How to use test_stuff method in green

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make_experiment.py

Source:make_experiment.py

1import argparse2from myutils.formatter import PrettyFormatter3parser=argparse.ArgumentParser(formatter_class=PrettyFormatter)4#5parser.add_argument('--output_core', type=str, default='experiments/def_result',6   help='Core part of the output files (in the form: output_core_appendix)')7#8parser.add_argument('--splits_checkpoint', type=str, default=None,9   help=('Checkpoint containing indeces of train/test splits. '10         'If present, will overriden splits generation and try to read from this file.'))11#12parser.add_argument('--data_checkpoint', type=str, default=None, 13   help=('Checkpoint containing preprocessed dataset. '14         'If present, will override preprocessing step and try to read from this file.'))15#16parser.add_argument('--scale_positive', type=float, default=0.5, 17   help=('Scale assigned to positive class. Value of 0.5 means that both negative and'18        ' positive classes are treated equally.'))19#20parser.add_argument('--config', type=str, default='config_files/def_rdkit_config.yaml', 21   help='YAML file defineing exeriment documentation (see README)')22#23parser.add_argument('--force', type=str, choices=['all','splits'], default=None, 24   help=('Forces data preprocess/splits calculation despite checkpoint being present.\n'25         '* all - force both data prerocess and splits generation\n'26         '* splits - force only splits generation\n'))27#28parser.add_argument('--epochs', type=int, default=100,29   help='Number of training epochs') 30#31parser.add_argument('--validation_mode', type=str, choices=['5cv_test','val_test'], 32   default='val_test', help=('Type of validation procedure. Validation score is '33   'used for model selection, which is than tested on the held-out test set.\n'34   '* val_test - train on 72%% of data, validate on 18%% of data and test on 10%% of data\n'35   '* 5cv_test - do 5-fold cross-validation on 90%% of data, test on 10%%%% of data\n'))36#37args=parser.parse_args()38#name checkoints of this run (if checkpoint file is not provided39if args.data_checkpoint is None:40   args.data_checkpoint = '%s_data_chk.pkz'%args.output_core41if args.splits_checkpoint is None:42   args.splits_checkpoint = '%s_splits_chk.pkz'%args.output_core43#set override flags; preprocessing and splits will be done,44#results will be written in checkpoints45args.force_resample=False46args.force_resplit=False47if args.force=='all':48   args.force_resample=True49   args.force_resplit=True50elif args.force=='splits':51   args.force_resplit=True52#===== These imports take time, so are placed here. Thanks to that printing help is quick53from data_preprocess import load_yaml, load_from_config, yaml, gz_pickle, gz_unpickle, tpr_tnr54from data_preprocess import balance_masked_weights, split_data, isfile, np, slice_data, make_test_data, scale_weights55from models import make_model, make_av_std, make_bayesian_prediction, SaveSelected, tasks_balanced_scores56import logging57#========= logging stuff ===========58logger=logging.getLogger()59level=logging.INFO60formatter=logging.Formatter('%(asctime)s: %(levelname)s): %(message)s')61log_name = '%s_%s.log'%(args.output_core, args.validation_mode)62handlers= logging.FileHandler(log_name), logging.StreamHandler()63for handler in handlers:64   handler.setFormatter(formatter)65   handler.setLevel(level)66   logger.addHandler(handler)67logger.setLevel(level)68#======= loading stuff ==========69logger.info('Start')70config = load_yaml(args.config)71config['loader_config']['data_checkpoint'] = args.data_checkpoint72x, y, weights = load_from_config(config, args.force_resample)73#======= split data =======74checkpoint_name = args.splits_checkpoint75cv_cfg = config['cross_validation']76cv_cfg['checkpoint'] = checkpoint_name77cv_splits, train_idx, test_idx, weights = split_data(y, weights, cv_cfg, 78                                   args.validation_mode, args.force_resplit)79data_stuff = [x, y, weights]80kind = config['model_params'].get('kind', 'any')81is_multitask = 'multitask' in kind82if is_multitask:83   axis = 184   N_outputs = len(y)85else:86   axis=087   N_outputs = -188to_relax = config['model_params'].get('relax', False)89#======= print info ======= 90config_str = yaml.dump(config, default_flow_style=False)91logger.info('Config file: %s'%args.config)92logger.info('Force resample/reload: %s   Force resplit: %s'%(args.force_resample, args.force_resplit))93logger.info('weights_are_none %s'%(weights is None))94logger.info('Validation mode: %s'%args.validation_mode)95logger.info('output_core: %s'%args.output_core)96logger.info('Epochs: %i'%args.epochs)97logger.info('Positive scaling: %8.3f'%args.scale_positive)98logger.info('Data loaded.\n== Config ==\n%s\n============'%config_str)99data_summary = [str(obj) for obj in [np.shape(y), np.sum(y, axis=axis)]]100logger.info('Y shape:%s  Y sum:%s'%tuple(data_summary))101#write all configuration to the YAML file102with open('%s_post.yaml'%args.output_core, 'w') as f:103   f.write(config_str)104#====== train =======105batch_size=100 ## add config?? later??106epochs=args.epochs107history=[]108N_inputs = config['model_params'].get('num_inputs', 1)109if N_inputs==1:110   input_shape = x.shape[1]111else:112   input_shape = [arr.shape for arr in x]113data_shapes = config.get('data_shapes', 'none')114if data_shapes!='none':115   input_shape = data_shapes116for cv_train_idx, cv_val_idx in cv_splits:117   train = slice_data(data_stuff, cv_train_idx, N_inputs)118   val = slice_data(data_stuff, cv_val_idx, N_inputs)119   if is_multitask:120      logger.info('Train Y: %s'%str(np.sum(train[1],axis=1)))121      for i,vy in enumerate(train[1]):122         key='out%i'%i123         train[2][key] = balance_masked_weights(vy,train[2][key])124         val[2][key] = balance_masked_weights(val[1][i],val[2][key])125   else:126      train[2] = scale_weights(train[1], train[2], args.scale_positive)127      val[2] = scale_weights(val[1], val[2], args.scale_positive)128      logger.info('Train Y: %s'%str(np.sum(train[1],axis=0)))129   model, metric = make_model(input_shape, np.shape(y), config['model_params']) 130   logger.info('Model build')131   result = model.fit(train[0], train[1], sample_weight = train[2],132                        validation_data = val,133                        batch_size=batch_size, epochs=epochs, shuffle=True, verbose=1)134   if to_relax:135      logger.info('Relaxing')136      tr_score, _ = make_av_std([result.history], metric, is_multitask, N_outputs)137      tst_score, _ =  make_av_std([result.history], 'val_%s'%metric, is_multitask, N_outputs)138      logger.info('Last stats: Train:  %8.3f   Val: %8.3f'%(tr_score.max(), tst_score.max()))139      w= model.get_weights()140      model, _ = make_model(input_shape, np.shape(y), config['model_params'])141      model.set_weights(w)142      for layer in model.layers: layer.trainable=True143      result = model.fit(train[0], train[1], sample_weight = train[2],144                         validation_data = val[:2],145                         batch_size=batch_size, epochs=epochs, shuffle=True, verbose=1)146      tr_score, _ = make_av_std([result.history], metric, is_multitask, N_outputs)147      tst_score, _ =  make_av_std([result.history], 'val_%s'%metric, is_multitask, N_outputs)148      logger.info('After relaxation: Train:  %8.3f   Val: %8.3f'%(tr_score.max(), tst_score.max()))149   history.append(result.history)150#====== Average ===============151if is_multitask:152   metric = 'out%i_'+metric153cv_av, cv_std = make_av_std(history, metric, is_multitask, N_outputs)154cv_val_av, cv_val_std = make_av_std(history, 'val_%s'%metric, is_multitask, N_outputs)155val_loss = np.array([x['val_loss'] for x in history]).mean(axis=0)156if is_multitask:157   best_cv_idx = np.argmax(val_loss)#cv_val_av.argmax()158else:159   best_cv_idx = cv_val_av.argmax()160logging.info('Val loss: %i-%8.6f'%(best_cv_idx,val_loss[best_cv_idx]))161test_epochs = args.epochs #best_cv_idx+1162#====== test ===========163logger.info('Testing')164test_stuff = make_test_data(data_stuff, test_idx, N_inputs, config)#slice_data(data_stuff, test_idx, N_inputs)165train_stuff = slice_data(data_stuff, train_idx, N_inputs)166test_stuff = list(test_stuff)167train_stuff = list(train_stuff)168#TODO: repetition-refactor169if is_multitask:170   for i,vy in enumerate(train_stuff[1]):171      key='out%i'%i172      train_stuff[2][key] = balance_masked_weights(vy, train_stuff[2][key])173      test_stuff[2][key] = balance_masked_weights(test_stuff[1][i], test_stuff[2][key])174else:175      train_stuff[2] = scale_weights(train_stuff[1], train_stuff[2], args.scale_positive)176      test_stuff[2] = scale_weights(test_stuff[1], test_stuff[2], args.scale_positive)177model, _ = make_model(input_shape, np.shape(y), config['model_params']) 178logger.info('Model build')179saver = SaveSelected(best_cv_idx)180try:181   result = model.fit(train_stuff[0], train_stuff[1], sample_weight=train_stuff[2],182                   validation_data = test_stuff,183                   batch_size=batch_size, epochs=test_epochs, shuffle=True, verbose=1, callbacks=[saver])184   if to_relax:185      logger.info('Relaxing')186      tr_score, _ = make_av_std([result.history], metric, is_multitask, N_outputs)187      tst_score, _ =  make_av_std([result.history], 'val_%s'%metric, is_multitask, N_outputs)188      logger.info('Last stats: Train:  %8.3f   Val: %8.3f'%(tr_score.max(), tst_score.max()))189      for layer in model.layers: layer.trainable=True190      result = model.fit(train_stuff[0], train_stuff[1], sample_weight=train_stuff[2],191                   validation_data = test_stuff[:2],192                   batch_size=batch_size, epochs=test_epochs, shuffle=True, verbose=1, callbacks=[saver])193      tr_score, _ = make_av_std([result.history], metric, is_multitask, N_outputs)194      tst_score, _ =  make_av_std([result.history], 'val_%s'%metric, is_multitask, N_outputs)195      logger.info('After relaxation: Train:  %8.3f   Val: %8.3f'%(tr_score.max(), tst_score.max()))196except:197   xx = list(test_stuff[0])198   yy = test_stuff[1]199   result = model.fit(train_stuff[0], train_stuff[1], sample_weight=train_stuff[2],200                       validation_data = (xx, yy, test_stuff[2]),201                       batch_size=batch_size, epochs=test_epochs, shuffle=True, verbose=1, callbacks=[saver])202   if to_relax:203      logger.info('Relaxing')204      tr_score, _ = make_av_std([result.history], metric, is_multitask, N_outputs)205      tst_score, _ =  make_av_std([result.history], 'val_%s'%metric, is_multitask, N_outputs)206      logger.info('Last stats: Train:  %8.3f   Val: %8.3f'%(tr_score.max(), tst_score.max()))207      for layer in model.layers: layer.trainable=True208      result = model.fit(train_stuff[0], train_stuff[1], sample_weight=train_stuff[2],209                         validation_data = (xx, yy),210                         batch_size=batch_size, epochs=test_epochs, shuffle=True, verbose=1, callbacks=[saver])211#====== save history =====212logger.info('Saving history...')213test_av, test_std = make_av_std([result.history], metric, is_multitask, N_outputs)214test_val_av, test_val_std = make_av_std([result.history], 'val_%s'%metric, is_multitask, N_outputs)215logger.info('Best CV:')216logger.info('epoch: %i'%(best_cv_idx+1))217cv_max_data = tuple(arr[best_cv_idx] for arr in [cv_av, cv_std, cv_val_av, cv_val_std])218logger.info('train: %8.3f (%4.3f)   val:%8.3f (%4.3f)'%cv_max_data)219logger.info('Test:')220test_max_data = tuple(arr[best_cv_idx] for arr in [test_av, test_val_av])221logger.info('train: %8.3f   val:%8.3f'%test_max_data)222logger.info('Resetting model weights from epoch with best cross-val score')223saver.reset()224if is_multitask:225   logger.info('Details at best epoch:')226   for i in range(N_outputs):227      out_trn = result.history[metric%i][best_cv_idx]228      out_tst = result.history['val_'+metric%i][best_cv_idx]229      logger.info('   out%-2i:  train: %8.3f  test %8.3f'%(i, out_trn, out_tst))230else:231   if type(test_stuff[0]).__name__=='tuple': 232      x_to_use = list(test_stuff[0])233   else:234      x_to_use = test_stuff[0]235   pred = model.predict(x_to_use)236   tpr, tnr = tpr_tnr(pred, test_stuff[1])237   logger.info('TPR: %8.3f  TNR: %8.3f'%(tpr, tnr))238with open('%s_%s_history.txt'%(args.output_core, args.validation_mode), 'w') as f:239   data_order = [cv_av, cv_std, cv_val_av, cv_val_std, test_av, test_val_av]240   titles = ('EPOCH', 'train_cv', 'train_cv_err', 'val_cv', 'val_cv_err', \241                      'test', 'test_val')242   line_format = '%5i %12.4f %12.4f %12.4f %12.4f %12.4f %12.4f\n'243   f.write('%5s %12s %12s %12s %12s %12s %12s\n'%titles)244   for i in range(args.epochs):245      to_write = [i+1] + [arr[i] for arr in data_order]246      f.write(line_format%tuple(to_write))247if is_multitask:248   prediction_train = model.predict(train_stuff[0])249   prediction_test = model.predict(test_stuff[0])250   score_train = tasks_balanced_scores(prediction_train, train_stuff[1], train_stuff[2])251   score_test = tasks_balanced_scores(prediction_test, test_stuff[1], test_stuff[2])252   auc_test = tasks_balanced_scores(prediction_test, test_stuff[1], test_stuff[2], auc=True)253   logger.info('Correcting for masking information')254   logger.info('Train mean: %8.3f  Test mean: %8.3f  Test mean auc %8.3f'%(score_train.mean(), score_test.mean(), np.mean(auc_test)))255   for i in range(N_outputs):256      logger.info('   out%-2i:  train: %8.3f  test %8.3f auc: %8.3f'%(i, score_train[i], score_test[i], auc_test[i]))257logger.info('Saving model weights')258gz_pickle(args.output_core+'_train_weights.pkz', model.get_weights())259#======= bayesian prediction =======260do_bayes = config['model_params'].get('dropout_flag',False)261if do_bayes:262   logger.info('Making bayesian prediction on %i samples'%test_stuff[1].shape[0])263   bayesian_result = make_bayesian_prediction(model, test_stuff[0])264   265   logger.info('Done. Saving...')266   with open('%s_%s_bayesian_result.txt'%(args.output_core, args.validation_mode), 'w') as f:267      order = ('true_flag','mean_prob', 'aleatoric', 'epistemic')268      f.write('%10s %10s %10s %10s \n'%order)269   270      for i in range(test_stuff[1].shape[0]):271         f.write('%10i '%test_stuff[1][i].argmax())272   273         for key in order[1:]:274            f.write('%10.4f '%bayesian_result[key][i])275         276         f.write('\n')277         ...

drops.py

Source:drops.py

1"""2System for managing dropped items, dropped knowledge, distributed NPCs.3For allowing map generators to create things that might appear elsewhere in the4world, thus allowing the kind of interconnectedness that the game would5otherwise lack. This is the focus of drops here, rather than the economic6distribution of in-game resources.7"""8import random9common = 1010uncommon = 511rare = 112super_rare = 0.113class DropRegister:14    """15    Tracks droppable items.16    """17    def __init__(self):18        self.drops = []19        self.total_weight = 020    def add(self, generator, rarity, limit = None):21        self.drops.append((generator, rarity, limit))22        self.total_weight += rarity23    def gen_drop(self):24        index = random.random()*self.total_weight25        current_weight = 026        for generator, weight, limit in self.drops:27            current_weight += weight28            if current_weight > index:29                if limit != None:30                    self.drops.remove((generator, weight, limit))31                    if limit > 1:32                        self.drops.append((generator, weight, limit-1))33                    else:34                        self.total_weight -= weight35                if callable(generator):36                    return generator()37                else:38                    return generator39loot = DropRegister()40keys = DropRegister()41def test_drops():42    test_stuff = DropRegister()43    test_stuff.add(lambda: "a")44    assert test_stuff.total_weight == common45    test_stuff.add(lambda: "b")46    assert test_stuff.total_weight == common*247    test_stuff.add(lambda: "c", limit = 1) 48    results = [test_stuff.gen_drop() for i in range(100)]49    for result in results:50        assert result in ["a", "b", "c"]51    assert results.count("c") <= 152    if results.count("c") == 1:...

test_import.py

Source:test_import.py

1from testmod import test_stuff2from testmod import test_fxns3s = "alice killed bob"4result = test_stuff.countWords(s, "alice")5print result6print(result)7o = test_stuff.OldStyleClass("alice")8print o9n = test_stuff.NewStyleClass("bob")10print n11l = []12for i in range(5):13	l.append(test_stuff.OldStyleClass(i))14print l15for i in l:16	print i17print test_fxns.A_GLOBAL18test_fxns.incr_global()...

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