Add a new test for sAHP extraction (#163)

.gitignore

@@ -14,3 +14,5 @@ test_run
 MouseCells/
 .ipynb_checkpoints/
 coverage.xml
+MouseCells_sAHP/
+tests/exp_data/X/

setup.py

@@ -34,7 +34,7 @@
     "the eFel library. BluePyEfe outputs protocols and features files in a "
     "format that can then be used by BluePyOpt for electrical model building "
     "purposes.",
-    packages=setuptools.find_packages(),
+    packages=setuptools.find_packages(exclude=["tests"]),
     python_requires=">=3.8",
     include_package_data=True,
     author="BlueBrain Project, EPFL",

tests/test_extractor.py

@@ -6,6 +6,7 @@
 
 import bluepyefe.extract
 import bluepyefe.tools
+from tests.utils import download_sahp_datafiles
 
 
 def get_config(absolute_amplitude=False):
@@ -74,6 +75,74 @@ def get_config(absolute_amplitude=False):
 
     return files_metadata, bluepyefe.extract.convert_legacy_targets(targets)
 
+def get_sahp_config(absolute_amplitude=False):
+    download_sahp_datafiles()
+
+    interesting_efeatures = {
+        "Spikecount": {},
+        "mean_frequency": {},
+        "ISI_CV": {},
+        "AP1_amp": {},
+        "AP_width": {},
+    }
+
+    files_metadata1 = []
+    for file in glob.glob("./tests/exp_data/X/X_sAHP_ch0_*.ibw"):
+        files_metadata1.append(
+            {
+                "i_file": file,
+                "v_file": file.replace("ch0", "ch1"),
+                "i_unit": "A",
+                "v_unit": "V",
+                "t_unit": "s",
+                "dt": 0.00025,
+                "ljp": 14,
+                "ton": 10,
+                "tmid": 260,
+                "tmid2": 360,
+                "toff": 1360,
+            }
+        )
+    files_metadata2 = []
+    for file in glob.glob("./tests/exp_data/X/X_IDthresh_ch0_*.ibw"):
+        files_metadata2.append(
+            {
+                "i_file": file,
+                "v_file": file.replace("ch0", "ch1"),
+                "i_unit": "A",
+                "v_unit": "V",
+                "t_unit": "s",
+                "dt": 0.00025,
+                "ljp": 14,
+            }
+        )
+
+    files_metadata = {
+        "MouseNeuron1": {"sAHP": files_metadata1, "IDthresh": files_metadata2},
+    }
+
+    if absolute_amplitude:
+        targets = {
+            "sAHP": {
+                "amplitudes": [0.315, 0.225, 0.5, 0.69, 0.41, 0.595],
+                "tolerances": [0.01],
+                "efeatures": interesting_efeatures,
+                "location": "soma",
+            }
+        }
+
+    else:
+        targets = {
+            "sAHP": {
+                "amplitudes": [285, 200, 450, 625, 370, 540],
+                "tolerances": [10.0],
+                "efeatures": interesting_efeatures,
+                "location": "soma",
+            }
+        }
+
+    return files_metadata, bluepyefe.extract.convert_legacy_targets(targets)
+
 
 class ExtractorTest(unittest.TestCase):
     def test_extract(self):
@@ -219,6 +288,62 @@ def test_extract_absolute(self):
             protocols = json.load(fp)
 
         self.assertEqual(len(features), len(protocols))
+
+    def test_extract_sahp(self):
+
+        files_metadata, targets = get_sahp_config()
+
+        cells = bluepyefe.extract.read_recordings(files_metadata=files_metadata)
+
+        cells = bluepyefe.extract.extract_efeatures_at_targets(
+            cells=cells, targets=targets
+        )
+
+        bluepyefe.extract.compute_rheobase(cells, protocols_rheobase=["IDthresh"])
+
+        self.assertEqual(len(cells), 1)
+        self.assertEqual(len(cells[0].recordings), 24)
+        self.assertLess(abs(cells[0].rheobase - 0.1103), 0.01)
+
+        # amplitude test for one recording
+        # sort the recordings because they can be in any order,
+        # and we want to select the same one each time we test
+        sahp_recs = [rec for rec in cells[0].recordings if rec.protocol_name == "sAHP"]
+        rec1 = sorted(sahp_recs, key=lambda x: x.amp2)[1]
+        self.assertLess(abs(rec1.amp - 0.0953), 0.01)
+        self.assertLess(abs(rec1.amp2 - 0.3153), 0.01)
+        self.assertLess(abs(rec1.amp_rel - 86.4), 0.1)
+        self.assertLess(abs(rec1.amp2_rel - 285.8), 0.1)
+
+
+        protocols = bluepyefe.extract.group_efeatures(
+            cells,
+            targets,
+            use_global_rheobase=True,
+            protocol_mode="mean"
+        )
+
+        _ = bluepyefe.extract.create_feature_protocol_files(
+            cells=cells, protocols=protocols, output_directory="MouseCells_sAHP"
+        )
+
+        for protocol in protocols:
+            if protocol.name == "sAHP" and protocol.amplitude == 625:
+                for target in protocol.feature_targets:
+                    if target.efel_feature_name == "Spikecount":
+                        self.assertEqual(target.mean, 6)
+                        break
+
+        bluepyefe.extract.plot_all_recordings_efeatures(
+            cells, protocols, output_dir="MouseCells_sAHP/"
+        )
+
+        with open("MouseCells_sAHP/features.json") as fp:
+            features = json.load(fp)
+        with open("MouseCells_sAHP/protocols.json") as fp:
+            protocols = json.load(fp)
+
+        self.assertEqual(len(features), len(protocols))
 
 
 if __name__ == "__main__":

tests/utils.py

@@ -0,0 +1,28 @@
+"""Utils"""
+
+import urllib.request
+import shutil
+from pathlib import Path
+
+
+def download_sahp_datafiles():
+    """Download data files for sAHP and IDthresh traces"""
+    output_dir = "./tests/exp_data/X/"
+    gb_url = "https://raw.githubusercontent.com/BlueBrain/SSCxEModelExamples/main/feature_extraction/input-traces/C060109A1-SR-C1/"
+    sahp_pathname = "X_sAHP"
+    sahp_ch = ["ch0", "ch1"]
+    sahp_numbers = list(range(320, 326))
+    idthresh_pathname = "X_IDthresh"
+    idthresh_ch = ["ch0", "ch1"]
+    idthresh_numbers = list(range(349, 358)) + list(range(362, 371))
+
+    sahp_paths = [f"{sahp_pathname}_{ch}_{n}.ibw" for ch in sahp_ch for n in sahp_numbers]
+    idthresh_paths = [f"{idthresh_pathname}_{ch}_{n}.ibw" for ch in idthresh_ch for n in idthresh_numbers]
+    pathnames = sahp_paths + idthresh_paths
+
+    Path(output_dir).mkdir(exist_ok=True, parents=True)
+    for pathname in pathnames:
+        output_path = f"{output_dir}{pathname}"
+        if not Path(output_path).is_file():
+            with urllib.request.urlopen(f"{gb_url}{pathname}") as response, open(output_path, "wb") as out_file:
+                shutil.copyfileobj(response, out_file)