class ArrayVolumePlot(qt.QWidget):
"""
Widget for plotting a n-D array (n >= 3) as a 3D scalar field.
Three axis arrays can be provided to calibrate the axes.
The signal array can have an arbitrary number of dimensions, the only
limitation being that the last 3 dimensions must have the same length as
the axes arrays.
Sliders are provided to select indices on the first (n - 3) dimensions of
the signal array, and the plot is updated to load the stack corresponding
to the selection.
"""
def __init__(self, parent=None):
"""
:param parent: Parent QWidget
"""
super(ArrayVolumePlot, self).__init__(parent)
self.__signal = None
self.__signal_name = None
# the Z, Y, X axes apply to the last three dimensions of the signal
# (in that order)
self.__z_axis = None
self.__z_axis_name = None
self.__y_axis = None
self.__y_axis_name = None
self.__x_axis = None
self.__x_axis_name = None
from silx.gui.plot3d.ScalarFieldView import ScalarFieldView
from silx.gui.plot3d import SFViewParamTree
self._view = ScalarFieldView(self)
def computeIsolevel(data):
data = data[numpy.isfinite(data)]
if len(data) == 0:
return 0
else:
return numpy.mean(data) + numpy.std(data)
self._view.addIsosurface(computeIsolevel, '#FF0000FF')
# Create a parameter tree for the scalar field view
options = SFViewParamTree.TreeView(self._view)
options.setSfView(self._view)
# Add the parameter tree to the main window in a dock widget
dock = qt.QDockWidget()
dock.setWidget(options)
self._view.addDockWidget(qt.Qt.RightDockWidgetArea, dock)
self._hline = qt.QFrame(self)
self._hline.setFrameStyle(qt.QFrame.HLine)
self._hline.setFrameShadow(qt.QFrame.Sunken)
self._legend = qt.QLabel(self)
self._selector = NumpyAxesSelector(self)
self._selector.setNamedAxesSelectorVisibility(False)
self.__selector_is_connected = False
layout = qt.QVBoxLayout()
layout.addWidget(self._view)
layout.addWidget(self._hline)
layout.addWidget(self._legend)
layout.addWidget(self._selector)
self.setLayout(layout)
def getVolumeView(self):
"""Returns the plot used for the display
:rtype: ScalarFieldView
"""
return self._view
def normalizeComplexData(self, data):
"""
Converts a complex data array to its amplitude, if necessary.
:param data: the data to normalize
:return:
"""
if hasattr(data, "dtype"):
isComplex = numpy.issubdtype(data.dtype, numpy.complexfloating)
else:
isComplex = isinstance(data, numbers.Complex)
if isComplex:
data = numpy.absolute(data)
return data
def setData(self,
signal,
x_axis=None,
y_axis=None,
z_axis=None,
signal_name=None,
xlabel=None,
ylabel=None,
zlabel=None,
title=None):
"""
:param signal: n-D dataset, whose last 3 dimensions are used as the
3D stack values.
:param x_axis: 1-D dataset used as the image's x coordinates. If
provided, its lengths must be equal to the length of the last
dimension of ``signal``.
:param y_axis: 1-D dataset used as the image's y. If provided,
its lengths must be equal to the length of the 2nd to last
dimension of ``signal``.
:param z_axis: 1-D dataset used as the image's z. If provided,
its lengths must be equal to the length of the 3rd to last
dimension of ``signal``.
:param signal_name: Label used in the legend
:param xlabel: Label for X axis
:param ylabel: Label for Y axis
:param zlabel: Label for Z axis
:param title: Graph title
"""
signal = self.normalizeComplexData(signal)
if self.__selector_is_connected:
self._selector.selectionChanged.disconnect(self._updateVolume)
self.__selector_is_connected = False
self.__signal = signal
self.__signal_name = signal_name or ""
self.__x_axis = x_axis
self.__x_axis_name = xlabel
self.__y_axis = y_axis
self.__y_axis_name = ylabel
self.__z_axis = z_axis
self.__z_axis_name = zlabel
self._selector.setData(signal)
self._selector.setAxisNames(["Y", "X", "Z"])
self._view.setAxesLabels(self.__x_axis_name or 'X', self.__y_axis_name
or 'Y', self.__z_axis_name or 'Z')
self._updateVolume()
# the legend label shows the selection slice producing the volume
# (only interesting for ndim > 3)
if signal.ndim > 3:
self._selector.setVisible(True)
self._legend.setVisible(True)
self._hline.setVisible(True)
else:
self._selector.setVisible(False)
self._legend.setVisible(False)
self._hline.setVisible(False)
if not self.__selector_is_connected:
self._selector.selectionChanged.connect(self._updateVolume)
self.__selector_is_connected = True
def _updateVolume(self):
"""Update displayed stack according to the current axes selector
data."""
data = self._selector.selectedData()
x_axis = self.__x_axis
y_axis = self.__y_axis
z_axis = self.__z_axis
offset = []
scale = []
for axis in [x_axis, y_axis, z_axis]:
if axis is None:
calibration = NoCalibration()
elif len(axis) == 2:
calibration = LinearCalibration(y_intercept=axis[0],
slope=axis[1])
else:
calibration = ArrayCalibration(axis)
if not calibration.is_affine():
_logger.warning("Axis has not linear values, ignored")
offset.append(0.)
scale.append(1.)
else:
offset.append(calibration(0))
scale.append(calibration.get_slope())
legend = self.__signal_name + "["
for sl in self._selector.selection():
if sl == slice(None):
legend += ":, "
else:
legend += str(sl) + ", "
legend = legend[:-2] + "]"
self._legend.setText("Displayed data: " + legend)
self._view.setData(data, copy=False)
self._view.setScale(*scale)
self._view.setTranslation(*offset)
self._view.setAxesLabels(self.__x_axis_name, self.__y_axis_name,
self.__z_axis_name)
def clear(self):
old = self._selector.blockSignals(True)
self._selector.clear()
self._selector.blockSignals(old)
self._view.setData(None)
class TestScalarFieldView(TestCaseQt, ParametricTestCase):
"""Tests of ScalarFieldView widget."""
def setUp(self):
super(TestScalarFieldView, self).setUp()
self.widget = ScalarFieldView()
self.widget.show()
paramTreeWidget = TreeView()
paramTreeWidget.setSfView(self.widget)
dock = qt.QDockWidget()
dock.setWidget(paramTreeWidget)
self.widget.addDockWidget(qt.Qt.BottomDockWidgetArea, dock)
# Commented as it slows down the tests
# self.qWaitForWindowExposed(self.widget)
def tearDown(self):
self.qapp.processEvents()
self.widget.setAttribute(qt.Qt.WA_DeleteOnClose)
self.widget.close()
del self.widget
super(TestScalarFieldView, self).tearDown()
@staticmethod
def _buildData(size):
"""Make a 3D dataset"""
coords = numpy.linspace(-10, 10, size)
z = coords.reshape(-1, 1, 1)
y = coords.reshape(1, -1, 1)
x = coords.reshape(1, 1, -1)
return numpy.sin(x * y * z) / (x * y * z)
def testSimple(self):
"""Set the data and an isosurface"""
data = self._buildData(size=32)
self.widget.setData(data)
self.widget.addIsosurface(0.5, (1., 0., 0., 0.5))
self.widget.addIsosurface(0.7, qt.QColor('green'))
self.qapp.processEvents()
def testNotFinite(self):
"""Test with NaN and inf in data set"""
# Some NaNs and inf
data = self._buildData(size=32)
data[8, :, :] = numpy.nan
data[16, :, :] = numpy.inf
data[24, :, :] = - numpy.inf
self.widget.addIsosurface(0.5, 'red')
self.widget.setData(data, copy=True)
self.qapp.processEvents()
self.widget.setData(None)
# All NaNs or inf
data = numpy.empty((4, 4, 4), dtype=numpy.float32)
for value in (numpy.nan, numpy.inf):
with self.subTest(value=str(value)):
data[:] = value
self.widget.setData(data, copy=True)
self.qapp.processEvents()
def testIsoSliderNormalization(self):
"""Test set TreeView with a different isoslider normalization"""
data = self._buildData(size=32)
self.widget.setData(data)
self.widget.addIsosurface(0.5, (1., 0., 0., 0.5))
self.widget.addIsosurface(0.7, qt.QColor('green'))
self.qapp.processEvents()
# Add a second TreeView
paramTreeWidget = TreeView(self.widget)
paramTreeWidget.setIsoLevelSliderNormalization('arcsinh')
paramTreeWidget.setSfView(self.widget)
dock = qt.QDockWidget()
dock.setWidget(paramTreeWidget)
self.widget.addDockWidget(qt.Qt.BottomDockWidgetArea, dock)
class TestScalarFieldView(TestCaseQt, ParametricTestCase):
"""Tests of ScalarFieldView widget."""
def setUp(self):
super(TestScalarFieldView, self).setUp()
self.widget = ScalarFieldView()
self.widget.show()
paramTreeWidget = TreeView()
paramTreeWidget.setSfView(self.widget)
dock = qt.QDockWidget()
dock.setWidget(paramTreeWidget)
self.widget.addDockWidget(qt.Qt.BottomDockWidgetArea, dock)
# Commented as it slows down the tests
# self.qWaitForWindowExposed(self.widget)
def tearDown(self):
self.qapp.processEvents()
self.widget.setAttribute(qt.Qt.WA_DeleteOnClose)
self.widget.close()
del self.widget
super(TestScalarFieldView, self).tearDown()
@staticmethod
def _buildData(size):
"""Make a 3D dataset"""
coords = numpy.linspace(-10, 10, size)
z = coords.reshape(-1, 1, 1)
y = coords.reshape(1, -1, 1)
x = coords.reshape(1, 1, -1)
return numpy.sin(x * y * z) / (x * y * z)
def testSimple(self):
"""Set the data and an isosurface"""
data = self._buildData(size=32)
self.widget.setData(data)
self.widget.addIsosurface(0.5, (1., 0., 0., 0.5))
self.widget.addIsosurface(0.7, qt.QColor('green'))
self.qapp.processEvents()
def testNotFinite(self):
"""Test with NaN and inf in data set"""
# Some NaNs and inf
data = self._buildData(size=32)
data[8, :, :] = numpy.nan
data[16, :, :] = numpy.inf
data[24, :, :] = -numpy.inf
self.widget.addIsosurface(0.5, 'red')
self.widget.setData(data, copy=True)
self.qapp.processEvents()
self.widget.setData(None)
# All NaNs or inf
data = numpy.empty((4, 4, 4), dtype=numpy.float32)
for value in (numpy.nan, numpy.inf):
with self.subTest(value=str(value)):
data[:] = value
self.widget.setData(data, copy=True)
self.qapp.processEvents()
def testIsoSliderNormalization(self):
"""Test set TreeView with a different isoslider normalization"""
data = self._buildData(size=32)
self.widget.setData(data)
self.widget.addIsosurface(0.5, (1., 0., 0., 0.5))
self.widget.addIsosurface(0.7, qt.QColor('green'))
self.qapp.processEvents()
# Add a second TreeView
paramTreeWidget = TreeView(self.widget)
paramTreeWidget.setIsoLevelSliderNormalization('arcsinh')
paramTreeWidget.setSfView(self.widget)
dock = qt.QDockWidget()
dock.setWidget(paramTreeWidget)
self.widget.addDockWidget(qt.Qt.BottomDockWidgetArea, dock)
# Start GUI
app = qt.QApplication([])
# Create the viewer main window
window = ScalarFieldView()
# Create a parameter tree for the scalar field view
treeView = SFViewParamTree.TreeView(window)
treeView.setSfView(window) # Attach the parameter tree to the view
# Add the parameter tree to the main window in a dock widget
dock = qt.QDockWidget()
dock.setWindowTitle('Parameters')
dock.setWidget(treeView)
window.addDockWidget(qt.Qt.RightDockWidgetArea, dock)
# Load data from file
if args.filename is not None:
data = load(args.filename)
_logger.info('Data:\n\tShape: %s\n\tRange: [%f, %f]', str(data.shape),
data.min(), data.max())
else:
# Create dummy data
_logger.warning('Not data file provided, creating dummy data')
coords = numpy.linspace(-10, 10, 64)
z = coords.reshape(-1, 1, 1)
y = coords.reshape(1, -1, 1)
x = coords.reshape(1, 1, -1)
data = numpy.sin(x * y * z) / (x * y * z)
def main(argv=None):
# Parse input arguments
parser = argparse.ArgumentParser(description=__doc__)
parser.add_argument('-l',
'--level',
nargs='?',
type=float,
default=float('nan'),
help="The value at which to generate the iso-surface")
parser.add_argument('-sx',
'--xscale',
nargs='?',
type=float,
default=1.,
help="The scale of the data on the X axis")
parser.add_argument('-sy',
'--yscale',
nargs='?',
type=float,
default=1.,
help="The scale of the data on the Y axis")
parser.add_argument('-sz',
'--zscale',
nargs='?',
type=float,
default=1.,
help="The scale of the data on the Z axis")
parser.add_argument('-ox',
'--xoffset',
nargs='?',
type=float,
default=0.,
help="The offset of the data on the X axis")
parser.add_argument('-oy',
'--yoffset',
nargs='?',
type=float,
default=0.,
help="The offset of the data on the Y axis")
parser.add_argument('-oz',
'--zoffset',
nargs='?',
type=float,
default=0.,
help="The offset of the data on the Z axis")
parser.add_argument('filename',
nargs='?',
default=None,
help="""Filename to open.
It supports 3D volume saved as .npy or in .h5 files.
It also support nD data set (n>=3) stored in a HDF5 file.
For HDF5, provide the filename and path as: <filename>::<path_in_file>.
If the data set has more than 3 dimensions, it is possible to choose a
3D data set as a subset by providing the indices along the first n-3
dimensions with '#':
<filename>::<path_in_file>#<1st_dim_index>...#<n-3th_dim_index>
E.g.: data.h5::/data_5D#1#1
""")
args = parser.parse_args(args=argv)
# Start GUI
global app # QApplication must be global to avoid seg fault on quit
app = qt.QApplication([])
# Create the viewer main window
window = ScalarFieldView()
window.setAttribute(qt.Qt.WA_DeleteOnClose)
# Create a parameter tree for the scalar field view
treeView = SFViewParamTree.TreeView(window)
treeView.setSfView(window) # Attach the parameter tree to the view
# Add the parameter tree to the main window in a dock widget
dock = qt.QDockWidget()
dock.setWindowTitle('Parameters')
dock.setWidget(treeView)
window.addDockWidget(qt.Qt.RightDockWidgetArea, dock)
# Load data from file
if args.filename is not None:
data = load(args.filename)
_logger.info('Data:\n\tShape: %s\n\tRange: [%f, %f]', str(data.shape),
data.min(), data.max())
else:
# Create dummy data
_logger.warning('Not data file provided, creating dummy data')
coords = numpy.linspace(-10, 10, 64)
z = coords.reshape(-1, 1, 1)
y = coords.reshape(1, -1, 1)
x = coords.reshape(1, 1, -1)
data = numpy.sin(x * y * z) / (x * y * z)
# Set ScalarFieldView data
window.setData(data)
# Set scale of the data
window.setScale(args.xscale, args.yscale, args.zscale)
# Set offset of the data
window.setTranslation(args.xoffset, args.yoffset, args.zoffset)
# Set axes labels
window.setAxesLabels('X', 'Y', 'Z')
# Add an iso-surface
if not numpy.isnan(args.level):
# Add an iso-surface at the given iso-level
window.addIsosurface(args.level, '#FF0000FF')
else:
# Add an iso-surface from a function
window.addIsosurface(default_isolevel, '#FF0000FF')
window.show()
return app.exec_()
# Start GUI
app = qt.QApplication([])
# Create the viewer main window
window = ScalarFieldView()
# Create a parameter tree for the scalar field view
treeView = SFViewParamTree.TreeView(window)
treeView.setSfView(window) # Attach the parameter tree to the view
# Add the parameter tree to the main window in a dock widget
dock = qt.QDockWidget()
dock.setWindowTitle('Parameters')
dock.setWidget(treeView)
window.addDockWidget(qt.Qt.RightDockWidgetArea, dock)
# Load data from file
if args.filename is not None:
data = load(args.filename)
_logger.info('Data:\n\tShape: %s\n\tRange: [%f, %f]',
str(data.shape), data.min(), data.max())
else:
# Create dummy data
_logger.warning('Not data file provided, creating dummy data')
coords = numpy.linspace(-10, 10, 64)
z = coords.reshape(-1, 1, 1)
y = coords.reshape(1, -1, 1)
x = coords.reshape(1, 1, -1)
data = numpy.sin(x * y * z) / (x * y * z)
class TestScalarFieldView(TestCaseQt, ParametricTestCase):
"""Tests of ScalarFieldView widget."""
def setUp(self):
super(TestScalarFieldView, self).setUp()
self.widget = ScalarFieldView()
self.widget.show()
# Create a parameter tree for the scalar field view
self.treeView = TreeView()
self.treeView.setSfView(
self.widget) # Attach the parameter tree to the view
self.treeView.show()
# Add the parameter tree to the main window in a dock widget
dock = qt.QDockWidget()
dock.setWindowTitle('Parameters')
dock.setWidget(self.treeView)
self.widget.addDockWidget(qt.Qt.RightDockWidgetArea, dock)
# Commented as it slows down the tests
# self.qWaitForWindowExposed(self.widget)
def tearDown(self):
self.qapp.processEvents()
self.widget.setAttribute(qt.Qt.WA_DeleteOnClose)
self.widget.close()
del self.widget
del self.treeView
super(TestScalarFieldView, self).tearDown()
@staticmethod
def _buildData(size):
"""Make a 3D dataset"""
coords = numpy.linspace(-10, 10, size)
z = coords.reshape(-1, 1, 1)
y = coords.reshape(1, -1, 1)
x = coords.reshape(1, 1, -1)
return numpy.sin(x * y * z) / (x * y * z)
def testSimple(self):
"""Set the data and an isosurface"""
data = self._buildData(size=32)
self.widget.setData(data)
self.widget.addIsosurface(0.5, (1., 0., 0., 0.5))
self.widget.addIsosurface(0.7, qt.QColor('green'))
self.qapp.processEvents()
def testNotFinite(self):
"""Test with NaN and inf in data set"""
# Some NaNs and inf
data = self._buildData(size=32)
data[8, :, :] = numpy.nan
data[16, :, :] = numpy.inf
data[24, :, :] = -numpy.inf
self.widget.addIsosurface(0.5, 'red')
self.widget.setData(data, copy=True)
self.qapp.processEvents()
self.widget.setData(None)
# All NaNs or inf
data = numpy.empty((4, 4, 4), dtype=numpy.float32)
for value in (numpy.nan, numpy.inf):
with self.subTest(value=str(value)):
data[:] = value
self.widget.setData(data, copy=True)
self.qapp.processEvents()