Merge pull request #7 from BlueBrain/som-val

Add somatic validation's feature extraction notebook
BlueBrain · Nov 8, 2022 · 15ceda6 · 15ceda6
2 parents 63c07d0 + 4d5cd88
commit 15ceda6
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Showing 155 changed files with 5,838 additions and 4 deletions.
diff --git a/.github/workflows/python-app.yml b/.github/workflows/python-app.yml
@@ -80,6 +80,23 @@ jobs:
         nrnivmodl mechanisms
         pytest -sx tests
 
+  somatic-validation:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v3
+      with:
+        python-version: "3.9"
+
+    - name: Test somatic validation
+      run: |
+        pip install -r test-requirements.txt
+        cd somatic_validation
+        pip install -r requirements.txt
+        pytest -sx tests
+
   code-style:
     runs-on: ubuntu-latest
     steps:

diff --git a/.gitignore b/.gitignore
@@ -16,4 +16,6 @@ model_management/mm_run_minimal/output_select
 model_management/mm_run_minimal/tests/tmp
 model_management/mm_run_minimal/tests/output
 model_management/mm_run_minimal/tests/output_select
+somatic_validation/L5PC
+somatic_validation/test_L5PC
 *.DS_Store
diff --git a/feature_extraction/feature-extraction.ipynb b/feature_extraction/feature-extraction.ipynb
@@ -23,7 +23,6 @@
     "import bluepyefe as bpefe\n",
     "import matplotlib.pyplot as plt\n",
     "from matplotlib.ticker import FormatStrFormatter\n",
-    "import numpy as np\n",
     "import pandas as pd\n",
     "import seaborn as sns\n",
     "\n",
@@ -1300,7 +1299,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3.9.12 ('sscx-paper')",
+   "display_name": "Python 3.9.7 ('py39-somatic-val')",
    "language": "python",
    "name": "python3"
   },
@@ -1314,12 +1313,12 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.12"
+   "version": "3.9.7"
   },
   "orig_nbformat": 4,
   "vscode": {
    "interpreter": {
-    "hash": "6b7b36ee16605864c8799b6b622a0b2f53fcdf7a7a694fd87b195fb2c2f0d792"
+    "hash": "01b95f356d58c0c62b01251923e22f925a6781b57cb9d5803cbdeff6a4cbb07f"
    }
   }
  },

diff --git a/feature_extraction/input-traces/C060109A1-SR-C1/X_APThreshold_ch0_254.ibw b/feature_extraction/input-traces/C060109A1-SR-C1/X_APThreshold_ch0_254.ibw
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diff --git a/feature_extraction/input-traces/C070109A4-C1/exp_sAHP_ch1_97.ibw b/feature_extraction/input-traces/C070109A4-C1/exp_sAHP_ch1_97.ibw
diff --git a/feature_extraction/input-traces/C070109A4-C1/exp_sAHP_ch1_98.ibw b/feature_extraction/input-traces/C070109A4-C1/exp_sAHP_ch1_98.ibw
diff --git a/feature_extraction/input-traces/C070109A4-C1/exp_sAHP_ch1_99.ibw b/feature_extraction/input-traces/C070109A4-C1/exp_sAHP_ch1_99.ibw
diff --git a/feature_extraction/input-traces/C080501A5-SR-C1/exp_APThreshold_ch0_857.ibw b/feature_extraction/input-traces/C080501A5-SR-C1/exp_APThreshold_ch0_857.ibw
diff --git a/feature_extraction/input-traces/C080501A5-SR-C1/exp_APThreshold_ch0_858.ibw b/feature_extraction/input-traces/C080501A5-SR-C1/exp_APThreshold_ch0_858.ibw
diff --git a/feature_extraction/input-traces/C080501A5-SR-C1/exp_APThreshold_ch0_859.ibw b/feature_extraction/input-traces/C080501A5-SR-C1/exp_APThreshold_ch0_859.ibw
diff --git a/feature_extraction/input-traces/C080501A5-SR-C1/exp_APThreshold_ch1_857.ibw b/feature_extraction/input-traces/C080501A5-SR-C1/exp_APThreshold_ch1_857.ibw
diff --git a/feature_extraction/input-traces/C080501A5-SR-C1/exp_APThreshold_ch1_858.ibw b/feature_extraction/input-traces/C080501A5-SR-C1/exp_APThreshold_ch1_858.ibw
diff --git a/feature_extraction/input-traces/C080501A5-SR-C1/exp_APThreshold_ch1_859.ibw b/feature_extraction/input-traces/C080501A5-SR-C1/exp_APThreshold_ch1_859.ibw
diff --git a/feature_extraction/input-traces/C080501A5-SR-C1/exp_IDhyperpol_ch0_954.ibw b/feature_extraction/input-traces/C080501A5-SR-C1/exp_IDhyperpol_ch0_954.ibw
diff --git a/feature_extraction/input-traces/C080501A5-SR-C1/exp_IDhyperpol_ch0_955.ibw b/feature_extraction/input-traces/C080501A5-SR-C1/exp_IDhyperpol_ch0_955.ibw
diff --git a/feature_extraction/input-traces/C080501A5-SR-C1/exp_IDhyperpol_ch0_956.ibw b/feature_extraction/input-traces/C080501A5-SR-C1/exp_IDhyperpol_ch0_956.ibw
diff --git a/feature_extraction/input-traces/C080501A5-SR-C1/exp_IDhyperpol_ch1_954.ibw b/feature_extraction/input-traces/C080501A5-SR-C1/exp_IDhyperpol_ch1_954.ibw
diff --git a/feature_extraction/input-traces/C080501A5-SR-C1/exp_IDhyperpol_ch1_955.ibw b/feature_extraction/input-traces/C080501A5-SR-C1/exp_IDhyperpol_ch1_955.ibw
diff --git a/feature_extraction/input-traces/C080501A5-SR-C1/exp_IDhyperpol_ch1_956.ibw b/feature_extraction/input-traces/C080501A5-SR-C1/exp_IDhyperpol_ch1_956.ibw
diff --git a/feature_extraction/input-traces/C080501A5-SR-C1/exp_sAHP_ch0_929.ibw b/feature_extraction/input-traces/C080501A5-SR-C1/exp_sAHP_ch0_929.ibw
diff --git a/feature_extraction/input-traces/C080501A5-SR-C1/exp_sAHP_ch0_930.ibw b/feature_extraction/input-traces/C080501A5-SR-C1/exp_sAHP_ch0_930.ibw
diff --git a/feature_extraction/input-traces/C080501A5-SR-C1/exp_sAHP_ch0_931.ibw b/feature_extraction/input-traces/C080501A5-SR-C1/exp_sAHP_ch0_931.ibw
diff --git a/feature_extraction/input-traces/C080501A5-SR-C1/exp_sAHP_ch0_932.ibw b/feature_extraction/input-traces/C080501A5-SR-C1/exp_sAHP_ch0_932.ibw
diff --git a/feature_extraction/input-traces/C080501A5-SR-C1/exp_sAHP_ch0_933.ibw b/feature_extraction/input-traces/C080501A5-SR-C1/exp_sAHP_ch0_933.ibw
diff --git a/feature_extraction/input-traces/C080501A5-SR-C1/exp_sAHP_ch0_934.ibw b/feature_extraction/input-traces/C080501A5-SR-C1/exp_sAHP_ch0_934.ibw
diff --git a/feature_extraction/input-traces/C080501A5-SR-C1/exp_sAHP_ch1_929.ibw b/feature_extraction/input-traces/C080501A5-SR-C1/exp_sAHP_ch1_929.ibw
diff --git a/feature_extraction/input-traces/C080501A5-SR-C1/exp_sAHP_ch1_930.ibw b/feature_extraction/input-traces/C080501A5-SR-C1/exp_sAHP_ch1_930.ibw
diff --git a/feature_extraction/input-traces/C080501A5-SR-C1/exp_sAHP_ch1_931.ibw b/feature_extraction/input-traces/C080501A5-SR-C1/exp_sAHP_ch1_931.ibw
diff --git a/feature_extraction/input-traces/C080501A5-SR-C1/exp_sAHP_ch1_932.ibw b/feature_extraction/input-traces/C080501A5-SR-C1/exp_sAHP_ch1_932.ibw
diff --git a/feature_extraction/input-traces/C080501A5-SR-C1/exp_sAHP_ch1_933.ibw b/feature_extraction/input-traces/C080501A5-SR-C1/exp_sAHP_ch1_933.ibw
diff --git a/feature_extraction/input-traces/C080501A5-SR-C1/exp_sAHP_ch1_934.ibw b/feature_extraction/input-traces/C080501A5-SR-C1/exp_sAHP_ch1_934.ibw
diff --git a/feature_extraction/input-traces/C080501B2-SR-C1/exp_APThreshold_ch0_857.ibw b/feature_extraction/input-traces/C080501B2-SR-C1/exp_APThreshold_ch0_857.ibw
diff --git a/feature_extraction/input-traces/C080501B2-SR-C1/exp_APThreshold_ch0_858.ibw b/feature_extraction/input-traces/C080501B2-SR-C1/exp_APThreshold_ch0_858.ibw
diff --git a/feature_extraction/input-traces/C080501B2-SR-C1/exp_APThreshold_ch0_859.ibw b/feature_extraction/input-traces/C080501B2-SR-C1/exp_APThreshold_ch0_859.ibw
diff --git a/feature_extraction/input-traces/C080501B2-SR-C1/exp_APThreshold_ch1_857.ibw b/feature_extraction/input-traces/C080501B2-SR-C1/exp_APThreshold_ch1_857.ibw
diff --git a/feature_extraction/input-traces/C080501B2-SR-C1/exp_APThreshold_ch1_858.ibw b/feature_extraction/input-traces/C080501B2-SR-C1/exp_APThreshold_ch1_858.ibw
diff --git a/feature_extraction/input-traces/C080501B2-SR-C1/exp_APThreshold_ch1_859.ibw b/feature_extraction/input-traces/C080501B2-SR-C1/exp_APThreshold_ch1_859.ibw
diff --git a/feature_extraction/input-traces/C080501B2-SR-C1/exp_IDhyperpol_ch0_956.ibw b/feature_extraction/input-traces/C080501B2-SR-C1/exp_IDhyperpol_ch0_956.ibw
diff --git a/feature_extraction/input-traces/C080501B2-SR-C1/exp_IDhyperpol_ch0_957.ibw b/feature_extraction/input-traces/C080501B2-SR-C1/exp_IDhyperpol_ch0_957.ibw
diff --git a/feature_extraction/input-traces/C080501B2-SR-C1/exp_IDhyperpol_ch0_958.ibw b/feature_extraction/input-traces/C080501B2-SR-C1/exp_IDhyperpol_ch0_958.ibw
diff --git a/feature_extraction/input-traces/C080501B2-SR-C1/exp_IDhyperpol_ch1_956.ibw b/feature_extraction/input-traces/C080501B2-SR-C1/exp_IDhyperpol_ch1_956.ibw
diff --git a/feature_extraction/input-traces/C080501B2-SR-C1/exp_IDhyperpol_ch1_957.ibw b/feature_extraction/input-traces/C080501B2-SR-C1/exp_IDhyperpol_ch1_957.ibw
diff --git a/feature_extraction/input-traces/C080501B2-SR-C1/exp_IDhyperpol_ch1_958.ibw b/feature_extraction/input-traces/C080501B2-SR-C1/exp_IDhyperpol_ch1_958.ibw
diff --git a/feature_extraction/input-traces/C080501B2-SR-C1/exp_sAHP_ch0_931.ibw b/feature_extraction/input-traces/C080501B2-SR-C1/exp_sAHP_ch0_931.ibw
diff --git a/feature_extraction/input-traces/C080501B2-SR-C1/exp_sAHP_ch0_932.ibw b/feature_extraction/input-traces/C080501B2-SR-C1/exp_sAHP_ch0_932.ibw
diff --git a/feature_extraction/input-traces/C080501B2-SR-C1/exp_sAHP_ch0_933.ibw b/feature_extraction/input-traces/C080501B2-SR-C1/exp_sAHP_ch0_933.ibw
diff --git a/feature_extraction/input-traces/C080501B2-SR-C1/exp_sAHP_ch0_934.ibw b/feature_extraction/input-traces/C080501B2-SR-C1/exp_sAHP_ch0_934.ibw
diff --git a/feature_extraction/input-traces/C080501B2-SR-C1/exp_sAHP_ch0_935.ibw b/feature_extraction/input-traces/C080501B2-SR-C1/exp_sAHP_ch0_935.ibw
diff --git a/feature_extraction/input-traces/C080501B2-SR-C1/exp_sAHP_ch0_936.ibw b/feature_extraction/input-traces/C080501B2-SR-C1/exp_sAHP_ch0_936.ibw
diff --git a/feature_extraction/input-traces/C080501B2-SR-C1/exp_sAHP_ch1_931.ibw b/feature_extraction/input-traces/C080501B2-SR-C1/exp_sAHP_ch1_931.ibw
diff --git a/feature_extraction/input-traces/C080501B2-SR-C1/exp_sAHP_ch1_932.ibw b/feature_extraction/input-traces/C080501B2-SR-C1/exp_sAHP_ch1_932.ibw
diff --git a/feature_extraction/input-traces/C080501B2-SR-C1/exp_sAHP_ch1_933.ibw b/feature_extraction/input-traces/C080501B2-SR-C1/exp_sAHP_ch1_933.ibw
diff --git a/feature_extraction/input-traces/C080501B2-SR-C1/exp_sAHP_ch1_934.ibw b/feature_extraction/input-traces/C080501B2-SR-C1/exp_sAHP_ch1_934.ibw
diff --git a/feature_extraction/input-traces/C080501B2-SR-C1/exp_sAHP_ch1_935.ibw b/feature_extraction/input-traces/C080501B2-SR-C1/exp_sAHP_ch1_935.ibw
diff --git a/feature_extraction/input-traces/C080501B2-SR-C1/exp_sAHP_ch1_936.ibw b/feature_extraction/input-traces/C080501B2-SR-C1/exp_sAHP_ch1_936.ibw
diff --git a/somatic_validation/__init__.py b/somatic_validation/__init__.py
diff --git a/somatic_validation/experiments.json b/somatic_validation/experiments.json
@@ -0,0 +1,121 @@
+{
+    "IDRest": {
+        "location": "soma.v",
+        "tolerances": [
+            20.0
+        ],
+        "targets": [
+            120
+        ],
+        "efeatures": [
+            "Spikecount",
+            "AP_amplitude",
+            "ISI_values"
+        ]
+    },
+    "IDthresh": {
+        "location": "soma.v",
+        "tolerances": [
+            20.0
+        ],
+        "targets": [
+            120
+        ],
+        "efeatures": [
+            "Spikecount",
+            "AP_amplitude",
+            "ISI_values"
+        ]
+    },
+    "IDhyperpol": {
+        "location": "soma.v",
+        "tolerances": [
+            20.0
+        ],
+        "targets": [
+            150,
+            170,
+            200,
+            220,
+            250,
+            270,
+            300,
+            350
+        ],
+        "efeatures": [
+            "Spikecount",
+            "AP_amplitude",
+            "ISI_values",
+            "AP_height",
+            "ISI_log_slope",
+            "sag_amplitude",
+            "sag_ratio1",
+            "minimum_voltage",
+            "steady_state_voltage_stimend"
+        ]
+    },
+    "sAHP": {
+        "location": "soma.v",
+        "tolerances": [
+            20.0
+        ],
+        "targets": [
+            150,
+            170,
+            200,
+            220,
+            250,
+            270,
+            300,
+            350
+        ],
+        "efeatures": [
+            "Spikecount",
+            "AP_amplitude",
+            "inv_first_ISI",
+            "AP_height",
+            "inv_time_to_first_spike",
+            "decay_time_constant_after_stim",
+            "AHP_depth_abs",
+            "sag_amplitude",
+            "sag_ratio1",
+            "steady_state_voltage",
+            "minimum_voltage",
+            "steady_state_voltage_stimend"
+        ]
+    },
+    "APThreshold": {
+        "location": "soma.v",
+        "tolerances": [
+            20.0
+        ],
+        "targets": [
+            100,
+            130,
+            150,
+            170,
+            200,
+            220,
+            250,
+            270,
+            300,
+            330,
+            360,
+            390,
+            400,
+            430,
+            460,
+            500,
+            530
+        ],
+        "efeatures": [
+            "Spikecount",
+            "AP_amplitude",
+            "inv_time_to_first_spike",
+            "ISI_log_slope",
+            "ISI_CV",
+            "AP1_amp",
+            "APlast_amp"
+        ]
+    }
+}