pyOPALTools issueshttps://gitlab.psi.ch/OPAL/pyOPALTools/-/issues2020-09-15T11:38:14+02:00https://gitlab.psi.ch/OPAL/pyOPALTools/-/issues/98Integrate UQ interface2020-09-15T11:38:14+02:00frey_mIntegrate UQ interfaceUpgrade the surrogate package with the new UQ interface.Upgrade the surrogate package with the new UQ interface.frey_mfrey_mhttps://gitlab.psi.ch/OPAL/pyOPALTools/-/issues/96Simplify file type checking2020-07-21T10:13:46+02:00frey_mSimplify file type checkingThe file type checking is quite error-prone. I suggest simplifying the interface with a function `check_file` for each parser.The file type checking is quite error-prone. I suggest simplifying the interface with a function `check_file` for each parser.frey_mfrey_mhttps://gitlab.psi.ch/OPAL/pyOPALTools/-/issues/93Update on FieldDataset2020-06-18T13:29:01+02:00frey_mUpdate on FieldDatasetThis issue should
- add the file FieldAnalysis.py
- provide the line plot functionality to FieldPlotter
- do some changes on FieldParser and FieldDatasetThis issue should
- add the file FieldAnalysis.py
- provide the line plot functionality to FieldPlotter
- do some changes on FieldParser and FieldDatasetfrey_mfrey_mhttps://gitlab.psi.ch/OPAL/pyOPALTools/-/issues/84Documentation: add last changed date2020-11-06T08:42:53+01:00snuverink_jjochem.snuverink@psi.chDocumentation: add last changed dateThe documentation is now automatically generated (#81), however there is no last changed date, so one is not sure if an update was successful.The documentation is now automatically generated (#81), however there is no last changed date, so one is not sure if an update was successful.snuverink_jjochem.snuverink@psi.chsnuverink_jjochem.snuverink@psi.chhttps://gitlab.psi.ch/OPAL/pyOPALTools/-/issues/81Auto deploy sphinx documentation2020-05-28T09:45:23+02:00snuverink_jjochem.snuverink@psi.chAuto deploy sphinx documentationSimilar to the OPAL manual, the sphinx documentation (#32) for pyOPALTools should be generated automatically on http://amas.web.psi.ch/docs/pyOPALTools/index.html
Note that the jupyter notebooks are now included (#79 !57) in the documen...Similar to the OPAL manual, the sphinx documentation (#32) for pyOPALTools should be generated automatically on http://amas.web.psi.ch/docs/pyOPALTools/index.html
Note that the jupyter notebooks are now included (#79 !57) in the documentation. The python package `nbsphinx` is needed, as well as `pandoc` and `latex`. There are some issues with the latex labels with matplotlib, therefore not all notebooks might build without problems, but this will then be fixed later.gsellgsellhttps://gitlab.psi.ch/OPAL/pyOPALTools/-/issues/79Add Jupyter Notebooks to Sphinx documentation2020-04-20T11:08:56+02:00snuverink_jjochem.snuverink@psi.chAdd Jupyter Notebooks to Sphinx documentationAs discussed in https://gitlab.psi.ch/OPAL/pyOPALTools/issues/32#note_19574, it would be good to include the jupyter notebooks in the sphinx documentation.As discussed in https://gitlab.psi.ch/OPAL/pyOPALTools/issues/32#note_19574, it would be good to include the jupyter notebooks in the sphinx documentation.snuverink_jjochem.snuverink@psi.chsnuverink_jjochem.snuverink@psi.chhttps://gitlab.psi.ch/OPAL/pyOPALTools/-/issues/76Additional arguments for the H5 version of plot_probe_histogram2020-04-20T08:09:39+02:00frey_mAdditional arguments for the H5 version of plot_probe_histogramBegin and end of steps to read by
```Python
begin = kwargs.pop('begin', 0)
end = kwargs.pop('end', self.ds.size)
```Begin and end of steps to read by
```Python
begin = kwargs.pop('begin', 0)
end = kwargs.pop('end', self.ds.size)
```frey_mfrey_mhttps://gitlab.psi.ch/OPAL/pyOPALTools/-/issues/74Selection of bunch in plot_probe_histogram2020-03-27T07:44:00+01:00frey_mSelection of bunch in plot_probe_histogramWe need to be able to select a single bunch in case of multi-bunch simulations.We need to be able to select a single bunch in case of multi-bunch simulations.frey_mfrey_mhttps://gitlab.psi.ch/OPAL/pyOPALTools/-/issues/72README: point to wiki2020-03-27T07:44:00+01:00frey_mREADME: point to wikifrey_mfrey_mhttps://gitlab.psi.ch/OPAL/pyOPALTools/-/issues/70Follow-up from "Resolve "Multiple steps in probe""2020-03-27T07:44:00+01:00frey_mFollow-up from "Resolve "Multiple steps in probe""The following discussions from !45 should be addressed:
- [x] @snuverink_j started a [discussion](https://gitlab.psi.ch/OPAL/pyOPALTools/merge_requests/45#note_14524): (+1 comment)
> sorry for being late with commenting. You could...The following discussions from !45 should be addressed:
- [x] @snuverink_j started a [discussion](https://gitlab.psi.ch/OPAL/pyOPALTools/merge_requests/45#note_14524): (+1 comment)
> sorry for being late with commenting. You could use the `hypot` function as well: https://docs.scipy.org/doc/numpy/reference/generated/numpy.hypot.html
- [x] @snuverink_j started a [discussion](https://gitlab.psi.ch/OPAL/pyOPALTools/merge_requests/45#note_14527): (+2 comments)
> Can the range become very large? In that case append might not be cpu efficient, and it is better to preallocate the array (e.g. https://stackoverflow.com/questions/2641691/building-up-an-array-in-numpy-scipy-by-iteration-in-python):
>
> ```python
> x = np.zeros(1,self.ds.size)
> for s in range(self.ds.size):
> x[i] = self.ds.getData('x', step=s)
> ```frey_mfrey_mhttps://gitlab.psi.ch/OPAL/pyOPALTools/-/issues/69Multiple steps in probe2020-04-07T10:41:36+02:00frey_mMultiple steps in probeWe need to update the `ProbePlotter` class since probe H5 files can now store multiple steps.We need to update the `ProbePlotter` class since probe H5 files can now store multiple steps.frey_mfrey_mhttps://gitlab.psi.ch/OPAL/pyOPALTools/-/issues/68H5 analysis: select last step if negative step number2020-03-27T07:44:00+01:00frey_mH5 analysis: select last step if negative step numberfrey_mfrey_mhttps://gitlab.psi.ch/OPAL/pyOPALTools/-/issues/67make YAML optional2019-10-14T15:44:24+02:00frey_mmake YAML optionalfrey_mfrey_mhttps://gitlab.psi.ch/OPAL/pyOPALTools/-/issues/62SDDS data set: Return a dataframe rather than a raw array2019-09-01T16:08:18+02:00frey_mSDDS data set: Return a dataframe rather than a raw arrayRelated to #60Related to #60frey_mfrey_mhttps://gitlab.psi.ch/OPAL/pyOPALTools/-/issues/60Access monitor in file2019-09-05T10:32:14+02:00frey_mAccess monitor in fileThe monitor stat file writes a row per monitor to a SDDS. We should add a routine that allows to return a full row of a stat file.The monitor stat file writes a row per monitor to a SDDS. We should add a routine that allows to return a full row of a stat file.frey_mfrey_mhttps://gitlab.psi.ch/OPAL/pyOPALTools/-/issues/59Matplotlib styles update2019-08-15T14:14:07+02:00frey_mMatplotlib styles update`mpl.rcParams['text.latex.unicode']` is deprecated in version > 2.1.`mpl.rcParams['text.latex.unicode']` is deprecated in version > 2.1.frey_mfrey_mhttps://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/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/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_m