def free():
#Loader.releaseAllCaches()
#System.out.println("Released all")
#
# Instead of releasing all, release half of all loaded images
try:
image_n_bytes = IMAGE_SIZE
projects = Project.getProjects()
if 0 == projects.size():
return
loader = projects[0].getLoader()
f = Loader.getDeclaredField("mawts")
f.setAccessible(True)
mawts = f.get(loader)
n_cached_images = mawts.size()
n_bytes_released = 0
if n_cached_images > 0:
n_bytes_to_release = int((n_cached_images * 0.5) * image_n_bytes)
n_bytes_released = loader.releaseMemory(n_bytes_to_release)
if 0 == n_bytes_released:
# There may be enough free memory so the loader refused to release anything,
# therefore ask the cache instance itself to actually remove the amount requested
n_bytes_released = mawts.removeAndFlushSome(n_bytes_to_release)
System.out.println("Released " + str(n_bytes_released) + " out of " + str(n_bytes_to_release))
loader.printCacheStatus()
if 0 == n_bytes_released:
# All memory retained is in the form of native arrays stored for loading images later
CachingThread.releaseAll()
System.out.println("Cleared CachingThread cache.")
except:
traceback.print_exc(file=sys.stdout)
def run():
projects = Project.getProjects()
if projects is None or projects.isEmpty():
IJ.log('No project open!')
return
ls = projects.get(0).getRootLayerSet()
trees = ls.getZDisplayables(Treeline)
trees.addAll(ls.getZDisplayables(AreaTree))
if trees.isEmpty():
IJ.log('No trees to process!')
return
dc = DirectoryChooser('Target folder')
targetFolder = dc.getDirectory()
if targetFolder is None:
return # user canceled
if targetFolder[len(targetFolder) -1] != '/':
targetFolder += '/'
fdir = File(targetFolder)
for f in fdir.listFiles():
if f.isHidden():
continue
yn = YesNoCancelDialog(IJ.getInstance(), "WARNING", "Folder not empty! Continue?")
if yn.yesPressed():
break
else:
return
process(trees, targetFolder)
def run():
global cal, pw, ph
projects = Project.getProjects()
if projects is None or projects.isEmpty():
IJ.log('No project open!')
return
p = projects.get(0)
ls = p.getRootLayerSet()
cal = ls.getCalibrationCopy()
pw = float(cal.pixelWidth)
ph = float(cal.pixelHeight)
rpt = p.getRootProjectThing()
add_recursively(rpt, None)
def run():
global cal, pw, ph
projects = Project.getProjects()
if projects is None or projects.isEmpty():
IJ.log('No project open!')
return
p = projects.get(0)
ls = p.getRootLayerSet()
cal = ls.getCalibrationCopy()
pw = float(cal.pixelWidth)
ph = float(cal.pixelHeight)
rpt = p.getRootProjectThing()
add_recursively(rpt,None)
add_connectors_recursively(rpt)
# print 'found', connector
if connector.intersectsOrigin(area, la):
if nd in outgoing:
outgoing[nd].append(connector)
else:
outgoing[nd] = [connector]
else:
if nd in incoming:
incoming[nd].append(connector)
else:
incoming[nd] = [connector]
return {'outgoing':outgoing, 'incoming':incoming}
# get the first open project
project = Project.getProjects().get(0)
projectRoot = project.getRootProjectThing()
neurites = projectRoot.findChildrenOfTypeR("neurite")
for neurite in neurites:
areatrees = neurite.findChildrenOfTypeR("areatree")
for areatree in areatrees:
areatree = areatree.getObject()
root = areatree.getRoot()
if root is None:
continue
layerset = areatree.getLayerSet()
calibration = layerset.getCalibration()
affine = areatree.getAffineTransform()
# outAndInArray = areatree.findConnectors()
from java.lang.reflect import Field
from java.lang import Runtime
from ini.trakem2.persistence import FSLoader
from ini.trakem2 import Project
loader = Project.getProjects()[0].getLoader()
f = FSLoader.getDeclaredField("regenerator")
f.setAccessible(True)
f.get(loader).shutdownNow()
loader.restartMipMapThreads(Runtime.getRuntime().availableProcessors())
f = FSLoader.getDeclaredField("regenerating_mipmaps")
f.setAccessible(True)
f.get(loader).clear()
f = FSLoader.getDeclaredField("n_regenerating")
f.setAccessible(True)
f.get(loader).set(0)
for node in tl.getRoot().getSubtreeNodes(): if node.getParent() is not None: if node.getConfidence() < 5: p = array([node.x, node.y], 'f') affine.transform(p, 0, p, 0, 1) x, y = p x *= cal.pixelWidth y *= cal.pixelHeight z = node.getLayer().getZ() * cal.pixelWidth locs.append([x, y, z]) print locs proj = Project.getProjects()[0] ls = proj.getRootLayerSet() neuToDisp = tl d3d = Display3D.get(ls) exe = Executors.newFixedThreadPool(Runtime.getRuntime().availableProcessors()) allOuts = [] allOuts.append(exe.submit(d3d.createMesh(proj.findProjectThing(neuToDisp), neuToDisp, 1))) ii = 0 for iffy in locs: print iffy[0], iffy[1], iffy[2] ii += 1 allOuts.append(exe.submit(ContentCreator(d3d, createFatPoint(iffy[0],iffy[1],iffy[2],300), Color3f(Color.red), "name" + str(ii))))
def exportWavefront(zds, filepath):
"""
Takes a sequence of ZDisplayable instances and saves all as meshes to disk in wavefront format.
A materials .mtl file is saved along with it.
See: https://github.com/fiji/3D_Viewer/blob/master/src/main/java/customnode/WavefrontExporter.java
"""
meshes = {
zd.getTitle(): d3d.createMesh(zd.project.findProjectThing(zd), zd,
resampling_factor).call()
for zd in zds
}
WavefrontExporter.save(meshes, filepath)
project = Project.getProjects()[0]
d3d = Display3D.getDisplay(project.getRootLayerSet())
def exportSelectedAsWavefront(project, filepath):
""" Select a node in the Project Tree, then run this function
to export the meshes of all ZDisplayable under the node
in Wavefront format. """
exportWavefront(list(loadFromSelectedTreeNode(project)), filepath)
# Strategy 1: provide a list of IDs
# The IDs of the AreaList (zDisplayables: arealists, balls etc.) instances
"""
to_add = [67163, 66596]
# To create envelopes for all lineages, do:
# regex = None
# ... and then don't show the plots (all will be together):
# show_3D = False
# ASSUMES pipes have the same exact name across all TrakEM2 projects.
# The 'name' is the title of the pipe node in the Project Tree
# and any of its parent nodes, chained. So if you want all DPM lineages
# and these are grouped in a DPM lineage group, then use "DPM".
from ini.trakem2 import Project
from java.awt import Color
from java.io import File
projects = [p for p in Project.getProjects()]
# Add more colors if you have more than 6 projects open
colors = [Color.white, Color.yellow, Color.magenta, Color.green, Color.blue, Color.orange]
sources_color_table = {}
for project, color in zip(projects, colors):
sources_color_table[project] = color
# 1. The project to use as reference--others are compared to it.
reference_project = projects[0]
# 2. The regular expression to match. Only pipes whose name matches it
# will be analyzed. If null, all are matched.
regex = None # For a single one, put its name: "DPMm2"
# 3. A list of text strings containing regular expressions.
# Any pipe whose name matches any will be ignored.
ignore = ["unknown.*", "poorly.*", "MB.*", "peduncle.*", "TR.*"]
from ini.trakem2 import Project
from ini.trakem2.display import Display
projects = Project.getProjects()
original = projects[0]
new_project = projects[1]
patches = None
layer2 = None
for display in Display.getDisplays():
if display.getProject() == original:
patches = display.getSelection().getSelected()
elif display.getProject() == new_project:
layer2 = display.getLayer()
for patch in patches:
layer2.add(patch.clone(new_project, True))
