## Import tiles
# Get all layers
f = open(os.path.join(data_dir, "tile_location.txt"), "r")
z_list = []
for l in f.readlines():
elem = l[:-1].split(" ")
fname = elem[0]
xloc = int(elem[1])
yloc = int(elem[2])
zloc = int(elem[3])
z_list.append(zloc)
imp = IJ.openImage(os.path.join(img_dir, fname))
patch = Patch(project, imp.title, xloc, yloc, imp)
patch.project.loader.addedPatchFrom(os.path.join(img_dir, fname),
patch)
layer = layerset.getLayer(zloc, 1, True)
layer.add(patch)
f.close()
front = Display.getFront()
bounds = Rectangle(x=0, y=0, width=20000, height=20000)
front.resizeCanvas(bounds)
z_list.sort()
if z_list[0] != 0:
layer = layerset.getLayer(0, 1, False)
preprocessor_script_path = "/tmp/trakem2-n5.bsh"
with open(preprocessor_script_path, 'w') as f:
f.write(script)
# Create as many layers as indices in the Z dimension
layers = []
for z in xrange(dimensions[2]):
layer = layerset.getLayer(z, 1.0, True) # create if not there
layerset.addSilently(layer)
layers.append(layer)
# Add a single Patch instance per Layer, whose image is a 2D crop of the N5 volume
if 0 == layer.getDisplayables().size():
index = layerset.getLayerIndex(layer.getId())
patch = Patch(project, str(z), dimensions[0], dimensions[1],
dimensions[0], dimensions[1], img_type, 1.0, Color.black,
True, 0, 255, AffineTransform(), "")
layer.add(patch, False) # don't update displays
project.getLoader().setPreprocessorScriptPathSilently(
patch, preprocessor_script_path)
layerset.recreateBuckets(layers, True)
Display.updateLayerScroller(layerset)
# Export for CATMAID from raw images (strategy=0)
"""
saver = Saver("jpg")
saver.setQuality(0.75)
ExportMultilevelTiles.makePrescaledTiles(layers, Patch, Rectangle(0, 0, dimensions[0], dimensions[1]),
-1, img_type, tgt_dir, 0, saver, tile_side, 1,
True, True,
