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 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)
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))
"/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 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
