Helveg
commented
1 year ago Hello and welcome Lorenzo, what version of the BSB are you using? Could you try installing bsb==4.0.0a55?
Closed LorenzoDeToni closed 10 months ago
Helveg
commented
1 year ago Hello and welcome Lorenzo, what version of the BSB are you using? Could you try installing bsb==4.0.0a55?
LorenzoDeToni
commented
1 year ago Hi, thank you for your answer, I already have that version.
Helveg
commented
1 year ago Oh, my bad, I see that the NEST simulation code hasn't been released yet. If you are interested in this feature, please install the BSB from the git repository:
git clone git@github.com:dbbs-lab/bsb
cd bsb
git checkout feature/nest3
pip install -e .If you need any further help please let me know (much of the documentation is still missing)
LorenzoDeToni
commented
1 year ago Hi, sorry ho bother, am I doing something wrong with the repository cloning o do I need some kind of permission?
I am able to clone it with https, but in the end it gives me an error.
Thank you for your help!
Helveg
commented
1 year ago Sorry, I missed your last reply! Is this still an issue? It seems like your Python environment is unable to write to some folders, you should create a virtual environment, this will solve your immediate problem. An alternative is to use pip install . instead, keep in mind that you would then have to repeat this command every time you change the git source code.
LorenzoDeToni
commented
11 months ago Hi Robin, let's start with a good new, with bsb4.0.0a55 and nest3.4 I'm currently able to run bsb till the scaffold generation. However I have another issue when I try to run the simulation.
It's seem like bsb has problem when calling nest features like neuron parameters and recording devices. Do you have any suggestion? I can't find any material on the bsb website related to this issue. Thanks in advances, best whises. Lorenzo
Helveg
commented
11 months ago Hi Lorenzo, good to hear there's some progress! Could you post this error as code formatted text? It is hard to work with these images. Post both the full code (and configuration), and full error log as code blocks and I will take a look!
From what I can tell so far it seems to be a bug that should be easy to reproduce :)
I can't find any material on the bsb website related to this issue.
Yes, sorry, the documentation is still missing, but starting from october up to february it will be the main focus of the development team to complete the documentation! 🎉
LorenzoDeToni
commented
11 months ago Hi Robin, here is the transcript.
import numpy as np
from bsb.core import Scaffold
from bsb.config import from_json
import bsb.options
bsb.options.verbosity = 2
from bsb.core import from_storage
from bsb.config import Configuration
from bsb.plotting import plot_network
from bsb.morphologies import Morphology
import json
import os
import scipy.io as sio
config = from_json("CPG_bsb4.json")
scaffold = Scaffold(config)
scaffold.compile(clear=True)
Compiling the following strategies: ...
Clearing data
Starting placement strategies: ...
Starting connectivity strategies: ...
Runtime: 0.25578784942626953 2
plot_network(scaffold,cubic=False)
scaffold.run_simulation("prova")
Importing NEST...
-- N E S T --
Copyright (C) 2004 The NEST Initiative
Version: 3.4
Built: Mar 7 2023 05:58:31
his program is provided AS IS and comes with
NO WARRANTY. See the file LICENSE for details.
Problems or suggestions?
Visit https://www.nest-simulator.org/
Type 'nest.help()' to find out more about NEST.
Installing NEST modules...
Creating neurons...
Creating connections...
A_to_B: 100%|█████████████████████████████████| 10/10 [00:00<00:00, 57.33it/s]
Creating devices...
------------------------------------------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
Cell In[6], line 1
----> 1 scaffold.run_simulation("prova")
File ~/bsb/bsb/profiling.py:157, in meter.<locals>.decorated(*args, **kwargs)
155 return r
156 else:
--> 157 return f(*args, **kwargs)
File ~/bsb/bsb/core.py:420, in Scaffold.run_simulation(self, simulation_name, quit)
418 simulation = self.get_simulation(simulation_name)
419 adapter = get_simulation_adapter(simulation.simulator)
--> 420 return adapter.simulate(simulation)
File ~/bsb/bsb/simulators/nest/adapter.py:77, in NestAdapter.simulate(self, simulation)
75 try:
76 self.reset_kernel()
---> 77 return super().simulate(simulation)
78 finally:
79 self.reset_kernel()
File ~/bsb/bsb/simulation/adapter.py:10, in SimulatorAdapter.simulate(self, simulation)
6 """
7 Simulate the given simulation.
8 """
9 with simulation.scaffold.storage.read_only():
---> 10 data = self.prepare(simulation)
11 for hook in simulation.post_prepare:
12 hook(self, simulation, data)
File ~/bsb/bsb/simulators/nest/adapter.py:93, in NestAdapter.prepare(self, simulation, comm)
91 self.connect_neurons(simulation)
92 report("Creating devices...", level=2)
---> 93 self.create_devices(simulation)
94 return self.simdata[simulation]
95 except Exception:
File ~/bsb/bsb/simulators/nest/adapter.py:187, in NestAdapter.create_devices(self, simulation)
185 simdata = self.simdata[simulation]
186 for device_model in simulation.devices.values():
--> 187 device_model.implement(self, simulation, simdata)
File ~/bsb/bsb/simulators/nest/devices/spike_recorder.py:14, in SpikeRecorder.implement(self, adapter, simulation, simdata)
11 def implement(self, adapter, simulation, simdata):
12 import nest
---> 14 nodes = self.get_target_nodes(adapter, simulation, simdata)
15 device = self.register_device(simdata, nest.Create("spike_recorder"))
16 self.connect_to_nodes(device, nodes)
File ~/bsb/bsb/simulators/nest/device.py:33, in NestDevice.get_target_nodes(self, adapter, simulation, simdata)
27 else:
28 node_collector = (
29 simdata.populations[model][targets]
30 for model, targets in simdata.populations.items()
31 if not self.targetting.cell_models or model in self.targetting.cell_models
32 )
---> 33 return sum(node_collector, start=adapter.nest.NodeCollection())
File ~/bsb/bsb/simulators/nest/device.py:31, in <genexpr>(.0)
24 node_collector = self.targetting.get_targets(
25 adapter, simulation, simdata
26 ).values()
27 else:
28 node_collector = (
29 simdata.populations[model][targets]
30 for model, targets in simdata.populations.items()
---> 31 if not self.targetting.cell_models or model in self.targetting.cell_models
32 )
33 return sum(node_collector, start=adapter.nest.NodeCollection())
AttributeError: 'NoneType' object has no attribute 'cell_models'
Thanks for your help. Lorenzo
Helveg
commented
11 months ago Can you show me the simulations configuration you have in CPG_bsb4.json?
LorenzoDeToni
commented
11 months ago "simulations": {
"prova": {
"simulator": "nest",
"duration": 3000,
"default_neuron_model": "ht_neuron",
"default_synapse_model": "static_synapse",
"cell_models": {
"A": {
},
"B": {
},
"C":{
},
"D":{
},
"E":{
}
},
"connection_models": {
"A_to_B": {
"synapse_model": "static_synapse",
"connection": {
"weight": 50.0,
"delay": 320.0
},
"synapse":{
"weight": 50.0,
"delay": 320.0
}
},
"A_to_B": {
"synapse_model": "static_synapse",
"connection": {
"weight": -20.0,
"delay": 320.0
},
"synapse":{
"weight": -20.0,
"delay": 320.0
}
},
"A_to_C": {
"synapse_model": "static_synapse",
"connection": {
"weight": 50.0,
"delay": 1.0
},
"synapse":{
"weight": 50.0,
"delay": 1.0
}
},
"B_to_A": {
"synapse_model": "static_synapse",
"connection": {
"weight": -50.0,
"delay": 1.0
},
"synapse":{
"weight": -50.0,
"delay": 1.0
}
},
"A_to_D": {
"synapse_model": "static_synapse",
"connection": {
"weight": 2.0,
"delay": 200.0
},
"synapse":{
"weight": 2.0,
"delay": 200.0
}
},
"B_to_D": {
"synapse_model": "static_synapse",
"connection": {
"weight": -8.0,
"delay": 200.0
},
"synapse":{
"weight": -8.0,
"delay": 200.0
}
},
"A_to_E": {
"synapse_model": "static_synapse",
"connection": {
"weight": 30.0,
"delay": 5.0
},
"synapse":{
"weight": 30.0,
"delay": 5.0
}
},
"B_to_A": {
"synapse_model": "static_synapse",
"connection": {
"weight": -100.0,
"delay": 1.0
},
"synapse":{
"weight": -100.0,
"delay": 1.0
}
},
"A_to_E": {
"synapse_model": "static_synapse",
"connection": {
"weight": -100.0,
"delay": 50.0
},
"synapse":{
"weight": -100.0,
"delay": 50.0
}
},
"E_to_A": {
"synapse_model": "static_synapse",
"connection": {
"weight": 2.0,
"delay": 1.0
},
"synapse":{
"weight": 2.0,
"delay": 1.0
}
},
"B_to_C": {
"synapse_model": "static_synapse",
"connection": {
"weight": -4.0,
"delay": 1.0
},
"synapse":{
"weight": -4.0,
"delay": 1.0
}
},
"C_to_B": {
"synapse_model": "static_synapse",
"connection": {
"weight": 10.0,
"delay": 300.0
},
"synapse":{
"weight": 10.0,
"delay": 300.0
}
},
"D_to_A": {
"synapse_model": "static_synapse",
"connection": {
"weight": 10.0,
"delay": 1.0
},
"synapse":{
"weight": 10.0,
"delay": 1.0
}
},
"E_to_D": {
"synapse_model": "static_synapse",
"connection": {
"weight": 2.0,
"delay": 200.0
},
"synapse":{
"weight": 2.0,
"delay": 200.0
}
}
},
"devices": {
"record_stimulus_spikes": {
"device": "spike_recorder",
"delay": 2.0
}
}
}
}Fixed it! Install bsb==4.0.0a57 to get the latest version where this shouldn't be an issue anymore.
PS: The default_neuron_model and default_synapse_model don't exist anymore, the default neuron model is iaf_psc_alpha and the default synapse is static_synapse. If you need different ones you have to give a neuron_model in each cell_model.
Helveg
commented
11 months ago Also, Lorenzo, I'm currently writing my dissertation on this software project. From the filename I'm guessing you're working on Central Pattern Generators? May I include a short description of what you're trying to model with the framework in my dissertation?
LorenzoDeToni
commented
10 months ago Hi Robin, Yes sure you can write about my project, I do work on central patterns generators (I am Lorenzo De Toni from NiLab, @ UNIMORE Jonathan Mapelli Lab) After I've installed the version you suggested, the device section is working (no error), however I still get errors compiling the cell parameters (like Vm...), it's seems like there is a mismatch between bsb version and the syntax indicated in the website. Here the error I get when I try to give some parameters to my cell model:
CastError Traceback (most recent call last)
Cell In[8], line 1
----> 1 config = from_json("PROVAbsbAB.json")
File ~/.local/lib/python3.10/site-packages/bsb/config/__init__.py:259, in parser_factory.<locals>.parser_method(self, file, data, path)
257 data = f.read()
258 tree, meta = parser().parse(data, path=path or file)
--> 259 return _from_parsed(self, name, tree, meta, file)
File ~/.local/lib/python3.10/site-packages/bsb/config/__init__.py:243, in _from_parsed(self, parser_name, tree, meta, file)
240 from ._config import _bootstrap_components
242 _bootstrap_components(tree["components"])
--> 243 conf = self.Configuration(tree)
244 conf._parser = parser_name
245 conf._meta = meta
File ~/.local/lib/python3.10/site-packages/bsb/config/_make.py:65, in make_metaclass.<locals>.ConfigArgRewrite.__call__(meta_subject, _parent, _key, *args, **kwargs)
63 raise ValueError(f"Unexpected positional argument '{primer}'")
64 # Call the base class's new with internal arguments
---> 65 instance = meta_subject.__new__(
66 meta_subject, *args, _parent=_parent, _key=_key, **kwargs
67 )
68 instance._config_pos_init = getattr(instance, "_config_pos_init", False)
69 # Call the end user's __init__ with the rewritten arguments, if one is defined
File ~/.local/lib/python3.10/site-packages/bsb/config/_make.py:218, in compile_new.<locals>.__new__(_cls, _parent, _key, *args, **kwargs)
216 if root:
217 instance._config_isfinished = False
--> 218 instance.__post_new__(**kwargs)
219 if _cls is not ncls:
220 instance.__init__(*args, **kwargs)
File ~/.local/lib/python3.10/site-packages/bsb/config/_make.py:318, in wrap_root_postnew.<locals>.__post_new__(self, _parent, _key, *args, **kwargs)
316 post_new(self, *args, _parent=None, _key=None, **kwargs)
317 except (CastError, RequirementError) as e:
--> 318 _bubble_up_exc(e, self._meta)
319 self._config_isfinished = True
320 _resolve_references(self)
File ~/.local/lib/python3.10/site-packages/bsb/config/_make.py:337, in _bubble_up_exc(exc, meta)
335 node = ""
336 attr = f".{exc.attr}" if hasattr(exc, "attr") and exc.attr else ""
--> 337 errr.wrap(type(exc), exc, append=node + attr)
File ~/.local/lib/python3.10/site-packages/errr/__init__.py:7, in wrap(err_type, *args, **kwargs)
6 def wrap(err_type, *args, **kwargs):
----> 7 return err_type.wrap(*args, **kwargs)
File ~/.local/lib/python3.10/site-packages/errr/exception.py:132, in DetailedException.wrap(err_type, e, prepend, append, *details)
130 err = err_type(msg, *details)
131 err.__traceback__ = e.__traceback__
--> 132 raise err from None
File ~/.local/lib/python3.10/site-packages/bsb/config/_make.py:316, in wrap_root_postnew.<locals>.__post_new__(self, _parent, _key, *args, **kwargs)
314 with warnings.catch_warnings(record=True) as log:
315 try:
--> 316 post_new(self, *args, _parent=None, _key=None, **kwargs)
317 except (CastError, RequirementError) as e:
318 _bubble_up_exc(e, self._meta)
File ~/.local/lib/python3.10/site-packages/bsb/config/_make.py:288, in compile_postnew.<locals>.__post_new__(self, _parent, _key, **kwargs)
286 attr.flag_pristine(self)
287 else:
--> 288 setattr(self, name, value)
289 attr.flag_dirty(self)
290 for key, value in leftovers.items():
File ~/.local/lib/python3.10/site-packages/bsb/config/_attrs.py:803, in ConfigurationDictAttribute.__set__(self, instance, value, _key)
799 def __set__(self, instance, value, _key=None):
800 _setattr(
801 instance,
802 self.attr_name,
--> 803 self.fill(value, _parent=instance, _key=_key or self.attr_name),
804 )
File ~/.local/lib/python3.10/site-packages/bsb/config/_attrs.py:812, in ConfigurationDictAttribute.fill(self, value, _parent, _key)
810 _cfgdict._config_attr = self
811 _cfgdict._elem_type = self.child_type
--> 812 _cfgdict.update(value or builtins.dict())
813 return _cfgdict
File ~/.local/lib/python3.10/site-packages/bsb/config/_attrs.py:753, in cfgdict.update(self, other)
751 def update(self, other):
752 for ckey, value in other.items():
--> 753 self[ckey] = value
File ~/.local/lib/python3.10/site-packages/bsb/config/_attrs.py:697, in cfgdict.__setitem__(self, key, value)
695 _unset_nodes(self[key])
696 try:
--> 697 value = self._elem_type(value, _parent=self, _key=key)
698 except (RequirementError, CastError) as e:
699 if not (hasattr(e, "node") and e.node):
File ~/.local/lib/python3.10/site-packages/bsb/config/_make.py:65, in make_metaclass.<locals>.ConfigArgRewrite.__call__(meta_subject, _parent, _key, *args, **kwargs)
63 raise ValueError(f"Unexpected positional argument '{primer}'")
64 # Call the base class's new with internal arguments
---> 65 instance = meta_subject.__new__(
66 meta_subject, *args, _parent=_parent, _key=_key, **kwargs
67 )
68 instance._config_pos_init = getattr(instance, "_config_pos_init", False)
69 # Call the end user's __init__ with the rewritten arguments, if one is defined
File ~/.local/lib/python3.10/site-packages/bsb/config/_make.py:218, in compile_new.<locals>.__new__(_cls, _parent, _key, *args, **kwargs)
216 if root:
217 instance._config_isfinished = False
--> 218 instance.__post_new__(**kwargs)
219 if _cls is not ncls:
220 instance.__init__(*args, **kwargs)
File ~/.local/lib/python3.10/site-packages/bsb/config/_make.py:288, in compile_postnew.<locals>.__post_new__(self, _parent, _key, **kwargs)
286 attr.flag_pristine(self)
287 else:
--> 288 setattr(self, name, value)
289 attr.flag_dirty(self)
290 for key, value in leftovers.items():
File ~/.local/lib/python3.10/site-packages/bsb/config/_attrs.py:803, in ConfigurationDictAttribute.__set__(self, instance, value, _key)
799 def __set__(self, instance, value, _key=None):
800 _setattr(
801 instance,
802 self.attr_name,
--> 803 self.fill(value, _parent=instance, _key=_key or self.attr_name),
804 )
File ~/.local/lib/python3.10/site-packages/bsb/config/_attrs.py:812, in ConfigurationDictAttribute.fill(self, value, _parent, _key)
810 _cfgdict._config_attr = self
811 _cfgdict._elem_type = self.child_type
--> 812 _cfgdict.update(value or builtins.dict())
813 return _cfgdict
File ~/.local/lib/python3.10/site-packages/bsb/config/_attrs.py:753, in cfgdict.update(self, other)
751 def update(self, other):
752 for ckey, value in other.items():
--> 753 self[ckey] = value
File ~/.local/lib/python3.10/site-packages/bsb/config/_attrs.py:697, in cfgdict.__setitem__(self, key, value)
695 _unset_nodes(self[key])
696 try:
--> 697 value = self._elem_type(value, _parent=self, _key=key)
698 except (RequirementError, CastError) as e:
699 if not (hasattr(e, "node") and e.node):
File ~/.local/lib/python3.10/site-packages/bsb/config/_make.py:65, in make_metaclass.<locals>.ConfigArgRewrite.__call__(meta_subject, _parent, _key, *args, **kwargs)
63 raise ValueError(f"Unexpected positional argument '{primer}'")
64 # Call the base class's new with internal arguments
---> 65 instance = meta_subject.__new__(
66 meta_subject, *args, _parent=_parent, _key=_key, **kwargs
67 )
68 instance._config_pos_init = getattr(instance, "_config_pos_init", False)
69 # Call the end user's __init__ with the rewritten arguments, if one is defined
File ~/.local/lib/python3.10/site-packages/bsb/config/_make.py:218, in compile_new.<locals>.__new__(_cls, _parent, _key, *args, **kwargs)
216 if root:
217 instance._config_isfinished = False
--> 218 instance.__post_new__(**kwargs)
219 if _cls is not ncls:
220 instance.__init__(*args, **kwargs)
File ~/.local/lib/python3.10/site-packages/bsb/config/_make.py:288, in compile_postnew.<locals>.__post_new__(self, _parent, _key, **kwargs)
286 attr.flag_pristine(self)
287 else:
--> 288 setattr(self, name, value)
289 attr.flag_dirty(self)
290 for key, value in leftovers.items():
File ~/.local/lib/python3.10/site-packages/bsb/config/_attrs.py:653, in ConfigurationListAttribute.__set__(self, instance, value, _key)
652 def __set__(self, instance, value, _key=None):
--> 653 _setattr(instance, self.attr_name, self.fill(value, _parent=instance))
File ~/.local/lib/python3.10/site-packages/bsb/config/_attrs.py:666, in ConfigurationListAttribute.fill(self, value, _parent, _key)
664 _cfglist._elem_type = self.child_type
665 if isinstance(value, builtins.dict):
--> 666 raise CastError(f"Dictionary `{value}` given where list is expected.")
667 _cfglist.extend(value or builtins.list())
668 if self.size is not None and len(_cfglist) != self.size:
CastError: Dictionary `<parsed json config '{'V_m': -70.0}' at '/simulations/prova/cell_models/B/parameters'>` given where list is expected. in {root}.simulations.prova.cell_models.BHi! The public documentation is definitely outdated, I think you can just change parameters to constants. In the new simulation features parameters is a list of Parameter, which can map generated BSB data to properties for the individual NEST nodes. When you set Vm for the entire node collection, it's considered a constant that you'd put in constants. Hope this helps.
Helveg
commented
10 months ago @LorenzoDeToni just checking in if everything is running smoothly now? Keep in mind that this is all very new stuff, and if you need any missing component, just open an issue with a feature request, or ask a question on StackOverflow tagged with bsb-framework and I'll make sure to reply and help out wherever I can 😄
LorenzoDeToni
commented
10 months ago Hi Robin, thank for your help, yes now everything it's ok and the simulation is running, but I've a problem in the visualisation of the result of the device, I don't know how to open the hdf5 file, do you have any suggest?
Helveg
commented
10 months ago The .hdf5 file is the network reconstruction file; it contains the cell positions, morphologies, connections, ... The simulation results should be stored in a .nio file.
from bsb.core import from_storage
my_network = from_storage("my_file.hdf5")from neo.io import NixIO
data = NixIO("my_file.nio").read()Each library contains their own functions that you can use to read the data. For the BSB (which can get you the structural data), try playing around with the my_network.get_placement_set("my_cell_type"), it has a .load_positions(), load_rotations, load_morphologies function. There's also the my_network.get_connectivity_set("my_conn_type").load_connections().all()
For Neo you can read their docs, they have a very consistent data model, the data should be in .blocks[0].segments[0].spiketrains or .blocks[0].segments[0].analogsignals
Helveg
commented
10 months ago Since you no longer face any technical issues, I'll close this thread, and we can continue in a question/answer format on StackOverflow! That way the questions and answers are easily publicly available to everyone! I will transcribe your questions there and post example links here for future reference.
(Make sure to tag your question with the bsb-framework tag, then I receive an email notification)
Helveg
commented
10 months ago I have transcribed your last comment as 2 separate questions on StackOverflow:
I'm trying to create a new network, I wrote the .json file. In Python I write:
I expected to get the simulation of the network but I stumbled in an error like is reported in the image.