Merge pull request #116 from alejoe91/fix_scipy

Remove decimate for instability

Author: alejoe91

MEArec/generators/recgensteps.py

@@ -6,8 +6,8 @@
 
 Important:
 
-When tmp_mode=='memmap' : theses functions must assign and add directly the buffer.
-When tmp_mode is Noe : theses functions return the buffer and the assignament is done externally.
+When tmp_mode=='memmap' : these functions must assign and add directly the buffer.
+When tmp_mode is None : these functions return the buffer and the assignament is done externally.
 
 
 

MEArec/generators/recordinggenerator.py

@@ -1,5 +1,6 @@
 # don't enter here without a good guide! (only one person in the world)
 
+from distutils.log import DEBUG
 import numpy as np
 import time
 from copy import deepcopy
@@ -34,9 +35,9 @@
     use_loader = False
 
 
-debug = True
+DEBUG = False
 
-if debug:
+if DEBUG:
     import matplotlib.pyplot as plt
     plt.ion()
     plt.show()
@@ -315,11 +316,14 @@ def generate_recordings(self, tmp_mode=None, tmp_folder=None, n_jobs=0, template
         else:
             params['recordings']['dtype'] = rec_params['dtype']
         dtype = params['recordings']['dtype']
+        
+        assert np.dtype(dtype).kind in ("i", "f"), "Only integers and float dtypes are supported"
+        
         params['recordings']['adc_bit_depth'] = rec_params.get('adc_bit_depth', None)
         adc_bit_depth = params['recordings']['adc_bit_depth']
         params['recordings']['lsb'] = rec_params.get('lsb', None)
         lsb = params['recordings']['lsb']
-        if lsb is None:
+        if lsb is None and np.dtype(dtype).kind == "i":
             lsb = 1
         params['recordings']['gain'] = rec_params.get('gain', None)
         gain = params['recordings']['gain']
@@ -1380,8 +1384,6 @@ def run_several_chunks(func, chunk_indexes, fs, lsb, args, n_jobs, tmp_mode, ass
     or in paralell if n_jobs>1
     
     The function can return
-    
-    
     """
 
     # create task list

MEArec/tests/test_generators.py

@@ -17,7 +17,12 @@
 else:
     use_loader = False
 
-LOCAL_TMP = True
+DEBUG = False
+
+if DEBUG:
+    import matplotlib.pyplot as plt
+    plt.ion()
+    plt.show()
 
 
 class TestGenerators(unittest.TestCase):
@@ -36,7 +41,7 @@ def setUpClass(self):
         # Set seed
         np.random.seed(2308)
 
-        if not LOCAL_TMP:
+        if not DEBUG:
             self.test_dir = Path(tempfile.mkdtemp())
         else:
             self.test_dir = Path('./tmp').absolute()
@@ -100,7 +105,7 @@ def setUpClass(self):
     @classmethod
     def tearDownClass(self):
         # Remove the directory after the test
-        if not LOCAL_TMP:
+        if not DEBUG:
             shutil.rmtree(self.test_dir)
 
     def test_gen_templates(self):
@@ -693,28 +698,30 @@ def test_recordings_backend(self):
         rec_params['spiketrains']['n_exc'] = ne
         rec_params['spiketrains']['n_inh'] = ni
         rec_params['spiketrains']['duration'] = duration
-        n_jitter = 2
+        n_jitter = 10
         rec_params['templates']['n_jitters'] = n_jitter
         rec_params['recordings']['modulation'] = 'none'
+        rec_params['recordings']['filter'] = False
+
 
         rec_params['seeds']['templates'] = 0
         rec_params['seeds']['spiketrains'] = 0
         rec_params['seeds']['convolution'] = 0
         rec_params['seeds']['noise'] = 0
 
+
         n_jobs = [1, 2]
         chunk_durations = [0, 1]
 
         for n in n_jobs:
             for ch in chunk_durations:
                 print('Test recording backend with', n, 'jobs - chunk', ch)
-                rec_params['chunk_duration'] = n
+                rec_params['recordings']['chunk_duration'] = ch
 
                 recgen_memmap = mr.gen_recordings(params=rec_params, tempgen=self.tempgen, tmp_mode='memmap',
                                                   verbose=False, n_jobs=n)
                 recgen_np = mr.gen_recordings(params=rec_params, tempgen=self.tempgen, tmp_mode=None, verbose=False,
                                               n_jobs=n)
-
                 assert np.allclose(np.array(recgen_np.recordings), recgen_memmap.recordings.copy(), atol=1e-4)
                 del recgen_memmap, recgen_np
 
@@ -955,4 +962,4 @@ def test_simulate_cell(self):
     TestGenerators().setUpClass()
     # TestGenerators().test_gen_recordings_drift()
     # TestGenerators().test_default_params()
-    TestGenerators().test_recording_custom_drifts()
+    TestGenerators().test_recordings_backend()

MEArec/tools.py

@@ -3457,7 +3457,7 @@ def _jitter_parallel(i, template, upsample, fs, n_jitters, jitter, drifting, ver
                 t_jitt = np.pad(temp_up, [(0, 0), (0, np.abs(shift))], 'constant')[:, -nsamples_up:]
             else:
                 t_jitt = temp_up
-            temp_down = ss.decimate(t_jitt, upsample, axis=1)
+            temp_down = t_jitt[:, ::upsample]
             templates_jitter[n] = temp_down
     else:
         if verbose:

MEArec/version.py

@@ -1 +1 @@
-version = '1.8.0.dev0'
+version = '1.8.0'