def createWidget(self, parent):
from silx.gui.plot3d import ScalarFieldView
from silx.gui.plot3d import SFViewParamTree
plot = ScalarFieldView.ScalarFieldView(parent)
plot.setAxesLabels(*reversed(self.axesNames(None, None)))
def computeIsolevel(data):
data = data[numpy.isfinite(data)]
if len(data) == 0:
return 0
else:
return numpy.mean(data) + numpy.std(data)
plot.addIsosurface(computeIsolevel, '#FF0000FF')
# Create a parameter tree for the scalar field view
options = SFViewParamTree.TreeView(plot)
options.setSfView(plot)
# Add the parameter tree to the main window in a dock widget
dock = qt.QDockWidget()
dock.setWidget(options)
plot.addDockWidget(qt.Qt.RightDockWidgetArea, dock)
return plot
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)
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=sys.argv[1:])
# 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
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_()