def run():
if 0 == Display.getSelected().size():
print "Nothing selected!"
return
tree = Display.getSelected()[0]
if not isinstance(tree, AreaTree):
print "Not an AreaTree!"
return
cal = tree.getLayerSet().getCalibration()
for nd in tree.getRoot().getSubtreeNodes():
area = nd.getData()
if area is None:
continue
pols = M.getPolygons(area)
if len(pols) > 1:
report(nd, pols, tree.getAffineTransform(), cal)
if remove_all_but_largest:
removeAllButLargest(area, pols)
elif len(pols) == 1:
print "Found a single polygon with bounds: "+str(pols[0].getBounds())
Display.repaint()
def importMask(evt=None):
display = Display.getFront()
# Obtain an image stack
#imp = IJ.getImage()
imp = WindowManager.getImage("Labels")
layerset = display.getLayerSet()
p = layerset.getProject()
ali = AreaList(p, "", 0, 0)
layerset.add(ali)
p.getProjectTree().insertSegmentations([ali])
# Obtain the image stack
stack = imp.getImageStack()
# Iterate every slice of the stack
for i in range(1, imp.getNSlices() + 1):
ip = stack.getProcessor(i) # 1-based
# Extract all areas (except background) into a map of value vs. java.awt.geom.Area
m = AreaUtils.extractAreas(ip)
# Report progress
if len(m) > 0:
IJ.log(str(i) + ":" + str(len(m)))
# Get the Layer instance at the corresponding index
layer = layerset.getLayers().get(i-1) # 0-based
# Add the first Area instance to the AreaList at the proper Layer
if ( m.values().iterator().hasNext() ):
ali.addArea(layer.getId(), m.values().iterator().next())
# Change the color of the AreaList
ali.setColor(Color.red)
ali.adjustProperties()
# Ensure bounds are as constrained as possible
ali.calculateBoundingBox(None)
# Repaint
Display.repaint()
# Translate any selected Displayable objects
dx = -90
dy = 129
from ini.trakem2.display import Display
# For any selected objected
for displ in Display.getFront().getSelected():
displ.getAffineTransform().translate(dx, dy)
Display.repaint()
print patch.getTitle()
if cp.containsKey(patch.getTitle()):
patch_title = patch.getTitle()[:-4]
print patch.getId(), patch_title
print patch.hasCoordinateTransform()
target_patch = cp.get(patch.getTitle())
target_patch.setCoordinateTransform(patch.getCoordinateTransform())
target_patch.getAffineTransform().setTransform(patch.getAffineTransform())
target_patch.updateInDatabase("transform")
target_patch.updateBucket()
# tform_file = folder + patch_title + '_original.xml'
# tform_xml = open(tform_file, 'w')
# tform_xml.write(patch.getCoordinateTransform().toXML('\t'))
# tform_xml.close()
# tform_file = folder + patch_title + '_target.xml'
# tform_xml = open(tform_file, 'w')
# tform_xml.write(target_patch.getCoordinateTransform().toXML('\t'))
# tform_xml.close()
print patch.getAffineTransform()
print target_patch.getAffineTransform()
target_layer.moveBottom(target_patch)
IJ.showProgress(i, original_patches.size())
Display.repaint()