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 initTrakem(path, nbLayers, mipmaps = False): #initialize a project
path = cleanLinuxPath(path)
ControlWindow.setGUIEnabled(False)
project = Project.newFSProject("blank", None, path)
project.getLoader().setMipMapsRegeneration(mipmaps)
layerset = project.getRootLayerSet()
for i in range(nbLayers): # create the layers
layerset.getLayer(i, 1, True)
project.getLayerTree().updateList(layerset) #update the LayerTree
Display.updateLayerScroller(layerset) # update the display slider
IJ.log('TrakEM project initialized with ' + str(nbLayers) + ' layers and stored in ' + path + ' (but not saved yet)')
return project
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 main(linearAlignmentDir,ImageDir,trackEMfile,verbose=False): """Run the main Fiji-based functionality. """ from jython_imports import AffineModel2D,InverseTransformMapping from ini.trakem2.display import Display, Patch from ini.trakem2 import Project #get a list of all pairwise files (has _to_ in midddle) transform_files = [f for f in os.listdir(linearAlignmentDir) if 'txt' in os.path.splitext(f)[1]] transform_files.sort() dirname=os.path.split(os.path.split(ImageDir)[0])[1] target = Project.newFSProject(dirname, None, ImageDir,True)
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)
def readWriteXMLTransform(projectPath,layerIndex,folder):
'''
1-Take the TrakEM project 'projectPath'
2-Read the transformation of the first patch of layer 'layerIndex'
3-Read the locations of the first patch of layer 'layerIndex' and layer '1-layerIndex'. This is used to calculate the offset of the EM and LM images in the initial transformation file
4-Write as a simple text file in folder + title of the project + InitialTransform.txt
'''
project = Project.openFSProject(projectPath, False)
layerset = project.getRootLayerSet()
layers = layerset.getLayers()
layer = layerset.getLayers().get(layerIndex)
patches = layer.getDisplayables(Patch)
t = patches.get(0).getAffineTransform()
transPath = folder + project.getTitle() + 'InitialTransform.txt.txt'
f = open(transPath,'w')
f.write( str(t.getScaleX()) + "\n")
f.write( str(t.getShearY())+ "\n")
f.write( str(t.getShearX())+ "\n")
f.write( str(t.getScaleY())+ "\n")
f.write( str(t.getTranslateX())+ "\n")
f.write( str(t.getTranslateY())+ "\n")
f.write ( str( layers.get(layerIndex).getDisplayables(Patch).get(0).getX() ) + '\n')
f.write ( str( layers.get(layerIndex).getDisplayables(Patch).get(0).getY() ) + '\n')
f.write ( str( layers.get(1-layerIndex).getDisplayables(Patch).get(0).getX() ) + '\n')
f.write ( str( layers.get(1-layerIndex).getDisplayables(Patch).get(0).getY() ) + '\n')
f.close()
IJ.log('Transformation saved in: ' + transPath)
# read the parameters of the transformations
trans = []
f = open(transPath,'r')
while 1:
line = f.readline()
if not line: break
IJ.log(line)
trans.append(float(line))
f.close
IJ.log('Transformation: ' + str(trans))
closeProject(project)
return trans
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))))
"/data/research/se/celegans/dataset3/N2DA_1430-2/M5/",
"/data/research/se/celegans/dataset3/N2DA_1430-2/N1/",
"/data/research/se/celegans/dataset3/N2DA_1430-2/N2/"
]
for i in range(len(proj_list)):
data_dir = proj_list[i]
proj_dir = os.path.join(data_dir, "montage_v1")
img_dir = os.path.join(data_dir, "clahe_new")
if not os.path.isdir(proj_dir):
os.makedirs(proj_dir)
## Create new project
project = Project.newFSProject("blank", None, proj_dir)
layerset = project.getRootLayerSet()
## 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)
from ini.trakem2.imaging.filters import CLAHE
from mpicbg.trakem2.align import AlignmentUtils
import os
import re
import math
import csv
from java.awt.geom import AffineTransform
wafer = "S2-W003-W008"
# bucket = "/usr/people/tmacrina/seungmount/research/"
bucket = "/mnt/data0/"
# writefile = bucket + "tommy/150528_zfish/" + wafer + "_import.txt"
project_folder = bucket + "tommy/150502_piriform/S2-W001/"
project = Project.getProject("150605_S2-W001_elastic_S2-W002_affine.xml")
loader = project.getLoader()
# loader.setMipMapsRegeneration(False) # disable mipmaps
layerset = project.getRootLayerSet()
layers = layerset.getLayers()
starting_index = len(layers) + 1
task = loader.importImages(
layerset.getLayers().get(0), # the first layer
project_folder + wafer + "_import.txt", # the absolute file path to the text file with absolute image file paths
"\t", # the column separator <path> <x> <y> <section index>
1.0, # section thickness, defaults to 1
1.0, # calibration, defaults to 1
# 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))
def openTrakemProject(path, mipmap = False): project = Project.openFSProject(cleanLinuxPath(path), False) return getProjectUtils(project, mipmap)
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)
# Adapted from:
# http://fiji.sc/TrakEM2_Scripting#Concatenating_multiple_project_XML_files_by_copying_all_their_layers
from ini.trakem2 import Project
from ini.trakem2.display import Patch
from ini.trakem2.utils import Utils
# Wafer
bucket = '/mnt/bucket/labs/seung/research/'
# project_folder = bucket + 'tommy/150528_zfish/'
# project_folder = bucket + 'tommy/150502_piriform/'
project_folder = bucket + 'tommy/trakem_test/150622_fix_rigid'
# Get the first open project
project = Project.getProject('turtle_rigid.xml')
# Get layerset
layerset = project.getRootLayerSet()
start = 0
finish = 2
layers = layerset.getLayers()[start:finish]
# Regenerate all image mipmaps
futures = []
for layer in layers:
for patch in layer.getDisplayables(Patch):
futures.append(patch.updateMipMaps())
Utils.wait(futures)
from ij import IJ
from ini.trakem2.imaging.filters import CLAHE
from mpicbg.trakem2.align import AlignmentUtils
import os
import re
import math
import csv
from java.awt.geom import AffineTransform
wafer = "W004"
bucket = "/usr/people/tmacrina/seungmount/research/"
project_folder = bucket + "tommy/150528_zfish/"
# project_folder = "/mnt/data0/tommy/tests/150501_trakem_project_creation/"
project = Project.newFSProject("blank", None, project_folder)
loader = project.getLoader()
# loader.setMipMapsRegeneration(False) # disable mipmaps
layerset = project.getRootLayerSet()
# layerset.setSnapshotsMode(1) # outlines
task = loader.importImages(
layerset.getLayers().get(0), # the first layer
project_folder + wafer + "_import.txt", # the absolute file path to the text file with absolute image file paths
"\t", # the column separator <path> <x> <y> <section index>
1.0, # section thickness, defaults to 1
1.0, # calibration, defaults to 1
False, # whether to homogenize contrast, avoid
1.0, # scaling factor, default to 1
0) # border width
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]
os.mkdir(out_folder + "/storm_merged/")
##determine image canvas size (query each image)
imp = IJ.openImage((imlist[0]))
#print imp.width
im_width = imp.width
print im_width
im_height = imp.height
print im_height
ControlWindow.setGUIEnabled(False)
# 1. Create a TrakEM2 project
project = Project.newFSProject("blank", None, out_folder)
loader = project.getLoader()
loader.setMipMapsRegeneration(True) # disable mipmaps
layerset = project.getRootLayerSet()
# 2. Create 10 layers (or as many as you need)
for i in range(num_sections):
layerset.getLayer(i, 1, True)
layerset.setDimensions(im_width, im_height, LayerSet.NORTHWEST)
# ... and update the LayerTree:
project.getLayerTree().updateList(layerset)
# ... and the display slider
Display.updateLayerScroller(layerset)
filenames = sorted(os.listdir(storm_merged_folder))
filenames1 = sorted(os.listdir(conv_561_folder))
filenames2 = sorted(os.listdir(conv_merged_folder))
from java.util.concurrent import Executors, TimeUnit
SPRING_LENGTH = 100
spring_triangle_height_twice = 2 * Math.sqrt(0.75*SPRING_LENGTH*SPRING_LENGTH)
LAYER_SCALE = 1.0
STIFFNESS = 0.1
MAX_STRETCH = 2000.0
DAMP = 0.9
MAX_ITERATIONS = 5000 #1000
MAX_PLATEAU_WIDTH = 200
MAX_EPSILON = 6
MIN_NUM_MATCHES = 1 # minimum for TranslationModel2D()
MAX_NUM_THREADS = 40
# project = Project.getProject('stack_import.xml')
project = Project.getProject('montage_align.xml')
bucket = "/usr/people/tmacrina/seungmount/research/"
# project_folder = bucket + "tommy/150502_piriform/"
project_folder = bucket + "tommy/trakem_tests/150709_elastic_montage/"
input_folder = project_folder + "affine_block_matching/points/"
# input_folder = project_folder + "affine_block_matching/layers/"
all_files = os.listdir(input_folder)
def get_tiles(layer):
po = ParamOptimize()
po.maxEpsilon = 25.0
po.minInlierRatio = 0.0
po.minNumInliers = 12
po.expectedModelIndex = 1
# 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()
"/data/research/se/celegans/dataset3/N2DA_1430-2/M5/",
"/data/research/se/celegans/dataset3/N2DA_1430-2/N1/",
"/data/research/se/celegans/dataset3/N2DA_1430-2/N2/"
]
for i in range(len(proj_list)):
data_dir = proj_list[i]
proj_dir = os.path.join(data_dir, "montage_v1")
img_dir = os.path.join(data_dir, "transformed")
if not os.path.isdir(img_dir):
os.makedirs(img_dir)
proj_name = os.path.join(proj_dir, "montage_v1.xml")
project = Project.openFSProject(proj_name)
layerset = project.getRootLayerSet()
layer_list = layerset.getLayers()
fname_trans = os.path.join(data_dir, "transform.csv")
fw = open(fname_trans, "w")
for j in range(len(layer_list)):
layer = layer_list[j]
tiles = layer.getDisplayables(Patch)
patches = layer.getDisplayables(Patch)
for k in range(len(patches)):