bluebrain / rtneuron Goto Github PK

When I run the MorphologyCollage, the morphologies appear cut.

This issue makes the visual check less clear and it should be fixed.

Errors and problems found on the site http://bluebrain.github.io/RTNeuron-3.0/python/gallery.html

1.- DONE In 'Getting Started': Not clear what the 'snapshot' function does:
rtneuron.snapshot_to_notebook(rtneuron.engine.views[0])

2.- In 'Getting Started' 7th code block I get a bunch of output that is not clear to me:
````In [5]: rtneuron.display_circuit(blueconfig, 6523)
...: # This function doesn't directly accept a dictionary for the attributes, it has to be
...: # an AttributeMap instead.
...: rtneuron.display_synapses(
...: 6523, attributes=rtneuron.AttributeMap({'color': [1, 1, 0, 1], 'radius': 3}))
...: rtneuron.snapshot_to_notebook(rtneuron.engine.views[0])
...:

['/gpfs/bbp.cscs.ch/project/proj3/resources/circuits/ReleaseL2_fixed']
Trying to load blue config: /gpfs/bbp.cscs.ch/project/proj3/resources/circuits/ReleaseL2_fixed... done
Error starting Servus client: Can't setup avahi client: Daemon not running
Error starting Servus client: Can't setup avahi client: Daemon not running
Error starting Servus client: Can't setup avahi client: Daemon not running
Error starting Servus client: Can't setup avahi client: Daemon not running
Creating 1 neurons
0%   10   20   30   40   50   60   70   80   90   100%
|----|----|----|----|----|----|----|----|----|----|
***************************************************
Adding 1 neurons to the scene
0%   10   20   30   40   50   60   70   80   90   100%
|----|----|----|----|----|----|----|----|----|----|
***************************************************
    1533 Only unmerged synapse files found for /gpfs/bbp.cscs.ch/release/l2/2012.07.23/circuit/O1/merged_circuit/ncsFunctionalAllRecipePathways/nrn_positions.h5; consider using merged files for better performance.
 11444 No merged file found in "/gpfs/bbp.cscs.ch/release/l2/2012.07.23/circuit/O1/merged_circuit/ncsFunctionalAllRecipePathways" to build lookup index; loading data will be very slow

Also it takes quite a long time (>1 minute) which is way too long for an user. It should be mentioned on the 

3.- DONE In 'Getting Started the command
view.attributes.help()
does not show anything.

4.- DONE In 'Coloring and Modes', code block 4: Syntax error, one bracket too much:
layer_ids.append(simulation.gids('Layer%d' % i)))

5.- DONE in Meshes and models, fifth code block:
scene.addMesh(vertices, indices, colors=colors, attributes=attributes)
AttributeError: 'Scene' object has no attribute 'addMesh'
6.- DONE This happens also in 'Getting Started' Cell 12.

7.- In "Simulation playback', block 1: rtneuron.display_circuit(brain.test.blue_config, ('MiniColumn_[0-5]', attributes))
AttributeError: 'module' object has no attribute 'test'

8.- In "Simulation playback', block 1, first line (rtneuron.apply_spike_data(rtneuron.simulation, view)):
RuntimeError: IO error reading spike times file: /out.dat
Unable to test remainder of the page ...

9.- In 'Synaptic afferent projections': blue.test again not defined. Also unable to load the blueconfig defined in other pages (Error: AttributeError: 'exceptions.RuntimeError' object has no attribute 'msg').
Unable to test remainder of the page ...

Hi,
I have tried multiple times to download the AppImage binary file but I could not do so. Each time, I get "Network Error".
So, I tried to install from source files. And when I issue make command after configure, it terminates with this message. [ 86%] Linking CXX executable attribute_map /usr/bin/x86_64-linux-gnu-ld: warning: libhdf5.so.101, needed by /usr/lib/libBrain.so.3.0.0, not found (try using -rpath or -rpath-link) /usr/bin/x86_64-linux-gnu-ld: //usr/lib/libBrionPlugins.so.9: undefined reference to H5P_CLS_DATASET_CREATE_ID_g'
/usr/bin/x86_64-linux-gnu-ld: /usr/lib/libBrain.so.3.0.0: undefined reference to H5Dread' /usr/bin/x86_64-linux-gnu-ld: //usr/lib/libBrionPlugins.so.9: undefined reference to H5Dget_create_plist'
/usr/bin/x86_64-linux-gnu-ld: /usr/lib/libBrain.so.3.0.0: undefined reference to H5Eget_major' /usr/bin/x86_64-linux-gnu-ld: /usr/lib/libBrain.so.3.0.0: undefined reference to H5Eset_auto2'
/usr/bin/x86_64-linux-gnu-ld: /usr/lib/libBrion.so.3.0.0: undefined reference to H5Fcreate' /usr/bin/x86_64-linux-gnu-ld: /usr/lib/libBrain.so.3.0.0: undefined reference to H5Eget_current_stack'
/usr/bin/x86_64-linux-gnu-ld: /usr/lib/libBrion.so.3.0.0: undefined reference to H5T_NATIVE_UCHAR_g' /usr/bin/x86_64-linux-gnu-ld: /usr/lib/libBrion.so.3.0.0: undefined reference to H5Gget_num_objs'
/usr/bin/x86_64-linux-gnu-ld: //usr/lib/libBrionPlugins.so.9: undefined reference to H5Pset_chunk' /usr/bin/x86_64-linux-gnu-ld: /usr/lib/libBrain.so.3.0.0: undefined reference to H5Sselect_hyperslab'
/usr/bin/x86_64-linux-gnu-ld: /usr/lib/libBrain.so.3.0.0: undefined reference to H5Iinc_ref' /usr/bin/x86_64-linux-gnu-ld: //usr/lib/libBrionPlugins.so.9: undefined reference to H5Pget_chunk'
/usr/bin/x86_64-linux-gnu-ld: /usr/lib/libBrain.so.3.0.0: undefined reference to H5Scopy' /usr/bin/x86_64-linux-gnu-ld: /usr/lib/libBrain.so.3.0.0: undefined reference to H5check_version'
/usr/bin/x86_64-linux-gnu-ld: //usr/lib/libBrionPlugins.so.9: undefined reference to H5Pset_chunk_cache' /usr/bin/x86_64-linux-gnu-ld: /usr/lib/libBrion.so.3.0.0: undefined reference to H5Lget_name_by_idx'
/usr/bin/x86_64-linux-gnu-ld: /usr/lib/libBrain.so.3.0.0: undefined reference to H5Dget_space' /usr/bin/x86_64-linux-gnu-ld: //usr/lib/libBrionPlugins.so.9: undefined reference to H5Aget_space'
/usr/bin/x86_64-linux-gnu-ld: /usr/lib/libBrion.so.3.0.0: undefined reference to H5Sselect_none' /usr/bin/x86_64-linux-gnu-ld: /usr/lib/libBrain.so.3.0.0: undefined reference to H5Dopen2'
/usr/bin/x86_64-linux-gnu-ld: //usr/lib/libBrionPlugins.so.9: undefined reference to H5P_CLS_FILE_ACCESS_ID_g' /usr/bin/x86_64-linux-gnu-ld: /usr/lib/libBrain.so.3.0.0: undefined reference to H5open'
/usr/bin/x86_64-linux-gnu-ld: /usr/lib/libBrain.so.3.0.0: undefined reference to H5Dvlen_reclaim' /usr/bin/x86_64-linux-gnu-ld: /usr/lib/libBrion.so.3.0.0: undefined reference to H5T_NATIVE_FLOAT_g'
/usr/bin/x86_64-linux-gnu-ld: /usr/lib/libBrain.so.3.0.0: undefined reference to H5Idec_ref' /usr/bin/x86_64-linux-gnu-ld: /usr/lib/libBrion.so.3.0.0: undefined reference to H5Gopen2'
/usr/bin/x86_64-linux-gnu-ld: /usr/lib/libBrion.so.3.0.0: undefined reference to H5T_NATIVE_USHORT_g' /usr/bin/x86_64-linux-gnu-ld: //usr/lib/libBrionPlugins.so.9: undefined reference to H5Pcreate'
/usr/bin/x86_64-linux-gnu-ld: /usr/lib/libBrain.so.3.0.0: undefined reference to H5Eget_auto2' /usr/bin/x86_64-linux-gnu-ld: /usr/lib/libBrain.so.3.0.0: undefined reference to H5Iis_valid'
/usr/bin/x86_64-linux-gnu-ld: /usr/lib/libBrain.so.3.0.0: undefined reference to H5Tset_size' /usr/bin/x86_64-linux-gnu-ld: /usr/lib/libBrain.so.3.0.0: undefined reference to H5T_NATIVE_ULONG_g'
/usr/bin/x86_64-linux-gnu-ld: /usr/lib/libBrain.so.3.0.0: undefined reference to H5Pclose' /usr/bin/x86_64-linux-gnu-ld: /usr/lib/libBrain.so.3.0.0: undefined reference to H5Screate_simple'
/usr/bin/x86_64-linux-gnu-ld: /usr/lib/libBrain.so.3.0.0: undefined reference to H5Sget_simple_extent_ndims' /usr/bin/x86_64-linux-gnu-ld: /usr/lib/libBrion.so.3.0.0: undefined reference to H5T_NATIVE_SCHAR_g'
/usr/bin/x86_64-linux-gnu-ld: //usr/lib/libBrionPlugins.so.9: undefined reference to H5Screate' /usr/bin/x86_64-linux-gnu-ld: /usr/lib/libBrion.so.3.0.0: undefined reference to H5T_NATIVE_UINT_g'
/usr/bin/x86_64-linux-gnu-ld: //usr/lib/libBrionPlugins.so.9: undefined reference to H5Dwrite' /usr/bin/x86_64-linux-gnu-ld: /usr/lib/libBrain.so.3.0.0: undefined reference to H5Ewalk2'
/usr/bin/x86_64-linux-gnu-ld: //usr/lib/libBrionPlugins.so.9: undefined reference to H5Fflush' /usr/bin/x86_64-linux-gnu-ld: //usr/lib/libBrionPlugins.so.9: undefined reference to H5Awrite'
/usr/bin/x86_64-linux-gnu-ld: /usr/lib/libBrain.so.3.0.0: undefined reference to H5Tset_cset' /usr/bin/x86_64-linux-gnu-ld: //usr/lib/libBrionPlugins.so.9: undefined reference to H5Aopen'
/usr/bin/x86_64-linux-gnu-ld: /usr/lib/libBrain.so.3.0.0: undefined reference to H5Eclear2' /usr/bin/x86_64-linux-gnu-ld: /usr/lib/libBrain.so.3.0.0: undefined reference to H5T_C_S1_g'
/usr/bin/x86_64-linux-gnu-ld: //usr/lib/libBrionPlugins.so.9: undefined reference to H5Gcreate2' /usr/bin/x86_64-linux-gnu-ld: /usr/lib/libBrion.so.3.0.0: undefined reference to H5T_NATIVE_INT_g'
/usr/bin/x86_64-linux-gnu-ld: /usr/lib/libBrain.so.3.0.0: undefined reference to H5Tcopy' /usr/bin/x86_64-linux-gnu-ld: /usr/lib/libBrain.so.3.0.0: undefined reference to H5Eget_minor'
/usr/bin/x86_64-linux-gnu-ld: /usr/lib/libBrain.so.3.0.0: undefined reference to H5T_NATIVE_DOUBLE_g' /usr/bin/x86_64-linux-gnu-ld: //usr/lib/libBrionPlugins.so.9: undefined reference to H5Aread'
/usr/bin/x86_64-linux-gnu-ld: //usr/lib/libBrionPlugins.so.9: undefined reference to H5P_CLS_DATASET_ACCESS_ID_g' /usr/bin/x86_64-linux-gnu-ld: //usr/lib/libBrionPlugins.so.9: undefined reference to H5Literate'
/usr/bin/x86_64-linux-gnu-ld: /usr/lib/libBrain.so.3.0.0: undefined reference to H5Sget_simple_extent_dims' /usr/bin/x86_64-linux-gnu-ld: //usr/lib/libBrionPlugins.so.9: undefined reference to H5Dcreate2'
/usr/bin/x86_64-linux-gnu-ld: /usr/lib/libBrain.so.3.0.0: undefined reference to H5Fopen' /usr/bin/x86_64-linux-gnu-ld: //usr/lib/libBrionPlugins.so.9: undefined reference to H5Acreate2'
collect2: error: ld returned 1 exit status
make[2]: *** [tests/unit/CMakeFiles/attribute_map.dir/build.make:143: tests/unit/attribute_map] Error 1
make[1]: *** [CMakeFiles/Makefile2:1322: tests/unit/CMakeFiles/attribute_map.dir/all] Error 2
make: *** [Makefile:163: all] Error 2
`
How can I fix the above problem? Thank you.

When I select to show only somas and play around with the graphics (work Linux box Ubuntu 16.04), then sometimes the app crashes and I have an error like follows:

terminate called after throwing an instance of 'std::runtime_error'
  what():  Could not open morphology file /home/adietz/Work/60_Other/62_RTNeuron/AppImage/shared_components/morphologies/Scnn1a_473845048_m.h5: Unable to open file /home/adietz/Work/60_Other/62_RTNeuron/AppImage/shared_components/morphologies/Scnn1a_473845048_m.h5 (File accessibilty) Unable to open file
/tmp/.mount_rtneurk1ttII/AppRun: line 5: 15873 Aborted                 LD_LIBRARY_PATH=${HERE}/usr/local/lib:${HERE}/usr/local/lib64:${HERE}/usr/local/lib/python3.7/site-packages/PyQt5/Qt/lib:$LD_LIBRARY_PATH PYTHONHOME=${HERE}/usr/local PYTHONPATH=${HERE}/usr/local/lib/python3.7/site-packages ${HERE}/usr/local/bin/python3.7 ${HERE}/usr/local/bin/rtneuron $@

Step to repduce:

1. Load only the soma
2. Start rotating the cells so they rotate automatically
   3 Stop rotation (left click) with mouse over a soma.

It looks like the application if looking for some morphology information (axon/dendrites) although only the SOMA is selected.

Strange: When I do the same selecting the correct config file (which have all the morphologies available), then when I stop the rotation (step 3) a single cell with morphology is shown.

Tab completion only works for the first level of nesting. For example this works:

In [1]: view.<TAB>

but this doesn't:

In [1]: view.attributes.<TAB>

Assigning view.attributes to a variable and then tabbing on it works.

Install and activate RTNeuron 3.0 in BB5.

If that has been done, testing can continue on the new system...

Hi,

Does RTNeuron support external models? I see that there is a requirement for blue brain project config file for the first argument in display_circuit command of RTNeuron.

I have detailed models in NEURON. Is it not possible to use them with RTNeuron?

In the "Meshes and models" tutorial http://bluebrain.github.io/RTNeuron-3.0/python/meshes_and_models.html it looks like some items are out of date.

In the second-to-last code block you have the following line of code:

scene.addMesh(numpy.array(vertices), numpy.array(indices), colors=[1, 1, 1, 1], attributes=attributes)

which generates the following error:

AttributeError: 'Scene' object has no attribute 'addMesh'.

According to the documentation a scene has no method addMesh...

Launching a use-case app from the command line sets up the Qt5 hook to integrate the QT event loop in the IPython shell event loop. However this setup is not done when the IPython console is started first and start_app() is called from there. The workaround is to type %gui qt5 in the console, but this should be done automatically by start_app.

Issue on Ubuntu 18.04.1:

When loading the circuit with just the soma I see the following image, with the soma (or whatever) very faint at the center of the image. When I zoom in, it gets even fainter:

Hi,

I've installed all the dependencies listed here : [http://bluebrain.github.io/RTNeuron-3.0/old/compilation.html], then downloaded the rtneuron AppImage and succesfully run it.
However, when I type

start_app()

then the following error is returned:

Unrecognized OpenGL version QOpenGLWidget: Failed to make context current composeAndFlush: makeCurrent() failed composeAndFlush: makeCurrent() failed composeAndFlush: makeCurrent() failed

A window actually prompted but was totally black and not reacting to any input.
I've tried to reinstall OpenGL using the following commands:

sudo apt-get install mesa-common-dev libgl1-mesa-dev libglu1-mesa-dev freeglut3-dev

but nothing changed.
I'm working on Ubuntu 18.10
What I'm doing wrong / missing?

Thanks in advance for help!

When I want to select a color (e.g. or background), the color selecting window appears behind the main window and can be easily missed (Ubuntu 16.04 Work).

Hey @hernando
When I try to execute the app Image using ./rtneuron_x86_64.AppImage --app I am getting this error

ImportError: libturbojpeg.so.0: cannot open shared object file: No such file or directory

Thanks

I have found some issues related to the RTNeuron 3.0 user guide, located here: https://bbpteam.epfl.ch/documentation/RTNeuron-3.0/user_guide.html

• The vizcluster is mentioned without reference. As a user not familiar with the vizcluster I would be confused what is it. Suggestion: Put in a link to a more general description of the vizcluster
• The mention of vglrun: What is it?
• The link to the page 'installations instructions' seems to be broken or not up-to-date
• Typo: Second paragraph in "If you are working in the vizcluster": 'cluter' -> 'cluster'
• Typo: First paragraph in "If you are working in your own machine": 'detais' -> 'details'

When the AppImage is double-clicked, no GUI is shown. RTNeutron should either show a default (example) image when invoked without command line parameters, or Terminal=true should be set in the desktop file to indicate that this is a command line tool rather than a GUI application.

Reference:
AppImage/appimage.github.io#1302

Regardless of the morphology used, the code fails at the assert at /home/hernando/dev/src/RTNeuron/rtneuron/rtneuron/render/DrawElementsPortions.cpp:173

Hi,

I am trying to install RT Neuron on Ubuntu with the compilation instructions provided, however I get this error "/home/krishna/Desktop/RTNeuron/Pression/pression/data/liblzf/lzf_c.c:157:5: error: this use of "defined" may not be portable [-Werror=expansion-to-defined]
#if STRICT_ALIGN
^~~~~~~~~~~~"

I have installed all the required packages as asked but could not understand the problem.

In the documentation https://bbpteam.epfl.ch/documentation/RTNeuron-3.0/user_guide.html#Introduction the command line options are given with one dash, but they work with two dashes:

On Ubuntu 18.04.1:

I am unable to see the detailed view. I cloned the whole sonata repository to be sure to have the up-to-date files, but when trying to open the 'Detailed' view from 300_cells I get the following error messages:

 12258 Unable to load data for neuron a2: Reading swc morphology file: /home/alex/Documents/AppImage/sonata/examples/shared_components/morphologies/Scnn1a_473845048_m.swc, parse error at line 4
 12258 Unable to load data for neuron a3: Reading swc morphology file: /home/alex/Documents/AppImage/sonata/examples/shared_components/morphologies/Rorb_325404214_m.swc, parse error at line 4
 12259 Unable to load data for neuron a4: Reading swc morphology file: /home/alex/Documents/AppImage/sonata/examples/shared_components/morphologies/Rorb_325404214_m.swc, parse error at line 4
```

I see two additional options on the screen: Extra models and Cell dyes.

They are neither documented, nor do they seem to do anything. Can they be taken out, or is there a plan to implement these options?

The documentation at http://bluebrain.github.io/RTNeuron-3.0/compilation.html requires some updates and clarification:

• Clean up dependencies.
• Make sure what really is required to install RTNeuron, and what must be installed manually:
• cmake version 3.0.0
• sphinx 1.3 (other version for BB5 or something?)
• lxml

Hi @hernando,
RTNeuron is finally working once I moved my graphics to the NVidia graphics card. But I can't save the images using
view.snapshot('5_neuron.png')
I am getting the error
Error writing file 5_neuron.png: Warning: Could not find plugin to write image to file "5_neuron.png".
Is it looking for the OSG plugin? I haven't tried the latest app image. Is it fixed there? You mentioned you uploaded the latest app image on the repo - but on the release page version is from December 14. Can you please point me where it is? Or do I have to build the image using docker?

Thanks