Merge pull request #1455 from flatironinstitute/dev-volpy_qt6

Addresses #1454 using pyside6

caiman/source_extraction/volpy/volpy_gui.py

@@ -6,6 +6,13 @@
 and spike extraction step of VolPy.
 @author: @caichangjia
 """
+
+# These imports apparently must come before importing pyqtgraph on some platforms
+import PySide6
+from PySide6 import QtWidgets
+from PySide6.QtWidgets import QApplication
+from PySide6.QtGui import QShortcut
+
 import cv2
 import h5py
 import numpy as np
@@ -15,18 +22,15 @@
 from pyqtgraph import FileDialog
 from pyqtgraph.Qt import QtGui
 from pyqtgraph.parametertree import Parameter, ParameterTree
-import PyQt5
-from PyQt5 import QtWidgets
-from PyQt5.QtWidgets import QApplication, QShortcut
 import random
 from skimage.draw import polygon
 import sys
 
 import caiman as cm
 from caiman.external.cell_magic_wand import cell_magic_wand_single_point
-    
+
 os.environ["QT_QPA_PLATFORM_PLUGIN_PATH"] = os.fspath(
-    Path(PyQt5.__file__).resolve().parent / "Qt5" / "plugins")
+    Path(PySide6.__file__).resolve().parent / "Qt6" / "plugins")
 
 
 def mouseClickEvent(event):
@@ -70,7 +74,7 @@ def mouseClickEvent(event):
             roi = roi * 1.
         except:
             pass
-    
+
     elif mode == 'CHOOSE NEURONS':
         pos = img.mapFromScene(event.pos())
         p1.clear()
@@ -104,7 +108,7 @@ def add():
         roi = np.zeros((dims[1], dims[0]))
         ff = np.array(polygon(np.array(pts)[:,0], np.array(pts)[:,1]))
         roi[ff[1],[ff[0]]] = 1
-    
+
     if len(pts) > 2 :
         flag = True
         while flag:
@@ -187,7 +191,7 @@ def load_rois():
     if (l_ROIs.shape[2], l_ROIs.shape[1]) != dims:
         print(dims);print(l_ROIs.shape[1:])
         raise ValueError('Dimentions of movie and rois do not accord')
-    
+
     for roi in l_ROIs:
         flag = True
         while flag:
@@ -213,7 +217,7 @@ def save():
     print(ffll[0])
     save_ROIs = np.array(list(all_ROIs.values())).copy()
     save_ROIs = np.flip(save_ROIs, axis=1)
-    
+
     if os.path.splitext(ffll[0])[1] == '.hdf5':
         cm.movie(save_ROIs).save(ffll[0])
     summary_images = summary_images.transpose([0, 2, 1])
@@ -293,11 +297,13 @@ def overlay(all_ROIs):
 
 if __name__ == "__main__":    
     ## Always start by initializing Qt (only once per application)
+    if sys.platform == 'darwin':
+        PySide6.QtWidgets.QApplication.setStyle("fusion")
     app = QApplication(sys.argv)
-    
+
     ## Define a top-level widget to hold everything
     w = QtWidgets.QWidget()
-    
+
     ## Create some widgets to be placed inside
     hist = pg.HistogramLUTItem()  # Contrast/color control
     win = pg.GraphicsLayoutWidget()
@@ -307,11 +313,11 @@ def overlay(all_ROIs):
     p1 = pg.PlotWidget()
     neuron_action = ParameterTree()
     neuron_list = QtWidgets.QListWidget()
-    
+
     ## Create a grid layout to manage the widgets size and position
     layout = QtWidgets.QGridLayout()
     w.setLayout(layout)
-    
+
     ## Add widgets to the layout in their proper positions
     layout.addWidget(win, 0, 1)  
     layout.addWidget(p1, 0, 2)  
@@ -320,27 +326,27 @@ def overlay(all_ROIs):
     img = pg.ImageItem()
     p1.addItem(img)
     hist.setImageItem(img)
-    
+
     # Add actions    
-    params_action = [{'name': 'LOAD DATA', 'type':'action'},
-                     {'name': 'LOAD ROIS', 'type':'action'},
-                     {'name': 'SAVE', 'type':'action'},                 
-                     {'name': 'ADD', 'type': 'action'}, 
-                     {'name': 'REMOVE', 'type': 'action'}, 
-                     {'name': 'SHOW ALL', 'type': 'action'},
-                     {'name': 'CLEAR', 'type': 'action'}, 
-                     {'name': 'IMAGES', 'type': 'list', 'values': ['MEAN','CORR']},
-                     {'name': 'DISPLAY', 'type': 'list', 'values': ['CONTOUR','SPATIAL FOOTPRINTS']},
-                     {'name': 'MODE', 'type': 'list', 'values': ['POLYGON','CELL MAGIC WAND', 'CHOOSE NEURONS']},
+    params_action = [{'name': 'LOAD DATA', 'type': 'action'},
+                     {'name': 'LOAD ROIS', 'type': 'action'},
+                     {'name': 'SAVE',      'type': 'action'},
+                     {'name': 'ADD',       'type': 'action'},
+                     {'name': 'REMOVE',    'type': 'action'},
+                     {'name': 'SHOW ALL',  'type': 'action'},
+                     {'name': 'CLEAR',     'type': 'action'},
+                     {'name': 'IMAGES',    'type': 'list', 'limits': ['MEAN','CORR']},
+                     {'name': 'DISPLAY',   'type': 'list', 'limits': ['CONTOUR', 'SPATIAL FOOTPRINTS']},
+                     {'name': 'MODE',      'type': 'list', 'limits': ['POLYGON', 'CELL MAGIC WAND', 'CHOOSE NEURONS']},
                      {'name': 'MAGIC WAND PARAMS', 'type': 'group', 'children': [{'name': 'MIN RADIUS', 'type': 'int', 'value': 4},
                                                                         {'name': 'MAX RADIUS', 'type': 'int', 'value': 10},
                                                                         {'name': 'ROUGHNESS', 'type': 'int', 'value': 1}]}]
-    
+
     pars_action = Parameter.create(name='params_action', type='group', children=params_action) 
     neuron_action.setParameters(pars_action, showTop=False)
     neuron_action.setWindowTitle('Parameter Action')
     mode = pars_action.getValues()['MODE'][0]
-    
+
     # Add event
     p1.mousePressEvent = mouseClickEvent
     p1.mouseReleaseEvent = release
@@ -358,20 +364,17 @@ def overlay(all_ROIs):
     shortcut_up = QShortcut(QtGui.QKeySequence("up"), w)
     shortcut_up.activated.connect(up)
     neuron_list.itemClicked.connect(show_neuron)
-    
+
     # Create dictionary for saving 
     F = FileDialog()
     all_pts = {}
     all_centers = {}
     all_ROIs = {}
     pts = []
     pen = pg.mkPen(color=(255, 255, 0), width=4)#, style=Qt.DashDotLine)
-    
+
     ## Display the widget as a new window
     w.show()
-    
+
     ## Start the Qt event loop
-    app.exec_()
-
-
-
+    app.exec()

environment.yml

@@ -27,6 +27,7 @@ dependencies:
 - psutil
 - pynwb
 - pyqtgraph
+- pyside6
 - scikit-image >=0.19.0
 - scikit-learn >=1.2
 - scipy >= 1.10.1

pyproject.toml

@@ -33,6 +33,7 @@ dependencies = [
   "pims",
   "psutil",
   "pynwb",
+  "pyside6",
   "scikit-image",
   "scikit-learn",
   "scipy",