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tkostov/HackCorona 11

Visualize the corona-outbreak in our area, region or country and simulate its spread in the nearest futures. Help COVID19 crisis teams identify future shortages such as ICUs & remedial actions.

RainerHeintzmann/StateModeling 5

a toolbox for modeling states and transition rates between them and fitting initial distributions, rates and alike using tensorflow

RainerHeintzmann/CudaMat 4

CudaMat enables fast computing on graphics cards that supports the CUDA programming language. Currently such cards are available from NVidia. CudaMat is, as much as possible, invisible to the user. The idea is that the user can transform any existing Matlab code into a CudaMat code with minimal effort. E.g. with a single line like a=cuda(a) the Matlab object 'a' gets transformed into a CudaMat object 'a'. This can be checked using the matlab command whos.

RainerHeintzmann/View5D 2

Julia interface to call the View5D Java application, an image viewer for up to 5-dim data www.nanoimaging.de/View5D

SimonLabouesse/BioFormatOpener.jl 1

Permit to open image with BioFormat in Julia (use java and JavaCall)

RainerHeintzmann/bioformats 0

Bio-Formats is a Java library for reading and writing data in life sciences image file formats. It is developed by the Open Microscopy Environment. Bio-Formats is released under the GNU General Public License (GPL); commercial licenses are available from Glencoe Software.

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Allows CudaMat to be called from Julia

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Dual-Stage Attention-Based Recurrent Neural Net for Time Series Prediction

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Give list of java available methods when wrong methods are call from Julia.

issue closedbionanoimaging/UC2-Software-GIT

GUI non-functional (possibly Kivy compatibility change)

Hi, love this project, just building one myself. Run into a bit of problem with the GUI. I've got Kivy installed on an RPI 2B+ and have verified that the installation is working through the kivy github tutorial. Worked through this GUI tutorial with no hiccups until running the GUI and got this error code: [ WARNING ] [ kivy ] stderr: Traceback (most recent call last): [ WARNING ] [ kivy ] stderr: File "/home/UC21/berryconda3/envs/UC2env/lib/python3.6/site-packages/kivy/lang/builder.py", line 706, in _apply_rule [ WARNING ] [ kivy ] stderr: setattr(widget_set, key, value) [ WARNING ] [ kivy ] stderr: File "kivy/weakproxy.pyx", line 35, in kivy.weakproxy.WeakProxy.__setattr__ [ WARNING ] [ kivy ] stderr: File "kivy/properties.pyx", line 498, in kivy.properties.Property.__set__ [ WARNING ] [ kivy ] stderr: File "kivy/properties.pyx", line 542, in kivy.properties.Property.set [ WARNING ] [ kivy ] stderr: File "kivy/properties.pyx", line 533, in kivy.properties.Property.set [ WARNING ] [ kivy ] stderr: File "kivy/properties.pyx", line 1253, in kivy.properties.OptionProperty.check [ WARNING ] [ kivy ] stderr: ValueError: GridLayout.orientation is set to an invalid option 'horizontal'. Must be one of: ['lr-tb', 'tb-lr', 'rl-tb', 'tb-rl', 'lr-bt', 'bt-lr', 'rl-bt', 'bt-rl'] [ WARNING ] [ kivy ] stderr: [ WARNING ] [ kivy ] stderr: During handling of the above exception, another exception occurred: [ WARNING ] [ kivy ] stderr: [ WARNING ] [ kivy ] stderr: Traceback (most recent call last): [ WARNING ] [ kivy ] stderr: File "main.py", line 318, in <module> [ WARNING ] [ kivy ] stderr: FluidiscopeApp().run() [ WARNING ] [ kivy ] stderr: File "/home/UC21/berryconda3/envs/UC2env/lib/python3.6/site-packages/kivy/app.py", line 949, in run [ WARNING ] [ kivy ] stderr: self._run_prepare() [ WARNING ] [ kivy ] stderr: File "/home/UC21/berryconda3/envs/UC2env/lib/python3.6/site-packages/kivy/app.py", line 919, in _run_prepare [ WARNING ] [ kivy ] stderr: root = self.build() [ WARNING ] [ kivy ] stderr: File "main.py", line 298, in build [ WARNING ] [ kivy ] stderr: self.fluidiscope = Fluidiscope(app=self) [ WARNING ] [ kivy ] stderr: File "main.py", line 248, in __init__ [ WARNING ] [ kivy ] stderr: super(Fluidiscope, self).__init__() # **kwargs [ WARNING ] [ kivy ] stderr: File "/home/UC21/berryconda3/envs/UC2env/lib/python3.6/site-packages/kivy/uix/boxlayout.py", line 145, in __init__ [ WARNING ] [ kivy ] stderr: super(BoxLayout, self).__init__(**kwargs) [ WARNING ] [ kivy ] stderr: File "/home/UC21/berryconda3/envs/UC2env/lib/python3.6/site-packages/kivy/uix/layout.py", line 76, in __init__ [ WARNING ] [ kivy ] stderr: super(Layout, self).__init__(**kwargs) [ WARNING ] [ kivy ] stderr: File "/home/UC21/berryconda3/envs/UC2env/lib/python3.6/site-packages/kivy/uix/widget.py", line 361, in __init__ [ WARNING ] [ kivy ] stderr: rule_children=rule_children) [ WARNING ] [ kivy ] stderr: File "/home/UC21/berryconda3/envs/UC2env/lib/python3.6/site-packages/kivy/uix/widget.py", line 465, in apply_class_lang_rules [ WARNING ] [ kivy ] stderr: rule_children=rule_children) [ WARNING ] [ kivy ] stderr: File "/home/UC21/berryconda3/envs/UC2env/lib/python3.6/site-packages/kivy/lang/builder.py", line 544, in apply [ WARNING ] [ kivy ] stderr: rule_children=rule_children) [ WARNING ] [ kivy ] stderr: File "/home/UC21/berryconda3/envs/UC2env/lib/python3.6/site-packages/kivy/lang/builder.py", line 713, in _apply_rule [ WARNING ] [ kivy ] stderr: e), cause=tb) [ WARNING ] [ kivy ] stderr: kivy.lang.builder.BuilderException: Parser: File "/home/UC21/UC2/UC2-GUI/fluidiscope.kv", line 1278: [ WARNING ] [ kivy ] stderr: ... [ WARNING ] [ kivy ] stderr: 1276: text: 'POS\nIM' [ WARNING ] [ kivy ] stderr: 1277: GridLayout: [ WARNING ] [ kivy ] stderr: >> 1278: orientation: 'horizontal' [ WARNING ] [ kivy ] stderr: 1279: cols: 3 [ WARNING ] [ kivy ] stderr: 1280: size_hint_x: 0.4 [ WARNING ] [ kivy ] stderr: ... [ WARNING ] [ kivy ] stderr: ValueError: GridLayout.orientation is set to an invalid option 'horizontal'. Must be one of: ['lr-tb', 'tb-lr', 'rl-tb', 'tb-rl', 'lr-bt', 'bt-lr', 'rl-bt', 'bt-rl'] [ WARNING ] [ kivy ] stderr: File "/home/UC21/berryconda3/envs/UC2env/lib/python3.6/site-packages/kivy/lang/builder.py", line 706, in _apply_rule [ WARNING ] [ kivy ] stderr: setattr(widget_set, key, value) [ WARNING ] [ kivy ] stderr: File "kivy/weakproxy.pyx", line 35, in kivy.weakproxy.WeakProxy.__setattr__ [ WARNING ] [ kivy ] stderr: File "kivy/properties.pyx", line 498, in kivy.properties.Property.__set__ [ WARNING ] [ kivy ] stderr: File "kivy/properties.pyx", line 542, in kivy.properties.Property.set [ WARNING ] [ kivy ] stderr: File "kivy/properties.pyx", line 533, in kivy.properties.Property.set [ WARNING ] [ kivy ] stderr: File "kivy/properties.pyx", line 1253, in kivy.properties.OptionProperty.check [ WARNING ] [ kivy ] stderr:

Seems one issue is that GridLayout.orientation no longer supports 'horizontal'. This could be a change in the kivy distribution? changing linke 1278 of fluidiscope.kv from 'horiztonal' to 'lr-tb' fixes the issue.

closed time in 3 hours

jhaliburton

issue commentbionanoimaging/UC2-Software-GIT

GUI non-functional (possibly Kivy compatibility change)

I will mark this closed as it seems that no further fix was needed.

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issue commentbionanoimaging/UC2-Software-GIT

GUI non-functional (possibly Kivy compatibility change)

@jhaliburton did you have any success? :)

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issue closedbionanoimaging/UC2-GIT

UC2 configurator issues

General issues

  • [x] Lenses: how shall we take into account that there are different holders for different lenses and that the user might need to create his own?

GitHub

  • [x] for v3 I omitted the version from the name of the module, since renaming everything everywhere is a hassle and this will save time in the future. However, all the modules that existed in git with ‘_v2’ in their name now appeared extra in the configurator and their folders also appeared again in the git CAD folder, with the only file in them being the ‘config.json’. The ‘_v2’ options in the configurator contain the v3 inserts that correspond to the module but not the cube and lid

STLs

  • [ ] is it necessary for each part to end with _v3? The .ipts and hence the generated .stls for which it matters do have it in their name already
  • [ ] The renaming is a very good solution, although except for changing the prefix from UC2_v3 to UC2 only and cutting off the suffix number that Inventor creates when generating the file, I don’t see much difference. The “main” file names (without the prefix and suffix number) were matched between the excel and RAW/STL folder. Wouldn’t it be then enough to just cut the suffix numbers?

Excel sheet

  • [x] there must be some confusion between the v2 and v3 version of the excel sheet. or did you use a different tab than v3?
  • [ ] the configurator doesn’t take into account the amount of parts stated in the excel sheet - shall the multiple parts be added as extra lines?
  • [ ] by making all the OPT parts default, the user might get more STL files than he needs - the question is whether printing some redundant parts makes him unhappy or whether it makes him unhappy not to find the parts in the zip folder when he needs them. I can’t decide what’s better

Configurator (general)

  • [x] it would be nice to have a ‘clear all’ option for the case when one added a lot off different modules and got lost in it

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issue commentbionanoimaging/UC2-GIT

UC2 configurator issues

Closing it for now, since all issues have been resolved here https://github.com/bionanoimaging/uc2-configurator/issues

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