Merge pull request #134 from AllenInstitute/dev

Dev

Author: rcpeene

docs/basics/use_nwbwidgets.ipynb

@@ -6,7 +6,7 @@
    "metadata": {},
    "source": [
     "# Exploring an NWB File\n",
-    "It can get cumbersome to manually dissect an NWB file with print statements. There are a few ways to view an NWB graphically instead. A great way to do this in a Jupyter notebook is with [NWBWidgets](https://github.com/NeurodataWithoutBorders/nwbwidgets). Here, you can use NWBWidgets to view a file from a location on your machine. If you don't want to download a file just to view it, you can still use NWBWidgets to view it remotely. Check out *Stream an NWB File with fsspec* to learn how to do this. Another way to explore an NWB file, that doesn't require Jupyter, is with [HDFView](https://www.hdfgroup.org/downloads/hdfview/)."
+    "It can get cumbersome to manually dissect an NWB file with print statements. There are a few ways to view an NWB graphically instead. A great way to do this in a Jupyter notebook is with [NWBWidgets](https://github.com/NeurodataWithoutBorders/nwbwidgets). Here, you can use NWBWidgets to view a file from a location on your machine. If you don't want to download a file just to view it, you can still use NWBWidgets to view it remotely. Check out [Streaming an NWB File with fsspec](./stream_nwb.ipynb) to learn how to do this. Another way to explore an NWB file, that doesn't require Jupyter, is with [HDFView](https://www.hdfgroup.org/downloads/hdfview/)."
    ]
   },
   {

docs/visualization/visualize_2p_raw.ipynb

@@ -29,13 +29,13 @@
     "import fsspec\n",
     "import h5py\n",
     "import numpy as np\n",
-    "import pynwb\n",
     "\n",
     "from dandi import dandiapi\n",
     "from fsspec.implementations.cached import CachingFileSystem\n",
     "from matplotlib import pyplot as plt\n",
     "from mpl_interactions import hyperslicer\n",
-    "from nwbwidgets import nwb2widget"
+    "from nwbwidgets import nwb2widget\n",
+    "from pynwb import NWBHDF5IO"
    ]
   },
   {
@@ -55,7 +55,7 @@
    "outputs": [],
    "source": [
     "dandiset_id = \"000336\"\n",
-    "dandi_filepath = \"1186140941/1212553658/1212705237_raw.nwb\"\n",
+    "dandi_filepath = \"sub_1186140941/sub_1186140941sess_1212553658/sub_1186140941+sess_1212553658+exp_1212705237+raw_ophys.nwb\"\n",
     "authenticate = True\n",
     "dandi_api_key = os.environ['DANDI_API_KEY']"
    ]
@@ -124,7 +124,7 @@
     "# opening may take awhile on a large file\n",
     "f = fs.open(file_url, \"rb\")\n",
     "file = h5py.File(f)\n",
-    "io = pynwb.NWBHDF5IO(file=file, mode='r', load_namespaces=True)\n",
+    "io = NWBHDF5IO(file=file, mode='r', load_namespaces=True)\n",
     "nwb = io.read()"
    ]
   },