mason/breeders_toolbox/drone_imagery/drone_imagery_analytics.mas

   1 <%args>
   2 </%args>
   3
   4 <div class="modal fade" id="drone_imagery_analytics_dialog" name="drone_imagery_analytics_dialog" tabindex="-1" role="dialog" aria-labelledby="droneImageryAnalyticsDialog" data-backdrop="static">
   5   <div class="modal-dialog modal-xl" role="document">
   6     <div class="modal-content">
   7       <div class="modal-header">
   8         <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">&times;</span></button>
   9         <h4 class="modal-title" id="droneImageryAnalyticsDialog">Perform analytics on aerial image phenotypes</h4>
  10       </div>
  11       <div class="modal-body">
  12         <div class="container-fluid">
  13
  14             <&| /util/workflow.mas, id=> "drone_imagery_analytics_workflow" &>
  15                 <&| /util/workflow.mas:step, title=> "Field Trial" &>
  16                     <& /page/page_title.mas, title=>"Select the field trial you are interested in. Select only one. Field trial MUST have row and column assigned and should be a rectangular design." &>
  17                     <br/><br/>
  18                     <form class="form-horizontal">
  19                         <div class="form-group">
  20                             <label class="col-sm-3 control-label">Field Trial(s): </label>
  21                             <div class="col-sm-9" >
  22                                 <div id="drone_imagery_analytics_trial_select_div"></div>
  23                             </div>
  24                         </div>
  25                     </form>
  26                     <center>
  27                     <button class="btn btn-primary" id="drone_imagery_analytics_field_trial_select_step">Go to Next Step</button>
  28                     </center>
  29                 </&>
  30                 <&| /util/workflow.mas:step, title=> "Analytics Reporting" &>
  31                     <& /page/page_title.mas, title=>"Select an Analytics Protocol to save the results to or create a new one" &>
  32
  33                     <div id="drone_imagery_analytics_analytics_protocols_select_div">Loading...</div>
  34
  35                     <& /page/page_title.mas, title=>"Select the type of analysis to run" &>
  36
  37                     <div class="well well-sm">
  38                         <select class="form-control" id="drone_imagery_analytics_select_input">
  39                             <!--option value="">Sommer Multi/Uni Spatial 2Dspl, REMLf90 RR Identiy/Env, ASREML Uni Spatial AR1xAR1</option-->
  40                             <!--option value="lmer_germplasmname_replicate">LMER BLUPs y~replicate+1|Germplasm. Univariate genetic effects</option-->
  41
  42                             <!--option value="sommer_grm_genetic_blups">Sommer GBLUPs Y~replicate+GRM. Multivariate genetic effects using GRM</option-->
  43
  44                             <option value="sommer_grm_spatial_genetic_blups">Sommer Spatial GBLUPs Y~replicate+GRM+Row+Col+2Dspline. Multivariate genetic + 2Dspl spatial effects</option>
  45                             <option value="sommer_grm_spatial_pure_2dspl_genetic_blups">Sommer Spatial GBLUPs Y~replicate+GRM+2Dspline. Multivariate genetic + 2Dspl spatial effects</option>
  46                             <option value="sommer_grm_univariate_spatial_genetic_blups">Sommer Spatial GBLUPs Y~replicate+GRM+Row+Col+2Dspline. Univariate genetic + 2Dspl spatial effects</option>
  47                             <option value="sommer_grm_univariate_spatial_pure_2dspl_genetic_blups">Sommer Spatial GBLUPs Y~replicate+GRM+2Dspline. Univariate genetic + 2Dspl spatial effects</option>
  48
  49                             <!--option value="blupf90_grm_random_regression_dap_blups">BLUPf90 GBLUPs Y~replicate+GRM+temporal random regression using days after planting. Multivariate genetic + permanent environment effects</option>
  50                             <option value="blupf90_grm_random_regression_gdd_blups">BLUPf90 GBLUPs Y~replicate+GRM+temporal random regression using growing degree days. Multivariate genetic + permanent environment effects</option-->
  51
  52                             <option value="airemlf90_grm_random_regression_dap_blups">AIREMLf90 GBLUPs Y~replicate+GRM+temporal random regression using days after planting. Multivariate genetic + permanent environment effects</option>
  53
  54                             <option value="asreml_grm_univariate_spatial_genetic_blups">ASREML Spatial GBLUPs Y~replicate+GRM+Row+Col+spatial. Univariate genetic + AR1xAR1 spatial effects</option>
  55                             <option value="asreml_grm_univariate_pure_spatial_genetic_blups">ASREML Spatial GBLUPs Y~replicate+GRM+spatial. Univariate genetic + AR1xAR1 spatial effects</option>
  56                             <option value="asreml_grm_multivariate_spatial_genetic_blups">ASREML Spatial GBLUPs Y~replicate+GRM+spatial. Multivariate genetic + AR1xAR1 spatial effects</option>
  57
  58                             <!--option value="airemlf90_grm_random_regression_gdd_blups">AIREMLf90 GBLUPs Y~replicate+GRM+temporal random regression using growing degree days. Multivariate genetic + permanent environment effects</option-->
  59
  60                             <!--option value="sommer_grm_temporal_random_regression_dap_genetic_blups">Sommer Temporal Random Regression GBLUPs Y~replicate+GRM+LegendrePoly. Multivariate genetic + permanent environment effects using days after planting</option>
  61                             <option value="sommer_grm_temporal_random_regression_gdd_genetic_blups">Sommer Temporal Random Regression GBLUPs Y~replicate+GRM+LegendrePoly. Multivariate genetic + permanent environment effects using growing degree days</option>
  62                             <option value="sommer_grm_genetic_only_random_regression_dap_genetic_blups">Sommer Random Regression GBLUPs Y~replicate+GRM+LegendrePoly. Multivariate genetic effects using days after planting</option>
  63                             <option value="sommer_grm_genetic_only_random_regression_gdd_genetic_blups">Sommer Random Regression GBLUPs Y~replicate+GRM+LegendrePoly. Multivariate genetic effects using growing degree days</option-->
  64
  65                         </select>
  66
  67                         <br/><br/>
  68                         <div class="form-horizontal">
  69                             <div class="form-group">
  70                                 <label class="col-sm-5 control-label">Simulated Environments (Linear, 1D-Normal, 2D-Normal, Random, AR1xAR1): </label>
  71                                 <div class="col-sm-7" >
  72                                     <select class="form-control" id="drone_imagery_analytics_select_sim_env_change_over_time_type">
  73                                         <option value="">Constant over timepoints</option>
  74                                         <option value="changing_gradual">Gradual change over timepoints</option>
  75                                     </select>
  76                                 </div>
  77                             </div>
  78                             <div class="form-group">
  79                                 <label class="col-sm-5 control-label">Perform Cross Validation (Can take a long time): </label>
  80                                 <div class="col-sm-7" >
  81                                     <select class="form-control" id="drone_imagery_analytics_select_perform_cv">
  82                                         <option value="0">No</option>
  83                                         <option value="1">Yes</option>
  84                                     </select>
  85                                 </div>
  86                             </div>
  87                         </div>
  88                     </div>
  89
  90                     <hr>
  91                     <center>
  92                         <button class="btn btn-default" id="drone_imagery_analytics_analytics_project_new_button">Create a New Analytics Protocol</button>
  93                     </center>
  94
  95                     <div id="drone_imagery_analytics_analytics_project_new_div" style="display:none">
  96                         <br/><br/>
  97                         <div class="well well-sm">
  98                             <div class="form-horizontal">
  99                                 <div class="form-group">
 100                                     <label class="col-sm-3 control-label">Analytics Name: </label>
 101                                     <div class="col-sm-9" >
 102                                         <input type="text" class="form-control" id="drone_imagery_analytics_select_analytics_name" />
 103                                     </div>
 104                                 </div>
 105                                 <div class="form-group">
 106                                     <label class="col-sm-3 control-label">Analytics Type: </label>
 107                                     <div class="col-sm-9" >
 108                                         <select class="form-control" id="drone_imagery_analytics_select_analytics_type">
 109                                             <option value="minimize_local_env_effect">Minimize Spatial or PE Effects</option>
 110                                             <!--option value="minimize_genetic_effect">Minimize Genetic Effects</option-->
 111                                         </select>
 112                                     </div>
 113                                 </div>
 114                                 <div class="form-group">
 115                                     <label class="col-sm-3 control-label">Analytics Description: </label>
 116                                     <div class="col-sm-9" >
 117                                         <input type="text" class="form-control" id="drone_imagery_analytics_select_analytics_desc" />
 118                                     </div>
 119                                 </div>
 120                                 <div class="form-group">
 121                                     <label class="col-sm-3 control-label">Number Interations: </label>
 122                                     <div class="col-sm-9" >
 123                                         <select class="form-control" id="drone_imagery_analytics_number_iterations">
 124                                             <option value="10">10</option>
 125                                             <option value="2">2</option>
 126                                             <option value="25">25</option>
 127                                             <option value="1">1</option>
 128                                         </select>
 129                                     </div>
 130                                 </div>
 131                                 <div class="form-group">
 132                                     <label class="col-sm-3 control-label">Env Variance: </label>
 133                                     <div class="col-sm-9" >
 134                                         <select class="form-control" id="drone_imagery_analytics_env_variance">
 135                                             <option value="0.2">0.2</option>
 136                                             <option value="0.1">0.1</option>
 137                                             <option value="0.05">0.05</option>
 138                                             <option value="0.01">0.01</option>
 139                                             <option value="0.3">0.3</option>
 140                                             <option value="0.2,0.1,0.05,0.01,0.3">0.2,0.1,0.05,0.01,0.3</option>
 141                                         </select>
 142                                     </div>
 143                                 </div>
 144                                 <div class="form-group">
 145                                     <label class="col-sm-3 control-label">Simulated Environment Correlation Through Time: </label>
 146                                     <div class="col-sm-9" >
 147                                         <select class="form-control" id="drone_imagery_analytics_sim_env_change_over_time_correlation">
 148                                             <option value="0.9">0.9</option>
 149                                             <option value="0.75">0.75</option>
 150                                             <option value="0.6">0.6</option>
 151                                         </select>
 152                                     </div>
 153                                 </div>
 154                             </div>
 155                         </div>
 156
 157                         <& /page/page_title.mas, title=>"Select the observation variable(s) you are interested in" &>
 158
 159                         <div class="well well-sm">
 160                             <div class="form-horizontal">
 161                                 <div class="form-group">
 162                                     <label class="col-sm-3 control-label">Observation Variable Type: </label>
 163                                     <div class="col-sm-9" >
 164                                         <select class="form-control" id="drone_imagery_analytics_select_observation_variable_type">
 165                                             <option value="time_ontology">Time Series</option>
 166                                             <option value="">Single Trait</option>
 167                                         </select>
 168                                     </div>
 169                                 </div>
 170                                 <div class="form-group">
 171                                     <label class="col-sm-3 control-label">Observation Variables Phenotyped in the Selected Field Trial: </label>
 172                                     <div class="col-sm-9" >
 173                                         <div id="drone_imagery_analytics_trait_select_div">Loading...</div>
 174                                     </div>
 175                                 </div>
 176                             </div>
 177                         </div>
 178
 179                         <& /page/page_title.mas, title=>"Statistics Parameters" &>
 180
 181                         <div class="well well-sm">
 182                             <div class="form-horizontal">
 183                                 <div class="form-group">
 184                                     <label class="col-sm-3 control-label">Relationship Matrix Type: </label>
 185                                     <div class="col-sm-9" >
 186                                         <select class="form-control" id="drone_imagery_analytics_relationship_matrix_type_select_div">
 187                                             <option value="">Identity</option>
 188                                             <option value="genotypes">Genotyping Data</option>
 189                                             <option value="htp_phenotypes">High-throughput Phenotyping Data</option>
 190                                         </select>
 191                                     </div>
 192                                 </div>
 193                             </div>
 194
 195                             <div id="drone_imagery_analytics_genotyping_protocol_div" class="well well-sm" style="display:none">
 196                                 <div class="form-horizontal">
 197                                     <div class="form-group">
 198                                         <label class="col-sm-3 control-label">Genotyping Protocol To Calculate Genomic Relationship Matrix (optional. If none selected, an identity matrix is used): </label>
 199                                         <div class="col-sm-9" >
 200                                             <div id="drone_imagery_analytics_genotyping_protocol_select_div"></div>
 201                                         </div>
 202                                     </div>
 203                                     <div class="form-group">
 204                                         <label class="col-sm-3 control-label">Compute Genotypes From Parents: </label>
 205                                         <div class="col-sm-9" >
 206                                             <select class="form-control" id="drone_image_analytics_genotyping_protocol_compute_from_parents_select">
 207                                                 <option value="no">No</option>
 208                                                 <option value="yes">Yes</option>
 209                                             </select>
 210                                         </div>
 211                                     </div>
 212                                     <div class="form-group" id="drone_image_analytics_genotyping_protocol_use_parental_grms_select_div" style="display:none">
 213                                         <label class="col-sm-3 control-label">Use Parental Relationship Matrices: </label>
 214                                         <div class="col-sm-9" >
 215                                             <select class="form-control" id="drone_image_analytics_genotyping_protocol_use_parental_grms_select">
 216                                                 <option value="no">No</option>
 217                                                 <option value="yes">Yes</option>
 218                                             </select>
 219                                         </div>
 220                                     </div>
 221                                     <div class="form-group" id="drone_image_analytics_genotyping_protocol_include_pedigree_select_div" style="display:none">
 222                                         <label class="col-sm-3 control-label">Include Pedigree Info Into Relationship Matrix: </label>
 223                                         <div class="col-sm-9" >
 224                                             <select class="form-control" id="drone_image_analytics_genotyping_protocol_include_pedigree_select">
 225                                                 <option value="no">No</option>
 226                                                 <option value="yes">Yes</option>
 227                                             </select>
 228                                         </div>
 229                                     </div>
 230                                 </div>
 231                             </div>
 232
 233                             <div id="drone_imagery_analytics_htp_phenotypes_rel_matrix_div" class="well well-sm" style="display:none">
 234                                 <div class="form-horizontal">
 235                                     <div class="form-group">
 236                                         <label class="col-sm-3 control-label">How to calculate the relationship matrix with high-throughput phenotypes: </label>
 237                                         <div class="col-sm-9" >
 238                                             <select class="form-control" id="drone_image_analytics_htp_phenotypes_rel_matrix_select">
 239                                                 <option value="correlations">Correlations</option>
 240                                                 <option value="blues">BLUEs</option>
 241                                             </select>
 242                                         </div>
 243                                     </div>
 244                                     <div class="form-group">
 245                                         <label class="col-sm-3 control-label">Time Points to Use: </label>
 246                                         <div class="col-sm-9" >
 247                                             <select class="form-control" id="drone_image_analytics_htp_phenotypes_rel_matrix_times_select">
 248                                                 <option value="all">All Available</option>
 249                                                 <option value="latest_trait">Up to latest days after planting selecting in traits</option>
 250                                                 <option value="vegetative" disabled>Vegetative Growth Stage</option>
 251                                                 <option value="reproductive" disabled>Reproductive Growth Stage</option>
 252                                                 <option value="mature" disabled>Mature Growth Stage</option>
 253                                             </select>
 254                                         </div>
 255                                     </div>
 256                                     <div class="form-group" id="drone_image_analytics_htp_phenotypes_rel_matrix_inversion_select_div" style="display:none">
 257                                         <label class="col-sm-3 control-label">HTP BLUEs Inversion Tolerance: </label>
 258                                         <div class="col-sm-9" >
 259                                             <select class="form-control" id="drone_image_analytics_htp_phenotypes_rel_matrix_inversion_select">
 260                                                 <option value="0.00001">0.00001</option>
 261                                                 <option value="0.0001">0.0001</option>
 262                                                 <option value="0.001">0.001</option>
 263                                                 <option value="0.01">0.01</option>
 264                                                 <option value="0.1">0.1</option>
 265                                                 <option value="0.5">0.5</option>
 266                                             </select>
 267                                         </div>
 268                                     </div>
 269                                 </div>
 270                             </div>
 271
 272                             <!--hr>
 273                             <div class="form-horizontal">
 274                                 <div class="form-group">
 275                                     <label class="col-sm-3 control-label">Use Cumulative Area-Under-Curve Phenotype in Analysis: </label>
 276                                     <div class="col-sm-9" >
 277                                         <select class="form-control" id="drone_image_analytics_use_area_under_curve_select">
 278                                             <option value="no">No</option>
 279                                             <option value="yes">Yes</option>
 280                                         </select>
 281                                     </div>
 282                                 </div>
 283                             </div-->
 284
 285                             <hr>
 286                             <div class="form-horizontal">
 287                                 <div class="form-group">
 288                                     <label class="col-sm-3 control-label">Inversion Tolerance: </label>
 289                                     <div class="col-sm-9" >
 290                                         <select class="form-control" id="drone_image_analytics_tolparinv_select">
 291                                             <option value="0.000001">0.000001</option>
 292                                             <option value="0.00001">0.00001</option>
 293                                             <option value="0.0001">0.0001</option>
 294                                             <option value="0.001">0.001</option>
 295                                             <option value="0.01">0.01</option>
 296                                             <option value="0.05">0.05</option>
 297                                             <option value="0.08">0.08</option>
 298                                             <option value="0.1">0.1</option>
 299                                             <option value="0.2">0.2</option>
 300                                             <option value="0.5">0.5</option>
 301                                         </select>
 302                                     </div>
 303                                 </div>
 304                                 <div class="form-group">
 305                                     <label class="col-sm-3 control-label">Legendre Polynomial Order: </label>
 306                                     <div class="col-sm-9" >
 307                                         <select class="form-control" id="drone_image_analytics_legendre_order_number_select">
 308                                             <option value="3">3</option>
 309                                             <!--option value="1">1</option>
 310                                             <option value="2">2</option>
 311                                             <option value="4">4</option>
 312                                             <option value="5">5</option-->
 313                                         </select>
 314                                     </div>
 315                                 </div>
 316                             </div>
 317
 318                             <hr>
 319                             <div class="form-horizontal">
 320                                 <div class="form-group">
 321                                     <label class="col-sm-3 control-label">AIMREMLf90 Permanent Environment Structure: </label>
 322                                     <div class="col-sm-9" >
 323                                         <select class="form-control" id="drone_image_analytics_permanent_env_structure_select">
 324                                             <option value="identity">Identity Matrix</option>
 325                                             <option value="env_corr_structure">Simulated Phenotype Correlation Matrix</option>
 326                                             <option value="phenotype_correlation">Phenotype Correlation Matrix</option>
 327                                             <option value="phenotype_2dspline_effect">2D-Spline Effect of Phenotype</option>
 328                                             <!--option value="phenotype_ar1xar1_effect">AR1xAR1 Effect of Phenotype</option-->
 329                                             <option value="euclidean_rows_and_columns">Euclidean Distance From Rows and Columns Matrix</option>
 330                                         </select>
 331                                     </div>
 332                                 </div>
 333                             </div>
 334
 335                             <div id="drone_imagery_analytics_permanent_env_structure_phenotype_correlation_div" style="display:none">
 336                                 <div class="form-horizontal">
 337                                     <div class="form-group">
 338                                         <label class="col-sm-3 control-label">Phenotypes For Correlation Matrix: </label>
 339                                         <div class="col-sm-9" >
 340                                             <div id="drone_imagery_analytics_permanent_env_structure_phenotype_correlation_select_div"></div>
 341                                         </div>
 342                                     </div>
 343                                 </div>
 344                             </div>
 345
 346                             <div id="drone_imagery_analytics_permanent_env_structure_phenotype_effect_select_div" style="display:none">
 347                                 <div class="form-horizontal">
 348                                     <div class="form-group">
 349                                         <label class="col-sm-3 control-label">Phenotype For 2D-spline of AR1xAR1 Effect in Permanent Environment Structure: </label>
 350                                         <div class="col-sm-9" >
 351                                             <div id="drone_imagery_analytics_permanent_env_structure_phenotype_select_div"></div>
 352                                         </div>
 353                                     </div>
 354                                 </div>
 355                             </div>
 356
 357                             <hr>
 358                             <div class="form-horizontal">
 359                                 <div class="form-group">
 360                                     <label class="col-sm-3 control-label">Simulated Environment Processes: </label>
 361                                     <div class="col-sm-9" >
 362                                         <select class="form-control" id="drone_imagery_analytics_simulated_environment_processes_select_div">
 363                                             <option value="">Linear, 1D Normal, 2D Normal, AR1xAR1, Random, Real Data</option>
 364                                         </select>
 365                                     </div>
 366                                 </div>
 367                                 <div class="form-group">
 368                                     <label class="col-sm-3 control-label">Trait For Real Data Environment Simulation: </label>
 369                                     <div class="col-sm-9" >
 370                                         <div id="drone_imagery_analytics_simulated_environment_real_data_trait_select_div"></div>
 371                                     </div>
 372                                 </div>
 373                             </div>
 374
 375                             <hr>
 376                             <div class="form-horizontal">
 377                                 <div class="form-group">
 378                                     <label class="col-sm-3 control-label">Fixed Effects: </label>
 379                                     <div class="col-sm-9" >
 380                                         <select class="form-control" id="drone_imagery_analytics_fixed_effect_select_div">
 381                                             <option value="replicate">Replicate</option>
 382                                             <option value="fixed_effect_trait">Select a continuous trait (e.g. soil elevation curvature)</option>
 383                                         </select>
 384                                     </div>
 385                                 </div>
 386                                 <div class="form-group" id="drone_imagery_analytics_fixed_effect_select_trait_div" style="display:none">
 387                                     <label class="col-sm-3 control-label">Fixed Effect Trait: </label>
 388                                     <div class="col-sm-9" >
 389                                         <div id="drone_imagery_analytics_fixed_effect_trait_select_div"></div>
 390                                     </div>
 391                                 </div>
 392                                 <div class="form-group" id="drone_imagery_analytics_fixed_effect_select_quantile_div" style="display:none">
 393                                     <label class="col-sm-3 control-label">Fixed Effect Continuous Trait Quantile Binning: </label>
 394                                     <div class="col-sm-9" >
 395                                         <select class="form-control" id="drone_imagery_analytics_fixed_effect_select_quantile">
 396                                             <option value="4">25% Quantiles</option>
 397                                             <option value="5">20% Quantiles</option>
 398                                             <option value="10">10% Quantiles</option>
 399                                             <option value="3">33% Quantiles</option>
 400                                         </select>
 401                                     </div>
 402                                 </div>
 403                             </div>
 404                         </div>
 405                     </div>
 406
 407                     <hr>
 408                     <center>
 409                     <button class="btn btn-primary" id="drone_imagery_analytics_select_step">Submit</button>
 410                     </center>
 411                 </&>
 412                 <&| /util/workflow.mas:step, title=> "Results" &>
 413                     <& /page/page_title.mas, title=>"Statistics results" &>
 414
 415                     <hr>
 416                     <button class="btn btn-primary" id="drone_imagery_analytics_analysis_save_blups_genetic_pe_residual" style="display:none">Go To Save Analysis Results For Genetic and Environment BLUPS and Residuals</button>
 417                     <button class="btn btn-primary" id="drone_imagery_analytics_analysis_save_blups_genetic" style="display:none">Go To Save Analysis Results For Genetic BLUPS</button>
 418                     <button class="btn btn-primary" id="drone_imagery_analytics_analysis_save_blups_spatial" style="display:none">Go To Save Analysis Results For Spatial BLUPS</button>
 419                     <button class="btn btn-primary" id="drone_imagery_analytics_analysis_save_blups_pe" style="display:none">Go To Save Analysis Results For Permanent Environmental BLUPS</button>
 420                     <button class="btn btn-primary" id="drone_imagery_analytics_analysis_save_residuals" style="display:none">Go To Save Analysis Results For Residuals</button>
 421                     <button class="btn btn-primary" id="drone_imagery_analytics_analysis_save_fitted" style="display:none">Go To Save Analysis Results For Fitted Values</button>
 422                     <hr>
 423
 424                     <div id ="drone_imagery_analytics_result_div">
 425                     </div>
 426                 </&>
 427             </&>
 428
 429         </div>
 430
 431       </div>
 432       <div class="modal-footer">
 433         <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>
 434       </div>
 435     </div>
 436   </div>
 437 </div>
 438
 439 <script>
 440 jQuery(document).ready(function() {
 441     jQuery('#drone_imagery_analytics_link').click(function(){
 442         get_select_box('trials', 'drone_imagery_analytics_trial_select_div', { 'name' : 'drone_imagery_analytics_field_trial_id', 'id' : 'drone_imagery_analytics_field_trial_id', 'empty':1, 'multiple':1 });
 443
 444         jQuery('#drone_imagery_analytics_dialog').modal('show');
 445     });
 446
 447     var manage_drone_imagery_analytics_field_trial_id_array = undefined;
 448     var manage_drone_imagery_analytics_field_trial_id_string = "";
 449     var manage_drone_imagery_analytics_observation_variable_type;
 450     var manage_drone_imagery_analytics_trait_ids = [];
 451     var manage_drone_imagery_analytics_trait_names = [];
 452     var manage_drone_imagery_analytics_accession_names = [];
 453     var manage_drone_imagery_analytics_plot_names = [];
 454     var manage_drone_imagery_analytics_statistics_select = '';
 455     var manage_drone_imagery_analytics_phenotype_training_file;
 456     var manage_drone_imagery_analytics_grm_training_file;
 457     var manage_drone_imagery_analytics_response = {};
 458     var manage_drone_imagery_analytics_name = "";
 459     var manage_drone_imagery_analytics_desc = "";
 460     var manage_drone_imagery_analytics_type = "";
 461     var manage_drone_imagery_analytics_protocol_id = undefined;
 462
 463     jQuery('#drone_imagery_analytics_field_trial_select_step').click(function(){
 464         manage_drone_imagery_analytics_field_trial_id_array = undefined;
 465         manage_drone_imagery_analytics_field_trial_id_string = "";
 466         manage_drone_imagery_analytics_field_trial_id_array = jQuery('#drone_imagery_analytics_field_trial_id').val();
 467
 468         if (!manage_drone_imagery_analytics_field_trial_id_array || manage_drone_imagery_analytics_field_trial_id_array.length > 1) {
 469             alert('Please only select a single field trial for now!');
 470             return false;
 471         }
 472
 473         manage_drone_imagery_analytics_field_trial_id_string = manage_drone_imagery_analytics_field_trial_id_array.join(",");
 474         manage_drone_imagery_analytics_observation_variable_type = jQuery('#drone_imagery_analytics_select_observation_variable_type').val();
 475         if (manage_drone_imagery_analytics_field_trial_id_string == '') {
 476             alert('Please select a field trial first!');
 477         } else {
 478             if (manage_drone_imagery_analytics_observation_variable_type == 'time_ontology') {
 479                 get_select_box('traits', 'drone_imagery_analytics_trait_select_div', { 'name' : 'drone_imagery_analytics_trait_id_select', 'id' : 'drone_imagery_analytics_trait_id_select', 'empty':1, 'multiple':1, 'size': 20, 'trial_ids':manage_drone_imagery_analytics_field_trial_id_string, 'stock_type':'plot', 'contains_composable_cv_type':manage_drone_imagery_analytics_observation_variable_type, 'select_format':'component_table_select' });
 480             }
 481             else {
 482                 get_select_box('traits', 'drone_imagery_analytics_trait_select_div', { 'name' : 'drone_imagery_analytics_trait_id_select', 'id' : 'drone_imagery_analytics_trait_id_select', 'empty':1, 'multiple':1, 'size': 20, 'trial_ids':manage_drone_imagery_analytics_field_trial_id_string, 'stock_type':'plot', 'contains_composable_cv_type':manage_drone_imagery_analytics_observation_variable_type });
 483             }
 484
 485             get_select_box('traits', 'drone_imagery_analytics_permanent_env_structure_phenotype_correlation_select_div', { 'name' : 'drone_imagery_analytics_permanent_env_structure_phenotype_correlation_select', 'id' : 'drone_imagery_analytics_permanent_env_structure_phenotype_correlation_select', 'empty':1, 'multiple':1, 'size': 20, 'trial_ids':manage_drone_imagery_analytics_field_trial_id_string, 'stock_type':'plot' });
 486
 487             get_select_box('traits', 'drone_imagery_analytics_permanent_env_structure_phenotype_select_div', { 'name' : 'drone_imagery_analytics_permanent_env_structure_phenotype_select', 'id' : 'drone_imagery_analytics_permanent_env_structure_phenotype_select', 'empty':1, 'multiple':1, 'size':20, 'trial_ids':manage_drone_imagery_analytics_field_trial_id_string, 'stock_type':'plot', 'contains_composable_cv_type':'time_ontology', 'select_format':'component_table_select' });
 488
 489             get_select_box('traits', 'drone_imagery_analytics_simulated_environment_real_data_trait_select_div', { 'name' : 'drone_imagery_analytics_simulated_environment_real_data_trait_select', 'id' : 'drone_imagery_analytics_simulated_environment_real_data_trait_select', 'empty':0, 'multiple':0, 'trial_ids':manage_drone_imagery_analytics_field_trial_id_string, 'stock_type':'plot' });
 490
 491             get_select_box('traits', 'drone_imagery_analytics_fixed_effect_trait_select_div', { 'name' : 'drone_imagery_analytics_fixed_effect_trait_select', 'id' : 'drone_imagery_analytics_fixed_effect_trait_select', 'empty':0, 'multiple':0, 'trial_ids':manage_drone_imagery_analytics_field_trial_id_string, 'stock_type':'plot' });
 492
 493             get_select_box('analytics_protocols', 'drone_imagery_analytics_analytics_protocols_select_div', { 'checkbox_name' : 'drone_imagery_analytics_analytics_protocols_select_id', 'analytics_protocol_type' : 'drone_imagery_analytics_env_simulation_protocol' });
 494
 495             get_select_box('genotyping_protocol', 'drone_imagery_analytics_genotyping_protocol_select_div', { 'name' : 'drone_image_analytics_genotyping_protocol_select', 'id' : 'drone_image_analytics_genotyping_protocol_select', 'empty':1 });
 496
 497             Workflow.complete("#drone_imagery_analytics_field_trial_select_step");
 498             Workflow.focus('#drone_imagery_analytics_workflow', 1);
 499         }
 500         return false;
 501     });
 502
 503     jQuery('#drone_imagery_analytics_select_observation_variable_type').change(function(){
 504         manage_drone_imagery_analytics_observation_variable_type = jQuery('#drone_imagery_analytics_select_observation_variable_type').val();
 505         if (manage_drone_imagery_analytics_observation_variable_type == 'time_ontology') {
 506             get_select_box('traits', 'drone_imagery_analytics_trait_select_div', { 'name' : 'drone_imagery_analytics_trait_id_select', 'id' : 'drone_imagery_analytics_trait_id_select', 'empty':1, 'multiple':1, 'size': 20, 'trial_ids':manage_drone_imagery_analytics_field_trial_id_string, 'stock_type':'plot', 'contains_composable_cv_type':manage_drone_imagery_analytics_observation_variable_type, 'select_format':'component_table_select' });
 507         }
 508         else {
 509             get_select_box('traits', 'drone_imagery_analytics_trait_select_div', { 'name' : 'drone_imagery_analytics_trait_id_select', 'id' : 'drone_imagery_analytics_trait_id_select', 'empty':1, 'multiple':1, 'size': 20, 'trial_ids':manage_drone_imagery_analytics_field_trial_id_string, 'stock_type':'plot', 'contains_composable_cv_type':manage_drone_imagery_analytics_observation_variable_type });
 510         }
 511     });
 512
 513     jQuery('#drone_imagery_analytics_analytics_project_new_button').click(function(){
 514         jQuery('#drone_imagery_analytics_analytics_project_new_div').show();
 515     });
 516
 517     jQuery('#drone_imagery_analytics_select_input').change(function(){
 518         jQuery("#drone_imagery_analytics_relationship_matrix_type_select_div").val('').change();
 519         jQuery("#drone_image_analytics_genotyping_protocol_compute_from_parents_select").val('no').change();
 520
 521         manage_drone_imagery_analytics_statistics_select = jQuery('#drone_imagery_analytics_select_input').val();
 522
 523         if (manage_drone_imagery_analytics_statistics_select == 'lmer_germplasmname_replicate') {
 524             jQuery('#drone_imagery_analytics_genotyping_protocol_div').hide();
 525             jQuery('#drone_imagery_analytics_analysis_save_blups_genetic_pe_residual').hide();
 526             jQuery('#drone_imagery_analytics_analysis_save_blups_genetic').show();
 527             jQuery('#drone_imagery_analytics_analysis_save_blups_spatial').hide();
 528             jQuery('#drone_imagery_analytics_analysis_save_blups_pe').hide();
 529             jQuery('#drone_imagery_analytics_analysis_save_residuals').hide();
 530             jQuery('#drone_imagery_analytics_analysis_save_fitted').hide();
 531         }
 532         else if (manage_drone_imagery_analytics_statistics_select == 'sommer_grm_spatial_genetic_blups' || manage_drone_imagery_analytics_statistics_select == 'sommer_grm_spatial_pure_2dspl_genetic_blups') {
 533             jQuery('#drone_imagery_analytics_genotyping_protocol_div').hide();
 534             jQuery('#drone_imagery_analytics_analysis_save_blups_genetic_pe_residual').show();
 535             jQuery('#drone_imagery_analytics_analysis_save_blups_genetic').hide();
 536             jQuery('#drone_imagery_analytics_analysis_save_blups_spatial').hide();
 537             jQuery('#drone_imagery_analytics_analysis_save_blups_pe').hide();
 538             jQuery('#drone_imagery_analytics_analysis_save_residuals').hide();
 539             jQuery('#drone_imagery_analytics_analysis_save_fitted').hide();
 540         }
 541         else if (manage_drone_imagery_analytics_statistics_select == 'sommer_grm_temporal_random_regression_dap_genetic_blups' || manage_drone_imagery_analytics_statistics_select == 'sommer_grm_temporal_random_regression_gdd_genetic_blups') {
 542             jQuery('#drone_imagery_analytics_genotyping_protocol_div').hide();
 543             jQuery('#drone_imagery_analytics_analysis_save_blups_genetic_pe_residual').hide();
 544             jQuery('#drone_imagery_analytics_analysis_save_blups_genetic').show();
 545             jQuery('#drone_imagery_analytics_analysis_save_blups_spatial').hide();
 546             jQuery('#drone_imagery_analytics_analysis_save_blups_pe').show();
 547             jQuery('#drone_imagery_analytics_analysis_save_residuals').hide();
 548             jQuery('#drone_imagery_analytics_analysis_save_fitted').hide();
 549         }
 550         else if (manage_drone_imagery_analytics_statistics_select == 'sommer_grm_genetic_only_random_regression_dap_genetic_blups' || manage_drone_imagery_analytics_statistics_select == 'sommer_grm_genetic_only_random_regression_gdd_genetic_blups') {
 551             jQuery('#drone_imagery_analytics_genotyping_protocol_div').hide();
 552             jQuery('#drone_imagery_analytics_analysis_save_blups_genetic_pe_residual').hide();
 553             jQuery('#drone_imagery_analytics_analysis_save_blups_genetic').show();
 554             jQuery('#drone_imagery_analytics_analysis_save_blups_spatial').hide();
 555             jQuery('#drone_imagery_analytics_analysis_save_blups_pe').hide();
 556             jQuery('#drone_imagery_analytics_analysis_save_residuals').hide();
 557             jQuery('#drone_imagery_analytics_analysis_save_fitted').hide();
 558         }
 559         else if (manage_drone_imagery_analytics_statistics_select == 'blupf90_grm_random_regression_dap_blups' || manage_drone_imagery_analytics_statistics_select == 'blupf90_grm_random_regression_gdd_blups' || manage_drone_imagery_analytics_statistics_select == 'airemlf90_grm_random_regression_dap_blups' || manage_drone_imagery_analytics_statistics_select == 'airemlf90_grm_random_regression_gdd_blups') {
 560             jQuery('#drone_imagery_analytics_genotyping_protocol_div').hide();
 561             jQuery('#drone_imagery_analytics_analysis_save_blups_genetic_pe_residual').show();
 562             jQuery('#drone_imagery_analytics_analysis_save_blups_genetic').hide();
 563             jQuery('#drone_imagery_analytics_analysis_save_blups_spatial').hide();
 564             jQuery('#drone_imagery_analytics_analysis_save_blups_pe').hide();
 565             jQuery('#drone_imagery_analytics_analysis_save_residuals').hide();
 566             jQuery('#drone_imagery_analytics_analysis_save_fitted').hide();
 567         }
 568         else if (manage_drone_imagery_analytics_statistics_select == 'sommer_grm_genetic_blups') {
 569             jQuery('#drone_imagery_analytics_genotyping_protocol_div').hide();
 570             jQuery('#drone_imagery_analytics_analysis_save_blups_genetic_pe_residual').hide();
 571             jQuery('#drone_imagery_analytics_analysis_save_blups_genetic').show();
 572             jQuery('#drone_imagery_analytics_analysis_save_blups_spatial').hide();
 573             jQuery('#drone_imagery_analytics_analysis_save_blups_pe').hide();
 574             jQuery('#drone_imagery_analytics_analysis_save_residuals').hide();
 575             jQuery('#drone_imagery_analytics_analysis_save_fitted').hide();
 576         }
 577         else {
 578             jQuery('#drone_imagery_analytics_genotyping_protocol_div').hide();
 579             jQuery('#drone_imagery_analytics_analysis_save_blups_genetic_pe_residual').hide();
 580             jQuery('#drone_imagery_analytics_analysis_save_blups_genetic').hide();
 581             jQuery('#drone_imagery_analytics_analysis_save_blups_spatial').hide();
 582             jQuery('#drone_imagery_analytics_analysis_save_blups_pe').hide();
 583             jQuery('#drone_imagery_analytics_analysis_save_residuals').hide();
 584             jQuery('#drone_imagery_analytics_analysis_save_fitted').hide();
 585         }
 586
 587         jQuery('#drone_imagery_analytics_genotyping_protocol_div').hide();
 588         jQuery('#drone_imagery_analytics_analysis_save_blups_genetic_pe_residual').hide();
 589         jQuery('#drone_imagery_analytics_analysis_save_blups_genetic').hide();
 590         jQuery('#drone_imagery_analytics_analysis_save_blups_spatial').hide();
 591         jQuery('#drone_imagery_analytics_analysis_save_blups_pe').hide();
 592         jQuery('#drone_imagery_analytics_analysis_save_residuals').hide();
 593         jQuery('#drone_imagery_analytics_analysis_save_fitted').hide();
 594     });
 595
 596     jQuery('#drone_imagery_analytics_relationship_matrix_type_select_div').change(function(){
 597         if (jQuery(this).val() == 'genotypes') {
 598             jQuery('#drone_imagery_analytics_genotyping_protocol_div').show();
 599             jQuery('#drone_imagery_analytics_htp_phenotypes_rel_matrix_div').hide();
 600         }
 601         else if (jQuery(this).val() == 'htp_phenotypes') {
 602             jQuery('#drone_imagery_analytics_genotyping_protocol_div').hide();
 603             jQuery('#drone_imagery_analytics_htp_phenotypes_rel_matrix_div').show();
 604         }
 605         else {
 606             jQuery('#drone_imagery_analytics_genotyping_protocol_div').hide();
 607             jQuery('#drone_imagery_analytics_htp_phenotypes_rel_matrix_div').hide();
 608         }
 609     });
 610
 611     jQuery('#drone_image_analytics_htp_phenotypes_rel_matrix_select').change(function(){
 612         if (jQuery(this).val() == 'blues') {
 613             jQuery('#drone_image_analytics_htp_phenotypes_rel_matrix_inversion_select_div').show();
 614         }
 615         else {
 616             jQuery('#drone_image_analytics_htp_phenotypes_rel_matrix_inversion_select_div').hide();
 617         }
 618     });
 619
 620     jQuery('#drone_image_analytics_genotyping_protocol_compute_from_parents_select').change(function(){
 621         if (jQuery(this).val() == 'yes') {
 622             jQuery('#drone_image_analytics_genotyping_protocol_include_pedigree_select_div').show();
 623             jQuery('#drone_image_analytics_genotyping_protocol_use_parental_grms_select_div').show();
 624         }
 625         if (jQuery(this).val() == 'no') {
 626             jQuery('#drone_image_analytics_genotyping_protocol_include_pedigree_select_div').hide();
 627             jQuery('#drone_image_analytics_genotyping_protocol_use_parental_grms_select_div').hide();
 628             jQuery('#drone_image_analytics_genotyping_protocol_include_pedigree_select option[value=no]').attr('selected','selected');
 629             jQuery('#drone_image_analytics_genotyping_protocol_use_parental_grms_select option[value=no]').attr('selected','selected');
 630         }
 631     });
 632
 633     jQuery('#drone_image_analytics_genotyping_protocol_use_parental_grms_select').change(function(){
 634         if (jQuery(this).val() == 'yes') {
 635             jQuery('#drone_image_analytics_genotyping_protocol_include_pedigree_select option[value=no]').attr('selected','selected');
 636             jQuery('#drone_image_analytics_genotyping_protocol_include_pedigree_select_div').hide();
 637         }
 638         if (jQuery(this).val() == 'no') {
 639             jQuery('#drone_image_analytics_genotyping_protocol_include_pedigree_select_div').show();
 640         }
 641     });
 642
 643     jQuery('#drone_image_analytics_permanent_env_structure_select').change(function(){
 644         if (jQuery(this).val() == 'euclidean_rows_and_columns') {
 645             jQuery('#drone_imagery_analytics_permanent_env_structure_phenotype_correlation_div').hide();
 646             jQuery('#drone_imagery_analytics_permanent_env_structure_phenotype_effect_select_div').hide();
 647         }
 648         else if (jQuery(this).val() == 'phenotype_correlation') {
 649             jQuery('#drone_imagery_analytics_permanent_env_structure_phenotype_correlation_div').show();
 650             jQuery('#drone_imagery_analytics_permanent_env_structure_phenotype_effect_select_div').hide();
 651         }
 652         else if (jQuery(this).val() == 'phenotype_2dspline_effect') {
 653             jQuery('#drone_imagery_analytics_permanent_env_structure_phenotype_correlation_div').hide();
 654             jQuery('#drone_imagery_analytics_permanent_env_structure_phenotype_effect_select_div').show();
 655         }
 656         else {
 657             jQuery('#drone_imagery_analytics_permanent_env_structure_phenotype_correlation_div').hide();
 658             jQuery('#drone_imagery_analytics_permanent_env_structure_phenotype_effect_select_div').hide();
 659         }
 660     });
 661
 662     jQuery('#drone_imagery_analytics_fixed_effect_select_div').change(function(){
 663         if (jQuery(this).val() == 'replicate') {
 664             jQuery('#drone_imagery_analytics_fixed_effect_select_trait_div').hide();
 665             jQuery('#drone_imagery_analytics_fixed_effect_select_quantile_div').hide();
 666         }
 667         if (jQuery(this).val() == 'fixed_effect_trait') {
 668             jQuery('#drone_imagery_analytics_fixed_effect_select_trait_div').show();
 669             jQuery('#drone_imagery_analytics_fixed_effect_select_quantile_div').show();
 670         }
 671     });
 672
 673     jQuery('#drone_imagery_analytics_select_step').click(function(){
 674
 675         manage_drone_imagery_analytics_statistics_select = jQuery('#drone_imagery_analytics_select_input').val();
 676
 677         var manage_drone_imagery_analytics_protocol_ids = [];
 678         jQuery('input[name="drone_imagery_analytics_analytics_protocols_select_id"]').each(function() {
 679             if (this.checked){
 680                 manage_drone_imagery_analytics_protocol_ids.push(jQuery(this).val());
 681             }
 682         });
 683
 684         if (manage_drone_imagery_analytics_protocol_ids.length > 1) {
 685             alert('Please select only one protocol!');
 686             return false;
 687         }
 688         if (manage_drone_imagery_analytics_protocol_ids.length == 1) {
 689             manage_drone_imagery_analytics_protocol_id = manage_drone_imagery_analytics_protocol_ids[0];
 690         }
 691
 692         manage_drone_imagery_analytics_name = jQuery('#drone_imagery_analytics_select_analytics_name').val();
 693         manage_drone_imagery_analytics_desc = jQuery('#drone_imagery_analytics_select_analytics_desc').val();
 694         manage_drone_imagery_analytics_type = jQuery('#drone_imagery_analytics_select_analytics_type').val();
 695
 696         if (!manage_drone_imagery_analytics_protocol_id && manage_drone_imagery_analytics_name == '') {
 697             alert('Please give an analytics name or select a previously saved analytics report.');
 698             return false;
 699         }
 700         if (!manage_drone_imagery_analytics_protocol_id && manage_drone_imagery_analytics_desc == '') {
 701             alert('Please give an analytics description.');
 702             return false;
 703         }
 704         if (manage_drone_imagery_analytics_protocol_id && manage_drone_imagery_analytics_name != '') {
 705             alert('Please give an analytics name OR select a previously saved analytics report, not both!');
 706             return false;
 707         }
 708
 709         manage_drone_imagery_analytics_trait_ids = [];
 710
 711         if (manage_drone_imagery_analytics_observation_variable_type == 'time_ontology') {
 712             jQuery('input[name="drone_imagery_analytics_trait_id_select"]').each(function() {
 713                 if (this.checked){
 714                     manage_drone_imagery_analytics_trait_ids.push(jQuery(this).val());
 715                 }
 716             });
 717         }
 718         else {
 719             manage_drone_imagery_analytics_trait_ids = jQuery('#drone_imagery_analytics_trait_id_select').val();
 720             if (manage_drone_imagery_analytics_trait_ids == null || manage_drone_imagery_analytics_trait_ids == undefined) {
 721                 alert('Please select at least one observation variable!');
 722                 return false;
 723             }
 724         }
 725
 726         if (!manage_drone_imagery_analytics_protocol_id && manage_drone_imagery_analytics_trait_ids.length < 1){
 727             alert('Please select at least one observation variable!');
 728             return false;
 729         }
 730
 731         if (jQuery('#drone_image_analytics_genotyping_protocol_include_pedigree_select').val() == 'yes' && jQuery('#drone_image_analytics_genotyping_protocol_compute_from_parents_select').val() != 'yes') {
 732             alert('You can only use pedigree info in the relationship matrix if you will compute the genotypes from the parents!');
 733             return false;
 734         }
 735         if (jQuery('#drone_image_analytics_genotyping_protocol_use_parental_grms_select').val() == 'yes' && jQuery('#drone_image_analytics_genotyping_protocol_compute_from_parents_select').val() != 'yes') {
 736             alert('You can only use parental relationship matrices if you will compute the genotypes from the parents!');
 737             return false;
 738         }
 739
 740         var manage_drone_imagery_analytics_rr_structure_phenotype_correlation = [];
 741         if (jQuery('#drone_image_analytics_permanent_env_structure_select').val() == 'phenotype_correlation') {
 742             manage_drone_imagery_analytics_rr_structure_phenotype_correlation = jQuery('#drone_imagery_analytics_permanent_env_structure_phenotype_correlation_select').val();
 743             if (!manage_drone_imagery_analytics_rr_structure_phenotype_correlation || manage_drone_imagery_analytics_rr_structure_phenotype_correlation.length < 3) {
 744                 alert('Please select at least three phenotypes to use in random regression permanent environment phenotype correlation structure!');
 745                 return false;
 746             }
 747         }
 748
 749         var manage_drone_imagery_analytics_rr_env_structure_trait_ids = [];
 750         jQuery('input[name="drone_imagery_analytics_permanent_env_structure_phenotype_select"]').each(function() {
 751             if (this.checked){
 752                 manage_drone_imagery_analytics_rr_env_structure_trait_ids.push(jQuery(this).val());
 753             }
 754         });
 755
 756         jQuery.ajax({
 757             url : '/api/drone_imagery/calculate_analytics',
 758             type : 'POST',
 759             data : {
 760                 'observation_variable_id_list':JSON.stringify(manage_drone_imagery_analytics_trait_ids),
 761                 'field_trial_id_list':JSON.stringify(manage_drone_imagery_analytics_field_trial_id_array),
 762                 'statistics_select':manage_drone_imagery_analytics_statistics_select,
 763                 'analytics_protocol_id':manage_drone_imagery_analytics_protocol_id,
 764                 'analytics_protocol_name':manage_drone_imagery_analytics_name,
 765                 'analytics_protocol_desc':manage_drone_imagery_analytics_desc,
 766                 'analytics_select':manage_drone_imagery_analytics_type,
 767                 'number_iterations':jQuery('#drone_imagery_analytics_number_iterations').val(),
 768                 'relationship_matrix_type':jQuery('#drone_imagery_analytics_relationship_matrix_type_select_div').val(),
 769                 'protocol_id':jQuery('#drone_image_analytics_genotyping_protocol_select').val(),
 770                 'compute_from_parents':jQuery('#drone_image_analytics_genotyping_protocol_compute_from_parents_select').val(),
 771                 'use_parental_grms_if_compute_from_parents':jQuery('#drone_image_analytics_genotyping_protocol_use_parental_grms_select').val(),
 772                 'include_pedgiree_info_if_compute_from_parents':jQuery('#drone_image_analytics_genotyping_protocol_include_pedigree_select').val(),
 773                 'htp_pheno_rel_matrix_type':jQuery('#drone_image_analytics_htp_phenotypes_rel_matrix_select').val(),
 774                 'htp_pheno_rel_matrix_time_points':jQuery('#drone_image_analytics_htp_phenotypes_rel_matrix_times_select').val(),
 775                 'htp_pheno_rel_matrix_blues_inversion':jQuery('#drone_image_analytics_htp_phenotypes_rel_matrix_inversion_select').val(),
 776                 'tolparinv':jQuery('#drone_image_analytics_tolparinv_select').val(),
 777                 'legendre_order_number':jQuery('#drone_image_analytics_legendre_order_number_select').val(),
 778                 'use_area_under_curve':jQuery('#drone_image_analytics_use_area_under_curve_select').val(),
 779                 'permanent_environment_structure':jQuery('#drone_image_analytics_permanent_env_structure_select').val(),
 780                 'permanent_environment_structure_phenotype_correlation_traits':JSON.stringify(manage_drone_imagery_analytics_rr_structure_phenotype_correlation),
 781                 'permanent_environment_structure_phenotype_trait_ids':JSON.stringify(manage_drone_imagery_analytics_rr_env_structure_trait_ids),
 782                 'sim_env_change_over_time':jQuery('#drone_imagery_analytics_select_sim_env_change_over_time_type').val(),
 783                 'env_variance_percent':jQuery('#drone_imagery_analytics_env_variance').val(),
 784                 'simulated_environment_real_data_trait_id':jQuery('#drone_imagery_analytics_simulated_environment_real_data_trait_select').val(),
 785                 'sim_env_change_over_time_correlation':jQuery('#drone_imagery_analytics_sim_env_change_over_time_correlation').val(),
 786                 'fixed_effect_type':jQuery('#drone_imagery_analytics_fixed_effect_select_div').val(),
 787                 'fixed_effect_trait_id':jQuery('#drone_imagery_analytics_fixed_effect_trait_select').val(),
 788                 'fixed_effect_quantiles':jQuery('#drone_imagery_analytics_fixed_effect_select_quantile').val()
 789             },
 790             beforeSend: function() {
 791                 jQuery("#working_modal").modal("show");
 792             },
 793             success: function(response){
 794                 console.log(response);
 795                 jQuery("#working_modal").modal("hide");
 796
 797                 if (response.error) {
 798                     alert(response.error);
 799                 }
 800                 else {
 801                     manage_drone_imagery_analytics_response = response;
 802                     manage_drone_imagery_analytics_protocol_id = response.analytics_protocol_id;
 803
 804                     var html = '<h4>Summary :</h4><ul>';
 805                     if (response.sum_square_residual_original) {
 806                         html = html + '<li>Sum square residual original: '+response.sum_square_residual_original+'</li>';
 807                     }
 808                     if (response.sum_square_residual_altered) {
 809                         html = html + '<li>Sum square residual altered: '+response.sum_square_residual_altered+'</li>';
 810                     }
 811                     if (response.genetic_effect_sum_original) {
 812                         html = html + '<li>Genetic effect sum original: '+response.genetic_effect_sum_original+'</li>';
 813                     }
 814                     if (response.genetic_effect_sum_altered) {
 815                         html = html + '<li>Genetic effect sum altered: '+response.genetic_effect_sum_altered+'</li>';
 816                     }
 817                     if (response.env_effect_sum_original) {
 818                         html = html + '<li>Env effect sum original: '+response.env_effect_sum_original+'</li>';
 819                     }
 820                     if (response.env_effect_sum_altered) {
 821                         html = html + '<li>Env effect sum altered: '+response.env_effect_sum_altered+'</li>';
 822                     }
 823                     html = html + '</ul>';
 824
 825                     if (response.simulated_environment_to_effect_correlations) {
 826                         html = html + '<h4>Simulated Env to Effects Correlations:</h4><ul>';
 827                         for(var i=0; i<response.simulated_environment_to_effect_correlations.length; i++) {
 828                             html = html + '<li>' + response.simulated_environment_to_effect_correlations[i] + '</li>';
 829                         }
 830                         html = html + '</ul><hr>';
 831                     }
 832
 833                     if (response.spatial_effects_plots) {
 834                         for (i=0; i<response.spatial_effects_plots.length; i++) {
 835                             html = html + '<p>'+response.spatial_effects_plots[i][1]+'</p><img src="'+response.spatial_effects_plots[i][0]+'"><hr>';
 836                         }
 837                     }
 838
 839                     if (response.unique_accessions.length > 0 && response.unique_traits.length > 0 && response.result_blup_genetic_data_altered) {
 840                         manage_drone_imagery_analytics_accession_names = response.unique_accessions;
 841                         manage_drone_imagery_analytics_trait_names = response.unique_traits;
 842                         manage_drone_imagery_analytics_phenotype_training_file = response.stats_tempfile;
 843                         manage_drone_imagery_analytics_grm_training_file = response.grm_file;
 844
 845                         html = html + '<table class="table table-bordered table-hover"><thead><tr><th>Accessions</th>';
 846                         for (var i=0; i<manage_drone_imagery_analytics_trait_names.length; i++) {
 847                             html = html + '<th>'+manage_drone_imagery_analytics_trait_names[i]+'</th>';
 848                         }
 849                         html = html + '</tr></thead><tbody>';
 850                         for (var k=0; k<response.unique_accessions.length; k++) {
 851                             var acc = response.unique_accessions[k];
 852                             html = html + '<tr><td>'+acc+'</td>';
 853                             for (var i=0; i<manage_drone_imagery_analytics_trait_names.length; i++) {
 854                                 if (response.result_blup_genetic_data_altered[acc] && response.result_blup_genetic_data_altered[acc][manage_drone_imagery_analytics_trait_names[i]]) {
 855                                     html = html + '<td>'+response.result_blup_genetic_data_altered[acc][manage_drone_imagery_analytics_trait_names[i]][0]+'</td>';
 856                                 }
 857                                 else {
 858                                     html = html + '<td>NA</td>';
 859                                 }
 860                             }
 861                             html = html + '</tr>';
 862                         }
 863                         html = html + '</tbody></table>';
 864                     }
 865
 866                     if (response.unique_plots.length > 0 && response.unique_traits.length > 0 && response.result_blup_spatial_data_altered) {
 867                         manage_drone_imagery_analytics_plot_names = response.unique_plots;
 868                         manage_drone_imagery_analytics_trait_names = response.unique_traits;
 869
 870                         html = html + '<table class="table table-bordered table-hover"><thead><tr><th>Plots</th>';
 871                         for (var i=0; i<response.unique_traits.length; i++) {
 872                             html = html + '<th>'+response.unique_traits[i]+'</th>';
 873                         }
 874                         html = html + '</tr></thead><tbody>';
 875                         for (var k=0; k<response.unique_plots.length; k++) {
 876                             var plot = response.unique_plots[k];
 877                             html = html + '<tr><td>'+plot+'</td>';
 878                             for (var i=0; i<response.unique_traits.length; i++) {
 879                                 html = html + '<td>'+response.result_blup_spatial_data_altered[plot][response.unique_traits[i]][0]+'</td>';
 880                             }
 881                             html = html + '</tr>';
 882                         }
 883                         html = html + '</tbody></table>';
 884                     }
 885
 886                     if (response.unique_plots.length > 0 && response.unique_traits.length > 0 && response.result_blup_pe_data_altered) {
 887                         manage_drone_imagery_analytics_plot_names = response.unique_plots;
 888                         manage_drone_imagery_analytics_trait_names = response.unique_traits;
 889
 890                         html = html + '<table class="table table-bordered table-hover"><thead><tr><th>Plots</th>';
 891                         for (var i=0; i<response.unique_traits.length; i++) {
 892                             html = html + '<th>'+response.unique_traits[i]+'</th>';
 893                         }
 894                         html = html + '</tr></thead><tbody>';
 895                         for (var k=0; k<response.unique_plots.length; k++) {
 896                             var plot = response.unique_plots[k];
 897                             html = html + '<tr><td>'+plot+'</td>';
 898                             for (var i=0; i<response.unique_traits.length; i++) {
 899                                 if (response.result_blup_pe_data_altered[plot] && response.result_blup_pe_data_altered[plot][response.unique_traits[i]]) {
 900                                     html = html + '<td>'+response.result_blup_pe_data_altered[plot][response.unique_traits[i]][0]+'</td>';
 901                                 }
 902                                 else {
 903                                     html = html + '<td>NA</td>';
 904                                 }
 905                             }
 906                             html = html + '</tr>';
 907                         }
 908                         html = html + '</tbody></table>';
 909                     }
 910
 911                     html = html + '<hr><a href="'+response.stats_out_tempfile_string+'.log" target=_blank>Stats file or log</a>';
 912
 913                     if (jQuery('#drone_imagery_analytics_relationship_matrix_type_select_div').val() == 'htp_phenotypes') {
 914                         html = html + '<hr><a href="'+response.stats_out_htp_rel_tempfile_out_string+'" target=_blank>HTP Relationship Matrix</a>';
 915                     }
 916
 917                     jQuery('#drone_imagery_analytics_result_div').html(html);
 918
 919                     Workflow.complete("#drone_imagery_analytics_select_step");
 920                     Workflow.focus('#drone_imagery_analytics_workflow', 2);
 921                 }
 922             },
 923             error: function(response){
 924                 jQuery("#working_modal").modal("hide");
 925                 alert('Error calculating statistics analytics!')
 926             }
 927         });
 928     });
 929
 930 });
 931 </script>