# 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 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
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