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Merged
merged 3 commits into from
Dec 19, 2022
Merged

Dev #114

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63dec9a
Relocated binder files
rcpeene Dec 8, 2022
7df7d15
Added download cells to basic notebooks
rcpeene Dec 14, 2022
f3e4f3b
Changed variable names for clarity
rcpeene Dec 19, 2022
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0 apt.txt → .binder/apt.txt
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2,876 changes: 1,438 additions & 1,438 deletions jupyter_notebook_config.py → .binder/jupyter_notebook_config.py
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3 changes: 3 additions & 0 deletions .binder/postBuild
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@@ -0,0 +1,3 @@
#!/bin/bash
mkdir ~/.jupyter
cp .binder/jupyter_notebook_config.py ~/.jupyter/
0 runtime.txt → .binder/runtime.txt
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8 changes: 4 additions & 4 deletions docs/basics/download_nwb.ipynb
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Expand Up @@ -86,7 +86,7 @@
"metadata": {},
"source": [
"### Downloading Just One File\n",
"Set `filepath` to the path of the file you want to download within the dandiset. You can get this by navigating to the file you want to download on the DANDI Archive website and pressing on the `i` icon. There, you can copy the filepath from the field labeled `path`. Don't include a leading `/`."
"Set `dandi_filepath` to the path of the file you want to download within the dandiset. You can get this by navigating to the file you want to download on the DANDI Archive website and pressing on the `i` icon. There, you can copy the filepath from the field labeled `path`. Don't include a leading `/`."
]
},
{
Expand All @@ -96,7 +96,7 @@
"metadata": {},
"outputs": [],
"source": [
"filepath = \"sub-699733573/sub-699733573_ses-715093703.nwb\""
"dandi_filepath = \"sub-699733573/sub-699733573_ses-715093703.nwb\""
]
},
{
Expand All @@ -114,8 +114,8 @@
}
],
"source": [
"filename = filepath.split(\"/\")[-1]\n",
"file = my_dandiset.get_asset_by_path(filepath)\n",
"filename = dandi_filepath.split(\"/\")[-1]\n",
"file = my_dandiset.get_asset_by_path(dandi_filepath)\n",
"# this may take awhile, especially if the file to download is large\n",
"file.download(f\"{download_loc}/{filename}\")\n",
"\n",
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140 changes: 50 additions & 90 deletions docs/basics/read_nwb.ipynb
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Expand Up @@ -6,7 +6,7 @@
"metadata": {},
"source": [
"# Reading an NWB File\n",
"After downloading an NWB file, you *may* want to view the data inside. You can do basic reading of the file with [PyNWB](https://github.com/NeurodataWithoutBorders/pynwb). This is a package designed to utilize, modify, and process NWB files. The basic read functionality of PyNWB is shown below. This notebook is intended to explore the NWB file which was specified for download in *Downloading an NWB file*. If you choose a different file, make sure it's already downloaded!"
"After downloading an NWB file, you *may* want to view the data inside. You can do basic reading of the file with [PyNWB](https://github.com/NeurodataWithoutBorders/pynwb). This is a package designed to utilize, modify, and process NWB files. The basic read functionality of PyNWB is shown below."
]
},
{
Expand All @@ -19,120 +19,80 @@
},
{
"cell_type": "code",
"execution_count": 1,
"execution_count": null,
"id": "d76f08a6",
"metadata": {},
"outputs": [],
"source": [
"from dandi import dandiapi\n",
"from pynwb import NWBHDF5IO"
]
},
{
"cell_type": "markdown",
"id": "0b6b0571",
"id": "4687824b",
"metadata": {},
"source": [
"### Reading an NWB File\n",
"You can read in a PyNWB file with `NWBHDF5IO` to retrieve an io object. You can use the `.read` method to actually read it in. From there, you can see the raw data of the NWB file and can print the fields you are interested in. "
"### Downloading an NWB File\n",
"To read an NWB File, it must first be downloaded. `dandiset_id` and `filepath` may be changed to select a different file off of DANDI. If the file of interest already downloaded, you don't need to run the download cell again. When trying to download an embargoed file, refer to the code from the [Downloading an NWB File](./download_nwb.ipynb) notebook."
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "7fbd4d6c",
"metadata": {},
"outputs": [],
"source": [
"dandiset_id = \"000021\"\n",
"dandi_filepath = \"sub-699733573/sub-699733573_ses-715093703.nwb\"\n",
"download_loc = \".\""
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "9da13c50",
"metadata": {},
"outputs": [],
"source": [
"filename = dandi_filepath.split(\"/\")[-1]\n",
"filepath = f\"{download_loc}/{filename}\""
]
},
{
"cell_type": "code",
"execution_count": 2,
"id": "400c411d",
"execution_count": null,
"id": "da61049a",
"metadata": {},
"outputs": [],
"source": [
"nwb_filepath = \"./sub-699733573_ses-715093703.nwb\""
"client = dandiapi.DandiAPIClient()\n",
"my_dandiset = client.get_dandiset(dandiset_id)\n",
"file = my_dandiset.get_asset_by_path(dandi_filepath)\n",
"# this may take awhile, especially if the file to download is large\n",
"file.download(filepath)\n",
"\n",
"print(f\"Downloaded file to {filepath}\")"
]
},
{
"cell_type": "markdown",
"id": "0b6b0571",
"metadata": {},
"source": [
"### Reading an NWB File\n",
"You can read in a PyNWB file with `NWBHDF5IO` to retrieve an io object. You can use the `.read` method to actually read it in. From there, you can see the raw data of the NWB file and can print the fields you are interested in. "
]
},
{
"cell_type": "code",
"execution_count": 3,
"execution_count": null,
"id": "7628e758",
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"C:\\Users\\carter.peene\\AppData\\Local\\Programs\\Python\\Python39\\lib\\site-packages\\hdmf\\spec\\namespace.py:531: UserWarning: Ignoring cached namespace 'hdmf-common' version 1.1.3 because version 1.5.1 is already loaded.\n",
" warn(\"Ignoring cached namespace '%s' version %s because version %s is already loaded.\"\n",
"C:\\Users\\carter.peene\\AppData\\Local\\Programs\\Python\\Python39\\lib\\site-packages\\hdmf\\spec\\namespace.py:531: UserWarning: Ignoring cached namespace 'core' version 2.2.2 because version 2.5.0 is already loaded.\n",
" warn(\"Ignoring cached namespace '%s' version %s because version %s is already loaded.\"\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"root pynwb.file.NWBFile at 0x2228950120912\n",
"Fields:\n",
" acquisition: {\n",
" raw_running_wheel_rotation <class 'pynwb.base.TimeSeries'>,\n",
" running_wheel_signal_voltage <class 'pynwb.base.TimeSeries'>,\n",
" running_wheel_supply_voltage <class 'pynwb.base.TimeSeries'>\n",
" }\n",
" devices: {\n",
" probeA <class 'abc.EcephysProbe'>,\n",
" probeB <class 'abc.EcephysProbe'>,\n",
" probeC <class 'abc.EcephysProbe'>,\n",
" probeD <class 'abc.EcephysProbe'>,\n",
" probeE <class 'abc.EcephysProbe'>,\n",
" probeF <class 'abc.EcephysProbe'>\n",
" }\n",
" electrode_groups: {\n",
" probeA <class 'abc.EcephysElectrodeGroup'>,\n",
" probeB <class 'abc.EcephysElectrodeGroup'>,\n",
" probeC <class 'abc.EcephysElectrodeGroup'>,\n",
" probeD <class 'abc.EcephysElectrodeGroup'>,\n",
" probeE <class 'abc.EcephysElectrodeGroup'>,\n",
" probeF <class 'abc.EcephysElectrodeGroup'>\n",
" }\n",
" electrodes: electrodes <class 'hdmf.common.table.DynamicTable'>\n",
" file_create_date: [datetime.datetime(2020, 5, 26, 0, 53, 26, 986608, tzinfo=tzoffset(None, -25200))]\n",
" identifier: 715093703\n",
" institution: Allen Institute for Brain Science\n",
" intervals: {\n",
" drifting_gratings_presentations <class 'pynwb.epoch.TimeIntervals'>,\n",
" flashes_presentations <class 'pynwb.epoch.TimeIntervals'>,\n",
" gabors_presentations <class 'pynwb.epoch.TimeIntervals'>,\n",
" invalid_times <class 'pynwb.epoch.TimeIntervals'>,\n",
" natural_movie_one_presentations <class 'pynwb.epoch.TimeIntervals'>,\n",
" natural_movie_three_presentations <class 'pynwb.epoch.TimeIntervals'>,\n",
" natural_scenes_presentations <class 'pynwb.epoch.TimeIntervals'>,\n",
" spontaneous_presentations <class 'pynwb.epoch.TimeIntervals'>,\n",
" static_gratings_presentations <class 'pynwb.epoch.TimeIntervals'>\n",
" }\n",
" invalid_times: invalid_times <class 'pynwb.epoch.TimeIntervals'>\n",
" processing: {\n",
" eye_tracking_rig_metadata <class 'pynwb.base.ProcessingModule'>,\n",
" optotagging <class 'pynwb.base.ProcessingModule'>,\n",
" running <class 'pynwb.base.ProcessingModule'>,\n",
" stimulus <class 'pynwb.base.ProcessingModule'>\n",
" }\n",
" session_description: Data and metadata for an Ecephys session\n",
" session_id: 715093703\n",
" session_start_time: 2019-01-19 00:54:18-08:00\n",
" stimulus_notes: brain_observatory_1.1\n",
" subject: subject abc.EcephysSpecimen at 0x2228949633056\n",
"Fields:\n",
" age: P118D\n",
" age_in_days: 118.0\n",
" genotype: Sst-IRES-Cre/wt;Ai32(RCL-ChR2(H134R)_EYFP)/wt\n",
" sex: M\n",
" species: Mus musculus\n",
" specimen_name: Sst-IRES-Cre;Ai32-386129\n",
" subject_id: 699733573\n",
"\n",
" timestamps_reference_time: 2019-01-19 00:54:18-08:00\n",
" units: units <class 'pynwb.misc.Units'>\n",
"\n"
]
}
],
"outputs": [],
"source": [
"io = NWBHDF5IO(nwb_filepath, mode=\"r\", load_namespaces=True)\n",
"io = NWBHDF5IO(f\"{download_loc}/{filename}\", mode=\"r\", load_namespaces=True)\n",
"nwb = io.read()\n",
"\n",
"print(nwb)"
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4 changes: 2 additions & 2 deletions docs/basics/stream_nwb.ipynb
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Expand Up @@ -54,7 +54,7 @@
"outputs": [],
"source": [
"dandiset_id = \"000021\"\n",
"filepath = \"sub-699733573/sub-699733573_ses-715093703.nwb\"\n",
"dandi_filepath = \"sub-699733573/sub-699733573_ses-715093703.nwb\"\n",
"authenticate = False\n",
"dandi_api_key = \"\""
]
Expand Down Expand Up @@ -105,7 +105,7 @@
}
],
"source": [
"file = my_dandiset.get_asset_by_path(filepath)\n",
"file = my_dandiset.get_asset_by_path(dandi_filepath)\n",
"base_url = file.client.session.head(file.base_download_url)\n",
"file_url = base_url.headers['Location']\n",
"\n",
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