rapidtide 3.0.11__py3-none-any.whl → 3.1__py3-none-any.whl

rapidtide/tests/test_fullrunhappy_v2.py

@@ -45,8 +45,6 @@ def test_fullrunhappy_v2(debug=False, local=False, displayplots=False):
         os.path.join(exampleroot, "sub-HAPPYTEST_smallmask.nii.gz"),
         "--mklthreads",
         "-1",
-        "--model",
-        "model_revised_tf2",
         "--fliparteries",
         "--temporalregression",
         "--cardiacfile",

rapidtide/tests/test_fullrunhappy_v3.py

@@ -45,6 +45,7 @@ def test_fullrunhappy_v3(debug=False, local=False, displayplots=False):
         os.path.join(exampleroot, "sub-HAPPYTEST_smallmask.nii.gz"),
         "--mklthreads",
         "-1",
+        "--usetensorflow",
         "--model",
         "model_revised_tf2",
         "--cardcalconly",

rapidtide/tests/test_fullrunhappy_v4.py

@@ -45,8 +45,8 @@ def test_fullrunhappy_v4(debug=False, local=False, displayplots=False):
         os.path.join(exampleroot, "sub-HAPPYTEST_smallmask.nii.gz"),
         "--mklthreads",
         "-1",
-        "--model",
-        "model_revised_tf2",
+        "--usetensorflow",
+        "--usenewvesselmethod",
         "--motionfile",
         os.path.join(exampleroot, "sub-HAPPYTEST_mcf.par"),
         "--aliasedcorrelation",

rapidtide/tests/test_fullrunrapidtide_v7.py

@@ -81,7 +81,7 @@ def test_fullrunrapidtide_v7(debug=False, local=False, displayplots=False):
     rapidtide_retroregress.retroregress(rapidtide_retroregress.process_args(inputargs=inputargs))
 
     # check to see that rapidtide and retroregress output match
-    msethresh = 1e-6
+    msethresh = 2e-6
     aethresh = 2
     tclist = ["brain", "GM", "WM", "CSF"]
     for timecourse in tclist:

rapidtide/tests/test_simroundtrip.py

@@ -37,7 +37,6 @@ def test_simroundtrip(debug=False, local=False, displayplots=False):
         exampleroot = get_examples_path()
         testtemproot = get_test_temp_path()
 
-
     # run initial rapidtide
     inputargs = [
         os.path.join(exampleroot, "sub-RAPIDTIDETEST.nii.gz"),
@@ -63,16 +62,18 @@ def test_simroundtrip(debug=False, local=False, displayplots=False):
     inputargs = [
         "1.5",
         "260",
-        os.path.join( testtemproot, "sub-RAPIDTIDETESTSIM_desc-unfiltmean_map.nii.gz"),
-        os.path.join( testtemproot, "simulatedfmri_vn05"),
+        os.path.join(testtemproot, "sub-RAPIDTIDETESTSIM_desc-unfiltmean_map.nii.gz"),
+        os.path.join(testtemproot, "simulatedfmri_vn05"),
         "--lfopctfile",
-        os.path.join( testtemproot, "sub-RAPIDTIDETESTSIM_desc-maxcorr_map.nii.gz"),
+        os.path.join(testtemproot, "sub-RAPIDTIDETESTSIM_desc-maxcorr_map.nii.gz"),
         "--lfolagfile",
-        os.path.join( testtemproot, "sub-RAPIDTIDETESTSIM_desc-maxtimerefined_map.nii.gz"),
+        os.path.join(testtemproot, "sub-RAPIDTIDETESTSIM_desc-maxtimerefined_map.nii.gz"),
         "--lforegressor",
-        os.path.join(testtemproot, "sub-RAPIDTIDETESTSIM_desc-movingregressor_timeseries.json:pass2"),
+        os.path.join(
+            testtemproot, "sub-RAPIDTIDETESTSIM_desc-movingregressor_timeseries.json:pass2"
+        ),
         "--voxelnoiselevel",
-        "5.0"
+        "5.0",
     ]
 
     pf.generic_init(rapidtide_simdata._get_parser, rapidtide_simdata.simdata, inputargs=inputargs)
@@ -118,7 +119,6 @@ def test_simroundtrip(debug=False, local=False, displayplots=False):
         )"""
 
 
-
 if __name__ == "__main__":
     mpl.use("TkAgg")
     test_simroundtrip(debug=True, local=True, displayplots=True)

rapidtide/tests/utils.py

@@ -23,9 +23,10 @@ Utility functions for testing rapidtide.
 import os
 
 import numpy as np
+import numpy.typing as npt
 
 
-def get_rapidtide_root():
+def get_rapidtide_root() -> str:
     """
     Returns the path to the base rapidtide directory, terminated with separator.
     Based on function by Yaroslav Halchenko used in Neurosynth Python package.
@@ -34,7 +35,7 @@ def get_rapidtide_root():
     return os.path.join(thisdir, "..") + os.path.sep
 
 
-def get_scripts_path():
+def get_scripts_path() -> str:
     """
     Returns the path to test datasets, terminated with separator. Test-related
     data are kept in tests folder in "testdata".
@@ -43,7 +44,7 @@ def get_scripts_path():
     return os.path.realpath(os.path.join(get_rapidtide_root(), "scripts")) + os.path.sep
 
 
-def get_test_data_path():
+def get_test_data_path() -> str:
     """
     Returns the path to test datasets, terminated with separator. Test-related
     data are kept in tests folder in "testdata".
@@ -52,7 +53,7 @@ def get_test_data_path():
     return os.path.realpath(os.path.join(get_rapidtide_root(), "tests", "testdata")) + os.path.sep
 
 
-def get_test_target_path():
+def get_test_target_path() -> str:
     """
     Returns the path to test comparison data, terminated with separator. Test-related
     data are kept in tests folder in "testtargets".
@@ -63,7 +64,7 @@ def get_test_target_path():
     )
 
 
-def get_test_temp_path():
+def get_test_temp_path() -> str:
     """
     Returns the path to test temporary directory, terminated with separator.
     Based on function by Yaroslav Halchenko used in Neurosynth Python package.
@@ -71,7 +72,7 @@ def get_test_temp_path():
     return os.path.realpath(os.path.join(get_rapidtide_root(), "tests", "tmp")) + os.path.sep
 
 
-def get_examples_path():
+def get_examples_path() -> str:
     """
     Returns the path to examples src directory, where larger test files live, terminated with separator. Test-related
     data are kept in tests folder in "data".
@@ -83,7 +84,7 @@ def get_examples_path():
     )
 
 
-def create_dir(thedir, debug=False):
+def create_dir(thedir: str, debug: bool = False) -> None:
     # create a directory if it doesn't exist
     try:
         os.makedirs(thedir)
@@ -96,7 +97,7 @@ def create_dir(thedir, debug=False):
             pass
 
 
-def mse(ndarr1, ndarr2):
+def mse(ndarr1: npt.NDArray, ndarr2: npt.NDArray) -> np.floating:
     """
     Compute mean-squared error.
     """

rapidtide/tidepoolTemplate.py

@@ -15,7 +15,9 @@ class Ui_MainWindow(object):
     def setupUi(self, MainWindow):
         MainWindow.setObjectName("MainWindow")
         MainWindow.resize(1129, 909)
-        sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.MinimumExpanding, QtWidgets.QSizePolicy.MinimumExpanding)
+        sizePolicy = QtWidgets.QSizePolicy(
+            QtWidgets.QSizePolicy.MinimumExpanding, QtWidgets.QSizePolicy.MinimumExpanding
+        )
         sizePolicy.setHorizontalStretch(1)
         sizePolicy.setVerticalStretch(1)
         sizePolicy.setHeightForWidth(MainWindow.sizePolicy().hasHeightForWidth())
@@ -27,7 +29,9 @@ class Ui_MainWindow(object):
         self.centralwidget.setObjectName("centralwidget")
         self.logOutput_groupBox = QtWidgets.QGroupBox(self.centralwidget)
         self.logOutput_groupBox.setGeometry(QtCore.QRect(440, 520, 671, 171))
-        sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Expanding)
+        sizePolicy = QtWidgets.QSizePolicy(
+            QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Expanding
+        )
         sizePolicy.setHorizontalStretch(0)
         sizePolicy.setVerticalStretch(0)
         sizePolicy.setHeightForWidth(self.logOutput_groupBox.sizePolicy().hasHeightForWidth())
@@ -44,7 +48,9 @@ class Ui_MainWindow(object):
         self.logOutput.setObjectName("logOutput")
         self.imageData_groupBox = QtWidgets.QGroupBox(self.centralwidget)
         self.imageData_groupBox.setGeometry(QtCore.QRect(10, 0, 1100, 312))
-        sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.MinimumExpanding, QtWidgets.QSizePolicy.Preferred)
+        sizePolicy = QtWidgets.QSizePolicy(
+            QtWidgets.QSizePolicy.MinimumExpanding, QtWidgets.QSizePolicy.Preferred
+        )
         sizePolicy.setHorizontalStretch(0)
         sizePolicy.setVerticalStretch(0)
         sizePolicy.setHeightForWidth(self.imageData_groupBox.sizePolicy().hasHeightForWidth())
@@ -60,11 +66,15 @@ class Ui_MainWindow(object):
         self.layoutWidget.setGeometry(QtCore.QRect(10, 20, 1074, 286))
         self.layoutWidget.setObjectName("layoutWidget")
         self.largeimage_horizontalLayout = QtWidgets.QHBoxLayout(self.layoutWidget)
-        self.largeimage_horizontalLayout.setSizeConstraint(QtCore.Qt.QLayout.SizeConstraint.SetNoConstraint)
+        self.largeimage_horizontalLayout.setSizeConstraint(
+            QtCore.Qt.QLayout.SizeConstraint.SetNoConstraint
+        )
         self.largeimage_horizontalLayout.setContentsMargins(0, 0, 0, 0)
         self.largeimage_horizontalLayout.setObjectName("largeimage_horizontalLayout")
         self.main_graphicsView_ax = GraphicsLayoutWidget(self.layoutWidget)
-        sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.MinimumExpanding, QtWidgets.QSizePolicy.MinimumExpanding)
+        sizePolicy = QtWidgets.QSizePolicy(
+            QtWidgets.QSizePolicy.MinimumExpanding, QtWidgets.QSizePolicy.MinimumExpanding
+        )
         sizePolicy.setHorizontalStretch(0)
         sizePolicy.setVerticalStretch(0)
         sizePolicy.setHeightForWidth(self.main_graphicsView_ax.sizePolicy().hasHeightForWidth())
@@ -77,7 +87,9 @@ class Ui_MainWindow(object):
         self.main_graphicsView_ax.setObjectName("main_graphicsView_ax")
         self.largeimage_horizontalLayout.addWidget(self.main_graphicsView_ax)
         self.main_graphicsView_cor = GraphicsLayoutWidget(self.layoutWidget)
-        sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.MinimumExpanding, QtWidgets.QSizePolicy.MinimumExpanding)
+        sizePolicy = QtWidgets.QSizePolicy(
+            QtWidgets.QSizePolicy.MinimumExpanding, QtWidgets.QSizePolicy.MinimumExpanding
+        )
         sizePolicy.setHorizontalStretch(0)
         sizePolicy.setVerticalStretch(0)
         sizePolicy.setHeightForWidth(self.main_graphicsView_cor.sizePolicy().hasHeightForWidth())
@@ -90,7 +102,9 @@ class Ui_MainWindow(object):
         self.main_graphicsView_cor.setObjectName("main_graphicsView_cor")
         self.largeimage_horizontalLayout.addWidget(self.main_graphicsView_cor)
         self.main_graphicsView_sag = GraphicsLayoutWidget(self.layoutWidget)
-        sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.MinimumExpanding, QtWidgets.QSizePolicy.MinimumExpanding)
+        sizePolicy = QtWidgets.QSizePolicy(
+            QtWidgets.QSizePolicy.MinimumExpanding, QtWidgets.QSizePolicy.MinimumExpanding
+        )
         sizePolicy.setHorizontalStretch(0)
         sizePolicy.setVerticalStretch(0)
         sizePolicy.setHeightForWidth(self.main_graphicsView_sag.sizePolicy().hasHeightForWidth())
@@ -103,7 +117,9 @@ class Ui_MainWindow(object):
         self.main_graphicsView_sag.setObjectName("main_graphicsView_sag")
         self.largeimage_horizontalLayout.addWidget(self.main_graphicsView_sag)
         self.graphicsView_colorbar = GraphicsView(self.layoutWidget)
-        sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.MinimumExpanding, QtWidgets.QSizePolicy.MinimumExpanding)
+        sizePolicy = QtWidgets.QSizePolicy(
+            QtWidgets.QSizePolicy.MinimumExpanding, QtWidgets.QSizePolicy.MinimumExpanding
+        )
         sizePolicy.setHorizontalStretch(0)
         sizePolicy.setVerticalStretch(0)
         sizePolicy.setHeightForWidth(self.graphicsView_colorbar.sizePolicy().hasHeightForWidth())
@@ -119,11 +135,17 @@ class Ui_MainWindow(object):
         self.verticalLayout_3.setSpacing(0)
         self.verticalLayout_3.setObjectName("verticalLayout_3")
         self.dispmax_doubleSpinBox = QtWidgets.QDoubleSpinBox(self.layoutWidget)
-        self.dispmax_doubleSpinBox.setAlignment(QtCore.Qt.Qt.AlignmentFlag.AlignRight|QtCore.Qt.Qt.AlignmentFlag.AlignTrailing|QtCore.Qt.Qt.AlignmentFlag.AlignVCenter)
+        self.dispmax_doubleSpinBox.setAlignment(
+            QtCore.Qt.Qt.AlignmentFlag.AlignRight
+            | QtCore.Qt.Qt.AlignmentFlag.AlignTrailing
+            | QtCore.Qt.Qt.AlignmentFlag.AlignVCenter
+        )
         self.dispmax_doubleSpinBox.setDecimals(3)
         self.dispmax_doubleSpinBox.setObjectName("dispmax_doubleSpinBox")
         self.verticalLayout_3.addWidget(self.dispmax_doubleSpinBox)
-        spacerItem = QtWidgets.QSpacerItem(20, 40, QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Expanding)
+        spacerItem = QtWidgets.QSpacerItem(
+            20, 40, QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Expanding
+        )
         self.verticalLayout_3.addItem(spacerItem)
         self.resetDispLimits_Button = QtWidgets.QPushButton(self.layoutWidget)
         self.resetDispLimits_Button.setObjectName("resetDispLimits_Button")
@@ -137,14 +159,20 @@ class Ui_MainWindow(object):
         self.setMask_Button = QtWidgets.QPushButton(self.layoutWidget)
         self.setMask_Button.setObjectName("setMask_Button")
         self.verticalLayout_3.addWidget(self.setMask_Button)
-        spacerItem1 = QtWidgets.QSpacerItem(20, 40, QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Expanding)
+        spacerItem1 = QtWidgets.QSpacerItem(
+            20, 40, QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Expanding
+        )
         self.verticalLayout_3.addItem(spacerItem1)
         self.transparency_checkBox = QtWidgets.QCheckBox(self.layoutWidget)
         self.transparency_checkBox.setChecked(False)
         self.transparency_checkBox.setObjectName("transparency_checkBox")
         self.verticalLayout_3.addWidget(self.transparency_checkBox)
         self.dispmin_doubleSpinBox = QtWidgets.QDoubleSpinBox(self.layoutWidget)
-        self.dispmin_doubleSpinBox.setAlignment(QtCore.Qt.Qt.AlignmentFlag.AlignRight|QtCore.Qt.Qt.AlignmentFlag.AlignTrailing|QtCore.Qt.Qt.AlignmentFlag.AlignVCenter)
+        self.dispmin_doubleSpinBox.setAlignment(
+            QtCore.Qt.Qt.AlignmentFlag.AlignRight
+            | QtCore.Qt.Qt.AlignmentFlag.AlignTrailing
+            | QtCore.Qt.Qt.AlignmentFlag.AlignVCenter
+        )
         self.dispmin_doubleSpinBox.setDecimals(3)
         self.dispmin_doubleSpinBox.setObjectName("dispmin_doubleSpinBox")
         self.verticalLayout_3.addWidget(self.dispmin_doubleSpinBox)
@@ -260,7 +288,9 @@ class Ui_MainWindow(object):
         self.largeimage_horizontalLayout.addLayout(self.verticalLayout_2)
         self.overlays_groupBox = QtWidgets.QGroupBox(self.centralwidget)
         self.overlays_groupBox.setGeometry(QtCore.QRect(10, 315, 421, 376))
-        sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Preferred)
+        sizePolicy = QtWidgets.QSizePolicy(
+            QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Preferred
+        )
         sizePolicy.setHorizontalStretch(0)
         sizePolicy.setVerticalStretch(0)
         sizePolicy.setHeightForWidth(self.overlays_groupBox.sizePolicy().hasHeightForWidth())
@@ -276,7 +306,9 @@ class Ui_MainWindow(object):
         self.overlay_radioButton_05.setObjectName("overlay_radioButton_05")
         self.overlay_graphicsView_01 = GraphicsLayoutWidget(self.overlays_groupBox)
         self.overlay_graphicsView_01.setGeometry(QtCore.QRect(10, 30, 198, 64))
-        sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Preferred, QtWidgets.QSizePolicy.Preferred)
+        sizePolicy = QtWidgets.QSizePolicy(
+            QtWidgets.QSizePolicy.Preferred, QtWidgets.QSizePolicy.Preferred
+        )
         sizePolicy.setHorizontalStretch(0)
         sizePolicy.setVerticalStretch(0)
         sizePolicy.setHeightForWidth(self.overlay_graphicsView_01.sizePolicy().hasHeightForWidth())
@@ -334,7 +366,9 @@ class Ui_MainWindow(object):
         self.overlay_radioButton_08.setObjectName("overlay_radioButton_08")
         self.overlay_graphicsView_04 = GraphicsLayoutWidget(self.overlays_groupBox)
         self.overlay_graphicsView_04.setGeometry(QtCore.QRect(10, 115, 192, 64))
-        sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Preferred, QtWidgets.QSizePolicy.Preferred)
+        sizePolicy = QtWidgets.QSizePolicy(
+            QtWidgets.QSizePolicy.Preferred, QtWidgets.QSizePolicy.Preferred
+        )
         sizePolicy.setHorizontalStretch(0)
         sizePolicy.setVerticalStretch(0)
         sizePolicy.setHeightForWidth(self.overlay_graphicsView_04.sizePolicy().hasHeightForWidth())
@@ -346,7 +380,9 @@ class Ui_MainWindow(object):
         self.overlay_graphicsView_04.setObjectName("overlay_graphicsView_04")
         self.overlay_graphicsView_06 = GraphicsLayoutWidget(self.overlays_groupBox)
         self.overlay_graphicsView_06.setGeometry(QtCore.QRect(220, 200, 192, 64))
-        sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Preferred, QtWidgets.QSizePolicy.Preferred)
+        sizePolicy = QtWidgets.QSizePolicy(
+            QtWidgets.QSizePolicy.Preferred, QtWidgets.QSizePolicy.Preferred
+        )
         sizePolicy.setHorizontalStretch(0)
         sizePolicy.setVerticalStretch(0)
         sizePolicy.setHeightForWidth(self.overlay_graphicsView_06.sizePolicy().hasHeightForWidth())
@@ -358,7 +394,9 @@ class Ui_MainWindow(object):
         self.overlay_graphicsView_06.setObjectName("overlay_graphicsView_06")
         self.overlay_graphicsView_03 = GraphicsLayoutWidget(self.overlays_groupBox)
         self.overlay_graphicsView_03.setGeometry(QtCore.QRect(220, 115, 192, 64))
-        sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Preferred, QtWidgets.QSizePolicy.Preferred)
+        sizePolicy = QtWidgets.QSizePolicy(
+            QtWidgets.QSizePolicy.Preferred, QtWidgets.QSizePolicy.Preferred
+        )
         sizePolicy.setHorizontalStretch(0)
         sizePolicy.setVerticalStretch(0)
         sizePolicy.setHeightForWidth(self.overlay_graphicsView_03.sizePolicy().hasHeightForWidth())
@@ -370,7 +408,9 @@ class Ui_MainWindow(object):
         self.overlay_graphicsView_03.setObjectName("overlay_graphicsView_03")
         self.overlay_graphicsView_08 = GraphicsLayoutWidget(self.overlays_groupBox)
         self.overlay_graphicsView_08.setGeometry(QtCore.QRect(220, 285, 192, 64))
-        sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Preferred, QtWidgets.QSizePolicy.Preferred)
+        sizePolicy = QtWidgets.QSizePolicy(
+            QtWidgets.QSizePolicy.Preferred, QtWidgets.QSizePolicy.Preferred
+        )
         sizePolicy.setHorizontalStretch(0)
         sizePolicy.setVerticalStretch(0)
         sizePolicy.setHeightForWidth(self.overlay_graphicsView_08.sizePolicy().hasHeightForWidth())
@@ -382,7 +422,9 @@ class Ui_MainWindow(object):
         self.overlay_graphicsView_08.setObjectName("overlay_graphicsView_08")
         self.overlay_graphicsView_05 = GraphicsLayoutWidget(self.overlays_groupBox)
         self.overlay_graphicsView_05.setGeometry(QtCore.QRect(10, 200, 192, 64))
-        sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Preferred, QtWidgets.QSizePolicy.Preferred)
+        sizePolicy = QtWidgets.QSizePolicy(
+            QtWidgets.QSizePolicy.Preferred, QtWidgets.QSizePolicy.Preferred
+        )
         sizePolicy.setHorizontalStretch(0)
         sizePolicy.setVerticalStretch(0)
         sizePolicy.setHeightForWidth(self.overlay_graphicsView_05.sizePolicy().hasHeightForWidth())
@@ -394,7 +436,9 @@ class Ui_MainWindow(object):
         self.overlay_graphicsView_05.setObjectName("overlay_graphicsView_05")
         self.overlay_graphicsView_02 = GraphicsLayoutWidget(self.overlays_groupBox)
         self.overlay_graphicsView_02.setGeometry(QtCore.QRect(220, 30, 192, 64))
-        sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Preferred, QtWidgets.QSizePolicy.Preferred)
+        sizePolicy = QtWidgets.QSizePolicy(
+            QtWidgets.QSizePolicy.Preferred, QtWidgets.QSizePolicy.Preferred
+        )
         sizePolicy.setHorizontalStretch(0)
         sizePolicy.setVerticalStretch(0)
         sizePolicy.setHeightForWidth(self.overlay_graphicsView_02.sizePolicy().hasHeightForWidth())
@@ -406,7 +450,9 @@ class Ui_MainWindow(object):
         self.overlay_graphicsView_02.setObjectName("overlay_graphicsView_02")
         self.overlay_graphicsView_07 = GraphicsLayoutWidget(self.overlays_groupBox)
         self.overlay_graphicsView_07.setGeometry(QtCore.QRect(10, 285, 192, 64))
-        sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Preferred, QtWidgets.QSizePolicy.Preferred)
+        sizePolicy = QtWidgets.QSizePolicy(
+            QtWidgets.QSizePolicy.Preferred, QtWidgets.QSizePolicy.Preferred
+        )
         sizePolicy.setHorizontalStretch(0)
         sizePolicy.setVerticalStretch(0)
         sizePolicy.setHeightForWidth(self.overlay_graphicsView_07.sizePolicy().hasHeightForWidth())
@@ -435,7 +481,9 @@ class Ui_MainWindow(object):
         self.overlay_graphicsView_07.raise_()
         self.histogram_groupBox = QtWidgets.QGroupBox(self.centralwidget)
         self.histogram_groupBox.setGeometry(QtCore.QRect(440, 315, 381, 201))
-        sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Expanding)
+        sizePolicy = QtWidgets.QSizePolicy(
+            QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Expanding
+        )
         sizePolicy.setHorizontalStretch(0)
         sizePolicy.setVerticalStretch(0)
         sizePolicy.setHeightForWidth(self.histogram_groupBox.sizePolicy().hasHeightForWidth())
@@ -445,7 +493,9 @@ class Ui_MainWindow(object):
         self.histogram_groupBox.setObjectName("histogram_groupBox")
         self.histogram_graphicsView = GraphicsLayoutWidget(self.histogram_groupBox)
         self.histogram_graphicsView.setGeometry(QtCore.QRect(10, 30, 361, 161))
-        sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.MinimumExpanding)
+        sizePolicy = QtWidgets.QSizePolicy(
+            QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.MinimumExpanding
+        )
         sizePolicy.setHorizontalStretch(0)
         sizePolicy.setVerticalStretch(0)
         sizePolicy.setHeightForWidth(self.histogram_graphicsView.sizePolicy().hasHeightForWidth())
@@ -461,7 +511,11 @@ class Ui_MainWindow(object):
         self.label_4.setObjectName("label_4")
         self.pixnumX_doubleSpinBox = QtWidgets.QDoubleSpinBox(self.mainimagedata_groupBox)
         self.pixnumX_doubleSpinBox.setGeometry(QtCore.QRect(30, 30, 67, 24))
-        self.pixnumX_doubleSpinBox.setAlignment(QtCore.Qt.Qt.AlignmentFlag.AlignRight|QtCore.Qt.Qt.AlignmentFlag.AlignTrailing|QtCore.Qt.Qt.AlignmentFlag.AlignVCenter)
+        self.pixnumX_doubleSpinBox.setAlignment(
+            QtCore.Qt.Qt.AlignmentFlag.AlignRight
+            | QtCore.Qt.Qt.AlignmentFlag.AlignTrailing
+            | QtCore.Qt.Qt.AlignmentFlag.AlignVCenter
+        )
         self.pixnumX_doubleSpinBox.setDecimals(0)
         self.pixnumX_doubleSpinBox.setObjectName("pixnumX_doubleSpinBox")
         self.label_7 = QtWidgets.QLabel(self.mainimagedata_groupBox)
@@ -472,7 +526,11 @@ class Ui_MainWindow(object):
         self.label_7.setObjectName("label_7")
         self.coordX_doubleSpinBox = QtWidgets.QDoubleSpinBox(self.mainimagedata_groupBox)
         self.coordX_doubleSpinBox.setGeometry(QtCore.QRect(100, 30, 67, 24))
-        self.coordX_doubleSpinBox.setAlignment(QtCore.Qt.Qt.AlignmentFlag.AlignRight|QtCore.Qt.Qt.AlignmentFlag.AlignTrailing|QtCore.Qt.Qt.AlignmentFlag.AlignVCenter)
+        self.coordX_doubleSpinBox.setAlignment(
+            QtCore.Qt.Qt.AlignmentFlag.AlignRight
+            | QtCore.Qt.Qt.AlignmentFlag.AlignTrailing
+            | QtCore.Qt.Qt.AlignmentFlag.AlignVCenter
+        )
         self.coordX_doubleSpinBox.setDecimals(3)
         self.coordX_doubleSpinBox.setObjectName("coordX_doubleSpinBox")
         self.label_9 = QtWidgets.QLabel(self.mainimagedata_groupBox)
@@ -483,22 +541,38 @@ class Ui_MainWindow(object):
         self.label_9.setObjectName("label_9")
         self.pixnumY_doubleSpinBox = QtWidgets.QDoubleSpinBox(self.mainimagedata_groupBox)
         self.pixnumY_doubleSpinBox.setGeometry(QtCore.QRect(30, 55, 67, 24))
-        self.pixnumY_doubleSpinBox.setAlignment(QtCore.Qt.Qt.AlignmentFlag.AlignRight|QtCore.Qt.Qt.AlignmentFlag.AlignTrailing|QtCore.Qt.Qt.AlignmentFlag.AlignVCenter)
+        self.pixnumY_doubleSpinBox.setAlignment(
+            QtCore.Qt.Qt.AlignmentFlag.AlignRight
+            | QtCore.Qt.Qt.AlignmentFlag.AlignTrailing
+            | QtCore.Qt.Qt.AlignmentFlag.AlignVCenter
+        )
         self.pixnumY_doubleSpinBox.setDecimals(0)
         self.pixnumY_doubleSpinBox.setObjectName("pixnumY_doubleSpinBox")
         self.coordY_doubleSpinBox = QtWidgets.QDoubleSpinBox(self.mainimagedata_groupBox)
         self.coordY_doubleSpinBox.setGeometry(QtCore.QRect(100, 55, 67, 24))
-        self.coordY_doubleSpinBox.setAlignment(QtCore.Qt.Qt.AlignmentFlag.AlignRight|QtCore.Qt.Qt.AlignmentFlag.AlignTrailing|QtCore.Qt.Qt.AlignmentFlag.AlignVCenter)
+        self.coordY_doubleSpinBox.setAlignment(
+            QtCore.Qt.Qt.AlignmentFlag.AlignRight
+            | QtCore.Qt.Qt.AlignmentFlag.AlignTrailing
+            | QtCore.Qt.Qt.AlignmentFlag.AlignVCenter
+        )
         self.coordY_doubleSpinBox.setDecimals(3)
         self.coordY_doubleSpinBox.setObjectName("coordY_doubleSpinBox")
         self.pixnumZ_doubleSpinBox = QtWidgets.QDoubleSpinBox(self.mainimagedata_groupBox)
         self.pixnumZ_doubleSpinBox.setGeometry(QtCore.QRect(30, 80, 67, 24))
-        self.pixnumZ_doubleSpinBox.setAlignment(QtCore.Qt.Qt.AlignmentFlag.AlignRight|QtCore.Qt.Qt.AlignmentFlag.AlignTrailing|QtCore.Qt.Qt.AlignmentFlag.AlignVCenter)
+        self.pixnumZ_doubleSpinBox.setAlignment(
+            QtCore.Qt.Qt.AlignmentFlag.AlignRight
+            | QtCore.Qt.Qt.AlignmentFlag.AlignTrailing
+            | QtCore.Qt.Qt.AlignmentFlag.AlignVCenter
+        )
         self.pixnumZ_doubleSpinBox.setDecimals(0)
         self.pixnumZ_doubleSpinBox.setObjectName("pixnumZ_doubleSpinBox")
         self.coordZ_doubleSpinBox = QtWidgets.QDoubleSpinBox(self.mainimagedata_groupBox)
         self.coordZ_doubleSpinBox.setGeometry(QtCore.QRect(100, 80, 67, 24))
-        self.coordZ_doubleSpinBox.setAlignment(QtCore.Qt.Qt.AlignmentFlag.AlignRight|QtCore.Qt.Qt.AlignmentFlag.AlignTrailing|QtCore.Qt.Qt.AlignmentFlag.AlignVCenter)
+        self.coordZ_doubleSpinBox.setAlignment(
+            QtCore.Qt.Qt.AlignmentFlag.AlignRight
+            | QtCore.Qt.Qt.AlignmentFlag.AlignTrailing
+            | QtCore.Qt.Qt.AlignmentFlag.AlignVCenter
+        )
         self.coordZ_doubleSpinBox.setDecimals(3)
         self.coordZ_doubleSpinBox.setObjectName("coordZ_doubleSpinBox")
         self.label_6 = QtWidgets.QLabel(self.mainimagedata_groupBox)
@@ -509,12 +583,20 @@ class Ui_MainWindow(object):
         self.label_8.setObjectName("label_8")
         self.coordT_doubleSpinBox = QtWidgets.QDoubleSpinBox(self.mainimagedata_groupBox)
         self.coordT_doubleSpinBox.setGeometry(QtCore.QRect(100, 130, 67, 24))
-        self.coordT_doubleSpinBox.setAlignment(QtCore.Qt.Qt.AlignmentFlag.AlignRight|QtCore.Qt.Qt.AlignmentFlag.AlignTrailing|QtCore.Qt.Qt.AlignmentFlag.AlignVCenter)
+        self.coordT_doubleSpinBox.setAlignment(
+            QtCore.Qt.Qt.AlignmentFlag.AlignRight
+            | QtCore.Qt.Qt.AlignmentFlag.AlignTrailing
+            | QtCore.Qt.Qt.AlignmentFlag.AlignVCenter
+        )
         self.coordT_doubleSpinBox.setDecimals(3)
         self.coordT_doubleSpinBox.setObjectName("coordT_doubleSpinBox")
         self.pixnumT_doubleSpinBox = QtWidgets.QDoubleSpinBox(self.mainimagedata_groupBox)
         self.pixnumT_doubleSpinBox.setGeometry(QtCore.QRect(30, 130, 67, 24))
-        self.pixnumT_doubleSpinBox.setAlignment(QtCore.Qt.Qt.AlignmentFlag.AlignRight|QtCore.Qt.Qt.AlignmentFlag.AlignTrailing|QtCore.Qt.Qt.AlignmentFlag.AlignVCenter)
+        self.pixnumT_doubleSpinBox.setAlignment(
+            QtCore.Qt.Qt.AlignmentFlag.AlignRight
+            | QtCore.Qt.Qt.AlignmentFlag.AlignTrailing
+            | QtCore.Qt.Qt.AlignmentFlag.AlignVCenter
+        )
         self.pixnumT_doubleSpinBox.setDecimals(0)
         self.pixnumT_doubleSpinBox.setObjectName("pixnumT_doubleSpinBox")
         self.label_3 = QtWidgets.QLabel(self.mainimagedata_groupBox)
@@ -541,7 +623,9 @@ class Ui_MainWindow(object):
         self.runMovieButton.setObjectName("runMovieButton")
         self.regressor_groupBox = QtWidgets.QGroupBox(self.centralwidget)
         self.regressor_groupBox.setGeometry(QtCore.QRect(10, 690, 1101, 181))
-        sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Expanding)
+        sizePolicy = QtWidgets.QSizePolicy(
+            QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Expanding
+        )
         sizePolicy.setHorizontalStretch(0)
         sizePolicy.setVerticalStretch(0)
         sizePolicy.setHeightForWidth(self.regressor_groupBox.sizePolicy().hasHeightForWidth())
@@ -551,10 +635,14 @@ class Ui_MainWindow(object):
         self.regressor_groupBox.setObjectName("regressor_groupBox")
         self.regressorspectrum_graphicsView = GraphicsLayoutWidget(self.regressor_groupBox)
         self.regressorspectrum_graphicsView.setGeometry(QtCore.QRect(490, 23, 472, 131))
-        sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.MinimumExpanding, QtWidgets.QSizePolicy.Preferred)
+        sizePolicy = QtWidgets.QSizePolicy(
+            QtWidgets.QSizePolicy.MinimumExpanding, QtWidgets.QSizePolicy.Preferred
+        )
         sizePolicy.setHorizontalStretch(0)
         sizePolicy.setVerticalStretch(0)
-        sizePolicy.setHeightForWidth(self.regressorspectrum_graphicsView.sizePolicy().hasHeightForWidth())
+        sizePolicy.setHeightForWidth(
+            self.regressorspectrum_graphicsView.sizePolicy().hasHeightForWidth()
+        )
         self.regressorspectrum_graphicsView.setSizePolicy(sizePolicy)
         self.regressorspectrum_graphicsView.setMinimumSize(QtCore.QSize(100, 100))
         self.regressorspectrum_graphicsView.setMaximumSize(QtCore.QSize(1000, 1000))
@@ -563,10 +651,14 @@ class Ui_MainWindow(object):
         self.regressortimecourse_graphicsView = GraphicsLayoutWidget(self.regressor_groupBox)
         self.regressortimecourse_graphicsView.setEnabled(True)
         self.regressortimecourse_graphicsView.setGeometry(QtCore.QRect(10, 23, 472, 131))
-        sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.MinimumExpanding, QtWidgets.QSizePolicy.Preferred)
+        sizePolicy = QtWidgets.QSizePolicy(
+            QtWidgets.QSizePolicy.MinimumExpanding, QtWidgets.QSizePolicy.Preferred
+        )
         sizePolicy.setHorizontalStretch(0)
         sizePolicy.setVerticalStretch(0)
-        sizePolicy.setHeightForWidth(self.regressortimecourse_graphicsView.sizePolicy().hasHeightForWidth())
+        sizePolicy.setHeightForWidth(
+            self.regressortimecourse_graphicsView.sizePolicy().hasHeightForWidth()
+        )
         self.regressortimecourse_graphicsView.setSizePolicy(sizePolicy)
         self.regressortimecourse_graphicsView.setMinimumSize(QtCore.QSize(100, 100))
         self.regressortimecourse_graphicsView.setMaximumSize(QtCore.QSize(1000, 1000))
@@ -628,12 +720,22 @@ class Ui_MainWindow(object):
         MainWindow.setWindowTitle(_translate("MainWindow", "MainWindow"))
         self.logOutput_groupBox.setTitle(_translate("MainWindow", "Information"))
         self.imageData_groupBox.setTitle(_translate("MainWindow", "Image Data"))
-        self.label.setText(_translate("MainWindow", "Click in image to position ROI.  Drag right or left to increase or decrease the ROI size"))
+        self.label.setText(
+            _translate(
+                "MainWindow",
+                "Click in image to position ROI.  Drag right or left to increase or decrease the ROI size",
+            )
+        )
         self.resetDispLimits_Button.setText(_translate("MainWindow", "Full Range"))
         self.resetDispSmart_Button.setText(_translate("MainWindow", "Smart"))
         self.saveDisp_Button.setText(_translate("MainWindow", "Save"))
         self.setMask_Button.setText(_translate("MainWindow", "No mask"))
-        self.transparency_checkBox.setToolTip(_translate("MainWindow", "With transparency on, map values outside the range limits are not displayed."))
+        self.transparency_checkBox.setToolTip(
+            _translate(
+                "MainWindow",
+                "With transparency on, map values outside the range limits are not displayed.",
+            )
+        )
         self.transparency_checkBox.setText(_translate("MainWindow", "Transparency"))
         self.label_2.setText(_translate("MainWindow", "Colormap"))
         self.gray_radioButton.setText(_translate("MainWindow", "Gray"))
@@ -681,4 +783,6 @@ class Ui_MainWindow(object):
         self.label_5.setText(_translate("MainWindow", "Timecourse (seconds)"))
         self.label_12.setText(_translate("MainWindow", "Power spectrum (Hz)"))
         self.actionQuit.setText(_translate("MainWindow", "Quit"))
+
+
 from pyqtgraph import GraphicsLayoutWidget, GraphicsView