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