how stimulate the sine wave in PointProcessManager(GUI)

Using the graphical user interface to build and exercise models. Includes customizing the GUI by writing a little bit of hoc.
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chalspark
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Joined: Tue Jun 01, 2010 1:19 am

how stimulate the sine wave in PointProcessManager(GUI)

Post by chalspark » Sun Jun 27, 2010 6:14 am

hello, I want to stiumate sine wave in soma with pointProcessManager(GUI).

I try that

amp : sin(t)

but amp value is -0.50637.

I saw this link. https://www.neuron.yale.edu/phpBB2/view ... ?f=8&t=897

But there are all~ MOD source.

Can i found the way that used GUI?

thank.

ted
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Re: how stimulate the sine wave in PointProcessManager(GUI)

Post by ted » Mon Jun 28, 2010 1:27 am

The best way is to use a mod file. The compiled mechanism will automatically appear in the GUI tool menus, including the PointProcessManager's "SelectPointProcess" menu. I have updated the mod file you mentioned, and packaged it with some hoc code and a GUI interface so you can play with it yourself--see
https://www.neuron.yale.edu/phpBB2/view ... 7314#p7314

Or is your computer unable to compile mod files?

chalspark
Posts: 17
Joined: Tue Jun 01, 2010 1:19 am

Re: how stimulate the sine wave in PointProcessManager(GUI)

Post by chalspark » Tue Jun 29, 2010 8:09 am

ted, Thanks for your answer.

But i have some problem. I had compiled "Izap.mod" used to mknrndll.

I can See izap select point process in initizap.hoc file.

but I start my project. turn on neuron and make single model.

add point process manager and then i try to inject sin wave.

but I can't found izap. Why happen this things?

compile results

gcc -DDLL_EXPORT -DPIC -I/cygdrive/c/nrn71/src/scopmath -I/cygdrive/c/nrn71/src/ nrnoc -I/cygdrive/c/nrn71/src/oc -I/cygdrive/c/nrn71/lib -I/cygdrive/c/nrn71/gcc inc -I/cygdrive/c/nrn71/gcc3inc -L/cygdrive/c/nrn71/gcclib -c mod_func.c
gcc -I/cygdrive/c/nrn71/lib -I/cygdrive/c/nrn71/gccinc -I/cygdrive/c/nrn71/gcc3i nc -L/cygdrive/c/nrn71/gcclib -shared -o nrnmech.dll mod_func.o SinClamp.o apcou nt.o exp2syn.o expsyn.o feature.o hh.o intfire1.o intfire2.o intfire4.o izap.o n etstim.o oclmp.o passive.o pattern.o ppmark.o stim.o svclmp.o syn.o vclmp.o xmec h.o \
-L/cygdrive/c/nrn71/bin -lnrniv
Info: resolving _nrn_point_prop_ by linking to __imp__nrn_point_prop_ (auto-impo rt)
ld: warning: auto-importing has been activated without --enable-auto-import spec ified on the command line.
This should work unless it involves constant data structures referencing symbols from auto-imported DLLs.Info: resolving _use_cachevec by linking to __imp__use_ cachevec (auto-import)
Info: resolving _pnt_receive by linking to __imp__pnt_receive (auto-import)
Info: resolving _pnt_receive_size by linking to __imp__pnt_receive_size (auto-im port)
Info: resolving _nrn_threads by linking to __imp__nrn_threads (auto-import)
Info: resolving _celsius by linking to __imp__celsius (auto-import)
Info: resolving _cvode_active_ by linking to __imp__cvode_active_ (auto-import)
rebase -b 0x64000000 -v nrnmech.dll
nrnmech.dll: new base = 64000000, new size = 20000

nrnmech.dll was built successfully.
Press Return key to exit

ted
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Re: how stimulate the sine wave in PointProcessManager(GUI)

Post by ted » Tue Jun 29, 2010 2:17 pm

Does initizap.hoc work?

chalspark
Posts: 17
Joined: Tue Jun 01, 2010 1:19 am

Re: how stimulate the sine wave in PointProcessManager(GUI)

Post by chalspark » Tue Jun 29, 2010 8:48 pm

Hello, Ted

I have solved this problem. but There are still a little problem.

I try remove NEURON 7.1 and then I have start from the beginning.

I had completed setup and copied Izap directory(c:\nrn71\chals\Izap).

then I try modlunit,mknrndll. I had success Izap setup.

After execute initizap.hoc, I can see graphs and control windows.

So, I try to make new hoc file(c:\nrn71\chals\Izap\test.hoc). fortunately I can see Izap point process.

but, I had some problem still. I retry to make new hoc file(c:\nrn71\chals\myproject\test2.hoc) or just execute nrngui.

then I can't see Izap point process. I think if my project file exist Izap directory, NEURON recognize Izap point process but if my project file exist the others directory or just executing nrngui, NEURON does not recognize Izap point process.

How add pathway for access at the others directory?

Thanks for your effort. Have a nice days.

ted
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Re: how stimulate the sine wave in PointProcessManager(GUI)

Post by ted » Wed Jun 30, 2010 1:22 pm

chalspark wrote:So, I try to make new hoc file(c:\nrn71\chals\Izap\test.hoc). fortunately I can see Izap point process.
Yes, because mknrndll created a nrnmech.dll file in c:\nrn71\chals\Izap. This file contains the compiled Izap mechanism. When you start NEURON by double clicking on a hoc file in that directory, NEURON reads the nrnmech.dll file, which adds the Izap mechanism to NEURON.
I retry to make new hoc file(c:\nrn71\chals\myproject\test2.hoc) or just execute nrngui.
then I can't see Izap point process.
because c:\nrn71\chals\myproject does not contain the nrnmech.dll file to tell it about the Izap mechanism.
How add pathway for access at the others directory?
That's not a good idea. Put a copy of izap.mod in c:\nrn71\chals\myproject and then run mknrndll in that directory.

The best way to organize model files is to give each modeling project its own directory. Put whatever hoc and ses files a project needs into the project's directory. Also put copies of whatever mod files you need in that directory, and run mknrndll. If you need to add more mod files, add them, and then run mknrndll again.

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