adding pyqt6 and switching to qtpy

Author: carsen-stringer

.github/workflows/test_and_deploy.yml

@@ -41,7 +41,8 @@ jobs:
           sudo apt-get update
           sudo apt-get install -y libdbus-1-3 libxkbcommon-x11-0 libxcb-icccm4 \
             libxcb-image0 libxcb-keysyms1 libxcb-randr0 libxcb-render-util0 \
-            libxcb-xinerama0 libxcb-xinput0 libxcb-xfixes0 pkg-config libhdf5-103 libhdf5-dev
+            libxcb-xinerama0 libxcb-xinput0 libxcb-xfixes0 pkg-config libhdf5-103 libhdf5-dev \
+            libegl1
       # strategy borrowed from vispy for installing opengl libs on windows
       - name: Install Windows OpenGL
         if: runner.os == 'Windows'

setup.py

@@ -11,17 +11,17 @@
         "scipy>=1.9.0",
         "scikit-learn",
         "cellpose",
+        "scanimage-tiff-reader>=1.4.1"
         ]
 
 gui_deps = [
-        "pyqt5",
-        "pyqt5-tools",
-        "pyqt5.sip",
+        "qtpy",
+        "pyqt6",
+        "pyqt6.sip",
         "pyqtgraph",
       ]
 
 io_deps = [
-    "scanimage-tiff-reader>=1.4.1",
     "paramiko",
     "nd2",
     "sbxreader",

suite2p/gui/buttons.py

@@ -2,8 +2,8 @@
 Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
 """
 import numpy as np
-from PyQt5 import QtGui, QtCore
-from PyQt5.QtWidgets import QPushButton, QButtonGroup, QLabel, QLineEdit
+from qtpy import QtGui, QtCore
+from qtpy.QtWidgets import QPushButton, QButtonGroup, QLabel, QLineEdit
 
 
 def make_selection(parent):

suite2p/gui/classgui.py

@@ -5,8 +5,8 @@
 import shutil
 
 import numpy as np
-from PyQt5 import QtGui
-from PyQt5.QtWidgets import QDialog, QLabel, QPushButton, QMessageBox, QFileDialog, QListWidget, QGridLayout, QWidget, QAbstractItemView
+from qtpy import QtGui
+from qtpy.QtWidgets import QDialog, QLabel, QPushButton, QMessageBox, QFileDialog, QListWidget, QGridLayout, QWidget, QAbstractItemView
 
 from . import masks
 from .. import classification

suite2p/gui/drawroi.py

@@ -6,8 +6,8 @@
 
 import numpy as np
 import pyqtgraph as pg
-from PyQt5 import QtGui, QtCore
-from PyQt5.QtWidgets import QPushButton, QLabel, QLineEdit, QMainWindow, QGridLayout, QButtonGroup, QMessageBox, QWidget
+from qtpy import QtGui, QtCore
+from qtpy.QtWidgets import QPushButton, QLabel, QLineEdit, QMainWindow, QGridLayout, QButtonGroup, QMessageBox, QWidget
 from matplotlib.colors import hsv_to_rgb
 from scipy import stats
 

suite2p/gui/graphics.py

@@ -3,7 +3,7 @@
 """
 import numpy as np
 import pyqtgraph as pg
-from PyQt5 import QtCore
+from qtpy import QtCore
 from pyqtgraph import Point
 from pyqtgraph import functions as fn
 from pyqtgraph.graphicsItems.ViewBox.ViewBoxMenu import ViewBoxMenu

suite2p/gui/gui2p.py

@@ -5,8 +5,8 @@
 
 import numpy as np
 import pyqtgraph as pg
-from PyQt5 import QtGui, QtCore
-from PyQt5.QtWidgets import QMainWindow, QApplication, QWidget, QGridLayout, QCheckBox, QLineEdit, QLabel
+from qtpy import QtGui, QtCore
+from qtpy.QtWidgets import QMainWindow, QApplication, QWidget, QGridLayout, QCheckBox, QLineEdit, QLabel
 
 from . import menus, io, merge, views, buttons, classgui, traces, graphics, masks
 from .. import run_s2p, default_ops

suite2p/gui/io.py

@@ -4,8 +4,8 @@
 import os, time
 import numpy as np
 import scipy.io
-from PyQt5 import QtGui
-from PyQt5.QtWidgets import QFileDialog, QMessageBox
+from qtpy import QtGui
+from qtpy.QtWidgets import QFileDialog, QMessageBox
 
 from . import utils, masks, views, graphics, traces, classgui
 from .. import io

suite2p/gui/masks.py

@@ -5,8 +5,8 @@
 import matplotlib.cm
 import numpy as np
 import pyqtgraph as pg
-from PyQt5 import QtGui, QtCore
-from PyQt5.QtWidgets import QPushButton, QButtonGroup, QLabel, QComboBox, QLineEdit
+from qtpy import QtGui, QtCore
+from qtpy.QtWidgets import QPushButton, QButtonGroup, QLabel, QComboBox, QLineEdit
 from matplotlib.colors import hsv_to_rgb
 
 import suite2p.gui.merge

suite2p/gui/menus.py

@@ -1,8 +1,8 @@
 """
 Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
 """
-from PyQt5 import QtGui
-from PyQt5.QtWidgets import QAction, QMenu
+from qtpy import QtGui
+from qtpy.QtWidgets import QAction, QMenu
 from pkg_resources import iter_entry_points
 
 from . import reggui, drawroi, merge, io, rungui, visualize, classgui

suite2p/gui/merge.py

@@ -4,8 +4,8 @@
 import os
 import numpy as np
 import pyqtgraph as pg
-from PyQt5 import QtGui
-from PyQt5.QtWidgets import QDialog, QLineEdit, QGridLayout, QMessageBox, QLabel, QPushButton, QWidget
+from qtpy import QtGui
+from qtpy.QtWidgets import QDialog, QLineEdit, QGridLayout, QMessageBox, QLabel, QPushButton, QWidget
 from scipy import stats
 
 from . import masks, io

suite2p/gui/reggui.py

@@ -7,9 +7,9 @@
 
 import numpy as np
 import pyqtgraph as pg
-from PyQt5 import QtGui, QtCore
-from PyQt5.QtWidgets import QStyle
-from PyQt5.QtWidgets import QMainWindow, QGridLayout, QCheckBox, QLabel, QLineEdit, QSlider, QFileDialog, QPushButton, QToolButton, QButtonGroup, QWidget
+from qtpy import QtGui, QtCore
+from qtpy.QtWidgets import QStyle
+from qtpy.QtWidgets import QMainWindow, QGridLayout, QCheckBox, QLabel, QLineEdit, QSlider, QFileDialog, QPushButton, QToolButton, QButtonGroup, QWidget
 from scipy.ndimage import gaussian_filter1d
 from natsort import natsorted
 from tifffile import imread

suite2p/gui/rungui.py

@@ -1,13 +1,13 @@
 """
 Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
 """
-import glob, json, os, shutil, pathlib
+import glob, json, os, shutil, pathlib, sys
 from datetime import datetime
 
 import numpy as np
 
-from PyQt5 import QtGui, QtCore
-from PyQt5.QtWidgets import QDialog, QLineEdit, QLabel, QPushButton, QWidget, QGridLayout, QButtonGroup, QComboBox, QTextEdit, QFileDialog
+from qtpy import QtGui, QtCore
+from qtpy.QtWidgets import QDialog, QLineEdit, QLabel, QPushButton, QWidget, QGridLayout, QButtonGroup, QComboBox, QTextEdit, QFileDialog
 
 from cellpose.models import get_user_models, model_path, MODEL_NAMES
 
@@ -444,11 +444,14 @@ def run_S2P(self):
         shutil.copy(os.path.join(self.ops_path, "ops%d.npy" % self.f), ops_file)
         shutil.copy(os.path.join(self.ops_path, "db%d.npy" % self.f), db_file)
         self.db = np.load(db_file, allow_pickle=True).item()
-        print("Running suite2p!")
-        print("starting process")
         print(self.db)
-        self.process.start('python -u -W ignore -m suite2p --ops "%s" --db "%s"' %
-                           (ops_file, db_file))
+        print("Running suite2p with command:")
+        cmd = f"-u -W ignore -m suite2p --ops {ops_file} --db {db_file}"
+        print("python " + cmd)
+        self.process.start(sys.executable, cmd.split(" "))
+
+        #self.process.start('python -u -W ignore -m suite2p --ops "%s" --db "%s"' %
+        #                   (ops_file, db_file))
 
     def stop(self):
         self.finish = False

suite2p/gui/traces.py

@@ -2,8 +2,8 @@
 Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
 """
 import numpy as np
-from PyQt5 import QtGui, QtCore
-from PyQt5.QtWidgets import QLabel, QComboBox, QPushButton, QLineEdit, QCheckBox
+from qtpy import QtGui, QtCore
+from qtpy.QtWidgets import QLabel, QComboBox, QPushButton, QLineEdit, QCheckBox
 
 
 def plot_trace(parent):

suite2p/gui/views.py

@@ -2,9 +2,9 @@
 Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
 """
 import numpy as np
-from PyQt5 import QtGui, QtCore
-from PyQt5.QtWidgets import QPushButton, QSlider, QButtonGroup, QLabel, QStyle, QStyleOptionSlider, QApplication
-from PyQt5.QtGui import QPainter
+from qtpy import QtGui, QtCore
+from qtpy.QtWidgets import QPushButton, QSlider, QButtonGroup, QLabel, QStyle, QStyleOptionSlider, QApplication
+from qtpy.QtGui import QPainter
 
 from .. import extraction
 

suite2p/gui/visualize.py

@@ -6,9 +6,9 @@
 
 import numpy as np
 import pyqtgraph as pg
-from PyQt5 import QtGui, QtCore
-from PyQt5.QtWidgets import QStyle
-from PyQt5.QtWidgets import QWidget, QSlider, QMainWindow, QGridLayout, QStyleOptionSlider, QApplication, QLabel, QLineEdit, QPushButton, QComboBox, QCheckBox
+from qtpy import QtGui, QtCore
+from qtpy.QtWidgets import QStyle
+from qtpy.QtWidgets import QWidget, QSlider, QMainWindow, QGridLayout, QStyleOptionSlider, QApplication, QLabel, QLineEdit, QPushButton, QComboBox, QCheckBox
 from matplotlib import cm
 from rastermap.rastermap import Rastermap
 from scipy.ndimage import gaussian_filter1d
@@ -634,8 +634,8 @@ def activate(self):
         #model = np.load(os.path.join(parent.ops["save_path0"], "embedding.npy"))
         #model = np.load("embedding.npy", allow_pickle=True).item()
         self.isort1 = np.argsort(self.model.embedding[:, 0])
-        self.u = self.model.u
-        self.v = self.model.v
+        self.Usv = self.model.Usv
+        self.Vsv = self.model.Vsv
         self.comboBox.addItem("rastermap")
         #self.isort1, self.isort2 = mapping.main(self.sp,None,self.u,self.sv,self.v)
 
@@ -678,19 +678,16 @@ def compute_map(self):
         self.mapOn.setEnabled(False)
         self.tic = time.time()
         try:
-            self.model = Rastermap(n_components=ops["n_components"], n_X=ops["n_X"],
-                                   nPC=ops["nPC"], init=ops["init"], alpha=ops["alpha"],
-                                   K=ops["K"], constraints=ops["constraints"],
-                                   annealing=ops["annealing"])
+            self.model = Rastermap()
             self.model.fit(self.sp)
             #proc  = {"embedding": model.embedding, "uv": [model.u, model.v],
             #         "ops": ops, "filename": args.S, "train_time": train_time}
             #basename, fname = os.path.split(args.S)
             #np.save(os.path.join(basename, "embedding.npy"), proc)
-            print("raster map computed in %3.2f s" % (time.time() - self.tic))
             self.activate()
-        except:
+        except Exception as e:
             print("Rastermap issue: Interrupted by error (not finished)\n")
+            print(e)
         #self.process.start("python -u -W ignore -m rastermap --S %s --ops %s"%
         #                    (spath, opspath))
 
@@ -740,13 +737,9 @@ def sort_time(self):
                     "end_time": -1
                 }
                 if not hasattr(self, "isort2"):
-                    self.model = Rastermap(n_components=ops["n_components"],
-                                           n_X=ops["n_X"], nPC=ops["nPC"],
-                                           init=ops["init"], alpha=ops["alpha"],
-                                           K=ops["K"], constraints=ops["constraints"],
-                                           annealing=ops["annealing"])
-                    unorm = (self.u**2).sum(axis=0)**0.5
-                    self.model.fit(self.sp.T, u=self.v * unorm, v=self.u / unorm)
+                    self.model = Rastermap()
+                    #unorm = (self.u**2).sum(axis=0)**0.5
+                    self.model.fit(self.sp.T, Usv=self.Vsv, Vsv=self.Usv)
                     self.isort2 = np.argsort(self.model.embedding[:, 0])
                 self.tsort = self.isort2.astype(np.int32)
             else:
@@ -755,7 +748,7 @@ def sort_time(self):
 
     def neural_sorting(self, i):
         if i == 0:
-            self.isort = np.argsort(self.u[:, int(self.PCedit.text()) - 1])
+            self.isort = np.argsort(self.Usv[:, int(self.PCedit.text()) - 1])
         elif i == 1:
             self.isort = self.isort1
         if i < 2: