Merge branch 'master' into add_time_grid_widget

CHANGELOG.md

@@ -1,5 +1,9 @@
 # Upcoming
 
+### New features
+* Improved browsing and reading local NWB files with Panel, using ipyfilechooser [PR #300](https://github.com/NeurodataWithoutBorders/nwbwidgets/pull/300)
+* Improve readibility of dandisets and files dropdown lists [PR #301](https://github.com/NeurodataWithoutBorders/nwbwidgets/pull/301)
+
 ### Fixes
 * Fix I/O issues when streaming data on Panel [PR #295](https://github.com/NeurodataWithoutBorders/nwbwidgets/pull/295)
 * Fix plotly Figure not showing up, pinned Plotly version [PR #297](https://github.com/NeurodataWithoutBorders/nwbwidgets/pull/297)

README.md

@@ -1,11 +1,28 @@
-# NWB Widgets
-A library of widgets for visualization NWB data in a Jupyter notebook (or lab). The widgets allow you to navigate through the hierarchical structure of the NWB file and visualize specific data elements. It is designed to work out-of-the-box with NWB 2.0 files and to be easy to extend.
-
 [![PyPI version](https://badge.fury.io/py/nwbwidgets.svg)](https://badge.fury.io/py/nwbwidgets)
 [![codecov](https://codecov.io/gh/NeurodataWithoutBorders/nwbwidgets/branch/master/graph/badge.svg)](https://codecov.io/gh/NeurodataWithoutBorders/nwbwidgets)
 [![License](https://img.shields.io/badge/License-BSD%203--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause)
 [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/NeurodataWithoutBorders/nwb-jupyter-widgets/master?filepath=examples%2FNWBWidgets-modality-demos.ipynb)
 
+<p align="center">
+  <img src="https://github.com/NeurodataWithoutBorders/nwbwidgets/assets/844306/f20b8c26-79c7-4c1c-a3b5-b49ecf8cce5d" width="350" alt="NWB Widgets"/>
+  <h3 align="center">Explore NWB data in Jupyter</h3>
+</p>
+<p align="center">
+   <a href="https://nwbwidgets.readthedocs.io/"><strong>Explore our documentation »</strong></a>
+</p>
+
+<!-- TABLE OF CONTENTS -->
+
+## Table of Contents
+
+- [About](#about)
+- [Installation](#installation)
+- [Usage](#usage)
+- [Demo](#demo)
+- [Documentation](#documentation)
+
+## About
+A library of widgets for visualization NWB data in a Jupyter notebook (or lab). The widgets allow you to navigate through the hierarchical structure of the NWB file and visualize specific data elements. It is designed to work out-of-the-box with NWB 2.0 files and to be easy to extend.
 
 
 ## Installation
@@ -37,6 +54,9 @@ nwb2widget(nwb)
 ## Demo
 ![](https://drive.google.com/uc?export=download&id=1JtI2KtT8MielIMvvtgxRzFfBTdc41LiE)
 
+## Documentation
+See our [ReadTheDocs page](https://nwbwidgets.readthedocs.io/en/main/) for full documentation, including a gallery of all supported formats.
+
 ## How it works
 All visualizations are controlled by the dictionary `neurodata_vis_spec`. The keys of this dictionary are pynwb neurodata types, and the values are functions that take as input that neurodata_type and output a visualization. The visualizations may be of type `Widget` or `matplotlib.Figure`. When you enter a neurodata_type instance into `nwb2widget`, it searches the `neurodata_vis_spec` for that instance's neurodata_type, progressing backwards through the parent classes of the neurodata_type to find the most specific neurodata_type in `neurodata_vis_spec`. Some of these types are containers for other types, and create accordian UI elements for its contents, which are then passed into the `neurodata_vis_spec` and rendered accordingly.
 

nwbwidgets/panel.py

@@ -6,6 +6,7 @@
 import ipywidgets as widgets
 from dandi.dandiapi import DandiAPIClient
 from fsspec.implementations.cached import CachingFileSystem
+from ipyfilechooser import FileChooser
 from pynwb import NWBHDF5IO
 from tqdm.notebook import tqdm
 
@@ -48,7 +49,6 @@ def __init__(
 
         self.source_options_names = list()
         if enable_local_source:
-            self.source_options_names.append("Local dir")
             self.source_options_names.append("Local file")
         if enable_dandi_source:
             self.source_options_names.append("DANDI")
@@ -83,8 +83,8 @@ def __init__(
         self.source_options_radio.observe(self.updated_source, "value")
 
         if enable_local_source:
-            self.source_options_radio.value = "Local dir"
-            self.create_components_local_dir_source()
+            self.source_options_radio.value = "Local file"
+            self.create_components_local_file_source()
         elif enable_dandi_source:
             self.source_options_radio.value = "DANDI"
             self.create_components_dandi_source()
@@ -95,8 +95,6 @@ def updated_source(self, args=None):
             self.create_components_dandi_source()
         elif args["new"] == "S3":
             self.create_components_s3_source()
-        elif args["new"] == "Local dir":
-            self.create_components_local_dir_source()
         elif args["new"] == "Local file":
             self.create_components_local_file_source()
 
@@ -111,7 +109,7 @@ def create_components_dandi_source(self, args=None):
             dandiset_options.append(item_name)
 
         self.source_dandi_id = widgets.Dropdown(
-            options=dandiset_options,
+            options=sorted(dandiset_options),
             description="Dandiset:",
             layout=widgets.Layout(width="400px", overflow=None),
         )
@@ -182,69 +180,28 @@ def create_components_s3_source(self):
         self.source_s3_button.on_click(self.stream_s3_file)
         self.cache_checkbox.observe(self.toggle_cache)
 
-    def create_components_local_dir_source(self):
-        """Create widgets components for Loca dir option"""
-        self.local_dir_path = widgets.Text(
-            value="",
-            description="Dir path:",
-            layout=widgets.Layout(width="400px", overflow=None),
-        )
-        self.local_dir_button = widgets.Button(description="Search")
-        self.local_dir_top = widgets.HBox(
-            children=[self.local_dir_path, self.local_dir_button],
-            layout=widgets.Layout(padding="5px 0px 5px 0px"),
-        )
-        self.local_dir_files = widgets.Dropdown(
-            options=[],
-            description="Files:",
-            layout=widgets.Layout(width="400px", overflow=None),
-        )
-        self.local_dir_file_button = widgets.Button(icon="check", description="Load file")
-        self.local_dir_panel = widgets.VBox(
-            children=[
-                self.local_dir_top,
-                self.local_dir_files,
-                self.local_dir_file_button,
-            ],
-            layout=widgets.Layout(padding="5px 0px 5px 0px"),
-        )
-        self.source_changing_panel.children = [self.local_dir_panel]
-        self.local_dir_button.on_click(self.list_local_dir_files)
-        self.local_dir_file_button.on_click(self.load_local_dir_file)
-
     def create_components_local_file_source(self):
         """Create widgets components for Local file option"""
-        self.local_file_path = widgets.Text(
-            value="",
-            description="File path:",
-            layout=widgets.Layout(width="400px", overflow=None),
-        )
-        self.local_file_button = widgets.Button(icon="check", description="Load file")
+        self.local_file_chooser = FileChooser()
+        self.local_file_chooser.sandbox_path = str(Path.cwd())
+        self.local_file_chooser.filter_pattern = ["*.nwb"]
+        self.local_file_chooser.title = "<b>Select local NWB file</b>"
+        self.local_file_chooser.register_callback(self.load_local_file)
         self.local_file_panel = widgets.VBox(
-            children=[self.local_file_path, self.local_file_button],
+            children=[self.local_file_chooser],
             layout=widgets.Layout(padding="5px 0px 5px 0px"),
         )
         self.source_changing_panel.children = [self.local_file_panel]
-        self.local_file_button.on_click(self.load_local_file)
 
     def list_dandiset_files_dropdown(self, args=None):
         """Populate dropdown with all files and text area with summary"""
         self.dandi_summary.value = "Loading dandiset info..."
         self.source_dandi_file_dropdown.options = []
         dandiset_id = self.source_dandi_id.value.split("-")[0].strip()
         self.source_dandi_file_dropdown.options = list_dandiset_files(dandiset_id=dandiset_id)
-
         metadata = get_dandiset_metadata(dandiset_id=dandiset_id)
         self.dandi_summary.value = "<style>p{word-wrap: break-word}</style> <p>" + metadata.description + "</p>"
 
-    def list_local_dir_files(self, args=None):
-        """List NWB files in local dir"""
-        if Path(self.local_dir_path.value).is_dir():
-            all_files = [f.name for f in Path(self.local_dir_path.value).glob("*.nwb")]
-            self.local_dir_files.options = all_files
-        else:
-            print("Invalid local dir path")
-
     def stream_dandiset_file(self, args=None):
         """Stream NWB file from DANDI"""
         self.widgets_panel.children = [widgets.Label("loading...")]
@@ -290,19 +247,14 @@ def _stream_s3_file(self, s3_url):
         self.nwbfile = self.io.read()
         self.widgets_panel.children = [nwb2widget(self.nwbfile)]
 
-    def load_local_dir_file(self, args=None):
-        """Load local NWB file"""
-        full_file_path = str(Path(self.local_dir_path.value) / self.local_dir_files.value)
-        io = NWBHDF5IO(full_file_path, mode="r", load_namespaces=True)
-        nwb = io.read()
-        self.widgets_panel.children = [nwb2widget(nwb)]
-
     def load_local_file(self, args=None):
         """Load local NWB file"""
-        full_file_path = str(Path(self.local_file_path.value))
-        io = NWBHDF5IO(full_file_path, mode="r", load_namespaces=True)
-        nwb = io.read()
-        self.widgets_panel.children = [nwb2widget(nwb)]
+        full_file_path = str(Path(self.local_file_chooser.selected))
+        if self.io:
+            self.io.close()
+        self.io = NWBHDF5IO(full_file_path, mode="r", load_namespaces=True)
+        self.nwbfile = self.io.read()
+        self.widgets_panel.children = [nwb2widget(self.nwbfile)]
 
     def process_dandiset(self, dandiset):
         try:

nwbwidgets/utils/dandi.py

@@ -11,7 +11,7 @@ def get_dandiset_metadata(dandiset_id: str):
 def list_dandiset_files(dandiset_id: str):
     with DandiAPIClient() as client:
         dandiset = client.get_dandiset(dandiset_id=dandiset_id, version_id="draft")
-        return [i.dict().get("path") for i in dandiset.get_assets() if i.dict().get("path").endswith(".nwb")]
+        return sorted([i.dict().get("path") for i in dandiset.get_assets() if i.dict().get("path").endswith(".nwb")])
 
 
 def get_file_url(dandiset_id: str, file_path: str):

requirements.txt

@@ -20,3 +20,4 @@ fsspec
 requests
 aiohttp
 ipydatawidgets==4.3.2
+ipyfilechooser==0.6.0

test/test_file.py

@@ -27,7 +27,6 @@ def test_panel():
     assert isinstance(panel, widgets.Widget)
 
     # Change dropdown options for coverage
-    panel.source_options_radio.value = "Local dir"
     panel.source_options_radio.value = "Local file"
     panel.source_options_radio.value = "S3"
     panel.source_options_radio.value = "DANDI"