Initial go at updating notebooks to use the logger we're calling caiman

flatironinstitute · Jul 24, 2024 · d3a89fc · d3a89fc
1 parent b3fafb5
commit d3a89fc
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Showing 13 changed files with 119 additions and 50 deletions.
diff --git a/demos/notebooks/demo_OnACID_mesoscope.ipynb b/demos/notebooks/demo_OnACID_mesoscope.ipynb
@@ -34,10 +34,16 @@
     "from caiman.source_extraction import cnmf\n",
     "from caiman.utils.utils import download_demo\n",
     "\n",
-    "logging.basicConfig(format=\n",
-    "                          \"%(relativeCreated)12d [%(filename)s:%(funcName)20s():%(lineno)s] [%(process)d] %(message)s\",\n",
-    "                    # filename=\"/tmp/caiman.log\",\n",
-    "                    level=logging.INFO)\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",
+    "logfmt = '%(relativeCreated)12d [%(filename)s:%(funcName)20s():%(lineno)s] [%(process)d] %(message)s'\n",
+    "if logfile is not None:\n",
+    "    handler = logging.FileHandler(logfile)\n",
+    "else:\n",
+    "    handler = logging.StreamHandler()\n",
+    "handler.setFormatter(logfmt)\n",
+    "logger.addHandler(handler)\n",
     "\n",
     "try:\n",
     "    if __IPYTHON__:\n",

diff --git a/demos/notebooks/demo_Ring_CNN.ipynb b/demos/notebooks/demo_Ring_CNN.ipynb
@@ -23,10 +23,16 @@
     "import numpy as np\n",
     "import os\n",
     "\n",
-    "logging.basicConfig(format=\n",
-    "                          \"%(relativeCreated)12d [%(filename)s:%(funcName)20s():%(lineno)s] [%(process)d] %(message)s\",\n",
-    "                    # filename=\"/tmp/caiman.log\",\n",
-    "                    level=logging.WARNING)\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",
+    "logfmt = '%(relativeCreated)12d [%(filename)s:%(funcName)20s():%(lineno)s] [%(process)d] %(message)s'\n",
+    "if logfile is not None:\n",
+    "    handler = logging.FileHandler(logfile)\n",
+    "else:\n",
+    "    handler = logging.StreamHandler()\n",
+    "handler.setFormatter(logfmt)\n",
+    "logger.addHandler(handler)\n",
     "\n",
     "import caiman as cm\n",
     "import caiman.base.movies\n",

diff --git a/demos/notebooks/demo_VST.ipynb b/demos/notebooks/demo_VST.ipynb
@@ -24,10 +24,16 @@
     "import os\n",
     "import timeit\n",
     "\n",
-    "logging.basicConfig(format=\n",
-    "                          \"%(relativeCreated)12d [%(filename)s:%(funcName)20s():%(lineno)s] [%(process)d] %(message)s\",\n",
-    "                    # filename=\"/tmp/caiman.log\",\n",
-    "                    level=logging.DEBUG)\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",
+    "logfmt = '%(relativeCreated)12d [%(filename)s:%(funcName)20s():%(lineno)s] [%(process)d] %(message)s'\n",
+    "if logfile is not None:\n",
+    "    handler = logging.FileHandler(logfile)\n",
+    "else:\n",
+    "    handler = logging.StreamHandler()\n",
+    "handler.setFormatter(logfmt)\n",
+    "logger.addHandler(handler)\n",
     "\n",
     "import caiman.external.houghvst.estimation as est\n",
     "from caiman.external.houghvst.gat import compute_gat, compute_inverse_gat\n",

diff --git a/demos/notebooks/demo_caiman_cnmf_3D.ipynb b/demos/notebooks/demo_caiman_cnmf_3D.ipynb
@@ -39,10 +39,15 @@
     "import bokeh.plotting as bpl\n",
     "bpl.output_notebook()\n",
     "\n",
-    "logging.basicConfig(format=\n",
-    "                          \"%(relativeCreated)12d [%(filename)s:%(funcName)20s():%(lineno)s] [%(process)d] %(message)s\",\n",
-    "                    # filename=\"/tmp/caiman.log\",\n",
-    "                    level=logging.WARNING)"
+    "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",
+    "logfmt = '%(relativeCreated)12d [%(filename)s:%(funcName)20s():%(lineno)s] [%(process)d] %(message)s'\n",
+    "if logfile is not None:\n",
+    "    handler = logging.FileHandler(logfile)\n",
+    "else:\n",
+    "    handler = logging.StreamHandler()\n",
+    "handler.setFormatter(logfmt)\n"
    ]
   },
   {

diff --git a/demos/notebooks/demo_dendritic.ipynb b/demos/notebooks/demo_dendritic.ipynb
@@ -69,10 +69,14 @@
     "    print(f\"Will save logging data to {log_file}\")\n",
     "else:\n",
     "    log_file = None\n",
-    "log_format = \"{asctime} - {levelname} - [{filename} {funcName}() {lineno}] - pid {process} - {message}\"\n",
-    "logging.basicConfig(format=log_format,\n",
-    "                    filename=log_file, \n",
-    "                    level=logging.WARNING, style=\"{\") #DEBUG, INFO, WARNING, ERROR, CRITICAL"
+    "logger = logging.getLogger('caiman')\n",
+    "logger.setLevel(logging.INFO)\n",
+    "logfmt = '%(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",
+    "else:\n",
+    "    handler = logging.StreamHandler()\n",
+    "handler.setFormatter(logfmt)\n"
    ]
   },
   {

diff --git a/demos/notebooks/demo_motion_correction.ipynb b/demos/notebooks/demo_motion_correction.ipynb
@@ -40,10 +40,15 @@
     "except NameError:\n",
     "    pass\n",
     "\n",
-    "logging.basicConfig(format=\n",
-    "                          \"%(relativeCreated)12d [%(filename)s:%(funcName)20s():%(lineno)s] [%(process)d] %(message)s\",\n",
-    "                    # filename=\"/tmp/caiman.log\",\n",
-    "                    level=logging.DEBUG)\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",
+    "logfmt = '%(relativeCreated)12d [%(filename)s:%(funcName)20s():%(lineno)s] [%(process)d] %(message)s'\n",
+    "if logfile is not None:\n",
+    "    handler = logging.FileHandler(logfile)\n",
+    "else:\n",
+    "    handler = logging.StreamHandler()\n",
+    "handler.setFormatter(logfmt)\n",
     "\n",
     "import caiman as cm\n",
     "from caiman.motion_correction import MotionCorrect, tile_and_correct, motion_correction_piecewise\n",

diff --git a/demos/notebooks/demo_online_3D.ipynb b/demos/notebooks/demo_online_3D.ipynb
@@ -36,10 +36,15 @@
     "import bokeh.plotting as bpl\n",
     "bpl.output_notebook()\n",
     "\n",
-    "logging.basicConfig(format=\n",
-    "                          \"%(relativeCreated)12d [%(filename)s:%(funcName)20s():%(lineno)s] [%(process)d] %(message)s\",\n",
-    "                    # filename=\"/tmp/caiman.log\",\n",
-    "                    level=logging.WARNING)"
+    "logfile = None # Replace with a path if you want to log to a file\n",
+    "logger = logging.getLogger('caiman')\n",
+    "logger.setLevel(logging.WARNING)\n",
+    "logfmt = '%(relativeCreated)12d [%(filename)s:%(funcName)20s():%(lineno)s] [%(process)d] %(message)s'\n",
+    "if logfile is not None:\n",
+    "    handler = logging.FileHandler(logfile)\n",
+    "else:\n",
+    "    handler = logging.StreamHandler()\n",
+    "handler.setFormatter(logfmt)\n"
    ]
   },
   {

diff --git a/demos/notebooks/demo_online_cnmfE.ipynb b/demos/notebooks/demo_online_cnmfE.ipynb
@@ -36,10 +36,15 @@
     "except NameError:\n",
     "    pass\n",
     "\n",
-    "logging.basicConfig(format=\n",
-    "                          \"%(relativeCreated)12d [%(filename)s:%(funcName)10s():%(lineno)s] [%(process)d] %(message)s\",\n",
-    "                    # filename=\"/tmp/caiman.log\",\n",
-    "                    level=logging.WARNING)\n",
+    "logfile = None # Replace with a path if you want to log to a file\n",
+    "logger = logging.getLogger('caiman')\n",
+    "logger.setLevel(logging.WARNING)\n",
+    "logfmt = '%(relativeCreated)12d [%(filename)s:%(funcName)20s():%(lineno)s] [%(process)d] %(message)s'\n",
+    "if logfile is not None:\n",
+    "    handler = logging.FileHandler(logfile)\n",
+    "else:\n",
+    "    handler = logging.StreamHandler()\n",
+    "handler.setFormatter(logfmt)\n",
     "\n",
     "bpl.output_notebook()\n",
     "hv.notebook_extension('bokeh')"

diff --git a/demos/notebooks/demo_pipeline.ipynb b/demos/notebooks/demo_pipeline.ipynb
@@ -93,9 +93,15 @@
    "outputs": [],
    "source": [
     "# set up logging\n",
-    "logging.basicConfig(format=\"{asctime} - {levelname} - [{filename} {funcName}() {lineno}] - pid {process} - {message}\",\n",
-    "                    filename=None, \n",
-    "                    level=logging.WARNING, style=\"{\") #logging level can be DEBUG, INFO, WARNING, ERROR, CRITICAL\n",
+    "logfile = None # Replace with a path if you want to log to a file\n",
+    "logger = logging.getLogger('caiman')\n",
+    "logger.setLevel(logging.WARNING)\n",
+    "logfmt = '%(relativeCreated)12d [%(filename)s:%(funcName)20s():%(lineno)s] [%(process)d] %(message)s'\n",
+    "if logfile is not None:\n",
+    "    handler = logging.FileHandler(logfile)\n",
+    "else:\n",
+    "    handler = logging.StreamHandler()\n",
+    "handler.setFormatter(logfmt)\n",
     "\n",
     "# set env variables \n",
     "os.environ[\"MKL_NUM_THREADS\"] = \"1\"\n",

diff --git a/demos/notebooks/demo_pipeline_cnmfE.ipynb b/demos/notebooks/demo_pipeline_cnmfE.ipynb
@@ -83,9 +83,15 @@
    "outputs": [],
    "source": [
     "# set up logging\n",
-    "logging.basicConfig(format=\"{asctime} - {levelname} - [{filename} {funcName}() {lineno}] - pid {process} - {message}\",\n",
-    "                    filename=None, \n",
-    "                    level=logging.WARNING, style=\"{\") #logging level can be DEBUG, INFO, WARNING, ERROR, CRITICAL\n",
+    "logfile = None # Replace with a path if you want to log to a file\n",
+    "logger = logging.getLogger('caiman')\n",
+    "logger.setLevel(logging.WARNING)\n",
+    "logfmt = '%(relativeCreated)12d [%(filename)s:%(funcName)20s():%(lineno)s] [%(process)d] %(message)s'\n",
+    "if logfile is not None:\n",
+    "    handler = logging.FileHandler(logfile)\n",
+    "else:\n",
+    "    handler = logging.StreamHandler()\n",
+    "handler.setFormatter(logfmt)\n",
     "\n",
     "# set env variables in case they weren't already set\n",
     "os.environ[\"MKL_NUM_THREADS\"] = \"1\"\n",

diff --git a/demos/notebooks/demo_pipeline_voltage_imaging.ipynb b/demos/notebooks/demo_pipeline_voltage_imaging.ipynb
@@ -60,10 +60,15 @@
     "from caiman.summary_images import mean_image\n",
     "from caiman.paths import caiman_datadir\n",
     "\n",
-    "logging.basicConfig(format=\n",
-    "                    \"%(relativeCreated)12d [%(filename)s:%(funcName)20s():%(lineno)s]\" \\\n",
-    "                    \"[%(process)d] %(message)s\",\n",
-    "                    level=logging.ERROR)"
+    "logfile = None # Replace with a path if you want to log to a file\n",
+    "logger = logging.getLogger('caiman')\n",
+    "logger.setLevel(logging.ERROR)\n",
+    "logfmt = '%(relativeCreated)12d [%(filename)s:%(funcName)20s():%(lineno)s] [%(process)d] %(message)s'\n",
+    "if logfile is not None:\n",
+    "    handler = logging.FileHandler(logfile)\n",
+    "else:\n",
+    "    handler = logging.StreamHandler()\n",
+    "handler.setFormatter(logfmt)\n"
    ]
   },
   {

diff --git a/demos/notebooks/demo_realtime_cnmfE.ipynb b/demos/notebooks/demo_realtime_cnmfE.ipynb
@@ -51,10 +51,15 @@
     "except NameError:\n",
     "    pass\n",
     "\n",
-    "logging.basicConfig(format=\n",
-    "                          \"%(relativeCreated)12d [%(filename)s:%(funcName)10s():%(lineno)s] [%(process)d] %(message)s\",\n",
-    "                    # filename=\"/tmp/caiman.log\",\n",
-    "                    level=logging.WARNING)\n",
+    "logfile = None # Replace with a path if you want to log to a file\n",
+    "logger = logging.getLogger('caiman')\n",
+    "logger.setLevel(logging.WARNING)\n",
+    "logfmt = '%(relativeCreated)12d [%(filename)s:%(funcName)20s():%(lineno)s] [%(process)d] %(message)s'\n",
+    "if logfile is not None:\n",
+    "    handler = logging.FileHandler(logfile)\n",
+    "else:\n",
+    "    handler = logging.StreamHandler()\n",
+    "handler.setFormatter(logfmt)\n",
     "\n",
     "import caiman as cm\n",
     "from caiman.source_extraction import cnmf\n",

diff --git a/demos/notebooks/demo_seeded_CNMF.ipynb b/demos/notebooks/demo_seeded_CNMF.ipynb
@@ -45,10 +45,15 @@
     "except NameError:\n",
     "    pass\n",
     "\n",
-    "logging.basicConfig(format=\n",
-    "                          \"%(relativeCreated)12d [%(filename)s:%(funcName)20s():%(lineno)s] [%(process)d] %(message)s\",\n",
-    "                    # filename=\"/tmp/caiman.log\",\n",
-    "                    level=logging.WARNING)\n",
+    "logfile = None # Replace with a path if you want to log to a file\n",
+    "logger = logging.getLogger('caiman')\n",
+    "logger.setLevel(logging.WARNING)\n",
+    "logfmt = '%(relativeCreated)12d [%(filename)s:%(funcName)20s():%(lineno)s] [%(process)d] %(message)s'\n",
+    "if logfile is not None:\n",
+    "    handler = logging.FileHandler(logfile)\n",
+    "else:\n",
+    "    handler = logging.StreamHandler()\n",
+    "handler.setFormatter(logfmt)\n",
     "\n",
     "import caiman as cm\n",
     "from caiman.motion_correction import MotionCorrect\n",