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reinstantiate point display overlay if we don't have a filter#1344

Merged
David-Baddeley merged 1 commit intopython-microscopy:masterfrom
barentine:overlayfilterinit
Sep 10, 2023
Merged

reinstantiate point display overlay if we don't have a filter#1344
David-Baddeley merged 1 commit intopython-microscopy:masterfrom
barentine:overlayfilterinit

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@barentine
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Addresses issue #1343 .

Is this a bugfix or an enhancement?
bugfix
Proposed changes:
if we have a PointsDisplayOverlay without a filter attribute when we run test frame, just go ahead and make a new PointsDisplayOverlay that does.

Checklist:
The below is a list of things what will be considered when reviewing PRs. It is not prescriptive, and does not
imply that PRs which touch any of these will be rejected but gives a rough indication of where there is a potential
for hangups (i.e. factors which could turn a 5 min review into a half hour or longer and shunt it to the bottom
of the TODO list).

  • Does the PR avoid variable renaming in existing code, whitespace changes, and other forms of tidying? [There is a place for code tidying, but it makes reviewing
    much simpler if this is kept separate from functional changes. The auto-formatting performed by some editors is particulaly egregious and can lead to files with thousands
    of non-functional changes with a few functional changes scattered amoungst them]

If an enhancement (or non-trivial bugfix):

  • Has this been discussed in advance (feature request, PR proposal, email, or direct conversation)?
  • Does this change how users interact with the software? How will these changes be communicated?
  • Does this maintain backwards compatibility with old data?
  • Does this change the required dependencies?
  • Are there any other side effects of the change?

@David-Baddeley
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Will merge, but this smells like this is a symptom of an upstream problem (failure of filter creation on a previous call). Is there a traceback that goes with this?

@barentine
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I agree - seems like a possible upstream issue

Traceback
PYMEImage
Detected a .git folder, assuming a development install
Starting main loop
DEBUG:PYME.DSView.dsviewer:Loading data
filename == None
/Users/andy/Downloads/FOV2_ER_500mW_647_p02exp_Gain300_X2.tif
(12446, 293, 293)
INFO:PYME.IO.DataSources.TiffDataSource:Tiff file does not fully specify axes (axes=XY?)
INFO:PYME.IO.DataSources.TiffDataSource:Assuming unknown axis is Z
DEBUG:PYME.IO.DataSources.TiffDataSource:sh = {'Z': 12446, 'T': 1, 'C': 1, 'Y': 293, 'X': 293}
DEBUG:PYME.IO.DataSources.TiffDataSource:raw TIFF axisOrder = XYZTC
[293, 293, 12446, 1, 1]
DEBUG:PYME.DSView.dsviewer:Data loaded, launching viewer
WARNING:PYME.ui.selection:Using units=UNITS_PIXELS
DEBUG:PYME.DSView.dsviewer:Optimising ...
DEBUG:PYME.DSView.dsviewer:Optimise done
quaternion module not found, disabling custom clip plane orientations
WARNING:PYME.DSView.modules:Plugin [arrayView] injects into parent namespace, could result in circular references
WARNING:PYME.DSView.modules:Plugin [shell] injects into parent namespace, could result in circular references
0
WARNING:PYME.DSView.modules:Plugin [metadataView] injects into parent namespace, could result in circular references
10:48:54: Debug: Adding duplicate image handler for 'Windows bitmap file'
10:48:54: Debug: Adding duplicate animation handler for '1' type
10:48:54: Debug: Adding duplicate animation handler for '2' type
Trying to load 3rd party recipe module ste_analysis.recipe_modules.delay_toggle
Loaded 3rd party recipe module ste_analysis.recipe_modules.delay_toggle
Trying to load 3rd party recipe module ste_analysis.recipe_modules.filtering
Loaded 3rd party recipe module ste_analysis.recipe_modules.filtering
0
WARNING:PYME.DSView.modules:Plugin [recipes] injects into parent namespace, could result in circular references
/Users/andy/code/python-microscopy
INFO:PYME.misc.check_for_updates:Detected a .git folder, assuming a development install
/Users/andy/code/python-microscopy/PYME/DSView/modules/LMAnalysis.py:580: PYMEDeprecationWarning: This will either disappear or change function as we move to a 5D data model. Use the explicit .data_xytc instead, or even better, change to using the 5D model as image.data_xyztc or image.voxels
  if 'bgRange' in dir(self.image.data):
WARNING:PYME.DSView.modules:Plugin [LMAnalysis] injects into parent namespace, could result in circular references
Creating fold panel
['AstigGaussFitFR', 'AstigGaussGPUFitFR', 'BeadConvolvedAstigGaussFit', 'ChecksumFR', 'ChecksumGPUFR', 'ChecksumMultifitSR', 'ConfocCOIR', 'DoubleHelixFitR', 'Dumbell3DFitR', 'DumbellFitR', 'Gauss3DFitR', 'GaussFitConstrR', 'GaussMultifitLinesR', 'GaussMultifitR', 'GaussMultifitSR', 'InterpFitR', 'InterpFitWFR', 'LatFitCOIR', 'LatGaussFitFR', 'LatObjFindFR', 'LatPSFFitR', 'MultiviewFitInterpNR', 'PRInterpFitQR', 'PRInterpFitR', 'ROIExtractNR', 'SpecGaussFitFR', 'SplitterFitCOIR', 'SplitterFitFNR', 'SplitterFitFusionR', 'SplitterFitInterpBNR', 'SplitterFitInterpNR', 'SplitterFitScavNR', 'SplitterMultifitSR', 'SplitterObjFindR', 'SplitterROIExtractNR', 'SplitterShiftEstFR']
10:48:55: Debug: Unknown accel modifier: '- 2D single'
10:48:55: Debug: Unrecognized accel key 'colour', accel string ignored.
10:48:55: Debug: Unrecognized accel key '- 3D via Astigmatism, with sCMOS noise model', accel string ignored.
10:48:55: Debug: Unrecognized accel key '- 3D astigmatism calibrations', accel string ignored.
10:48:55: Debug: Unrecognized accel key '- Debugging to ensure reproducible ROI extraction and background correction', accel string ignored.
10:48:55: Debug: Unrecognized accel key '- Debugging to ensure frame data and background are reproducible', accel string ignored.
10:48:55: Debug: Unrecognized accel key '- Debugging to ensure frame data and background are reproducible', accel string ignored.
10:48:55: Debug: Unknown accel modifier: '- 2D single'
10:48:55: Debug: Unrecognized accel key 'colour', accel string ignored.
10:48:55: Debug: Unknown accel modifier: '- 3D single'
10:48:55: Debug: Unrecognized accel key 'colour', accel string ignored.
10:48:55: Debug: Unknown accel modifier: '- 2D single'
10:48:55: Debug: Unrecognized accel key 'colour', accel string ignored.
10:48:55: Debug: Unknown accel modifier: '- 2D single'
10:48:55: Debug: Unrecognized accel key 'colour', accel string ignored.
10:48:55: Debug: Unknown accel modifier: '- 2D multi'
10:48:55: Debug: Unrecognized accel key 'emitter', accel string ignored.
10:48:55: Debug: Unknown accel modifier: '- 2D multi'
10:48:55: Debug: Unrecognized accel key 'emitter', accel string ignored.
10:48:55: Debug: Unknown accel modifier: '- 3D single'
10:48:55: Debug: Unrecognized accel key 'colour', accel string ignored.
10:48:55: Debug: Unknown accel modifier: '- 2D single'
10:48:55: Debug: Unrecognized accel key 'colour', accel string ignored.
10:48:55: Debug: Unrecognized accel key '- PSF extraction', accel string ignored.
10:48:55: Debug: Unknown accel modifier: '- 2D multi'
10:48:55: Debug: Unrecognized accel key 'colour', accel string ignored.
10:48:55: Debug: Unknown accel modifier: '- 2D multi'
10:48:55: Debug: Unrecognized accel key 'colour', accel string ignored.
10:48:55: Debug: Unknown accel modifier: '- 2D multi'
10:48:55: Debug: Unrecognized accel key 'colour', accel string ignored.
10:48:55: Debug: Unknown accel modifier: '- 2D multi'
10:48:55: Debug: Unrecognized accel key 'colour', accel string ignored.
10:48:55: Debug: Unrecognized accel key '- Calibrating the splitter', accel string ignored.
Traceback (most recent call last):
  File "/Users/andy/code/python-microscopy/PYME/localization/MetaDataEdit.py", line 53, in <lambda>
    self.tValue.Bind(wx.EVT_TEXT, lambda e : self.retrieveValue(mdh))
  File "/Users/andy/code/python-microscopy/PYME/localization/MetaDataEdit.py", line 58, in retrieveValue
    mdh[self.paramName] = float(self.tValue.GetValue())
ValueError: could not convert string to float: '0.75E'
DEBUG:PYME.DSView.modules.LMAnalysis:use_cluster: newStyle=True, tq=None
DEBUG:asyncio:Using selector: KqueueSelector
/Users/andy/miniconda3/envs/pyme38/lib/python3.8/site-packages/zeroconf/_services/browser.py:168: FutureWarning: <PYME.misc.pyme_zeroconf.ZCListener object at 0x17597a0d0> has no update_service method. Provide one (it can be empty if you don't care about the updates), it'll become mandatory.
  warnings.warn(
DEBUG:PYME.IO.cluster_directory:Request for b'http://127.0.0.1:53825//Users/andy/Downloads/analysis/' failed with error: 404
DEBUG:PYME.IO.cluster_directory:Request for b'http://127.0.0.1:53825/Users/andy/Downloads/analysis/' failed with error: 404
DEBUG:root:Results file: /Users/andy/Downloads/analysis/FOV2_ER_500mW_647_p02exp_Gain300_X2.h5r
DEBUG:PYME.IO.cluster_directory:Request for b'http://127.0.0.1:53825//Users/andy/Downloads/analysis/' failed with error: 404
DEBUG:PYME.IO.cluster_directory:Request for b'http://127.0.0.1:53825/Users/andy/Downloads/analysis/' failed with error: 404
INFO:PYME.cluster.rules:Results file: /Users/andy/Downloads/analysis/FOV2_ER_500mW_647_p02exp_Gain300_X2.h5r
ERROR:PYME.cluster.rules:Raw file metadata (/Users/andy/Downloads/FOV2_ER_500mW_647_p02exp_Gain300_X2.tif/metadata.json) not found, continuing with analysis metadata alone. Can probably be ignored for .tiff analysis
Traceback (most recent call last):
  File "/Users/andy/code/python-microscopy/PYME/cluster/rules.py", line 695, in __init__
    resultsMdh.update(json.loads(unifiedIO.read(seriesName + '/metadata.json')))
  File "/Users/andy/code/python-microscopy/PYME/IO/unifiedIO.py", line 270, in read
    raise IOError('File does not exist or URI not understood: %s' % filename)
OSError: File does not exist or URI not understood: /Users/andy/Downloads/FOV2_ER_500mW_647_p02exp_Gain300_X2.tif/metadata.json
DEBUG:PYME.IO.cluster_directory:Request for b'http://127.0.0.1:53825//Users/andy/Downloads/analysis/' failed with error: 404
/Users/andy/Downloads/FOV2_ER_500mW_647_p02exp_Gain300_X2.tif
(12446, 293, 293)
INFO:PYME.IO.DataSources.TiffDataSource:Tiff file does not fully specify axes (axes=XY?)
INFO:PYME.IO.DataSources.TiffDataSource:Assuming unknown axis is Z
DEBUG:PYME.IO.DataSources.TiffDataSource:sh = {'Z': 12446, 'T': 1, 'C': 1, 'Y': 293, 'X': 293}
DEBUG:PYME.IO.DataSources.TiffDataSource:raw TIFF axisOrder = XYZTC
DEBUG:PYME.cluster.rules:DataSource.__class__: <class 'PYME.IO.DataSources.TiffDataSource.DataSource'>
DEBUG:asyncio:Using selector: KqueueSelector
/Users/andy/miniconda3/envs/pyme38/lib/python3.8/site-packages/zeroconf/_services/browser.py:168: FutureWarning: <PYME.misc.pyme_zeroconf.ZCListener object at 0x17471ba60> has no update_service method. Provide one (it can be empty if you don't care about the updates), it'll become mandatory.
  warnings.warn(
DEBUG:PYME.cluster.rules:local_queues: ['PYMERuleServer:Andrews-MacBook-Pro - PID:3536']
DEBUG:root:resultsURI: http://127.0.0.1:53825/__aggregate_h5r//Users/andy/Downloads/analysis/FOV2_ER_500mW_647_p02exp_Gain300_X2.h5r
DEBUG:root:fileFormattedResults - URI: http://127.0.0.1:53825/__aggregate_h5r//Users/andy/Downloads/analysis/FOV2_ER_500mW_647_p02exp_Gain300_X2.h5r/MetaData
'http://127.0.0.1:53825//Users/andy/Downloads/analysis/FOV2_ER_500mW_647_p02exp_Gain300_X2.h5r.json'
DEBUG:PYME.cluster.rules:Successfully created rule
DEBUG:root:task pusher poll loop started
Queue created
Images pushed
DEBUG:root:numTotalFrames: 12446, _next_release_start: 30
DEBUG:root:we have unpublished frames - push them
DEBUG:root:Successfully released tasks (30:12446)
DEBUG:PYME.cluster.rules:input data complete, calling on_data_complete
DEBUG:PYME.cluster.rules:Data complete, copying events to output file
WARNING:root:No handler for data type found, using pickle
DEBUG:root:fileFormattedResults - URI: http://127.0.0.1:53825/__aggregate_h5r//Users/andy/Downloads/analysis/FOV2_ER_500mW_647_p02exp_Gain300_X2.h5r/Events
DEBUG:PYME.cluster.rules:input data complete
DEBUG:root:numTotalFrames: 12446, _next_release_start: 12446
DEBUG:PYME.cluster.rules:all tasks pushed, marking rule as complete
DEBUG:root:Successfully marked rule as complete
DEBUG:root:ending polling loop.
quaternion module not found, disabling custom clip plane orientations
New Canvas
0
DEBUG:PYME.LMVis.visCore:Creating VisGUI menu bar
DEBUG:PYME.LMVis.visCore:Calling AddMenuItem from visCore
DEBUG:PYME.LMVis.visCore:Calling AddMenuItem from visCore
DEBUG:PYME.LMVis.visCore:Calling AddMenuItem from visCore
DEBUG:PYME.LMVis.visCore:Calling AddMenuItem from visCore
DEBUG:PYME.LMVis.visCore:Calling AddMenuItem from visCore
DEBUG:PYME.LMVis.visCore:Calling AddMenuItem from visCore
DEBUG:PYME.LMVis.visCore:Calling AddMenuItem from visCore
DEBUG:PYME.LMVis.visCore:Calling AddMenuItem from visCore
DEBUG:PYME.LMVis.visCore:Calling AddMenuItem from visCore
DEBUG:PYME.LMVis.visCore:Calling AddMenuItem from visCore
DEBUG:PYME.LMVis.visCore:Calling AddMenuItem from visCore
DEBUG:PYME.LMVis.visCore:Calling AddMenuItem from visCore
DEBUG:PYME.LMVis.visCore:Calling AddMenuItem from visCore
DEBUG:PYME.LMVis.visCore:Calling AddMenuItem from visCore
DEBUG:PYME.LMVis.visCore:Calling AddMenuItem from visCore
DEBUG:PYME.LMVis.visCore:Calling AddMenuItem from visCore
DEBUG:PYME.LMVis.visCore:Calling AddMenuItem from visCore
DEBUG:PYME.LMVis.visCore:Calling AddMenuItem from visCore
DEBUG:PYME.LMVis.visCore:Calling AddMenuItem from visCore
DEBUG:PYME.LMVis.visCore:Calling AddMenuItem from visCore
DEBUG:PYME.LMVis.visCore:Calling AddMenuItem from visCore
DEBUG:PYME.LMVis.visCore:Calling AddMenuItem from visCore
DEBUG:PYME.LMVis.Extras:Initializing QPobjectSegment plugin
DEBUG:PYME.LMVis.visCore:Calling AddMenuItem from visCore
DEBUG:PYME.LMVis.visCore:Calling AddMenuItem from visCore
DEBUG:PYME.LMVis.visCore:Calling AddMenuItem from visCore
DEBUG:PYME.LMVis.visCore:Calling AddMenuItem from visCore
DEBUG:PYME.LMVis.visCore:Calling AddMenuItem from visCore
DEBUG:PYME.LMVis.Extras:Initializing animation plugin
DEBUG:PYME.LMVis.visCore:Calling AddMenuItem from visCore
DEBUG:PYME.LMVis.Extras:Initializing annotation plugin
DEBUG:PYME.LMVis.visCore:Calling AddMenuItem from visCore
DEBUG:PYME.LMVis.visCore:Calling AddMenuItem from visCore
DEBUG:PYME.LMVis.visCore:Calling AddMenuItem from visCore
DEBUG:PYME.LMVis.visCore:Calling AddMenuItem from visCore
DEBUG:PYME.LMVis.visCore:Calling AddMenuItem from visCore
Traceback (most recent call last):
  File "/Users/andy/code/python-microscopy/PYME/DSView/modules/LMAnalysis.py", line 265, in <lambda>
    self.bGo.Bind(wx.EVT_BUTTON, lambda e : self.lmanal.OnGo(e))
  File "/Users/andy/code/python-microscopy/PYME/DSView/modules/LMAnalysis.py", line 658, in OnGo
    self.analysisController.pushImagesCluster(self.image)
  File "/Users/andy/code/python-microscopy/PYME/DSView/modules/LMAnalysis.py", line 354, in pushImagesCluster
    self.onImagesPushed.send(self)
  File "/Users/andy/code/python-microscopy/PYME/contrib/dispatch/dispatcher.py", line 172, in send
    return [
  File "/Users/andy/code/python-microscopy/PYME/contrib/dispatch/dispatcher.py", line 173, in <listcomp>
    (receiver, receiver(signal=self, sender=sender, **named))
  File "/Users/andy/code/python-microscopy/PYME/DSView/modules/LMAnalysis.py", line 681, in OnImagesPushed
    self.dsviewer.LoadModule('LMDisplay')
  File "/Users/andy/code/python-microscopy/PYME/DSView/dsviewer.py", line 241, in LoadModule
    modules.loadModule(moduleName, self)
  File "/Users/andy/code/python-microscopy/PYME/DSView/modules/__init__.py", line 117, in loadModule
    _load_mod(mod, modName, dsviewer)
  File "/Users/andy/code/python-microscopy/PYME/DSView/modules/__init__.py", line 128, in _load_mod
    ret = mod.Plug(parent)
  File "/Users/andy/code/python-microscopy/PYME/DSView/modules/LMDisplay.py", line 194, in Plug
    return LMDisplay(dsviewer)
  File "/Users/andy/code/python-microscopy/PYME/DSView/modules/LMDisplay.py", line 77, in __init__
    self.CreateMenuBar(subMenu=True, use_shaders=use_shaders)
  File "/Users/andy/code/python-microscopy/PYME/LMVis/visCore.py", line 300, in CreateMenuBar
    Extras.InitPlugins(self)
  File "/Users/andy/code/python-microscopy/PYME/LMVis/Extras/__init__.py", line 45, in InitPlugins
    _load_mod(m, mn, visFr)
  File "/Users/andy/code/python-microscopy/PYME/DSView/modules/__init__.py", line 128, in _load_mod
    ret = mod.Plug(parent)
  File "/Users/andy/code/python-microscopy/PYME/LMVis/Extras/annotation.py", line 78, in Plug
    return Annotator(vis_fr)
  File "/Users/andy/code/python-microscopy/PYME/LMVis/Extras/annotation.py", line 35, in __init__
    ann.AnnotateBase.__init__(self, vis_fr, vis_fr.glCanvas.selectionSettings, minimize=True)
  File "/Users/andy/code/python-microscopy/PYME/DSView/modules/annotation.py", line 336, in __init__
    self.labelPanel = LabelPanel(win, self)
  File "/Users/andy/code/python-microscopy/PYME/DSView/modules/annotation.py", line 47, in __init__
    wx.Panel.__init__(self, parent, **kwargs)
TypeError: Panel(): arguments did not match any overloaded call:
  overload 1: too many arguments
  overload 2: argument 1 has unexpected type 'LMDisplay'
OpenGL - Version: b'2.1 Metal - 76.3'
Shader - Version: b'1.20'
GL.GL_MAX_SAMPLES: 4, GL.GL_SAMPLES: 4
DEBUG:PYME.LMVis.shader_programs.ShaderProgramFactory:New shader program created: <class 'PYME.LMVis.shader_programs.DefaultShaderProgram.DefaultShaderProgram'>
DEBUG:PYME.DSView.modules.LMAnalysis:use_cluster: newStyle=True, tq=None
Traceback (most recent call last):
  File "/Users/andy/code/python-microscopy/PYME/ui/mytimer.py", line 42, in Notify
    a()
  File "/Users/andy/code/python-microscopy/PYME/DSView/modules/LMAnalysis.py", line 710, in refresh_analysis
    self._refresh_analysis_cluster()
  File "/Users/andy/code/python-microscopy/PYME/DSView/modules/LMAnalysis.py", line 768, in _refresh_analysis_cluster
    newNumAnalysed = int(queueInfo[self.analysisController.pusher._ruleID]['tasksCompleted'])
KeyError: '000000-b36a32e82ed24cf49905075807340511'
Ev Idle
('points', 't')
refreshed
DEBUG:PYME.DSView.modules.LMAnalysis:use_cluster: newStyle=True, tq=None
DEBUG:PYME.recipes.recipe:recipe.execute()
DEBUG:PYME.recipes.recipe:Executing <PYME.recipes.localisations.Pipelineify object at 0x2a2208630>
/Users/andy/code/python-microscopy/PYME/IO/MetaDataHandler.py:666: UserWarning: DictMDHandler is not yet fully supported, and will likely cause failures for anything related to localisation fitting
  warnings.warn('DictMDHandler is not yet fully supported, and will likely cause failures for anything related to localisation fitting')
DEBUG:PYME.recipes.localisations:no events found
<DictMDHandler>:

Analysis.BGRange: (-30, 0)
Analysis.DebounceRadius: 4
Analysis.DetectionFilterMag: 0.15
Analysis.DetectionThreshold: 750000.0
Analysis.FiducialROISize: 11
Analysis.FiducialSize: 1000.0
Analysis.FiducialThreshold: 1.8
Analysis.FitModule: DoubleHelixFitR
Analysis.LobeSepGuess: 900.0
Analysis.PCTBackground: 0.25
Analysis.ROISize: 10
Analysis.StartAt: 30
Analysis.TrackFiducials: False
Analysis.subtractBackground: True
Camera.ADOffset: 110
Camera.DarkMapID: 
Camera.ElectronsPerCount: 12.9
Camera.FlatfieldMapID: 
Camera.NoiseFactor: 1.4
Camera.ReadNoise: 0
Camera.TrueEMGain: 272
Camera.VarianceMapID: 
PYME.Version: 23.03.02.post0.dev[git]9f779019dd36
tIndex: 0
voxelsize.units: um
voxelsize.x: 0.1177
voxelsize.y: 0.1177
voxelsize.z: 0.2
DataFileID: 760605515 <DictMDHandler>:

Processing.AddPipelineDerivedVars.Pixelsizenm: 1.0
DEBUG:PYME.recipes.recipe:Executing <PYME.recipes.localisations.ProcessColour object at 0x2a626d0e0>
<DictMDHandler>:

Analysis.BGRange: (-30, 0)
Analysis.DebounceRadius: 4
Analysis.DetectionFilterMag: 0.15
Analysis.DetectionThreshold: 750000.0
Analysis.FiducialROISize: 11
Analysis.FiducialSize: 1000.0
Analysis.FiducialThreshold: 1.8
Analysis.FitModule: DoubleHelixFitR
Analysis.LobeSepGuess: 900.0
Analysis.PCTBackground: 0.25
Analysis.ROISize: 10
Analysis.StartAt: 30
Analysis.TrackFiducials: False
Analysis.subtractBackground: True
Camera.ADOffset: 110
Camera.DarkMapID: 
Camera.ElectronsPerCount: 12.9
Camera.FlatfieldMapID: 
Camera.NoiseFactor: 1.4
Camera.ReadNoise: 0
Camera.TrueEMGain: 272
Camera.VarianceMapID: 
PYME.Version: 23.03.02.post0.dev[git]9f779019dd36
tIndex: 0
voxelsize.units: um
voxelsize.x: 0.1177
voxelsize.y: 0.1177
voxelsize.z: 0.2
DataFileID: 760605515
Processing.AddPipelineDerivedVars.Pixelsizenm: 1.0 <DictMDHandler>:

Processing.ProcessColour.RatiosFromMetadata: True
Processing.ProcessColour.SpeciesDyes: {}
Processing.ProcessColour.SpeciesRatios: {}
DEBUG:PYME.recipes.recipe:Executing <PYME.recipes.tablefilters.FilterTable object at 0x14c70b5e0>
<DictMDHandler>:

Analysis.BGRange: (-30, 0)
Analysis.DebounceRadius: 4
Analysis.DetectionFilterMag: 0.15
Analysis.DetectionThreshold: 750000.0
Analysis.FiducialROISize: 11
Analysis.FiducialSize: 1000.0
Analysis.FiducialThreshold: 1.8
Analysis.FitModule: DoubleHelixFitR
Analysis.LobeSepGuess: 900.0
Analysis.PCTBackground: 0.25
Analysis.ROISize: 10
Analysis.StartAt: 30
Analysis.TrackFiducials: False
Analysis.subtractBackground: True
Camera.ADOffset: 110
Camera.DarkMapID: 
Camera.ElectronsPerCount: 12.9
Camera.FlatfieldMapID: 
Camera.NoiseFactor: 1.4
Camera.ReadNoise: 0
Camera.TrueEMGain: 272
Camera.VarianceMapID: 
PYME.Version: 23.03.02.post0.dev[git]9f779019dd36
tIndex: 0
voxelsize.units: um
voxelsize.x: 0.1177
voxelsize.y: 0.1177
voxelsize.z: 0.2
DataFileID: 760605515
Processing.AddPipelineDerivedVars.Pixelsizenm: 1.0
Processing.ProcessColour.RatiosFromMetadata: True
Processing.ProcessColour.SpeciesDyes: {}
Processing.ProcessColour.SpeciesRatios: {} <DictMDHandler>:

Processing.FilterTable.Filters: {'error_x': [0, 30], 'error_y': [0, 30], 'A': [5, 20000], 'sig': [95, 200]}
DEBUG:PYME.recipes.recipe:Module timings: {'localisations.AddPipelineDerivedVars': 0.0013990402221679688, 'localisations.ProcessColour': 0.00019097328186035156, 'tablefilters.FilterTable': 0.00022292137145996094}
Traceback (most recent call last):
  File "/Users/andy/code/python-microscopy/PYME/ui/mytimer.py", line 42, in Notify
    a()
  File "/Users/andy/code/python-microscopy/PYME/DSView/modules/LMAnalysis.py", line 710, in refresh_analysis
    self._refresh_analysis_cluster()
  File "/Users/andy/code/python-microscopy/PYME/DSView/modules/LMAnalysis.py", line 779, in _refresh_analysis_cluster
    self._add_new_results(newResults)
  File "/Users/andy/code/python-microscopy/PYME/DSView/modules/LMAnalysis.py", line 740, in _add_new_results
    self._ovl.filter.setResults(self.fitResults)
AttributeError: 'LMAnalyser2' object has no attribute '_ovl'
DEBUG:PYME.DSView.modules.LMAnalysis:use_cluster: newStyle=True, tq=None
DEBUG:PYME.recipes.recipe:recipe.execute()
DEBUG:PYME.recipes.recipe:Executing <PYME.recipes.localisations.ProcessColour object at 0x2a626d0e0>
<DictMDHandler>:

Analysis.BGRange: (-30, 0)
Analysis.DebounceRadius: 4
Analysis.DetectionFilterMag: 0.15
Analysis.DetectionThreshold: 750000.0
Analysis.FiducialROISize: 11
Analysis.FiducialSize: 1000.0
Analysis.FiducialThreshold: 1.8
Analysis.FitModule: DoubleHelixFitR
Analysis.LobeSepGuess: 900.0
Analysis.PCTBackground: 0.25
Analysis.ROISize: 10
Analysis.StartAt: 30
Analysis.TrackFiducials: False
Analysis.subtractBackground: True
Camera.ADOffset: 110
Camera.DarkMapID: 
Camera.ElectronsPerCount: 12.9
Camera.FlatfieldMapID: 
Camera.NoiseFactor: 1.4
Camera.ReadNoise: 0
Camera.TrueEMGain: 272
Camera.VarianceMapID: 
PYME.Version: 23.03.02.post0.dev[git]9f779019dd36
tIndex: 0
voxelsize.units: um
voxelsize.x: 0.1177
voxelsize.y: 0.1177
voxelsize.z: 0.2
DataFileID: 760605515
Processing.AddPipelineDerivedVars.Pixelsizenm: 1.0
Processing.ProcessColour.RatiosFromMetadata: True
Processing.ProcessColour.SpeciesDyes: {}
Processing.ProcessColour.SpeciesRatios: {} <DictMDHandler>:

Processing.ProcessColour.RatiosFromMetadata: True
Processing.ProcessColour.SpeciesDyes: {}
Processing.ProcessColour.SpeciesRatios: {}
DEBUG:PYME.recipes.recipe:Executing <PYME.recipes.tablefilters.FilterTable object at 0x14c70b5e0>
<DictMDHandler>:

Analysis.BGRange: (-30, 0)
Analysis.DebounceRadius: 4
Analysis.DetectionFilterMag: 0.15
Analysis.DetectionThreshold: 750000.0
Analysis.FiducialROISize: 11
Analysis.FiducialSize: 1000.0
Analysis.FiducialThreshold: 1.8
Analysis.FitModule: DoubleHelixFitR
Analysis.LobeSepGuess: 900.0
Analysis.PCTBackground: 0.25
Analysis.ROISize: 10
Analysis.StartAt: 30
Analysis.TrackFiducials: False
Analysis.subtractBackground: True
Camera.ADOffset: 110
Camera.DarkMapID: 
Camera.ElectronsPerCount: 12.9
Camera.FlatfieldMapID: 
Camera.NoiseFactor: 1.4
Camera.ReadNoise: 0
Camera.TrueEMGain: 272
Camera.VarianceMapID: 
PYME.Version: 23.03.02.post0.dev[git]9f779019dd36
tIndex: 0
voxelsize.units: um
voxelsize.x: 0.1177
voxelsize.y: 0.1177
voxelsize.z: 0.2
DataFileID: 760605515
Processing.AddPipelineDerivedVars.Pixelsizenm: 1.0
Processing.ProcessColour.RatiosFromMetadata: True
Processing.ProcessColour.SpeciesDyes: {}
Processing.ProcessColour.SpeciesRatios: {} <DictMDHandler>:

Processing.FilterTable.Filters: {'error_x': [0, 30], 'error_y': [0, 30], 'A': [5, 20000], 'sig': [95, 200]}
DEBUG:PYME.recipes.recipe:Module timings: {'localisations.AddPipelineDerivedVars': 0.0013990402221679688, 'localisations.ProcessColour': 0.00028395652770996094, 'tablefilters.FilterTable': 0.0011799335479736328}
Traceback (most recent call last):
  File "/Users/andy/code/python-microscopy/PYME/ui/mytimer.py", line 42, in Notify
    a()
  File "/Users/andy/code/python-microscopy/PYME/DSView/modules/LMAnalysis.py", line 710, in refresh_analysis
    self._refresh_analysis_cluster()
  File "/Users/andy/code/python-microscopy/PYME/DSView/modules/LMAnalysis.py", line 779, in _refresh_analysis_cluster
    self._add_new_results(newResults)
  File "/Users/andy/code/python-microscopy/PYME/DSView/modules/LMAnalysis.py", line 740, in _add_new_results
    self._ovl.filter.setResults(self.fitResults)
AttributeError: 'LMAnalyser2' object has no attribute '_ovl'
DEBUG:PYME.DSView.modules.LMAnalysis:use_cluster: newStyle=True, tq=None
DEBUG:PYME.recipes.recipe:recipe.execute()
DEBUG:PYME.recipes.recipe:Executing <PYME.recipes.localisations.ProcessColour object at 0x2a626d0e0>
<DictMDHandler>:

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