def init_ui(self):
FslWidget.init_ui(self)
data = self.options.add("Input data", DataOption(self.ivm), key="data")
data.sig_changed.connect(self._data_changed)
self.options.add("Output extracted brain image",
OutputNameOption(src_data=data, suffix="_brain"),
key="output-brain",
checked=True,
enabled=True)
self.options.add("Output brain mask",
OutputNameOption(src_data=data, suffix="_brain_mask"),
key="output-mask",
checked=True)
self.options.add("Intensity threshold",
NumericOption(minval=0, maxval=1, default=0.5),
key="thresh")
self.options.add("Head radius (mm)",
NumericOption(intonly=True,
minval=0,
maxval=300,
default=200),
key="radius",
checked=True)
self.centre = self.options.add("Brain centre (raw co-ordinates)",
PickPointOption(self.ivl),
key="centre",
checked=True)
def init_ui(self):
layout = QtGui.QVBoxLayout()
self.setLayout(layout)
title = TitleWidget(self, help="reg")
layout.addWidget(title)
if not self.reg_methods:
layout.addWidget(QtGui.QLabel("No registration methods found"))
layout.addStretch(1)
return
self.options = OptionBox("General Options")
self.options.add("Transform", TransformOption(self.ivm), key="transform")
self.options.add("Apply to data", DataOption(self.ivm), key="data")
self.options.add("Interpolation", ChoiceOption(["Nearest neighbour", "Linear", "Spline"], [0, 1, 3], default=1), key="interp-order")
self.options.add("Output name", OutputNameOption(src_data=self.options.option("data"), suffix="_reg"), key="output-name")
self.options.option("transform").sig_changed.connect(self._transform_changed)
layout.addWidget(self.options)
self.details = TransformDetails()
layout.addWidget(self.details)
layout.addWidget(RunButton(self))
layout.addStretch(1)
self._transform_changed()
def init_ui(self):
layout = QtGui.QVBoxLayout()
self.setLayout(layout)
title = TitleWidget(self, help="simple_maths")
layout.addWidget(title)
info = QtGui.QLabel(MATHS_INFO)
info.setWordWrap(True)
layout.addWidget(info)
self.optbox = OptionBox()
self.optbox.add("Data space from", DataOption(self.ivm), key="grid")
self.optbox.add("Command", TextOption(), key="cmd")
self.optbox.add("Output name",
OutputNameOption(src_data=self.optbox.option("grid")),
key="output-name")
self.optbox.add("Output is an ROI", BoolOption(), key="output-is-roi")
layout.addWidget(self.optbox)
hbox = QtGui.QHBoxLayout()
self.go_btn = RunButton(self)
hbox.addWidget(self.go_btn)
hbox.addStretch(1)
layout.addLayout(hbox)
layout.addStretch(1)
def init_ui(self):
layout = QtGui.QVBoxLayout()
self.setLayout(layout)
title = TitleWidget(self, title="Registration and Motion Correction", help="reg")
layout.addWidget(title)
if not self.reg_methods:
layout.addWidget(QtGui.QLabel("No registration methods found"))
layout.addStretch(1)
return
self.options = OptionBox("General Options")
self.options.add("Mode", ChoiceOption(["Registration", "Motion Correction"], ["reg", "moco"]), key="mode")
self.options.add("Method", ChoiceOption([method.display_name for method in self.reg_methods], self.reg_methods), key="method")
self.options.add("Registration data", DataOption(self.ivm), key="reg")
self.options.add("Reference data", DataOption(self.ivm), key="ref")
self.options.add("Reference volume", ChoiceOption(["Middle volume", "Mean volume", "Specified volume"], ["median", "mean", "idx"]), key="ref-vol")
self.options.add("Reference volume index", NumericOption(intonly=True), key="ref-idx")
self.options.add("Output space", ChoiceOption(["Reference", "Registration", "Transformed"], ["ref", "reg", "trans"]), key="output-space")
self.options.add("Output name", OutputNameOption(src_data=self.options.option("reg"), suffix="_reg"), key="output-name", checked=True)
self.options.add("Also apply transform to", DataOption(self.ivm, multi=True), key="add-reg")
self.options.add("Save transformation", TextOption(), key="save-transform", checked=True, default=False)
self.options.option("mode").sig_changed.connect(self._update_option_visibility)
self.options.option("method").sig_changed.connect(self._method_changed)
self.options.option("ref").sig_changed.connect(self._update_option_visibility)
self.options.option("ref-vol").sig_changed.connect(self._update_option_visibility)
self.options.option("reg").sig_changed.connect(self._update_option_visibility)
layout.addWidget(self.options)
# Create the options boxes for reg methods - only one visible at a time!
self.opt_boxes = {}
for method in self.reg_methods:
hbox = QtGui.QHBoxLayout()
opt_box = QtGui.QGroupBox()
opt_box.setTitle(method.display_name)
vbox = QtGui.QVBoxLayout()
opt_box.setLayout(vbox)
vbox.addWidget(method.interface())
hbox.addWidget(opt_box)
opt_box.setVisible(False)
layout.addLayout(hbox)
self.opt_boxes[method.name] = opt_box
layout.addWidget(RunWidget(self))
layout.addStretch(1)
self._method_changed()
def init_ui(self):
vbox = QtGui.QVBoxLayout()
self.setLayout(vbox)
title = TitleWidget(
self,
title="PCA reduction",
subtitle="Principal Component Analysis for 4D data")
vbox.addWidget(title)
self._options = OptionBox("Options")
self._options.add("Data",
DataOption(self.ivm, include_3d=False),
key="data")
self._options.add("ROI",
DataOption(self.ivm, data=False, rois=True),
key="roi")
self._options.add("Number of components",
NumericOption(minval=1, intonly=True, default=4),
key="n-components")
self._options.add("Output name",
OutputNameOption(
src_data=self._options.option("data"),
suffix="_pca"),
key="output-name")
self._options.option("data").sig_changed.connect(self._data_changed)
vbox.addWidget(self._options)
self._run = RunWidget(self)
self._run.sig_postrun.connect(self._postrun)
vbox.addWidget(self._run)
self.plot = Plot(qpo=None, parent=self, title="PCA modes")
self.variance_model = QtGui.QStandardItemModel()
variance_table = QtGui.QTableView()
variance_table.verticalHeader().hide()
variance_table.setModel(self.variance_model)
tabs = QtGui.QTabWidget()
tabs.addTab(self.plot, "PCA modes")
tabs.addTab(variance_table, "Explained variance")
tabs.setCurrentWidget(self.plot)
vbox.addWidget(tabs)
vbox.addStretch(1)
self._data_changed()
def init_ui(self):
vbox = QtGui.QVBoxLayout()
self.setLayout(vbox)
title = TitleWidget(self, title="Simulate Motion", help="sim_motion")
vbox.addWidget(title)
self.option_box = OptionBox("Options")
data = self.option_box.add("Data set",
DataOption(self.ivm,
include_4d=True,
include_3d=False),
key="data")
self.option_box.add("Random translation standard deviation (mm)",
NumericOption(minval=0,
maxval=5,
default=1,
decimals=2),
key="std")
self.option_box.add(
"Random rotation standard deviation (\N{DEGREE SIGN})",
NumericOption(minval=0, maxval=10, default=1, decimals=2),
key="std_rot")
self.option_box.add("Padding (mm)",
NumericOption(minval=0,
maxval=10,
default=5,
decimals=1),
key="padding",
checked=True)
self.option_box.add(
"Interpolation",
ChoiceOption(["Nearest neighbour", "Linear", "Quadratic", "Cubic"],
return_values=range(4),
default=3),
key="order")
self.option_box.add("Output name",
OutputNameOption(src_data=data, suffix="_moving"),
key="output-name")
vbox.addWidget(self.option_box)
run_btn = QtGui.QPushButton('Run', self)
run_btn.clicked.connect(self.run)
vbox.addWidget(run_btn)
vbox.addStretch(1)
def init_ui(self):
vbox = QtGui.QVBoxLayout()
self.setLayout(vbox)
vbox.addWidget(TitleWidget(self))
self.optbox = OptionBox("Resampling options")
self.data = self.optbox.add("Data to resample",
DataOption(self.ivm),
key="data")
self.resample_type = self.optbox.add(
"Resampling method",
ChoiceOption(
["On to grid from another data set", "Upsample", "Downsample"],
["data", "up", "down"]),
key="type")
self.grid_data = self.optbox.add("Use grid from",
DataOption(self.ivm),
key="grid")
self.factor = self.optbox.add("Factor",
NumericOption(default=2,
minval=2,
maxval=10,
intonly=True),
key="factor")
self.slicewise = self.optbox.add("2D only", BoolOption(), key="2d")
self.order = self.optbox.add(
"Interpolation",
ChoiceOption(["Nearest neighbour", "Linear", "Quadratic", "Cubic"],
[0, 1, 2, 3],
default=1),
key="order")
self.output_name = self.optbox.add("Output name",
OutputNameOption(src_data=self.data,
suffix="_res"),
key="output-name")
vbox.addWidget(self.optbox)
self.resample_type.sig_changed.connect(self._resample_type_changed)
self.run = RunButton("Resample", self._run)
vbox.addWidget(self.run)
vbox.addStretch(1)
self._resample_type_changed()
def init_ui(self):
FabberWidget.init_ui(self)
self.param_values_box = OptionBox("Parameter values")
self.param_values_box.sig_changed.connect(self._param_values_changed)
self.vbox.addWidget(self.param_values_box)
run_btn = QtGui.QPushButton('Generate test data', self)
run_btn.clicked.connect(self._run)
self.vbox.addWidget(run_btn)
self.vbox.addStretch(1)
model_opts_btn = QtGui.QPushButton('Model Options')
model_opts_btn.clicked.connect(self._show_model_options)
self.options.add("Model group", ChoiceOption(), key="model-group")
self.options.add("Model", ChoiceOption(), model_opts_btn, key="model")
self.options.add("Number of volumes (time points)", NumericOption(intonly=True, minval=1, maxval=100, default=10), key="num-vols")
self.options.add("Voxels per patch (approx)", NumericOption(intonly=True, minval=1, maxval=10000, default=1000), key="num-voxels")
self.options.add("Noise (Gaussian std.dev)", NumericOption(intonly=True, minval=0, maxval=1000, default=0), key="noise")
self.options.add("Output data name", OutputNameOption(initial="fabber_test_data"), key="output-name")
self.options.add("Output noise-free data", BoolOption(), key="save-clean")
self.options.add("Output parameter ROIs", BoolOption(), key="save-rois")
self.options.option("model-group").sig_changed.connect(self._model_group_changed)
model_groups = ["ALL"]
for group in FabberProcess.api().get_model_groups():
model_groups.append(group.upper())
self.options.option("model-group").setChoices(model_groups)
self.options.option("model-group").value = "ALL"
self._model_group_changed()
self.options.option("model").value = "poly"
self._options_changed()
# Start with something sensible for the polynomial model
self._param_test_values = {"c0" : [-100, 0, 100], "c1" : [-10, 0, 10], "c2" : [-1, 0, 1]}
self._update_params()
def init_ui(self):
vbox = QtGui.QVBoxLayout()
self.setLayout(vbox)
vbox.addWidget(TitleWidget(self))
optbox = OptionBox("Resampling options")
self.data = optbox.add("Data to resample", DataOption(self.ivm))
self.grid_data = optbox.add("Resample onto grid from",
DataOption(self.ivm))
self.order = optbox.add(
"Interpolation",
ChoiceOption(["Nearest neighbour", "Linear", "Quadratic", "Cubic"],
[0, 1, 2, 3]))
self.output_name = optbox.add(
"Output name", OutputNameOption(src_data=self.data, suffix="_res"))
vbox.addWidget(optbox)
self.run = RunButton("Resample", self._run)
vbox.addWidget(self.run)
vbox.addStretch(1)
def init_ui(self):
vbox = QtGui.QVBoxLayout()
self.setLayout(vbox)
title = TitleWidget(self, title="Add Noise", help="noise")
vbox.addWidget(title)
self.option_box = OptionBox("Options")
data = self.option_box.add("Data set",
DataOption(self.ivm),
key="data")
self.option_box.add("Gaussian standard deviation",
NumericOption(minval=0, maxval=100, default=50),
key="std")
self.option_box.add("Output name",
OutputNameOption(src_data=data, suffix="_noisy"),
key="output-name")
vbox.addWidget(self.option_box)
run_btn = QtGui.QPushButton('Run', self)
run_btn.clicked.connect(self.run)
vbox.addWidget(run_btn)
vbox.addStretch(1)
def init_ui(self):
vbox = QtGui.QVBoxLayout()
self.setLayout(vbox)
title = TitleWidget(self, title="Simulate Motion", help="sim_motion")
vbox.addWidget(title)
self.option_box = OptionBox("Options")
data = self.option_box.add("Data set",
DataOption(self.ivm,
include_4d=True,
include_3d=False),
key="data")
self.option_box.add("Motion standard deviation (mm)",
NumericOption(minval=0,
maxval=5,
default=1,
decimals=2),
key="std")
self.option_box.add("Padding (mm)",
NumericOption(minval=0,
maxval=10,
default=5,
decimals=1),
key="padding",
checked=True)
self.option_box.add("Output name",
OutputNameOption(src_data=data, suffix="_moving"),
key="output-name")
vbox.addWidget(self.option_box)
run_btn = QtGui.QPushButton('Run', self)
run_btn.clicked.connect(self.run)
vbox.addWidget(run_btn)
vbox.addStretch(1)