mason/tools/nirs/nirs_analysis_train_dialogs.mas

   1
   2
   3 <!--button class="btn btn-success" id="nirs_analysis_training_dialog_show">Train NIRS Model</button-->
   4
   5 <div class="modal fade" id="nirs_analysis_training_dialog" name="nirs_analysis_training_dialog" tabindex="-1" role="dialog" aria-labelledby="nirsAnalysisTrainingDialog" data-backdrop="static">
   6   <div class="modal-dialog modal-xl" role="document">
   7     <div class="modal-content">
   8       <div class="modal-header">
   9         <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">&times;</span></button>
  10         <h4 class="modal-title" id="nirsAnalysisTrainingDialog">Train Spectral Model</h4>
  11       </div>
  12       <div class="modal-body">
  13         <div class="container-fluid">
  14
  15             <&| /util/workflow.mas, id=> "nirs_analysis_training_workflow" &>
  16                 <&| /util/workflow.mas:step, title=> "Intro" &>
  17                     <& /page/page_title.mas, title=>"This workflow will guide you through the training of a model using spectra and phenotypes in the database." &>
  18                     <br/><br/>
  19                     <center>
  20                     <button class="btn btn-primary" onclick="Workflow.complete(this); return false;">Go to Next Step</button>
  21                     </center>
  22                 </&>
  23                 <&| /util/workflow.mas:step, title=> "Train Dataset" &>
  24                     <& /page/page_title.mas, title=>"Select the dataset you are interested in training (the accessions or plots or tissues samples in the dataset need to have spectra uploaded)" &>
  25                     <br/><br/>
  26                     <form class="form-horizontal">
  27                         <div class="form-group">
  28                             <label class="col-sm-1 control-label">Dataset: </label>
  29                             <div class="col-sm-11" >
  30                                 <div id="nirs_analysis_training_dataset_train_select_div"></div>
  31                             </div>
  32                         </div>
  33                     </form>
  34                     <br/><br/>
  35                     <center>
  36                     <button class="btn btn-primary" id="nirs_analysis_training_dataset_train_select_step">Go to Next Step</button>
  37                     </center>
  38                 </&>
  39                 <&| /util/workflow.mas:step, title=> "Test Dataset" &>
  40                     <& /page/page_title.mas, title=>"Select the dataset you are interested in testing (optional)" &>
  41                     <br/><br/>
  42
  43                     <div class="form-horizontal" >
  44                         <div class="form-group">
  45                             <label class="col-sm-7 control-label">Select Custom Dataset for Testing? If No, the training and test set will be partitioned from the training dataset you already selected: </label>
  46                             <div class="col-sm-5" >
  47                                 <select class="form-control" id="nirs_analysis_training_dataset_test_select_option">
  48                                     <option value="No">No</option>
  49                                     <option value="Yes">Yes</option>
  50                                 </select>
  51                             </div>
  52                         </div>
  53                     </div>
  54
  55                     <center>
  56                     <button class="btn btn-primary" id="nirs_analysis_training_dataset_test_select_step">Go to Next Step</button>
  57                     </center>
  58                     <br/><br/>
  59
  60                     <div class="form-horizontal" id="nirs_analysis_training_dataset_test_div" style="display:none">
  61                         <div class="form-group">
  62                             <label class="col-sm-1 control-label">Dataset (Optional) (the accessions or plots or tissues samples in the dataset need to have spectra uploaded): </label>
  63                             <div class="col-sm-11" >
  64                                 <div id="nirs_analysis_training_dataset_test_select_div"></div>
  65                             </div>
  66                         </div>
  67                     </div>
  68
  69                 </&>
  70                 <&| /util/workflow.mas:step, title=> "Trait" &>
  71                     <& /page/page_title.mas, title=>"Select the trait you are interested in. If there are no available options, the training and test datasets you selected do not share any traits in common!" &>
  72                     <br/><br/>
  73                     <form class="form-horizontal">
  74                         <div class="form-group">
  75                             <label class="col-sm-1 control-label">Trait: </label>
  76                             <div class="col-sm-11" >
  77                                 <div id="nirs_analysis_training_trait_select_div"></div>
  78                             </div>
  79                         </div>
  80                     </form>
  81                     <br/><br/>
  82                     <center>
  83                     <button class="btn btn-primary" id="nirs_analysis_training_trait_select_step">Go to Next Step</button>
  84                     </center>
  85                 </&>
  86                 <&| /util/workflow.mas:step, title=> "Model Settings" &>
  87                     <& /page/page_title.mas, title=>"Select parameters for spectral modeling" &>
  88
  89                     <center>
  90                     <button class="btn btn-info" id="nirs_analysis_training_dataset_info">More Info</button>
  91                     </center>
  92                     <hr>
  93
  94                     <div class="form-horizontal">
  95                         <div class="form-group">
  96                             <label class="col-sm-3 control-label">Spectrometer format: </label>
  97                             <div class="col-sm-9" >
  98
  99                                 <select class="form-control input-sm" id="nirs_analysis_training_format_select">
 100                                     <option value="">Select spectrometer format</option>
 101                                     <option selected value="SCIO">SCIO</option>
 102                                     <option value="QST">QST</option>
 103                                     <option value="Foss6500">Foss6500</option>
 104                                     <option value="Foss DS2500">Foss DS2500</option>
 105                                     <option value="Foss XDS">Foss XDS</option>
 106                                     <option value="BunchiN500">BunchiN500</option>
 107                                     <option value="LinkSquare">LinkSquare</option>
 108                                     <option value="ASD Qualityspec">ASD Qualityspec</option>
 109                                     <option value="ASD LabSpec">ASD LabSpec</option>
 110                                     <option value="Specim FX17">Specim FX17</option>
 111                                 </select>
 112                             </div>
 113                         </div>
 114                         <div class="form-group">
 115                             <label class="col-sm-3 control-label">Cross-validation methods: </label>
 116                             <div class="col-sm-9" >
 117
 118                                 <select class="form-control input-sm" id="nirs_analysis_training_cv_select">
 119                                     <option value="">Select cross-validation</option>
 120                                     <option selected value="random">Random</option>
 121                                     <option value="stratified">Stratified</option>
 122                                     <option value="CV1">CV1</option>
 123                                     <option value="CV2">CV2</option>
 124                                     <option value="CV0">CV0</option>
 125                                     <option value="CV00">CV00</option>
 126                                 </select>
 127                             </div>
 128                         </div>
 129                         <div class="form-group">
 130                             <label class="col-sm-3 control-label">Algorithm: </label>
 131                             <div class="col-sm-9" >
 132                                 <select class="form-control" id="nirs_analysis_training_nirs_model_algorithm">
 133                                     <option value="pls">PLSR</option>
 134                                     <option value="rf">Random Forest</option>
 135                                     <option value="svmLinear">SVM with Linear Kernel</option>
 136                                     <option value="svmRadial">SVM with Radial Kernel</option>
 137                                 </select>
 138                             </div>
 139                         </div>
 140                         <div class="form-group">
 141                             <label class="col-sm-3 control-label">Number of sampling iterations: </label>
 142                             <div class="col-sm-9" >
 143                                 <input class="form-control" type="number" id="nirs_analysis_training_niter_select" name="niter_select" min="1" max="100" step="1" value="10">
 144                             </div>
 145                         </div>
 146                         <div class="form-group">
 147                             <label class="col-sm-3 control-label">Tuning length: </label>
 148                             <div class="col-sm-9" >
 149                                 <input class="form-control" type="number" id="nirs_analysis_training_tuneLength_select" name="tuneLength_select" min="1" max="30" step="1" value="10">
 150                             </div>
 151                         </div>
 152                         <div class="form-group">
 153                             <label class="col-sm-3 control-label">Include preprocessing?: </label>
 154                             <div class="col-sm-9" >
 155                                 <input type="checkbox" id="nirs_analysis_training_preprocessing_select" name="preprocessing_select" >
 156                             </div>
 157                         </div>
 158                         <div class="form-group">
 159                             <label class="col-sm-3 control-label">Show random forest variable importance? (Note this may take a long time to run): </label>
 160                             <div class="col-sm-9" >
 161                                 <input type="checkbox" id="nirs_analysis_training_rf_var_imp_select" name="rf_var_imp_select" >
 162                             </div>
 163                         </div>
 164                     </div>
 165
 166                     <br/><br/>
 167                     <center>
 168                     <button class="btn btn-primary" id="nir_analysis_training_model_step">Train the Model</button>
 169                     </center>
 170                 </&>
 171                 <&| /util/workflow.mas:step, title=> "Summary" &>
 172                     <& /page/page_title.mas, title=>"Summary of the parameters selected for model creation" &>
 173
 174                     <div id="nir_analysis_training_model_performance_results"></div>
 175
 176                     <div class="form-horizontal">
 177                         <div class="form-group">
 178                             <label class="col-sm-3 control-label">Do you want to save the model for future predictions?: </label>
 179                             <div class="col-sm-9" >
 180                                 <button class="btn btn-primary" id="nir_analysis_training_model_save_step">Save the Model</button>
 181                             </div>
 182                         </div>
 183                     </div>
 184
 185                 </&>
 186             </&>
 187
 188         </div>
 189
 190       </div>
 191       <div class="modal-footer">
 192         <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>
 193       </div>
 194     </div>
 195   </div>
 196 </div>
 197
 198 <div class="modal fade" id="nirs_analysis_training_dialog_info" name="nirs_analysis_training_dialog_info" tabindex="-1" role="dialog" aria-labelledby="nirsAnalysisTrainingInfoDialog" data-backdrop="static">
 199   <div class="modal-dialog" role="document">
 200     <div class="modal-content">
 201       <div class="modal-header">
 202         <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">&times;</span></button>
 203         <h4 class="modal-title" id="nirsAnalysisTrainingInfoDialog">Train Spectral Model</h4>
 204       </div>
 205       <div class="modal-body">
 206         <div class="container-fluid">
 207
 208             <h1>More </h1>
 209             <ul>
 210               <li>"CV1": untested lines in tested environments</li>
 211               <li>"CV2": tested lines in tested environments</li>
 212               <li>"CV0": tested lines in untested environments</li>
 213               <li>"CV00": untested lines in untested environments</li>
 214             </ul>
 215         </div>
 216       </div>
 217       <div class="modal-footer">
 218         <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>
 219       </div>
 220     </div>
 221   </div>
 222 </div>
 223
 224 <script>
 225 jQuery(document).ready(function(){
 226
 227     jQuery('#nirs_analysis_training_dataset_info').click(function(){
 228         jQuery('#nirs_analysis_training_dialog_info').modal('show');
 229     });
 230
 231     jQuery('#nirs_analysis_training_dialog_show').click(function(){
 232         jQuery('#nirs_analysis_training_dialog').modal('show');
 233
 234         get_select_box('datasets','nirs_analysis_training_dataset_train_select_div', {'checkbox_name':'nirs_analysis_training_dataset_train_select_id'});
 235         get_select_box('datasets','nirs_analysis_training_dataset_test_select_div', {'checkbox_name':'nirs_analysis_training_dataset_test_select_id'});
 236     });
 237
 238     var nirs_analysis_training_dataset_train_id;
 239     jQuery('#nirs_analysis_training_dataset_train_select_step').click(function(){
 240         var selected_train = [];
 241         jQuery('input[name="nirs_analysis_training_dataset_train_select_id"]:checked').each(function() {
 242             selected_train.push(jQuery(this).val());
 243         });
 244
 245         if(selected_train.length > 1 || selected_train.length == 0) {
 246             alert('Please select one dataset!');
 247             return false;
 248         }
 249         else {
 250             nirs_analysis_training_dataset_train_id = selected_train[0];
 251             Workflow.complete("#nirs_analysis_training_dataset_train_select_step");
 252             Workflow.focus('#nirs_analysis_training_workflow', 2);
 253         }
 254     });
 255
 256     jQuery('#nirs_analysis_training_dataset_test_select_option').change(function(){
 257         var opt = jQuery(this).val();
 258         if (opt == 'Yes') {
 259             jQuery('#nirs_analysis_training_dataset_test_div').show();
 260         }
 261         else {
 262             jQuery('#nirs_analysis_training_dataset_test_div').hide();
 263         }
 264     });
 265
 266     var nirs_analysis_training_dataset_test_id;
 267     jQuery('#nirs_analysis_training_dataset_test_select_step').click(function(){
 268
 269         var selected_test = [];
 270         jQuery('input[name="nirs_analysis_training_dataset_test_select_id"]:checked').each(function() {
 271             selected_test.push(jQuery(this).val());
 272         });
 273
 274         if(selected_test.length > 1) {
 275             alert('Please select one dataset!');
 276             return false;
 277         }
 278         else {
 279             nirs_analysis_training_dataset_test_id = selected_test[0];
 280
 281             get_select_box('datasets_intersect', 'nirs_analysis_training_trait_select_div', {'name':'nirs_analysis_training_trait_select_id', 'id':'nirs_analysis_training_trait_select_id', 'param':'traits', 'dataset_ids':JSON.stringify([nirs_analysis_training_dataset_train_id,nirs_analysis_training_dataset_test_id]) });
 282
 283             Workflow.complete("#nirs_analysis_training_dataset_test_select_step");
 284             Workflow.focus('#nirs_analysis_training_workflow', 3);
 285         }
 286     });
 287
 288     var nirs_analysis_training_trait_id;
 289     jQuery('#nirs_analysis_training_trait_select_step').click(function(){
 290         nirs_analysis_training_trait_id = jQuery('#nirs_analysis_training_trait_select_id').val();
 291         console.log(nirs_analysis_training_trait_id);
 292
 293         Workflow.complete("#nirs_analysis_training_trait_select_step");
 294         Workflow.focus('#nirs_analysis_training_workflow', 4);
 295     });
 296
 297     var nirs_analysis_training_format_select;
 298     var nirs_analysis_training_cv_select;
 299     var nirs_analysis_training_nirs_model_algorithm;
 300     var nirs_analysis_training_tuneLength_select;
 301     var nirs_analysis_training_preprocessing_select;
 302     var nirs_analysis_training_niter_select;
 303     var nirs_analysis_training_rf_var_imp_select;
 304     var nirs_analysis_training_response;
 305
 306     jQuery('#nir_analysis_training_model_step').click(function(){
 307         nirs_analysis_training_format_select = jQuery('#nirs_analysis_training_format_select').val();
 308         nirs_analysis_training_cv_select = jQuery('#nirs_analysis_training_cv_select').val();
 309         nirs_analysis_training_nirs_model_algorithm = jQuery('#nirs_analysis_training_nirs_model_algorithm').val();
 310         nirs_analysis_training_tuneLength_select = jQuery('#nirs_analysis_training_tuneLength_select').val();
 311         nirs_analysis_training_preprocessing_select = 0;
 312         if (jQuery('#nirs_analysis_training_preprocessing_select').is(":checked")) {
 313             nirs_analysis_training_preprocessing_select = 1;
 314         }
 315         nirs_analysis_training_niter_select = jQuery('#nirs_analysis_training_niter_select').val();
 316         nirs_analysis_training_rf_var_imp_select = 0;
 317         if (jQuery('#nirs_analysis_training_rf_var_imp_select').is(":checked")) {
 318             nirs_analysis_training_rf_var_imp_select = 1;
 319         }
 320
 321         jQuery.ajax({
 322             url : '/ajax/Nirs/generate_results',
 323             type : 'POST',
 324             data : {
 325                 'train_dataset_id' : nirs_analysis_training_dataset_train_id,
 326                 'test_dataset_id' : nirs_analysis_training_dataset_test_id,
 327                 'trait_id' : nirs_analysis_training_trait_id,
 328                 'format' : nirs_analysis_training_format_select,
 329                 'cv' : nirs_analysis_training_cv_select,
 330                 'algorithm' : nirs_analysis_training_nirs_model_algorithm,
 331                 'niter' : nirs_analysis_training_niter_select,
 332                 'tune' : nirs_analysis_training_tuneLength_select,
 333                 'preprocessing' : nirs_analysis_training_preprocessing_select,
 334                 'rf' : nirs_analysis_training_rf_var_imp_select
 335             },
 336             beforeSend: function(){
 337                 jQuery('#working_modal').modal('show');
 338             },
 339             success: function(response){
 340                 console.log(response);
 341                 if (response.error) {
 342                     alert(response.error);
 343                 }
 344                 nirs_analysis_training_response = response;
 345
 346                 jQuery('#working_modal').modal('hide');
 347
 348                 jQuery('#nir_analysis_training_model_performance_results').html("<div class='well'>"+response.performance_output+"</div>");
 349
 350                 Workflow.complete("#nir_analysis_training_model_step");
 351                 Workflow.focus('#nirs_analysis_training_workflow', 5);
 352             },
 353             error: function(response){
 354                 alert('Error training NIRS!');
 355                 jQuery('#working_modal').modal('hide');
 356             }
 357         });
 358     });
 359
 360
 361     jQuery('#nir_analysis_training_model_save_step').click(function(){
 362         jQuery('#generic_save_analysis_analysis_to_save').prop('disabled', 'disabled');
 363         jQuery('#generic_save_analysis_model_language').val('R');
 364         jQuery('#generic_save_analysis_model_type').val('waves_nirs_spectral_predictions');
 365         jQuery('#generic_save_analysis_model_properties').val(JSON.stringify(nirs_analysis_training_response.model_properties));
 366         jQuery('#generic_save_analysis_model_application_name').val("Jenna's Waves R Package NIRs Analysis");
 367         jQuery('#generic_save_analysis_model_application_version').val("V1.01");
 368         jQuery('#generic_save_analysis_model_file').val(nirs_analysis_training_response.model_file);
 369         jQuery('#generic_save_analysis_model_archived_model_file_type').val(nirs_analysis_training_response.model_file_type);
 370         jQuery('#generic_save_analysis_model_training_data_file').val(nirs_analysis_training_response.training_data_file);
 371         jQuery('#generic_save_analysis_model_archived_training_data_file_type').val(nirs_analysis_training_response.training_data_file_type);
 372         jQuery('#generic_save_analysis_model_auxiliary_files').val(JSON.stringify(nirs_analysis_training_response.model_aux_files));
 373         jQuery('#generic_save_analysis_dataset_id').val(nirs_analysis_training_dataset_train_id);
 374
 375         jQuery('#generic_save_analysis_dialog').modal('show');
 376     });
 377
 378 });
 379 </script>