sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
f347f33afcc4b0f87865f1f925ae0b4132d6f0a7fbedd1116803f2c3ecfcb657 | Java | 1,389 | 64 | package org.jeecg.modules.system.entity;
import com.baomidou.mybatisplus.annotation.TableId;
import com.baomidou.mybatisplus.annotation.TableName;
import com.fasterxml.jackson.annotation.JsonFormat;
import lombok.Data;
import org.jeecg.common.aspect.annotation.Dict;
import org.springframework.format.annotation.DateTim... |
216128399ebcf196113bb57782b394ba035575ded38f7ef681a1b7dd521bc5af | Java | 1,394 | 52 | package jaolho.data.lma.implementations;
import jaolho.data.lma.LMA;
import jaolho.data.lma.LMAMultiDimFunction;
/**
* An example fit which fits a plane to some data points
* and prints out the resulting fit parameters.
*/
public class MultiDimExampleFit {
/** An example function with a form of y = a0 * x0 + a... |
0f820b69d7330c733b357d41f75c547a28838d3d5c6f4f829d400341b907c840 | Java | 1,397 | 71 | package org.jeecg.modules.system.entity;
import java.io.Serializable;
import java.util.Date;
import com.baomidou.mybatisplus.annotation.IdType;
import com.baomidou.mybatisplus.annotation.TableId;
import com.fasterxml.jackson.annotation.JsonFormat;
import lombok.Data;
import lombok.EqualsAndHashCode;
import lombok.ex... |
8b65cfc8c664f14f8b25af398f8529d1a178d13aa5752000edbeee8ab6330c69 | Java | 1,408 | 62 | package org.jeecg.modules.system.service;
import java.util.List;
import java.util.Map;
import org.jeecg.common.exception.JeecgBootException;
import org.jeecg.modules.system.entity.SysCategory;
import org.jeecg.modules.system.model.TreeSelectModel;
import com.baomidou.mybatisplus.extension.service.IService;
/**
* @... |
7cd8900c7f4dc698b5641925468ce386539084fdbd6eb32bd33c1c913af70c93 | Java | 1,409 | 93 | package org.jeecg.modules.system.model;
import java.io.Serializable;
import java.util.List;
/**
* 树形下拉框
*/
public class TreeSelectModel implements Serializable {
private static final long serialVersionUID = 9016390975325574747L;
private String key;
private String title;
private boolean isLeaf;
private... |
29c808a69e161178a91b7e3dbb967950e0dd62ce21701c8179e69bdcfe8ce6ef | Java | 1,431 | 40 | package org.janelia.colormipsearch.api_v2.cdsearch;
import org.junit.Test;
import static org.junit.Assert.assertEquals;
public class GradientAreaGapUtilsTest {
@Test
public void scoreCalculator() {
class TestData {
final int pix;
final long gap;
final long highExp... |
b47283970c459e8f6d97f6a1cfe7f085bb8b3f64f15e5a750067791887e12715 | Java | 1,448 | 44 | package org.janelia.colormipsearch.dao.mongo.support;
import com.fasterxml.jackson.databind.ObjectMapper;
import org.bson.BsonReader;
import org.bson.BsonWriter;
import org.bson.codecs.Codec;
import org.bson.codecs.DecoderContext;
import org.bson.codecs.EncoderContext;
import org.janelia.colormipsearch.model.FileData... |
7480ab5eb074f1d9e26cbd8954ea7b43a71def1ada7b14b238e17ab54527debb | Java | 1,452 | 50 | package org.janelia.colormipsearch.cmd_v2;
import java.util.Arrays;
import java.util.List;
import java.util.stream.Collectors;
import com.beust.jcommander.IStringConverter;
import org.apache.commons.lang3.StringUtils;
class MappedFieldArg {
static class MappedFieldArgConverter implements IStringConverter<Mappe... |
29956ef27e679138b853e559697505688410429cc45a8b637e86b8065b9eaaa2 | Java | 1,453 | 50 | package org.janelia.colormipsearch.dao.mongo;
import java.util.List;
import com.mongodb.client.model.Filters;
import org.janelia.colormipsearch.AbstractITest;
import org.janelia.colormipsearch.dao.Dao;
import org.janelia.colormipsearch.dao.DaosProvider;
import org.janelia.colormipsearch.model.BaseEntity;
import org.... |
1d406cc5d15bfefafa7df4f7f04ae4f6f0644f93edbe520b3300e80d201b767f | Java | 1,470 | 51 | package org.jeecg.modules.system.util;
import cn.hutool.core.util.CharsetUtil;
import cn.hutool.crypto.symmetric.SymmetricAlgorithm;
import cn.hutool.crypto.symmetric.SymmetricCrypto;
/**
* @Description: 密码加密解密
* @author: lsq
* @date: 2020年09月07日 14:26
*/
public class SecurityUtil {
/**加密key*/
private st... |
2b847d442c9eb416b7dce93e1573d44570f147109bc99595a913e5e6d786eb44 | Java | 1,470 | 30 | package cn.sdaict.fldatauploader.config;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.scheduling.annotation.EnableAsync;
import org.springframework.scheduling.concurrent.ThreadPoolTaskExecutor;
import java.util.concurrent.T... |
0f6526ac76f026eecaa9fa8adae67d3f261edbc47ec6c62e97f8fc80d7f00208 | Java | 1,472 | 34 | package org.janelia.colormipsearch.model.json;
import java.io.IOException;
import com.fasterxml.jackson.core.JsonParser;
import com.fasterxml.jackson.core.JsonToken;
import com.fasterxml.jackson.databind.DeserializationContext;
import com.fasterxml.jackson.databind.JsonDeserializer;
import com.fasterxml.jackson.datab... |
7e256fead45076023813c0635a66f24be1c1efe7bcfe5b1817d7720313560d94 | Java | 1,476 | 49 | package org.janelia.colormipsearch.cds;
import org.apache.commons.lang3.builder.ToStringBuilder;
public class ShapeMatchScore implements ColorDepthMatchScore {
private final long gradientAreaGap;
private final long highExpressionArea;
private final long maxGradientAreaGap;
private final boolean mirror... |
5ca6989d547cdd2b2f639577114afb9af5ad80d40f1bd8854d2cb104d7ff8352 | Java | 1,477 | 55 | package org.jeecg.modules.system.mapper;
import com.baomidou.mybatisplus.core.mapper.BaseMapper;
import org.apache.ibatis.annotations.Select;
import org.jeecg.modules.system.entity.SysDepart;
import org.jeecg.modules.system.model.SysDepartTreeModel;
import org.jeecg.modules.system.model.TreeModel;
import org.springfra... |
03105a6dec57210662e7ff197157bc3bcf72c386e722563c052dc7613382eac8 | Java | 1,481 | 58 | package org.janelia.colormipsearch.cmd.jacsdata;
import java.util.List;
import java.util.Map;
import java.util.stream.Collectors;
import com.fasterxml.jackson.annotation.JsonProperty;
import org.apache.commons.lang3.builder.ToStringBuilder;
/**
* This is the representation of a JACS EM Body.
*/
public class CDMIP... |
c39f4f26c8e64581e50ccc75a6374b5d188fa6984f78b8fb515e76a4f35e9744 | Java | 1,483 | 35 | package org.janelia.colormipsearch.cmd.dataexport;
import java.util.Map;
import org.janelia.colormipsearch.dto.AbstractNeuronMetadata;
public class ImageStoreMapping {
private final String defaultImageStore;
private final Map<ImageStoreKey, String> imageStoreByMetadataFields;
public ImageStoreMapping(St... |
73e51ddba1d8d73ac02fd0fd3926c96b6130eb7674eba32cb0f5dc07d41db05b | Java | 1,485 | 41 | package org.janelia.colormipsearch.cmd;
import java.util.Collections;
import java.util.Set;
import java.util.stream.Collectors;
import com.beust.jcommander.Parameter;
import org.apache.commons.collections4.CollectionUtils;
import org.apache.commons.lang3.StringUtils;
class CommonArgs {
@Parameter(names = {"--ou... |
113c6b11944962d3a76a4343241a99ab87695f23fe16690fab9fa39c10892df1 | Java | 1,492 | 68 | package org.janelia.colormipsearch.imageprocessing;
import java.io.Serializable;
import org.apache.commons.lang3.builder.ToStringBuilder;
/**
* Image array representation containing image type, image width, height and image pixel arrays.
*
* @param <T> pixel array type
*/
public abstract class ImageArray<T> impl... |
4920b16938e5f6374f76fa86e3003406ebb6c877a8220a0409d4e56733fc27e4 | Java | 1,498 | 35 | package org.janelia.colormipsearch.model.json;
import java.io.IOException;
import com.fasterxml.jackson.core.JsonParser;
import com.fasterxml.jackson.core.JsonToken;
import com.fasterxml.jackson.databind.DeserializationContext;
import com.fasterxml.jackson.databind.JsonDeserializer;
import com.fasterxml.jackson.datab... |
6f08fa2e204c214e941d76a3c8a96d02091a263788f82dd3616ff2c40c998fae | Java | 1,505 | 40 | package org.janelia.colormipsearch.dataio.db;
import java.util.List;
import java.util.Map;
import java.util.function.Function;
import java.util.stream.Collectors;
import org.apache.commons.lang3.tuple.Pair;
import org.janelia.colormipsearch.config.Config;
import org.janelia.colormipsearch.dao.DaosProvider;
import org... |
55dd3de9e716b20391444b8efb457ddbefd97e3a3e1d26e1ca0f60519adde828 | Java | 1,507 | 42 | package org.jeecg.modules.system.mapper;
import java.util.List;
import org.apache.ibatis.annotations.Param;
import org.apache.ibatis.annotations.Select;
import org.jeecg.modules.system.entity.SysUserRole;
import com.baomidou.mybatisplus.core.mapper.BaseMapper;
/**
* <p>
* 用户角色表 Mapper 接口
* </p>
*
* @Author scot... |
8f7ded386c7a2b70c3ccb17795a0317240b4400d5f74307d007bd6ab0a94410e | Java | 1,509 | 82 | package org.jeecg.modules.system.entity;
import java.io.Serializable;
import java.math.BigDecimal;
import java.util.Date;
import com.baomidou.mybatisplus.annotation.IdType;
import com.baomidou.mybatisplus.annotation.TableId;
import lombok.Data;
import lombok.EqualsAndHashCode;
import lombok.experimental.Accessors;
i... |
f8913b27df9930bcac04642ceba30ed7f852562fccf03b504dfa22eae31ff94b | Java | 1,512 | 60 | package jaolho.data.lma.implementations;
import jaolho.data.lma.LMAMatrix;
import java.io.PrintWriter;
import java.io.StringWriter;
import java.text.NumberFormat;
import Jama.Matrix;
public class JAMAMatrix extends Matrix implements LMAMatrix {
private static final long serialVersionUID = -8925816623803983503L;
... |
4fe78dd40144c3b663254c39861edbeecb464c8432d34c263610370aec41725b | Java | 1,520 | 51 | package org.janelia.colormipsearch.mips;
import org.apache.commons.lang3.builder.EqualsBuilder;
import org.apache.commons.lang3.builder.HashCodeBuilder;
import org.janelia.colormipsearch.imageprocessing.ImageArray;
import org.janelia.colormipsearch.model.AbstractNeuronEntity;
import org.janelia.colormipsearch.model.Fi... |
c6b9d96d4c06282a01ae427728ee1ac1272633a4ebbfc4f1488ccb66e8e1a47a | Java | 1,523 | 85 | package org.jeecg.modules.system.entity;
import java.io.Serializable;
import java.util.Date;
import com.baomidou.mybatisplus.annotation.IdType;
import com.baomidou.mybatisplus.annotation.TableId;
import com.baomidou.mybatisplus.annotation.TableLogic;
import lombok.Data;
import lombok.EqualsAndHashCode;
import lombok... |
05ec680c44f81c7c9186c9e22e52044b795cd7e4834b03cf4d508432cf726f17 | Java | 1,528 | 52 | package org.jeecg.modules.system.entity;
import java.io.Serializable;
import java.util.Date;
import com.baomidou.mybatisplus.annotation.IdType;
import com.baomidou.mybatisplus.annotation.TableId;
import com.baomidou.mybatisplus.annotation.TableName;
import com.baomidou.mybatisplus.annotation.TableField;
import io.swag... |
7ce2d0b76d60c2128d2c721712af3820acef8ad72b1caf0a1c8cb4f6e63ea408 | Java | 1,545 | 60 | package org.janelia.colormipsearch.cmd.jacsdata;
import java.util.List;
import java.util.Map;
import java.util.stream.Collectors;
import com.fasterxml.jackson.annotation.JsonProperty;
import org.apache.commons.lang3.builder.ToStringBuilder;
/**
* This is the representation of a JACS EM Body.
*/
public class CDMIP... |
eace124b6399bf9985a61928bd5788371a972c049b1ebbc2f586573d7bc19e43 | Java | 1,578 | 51 | package org.jeecg.modules.system.entity;
import java.io.Serializable;
import java.util.Date;
import com.baomidou.mybatisplus.annotation.IdType;
import com.baomidou.mybatisplus.annotation.TableId;
import com.baomidou.mybatisplus.annotation.TableName;
import lombok.Data;
import com.fasterxml.jackson.annotation.JsonForma... |
f636cf2ac0072e91157c9d6e9132ebe31ba2142bb13b62c88fe9cf29e2d97e4b | Java | 1,587 | 49 | package org.janelia.colormipsearch.dataio.db;
import java.util.List;
import java.util.Set;
import java.util.stream.Collectors;
import org.janelia.colormipsearch.dao.NeuronMetadataDao;
import org.janelia.colormipsearch.dataio.CDMIPsWriter;
import org.janelia.colormipsearch.model.AbstractNeuronEntity;
import org.janeli... |
05855ef72260f4146f0abd5d3a9a8dfeab45def35e9584f4afd25d0badbb2b5a | Java | 1,590 | 39 | package org.janelia.colormipsearch.dataio.db;
import java.util.List;
import java.util.Map;
import java.util.Set;
import org.janelia.colormipsearch.config.Config;
import org.janelia.colormipsearch.dao.DaosProvider;
import org.janelia.colormipsearch.dao.MatchSessionDao;
import org.janelia.colormipsearch.dataio.CDSSessi... |
0ef6eac5af73b6262cb49660090f020cc57e19de14a26866b24f773743654ccc | Java | 1,597 | 60 | package org.janelia.colormipsearch.dao.mongo;
import java.util.Collection;
import java.util.Set;
import java.util.function.Supplier;
import org.janelia.colormipsearch.model.AbstractNeuronEntity;
import org.janelia.colormipsearch.model.ComputeFileType;
import org.janelia.colormipsearch.model.FileData;
import org.jane... |
ee42d670b0b4e5f41054b52ddf13c2b229187a6dc4a55bbe99b72ad29b7b498a | Java | 1,605 | 53 | package org.janelia.colormipsearch.cmd_v2;
import java.util.List;
import com.fasterxml.jackson.annotation.JsonCreator;
import com.fasterxml.jackson.annotation.JsonProperty;
import org.apache.commons.collections4.CollectionUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.builder.ToS... |
09a1c254ab3b81c8f404c980b42f3b8d69c02c9ff3527dfb7063e5b9bb92e005 | Java | 1,608 | 43 | package org.janelia.colormipsearch.dao.mongo.support;
import com.mongodb.MongoClientSettings;
import com.mongodb.client.MongoClient;
import com.mongodb.client.MongoClients;
import com.mongodb.client.MongoDatabase;
public class MongoClientProvider {
public static MongoClient createMongoClient(
String ... |
8e6c9448a8a361dd2d4caf252874005fc9b14adcaaf1b83273f4ecc366f4ef15 | Java | 1,625 | 58 | package org.janelia.colormipsearch.cmd;
import java.util.Arrays;
import java.util.List;
import java.util.stream.Collectors;
import com.beust.jcommander.IStringConverter;
import org.apache.commons.lang3.StringUtils;
public class NameValueArg {
static class NameArgConverter implements IStringConverter<NameValueA... |
d038e5a6646c7077a82b8ce38238bc9cf53fce5ff4bf8f81bea458bb74adc565 | Java | 1,629 | 61 | package org.jeecg.modules.system.mapper;
import com.baomidou.mybatisplus.core.mapper.BaseMapper;
import org.apache.ibatis.annotations.Param;
import org.apache.ibatis.annotations.Select;
import org.apache.ibatis.annotations.Update;
import org.jeecg.modules.system.entity.SysPermission;
import org.jeecg.modules.system.mo... |
4b8ad65eb276b89d475ac2e2520cd2a8009dd2475a62eb4a222cc8deaf5b8664 | Java | 1,639 | 55 | package org.jeecg.modules.system.entity;
import java.io.Serializable;
import java.util.Date;
import com.baomidou.mybatisplus.annotation.IdType;
import com.baomidou.mybatisplus.annotation.TableId;
import com.baomidou.mybatisplus.annotation.TableName;
import com.baomidou.mybatisplus.annotation.TableField;
import io.swag... |
762f10821c5fc4b56bcac9e1fe86be297e316745b845da8ca5445016d148e22a | Java | 1,642 | 38 | package org.janelia.colormipsearch.cds;
import java.io.Serializable;
import org.janelia.colormipsearch.imageprocessing.ImageArray;
/**
* Creator of a ColorMIPQuerySearch for a given mask that generates a certain score type.
*
* @param <S> color depth match score type
*/
public interface ColorDepthSearchAlgorithm... |
4669118f155f50504eda7ad1e72190dd6986f4b91fb7ffc03cb42faaed2f0e31 | Java | 1,645 | 43 | package org.jeecg.modules.oss.service.impl;
import com.baomidou.mybatisplus.extension.service.impl.ServiceImpl;
import org.jeecg.common.util.CommonUtils;
import org.jeecg.common.util.oss.OssBootUtil;
import org.jeecg.modules.oss.entity.OSSFile;
import org.jeecg.modules.oss.mapper.OSSFileMapper;
import org.jeecg.module... |
50e5aa6cca1fb318e5b89c8d0be1d148c0c36d7c05bd75f47aebaef2208afacd | Java | 1,649 | 64 | package org.jeecg.modules.system.service;
import com.baomidou.mybatisplus.extension.service.IService;
import org.jeecg.common.exception.JeecgBootException;
import org.jeecg.modules.system.entity.SysPermission;
import org.jeecg.modules.system.model.TreeModel;
import java.util.List;
/**
* <p>
* 菜单权限表 服务类
* </p>
*
... |
df4b90d9f39a14f8fc0c7e5724aa2996beedf367ab3f0dd3dbdb89d1a908c910 | Java | 1,649 | 38 | package org.janelia.colormipsearch.cds;
import java.io.Serializable;
import org.janelia.colormipsearch.imageprocessing.ImageArray;
/**
* Creator of a ColorMIPQuerySearch for a given mask that generates a certain score type.
*
* @param <S> color depth match score type
*/
public interface ColorDepthSearchAlgorithm... |
49d70e4bc31e97f2f1a30655fb7c5d3943aa2de29073f2880903c97016853bc1 | Java | 1,652 | 82 | package org.jeecg.modules.system.entity;
import java.io.Serializable;
import java.time.LocalDateTime;
import java.util.Date;
import org.jeecgframework.poi.excel.annotation.Excel;
import org.springframework.format.annotation.DateTimeFormat;
import com.baomidou.mybatisplus.annotation.IdType;
import com.baomidou.mybati... |
1a9e4bf51b96d9aed09575e7400222fe468b175d4572f519bf979cd372eb9eeb | Java | 1,654 | 42 | package org.janelia.colormipsearch.api_v2.cdsearch;
import java.util.Collections;
import ij.ImagePlus;
import ij.io.Opener;
import org.janelia.colormipsearch.imageprocessing.ImageArray;
import org.janelia.colormipsearch.imageprocessing.ImageArrayUtils;
import org.junit.Test;
import static org.junit.Assert.assertEqua... |
250c1653dca1e39c4f9c13d984502a08ead3a23863b603525e984e1d18fe423e | Java | 1,657 | 74 | package org.janelia.colormipsearch.model;
public class TestLMNeuronEntity extends LMNeuronEntity {
private String sampleRef;
private String sampleName;
private String objective;
private Gender gender;
private String anatomicalArea;
private String mountingProtocol;
private Integer channel;
... |
fe61ae98170223b2542c8efba79fbfeb91ee3eab465f051352e12d9f692c59f3 | Java | 1,663 | 38 | package fiji.plugin.DOM;
//error function realization
//taken from http://introcs.cs.princeton.edu/java/21function/ErrorFunction.java.html
public class ErrorFunction {
// fractional error in math formula less than 1.2 * 10 ^ -7.
// although subject to catastrophic cancellation when z in very close to 0
// f... |
2798de6543a1f81e4da81118b9fcabbe74d3ccf371acab26db6bae7e6f2091cd | Java | 1,667 | 60 | //package cn.sdaict.fldatauploader.utils;
//
//import com.esotericsoftware.yamlbeans.YamlException;
//import com.esotericsoftware.yamlbeans.YamlReader;
//import com.esotericsoftware.yamlbeans.YamlWriter;
//import org.springframework.stereotype.Service;
//
//import java.io.FileNotFoundException;
//import java.io.FileRea... |
16ac9b17e727775d8453865c55bc416f73f9125125b74f4623dd2e386e257f67 | Java | 1,671 | 71 | package org.janelia.colormipsearch.datarequests;
import java.util.List;
import com.fasterxml.jackson.annotation.JsonIgnore;
import org.apache.commons.collections4.CollectionUtils;
public class PagedResult<T> {
private long pageOffset;
private long pageNumber;
private int pageSize;
private List<SortC... |
1cc77cd99fe110f26d4c239cefaa3dd74e8bad535c5f9682337f476c272be3f8 | Java | 1,682 | 50 | package org.janelia.colormipsearch.dataio.fs;
import java.io.IOException;
import java.io.UncheckedIOException;
import java.nio.file.Path;
import com.fasterxml.jackson.databind.JsonNode;
import com.fasterxml.jackson.databind.ObjectWriter;
import org.janelia.colormipsearch.dataio.fileutils.FSUtils;
import org.slf4j.Lo... |
1ab9d12401747d58ee8e259fb703a4ea337832bbb5708a36003821e3c35d08ab | Java | 1,683 | 51 | package org.janelia.colormipsearch.imageprocessing;
import java.util.function.BinaryOperator;
/**
* Utils for lazy image data type
*/
public class LImageUtils {
public static LImage create(ImageArray<?> imageArray) {
return create(imageArray, 0, 0, 0, 0);
}
public static LImage create(ImageArr... |
7a74096f2b3c63254eeba63816bf4dc4858580b6119cb686f5287206bbe93994 | Java | 1,683 | 37 | package org.janelia.colormipsearch.dataio.db;
import java.util.List;
import org.janelia.colormipsearch.dao.NeuronMetadataDao;
import org.janelia.colormipsearch.dao.NeuronSelector;
import org.janelia.colormipsearch.dataio.CDMIPsReader;
import org.janelia.colormipsearch.dataio.DataSourceParam;
import org.janelia.colorm... |
637dfe01b5fb7c675820d1e0b57a160c9e3db0855f66e0cab7f61cc1ba7ed8ac | Java | 1,685 | 48 | package org.janelia.colormipsearch.cmd;
import java.util.Collections;
import java.util.List;
import com.beust.jcommander.IStringConverter;
import com.google.common.base.Splitter;
import com.google.common.collect.ImmutableList;
import org.apache.commons.collections4.CollectionUtils;
import org.apache.commons.lang3.St... |
9a5cdadf12969702e212312c6fd1946c72f7133dcaf06c1efef2f94b0eeae6ad | Java | 1,685 | 48 | package org.janelia.colormipsearch.cmd;
import java.util.Collections;
import java.util.List;
import com.beust.jcommander.IStringConverter;
import com.google.common.base.Splitter;
import com.google.common.collect.ImmutableList;
import org.apache.commons.collections4.CollectionUtils;
import org.apache.commons.lang3.St... |
80a1d41c1417e72b8c7b565fb07c0e1c4e8ddf91fcdfd6c696e12049d3e2642d | Java | 1,686 | 38 | package org.janelia.colormipsearch.api_v2.cdsearch;
import java.io.Serializable;
import org.janelia.colormipsearch.imageprocessing.ImageArray;
/**
* Creator of a ColorMIPQuerySearch for a given mask that generates a certain score type.
*
* @param <S> color depth match score type
*/
public interface ColorDepthSea... |
d127ca8d1f61689c960038e0b6242ce6570247ed6543afe84655705a3b5900f9 | Java | 1,697 | 63 | package org.janelia.colormipsearch.dao.mongo;
import java.util.Collection;
import java.util.Set;
import java.util.function.Supplier;
import org.janelia.colormipsearch.model.AbstractNeuronEntity;
import org.janelia.colormipsearch.model.ComputeFileType;
import org.janelia.colormipsearch.model.FileData;
import org.janel... |
1cc219960a07b51782ccc05e9a4181eee031f543050d014fb9bc2defb186af36 | Java | 1,698 | 65 | package org.janelia.colormipsearch.cmd_v2;
import java.io.Serializable;
import java.util.Set;
import com.fasterxml.jackson.annotation.JsonProperty;
import org.apache.commons.collections4.CollectionUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.builder.ToStringBuilder;
class Colo... |
696a5027b66169361b217ea34c42d320318ad4acda3e057a63e2aec9b753fa14 | Java | 1,715 | 69 | package org.janelia.colormipsearch.datarequests;
import java.util.List;
import org.apache.commons.lang3.builder.ToStringBuilder;
public class PagedRequest {
private long firstPageOffset;
private long pageNumber;
private int pageSize;
private List<SortCriteria> sortCriteria;
public long getFirstP... |
ecbea3887d0820c912027ea243721ccd827adeddbb5ae5c420f32a992b5faf64 | Java | 1,715 | 51 | package org.janelia.colormipsearch.dataio.db;
import java.util.List;
import java.util.Set;
import java.util.stream.Collectors;
import org.janelia.colormipsearch.dao.NeuronMetadataDao;
import org.janelia.colormipsearch.dataio.CDMIPsWriter;
import org.janelia.colormipsearch.model.AbstractNeuronEntity;
import org.janeli... |
60c87dd9b2f143725b4d9321b9ad619496e99fba6003400e0c21312cc7e1c6aa | Java | 1,739 | 36 | package fiji.plugin.DOM;
//import jaolho.data.lma.LMA;
import jaolho.data.lma.LMAMultiDimFunction;
//public class SMLGFit {
/** Two-dimensional gaussian function with a form of y = a0 + a1*exp-((x1-a2)^2/(2*a4) + (x2-a3)^2/(2*a5))*/
// a[0] - Background
// a[1] - Amplitude
// a[2] - x0
// a[3] - y0
// ... |
c5692b546715c14718ac5f44e71045e97e613b14de16e66610f5a405a6d5f573 | Java | 1,743 | 53 | package org.janelia.colormipsearch.dataio.db;
import java.util.Collection;
import java.util.List;
import java.util.Set;
import java.util.stream.Collectors;
import org.janelia.colormipsearch.dao.NeuronMetadataDao;
import org.janelia.colormipsearch.dataio.CDMIPsWriter;
import org.janelia.colormipsearch.model.AbstractNe... |
3d86f78881c3969741c0263734c7eb2200f3ea4de5987bb0418f9900a9533fa5 | Java | 1,747 | 45 | package org.jeecg.modules.message.handle.impl;
import org.jeecg.common.util.SpringContextUtils;
import org.jeecg.common.util.oConvertUtils;
import org.jeecg.config.StaticConfig;
import org.jeecg.modules.message.handle.ISendMsgHandle;
import org.springframework.mail.SimpleMailMessage;
import org.springframework.mail.ja... |
b743f3a1392d39e572dc93ed8bf4d0f786cdf4920b1d56a5000409ca4e90cd3e | Java | 1,765 | 48 | package org.jeecg.modules.message.websocket;
import org.jeecg.common.api.vo.Result;
import org.jeecg.common.constant.WebsocketConst;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.web.bind.annotation.PostMapping;
import org.springframework.web.bind.annotation.RequestBody;
imp... |
c100c326bcf0e23df1b64a0b0089b3f8c3fdc3a52a470c62607bddd007541bc3 | Java | 1,770 | 62 | package org.janelia.colormipsearch.api_v2.cdsearch;
import javax.annotation.Nullable;
/**
* ColorMIPCompareOutput represents the color depth match summary result.
*/
public class ColorMIPMatchScore implements ColorDepthMatchScore {
public static ColorMIPMatchScore NO_MATCH = new ColorMIPMatchScore(0, 0, false, ... |
a0e5c7efab13e1b5afe3bb8aed5e01723ad1f66ce43b80b7afef4f4b573c4803 | Java | 1,779 | 46 | package org.jeecg.modules.ngalain.aop;
import javax.servlet.http.HttpServletRequest;
import org.aspectj.lang.ProceedingJoinPoint;
import org.aspectj.lang.annotation.Around;
import org.aspectj.lang.annotation.Aspect;
import org.aspectj.lang.annotation.Pointcut;
import org.springframework.context.annotation.Configurati... |
f17d0529605503893e4049a84cb675d26940aca2241a1644e38b6fa6c30a4549 | Java | 1,779 | 44 | package org.janelia.colormipsearch.cmd;
import java.util.Collection;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
import java.util.function.Function;
import java.util.stream.Collectors;
import com.google.common.util.concurrent.ThreadFactoryBuilder;
import org.slf4j.Logger;
impo... |
689b97619fab1343347968ca8a7a22185815efc4478a315fa7f33bc9cfb5b66d | Java | 1,790 | 69 | package org.janelia.colormipsearch.dto;
import javax.validation.constraints.NotBlank;
import org.apache.commons.lang3.builder.ToStringBuilder;
public class LMNeuronMetadata extends AbstractNeuronMetadata {
private String slideCode;
private String objective;
private String mountingProtocol;
private In... |
e0ca63bad6861841251ec5700ecd6cb56f6d81321ca2d4e20a5f552653a36aab | Java | 1,795 | 66 | package org.jeecg.modules.system.service.impl;
import java.sql.SQLException;
import java.util.Date;
import java.util.List;
import java.util.Map;
import javax.annotation.Resource;
import org.jeecg.common.system.api.ISysBaseAPI;
import org.jeecg.common.util.CommonUtils;
import org.jeecg.modules.system.entity.SysLog;
i... |
489c40639e12846bec80b1f288cae932c51b64f6192f1f1c11a18a5614afc4d8 | Java | 1,802 | 96 | package org.jeecg.modules.system.model;
import java.io.Serializable;
import java.util.Date;
import org.jeecg.modules.system.entity.SysDict;
import com.baomidou.mybatisplus.annotation.IdType;
import com.baomidou.mybatisplus.annotation.TableId;
import lombok.Data;
import lombok.EqualsAndHashCode;
import lombok.experi... |
a9482db0914c7efaa5584cccb0a3c5e2e72792a258fb132ef0a00684f6eb5595 | Java | 1,805 | 60 | package org.janelia.colormipsearch.mips;
import org.apache.commons.lang3.builder.EqualsBuilder;
import org.apache.commons.lang3.builder.HashCodeBuilder;
import org.apache.commons.lang3.builder.ToStringBuilder;
import org.janelia.colormipsearch.imageprocessing.ImageArray;
import org.janelia.colormipsearch.model.Abstrac... |
9c24ac7d3b4388ab153fd0cfcbb383527b71e393018909922e85a899ad564cc1 | Java | 1,814 | 54 | package org.janelia.colormipsearch.dataio.db;
import java.util.Collection;
import java.util.List;
import java.util.Set;
import java.util.stream.Collectors;
import org.janelia.colormipsearch.dao.NeuronMetadataDao;
import org.janelia.colormipsearch.dataio.CDMIPsWriter;
import org.janelia.colormipsearch.model.AbstractNe... |
5417dcc07a94f845df96d3df2dcda0d396da0a5126afc4fc7bf9fa82c0c2ca30 | Java | 1,829 | 54 | package org.janelia.colordepthsearch;
import java.net.URI;
import com.fasterxml.jackson.annotation.JsonProperty;
import org.junit.Before;
import org.junit.Test;
import org.mockito.ArgumentMatcher;
import software.amazon.awssdk.core.sync.RequestBody;
import software.amazon.awssdk.services.s3.S3Client;
import software... |
21a5cc03cce88fd42121dc3a34e3e191bc6754e14a231a4c6f2f83082c70f58e | Java | 1,861 | 35 | package org.janelia.colormipsearch.cmd.cdsprocess;
import java.util.List;
import java.util.stream.Collectors;
import org.janelia.colormipsearch.model.AbstractNeuronEntity;
import org.janelia.colormipsearch.model.CDMatchEntity;
import org.janelia.colormipsearch.results.ItemsHandling;
import org.janelia.colormipsearch.... |
3155c4eb2e1640f0a22fa0ec013bcc2d84530557c3a176e3fbf25f86df0ea8cd | Java | 1,865 | 58 | package org.janelia.colormipsearch.cmd.dataexport;
import java.util.List;
import java.util.Objects;
import org.apache.commons.collections4.CollectionUtils;
import org.apache.commons.lang3.builder.EqualsBuilder;
import org.apache.commons.lang3.builder.HashCodeBuilder;
import org.apache.commons.lang3.builder.ToStringBu... |
7e0a967fa932047749f8793ddda761d29a5049727392b1373e56ed84ad85716f | Java | 1,867 | 46 | package org.janelia.colormipsearch.dataio.db;
import java.util.List;
import java.util.function.Function;
import java.util.stream.Collectors;
import org.apache.commons.lang3.tuple.Pair;
import org.janelia.colormipsearch.dao.NeuronMatchesDao;
import org.janelia.colormipsearch.dao.NeuronsMatchFilter;
import org.janelia.... |
4db12a63466e841bc3e444468676e65442149b37194d94b765d44b2e96f02669 | Java | 1,868 | 80 | package org.jeecg.modules.system.model;
import java.io.Serializable;
import org.springframework.format.annotation.DateTimeFormat;
import com.baomidou.mybatisplus.annotation.IdType;
import com.baomidou.mybatisplus.annotation.TableId;
import com.baomidou.mybatisplus.annotation.TableName;
import com.fasterxml.jackson.a... |
cf10d4313d9349f2be72b1d3f111270904f38bfca01178d46b052a95e3efd647 | Java | 1,869 | 112 | package org.jeecg.modules.system.entity;
import java.util.Date;
import org.jeecg.common.aspect.annotation.Dict;
import org.springframework.format.annotation.DateTimeFormat;
import com.baomidou.mybatisplus.annotation.IdType;
import com.baomidou.mybatisplus.annotation.TableId;
import com.fasterxml.jackson.annotation.Js... |
c04017a32baaa9363154e239089481893e7c6ecdc06f9d74713228320c94878f | Java | 1,874 | 62 | package org.jeecg.modules.quartz.entity;
import java.io.Serializable;
import org.jeecg.common.aspect.annotation.Dict;
import org.jeecgframework.poi.excel.annotation.Excel;
import org.springframework.format.annotation.DateTimeFormat;
import com.baomidou.mybatisplus.annotation.IdType;
import com.baomidou.mybatisplus.a... |
a960e10ec5629065737a1cb586ac9d31bbbfd289ad76199b8c1aa18f63cff7b0 | Java | 1,879 | 71 | package org.janelia.colormipsearch.api_v2.pppsearch;
import com.fasterxml.jackson.annotation.JsonClassDescription;
import com.fasterxml.jackson.annotation.JsonInclude;
import com.fasterxml.jackson.annotation.JsonProperty;
import com.fasterxml.jackson.annotation.JsonPropertyOrder;
/**
* These are the source PPP match... |
e7617e03855db778ad2910dc6492de02913271ffa1b34d6da68f2d87c804d55e | Java | 1,891 | 55 | package org.janelia.colormipsearch.imageprocessing;
import java.io.Serializable;
/**
* Wrapper for composing multiple image transformations.
*/
public class ImageProcessing implements Serializable {
public static ImageProcessing create(ImageTransformation imageTransformation) {
return new ImageProcessi... |
4999f2e4514d6cb07d59c2f531de1526617f289bc07bff44ab324b7ba40addf6 | Java | 1,912 | 45 | package org.jeecg;
import java.net.InetAddress;
import java.net.UnknownHostException;
import org.jeecg.common.util.oConvertUtils;
import org.springframework.boot.SpringApplication;
import org.springframework.boot.autoconfigure.SpringBootApplication;
import org.springframework.boot.builder.SpringApplicationBuilder;
im... |
99ee2a7d247f1516bcd86d40b14d14858d610be3a6f1ff6bc48bfb6d5e1e940f | Java | 1,928 | 35 | package org.janelia.colormipsearch.cmd.cdsprocess;
import java.util.List;
import java.util.stream.Collectors;
import org.janelia.colormipsearch.model.AbstractNeuronEntity;
import org.janelia.colormipsearch.model.CDMatchEntity;
import org.janelia.colormipsearch.results.ItemsHandling;
import org.janelia.colormipsearch.... |
8d476ecd549868e729845c6b713905ae2ce17704532287f3372ff9e9699706ef | Java | 1,940 | 92 | package org.jeecg.modules.system.model;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.List;
import org.jeecg.modules.system.entity.SysDepart;
/**
* <p>
* 部门表 封装树结构的部门的名称的实体类
* <p>
*
* @Author Steve
* @Since 2019-01-22
*
*/
public class DepartIdModel implements Serializable {
... |
9c0d42add97f3ea962fcba6cda89ef0697ef3010b9c87ed17fe77e48b2436947 | Java | 1,949 | 52 | package org.janelia.colormipsearch.cds;
import org.junit.Test;
import static org.junit.Assert.assertEquals;
public class GradientAreaGapUtilsTest {
@Test
public void scoreCalculator() {
class TestData {
final int pix;
final long gap;
final long highExpr;
... |
cb74fc7f1379f1e022752d1eff32a1cc063b45d176793b845c20ebe695d07fa6 | Java | 1,954 | 80 | package org.janelia.colordepthsearch;
import org.apache.commons.lang3.builder.ToStringBuilder;
/**
* Search parameters for a burst parallel search.
*
* @author <a href="mailto:rokickik@janelia.hhmi.org">Konrad Rokicki</a>
*/
public class BatchSearchParameters {
private String tasksTableName;
private Stri... |
fd29821bfb549a7729c980e5fb5ca9f8517dd34070a8c7cc52269464c8cc0c41 | Java | 1,962 | 67 | package org.janelia.colormipsearch.model;
import java.util.HashMap;
import java.util.Map;
import org.janelia.colormipsearch.dto.EMNeuronMetadata;
public class EMNeuronEntity extends AbstractNeuronEntity {
// neuronType and the neuronInstance are only for reference purposes here
private String neuronType;
... |
d26796e40b470917a07f2609978172e98792ea5135d7242bdc7e119990028fe2 | Java | 1,963 | 65 | package org.jeecg.modules.system.service.impl;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import org.jeecg.common.system.vo.DictModel;
import org.jeecg.common.util.oConvertUtils;
import org.jeecg.modules.system.mapper.SysDictMapper;
import org.jeecgframework.dict.service.AutoPoiDictServi... |
584a6dfca0346b492955579eb12612914b2e64734c12cfb0d909f0bc7b4bd8db | Java | 1,973 | 46 | package org.janelia.colormipsearch.dao.mongo.support;
import com.fasterxml.jackson.databind.PropertyNamingStrategy;
import com.fasterxml.jackson.databind.cfg.MapperConfig;
import com.fasterxml.jackson.databind.introspect.AnnotatedField;
import com.fasterxml.jackson.databind.introspect.AnnotatedMethod;
public class Mo... |
666b00a66337164a63674215849b57323d3d8a6539ac19cd69402c4b9c0990f2 | Java | 1,994 | 65 | package org.janelia.colormipsearch.cds;
import org.apache.commons.lang3.builder.ToStringBuilder;
public class ShapeMatchScore implements ColorDepthMatchScore {
private final long bidirectionalAreaGap;
private final long gradientAreaGap;
private final long highExpressionArea;
private final long maxGrad... |
dd64cd952bad4b075a56e40e0684f445b54db90b9fbabe4dd054f9db2c669f4c | Java | 2,016 | 63 | package org.janelia.colormipsearch.cmd;
import org.apache.commons.lang3.StringUtils;
import org.janelia.colormipsearch.config.Config;
import org.janelia.colormipsearch.config.ConfigProvider;
import org.janelia.colormipsearch.dao.DaosProvider;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
abstract class Abs... |
9e14c6f42080d2fa24f8db98247d7ce0d5554681a41e6d4d1f7c2d2850cccb2e | Java | 2,031 | 66 | package org.jeecg.modules.system.entity;
import com.baomidou.mybatisplus.annotation.IdType;
import com.baomidou.mybatisplus.annotation.TableId;
import com.baomidou.mybatisplus.annotation.TableName;
import com.fasterxml.jackson.annotation.JsonFormat;
import lombok.Data;
import org.jeecgframework.poi.excel.annotation.Ex... |
bdd13ba13ca92c820694994ba1342287802fea5b3f64023db3698934a46a6abf | Java | 2,045 | 60 | package org.jeecg.modules.message.entity;
import org.jeecg.common.aspect.annotation.Dict;
import org.jeecg.common.system.base.entity.JeecgEntity;
import org.jeecgframework.poi.excel.annotation.Excel;
import org.springframework.format.annotation.DateTimeFormat;
import com.baomidou.mybatisplus.annotation.TableName;
imp... |
73ec53bcb121555c810b8368f58840a9ec95b2ea63cfbd248e1bb8c9dac85ffb | Java | 2,071 | 68 | package org.janelia.colormipsearch.model;
import java.util.ArrayList;
import java.util.List;
import org.janelia.colormipsearch.dto.EMNeuronMetadata;
public class EMNeuronEntity extends AbstractNeuronEntity {
// neuronType and the neuronInstance are only for reference purposes here
private String neuronType;... |
9f02004c05cc35b2e1c3fb897bbe7b4d2a38bc57ba06c0dc56d8c76e0c206e21 | Java | 2,078 | 57 | package org.jeecg.modules.system.controller;
import lombok.extern.slf4j.Slf4j;
import org.jeecg.common.api.vo.Result;
import org.jeecg.common.util.CommonUtils;
import org.jeecg.common.util.MinioUtil;
import org.jeecg.common.util.oConvertUtils;
import org.jeecg.modules.oss.entity.OSSFile;
import org.jeecg.modules.oss.s... |
b55c2a6162c52bef06d038eb30a4b07178abdb1515811a2a378e4e688daad352 | Java | 2,085 | 74 | package org.janelia.colormipsearch.cmd;
import javax.annotation.Nonnull;
import org.janelia.colormipsearch.cmd.jacsdata.CDMIPBody;
import org.janelia.colormipsearch.cmd.jacsdata.CDMIPSample;
import org.janelia.colormipsearch.cmd.jacsdata.ColorDepthMIP;
import org.janelia.colormipsearch.model.AbstractNeuronEntity;
imp... |
77c18faddfe5a98d74ad793d480c3264987169f20afa477e2ce60bf0714046f0 | Java | 2,102 | 58 | package org.janelia.colormipsearch.dao;
import java.util.Collection;
import java.util.List;
import java.util.Map;
import java.util.Set;
import org.janelia.colormipsearch.datarequests.PagedRequest;
import org.janelia.colormipsearch.datarequests.PagedResult;
import org.janelia.colormipsearch.model.AbstractNeuronEntity;... |
6e75729586af7637df2e5c7862eefd7b079d450a286be5841f41083aca9691bf | Java | 2,108 | 59 | package jaolho.data.lma;
import java.util.Arrays;
/**
* Implement this for your fit function.
*
* @author Janne Holopainen (jaolho@utu.fi, tojotamies@gmail.com)
* @version 1.2, 16.11.2006
*/
public abstract class LMAFunction {
/**
* @return The <i>y</i>-value of the function.
* @param x The <i>x</i>-value... |
a397365c2b6c2bf4d38e7ed0a3f0601f9f9684e0934217a2aa72ff2f0d9389bc | Java | 2,119 | 89 | package org.janelia.colormipsearch.dto;
import java.util.HashSet;
import java.util.Set;
import javax.validation.constraints.NotNull;
import com.fasterxml.jackson.annotation.JsonIgnore;
import com.fasterxml.jackson.annotation.JsonProperty;
import org.janelia.colormipsearch.model.PPPScreenshotType;
/**
* Metadata a... |
20015cd196eb07dbabc8b5f8e06da83bc9d26f136b8eb86f843680626a1b6bb9 | Java | 2,148 | 58 | package org.janelia.colormipsearch.cmd_v2;
import java.io.File;
import java.io.IOException;
import java.nio.file.Path;
import java.util.Collections;
import java.util.List;
import com.fasterxml.jackson.databind.DeserializationFeature;
import com.fasterxml.jackson.databind.ObjectMapper;
import org.apache.commons.lang3... |
805db6ef03cd403ce82e90c16892ca877462f599ee08ccab1006b4db438d206d | Java | 2,163 | 88 | package fiji.plugin.DOM;
import ij.IJ;
import ij.ImagePlus;
import ij.gui.Overlay;
import ij.plugin.PlugIn;
public class ShowTracks implements PlugIn{
ImagePlus imp;
SMLAnalysis sml = new SMLAnalysis();
int indX, indY, indFrame, indTrack, indTrLength;
@Override
public void run(String arg) {
imp = IJ.getI... |
a79bec228da3ac0f5b334a9c6ae90b7c5a4063c4d235b22a5f7556ea272f0564 | Java | 2,164 | 66 | package org.jeecg.modules.system.controller;
import io.swagger.annotations.Api;
import io.swagger.annotations.ApiOperation;
import lombok.extern.slf4j.Slf4j;
import org.apache.commons.lang.StringUtils;
import org.jeecg.common.api.vo.Result;
import org.jeecg.common.util.SqlInjectionUtil;
import org.jeecg.modules.system... |
408cbcc80ad40986d0c9f5cf52a055cae9553ee38e2d54f7a7de90e5f7f1e64a | Java | 2,168 | 47 | package org.janelia.colormipsearch.cds;
import java.io.Serializable;
import java.util.LinkedHashMap;
import java.util.Map;
import org.janelia.colormipsearch.imageprocessing.ImageArray;
/**
* Creates a color depth search for a given mask.
*/
public class ColorMIPSearch implements Serializable {
private final C... |
acd7f5dd1d42eddb56a12c117aa0820cb49283d0f995194d2838ce427ae93d7d | Java | 2,172 | 67 | package org.jeecg.modules.system.entity;
import java.io.Serializable;
import java.util.Date;
import com.baomidou.mybatisplus.annotation.IdType;
import com.baomidou.mybatisplus.annotation.TableId;
import com.baomidou.mybatisplus.annotation.TableName;
import com.baomidou.mybatisplus.annotation.TableField;
import io.swag... |
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