pyOPALTools issueshttps://gitlab.psi.ch/OPAL/pyOPALTools/-/issues2020-04-07T10:46:34+02:00https://gitlab.psi.ch/OPAL/pyOPALTools/-/issues/58update of probe plotting utilities2020-04-07T10:46:34+02:00frey_mupdate of probe plotting utilitiesDue to the changes made in https://gitlab.psi.ch/OPAL/src/merge_requests/161 the plotting functions of the probe dataset (H5) are not valid anymore if the probe is saved with `OPTION,PSDUMPEACHTURN=TRUE`. However, we need to guarantee bo...Due to the changes made in https://gitlab.psi.ch/OPAL/src/merge_requests/161 the plotting functions of the probe dataset (H5) are not valid anymore if the probe is saved with `OPTION,PSDUMPEACHTURN=TRUE`. However, we need to guarantee both versions.https://gitlab.psi.ch/OPAL/pyOPALTools/-/issues/57H5Parser::getNSteps() counts one too many2019-08-13T10:22:48+02:00snuverink_jjochem.snuverink@psi.chH5Parser::getNSteps() counts one too manyThe H5Parser counts one too many, this is because header `Attachment` is in the keys as well:
```python
self.__nsteps = len(self.__h5f.keys())
print(list(self.__h5f.keys()))
['Attachment', 'Step#0']
```
I propose to simply do:
```pyth...The H5Parser counts one too many, this is because header `Attachment` is in the keys as well:
```python
self.__nsteps = len(self.__h5f.keys())
print(list(self.__h5f.keys()))
['Attachment', 'Step#0']
```
I propose to simply do:
```python
self.__nsteps = len(self.__h5f.keys()) - 1 #don't count header
```snuverink_jjochem.snuverink@psi.chsnuverink_jjochem.snuverink@psi.chhttps://gitlab.psi.ch/OPAL/pyOPALTools/-/issues/56Add H5 Probe Jupyter Notebook2019-08-12T17:35:52+02:00frey_mAdd H5 Probe Jupyter Notebookfrey_mfrey_mhttps://gitlab.psi.ch/OPAL/pyOPALTools/-/issues/55Plotting style gives error for matplotlib version < 2.12019-08-15T14:14:07+02:00snuverink_jjochem.snuverink@psi.chPlotting style gives error for matplotlib version < 2.1```python
from opal.visualization.styles import load_style
load_style('jupyter')
```
gives an error:
`KeyError: 'axes.formatter.min_exponent is not a valid rc parameter.See rcParams.keys() for a list of valid parameters.'````python
from opal.visualization.styles import load_style
load_style('jupyter')
```
gives an error:
`KeyError: 'axes.formatter.min_exponent is not a valid rc parameter.See rcParams.keys() for a list of valid parameters.'`snuverink_jjochem.snuverink@psi.chsnuverink_jjochem.snuverink@psi.chhttps://gitlab.psi.ch/OPAL/pyOPALTools/-/issues/54sampler files not properly loaded2019-08-12T16:20:41+02:00frey_msampler files not properly loadedIn case of multiple masters we obtain multiple sampler output files. However, they are not properly parsed causing the program to crash if it tries to access an individual from another master.In case of multiple masters we obtain multiple sampler output files. However, they are not properly parsed causing the program to crash if it tries to access an individual from another master.frey_mfrey_mhttps://gitlab.psi.ch/OPAL/pyOPALTools/-/issues/53JobHandler: Use of less used symbol2019-08-12T10:20:07+02:00frey_mJobHandler: Use of less used symbolUse `@` to replace keywords instead of `_`.Use `@` to replace keywords instead of `_`.frey_mfrey_mhttps://gitlab.psi.ch/OPAL/pyOPALTools/-/issues/52add missing import2019-08-07T14:59:44+02:00frey_madd missing importfrey_mfrey_mhttps://gitlab.psi.ch/OPAL/pyOPALTools/-/issues/51Follow-up from "Resolve "Performance improvement in H5""2019-08-07T13:32:46+02:00frey_mFollow-up from "Resolve "Performance improvement in H5""The following discussion from !27 should be addressed:
- [ ] @snuverink_j started a [discussion](https://gitlab.psi.ch/OPAL/pyOPALTools/merge_requests/27#note_11978): (+2 comments)
> Should there be a check on the validity of `ste...The following discussion from !27 should be addressed:
- [ ] @snuverink_j started a [discussion](https://gitlab.psi.ch/OPAL/pyOPALTools/merge_requests/27#note_11978): (+2 comments)
> Should there be a check on the validity of `step` like in `getStepDataset()` ?frey_mfrey_mhttps://gitlab.psi.ch/OPAL/pyOPALTools/-/issues/50Performance improvement in H52019-08-15T14:14:07+02:00frey_mPerformance improvement in H5We currently do not use h5py properly leading to a performance bottleneck for large files.We currently do not use h5py properly leading to a performance bottleneck for large files.frey_mfrey_mhttps://gitlab.psi.ch/OPAL/pyOPALTools/-/issues/49SDDS dataset dataframe access2019-08-15T14:14:07+02:00frey_mSDDS dataset dataframe access* use pandas dataframe also in master
* add function to get direct access to the pandas dataframe* use pandas dataframe also in master
* add function to get direct access to the pandas dataframefrey_mfrey_mhttps://gitlab.psi.ch/OPAL/pyOPALTools/-/issues/48Additional radial statistics2019-08-15T14:14:07+02:00frey_mAdditional radial statisticsAdd the evaluation of radial moments and the radial projected emittanceAdd the evaluation of radial moments and the radial projected emittancefrey_mfrey_mhttps://gitlab.psi.ch/OPAL/pyOPALTools/-/issues/47Select turn and bunch number from H52019-07-25T13:59:18+02:00frey_mSelect turn and bunch number from H5Currently we can only select a turn or a bunch from H5. It should be made a bit more general: First select a bunch and then a turn (if available).Currently we can only select a turn or a bunch from H5. It should be made a bit more general: First select a bunch and then a turn (if available).frey_mfrey_mhttps://gitlab.psi.ch/OPAL/pyOPALTools/-/issues/46confidence interval using bootstrap2019-08-15T14:14:07+02:00frey_mconfidence interval using bootstrapWhen we have a surrogate model we might plot a confindence interval. In order to do the confidence interval of a surrogate model the bootstrap method can be applied.When we have a surrogate model we might plot a confindence interval. In order to do the confidence interval of a surrogate model the bootstrap method can be applied.frey_mfrey_mhttps://gitlab.psi.ch/OPAL/pyOPALTools/-/issues/45Use function to extract data2019-07-22T20:24:29+02:00frey_mUse function to extract dataInstead of
```Python
data = data[val == attrval]
```
we should use
```Python
data = self._select(data, turns, turn)
```
that checks if ```data``` is not empty.Instead of
```Python
data = data[val == attrval]
```
we should use
```Python
data = self._select(data, turns, turn)
```
that checks if ```data``` is not empty.frey_mfrey_mhttps://gitlab.psi.ch/OPAL/pyOPALTools/-/issues/43Add merlin 6 template2019-07-18T15:33:50+02:00frey_mAdd merlin 6 templateAdd jobhandler template for Merlin 6Add jobhandler template for Merlin 6frey_mfrey_mhttps://gitlab.psi.ch/OPAL/pyOPALTools/-/issues/42turn number as argument to compute halo2019-07-20T15:49:58+02:00frey_mturn number as argument to compute haloThe turn number is part of the probe H5 file. It missing however the step number. Therefore, we should be able to call the function with the turn number as well.The turn number is part of the probe H5 file. It missing however the step number. Therefore, we should be able to call the function with the turn number as well.frey_mfrey_mhttps://gitlab.psi.ch/OPAL/pyOPALTools/-/issues/412d_halo_projection2019-07-20T15:49:58+02:00frey_m2d_halo_projectionfrey_mfrey_mhttps://gitlab.psi.ch/OPAL/pyOPALTools/-/issues/40Simplify interface2019-07-17T15:30:04+02:00frey_mSimplify interfacehttps://gitlab.psi.ch/OPAL/pyOPALTools/-/issues/38Built ML database from sampler objectives2019-07-03T09:18:40+02:00frey_mBuilt ML database from sampler objectivesCurrently, we can only build ML databases from sampler output with stat-files. However, the sampler can write objectives to the JSON file like the optimizer.Currently, we can only build ML databases from sampler output with stat-files. However, the sampler can write objectives to the JSON file like the optimizer.frey_mfrey_mhttps://gitlab.psi.ch/OPAL/pyOPALTools/-/issues/36Analyse Optimizer output2019-06-29T18:15:22+02:00frey_mAnalyse Optimizer outputSince https://gitlab.psi.ch/OPAL/src/merge_requests/102 OPAL writes a Pareto file. It would be nice having some tools to evaluate e.g. the *best* individual etc. A user might give function handles to be evaluated on the data set.Since https://gitlab.psi.ch/OPAL/src/merge_requests/102 OPAL writes a Pareto file. It would be nice having some tools to evaluate e.g. the *best* individual etc. A user might give function handles to be evaluated on the data set.frey_mfrey_m