Merge branch 'main' of github.com:MouseLand/Kilosort

Author: jacobpennington

kilosort/gui/converter.py

@@ -2,7 +2,7 @@
 from pathlib import Path
 
 import numpy as np
-from PyQt5 import QtCore, QtWidgets
+from qtpy import QtCore, QtWidgets
 from kilosort.io import (
     RecordingExtractorAsArray, BinaryRWFile, spikeinterface_to_binary, load_probe
     )
@@ -22,8 +22,8 @@
 
 
 class DataConversionBox(QtWidgets.QWidget):
-    disableInput = QtCore.pyqtSignal(bool)
-    fileObjectLoaded = QtCore.pyqtSignal(bool)
+    disableInput = QtCore.Signal(bool)
+    fileObjectLoaded = QtCore.Signal(bool)
 
     def __init__(self, gui):
         super().__init__()
@@ -134,7 +134,7 @@ def __init__(self, gui):
         self.setLayout(layout)
 
 
-    @QtCore.pyqtSlot()
+    @QtCore.Slot()
     def select_file(self):
         options = QtWidgets.QFileDialog.DontUseNativeDialog
         filename, _ = QtWidgets.QFileDialog.getOpenFileName(
@@ -148,7 +148,7 @@ def select_file(self):
         data_location = Path(filename).parent.as_posix()
         self.gui.qt_settings.setValue('last_data_location', data_location)
 
-    @QtCore.pyqtSlot()
+    @QtCore.Slot()
     def select_folder(self):
         options = QtWidgets.QFileDialog.DontUseNativeDialog
         directory = QtWidgets.QFileDialog.getExistingDirectory(
@@ -162,11 +162,11 @@ def select_folder(self):
         data_location = Path(directory).as_posix()
         self.gui.qt_settings.setValue('last_data_location', data_location)
 
-    @QtCore.pyqtSlot()
+    @QtCore.Slot()
     def select_filetype(self):
         self.filetype = self.filetype_selector.currentText()
 
-    @QtCore.pyqtSlot()
+    @QtCore.Slot()
     def set_stream_id(self):
         stream_id = self.stream_id_input.text()
         if stream_id is None or stream_id == '':
@@ -175,18 +175,18 @@ def set_stream_id(self):
             stream_id = stream_id
         self.stream_id = stream_id
 
-    @QtCore.pyqtSlot()
+    @QtCore.Slot()
     def set_stream_name(self):
         stream_name = self.stream_name_input.text()
         if stream_name == '':
             stream_name = None
         self.stream_name = stream_name
 
-    @QtCore.pyqtSlot()
+    @QtCore.Slot()
     def set_dtype(self):
         self.data_dtype = self.dtype_selector.currentText()
 
-    @QtCore.pyqtSlot()
+    @QtCore.Slot()
     def load_as_wrapper(self):
         if None in [self.filename, self.filetype, self.data_dtype]:
             logger.exception(
@@ -230,7 +230,7 @@ def load_as_wrapper(self):
             )
         self.gui.settings_box.check_load()
 
-    @QtCore.pyqtSlot()
+    @QtCore.Slot()
     def convert_to_binary(self):
         # TODO: add option to specify chunksize for conversion
         if None in [self.filename, self.filetype, self.data_dtype]:

kilosort/gui/data_view_box.py

@@ -2,16 +2,16 @@
 import pyqtgraph as pg
 from kilosort.gui.logger import setup_logger
 from kilosort.gui.palettes import COLORMAP_COLORS
-from PyQt5 import QtCore, QtWidgets
+from qtpy import QtCore, QtWidgets
 
 logger = setup_logger(__name__)
 
 
 class DataViewBox(QtWidgets.QGroupBox):
-    channelChanged = QtCore.pyqtSignal(int, int)
-    modeChanged = QtCore.pyqtSignal(str, int)
-    updateContext = QtCore.pyqtSignal(object)
-    intervalUpdated = QtCore.pyqtSignal()
+    channelChanged = QtCore.Signal(int, int)
+    modeChanged = QtCore.Signal(str, int)
+    updateContext = QtCore.Signal(object)
+    intervalUpdated = QtCore.Signal()
 
     def __init__(self, parent):
         QtWidgets.QGroupBox.__init__(self, parent=parent)
@@ -191,7 +191,7 @@ def setup(self):
 
         self.setLayout(layout)
 
-    @QtCore.pyqtSlot()
+    @QtCore.Slot()
     def on_tmin_edited(self):
         try:
             self.tmin = float(self.tmin_input.text())
@@ -201,7 +201,7 @@ def on_tmin_edited(self):
         except AssertionError:
             logger.exception('Invalid tmin,tmax: must have 0 <= tmin < tmax')
 
-    @QtCore.pyqtSlot()
+    @QtCore.Slot()
     def on_tmax_edited(self):
         try:
             self.tmax = float(self.tmax_input.text())
@@ -216,7 +216,7 @@ def check_time_interval(self):
         assert self.tmin >= 0
         assert self.tmin < self.tmax
 
-    @QtCore.pyqtSlot()
+    @QtCore.Slot()
     def on_views_clicked(self):
         current_state = {key: self.view_buttons[key].isChecked() for key in self._keys}
 
@@ -242,22 +242,22 @@ def on_views_clicked(self):
 
             self.update_plot()
 
-    @QtCore.pyqtSlot(float)
+    @QtCore.Slot(float)
     def on_wheel_scroll(self, direction):
         if self.context_set():
             self.shift_current_time(direction)
 
-    @QtCore.pyqtSlot(float)
+    @QtCore.Slot(float)
     def on_wheel_scroll_plus_control(self, direction):
         if self.context_set():
             self.change_displayed_channel_count(direction)
 
-    @QtCore.pyqtSlot(float)
+    @QtCore.Slot(float)
     def on_wheel_scroll_plus_shift(self, direction):
         if self.context_set():
             self.change_plot_range(direction)
 
-    @QtCore.pyqtSlot(float)
+    @QtCore.Slot(float)
     def on_wheel_scroll_plus_alt(self, direction):
         if self.context_set():
             self.change_plot_scaling(direction)
@@ -430,7 +430,7 @@ def change_sorting_status(self, status_dict):
         self.sorting_status = status_dict
         self.enable_view_buttons()
 
-    @QtCore.pyqtSlot()
+    @QtCore.Slot()
     def enable_view_buttons(self):
         self.raw_button.click()
 
@@ -474,11 +474,11 @@ def add_image_to_plot(self, raw_traces, level_min, level_max):
         self.colormap_image = image_item
         self.plot_item.addItem(image_item)
 
-    @QtCore.pyqtSlot(object)
+    @QtCore.Slot(object)
     def set_whitening_matrix(self, array):
         self.whitening_matrix = array
 
-    @QtCore.pyqtSlot(object)
+    @QtCore.Slot(object)
     def set_highpass_filter(self, filter):
         self.highpass_filter = filter
 
@@ -579,10 +579,10 @@ def _update_colormap(
 
 
 class KSPlotWidget(pg.PlotWidget):
-    signalChangeTimePoint = QtCore.pyqtSignal(float)
-    signalChangeChannel = QtCore.pyqtSignal(float)
-    signalChangeTimeRange = QtCore.pyqtSignal(float)
-    signalChangeScaling = QtCore.pyqtSignal(float)
+    signalChangeTimePoint = QtCore.Signal(float)
+    signalChangeChannel = QtCore.Signal(float)
+    signalChangeTimeRange = QtCore.Signal(float)
+    signalChangeScaling = QtCore.Signal(float)
 
     def __init__(self, *args, **kwargs):
         super(KSPlotWidget, self).__init__(*args, **kwargs)

kilosort/gui/header_box.py

@@ -1,6 +1,6 @@
 from kilosort import __version__
 from kilosort.gui.minor_gui_elements import help_popup_text, controls_popup_text
-from PyQt5 import QtCore, QtGui, QtWidgets
+from qtpy import QtCore, QtGui, QtWidgets
 
 
 class HeaderBox(QtWidgets.QWidget):
@@ -55,17 +55,17 @@ def __init__(self, parent):
         self.setLayout(self.layout)
 
 
-    @QtCore.pyqtSlot()
+    @QtCore.Slot()
     def check_auto_load(self):
         self.gui.auto_load = self.auto_load_check.isChecked()
         self.gui.qt_settings.setValue('auto_load', self.gui.auto_load)
 
-    @QtCore.pyqtSlot()
+    @QtCore.Slot()
     def check_show_plots(self):
         self.gui.show_plots = self.show_plots_check.isChecked()
         self.gui.qt_settings.setValue('show_plots', self.gui.show_plots)
 
-    @QtCore.pyqtSlot()
+    @QtCore.Slot()
     def clear_cache(self):
         self.gui.qt_settings.clear()
 

kilosort/gui/launch.py

@@ -2,7 +2,9 @@
 
 import pyqtgraph as pg
 from kilosort.gui import DarkPalette, KiloSortGUI
-from PyQt5 import QtWidgets
+from qtpy import QtWidgets, QtGui, QtCore
+from pathlib import Path
+from kilosort.utils import DOWNLOADS_DIR, download_url_to_file
 
 # TODO: figure out how to fix margin/padding around tooltip text.
 #       property-margin, margin-right not working as expected.
@@ -20,6 +22,25 @@ def launcher(filename=None):
     kilosort_application.setStyle("Fusion")
     kilosort_application.setPalette(DarkPalette())
     kilosort_application.setStyleSheet(_QSS)
+    
+    # get icon
+    DOWNLOADS_DIR.mkdir(parents=True, exist_ok=True)
+    icon_path = DOWNLOADS_DIR / "logo.png"
+    if not icon_path.is_file():
+        print("downloading logo")
+        download_url_to_file(
+            "https://www.kilosort.org/static/downloads/kilosort_logo_small.png",
+            icon_path, progress=True)
+    icon_path = str(icon_path.resolve())
+    app_icon = QtGui.QIcon()
+    app_icon.addFile(icon_path, QtCore.QSize(16, 16))
+    app_icon.addFile(icon_path, QtCore.QSize(24, 24))
+    app_icon.addFile(icon_path, QtCore.QSize(32, 32))
+    app_icon.addFile(icon_path, QtCore.QSize(48, 48))
+    app_icon.addFile(icon_path, QtCore.QSize(64, 64))
+    app_icon.addFile(icon_path, QtCore.QSize(256, 256))
+    
+    kilosort_application.setWindowIcon(app_icon)
 
     pg.setConfigOption("background", "k")
     pg.setConfigOption("foreground", "w")

kilosort/gui/logger.py

@@ -1,7 +1,7 @@
 import logging
 import sys
 
-from PyQt5 import QtCore
+from qtpy import QtCore
 
 
 class QtHandler(logging.Handler):
@@ -17,7 +17,7 @@ def emit(self, record):
 class XStream(QtCore.QObject):
     _stdout = None
     _stderr = None
-    messageWritten = QtCore.pyqtSignal(str)
+    messageWritten = QtCore.Signal(str)
 
     def flush(self):
         pass

kilosort/gui/main.py

@@ -13,7 +13,7 @@
 from kilosort.gui.logger import setup_logger
 from kilosort.io import BinaryFiltered
 from kilosort.utils import DOWNLOADS_DIR, download_probes
-from PyQt5 import QtCore, QtGui, QtWidgets
+from qtpy import QtCore, QtGui, QtWidgets
 
 logger = setup_logger(__name__)
 
@@ -275,7 +275,7 @@ def toggle_mode(self, mode):
         else:
             raise ValueError("Invalid mode requested!")
 
-    @QtCore.pyqtSlot(bool)
+    @QtCore.Slot(bool)
     def disable_all_input(self, value):
         self.settings_box.disable_all_input(value)
         self.run_box.disable_all_input(value)
@@ -417,13 +417,13 @@ def setup_context_for_run(self):
         self.load_data()
         self.context["params"] = self.params
 
-    @QtCore.pyqtSlot(object)
+    @QtCore.Slot(object)
     def update_context(self, context):
         self.context = context
         self.update_probe_view()
         self.update_data_view()
 
-    @QtCore.pyqtSlot()
+    @QtCore.Slot()
     def update_probe_view(self):
         self.probe_view_box.set_layout(self.context)
 
@@ -435,15 +435,15 @@ def update_run_box(self):
         self.run_box.set_data_path(self.data_path)
         self.run_box.set_results_directory(self.results_directory)
 
-    @QtCore.pyqtSlot()
+    @QtCore.Slot()
     def disable_run(self):
         self.run_box.disable_all_buttons()
 
-    @QtCore.pyqtSlot()
+    @QtCore.Slot()
     def enable_run(self):
         self.run_box.reenable_buttons()
 
-    @QtCore.pyqtSlot(dict)
+    @QtCore.Slot(dict)
     def update_sorting_status(self, status_dict):
         self.run_box.change_sorting_status(status_dict)
         self.data_view_box.change_sorting_status(status_dict)

kilosort/gui/message_log_box.py

@@ -1,7 +1,7 @@
 from pathlib import Path
 
 from kilosort.gui.logger import XStream
-from PyQt5 import QtCore, QtGui, QtWidgets
+from qtpy import QtCore, QtGui, QtWidgets
 
 
 class MessageLogBox(QtWidgets.QGroupBox):
@@ -35,18 +35,18 @@ def __init__(self, parent):
         XStream.stderr().messageWritten.connect(self.update_text)
 
 
-    @QtCore.pyqtSlot(str)
+    @QtCore.Slot(str)
     def update_text(self, text):
         self.log_box.moveCursor(QtGui.QTextCursor.End)
         self.log_box.appendPlainText(text)
         self.log_box.ensureCursorVisible()
         self.popout_window.update_text(text)
 
-    @QtCore.pyqtSlot()
+    @QtCore.Slot()
     def show_log_popout(self):
         self.popout_window.show()
 
-    @QtCore.pyqtSlot()
+    @QtCore.Slot()
     def dump_settings(self):
         # For debugging purposes, check for mismatch between displayed parameter
         # values and the values that are actually being used.

kilosort/gui/minor_gui_elements.py

@@ -1,6 +1,6 @@
 import numpy as np
 from kilosort.gui.logger import setup_logger
-from PyQt5 import QtGui, QtWidgets, QtCore
+from qtpy import QtGui, QtWidgets, QtCore
 
 logger = setup_logger(__name__)
 
@@ -247,8 +247,7 @@ def get_probe(self):
 Welcome to Kilosort4!
 
 ##### Documentation #####
-Pykilosort is the Python port of Kilosort2, which was originally written in Matlab.
-For documentation of the underlying algorithm or the GUI, please visit https://github.com/MouseLand/Kilosort/wiki
+For documentation of the underlying algorithm or the GUI, please visit https://github.com/MouseLand/Kilosort/
 or https://www.biorxiv.org/content/10.1101/2023.01.07.523036v1.
 
 ##### Troubleshooting #####

kilosort/gui/palettes.py

@@ -1,5 +1,5 @@
 import numpy as np
-from PyQt5 import QtGui
+from qtpy import QtGui
 
 
 class DarkPalette(QtGui.QPalette):