Qt gui

qt/README.md

@@ -0,0 +1,15 @@
+## Running locally from source
+
+Install the dependencies and run the `application.py` script:
+```bash
+$ pip install -r requirements.txt
+$ python application.py
+```
+
+## Packaging the GUI as executable
+
+Further reference and options: https://pyinstaller.org/en/stable/index.html
+
+```bash
+$ pyinstaller application.py
+```

qt/application.py

@@ -0,0 +1,273 @@
+from PySide6.QtWidgets import (
+    QApplication, 
+    QMainWindow, 
+    QPushButton, 
+    QWidget,
+    QVBoxLayout, 
+    QHBoxLayout, 
+    QComboBox, 
+    QStyle,
+    QTextBrowser,
+    QLineEdit,
+    QFileDialog
+)
+from PySide6.QtCore import Qt
+from qtvoila import QtVoila
+import sys
+import webbrowser
+from pathlib import Path
+
+from utils.dandi import (
+    get_all_dandisets_metadata, 
+    get_dandiset_metadata,
+    list_dandiset_files, 
+    get_file_url
+)
+
+
+class MyApp(QMainWindow):
+    def __init__(self, parent=None):
+        super().__init__(parent)
+        self.resize(800, 800)
+        self.setWindowTitle('Desktop DANDI Explorer')
+
+        try:
+            self.all_dandisets_metadata = get_all_dandisets_metadata()
+        except BaseException as e:
+            self.all_dandisets_metadata = list()
+            print("Failed to fetch DANDI archive datasets: ", e)
+
+        # Voila widget
+        self.voila_widget = QtVoila(
+            parent=self,
+            strip_sources=True,
+        )
+
+        # Select source
+        self.source_choice = QComboBox()
+        self.source_choice.currentTextChanged.connect(self.change_data_source)
+        # self.source_choice.addItem(QIcon(':/static/icon_dandi.svg'), "DANDI")
+        self.source_choice.addItem("Local dir")
+        self.source_choice.addItem("Local file")
+        self.source_choice.addItem("DANDI archive")
+
+        # Main Layout
+        self.layout = QVBoxLayout()
+        self.layout.addWidget(self.source_choice, stretch=0)
+        self.layout.addWidget(self.voila_widget, stretch=1)
+
+        self.create_folder_layout()
+
+        self.main_widget = QWidget(self)
+        self.main_widget.setLayout(self.layout)
+        self.setCentralWidget(self.main_widget)
+        self.show()
+
+
+    def change_data_source(self, value):
+        self.delete_item_from_layout()
+        if value == "DANDI archive":
+            self.create_dandi_layout()
+        elif value == "Local dir":
+            self.create_folder_layout()
+        elif value == "Local file":
+            self.create_file_layout()
+
+
+    def delete_item_from_layout(self):
+        # Ref: https://stackoverflow.com/a/9899475/11483674
+        child = self.layout.takeAt(1)
+        child.widget().deleteLater()
+
+
+    def browser_local_folder(self):
+        folder_path = QFileDialog.getExistingDirectory(parent=self, caption='Open folder', dir=str(Path.home()))
+        if folder_path:
+            for f in Path(folder_path).glob("*.nwb"):
+                 self.all_folder_files.addItem(str(f))
+
+
+    def browser_local_file(self):
+        filename, filter = QFileDialog.getOpenFileName(parent=self, caption='Open file', dir=str(Path.home()), filter='NWB Files (*.nwb)')
+        if filename:
+            self.chosen_file.setText(filename)
+
+
+    def create_folder_layout(self):
+        browser_folder_button = QPushButton()
+        icon = self.style().standardIcon(QStyle.SP_DialogOpenButton)
+        browser_folder_button.setIcon(icon)
+        browser_folder_button.setToolTip("Browser local dir")
+        browser_folder_button.clicked.connect(self.browser_local_folder)
+
+        self.all_folder_files = QComboBox()
+
+        accept_folder_file_button = QPushButton()
+        icon_2 = self.style().standardIcon(QStyle.SP_FileDialogContentsView)
+        accept_folder_file_button.setIcon(icon_2)
+        accept_folder_file_button.setToolTip("Visualize NWB file")
+        accept_folder_file_button.clicked.connect(self.pass_code_to_voila_widget)        
+
+        hbox = QHBoxLayout()
+        hbox.addWidget(browser_folder_button, stretch=0)
+        hbox.addWidget(self.all_folder_files, stretch=1)
+        hbox.addWidget(accept_folder_file_button, stretch=0)
+        w = QWidget()
+        w.setLayout(hbox)
+
+        self.layout.insertWidget(1, w)
+
+
+    def create_file_layout(self):
+        browser_file_button = QPushButton()
+        icon = self.style().standardIcon(QStyle.SP_DialogOpenButton)
+        browser_file_button.setIcon(icon)
+        browser_file_button.setToolTip("Browser local dir")
+        browser_file_button.clicked.connect(self.browser_local_file)
+
+        self.chosen_file = QLineEdit()
+
+        accept_file_button = QPushButton()
+        icon_2 = self.style().standardIcon(QStyle.SP_FileDialogContentsView)
+        accept_file_button.setIcon(icon_2)
+        accept_file_button.setToolTip("Visualize NWB file")
+        accept_file_button.clicked.connect(self.pass_code_to_voila_widget)
+
+        hbox = QHBoxLayout()
+        hbox.addWidget(browser_file_button, stretch=0)
+        hbox.addWidget(self.chosen_file, stretch=1)
+        hbox.addWidget(accept_file_button, stretch=0)
+        w = QWidget()
+        w.setLayout(hbox)
+
+        self.layout.insertWidget(1, w)
+
+
+    def create_dandi_layout(self):
+        self.dandiset_choice = QComboBox()
+        for m in self.all_dandisets_metadata:
+            item_name = m.id.split(":")[1].split("/")[0] + " - " + m.name
+            self.dandiset_choice.addItem(item_name)
+        self.dandiset_choice.view().setVerticalScrollBarPolicy(Qt.ScrollBarPolicy.ScrollBarAsNeeded)
+
+        accept_dandiset_choice = QPushButton()
+        icon_1 = self.style().standardIcon(QStyle.SP_ArrowDown)
+        accept_dandiset_choice.setIcon(icon_1)
+        accept_dandiset_choice.setToolTip("Read DANDI set")
+        accept_dandiset_choice.clicked.connect(self.list_dandiset_files)
+
+        open_dandiset_choice = QPushButton()
+        icon_2 = self.style().standardIcon(QStyle.SP_ComputerIcon)
+        open_dandiset_choice.setIcon(icon_2)
+        open_dandiset_choice.setToolTip("Open in DANDI Archive")
+        open_dandiset_choice.clicked.connect(self.open_webbrowser)
+
+        hbox1 = QHBoxLayout()
+        hbox1.addWidget(self.dandiset_choice, stretch=1)
+        hbox1.addWidget(accept_dandiset_choice, stretch=0)
+        hbox1.addWidget(open_dandiset_choice, stretch=0)
+        hbox1_w = QWidget()
+        hbox1_w.setLayout(hbox1)
+
+        # Summary info
+        self.info_summary = QTextBrowser()
+        self.info_summary.setOpenExternalLinks(True)
+        self.info_summary.setStyleSheet("font-size: 14px; background: rgba(0,0,0,0%);")
+        self.info_summary.setFixedHeight(100)
+
+        # Select file
+        self.dandi_file_choice = QComboBox()
+        self.dandi_file_choice.view().setVerticalScrollBarPolicy(Qt.ScrollBarPolicy.ScrollBarAsNeeded)
+        accept_file_choice = QPushButton()
+        icon_3 = self.style().standardIcon(QStyle.SP_FileDialogContentsView)
+        accept_file_choice.setIcon(icon_3)
+        accept_file_choice.setToolTip("Visualize NWB file")
+        accept_file_choice.clicked.connect(self.pass_code_to_voila_widget)
+
+        hbox2 = QHBoxLayout()
+        hbox2.addWidget(self.dandi_file_choice, stretch=1)
+        hbox2.addWidget(accept_file_choice, stretch=0)
+        hbox2_w = QWidget()
+        hbox2_w.setLayout(hbox2)
+
+        dandi_source_layout = QVBoxLayout()
+        dandi_source_layout.addWidget(hbox1_w, stretch=0)
+        dandi_source_layout.addWidget(self.info_summary, stretch=0)
+        dandi_source_layout.addWidget(hbox2_w, stretch=0)
+        w = QWidget()
+        w.setLayout(dandi_source_layout)
+
+        self.layout.insertWidget(1, w)
+
+
+    def open_webbrowser(self):
+        dandiset_id = self.dandiset_choice.currentText().split("-")[0].strip()
+        metadata = get_dandiset_metadata(dandiset_id=dandiset_id)
+        webbrowser.open(metadata.url)
+
+
+    def list_dandiset_files(self):
+        self.dandi_file_choice.clear()
+        dandiset_id = self.dandiset_choice.currentText().split("-")[0].strip()
+        self.info_summary.clear()
+        metadata = get_dandiset_metadata(dandiset_id=dandiset_id)
+        self.info_summary.append(metadata.description)
+        all_files = list_dandiset_files(dandiset_id=dandiset_id)
+        for f in all_files:
+            self.dandi_file_choice.addItem(f)
+
+
+    def pass_code_to_voila_widget(self):
+        self.voila_widget.external_notebook = None
+        self.voila_widget.clear()
+
+        if self.source_choice.currentText() == "DANDI archive":
+            file_url = get_file_url(
+                dandiset_id=self.dandiset_choice.currentText().split("-")[0].strip(), 
+                file_path=self.dandi_file_choice.currentText().strip()
+            )
+            code = f"""import fsspec
+import pynwb
+import h5py
+from fsspec.implementations.cached import CachingFileSystem
+from nwbwidgets import nwb2widget
+
+fs = CachingFileSystem(
+    fs=fsspec.filesystem("http"),
+    cache_storage="nwb-cache",  # Local folder for the cache
+)
+
+# next, open the file
+f = fs.open('{file_url}', "rb")
+file = h5py.File(f)
+io = pynwb.NWBHDF5IO(file=file, load_namespaces=True)
+nwbfile = io.read()
+nwb2widget(nwbfile)"""
+
+        elif self.source_choice.currentText() == "Local dir":
+            file_path = self.all_folder_files.currentText()
+            code = f"""import pynwb
+from nwbwidgets import nwb2widget
+
+io = pynwb.NWBHDF5IO('{file_path}', load_namespaces=True)
+nwbfile = io.read()
+nwb2widget(nwbfile)"""
+
+        elif self.source_choice.currentText() == "Local file":
+            file_path = self.chosen_file.text()
+            code = f"""import pynwb
+from nwbwidgets import nwb2widget
+
+io = pynwb.NWBHDF5IO('{file_path}', load_namespaces=True)
+nwbfile = io.read()
+nwb2widget(nwbfile)"""
+
+        self.voila_widget.add_notebook_cell(code=code, cell_type='code')
+        # Run Voila
+        self.voila_widget.run_voila()
+
+
+if __name__ == '__main__':
+    app = QApplication(sys.argv)
+    my_app = MyApp()
+    sys.exit(app.exec())

qt/requirements.txt

@@ -0,0 +1,3 @@
+qtvoila
+PySide6
+nwbwidgets

qt/utils/dandi.py

@@ -0,0 +1,33 @@
+from dandi.dandiapi import DandiAPIClient
+
+
+def get_all_dandisets_metadata():
+    with DandiAPIClient() as client:
+        all_metadata = list()
+        for ii, m in enumerate(client.get_dandisets()):
+            if ii > 150 and ii < 160:
+                try:
+                    all_metadata.append(m.get_metadata())
+                except:
+                    pass
+            else:
+                pass
+    return all_metadata
+
+
+def get_dandiset_metadata(dandiset_id: str):
+    with DandiAPIClient() as client:
+        dandiset = client.get_dandiset(dandiset_id=dandiset_id, version_id="draft")
+        return dandiset.get_metadata()
+
+
+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()]
+
+
+def get_file_url(dandiset_id:str, file_path: str):
+    with DandiAPIClient() as client:
+        asset = client.get_dandiset(dandiset_id, 'draft').get_asset_by_path(file_path)
+        return asset.get_content_url(follow_redirects=1, strip_query=True)