def value(self, pos, grid=None, as_str=False):
"""
Return the data value at a point
:param pos: Position as a 3D or 4D vector. If 4D last value is the volume index
(0 for 3D). If ``grid`` not specified, position is in world space
:param grid: If specified, interpret position in this ``DataGrid`` co-ordinate space.
:param str: If True, return value as string to appropriate number of decimal places.
"""
if grid is None:
grid = DataGrid([1, 1, 1], np.identity(4))
if len(pos) == 3:
pos = list(pos) + [
0,
]
data_pos = [
int(math.floor(v + 0.5))
for v in self.grid.grid_to_grid(pos[:3], from_grid=grid)
]
if min(data_pos) < 0:
# Out of range but will be misinterpreted by indexing!
value = 0
else:
rawdata = self.volume(pos[3])
try:
value = rawdata[tuple(data_pos)]
except IndexError:
value = 0
if as_str:
return sf(value)
else:
return value
def _update_table(self):
self.variance_model.clear()
extra = self.ivm.extras.get(
self._options.option("output-name").value + "_variance", None)
if extra is not None:
self.debug(str(extra))
for idx, header in enumerate(extra.col_headers):
self.variance_model.setHorizontalHeaderItem(
idx, QtGui.QStandardItem(header))
for idx, variance in enumerate(extra.arr):
self.variance_model.setItem(
idx, 0, QtGui.QStandardItem(str(variance[0])))
self.variance_model.setItem(
idx, 1, QtGui.QStandardItem(sf(variance[1])))
self.variance_model.setItem(
idx, 2, QtGui.QStandardItem(sf(variance[2])))
def _update_table(self):
"""
Set the data parameter values in the table based on the current point clicked
"""
self.values_table.clear()
self.values_table.setHorizontalHeaderItem(0, QtGui.QStandardItem("Value"))
data_vals = self.ivm.values(self.ivl.focus(), self.ivl.grid)
for ii, ovl in enumerate(sorted(data_vals.keys())):
if self.ivm.data[ovl].ndim == 3:
self.values_table.setVerticalHeaderItem(ii, QtGui.QStandardItem(ovl))
self.values_table.setItem(ii, 0, QtGui.QStandardItem(sf(data_vals[ovl])))
def _focus_changed(self, focus):
if self._qpdata is not None:
value = self._qpdata.value(focus, self.ivl.grid)
if self._qpdata.roi:
region = int(value)
if region == 0:
text = "(outside ROI)"
else:
text = self._qpdata.regions.get(region, "")
if text == "":
text = "1"
else:
text = sf(value, 4)
self._value_label.setText(text)
def _update_rms_table(self):
try:
self.updating = True # Hack to prevent plot being refreshed during table update
self.rms_table.clear()
self.rms_table.setHorizontalHeaderItem(0,
QtGui.QStandardItem("Name"))
self.rms_table.setHorizontalHeaderItem(
1, QtGui.QStandardItem("RMS (Position)"))
pos = self.ivl.focus()
sigs = self.ivm.timeseries(pos, self.ivl.grid)
max_length = max([
0,
] + [len(sig) for sig in sigs.values()])
if self.ivm.main is not None:
main_curve = self.ivm.main.timeseries(pos, grid=self.ivl.grid)
main_curve.extend([0] * max_length)
main_curve = main_curve[:max_length]
for idx, name in enumerate(sorted(sigs.keys())):
# Make sure data curve is correct length
data_curve = sigs[name]
data_curve.extend([0] * max_length)
data_curve = data_curve[:max_length]
if self.ivm.main is not None:
data_rms = np.sqrt(
np.mean(
np.square([
v1 - v2
for v1, v2 in zip(main_curve, data_curve)
])))
else:
data_rms = 0
name_item = QtGui.QStandardItem(name)
name_item.setCheckable(True)
name_item.setEditable(False)
if name not in self.data_enabled:
self.data_enabled[name] = QtCore.Qt.Checked
name_item.setCheckState(self.data_enabled[name])
self.rms_table.setItem(idx, 0, name_item)
item = QtGui.QStandardItem(sf(data_rms))
item.setEditable(False)
self.rms_table.setItem(idx, 1, item)
finally:
self.updating = False
def _update_pool_list(self):
self._updating = True
try:
self.pools_table.clear()
self.pools_table.setHorizontalHeaderItem(
0, QtGui.QStandardItem("Name"))
self.pools_table.setHorizontalHeaderItem(
1, QtGui.QStandardItem("PPM offset"))
self.pools_table.setHorizontalHeaderItem(
2, QtGui.QStandardItem("Exchange rate"))
self.pools_table.setHorizontalHeaderItem(3,
QtGui.QStandardItem("T1"))
self.pools_table.setHorizontalHeaderItem(4,
QtGui.QStandardItem("T2"))
self.pools_table_view.horizontalHeader().setSectionResizeMode(
0, QtGui.QHeaderView.Stretch)
for idx, pool in enumerate(self._pools):
name_item = QtGui.QStandardItem(pool.name)
name_item.setCheckable(True)
name_item.setEditable(False)
name_item.setCheckState(
QtCore.Qt.Checked if pool.enabled else QtCore.Qt.Unchecked)
name_item.setData(pool)
self.pools_table.setItem(idx, 0, name_item)
vals = pool.vals[self._b0_str]
for col, val in enumerate(vals):
item = QtGui.QStandardItem(sf(val))
item.setEditable(True)
item.setData(pool)
self.pools_table.setItem(idx, col + 1, item)
self.pools_table_view.resizeColumnsToContents()
finally:
self._updating = False
self.sig_pools_changed.emit(self.pools)
def _update_edit(self, value):
if self.rtype == int:
self.val_edit.setText(str(int(value)))
else:
self.val_edit.setText(sf(value, sig_fig=self.decimals))
def run(self, options):
data_name = options.pop('data', None)
output_name = options.pop('output-name', None)
if data_name is None:
data_items = self.ivm.data.keys()
elif isinstance(data_name, six.string_types):
data_items = [
data_name,
]
if output_name is None:
output_name = "%s_stats" % data_name
else:
data_items = data_name
data_items = [self.ivm.data[name] for name in data_items]
if output_name is None:
output_name = "stats"
roi_name = options.pop('roi', None)
roi = None
if roi_name is not None:
roi = self.ivm.rois[roi_name]
slice_dir = options.pop('slice-dir', None)
slice_pos = options.pop('slice-pos', 0)
sl = None
if slice_dir is not None:
sl = OrthoSlice(self.ivm.main.grid, slice_dir, slice_pos)
vol = options.pop('vol', None)
no_extra = options.pop('no-extras', False)
exact_median = options.pop('exact-median', False)
self.model.clear()
self.model.setVerticalHeaderItem(0, QtGui.QStandardItem("Mean"))
self.model.setVerticalHeaderItem(1, QtGui.QStandardItem("Median"))
self.model.setVerticalHeaderItem(2, QtGui.QStandardItem("STD"))
self.model.setVerticalHeaderItem(3, QtGui.QStandardItem("Min"))
self.model.setVerticalHeaderItem(4, QtGui.QStandardItem("Max"))
col = 0
for data in data_items:
stats, roi_labels = self.get_summary_stats(
data, roi, slice_loc=sl, vol=vol, exact_median=exact_median)
for ii in range(len(stats['mean'])):
self.model.setHorizontalHeaderItem(
col,
QtGui.QStandardItem("%s\n%s" %
(data.name, roi_labels[ii])))
self.model.setItem(0, col,
QtGui.QStandardItem(sf(stats['mean'][ii])))
self.model.setItem(
1, col, QtGui.QStandardItem(sf(stats['median'][ii])))
self.model.setItem(2, col,
QtGui.QStandardItem(sf(stats['std'][ii])))
self.model.setItem(3, col,
QtGui.QStandardItem(sf(stats['min'][ii])))
self.model.setItem(4, col,
QtGui.QStandardItem(sf(stats['max'][ii])))
col += 1
if not no_extra:
self.ivm.add_extra(output_name,
table_to_extra(self.model, output_name))