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public Trajectory generateTrajectory() { | |
Trajectory t = new Trajectory(dimension); | |
t.add(new Point3d(0, 0, 0)); | |
double[] incrx = generateIncrements(); | |
double[] incry = generateIncrements(); | |
for(int i = 1; i <= numberOfSteps; i++) { | |
Point3d pos = new Point3d(); | |
pos.setX(t.get(i-1).x + incrx[i-1]); | |
pos.setY(t.get(i-1).y + incry[i-1]); | |
t.add(pos); |
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package fiji.plugin.trackmate.detection.findmaxima; | |
import ij.IJ; | |
import java.util.ArrayList; | |
import java.util.Collections; | |
import java.util.List; | |
import java.util.Stack; | |
import java.util.concurrent.ExecutorService; | |
import java.util.concurrent.Executors; |
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<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi= | |
"http://www.w3.org/2001/XMLSchema-instance" | |
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 | |
http://maven.apache.org/xsd/maven-4.0.0.xsd"> | |
<modelVersion>4.0.0</modelVersion> | |
<groupId>de.biomedical-imaging.imagej</groupId> | |
<artifactId>ij_trajectory_classifier</artifactId> | |
<version>0.0.1-SNAPSHOT</version> | |
<packaging>jar</packaging> |
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java.lang.IllegalArgumentException: Cannot handle replace call to list in ij.Menus's public static synchronized java.lang.String[] getPlugins() | |
at net.imagej.patcher.CodeHacker.replaceCallInMethod(CodeHacker.java:725) | |
at net.imagej.patcher.CodeHacker.replaceCallInMethod(CodeHacker.java:650) | |
at net.imagej.patcher.LegacyExtensions.addExtraPlugins(LegacyExtensions.java:477) | |
at net.imagej.patcher.LegacyExtensions.injectHooks(LegacyExtensions.java:175) | |
at net.imagej.patcher.LegacyInjector.inject(LegacyInjector.java:308) | |
at net.imagej.patcher.LegacyInjector.injectHooks(LegacyInjector.java:109) | |
at net.imagej.patcher.LegacyEnvironment.initialize(LegacyEnvironment.java:101) | |
at net.imagej.patcher.LegacyEnvironment.applyPatches(LegacyEnvironment.java:495) | |
at net.imagej.patcher.LegacyInjector.preinit(LegacyInjector.java:397) |
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{ | |
"model" : { | |
"architecture": "Full Yolo", | |
"input_size": 4096, | |
"anchors": [260, 260], | |
"max_box_per_image": 150, | |
"labels": ["box"] | |
}, |
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<?xml version="1.0" encoding="UTF-8" standalone="no"?><annotation verified="no"><folder>boxes</folder><filename>TcdA1-0010_frames_sum.jpg</filename><path>/Users/twagner/Documents/Datasets/deep_training_set/training/img/TcdA1-0010_frames_sum.jpg</path><source><database>unknown</database></source><size><width>4096</width><height>4096</height><depth>1</depth></size><segmented>0</segmented><object><name>box</name><pose>Unspecified</pose><truncated>0</truncated><difficult>0</difficult><bndbox><xmin>3170</xmin><ymin>3324</ymin><xmax>3430</xmax><ymax>3584</ymax></bndbox></object><object><name>box</name><pose>Unspecified</pose><truncated>0</truncated><difficult>0</difficult><bndbox><xmin>917</xmin><ymin>952</ymin><xmax>1177</xmax><ymax>1212</ymax></bndbox></object><object><name>box</name><pose>Unspecified</pose><truncated>0</truncated><difficult>0</difficult><bndbox><xmin>541</xmin><ymin>3348</ymin><xmax>801</xmax><ymax>3608</ymax></bndbox></object><object><name>box</name><pose>Unspecified</pose><truncated>0</truncat |
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public FloatProcessor generateMask(int mask_size, int filamentwidth, int maskwidth, int type){ | |
FloatProcessor fp = new FloatProcessor(mask_size, mask_size); | |
double x0 = fp.getWidth()/2 + 0.5; | |
double y0 = fp.getHeight()/2 + 0.5; | |
double sigmax = maskwidth/2.355; //Full width at half maximum | |
double varx = sigmax*sigmax; | |
double sigmay = filamentwidth/2.355; | |
double vary = sigmay*sigmay; | |
for(int i = 0; i < mask_size; i++){ |
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from . import imagereader | |
from .augmentation import Augmentation | |
import cv2 | |
import copy | |
from .utils import BoundBox, bbox_iou | |
import numpy as np | |
from keras.utils import Sequence | |
import threading | |
import multiprocessing | |
from multiprocessing import sharedctypes |
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from __future__ import print_function | |
import argparse | |
import json | |
import os | |
from keras.utils import multi_gpu_model | |
import numpy as np | |
import time | |
from . import imagereader | |
from .frontend import YOLO | |
from .preprocessing import parse_annotation2 |
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from scipy.spatial.transform import Rotation as R | |
import numpy as np | |
import star | |
import transphire_transform.dump_load.star as trs | |
import os | |
input_path = "data/run_it024_data.star" | |
results_path = "results/test_results/" | |
result_filename = "run_it024_data" |
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