tomwer issueshttps://gitlab.esrf.fr/tomotools/tomwer/-/issues2024-03-28T16:00:18+01:00https://gitlab.esrf.fr/tomotools/tomwer/-/issues/1155move to native namespace packages2024-03-28T16:00:18+01:00paynomove to native namespace packagessee example in https://gitlab.esrf.fr/workflow/ewoksapps/est/-/merge_requests/136 and details in https://confluence.esrf.fr/display/AAWWK/2024-03-27+Meeting+notessee example in https://gitlab.esrf.fr/workflow/ewoksapps/est/-/merge_requests/136 and details in https://confluence.esrf.fr/display/AAWWK/2024-03-27+Meeting+notes1.4https://gitlab.esrf.fr/tomotools/tomwer/-/issues/1145issue multi-cor2024-03-19T08:33:20+01:00paynoissue multi-cor```
^CERROR:silx.gui.qt._qt:<class 'AttributeError'> 'super' object has no attribute 'stop' File "/cvmfs/tomo.esrf.fr/software/packages/linux/ppc64le/tomotools/2024_03_04/lib/python3.11/site-packages/tomwer/app/multicor.py", line 123, ...```
^CERROR:silx.gui.qt._qt:<class 'AttributeError'> 'super' object has no attribute 'stop' File "/cvmfs/tomo.esrf.fr/software/packages/linux/ppc64le/tomotools/2024_03_04/lib/python3.11/site-packages/tomwer/app/multicor.py", line 123, in stop
super().stop()
```https://gitlab.esrf.fr/tomotools/tomwer/-/issues/1149volume viewer: infinite loop when try to load a non-existing tiff file2024-03-13T14:15:32+01:00paynovolume viewer: infinite loop when try to load a non-existing tiff fileif this happen then we end up with something like:
```bash
File not found [tomoscan.esrf.volume.singleframebase](singleframebase.py:158)
2024-03-13 11:43:42,338 [WARNING] Attempt to set a non HDF5 volume to the viewer. This requires to l...if this happen then we end up with something like:
```bash
File not found [tomoscan.esrf.volume.singleframebase](singleframebase.py:158)
2024-03-13 11:43:42,338 [WARNING] Attempt to set a non HDF5 volume to the viewer. This requires to load all the data in memory. This can take a while [tomwer.gui.visualization.volumeviewer](volumeviewer.py:321)
2024-03-13 11:43:42,338 [WARNING] Failed to load any data for <bound method BaseFolderAndfilePrefixIdentifierMixIn.short_description of <tomwer.core.volume.tiffvolume.TIFFVolumeIdentifier object at 0x7f7d47713fa0>> [tomoscan.esrf.volume.singleframebase](singleframebase.py:316)
2024-03-13 11:43:42,339 [ERROR ] Failed to load volume tiff:volume:/tmp_14_days/payno/training_2024/reconstructed_volumes/cast_volume/bambou_hercules_0001_vol [tomwer.gui.visualization.volumeviewer](volumeviewer.py:338)
2024-03-13 11:43:42,339:ERROR:tomwer.gui.visualization.volumeviewer: Failed to load volume tiff:volume:/tmp_14_days/payno/training_2024/reconstructed_volumes/cast_volume/bambou_hercules_0001_vol
2024-03-13 11:43:42,340 [WARNING] unable to load metadata from /tmp_14_days/payno/training_2024/reconstructed_volumes/cast_volume/bambou_hercules_0001_vol/bambou_hercules_0001_vol_infos.txt - File not found [tomoscan.esrf.volume.singleframebase](singleframebase.py:158)
2024-03-13 11:43:42,340 [WARNING] Attempt to set a non HDF5 volume to the viewer. This requires to load all the data in memory. This can take a while [tomwer.gui.visualization.volumeviewer](volumeviewer.py:321)
2024-03-13 11:43:42,341 [WARNING] Failed to load any data for <bound method BaseFolderAndfilePrefixIdentifierMixIn.short_description of <tomwer.core.volume.tiffvolume.TIFFVolumeIdentifier object at 0x7f7d47713820>> [tomoscan.esrf.volume.singleframebase](singleframebase.py:316)
2024-03-13 11:43:42,341 [ERROR ] Failed to load volume tiff:volume:/tmp_14_days/payno/training_2024/reconstructed_volumes/cast_volume/bambou_hercules_0001_vol [tomwer.gui.visualization.volumeviewer](volumeviewer.py:338)
2024-03-13 11:43:42,341:ERROR:tomwer.gui.visualization.volumeviewer: Failed to load volume tiff:volume:/tmp_14_days/payno/training_2024/reconstructed_volumes/cast_volume/bambou_hercules_0001_vol
```https://gitlab.esrf.fr/tomotools/tomwer/-/issues/1146issue hdf52024-03-13T09:22:23+01:00paynoissue hdf5```
self._centralWidget.setData(volume)
File "/cvmfs/tomo.esrf.fr/software/packages/linux/ppc64le/tomotools/2024_03_04/lib/python3.11/site-packages/silx/gui/data/DataViewerFrame.py", line 188, in setData
self.__dataViewer.setDa...```
self._centralWidget.setData(volume)
File "/cvmfs/tomo.esrf.fr/software/packages/linux/ppc64le/tomotools/2024_03_04/lib/python3.11/site-packages/silx/gui/data/DataViewerFrame.py", line 188, in setData
self.__dataViewer.setData(data)
File "/cvmfs/tomo.esrf.fr/software/packages/linux/ppc64le/tomotools/2024_03_04/lib/python3.11/site-packages/silx/gui/data/DataViewer.py", line 536, in setData
self.__updateView()
File "/cvmfs/tomo.esrf.fr/software/packages/linux/ppc64le/tomotools/2024_03_04/lib/python3.11/site-packages/silx/gui/data/DataViewer.py", line 442, in __updateView
self.__updateAvailableViews()
File "/cvmfs/tomo.esrf.fr/software/packages/linux/ppc64le/tomotools/2024_03_04/lib/python3.11/site-packages/silx/gui/data/DataViewer.py", line 424, in __updateAvailableViews
info = self._getInfo()
^^^^^^^^^^^^^^^
File "/cvmfs/tomo.esrf.fr/software/packages/linux/ppc64le/tomotools/2024_03_04/lib/python3.11/site-packages/silx/gui/data/DataViewer.py", line 569, in _getInfo
self.__info = DataViews.DataInfo(self.__data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/cvmfs/tomo.esrf.fr/software/packages/linux/ppc64le/tomotools/2024_03_04/lib/python3.11/site-packages/silx/gui/data/DataViews.py", line 166, in __init__
self.interpretation = get_attr_as_unicode(data, "interpretation")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/cvmfs/tomo.esrf.fr/software/packages/linux/ppc64le/tomotools/2024_03_04/lib/python3.11/site-packages/silx/io/nxdata/_utils.py", line 66, in get_attr_as_unicode
attr = item.attrs.get(attr_name, default)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "<frozen _collections_abc>", line 774, in get
File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
File "/cvmfs/tomo.esrf.fr/software/packages/linux/ppc64le/tomotools/2024_03_04/lib/python3.11/site-packages/h5py/_hl/attrs.py", line 78, in __getitem__
attr.read(arr, mtype=htype)
File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
File "h5py/h5a.pyx", line 362, in h5py.h5a.AttrID.read
File "h5py/_proxy.pyx", line 61, in h5py._proxy.attr_rw
OSError: Can't synchronously read data (Expected global heap object size does not match)
-------------------------------------------------------------------------------
------------------------------ OSError Exception ------------------------------
Traceback (most recent call last):
File "/cvmfs/tomo.esrf.fr/software/packages/linux/ppc64le/tomotools/2024_03_04/lib/python3.11/site-packages/orangecanvas/scheme/signalmanager.py", line 1180, in __process_next
if self.__process_next_helper(use_max_active=True):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/cvmfs/tomo.esrf.fr/software/packages/linux/ppc64le/tomotools/2024_03_04/lib/python3.11/site-packages/orangecanvas/scheme/signalmanager.py", line 1218, in __process_next_helper
self.process_node(selected_node)
File "/cvmfs/tomo.esrf.fr/software/packages/linux/ppc64le/tomotools/2024_03_04/lib/python3.11/site-packages/orangecanvas/scheme/signalmanager.py", line 846, in process_node
self.send_to_node(node, signals_in)
File "/cvmfs/tomo.esrf.fr/software/packages/linux/ppc64le/tomotools/2024_03_04/lib/python3.11/site-packages/orangewidget/workflow/widgetsscheme.py", line 806, in send_to_node
self.process_signals_for_widget(node, widget, signals)
File "/cvmfs/tomo.esrf.fr/software/packages/linux/ppc64le/tomotools/2024_03_04/lib/python3.11/site-packages/orangewidget/workflow/widgetsscheme.py", line 820, in process_signals_for_widget
process_signals_for_widget(widget, signals, workflow)
File "/cvmfs/tomo.esrf.fr/software/packages/linux/ppc64le/tomotools/2024_03_04/lib/python3.11/functools.py", line 909, in wrapper
return dispatch(args[0].__class__)(*args, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/cvmfs/tomo.esrf.fr/software/packages/linux/ppc64le/tomotools/2024_03_04/lib/python3.11/site-packages/orangewidget/workflow/widgetsscheme.py", line 923, in process_signals_for_widget
process_signal_input(input_meta, widget, signal, workflow)
File "/cvmfs/tomo.esrf.fr/software/packages/linux/ppc64le/tomotools/2024_03_04/lib/python3.11/functools.py", line 909, in wrapper
return dispatch(args[0].__class__)(*args, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/cvmfs/tomo.esrf.fr/software/packages/linux/ppc64le/tomotools/2024_03_04/lib/python3.11/site-packages/orangewidget/workflow/widgetsscheme.py", line 886, in process_signal_input_default
notify_input_helper(
File "/cvmfs/tomo.esrf.fr/software/packages/linux/ppc64le/tomotools/2024_03_04/lib/python3.11/functools.py", line 909, in wrapper
return dispatch(args[0].__class__)(*args, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/cvmfs/tomo.esrf.fr/software/packages/linux/ppc64le/tomotools/2024_03_04/lib/python3.11/site-packages/orangewidget/utils/signals.py", line 735, in set_input_helper
handler(*args)
File "/cvmfs/tomo.esrf.fr/software/packages/linux/ppc64le/tomotools/2024_03_04/lib/python3.11/site-packages/orangewidget/utils/signals.py", line 208, in summarize_wrapper
method(widget, value)
File "/cvmfs/tomo.esrf.fr/software/packages/linux/ppc64le/tomotools/2024_03_04/lib/python3.11/site-packages/orangecontrib/tomwer/widgets/visualization/VolumeViewerOW.py", line 50, in addScan
self.viewer.setScan(scan)
File "/cvmfs/tomo.esrf.fr/software/packages/linux/ppc64le/tomotools/2024_03_04/lib/python3.11/site-packages/tomwer/gui/visualization/volumeviewer.py", line 280, in setScan
self._set_volumes(volumes=scan.latest_vol_reconstructions)
File "/cvmfs/tomo.esrf.fr/software/packages/linux/ppc64le/tomotools/2024_03_04/lib/python3.11/site-packages/tomwer/gui/visualization/volumeviewer.py", line 401, in _set_volumes
self._set_volume(data)
File "/cvmfs/tomo.esrf.fr/software/packages/linux/ppc64le/tomotools/2024_03_04/lib/python3.11/site-packages/tomwer/gui/visualization/volumeviewer.py", line 410, in _set_volume
self._centralWidget.setData(volume)
File "/cvmfs/tomo.esrf.fr/software/packages/linux/ppc64le/tomotools/2024_03_04/lib/python3.11/site-packages/silx/gui/data/DataViewerFrame.py", line 188, in setData
self.__dataViewer.setData(data)
File "/cvmfs/tomo.esrf.fr/software/packages/linux/ppc64le/tomotools/2024_03_04/lib/python3.11/site-packages/silx/gui/data/DataViewer.py", line 536, in setData
self.__updateView()
File "/cvmfs/tomo.esrf.fr/software/packages/linux/ppc64le/tomotools/2024_03_04/lib/python3.11/site-packages/silx/gui/data/DataViewer.py", line 442, in __updateView
self.__updateAvailableViews()
File "/cvmfs/tomo.esrf.fr/software/packages/linux/ppc64le/tomotools/2024_03_04/lib/python3.11/site-packages/silx/gui/data/DataViewer.py", line 424, in __updateAvailableViews
info = self._getInfo()
^^^^^^^^^^^^^^^
File "/cvmfs/tomo.esrf.fr/software/packages/linux/ppc64le/tomotools/2024_03_04/lib/python3.11/site-packages/silx/gui/data/DataViewer.py", line 569, in _getInfo
self.__info = DataViews.DataInfo(self.__data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/cvmfs/tomo.esrf.fr/software/packages/linux/ppc64le/tomotools/2024_03_04/lib/python3.11/site-packages/silx/gui/data/DataViews.py", line 166, in __init__
self.interpretation = get_attr_as_unicode(data, "interpretation")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/cvmfs/tomo.esrf.fr/software/packages/linux/ppc64le/tomotools/2024_03_04/lib/python3.11/site-packages/silx/io/nxdata/_utils.py", line 66, in get_attr_as_unicode
attr = item.attrs.get(attr_name, default)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "<frozen _collections_abc>", line 774, in get
File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
File "/cvmfs/tomo.esrf.fr/software/packages/linux/ppc64le/tomotools/2024_03_04/lib/python3.11/site-packages/h5py/_hl/attrs.py", line 78, in __getitem__
attr.read(arr, mtype=htype)
File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
File "h5py/h5a.pyx", line 362, in h5py.h5a.AttrID.read
File "h5py/_proxy.pyx", line 61, in h5py._proxy.attr_rw
OSError: Can't synchronously read data (Expected global heap object size does not match)
-------------------------------------------------------------------------------
```https://gitlab.esrf.fr/tomotools/tomwer/-/issues/1140integrate ewoksnotify2024-03-11T16:22:34+01:00paynointegrate ewoksnotify1.4https://gitlab.esrf.fr/tomotools/tomwer/-/issues/1142issue h52nx conversion2024-03-11T15:47:37+01:00paynoissue h52nx conversionWhen provide a configuration file end up with
```
Traceback (most recent call last):
File "/cvmfs/tomo.esrf.fr/software/packages/linux/ppc64le/tomotools/2024_03_04/lib/python3.11/site-packages/orangecontrib/tomwer/widgets/control/NXTom...When provide a configuration file end up with
```
Traceback (most recent call last):
File "/cvmfs/tomo.esrf.fr/software/packages/linux/ppc64le/tomotools/2024_03_04/lib/python3.11/site-packages/orangecontrib/tomwer/widgets/control/NXTomomillOW.py", line 316, in _sendAll
self._convertAndSend(identifier.to_str())
File "/cvmfs/tomo.esrf.fr/software/packages/linux/ppc64le/tomotools/2024_03_04/lib/python3.11/site-packages/orangecontrib/tomwer/widgets/control/NXTomomillOW.py", line 209, in _convertAndSend
self._processBlissScan(bliss_scan)
File "/cvmfs/tomo.esrf.fr/software/packages/linux/ppc64le/tomotools/2024_03_04/lib/python3.11/site-packages/orangecontrib/tomwer/widgets/control/NXTomomillOW.py", line 252, in _processBlissScan
self._execute_ewoks_task(propagate=True)
TypeError: OWEwoksWidgetWithTaskStack._execute_ewoks_task() missing 1 required positional argument: 'log_missing_inputs'
```https://gitlab.esrf.fr/tomotools/tomwer/-/issues/1111copy dark / flat2024-02-26T19:43:20+01:00paynocopy dark / flat"remove raw files when done": add information that is for spec only"remove raw files when done": add information that is for spec only1.3https://gitlab.esrf.fr/tomotools/tomwer/-/issues/1128multi-cor: score2024-02-23T08:57:32+01:00paynomulti-cor: scoremodifying the score does not modify the plotmodifying the score does not modify the plot1.3https://gitlab.esrf.fr/tomotools/tomwer/-/issues/1129multi-delta-beta: no display2024-02-22T16:57:59+01:00paynomulti-delta-beta: no displaydisplay of delta / beta values is not working. But the slice are reconstructed. Most likely something file_name mapping faillingdisplay of delta / beta values is not working. But the slice are reconstructed. Most likely something file_name mapping failling1.3https://gitlab.esrf.fr/tomotools/tomwer/-/issues/1124connect data discovery / HDF5 nxtomomill2024-02-22T16:27:03+01:00paynoconnect data discovery / HDF5 nxtomomill```txt
Traceback (most recent call last):
File "/cvmfs/tomo.esrf.fr/software/packages/linux/ppc64le/tomotools/2023_11_24/lib/python3.11/site-packages/orangecanvas/scheme/signalmanager.py", line 1180, in __process_next
if self.__pro...```txt
Traceback (most recent call last):
File "/cvmfs/tomo.esrf.fr/software/packages/linux/ppc64le/tomotools/2023_11_24/lib/python3.11/site-packages/orangecanvas/scheme/signalmanager.py", line 1180, in __process_next
if self.__process_next_helper(use_max_active=True):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/cvmfs/tomo.esrf.fr/software/packages/linux/ppc64le/tomotools/2023_11_24/lib/python3.11/site-packages/orangecanvas/scheme/signalmanager.py", line 1218, in __process_next_helper
self.process_node(selected_node)
File "/cvmfs/tomo.esrf.fr/software/packages/linux/ppc64le/tomotools/2023_11_24/lib/python3.11/site-packages/orangecanvas/scheme/signalmanager.py", line 846, in process_node
self.send_to_node(node, signals_in)
File "/cvmfs/tomo.esrf.fr/software/packages/linux/ppc64le/tomotools/2023_11_24/lib/python3.11/site-packages/orangewidget/workflow/widgetsscheme.py", line 806, in send_to_node
self.process_signals_for_widget(node, widget, signals)
File "/cvmfs/tomo.esrf.fr/software/packages/linux/ppc64le/tomotools/2023_11_24/lib/python3.11/site-packages/orangewidget/workflow/widgetsscheme.py", line 820, in process_signals_for_widget
process_signals_for_widget(widget, signals, workflow)
File "/cvmfs/tomo.esrf.fr/software/packages/linux/ppc64le/tomotools/2023_11_24/lib/python3.11/functools.py", line 909, in wrapper
return dispatch(args[0].__class__)(*args, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/cvmfs/tomo.esrf.fr/software/packages/linux/ppc64le/tomotools/2023_11_24/lib/python3.11/site-packages/orangewidget/workflow/widgetsscheme.py", line 925, in process_signals_for_widget
handle_new_signals(widget, workflow)
File "/cvmfs/tomo.esrf.fr/software/packages/linux/ppc64le/tomotools/2023_11_24/lib/python3.11/functools.py", line 909, in wrapper
return dispatch(args[0].__class__)(*args, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/cvmfs/tomo.esrf.fr/software/packages/linux/ppc64le/tomotools/2023_11_24/lib/python3.11/site-packages/orangewidget/workflow/widgetsscheme.py", line 912, in handle_new_signals
widget.handleNewSignals()
File "/cvmfs/tomo.esrf.fr/software/packages/linux/ppc64le/tomotools/2023_11_24/lib/python3.11/site-packages/orangecontrib/tomwer/widgets/control/NXTomomillOW.py", line 160, in handleNewSignals
raise TypeError(
TypeError: hdf5_scan is expected to be an instance of HDF5TomoScan
-------------------------------------------------------------------------------
```1.3https://gitlab.esrf.fr/tomotools/tomwer/-/issues/1123volume viewer: some metadata not displayed2024-02-22T16:26:19+01:00paynovolume viewer: some metadata not displayedLooks like the `estimated cor`, `pixel size` and `energy` are not displayedLooks like the `estimated cor`, `pixel size` and `energy` are not displayed1.3https://gitlab.esrf.fr/tomotools/tomwer/-/issues/1126Doc: add warning about python script and if triggerered before the processing...2024-02-22T16:21:11+01:00paynoDoc: add warning about python script and if triggerered before the processing is finished1.3https://gitlab.esrf.fr/tomotools/tomwer/-/issues/1125python script2024-02-22T15:38:39+01:00paynopython scriptGui is freezing when converting bliss scan to hdf5 from a python widget.
Mayeb multiprocessing should be allowed in orange canvas sideGui is freezing when converting bliss scan to hdf5 from a python widget.
Mayeb multiprocessing should be allowed in orange canvas sidehttps://gitlab.esrf.fr/tomotools/tomwer/-/issues/1119volume viewer: no metadata displayed2024-02-19T09:34:25+01:00paynovolume viewer: no metadata displayed1.3https://gitlab.esrf.fr/tomotools/tomwer/-/issues/1106update jira issues2024-02-14T13:53:44+01:00paynoupdate jira issuesonce the release done, update existing kanban issuesonce the release done, update existing kanban issues1.3paynopaynohttps://gitlab.esrf.fr/tomotools/tomwer/-/issues/1109iccbm051: redirect /nobackup/.../tomwer/dev to /nobackup/.../venv/dev2024-02-09T10:42:11+01:00paynoiccbm051: redirect /nobackup/.../tomwer/dev to /nobackup/.../venv/devthe tomwer contains the old installation which are outdated. Better to keep it and create a link to recent virtual environmentthe tomwer contains the old installation which are outdated. Better to keep it and create a link to recent virtual environmentpaynopaynohttps://gitlab.esrf.fr/tomotools/tomwer/-/issues/1072slurm: check 'module load tomotools' and 'source /scisoft/activate' are both ...2024-02-08T11:15:56+01:00paynoslurm: check 'module load tomotools' and 'source /scisoft/activate' are both working as expected.when try to activate a venv (instead of a module load) seems to fails...when try to activate a venv (instead of a module load) seems to fails...1.3paynopaynohttps://gitlab.esrf.fr/tomotools/tomwer/-/issues/1104hook to publish to readthedocs automatically2024-02-08T09:56:37+01:00paynohook to publish to readthedocs automatically1.3paynopaynohttps://gitlab.esrf.fr/tomotools/tomwer/-/issues/1107remove doc from silx.org2024-02-08T09:56:19+01:00paynoremove doc from silx.orgLet's focus on readthedocs for nowLet's focus on readthedocs for now1.3https://gitlab.esrf.fr/tomotools/tomwer/-/issues/936stitching: normalize projections from a ROI2024-02-08T09:52:58+01:00paynostitching: normalize projections from a ROIadd an option to normalize projection from a left or right border with a specific widthadd an option to normalize projection from a left or right border with a specific widthstitching public beta version