Adding thumbnail generating function #19
Conversation
darshanmandge
requested review from
AurelienJaquier and
ilkilic
and removed request for
AurelienJaquier
| # we use calculate_rheobase() to find the threshold_current. | ||
| # For this case, we set the holding_current to 0.0 nA. | ||
| # if threshold_current is None: | ||
| threshold_current = 1.0 |
There was a problem hiding this comment.
Why are you overwriting this value?
There was a problem hiding this comment.
The threshold current calculation should be done every time as the morphology of the me-combination will change and it won't be emodel threshold to be sure we are not using the emodel threshold. The value was overwritten just to initialise of the cell.
There was a problem hiding this comment.
this can be called after we compute the threshold, and we just get it from MEModelCalibration. So we can remove the threshold computation
There was a problem hiding this comment.
Ok. I will not overwrite the threshold and holding currents. I will pass the emodel_properties instead.
| template_format=template_format, | ||
| emodel_properties=emodel_properties, | ||
| ) | ||
| holding_current = 0.0 |
There was a problem hiding this comment.
Here also, you are overwriting holding current and computing rheobase even if we have passed those values to the function
There was a problem hiding this comment.
same but for holding current.
| section="soma[0]", | ||
| segx=0.5 | ||
| ) | ||
| print(f"Threshold current: {newthreshold_current}") |
There was a problem hiding this comment.
use logger.info instead of print
| ) | ||
|
|
||
| # Create cell | ||
| thumbnail_cell = Cell( |
There was a problem hiding this comment.
you don't need to re-create the cell
There was a problem hiding this comment.
If you don't recreate the cell, the thumbnail generation step protocol would persist even after the thumbnail was generated. I also delete the cell at the end.
| emodel_properties=emodel_properties, | ||
| ) | ||
|
|
||
| # Add 130% threshold current injection |
There was a problem hiding this comment.
comment is not consistent with code
| sim.add_cell(thumbnail_cell) | ||
|
|
||
| neuron_globals = NeuronGlobals.get_instance() | ||
| # neuron_globals.temperature = celsius |
There was a problem hiding this comment.
why are those commented out?
|
|
||
|
|
||
| def generate_cell_thumbnail( | ||
| template_path: str, |
There was a problem hiding this comment.
Could you reduce the number of function arguments by passing template_params instead?
See https://github.com/openbraininstitute/BlueCelluLab/blob/main/bluecellulab/cell/template.py#L48
|
Closing in favour of #27 |
No description provided.