def __init__(self, ivm, parent, acq_options):
OptionsWidget.__init__(self, ivm, parent)
self.acq_options = acq_options
vbox = QtWidgets.QVBoxLayout()
self.setLayout(vbox)
self._optbox = OptionBox()
self._optbox.add("<b>Model options</b>")
self._optbox.add("Delay minimum (s)",
NumericOption(minval=-100, maxval=100, default=0),
key="delay-min")
self._optbox.add("Delay maximum (s)",
NumericOption(minval=-100, maxval=100, default=0),
key="delay-max")
self._optbox.add("Delay step (s)",
NumericOption(minval=-5, maxval=5, default=1),
key="delay-step")
self._optbox.add("<b>Output options</b>")
self._optbox.add("Output data name suffix",
TextOption(),
checked=True,
key="output-suffix")
vbox.addWidget(self._optbox)
vbox.addWidget(RunWidget(self, save_option=True))
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):
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 __init__(self, ivm, parent, acq_options):
OptionsWidget.__init__(self, ivm, parent)
self.acq_options = acq_options
vbox = QtWidgets.QVBoxLayout()
self.setLayout(vbox)
cite = Citation(FAB_CITE_TITLE, FAB_CITE_AUTHOR, FAB_CITE_JOURNAL)
vbox.addWidget(cite)
self._optbox = OptionBox()
self._optbox.add("<b>Model options</b>")
self._optbox.add("Infer constant signal offset",
BoolOption(default=True),
key="infer-sig0")
self._optbox.add("Infer delay",
BoolOption(default=True),
key="infer-delay")
#self._optbox.add("<b>Model fitting options</b>")
#self._optbox.add("Spatial regularization", BoolOption(default=True), key="spatial")
self._optbox.add("<b>Output options</b>")
self._optbox.add("Output data name suffix",
TextOption(),
checked=True,
key="output-suffix")
vbox.addWidget(self._optbox)
vbox.addWidget(RunWidget(self, save_option=True))
vbox.addStretch(1)
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, 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, fsldir, fsldevdir):
super(FslDirDialog, self).__init__(quantiphyse.gui.dialogs.MAINWIN)
self.setWindowTitle("Choose location of FSL installation")
vbox = QtGui.QVBoxLayout()
self.optbox = OptionBox()
self.optbox.add("FSL installation",
FileOption(dirs=True, initial=fsldir),
key="fsldir")
self.optbox.add("FSL development code",
FileOption(dirs=True, initial=fsldevdir),
checked=True,
enabled=bool(fsldevdir),
key="fsldevdir")
self.optbox.option("fsldir").sig_changed.connect(self._fsldir_changed)
self.optbox.option("fsldevdir").sig_changed.connect(
self._fsldevdir_changed)
vbox.addWidget(self.optbox)
hbox = QtGui.QHBoxLayout()
hbox.addStretch(1)
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)
hbox.addWidget(self.button_box)
vbox.addLayout(hbox)
self.setLayout(vbox)
def init_ui(self, run_box=True):
self.vbox = QtGui.QVBoxLayout()
self.setLayout(self.vbox)
title = TitleWidget(self,
help="fsl",
subtitle="%s %s" % (self.description, __version__))
self.vbox.addWidget(title)
cite = Citation(*CITATIONS.get(self.prog, CITATIONS["fsl"]))
self.vbox.addWidget(cite)
self.options = OptionBox("%s options" % self.prog.upper())
self.vbox.addWidget(self.options)
if run_box:
self.run_box = RunBox(self.get_process, self.get_options)
self.vbox.addWidget(self.run_box)
self.vbox.addStretch(1)
fsldir = FslDirWidget()
self.vbox.addWidget(fsldir)
fsldir.sig_changed.connect(self._fsldir_changed)
self._fsldir_changed(fsldir.fsldir)
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 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__(self, ivm, parent, model_type, abbrev, model_classes):
OptionsWidget.__init__(self, ivm, parent)
self._views = {}
self.model = None
self.view = None
self._option_name = "%s-model" % abbrev
for name, cls in model_classes.items():
self._views[name] = get_view_class(cls)(ivm)
main_vbox = QtGui.QVBoxLayout()
self.setLayout(main_vbox)
self.options = OptionBox()
self.options.add(
"%s model" % model_type,
ChoiceOption([v.model.display_name for v in self._views.values()],
self._views.keys()),
key=self._option_name)
self.options.option(self._option_name).sig_changed.connect(
self._model_changed)
main_vbox.addWidget(self.options)
self._create_guis(main_vbox)
main_vbox.addStretch(1)
self._model_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):
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):
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):
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, ivm):
self.ivm = ivm
self.model = UserPvModel(ivm)
self.model.options.update({
"pvmaps" : {},
"additional" : {},
})
self.gui = OptionBox()
self.gui.sig_changed.connect(self._update_options)
self._refresh_gui()
class CheckerboardModelView:
"""
View for CheckerboardModel
"""
def __init__(self, ivm):
self.model = CheckerboardModel(ivm)
self.gui = OptionBox()
self.gui.add("Number of voxels per patch (approx)", NumericOption(minval=1, maxval=1000, default=20, intonly=True), key="voxels-per-patch")
self.gui.sig_changed.connect(self._update_options)
def _update_options(self):
self.model.options.update(self.gui.values())
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__(self, ivm):
self.model = DceDataModel(ivm)
self.gui = OptionBox()
self.gui.add(
"Model",
ChoiceOption([
"Standard Tofts model", "Extended Tofts model (ETM)",
"2 Compartment exchange model",
"Compartmental Tissue Update (CTU) model",
"Adiabatic Approximation to Tissue Homogeneity (AATH) Model"
], ["dce_tofts", "dce_ETM", "dce_2CXM", "dce_CTU", "dce_AATH"]),
key="model")
self.gui.add("Contrast agent R1 relaxivity (l/mmol s)",
NumericOption(minval=0, maxval=10, default=3.7),
key="r1")
self.gui.add("Flip angle (\N{DEGREE SIGN})",
NumericOption(minval=0, maxval=90, default=12),
key="fa")
self.gui.add("TR (ms)",
NumericOption(minval=0, maxval=10, default=4.108),
key="tr")
self.gui.add("Time between volumes (s)",
NumericOption(minval=0, maxval=30, default=12),
key="delt")
self.gui.add("AIF",
ChoiceOption([
"Population (Orton 2008)", "Population (Parker)",
"Measured DCE signal", "Measured concentration curve"
], ["orton", "parker", "signal", "conc"]),
key="aif")
self.gui.add("Number of volumes",
NumericOption(minval=0,
maxval=100,
default=20,
intonly=True),
key="nt")
self.gui.add("Bolus injection time (s)",
NumericOption(minval=0, maxval=60, default=30),
key="tinj")
self.gui.add("AIF data values",
NumberListOption([
0,
]),
key="aif-data")
self.gui.add("Arterial transit time (s)",
NumericOption(minval=0, maxval=1.0, default=0),
key="delay")
self.gui.option("model").sig_changed.connect(self._model_changed)
self.gui.option("aif").sig_changed.connect(self._aif_changed)
self._aif_changed()
self._model_changed()
self.gui.sig_changed.connect(self._update_options)
self._update_options()
def __init__(self, ivm):
self.model = DscDataModel(ivm)
self.gui = OptionBox()
self.gui.add("Time between volumes (s)",
NumericOption(minval=0, maxval=5, default=1.0),
key="delt")
self.gui.add("TE (s)",
NumericOption(minval=0, maxval=5, default=1.0),
key="te")
self.gui.add("AIF", NumberListOption(), key="aif")
self.gui.sig_changed.connect(self._update_options)
self._update_options()
class FastStructureModelView:
"""
View for FastStructureModel
"""
def __init__(self, ivm):
self.model = FastStructureModel(ivm)
self.gui = OptionBox()
self.gui.add("Structural image (brain extracted)", DataOption(self.model._ivm, explicit=True), key="struc")
self.gui.add("Image type", ChoiceOption(["T1 weighted", "T2 weighted", "Proton Density"], return_values=[1, 2, 3]), key="type")
self.gui.sig_changed.connect(self._update_options)
def _update_options(self):
self.model.options.update(self.gui.values())
def __init__(self, ivm=None):
QtGui.QWidget.__init__(self)
self.ivm = ivm
self.vbox = QtGui.QVBoxLayout()
self.setLayout(self.vbox)
if hasattr(self, "CITE"):
self.vbox.addWidget(Citation(*self.CITE))
self.optbox = OptionBox()
self.vbox.addWidget(self.optbox)
self._init_ui()
self.vbox.addStretch(1)
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__(self, ivm):
self.model = AslDataModel(ivm)
self.gui = OptionBox()
self.gui.add("Bolus duration",
NumericOption(minval=0, maxval=5, default=1.8),
key="tau")
self.gui.add("Labelling",
ChoiceOption(["CASL/pCASL", "PASL"], [True, False],
default=True),
key="casl")
self.gui.add("PLDs",
NumberListOption([0.25, 0.5, 0.75, 1.0, 1.25, 1.5]),
key="plds")
self.gui.add("Time per slice (ms)",
NumericOption(minval=0,
maxval=1000,
default=0,
intonly=True),
key="slicedt")
self.gui.add("Data format",
ChoiceOption(["Differenced data", "Label/Control pairs"],
["diff", "tc"]),
key="iaf")
self.gui.add("Repeats",
NumericOption(minval=1,
maxval=100,
default=1,
intonly=True),
key="repeats")
self.gui.add("Group by",
ChoiceOption(["PLDs", "Repeats"], ["tis", "rpt"]),
key="ibf")
self.gui.add("Inversion efficiency",
NumericOption(minval=0.5, maxval=1.0, default=0.85),
key="alpha")
self.gui.add("M0",
NumericOption(minval=0, maxval=2000, default=1000),
key="m0")
self.gui.add("TR (s)",
NumericOption(minval=0, maxval=10, default=4),
key="tr")
self.gui.add("TE (ms)",
NumericOption(minval=0, maxval=1000, default=13),
key="te")
self.gui.add("Tissue/arterial partition coefficient",
NumericOption(minval=0, maxval=1, default=0.9),
key="pct")
#self.gui.add("Arterial component", BoolOption(), key="incart")
self.gui.sig_changed.connect(self._update_options)
self._update_options()
def __init__(self, ivm):
self.model = SpinEchoDataModel(ivm)
self.gui = OptionBox()
self.gui.add("TR (s)",
NumericOption(minval=0, maxval=10, default=4.8),
key="tr")
self.gui.add("TE (ms)",
NumericOption(minval=0, maxval=1000, default=0),
key="te")
self.gui.add("M0",
NumericOption(minval=0, maxval=10000, default=1000),
key="m0")
self.gui.sig_changed.connect(self._update_options)
self._update_options()
class ModelOptions(OptionsWidget):
def __init__(self, ivm, parent, model_type, abbrev, model_classes):
OptionsWidget.__init__(self, ivm, parent)
self._views = {}
self.model = None
self.view = None
self._option_name = "%s-model" % abbrev
for name, cls in model_classes.items():
self._views[name] = get_view_class(cls)(ivm)
main_vbox = QtGui.QVBoxLayout()
self.setLayout(main_vbox)
self.options = OptionBox()
self.options.add(
"%s model" % model_type,
ChoiceOption([v.model.display_name for v in self._views.values()],
self._views.keys()),
key=self._option_name)
self.options.option(self._option_name).sig_changed.connect(
self._model_changed)
main_vbox.addWidget(self.options)
self._create_guis(main_vbox)
main_vbox.addStretch(1)
self._model_changed()
def _create_guis(self, main_vbox):
# Create the GUIs for models - only one visible at a time!
for view in self._views.values():
if view.gui is not None:
view.gui.setVisible(False)
if isinstance(view.gui, QtGui.QWidget):
main_vbox.addWidget(view.gui)
else:
main_vbox.addLayout(view.gui)
view.model.options.sig_changed.connect(
self._model_option_changed)
def _model_changed(self):
chosen_name = self.options.option(self._option_name).value
self.view = self._views[chosen_name]
self.model = self.view.model
for name, view in self._views.items():
view.gui.setVisible(chosen_name == name)
self.sig_changed.emit()
def _model_option_changed(self, _key, _value):
self.sig_changed.emit()
def __init__(self, ivm, parent):
OptionsWidget.__init__(self, ivm, parent)
main_vbox = QtGui.QVBoxLayout()
self.setLayout(main_vbox)
self.options = OptionBox()
self.options.add("Add noise with SNR",
NumericOption(minval=0.1, maxval=100, default=10),
checked=True,
key="snr")
self.options.sig_changed.connect(self.sig_changed.emit)
main_vbox.addWidget(self.options)
main_vbox.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__(self, parent):
super(NewPoolDialog, self).__init__(parent)
self.setWindowTitle("New Pool")
vbox = QtGui.QVBoxLayout()
self.optbox = OptionBox()
vbox.addWidget(self.optbox)
self.optbox.add("Name", TextOption(), key="name")
self.optbox.add("PPM",
NumericOption(minval=0,
maxval=20,
default=0,
decimals=3,
slider=False),
key="ppm")
self.optbox.add("Exchange rate",
NumericOption(minval=0,
maxval=1000,
default=0,
decimals=1,
slider=False),
key="exch")
self.optbox.add("T1 (s)",
NumericOption(minval=0,
maxval=10,
default=1.0,
decimals=2,
slider=False),
key="t1")
self.optbox.add("T2 (s)",
NumericOption(minval=0,
maxval=1.0,
default=0.07,
decimals=6,
slider=False),
key="t2")
self.optbox.option("name").sig_changed.connect(self._validate)
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)
vbox.addWidget(self.button_box)
self.setLayout(vbox)
self._validate()
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()
