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Auto-deduce wether file contains morphology or cell, load accordingly.
This is on current master, perhaps properly loading these files depends on Arobr v0.6, but I thought I'd mention it anyway.
E.g.: [error] NML file /home/brent/sync/julich/code/arbor-gui/data/c302-dd1-cell.nml has no morphologies.
In the open-morph file chooser, could we guess that .acc are Cable Cells?
GUI crashes "Unknown locset" loading ACC
Loading the attached acc file crashes with:
[2021-09-14 11:11:08.981] [error] Unknown locset
terminate called after throwing an instance of 'std::runtime_error'
what(): Unknown locset
[1] 152076 abort (core dumped) ~/Downloads/Arbor_GUI-x86_64.AppImage
Feature: Add a mode to color morph by trace
Sketch:
- traces color relevant cables by value % lut
- interface to scrub through traces with a draggable handle
- box to choose the probes
GUI crashes reading mech/g=v format
Loading
crashes without error messages.
Explanation by @thorstenhater in chat:
ACC does not say which catalogues to use, so I have to manage that in the GUI myself.
Therefore, mechanisms are written "catalogue::mechanism", thus need to use default::pas
The globals are converted to but not from the mech/g=v format; that's a bug
Wrong Potassium internal concentration
Hi.
I have installed the gui and it runs without issues, so far.
I loaded an ASC morphology and than looked around to understand the various tabs.
Under "ion settings", the other default values are correct but "k" (the internal potassium concentration) has a default value of only 54.4mM.
The average concentration has been estimated to be 150mM.
Feature: graphical dynamics painter
In addition to writing S-expressions, graphical delineation (use a mouse to 'draw' a region and generate an S-expression consequently) of regions and assigning dynamics (and parameters, etc) would be of great help designing cells.
Pan and rotation handles out of view
Some morphologies open up with a viewport very much off centre. When that is the case, the handles for rotation and panning are not in the viewport and thus not usable.
Proposal: always places the handles in the center of the viewport.
Alternatively, center morphs that apparently are not centered (stellate.asc is the file in question).
Unable to install in Ubuntu 20.04
OS: Ubuntu 20.04
cmake: 3.24
Unable to install the gui. I followed the steps for Linux (Ubuntu). That is, after
git clone --recursive https://github.com/arbor-sim/gui.git
cd gui
mkdir build
cd build
and then
sudo apt update
sudo apt install libxml2-dev libxrandr-dev libxinerama-dev \
libxcursor-dev libxi-dev libglu1-mesa-dev \
freeglut3-dev mesa-common-dev gcc-10 g++-10
sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-10 10
sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-10 10
when I run
cmake ..
sudo make install -j 4
I get
[ 92%] Building CXX object CMakeFiles/arbor-gui.dir/src/cell_builder.cpp.o
In file included from /home/gui/src/component.hpp:3,
from /home/gui/src/gui_state.hpp:11,
from /home/gui/src/main.cpp:1:
/home/gui/src/id.hpp:3:10: fatal error: compare: No such file or directory
3 | #include <compare>
| ^~~~~~~~~
compilation terminated.
In file included from /home/gui/src/component.hpp:3,
from /home/gui/src/gui_state.hpp:11,
from /home/gui/src/gui_state.cpp:1:
/home/gui/src/id.hpp:3:10: fatal error: compare: No such file or directory
3 | #include <compare>
| ^~~~~~~~~
compilation terminated.
make[2]: *** [CMakeFiles/arbor-gui.dir/build.make:76: CMakeFiles/arbor-gui.dir/src/main.cpp.o] Error 1
make[2]: *** Waiting for unfinished jobs....
make[2]: *** [CMakeFiles/arbor-gui.dir/build.make:104: CMakeFiles/arbor-gui.dir/src/gui_state.cpp.o] Error 1
In file included from /home/gui/src/window.hpp:14,
from /home/gui/src/window.cpp:1:
/home/gui/src/utils.hpp:20:21: warning: use of 'auto' in parameter declaration only available with '-fconcepts'
20 | inline double to_us(auto dt) { return std::chrono::duration_cast<std::chrono::microseconds>(dt).count(); }
| ^~~~
In file included from /home/gui/src/location.hpp:13,
from /home/gui/src/cell_builder.hpp:12,
from /home/gui/src/cell_builder.cpp:1:
/home/gui/src/utils.hpp:20:21: warning: use of 'auto' in parameter declaration only available with '-fconcepts'
20 | inline double to_us(auto dt) { return std::chrono::duration_cast<std::chrono::microseconds>(dt).count(); }
| ^~~~
make[1]: *** [CMakeFiles/Makefile2:653: CMakeFiles/arbor-gui.dir/all] Error 2
make: *** [Makefile:136: all] Error 2
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