empyre issueshttps://iffgit.fz-juelich.de/empyre/empyre/-/issues2021-09-03T15:01:37Zhttps://iffgit.fz-juelich.de/empyre/empyre/-/issues/58Loading vtk data as 2D data set2021-09-03T15:01:37ZTeresa WeßelsLoading vtk data as 2D data set### Summary
I am trying to load an unstructured vtk data set. I would like to have a 2D array as an output. However, field setter complains because it gets a 3D scale for the 2D output.
### Steps to reproduce
Use emp.ip.load_field() a...### Summary
I am trying to load an unstructured vtk data set. I would like to have a 2D array as an output. However, field setter complains because it gets a 3D scale for the 2D output.
### Steps to reproduce
Use emp.ip.load_field() and set the scale in such a way that an output grid of (1, z, x, 3) is generated.
### What is the current *bug* behavior?
```AssertionError: Each of the 2 dimensions needs a scale, but (20, 20, 20) was given!```
### Relevant logs and/or screenshots
![loading_2d_from_vtk](/uploads/b38b752a5c78f8bf78dead7527b2f4d1/loading_2d_from_vtk.png)
~bug ~io ~fieldshttps://iffgit.fz-juelich.de/empyre/empyre/-/issues/57Loading Pyramid dataset with Empyre2021-08-04T09:32:18ZTeresa WeßelsLoading Pyramid dataset with Empyre## Summary
When loading Pyramid datasets with Empyre, the component axis needs to be shifted. This can be done by setting the parameter comp_pos which works for hdf5 files. However, it is not working for npy files.
### Steps to reprodu...## Summary
When loading Pyramid datasets with Empyre, the component axis needs to be shifted. This can be done by setting the parameter comp_pos which works for hdf5 files. However, it is not working for npy files.
### Steps to reproduce
Load any dataset save in numpy with "emp.io.load_field('dataset.npy',comp_pos=3)" while setting the parameter comp_pos
### What is the current *bug* behavior?
Numpy.load() gets the parameter comp_pos which it does not know and throws an error.
### Relevant logs and/or screenshots
```
TypeError Traceback (most recent call last)
<ipython-input-10-5fcc66790585> in <module>
----> 1 field_sum = emp.io.load_field('Hdem-45deg_10100100_step3.npy',comp_pos=3)
~/.conda/envs/empyre_1/lib/python3.8/site-packages/empyre/io/io_field.py in load_field(filename, scale, vector, **kwargs)
67 for plugin in plugin_list: # Iterate over all plugins:
68 if extension in plugin.file_extensions: # Check if extension is recognised:
---> 69 return plugin.reader(filename, scale=scale, vector=vector, **kwargs)
70 # If nothing was found, try HyperSpy
71 _log.debug('Using HyperSpy')
~/.conda/envs/empyre_1/lib/python3.8/site-packages/empyre/io/field_plugins/numpy.py in reader(filename, scale, vector, **kwargs)
24 if scale is None:
25 scale = 1.0
---> 26 return Field(np.load(filename, **kwargs), scale, vector)
27
28
TypeError: load() got an unexpected keyword argument 'comp_pos'
```
### Possible fixes
Exclude comp_pos from kwargs for numpy.
Workaround: only use hdf5 format to save files
~bug ~iohttps://iffgit.fz-juelich.de/empyre/empyre/-/issues/563d plot only partly shown using png backend2021-01-12T09:33:48ZTeresa Weßels3d plot only partly shown using png backend### Summary
When plotting a 3d image using the png backend, only a part of the whole plot is displayed.
### Steps to reproduce
```python
import empyre as emp
from mayavi import mlab
import numpy as np
mlab.init_notebook('png')
test = ...### Summary
When plotting a 3d image using the png backend, only a part of the whole plot is displayed.
### Steps to reproduce
```python
import empyre as emp
from mayavi import mlab
import numpy as np
mlab.init_notebook('png')
test = emp.fields.Field(np.ones((20,20,20)))
emp.vis.mask3d(test)
```
### What is the current *bug* behavior?
Only the lower left quarter of the image is shown, the rest stays black.
### What is the expected *correct* behavior?
The full image should be visible.
### Relevant logs and/or screenshots
![issue_png_back](/uploads/02d9e7e1756b9933cb10fe5eba2ef63f/issue_png_back.png)
~bug ~vishttps://iffgit.fz-juelich.de/empyre/empyre/-/issues/55Speed up CI pipeline2020-10-21T12:55:01ZAlexander Clausena.clausen@fz-juelich.deSpeed up CI pipelineCould create a docker image in a first stage with the conda environment, which is only rebuilt if the dependencies change.
Building the docker image may need Docker-in-Docker support, so probably a good idea to do a first simple test if...Could create a docker image in a first stage with the conda environment, which is only rebuilt if the dependencies change.
Building the docker image may need Docker-in-Docker support, so probably a good idea to do a first simple test if we can even build a docker image in CI.
See also: https://iffgit.fz-juelich.de/docker-images/gr-build-images/-/blob/master/.gitlab-ci.ymlAlexander Clausena.clausen@fz-juelich.deAlexander Clausena.clausen@fz-juelich.dehttps://iffgit.fz-juelich.de/empyre/empyre/-/issues/54Too small `coords` for some reason2020-10-16T11:11:40ZAlexander Clausena.clausen@fz-juelich.deToo small `coords` for some reasonEnvironment: Windows
Looks something like this:
![image](/uploads/328acd4762f9c989b110337bde39e4f1/image.png)Environment: Windows
Looks something like this:
![image](/uploads/328acd4762f9c989b110337bde39e4f1/image.png)https://iffgit.fz-juelich.de/empyre/empyre/-/issues/51New functions for electric field and charges2020-09-11T18:22:30ZFengshan ZhengNew functions for electric field and charges### Problem to solve
<!-- What problem do we solve? --> Plot electric field from phase, calculate charge density from phase
### Intended users
<!-- Who will use this feature? . It's okay to write "Unknown" and fill this field in later...### Problem to solve
<!-- What problem do we solve? --> Plot electric field from phase, calculate charge density from phase
### Intended users
<!-- Who will use this feature? . It's okay to write "Unknown" and fill this field in later. --> People who are working on electric field mapping
### Further details
<!-- Include use cases, benefits, and/or goals -->
### Proposal
<!-- How are we going to solve the problem? -->
### Documentation
<!-- Add all known Documentation Requirements here. --> Electric field corresponds to EXACTLY the gradient of the phase, and charge density corresponds to laplacian of the phase.
~featurehttps://iffgit.fz-juelich.de/empyre/empyre/-/issues/46Mistake in Docstring in Pyramid2020-06-26T08:41:01ZTeresa WeßelsMistake in Docstring in PyramidThis issues is for a function which is currently only available in Pyramid, not in Empyre.
In the docstring of the diagnostics.py, there is a mistake when looking at the averaging kernel with calculate_fwhm(). There it is stated that "T...This issues is for a function which is currently only available in Pyramid, not in Empyre.
In the docstring of the diagnostics.py, there is a mistake when looking at the averaging kernel with calculate_fwhm(). There it is stated that "The inverse [of the given FWHM] corresponds to the number of pixels over which is approximately averaged.". However, the FWHM needs to be divided by a to get from nm to pixel.Jan CaronJan Caronhttps://iffgit.fz-juelich.de/empyre/empyre/-/issues/44Complete documentation!2020-03-20T10:49:38ZJan CaronComplete documentation!Add ~docs to:
* [ ] ~vis subpackage
* [ ] ~fields subpackage
* [ ] ~io subpackageAdd ~docs to:
* [ ] ~vis subpackage
* [ ] ~fields subpackage
* [ ] ~io subpackageJan CaronJan Caronhttps://iffgit.fz-juelich.de/empyre/empyre/-/issues/43Add tests!2020-09-23T11:46:46ZJan CaronAdd tests!Add ~tests to:
* [ ] ~vis subpackage
* [ ] ~fields subpackage
* [ ] ~io subpackageAdd ~tests to:
* [ ] ~vis subpackage
* [ ] ~fields subpackage
* [ ] ~io subpackageJan CaronJan Caronhttps://iffgit.fz-juelich.de/empyre/empyre/-/issues/41Use tox for testing2020-03-17T10:40:02ZJan CaronUse tox for testingSuggestion by @clausen : use [tox-conda](https://github.com/tox-dev/tox-conda) !Suggestion by @clausen : use [tox-conda](https://github.com/tox-dev/tox-conda) !https://iffgit.fz-juelich.de/empyre/empyre/-/issues/38pip install .[io] not working due to hyperspy depending on traits (no wheels ...2020-03-17T23:27:39ZJan Caronpip install .[io] not working due to hyperspy depending on traits (no wheels on PyPI)Currently, `pip install .[io]` is not working, due to hyperspy depending on traits, which does not have precompiled wheels on PyPI. The `test_install` job does not work without a wheel, or without getting Microsoft Visual C++ 14 for its ...Currently, `pip install .[io]` is not working, due to hyperspy depending on traits, which does not have precompiled wheels on PyPI. The `test_install` job does not work without a wheel, or without getting Microsoft Visual C++ 14 for its gcc (which is a large download and would complicate `gitlab-ci.yml`).
The [issue](https://github.com/hyperspy/hyperspy/issues/2315) is known to the HyperSpy guys and traits also has a [request to build wheels for PyPI](https://github.com/enthought/traits/issues/357), but it does not look like this will be fixed in the near future...
For now, hyperspy is removed from `[all]`, if people want to use hyperspy for io, they need to install it with conda for now (or
get a wheel for Windows from [gohlke](https://www.lfd.uci.edu/~gohlke/pythonlibs/).
~bug
UPDATE: `mayavi` has the same problem and `tvtk` is also not easily installable via pip. As it stands, the `[all]` is quite empty...https://iffgit.fz-juelich.de/empyre/empyre/-/issues/37Publish in JOSS2020-02-19T14:59:43ZJan CaronPublish in JOSS@weber and @clausen should have a lot of expertise due to LiberTEM.
This can wait until a later stage, I just wanted to have it documented here that this is a goal!
[](https://joss.theoj.org/)
@rafaldb @unger@weber and @clausen should have a lot of expertise due to LiberTEM.
This can wait until a later stage, I just wanted to have it documented here that this is a goal!
[](https://joss.theoj.org/)
@rafaldb @ungerhttps://iffgit.fz-juelich.de/empyre/empyre/-/issues/34Implement lorentz forward model2020-02-14T08:28:59ZJan CaronImplement lorentz forward modelJacobi calculations not necessary for now!Jacobi calculations not necessary for now!Minimum viable product: Create magnetic skyrmion distributions, visualize and export themhttps://iffgit.fz-juelich.de/empyre/empyre/-/issues/33Implement phase mapper forward model2020-02-14T08:28:21ZJan CaronImplement phase mapper forward modelMinimum viable product: Create magnetic skyrmion distributions, visualize and export themhttps://iffgit.fz-juelich.de/empyre/empyre/-/issues/32Implement projector forward model2020-02-14T08:27:45ZJan CaronImplement projector forward modelMinimum viable product: Create magnetic skyrmion distributions, visualize and export themhttps://iffgit.fz-juelich.de/empyre/empyre/-/issues/30jutil dependency2020-02-19T14:23:12ZJan Caronjutil dependencyDo you still need jutil? If yes, should I then also work on moving it to pypi/anaconda? @ungerDo you still need jutil? If yes, should I then also work on moving it to pypi/anaconda? @ungerMinimum viable product: Create magnetic skyrmion distributions, visualize and export themJan CaronJan Caronhttps://iffgit.fz-juelich.de/empyre/empyre/-/issues/29Announcements2020-03-20T10:38:10ZJan CaronAnnouncements@empyre
This issue is to keep everyone in the group up to date with announcements etc.@empyre
This issue is to keep everyone in the group up to date with announcements etc.https://iffgit.fz-juelich.de/empyre/empyre/-/issues/28Proper use of snippets2020-02-12T13:20:13ZJan CaronProper use of snippetsWhat should be put into the snippets category? Full tutorials or only short things like "How to quickly load some specific data"?What should be put into the snippets category? Full tutorials or only short things like "How to quickly load some specific data"?https://iffgit.fz-juelich.de/empyre/empyre/-/issues/24Define FwdModel base class / interface2020-03-02T11:53:33ZJan CaronDefine FwdModel base class / interfacePut resources here for linear operators (inherit from or wrap them?)
* [ ] [PyLops](https://pylops.readthedocs.io/en/latest/)
* [ ] FMComposite as a structure with children and parents (concatenation: same level, stacking: parallel)? N...Put resources here for linear operators (inherit from or wrap them?)
* [ ] [PyLops](https://pylops.readthedocs.io/en/latest/)
* [ ] FMComposite as a structure with children and parents (concatenation: same level, stacking: parallel)? NOT a tree, one node can have several parents (i.e. input from more than one submodel, e.g. summation of phase ramp and magnetic ramp).Minimum viable product: Create magnetic skyrmion distributions, visualize and export themhttps://iffgit.fz-juelich.de/empyre/empyre/-/issues/23Implement diagnostics.py2020-02-14T08:15:13ZJan CaronImplement diagnostics.py* [ ] Implementation
* [ ] Documentation
* [ ] Testing* [ ] Implementation
* [ ] Documentation
* [ ] Testing