class Launcher(Runnable,SNTListener):
def __init__(self, imp, roi, layers):
self.imp = imp
self.roi = roi
self.layers = layers
def run(self):
self.plugin = Simple_Neurite_Tracer()
self.plugin.addListener(self)
self.plugin.run("")
def onEvent(self, event):
global front
if event.getType() != SNTEvent.SEND_TO_TRAKEM2:
return
d = tempfile.mkdtemp()
pafm = self.plugin.getPathAndFillManager()
pixel_width = self.imp.getCalibration().pixelWidth
pafm.downsampleAll(pixel_width)
output_prefix = os.path.join(d,'snt-export')
if not pafm.exportAllAsSWC(output_prefix):
IJ.error('Exporting SNT paths as SWC files to "%s" failed' % (output_prefix,))
return
tlines = []
cal = self.imp.getCalibration().copy()
lset = front.getLayerSet()
for e in os.listdir(d):
filename = os.path.join(d, e)
tl = Treeline(front.project, filename)
nodes = {}
offset = self.roi.getBounds()
fp = open(filename)
root = None
for line in fp:
line = re.sub('\s*#.*$', '', line)
line = line.strip()
if not line:
continue
point_id, point_type, x, y, z, radius, parent_id = re.split('\s+', line)
node = tl.newNode(offset.x + float(x) / cal.pixelWidth,
offset.y + float(y) / cal.pixelHeight,
self.layers[int(float(z) / cal.pixelDepth + 0.5)],
None)
nodes[int(point_id)] = node
pid = int(parent_id)
parent = nodes.get(pid, None)
if parent:
parent.add(node, 5)
elif -1 == pid:
root = node
if root:
tl.setRoot(root) # caches all subtree nodes in the Treeline
tl.calculateBoundingBox(None)
tlines.append(tl)
lset.addAll(tlines)
front.project.getProjectTree().insertSegmentations(tlines)
shutil.rmtree(d)
def run(self):
self.plugin = Simple_Neurite_Tracer()
self.plugin.addListener(self)
self.plugin.run("")
