Maybe you can rlook for the dot?

/media/terror/code/source/MEAutility/MEAutility/core.py in reset_currents(self, amp)
324 else:
325 currents = amp*np.ones(self.number_electrode)
--> 326 self.currents(currents)
327
328

TypeError: 'numpy.ndarray' object is not callable

/media/terror/code/source/MEAutility/MEAutility/core.py in set_current_matrix(self, currents)
503 # for zz in range(self.dim):
504 # current_array[self.dim * yy + zz] = currents[zz, yy]
--> 505 self.set_currents(currents=np.reshape(currents, self.dim))
506
507

AttributeError: 'RectMEA' object has no attribute 'set_currents'

Yes. No need to say more. Security issue. Defcon 1.

I believe it is somehow related to mea.move(). The green plane is displayed at z=0, the electrode plane is where it should be. x and y displacement look fine.
Why?

This due in 2 weeks.

Running the test suite now results in some DeprecationWarning in MEAutility:

/Users/espenhagen/miniforge3/envs/lfpy/lib/python3.9/site-packages/MEAutility/core.py:23: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
    if StrictVersion(yaml.__version__) >= StrictVersion('5.0.0'):

This was with (truncated list):

matplotlib                3.5.1           py310hb6292c7_0    conda-forge
meautility                1.5.0                    pypi_0    pypi
numpy                     1.22.2          py310h567df17_0    conda-forge
packaging                 21.3               pyhd8ed1ab_0    conda-forge
pytest                    7.0.0           py310hbe9552e_0    conda-forge
python                    3.10.2          h38ef502_3_cpython    conda-forge

after a mea.move([0, 2000, 50]) and a mea.plot_probe_3d() the electrodes (correctly at -2000) are not overlapped by the probe (seems to be at -4000).
Furthermore, the x and y axes (I had set the range of the z axis) are huge: x:[0, -8000] and y:[0, -10000] even though there does not seem to be anything there.

Hi @alejoe91 ;
The LFPy tests now throws a bunch of DeprecationWarnings from numpy (>v1.20) via MEAutility. np.float should just be float presumably:

  /Users/ehagen/anaconda3/envs/lfpy/lib/python3.9/site-packages/MEAutility/core.py:542: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    if isinstance(current_value, (float, int, np.float, np.integer)):

Catastrophic failure!!!! I have been hacked! VIRUS!

when using negative currents, then all the electrodes are plotted as negative, even the ones set to 0.
It is terrible.

Save me.

with a nice function to return a movie of the current dynamics. Fantastic.(:

when I assign new positions to the electrodes, like
for i in range(bisc.get_electrodes_number()): bisc.electrodes[i].current = params.sim['ampere'] bisc.electrodes[i].position[2] = pia_height
and I then ask for:
mea.plot_probe_3d(bisc, ax=ax1, xlim=[-300, 300], ylim=[-300, 300], zlim=[np.min(cell.zmid) - 50, 200])
the green plane is not aligned (still at z=0) with the electrode plane (correctly at z=pia_height)

Hi,
in LFPy, I got an error when I tried to make a 3D grid of electrodes:

"
....
File "/home/tone/work/LFPykit/lfpykit/models.py", line 841, in init
self.probe = mu.MEA(positions=positions, info=probe_info,
File "/home/tone/.local/lib/python3.8/site-packages/MEAutility/core.py", line 379, in init
normal /= np.linalg.norm(normal)
TypeError: ufunc 'true_divide' output (typecode 'd') could not be coerced to provided output parameter (typecode 'l') according to the casting rule ''same_kind''
"
I'm not sure what is causing the error, but an easy fix seems to be to change from
normal /= np.linalg.norm(normal)
to
normal = normal / np.linalg.norm(normal)
at this line:

Here is a notebook example that reproduces the error locally:
https://www.dropbox.com/s/k22jnskumzi9o9k/LFPy-example-02-Copy1.ipynb?dl=0

Do you also have this issue?

We should extend the code to include finite size electrodes such as, at least, squares.

• allow to pass positions in the yaml file
• (alternatively) pass plane (xy, yz, xz), dim [2D]
• do not hard-code get_elcoords: this should be independent on the electrode type (some sample electrode design could be included)
• command line interface to add a user defined yaml MEA file

easy access to pitch, dimension, position and possibility to create "standard" MEA in one line.

e.g.

mea = MEAutility.create_mea('Neuronexus-32')

Would not it be fantastic if the MEA plot would color the active electrodes differently from the inactive ones?
currents == 0 Vs currents!= 0
I believe it would be amazing.

the user should be able to upload/save new MEA configurations

In principle in the yaml file one could also put the location array

Hi,
Could I build a 3D electrodes in LFPy through MEA? I have read the documentation, but I only found the way of 2D electrodes building which means that put electrodes on same plane.
An idea come to me is build multiple 2D electrodes(xy plane), put them to different position on z-axis and superpose it.
Does it work or can I build 3D directly?
Thanks.

copy and organize methods for:

• plotting recordings/waveforms
• rotate probe in 3d
• 2D and 3d plot of the probe

in the 3d plots: plane
and a 2d option.

I am trying to create a MEArec file, but I first want to define my MEA geometry with arbitrary locations (no regular pattern). I can not figure out how to create this in MEAutility from the documentation. I was wondering if you might have any insights into how to make this? Would it be possible to import a list of points?