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Issue loading a volume #4190

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payno opened this issue Oct 31, 2024 · 5 comments
Open

Issue loading a volume #4190

payno opened this issue Oct 31, 2024 · 5 comments

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@payno
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payno commented Oct 31, 2024

when trying to display the following file /data/visitor/ihma551/bm05/20240920/PROCESSED_DATA/SSD_battery/SSD_battery_0001/reconstructed_volumes/SSD_battery_0001_1_1_0000pag_db0020_vol.hdf5 as 3D / cube we get the following error:

hpc5-0204:PROCESSED_DATA/SSD_battery/SSD_battery_0001 % silx view reconstructed_volumes/SSD_battery_0001_1_1_0000pag_db0020_vol.hdf5 
QStandardPaths: XDG_RUNTIME_DIR points to non-existing path '/run/user/81067', please create it with 0700 permissions.
ERROR:silx.gui.qt._qt:<class 'ValueError'> Zero-size array   File "/usr/lib/python3/dist-packages/silx/gui/data/DataViewer.py", line 287, in __setDataInView
    self.__currentView.setData(self.__displayedData)
  File "/usr/lib/python3/dist-packages/silx/gui/data/DataViews.py", line 1119, in setData
    self.getWidget().setData(data)
  File "/usr/lib/python3/dist-packages/silx/gui/data/_VolumeWindow.py", line 111, in setData
    volume = sceneWidget.addVolume(data, copy=False)
  File "/usr/lib/python3/dist-packages/silx/gui/plot3d/SceneWidget.py", line 504, in addVolume
    volume.setData(data, copy=copy)
  File "/usr/lib/python3/dist-packages/silx/gui/plot3d/items/volume.py", line 536, in setData
    self._dataRange = self._computeRangeFromData(self._data)
  File "/usr/lib/python3/dist-packages/silx/gui/plot3d/items/volume.py", line 503, in _computeRangeFromData
    dataRange = min_max(data, min_positive=True, finite=True)
  File "src/silx/math/combo.pyx", line 326, in silx.math.combo.min_max
  File "src/silx/math/combo.pyx", line 224, in silx.math.combo._finite_min_max

Tested with 128Go of ram. Crashes after waiting a 'long time'. So probably when initiate the display

@t20100
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t20100 commented Nov 4, 2024

What is the size of the dataset?
Do you select the 3D view manually or is it opened automatically when opening the dataset?
Is it only with the 3D view? or with other as well?

@payno
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payno commented Nov 4, 2024

The volume is 2048x2048x2048.

Other display mode (image stack...) works well.

The error arrives after a couple of minutes once clicked on the 'cube' view.

@payno
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payno commented Nov 4, 2024

After discussion with @t20100 this clearly comes from the size of the volume. A warning could be add.

@payno
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payno commented Feb 6, 2025

Do we close it or do we want to add a warning for the next release ?
If we want to add a warning we will need to have a estimate on how much a system can handle or define an arbitrary threshold (number of cubes) to define when raising the warning

@payno
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payno commented Feb 10, 2025

So the idea would be to warm the user if the volume exceed a certain size (2k*2k).
It can be either a warning in the terminal or a pop-up dialog.

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