ECP module not recording consistently

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Assessment

Difficulty
4/5
Estimated time
3-5 days
Newbie friendliness
30/100
Issue type
Bug
Clarity
Needs clarification
Activity status
Stale
Tech stack
python
Domain
data

Research direction

Start with the ECP configurations in the issue and the Python h5py comparison of ecp_pv1.h5 and ecp_pv2.h5. Reproduce the two recordings using identical settings, then inspect the ECP recording path and determine why repeated recordings differ; done means the inconsistency is explained and the repeated outputs behave consistently.

Written by the indexing model from the issue text.

Description

I am recording a biophysical model's ECP using the ECP module

  "reports": {
    "ecp1": {
      "cells": {"pop_name": "PV"},
      "variable_name": "v",
      "module": "extracellular",
      "tmp_dir": "$OUTPUT_DIR",
      "electrode_positions": "$COMPONENTS_DIR/recXelectrodes/linear_electrode.csv",
      "file_name": "ecp_pv1.h5",
      "electrode_channels": "all",
      "contributions_dir": "ecp_pv1"
      },
    "ecp2": {
      "cells": {"pop_name": "PV"},
      "variable_name": "v",
      "module": "extracellular",
      "tmp_dir": "$OUTPUT_DIR",
      "electrode_positions": "$COMPONENTS_DIR/recXelectrodes/linear_electrode.csv",
      "file_name": "ecp_pv2.h5",
      "electrode_channels": "all",
      "contributions_dir": "ecp_pv2"
      },
    "ecp3": {
      "cells": "all",
      "variable_name": "v",
      "module": "extracellular",
      "tmp_dir": "$OUTPUT_DIR",
      "electrode_positions": "$COMPONENTS_DIR/recXelectrodes/linear_electrode.csv",
      "file_name": "ecp_all1.h5",
      "electrode_channels": "all",
      "contributions_dir": "ecp_all1"
      },
    "ecp4": {
      "cells": "all",
      "variable_name": "v",
      "module": "extracellular",
      "tmp_dir": "$OUTPUT_DIR",
      "electrode_positions": "$COMPONENTS_DIR/recXelectrodes/linear_electrode.csv",
      "file_name": "ecp_all2.h5",
      "electrode_channels": "all",
      "contributions_dir": "ecp_all2"
      }
  },

Then when I compare either the two ECPs that recorded only PV cells or the two ECPs that recorded all cells the signal is different. The signal looks largely the same but once closes examined it's clear that it is different. To analysis the output I did

import h5py
import matplotlib.pyplot as plt
%matplotlib inline

path1  = "outputECP1/ecp_pv1.h5"
path2 = "outputECP1/ecp_pv2.h5"

f1 = h5py.File(path1)
f2 = h5py.File(path2)

fig, ax = plt.subplots(2,1,figsize=(15,4.8))
ax[0].plot(f1["ecp/data"][:])
ax[0].title.set_text("PV recording 1")
ax[0].set_xlim(4000,5000)
ax[1].plot(f2["ecp/data"][:])
ax[1].title.set_text("PV recording 2")
ax[1].set_xlim(4000,5000)

plt.show()

The result was

output

You can see that the signals are different when they recorded the same thing.

Dominant language
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Merged PRs (30d)
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