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Addresses #1454 using pyside6 #1455

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merged 6 commits into from
Feb 5, 2025
Merged

Addresses #1454 using pyside6 #1455

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8090e27
Addresses #1454 using pyside6
pgunn Jan 22, 2025
db6ddac
volpy_gui: change import errors based on a stackoverflow suggestion
pgunn Jan 22, 2025
96d8a06
Add pyside6 to pyproject - so many places to update things!
pgunn Jan 24, 2025
d1236ec
Add workaround to fix pyqtgraph issue 2380
pgunn Jan 27, 2025
66120c7
volpy_gui: use limits keyword, which makes the menu actually work
pgunn Jan 27, 2025
6ef1051
If we're going qt6, let's go qt6. Fix plugin path
pgunn Jan 27, 2025
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69 changes: 36 additions & 33 deletions caiman/source_extraction/volpy/volpy_gui.py
100644 → 100755
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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):
Expand Down Expand Up @@ -70,7 +74,7 @@ def mouseClickEvent(event):
roi = roi * 1.
except:
pass

elif mode == 'CHOOSE NEURONS':
pos = img.mapFromScene(event.pos())
p1.clear()
Expand Down Expand Up @@ -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:
Expand Down Expand Up @@ -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:
Expand All @@ -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])
Expand Down Expand Up @@ -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()
Expand All @@ -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)
Expand All @@ -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
Expand All @@ -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()
1 change: 1 addition & 0 deletions environment.yml
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Expand Up @@ -27,6 +27,7 @@ dependencies:
- psutil
- pynwb
- pyqtgraph
- pyside6
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I wonder if including this in the deps could create issues with opencv, last time I remember it wants to have its own qt installed. That's why I always use opencv-python-headless but I'm not sure if opencv windowed stuff still works but just using the existing qt then.

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Looks like it pulls in qt6-main, so it's at least a closer version; more likely than sticking with qt5-based distros but something to watch out for.

Unfortunately, right now I think some of the code uses opencv's ability to launch a qt-based GUI, I think. I'd need to check to find out where but I'm pretty sure we do it.

- scikit-image >=0.19.0
- scikit-learn >=1.2
- scipy >= 1.10.1
Expand Down
1 change: 1 addition & 0 deletions pyproject.toml
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Expand Up @@ -32,6 +32,7 @@ dependencies = [
"pims",
"psutil",
"pynwb",
"pyside6",
"scikit-image",
"scikit-learn",
"scipy",
Expand Down
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