Merge pull request #1380 from flatironinstitute/dev

dev to main for release 1.11.3

VERSION

@@ -1 +1 @@
-1.11.2
+1.11.3

caiman/utils/image_preprocessing_keras.py

@@ -14,7 +14,6 @@
 import re
 from scipy import linalg
 import scipy.ndimage as ndi
-from six.moves import range
 import threading
 import warnings
 

demos/notebooks/demo_OnACID_mesoscope.ipynb

@@ -37,7 +37,7 @@
     "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",
+    "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",
     "else:\n",

demos/notebooks/demo_Ring_CNN.ipynb

@@ -26,7 +26,7 @@
     "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",
+    "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",
     "else:\n",

demos/notebooks/demo_VST.ipynb

@@ -27,7 +27,7 @@
     "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",
+    "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",
     "else:\n",

demos/notebooks/demo_caiman_cnmf_3D.ipynb

@@ -42,7 +42,7 @@
     "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",
+    "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",
     "else:\n",

demos/notebooks/demo_dendritic.ipynb

@@ -71,7 +71,7 @@
     "    log_file = None\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",
+    "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",
     "else:\n",

demos/notebooks/demo_motion_correction.ipynb

@@ -43,7 +43,7 @@
     "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",
+    "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",
     "else:\n",

demos/notebooks/demo_online_3D.ipynb

@@ -39,7 +39,7 @@
     "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",
+    "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",
     "else:\n",

demos/notebooks/demo_online_cnmfE.ipynb

@@ -39,7 +39,7 @@
     "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",
+    "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",
     "else:\n",

demos/notebooks/demo_pipeline.ipynb

@@ -96,7 +96,7 @@
     "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",
+    "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",
     "else:\n",

demos/notebooks/demo_pipeline_cnmfE.ipynb

@@ -86,7 +86,7 @@
     "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",
+    "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",
     "else:\n",

demos/notebooks/demo_pipeline_voltage_imaging.ipynb

@@ -63,7 +63,7 @@
     "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",
+    "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",
     "else:\n",

demos/notebooks/demo_realtime_cnmfE.ipynb

@@ -54,7 +54,7 @@
     "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",
+    "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",
     "else:\n",

demos/notebooks/demo_seeded_CNMF.ipynb

@@ -48,7 +48,7 @@
     "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",
+    "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",
     "else:\n",

requirements_gpu.txt

@@ -1,7 +1,6 @@
 av
 coverage
 cython
-future
 h5py
 ipykernel
 ipython