alejoe91
commented
4 years ago HI @paglabhola
I think there is probably some issues with NEURON or LFPy. The output should print the templates that are being simulated:
Cell: L5_LBC_bAC217_1 Progress: [3/30]
Cell: L5_SBC_bNAC219_1 Progress: [6/30]
Cell: L5_ChC_cACint209_1 Progress: [10/30]
Cell: L5_STPC_cADpyr232_1 Progress: [8/30]
Cell: L5_UTPC_cADpyr232_1 Progress: [5/30]
Cell: L5_TTPC2_cADpyr232_1 Progress: [4/30]
Cell: L5_TTPC1_cADpyr232_1 Progress: [3/30]
Cell: L5_SBC_bNAC219_1 Progress: [7/30]
Cell: L5_STPC_cADpyr232_1 Progress: [9/30]
Cell: L5_SBC_bNAC219_1 Progress: [8/30]
Cell: L5_DBC_bAC217_1 Progress: [11/30]
Cell: L5_ChC_cACint209_1 Progress: [11/30]
Cell: L5_MC_bAC217_1 Progress: [7/30]
Cell: L5_DBC_bAC217_1 Progress: [12/30]
Cell: L5_UTPC_cADpyr232_1 Progress: [6/30]
Cell: L5_BTC_bAC217_1 Progress: [9/30]
Cell: L5_MC_bAC217_1 Progress: [8/30]
Cell: L5_ChC_cACint209_1 Progress: [12/30]
Cell: L5_TTPC2_cADpyr232_1 Progress: [5/30]but it doesn't show in your output. Also the simulation should take ~20 minutes, and you output shows that it only took 0.76 s. The templates were not correctly simulated.
What is the output of running mearec default-config from terminal?
paglabhola
espenhgn
Code run and error obtained are given below. It seems that temporary template files are not getting generated resulting in: FileNotFoundError: [Errno 2] No such file or directory: '/home/neuroelectronics/.config/spyder-py3/physrot/tmp_30_Neuronexus-32' Kindly help me to resolve this issue.
Code Run: import MEArec as mr import MEAutility
generate templates
templates_params = mr.get_default_templates_params() cell_models_folder = mr.get_default_cell_models_folder()
templates_params['probe']='Neuronexus-32' templates_params['n']=30 templates_params['seed']=0 tempgen = mr.gen_templates(cell_models_folder=cell_models_folder, params= templates_params, verbose=True, delete_tmp=True)
mr.save_template_generator(tempgen, '/home/neuroelectronics/path_to_templates.h5')
generate recordings
recordings_params= mr.get_default_recordings_params() recordings_params['spiketrains']['n_exc'] = 4 recordings_params['spiketrains']['n_inh'] = 2 recordings_params['spiketrains']['duration'] = 30 recordings_params['spiketrains']['seed'] = 0 recordings_params['templates']['seed'] = 1 recordings_params['recordings']['seed'] = 2
recgen= mr.gen_recordings(params=recordings_params, templates='path_to_templates.h5') mr.save_recording_generator(recgen,'path_to_recordings.h5')
Error Obtained:
runfile('/home/neuroelectronics/.config/spyder-py3/temp.py', wdir='/home/neuroelectronics/.config/spyder-py3') Compiling NEURON models Starting 1
Starting 2 L5_TTPC2_cADpyr232_1 1 / 13
L5_NGC_bNAC219_1 2 / 13
Starting 3
L5_TTPC1_cADpyr232_1 3 / 13
Starting 4
Starting 5 L5_STPC_cADpyr232_1 4 / 13
Starting 6
L5_SBC_bNAC219_1 5 / 13
L5_BP_bAC217_1 6 / 13
Starting 8 Starting 7
L5_DBC_bAC217_1 8 / 13
Starting 9 Starting 11 L5_NBC_bAC217_1 7 / 13
Starting 10
L5_BTC_bAC217_1 11 / 13
L5_MC_bAC217_1 10 / 13
Starting 13
Starting 12 L5_UTPC_cADpyr232_1 13 / 13
L5_ChC_cACint209_1 9 / 13
L5_LBC_bAC217_1 12 / 13
Exiting 1 Exiting 2 Exiting 3 Exiting 7 Exiting 5 Exiting 8 Exiting 4 Exiting 6 Exiting 13 Exiting 10 Exiting 11 Exiting 12 Exiting 9
Simulation time: 0.7660350799560547
Traceback (most recent call last):
File "", line 1, in
runfile('/home/neuroelectronics/.config/spyder-py3/temp.py', wdir='/home/neuroelectronics/.config/spyder-py3')
File "/usr/lib/python3/dist-packages/spyder/utils/site/sitecustomize.py", line 705, in runfile execfile(filename, namespace)
File "/usr/lib/python3/dist-packages/spyder/utils/site/sitecustomize.py", line 102, in execfile exec(compile(f.read(), filename, 'exec'), namespace)
File "/home/neuroelectronics/.config/spyder-py3/temp.py", line 18, in
tempgen = mr.gen_templates(cell_models_folder=cell_models_folder, params= templates_params, verbose=True, delete_tmp=True)
File "/usr/local/lib/python3.6/dist-packages/MEArec/generation_tools.py", line 198, in gen_templates tempgen.generate_templates()
File "/usr/local/lib/python3.6/dist-packages/MEArec/generators/templategenerator.py", line 188, in generate_templates templates, locations, rotations, celltypes = load_tmp_eap(tmp_folder)
File "/usr/local/lib/python3.6/dist-packages/MEArec/tools.py", line 148, in load_tmp_eap eaplist = [f for f in os.listdir(templates_folder) if f.startswith('eap')]
FileNotFoundError: [Errno 2] No such file or directory: '/home/neuroelectronics/.config/spyder-py3/physrot/tmp_30_Neuronexus-32'