def testMarkInclusions(self):
from ImageProcessing.LoadZStack import LoadZStack
from ImageProcessing.MarkInclusions import MarkInclusions
loader = LoadZStack()
loader.paramPath.value = importDir
loader.paramDz.value = '100.0 mum'
loader.paramDy.value = '1.29 mum'
loader.paramDx.value = '1.29 mum'
zstack = loader.loadImageAsGreyScale()
from ImageProcessing.AutoFocus import AutoFocus
afw = AutoFocus()
statistics = afw.getStatistics(zstack)
minc = MarkInclusions()
marked = minc.markInclusions(zstack, statistics)
self.assertEqual(zstack.dimensions, marked.dimensions)
self.assertEqual(zstack.unit, marked.unit)
def testSingle(self):
print "Importing single image..."
from ImageProcessing.LoadZStack import LoadZStack
loader = LoadZStack()
loader.paramPath.value = os.path.join(importDir, 'TestZStack_z00.tif')
loader.paramDz.value = '100.0 mum'
loader.paramDy.value = '1.29 mum'
loader.paramDx.value = '1.29 mum'
loader.paramStartz.value = '300.0 mum'
loader.paramZClip.value = '3:4'
zstack = loader.loadImageAsGreyScale()
print "Done."
print "Calculating single image statistics..."
from ImageProcessing.AutoFocus import AutoFocus
afw = AutoFocus()
statistics = afw.getStatistics(zstack)
print "Done."
assert len(statistics['diameter'].data) == 2
imax = statistics['diameter'].data.argmax()
imin = statistics['diameter'].data.argmin()
mul = 1.29
self.check((200.0 * mul, mul), statistics['xPos'].data[imax])
self.check((200.0 * mul, mul), statistics['yPos'].data[imax])
self.check((300.0, 0.0), statistics['zPos'].data[imax])
self.check((20.7 * mul, 3 * mul), statistics['diameter'].data[imax])
self.check((53.0 * mul, mul), statistics['xPos'].data[imin])
self.check((53.0 * mul, mul), statistics['yPos'].data[imin])
self.check((300.0, 0.0), statistics['zPos'].data[imin])
self.check((7.0 * mul, mul), statistics['diameter'].data[imin])