sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
ca666d51026d71109c8f9cc2486070528592ccc744a9f72036b2779710d3eddd | Java | 10,560 | 278 | package org.janelia.colormipsearch.imageprocessing;
import java.io.InputStream;
import java.util.Arrays;
import javax.imageio.ImageIO;
import ij.ImagePlus;
import ij.io.FileInfo;
import ij.io.Opener;
import ij.io.RandomAccessStream;
import ij.process.ByteProcessor;
import ij.process.ColorProcessor;
import ij.process... |
e44402ec1f8dc8d0c35f77ecc384974fa8312085637bff6995bc65ba0063a6b4 | Java | 10,672 | 253 | package org.janelia.colormipsearch.cmd_v2;
import java.io.File;
import java.io.IOException;
import java.io.UncheckedIOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashSet;
import java.util.List;
... |
3039f17fc3b753cf45f78e68053d557eac4176cb42786f8d6f5832b514034aee | Java | 10,689 | 239 | package org.janelia.colormipsearch.cds;
import java.util.EnumSet;
import java.util.Map;
import java.util.Set;
import java.util.function.Supplier;
import javax.annotation.Nonnull;
import org.janelia.colormipsearch.imageprocessing.ColorTransformation;
import org.janelia.colormipsearch.imageprocessing.ImageArray;
impor... |
b864a7e074b1ada5b32ee3853cab6159c1d0a452405b6952456bb664a57f6c71 | Java | 10,710 | 293 | package org.jeecg.modules.system.controller;
import java.util.*;
import java.util.stream.Collectors;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import com.alibaba.fastjson.JSONObject;
import com.baomidou.mybatisplus.core.conditions.query.LambdaQueryWrapper;
import org... |
2d439eb899ed4ef8bfc84b79b8b8091173b1d146ed28fef1279319fe1ede977f | Java | 10,719 | 204 | package org.janelia.colormipsearch.results;
import java.util.Comparator;
import java.util.EnumSet;
import java.util.List;
import java.util.function.Function;
import java.util.function.Predicate;
import java.util.stream.Collectors;
import org.janelia.colormipsearch.model.AbstractMatchEntity;
import org.janelia.colormi... |
0c8a77b9c9ef11cef86de5ab5669b4d37c9e402123ef9b75e1a4cca735472439 | Java | 10,754 | 280 | package org.jeecg.modules.system.controller;
import com.alibaba.fastjson.JSON;
import com.baomidou.mybatisplus.core.conditions.query.QueryWrapper;
import com.baomidou.mybatisplus.core.metadata.IPage;
import com.baomidou.mybatisplus.extension.plugins.pagination.Page;
import io.swagger.annotations.Api;
import io.swagger... |
c6c64c2bb2c677f9d6a12a4d7d2e06422ff162e8faeab1e54b5d0b70aadab7e3 | Java | 10,813 | 280 | package org.jeecg.modules.system.controller;
import cn.hutool.crypto.SecureUtil;
import com.alibaba.fastjson.JSONObject;
import com.baomidou.mybatisplus.core.conditions.query.LambdaQueryWrapper;
import com.xkcoding.justauth.AuthRequestFactory;
import io.swagger.annotations.ApiOperation;
import lombok.extern.slf4j.Slf4... |
3c40ec0aa0c40b6290432eeda57746d68029209a73f76e17ebce79e7624468d2 | Java | 10,901 | 183 | package org.janelia.colormipsearch.cmd_v2.cmsdrivers;
import java.util.Collection;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.concurrent.CompletableFuture;
import java.util.concurrent.Executor;
import java.util.function.Su... |
f1949a3467fb4a26e98cd4ded15806aad83008c8fa9e24db5f1e6a9db7320c20 | Java | 10,946 | 207 | package org.janelia.colormipsearch.dataio.db;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.List;
import java.util.Map;
import java.util.stream.Collectors;
import org.janelia.colormipsearch.dao.NeuronMatchesDao;
import org.janelia.colormipsearch.dao.NeuronMeta... |
fcaeff249929913d68bb3a9ff38553af3706503255617d1f4068eb8ff1c3185b | Java | 10,996 | 224 | package org.janelia.colormipsearch.mips;
import java.io.IOException;
import java.io.UncheckedIOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.HashMap;
import java.util.... |
112ab2e61b7513166ddc380275895957eac3071c2a3a60fb5b5ca832754ddac7 | Java | 11,065 | 292 | package org.jeecg.modules.cas.util;
import java.io.StringReader;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
import javax.xml.XMLConstants;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.x... |
02388118ed4d724f9443ef2977e861f3ae65495eef4f2f40d384c3dc8ff57ee7 | Java | 11,069 | 243 | package org.janelia.colormipsearch.api_v2.cdsearch;
import java.util.HashSet;
import java.util.Map;
import java.util.Set;
import java.util.function.Supplier;
import javax.annotation.Nonnull;
import org.janelia.colormipsearch.imageprocessing.ColorTransformation;
import org.janelia.colormipsearch.imageprocessing.Image... |
2f26249903148c8063ef234c8057d7d7cdbf93b060d96cfc87c08042f5f63931 | Java | 11,174 | 191 | package org.janelia.colormipsearch.cmd.dataexport;
import java.io.File;
import java.nio.file.Path;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.concurrent.Executor;
import java.util.function.BiConsumer;
import java.util.regex.Pattern;
import java.util.... |
f3989e18b1907d98ab0104d0f62755570157e1f6654caee2cf528b6f0c8445de | Java | 11,237 | 341 | package org.janelia.colormipsearch.dao;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.stream.Collectors;
import org.apache.commons.collections4.CollectionUtils;
import org... |
e28095d6f0f49826b96da00d2e40dee9d312aa12e70079088dfe157230f75aa2 | Java | 11,387 | 231 | package org.janelia.colormipsearch.cmd_v2;
import java.util.List;
import java.util.function.Supplier;
import java.util.stream.Collectors;
import com.beust.jcommander.Parameter;
import com.beust.jcommander.Parameters;
import com.fasterxml.jackson.databind.DeserializationFeature;
import com.fasterxml.jackson.databind.O... |
04b59382bfc01db377388b6cc4d8c6d493249da72d92d1a0474c1ff2a0dd2dbe | Java | 11,409 | 321 | package org.janelia.colormipsearch.cmd.jacsdata;
import java.io.Serializable;
import java.util.Collections;
import java.util.List;
import java.util.Set;
import java.util.function.Consumer;
import com.fasterxml.jackson.annotation.JsonProperty;
import org.apache.commons.collections4.CollectionUtils;
import org.apache.... |
bb36f5106b3f9befcba597ada2693297c36aca4cf964168dea5522c1ab1ad162 | Java | 11,528 | 265 | package org.janelia.colormipsearch.cds;
import java.util.Collections;
import java.util.Map;
import java.util.Set;
import java.util.function.Supplier;
import javax.annotation.Nonnull;
import org.janelia.colormipsearch.imageprocessing.ImageArray;
import org.janelia.colormipsearch.imageprocessing.ImageRegionDefinition;... |
00b6d762e84f964e26dd7cde8891ac79ca88b35f7bfdd75b257ad51fb9ef5394 | Java | 11,787 | 234 | package org.janelia.colormipsearch.api_v2.cdsearch;
import java.io.File;
import java.io.IOException;
import java.io.UncheckedIOException;
import java.nio.channels.Channels;
import java.nio.channels.FileChannel;
import java.nio.file.Path;
import java.util.Comparator;
import java.util.List;
import java.util.Map;
import ... |
36e3f207eba3e6e5863b51e1356b868c4182857cb30d781bd5a0278396bf04d5 | Java | 11,837 | 315 | package org.jeecg.modules.system.controller;
import java.util.*;
import java.util.stream.Collectors;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import com.alibaba.fastjson.JSONObject;
import com.baomidou.mybatisplus.core.conditions.query.LambdaQueryWrapper;
import org... |
0b1a3424c94777a9a478197e281299b4c47b3da7ab8341c0efc3ab46e3adcf9f | Java | 11,844 | 333 | package org.janelia.colormipsearch.model;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import javax.annotation.Nullable;
import com.fasterxml.jackson.annotation.JsonIgnore;
import com.fa... |
855c1acabec5c53e9fc681a9a0f101d715bb154d474bfd922fc33ae8b42239ae | Java | 11,932 | 298 | package de.biovoxxel.toolbox;
import java.awt.AWTEvent;
import java.awt.Checkbox;
import java.awt.Color;
import java.util.ArrayList;
import ij.IJ;
import ij.ImagePlus;
import ij.Prefs;
import ij.blob.Blob;
import ij.blob.ManyBlobs;
import ij.gui.DialogListener;
import ij.gui.GenericDialog;
import ij.gui.Roi;
import... |
6a7ba0bcc5ebb91a1d965362a4fb2ee1d3f12cfb0ed03bab61bf75e5a3c6ad13 | Java | 11,985 | 263 | package org.janelia.colormipsearch.api_v2.cdsearch;
import java.util.Collections;
import java.util.Map;
import java.util.Set;
import java.util.function.Supplier;
import javax.annotation.Nonnull;
import org.janelia.colormipsearch.imageprocessing.ImageArray;
/**
* PixelMatchColorDepthQuerySearchAlgorithm - implement... |
bd1402e0d7cf069a0e9d66022cb2acf026e81f2142478c05051c36a8b527df52 | Java | 11,988 | 209 | package org.janelia.colormipsearch.cmd.v2dataimport;
import java.io.File;
import java.io.IOException;
import java.io.UncheckedIOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.Collection;
import java.util.Collections;
import java.util.List;
import java.uti... |
ac48bb7c1fabcaec1f55d9f299fd5017bb3a20188cab3ac32ce9e11d13827e75 | Java | 12,082 | 265 | package org.janelia.colormipsearch.cds;
import java.util.Collections;
import java.util.Map;
import java.util.Set;
import java.util.function.Supplier;
import javax.annotation.Nonnull;
import org.janelia.colormipsearch.imageprocessing.ImageArray;
import org.janelia.colormipsearch.imageprocessing.ImageRegionDefinition;... |
4ca181de8dc53693b9f52e352194577ede201ef02aef330b58bc286d53c18bbb | Java | 12,187 | 241 | package org.janelia.colordepthsearch;
import com.amazonaws.services.lambda.runtime.Context;
import com.amazonaws.services.lambda.runtime.RequestHandler;
import org.apache.commons.collections4.CollectionUtils;
import org.apache.commons.collections4.IterableUtils;
import org.apache.commons.lang3.StringUtils;
import org... |
0cbd87a54456bc6df5e72c2e707ca09772bc25cf3c60a3d629f4c07952315d75 | Java | 12,213 | 263 | package org.janelia.colormipsearch.dao.mongo;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.function.Function;
import java.util.stream.Collectors;
import java.util.strea... |
f53a1ae64215eefb22b315c8e5a528c39c2fb4e975f1b71f67579eb7341a8b2a | Java | 12,245 | 221 | package org.janelia.colormipsearch.cmd.dataexport;
import java.nio.file.Path;
import java.util.Collection;
import java.util.Collections;
import java.util.Comparator;
import java.util.List;
import java.util.Map;
import java.util.Objects;
import java.util.concurrent.CompletableFuture;
import java.util.concurrent.Executo... |
9e09bc448401141c5a26c7fe09ffe9515b3592d4f6daa52e05bdf1762e1ff42b | Java | 12,565 | 237 | package org.janelia.colormipsearch.cds;
/**
* Utils for calculating gradient area gap scores.
*/
public class GradientAreaGapUtils {
private static final double LOW_NORMALIZED_NEGATIVE_SCORE = 0.002;
private static final double HIGH_NORMALIZED_NEGATIVE_SCORE = 1.;
private enum Color {
BLACK,
... |
170c3e930bb598ba5e425d17447ca300af961bf8481b3968e119c20893e187fb | Java | 12,585 | 224 | package org.janelia.colormipsearch.cmd.dataexport;
import java.nio.file.Path;
import java.util.Collection;
import java.util.Collections;
import java.util.Comparator;
import java.util.List;
import java.util.Map;
import java.util.Objects;
import java.util.concurrent.CompletableFuture;
import java.util.concurrent.Executo... |
e747e49b7589984c380f4e7389abc1213b691a5f2796b626ad61e1dd31eef24e | Java | 12,751 | 315 | package org.jeecg.modules.federalml.controller;
import java.io.IOException;
import java.util.Arrays;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import org.jeecg.common.api.vo.Result;
import org.je... |
e6bee413f3819e937981276a1cc36a73d9cf7cfa4892632c553733fc8925234a | Java | 12,806 | 331 | package org.jeecg.modules.federalml.controller;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.Map;
import java.util.stream.Collectors;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import org.apa... |
6f6b0bc96be21bc1b4353b96076cc83bb98814e5dde2a4d63a6edfaaa27a4311 | Java | 13,259 | 246 | package org.janelia.colormipsearch.cds;
/**
* Utils for calculating gradient area gap scores.
*/
public class GradientAreaGapUtils {
public static final int HIGH_EXPRESSION_FACTOR = 2;
private static final double LOW_NORMALIZED_NEGATIVE_SCORE = 0.002;
private static final double HIGH_NORMALIZED_NEGATIVE... |
0b3aff768667db6bd2ee7698283605fc151d31a22d313692bb0e60dbdcc6a010 | Java | 13,265 | 320 | package org.janelia.colormipsearch.dao.mongo;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import java.util.Objects;
import java.util.Set;
import java.util.function.Function;
... |
a3389f5ef28d758e2094abb6fdd61e5e6834615f31acce79e44ea791acc286ef | Java | 13,271 | 246 | package org.janelia.colormipsearch.api_v2.cdsearch;
/**
* Utils for calculating gradient area gap scores.
*/
public class GradientAreaGapUtils {
public static final int HIGH_EXPRESSION_FACTOR = 2;
private static final double LOW_NORMALIZED_NEGATIVE_SCORE = 0.002;
private static final double HIGH_NORMALI... |
6a2761bd4770430a4a70a219442fa6a7e586ab0a969ad5f74b1d2e64e57971e7 | Java | 13,798 | 313 | package org.janelia.colormipsearch.dao.mongo;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
import java.util.Date;
import java.util.List;
import java.util.Map;
import java.util.function.Function;
import java.util.stream.Collectors;
import java.util.stre... |
90be158aa820982ce4742981058b49c42db00573a25dc816228fa4c92794fed4 | Java | 13,808 | 303 | package org.janelia.colormipsearch.cmd_v2;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.nio.file.StandardCopyOption;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Objects;
import java.util.Set;
import ... |
d60228de68bd5f1c7f92044eb639b1f6583c173d4940a73265aac533fc70f487 | Java | 14,122 | 391 | package org.janelia.colormipsearch.api_v2.cdsearch;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.List;
import java.util.function.BiPredicate;
import org.janelia.colormipsearch.imageprocessing.ImageArray;
/**
* Common methods that can be used by various ColorDepthQuerySearchAlgorithm imp... |
32221ea05a4b03bd4736d779549617e15430766aa2ce1c382d0ba875c54ba736 | Java | 14,150 | 392 | package org.janelia.colormipsearch.cds;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.List;
import java.util.function.BiPredicate;
import org.janelia.colormipsearch.imageprocessing.ImageArray;
import org.janelia.colormipsearch.imageprocessing.ImageRegionDefinition;
/**
* Common methods t... |
22850d28d57c0920ce8715176855efd26963a13bc6403f14e085098b28b06f4d | Java | 14,182 | 409 | package org.jeecg.modules.system.controller;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Date;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.Http... |
59048b0a0c549dee42c51cf6ff654ccbe6bbfbd5219b612b8f1f876030cae4ef | Java | 14,248 | 282 | package org.janelia.colordepthsearch;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.Collection;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.function.Supplier;
import java.util.regex.Matcher;
import... |
f35cbeebd17abee433af25ee448d9209544babdc39985d399c4d96b44ae8b811 | Java | 14,481 | 256 | package org.janelia.colormipsearch.cmd.dataexport;
import java.io.File;
import java.nio.file.Path;
import java.util.Collection;
import java.util.Comparator;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.concurrent.Executor;
import java.util.function.BiConsumer;
import java.util.re... |
a359a43013294e26ed8c7d29d35dc7b3165981348f58b70070418593a74e73e1 | Java | 14,543 | 486 | package fiji.plugin.DOM;
import java.awt.Rectangle;
import ij.ImagePlus;
import ij.ImageStack;
import ij.Undo;
import ij.process.FHT;
import ij.process.FloatProcessor;
import ij.process.ImageProcessor;
import ij.process.ImageStatistics;
import ij.process.StackProcessor;
public class ImCrossCorrelation {
public ... |
845d7789af411d275edbaf7067923096b110cba450d0011362fbc39a7f3c27dc | Java | 14,576 | 435 | package org.janelia.colormipsearch.api_v2.cdsearch;
import java.nio.file.Paths;
import java.util.function.Consumer;
import com.fasterxml.jackson.annotation.JsonClassDescription;
import com.fasterxml.jackson.annotation.JsonIgnore;
import com.fasterxml.jackson.annotation.JsonProperty;
import org.apache.commons.lang3.S... |
4759cb4af1090c0a491f9fab8937255b7968e84cd0b903ae987af47234d6afd5 | Java | 14,634 | 258 | package org.janelia.colormipsearch.cmd.dataexport;
import java.nio.file.Path;
import java.util.Collections;
import java.util.Comparator;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.concurrent.CompletableFuture;
import java.util.concurrent.Executor;
import java.util.function.Func... |
ad9207a96dec3f8f208da4b8fb06671b00b541b501c6aa4e943c750bc276c79a | Java | 14,729 | 509 | import java.awt.*;
import java.io.IOException;
import java.net.*;
import javax.imageio.ImageIO;
import javax.swing.*;
import netscape.javascript.*;
/**
* This class is a component of myProMS software and display
* a gel image in an html page with its annotation whether it
* was annotated or not by ImageMaster.
* @a... |
19a45e5cceaff9b3febd6ff8542233b577e27998e719e8aa056194f8915d2b74 | Java | 14,750 | 321 | package org.janelia.colormipsearch.cmd;
import java.io.IOException;
import java.io.InputStream;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.nio.file.StandardCopyOption;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Set;
import... |
c1e6612642c3156a23c41d989fe89269aed0ddcb26b6b26731153217dfea2098 | Java | 14,893 | 347 | package de.biovoxxel.toolbox;
import java.util.Arrays;
import ij.IJ;
import ij.ImagePlus;
import ij.Prefs;
import ij.WindowManager;
import ij.gui.GenericDialog;
import ij.measure.Calibration;
import ij.measure.Measurements;
import ij.measure.ResultsTable;
import ij.plugin.filter.EDM;
import ij.plugin.fil... |
48a4a88c1e9b2577592bf7c28f522b2edd983c84229445befc36269a76d853d0 | Java | 15,106 | 289 | package org.janelia.colormipsearch.cmd;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import java.util.Objects;
import java.util.function.Function;
import java.util.stream.Collectors;
import java.util.str... |
f81a2c5d01a60b6cd173a35b3fcdce4354ba4c135731918c8cedc16987add41f | Java | 15,139 | 357 | package de.biovoxxel.toolbox;
import java.util.Arrays;
import ij.IJ;
import ij.ImagePlus;
import ij.Prefs;
import ij.WindowManager;
import ij.gui.GenericDialog;
import ij.measure.Calibration;
import ij.measure.Measurements;
import ij.measure.ResultsTable;
import ij.plugin.filter.EDM;
import ij.plugin.f... |
6a02f4f7ca7de7e9579e4455d5dbff15d022861f986aac6e23597701f94982fe | Java | 15,170 | 315 | package org.janelia.colormipsearch.imageprocessing;
import java.util.function.BiPredicate;
import ij.ImagePlus;
import ij.io.Opener;
import ij.plugin.filter.RankFilters;
import ij.process.ImageConverter;
import ij.process.ImageProcessor;
import org.junit.Assert;
import org.junit.Test;
import static org.junit.Assert.... |
99230a99f3eab3b277490ead7cad9e82b61757f5957c4ab78ab706ca9307d017 | Java | 15,234 | 319 | package org.janelia.colormipsearch.cmd;
import java.util.Collections;
import java.util.Comparator;
import java.util.List;
import java.util.Optional;
import java.util.Set;
import java.util.function.Supplier;
import java.util.stream.Collectors;
import com.beust.jcommander.Parameter;
import com.beust.jcommander.Paramete... |
417f40238d588e5d0991da7e31b624ba309c6b8516cc4bd8670d9b214bbfa8a9 | Java | 15,270 | 524 | package org.jeecg.modules.api.controller;
import com.alibaba.fastjson.JSONObject;
import org.jeecg.common.api.dto.OnlineAuthDTO;
import org.jeecg.common.api.dto.message.*;
import org.jeecg.common.system.api.ISysBaseAPI;
import org.jeecg.common.system.vo.*;
import org.jeecg.modules.system.service.ISysUserService;
impor... |
e7ef7d2092be2ab986f187cf516bf25993b79d66d63bd7c4db8e12602884b16d | Java | 15,519 | 530 | package org.janelia.colormipsearch.api_v2.cdmips;
import java.io.Serializable;
import java.nio.file.Paths;
import java.util.Collections;
import java.util.LinkedHashMap;
import java.util.Map;
import java.util.Set;
import java.util.function.Consumer;
import com.fasterxml.jackson.annotation.JsonAnySetter;
import com.fas... |
aa460fd9677099f891cc34cef1fa741ab37da3adff3d09724b9fe6472b061175 | Java | 15,576 | 312 | package org.janelia.colormipsearch.cmd;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import java.util.Set;
import java.util.concurrent.CompletableFuture;
import java.util.concurrent.Executor;
import java.util.stream.Collectors;
import com.beust.jcommander.Parameter;
import com.beus... |
437b04b46f50e03e88cda663a9d9a06265a6145e18f06b295d5ec7855136e297 | Java | 15,745 | 321 | package org.janelia.colormipsearch.cmd_v2;
import java.io.File;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import java.util.Map;
import java.util.Optional;
import java.util.concurrent.CompletableFuture;
import java.util.concur... |
d135a9581109de08c06206a2b265a3cba5a4fe9585569e08d762218da319fe9b | Java | 15,797 | 277 | package org.janelia.colormipsearch.cmd.dataexport;
import java.nio.file.Path;
import java.util.Collection;
import java.util.Collections;
import java.util.Comparator;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.concurrent.CompletableFuture;
import java.util.concurrent.Executor;
i... |
1258b571ce197cfdfb7c353c5398ab6d911ff195105e93fc225648645ac334cc | Java | 15,922 | 363 | package org.jeecg.modules.federalml.controller;
import static org.jeecg.common.constant.CommonConstant.*;
import java.util.*;
import javax.servlet.http.HttpServletRequest;
import org.apache.shiro.SecurityUtils;
import org.jeecg.common.api.vo.Result;
import org.jeecg.common.aspect.annotation.AutoLog;
import org.jeec... |
8a38dac3efd5cb2c981e024111724bec13437e74038fd5876ba0ee5926978aad | Java | 16,106 | 333 | package org.janelia.colormipsearch.imageprocessing;
import java.util.function.BiPredicate;
import ij.ImagePlus;
import ij.Prefs;
import ij.io.Opener;
import ij.plugin.filter.RankFilters;
import ij.process.ImageConverter;
import ij.process.ImageProcessor;
import org.junit.Assert;
import org.junit.Test;
import org.slf4... |
121895daca389c32a2f312530351e6ad20e5458a12827599777117a3aaf9f094 | Java | 16,145 | 344 | package org.janelia.colormipsearch.cmd;
import java.io.IOException;
import java.io.InputStream;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.nio.file.StandardCopyOption;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Set;
import... |
091e0445f23ce08d32e86621e0fedc043bcac3c72f3eeedde034bf144b824b1c | Java | 16,292 | 349 | package org.janelia.colormipsearch.cmd;
import java.io.File;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.Collection;
import java.util.Collections;
import java.util.List;
import java.util.Map;
import java.util.function.Predicate;
import... |
4e5b77427b38987e9450e580233555b9623d847236cce78ef16d755a8535754b | Java | 16,385 | 336 | package org.janelia.colormipsearch.cmd_v2;
import java.io.File;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.function.Function;
import ... |
719b7e10dd0cb06e562b52cc91e3373bf7609cb50a08f8c2acfbd451caf8c34a | Java | 16,818 | 321 | package org.janelia.colormipsearch.cmd;
import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
import java.util.Comparator;
import java.util.Date;
import java.util.List;
import java.util.Set;
import java.util.concurrent.ExecutorService;
import java.util.function.Function;
import java.util.... |
bc078ab70fa4ffdfe63719d996d38f7771c3c955fb52443dd84a017ab3b5a7ee | Java | 16,819 | 484 | package org.jeecg.modules.system.controller;
import com.alibaba.fastjson.JSON;
import com.baomidou.mybatisplus.core.conditions.query.LambdaQueryWrapper;
import com.baomidou.mybatisplus.core.conditions.query.QueryWrapper;
import com.baomidou.mybatisplus.core.metadata.IPage;
import com.baomidou.mybatisplus.extension.plu... |
12c4867c2b30a97cf9d2aa825fe873f86c1eaf600464096344241c78960eea66 | Java | 17,061 | 366 | package org.janelia.colormipsearch.cmd;
import java.nio.file.Path;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.concurrent.Executor;
import java.util.stream.Collectors;
import javax.annotation.Nullable;
import javax.validation.Validation;
import javax... |
0f8b37acb7d02004bad62e4e8e4383b7be5ccabf1988c4a6c1558fcc7c734fc7 | Java | 17,274 | 396 | package org.janelia.colormipsearch.dao.mongo;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
import java.util.Date;
import java.util.List;
import java.util.function.Function;
import java.util.stream.Collectors;
import java.util.stream.Stream;
import com... |
747f146aa9514476994c152cb2286f04ade0817e93a84a3c93daffab943734b6 | Java | 17,522 | 563 |
package fiji.plugin.DOM;
public class LevenbergMarquardt
{
/**
* Constants
*/
public static final int GAUSSIAN_2D_PARAMETERS = 6;
public static final int PARAM_BACKGROUND = 0;
public static final int PARAM_AMPLITUDE = 1;
public static final int PARAM_X_SPOS = 2;
public static final int PARAM_Y_SPOS = 3;
pu... |
ad502a5301c5646ffaf6b3cc56aaf88127bb3a6ec2b80d0482073d99376f4726 | Java | 17,739 | 382 | package org.janelia.colormipsearch.dao.mongo;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.function.Supplier;
import com.google.common.collec... |
0ca2f3b2405680d464e48b7e28c41db89cfa73fdc7de33a60722eb48fa694cb0 | Java | 17,868 | 457 | package org.jeecg.modules.federalml.controller;
import static org.jeecg.common.constant.CommonConstant.*;
import java.io.IOException;
import java.util.Arrays;
import java.util.List;
import java.util.Map;
import java.util.stream.Collectors;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpS... |
95891142afe760c644652bb0ef1409166f7fd552f3001f4cea7e75d4cb8c7168 | Java | 18,045 | 648 | package fiji.plugin.DOM;
import java.awt.Color;
import java.util.ArrayList;
import ij.ImagePlus;
import ij.gui.OvalRoi;
import ij.gui.Overlay;
import ij.gui.PolygonRoi;
import ij.gui.Roi;
public class SMLLinker {
ImagePlus implnk;
SMLDialog settings;
SMLAnalysis smllink;
double [] x;
double [] y;
double [] f... |
7fc31c5063f7a7085fc3fbd7a01ea6a7da660b17523d9c541236951c89795d4b | Java | 18,296 | 354 | package org.janelia.colormipsearch.cmd;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.atomic.AtomicLong;
import java.util.function.Fun... |
f777266f1487835eff763e9d8a9b50c0b617d0c01ecb2a7d13c93b9889044f20 | Java | 18,336 | 473 | package org.jeecg.modules.system.service.impl;
import com.baomidou.mybatisplus.core.conditions.query.LambdaQueryWrapper;
import com.baomidou.mybatisplus.core.conditions.query.QueryWrapper;
import com.baomidou.mybatisplus.core.metadata.IPage;
import com.baomidou.mybatisplus.extension.plugins.pagination.Page;
import com... |
67da7ad87c0ff25356d9955a8e63b781ef99d0e3846720fb72baf63f7fc8a031 | Java | 18,378 | 480 | package org.jeecg.modules.system.controller;
import cn.hutool.core.io.FileTypeUtil;
import com.alibaba.fastjson.JSON;
import com.alibaba.fastjson.JSONObject;
import com.github.xiaoymin.knife4j.annotations.DynamicParameter;
import com.github.xiaoymin.knife4j.annotations.DynamicResponseParameters;
import io.swagger.anno... |
440760b0936499f92e163aae3973f9b4f098b443567dda58625a9f265fd9b1cf | Java | 18,542 | 675 | package fiji.plugin.DOM;
// Java
import java.util.Arrays;
//import java.io.InputStream;
//import java.io.InputStreamReader;
//import java.io.BufferedReader;
//import java.io.IOException;
// ImageJ
import ij.IJ;
import ij.ImageJ;
import ij.ImagePlus;
import ij.gui.Overlay;
import ij.gui.Roi;
import ij.plugin.PlugIn;... |
75ac7bb602ffa8bc8602f3acf2e64fd1af32458a1103551e3375dd59eb1badb9 | Java | 18,983 | 488 | package de.biovoxxel.toolbox;
import java.awt.Color;
import ij.IJ;
import ij.ImagePlus;
import ij.Prefs;
import ij.WindowManager;
import ij.gui.GenericDialog;
import ij.gui.NewImage;
import ij.gui.OvalRoi;
import ij.gui.Overlay;
import ij.gui.Roi;
import ij.measure.Calibration;
import ij.measure.Measu... |
6d8f5fa56ff297411c52f5f362ae65003247717efdae9cc4b53ed88eb60e6d35 | Java | 19,637 | 370 | package org.janelia.colormipsearch.cmd;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import java.util.concurrent.CompletableFuture;
import java.util.concurrent.Executor;
import java.util.function.Function;
... |
f3713c6c6e519f5d5fba320e191dc11537aa40c3e1ebf95cb7d065c6ca1a836b | Java | 20,025 | 474 | package org.jeecg.modules.system.controller;
import java.io.IOException;
import java.util.Date;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import javax.annotation.Resource;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import io.swagger.annot... |
8833cf66ad0c6aa10b1fb371d47246054a73d7090b70c38c25fdbbf0a7631d1b | Java | 20,047 | 487 | package org.jeecg.modules.system.controller;
import java.io.IOException;
import java.util.*;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import com.baomidou.mybatisplus.core.conditions.query.LambdaQueryWrapper;
import org.apache.shiro.SecurityUtils;
import org.apache.... |
165be559bf9ec7ce12309573b5041ee243486232431232d8d509531bcc81846c | Java | 20,076 | 565 | package org.jeecg.modules.system.controller;
import com.alibaba.fastjson.JSON;
import com.baomidou.mybatisplus.core.conditions.query.LambdaQueryWrapper;
import com.baomidou.mybatisplus.core.conditions.query.QueryWrapper;
import com.baomidou.mybatisplus.core.metadata.IPage;
import com.baomidou.mybatisplus.extension.pl... |
3b8938e960ff66ed4535c5f08b3b70b158023b99cf08b13abda18fa67f9c6a38 | Java | 20,138 | 390 | package org.janelia.colormipsearch.dao.mongo;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.Comparator;
import java.util.List;
import java.util.function.Function;
import java.util.stream.Collectors;
import java.util.stream.Stream;
import org.apache.commons.lang3.t... |
4dc7a8ad6c1a69b1357d4d8cd84b82c9f1b2a0642e473ba15fa9a52992df3822 | Java | 20,337 | 426 | package org.janelia.colormipsearch.cmd;
import java.nio.file.Path;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.concurrent.Executor;
import java.util.stream.Collectors;
import javax.annotation.Nullable;
import javax.validation.Validation;
import javax... |
fa6872362c626bfaf23af174f111af50ba715982b9d4c80ed07cb3148cfa3442 | Java | 20,418 | 493 | package de.biovoxxel.toolbox;
import java.awt.Color;
import java.awt.Font;
import ij.IJ;
import ij.ImagePlus;
import ij.Macro;
import ij.WindowManager;
import ij.gui.GenericDialog;
import ij.gui.Roi;
import ij.measure.Calibration;
import ij.measure.Measurements;
import ij.measure.ResultsTable;
import ij.plugin.filte... |
b0695456972feee632cfd9be96bbe438ca846883de571996ec11e23323d4b3d7 | Java | 20,693 | 423 | package org.janelia.colormipsearch.cmd;
import java.io.File;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.Collections;
import java.util.List;
import java.util.Map;
import java.util.function.Function;
import java.util.function.Predicate;... |
764318c6dff7859d9e5388b10fa6de22aaedc4e536bfa2e047c3fe5a5c22a7de | Java | 20,786 | 494 | package org.jeecg.modules.system.service.impl;
import java.util.*;
import com.alibaba.fastjson.JSONObject;
import org.apache.commons.lang.StringUtils;
import org.jeecg.common.constant.CacheConstant;
import org.jeecg.common.constant.CommonConstant;
import org.jeecg.common.constant.FillRuleConstant;
import org.jeecg.co... |
5f8953889afd12a0bc23c813f19de170ea84b2fa490a3202ad4f8ef05dc21e26 | Java | 21,298 | 445 | package org.janelia.colormipsearch.dao.mongo;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.function.Supplier;
import com.google.common.collec... |
b15ac914e32e860e418a8217085b5c08796b1af578db90c2d018d783fe0003cf | Java | 21,517 | 469 | package org.janelia.colormipsearch.cmd_v2;
import java.io.File;
import java.io.IOException;
import java.io.UncheckedIOException;
import java.nio.file.DirectoryStream;
import java.nio.file.FileVisitResult;
import java.nio.file.FileVisitor;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Path... |
32330e4ed866659f9a6c0d66afcb7763e24c217e78e2a92d5b3e4baa101d7126 | Java | 21,917 | 406 | package org.janelia.colormipsearch.cmd;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.Comparator;
import java.util.List;
import java.util.Set;
import java.util.concurrent.CompletableFuture;
import java.util.concurrent.Executor;
import java.util.function.Supplier;
i... |
ec5c0daedf8f92c905ddaf3545f900288d1fa3644ed35e089dee2cd142f62dbc | Java | 22,048 | 441 | package org.janelia.colormipsearch.cmd;
import java.io.File;
import java.io.IOException;
import java.io.UncheckedIOException;
import java.nio.file.DirectoryStream;
import java.nio.file.FileVisitResult;
import java.nio.file.FileVisitor;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
... |
d9e07ac660891ce57abdc1bc14c34cffdd07638f73a1a676bd1d22f4ed94f151 | Java | 22,063 | 441 | package org.janelia.colormipsearch.cmd;
import java.io.File;
import java.io.IOException;
import java.io.UncheckedIOException;
import java.nio.file.DirectoryStream;
import java.nio.file.FileVisitResult;
import java.nio.file.FileVisitor;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
... |
aebc7b186be2b38cc304d7e0f135c09fa59560ca7fd0697cb792db88362d1e7b | Java | 22,115 | 373 | package org.janelia.colormipsearch.cds;
import java.util.HashMap;
import java.util.Map;
import java.util.function.Supplier;
import ij.ImagePlus;
import ij.io.Opener;
import org.janelia.colormipsearch.ImageTestUtils;
import org.janelia.colormipsearch.imageprocessing.ColorTransformation;
import org.janelia.colormipsear... |
0183c0d0953369a88ad1208f83932e134c74cd7a5a6aba5f6a6112bb9db1611e | Java | 22,713 | 385 | package org.janelia.colormipsearch.cmd_v2;
import java.io.File;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.concurrent.CompletableFuture;
im... |
f1aa7738388a5de94e1e754c8866f8390c1804cd24829e29375801f80b97af33 | Java | 22,855 | 485 | package org.jeecg.modules.federalml.controller;
import static org.jeecg.common.constant.CommonConstant.*;
import java.io.IOException;
import java.util.*;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import org.jeecg.common.api.vo.Result;
import org.jeecg.common.aspect... |
bac626c5846ecfa68b59e2c297758f954fd144cd91d3773a81275c452c961303 | Java | 23,669 | 510 | package org.janelia.colormipsearch.api_v2.cdmips;
import java.io.File;
import java.io.IOException;
import java.io.InputStream;
import java.io.UncheckedIOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.Arrays;
import java.util.Collections;
import java.util.... |
ca307e08eddff946efabf9b41a9f56284aed77ff00f84857592a347d751cd666 | Java | 23,736 | 467 | package org.janelia.colormipsearch.cmd;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Comparator;
import java.util.List;
import java.util.Map;
import java.util.Optional;
import java.util.Set;
import java.util.function.Supplier;
import java.util.stream.Collectors;
import java.util.stream.St... |
7b74c6c1541ea447ed6b35d1f68da3efa8c10cacf279d8af691ed6bbccee41b6 | Java | 25,992 | 629 | package org.janelia.colormipsearch.imageprocessing;
import java.io.Serializable;
import java.util.Arrays;
import java.util.function.BiFunction;
import java.util.function.BiPredicate;
import java.util.function.Function;
/**
* ImageTransformation - image transformations that take both pixel value and pixel position in... |
6ddf30a110107228ad7759f66b29ef91c6a5ba709cd89f6ab3ec06c93b70c124 | Java | 26,212 | 689 | package jaolho.data.lma;
import jaolho.data.lma.ArrayConverter.SeparatedData;
import jaolho.data.lma.implementations.JAMAMatrix;
import java.util.Arrays;
/**
* A class which implements the <i>Levenberg-Marquardt Algorithm</i>
* (LMA) fit for non-linear, multidimensional parameter space
* for any multidimensional... |
b36baed3a3ccb77ef3c83b442e01b49d5e21faf3e9b0c4219704501b8e5ef187 | Java | 26,426 | 639 | package org.janelia.colormipsearch.imageprocessing;
import java.io.Serializable;
import java.util.Arrays;
import java.util.function.BiFunction;
import java.util.function.BiPredicate;
import java.util.function.Function;
/**
* ImageTransformation - image transformations that take both pixel value and pixel position in... |
72c14634026a03456693a260925e6ea164cead8c6608b81fe12579f07a052189 | Java | 29,889 | 731 | package fiji.plugin.DOM;
import java.awt.AWTEvent;
import java.text.DecimalFormat;
import ij.IJ;
import ij.ImagePlus;
import ij.Prefs;
import ij.gui.DialogListener;
import ij.gui.GenericDialog;
import ij.gui.Overlay;
import ij.gui.Roi;
import ij.process.ImageProcessor;
import ij.util.Tools;
public class SMLDialog i... |
82ccd8f3bb109f3746f8592c746457199774eba5a1d247ec474f1088f2d891e2 | Java | 30,335 | 624 | package org.janelia.colormipsearch.cmd_v2;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.OutputStream;
import java.io.RandomAccessFile;
import java.net.URI;
import java.nio.channels.Channels;
import java.nio.file.Files;
import java.nio.file.Path;
impo... |
69f96741c048fed21e1256e6830c0b69a8be70cb1d000e7d76488b89aac7cc13 | Java | 31,699 | 873 | package org.jeecg.modules.system.controller;
import com.alibaba.fastjson.JSONArray;
import com.alibaba.fastjson.JSONObject;
import com.baomidou.mybatisplus.core.conditions.query.LambdaQueryWrapper;
import com.baomidou.mybatisplus.core.conditions.query.QueryWrapper;
import io.swagger.annotations.Api;
import io.swagger.... |
2b52ea7f00d3229be1e5e5be06691db7e42d771677ac4c3dd40fb6697e139a31 | Java | 32,684 | 725 | package org.jeecg.modules.system.controller;
import cn.hutool.core.util.RandomUtil;
import com.alibaba.fastjson.JSONObject;
import com.aliyuncs.exceptions.ClientException;
import com.baomidou.mybatisplus.core.conditions.query.LambdaQueryWrapper;
import com.github.xiaoymin.knife4j.annotations.ApiOperationSupport;
impor... |
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