
|
|
750
|
+
else:
|
|
751
|
+
try:
|
|
752
|
+
clientid = str(d['lockinfo']['owner']['href'])[7:] # temp: need Change other method!!!
|
|
753
|
+
except KeyError:
|
|
754
|
+
pass
|
|
755
|
+
clientid = 'foo'
|
|
756
|
+
lockid = str(uuid.uuid1())
|
|
757
|
+
|
|
758
|
+
retstr = '<?xml version="1.0" encoding="utf-8" ?>\n<D:prop xmlns:D="DAV:">\n<D:lockdiscovery>\n<D:activelock>\n<D:locktype><D:write/></D:locktype>\n<D:lockscope><D:exclusive/></D:lockscope>\n<D:depth>Infinity</D:depth>\n<D:owner>\n<D:href>'+clientid+'</D:href>\n</D:owner>\n<D:timeout>3600</D:timeout>\n<D:locktoken><D:href>opaquelocktoken:'+lockid+'</D:href></D:locktoken>\n</D:activelock>\n</D:lockdiscovery>\n</D:prop>\n'
|
|
759
|
+
self.send_response(200,'OK')
|
|
760
|
+
self.send_header("Content-type",'text/xml')
|
|
761
|
+
self.send_header("charset",'"utf-8"')
|
|
762
|
+
self.send_header("Lock-Token",'<opaquelocktoken:'+lockid+'>')
|
|
763
|
+
self.send_header('Content-Length',len(retstr))
|
|
764
|
+
self.end_headers()
|
|
765
|
+
self.wfile.write(retstr)
|
|
766
|
+
self.wfile.flush()
|
|
767
|
+
|
|
768
|
+
def do_UNLOCK(self):
|
|
769
|
+
# frome self.headers get Lock-Token:
|
|
770
|
+
logger.debug('do_UNLOCK')
|
|
771
|
+
self.send_response(204, 'No Content') # unlock using 204 for sucess.
|
|
772
|
+
self.send_header('Content-length', '0')
|
|
773
|
+
self.end_headers()
|
|
774
|
+
|
|
775
|
+
def do_PROPFIND(self):
|
|
776
|
+
if self.WebAuth():
|
|
777
|
+
return
|
|
778
|
+
depth = 'infinity'
|
|
779
|
+
if 'Depth' in self.headers:
|
|
780
|
+
depth = self.headers['Depth'].lower()
|
|
781
|
+
if 'Content-length' in self.headers:
|
|
782
|
+
req = self.rfile.read(int(self.headers['Content-length']))
|
|
783
|
+
else:
|
|
784
|
+
req = self.rfile.read()
|
|
785
|
+
d = builddict(req) # change all http.request to dict stru
|
|
786
|
+
wished_all = False
|
|
787
|
+
if len(d) == 0:
|
|
788
|
+
wished_props = DAVRequestHandler.basic_props
|
|
789
|
+
else:
|
|
790
|
+
if 'allprop' in d['propfind']:
|
|
791
|
+
wished_props = DAVRequestHandler.all_props
|
|
792
|
+
wished_all = True
|
|
793
|
+
else:
|
|
794
|
+
wished_props = []
|
|
795
|
+
for prop in d['propfind']['prop']:
|
|
796
|
+
### 2017/9/7 Edit By LCJ , Old is [ wished_props.append(prop) ]
|
|
797
|
+
### for IOS Coda Webdav support ###
|
|
798
|
+
wished_props.append(prop.split(' ')[0])
|
|
799
|
+
path, elem = self.path_elem()
|
|
800
|
+
if not elem:
|
|
801
|
+
if len(path) >= 1: # it's a non-existing file
|
|
802
|
+
self.send_response(404, 'Not Found')
|
|
803
|
+
self.send_header('Content-length', '0')
|
|
804
|
+
self.end_headers()
|
|
805
|
+
return
|
|
806
|
+
else:
|
|
807
|
+
elem = self.server.root # fixup root lookups?
|
|
808
|
+
if depth != '0' and not elem: #or elem.type != Member.M_COLLECTION:
|
|
809
|
+
self.send_response(406, 'This is not allowed')
|
|
810
|
+
self.send_header('Content-length', '0')
|
|
811
|
+
self.end_headers()
|
|
812
|
+
return
|
|
813
|
+
self.send_response(207, 'Multi-Status') #Multi-Status
|
|
814
|
+
self.send_header('Content-Type', 'text/xml')
|
|
815
|
+
self.send_header("charset",'"utf-8"')
|
|
816
|
+
# !!! if need debug output xml info,please set last var from False to True.
|
|
817
|
+
w = BufWriter(self.wfile, True)
|
|
818
|
+
w.write('<?xml version="1.0" encoding="utf-8" ?>\n')
|
|
819
|
+
w.write('<D:multistatus xmlns:D="DAV:" xmlns:Z="urn:schemas-microsoft-com:">\n')
|
|
820
|
+
|
|
821
|
+
def write_props_member(w, m):
|
|
822
|
+
w.write('<D:response>\n<D:href>%s</D:href>\n<D:propstat>\n<D:prop>\n' % urllib.quote(m.virname)) #add urllib.quote for chinese
|
|
823
|
+
props = m.getProperties() # get the file or dir props
|
|
824
|
+
# For OSX Finder : getlastmodified,getcontentlength,resourceType
|
|
825
|
+
if ('quota-available-bytes' in wished_props) or ('quota-used-bytes'in wished_props) or ('quota' in wished_props) or ('quotaused'in wished_props):
|
|
826
|
+
sDisk = os.statvfs('/') #TODO - FIXME
|
|
827
|
+
props['quota-used-bytes'] = (sDisk.f_blocks - sDisk.f_bavail) * sDisk.f_frsize
|
|
828
|
+
props['quotaused'] = (sDisk.f_blocks - sDisk.f_bavail) * sDisk.f_frsize
|
|
829
|
+
props['quota-available-bytes'] = sDisk.f_bavail * sDisk.f_frsize
|
|
830
|
+
props['quota'] = sDisk.f_bavail * sDisk.f_frsize
|
|
831
|
+
|
|
832
|
+
#print props
|
|
833
|
+
for wp in wished_props:
|
|
834
|
+
if props.has_key(wp) == False:
|
|
835
|
+
w.write(' <D:%s/>\n' % wp)
|
|
836
|
+
else:
|
|
837
|
+
w.write(' <D:%s>%s</D:%s>\n' % (wp, str(props[wp]), wp))
|
|
838
|
+
w.write('</D:prop>\n<D:status>HTTP/1.1 200 OK</D:status>\n</D:propstat>\n</D:response>\n')
|
|
839
|
+
|
|
840
|
+
#print props
|
|
841
|
+
|
|
842
|
+
write_props_member(w, elem)
|
|
843
|
+
if depth == '1':
|
|
844
|
+
for m in elem.getMembers():
|
|
845
|
+
write_props_member(w,m)
|
|
846
|
+
w.write('</D:multistatus>')
|
|
847
|
+
self.send_header('Content-Length', str(w.getSize()))
|
|
848
|
+
self.end_headers()
|
|
849
|
+
w.flush()
|
|
850
|
+
|
|
851
|
+
def do_PROPPATCH(self):
|
|
852
|
+
if self.WebAuth():
|
|
853
|
+
return
|
|
854
|
+
|
|
855
|
+
if 'Content-length' in self.headers:
|
|
856
|
+
req = self.rfile.read(int(self.headers['Content-length']))
|
|
857
|
+
else:
|
|
858
|
+
req = self.rfile.read()
|
|
859
|
+
|
|
860
|
+
logger.debug('Attempting to proppatch %s' % self.path)
|
|
861
|
+
logger.debug('do_PROPPATCH: req = ' + req)
|
|
862
|
+
|
|
863
|
+
self.send_error(403, 'Forbidden')
|
|
864
|
+
self.send_header('Content-length', '0')
|
|
865
|
+
self.end_headers()
|
|
866
|
+
return
|
|
867
|
+
|
|
868
|
+
# path = urllib.unquote(self.path)
|
|
869
|
+
# if path == '':
|
|
870
|
+
# self.send_error(404, 'Object not found')
|
|
871
|
+
# self.send_header('Content-length', '0')
|
|
872
|
+
# self.end_headers()
|
|
873
|
+
# return
|
|
874
|
+
# path = self.server.root.rootdir() + path
|
|
875
|
+
# if os.path.isfile(path):
|
|
876
|
+
# os.remove(path) #delete file
|
|
877
|
+
# elif os.path.isdir(path):
|
|
878
|
+
# shutil.rmtree(path) #delete dir
|
|
879
|
+
# else:
|
|
880
|
+
# self.send_response(404,'Not Found')
|
|
881
|
+
# self.send_header('Content-length', '0')
|
|
882
|
+
# self.end_headers()
|
|
883
|
+
# return
|
|
884
|
+
# self.send_response(204, 'No Content')
|
|
885
|
+
# self.send_header('Content-length', '0')
|
|
886
|
+
# self.end_headers()
|
|
887
|
+
|
|
888
|
+
def do_GET(self, onlyhead=False):
|
|
889
|
+
if self.WebAuth():
|
|
890
|
+
return
|
|
891
|
+
path, elem = self.path_elem()
|
|
892
|
+
if not elem:
|
|
893
|
+
self.send_error(404, 'Object not found')
|
|
894
|
+
return
|
|
895
|
+
try:
|
|
896
|
+
props = elem.getProperties()
|
|
897
|
+
except:
|
|
898
|
+
self.send_response(500, "Error retrieving properties")
|
|
899
|
+
self.end_headers()
|
|
900
|
+
return
|
|
901
|
+
# when the client had Range: bytes=3156-3681
|
|
902
|
+
bpoint = 0
|
|
903
|
+
epoint = 0
|
|
904
|
+
fullen = props['getcontentlength']
|
|
905
|
+
logger.debug('do_GET: fullen = ' + str(fullen))
|
|
906
|
+
if 'Range' in self.headers:
|
|
907
|
+
stmp = self.headers['Range'][6:]
|
|
908
|
+
stmp = stmp.split('-')
|
|
909
|
+
try:
|
|
910
|
+
bpoint = int(stmp[0])
|
|
911
|
+
except:
|
|
912
|
+
bpoint = 0
|
|
913
|
+
try:
|
|
914
|
+
epoint = int(stmp[1])
|
|
915
|
+
except:
|
|
916
|
+
epoint = fullen - 1
|
|
917
|
+
if (epoint<=bpoint):
|
|
918
|
+
bpoint = 0
|
|
919
|
+
epoint = fullen - 1
|
|
920
|
+
fullen = epoint - bpoint + 1
|
|
921
|
+
if epoint>0:
|
|
922
|
+
self.send_response(206, 'Partial Content')
|
|
923
|
+
self.send_header("Content-Range", " Bytes %s-%s/%s" % (bpoint, epoint, fullen))
|
|
924
|
+
else:
|
|
925
|
+
self.send_response(200, 'OK')
|
|
926
|
+
if elem.type == Member.M_MEMBER:
|
|
927
|
+
self.send_header("Content-type", props['getcontenttype'])
|
|
928
|
+
self.send_header("Last-modified", props['getlastmodified'])
|
|
929
|
+
self.send_header("Content-length", fullen)
|
|
930
|
+
else:
|
|
931
|
+
try:
|
|
932
|
+
ctype = props['getcontenttype']
|
|
933
|
+
except:
|
|
934
|
+
ctype = DirCollection.COLLECTION_MIME_TYPE
|
|
935
|
+
self.send_header("Content-type", ctype)
|
|
936
|
+
self.end_headers()
|
|
937
|
+
if not onlyhead:
|
|
938
|
+
if fullen >0 : # all 0 size file don't need this
|
|
939
|
+
elem.sendData(self.wfile,bpoint,epoint)
|
|
940
|
+
|
|
941
|
+
def do_HEAD(self):
|
|
942
|
+
self.do_GET(True) # HEAD should behave like GET, only without contents
|
|
943
|
+
|
|
944
|
+
def do_PUT(self):
|
|
945
|
+
if self.WebAuth():
|
|
946
|
+
return
|
|
947
|
+
try:
|
|
948
|
+
if 'Content-length' in self.headers:
|
|
949
|
+
size = int(self.headers['Content-length'])
|
|
950
|
+
elif 'Transfer-Encoding' in self.headers:
|
|
951
|
+
if self.headers['Transfer-Encoding'].lower()=='chunked':
|
|
952
|
+
size = -2
|
|
953
|
+
else:
|
|
954
|
+
size = -1
|
|
955
|
+
path, elem = self.path_elem_prev()
|
|
956
|
+
ename = path[-1]
|
|
957
|
+
except:
|
|
958
|
+
logger.exception('Error parsing request on: %s' % self.path)
|
|
959
|
+
self.send_response(400, 'Cannot parse request')
|
|
960
|
+
self.send_header('Content-length', '0')
|
|
961
|
+
self.end_headers()
|
|
962
|
+
return
|
|
963
|
+
# for OSX finder, it's first send a 0 byte file,and you need response a 201 code,and then osx send real file.
|
|
964
|
+
# OSX finder don't using content-length.
|
|
965
|
+
if ename == '.DS_Store':
|
|
966
|
+
logger.debug('Trying to save .DS_Store')
|
|
967
|
+
self.send_response(403, 'Forbidden')
|
|
968
|
+
self.send_header('Content-length', '0')
|
|
969
|
+
self.end_headers()
|
|
970
|
+
elif ename.startswith('._'):
|
|
971
|
+
#block OSX resource forks
|
|
972
|
+
logger.debug('Trying to save resource fork')
|
|
973
|
+
self.send_response(403, 'Forbidden')
|
|
974
|
+
self.send_header('Content-length', '0')
|
|
975
|
+
self.end_headers()
|
|
976
|
+
else:
|
|
977
|
+
try:
|
|
978
|
+
#if not size == 0:
|
|
979
|
+
elem.recvMember(self.rfile, ename, size, self)
|
|
980
|
+
except:
|
|
981
|
+
logger.exception('Error saving file: %s' % self.path)
|
|
982
|
+
self.send_response(500, 'Cannot save file')
|
|
983
|
+
self.send_header('Content-length', '0')
|
|
984
|
+
self.end_headers()
|
|
985
|
+
return
|
|
986
|
+
if size == 0:
|
|
987
|
+
logger.debug('File created %s' % path)
|
|
988
|
+
self.send_response(201, 'Created')
|
|
989
|
+
else:
|
|
990
|
+
logger.debug('File saved %s' % path)
|
|
991
|
+
self.send_response(200, 'OK')
|
|
992
|
+
self.send_header('Content-length', '0')
|
|
993
|
+
self.end_headers()
|
|
994
|
+
|
|
995
|
+
def split_path(self, path):
|
|
996
|
+
"""Splits path string in form '/dir1/dir2/file' into parts"""
|
|
997
|
+
p = path.split('/')[1:]
|
|
998
|
+
while p and p[-1] in ('','/'):
|
|
999
|
+
p = p[:-1]
|
|
1000
|
+
if len(p) > 0:
|
|
1001
|
+
p[-1] += '/'
|
|
1002
|
+
return p
|
|
1003
|
+
|
|
1004
|
+
def path_elem(self):
|
|
1005
|
+
"""Returns split path (see split_path()) and Member object of the last element"""
|
|
1006
|
+
path = self.split_path(urllib.unquote(self.path))
|
|
1007
|
+
elem = self.server.root
|
|
1008
|
+
for e in path:
|
|
1009
|
+
elem = elem.findMember(e)
|
|
1010
|
+
if elem == None:
|
|
1011
|
+
break
|
|
1012
|
+
return (path, elem)
|
|
1013
|
+
|
|
1014
|
+
def path_elem_prev(self):
|
|
1015
|
+
"""Returns split path (see split_path()) and Member object of the next-to-last element"""
|
|
1016
|
+
path = self.split_path(urllib.unquote(self.path))
|
|
1017
|
+
elem = self.server.root
|
|
1018
|
+
for e in path[:-1]:
|
|
1019
|
+
elem = elem.findMember(e)
|
|
1020
|
+
if elem == None:
|
|
1021
|
+
break
|
|
1022
|
+
return (path, elem)
|
|
1023
|
+
|
|
1024
|
+
# disable log info output to screen
|
|
1025
|
+
def log_message(self,format,*args):
|
|
1026
|
+
if True:
|
|
1027
|
+
logger.info("%s - - [%s] %s\n" %
|
|
1028
|
+
(self.client_address[0],
|
|
1029
|
+
self.log_date_time_string(),
|
|
1030
|
+
format % args))
|
|
1031
|
+
|
|
1032
|
+
class BufWriter:
|
|
1033
|
+
def __init__(self, w, debug=True):
|
|
1034
|
+
self.w = w
|
|
1035
|
+
self.buf = StringIO(u'')
|
|
1036
|
+
self.debug = debug
|
|
1037
|
+
|
|
1038
|
+
def write(self, s):
|
|
1039
|
+
if self.debug:
|
|
1040
|
+
sys.stderr.write(s)
|
|
1041
|
+
self.buf.write(s)
|
|
1042
|
+
#self.buf.write(unicode(s,'utf-8')) # add unicode(s,'utf-8') for chinese code.
|
|
1043
|
+
|
|
1044
|
+
def flush(self):
|
|
1045
|
+
self.w.write(self.buf.getvalue().encode('utf-8'))
|
|
1046
|
+
self.w.flush()
|
|
1047
|
+
|
|
1048
|
+
def getSize(self):
|
|
1049
|
+
return len(self.buf.getvalue().encode('utf-8'))
|
|
1050
|
+
|
|
1051
|
+
class DAVServer(ThreadingMixIn, HTTPServer):
|
|
1052
|
+
def __init__(self, addr, handler, root, userpwd):
|
|
1053
|
+
HTTPServer.__init__(self, addr, handler)
|
|
1054
|
+
self.root = root
|
|
1055
|
+
self.userpwd = userpwd # WebDav Auth user:passwd
|
|
1056
|
+
if len(userpwd)>0:
|
|
1057
|
+
self.auth_enable = True
|
|
1058
|
+
else:
|
|
1059
|
+
self.auth_enable = False
|
|
1060
|
+
|
|
1061
|
+
# disable the broken pipe error message
|
|
1062
|
+
def finish_request(self,request,client_address):
|
|
1063
|
+
try:
|
|
1064
|
+
HTTPServer.finish_request(self, request, client_address)
|
|
1065
|
+
except socket.error as e:
|
|
1066
|
+
pass
|
|
1067
|
+
|
|
1068
|
+
|
|
1069
|
+
|
|
1070
|
+
def main():
|
|
1071
|
+
# WebDav TCP Port
|
|
1072
|
+
srvport = 9090
|
|
1073
|
+
# Get local IP address
|
|
1074
|
+
import socket
|
|
1075
|
+
myaddr = get_localip()
|
|
1076
|
+
print('PYMECluster WebDav Server run at '+myaddr+':'+str(srvport)+'...')
|
|
1077
|
+
server_address = ('', srvport)
|
|
1078
|
+
# WebDav Auth User/Password file
|
|
1079
|
+
# if not this file ,the auth function disable.
|
|
1080
|
+
# file format: user:passwd\n user:passwd\n
|
|
1081
|
+
# or you can change your auth mode and file save format
|
|
1082
|
+
userpwd = []
|
|
1083
|
+
try:
|
|
1084
|
+
with open('wdusers.conf', 'r') as f:
|
|
1085
|
+
for uinfo in f.readlines():
|
|
1086
|
+
uinfo = uinfo.replace('\n','')
|
|
1087
|
+
if len(uinfo)>2:
|
|
1088
|
+
userpwd.append(base64.b64encode(uinfo))
|
|
1089
|
+
except:
|
|
1090
|
+
userpwd.append(base64.b64encode('test:test'))
|
|
1091
|
+
pass
|
|
1092
|
+
# first is Server root dir, Second is virtual dir
|
|
1093
|
+
# **** Change first ./ to your dir , etc :/mnt/flash/public
|
|
1094
|
+
root = DirCollection('/', '/')
|
|
1095
|
+
httpd = DAVServer(server_address, DAVRequestHandler, root, userpwd)
|
|
1096
|
+
|
|
1097
|
+
#httpd.socket = ssl.wrap_socket (httpd.socket, certfile='./server.pem', server_side=True)
|
|
1098
|
+
|
|
1099
|
+
httpd.serve_forever() # todo: add some control over starting and stopping the server
|
|
1100
|
+
|
|
1101
|
+
if __name__ == '__main__':
|
|
1102
|
+
main()
|