Notebooks: set default logging level to logging.WARNING, add a blurb.

caiman/source_extraction/cnmf/initialization.py

@@ -541,7 +541,7 @@ def sparseNMF(Y_ds, nr, max_iter_snmf=200, alpha=0.5, sigma_smooth=(.5, .5, .5),
     d = np.prod(dims)
     yr = np.reshape(m1, [T, d], order='F')
 
-    logger.debug(f"Running SparseNMF with alpha_W={alpha} and l1_ratio={l1_ratio}")
+    logger.info(f"Running SparseNMF with alpha_W={alpha} and l1_ratio={l1_ratio}")
     mdl = NMF(n_components=nr, 
               verbose=False, 
               init='nndsvd', 

demos/notebooks/demo_OnACID_mesoscope.ipynb

@@ -36,7 +36,8 @@
     "\n",
     "logfile = None # Replace with a path if you want to log to a file\n",
     "logger = logging.getLogger('caiman')\n",
-    "logger.setLevel(logging.INFO)\n",
+    "# Set to logging.INFO if you want much output, potentially much more output\n",
+    "logger.setLevel(logging.WARNING)\n",
     "logfmt = logging.Formatter('%(relativeCreated)12d [%(filename)s:%(funcName)20s():%(lineno)s] [%(process)d] %(message)s')\n",
     "if logfile is not None:\n",
     "    handler = logging.FileHandler(logfile)\n",

demos/notebooks/demo_Ring_CNN.ipynb

@@ -25,7 +25,8 @@
     "\n",
     "logfile = None # Replace with a path if you want to log to a file\n",
     "logger = logging.getLogger('caiman')\n",
-    "logger.setLevel(logging.INFO)\n",
+    "# Set to logging.INFO if you want much output, potentially much more output\n",
+    "logger.setLevel(logging.WARNING)\n",
     "logfmt = logging.Formatter('%(relativeCreated)12d [%(filename)s:%(funcName)20s():%(lineno)s] [%(process)d] %(message)s')\n",
     "if logfile is not None:\n",
     "    handler = logging.FileHandler(logfile)\n",

demos/notebooks/demo_VST.ipynb

@@ -26,7 +26,8 @@
     "\n",
     "logfile = None # Replace with a path if you want to log to a file\n",
     "logger = logging.getLogger('caiman')\n",
-    "logger.setLevel(logging.INFO)\n",
+    "# Set to logging.INFO if you want much output, potentially much more output\n",
+    "logger.setLevel(logging.WARNING)\n",
     "logfmt = logging.Formatter('%(relativeCreated)12d [%(filename)s:%(funcName)20s():%(lineno)s] [%(process)d] %(message)s')\n",
     "if logfile is not None:\n",
     "    handler = logging.FileHandler(logfile)\n",

demos/notebooks/demo_caiman_cnmf_3D.ipynb

@@ -41,7 +41,8 @@
     "\n",
     "logfile = None # Replace with a path if you want to log to a file\n",
     "logger = logging.getLogger('caiman')\n",
-    "logger.setLevel(logging.INFO)\n",
+    "# Set to logging.INFO if you want much output, potentially much more output\n",
+    "logger.setLevel(logging.WARNING)\n",
     "logfmt = logging.Formatter('%(relativeCreated)12d [%(filename)s:%(funcName)20s():%(lineno)s] [%(process)d] %(message)s')\n",
     "if logfile is not None:\n",
     "    handler = logging.FileHandler(logfile)\n",

demos/notebooks/demo_dendritic.ipynb

@@ -70,7 +70,8 @@
     "else:\n",
     "    log_file = None\n",
     "logger = logging.getLogger('caiman')\n",
-    "logger.setLevel(logging.INFO)\n",
+    "# Set to logging.INFO if you want much output, potentially much more output\n",
+    "logger.setLevel(logging.WARNING)\n",
     "logfmt = logging.Formatter('%(relativeCreated)12d [%(filename)s:%(funcName)20s():%(lineno)s] [%(process)d] %(message)s')\n",
     "if log_file is not None:\n",
     "    handler = logging.FileHandler(log_file)\n",

demos/notebooks/demo_motion_correction.ipynb

@@ -42,7 +42,8 @@
     "\n",
     "logfile = None # Replace with a path if you want to log to a file\n",
     "logger = logging.getLogger('caiman')\n",
-    "logger.setLevel(logging.INFO)\n",
+    "# Set to logging.INFO if you want much output, potentially much more output\n",
+    "logger.setLevel(logging.WARNING)\n",
     "logfmt = logging.Formatter('%(relativeCreated)12d [%(filename)s:%(funcName)20s():%(lineno)s] [%(process)d] %(message)s')\n",
     "if logfile is not None:\n",
     "    handler = logging.FileHandler(logfile)\n",

demos/notebooks/demo_online_3D.ipynb

@@ -38,6 +38,7 @@
     "\n",
     "logfile = None # Replace with a path if you want to log to a file\n",
     "logger = logging.getLogger('caiman')\n",
+    "# Set to logging.INFO if you want much output, potentially much more output\n",
     "logger.setLevel(logging.WARNING)\n",
     "logfmt = logging.Formatter('%(relativeCreated)12d [%(filename)s:%(funcName)20s():%(lineno)s] [%(process)d] %(message)s')\n",
     "if logfile is not None:\n",

demos/notebooks/demo_online_cnmfE.ipynb

@@ -38,6 +38,7 @@
     "\n",
     "logfile = None # Replace with a path if you want to log to a file\n",
     "logger = logging.getLogger('caiman')\n",
+    "# Set to logging.INFO if you want much output, potentially much more output\n",
     "logger.setLevel(logging.WARNING)\n",
     "logfmt = logging.Formatter('%(relativeCreated)12d [%(filename)s:%(funcName)20s():%(lineno)s] [%(process)d] %(message)s')\n",
     "if logfile is not None:\n",

demos/notebooks/demo_pipeline.ipynb

@@ -95,6 +95,7 @@
     "# set up logging\n",
     "logfile = None # Replace with a path if you want to log to a file\n",
     "logger = logging.getLogger('caiman')\n",
+    "# Set to logging.INFO if you want much output, potentially much more output\n",
     "logger.setLevel(logging.WARNING)\n",
     "logfmt = logging.Formatter('%(relativeCreated)12d [%(filename)s:%(funcName)20s():%(lineno)s] [%(process)d] %(message)s')\n",
     "if logfile is not None:\n",

demos/notebooks/demo_pipeline_cnmfE.ipynb

@@ -85,6 +85,7 @@
     "# set up logging\n",
     "logfile = None # Replace with a path if you want to log to a file\n",
     "logger = logging.getLogger('caiman')\n",
+    "# Set to logging.INFO if you want much output, potentially much more output\n",
     "logger.setLevel(logging.WARNING)\n",
     "logfmt = logging.Formatter('%(relativeCreated)12d [%(filename)s:%(funcName)20s():%(lineno)s] [%(process)d] %(message)s')\n",
     "if logfile is not None:\n",

demos/notebooks/demo_pipeline_voltage_imaging.ipynb

@@ -62,6 +62,7 @@
     "\n",
     "logfile = None # Replace with a path if you want to log to a file\n",
     "logger = logging.getLogger('caiman')\n",
+    "# Set to logging.INFO if you want much output, potentially much more output\n",
     "logger.setLevel(logging.ERROR)\n",
     "logfmt = logging.Formatter('%(relativeCreated)12d [%(filename)s:%(funcName)20s():%(lineno)s] [%(process)d] %(message)s')\n",
     "if logfile is not None:\n",

demos/notebooks/demo_realtime_cnmfE.ipynb

@@ -53,6 +53,7 @@
     "\n",
     "logfile = None # Replace with a path if you want to log to a file\n",
     "logger = logging.getLogger('caiman')\n",
+    "# Set to logging.INFO if you want much output, potentially much more output\n",
     "logger.setLevel(logging.WARNING)\n",
     "logfmt = logging.Formatter('%(relativeCreated)12d [%(filename)s:%(funcName)20s():%(lineno)s] [%(process)d] %(message)s')\n",
     "if logfile is not None:\n",

demos/notebooks/demo_seeded_CNMF.ipynb

@@ -47,6 +47,7 @@
     "\n",
     "logfile = None # Replace with a path if you want to log to a file\n",
     "logger = logging.getLogger('caiman')\n",
+    "# Set to logging.INFO if you want much output, potentially much more output\n",
     "logger.setLevel(logging.WARNING)\n",
     "logfmt = logging.Formatter('%(relativeCreated)12d [%(filename)s:%(funcName)20s():%(lineno)s] [%(process)d] %(message)s')\n",
     "if logfile is not None:\n",