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, 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):
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)
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 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__(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()
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__(self, ivm, parent):
OptionsWidget.__init__(self, ivm, parent)
main_vbox = QtGui.QVBoxLayout()
self.setLayout(main_vbox)
self.options = OptionBox()
self.options.add("Output name", TextOption("sim_data"), key="output")
self.options.add("Output parameter maps",
BoolOption(),
default=False,
key="output-param-maps")
self.options.add("Output clean data (no noise/motion)",
TextOption("sim_data_clean"),
checked=True,
default=True,
key="output-clean")
main_vbox.addWidget(self.options)
main_vbox.addStretch(1)
def init_ui(self):
FslWidget.init_ui(self, run_box=False)
run_btn = QtGui.QPushButton("Run")
run_btn.clicked.connect(self._run)
self.options.add("Command string", TextOption(), run_btn, key="cmd")
doc = QtGui.QLabel(
"Enter the fslmaths command line string as you would normally. Use the names of the Quantiphyse data sets you want to use as filenames"
)
doc.setWordWrap(True)
self.vbox.insertWidget(self.vbox.count() - 1, doc)
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):
self.optbox.add("<b>Default outputs</b>")
self.optbox.add("Prefix for output data names",
TextOption(),
key="output-prefix",
checked=True)
self.optbox.add("Output in native (ASL) space",
BoolOption(default=True),
key="output_native")
self.optbox.add("Output in structural space",
BoolOption(),
key="output_struc")
self.optbox.add("Output in standard (MNI) space",
BoolOption(),
key="output_mni")
self.optbox.add("")
self.optbox.add("<b>Additional outputs</b>")
self.optbox.add("Output parameter variance maps",
BoolOption(),
key="output_var")
self.optbox.add("Output mask",
BoolOption(default=True),
key="save_mask")
self.optbox.add("Output calibration data",
BoolOption(),
key="save_calib")
self.optbox.add("Output corrected input data",
BoolOption(),
key="save_corrected")
self.optbox.add("Output registration data",
BoolOption(),
key="save_reg")
self.optbox.add("Output structural segmentation",
BoolOption(),
key="save_struc")
self.optbox.add("Output model fitting data",
BoolOption(),
key="save_basil")
self.optbox.add("")
self.optbox.add("<b>Summary report</b>")
self.optbox.add("Save HTML report",
FileOption(dirs=True),
key="report",
checked=True)
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()
def __init__(self, ivm):
QtGui.QWidget.__init__(self)
self.ivm = ivm
vbox = QtGui.QVBoxLayout()
self.setLayout(vbox)
self.optbox = OptionBox()
self.optbox.add("DSC Data", DataOption(self.ivm), key="data")
self.optbox.add("ROI",
DataOption(self.ivm, rois=True, data=False),
key="mask")
self.optbox.add(
"Model choice",
ChoiceOption(["Standard", "Control point interpolation"],
["dsc", "dsc_cpi"]),
key="model")
self.optbox.add("TE (s)",
NumericOption(minval=0, maxval=0.1, default=0.065),
key="te")
self.optbox.add("Time interval between volumes (s)",
NumericOption(minval=0, maxval=10, default=1.5),
key="delt")
self.optbox.add("Apply dispersion to AIF", BoolOption(), key="disp")
self.optbox.add("Infer delay parameter",
BoolOption(default=True),
key="inferdelay")
self.optbox.add("Infer arterial component",
BoolOption(),
key="inferart")
self.optbox.add("Log transform on rCBF", BoolOption(), key="log-cbf")
self.optbox.add("Output residue function",
BoolOption(),
key="save-model-extras")
self.optbox.add("Spatial regularization",
ChoiceOption(("None", "Standard", "Full"),
default="Standard"),
key="spatial")
self.optbox.add("Output data suffix",
TextOption(),
checked=True,
key="output-suffix")
self.optbox.option("model").sig_changed.connect(self._model_changed)
vbox.addWidget(self.optbox)
hbox = QtGui.QHBoxLayout()
self.classic_options = OptionBox("Standard model")
self.classic_options.add("Infer MTT",
BoolOption(default=True),
key="infermtt")
self.classic_options.add("Infer lambda",
BoolOption(default=True),
key="inferlambda")
hbox.addWidget(self.classic_options)
hbox.addStretch(1)
vbox.addLayout(hbox)
hbox = QtGui.QHBoxLayout()
self.cpi_options = OptionBox("CPI model")
self.cpi_options.setVisible(False)
self.cpi_options.add("Number of control points",
NumericOption(minval=3,
maxval=20,
default=5,
intonly=True),
key="num-cps")
self.cpi_options.add("Infer control point time position",
BoolOption(),
key="infer-cpt")
hbox.addWidget(self.cpi_options)
hbox.addStretch(1)
vbox.addLayout(hbox)
vbox.addStretch()
def __init__(self, parent, registry):
super(AtlasDescription, self).__init__(parent)
self._registry = registry
self.ivm = parent.ivm
self._desc = None
grid = QtGui.QGridLayout()
self.setLayout(grid)
grid.addWidget(QtGui.QLabel("Name"), 0, 0)
self._name = QtGui.QLabel()
grid.addWidget(self._name, 0, 1)
grid.addWidget(QtGui.QLabel("Type"), 1, 0)
self._type = QtGui.QLabel()
grid.addWidget(self._type, 1, 1)
grid.addWidget(QtGui.QLabel("Resolutions"), 2, 0)
self._imgs = QtGui.QComboBox()
grid.addWidget(self._imgs, 2, 1)
self._label_table = QtGui.QTableView()
self._label_model = QtGui.QStandardItemModel()
self._label_table.setModel(self._label_model)
self._label_table.setSelectionBehavior(
QtGui.QAbstractItemView.SelectRows)
self._label_table.setSelectionMode(
QtGui.QAbstractItemView.SingleSelection)
self._label_table.setEditTriggers(
QtGui.QAbstractItemView.NoEditTriggers)
self._label_table.selectionModel().selectionChanged.connect(
self._region_changed)
self._label_table.setStyleSheet(
"font-size: 10px; alternate-background-color: #6c6c6c;")
self._label_table.setShowGrid(False)
self._label_table.setTextElideMode(QtCore.Qt.ElideLeft)
self._label_table.setAlternatingRowColors(True)
self._label_table.ensurePolished()
fm = QtGui.QFontMetrics(self._label_table.font())
self._label_table.verticalHeader().setVisible(False)
self._label_table.verticalHeader().setSectionResizeMode(
QtGui.QHeaderView.Fixed)
self._label_table.verticalHeader().setDefaultSectionSize(fm.height() +
2)
grid.addWidget(self._label_table, 3, 0, 1, 2)
grid.setRowStretch(3, 1)
self._load_options = OptionBox()
self._load_options.add("Regions",
ChoiceOption(["Selected region", "All regions"],
["sel", "all"]),
key="regions")
self._load_options.add(
"Load as",
ChoiceOption(["New dataset", "Add to existing dataset"],
["new", "add"]),
key="add")
self._load_options.add("Dataset name", TextOption("atlas"), key="name")
self._load_options.add("Existing dataset",
DataOption(self.ivm),
key="data")
self._load_options.option("regions").sig_changed.connect(
self._load_regions_changed)
self._load_options.option("add").sig_changed.connect(self._add_changed)
grid.addWidget(self._load_options, 4, 0, 1, 2)
hbox = QtGui.QHBoxLayout()
btn = QtGui.QPushButton("Load")
btn.clicked.connect(self._load)
hbox.addWidget(btn)
hbox.addStretch(1)
grid.addLayout(hbox, 5, 0, 1, 2)
self._add_changed()