perf improvements and working loc

data_ome_tif/net/1_MMStack_Pos0.ome_locs.yaml

@@ -0,0 +1,276 @@
+Byte Order: <
+Camera: HamamatsuHam_DCAM
+Data Type: uint16
+File: /home/nicolas/Bureau/MicroscopyImaging/DatasetMicroscopy/data_ome_tif/net/1_MMStack_Pos0.ome.tif
+Frames: 50
+Height: 512
+Micro-Manager Acquisiton Comments:
+- ''
+Micro-Manager Metadata:
+  AutoFocusZDC-ContinuousMode: 'Off'
+  AutoFocusZDC-Description: ZDC Auto Focus accessory
+  AutoFocusZDC-MeasureOffset: 'Off'
+  AutoFocusZDC-Name: AutoFocusZDC
+  AutoFocusZDC-ObjectiveTypeSetting: UPlanSApo100XO
+  AutoFocusZDC-Offset: '4241.4400'
+  AutoFocusZDC-SearchRange: '0.0000'
+  AxisPositions: null
+  Binning: 1x1
+  BitDepth: 16
+  COM10-AnswerTimeout: '500.0000'
+  COM10-BaudRate: '9600'
+  COM10-DataBits: '8'
+  COM10-DelayBetweenCharsMs: '0.0000'
+  COM10-Description: Serial port driver (boost:asio)
+  COM10-Handshaking: 'Off'
+  COM10-Name: COM10
+  COM10-Parity: None
+  COM10-StopBits: '1'
+  COM10-Verbose: '1'
+  COM11-AnswerTimeout: '500.0000'
+  COM11-BaudRate: '9600'
+  COM11-DataBits: '8'
+  COM11-DelayBetweenCharsMs: '0.0000'
+  COM11-Description: Serial port driver (boost:asio)
+  COM11-Handshaking: 'Off'
+  COM11-Name: COM11
+  COM11-Parity: None
+  COM11-StopBits: '1'
+  COM11-Verbose: '1'
+  COM12-AnswerTimeout: '500.0000'
+  COM12-BaudRate: '19200'
+  COM12-DataBits: '8'
+  COM12-DelayBetweenCharsMs: '0.0000'
+  COM12-Description: Serial port driver (boost:asio)
+  COM12-Handshaking: 'Off'
+  COM12-Name: COM12
+  COM12-Parity: None
+  COM12-StopBits: '1'
+  COM12-Verbose: '0'
+  COM13-AnswerTimeout: '500.0000'
+  COM13-BaudRate: '9600'
+  COM13-DataBits: '8'
+  COM13-DelayBetweenCharsMs: '0.0000'
+  COM13-Description: Serial port driver (boost:asio)
+  COM13-Handshaking: 'Off'
+  COM13-Name: COM13
+  COM13-Parity: None
+  COM13-StopBits: '1'
+  COM13-Verbose: '1'
+  COM15-AnswerTimeout: '500.0000'
+  COM15-BaudRate: '9600'
+  COM15-DataBits: '8'
+  COM15-DelayBetweenCharsMs: '0.0000'
+  COM15-Description: Serial port driver (boost:asio)
+  COM15-Handshaking: 'Off'
+  COM15-Name: COM15
+  COM15-Parity: None
+  COM15-StopBits: '1'
+  COM15-Verbose: '1'
+  COM18-AnswerTimeout: '500.0000'
+  COM18-BaudRate: '19200'
+  COM18-DataBits: '8'
+  COM18-DelayBetweenCharsMs: '0.0000'
+  COM18-Description: Serial port driver (boost:asio)
+  COM18-Handshaking: 'Off'
+  COM18-Name: COM18
+  COM18-Parity: Even
+  COM18-StopBits: '2'
+  COM18-Verbose: '1'
+  Camera: HamamatsuHam_DCAM
+  CameraChannelIndex: 0
+  Channel: Default
+  ChannelIndex: 0
+  Core-AutoFocus: AutoFocusZDC
+  Core-AutoShutter: '1'
+  Core-Camera: HamamatsuHam_DCAM
+  Core-ChannelGroup: ''
+  Core-Focus: ManualFocus
+  Core-Galvo: ''
+  Core-ImageProcessor: ''
+  Core-Initialize: '1'
+  Core-SLM: ''
+  Core-Shutter: Shutter532
+  Core-TimeoutMs: '5000'
+  Core-XYStage: XYStage
+  ElapsedTime-ms: 1953
+  Exposure-ms: 40
+  FileName: pos1DO0p1_1_MMStack_Pos0.ome.tif
+  Frame: 0
+  FrameIndex: 0
+  HamamatsuHam_DCAM-Binning: 1x1
+  HamamatsuHam_DCAM-CCDMode: EM CCD
+  HamamatsuHam_DCAM-CCDTemperature: '1.7000'
+  HamamatsuHam_DCAM-CONTRAST GAIN: '1'
+  HamamatsuHam_DCAM-Camera Bus: AS-PHX-D24CL-PE1
+  HamamatsuHam_DCAM-Camera Version: '2.0'
+  HamamatsuHam_DCAM-CameraID: 'S/N: 230387'
+  HamamatsuHam_DCAM-CameraName: C9100-13
+  HamamatsuHam_DCAM-Description: Hamamatsu device adapter 1.8.12.52
+  HamamatsuHam_DCAM-Driver Version: 5.58.240.5162
+  HamamatsuHam_DCAM-EM GAIN PROTECT AFTER FRAMES: '1'
+  HamamatsuHam_DCAM-EM GAIN PROTECT MODE: 'OFF'
+  HamamatsuHam_DCAM-EM GAIN WARNING ALARM: 'OFF'
+  HamamatsuHam_DCAM-EM GAIN WARNING LEVEL: '3'
+  HamamatsuHam_DCAM-EM GAIN WARNING STATUS: NORMAL
+  HamamatsuHam_DCAM-EMGain: '400'
+  HamamatsuHam_DCAM-EXPOSURE FULL RANGE: DISABLE
+  HamamatsuHam_DCAM-EXPOSURE TIME UNITS: MILLISECONDS
+  HamamatsuHam_DCAM-Exposure: '40.00'
+  HamamatsuHam_DCAM-FRAME AVERAGING FRAMES: '2'
+  HamamatsuHam_DCAM-FRAME AVERAGING MODE: 'OFF'
+  HamamatsuHam_DCAM-High Dynamic Range Mode: 'OFF'
+  HamamatsuHam_DCAM-MINIMUM ACQUISITION TIMEOUT: '60000'
+  HamamatsuHam_DCAM-Module Version: 16.10.642.5162
+  HamamatsuHam_DCAM-Name: HamamatsuHam_DCAM
+  HamamatsuHam_DCAM-OUTPUT TRIGGER DELAY: '0.0000'
+  HamamatsuHam_DCAM-OUTPUT TRIGGER DELAY UNITS: SECONDS
+  HamamatsuHam_DCAM-OUTPUT TRIGGER PERIOD: '0.0010'
+  HamamatsuHam_DCAM-OUTPUT TRIGGER PERIOD UNITS: SECONDS
+  HamamatsuHam_DCAM-OUTPUT TRIGGER POLARITY: NEGATIVE
+  HamamatsuHam_DCAM-PhotonImagingMode: '0'
+  HamamatsuHam_DCAM-PixelType: 16bit
+  HamamatsuHam_DCAM-RECURSIVE FILTER: 'OFF'
+  HamamatsuHam_DCAM-RECURSIVE FILTER FRAMES: '2'
+  HamamatsuHam_DCAM-ReadoutTime: '0.0313'
+  HamamatsuHam_DCAM-SENSOR MODE: AREA
+  HamamatsuHam_DCAM-SHADING CORRECTION: 'OFF'
+  HamamatsuHam_DCAM-SHADING DATA MEMORY: '1'
+  HamamatsuHam_DCAM-SPOT NOISE REDUCER: 'OFF'
+  HamamatsuHam_DCAM-STORE SHADING DATA TO MEMORY: '1'
+  HamamatsuHam_DCAM-STORE SUBTRACT IMAGE TO MEMORY: '1'
+  HamamatsuHam_DCAM-SUBTRACT: 'OFF'
+  HamamatsuHam_DCAM-SUBTRACT IMAGE MEMORY: '1'
+  HamamatsuHam_DCAM-SUBTRACT OFFSET: '0'
+  HamamatsuHam_DCAM-ScanMode: '3'
+  HamamatsuHam_DCAM-Sensor Cooler: 'ON'
+  HamamatsuHam_DCAM-Sensor Cooler Fan: 'ON'
+  HamamatsuHam_DCAM-TRIGGER ACTIVE: EDGE
+  HamamatsuHam_DCAM-TRIGGER SOURCE: INTERNAL
+  HamamatsuHam_DCAM-TRIGGER TIMES: '1'
+  HamamatsuHam_DCAM-Temperature Set Point: '-65.0000'
+  HamamatsuHam_DCAM-TransposeCorrection: '0'
+  HamamatsuHam_DCAM-TransposeMirrorX: '0'
+  HamamatsuHam_DCAM-TransposeMirrorY: '0'
+  HamamatsuHam_DCAM-TransposeXY: '0'
+  HamamatsuHam_DCAM-Trigger: NORMAL
+  HamamatsuHam_DCAM-TriggerPolarity: NEGATIVE
+  HamamatsuImageNr: '0'
+  Height: 512
+  ImageNumber: '0'
+  LightPath-ClosedPosition: ''
+  LightPath-Description: Light Path Prism
+  LightPath-Label: Side Port
+  LightPath-Name: LightPath
+  LightPath-State: '1'
+  ManualFocus-Description: Manual Focus (Z-Drive)
+  ManualFocus-FarLimit: '0.0100'
+  ManualFocus-FocusSensitivity: '100'
+  ManualFocus-FocusWheel: 'Off'
+  ManualFocus-Name: ManualFocus
+  ManualFocus-NearLimit: '30000.0000'
+  ManualFocus-Position: '4613.1400'
+  NextFrame: 1
+  OlympusHub-Control: Manual + Computer
+  OlympusHub-Description: Olympus Hub
+  OlympusHub-Model: IX2
+  OlympusHub-Name: OlympusHub
+  OlympusHub-Port: COM18
+  OlympusHub-Version: V02.01.01,V01.02.01,V01.02.01,---.--.--
+  Oxxius LBX-LD-Analog mod: Enable
+  Oxxius LBX-LD-Base Temperature: '21.8000'
+  Oxxius LBX-LD-Control mode: APC
+  Oxxius LBX-LD-Current: '1.5000'
+  Oxxius LBX-LD-CurrentSetPoint: '100.0000'
+  Oxxius LBX-LD-Description: Oxxius Laser Controller
+  Oxxius LBX-LD-Digital mod: Disable
+  Oxxius LBX-LD-Fault: No Fault
+  Oxxius LBX-LD-Hours: '16.0000'
+  Oxxius LBX-LD-Interlock: Interlock Closed
+  Oxxius LBX-LD-Laser: 'Off'
+  Oxxius LBX-LD-LaserStatus: Standby
+  Oxxius LBX-LD-Max Current: '100.5000'
+  Oxxius LBX-LD-Max Power: '55.0000'
+  Oxxius LBX-LD-Name: Oxxius LBX-LD
+  Oxxius LBX-LD-Port: COM12
+  Oxxius LBX-LD-Power: '0.0000'
+  Oxxius LBX-LD-PowerSetPoint: '30.0000'
+  Oxxius LBX-LD-Serial Number: LAS-05132
+  Oxxius LBX-LD-Soft Version: 3.2.23
+  Oxxius LBX-LD-Wavelength: '405'
+  PixelSizeUm: 0
+  PixelType: GRAY16
+  Position: Default
+  PositionIndex: 0
+  PositionName: null
+  ROI: 0-0-512-512
+  Shutter405-Address: x
+  Shutter405-Command: Close
+  Shutter405-Description: Vincent D1 controller adapter
+  Shutter405-Name: Vincent-D1
+  Shutter405-Port: COM10
+  Shutter405-Shutter A or B: A
+  Shutter405-Time to close (ms): '35.0000'
+  Shutter405-Time to open (ms): '35.0000'
+  Shutter488-Delay_ms: '50.0000'
+  Shutter488-Description: SIGMA-KOKI shutter adapter
+  Shutter488-Name: Shutter-1
+  Shutter488-Port: COM11
+  Shutter488-ShutterModel: Release
+  Shutter488-State: '0'
+  Shutter532-Delay_ms: '50.0000'
+  Shutter532-Description: SIGMA-KOKI shutter adapter
+  Shutter532-Name: Shutter-2
+  Shutter532-Port: COM11
+  Shutter532-ShutterModel: Release
+  Shutter532-State: '0'
+  Shutter561-Delay_ms: '50.0000'
+  Shutter561-Description: SIGMA-KOKI shutter adapter
+  Shutter561-Name: Shutter-3
+  Shutter561-Port: COM11
+  Shutter561-ShutterModel: Release
+  Shutter561-State: '0'
+  Shutter645-Delay_ms: '50.0000'
+  Shutter645-Description: SIGMA-KOKI shutter adapter
+  Shutter645-Name: Shutter-4
+  Shutter645-Port: COM11
+  Shutter645-ShutterModel: Release
+  Shutter645-State: '0'
+  Slice: 0
+  SliceIndex: 0
+  SlicePosition: null
+  Source: HamamatsuHam_DCAM
+  Time: 2019-08-19 13:58:15 +0200
+  TransmittedLamp-ClosedPosition: ''
+  TransmittedLamp-Description: ''
+  TransmittedLamp-Label: 'Off'
+  TransmittedLamp-Name: ''
+  TransmittedLamp-State: '0'
+  TransmittedLamp-Voltage: '9.7000'
+  UUID: daa20162-48be-4ddb-8ecf-90cb6ebe2a40
+  WaitInterval: 0
+  Width: 512
+  XPositionUm: 13573.5
+  XYStage-Acceleration X [m/s^2]: '0.2000'
+  XYStage-Acceleration Y [m/s^2]: '0.2000'
+  XYStage-Backlash X [um]: '0.0000'
+  XYStage-Backlash Y [um]: '0.0000'
+  XYStage-Description: Tango XY stage driver adapter
+  XYStage-Name: XYStage
+  XYStage-Port: COM13
+  XYStage-SpeedX [mm/s]: '10.0000'
+  XYStage-SpeedY [mm/s]: '10.0000'
+  XYStage-StepSizeX [um]: '0.0024'
+  XYStage-StepSizeY [um]: '0.0024'
+  XYStage-TransposeMirrorX: '0'
+  XYStage-TransposeMirrorY: '0'
+  YPositionUm: -3596.60009765625
+  ZPositionUm: 4241.44
+Width: 512
+---
+Box Size: 7
+Convergence Criterion: 0.001
+Generated by: Picasso Localize
+Max. Iterations: 1000
+Min. Net Gradient: 5000
+ROI: null

generateData.py

@@ -9,7 +9,9 @@
 from csbdeep.data.generate import no_background_patches
 from csbdeep.utils import plot_some
 
+from localizeDots.localize import launchLocalize
 
+launchLocalize("data_ome_tif/net/1_MMStack_Pos0.ome.tif")
 #################
 # TRAINING DATA #
 #################