Changeset 1034

Timestamp:

12/15/11 17:31:04 (5 months ago)

Author:

apdavison

Message:

Fixed some broken unittests in neo_output branch. Recovered recording.files as it is still needed for saving connections, positions, etc.

Location:

branches/neo_output

Files:

• src/common/projections.py (modified) (2 diffs)
• src/connectors.py (modified) (1 diff)
• src/neuron/electrodes.py (modified) (1 diff)
• src/recording/__init__.py (modified) (2 diffs)
• src/recording/files.py (copied) (copied from branches/neo_output/src/recording/files.py)
• test/unittests/test_files.py (copied) (copied from branches/neo_output/test/unittests/test_files.py)
• test/unittests/test_neuron.py (modified) (3 diffs)
• test/unittests/test_recording.py (modified) (9 diffs)
• test/unittests/test_simulation_control.py (modified) (1 diff)

branches/neo_output/src/common/projections.py

@@ -276 +276 @@
         
         if isinstance(file, basestring):
-            file = files.StandardTextFile(file, mode='w')
+            file = recording.files.StandardTextFile(file, mode='w')
         
         lines = []
@@ -309 +309 @@
         
         if isinstance(file, basestring):
-            file = files.StandardTextFile(file, mode='w')
+            file = recording.files.StandardTextFile(file, mode='w')
         
         if format == 'array':

branches/neo_output/src/connectors.py

@@ -12 +12 @@
 from pyNN import errors, common, core, random, utility, recording, descriptions
 from pyNN.space import Space
-#from pyNN.recording import files
+from pyNN.recording import files
 from pyNN.random import RandomDistribution
 from numpy import arccos, arcsin, arctan, arctan2, ceil, cos, cosh, e, exp, \

branches/neo_output/src/neuron/electrodes.py

@@ -72 +72 @@
         for iclamp in self._devices:
             iclamp.dur = value - self._start
-    stop = property(fget=lambda self: self._start,
+    stop = property(fget=lambda self: self._stop,
                     fset=_set_stop)
 

branches/neo_output/src/recording/__init__.py

@@ -50 +50 @@
         logger.warning("File %s already exists. Renaming the original file to %s_old" % (filename, filename))
 
-def gather(data):
+def gather_array(data):
     # gather 1D or 2D numpy arrays
     if MPI is None:
@@ -193 +193 @@
         data.annotate(**self.metadata)
         if gather and self._simulator.state.num_processes > 1:
-            data = recording.gather(data)
+            data = gather_array(data)
         return data
     

branches/neo_output/test/unittests/test_neuron.py

@@ -268 +268 @@
         self.cells[1]._cell.vtrace = numpy.arange(-64.0, -65.0, -0.1)
         self.cells[0]._cell.record_times = self.cells[1]._cell.record_times = numpy.arange(0.0, 1.0, 0.1)
-        vdata = self.rv._get(['v'], gather=False, filter_ids=None)
-        assert_equal(len(vdata.segments[0].analogsignals), 2)
-        assert_arrays_equal(numpy.array(vdata.segments[0].analogsignals[0]), self.cells[0]._cell.vtrace)
+        simulator.state.t = simulator.state.dt * len(self.cells[0]._cell.vtrace)
+        vdata = self.rv._get_current_segment(variables=['v'], filter_ids=None)
+        assert_equal(len(vdata.analogsignalarrays), 1)
+        assert_arrays_equal(numpy.array(vdata.analogsignalarrays[0]),
+                            numpy.vstack((self.cells[0]._cell.vtrace, self.cells[1]._cell.vtrace)).T)
         
     def test__get_spikes(self):
@@ -277 +279 @@
         self.cells[1]._cell.spike_times = numpy.arange(13.0, 23.0)
         simulator.state.t = 111.0
-        sdata = self.rs._get(['spikes'], gather=False, filter_ids=None)
-        assert_equal(len(sdata.segments[0].spiketrains), 2)
-        assert_arrays_equal(numpy.array(sdata.segments[0].spiketrains[0]), self.cells[0]._cell.spike_times)
+        sdata = self.rs._get_current_segment(variables=['spikes'], filter_ids=None)
+        assert_equal(len(sdata.spiketrains), 2)
+        assert_arrays_equal(numpy.array(sdata.spiketrains[0]), self.cells[0]._cell.spike_times)
         
     def test__get_gsyn(self):
+        self.rg.recorded['gsyn_exc'] = self.cells
         self.rg.recorded['gsyn_inh'] = self.cells
         for cell in self.cells:
@@ -290 +293 @@
             cell._cell.gsyn_trace['inhibitory_TM'] = numpy.arange(4.01, 4.0199, 0.001)
             cell._cell.record_times = self.cells[1]._cell.record_times = numpy.arange(0.0, 1.0, 0.1)
-        gdata = self.rg._get(['gsyn_inh'], gather=False, filter_ids=None)
-        assert_equal(gdata.shape, (20,4))
+        simulator.state.t = simulator.state.dt * len(cell._cell.gsyn_trace['excitatory'])
+        gdata = self.rg._get_current_segment(variables=['gsyn_exc', 'gsyn_inh'], filter_ids=None)
+        assert_equal(len(gdata.analogsignalarrays), 2)
+        assert_arrays_equal(numpy.array(gdata.analogsignalarrays[0][:,0]),
+                            cell._cell.gsyn_trace['excitatory'])
+        assert_arrays_equal(numpy.array(gdata.analogsignalarrays[1][:,0]),
+                            cell._cell.gsyn_trace['inhibitory'])
     
     def test__local_count(self):

branches/neo_output/test/unittests/test_recording.py

@@ -4 +4 @@
 import numpy
 import os
+from datetime import datetime
 from collections import defaultdict
 from pyNN.utility import assert_arrays_equal
@@ -35 +36 @@
 #def test_mpi_sum():
 
+class MockState(object):
+    def __init__(self, mpi_rank):
+        self.mpi_rank = mpi_rank
+        self.num_processes = 9
+        self.dt = 0.123
+        self.running = True
+class MockSimulator(object):
+    def __init__(self, mpi_rank):
+        self.state = MockState(mpi_rank)
+        self.recorders = set([])
+
+class MockNeoIO(object):
+    filename = "fake_file"
+    write = Mock()
+
+class MockRecorder(recording.Recorder):
+    _simulator = MockSimulator(mpi_rank=0)
+
 class MockPopulation(object):
     size = 11
@@ -41 +60 @@
     label = "mock population"
     celltype = Mock()
+    annotations = {'knights_say': 'Ni!'}
     def __len__(self):
         return self.size
@@ -58 +78 @@
         self.description = None
         self.segments = [Mock()]
+        self.rec_datetime = datetime.now()
     def annotate(self, **annotations):
         pass
@@ -63 +84 @@
 def test_Recorder_create():
     p = MockPopulation()
-    r = recording.Recorder(p)
+    r = MockRecorder(p)
     assert_equal(r.population, p)
     assert_equal(r.file, None)
@@ -70 +91 @@
 def test_Recorder_invalid_variable():
     p = MockPopulation()
-    r = recording.Recorder(p)
+    r = MockRecorder(p)
     all_ids = (MockID(0, True), MockID(1, False), MockID(2, True), MockID(3, True), MockID(4, False))
     assert_raises(errors.RecordingError,
@@ -82 +103 @@
 def test_record():
     p = MockPopulation()
-    r = recording.Recorder(p)
+    r = MockRecorder(p)
     r._record = Mock()
     assert_equal(r.recorded, defaultdict(set))
@@ -101 +122 @@
 def test_filter_recorded():
     p = MockPopulation()
-    r = recording.Recorder(p)
+    r = MockRecorder(p)
     r._record = Mock()
     all_ids = (MockID(0, True), MockID(1, False), MockID(2, True), MockID(3, True), MockID(4, False))
@@ -116 +137 @@
 def test_get():
     p = MockPopulation()
-    r = recording.Recorder(p)
-    r._simulator = MockSimulator(mpi_rank=0)
-    fake_data = MockNeoBlock()
-    r._get = Mock(return_value=fake_data)
-    r.get('spikes')
-    assert_equal(fake_data.name, p.label)
-    assert_equal(fake_data.description, p.describe())
-
-
-class MockState(object):
-    def __init__(self, mpi_rank):
-        self.mpi_rank = mpi_rank
-        self.dt = 0.123
-class MockSimulator(object):
-    def __init__(self, mpi_rank):
-        self.state = MockState(mpi_rank)
-
-class MockNeoIO(object):
-    filename = "fake_file"
-    write = Mock()
+    r = MockRecorder(p)
+    r._get_current_segment = Mock()
+    data = r.get('spikes')
+    assert_equal(data.name, p.label)
+    assert_equal(data.description, p.describe())
 
 def test_write__with_filename__compatible_output__gather__onroot():
     orig_metadata = recording.Recorder.metadata
-    recording.Recorder.metadata = {'a': 2, 'b':3}
+    #recording.Recorder.metadata = {'a': 2, 'b':3}
     p = MockPopulation()
-    r = recording.Recorder(p)
-    r._simulator = MockSimulator(mpi_rank=0)
-    fake_data = MockNeoBlock()
-    r._get = Mock(return_value=fake_data)
+    r = MockRecorder(p)
+    #fake_data = MockNeoBlock()
+    r._get_current_segment = Mock() #return_value=fake_data)
     output_io = MockNeoIO()
     r.write("spikes", file=output_io, gather=True)
-    recording.Recorder.metadata = orig_metadata
+    #recording.Recorder.metadata = orig_metadata
     output_io.write.assert_called_with(fake_data)
 
 def test_metadata_property():
     p = MockPopulation()
-    r = recording.Recorder(population=p)
-    r._simulator = MockSimulator(mpi_rank=0)
+    r = MockRecorder(p)
     assert_equal(r.metadata,
                  {'first_id': 2454, 'label': 'mock population',
                   'dt': 0.123, 'last_id': 2465, 'size': 11,
-                  'first_index': 0, 'last_index': 11})
+                  'first_index': 0, 'last_index': 11, 'knights_say': 'Ni!'})
 
 

branches/neo_output/test/unittests/test_simulation_control.py

@@ -15 +15 @@
         self.reset_called = False
         self.state = MockState()
+        self.recorders = []
     def reset(self):
         self.reset_called = True