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cnmodel/cells/tests/cell_data/bushy_guineapig-typeII-I.pk

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cnmodel/cells/tests/cell_data/dstellate_guineapig-typeI-II.pk

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cnmodel/cells/tests/cell_data/octopus_guineapig-typeII-o.pk

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cnmodel/cells/tests/cell_data/pyramidal_rat_I.pk

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cnmodel/cells/tests/cell_data/tstellate_guineapig-typeI-t.pk

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cnmodel/cells/tests/cell_data/tstellate_mouse-typeI-c.pk

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cnmodel/cells/tests/cell_data/tuberculoventral_mouse_I.pk

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cnmodel/cells/tests/test_cells.py

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+import os, pickle, pprint
+import numpy as np
+import neuron
+
+import cnmodel
+import cnmodel.cells as cells
+from cnmodel.util import UserTester, reset
+from cnmodel.protocols import IVCurve
+
+"""
+Cell-type tests
+"""
+
+
+def test_bushy():
+    reset(raiseError=False)
+    cell = cells.Bushy.create(species="guineapig", modelType="II")
+    CellTester("bushy_guineapig-typeII", cell)
+
+
+def test_bushy21():
+    reset(raiseError=False)
+    cell = cells.Bushy.create(species="guineapig", modelType="II-I")
+    CellTester("bushy_guineapig-typeII-I", cell)
+
+
+def test_bushy_mouse():
+    reset(raiseError=False)
+    cell = cells.Bushy.create(species="mouse", modelType="II")
+    CellTester("bushy-mouse-typeII", cell)
+
+
+def test_tstellate():
+    reset(raiseError=False)
+    cell = cells.TStellate.create(species="guineapig", modelType="I-c")
+    CellTester("tstellate_guineapig-typeI-c", cell)
+
+
+def test_tstellate_mouse():
+    reset(raiseError=False)
+    cell = cells.TStellate.create(species="mouse", modelType="I-c")
+    CellTester("tstellate_mouse-typeI-c", cell)
+
+
+def test_tstellatet():
+    reset(raiseError=False)
+    cell = cells.TStellate.create(species="guineapig", modelType="I-t")
+    CellTester("tstellate_guineapig-typeI-t", cell)
+
+
+# not implemented yet
+# def test_tstellatet_mouse():
+#     reset(raiseError=False)
+#     cell = cells.TStellate.create(species='mouse', modelType='I-t')
+#     CellTester('tstellate_mouse-typeI-t', cell)
+
+
+def test_dstellate():
+    reset(raiseError=False)
+    cell = cells.DStellate.create(species="guineapig", modelType="I-II")
+    CellTester("dstellate_guineapig-typeI-II", cell)
+
+
+def test_dstellate_mouse():
+    reset(raiseError=False)
+    cell = cells.DStellate.create(species="mouse", modelType="I-II")
+    CellTester("dstellate_mouse-typeI-II", cell)
+
+
+def test_octopus():
+    reset(raiseError=False)
+    cell = cells.Octopus.create(species="guineapig", modelType="II-o")
+    CellTester("octopus_guineapig-typeII-o", cell)
+
+
+def test_pyramidal():
+    reset(raiseError=False)
+    cell = cells.Pyramidal.create(species="rat", modelType="I")
+    CellTester("pyramidal_rat_I", cell)
+
+
+def test_tuberculoventral():
+    reset(raiseError=False)
+    cell = cells.Tuberculoventral.create(species="mouse", modelType="TVmouse")
+    CellTester("tuberculoventral_mouse_I", cell)
+
+
+def test_cartwheel():
+    reset(raiseError=False)
+    cell = cells.Cartwheel.create(species="mouse", modelType="I")
+    CellTester("cartwheel_rat_I", cell)
+
+
+def test_sgc_basal_middle():
+    reset(raiseError=False)
+    cell = cells.SGC.create(species="mouse", modelType="bm")
+    CellTester("SGC_rat_bm", cell)
+
+
+def test_sgc_apical():
+    reset(raiseError=False)
+    cell = cells.SGC.create(species="mouse", modelType="a")
+    CellTester("SGC_rat_a", cell)
+
+
+#
+# Supporting functions
+#
+
+
+class CellTester(UserTester):
+    data_dir = "cell_data"
+
+    def run_test(self, cell):
+        # run I/V test on cell
+        V0 = cell.find_i0(showinfo=True)
+        rmrintau = cell.compute_rmrintau(auto_initialize=False, vrange=None)
+        iv = IVCurve()
+        self.iv = iv
+        iv.run(cell.i_test_range, cell)
+        if self.audit:
+            iv.show(cell)
+
+        info = dict(
+            temp=iv.temp,
+            icmd=iv.current_cmd,
+            spikes=iv.spike_times(),
+            rmp=iv.rest_vm(),
+            rm_taum=iv.input_resistance_tau(),
+            vpeak=iv.peak_vm(),
+            vss=iv.steady_vm(),
+            rmrintau=rmrintau,
+        )
+        return info
+
+    def assert_test_info(self, *args, **kwds):
+        try:
+            super(CellTester, self).assert_test_info(*args, **kwds)
+        finally:
+            if hasattr(self, "iv") and hasattr(self.iv, "win"):
+                self.iv.win.hide()
+
+
+# def result_file(key):
+# """
+# Return a file name to be used for storing / retrieving test results
+# given *key*.
+# """
+# path = os.path.dirname(__file__)
+# return os.path.join(path, 'cell_data', key + '.pk')
+
+# def load_cell_info(key):
+# """
+# Load prior test results for *key*.
+# If there are no prior results, return None.
+# """
+# fn = result_file(key)
+# if os.path.isfile(fn):
+# return pickle.load(open(fn, 'rb'))
+# return None
+
+# def save_cell_info(info, key):
+# """
+# Store test results for *key*.
+# """
+# fn = result_file(key)
+# dirname = os.path.dirname(fn)
+# if not os.path.isdir(dirname):
+# os.mkdir(dirname)
+# pickle.dump(info, open(fn, 'wb'))
+
+
+# The following is superseeded by the built in unit tests.
+# def CellTester(key):
+# """
+# Test *cell* and raise exception if the results do not match prior
+# data.
+# """
+# audit = cnmodel.AUDIT_TESTS
+
+## run I/V test on cell
+# iv = IVCurve()
+# iv.run(cell.i_test_range, cell)
+# iv.show(cell)
+
+# try:
+# info = dict(
+# icmd=iv.current_cmd,
+# spikes=iv.spike_times(),
+# rmp=iv.rest_vm(),
+# rm=iv.input_resistance(),
+# vpeak=iv.peak_vm(),
+# vss=iv.steady_vm(),
+# )
+
+# expect = load_cell_info(key)
+
+# if expect is not None:
+
+## Check test structures are the same
+# assert len(info) == len(expect)
+# for k in info:
+# assert k in expect
+
+## Check data matches
+# for k in info:
+# if isinstance(info[k], list):
+# assert len(info[k]) == len(expect[k])
+# for i in range(len(info[k])):
+# assert np.allclose(info[k][i], expect[k][i])
+# else:
+# assert np.allclose(info[k], expect[k])
+# else:
+# if not audit:
+# raise Exception("No prior test results for cell type '%s'. "
+# "Run test.py --audit store new test data." % key)
+
+# print "\n=== New test results for %s: ===\n" % key
+# pprint.pprint(info)
+# print "Store new test results? [y/n]",
+# yn = raw_input()
+# if yn.lower().startswith('y'):
+# save_cell_info(info, key)
+# else:
+# raise Exception("Rejected test results for '%s'" % key)
+# finally:
+# iv.win.hide()