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Saner workaround for #1292#1305

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David-Baddeley merged 2 commits into
python-microscopy:masterfrom
David-Baddeley:traitsui_stuff
Oct 17, 2022
Merged

Saner workaround for #1292#1305
David-Baddeley merged 2 commits into
python-microscopy:masterfrom
David-Baddeley:traitsui_stuff

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@David-Baddeley
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Fixes #1292, adds saner default for DensityMapping on multicolour datasets

@David-Baddeley David-Baddeley merged commit 2d9617b into python-microscopy:master Oct 17, 2022
@barentine
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barentine commented Oct 18, 2022

Seeing an issue in datawrap for what should be a 2D histogram (both through PYMEVis as well as run on a clusterofone) generated using PYMEAcquire -i init_sim_htsms.py

Details
===========================================================================
Error in rule: 000005-d1ae662e5c40446493f1b7d9f3ed5969 running task: 0 on WEM24C:18632

taskDescr:
----------
id: 000005-d1ae662e5c40446493f1b7d9f3ed5969~0
inputs:
  input: PYME-CLUSTER://WEM24C/aesb/2022_10_18/analysis/18_10_series_C.h5r
optimal-chunk-size: 1
output_dir: PYME-CLUSTER:///aesb/2022_10_18/analysis
taskdef:
  recipe: |
    - multiview.Fold:
        input_name: FitResults
        output_name: folded
    - localisations.DensityMapping:
        inputLocalizations: folded
        outputImage: output
        renderingModule: Histogram
    - output.ImageOutput:
        filePattern: '{output_dir}/{file_stub}.tif'
        inputName: output
        scheme: pyme-cluster://
type: recipe


Traceback:
----------
Traceback (most recent call last):
  File "C:\Users\aesb\AppData\Local\python-microscopy\lib\site-packages\PYME\recipes\recipe.py", line 222, in execute
    m.execute(self.namespace)
  File "C:\Users\aesb\AppData\Local\python-microscopy\lib\site-packages\PYME\recipes\localisations.py", line 102, in execute
    out = renderer.Generate(self.trait_get())
  File "C:\Users\aesb\AppData\Local\python-microscopy\lib\site-packages\PYME\LMVis\renderers.py", line 285, in Generate
    return GeneratedImage(ims, imb, pixelSize, sliceThickness, colours, mdh=mdh)
  File "C:\Users\aesb\AppData\Local\python-microscopy\lib\site-packages\PYME\IO\image.py", line 1356, in GeneratedImage
    image = ImageStack(img, mdh=mdh)
  File "C:\Users\aesb\AppData\Local\python-microscopy\lib\site-packages\PYME\IO\image.py", line 254, in __init__
    self.SetData(self._data)
  File "C:\Users\aesb\AppData\Local\python-microscopy\lib\site-packages\PYME\IO\image.py", line 295, in SetData
    self._data = dataWrap.Wrap(data)
  File "C:\Users\aesb\AppData\Local\python-microscopy\lib\site-packages\PYME\IO\dataWrap.py", line 101, in Wrap
    datasource = ListWrapper(datasource, strict_dims=strict_dims)
  File "C:\Users\aesb\AppData\Local\python-microscopy\lib\site-packages\PYME\IO\dataWrap.py", line 35, in __init__
    self.listDim = self.wrapList[0].ndim
IndexError: list index out of range

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "C:\Users\aesb\AppData\Local\python-microscopy\lib\site-packages\PYME\cluster\taskWorkerHTTP.py", line 361, in computeLoop
    recipe.execute()
  File "C:\Users\aesb\AppData\Local\python-microscopy\lib\site-packages\PYME\recipes\recipe.py", line 263, in execute
    raise RecipeExecutionError('Recipe execution failed in module %s' % self._failing_module._module_name, self ) from e
PYME.recipes.recipe.RecipeExecutionError: Recipe execution failed in module localisations.DensityMapping

@David-Baddeley
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@barentine - suspect it's the lack of a ProcessColour and/or 'Pipelineify' modules in the recipe, but we should see if we can make it more robust ... If you actually want to get a two colour image, I suspect you'll need a little bit more (MergeClumps etc ... beforehand too).

David-Baddeley added a commit to David-Baddeley/python-microscopy that referenced this pull request Oct 24, 2022
David-Baddeley added a commit that referenced this pull request Oct 24, 2022
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[BUG] Traitsui list editor causes hard crash (segfault)

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