def run(self):
try:
filepath = self.makeFilePath()
if os.path.exists(filepath):
return
x, y, k = self.coords
width, height, n_layers = self.dimensions
# Cube's field of view in XY
fov = Rectangle(x, y, width, height)
# Join the bounds of the layers
r = None
for b in self.bounds[k:min(k + n_layers, len(bounds))]:
if r is None:
r = Rectangle(b.x, b.y, b.width, b.height)
else:
r.add(b)
if not fov.intersects(r):
# Would be empty
return
drawImage = Graphics2D.getDeclaredMethod(
"drawImage", [Image, AffineTransform, ImageObserver])
drawImage.setAccessible(True)
dispose = Graphics.getDeclaredMethod("dispose", [])
dispose.setAccessible(True)
# Populate and write cube
stack = ImageStack(width, height)
for layer in self.layers[k:min(k + n_layers, len(self.layers))]:
img = layer.getProject().getLoader().getFlatAWTImage(
layer, fov, 1.0, -1, ImagePlus.GRAY8, Patch, None, False,
Color.black)
bi = BufferedImage(img.getWidth(None), img.getHeight(None),
BufferedImage.TYPE_BYTE_GRAY)
g = bi.createGraphics()
aff = AffineTransform(1, 0, 0, 1, 0, 0)
#g.drawImage(img, aff, None) # Necessary to bypass issues that result in only using 7-bits and with the ByteProcessor constructor
drawImage.invoke(g, [img, aff, None])
#g.dispose()
dispose.invoke(g, [])
g = None
img = None
stack.addSlice("", ByteProcessor(bi))
bi.flush()
bi = None
imp = ImagePlus("x=%s y=%s k=%s" % (x, y, k), stack)
Utils.ensure(filepath)
FileSaver(imp).saveAsZip(filepath)
imp.flush()
imp = None
except:
e = sys.exc_info()
System.out.println("Error:" + str(e[0]) + "\n" + str(e[1]) + "\n" +
str(e[2]))
System.out.println(traceback.format_exception(e[0], e[1], e[2]))
def isEmpty(self):
# Check if the cube would have any data
x, y, k = self.coords
width, height, n_layers = self.dimensions
# Cube's field of view in XY
fov = Rectangle(x, y, width, height)
# Join the bounds of the layers
r = None
for b in self.bounds[k:min(k + n_layers, len(bounds))]:
if r is None and b is not None: # can be none when the Layer is empty
r = Rectangle(b.x, b.y, b.width, b.height)
elif b is not None:
r.add(b)
# Return True if not intersecting
return r is None or not fov.intersects(r)
