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bug 处理

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This commit is contained in:
13405411873 2025-01-12 15:50:20 +08:00
parent 0ee8fb05b8
commit f1fe30920f
11 changed files with 153 additions and 69 deletions
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4
asd-wx/common/utils/config.js
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@ -2,8 +2,8 @@
// const baseUrl = "https://www.jieyi-autism.com/asdProject"
//const baseUrl = "https://www.jieyi-autism.com/asdProject"
//const baseUrl = "http://192.168.31.25:8082/asdProject"
const baseUrl = "https://www.jieyi-autism.com/asdProject"
//const baseUrl = "http://192.168.31.25:8082/asdProject"
// const baseUrl = "https://www.jieyi-autism.com/asdProject"
const baseUrl = "http://127.0.0.1:8082/asdProject"
// const baseUrl = "https://localhost/asdProject"
// const baseUrl = "https://43.140.199.34/jeecg-boot"
// const baseUrl = "http://43.140.199.34:8080/jeecg-boot"

4
asd-wx/util/config.js
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@ -1,7 +1,7 @@
// const baseUrl = "http://localhost:8080/asdProject"
const baseUrl = "https://www.jieyi-autism.com/asdProject"
//const baseUrl = "http://192.168.31.25:8082/asdProject"
//const baseUrl = "https://www.jieyi-autism.com/asdProject"
const baseUrl = "http://127.0.0.1:8082/asdProject"
export {
baseUrl
}

5
ruoyi-admin/src/main/java/com/ruoyi/script/entity/PatientScript.java
View File

@ -34,10 +34,9 @@ public class PatientScript extends BaseEntity {
private String scanPosition;
//扫描医生
private String scanDoctor;
//结构像地址
private String structureImage;
//功能像地址
private String featureImage;
private String filePath;
//TR
private String repetitionTime;
//扫描顺序

33
ruoyi-admin/src/main/java/com/ruoyi/script/service/impl/PatientScriptServiceImpl.java
View File

@ -63,29 +63,20 @@ public class PatientScriptServiceImpl implements PatientScriptService {
@SneakyThrows
@Override
public void run() {
if (!patientScript.getType().equals("dti")){
//准备动态yml
if (!patientScript.getType().equals("mri")){
String unique_id = generateOtp();
String playground = "playground"+patientScript.getPatientName()+unique_id;
String format = DateUtil.format(new Date(), "yyyy-MM-dd");
Map<String, Object> yamlMap = new LinkedHashMap<>();
yamlMap.put("uniqueId", "'"+unique_id+"'");
yamlMap.put("anatPath", patientScript.getStructureImage());
yamlMap.put("scanPath", patientScript.getFeatureImage());
//扫描顺序
yamlMap.put("scanningOrder", patientScript.getScanningOrder());
yamlMap.put("sliceNumber", patientScript.getSliceNumber());
yamlMap.put("repetitionTime", patientScript.getRepetitionTime());
String dataYmlPath ="/data/"+format+"/config/datainfo"+"-"+unique_id+".yml";
Boolean flag = createFile(yamlMap, dataYmlPath,"yml.ftl");
if (flag){
Map<String, Object> shMap = new LinkedHashMap<>();
shMap.put("outPath",format+"/output-"+unique_id);
shMap.put("dataInfoPath",dataYmlPath);
shMap.put("filePath", patientScript.getFilePath());
shMap.put("subId",unique_id);
shMap.put("fmriFileMb",format+"/output-"+unique_id+"/output/pipeline_cpac-default-pipeline/sub/ses-"+unique_id+"/func/sub-sub_ses-"+unique_id+"_task-scan_desc-mean_bold.nii.gz");
shMap.put("fmriFileMb",format+"/"+playground+"/preprocessed/sub001/func/sub-001_task-rest_space-MNI152NLin2009cAsym_boldref.nii");
shMap.put("fmriRegOutFile",format+"/output-"+unique_id+"/bold_2_struct.mat");
shMap.put("fmriFileDpp",format+"/output-"+unique_id+"/output/pipeline_cpac-default-pipeline/sub/ses-"+unique_id+"/func/sub-sub_ses-"+unique_id+"_task-scan_reg-default_desc-preproc_bold.nii.gz");
shMap.put("fmriFileDpp",format+"/"+playground+"/preprocessed/sub001/func/sub-001_task-rest_space-MNI152NLin2009cAsym_desc-preproc_bold.nii");
shMap.put("fmriR2t1OutFile",format+"/output-"+unique_id+"/reg2_Template.nii.gz");
shMap.put("smriFileMb",format+"/"+playground+"/preprocessed/sub001/anat/sub-001_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz");
shMap.put("smriOutFile",format+"/output-"+unique_id+"/anat2_Template.nii");
String fmriOutPath = "/data/"+format+"/output-"+unique_id+"/fmriOut/";
shMap.put("fmriOutPath",fmriOutPath);
shMap.put("matrixPath","/data/"+format+"/output-"+unique_id+"/");
@ -95,9 +86,6 @@ public class PatientScriptServiceImpl implements PatientScriptService {
String alignPath="/data/"+format+"/align"+"-"+unique_id+".py";
shMap.put("alignPath",alignPath);
shMap.put("fucDataPath",format+"/output-"+unique_id+"/reg2_Template.nii.gz");
shMap.put("anatPath",patientScript.getStructureImage());
shMap.put("smriFileMb",format+"/output-"+unique_id+"/output/pipeline_cpac-default-pipeline/sub/ses-"+unique_id+"/anat/sub-sub_ses-"+unique_id+"_desc-preproc_T1w.nii.gz");
shMap.put("smriOutFile",format+"/output-"+unique_id+"/anat2_Template.nii");
//创建alignPy
createFile(shMap, alignPath,"alignTemplate.ftl");
//创建总脚本
@ -131,8 +119,6 @@ public class PatientScriptServiceImpl implements PatientScriptService {
}
}
}
});
@ -156,8 +142,7 @@ public class PatientScriptServiceImpl implements PatientScriptService {
String format = DateUtil.format(new Date(), "yyyy-MM-dd");
Map<String, Object> yamlMap = new LinkedHashMap<>();
yamlMap.put("uniqueId", "'"+unique_id+"'");
yamlMap.put("anatPath", patientScript.getStructureImage());
yamlMap.put("scanPath", patientScript.getFeatureImage());
//扫描顺序
yamlMap.put("scanningOrder", patientScript.getScanningOrder());
yamlMap.put("sliceNumber", patientScript.getSliceNumber());
@ -182,7 +167,7 @@ public class PatientScriptServiceImpl implements PatientScriptService {
String alignPath="/data/"+format+"/align"+"-"+unique_id+".py";
shMap.put("alignPath",alignPath);
shMap.put("fucDataPath",format+"/output-"+unique_id+"/reg2_Template.nii.gz");
shMap.put("anatPath",patientScript.getStructureImage());
shMap.put("smriFileMb",format+"/output-"+unique_id+"/output/pipeline_cpac-default-pipeline/sub/ses-"+unique_id+"/anat/sub-sub_ses-"+unique_id+"_desc-preproc_T1w.nii.gz");
shMap.put("smriOutFile",format+"/output-"+unique_id+"/anat2_Template.nii");
//创建alignPy

2
ruoyi-admin/src/main/resources/application-druid.yml
View File

@ -6,7 +6,7 @@ spring:
druid:
# 主库数据源
master:
url: jdbc:mysql://127.0.0.1:3306/asd-project?useUnicode=true&characterEncoding=utf8&zeroDateTimeBehavior=convertToNull&useSSL=true&serverTimezone=GMT%2B8
url: jdbc:mysql://81.70.190.166:3306/asd-project?useUnicode=true&characterEncoding=utf8&zeroDateTimeBehavior=convertToNull&useSSL=true&serverTimezone=GMT%2B8
# username: root
# password: qqzcy@1014
# url: jdbc:mysql://81.70.190.166:3306/asd-project?useUnicode=true&characterEncoding=utf8&zeroDateTimeBehavior=convertToNull&useSSL=true&serverTimezone=GMT%2B8

10
ruoyi-admin/src/main/resources/mapper/system/PatientScriptMapper.xml
View File

@ -13,9 +13,7 @@ PUBLIC "-//mybatis.org//DTD Mapper 3.0//EN"
<result property="scanTime" column="scan_time" />
<result property="scanPosition" column="scan_position" />
<result property="scanDoctor" column="scan_doctor" />
<result property="structureImage" column="structure_image" />
<result property="featureImage" column="feature_image" />
<result property="filePath" column="filePath" />
<result property="repetitionTime" column="repetition_time" />
<result property="scanningOrder" column="scanning_order" />
<result property="sliceNumber" column="slice_number" />
@ -79,8 +77,7 @@ PUBLIC "-//mybatis.org//DTD Mapper 3.0//EN"
<if test="scanTime != null">scan_time,</if>
<if test="scanPosition != null">scan_position,</if>
<if test="scanDoctor != null">scan_doctor,</if>
<if test="structureImage != null">structure_image,</if>
<if test="featureImage != null">feature_image,</if>
<if test="filePath != null">file_path,</if>
<if test="repetitionTime != null">repetition_time,</if>
<if test="scanningOrder != null">scanning_order,</if>
<if test="blOrder != null">bl_order,</if>
@ -108,8 +105,7 @@ PUBLIC "-//mybatis.org//DTD Mapper 3.0//EN"
<if test="scanTime != null">#{scanTime},</if>
<if test="scanPosition != null">#{scanPosition},</if>
<if test="scanDoctor != null">#{scanDoctor},</if>
<if test="structureImage != null">#{structureImage},</if>
<if test="featureImage != null">#{featureImage},</if>
<if test="filePath != null">#{filePath},</if>
<if test="repetitionTime != null">#{repetitionTime},</if>
<if test="scanningOrder != null">#{scanningOrder},</if>
<if test="blOrder != null">#{blOrder},</if>

24
ruoyi-admin/src/main/resources/static/cpacSh.ftl
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@ -2,18 +2,32 @@
echo "Hello, output-43207!"
cd /data
source ~/.bashrc
mkdir ${playground}
echo "复制源文件到指定个体下"
cp ${filePath} ${playground}/file.zip
echo "解压源文件"
cd ${playground}
unzip file.zip
cd /data
echo "执行源文件处理脚本"
python dealTest.py --base_dir ${playground} --output_dir ${playground}/BIDS_output
echo "通过源文件进行二次处理"
fmriprep-docker ${playground}/BIDS_output/sub-001 ${playground}/preprocessed/ participant --participant-label 001 --fs-license-file /data/license.txt --fs-no-reconall
echo "激活py环境"
export PYTHONPATH=/usr/local/python3/lib/python3.8/site-packages:$PYTHONPATH
cpac run /data/ABIDEII-EMC_1 ${outPath} participant --pipeline_file /data/config/default.yml --data_config_file ${dataInfoPath} --mem_gb 10 --platform docker
echo "cpac handle end!"
conda activate myenv
export PYTHONPATH=/root/anaconda3/envs/myenv/lib/python3.7/site-packages:$PYTHONPATH
python ${alignPath}
python /data/test2.py --sub_id ${subId} --TR ${tr} --root_dir ${fucDataPath} --out_dir ${fmriOutPath} --anat_dir ${anatPath}
python /data/test2.py --sub_id ${subId} --TR ${tr} --root_dir ${fmriR2t1OutFile} --out_dir ${fmriOutPath} --anat_dir ${smriOutFile}
echo "fmri handle end!"

4
ruoyi-ui/.env.development
View File

@ -5,8 +5,8 @@ VUE_APP_TITLE = 北京北山医疗科技有限公司
ENV = 'development'
# 孑医测评管理系统/开发环境
#VUE_APP_BASE_API = 'https://www.jieyi-autism.com/asdProject'
VUE_APP_BASE_API = 'http://127.0.0.1:8082/asdProject'
VUE_APP_BASE_API = 'https://www.jieyi-autism.com/asdProject'
#VUE_APP_BASE_API = 'http://127.0.0.1:8082/asdProject'
# 路由懒加载
VUE_CLI_BABEL_TRANSPILE_MODULES = true

3
ruoyi-ui/.env.production
View File

@ -6,4 +6,5 @@ VUE_APP_TITLE = 北京北山医疗科技有限公司
ENV = 'production'
# ASD小程序管理系统/生产环境
VUE_APP_BASE_API = 'https://www.jieyi-autism.com/asdProject'
#VUE_APP_BASE_API = 'https://www.jieyi-autism.com/asdProject'
VUE_APP_BASE_API = 'http://192.168.1.71:8082/asdProject'

2
ruoyi-ui/src/components/BrainUpload/index.vue
View File

@ -50,7 +50,7 @@
// 文件类型, 例如['png', 'jpg', 'jpeg']
fileType: {
type: Array,
default: () => ["gz"],
default: () => ["zip"],
},
// 是否显示提示
isShowTip: {

131
ruoyi-ui/src/views/system/shMenu/index.vue
View File

@ -115,35 +115,32 @@
<el-input v-model="form.scanDoctor" placeholder="扫描医生" />
</el-form-item>
<el-form-item label="诊断医师" prop="zdDoctor">
<el-input v-model="form.zdDoctor" placeholder="扫描医生" />
<el-input v-model="form.zdDoctor" placeholder="诊断医师" />
</el-form-item>
<el-form-item label="审核医生" prop="shDoctor">
<el-input v-model="form.shDoctor" placeholder="扫描医生" />
<el-input v-model="form.shDoctor" placeholder="审核医生" />
</el-form-item>
<el-form-item label="TR" prop="repetitionTime">
<el-input v-model="form.repetitionTime" placeholder="TR" />
</el-form-item>
<el-form-item label="扫描顺序" prop="scanningOrder">
<el-select v-model="form.scanningOrder" placeholder="请选择扫描顺序">
<el-option
v-for="item in options"
:key="item.value"
:label="item.label"
:value="item.value">
</el-option>
</el-select>
</el-form-item>
<el-form-item label="参考切片层数" prop="sliceNumber">
<el-input-number v-model="form.sliceNumber" placeholder="参考切片层数" />
</el-form-item>
<el-form-item label="结构像" prop="structureImage">
<brain-upload :limit="1" v-model="form.structureImage" />
<!-- <el-form-item label="扫描顺序" prop="scanningOrder">-->
<!-- <el-select v-model="form.scanningOrder" placeholder="请选择扫描顺序">-->
<!-- <el-option-->
<!-- v-for="item in options"-->
<!-- :key="item.value"-->
<!-- :label="item.label"-->
<!-- :value="item.value">-->
<!-- </el-option>-->
<!-- </el-select>-->
<!-- </el-form-item>-->
<!-- <el-form-item label="参考切片层数" prop="sliceNumber">-->
<!-- <el-input-number v-model="form.sliceNumber" placeholder="参考切片层数" />-->
<!-- </el-form-item>-->
<el-form-item label="扫描文件" prop="filePath">
<brain-upload :limit="1" v-model="form.filePath" />
</el-form-item>
<el-form-item label="功能像" prop="featureImage">
<brain-upload :limit="1" v-model="form.featureImage" />
</el-form-item>
</el-form>
@ -228,7 +225,99 @@
scanTime: ''
},
// 表单校验
rules: {},
rules: {
patientName: [
{
required: true,
message: "患者姓名不能为空",
trigger: "blur",
},
],
patientAge: [
{
required: true,
message: "患者年龄不能为空",
trigger: "blur",
},
],
patientCard: [
{
required: true,
message: "证件信息号不能为空",
trigger: "blur",
},
],
scanTime: [
{
required: true,
message: "扫描时间不能为空",
trigger: "blur",
},
],
blOrder: [
{
required: true,
message: "病历号不能为空",
trigger: "blur",
},
],
scanPosition: [
{
required: true,
message: "扫描地点不能为空",
trigger: "blur",
},
],
scanDoctor: [
{
required: true,
message: "扫描医生不能为空",
trigger: "blur",
},
],
zdDoctor: [
{
required: true,
message: "诊断医师不能为空",
trigger: "blur",
},
],
shDoctor: [
{
required: true,
message: "审核医生不能为空",
trigger: "blur",
},
],
repetitionTime: [
{
required: true,
message: "TR不能为空",
trigger: "blur",
},
],
scanningOrder: [
{
required: true,
message: "扫描顺序不能为空",
trigger: "blur",
},
],
sliceNumber: [
{
required: true,
message: "参考切片层数不能为空",
trigger: "blur",
},
],
filePath: [
{
required: true,
message: "扫描文件不能为空",
trigger: "blur",
},
],
},
jsonOpen: false,
jsonData: {},
jsonType: ''