tomwer issueshttps://gitlab.esrf.fr/tomotools/tomwer/-/issues2024-03-27T15:58:12+01:00https://gitlab.esrf.fr/tomotools/tomwer/-/issues/1154Add ID16b workflows to tomwer canvas2024-03-27T15:58:12+01:00paynoAdd ID16b workflows to tomwer canvasAdd ID16B insitu workflow to the examplesAdd ID16B insitu workflow to the examples1.4https://gitlab.esrf.fr/tomotools/tomwer/-/issues/1153Volume viewer: read metadata from the volume2024-03-21T09:08:06+01:00paynoVolume viewer: read metadata from the volumeFor on the right side of the volume viewer we are displaying some information like distance, padding type...
This information is read from the scan only but also contained by the volume now.
So we should have the same information if the ...For on the right side of the volume viewer we are displaying some information like distance, padding type...
This information is read from the scan only but also contained by the volume now.
So we should have the same information if the input of the widget is a volume.
It can either always read from the volume. Or read from the volume as a fallback in the case of a scan.
## metadata when the link is done over a `scan`
![image](/uploads/3ea6b95ee28bd0a89bff4247b0116997/image.png)
## metadata when the link is done over a `volume`
![image](/uploads/007dc3e7f268d7bd191b9864927f151e/image.png)https://gitlab.esrf.fr/tomotools/tomwer/-/issues/1152integrate ewoksorange >= 0.72024-03-18T13:34:54+01:00paynointegrate ewoksorange >= 0.7remove usage of `pkgutil` as wellremove usage of `pkgutil` as well1.4https://gitlab.esrf.fr/tomotools/tomwer/-/issues/1151Error on default center of rotation widget after loading .ows file2024-03-18T09:45:20+01:00Pierre-Olivier AutranError on default center of rotation widget after loading .ows fileHi,
Seems like the widget is not loading properly, removing and adding a fresh one fixes the issue.
Path of the .ows: `/data/visitor/ihmi1549/id11/20240305/SCRIPTS/POA/tomo.ows`
Version used: module load tomotools,
tomwer version is ...Hi,
Seems like the widget is not loading properly, removing and adding a fresh one fixes the issue.
Path of the .ows: `/data/visitor/ihmi1549/id11/20240305/SCRIPTS/POA/tomo.ows`
Version used: module load tomotools,
tomwer version is 1.2.8
tomoscan version is 1.3.5
nxtomomill version is 0.13.5
nabu version is 2023.2.1
Error log:
```
2024-03-18 09:32:08,972:CRITICAL:orangecanvas.scheme.widgetmanager: Traceback (most recent call last): File "/cvmfs/tomo.esrf.fr/software/packages/linux/x86_64/tomotools/2023_11_24/lib/python3.11/site-packages/orangecanvas/scheme/widgetmanager.py", line 243, in \__add_widget_for_node w = self.create_widget_for_node(node) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/cvmfs/tomo.esrf.fr/software/packages/linux/x86_64/tomotools/2023_11_24/lib/python3.11/site-packages/orangewidget/workflow/widgetsscheme.py", line 300, in create_widget_for_node widget = self.create_widget_instance(node) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/cvmfs/tomo.esrf.fr/software/packages/linux/x86_64/tomotools/2023_11_24/lib/python3.11/site-packages/orangewidget/workflow/widgetsscheme.py", line 413, in create_widget_instance widget.**init**() File "/cvmfs/tomo.esrf.fr/software/packages/linux/x86_64/tomotools/2023_11_24/lib/python3.11/site-packages/orangecontrib/tomwer/widgets/reconstruction/AxisOW.py", line 161, in **init** self.\_widget = AxisWindow(parent=self, axis_params=self.\_axis_params) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/cvmfs/tomo.esrf.fr/software/packages/linux/x86_64/tomotools/2023_11_24/lib/python3.11/site-packages/tomwer/gui/reconstruction/axis/axis.py", line 122, in **init** self.\_axisWidget = \_AxisWidget( ^^^^^^^^^^^^ File "/cvmfs/tomo.esrf.fr/software/packages/linux/x86_64/tomotools/2023_11_24/lib/python3.11/site-packages/tomwer/gui/reconstruction/axis/axis.py", line 258, in **init** self.\_radioAxis = RadioAxisWindow( ^^^^^^^^^^^^^^^^ File "/cvmfs/tomo.esrf.fr/software/packages/linux/x86_64/tomotools/2023_11_24/lib/python3.11/site-packages/tomwer/gui/reconstruction/axis/radioaxis.py", line 119, in **init** self.\_controlWidget = \_AxisManual( ^^^^^^^^^^^^ File "/cvmfs/tomo.esrf.fr/software/packages/linux/x86_64/tomotools/2023_11_24/lib/python3.11/site-packages/tomwer/gui/reconstruction/axis/radioaxis.py", line 654, in **init** self.\_mainWidget = AxisTabWidget( ^^^^^^^^^^^^^^ File "/cvmfs/tomo.esrf.fr/software/packages/linux/x86_64/tomotools/2023_11_24/lib/python3.11/site-packages/tomwer/gui/reconstruction/axis/radioaxis.py", line 1464, in **init** self.\_calculationWidget = \_CalculationWidget( ^^^^^^^^^^^^^^^^^^^ File "/cvmfs/tomo.esrf.fr/software/packages/linux/x86_64/tomotools/2023_11_24/lib/python3.11/site-packages/tomwer/gui/reconstruction/axis/radioaxis.py", line 1727, in **init** self.setAxisParams(axis_params) File "/cvmfs/tomo.esrf.fr/software/packages/linux/x86_64/tomotools/2023_11_24/lib/python3.11/site-packages/tomwer/gui/reconstruction/axis/radioaxis.py", line 1973, in setAxisParams self.\_sideChanged() File "/cvmfs/tomo.esrf.fr/software/packages/linux/x86_64/tomotools/2023_11_24/lib/python3.11/site-packages/tomwer/gui/reconstruction/axis/radioaxis.py", line 1932, in \_sideChanged self.\_axis_params.side = side ^^^^^^^^^^^^^^^^^^^^^^ File "/cvmfs/tomo.esrf.fr/software/packages/linux/x86_64/tomotools/2023_11_24/lib/python3.11/site-packages/tomwer/core/process/reconstruction/axis/params.py", line 434, in side raise ValueError(f"side '{side}' is not managed") ValueError: side '' is not managed ---------------------------- ValueError Exception ----------------------------- Traceback (most recent call last): File "/cvmfs/tomo.esrf.fr/software/packages/linux/x86_64/tomotools/2023_11_24/lib/python3.11/site-packages/orangecanvas/scheme/widgetmanager.py", line 404, in \__process_init_queue self.ensure_created(node) File "/cvmfs/tomo.esrf.fr/software/packages/linux/x86_64/tomotools/2023_11_24/lib/python3.11/site-packages/orangecanvas/scheme/widgetmanager.py", line 350, in ensure_created self.\__add_widget_for_node(node) File "/cvmfs/tomo.esrf.fr/software/packages/linux/x86_64/tomotools/2023_11_24/lib/python3.11/site-packages/orangecanvas/scheme/widgetmanager.py", line 243, in \__add_widget_for_node w = self.create_widget_for_node(node) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/cvmfs/tomo.esrf.fr/software/packages/linux/x86_64/tomotools/2023_11_24/lib/python3.11/site-packages/orangewidget/workflow/widgetsscheme.py", line 300, in create_widget_for_node widget = self.create_widget_instance(node) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/cvmfs/tomo.esrf.fr/software/packages/linux/x86_64/tomotools/2023_11_24/lib/python3.11/site-packages/orangewidget/workflow/widgetsscheme.py", line 413, in create_widget_instance widget.**init**() File "/cvmfs/tomo.esrf.fr/software/packages/linux/x86_64/tomotools/2023_11_24/lib/python3.11/site-packages/orangecontrib/tomwer/widgets/reconstruction/AxisOW.py", line 161, in **init** self.\_widget = AxisWindow(parent=self, axis_params=self.\_axis_params) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/cvmfs/tomo.esrf.fr/software/packages/linux/x86_64/tomotools/2023_11_24/lib/python3.11/site-packages/tomwer/gui/reconstruction/axis/axis.py", line 122, in **init** self.\_axisWidget = \_AxisWidget( ^^^^^^^^^^^^ File "/cvmfs/tomo.esrf.fr/software/packages/linux/x86_64/tomotools/2023_11_24/lib/python3.11/site-packages/tomwer/gui/reconstruction/axis/axis.py", line 258, in **init** self.\_radioAxis = RadioAxisWindow( ^^^^^^^^^^^^^^^^ File "/cvmfs/tomo.esrf.fr/software/packages/linux/x86_64/tomotools/2023_11_24/lib/python3.11/site-packages/tomwer/gui/reconstruction/axis/radioaxis.py", line 119, in **init** self.\_controlWidget = \_AxisManual( ^^^^^^^^^^^^ File "/cvmfs/tomo.esrf.fr/software/packages/linux/x86_64/tomotools/2023_11_24/lib/python3.11/site-packages/tomwer/gui/reconstruction/axis/radioaxis.py", line 654, in **init** self.\_mainWidget = AxisTabWidget( ^^^^^^^^^^^^^^ File "/cvmfs/tomo.esrf.fr/software/packages/linux/x86_64/tomotools/2023_11_24/lib/python3.11/site-packages/tomwer/gui/reconstruction/axis/radioaxis.py", line 1464, in **init** self.\_calculationWidget = \_CalculationWidget( ^^^^^^^^^^^^^^^^^^^ File "/cvmfs/tomo.esrf.fr/software/packages/linux/x86_64/tomotools/2023_11_24/lib/python3.11/site-packages/tomwer/gui/reconstruction/axis/radioaxis.py", line 1727, in **init** self.setAxisParams(axis_params) File "/cvmfs/tomo.esrf.fr/software/packages/linux/x86_64/tomotools/2023_11_24/lib/python3.11/site-packages/tomwer/gui/reconstruction/axis/radioaxis.py", line 1973, in setAxisParams self.\_sideChanged() File "/cvmfs/tomo.esrf.fr/software/packages/linux/x86_64/tomotools/2023_11_24/lib/python3.11/site-packages/tomwer/gui/reconstruction/axis/radioaxis.py", line 1932, in \_sideChanged self.\_axis_params.side = side ^^^^^^^^^^^^^^^^^^^^^^ File "/cvmfs/tomo.esrf.fr/software/packages/linux/x86_64/tomotools/2023_11_24/lib/python3.11/site-packages/tomwer/core/process/reconstruction/axis/params.py", line 434, in side raise ValueError(f"side '{side}' is not managed") ValueError: side '' is not managed
```https://gitlab.esrf.fr/tomotools/tomwer/-/issues/1150examples: add a remote cast example in examples / remote processing2024-03-13T14:10:14+01:00paynoexamples: add a remote cast example in examples / remote processing1.4https://gitlab.esrf.fr/tomotools/tomwer/-/issues/1148get images along different axis2024-03-13T14:28:43+01:00paynoget images along different axisIt would be nice to have a widget taking a volume as input and and select some slices.
Then this will create .tiff or something else of the volume.
Behavior to be clearly definedIt would be nice to have a widget taking a volume as input and and select some slices.
Then this will create .tiff or something else of the volume.
Behavior to be clearly defined1.4https://gitlab.esrf.fr/tomotools/tomwer/-/issues/1147nabu slice: reconstruction over different axis2024-03-13T14:28:39+01:00paynonabu slice: reconstruction over different axisFor now we can reconstruct over different axis. But only one axis can be selected. It would be nice to let the user selected the axis by something like:
```bash
XY:middle, YZ:middle...
```For now we can reconstruct over different axis. But only one axis can be selected. It would be nice to let the user selected the axis by something like:
```bash
XY:middle, YZ:middle...
```1.4https://gitlab.esrf.fr/tomotools/tomwer/-/issues/1144failed to launch on iccbm1912024-03-12T09:13:55+01:00paynofailed to launch on iccbm191Failed on launchFailed on launchhttps://gitlab.esrf.fr/tomotools/tomwer/-/issues/1143improve tilt2024-03-11T10:32:31+01:00paynoimprove tiltIt would be nice to allow the user to provide the center of the tilt not from the center of the radio but from the center of rotation.It would be nice to allow the user to provide the center of the tilt not from the center of the radio but from the center of rotation.https://gitlab.esrf.fr/tomotools/tomwer/-/issues/1141Axis widget fails if `side=near`, `Updata automaticall...` ticked and `estima...2024-03-07T14:22:00+01:00Jerome LesaintAxis widget fails if `side=near`, `Updata automaticall...` ticked and `estimated_value` set to 0.0.It fails if `estimated_value=0.0` or `1.` (see log below). It works fine if `estimated_value=800.` (the value in the NX) or `799.0`.
```
2024-03-07 14:17:15,437 [PROCESS_FAILED] fail to compute axis position for scan /home/esrf/lesaint/...It fails if `estimated_value=0.0` or `1.` (see log below). It works fine if `estimated_value=800.` (the value in the NX) or `799.0`.
```
2024-03-07 14:17:15,437 [PROCESS_FAILED] fail to compute axis position for scan /home/esrf/lesaint/tomo_training_march_2024/Intro reason is Fail to compute axis position for /home/esrf/lesaint/tomo_training_march_2024/Intro reason is operands could not be broadcast together with shapes (2160,0) (2160,1025) [tomwer.core.process.reconstruction.axis.axis](axis.py:962)
```https://gitlab.esrf.fr/tomotools/tomwer/-/issues/1139multi-cor: add an option to run all cor algorithm and run the reconstruction2024-03-07T14:01:05+01:00paynomulti-cor: add an option to run all cor algorithm and run the reconstructionIt could be interesting to have a n option that run all the different cor algorithm and use the found cor in the `multi-cor` widget.It could be interesting to have a n option that run all the different cor algorithm and use the found cor in the `multi-cor` widget.https://gitlab.esrf.fr/tomotools/tomwer/-/issues/1138slurm widget: provide nice*2024-03-04T15:13:17+01:00paynoslurm widget: provide nice*nice* should never be used because doesn't existsnice* should never be used because doesn't existshttps://gitlab.esrf.fr/tomotools/tomwer/-/issues/1137remove nb tasks from the GUI2024-03-04T15:04:40+01:00paynoremove nb tasks from the GUIlooks like this is still displayed to the user but ignored when processedlooks like this is still displayed to the user but ignored when processedhttps://gitlab.esrf.fr/tomotools/tomwer/-/issues/1136Make COR conversion from rel to abs consistent with Nabu2024-03-07T15:27:52+01:00Jerome LesaintMake COR conversion from rel to abs consistent with NabuThe output of the COR estimators is a relative COR position, i.e. a position relative to the center of the detector. Then, this relative position is converted to an absolute one, i.e. with respect to the left side of the detector. The co...The output of the COR estimators is a relative COR position, i.e. a position relative to the center of the detector. Then, this relative position is converted to an absolute one, i.e. with respect to the left side of the detector. The conversion is done with:
`abs = rel + (detector_width - 1)// 2`.
This corresponds to taking the origin of the detector at the center of the pixel of the first column.
In `nabu`, the `CompositeCORFinder` does the same conversion, contrary to `CORFinder` and `SinoCORFinder` classes (see Nabu [#486](https://gitlab.esrf.fr/tomotools/nabu/-/issues/486#:~:text=Issues-,%23486,-Make%20COR%20conversion)).https://gitlab.esrf.fr/tomotools/tomwer/-/issues/1135tomwer stitching2024-03-04T15:00:05+01:00paynotomwer stitchingoutput directory does not seem to be take into accountsoutput directory does not seem to be take into accountshttps://gitlab.esrf.fr/tomotools/tomwer/-/issues/1134Doc: installation: warning about only linux supported2024-03-01T08:20:35+01:00paynoDoc: installation: warning about only linux supportedhttps://gitlab.esrf.fr/tomotools/tomwer/-/issues/1133waiter overlay: not visible enought when has something on the background2024-02-26T16:26:27+01:00paynowaiter overlay: not visible enought when has something on the backgroundhttps://gitlab.esrf.fr/tomotools/tomwer/-/issues/1132ImageKeyEditor: ewoksify2024-02-23T15:06:36+01:00paynoImageKeyEditor: ewoksifythere is no reason why this process couldn't be ewoksifythere is no reason why this process couldn't be ewoksify1.4https://gitlab.esrf.fr/tomotools/tomwer/-/issues/1131volum reprocess: reprocessing fails because no nabu existing2024-03-07T10:44:39+01:00paynovolum reprocess: reprocessing fails because no nabu existingAs the reprocessing from the slurm supervisor is simply creating the object he doesn't keep trace of the latest nabu reconstruction parameters used.
So he cannot reprocessAs the reprocessing from the slurm supervisor is simply creating the object he doesn't keep trace of the latest nabu reconstruction parameters used.
So he cannot reprocess1.4https://gitlab.esrf.fr/tomotools/tomwer/-/issues/1130fix coherence `clear_cache` vs `clear_caches`2024-02-23T08:35:35+01:00paynofix coherence `clear_cache` vs `clear_caches`Looks like for scan this is named \`clear_caches\` as for the TomwerObject when for Volume this is named \`clear_cache\`. There should be only oneLooks like for scan this is named \`clear_caches\` as for the TomwerObject when for Volume this is named \`clear_cache\`. There should be only one1.4