def measureCustom(layerset):
# Obtain a list of all AreaLists:
alis = layerset.getZDisplayables(AreaList)
# The loader
loader = layerset.getProject().getLoader()
# The ResultsTable
table = Utils.createResultsTable("AreaLists",
["id", "layer", "Z", "area", "mean"])
# The LayerSet's Calibration (units in microns, etc)
calibration = layerset.getCalibrationCopy()
# The measurement options as a bit mask:
moptions = Measurements.AREA | Measurements.MEAN
for ali in alis:
affine = ali.getAffineTransformCopy()
box = ali.getBoundingBox()
index = 0
for layer in layerset.getLayers():
index += 1 # layer index starts at 1, so sum before
# The java.awt.geom.Area object for the AreaList 'ali'
# at the given Layer 'layer':
area = ali.getArea(layer)
if area:
# Bring the area to world coordinates,
# and then local to its own data:
tr = AffineTransform()
tr.translate(-box.x, -box.y)
tr.concatenate(affine)
area = area.createTransformedArea(tr)
# Create a snapshot of the images under the area:
imp = loader.getFlatImage(layer, box, 1, 0xffffffff,
ImagePlus.GRAY8, Patch, False)
# Set the area as a roi
imp.setRoi(ShapeRoi(area))
# Perform measurements (uncalibrated)
# (To get the calibration, call layerset.getCalibrationCopy())
stats = ByteStatistics(imp.getProcessor(), moptions,
calibration)
table.incrementCounter()
table.addLabel("Name", ali.getTitle())
table.addValue(0, ali.getId())
table.addValue(1, index) # the layer index
table.addValue(2, layer.getZ())
table.addValue(3, stats.area)
table.addValue(4, stats.mean)
# Update and show the table
table.show("AreaLists")
def measureCustom(layerset):
# Obtain a list of all AreaLists:
alis = layerset.getZDisplayables(AreaList)
# The loader
loader = layerset.getProject().getLoader()
# The ResultsTable
table = Utils.createResultsTable("AreaLists", ["id", "layer", "Z", "area", "mean"])
# The LayerSet's Calibration (units in microns, etc)
calibration = layerset.getCalibrationCopy()
# The measurement options as a bit mask:
moptions = Measurements.AREA | Measurements.MEAN
for ali in alis:
affine = ali.getAffineTransformCopy()
box = ali.getBoundingBox()
index = 0
for layer in layerset.getLayers():
index += 1 # layer index starts at 1, so sum before
# The java.awt.geom.Area object for the AreaList 'ali'
# at the given Layer 'layer':
area = ali.getArea(layer)
if area:
# Bring the area to world coordinates,
# and then local to its own data:
tr = AffineTransform()
tr.translate(-box.x, -box.y)
tr.concatenate(affine)
area = area.createTransformedArea(tr)
# Create a snapshot of the images under the area:
imp = loader.getFlatImage(layer, box, 1, 0xffffffff,
ImagePlus.GRAY8, Patch, False)
# Set the area as a roi
imp.setRoi(ShapeRoi(area))
# Perform measurements (uncalibrated)
# (To get the calibration, call layerset.getCalibrationCopy())
stats = ByteStatistics(imp.getProcessor(), moptions, calibration)
table.incrementCounter()
table.addLabel("Name", ali.getTitle())
table.addValue(0, ali.getId())
table.addValue(1, index) # the layer index
table.addValue(2, layer.getZ())
table.addValue(3, stats.area)
table.addValue(4, stats.mean)
# Update and show the table
table.show("AreaLists")
def transform(self, t): t = AffineTransform(t) t.concatenate(self.preTransformation) tile = Trimorphic(t) tile.getUI().setBackground(self.getUI().getBackground()) return tile
def transform(self, t): t = AffineTransform(t) t.concatenate(self.preTransformation) w = SHorn(self.n, t) w.getUI().setBackground(self.getUI().getBackground()) return w
