updated from review bits

flatironinstitute · Aug 25, 2023 · e7055c0 · e7055c0
1 parent e8aaef2
commit e7055c0
Show file tree

Hide file tree

Showing 2 changed files with 7 additions and 21 deletions.
diff --git a/caiman/motion_correction.py b/caiman/motion_correction.py
@@ -3076,9 +3076,6 @@ def tile_and_correct_wrapper(params):
     extension = extension.lower()
     shift_info = []
 
-    print("In tile and correct wrapper about to call load with subidxs")
-    print(f"subidx type: {type(idxs)}")
-
     imgs = cm.load(img_name, subindices=idxs, var_name_hdf5=var_name_hdf5,is3D=is3D)
     imgs = imgs[(slice(None),) + indices]
     mc = np.zeros(imgs.shape, dtype=np.float32)

diff --git a/demos/notebooks/demo_online_cnmfE.ipynb b/demos/notebooks/demo_online_cnmfE.ipynb
@@ -28,6 +28,7 @@
     "import logging\n",
     "import matplotlib.pyplot as plt\n",
     "import numpy as np\n",
+    "from time import time\n",
     "\n",
     "import caiman as cm\n",
     "from caiman.source_extraction import cnmf as cnmf\n",
@@ -174,8 +175,7 @@
     "                    cm.load(mc.mmap_file).resize(1, 1, temporal_downsampling)), axis=2).play(fr=30,\n",
     "                                                         magnification=1,\n",
     "                                                         gain=0.6,\n",
-    "                                                         plot_text=True,\n",
-    "                                                         do_loop=True)\n",
+    "                                                         plot_text=True)\n",
     "#plt.figure(); plt.plot(mc.shifts_rig); plt.legend(['x-shifts', 'y-shifts'])    "
    ]
   },
@@ -202,7 +202,8 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Inspect correlation and PNR images to set relevant thresholds"
+    "### Inspect correlation and PNR images to set relevant thresholds\n",
+    "First, extract correlation and pnr images."
    ]
   },
   {
@@ -212,12 +213,9 @@
    "outputs": [],
    "source": [
     "gSig = (6, 6)\n",
-    "\n",
     "cn_filter, pnr = cm.summary_images.correlation_pnr(images[::max(T//1000, 1)], \n",
     "                                                   gSig=gSig[0], \n",
-    "                                                   swap_dim=False) # change swap dim if output looks weird, it is a problem with tiffile\n",
-    "\n",
-    "\n"
+    "                                                   swap_dim=False) # change swap dim if output looks weird, it is a problem with tiffile"
    ]
   },
   {
@@ -294,20 +292,11 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from time import time\n",
     "t1 = -time()\n",
     "cnm = cnmf.CNMF(n_processes=n_processes, dview=dview, params=opts)\n",
     "cnm.fit(images)\n",
-    "t1 += time()"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "print(f\"Wall time: {t1: 0.2f} seconds\")"
+    "t1 += time()\n",
+    "print(f\"Elapsed time: {t1: 0.2f} seconds\")"
    ]
   },
   {