bliss-tomo merge requestshttps://gitlab.esrf.fr/tomo/bliss-tomo/-/merge_requests2022-04-29T08:37:54+02:00https://gitlab.esrf.fr/tomo/bliss-tomo/-/merge_requests/79Fix typo2022-04-29T08:37:54+02:00Valentin VallsFix typo- Use `float32` instead of `numpy.float` (they prefer to specify the size, else to use python `float`)
- Fix actual detector size to return python int instead of numpy data- Use `float32` instead of `numpy.float` (they prefer to specify the size, else to use python `float`)
- Fix actual detector size to return python int instead of numpy dataValentin VallsValentin Vallshttps://gitlab.esrf.fr/tomo/bliss-tomo/-/merge_requests/135Draft: Test robustness2022-11-09T18:13:31+01:00Valentin VallsDraft: Test robustnessTry to have a CI a bit more robust.Try to have a CI a bit more robust.Valentin VallsValentin Vallshttps://gitlab.esrf.fr/tomo/bliss-tomo/-/merge_requests/196Fix tomosynch with BLISS 1.112023-10-23T14:15:08+02:00Valentin VallsFix tomosynch with BLISS 1.11Closes #89
info["state"] is an enum name (a string) in BLISS 1.11
This PR make sure the state comparison are still working.
FYI @paynoCloses #89
info["state"] is an enum name (a string) in BLISS 1.11
This PR make sure the state comparison are still working.
FYI @paynoValentin VallsValentin Vallshttps://gitlab.esrf.fr/tomo/bliss-tomo/-/merge_requests/144Improve icat testability2023-10-23T14:16:35+02:00Valentin VallsImprove icat testabilityThis PR split the cooking of the icat metadata and the way to push the result.
This improve the readability and will allow to check the result in the future without triggering icat.
- `_send_icat_metadata` is not supposed to be overwri...This PR split the cooking of the icat metadata and the way to push the result.
This improve the readability and will allow to check the result in the future without triggering icat.
- `_send_icat_metadata` is not supposed to be overwritten
- `_get_icat_metadata` can be overrided and returns an intermediate dict containing the whole icat metadata
!142 have to be merged first.Valentin VallsValentin Vallshttps://gitlab.esrf.fr/tomo/bliss-tomo/-/merge_requests/225Few improvements2024-03-21T10:41:42+01:00Valentin VallsFew improvementsThis PR clean few things on the project.
This should not break anything.
The remaining presets from `tomo.presets` was moved inside `tomo.chain_presets.*`
As result `tomo.presets` is empty and could be deprecated in the future.This PR clean few things on the project.
This should not break anything.
The remaining presets from `tomo.presets` was moved inside `tomo.chain_presets.*`
As result `tomo.presets` is empty and could be deprecated in the future.Valentin VallsValentin Vallshttps://gitlab.esrf.fr/tomo/bliss-tomo/-/merge_requests/224Draft: Rework align2024-03-26T19:07:28+01:00Valentin VallsDraft: Rework alignRework the alignment script in order to be used in Daiquiri.
- [x] Clean up the actual code
- [ ] Rework it as a "normalized" sequence
- [ ] Add some regression tests
- [ ] Check what we can do with daiquiriRework the alignment script in order to be used in Daiquiri.
- [x] Clean up the actual code
- [ ] Rework it as a "normalized" sequence
- [ ] Add some regression tests
- [ ] Check what we can do with daiquiriValentin VallsValentin Vallshttps://gitlab.esrf.fr/tomo/bliss-tomo/-/merge_requests/212Enable machinfo counters at the beginning of tomo sequence2023-11-24T18:03:18+01:00Clemence MuzelleEnable machinfo counters at the beginning of tomo sequenceAdd security to avoid saving tomo data without current info (needed for reconstruction)Add security to avoid saving tomo data without current info (needed for reconstruction)Clemence MuzelleClemence Muzellehttps://gitlab.esrf.fr/tomo/bliss-tomo/-/merge_requests/211Resolve "Move reference motors in serial"2023-11-27T18:53:36+01:00Clemence MuzelleResolve "Move reference motors in serial"Closes #100Closes #100Clemence MuzelleClemence Muzellehttps://gitlab.esrf.fr/tomo/bliss-tomo/-/merge_requests/209Improve half menu2023-11-03T10:15:00+01:00Valentin VallsImprove half menuThis reworks a bit the menu to hanle half tomo menu is a single menu.
The configuration will only be visible if the half acquisition is enabled (to make it obvious that it is disabled)
![image](/uploads/0cd1cf4997368a5110662d74debbf98b...This reworks a bit the menu to hanle half tomo menu is a single menu.
The configuration will only be visible if the half acquisition is enabled (to make it obvious that it is disabled)
![image](/uploads/0cd1cf4997368a5110662d74debbf98b/image.png)Valentin VallsValentin Vallshttps://gitlab.esrf.fr/tomo/bliss-tomo/-/merge_requests/204Rework half tomo setup2023-10-23T09:00:04+02:00Valentin VallsRework half tomo setupThis PR rework a bit the half tomo setup.
Enum for `ShiftType` was addedThis PR rework a bit the half tomo setup.
Enum for `ShiftType` was addedValentin VallsValentin Vallshttps://gitlab.esrf.fr/tomo/bliss-tomo/-/merge_requests/203Improve zseries for daiquiri2023-10-18T11:16:56+02:00Valentin VallsImprove zseries for daiquiriThe `zseries` was creating an unused `collection/dataset` at start.
Daiquiri was also creating stuff at the same place.
As result instead of having a layer named `mydataset_000`, the layer was called `mydataset_0002_000`.
This PR is a...The `zseries` was creating an unused `collection/dataset` at start.
Daiquiri was also creating stuff at the same place.
As result instead of having a layer named `mydataset_000`, the layer was called `mydataset_0002_000`.
This PR is a workaround to make it work for daiquiri, without changing much things.
Plus blackValentin VallsValentin Vallshttps://gitlab.esrf.fr/tomo/bliss-tomo/-/merge_requests/201tiling: Tune the the presets to make sure the axis metadata are right2023-08-30T16:24:06+02:00Valentin Vallstiling: Tune the the presets to make sure the axis metadata are rightCloses https://gitlab.esrf.fr/ui/tomovis/-/issues/11Closes https://gitlab.esrf.fr/ui/tomovis/-/issues/11Valentin VallsValentin Vallshttps://gitlab.esrf.fr/tomo/bliss-tomo/-/merge_requests/199Replace enum prop by bliss2023-10-23T14:20:04+02:00Valentin VallsReplace enum prop by blissNow we know BLISS 1.11 is used, we can replace the local code which was moved into BLISS.Now we know BLISS 1.11 is used, we can replace the local code which was moved into BLISS.Valentin VallsValentin Vallshttps://gitlab.esrf.fr/tomo/bliss-tomo/-/merge_requests/188Rework the tomoconfig default chains2023-07-21T08:59:01+02:00Valentin VallsRework the tomoconfig default chainsThis PR is intent to solve timeout on slow scans with some Lima detectors.
This fix have to be applied by configuration in each beamlines and detectors.
- `tomoconfig` can be setup with 2 new chain settings:
- `default_slow_single_...This PR is intent to solve timeout on slow scans with some Lima detectors.
This fix have to be applied by configuration in each beamlines and detectors.
- `tomoconfig` can be setup with 2 new chain settings:
- `default_slow_single_chain` and `default_slow_accumulation_chain`
- This chains are only used for slow runners: `return_ref`, `mesh` and `tiling` for now
- If a detector is not defined in this chains, the default one are anyway used
- Runners was reworked to property setup and cleanup `DEFAULT_CHAIN`
# Example of setup
```
- name: HRTOMO_ext_chain
plugin: default
chain_config:
- device: $pcolinux
acquisition_settings:
acq_trigger_mode: EXTERNAL_TRIGGER_MULTI
master: $musst
- name: HRTOMO_ext_chain_acc
plugin: default
chain_config:
- device: $pcolinux
acquisition_settings:
acq_trigger_mode: EXTERNAL_TRIGGER_MULTI
acq_mode: ACCUMULATION
master: $musst_acc
- name: HRTOMO_int_chain
plugin: default
chain_config:
- device: $pcolinux
acquisition_settings:
acq_trigger_mode: INTERNAL_TRIGGER
acq_mode: SINGLE
- name: HRTOMO_int_chain_acc
plugin: default
chain_config:
- device: $pcolinux
acquisition_settings:
acq_trigger_mode: INTERNAL_TRIGGER
acq_mode: ACCUMULATION
- name: hrtomo_config
plugin: bliss
class: TomoConfig
package: tomo.tomoconfig
default_single_chain: $HRTOMO_ext_chain
default_accumulation_chain: $HRTOMO_ext_chain_acc
default_slow_single_chain: $HRTOMO_int_chain
default_slow_accumulation_chain: $HRTOMO_int_chain_acc
```Valentin VallsValentin Vallshttps://gitlab.esrf.fr/tomo/bliss-tomo/-/merge_requests/174Expose and share energy from tomoconfig2023-04-24T16:08:41+02:00Valentin VallsExpose and share energy from tomoconfigThis PR expose and share the energy from the tomo config object
```
DEMO_SESSION [5]: ACTIVE_TOMOCONFIG.energy = 100
DEMO_SESSION [6]: ACTIVE_TOMOCONFIG.pars.energy
Out [6]: 100.0
DEMO_SESSION [7]: ENERGY(99)
DEMO_SESSION [8]:...This PR expose and share the energy from the tomo config object
```
DEMO_SESSION [5]: ACTIVE_TOMOCONFIG.energy = 100
DEMO_SESSION [6]: ACTIVE_TOMOCONFIG.pars.energy
Out [6]: 100.0
DEMO_SESSION [7]: ENERGY(99)
DEMO_SESSION [8]: ACTIVE_TOMOCONFIG.pars.energy
Out [8]: 99.0
DEMO_SESSION [9]: ACTIVE_TOMOCONFIG.energy
Out [9]: 99.0
DEMO_SESSION [10]: ENERGY()
Out [10]: 99.0
DEMO_SESSION [11]: ACTIVE_TOMOCONFIG.energy = 11
DEMO_SESSION [12]: ENERGY()
Out [12]: 11
```Valentin VallsValentin Vallshttps://gitlab.esrf.fr/tomo/bliss-tomo/-/merge_requests/164tomo_detector: Make sure the detector axis use a proper unit2023-03-27T18:01:07+02:00Valentin Vallstomo_detector: Make sure the detector axis use a proper unitBetter error handling.
Noticed at BM05.Better error handling.
Noticed at BM05.Valentin VallsValentin Vallshttps://gitlab.esrf.fr/tomo/bliss-tomo/-/merge_requests/160Fix async inconsistency with optics2023-03-03T16:14:35+01:00Valentin VallsFix async inconsistency with opticsCloses https://gitlab.esrf.fr/ui/daiquiri-tomo/-/issues/252
This PR just mitigate an async issue between BLISS and the tomo simulator.
When an optic magnification is `None` we can wait some time for a better value.Closes https://gitlab.esrf.fr/ui/daiquiri-tomo/-/issues/252
This PR just mitigate an async issue between BLISS and the tomo simulator.
When an optic magnification is `None` we can wait some time for a better value.Valentin VallsValentin Vallshttps://gitlab.esrf.fr/tomo/bliss-tomo/-/merge_requests/146doc: Added graphical modelization of the sample stage2022-11-29T10:25:51+01:00Valentin Vallsdoc: Added graphical modelization of the sample stageValentin VallsValentin Vallshttps://gitlab.esrf.fr/tomo/bliss-tomo/-/merge_requests/141Use BEACON_HOST var for the redis server2022-11-29T10:29:55+01:00Valentin VallsUse BEACON_HOST var for the redis server(cherry picked from commit a72a879c7bc46003d8bf86e7baecb34ac8daebd7)
The simulator was not able to be installed into another machine than the one with Redis.
That's not the case at the BCU lab.
This PR use an extra `BEACON_HOST` var t...(cherry picked from commit a72a879c7bc46003d8bf86e7baecb34ac8daebd7)
The simulator was not able to be installed into another machine than the one with Redis.
That's not the case at the BCU lab.
This PR use an extra `BEACON_HOST` var to allow to use another machine name.Valentin VallsValentin Vallshttps://gitlab.esrf.fr/tomo/bliss-tomo/-/merge_requests/140tiling: Rework the sequence without a simultaneous set of presets2022-11-22T14:16:37+01:00Valentin Vallstiling: Rework the sequence without a simultaneous set of presetsCloses https://gitlab.esrf.fr/ui/daiquiri-tomo/-/issues/192
In BLISS, the scan presets a executed simultaneously with a gevent spawn.
I was not expecting this behavior for the tiling scan. So in some cases, the execution of the list of...Closes https://gitlab.esrf.fr/ui/daiquiri-tomo/-/issues/192
In BLISS, the scan presets a executed simultaneously with a gevent spawn.
I was not expecting this behavior for the tiling scan. So in some cases, the execution of the list of preset
results in a fail, or an unexpected position of motors.
So instead, a new preset `OrderedPresetsPreset` was create.
- It behave like a preset (it can be used normally by the BLISS scan)
- And can contain sub presets
Here we order the execution of the sub presets in a synchronous order.
The tiling scan was reworked to use this new preset.Valentin VallsValentin Valls