def init_ui(self):
vbox = QtGui.QVBoxLayout()
self.setLayout(vbox)
title = TitleWidget(self)
vbox.addWidget(title)
self.options = OptionBox("Options")
self.options.add("Data", DataOption(self.ivm, multi=True), key="data")
self.options.add("Within ROI", DataOption(self.ivm, data=False, rois=True, none_option=True), key="roi")
self.options.add("All volumes", BoolOption(default=False), key="allvols")
self.options.add("Y-axis scale", ChoiceOption(["Count", "Probability"]), key="yscale")
self.options.add("Number of bins", NumericOption(minval=5, maxval=500, default=100, intonly=True), key="bins")
self.options.add("Min value", NumericOption(minval=0, maxval=100, default=0), key="min")
self.options.add("Max value", NumericOption(minval=0, maxval=500, default=100), key="max")
self.options.option("yscale").sig_changed.connect(self._yscale_changed)
self.options.option("min").sig_changed.connect(self._min_changed)
self.options.option("min").sig_changed.connect(self._max_changed)
vbox.addWidget(self.options)
self.plot = Plot(qpo=None, parent=self, title="Data histogram", display_mode=False)
self.plot.set_xlabel("Data value")
self.plot.set_ylabel("Count")
vbox.addWidget(self.plot)
vbox.addStretch(1)
def init_ui(self):
vbox = QtGui.QVBoxLayout()
self.setLayout(vbox)
title = TitleWidget(self)
vbox.addWidget(title)
self._options = OptionBox("Options")
self._options.add("Signal data", DataOption(self.ivm), key="data")
self._clear_btn = QtGui.QPushButton("Clear points")
self._options.add("Method", ChoiceOption(["Pick points", "Use existing ROI"], ["points", "roi"]), self._clear_btn, key="method")
self._options.add("ROI", DataOption(self.ivm, data=False, rois=True), key="roi")
self._view_btn = QtGui.QPushButton("View")
self._view_btn.setEnabled(False)
self._save_btn = QtGui.QPushButton("Save")
self._save_btn.setEnabled(False)
self._options.add("AIF name", TextOption("aif"), self._view_btn, self._save_btn, key="output-name")
self._options.option("method").sig_changed.connect(self._method_changed)
self._options.option("data").sig_changed.connect(self._recalc_aif)
self._options.option("roi").sig_changed.connect(self._recalc_aif)
self._clear_btn.clicked.connect(self._clear_btn_clicked)
self._save_btn.clicked.connect(self._save_btn_clicked)
self._view_btn.clicked.connect(self._view_btn_clicked)
vbox.addWidget(self._options)
self._plot = Plot(qpo=None, parent=self, title="AIF", display_mode=False)
self._plot.set_xlabel("Volume")
self._plot.set_ylabel("Signal")
vbox.addWidget(self._plot)
vbox.addStretch(1)
def interface(self, generic_options=None):
if generic_options is None:
generic_options = {}
if self.options_widget is None:
self.options_widget = QtGui.QWidget()
vbox = QtGui.QVBoxLayout()
self.options_widget.setLayout(vbox)
cite = Citation(CITE_TITLE, CITE_AUTHOR, CITE_JOURNAL)
vbox.addWidget(cite)
self.optbox = OptionBox()
self.optbox.add("Mask for registration data",
DataOption(self.ivm, rois=True, data=False),
key="inmask",
checked=True)
self.optbox.add("Mask for reference data",
DataOption(self.ivm, rois=True, data=False),
key="refmask",
checked=True)
self.optbox.add("Spline order",
ChoiceOption([2, 3]),
key="splineorder",
checked=True)
self.optbox.add("Use pre-defined configuration",
ChoiceOption(
["T1_2_MNI152_2mm", "FA_2_FMRIB58_1mm"]),
key="config",
checked=True)
vbox.addWidget(self.optbox)
return self.options_widget
def _init_ui(self):
self.optbox.add("Minimum number of repeats per time point",
NumericOption(intonly=True,
default=3,
minval=1,
maxval=20),
key="min_nvols")
self.optbox.add("Custom grey matter ROI",
DataOption(self.ivm,
rois=True,
data=False,
explicit=True),
checked=True,
key="gm_roi")
self.optbox.add("Custom noise ROI",
DataOption(self.ivm,
rois=True,
data=False,
explicit=True),
checked=True,
key="noise_roi")
self.vbox.addWidget(QtGui.QLabel("Quality measures"))
self.qms_table = QtGui.QTableView()
self.qms_table.setModel(self.qms_model)
self.vbox.addWidget(self.qms_table)
def init_ui(self):
vbox = QtGui.QVBoxLayout()
self.setLayout(vbox)
title = TitleWidget(self)
vbox.addWidget(title)
self.options = OptionBox("Options")
self.options.add("Data", DataOption(self.ivm, multi=True), key="data")
self.options.add("Within ROI",
DataOption(self.ivm,
data=False,
rois=True,
none_option=True),
key="roi")
self.options.add("All volumes",
BoolOption(default=False),
key="allvols")
self.options.add("Number of bins",
NumericOption(minval=5,
maxval=250,
default=50,
intonly=True),
key="bins")
vbox.addWidget(self.options)
self.plot = Plot(qpo=None,
parent=self,
title="Radial profile",
display_mode=False)
self.plot.set_xlabel("Distance (mm)")
self.plot.set_ylabel("Mean data value")
vbox.addWidget(self.plot)
vbox.addStretch(1)
def _refresh_gui(self):
options = dict(self.model.options)
self.gui.clear()
for struc in self.model.default_strucs:
data_opt = self.gui.add("%s map" % struc.name.upper(), DataOption(self.model._ivm, explicit=True), checked=True, enabled=struc.name in options["pvmaps"], key=struc.name)
data_opt.value = options["pvmaps"].get(struc.name, None)
for struc in options["additional"].values():
del_btn = self._struc_delete_btn(struc)
display_type = {"add" : "map", "embed" : "embedding", "act" : "mask"}.get(struc["struc_type"], "map")
data_opt = self.gui.add("%s %s" % (struc["name"], display_type), DataOption(self.model._ivm, explicit=True, rois=True), del_btn, key=struc["name"])
data_opt.value = struc.get("pvmap", None)
res_opts = options.get("resampling", {})
self.gui.add("Resampling", ChoiceOption(["Downsample", "From another data set", "Specified resolution"], ["down", "data", "res"],
default=res_opts.get("type", "res")), checked=True, enabled="type" in res_opts, key="type")
self.gui.add("Output space from", DataOption(self.ivm), key="grid")
self.gui.add("Output resample factor", NumericOption(intonly=True, minval=1, maxval=10, default=2), key="factor")
self.gui.add("Voxel sizes (mm)", NumberListOption(load_btn=False), key="voxel-sizes")
for opt in ("grid", "factor", "voxel-sizes"):
if opt in res_opts:
self.gui.option(opt).value = res_opts[opt]
self.gui.add(None, RunButton("Add user-defined structure", callback=self._add_embedding), key="add_embedding")
self._update_resamp_visibility()
def _init_ui(self):
self.optbox.add("Motion correction",
BoolOption(default=True),
key="mc")
#opt = self.optbox.add("Deblurring", BoolOption(), key="deblur")
#opt.sig_changed.connect(self._deblur_changed)
opt = self.optbox.add("ENABLE volume selection",
BoolOption(),
key="use_enable")
opt.sig_changed.connect(self._enable_changed)
self.optbox.add(
"Distortion correction",
ChoiceOption(["Fieldmap", "Phase encoding reversed calibration"],
["fmap", "cblip"]),
key="distcorr",
checked=True)
self.optbox.option("distcorr").sig_changed.connect(
self._distcorr_changed)
self.optbox.add("Phase encode direction",
ChoiceOption(["x", "y", "z", "-x", "-y", "-z"]),
key="pedir")
self.optbox.add("Echo spacing (ms)",
NumericOption(minval=0,
maxval=1,
step=0.01,
decimals=3),
key="echospacing")
self.fmap_opts = OptionBox("Fieldmap distortion correction")
self.fmap_opts.add("Fieldmap image (rads)",
DataOption(self.ivm,
include_4d=False,
explicit=True),
key="fmap")
self.fmap_opts.add("Fieldmap magnitude image (rads)",
DataOption(self.ivm,
include_4d=False,
explicit=True),
key="fmapmag")
self.fmap_opts.add("Fieldmap magnitude brain image (rads)",
DataOption(self.ivm,
include_4d=False,
explicit=True),
key="fmapmagbrain")
self.vbox.addWidget(self.fmap_opts)
self.cblip_opts = OptionBox(
"Phase-encoding reversed distortion correction")
self.cblip_opts.add("Phase-encode reversed image",
DataOption(self.ivm,
include_4d=False,
explicit=True),
key="cblip")
self.vbox.addWidget(self.cblip_opts)
self._distcorr_changed()
def __init__(self, ivl, rois=True, data=True):
OptionBox.__init__(self, border=True)
self.ivl = ivl
self.ivm = ivl.ivm
self._qpdata = None
self._no_update = False
self.grid.setVerticalSpacing(2)
self._view_btn = QtGui.QPushButton()
self._view_btn.setIcon(QtGui.QIcon(get_icon("visible.png")))
self._view_btn.setFixedSize(16, 16)
self._view_btn.setToolTip("Visibility")
self._view_btn.clicked.connect(self._view_btn_clicked)
self._data = self.add("Data" if data else "ROI",
DataOption(self.ivm,
data=data,
rois=rois,
follow_current=True),
self._view_btn,
key="data")
self._view_roi = self.add("View ROI",
DataOption(self.ivm, data=False, rois=True),
checked=True,
key="view_roi")
self._levels_btn = QtGui.QPushButton()
self._levels_btn.setIcon(QtGui.QIcon(get_icon("levels.png")))
self._levels_btn.setFixedSize(16, 16)
self._levels_btn.setToolTip("Adjust colour map levels")
self._levels_btn.clicked.connect(self._levels_clicked)
self._cmap = self.add("Colour map",
ChoiceOption([
"jet", "hot", "gist_heat", "flame",
"bipolar", "spectrum", "custom"
]),
self._levels_btn,
key="cmap")
self._alpha = self.add("Alpha",
NumericOption(minval=0,
maxval=255,
default=255,
edit=False,
intonly=True),
key="alpha")
self._value_label = QtGui.QLabel()
self.add("Value", self._value_label)
self.add("", stretch=2)
self._data.sig_changed.connect(self._data_changed)
self._view_roi.sig_changed.connect(self._view_roi_changed)
self._cmap.sig_changed.connect(self._cmap_changed)
self._alpha.sig_changed.connect(self._alpha_changed)
self.ivl.sig_focus_changed.connect(self._focus_changed)
self.qpdata = None
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):
FslWidget.init_ui(self)
self.options.add("Input structural data",
DataOption(self.ivm),
key="data")
self.options.add("Image type",
ChoiceOption(
["T1 weighted", "T2 weighted", "Proton Density"],
return_values=["T1", "T2", "PD"]),
key="img_type")
self.options.add("Strong bias field", BoolOption(), key="strongbias")
self.options.add("Re-orientation to standard space",
BoolOption(invert=True),
key="noreorient")
self.options.add("Automatic cropping",
BoolOption(invert=True),
key="nocrop")
self.options.add("Bias field correction",
BoolOption(invert=True),
key="nobias")
#self.options.add("Registration to standard space", BoolOption(invert=True), key="noreg")
#self.options.add("Non-linear registration", BoolOption(invert=True), key="nononlinreg")
self.options.add("Segmentation", BoolOption(invert=True), key="noseg")
self.options.add("Sub-cortical segmentation",
BoolOption(invert=True),
key="nosubcortseg")
self.options.add("BET Intensity threshold",
NumericOption(minval=0, maxval=1, default=0.5),
key="betfparam")
self.options.add("Bias field smoothing extent (mm)",
NumericOption(minval=0, maxval=100, default=20),
key="bias_smoothing")
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__(self, parent, ivm, existing_strucs):
super(AddEmbeddingDialog, self).__init__(parent)
self.ivm = ivm
self.sel_text = None
self.sel_data = None
self.existing_names = [struc.name for struc in existing_strucs]
self.setWindowTitle("Add embedding")
vbox = QtGui.QVBoxLayout()
self.setLayout(vbox)
self._opts = OptionBox()
pvmap = self._opts.add("PV map / mask", DataOption(ivm, data=True, rois=True), key="pvmap")
pvmap.sig_changed.connect(self._pvmap_changed)
self._opts.add("ROI region", ChoiceOption([]), key="region")
name = self._opts.add("Name of embedded structure", TextOption(), key="name")
name.textChanged.connect(self._name_changed)
self._opts.add("Structure type", ChoiceOption(["Embedding", "Activation mask", "Additional PVE"], return_values=["embed", "act", "add"]), key="type")
self._opts.add("Parent structure", ChoiceOption([s.display_name for s in existing_strucs], [s.name for s in existing_strucs]), key="parent")
self._opts.add("Edge smoothing sigma (mm)", NumericOption(minval=0, maxval=10, default=1, decimals=2), checked=True, enabled=False, key="sigma")
vbox.addWidget(self._opts)
self._warning = QtWidgets.QLabel(parent=self)
self._warning.setStyleSheet("color: red;")
vbox.addWidget(self._warning)
self.button_box = QtGui.QDialogButtonBox(QtGui.QDialogButtonBox.Ok | QtGui.QDialogButtonBox.Cancel)
self.button_box.accepted.connect(self.accept)
self.button_box.rejected.connect(self.reject)
self.button_box.button(QtGui.QDialogButtonBox.Ok).setEnabled(False)
vbox.addWidget(self.button_box)
self._pvmap_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):
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 _new_roi(self):
dialog = QtGui.QDialog(self)
dialog.setWindowTitle("New ROI")
vbox = QtGui.QVBoxLayout()
dialog.setLayout(vbox)
optbox = OptionBox()
optbox.add("ROI name", TextOption(), key="name")
optbox.add("Data space from", DataOption(self.ivm), key="grid")
vbox.addWidget(optbox)
buttons = QtGui.QDialogButtonBox(QtGui.QDialogButtonBox.Ok
| QtGui.QDialogButtonBox.Cancel)
buttons.accepted.connect(dialog.accept)
buttons.rejected.connect(dialog.reject)
vbox.addWidget(buttons)
ok = dialog.exec_()
if ok:
roiname = optbox.option("name").value
grid = self.ivm.data[optbox.option("grid").value].grid
roidata = np.zeros(grid.shape, dtype=np.int)
self.ivm.add(NumpyData(roidata, grid=grid, roi=True, name=roiname),
make_current=True)
# Throw away old history. FIXME is this right, should we keep existing data and history?
# Also should we cache old history in case we go back to this ROI?
self._history = []
self._undo_btn.setEnabled(False)
self.options.option("roi").value = roiname
def init_ui(self):
self.setStatusTip("Click points on the 4D volume to see data curve")
vbox = QtGui.QVBoxLayout()
self.setLayout(vbox)
title = TitleWidget(self, "Multi-Voxel Visualisation", help="curve_compare", batch_btn=False)
vbox.addWidget(title)
self.plot = Plot(clear_btn=True)
self.plot.clear_btn.clicked.connect(self._clear)
self.plot.options.sig_options_changed.connect(self._options_changed)
vbox.addWidget(self.plot)
self.options = OptionBox("Options")
self.options.add("Data set", DataOption(self.ivm, include_3d=False), key="data")
col_names = [text for text in self.colors]
cols = [col for text, col in self.colors.items()]
self.options.add("Plot colour", ChoiceOption(col_names, cols, default="red"), key="col")
self.options.add("Show individual curves", BoolOption(default=True), key="indiv")
self.options.add("Show mean curve", BoolOption(), key="mean")
self.options.option("data").sig_changed.connect(self._data_changed)
self.options.option("indiv").sig_changed.connect(self._indiv_changed)
self.options.option("mean").sig_changed.connect(self._mean_changed)
self.options.option("col").sig_changed.connect(self._col_changed)
hbox = QtGui.QHBoxLayout()
hbox.addWidget(self.options)
hbox.addStretch()
vbox.addLayout(hbox)
vbox.addStretch(1)
self._options_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):
layout = QtGui.QVBoxLayout()
title = TitleWidget(self, help="roibuilder", batch_btn=False)
layout.addWidget(title)
self.options = OptionBox("Options")
btn = QtGui.QPushButton("New")
btn.clicked.connect(self._new_roi)
self.options.add("ROI", DataOption(self.ivm, rois=True, data=False), btn, key="roi")
self.options.add("Current label", NumericOption(minval=1, slider=False, intonly=True), key="label")
self.options.add("Label description", TextOption(), key="label_text")
self.options.option("roi").sig_changed.connect(self._roi_changed)
self.options.option("label").sig_changed.connect(self._label_changed)
self.options.option("label_text").sig_changed.connect(self._label_text_changed)
layout.addWidget(self.options)
# Add toolbox buttons in a grid
hbox = QtGui.QHBoxLayout()
self._toolbox = QtGui.QGroupBox()
self._toolbox.setTitle("Toolbox")
self.tools_grid = QtGui.QGridLayout()
self._toolbox.setLayout(self.tools_grid)
x, y, cols = 0, 0, 4
for tool in TOOLS:
self._add_tool(tool, y, x)
x += 1
if x == cols:
y += 1
x = 0
self._undo_btn = QtGui.QPushButton()
self._undo_btn.clicked.connect(self.undo)
self._undo_btn.setEnabled(False)
undo_icon = QtGui.QIcon(get_icon("undo"))
self._undo_btn.setIcon(undo_icon)
self._undo_btn.setToolTip("Undo last action")
self._undo_btn.setFixedSize(32, 32)
self.tools_grid.addWidget(self._undo_btn, y, x)
hbox.addWidget(self._toolbox)
self._toolbox.setEnabled(False)
hbox.addStretch(1)
layout.addLayout(hbox)
# Tool options box - initially invisible
hbox = QtGui.QHBoxLayout()
self._tool_options = QtGui.QGroupBox()
self._tool_options.setVisible(False)
hbox.addWidget(self._tool_options)
hbox.addStretch(1)
layout.addLayout(hbox)
layout.addStretch(1)
self.setLayout(layout)
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):
self._batdefault = 1.3
self.optbox.add("<b>Model fitting options</b>")
self.optbox.add("Custom ROI",
DataOption(self.ivm,
data=False,
rois=True,
explicit=True),
key="roi",
checked=True)
self.optbox.add("Spatial regularization",
BoolOption(default=True),
key="spatial")
self.optbox.add("Fix label duration",
BoolOption(default=False, invert=True),
key="infertau")
self.optbox.add("Fix arterial transit time",
BoolOption(default=True, invert=True),
key="inferbat")
self.optbox.add("T1 value uncertainty",
BoolOption(default=False),
key="infert1")
self.optbox.add("Macro vascular component",
BoolOption(default=True),
key="inferart")
self.optbox.add("Partial volume correction",
BoolOption(default=False),
key="pvcorr")
self.optbox.add("")
self.optbox.add("<b>Default parameters</b>")
self.optbox.add("Arterial Transit Time",
NumericOption(minval=0,
maxval=2.5,
default=self._batdefault,
decimals=3),
key="bat",
checked=True)
self.optbox.add("T1 (s)",
NumericOption(minval=0,
maxval=3,
default=1.3,
decimals=3),
key="t1",
checked=True)
self.optbox.add("T1b (s)",
NumericOption(minval=0,
maxval=3,
default=1.65,
decimals=3),
key="t1b",
checked=True)
self.optbox.add("")
self.optbox.add(
"<b>White paper mode</b> (defaults from Alsop, 2015 consensus paper)"
)
self.optbox.add("Enable white paper mode", BoolOption(), key="wp")
def init_ui(self):
FslWidget.init_ui(self)
self.options.add("Structural image (brain extracted)",
DataOption(self.ivm, include_4d=False),
key="data")
self.options.add("Image type",
ChoiceOption(
["T1 weighted", "T2 weighted", "Proton Density"],
return_values=[1, 2, 3]),
key="type")
self.options.add("Number of tissue type classes",
NumericOption(intonly=True,
minval=2,
maxval=10,
default=3),
key="class")
self.options.add("Output estimated bias field",
BoolOption(),
key="biasfield")
self.options.add("Output bias-corrected image",
BoolOption(),
key="biascorr")
self.options.add("Remove bias field",
BoolOption(default=True),
key="nobias")
self.options.add("Bias field smoothing extent (mm)",
NumericOption(minval=0, maxval=100, default=20),
key="lowpass")
self.options.add(
"Number of main-loop iterations during bias-field removal",
NumericOption(intonly=True, minval=1, maxval=10, default=4),
key="iter")
self.options.add(
"Number of main-loop iterations after bias-field removal",
NumericOption(intonly=True, minval=1, maxval=10, default=4),
key="fixed")
self.options.add("Number of segmentation iterations",
NumericOption(intonly=True,
minval=1,
maxval=100,
default=15),
key="init")
self.options.add("Initial segmentation spatial smoothness",
NumericOption(minval=0, maxval=1, default=0.02),
key="fHard")
self.options.add("Spatial smoothness for mixeltype",
NumericOption(minval=0, maxval=5, default=0.3),
key="mixel")
self.options.add("Segmentation spatial smoothness",
NumericOption(minval=0, maxval=5, default=0.1),
key="Hyper")
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):
self.optbox.add(
"Structural data from",
ChoiceOption(
["No structural data", "Structural image", "FSL_ANAT output"],
[None, "img", "fsl_anat"]),
key="struc_src")
self.optbox.option("struc_src").sig_changed.connect(
self._data_from_changed)
self.optbox.add("Structural image",
DataOption(self.ivm, include_4d=False, explicit=True),
key="struc")
self.optbox.add("FSL_ANAT directory",
FileOption(dirs=True),
key="fslanat")
self.optbox.set_visible("fslanat", False)
self.optbox.add("")
self.optbox.add("<b>Override automatic segmentation</b>",
key="override_label")
self.optbox.add("Brain image",
DataOption(self.ivm, include_4d=False, explicit=True),
key="struc_bet",
checked=True)
self.optbox.add("White matter",
DataOption(self.ivm, include_4d=False, explicit=True),
key="wmseg",
checked=True)
self.optbox.add("Grey matter",
DataOption(self.ivm, include_4d=False, explicit=True),
key="gmseg",
checked=True)
self.optbox.add("CSF",
DataOption(self.ivm, include_4d=False, explicit=True),
key="csfseg",
checked=True)
self._data_from_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)
title = TitleWidget(self)
vbox.addWidget(title)
hbox = QtGui.QHBoxLayout()
self.options = OptionBox("Re-orient data")
data = self.options.add("Data item", DataOption(self.ivm), key="data")
data.sig_changed.connect(self._data_changed)
self.trans, self.rot = {}, {}
self.options.add("Translation")
for axis, label in {2: "axial", 0: "sagittal", 1: "coronal"}.items():
trans = self.options.add(" %s (mm)" % label.title(),
NumericOption(minval=-100,
maxval=100,
default=0),
key="trans-%s" % label)
trans.sig_changed.connect(self._translate(axis, label))
self.trans[axis] = trans
self.options.add("Rotation")
for axis, label in {2: "axial", 0: "sagittal", 1: "coronal"}.items():
rot = self.options.add(" %s (degrees)" % label.title(),
NumericOption(minval=-180,
maxval=180,
default=0),
key="rot-%s" % label)
rot.sig_changed.connect(self._rotate(axis, label))
self.rot[axis] = rot
hbox.addWidget(self.options)
vbox.addLayout(hbox)
self.gridview = GridView(self.ivm, self.ivl)
vbox.addWidget(self.gridview)
hbox = QtGui.QHBoxLayout()
reset_btn = QtGui.QPushButton("Reset to original")
reset_btn.clicked.connect(self._reset)
hbox.addWidget(reset_btn)
hbox.addStretch(1)
vbox.addLayout(hbox)
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)
def init_ui(self):
FabberWidget.init_ui(self)
self.run_box = RunBox(self.get_process, self.get_options, title="Run Fabber", save_option=True)
self.vbox.addWidget(self.run_box)
self.vbox.addStretch(1)
model_opts_btn = QtGui.QPushButton('Model Options')
method_opts_btn = QtGui.QPushButton('Method Options')
edit_priors_btn = QtGui.QPushButton('Edit Priors')
options_btn = QtGui.QPushButton('Edit')
self.options.add("Main input data", DataOption(self.ivm), key="data")
self.options.add("Model group", ChoiceOption(), key="model-group")
self.options.add("Model", ChoiceOption(), model_opts_btn, key="model")
self.options.add("Parameter priors", edit_priors_btn)
self.options.add("Inference method", ChoiceOption(), method_opts_btn, key="method")
self.options.add("General options", options_btn)
self.options.option("model-group").sig_changed.connect(self._model_group_changed)
method_opts_btn.clicked.connect(self._show_method_options)
model_opts_btn.clicked.connect(self._show_model_options)
edit_priors_btn.clicked.connect(self._show_prior_options)
options_btn.clicked.connect(self._show_general_options)
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.option("method").setChoices(FabberProcess.api().get_methods())
self.options.option("method").value = "vb"
self._options_changed()
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__(self, ivm):
QtGui.QWidget.__init__(self)
self.ivm = ivm
vbox = QtGui.QVBoxLayout()
self.setLayout(vbox)
self.optbox = OptionBox()
self.optbox.add(
"AIF source",
ChoiceOption(["Global sequence of values", "Voxelwise image"],
["global", "voxelwise"]),
key="aif_source")
self.optbox.option("aif_source").sig_changed.connect(
self._aif_source_changed)
self.optbox.add("AIF", NumberListOption(), key="aif")
self.optbox.add("AIF image", DataOption(self.ivm), key="suppdata")
self.optbox.add("AIF type",
ChoiceOption(["DSC signal", "Concentration"],
[False, True]),
key="aifconc")
vbox.addWidget(self.optbox)
vbox.addStretch()
self._aif_source_changed()
def __init__(self, ivm=None):
QtGui.QWidget.__init__(self)
self._ivm = ivm
self._poolvals_edited = False
vbox = QtGui.QVBoxLayout()
self.setLayout(vbox)
self.optbox = OptionBox()
vbox.addWidget(self.optbox)
self.optbox.add("<b>Output options</b>")
self.optbox.add("CEST R*",
BoolOption(default=True),
key="save-model-extras")
self.optbox.add("Parameter maps",
BoolOption(default=False),
key="save-mean")
#self.optbox.add("Parameter variance", BoolOption(default=False), key="var")
self.optbox.add("Model fit",
BoolOption(default=False),
key="save-model-fit")
self.optbox.add("Prefix for output",
TextOption(),
checked=True,
key="output-prefix")
self.optbox.add(" ")
self.optbox.add("<b>Analysis options</b>")
self.optbox.add("Spatial Regularization", BoolOption(), key="spatial")
self.optbox.add("Allow uncertainty in T1/T2 values",
BoolOption(),
key="t12prior")
self.optbox.add("Prior T1 map",
DataOption(self._ivm),
key="t1img",
checked=True)
self.optbox.add("Prior T2 map",
DataOption(self._ivm),
key="t2img",
checked=True)
self.optbox.add("Tissue PV map (GM+WM)",
DataOption(self._ivm),
key="pvimg",
checked=True)
self.optbox.option("t12prior").sig_changed.connect(self._update_ui)
self.optbox.add("Use steady state solution for MT bias reduction",
BoolOption(default=False),
key="new-ss")
self.optbox.option("new-ss").sig_changed.connect(self._update_ui)
self.optbox.add("TR (s)",
NumericOption(default=3.0,
minval=0,
maxval=5,
digits=3,
step=0.1),
key="tr")
self.optbox.add("Excitation flip angle (\N{DEGREE SIGN})",
NumericOption(default=12.0,
minval=0,
maxval=25,
digits=3,
step=1.0),
key="fa")
self.optbox.add(
"MT pool Line shape",
ChoiceOption(
["None", "Gaussian", "Lorentzian", "Super Lorentzian"],
["none", "gaussian", "lorentzian", "superlorentzian"]),
key="lineshape")
self.alexmt_cite = Citation(ALEXMT_CITE_TITLE, ALEXMT_CITE_AUTHOR,
ALEXMT_CITE_JOURNAL)
vbox.addWidget(self.alexmt_cite)
vbox.addStretch(1)
self._update_ui()