class TestScalarFieldView(TestCaseQt, ParametricTestCase):
"""Tests of ScalarFieldView widget."""
def setUp(self):
super(TestScalarFieldView, self).setUp()
self.widget = ScalarFieldView()
self.widget.show()
# 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()
class TestScalarFieldView(TestCaseQt, ParametricTestCase):
"""Tests of ScalarFieldView widget."""
def setUp(self):
super(TestScalarFieldView, self).setUp()
self.widget = ScalarFieldView()
self.widget.show()
# 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()
class TestScalarFieldView(TestCaseQt):
"""Tests StatsWidget combined with ScalarFieldView"""
def setUp(self):
super(TestScalarFieldView, self).setUp()
self.scalarFieldView = ScalarFieldView()
self.scalarFieldView.resize(300, 300)
self.scalarFieldView.show()
self.statsWidget = BasicStatsWidget()
self.statsWidget.setPlot(self.scalarFieldView)
# self.qWaitForWindowExposed(self.sceneWidget)
def tearDown(self):
Stats._getContext.cache_clear()
self.qapp.processEvents()
self.scalarFieldView.setAttribute(qt.Qt.WA_DeleteOnClose)
self.scalarFieldView.close()
del self.scalarFieldView
self.statsWidget.setAttribute(qt.Qt.WA_DeleteOnClose)
self.statsWidget.close()
del self.statsWidget
super(TestScalarFieldView, self).tearDown()
def _getTextFor(self, row, name):
"""Returns text in table at given row for column name
:param int row: Row number in the table
:param str name: Column id
:rtype: Union[str,None]
"""
statsTable = self.statsWidget._getStatsTable()
for column in range(statsTable.columnCount()):
headerItem = statsTable.horizontalHeaderItem(column)
if headerItem.data(qt.Qt.UserRole) == name:
tableItem = statsTable.item(row, column)
return tableItem.text()
return None
def test(self):
"""Test StatsWidget with ScalarFieldView"""
data = numpy.arange(64**3, dtype=numpy.float64).reshape(64, 64, 64)
self.scalarFieldView.setData(data)
statsTable = self.statsWidget._getStatsTable()
# Test selection only
self.statsWidget.setDisplayOnlyActiveItem(True)
self.assertEqual(statsTable.rowCount(), 1)
# Test all data
self.statsWidget.setDisplayOnlyActiveItem(False)
self.assertEqual(statsTable.rowCount(), 1)
for column in range(statsTable.columnCount()):
self.assertEqual(float(self._getTextFor(0, 'min')),
numpy.min(data))
self.assertEqual(float(self._getTextFor(0, 'max')),
numpy.max(data))
sum_ = numpy.sum(data)
comz = numpy.sum(
numpy.arange(data.shape[0]) *
numpy.sum(data, axis=(1, 2))) / sum_
comy = numpy.sum(
numpy.arange(data.shape[1]) *
numpy.sum(data, axis=(0, 2))) / sum_
comx = numpy.sum(
numpy.arange(data.shape[2]) *
numpy.sum(data, axis=(0, 1))) / sum_
self.assertEqual(self._getTextFor(0, 'COM'), str(
(comx, comy, comz)))
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_()
class TestScalarFieldView(TestCaseQt):
"""Tests StatsWidget combined with ScalarFieldView"""
def setUp(self):
super(TestScalarFieldView, self).setUp()
self.scalarFieldView = ScalarFieldView()
self.scalarFieldView.resize(300, 300)
self.scalarFieldView.show()
self.statsWidget = BasicStatsWidget()
self.statsWidget.setPlot(self.scalarFieldView)
# self.qWaitForWindowExposed(self.sceneWidget)
def tearDown(self):
self.qapp.processEvents()
self.scalarFieldView.setAttribute(qt.Qt.WA_DeleteOnClose)
self.scalarFieldView.close()
del self.scalarFieldView
self.statsWidget.setAttribute(qt.Qt.WA_DeleteOnClose)
self.statsWidget.close()
del self.statsWidget
super(TestScalarFieldView, self).tearDown()
def _getTextFor(self, row, name):
"""Returns text in table at given row for column name
:param int row: Row number in the table
:param str name: Column id
:rtype: Union[str,None]
"""
statsTable = self.statsWidget._getStatsTable()
for column in range(statsTable.columnCount()):
headerItem = statsTable.horizontalHeaderItem(column)
if headerItem.data(qt.Qt.UserRole) == name:
tableItem = statsTable.item(row, column)
return tableItem.text()
return None
def test(self):
"""Test StatsWidget with ScalarFieldView"""
data = numpy.arange(64**3, dtype=numpy.float64).reshape(64, 64, 64)
self.scalarFieldView.setData(data)
statsTable = self.statsWidget._getStatsTable()
# Test selection only
self.statsWidget.setDisplayOnlyActiveItem(True)
self.assertEqual(statsTable.rowCount(), 1)
# Test all data
self.statsWidget.setDisplayOnlyActiveItem(False)
self.assertEqual(statsTable.rowCount(), 1)
for column in range(statsTable.columnCount()):
self.assertEqual(float(self._getTextFor(0, 'min')), numpy.min(data))
self.assertEqual(float(self._getTextFor(0, 'max')), numpy.max(data))
sum_ = numpy.sum(data)
comz = numpy.sum(numpy.arange(data.shape[0]) * numpy.sum(data, axis=(1, 2))) / sum_
comy = numpy.sum(numpy.arange(data.shape[1]) * numpy.sum(data, axis=(0, 2))) / sum_
comx = numpy.sum(numpy.arange(data.shape[2]) * numpy.sum(data, axis=(0, 1))) / sum_
self.assertEqual(self._getTextFor(0, 'COM'), str((comx, comy, comz)))