def _get_widgets(self, idx):
prior_idx = self._get_prior_idx(self.params[idx])
ptype = self.rundata.get("PSP_byname%i_type" % prior_idx, "N")
image = self.rundata.get("PSP_byname%i_image" % prior_idx, "")
mean = self.rundata.get("PSP_byname%i_mean" % prior_idx, "")
prec = self.rundata.get("PSP_byname%i_prec" % prior_idx, "")
trans = self.rundata.get("PSP_byname%i_transform" % prior_idx, "")
type_combo = QtGui.QComboBox()
type_combo.addItem("Normal", "N")
type_combo.addItem("Image Prior", "I")
type_combo.addItem("Spatial prior, type M", "M")
type_combo.addItem("Spatial prior , type P", "P")
type_combo.addItem("Spatial prior, type m", "m")
type_combo.addItem("Spatial prior , type p", "p")
type_combo.addItem("ARD prior", "A")
type_combo.setSizeAdjustPolicy(QtGui.QComboBox.AdjustToContents)
type_combo.setCurrentIndex(type_combo.findData(ptype))
type_combo.currentIndexChanged.connect(self._changed)
image_combo = OverlayCombo(self.ivm, static_only=True)
image_combo.setSizeAdjustPolicy(QtGui.QComboBox.AdjustToContents)
if image != "":
image_combo.setCurrentIndex(image_combo.findText(image))
image_combo.currentIndexChanged.connect(self._changed)
mean_cb = QtGui.QCheckBox()
mean_cb.setChecked(ptype != "I" and mean != "")
mean_cb.stateChanged.connect(self._changed)
mean_edit = QtGui.QLineEdit(mean)
mean_edit.editingFinished.connect(self._changed)
prec_cb = QtGui.QCheckBox()
prec_cb.setChecked(prec != "")
prec_cb.stateChanged.connect(self._changed)
prec_edit = QtGui.QLineEdit(prec)
prec_edit.editingFinished.connect(self._changed)
trans_combo = QtGui.QComboBox()
trans_combo.addItem("Default transformation", "")
trans_combo.addItem("No transformation", "I")
trans_combo.addItem("Log transformation", "L")
trans_combo.addItem("Soft-plus transformation", "S")
trans_combo.addItem("Fractional transformation", "F")
trans_combo.setSizeAdjustPolicy(QtGui.QComboBox.AdjustToContents)
trans_combo.setCurrentIndex(trans_combo.findData(trans))
trans_combo.currentIndexChanged.connect(self._changed)
return (type_combo, QtGui.QLabel("Image: "), image_combo, mean_cb,
QtGui.QLabel("Custom mean: "), mean_edit, prec_cb,
QtGui.QLabel("Custom precision: "), prec_edit, trans_combo)
class ImageOptionWidget(OptionWidget):
"""
OptionWidget subclass which allows image options to be chosen
from the current list of overlays
"""
def __init__(self, opt, **kwargs):
OptionWidget.__init__(self, opt, **kwargs)
self.combo = OverlayCombo(self.ivm, static_only=True)
self.widgets.append(self.combo)
def get_value(self):
return self.combo.currentText()
def set_value(self, value):
idx = self.combo.findText(value)
self.combo.setCurrentIndex(idx)
def add(self, grid, row):
OptionWidget.add(self, grid, row)
grid.addWidget(self.combo, row, 1)
class AslImageWidget(QtGui.QWidget, LogSource):
"""
QWidget which allows an ASL data set to be described
This is intended to be embedded into a QpWidget which supports processing of ASL data
"""
# Signal emitted when the data or metadata is changed
sig_changed = QtCore.Signal()
def __init__(self, ivm, parent=None, **kwargs):
LogSource.__init__(self)
QtGui.QWidget.__init__(self, parent)
self.ivm = ivm
self.data = None
self.default_md = kwargs.get("default_metadata", DEFAULT_METADATA)
self.md = dict(self.default_md)
self.aslimage = None
self.valid = True
vbox = QtGui.QVBoxLayout()
self.setLayout(vbox)
grid = QtGui.QGridLayout()
grid.addWidget(QtGui.QLabel("ASL data"), 0, 0)
self.data_combo = OverlayCombo(self.ivm)
self.data_combo.currentIndexChanged.connect(self._data_changed)
grid.addWidget(self.data_combo, 0, 1)
view_classes = [
LabelType, RepeatsChoice, NumPhases, NumEncodings, BlockFormat,
DataStructure, SignalView, Labelling, Readout, SliceTime,
Multiband, Times, BolusDurations, VariableRepeats
]
self.views = []
for idx, view_class in enumerate(view_classes):
if view_class in kwargs.get("ignore_views", ()):
continue
view = view_class(grid, ypos=idx + 2)
view.ivm = self.ivm
view.sig_md_changed.connect(self._metadata_changed)
self.views.append(view)
#grid.addWidget(QtGui.QLabel("Data order preview"), 5, 0)
# Code below is for specific multiple phases
#self.phases_lbl = QtGui.QLabel("Phases (\N{DEGREE SIGN})")
#grid.addWidget(self.phases_lbl, 3, 0)
#self.phases_lbl.setVisible(False)
#self.phases = NumberList([float(x)*360/8 for x in range(8)])
#grid.addWidget(self.phases, 3, 1)
#self.phases.setVisible(False)
grid.setColumnStretch(0, 0)
grid.setColumnStretch(1, 1)
grid.setColumnStretch(2, 0)
grid.setRowStretch(len(view_classes) + 2, 1)
self.grid = grid
vbox.addLayout(grid)
self.warn_label = WarningBox()
vbox.addWidget(self.warn_label)
self._update_ui()
self._data_changed()
def set_data_name(self, name):
""" Set the name of the data item being displayed """
if name not in self.ivm.data:
raise QpException("Data not found: %s" % name)
else:
idx = self.data_combo.findText(name)
self.data_combo.setCurrentIndex(idx)
def _data_changed(self):
"""
New data selected - load any previously defined metadata, and validate it
"""
self.data = self.ivm.data.get(self.data_combo.currentText(), None)
for idx in range(self.grid.count()):
if idx > 1:
w = self.grid.itemAt(idx).widget()
if w is not None:
w.setEnabled(self.data is not None)
if self.data is not None:
self.md = self.data.metadata.get("AslData", None)
if self.md is None:
self.md = dict(self.default_md)
if self.data.nvols % 2 == 0:
# Even number of volumes - guess TC pairs
# FIXME don't need block format for single TI
self.md["iaf"] = "tc"
self.md["ibf"] = "tis"
for view in self.views:
view.set_data(self.data, self.md)
self._validate_metadata()
self.sig_changed.emit()
def _metadata_changed(self, sender):
"""
Called when a view has changed the metadata
"""
self.debug("Metadata changed %s", sender)
if self.data is not None:
self.debug("Current metadata: %s", self.md)
self.debug("New metadata: %s", sender.md)
self.md = sender.md
self._validate_metadata()
self._save_metadata()
self.sig_changed.emit()
def _save_metadata(self):
"""
Set the metadata on the dataset
"""
if self.data is not None:
current_md = self.data.metadata.get("AslData", {})
self.debug("Save: Current metadata: %s", current_md)
if self.md != current_md:
self.debug("Different!")
self.data.metadata["AslData"] = dict(self.md)
self.debug("Saved: %s ", self.md)
self._update_ui()
def _update_ui(self, ignore=()):
"""
Update user interface from the current metadata
"""
try:
for view in self.views:
if view not in ignore:
view.set_data(self.data, self.md)
finally:
self.updating_ui = False
def _validate_metadata(self):
"""
Validate data against specified TIs, etc
"""
try:
if self.md and self.data is not None:
self.debug("Validating metadata: %s", str(self.md))
self.aslimage, _ = qpdata_to_aslimage(self.data,
metadata=self.md)
self.warn_label.clear()
self.valid = True
except ValueError as e:
self.debug("Failed: %s", str(e))
self.aslimage = None
self.warn_label.warn(str(e))
self.valid = False
def get_options(self):
""" Get batch options """
options = {}
if self.data is not None:
options["data"] = self.data.name
options.update(self.md)
return options
class ClusteringWidget(QpWidget):
"""
Widget for doing K-means clustering on 3D or 4D data
"""
def __init__(self, **kwargs):
super(ClusteringWidget,
self).__init__(name="KMeans Clustering",
icon="clustering",
desc="Generate clusters from 3D or 4D data",
group="Clustering",
position=2,
**kwargs)
self.curves = {}
def init_ui(self):
self.process = KMeansProcess(self.ivm)
layout = QtGui.QVBoxLayout()
self.setLayout(layout)
title = TitleWidget(self, help="cluster")
layout.addWidget(title)
DESC = """
<i>Performs clustering of 3D or 4D data using the K-means algorithm.
PCA reduction is used on 4D data to extract representative curves
"""
desc = QtGui.QLabel(DESC)
desc.setWordWrap(True)
layout.addWidget(desc)
gbox = QtGui.QGroupBox()
gbox.setTitle('Clustering options')
grid = QtGui.QGridLayout()
gbox.setLayout(grid)
# Data to cluster
grid.addWidget(QtGui.QLabel("Data"), 0, 0)
self.data_combo = OverlayCombo(self.ivm)
self.data_combo.currentIndexChanged.connect(self._data_changed)
grid.addWidget(self.data_combo, 0, 1)
grid.addWidget(QtGui.QLabel("ROI"), 1, 0)
self.roi_combo = RoiCombo(self.ivm, none_option=True)
grid.addWidget(self.roi_combo, 1, 1)
# Number of clusters inside the ROI
self.n_clusters = NumericOption("Number of clusters",
grid,
xpos=2,
ypos=0,
minval=2,
maxval=20,
default=4,
intonly=True)
self.n_clusters.spin.setToolTip("")
# Number of PCA modes
self.n_pca = NumericOption("Number of PCA modes",
grid,
xpos=2,
ypos=1,
minval=1,
maxval=10,
default=3,
intonly=True)
self.n_pca.spin.setToolTip("")
# Output ROI name
grid.addWidget(QtGui.QLabel("Output name"), 2, 0)
self.output_name = QtGui.QLineEdit("clusters")
grid.addWidget(self.output_name, 2, 1)
layout.addWidget(gbox)
# Run clustering button
hbox = QtGui.QHBoxLayout()
self.run_btn = QtGui.QPushButton('Run', self)
self.run_btn.clicked.connect(self.run_clustering)
hbox.addWidget(self.run_btn)
hbox.addStretch(1)
layout.addLayout(hbox)
# Plot window, showing representative curves for 4D data
self.show_curves_btn = QtGui.QPushButton('Show representative curves',
self)
self.show_curves_btn.clicked.connect(self._show_curves)
layout.addWidget(self.show_curves_btn)
self.plotwin = pg.GraphicsLayoutWidget()
self.plotwin.setBackground(background=None)
self.plot = self.plotwin.addPlot(title="Cluster representative curves")
self.plot.setLabel('left', "Signal Enhancement")
self.plotwin.setVisible(False)
layout.addWidget(self.plotwin)
# Statistics
self.show_count_btn = QtGui.QPushButton('Show voxel counts', self)
self.show_count_btn.clicked.connect(self._show_counts)
layout.addWidget(self.show_count_btn)
self.stats_gbox = QtGui.QGroupBox()
self.stats_gbox.setTitle('Voxel count')
self.count_table = QtGui.QStandardItemModel()
self.count_view = QtGui.QTableView()
self.count_view.resizeColumnsToContents()
self.count_view.setModel(self.count_table)
hbox = QtGui.QHBoxLayout()
hbox.addWidget(self.count_view)
self.stats_gbox.setLayout(hbox)
self.stats_gbox.setVisible(False)
layout.addWidget(self.stats_gbox)
# Merge regions
self.show_merge_btn = QtGui.QPushButton('Show merge options', self)
self.show_merge_btn.clicked.connect(self._show_merge)
layout.addWidget(self.show_merge_btn)
self.merge_gbox = QtGui.QGroupBox()
self.merge_gbox.setTitle('Merge regions')
vbox = QtGui.QVBoxLayout()
self.merge_gbox.setLayout(vbox)
hbox = QtGui.QHBoxLayout()
self.merge_btn = QtGui.QPushButton('Merge', self)
self.merge_btn.clicked.connect(self._run_merge)
hbox.addWidget(self.merge_btn)
hbox.addWidget(QtGui.QLabel('Merge region '))
self.merge_region1 = QtGui.QLineEdit('1', self)
hbox.addWidget(self.merge_region1)
hbox.addWidget(QtGui.QLabel(' with '))
self.merge_region2 = QtGui.QLineEdit('2', self)
hbox.addWidget(self.merge_region2)
vbox.addLayout(hbox)
hbox = QtGui.QHBoxLayout()
self.auto_merge_btn = QtGui.QPushButton('AutoMerge', self)
self.auto_merge_btn.clicked.connect(self._run_automerge)
hbox.addWidget(self.auto_merge_btn)
hbox.addStretch(1)
vbox.addLayout(hbox)
self.merge_gbox.setVisible(False)
layout.addWidget(self.merge_gbox)
layout.addStretch(1)
def activate(self):
self.ivl.sig_focus_changed.connect(self._focus_changed)
self.ivm.sig_current_roi.connect(self._current_roi_changed)
self.ivm.sig_main_data.connect(self._main_data_changed)
self._data_changed()
def deactivate(self):
self.ivl.sig_focus_changed.disconnect(self._focus_changed)
self.ivm.sig_current_roi.disconnect(self._current_roi_changed)
self.ivm.sig_main_data.disconnect(self._main_data_changed)
def _current_roi_changed(self, roi):
if roi is not None and roi.name != self.output_name.text():
self.roi_combo.setCurrentIndex(self.roi_combo.findText(roi.name))
def _main_data_changed(self, data):
if data is not None:
idx = self.data_combo.findText(data.name)
else:
idx = 0
self.data_combo.setCurrentIndex(idx)
def _data_changed(self):
data = self.ivm.data.get(self.data_combo.currentText(), None)
if data is not None:
is4d = data.nvols > 1
self.debug("Number of vols: %i, 4d=%s", data.nvols, is4d)
self.n_pca.label.setVisible(is4d)
self.n_pca.spin.setVisible(is4d)
self.show_curves_btn.setVisible(is4d)
self.plotwin.setVisible(is4d and self.plotwin.isVisible())
self.auto_merge_btn.setEnabled(is4d)
self.run_btn.setEnabled(data is not None)
def _focus_changed(self):
self._update_voxel_count()
def _show_curves(self):
if self.plotwin.isVisible():
self.plotwin.setVisible(False)
self.show_curves_btn.setText("Show representative curves")
else:
self.plotwin.setVisible(True)
self.show_curves_btn.setText("Hide representative curves")
def _show_counts(self):
if self.stats_gbox.isVisible():
self.stats_gbox.setVisible(False)
self.show_count_btn.setText("Show voxel counts")
else:
self.stats_gbox.setVisible(True)
self.show_count_btn.setText("Hide voxel counts")
def _show_merge(self):
if self.merge_gbox.isVisible():
self.merge_gbox.setVisible(False)
self.show_merge_btn.setText("Show merge_options")
else:
self.merge_gbox.setVisible(True)
self.show_merge_btn.setText("Hide merge options")
def batch_options(self):
options = {
"data": self.data_combo.currentText(),
"roi": self.roi_combo.currentText(),
"n-clusters": self.n_clusters.spin.value(),
"output-name": self.output_name.text(),
"invert-roi": False,
}
if options["roi"] == "<none>":
del options["roi"]
if self.n_pca.label.isVisible():
# 4D PCA options
options["n-pca"] = self.n_pca.spin.value()
options["reduction"] = "pca"
options["norm-data"] = True
return "KMeans", options
def run_clustering(self):
"""
Run kmeans clustering using normalised PCA modes
"""
options = self.batch_options()[1]
self.process.run(options)
self._update_voxel_count()
if self.n_pca.label.isVisible():
self.update_plot()
def _update_voxel_count(self):
self.count_table.clear()
self.count_table.setVerticalHeaderItem(
0, QtGui.QStandardItem("Voxel count"))
roi = self.ivm.rois.get(self.output_name.text(), None)
if roi is not None:
col_idx = 0
for region, name in roi.regions.items():
self.count_table.setHorizontalHeaderItem(
col_idx, QtGui.QStandardItem(name))
# Volume count
voxel_count = np.sum(roi.raw() == region)
self.count_table.setItem(
0, col_idx,
QtGui.QStandardItem(str(np.around(voxel_count))))
col_idx += 1
def update_plot(self):
"""
Plot the cluster curves
:return:
"""
# Clear graph
self.plot.clear()
self.plot.setLabel('bottom', "Volume", "")
if self.plot.legend is not None:
# Work around pyqtgraph legend bug - the legend is recreated multiple times!
# https://stackoverflow.com/questions/42792858/pyqtgraph-delete-persisting-legend-in-pyqt4-gui
self.plot.legend.scene().removeItem(self.plot.legend)
data = self.ivm.data.get(self.data_combo.currentText(), None)
roi = self.ivm.rois.get(self.output_name.text(), None)
if roi is not None and data is not None and data.nvols > 1:
# Generate mean curve for each cluster
self._generate_cluster_means(roi, data)
self.plot.addLegend()
# Plotting using single or multiple plots
for region, name in roi.regions.items():
if np.sum(self.curves[region]) == 0:
continue
pencol = get_pencol(roi, region)
curve = self.plot.plot(pen=pencol, width=8.0, name=name)
xx = np.arange(len(self.curves[region]))
curve.setData(xx, self.curves[region])
def _run_merge(self):
m1 = int(self.merge_region1.text())
m2 = int(self.merge_region2.text())
self._merge(m1, m2)
def _run_automerge(self):
# Use PCA features or true curves?
# Mean features from each cluster
# Distance matrix between features
if len(self.curves) < 2: return
curvemat = np.zeros((len(self.curves), self.ivm.main.nvols))
row_region = {}
idx = 0
for region, curve in self.curves.items():
row_region[idx] = region
curvemat[idx, :] = curve
idx += 1
distmat = pairwise.euclidean_distances(curvemat)
distmat[distmat == 0] = np.inf
loc1 = np.where(distmat == distmat.min())[0]
self._merge(row_region[loc1[0]], row_region[loc1[1]])
def _generate_cluster_means(self, roi, data):
"""
Generate the mean curves for each cluster
Returns:
"""
self.curves = {}
for region in roi.regions:
roi_data = data.mask(roi, region=region, output_flat=True)
mean = np.median(roi_data, axis=0)
self.curves[region] = mean
def _merge(self, m1, m2):
roi = self.ivm.rois.get(self.output_name.text(), None)
if roi is not None:
roi_data = roi.raw()
roi_data[roi_data == m1] = m2
# signal the change
self.ivm.add(NumpyData(roi_data,
grid=roi.grid,
name=self.output_name.text(),
roi=True),
make_current=True)
# replot
self.update_plot()
self._update_voxel_count()
class OverlayViewWidget(QtGui.QGroupBox):
""" Change view options for ROI """
def __init__(self, ivl, view):
QtGui.QGroupBox.__init__(self)
self.ivl = ivl
self.ivm = ivl.ivm
self.view = view
grid = QtGui.QGridLayout()
grid.setVerticalSpacing(2)
grid.setContentsMargins(5, 5, 5, 5)
self.setLayout(grid)
grid.addWidget(QtGui.QLabel("Overlay"), 0, 0)
self.overlay_combo = OverlayCombo(self.ivm,
none_option=True,
set_first=False)
grid.addWidget(self.overlay_combo, 0, 1)
grid.addWidget(QtGui.QLabel("View"), 1, 0)
self.ov_view_combo = QtGui.QComboBox()
self.ov_view_combo.addItem("All")
self.ov_view_combo.addItem("Only in ROI")
self.ov_view_combo.addItem("None")
grid.addWidget(self.ov_view_combo, 1, 1)
grid.addWidget(QtGui.QLabel("Color map"), 2, 0)
hbox = QtGui.QHBoxLayout()
self.ov_cmap_combo = QtGui.QComboBox()
self.ov_cmap_combo.addItem("jet")
self.ov_cmap_combo.addItem("hot")
self.ov_cmap_combo.addItem("gist_heat")
self.ov_cmap_combo.addItem("flame")
self.ov_cmap_combo.addItem("bipolar")
self.ov_cmap_combo.addItem("spectrum")
hbox.addWidget(self.ov_cmap_combo)
self.ov_levels_btn = QtGui.QPushButton()
self.ov_levels_btn.setIcon(QtGui.QIcon(get_icon("levels.png")))
self.ov_levels_btn.setFixedSize(16, 16)
self.ov_levels_btn.setToolTip("Adjust colour map levels")
self.ov_levels_btn.clicked.connect(self._show_ov_levels)
self.ov_levels_btn.setEnabled(False)
hbox.addWidget(self.ov_levels_btn)
grid.addLayout(hbox, 2, 1)
grid.addWidget(QtGui.QLabel("Alpha"), 3, 0)
self.ov_alpha_sld = QtGui.QSlider(QtCore.Qt.Horizontal, self)
self.ov_alpha_sld.setFocusPolicy(QtCore.Qt.NoFocus)
self.ov_alpha_sld.setRange(0, 255)
self.ov_alpha_sld.setValue(255)
grid.addWidget(self.ov_alpha_sld, 3, 1)
grid.setRowStretch(4, 1)
self.overlay_combo.currentIndexChanged.connect(self._combo_changed)
self.ov_view_combo.currentIndexChanged.connect(self._view_changed)
self.ov_cmap_combo.currentIndexChanged.connect(self._cmap_changed)
self.ov_alpha_sld.valueChanged.connect(self._alpha_changed)
self.view.sig_view_changed.connect(self._update)
def _update(self, view):
widgets = [
self.ov_view_combo, self.ov_cmap_combo, self.ov_alpha_sld,
self.overlay_combo
]
try:
for widget in widgets:
widget.blockSignals(True)
if not view.get("visible"):
self.ov_view_combo.setCurrentIndex(2)
elif view.get("roi_only"):
self.ov_view_combo.setCurrentIndex(1)
else:
self.ov_view_combo.setCurrentIndex(0)
# 'Custom' only appears as a flag to indicate the user has messed with the
# LUT using the histogram widget. Otherwise is is hidden
cmap = view.get("cmap")
if cmap == "custom":
idx = self.ov_cmap_combo.findText("custom")
if idx >= 0:
self.ov_cmap_combo.setCurrentIndex(idx)
else:
self.ov_cmap_combo.addItem("custom")
idx = self.ov_cmap_combo.findText("custom")
self.ov_cmap_combo.setCurrentIndex(idx)
else:
idx = self.ov_cmap_combo.findText("custom")
if idx >= 0:
self.ov_cmap_combo.removeItem(idx)
idx = self.ov_cmap_combo.findText(view.get("cmap"))
self.ov_cmap_combo.setCurrentIndex(idx)
self.ov_alpha_sld.setValue(view.get("alpha"))
self.ov_levels_btn.setEnabled(view.data is not None)
if view.data is not None:
idx = self.overlay_combo.findText(view.data.name)
self.overlay_combo.setCurrentIndex(idx)
else:
self.overlay_combo.setCurrentIndex(-1)
except:
import traceback
traceback.print_exc()
finally:
for widget in widgets:
widget.blockSignals(False)
def _combo_changed(self, idx):
if idx > 0:
data_name = self.overlay_combo.itemText(idx)
self.ivm.set_current_data(data_name)
else:
self.ivl.ivm.set_current_data(None)
def _cmap_changed(self, idx):
cmap = self.ov_cmap_combo.itemText(idx)
self.view.set("cmap", cmap)
def _view_changed(self, idx):
""" Viewing style (all or within ROI only) changed """
self.view.set("visible", idx in (0, 1))
self.view.set("roi_only", (idx == 1))
def _alpha_changed(self, alpha):
""" Set the data transparency """
self.view.set("alpha", alpha)
def _show_ov_levels(self):
dlg = LevelsDialog(self, self.ivl, self.ivm, self.view)
dlg.exec_()