def createRois(self):
self._1Droi = ROI(name='my1DRoi', fromdata=2.0, todata=5.0)
self._2Droi_rect = RectangleROI()
self._2Droi_rect.setGeometry(size=(10, 10), origin=(10, 0))
self._2Droi_poly = PolygonROI()
points = numpy.array(((0, 20), (0, 0), (10, 0)))
self._2Droi_poly.setPoints(points=points)
class _TestRoiStatsBase(TestCaseQt):
"""Base class for several unittest relative to ROIStatsWidget"""
def setUp(self):
TestCaseQt.setUp(self)
# define plot
self.plot = PlotWindow()
self.plot.addImage(numpy.arange(10000).reshape(100, 100),
legend='img1')
self.img_item = self.plot.getImage('img1')
self.plot.addCurve(x=numpy.linspace(0, 10, 56),
y=numpy.arange(56),
legend='curve1')
self.curve_item = self.plot.getCurve('curve1')
self.plot.addHistogram(edges=numpy.linspace(0, 10, 56),
histogram=numpy.arange(56),
legend='histo1')
self.histogram_item = self.plot.getHistogram(legend='histo1')
self.plot.addScatter(x=numpy.linspace(0, 10, 56),
y=numpy.linspace(0, 10, 56),
value=numpy.arange(56),
legend='scatter1')
self.scatter_item = self.plot.getScatter(legend='scatter1')
# stats widget
self.statsWidget = ROIStatsWidget(plot=self.plot)
# define stats
stats = [
('sum', numpy.sum),
('mean', numpy.mean),
]
self.statsWidget.setStats(stats=stats)
# define rois
self.roi1D = ROI(name='range1', fromdata=0, todata=4, type_='energy')
self.rectangle_roi = RectangleROI()
self.rectangle_roi.setGeometry(origin=(0, 0), size=(20, 20))
self.rectangle_roi.setName('Initial ROI')
self.polygon_roi = PolygonROI()
points = numpy.array([[0, 5], [5, 0], [10, 5], [5, 10]])
self.polygon_roi.setPoints(points)
def statsTable(self):
return self.statsWidget._statsROITable
def tearDown(self):
Stats._getContext.cache_clear()
self.statsWidget.setAttribute(qt.Qt.WA_DeleteOnClose, True)
self.statsWidget.close()
self.statsWidget = None
self.plot.setAttribute(qt.Qt.WA_DeleteOnClose, True)
self.plot.close()
self.plot = None
TestCaseQt.tearDown(self)
def test(self):
"""Test stats result on an image context with different scale and
origins"""
roi_origins = [(0, 0), (2, 10), (14, 20)]
img_origins = [(0, 0), (14, 20), (2, 10)]
img_scales = [1.0, 0.5, 2.0]
_stats = {
'sum': stats.Stat(name='sum', fct=numpy.sum),
}
for roi_origin in roi_origins:
for img_origin in img_origins:
for img_scale in img_scales:
with self.subTest(roi_origin=roi_origin,
img_origin=img_origin,
img_scale=img_scale):
self.plot.addImage(self.data,
legend='img',
origin=img_origin,
scale=img_scale)
roi = RectangleROI()
roi.setGeometry(origin=roi_origin, size=(20, 20))
context = stats._ImageContext(
item=self.plot.getImage('img'),
plot=self.plot,
onlimits=False,
roi=roi)
x_start = int(
(roi_origin[0] - img_origin[0]) / img_scale)
x_end = int(x_start + (20 / img_scale)) + 1
y_start = int(
(roi_origin[1] - img_origin[1]) / img_scale)
y_end = int(y_start + (20 / img_scale)) + 1
x_start = max(x_start, 0)
x_end = min(max(x_end, 0), self.data_dims[1])
y_start = max(y_start, 0)
y_end = min(max(y_end, 0), self.data_dims[0])
th_sum = numpy.sum(self.data[y_start:y_end,
x_start:x_end])
self.assertAlmostEqual(
_stats['sum'].calculate(context), th_sum)
def setUp(self):
TestCaseQt.setUp(self)
# define plot
self.plot = PlotWindow()
self.plot.addImage(numpy.arange(10000).reshape(100, 100),
legend='img1')
self.img_item = self.plot.getImage('img1')
self.plot.addCurve(x=numpy.linspace(0, 10, 56),
y=numpy.arange(56),
legend='curve1')
self.curve_item = self.plot.getCurve('curve1')
self.plot.addHistogram(edges=numpy.linspace(0, 10, 56),
histogram=numpy.arange(56),
legend='histo1')
self.histogram_item = self.plot.getHistogram(legend='histo1')
self.plot.addScatter(x=numpy.linspace(0, 10, 56),
y=numpy.linspace(0, 10, 56),
value=numpy.arange(56),
legend='scatter1')
self.scatter_item = self.plot.getScatter(legend='scatter1')
# stats widget
self.statsWidget = ROIStatsWidget(plot=self.plot)
# define stats
stats = [
('sum', numpy.sum),
('mean', numpy.mean),
]
self.statsWidget.setStats(stats=stats)
# define rois
self.roi1D = ROI(name='range1', fromdata=0, todata=4, type_='energy')
self.rectangle_roi = RectangleROI()
self.rectangle_roi.setGeometry(origin=(0, 0), size=(20, 20))
self.rectangle_roi.setName('Initial ROI')
self.polygon_roi = PolygonROI()
points = numpy.array([[0, 5], [5, 0], [10, 5], [5, 10]])
self.polygon_roi.setPoints(points)
def get_2D_rois():
"""return some RectangleROI instance"""
rectangle_roi = RectangleROI()
rectangle_roi.setGeometry(origin=(0, 100), size=(20, 20))
rectangle_roi.setName('Initial ROI')
polygon_roi = PolygonROI()
polygon_points = numpy.array([(0, 10), (10, 20), (45, 30), (35, 0)])
polygon_roi.setPoints(polygon_points)
polygon_roi.setName('polygon ROI')
arc_roi = ArcROI()
arc_roi.setName('arc ROI')
arc_roi.setFirstShapePoints(numpy.array([[50, 10], [80, 120]]))
arc_roi.setGeometry(*arc_roi.getGeometry())
return rectangle_roi, polygon_roi, arc_roi
"""Called for each added region of interest: set the name"""
if roi.getName() == '':
roi.setName('ROI %d' % len(roiManager.getRois()))
if isinstance(roi, LineMixIn):
roi.setLineWidth(1)
roi.setLineStyle('--')
if isinstance(roi, SymbolMixIn):
roi.setSymbolSize(5)
roi.setSelectable(True)
roi.setEditable(True)
roiManager.sigRoiAdded.connect(updateAddedRegionOfInterest)
# Add a rectangular region of interest
roi = RectangleROI()
roi.setGeometry(origin=(50, 50), size=(200, 200))
roi.setName('Initial ROI')
roiManager.addRoi(roi)
# Create the table widget displaying
roiTable = RegionOfInterestTableWidget()
roiTable.setRegionOfInterestManager(roiManager)
# Create a toolbar containing buttons for all ROI 'drawing' modes
roiToolbar = qt.QToolBar() # The layout to store the buttons
roiToolbar.setIconSize(qt.QSize(16, 16))
for roiClass in roiManager.getSupportedRoiClasses():
# Create a tool button and associate it with the QAction of each mode
action = roiManager.getInteractionModeAction(roiClass)
def updateAddedRegionOfInterest(roi):
"""Called for each added region of interest: set the name"""
if roi.getLabel() == '':
roi.setLabel('ROI %d' % len(roiManager.getRois()))
if isinstance(roi, LineMixIn):
roi.setLineWidth(2)
roi.setLineStyle('--')
if isinstance(roi, SymbolMixIn):
roi.setSymbol('o')
roi.setSymbolSize(5)
roiManager.sigRoiAdded.connect(updateAddedRegionOfInterest)
# Add a rectangular region of interest
roi = RectangleROI()
roi.setGeometry(origin=(50, 50), size=(200, 200))
roi.setLabel('Initial ROI')
roiManager.addRoi(roi)
# Create the table widget displaying
roiTable = RegionOfInterestTableWidget()
roiTable.setRegionOfInterestManager(roiManager)
# Create a toolbar containing buttons for all ROI 'drawing' modes
roiToolbar = qt.QToolBar() # The layout to store the buttons
roiToolbar.setIconSize(qt.QSize(16, 16))
for roiClass in roiManager.getSupportedRoiClasses():
# Create a tool button and associate it with the QAction of each mode
action = roiManager.getInteractionModeAction(roiClass)
class TestStatsROI(TestStatsBase, TestCaseQt):
"""
Test stats based on ROI
"""
def setUp(self):
TestCaseQt.setUp(self)
self.createRois()
TestStatsBase.setUp(self)
self.createHistogramContext()
self.roiManager = RegionOfInterestManager(self.plot2d)
self.roiManager.addRoi(self._2Droi_rect)
self.roiManager.addRoi(self._2Droi_poly)
def tearDown(self):
self.roiManager.clear()
self.roiManager = None
self._1Droi = None
self._2Droi_rect = None
self._2Droi_poly = None
self.plotHisto.setAttribute(qt.Qt.WA_DeleteOnClose)
self.plotHisto.close()
self.plotHisto = None
TestStatsBase.tearDown(self)
TestCaseQt.tearDown(self)
def createRois(self):
self._1Droi = ROI(name='my1DRoi', fromdata=2.0, todata=5.0)
self._2Droi_rect = RectangleROI()
self._2Droi_rect.setGeometry(size=(10, 10), origin=(10, 0))
self._2Droi_poly = PolygonROI()
points = numpy.array(((0, 20), (0, 0), (10, 0)))
self._2Droi_poly.setPoints(points=points)
def createCurveContext(self):
TestStatsBase.createCurveContext(self)
self.curveContext = stats._CurveContext(
item=self.plot1d.getCurve('curve0'),
plot=self.plot1d,
onlimits=False,
roi=self._1Droi)
def createHistogramContext(self):
self.plotHisto = Plot1D()
x = range(20)
y = range(20)
self.plotHisto.addHistogram(x, y, legend='histo0')
self.histoContext = stats._HistogramContext(
item=self.plotHisto.getHistogram('histo0'),
plot=self.plotHisto,
onlimits=False,
roi=self._1Droi)
def createScatterContext(self):
TestStatsBase.createScatterContext(self)
self.scatterContext = stats._ScatterContext(
item=self.scatterPlot.getScatter('scatter plot'),
plot=self.scatterPlot,
onlimits=False,
roi=self._1Droi)
def createImageContext(self):
TestStatsBase.createImageContext(self)
self.imageContext = stats._ImageContext(item=self.plot2d.getImage(
self._imgLgd),
plot=self.plot2d,
onlimits=False,
roi=self._2Droi_rect)
self.imageContext_2 = stats._ImageContext(item=self.plot2d.getImage(
self._imgLgd),
plot=self.plot2d,
onlimits=False,
roi=self._2Droi_poly)
def testErrors(self):
# test if onlimits is True and give also a roi
with self.assertRaises(ValueError):
stats._CurveContext(item=self.plot1d.getCurve('curve0'),
plot=self.plot1d,
onlimits=True,
roi=self._1Droi)
# test if is a curve context and give an invalid 2D roi
with self.assertRaises(TypeError):
stats._CurveContext(item=self.plot1d.getCurve('curve0'),
plot=self.plot1d,
onlimits=False,
roi=self._2Droi_rect)
def testBasicStatsCurve(self):
"""Test result for simple stats on a curve"""
_stats = self.getBasicStats()
xData = yData = numpy.array(range(0, 10))
self.assertEqual(_stats['min'].calculate(self.curveContext), 2)
self.assertEqual(_stats['max'].calculate(self.curveContext), 5)
self.assertEqual(_stats['minCoords'].calculate(self.curveContext),
(2, ))
self.assertEqual(_stats['maxCoords'].calculate(self.curveContext),
(5, ))
self.assertEqual(_stats['std'].calculate(self.curveContext),
numpy.std(yData[2:6]))
self.assertEqual(_stats['mean'].calculate(self.curveContext),
numpy.mean(yData[2:6]))
com = numpy.sum(xData[2:6] * yData[2:6]) / numpy.sum(yData[2:6])
self.assertEqual(_stats['com'].calculate(self.curveContext), com)
def testBasicStatsImageRectRoi(self):
"""Test result for simple stats on an image"""
self.assertEqual(self.imageContext.values.compressed().size, 121)
_stats = self.getBasicStats()
self.assertEqual(_stats['min'].calculate(self.imageContext), 10)
self.assertEqual(_stats['max'].calculate(self.imageContext), 1300)
self.assertEqual(_stats['minCoords'].calculate(self.imageContext),
(10, 0))
self.assertEqual(_stats['maxCoords'].calculate(self.imageContext),
(20.0, 10.0))
self.assertAlmostEqual(_stats['std'].calculate(self.imageContext),
numpy.std(self.imageData[0:11, 10:21]))
self.assertAlmostEqual(_stats['mean'].calculate(self.imageContext),
numpy.mean(self.imageData[0:11, 10:21]))
compressed_values = self.imageContext.values.compressed()
compressed_values = compressed_values.reshape(11, 11)
yData = numpy.sum(compressed_values.astype(numpy.float64), axis=1)
xData = numpy.sum(compressed_values.astype(numpy.float64), axis=0)
dataYRange = range(11)
dataXRange = range(10, 21)
ycom = numpy.sum(yData * dataYRange) / numpy.sum(yData)
xcom = numpy.sum(xData * dataXRange) / numpy.sum(xData)
self.assertEqual(_stats['com'].calculate(self.imageContext),
(xcom, ycom))
def testBasicStatsImagePolyRoi(self):
"""Test a simple rectangle ROI"""
_stats = self.getBasicStats()
self.assertEqual(_stats['min'].calculate(self.imageContext_2), 0)
self.assertEqual(_stats['max'].calculate(self.imageContext_2), 2432)
self.assertEqual(_stats['minCoords'].calculate(self.imageContext_2),
(0.0, 0.0))
# not 0.0, 19.0 because not fully in. Should all pixel have a weight,
# on to manage them in stats. For now 0 if the center is not in, else 1
self.assertEqual(_stats['maxCoords'].calculate(self.imageContext_2),
(0.0, 19.0))
def testBasicStatsScatter(self):
self.assertEqual(self.scatterContext.values.compressed().size, 2)
_stats = self.getBasicStats()
self.assertEqual(_stats['min'].calculate(self.scatterContext), 6)
self.assertEqual(_stats['max'].calculate(self.scatterContext), 7)
self.assertEqual(_stats['minCoords'].calculate(self.scatterContext),
(2, 3))
self.assertEqual(_stats['maxCoords'].calculate(self.scatterContext),
(3, 4))
self.assertEqual(_stats['std'].calculate(self.scatterContext),
numpy.std([6, 7]))
self.assertEqual(_stats['mean'].calculate(self.scatterContext),
numpy.mean([6, 7]))
def testBasicHistogram(self):
_stats = self.getBasicStats()
xData = yData = numpy.array(range(2, 6))
self.assertEqual(_stats['min'].calculate(self.histoContext), 2)
self.assertEqual(_stats['max'].calculate(self.histoContext), 5)
self.assertEqual(_stats['minCoords'].calculate(self.histoContext),
(2, ))
self.assertEqual(_stats['maxCoords'].calculate(self.histoContext),
(5, ))
self.assertEqual(_stats['std'].calculate(self.histoContext),
numpy.std(yData))
self.assertEqual(_stats['mean'].calculate(self.histoContext),
numpy.mean(yData))
com = numpy.sum(xData * yData) / numpy.sum(yData)
self.assertEqual(_stats['com'].calculate(self.histoContext), com)
signal += 0.3 * numpy.random.random(size=signal.shape)
return signal
app = qt.QApplication([]) # Start QApplication
# Create the plot widget and add an image
plot = Plot2D()
roiManager = RegionOfInterestManager(plot)
# plot = StackView()
# roiManager = RegionOfInterestManager(plot._plot)
roiManager.setColor('pink') # Set the color of ROI
# Add a rectangular region of interest
roi = RectangleROI()
roi.setGeometry(origin=(500, 500), size=(200, 200))
roi.setEditable(True)
roi.setVisible(True)
roi.setName('Initial ROI')
roiManager.addRoi(roi)
# Show the widget and start the application
plot.addImage(dummy_image())
plot.show()
result = app.exec_()
app.deleteLater()
sys.exit(result)