Logging cleanup diffset: Get rid of almost all calls to global logger

caiman/tests/comparison/comparison.py

@@ -23,7 +23,8 @@
 # You can log to a file using the filename parameter, or make the output more or less
 # verbose by setting level to logging.DEBUG, logging.INFO, logging.WARNING, or logging.ERROR
 
-logging.getLogger("caiman").setLevel(logging.DEBUG)
+logger = logging.getLogger("caiman")
+logger.setLevel(logging.DEBUG)
 
 import caiman as cm
 from caiman.paths import caiman_datadir
@@ -190,7 +191,7 @@ def save_with_compare(self, istruth=False, params=None, dview=None, Cn=None):
                 """
         # getting the DATA FOR COMPARISONS
         assert (params != None and self.cnmpatch != None)
-        logging.info('we need the parameters in order to save anything\n')
+        logger.info('Parameters must be set in order to save anything\n')
         # actions on the sparse matrix
         cnm = self.cnmpatch.__dict__
         cnmpatch = deletesparse(cnm)
@@ -227,15 +228,15 @@ def save_with_compare(self, istruth=False, params=None, dview=None, Cn=None):
             if os.path.exists(file_path):
                 os.remove(file_path)
             else:
-                logging.debug("nothing to remove\n")
+                logger.debug("nothing to remove\n")
             np.savez_compressed(file_path,
                                 information=information,
                                 A_full=self.comparison['cnmf_full_frame']['ourdata'][0],
                                 C_full=self.comparison['cnmf_full_frame']['ourdata'][1],
                                 A_patch=self.comparison['cnmf_on_patch']['ourdata'][0],
                                 C_patch=self.comparison['cnmf_on_patch']['ourdata'][1],
                                 rig_shifts=self.comparison['rig_shifts']['ourdata'])
-            logging.info('we now have ground truth\n')
+            logger.info('we now have ground truth\n')
             return
 
         else:                                                                                               # if not we create a comparison first
@@ -250,7 +251,7 @@ def save_with_compare(self, istruth=False, params=None, dview=None, Cn=None):
                                                                                                             # if we cannot manage to open it or it doesn't exist:
             except (IOError, OSError):
                                                                                                             # we save but we explain why there were a problem
-                logging.warning('we were not able to read the file ' + str(file_path) + ' to compare it\n')
+                logger.warning(f'We were not able to read the file {file_path} to compare it\n')
                 file_path = os.path.join(caiman_datadir(), "testdata", "NC" + dt + ".npz")
                 np.savez_compressed(file_path,
                                     information=information,
@@ -273,26 +274,26 @@ def save_with_compare(self, istruth=False, params=None, dview=None, Cn=None):
         information.update({'differences': {'proc': False, 'params_movie': False, 'params_cnm': False}})
 
         if data['processor'] != information['processor']:
-            logging.info("You don't have the same processor as was used to generate the ground truth. The processing time can vary.\n" +
+            logger.info("You don't have the same processor as was used to generate the ground truth. The processing time can vary.\n" +
                          "For time comparison, Create your own groundtruth standard for future testing.\n" +
                          f"Compare: {data['processor']} to {information['processor']}\n")
             information['differences']['proc'] = True
         if data['params'] != information['params']:
-            logging.warning("You are not using the same movie parameters. Results will not be comparable.")
-            logging.warning('You must use the same parameters as the groundtruth.\n' +
+            logger.warning("You are not using the same movie parameters. Results will not be comparable.")
+            logger.warning('You must use the same parameters as the groundtruth.\n' +
                             'examine the groundtruth parameters with the see() method\n')
             information['differences']['params_movie'] = True
                                                                                                             # We must cleanup some fields to permit an accurate comparison
         if not normalised_compare_cnmpatches(data['cnmpatch'], cnmpatch):
             if data['cnmpatch'].keys() != cnmpatch.keys():
-                logging.error(
+                logger.error(
                     'DIFFERENCES IN THE FIELDS OF CNMF'
                 )                                                                                           # TODO: Now that we have deeply nested data structures, find a module that gives you tight differences.
             diffkeys = [k for k in data['cnmpatch'] if data['cnmpatch'][k] != cnmpatch[k]]
             for k in diffkeys:
-                logging.info(f"{k}:{data['cnmpatch'][k]}->{cnmpatch[k]}")
+                logger.info(f"{k}:{data['cnmpatch'][k]}->{cnmpatch[k]}")
 
-            logging.warning('You are not using the same parameters in your cnmf on patches initialization\n')
+            logger.warning('You are not using the same parameters in your cnmf on patches initialization\n')
             information['differences']['params_cnm'] = True
 
         # for rigid
@@ -373,7 +374,7 @@ def see(filename=None):
         dr = os.path.join(caiman_datadir(), "testdata", "groundtruth.npz")
     else:
         dr = os.path.join(caiman_datadir(), "testdata", filename, filename + ".npz")
-        logging.debug("Loading GT file " + str(dr))
+        logger.debug("Loading GT file " + str(dr))
     with np.load(dr) as dt:
         print('Info :\n')
         see_it(dt)
@@ -403,7 +404,7 @@ def deletesparse(cnm):
             val = deletesparse(val)
         if not isinstance(val, scipy.sparse.coo.coo_matrix) and not isinstance(val, np.ndarray) \
                 and not isinstance(val, scipy.sparse.csc.csc_matrix) and not keys == 'dview':
-            logging.debug(f"type of val is {type(val)}")
+            logger.debug(f"type of val is {type(val)}")
             cnm[keys] = val
         else:
 
@@ -483,28 +484,13 @@ def cnmf(Cn, A_gt, A_test, C_gt, C_test, dims_gt, dims_test, dview=None, sensiti
 
 
 def plotrig(init, curr, timer, sensitivity):
-
     diff = np.linalg.norm(np.asarray(init) - np.asarray(curr)) / np.linalg.norm(init)
     isdiff = diff > sensitivity
     info = {'isdifferent': int(isdiff), 'diff_data': diff, 'diff_timing': timer}
     curr = np.asarray(curr).transpose([1, 0])
     init = init.transpose([1, 0])
     xc = np.arange(curr.shape[1])
     xi = np.arange(init.shape[1])
-    #try:
-    #    pl.figure()
-    #    pl.subplot(1, 2, 1)
-    #    pl.plot(xc, curr[0], 'r', xi, init[0], 'b')
-    #    pl.legend(['x shifts curr', 'x shifts init'])
-    #    pl.xlabel('frames')
-    #    pl.ylabel('pixels')
-    #    pl.subplot(1, 2, 2)
-    #    pl.plot(xc, curr[1], 'r', xi, init[1], 'b')
-    #    pl.legend(['yshifts curr', 'y shifts init'])
-    #    pl.xlabel('frames')
-    #    pl.ylabel('pixels')
-    #except:
-    #    logging.warning("not able to plot")
     return info
 
 

caiman/tests/comparison_general.py

@@ -6,15 +6,7 @@
 See Also
 ------------
 caiman/tests/comparison/comparison.py
-
-
 """
-#%%
-#\package None
-#\version   1.0
-#\copyright GNU General Public License v2.0
-#\date Created on june 2017
-#\author: Jremie KALFON
 
 import copy
 import cv2
@@ -49,7 +41,8 @@
 # You can log to a file using the filename parameter, or make the output more or less
 # verbose by setting level to logging.DEBUG, logging.INFO, logging.WARNING, or logging.ERROR
 
-logging.getLogger("caiman").setLevel(logging.DEBUG)
+logger = logging.getLogger("caiman")
+logger.setLevel(logging.DEBUG)
 
 # GLOBAL VAR
 params_movie = {
@@ -201,7 +194,7 @@ def test_general():
     if len(name_new) > 1:
         fname_new = cm.save_memmap_join(name_new, base_name='Yr', n_chunks=params_movie['n_chunks'], dview=None)
     else:
-        logging.warning('One file only, not saving!')
+        logger.warning('One file only, not saving!')
         fname_new = name_new[0]
 
     Yr, dims, T = cm.load_memmap(fname_new)
@@ -256,7 +249,7 @@ def test_general():
     b_tot = cnm.estimates.b
     f_tot = cnm.estimates.f
     # DISCARDING
-    logging.info(('Number of components:' + str(A_tot.shape[-1])))
+    logger.info(('Number of components:' + str(A_tot.shape[-1])))
     final_frate = params_movie['final_frate']
     # threshold on space consistency
     r_values_min = params_movie['r_values_min_patch']
@@ -332,29 +325,29 @@ def test_general():
         for log_file in log_files:
             os.remove(log_file)
     except:
-        logging.warning('Cannot remove log files')
+        logger.warning('Cannot remove log files')
 
 
 ############ assertions ##################
     pb = False
     if (comp.information['differences']['params_movie']):
-        logging.error(
-            "you need to set the same movie parameters than the ground truth to have a real comparison (use the comp.see() function to explore it)"
+        logger.error(
+            "You must set the same movie parameters as the ground truth to have a real comparison (use the comp.see() function to explore it)"
         )
         pb = True
     if (comp.information['differences']['params_cnm']):
-        logging.warning(
-            "you need to set the same cnmf parameters than the ground truth to have a real comparison (use the comp.see() function to explore it)"
+        logger.warning(
+            "You must set the same cnmf parameters as the ground truth to have a real comparison (use the comp.see() function to explore it)"
         )
         # pb = True
     if (comp.information['diff']['rig']['isdifferent']):
-        logging.error("the rigid shifts are different from the groundtruth ")
+        logger.error("the rigid shifts are different from the groundtruth ")
         pb = True
     if (comp.information['diff']['cnmpatch']['isdifferent']):
-        logging.error("the cnmf on patch produces different results than the groundtruth ")
+        logger.error("the cnmf on patch produces different results than the groundtruth ")
         pb = True
     if (comp.information['diff']['cnmfull']['isdifferent']):
-        logging.error("the cnmf full frame produces different  results than the groundtruth ")
+        logger.error("the cnmf full frame produces different  results than the groundtruth ")
         pb = True
 
     assert (not pb)

caiman/tests/test_deconvolution.py

@@ -11,7 +11,8 @@
 # You can log to a file using the filename parameter, or make the output more or less
 # verbose by setting level to logging.DEBUG, logging.INFO, logging.WARNING, or logging.ERROR
 
-logging.getLogger("caiman").setLevel(logging.DEBUG)
+logger = logging.getLogger("caiman")
+logger.setLevel(logging.DEBUG)
 
 def gen_data(g=[.95], sn=.2, T=1000, framerate=30, firerate=.5, b=10, N=1, seed=0):
     """
@@ -67,7 +68,7 @@ def foo(method, p):
         res = constrained_foopsi(y, g=g, sn=sn, p=p, method=method)
         npt.assert_allclose(np.corrcoef(res[0], c)[0, 1], 1, [.01, .1][i])
         npt.assert_allclose(np.corrcoef(res[-2], s)[0, 1], 1, [.03, .3][i])
-    logging.debug(['\n', ''][p - 1] + ' %5s AR%d   %.4fs' % (method, p, time() - t))
+    logger.debug(['\n', ''][p - 1] + ' %5s AR%d   %.4fs' % (method, p, time() - t))
 
 
 def test_oasis():

demos/general/demo_OnACID.py

@@ -57,7 +57,7 @@ def main():
     cnm.fit_online()
 
     # plot contours
-    logging.info(f"Number of components: {cnm.estimates.A.shape[-1]}")
+    logger.info(f"Number of components: {cnm.estimates.A.shape[-1]}")
     Cn = cm.load(fnames[0], subindices=slice(0,500)).local_correlations(swap_dim=False)
     cnm.estimates.plot_contours(img=Cn)
 

demos/general/demo_OnACID_mesoscope.py

@@ -69,7 +69,7 @@ def main():
     cnm.fit_online()
 
     # plot contours (this may take time)
-    logging.info(f"Number of components: {cnm.estimates.A.shape[-1]}")
+    logger.info(f"Number of components: {cnm.estimates.A.shape[-1]}")
     images = cm.load(fnames)
     Cn = images.local_correlations(swap_dim=False, frames_per_chunk=500)
     cnm.estimates.plot_contours(img=Cn, display_numbers=False)

demos/notebooks/demo_OnACID_mesoscope.ipynb

@@ -175,7 +175,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "logging.info('Number of components: ' + str(cnm.estimates.A.shape[-1]))\n",
+    "logger.info('Number of components: ' + str(cnm.estimates.A.shape[-1]))\n",
     "Cn = cm.load(fnames[0], subindices=slice(0,500)).local_correlations(swap_dim=False)\n",
     "cnm.estimates.plot_contours(img=Cn)"
    ]