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How to use save_cfg method in yandex-tank
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analysis.py
Source:analysis.py 
1"""Functions to plot and compute results for the literature review.2"""3import os4import logging5import logging.config6from collections import OrderedDict7import subprocess8import pandas as pd9import geopandas as gpd10import matplotlib.pyplot as plt11from matplotlib.ticker import MaxNLocator12import matplotlib.patches as patches13import matplotlib as mpl14import seaborn as sns15import numpy as np16from PIL import Image17from wordcloud import WordCloud, STOPWORDS18from graphviz import Digraph19import config as cfg20import utils as ut21# Set style, context and palette22sns.set_style(rc=cfg.axes_styles)23sns.set_context(rc=cfg.plotting_context)24sns.set_palette(cfg.palette)25for key, val in cfg.axes_styles.items():26 mpl.rcParams[key] = val27for key, val in cfg.plotting_context.items():28 mpl.rcParams[key] = val29# Initialize logger for saving results and stats. Use `logger.info('message')`30# to log results.31logging.config.dictConfig({32 'version': 1,33 'disable_existing_loggers': True,34})35logger = logging.getLogger()36log_savename = os.path.join(cfg.saving_config['savepath'], 'results') + '.log'37handler = logging.FileHandler(log_savename, mode='w')38formatter = logging.Formatter(39 '%(asctime)s %(name)-12s %(levelname)-8s %(message)s')40handler.setFormatter(formatter)41logger.addHandler(handler)42logger.setLevel(logging.INFO)43def plot_prisma_diagram(save_cfg=cfg.saving_config):44 """Plot diagram showing the number of selected articles.45 TODO:46 - Use first two colors of colormap instead of gray47 - Reduce white space48 - Reduce arrow width49 """50 # save_format = save_cfg['format'] if isinstance(save_cfg, dict) else 'svg'51 save_format = 'pdf'52 # save_format = 'eps'53 size = '{},{}!'.format(0.5 * save_cfg['page_width'], 0.2 * save_cfg['page_height'])54 dot = Digraph(format=save_format)55 dot.attr('graph', rankdir='TB', overlap='false', size=size, margin='0')56 dot.attr('node', fontname='Liberation Sans', fontsize=str(9), shape='box', 57 style='filled', margin='0.15,0.07', penwidth='0.1')58 # dot.attr('edge', arrowsize=0.5)59 fillcolor = 'gray98'60 dot.node('A', 'PubMed (n=39)\nGoogle Scholar (n=409)\narXiv (n=105)', 61 fillcolor='gray95')62 dot.node('B', 'Articles identified\nthrough database\nsearching\n(n=553)', 63 fillcolor=fillcolor)64 # dot.node('B2', 'Excluded\n(n=446)', fillcolor=fillcolor)65 dot.node('C', 'Articles after content\nscreening and\nduplicate removal\n(n=105) ', 66 fillcolor=fillcolor)67 dot.node('D', 'Articles included in\nthe analysis\n(n=154)', 68 fillcolor=fillcolor)69 dot.node('E', 'Additional articles\nidentified through\nbibliography search\n(n=49)', 70 fillcolor=fillcolor)71 dot.edge('B', 'C')72 # dot.edge('B', 'B2')73 dot.edge('C', 'D')74 dot.edge('E', 'D')75 if save_cfg is not None:76 fname = os.path.join(save_cfg['savepath'], 'prisma_diagram')77 dot.render(filename=fname, view=False, cleanup=False)78 79 return dot80def plot_domain_tree(df, first_box='DL + EEG studies', min_font_size=10, 81 max_font_size=14, max_char=16, min_n_items=2, 82 postprocess=True, save_cfg=cfg.saving_config):83 """Plot tree graph showing the breakdown of study domains.84 Args:85 df (pd.DataFrame): data items table86 Keyword Args:87 first_box (str): text of the first box88 min_font_size (int): minimum font size89 max_font_size (int): maximum font size90 max_char (int): maximum number of characters per line91 min_n_items (int): if a node has less than this number of elements, 92 put it inside a node called "Others".93 postpocess (bool): if True, convert PNG to EPS using inkscape in a 94 system call.95 save_cfg (dict or None):96 97 Returns:98 (graphviz.Digraph): graphviz object99 NOTES:100 - To unflatten automatically, apply the following on the .dot file:101 >> unflatten -l 3 -c 10 dom_domains_tree | dot -Teps -o domains_unflattened.eps102 - To produce a circular version instead (uses space more efficiently):103 >> neato -Tpdf dom_domains_tree -o domains_neato.pdf104 """105 df = df[['Domain 1', 'Domain 2', 'Domain 3', 'Domain 4']].copy()106 df = df[~df['Domain 1'].isnull()]107 df[df == ' '] = None108 n_samples, n_levels = df.shape109 format = save_cfg['format'] if isinstance(save_cfg, dict) else 'svg'110 size = '{},{}!'.format(save_cfg['page_width'], 0.7 * save_cfg['page_height'])111 112 dot = Digraph(format=format)113 dot.attr('graph', rankdir='TB', overlap='false', ratio='fill', size=size) # LR (left to right), TB (top to bottom)114 dot.attr('node', fontname='Liberation Sans', fontsize=str(max_font_size), 115 shape='box', style='filled, rounded', margin='0.2,0.01', 116 penwidth='0.5')117 dot.node('A', '{}\n({})'.format(first_box, len(df)), 118 fillcolor='azure')119 120 min_sat, max_sat = 0.05, 0.4121 122 sub_df = df['Domain 1'].value_counts()123 n_categories = len(sub_df)124 for i, (d1, count1) in enumerate(sub_df.iteritems()):125 node1, hue = ut.make_box(126 dot, d1, max_char, count1, n_samples, 0, n_levels, min_sat, max_sat, 127 min_font_size, max_font_size, 'A', counter=i, 128 n_categories=n_categories)129 130 for d2, count2 in df[df['Domain 1'] == d1]['Domain 2'].value_counts().iteritems():131 node2, _ = ut.make_box(132 dot, d2, max_char, count2, n_samples, 1, n_levels, min_sat, 133 max_sat, min_font_size, max_font_size, node1, hue=hue)134 135 n_others3 = 0136 for d3, count3 in df[df['Domain 2'] == d2]['Domain 3'].value_counts().iteritems():137 if isinstance(d3, str) and d3 != 'TBD':138 if count3 < min_n_items:139 n_others3 += 1140 else:141 node3, _ = ut.make_box(142 dot, d3, max_char, count3, n_samples, 2, n_levels,143 min_sat, max_sat, min_font_size, max_font_size, 144 node2, hue=hue)145 n_others4 = 0146 for d4, count4 in df[df['Domain 3'] == d3]['Domain 4'].value_counts().iteritems():147 if isinstance(d4, str) and d4 != 'TBD':148 if count4 < min_n_items:149 n_others4 += 1150 else:151 ut.make_box(152 dot, d4, max_char, count4, n_samples, 3, 153 n_levels, min_sat, max_sat, min_font_size, 154 max_font_size, node3, hue=hue)155 if n_others4 > 0:156 ut.make_box(157 dot, 'Others', max_char, n_others4, n_samples, 158 3, n_levels, min_sat, max_sat, min_font_size, 159 max_font_size, node3, hue=hue, 160 node_name=node3+'others')161 if n_others3 > 0:162 ut.make_box(163 dot, 'Others', max_char, n_others3, n_samples, 2, n_levels,164 min_sat, max_sat, min_font_size, max_font_size, node2, hue=hue, 165 node_name=node2+'others')166 if save_cfg is not None:167 fname = os.path.join(save_cfg['savepath'], 'dom_domains_tree')168 dot.render(filename=fname, cleanup=False)169 if postprocess:170 subprocess.call(171 ['neato', '-Tpdf', fname, '-o', fname + '.pdf'])172 173 return dot174def plot_model_comparison(df, save_cfg=cfg.saving_config):175 """Plot bar graph showing the types of baseline models used.176 """177 fig, ax = plt.subplots(figsize=(save_cfg['text_width'] / 4 * 2, 178 save_cfg['text_height'] / 5))179 sns.countplot(y=df['Baseline model type'].dropna(axis=0), ax=ax)180 ax.set_xlabel('Number of papers')181 ax.set_ylabel('')182 plt.tight_layout()183 model_prcts = df['Baseline model type'].value_counts() / df.shape[0] * 100184 logger.info('% of studies that used at least one traditional baseline: {}'.format(185 model_prcts['Traditional pipeline'] + model_prcts['DL & Trad.']))186 logger.info('% of studies that used at least one deep learning baseline: {}'.format(187 model_prcts['DL'] + model_prcts['DL & Trad.']))188 logger.info('% of studies that did not report baseline comparisons: {}'.format(189 model_prcts['None']))190 if save_cfg is not None:191 fname = os.path.join(save_cfg['savepath'], 'model_comparison')192 fig.savefig(fname + '.' + save_cfg['format'], **save_cfg)193 return ax194def plot_performance_metrics(df, cutoff=3, eeg_clf=None, 195 save_cfg=cfg.saving_config):196 """Plot bar graph showing the types of performance metrics used.197 Args:198 df (DataFrame)199 Keyword Args:200 cutoff (int): Metrics with less than this number of papers will be cut201 off from the bar graph.202 eeg_clf (bool): If True, only use studies that focus on EEG 203 classification. If False, only use studies that did not focus on 204 EEG classification. If None, use all studies.205 save_cfg (dict)206 Assumptions, simplifications:207 - Rates have been simplified (e.g., "false positive rate" -> "false positives")208 - RMSE and MSE have been merged under MSE209 - Training/testing times have been simplified to "time"210 - Macro f1-score === f1=score211 """212 if eeg_clf is True:213 metrics = df[df['Domain 1'] == 'Classification of EEG signals'][214 'Performance metrics (clean)']215 elif eeg_clf is False:216 metrics = df[df['Domain 1'] != 'Classification of EEG signals'][217 'Performance metrics (clean)']218 elif eeg_clf is None:219 metrics = df['Performance metrics (clean)']220 metrics = metrics.str.split(',').apply(ut.lstrip)221 metric_per_article = list()222 for i, metric_list in metrics.iteritems():223 for m in metric_list:224 metric_per_article.append([i, m])225 metrics_df = pd.DataFrame(metric_per_article, columns=['paper nb', 'metric'])226 # Replace equivalent terms by standardized term227 equivalences = {'selectivity': 'specificity',228 'true negative rate': 'specificity',229 'sensitivitiy': 'sensitivity',230 'sensitivy': 'sensitivity',231 'recall': 'sensitivity',232 'hit rate': 'sensitivity', 233 'true positive rate': 'sensitivity',234 'sensibility': 'sensitivity',235 'positive predictive value': 'precision',236 'f-measure': 'f1-score',237 'f-score': 'f1-score',238 'f1-measure': 'f1-score',239 'macro f1-score': 'f1-score',240 'macro-averaging f1-score': 'f1-score',241 'kappa': 'cohen\'s kappa',242 'mae': 'mean absolute error',243 'false negative rate': 'false negatives',244 'fpr': 'false positives',245 'false positive rate': 'false positives',246 'false prediction rate': 'false positives',247 'roc': 'ROC curves',248 'roc auc': 'ROC AUC',249 'rmse': 'mean squared error',250 'mse': 'mean squared error',251 'training time': 'time',252 'testing time': 'time',253 'test error': 'error'}254 metrics_df = metrics_df.replace(equivalences)255 metrics_df['metric'] = metrics_df['metric'].apply(lambda x: x[0].upper() + x[1:])256 # Removing low count categories257 metrics_counts = metrics_df['metric'].value_counts()258 metrics_df = metrics_df[metrics_df['metric'].isin(259 metrics_counts[(metrics_counts >= cutoff)].index)]260 fig, ax = plt.subplots(figsize=(save_cfg['text_width'] / 2, 261 save_cfg['text_height'] / 5))262 ax = sns.countplot(y='metric', data=metrics_df, 263 order=metrics_df['metric'].value_counts().index)264 ax.set_xlabel('Number of papers')265 ax.set_ylabel('')266 plt.tight_layout()267 if save_cfg is not None:268 savename = 'performance_metrics'269 if eeg_clf is True:270 savename += '_eeg_clf'271 elif eeg_clf is False:272 savename += '_not_eeg_clf'273 fname = os.path.join(save_cfg['savepath'], savename)274 fig.savefig(fname + '.' + save_cfg['format'], **save_cfg)275 return ax276def plot_reported_results(df, data_items_df=None, save_cfg=cfg.saving_config):277 """Plot figures to described the reported results in the studies.278 Args:279 df (DataFrame): contains reported results (second tab in spreadsheet)280 Keyword Args:281 data_items_df (DataFrame): contains data items (first tab in spreadsheet)282 save_cfg (dict)283 Returns:284 (list): list of axes to created figures285 TODO:286 - This function is starting to be a bit too big. Should probably split it up.287 """288 acc_df = df[df['Metric'] == 'accuracy'] # Extract accuracy rows only289 # Create new column that contains both citation and task information290 acc_df.loc[:, 'citation_task'] = acc_df[['Citation', 'Task']].apply(291 lambda x: ' ['.join(x) + ']', axis=1)292 # Create a new column with the year293 acc_df.loc[:, 'year'] = acc_df['Citation'].apply(294 lambda x: int(x[x.find('2'):x.find('2') + 4]))295 # Order by average proposed model accuracy296 acc_ind = acc_df[acc_df['model_type'] == 'Proposed'].groupby(297 'Citation').mean().sort_values(by='Result').index298 acc_df.loc[:, 'Citation'] = acc_df['Citation'].astype('category')299 acc_df['Citation'].cat.set_categories(acc_ind, inplace=True)300 acc_df = acc_df.sort_values(['Citation'])301 # Only keep 2 best per task and model type302 acc2_df = acc_df.sort_values(303 ['Citation', 'Task', 'model_type', 'Result'], ascending=True).groupby(304 ['Citation', 'Task', 'model_type']).tail(2)305 axes = list()306 axes.append(_plot_results_per_citation_task(acc2_df, save_cfg))307 # Only keep the maximum accuracy per citation & task308 best_df = acc_df.groupby(309 ['Citation', 'Task', 'model_type'])[310 'Result'].max().reset_index()311 # Only keep citations/tasks that have a traditional baseline312 best_df = best_df.groupby(['Citation', 'Task']).filter(313 lambda x: 'Baseline (traditional)' in x.values).reset_index()314 # Add back architecture315 best_df = pd.merge(316 best_df, acc_df[['Citation', 'Task', 'model_type', 'Result', 'Architecture']], 317 how='inner').drop_duplicates() # XXX: why are there duplicates?318 # Compute difference between proposed and traditional baseline319 def acc_diff_and_arch(x):320 diff = x[x['model_type'] == 'Proposed']['Result'].iloc[0] - \321 x[x['model_type'] == 'Baseline (traditional)']['Result'].iloc[0]322 arch = x[x['model_type'] == 'Proposed']['Architecture']323 return pd.Series(diff, arch)324 diff_df = best_df.groupby(['Citation', 'Task']).apply(325 acc_diff_and_arch).reset_index()326 diff_df = diff_df.rename(columns={0: 'acc_diff'})327 axes.append(_plot_results_accuracy_diff_scatter(diff_df, save_cfg))328 axes.append(_plot_results_accuracy_diff_distr(diff_df, save_cfg))329 # Pivot dataframe to plot proposed vs. baseline accuracy as a scatterplot330 best_df['citation_task'] = best_df[['Citation', 'Task']].apply(331 lambda x: ' ['.join(x) + ']', axis=1)332 acc_comparison_df = best_df.pivot_table(333 index='citation_task', columns='model_type', values='Result')334 axes.append(_plot_results_accuracy_comparison(acc_comparison_df, save_cfg))335 if data_items_df is not None:336 domains_df = data_items_df.filter(337 regex='(?=Domain*|Citation|Main domain|Journal / Origin|Dataset name|'338 'Data - samples|Data - time|Data - subjects|Preprocessing \(clean\)|'339 'Artefact handling \(clean\)|Features \(clean\)|Architecture \(clean\)|'340 'Layers \(clean\)|Regularization \(clean\)|Optimizer \(clean\)|'341 'Intra/Inter subject|Training procedure)')342 # Concatenate domains into one string343 def concat_domains(x):344 domain = ''345 for i in x[1:]:346 if isinstance(i, str):347 domain += i + '/'348 return domain[:-1]349 domains_df.loc[:, 'domain'] = data_items_df.filter(350 regex='(?=Domain*)').apply(concat_domains, axis=1)351 diff_domain_df = diff_df.merge(domains_df, on='Citation', how='left')352 diff_domain_df = diff_domain_df.sort_values(by='domain')353 diff_domain_df.loc[:, 'arxiv'] = diff_domain_df['Journal / Origin'] == 'Arxiv'354 axes.append(_plot_results_accuracy_per_domain(355 diff_domain_df, diff_df, save_cfg))356 axes.append(_plot_results_stats_impact_on_acc_diff(357 diff_domain_df, save_cfg))358 axes.append(_compute_acc_diff_for_preprints(diff_domain_df, save_cfg))359 360 return axes361def _plot_results_per_citation_task(results_df, save_cfg):362 """Plot scatter plot of accuracy for each condition and task.363 """364 fig, ax = plt.subplots(figsize=(save_cfg['text_width'], 365 save_cfg['text_height'] * 1.3))366 # figsize = plt.rcParams.get('figure.figsize')367 # fig, ax = plt.subplots(figsize=(figsize[0], figsize[1] * 4))368 # Need to make the graph taller otherwise the y axis labels are on top of369 # each other.370 sns.catplot(y='citation_task', x='Result', hue='model_type', data=results_df, 371 ax=ax)372 ax.set_xlabel('accuracy')373 ax.set_ylabel('')374 plt.tight_layout()375 if save_cfg is not None:376 savename = 'reported_results'377 fname = os.path.join(save_cfg['savepath'], savename)378 fig.savefig(fname + '.' + save_cfg['format'], **save_cfg)379 return ax380def _plot_results_accuracy_diff_scatter(results_df, save_cfg):381 """Plot difference in accuracy for each condition/task as a scatter plot.382 """383 fig, ax = plt.subplots(figsize=(save_cfg['text_width'], 384 save_cfg['text_height'] * 1.3))385 # figsize = plt.rcParams.get('figure.figsize')386 # fig, ax = plt.subplots(figsize=(figsize[0], figsize[1] * 2))387 sns.catplot(y='Task', x='acc_diff', data=results_df, ax=ax)388 ax.set_xlabel('Accuracy difference')389 ax.set_ylabel('')390 ax.axvline(0, c='k', alpha=0.2)391 plt.tight_layout()392 if save_cfg is not None:393 savename = 'reported_accuracy_diff_scatter'394 fname = os.path.join(save_cfg['savepath'], savename)395 fig.savefig(fname + '.' + save_cfg['format'], **save_cfg)396 return ax397def _plot_results_accuracy_diff_distr(results_df, save_cfg):398 """Plot the distribution of difference in accuracy.399 """400 fig, ax = plt.subplots(figsize=(save_cfg['text_width'], 401 save_cfg['text_height'] * 0.5))402 sns.distplot(results_df['acc_diff'], kde=False, rug=True, ax=ax)403 ax.set_xlabel('Accuracy difference')404 ax.set_ylabel('Number of studies')405 plt.tight_layout()406 if save_cfg is not None:407 savename = 'reported_accuracy_diff_distr'408 fname = os.path.join(save_cfg['savepath'], savename)409 fig.savefig(fname + '.' + save_cfg['format'], **save_cfg)410 return ax411def _plot_results_accuracy_comparison(results_df, save_cfg):412 """Plot the comparison between the best model and best baseline.413 """414 fig, ax = plt.subplots(figsize=(save_cfg['text_width'], 415 save_cfg['text_height'] * 0.5))416 sns.scatterplot(data=results_df, x='Baseline (traditional)', y='Proposed', 417 ax=ax)418 ax.plot([0, 1.1], [0, 1.1], c='k', alpha=0.2)419 plt.axis('square')420 ax.set_xlim([0, 1.1])421 ax.set_ylim([0, 1.1])422 plt.tight_layout()423 if save_cfg is not None:424 savename = 'reported_accuracy_comparison'425 fname = os.path.join(save_cfg['savepath'], savename)426 fig.savefig(fname + '.' + save_cfg['format'], **save_cfg)427 return ax428def _plot_results_accuracy_per_domain(results_df, diff_df, save_cfg):429 """Make scatterplot + boxplot to show accuracy difference by domain.430 """431 fig, axes = plt.subplots(432 nrows=2, ncols=1, sharex=True, 433 figsize=(save_cfg['text_width'], save_cfg['text_height'] / 3), 434 gridspec_kw = {'height_ratios':[5, 1]})435 results_df['Main domain'] = results_df['Main domain'].apply(436 ut.wrap_text, max_char=20)437 sns.catplot(y='Main domain', x='acc_diff', s=3, jitter=True, 438 data=results_df, ax=axes[0])439 axes[0].set_xlabel('')440 axes[0].set_ylabel('')441 axes[0].axvline(0, c='k', alpha=0.2)442 sns.boxplot(x='acc_diff', data=diff_df, ax=axes[1])443 sns.swarmplot(x='acc_diff', data=diff_df, color="0", size=2, ax=axes[1])444 axes[1].axvline(0, c='k', alpha=0.2)445 axes[1].set_xlabel('Accuracy difference')446 fig.subplots_adjust(wspace=0, hspace=0.02)447 plt.tight_layout()448 logger.info('Number of studies included in the accuracy improvement analysis: {}'.format(449 results_df.shape[0]))450 median = diff_df['acc_diff'].median()451 iqr = diff_df['acc_diff'].quantile(.75) - diff_df['acc_diff'].quantile(.25)452 logger.info('Median gain in accuracy: {:.6f}'.format(median))453 logger.info('Interquartile range of the gain in accuracy: {:.6f}'.format(iqr))454 best_improvement = diff_df.nlargest(3, 'acc_diff')455 logger.info('Best improvement in accuracy: {}, in {}'.format(456 best_improvement['acc_diff'].values[0], 457 best_improvement['Citation'].values[0]))458 logger.info('Second best improvement in accuracy: {}, in {}'.format(459 best_improvement['acc_diff'].values[1], 460 best_improvement['Citation'].values[1]))461 logger.info('Third best improvement in accuracy: {}, in {}'.format(462 best_improvement['acc_diff'].values[2], 463 best_improvement['Citation'].values[2]))464 if save_cfg is not None:465 savename = 'reported_accuracy_per_domain'466 fname = os.path.join(save_cfg['savepath'], savename)467 fig.savefig(fname + '.' + save_cfg['format'], **save_cfg)468 return axes469def _plot_results_stats_impact_on_acc_diff(results_df, save_cfg):470 """Run statistical analysis to see which data items correlate with acc diff.471 NOTE: This analysis is not perfectly accurate as there are several papers 472 which contrasted results based on data items (e.g., testing the impact473 of number of layers on performance), but our summaries are not at this474 level of granularity. Therefore the results are not to be taken at face475 value.476 """477 binary_data_items = {'Preprocessing (clean)': ['Yes', 'No'],478 'Artefact handling (clean)': ['Yes', 'No'],479 'Features (clean)': ['Raw EEG', 'Frequency-domain'],480 'Regularization (clean)': ['Yes', 'N/M'],481 'Intra/Inter subject': ['Intra', 'Inter']}482 multiclass_data_items = ['Architecture', # Architecture (clean)',483 'Optimizer (clean)']484 continuous_data_items = {'Layers (clean)': False,485 'Data - subjects': True,486 'Data - time': True,487 'Data - samples': True}488 results = dict()489 for key, val in binary_data_items.items():490 results[key] = ut.run_mannwhitneyu(results_df, key, val, plot=True)491 for i in multiclass_data_items:492 results[i] = ut.run_kruskal(results_df, i, plot=True)493 for i in continuous_data_items:494 single_df = ut.keep_single_valued_rows(results_df, i)495 single_df = single_df[single_df[i] != 'N/M']496 single_df[i] = single_df[i].astype(float)497 results[i] = ut.run_spearmanr(single_df, i, log=val, plot=True)498 499 stats_df = pd.DataFrame(results).T500 logger.info('Results of statistical tests on impact of data items:\n{}'.format(501 stats_df))502 # Categorical plot for each "significant" data item503 significant_items = stats_df[stats_df['pvalue'] < 0.05].index504 if save_cfg is not None and len(significant_items) > 0:505 for i in significant_items:506 savename = 'stat_impact_{}_on_acc_diff'.format(507 i.replace(' ', '_').replace('/', '_'))508 fname = os.path.join(save_cfg['savepath'], savename)509 stats_df.loc[i, 'fig'].savefig(510 fname + '.' + save_cfg['format'], **save_cfg)511 return None512def _compute_acc_diff_for_preprints(results_df, save_cfg):513 """Analyze the acc diff for preprints vs. peer-reviewed articles.514 """515 results_df['preprint'] = results_df['Journal / Origin'].isin(['Arxiv', 'BioarXiv'])516 preprints = results_df.groupby('Citation').first()['preprint'].value_counts()517 logger.info(518 'Number of preprints included in the accuracy difference comparison: '519 '{}/{} papers'.format(preprints[True], sum(preprints)))520 logger.info('Median acc diff for preprints vs. non-preprint:\n{}'.format(521 results_df.groupby('preprint').median()['acc_diff']))522 results = ut.run_mannwhitneyu(results_df, 'preprint', [True, False])523 logger.info('Mann-Whitney test on preprint vs. not preprint: {:0.3f}'.format(524 results['pvalue']))525 return results526def generate_wordcloud(df, save_cfg=cfg.saving_config):527 brain_mask = np.array(Image.open("./img/brain_stencil.png"))528 def transform_format(val):529 if val == 0:530 return 255531 else:532 return val533 text = (df['Title']).to_string()534 stopwords = set(STOPWORDS)535 stopwords.add("using")536 stopwords.add("based")537 wc = WordCloud(538 background_color="white", max_words=2000, max_font_size=50, mask=brain_mask,539 stopwords=stopwords, contour_width=1, contour_color='steelblue')540 wc.generate(text)541 # store to file542 if save_cfg is not None:543 fname = os.path.join(save_cfg['savepath'], 'DL-EEG_WordCloud')544 wc.to_file(fname + '.' + save_cfg['format']) #, **save_cfg)545def plot_model_inspection_and_table(df, cutoff=1, save_cfg=cfg.saving_config):546 """Make bar graph and table listing method inspection techniques.547 Args:548 df (DataFrame)549 Keyword Args:550 cutoff (int): Metrics with less than this number of papers will be cut551 off from the bar graph.552 save_cfg (dict)553 """554 df['inspection_list'] = df[555 'Model inspection (clean)'].str.split(',').apply(ut.lstrip)556 inspection_per_article = list()557 for i, items in df[['Citation', 'inspection_list']].iterrows():558 for m in items['inspection_list']:559 inspection_per_article.append([i, items['Citation'], m])560 561 inspection_df = pd.DataFrame(562 inspection_per_article, 563 columns=['paper nb', 'Citation', 'inspection method'])564 # Remove "no" entries, because they make it really hard to see the 565 # actual distribution566 n_nos = inspection_df['inspection method'].value_counts()['no']567 n_papers = inspection_df.shape[0]568 logger.info('Number of papers without model inspection method: {}'.format(n_nos))569 inspection_df = inspection_df[inspection_df['inspection method'] != 'no']570 # # Replace "no" by "None"571 # inspection_df['inspection method'][572 # inspection_df['inspection method'] == 'no'] = 'None'573 # Removing low count categories574 inspection_counts = inspection_df['inspection method'].value_counts()575 inspection_df = inspection_df[inspection_df['inspection method'].isin(576 inspection_counts[(inspection_counts >= cutoff)].index)]577 578 inspection_df['inspection method'] = inspection_df['inspection method'].apply(579 lambda x: x.capitalize())580 print(inspection_df['inspection method'])581 # Making table582 inspection_table = inspection_df.groupby(['inspection method'])[583 'Citation'].apply(list)584 order = inspection_df['inspection method'].value_counts().index585 inspection_table = inspection_table.reindex(order)586 inspection_table = inspection_table.apply(lambda x: r'\cite{' + ', '.join(x) + '}')587 with open(os.path.join(save_cfg['table_savepath'], 'inspection_methods.tex'), 'w') as f:588 with pd.option_context("max_colwidth", 1000):589 f.write(inspection_table.to_latex(escape=False))590 fig, ax = plt.subplots(figsize=(save_cfg['text_width'] / 4 * 3, 591 save_cfg['text_height'] / 2))592 ax = sns.countplot(y='inspection method', data=inspection_df, 593 order=inspection_df['inspection method'].value_counts().index)594 ax.set_xlabel('Number of papers')595 ax.set_ylabel('')596 ax.xaxis.set_major_locator(MaxNLocator(integer=True))597 plt.tight_layout()598 logger.info('% of studies that used model inspection techniques: {}'.format(599 100 - 100 * (n_nos / n_papers)))600 if save_cfg is not None:601 savename = 'model_inspection'602 fname = os.path.join(save_cfg['savepath'], savename)603 fig.savefig(fname + '.' + save_cfg['format'], **save_cfg)604 return ax605def plot_type_of_paper(df, save_cfg=cfg.saving_config):606 """Plot bar graph showing the type of each paper (journal, conference, etc.).607 """608 # Move supplements to journal paper category for the plot (a value of one is609 # not visible on a bar graph).610 df_plot = df.copy()611 df_plot.loc[df['Type of paper'] == 'Supplement', :] = 'Journal'612 fig, ax = plt.subplots(figsize=(save_cfg['text_width'] / 4, 613 save_cfg['text_height'] / 5))614 sns.countplot(x=df_plot['Type of paper'], ax=ax)615 ax.set_xlabel('')616 ax.set_ylabel('Number of papers')617 ax.set_xticklabels(ax.get_xticklabels(), rotation=90)618 plt.tight_layout()619 counts = df['Type of paper'].value_counts()620 logger.info('Number of journal papers: {}'.format(counts['Journal']))621 logger.info('Number of conference papers: {}'.format(counts['Conference']))622 logger.info('Number of preprints: {}'.format(counts['Preprint']))623 logger.info('Number of papers that were initially published as preprints: '624 '{}'.format(df[df['Type of paper'] != 'Preprint'][625 'Preprint first'].value_counts()['Yes']))626 if save_cfg is not None:627 fname = os.path.join(save_cfg['savepath'], 'type_of_paper')628 fig.savefig(fname + '.' + save_cfg['format'], **save_cfg)629 return ax630def plot_country(df, save_cfg=cfg.saving_config):631 """Plot bar graph showing the country of the first author's affiliation.632 """633 fig, ax = plt.subplots(figsize=(save_cfg['text_width'] / 4 * 3, 634 save_cfg['text_height'] / 5))635 sns.countplot(x=df['Country'], ax=ax,636 order=df['Country'].value_counts().index)637 ax.set_ylabel('Number of papers')638 ax.set_xlabel('')639 ax.set_xticklabels(ax.get_xticklabels(), rotation=90)640 plt.tight_layout()641 top3 = df['Country'].value_counts().index[:3]642 logger.info('Top 3 countries of first author affiliation: {}'.format(top3.values))643 if save_cfg is not None:644 fname = os.path.join(save_cfg['savepath'], 'country')645 fig.savefig(fname + '.' + save_cfg['format'], **save_cfg)646 return ax647def plot_countrymap(dfx, postprocess=True, save_cfg=cfg.saving_config):648 """Plot world map with colour indicating number of papers.649 Plot a world map where the colour of each country indicates how many papers650 were published in which the first author's affiliation was from that country.651 When saved as .eps this figure is well over the 6 MB limit allowed by arXiv.652 To solve this, we first save it as a .png (with high enough dpi), then use653 inkscape to convert it to .eps (leading to a file of ~1.6 MB):654 >> inkscape countrymap.png --export-eps=countrymap.eps655 Keyword Args:656 postpocess (bool): if True, convert PNG to EPS using inkscape in a 657 system call.658 """659 dirname = os.path.dirname(__file__)660 shapefile = os.path.join(dirname, '../img/countries/ne_10m_admin_0_countries.shp')661 gdf = gpd.read_file(shapefile)[['ADMIN', 'geometry']] #.to_crs('+proj=robin')662 # gdf = gdf.to_crs(epsg=4326)663 gdf.crs = '+init=epsg:4326'664 dfx = dfx.Country.value_counts().reset_index().rename(665 columns={'index': 'Country', 'Country': 'Count'})666 #print("Renaming Exceptions!")667 #print(dfx.loc[~dfx['Country'].isin(gdf['ADMIN'])])668 # Exception #1 - USA: United States of America669 dfx.loc[dfx['Country'] == 'USA', 'Country'] = 'United States of America'670 # Exception #2 - UK: United Kingdom671 dfx.loc[dfx['Country'] == 'UK', 'Country'] = 'United Kingdom'672 # Exception #3 - Bosnia: Bosnia and Herzegovina673 dfx.loc[dfx['Country'] == 'Bosnia', 'Country'] = 'Bosnia and Herzegovina'674 if len(dfx.loc[~dfx['Country'].isin(gdf['ADMIN'])]) > 0:675 print("## ERROR ## - Unhandled Countries!")676 # Adding 0 to all other countries!677 gdf['Count'] = 0678 for c in gdf['ADMIN']:679 if any(dfx['Country'].str.contains(c)):680 gdf.loc[gdf['ADMIN'] == c, 'Count'] = dfx[681 dfx['Country'].str.contains(c)]['Count'].values[0]682 else:683 gdf.loc[gdf['ADMIN'] == c, 'Count'] = 0684 # figsize = (16, 10)685 figsize = (save_cfg['text_width'], save_cfg['text_height'] / 2)686 ax = gdf.plot(column='Count', figsize=figsize, cmap='Blues', 687 scheme='Fisher_Jenks', k=10, legend=True, edgecolor='k',688 linewidth=0.3, categorical=False, vmin=0,689 legend_kwds={'loc': 'lower left', 'title': 'Number of studies',690 'framealpha': 1},691 rasterized=False)692 # Remove floating points in legend693 leg = ax.get_legend()694 for t in leg.get_texts():695 t.set_text(t.get_text().replace('.00', ''))696 ax.set_axis_off()697 fig = ax.get_figure()698 plt.tight_layout()699 700 if save_cfg is not None:701 fname = os.path.join(save_cfg['savepath'], 'countrymap')702 save_cfg2 = save_cfg.copy()703 save_cfg2['dpi'] = 1000704 save_cfg2['format'] = 'png'705 fig.savefig(fname + '.png', **save_cfg2)706 if postprocess:707 subprocess.call(708 ['inkscape', fname + '.png', '--export-eps=' + fname + '.eps'])709 return ax710def compute_prct_statistical_tests(df):711 """Compute the number of studies that used statistical tests.712 """713 prct = 100 - 100 * df['Statistical analysis of performance'].value_counts(714 )['No'] / df.shape[0]715 logger.info('% of studies that used statistical test: {}'.format(prct))716def make_domain_table(df, save_cfg=cfg.saving_config):717 """Make domain table that contains every reference.718 """719 # Replace NaNs by ' ' in 'Domain 3' and 'Domain 4' columns720 df = ut.replace_nans_in_column(df, 'Domain 3', replace_by=' ')721 df = ut.replace_nans_in_column(df, 'Domain 4', replace_by=' ')722 cols = ['Domain 1', 'Domain 2', 'Domain 3', 'Domain 4', 'Architecture (clean)']723 df[cols] = df[cols].applymap(ut.tex_escape)724 # Make tuple of first 2 domain levels725 domains_df = df.groupby(cols)['Citation'].apply(list).apply(726 lambda x: '\cite{' + ', '.join(x) + '}').unstack()727 domains_df = domains_df.applymap(728 lambda x: ' ' if isinstance(x, float) and np.isnan(x) else x)729 fname = os.path.join(save_cfg['table_savepath'], 'domains_architecture_table.tex')730 with open(fname, 'w') as f:731 with pd.option_context("max_colwidth", 1000):732 f.write(domains_df.to_latex(733 escape=False, 734 column_format='p{1.5cm}' * 4 + 'p{0.6cm}' * domains_df.shape[1]))735def plot_preprocessing_proportions(df, save_cfg=cfg.saving_config):736 """Plot proportions for preprocessing-related data items.737 """738 data = dict()739 data['(a) Preprocessing of EEG data'] = df[740 'Preprocessing (clean)'].value_counts().to_dict()741 data['(b) Artifact handling'] = df[742 'Artefact handling (clean)'].value_counts().to_dict()743 data['(c) Extracted features'] = df[744 'Features (clean)'].value_counts().to_dict()745 fig, ax = ut.plot_multiple_proportions(746 data, print_count=5, respect_order=['Yes', 'No', 'Other', 'N/M'],747 figsize=(save_cfg['text_width'] / 4 * 4, save_cfg['text_height'] / 7 * 2))748 749 if save_cfg is not None:750 fname = os.path.join(save_cfg['savepath'], 'preprocessing')751 fig.savefig(fname + '.' + save_cfg['format'], **save_cfg)752 return ax753def plot_hyperparams_proportions(df, save_cfg=cfg.saving_config):754 """Plot proportions for hyperparameter-related data items.755 """756 data = dict()757 data['(a) Training procedure'] = df[758 'Training procedure (clean)'].value_counts().to_dict()759 data['(b) Regularization'] = df[760 'Regularization (clean)'].value_counts().to_dict()761 data['(c) Optimizer'] = df[762 'Optimizer (clean)'].value_counts().to_dict()763 fig, ax = ut.plot_multiple_proportions(764 data, print_count=5, respect_order=['Yes', 'No', 'Other', 'N/M'],765 figsize=(save_cfg['text_width'] / 4 * 4, save_cfg['text_height'] / 7 * 2))766 767 if save_cfg is not None:768 fname = os.path.join(save_cfg['savepath'], 'hyperparams')769 fig.savefig(fname + '.' + save_cfg['format'], **save_cfg)770 return ax771def plot_reproducibility_proportions(df, save_cfg=cfg.saving_config):772 """Plot proportions for reproducibility-related data items.773 """774 df['Code hosted on'] = df['Code hosted on'].replace(np.nan, 'N/M', regex=True)775 df['Limited data'] = df['Limited data'].replace(np.nan, 'N/M', regex=True)776 df['Code available'] = df['Code available'].replace(np.nan, 'N/M', regex=True)777 data = dict()778 data['(a) Dataset availability'] = df[779 'Dataset accessibility'].value_counts().to_dict()780 data['(b) Code availability'] = df[781 'Code hosted on'].value_counts().to_dict()782 data['(c) Type of baseline'] = df[783 'Baseline model type'].value_counts().to_dict()784 df['reproducibility'] = 'Hard'785 df.loc[(df['Code available'] == 'Yes') & 786 (df['Dataset accessibility'] == 'Public'), 'reproducibility'] = 'Easy' 787 df.loc[(df['Code available'] == 'Yes') & 788 (df['Dataset accessibility'] == 'Both'), 'reproducibility'] = 'Medium' 789 df.loc[(df['Code available'] == 'No') & 790 (df['Dataset accessibility'] == 'Private'), 'reproducibility'] = 'Impossible' 791 data['(d) Reproducibility'] = df[792 'reproducibility'].value_counts().to_dict()793 logger.info('Stats on reproducibility - Dataset Accessibility: {}'.format(794 data['(a) Dataset availability']))795 logger.info('Stats on reproducibility - Code Accessibility: {}'.format(796 df['Code available'].value_counts().to_dict()))797 logger.info('Stats on reproducibility - Code Hosted On: {}'.format(798 data['(b) Code availability']))799 logger.info('Stats on reproducibility - Baseline: {}'.format(800 data['(c) Type of baseline']))801 logger.info('Stats on reproducibility - Reproducibility Level: {}'.format(802 data['(d) Reproducibility']))803 logger.info('Stats on reproducibility - Limited data: {}'.format(804 df['Limited data'].value_counts().to_dict()))805 logger.info('Stats on reproducibility - Shared their Code: {}'.format(806 df[df['Code available'] == 'Yes']['Citation'].to_dict()))807 fig, ax = ut.plot_multiple_proportions(808 data, print_count=5, respect_order=['Easy', 'Medium', 'Hard', 'Impossible'],809 figsize=(save_cfg['text_width'] / 4 * 4, save_cfg['text_height'] * 0.4))810 811 if save_cfg is not None:812 fname = os.path.join(save_cfg['savepath'], 'reproducibility')813 fig.savefig(fname + '.' + save_cfg['format'], **save_cfg)814 return ax815def plot_domains_per_year(df, save_cfg=cfg.saving_config):816 """Plot stacked bar graph of domains per year.817 """818 fig, ax = plt.subplots(819 figsize=(save_cfg['text_width'] / 4 * 2, save_cfg['text_height'] / 4))820 df['Year'] = df['Year'].astype('int32')821 main_domains = ['Epilepsy', 'Sleep', 'BCI', 'Affective', 'Cognitive', 822 'Improvement of processing tools', 'Generation of data']823 domains_df = df[['Domain 1', 'Domain 2', 'Domain 3', 'Domain 4']]824 df['Main domain'] = [row[row.isin(main_domains)].values[0] 825 if any(row.isin(main_domains)) else 'Others' 826 for ind, row in domains_df.iterrows()]827 df.groupby(['Year', 'Main domain']).size().unstack('Main domain').plot(828 kind='bar', stacked=True, title='', ax=ax)829 ax.set_ylabel('Number of papers')830 ax.set_xlabel('')831 legend = plt.legend()832 for l in legend.get_texts():833 l.set_text(ut.wrap_text(l.get_text(), max_char=14))834 if save_cfg is not None:835 fname = os.path.join(save_cfg['savepath'], 'domains_per_year')836 fig.savefig(fname + '.' + save_cfg['format'], **save_cfg)837 return ax838def plot_hardware(df, save_cfg=cfg.saving_config):839 """Plot bar graph showing the hardware used in the study.840 """841 col = 'EEG Hardware'842 hardware_df = ut.split_column_with_multiple_entries(843 df, col, ref_col='Citation', sep=',', lower=False)844 # Remove N/Ms because they make it hard to see anything845 hardware_df = hardware_df[hardware_df[col] != 'N/M']846 847 # Add low cost column848 hardware_df['Low-cost'] = False849 low_cost_devices = ['EPOC (Emotiv)', 'OpenBCI (OpenBCI)', 'Muse (InteraXon)', 850 'Mindwave Mobile (Neurosky)', 'Mindset (NeuroSky)']851 hardware_df.loc[hardware_df[col].isin(low_cost_devices), 852 'Low-cost'] = True853 fig, ax = plt.subplots(figsize=(save_cfg['text_width'] / 4 * 2, 854 save_cfg['text_height'] / 5 * 2))855 sns.countplot(hue=hardware_df['Low-cost'], y=hardware_df[col], ax=ax,856 order=hardware_df[col].value_counts().index, 857 dodge=False)858 # sns.catplot(row=hardware_df['low_cost'], y=hardware_df['hardware'])859 ax.set_xlabel('Number of papers')860 ax.set_ylabel('')861 plt.tight_layout()862 if save_cfg is not None:863 fname = os.path.join(save_cfg['savepath'], 'hardware')864 fig.savefig(fname + '.' + save_cfg['format'], **save_cfg)865 return ax866def plot_architectures(df, save_cfg=cfg.saving_config):867 """Plot bar graph showing the architectures used in the study.868 """869 fig, ax = plt.subplots(figsize=(save_cfg['text_width'] / 3, 870 save_cfg['text_width'] / 3))871 colors = sns.color_palette()872 counts = df['Architecture (clean)'].value_counts()873 _, _, pct = ax.pie(counts.values, labels=counts.index, autopct='%1.1f%%',874 wedgeprops=dict(width=0.3, edgecolor='w'), colors=colors,875 pctdistance=0.55)876 for i in pct:877 i.set_fontsize(5)878 ax.axis('equal')879 plt.tight_layout()880 if save_cfg is not None:881 fname = os.path.join(save_cfg['savepath'], 'architectures')882 fig.savefig(fname + '.' + save_cfg['format'], **save_cfg)883 return ax884 885def plot_architectures_per_year(df, save_cfg=cfg.saving_config):886 """Plot stacked bar graph of architectures per year.887 """888 fig, ax = plt.subplots(889 figsize=(save_cfg['text_width'] / 3 * 2, save_cfg['text_width'] / 3))890 colors = sns.color_palette()891 df['Year'] = df['Year'].astype('int32')892 col_name = 'Architecture (clean)'893 df['Arch'] = df[col_name]894 order = df[col_name].value_counts().index895 counts = df.groupby(['Year', 'Arch']).size().unstack('Arch')896 counts = counts[order]897 counts.plot(kind='bar', stacked=True, title='', ax=ax, color=colors)898 ax.legend(loc='upper left', bbox_to_anchor=(1, 1))899 ax.set_ylabel('Number of papers')900 ax.set_xlabel('')901 plt.tight_layout()902 if save_cfg is not None:903 fname = os.path.join(save_cfg['savepath'], 'architectures_per_year')904 fig.savefig(fname + '.' + save_cfg['format'], **save_cfg)905 return ax906def plot_architectures_vs_input(df, save_cfg=cfg.saving_config):907 """Plot stacked bar graph of architectures vs input type.908 """909 fig, ax = plt.subplots(910 figsize=(save_cfg['text_width'] / 4 * 2, save_cfg['text_width'] / 3))911 df['Input'] = df['Features (clean)']912 col_name = 'Architecture (clean)'913 df['Arch'] = df[col_name]914 order = df[col_name].value_counts().index915 counts = df.groupby(['Input', 'Arch']).size().unstack('Input')916 counts = counts.loc[order, :]917 # To reduce the height of the figure, wrap long xticklabels918 counts = counts.rename({'CNN+RNN': 'CNN+\nRNN'}, axis='index')919 counts.plot(kind='bar', stacked=True, title='', ax=ax)920 # ax.legend(loc='upper left', bbox_to_anchor=(1, 1))921 ax.set_ylabel('Number of papers')922 ax.set_xlabel('')923 plt.tight_layout()924 if save_cfg is not None:925 fname = os.path.join(save_cfg['savepath'], 'architectures_vs_input')926 fig.savefig(fname + '.' + save_cfg['format'], **save_cfg)927 save_cfg2 = save_cfg.copy()928 save_cfg2['format'] = 'png'929 fig.savefig(fname + '.png', **save_cfg2)930 return ax931def plot_optimizers_per_year(df, save_cfg=cfg.saving_config):932 """Plot stacked bar graph of optimizers per year.933 """934 fig, ax = plt.subplots(935 figsize=(save_cfg['text_width'] / 4 * 2, save_cfg['text_width'] / 5 * 2))936 df['Input'] = df['Features (clean)']937 col_name = 'Optimizer (clean)'938 df['Opt'] = df[col_name]939 order = df[col_name].value_counts().index940 counts = df.groupby(['Year', 'Opt']).size().unstack('Opt')941 counts = counts[order]942 counts.plot(kind='bar', stacked=True, title='', ax=ax)943 ax.legend(loc='upper left', bbox_to_anchor=(1, 1))944 ax.set_ylabel('Number of papers')945 ax.set_xlabel('')946 plt.tight_layout()947 if save_cfg is not None:948 fname = os.path.join(save_cfg['savepath'], 'optimizers_per_year')949 fig.savefig(fname + '.' + save_cfg['format'], **save_cfg)950 return ax951def plot_intra_inter_per_year(df, save_cfg=cfg.saving_config):952 """Plot stacked bar graph of intra-/intersubject studies per year.953 """954 fig, ax = plt.subplots(955 figsize=(save_cfg['text_width'] / 4 * 2, save_cfg['text_height'] / 4))956 df['Year'] = df['Year'].astype(int)957 col_name = 'Intra/Inter subject'958 order = df[col_name].value_counts().index959 counts = df.groupby(['Year', col_name]).size().unstack(col_name)960 counts = counts[order]961 logger.info('Stats on inter/intra subjects: {}'.format(962 df[col_name].value_counts() / df.shape[0] * 100))963 counts.plot(kind='bar', stacked=True, title='', ax=ax)964 # ax.legend(loc='upper left', bbox_to_anchor=(1, 1))965 ax.set_ylabel('Number of papers')966 ax.set_xlabel('')967 plt.tight_layout()968 if save_cfg is not None:969 fname = os.path.join(save_cfg['savepath'], 'intra_inter_per_year')970 fig.savefig(fname + '.' + save_cfg['format'], **save_cfg)971 return ax972def plot_number_layers(df, save_cfg=cfg.saving_config):973 """Plot histogram of number of layers.974 """975 fig, ax = plt.subplots(976 figsize=(save_cfg['text_width'] / 4 * 2, save_cfg['text_width'] / 3))977 n_layers_df = df['Layers (clean)'].value_counts().reindex(978 [str(i) for i in range(1, 32)] + ['N/M'])979 n_layers_df = n_layers_df.dropna().astype(int)980 from matplotlib.colors import ListedColormap981 cmap = ListedColormap(sns.color_palette(None).as_hex())982 n_layers_df.plot(kind='bar', width=0.8, rot=0, colormap=cmap, ax=ax)983 ax.set_xlabel('Number of layers')984 ax.set_ylabel('Number of papers')985 plt.tight_layout()986 if save_cfg is not None:987 fname = os.path.join(save_cfg['savepath'], 'number_layers')988 fig.savefig(fname + '.' + save_cfg['format'], **save_cfg)989 save_cfg2 = save_cfg.copy()990 save_cfg2['format'] = 'png'991 save_cfg2['dpi'] = 300992 fig.savefig(fname + '.png', **save_cfg2)993 return ax 994def plot_number_subjects_by_domain(df, save_cfg=cfg.saving_config):995 """Plot number of subjects in studies by domain.996 """997 # Split values into separate rows and remove invalid values998 col = 'Data - subjects'999 nb_subj_df = ut.split_column_with_multiple_entries(1000 df, col, ref_col='Main domain')1001 nb_subj_df = nb_subj_df.loc[~nb_subj_df[col].isin(['n/m', 'tbd'])]1002 nb_subj_df[col] = nb_subj_df[col].astype(int)1003 nb_subj_df = nb_subj_df.loc[nb_subj_df[col] > 0, :]1004 nb_subj_df['Main domain'] = nb_subj_df['Main domain'].apply(1005 ut.wrap_text, max_char=13)1006 fig, ax = plt.subplots(1007 figsize=(save_cfg['text_width'] / 3 * 2, save_cfg['text_height'] / 3))1008 ax.set(xscale='log', yscale='linear')1009 sns.swarmplot(1010 y='Main domain', x=col, data=nb_subj_df, 1011 ax=ax, size=3, order=nb_subj_df.groupby(['Main domain'])[1012 col].median().sort_values().index)1013 ax.set_xlabel('Number of subjects')1014 ax.set_ylabel('')1015 1016 logger.info('Stats on number of subjects per model: {}'.format(1017 nb_subj_df[col].describe()))1018 plt.tight_layout()1019 if save_cfg is not None:1020 fname = os.path.join(save_cfg['savepath'], 'nb_subject_per_domain')1021 fig.savefig(fname + '.' + save_cfg['format'], **save_cfg)1022 return ax 1023def plot_number_channels(df, save_cfg=cfg.saving_config):1024 """Plot histogram of number of channels.1025 """1026 nb_channels_df = ut.split_column_with_multiple_entries(1027 df, 'Nb Channels', ref_col='Citation', sep=';\n', lower=False)1028 nb_channels_df['Nb Channels'] = nb_channels_df['Nb Channels'].astype(int)1029 nb_channels_df = nb_channels_df.loc[nb_channels_df['Nb Channels'] > 0, :]1030 fig, ax = plt.subplots(1031 figsize=(save_cfg['text_width'] / 2, save_cfg['text_height'] / 4))1032 sns.distplot(nb_channels_df['Nb Channels'], kde=False, norm_hist=False, ax=ax)1033 ax.set_xlabel('Number of EEG channels')1034 ax.set_ylabel('Number of papers')1035 logger.info('Stats on number of channels per model: {}'.format(1036 nb_channels_df['Nb Channels'].describe()))1037 plt.tight_layout()1038 if save_cfg is not None:1039 fname = os.path.join(save_cfg['savepath'], 'nb_channels')1040 fig.savefig(fname + '.' + save_cfg['format'], **save_cfg)1041 return ax1042def compute_stats_sampling_rate(df):1043 """Compute the statistics for hardware sampling rate.1044 """1045 fs_df = ut.split_column_with_multiple_entries(1046 df, 'Sampling rate', ref_col='Citation', sep=';\n', lower=False)1047 fs_df['Sampling rate'] = fs_df['Sampling rate'].astype(float)1048 fs_df = fs_df.loc[fs_df['Sampling rate'] > 0, :]1049 logger.info('Stats on sampling rate per model: {}'.format(1050 fs_df['Sampling rate'].describe()))1051def plot_cross_validation(df, save_cfg=cfg.saving_config):1052 """Plot bar graph of cross validation approaches.1053 """1054 col = 'Cross validation (clean)'1055 df[col] = df[col].fillna('N/M')1056 cv_df = ut.split_column_with_multiple_entries(1057 df, col, ref_col='Citation', sep=';\n', lower=False)1058 1059 fig, ax = plt.subplots(1060 figsize=(save_cfg['text_width'] / 2, save_cfg['text_height'] / 5))1061 sns.countplot(y=cv_df[col], order=cv_df[col].value_counts().index, ax=ax)1062 ax.set_xlabel('Number of papers')1063 ax.set_ylabel('')1064 1065 plt.tight_layout()1066 if save_cfg is not None:1067 fname = os.path.join(save_cfg['savepath'], 'cross_validation')1068 fig.savefig(fname + '.' + save_cfg['format'], **save_cfg)1069 return ax1070def make_dataset_table(df, min_n_articles=2, save_cfg=cfg.saving_config):1071 """Make table that reports most used datasets.1072 Args:1073 df1074 Keyword Args:1075 min_n_articles (int): minimum number of times a dataset must have been1076 used to be listed in the table. If under that number, will appear as1077 'Other' in the table.1078 save_cfg (dict)1079 """1080 def merge_dataset_names(s):1081 if 'bci comp' in s.lower():1082 s = 'BCI Competition'1083 elif 'tuh' in s.lower():1084 s = 'TUH'1085 elif 'mahnob' in s.lower():1086 s = 'MAHNOB'1087 return s1088 col = 'Dataset name'1089 datasets_df = ut.split_column_with_multiple_entries(1090 df, col, ref_col=['Main domain', 'Citation'], sep=';\n', lower=False)1091 # Remove not mentioned and internal recordings, as readers won't be able to 1092 # use these datasets anyway1093 datasets_df = datasets_df.loc[~datasets_df[col].isin(1094 ['N/M', 'Internal Recordings', 'TBD'])]1095 datasets_df['Dataset'] = datasets_df[col].apply(merge_dataset_names).apply(1096 ut.tex_escape)1097 # Replace datasets that were used rarely by 'Other'1098 counts = datasets_df['Dataset'].value_counts()1099 datasets_df.loc[datasets_df['Dataset'].isin(1100 counts[counts < min_n_articles].index), 'Dataset'] = 'Other'1101 # Remove duplicates (due to grouping of Others and BCI Comp)1102 datasets_df = datasets_df.drop(labels=col, axis=1)1103 datasets_df = datasets_df.drop_duplicates()1104 # Group by dataset and order by number of articles1105 dataset_table = datasets_df.groupby(1106 ['Main domain', 'Dataset'], as_index=True)['Citation'].apply(list)1107 dataset_table = pd.concat([dataset_table.apply(len), dataset_table], axis=1)1108 dataset_table.columns = [r'\# articles', 'References']1109 dataset_table = dataset_table.sort_values(1110 by=['Main domain', r'\# articles'], ascending=[True, False])1111 dataset_table['References'] = dataset_table['References'].apply(1112 lambda x: r'\cite{' + ', '.join(x) + '}')1113 with open(os.path.join(save_cfg['table_savepath'], 'dataset_table.tex'), 'w') as f:1114 with pd.option_context("max_colwidth", 1000):1115 f.write(dataset_table.to_latex(escape=False, multicolumn=False))1116def plot_data_quantity(df, save_cfg=cfg.saving_config):1117 """Plot the quantity of data used by domain.1118 """1119 data_df = ut.split_column_with_multiple_entries(1120 df, ['Data - samples', 'Data - time'], ref_col=['Citation', 'Main domain'], 1121 sep=';\n', lower=False)1122 # Remove N/M and TBD1123 col = 'Data - samples'1124 data_df.loc[data_df[col].isin(['N/M', 'TBD', '[TBD]']), col] = np.nan1125 data_df[col] = data_df[col].astype(float)1126 col2 = 'Data - time'1127 data_df.loc[data_df[col2].isin(['N/M', 'TBD', '[TBD]']), col2] = np.nan1128 data_df[col2] = data_df[col2].astype(float)1129 # Wrap main domain text1130 data_df['Main domain'] = data_df['Main domain'].apply(1131 ut.wrap_text, max_char=13)1132 # Extract ratio1133 data_df['data_ratio'] = data_df['Data - samples'] / data_df['Data - time']1134 data_df = data_df.sort_values(['Main domain', 'data_ratio'])1135 # Plot1136 fig, axes = plt.subplots(1137 ncols=3, 1138 figsize=(save_cfg['text_width'], save_cfg['text_height'] / 3))1139 axes[0].set(xscale='log', yscale='linear')1140 sns.swarmplot(y='Main domain', x=col2, data=data_df, ax=axes[0], size=3)1141 axes[0].set_xlabel('Recording time (min)')1142 axes[0].set_ylabel('')1143 max_val = int(np.ceil(np.log10(data_df[col2].max())))1144 axes[0].set_xticks(np.power(10, range(0, max_val + 1)))1145 axes[1].set(xscale='log', yscale='linear')1146 sns.swarmplot(y='Main domain', x=col, data=data_df, ax=axes[1], size=3)1147 axes[1].set_xlabel('Number of examples')1148 axes[1].set_yticklabels('')1149 axes[1].set_ylabel('')1150 min_val = int(np.floor(np.log10(data_df[col].min())))1151 max_val = int(np.ceil(np.log10(data_df[col].max())))1152 axes[1].set_xticks(np.power(10, range(min_val, max_val + 1)))1153 axes[2].set(xscale='log', yscale='linear')1154 sns.swarmplot(y='Main domain', x='data_ratio', data=data_df, ax=axes[2], 1155 size=3)1156 axes[2].set_xlabel('Ratio (examples/min)')1157 axes[2].set_ylabel('')1158 axes[2].set_yticklabels('')1159 min_val = int(np.floor(np.log10(data_df['data_ratio'].min())))1160 max_val = int(np.ceil(np.log10(data_df['data_ratio'].max())))1161 axes[2].set_xticks(np.power(10, np.arange(min_val, max_val + 1, dtype=float)))1162 plt.tight_layout()1163 if save_cfg is not None:1164 fname = os.path.join(save_cfg['savepath'], 'data_quantity')1165 fig.savefig(fname + '.' + save_cfg['format'], **save_cfg)1166 return axes1167def plot_eeg_intro(save_cfg=cfg.saving_config):1168 """Plot a figure that shows basic EEG notions such as epochs and samples.1169 """1170 # Visualization parameters1171 win_len = 1 # in s1172 step = 0.5 # in s1173 first_epoch = 11174 data, t, fs = ut.get_real_eeg_data(start=30, stop=34, chans=[0, 10, 20, 30])1175 t = t - t[0]1176 # Offset data for visualization1177 data -= data.mean(axis=0)1178 max_std = np.max(data.std(axis=0))1179 offsets = np.arange(data.shape[1])[::-1] * 4 * max_std1180 data += offsets1181 rect_y_border = 0.6 * max_std1182 min_y = data.min() - rect_y_border1183 max_y = data.max() + rect_y_border1184 # Make figure1185 fig, ax = plt.subplots(1186 figsize=(save_cfg['text_width'] / 4 * 3, save_cfg['text_height'] / 3))1187 ax.plot(t, data)1188 ax.set_xlabel('Time (s)')1189 ax.set_ylabel(r'Amplitude (e.g., $\mu$V)')1190 ax.set_yticks(offsets)1191 ax.set_yticklabels(['channel {}'.format(i + 1) for i in range(data.shape[1])])1192 ax.spines['top'].set_visible(False)1193 ax.spines['right'].set_visible(False)1194 # Display epochs as dashed line rectangles1195 rect1 = patches.Rectangle((first_epoch, min_y + rect_y_border / 4), 1196 win_len, max_y - min_y, 1197 linewidth=1, linestyle='--', edgecolor='k',1198 facecolor='none')1199 rect2 = patches.Rectangle((first_epoch + step, min_y - rect_y_border / 4), 1200 win_len, max_y - min_y, 1201 linewidth=1, linestyle='--', edgecolor='k',1202 facecolor='none')1203 ax.add_patch(rect1)1204 ax.add_patch(rect2)1205 # Annotate epochs1206 ax.annotate(1207 r'$\bf{Window}$ or $\bf{epoch}$ or $\bf{trial}$' +1208 '\n({:.0f} points in a \n1-s window at {:.0f} Hz)'.format(fs, fs), #fontsize=14, 1209 xy=(first_epoch, min_y), 1210 arrowprops=dict(facecolor='black', shrink=0.05, width=2, headwidth=6),1211 xytext=(0, min_y - 3.5 * max_std),1212 xycoords='data', ha='center', va='top')1213 1214 # Annotate input1215 ax.annotate(r'Neural network input' + '\n'1216 r'$X_i \in \mathbb{R}^{c \times l}$', #fontsize=14,1217 xy=(first_epoch+1.5, min_y),1218 arrowprops=dict(facecolor='black', shrink=0.05, width=2),1219 xytext=(4, min_y - 5.3 * max_std),1220 xycoords='data', ha='right', va='bottom')1221 # Annotate sample1222 special_ind = np.where((t >= 2.4) & (t < 2.5))[0][0]1223 special_point = data[special_ind, 0]1224 ax.plot(t[special_ind], special_point, '.', c='k')1225 ax.annotate(1226 r'$\bf{Point}$ or $\bf{sample}$', #fontsize=14, 1227 xy=(t[special_ind], special_point), 1228 arrowprops=dict(facecolor='black', shrink=0.05, width=2, headwidth=6),1229 xytext=(3, max_y),1230 xycoords='data', ha='left', va='bottom')1231 # Annotate overlap1232 ut.draw_brace(ax, (first_epoch + step, first_epoch + step * 2), 1233 r'0.5-s $\bf{overlap}$' + '\nbetween windows', 1234 beta_factor=300, y_offset=max_y)1235 plt.tight_layout()1236 if save_cfg is not None:1237 fname = os.path.join(save_cfg['savepath'], 'eeg_intro')1238 fig.savefig(fname + '.' + save_cfg['format'], **save_cfg)...
utils.py
Source:utils.py
...119 }120 'optimizer_state_dict': xxx121 }122 Args:123 save_cfg(namedtuple): The configuration object of the saving process. It must contain the follows:124 save_cfg.output_dir: the output directory of the model or checkpoint125 save_cfg.low: the lowest value of the metric to save126 save_cfg.cfg_name: the name of the configuration127 save_cfg.dataset_name: the name of the dataset128 save_cfg.model_name: the name of the model129 save_cfg.time_stamp: the time when the engine start130 cfg_name: the name of the configuration file # will be deprecated in the future131 current_step(int): Which step stores the ckpt or model132 saved_stuff(dict): The saving things incules the model, epoch, loss, optimizer. At least, it contains the model. For example:133 {134 'step': 0,135 'loss':0,136 $model_name: xxxx,137 $optimizer_name: xxx
...
save_img.py
Source:save_img.py
1import glob2import os3import SimpleITK as sitk4import imageio5import matplotlib6import matplotlib.pyplot as plt7import numpy as np8matplotlib.use('Agg')9import torch10def plot_save_img(input_img, pred_img, target_img, save_cfg):11 input_img = input_img.squeeze()12 pred_img = pred_img.squeeze()13 target_img = target_img.squeeze()14 input_img = torch.clamp(input_img, min=0, max=1.)15 pred_img = torch.clamp(pred_img, min=0, max=1.)16 target_img = torch.clamp(target_img, min=0, max=1.)17 if len(input_img) == 3:18 input_img = input_img.squeeze().permute(1, 2, 0).cpu().numpy()19 pred_img = pred_img.squeeze().permute(1, 2, 0).cpu().numpy()20 target_img = target_img.squeeze().permute(1, 2, 0).cpu().numpy()21 else:22 input_img = input_img.squeeze().cpu().numpy()23 pred_img = pred_img.squeeze().cpu().numpy()24 target_img = target_img.squeeze().cpu().numpy()25 fig, ax = plt.subplots(1, 3, figsize=(30, 10))26 fig.suptitle(save_cfg['name'], fontsize=20)27 ax[0].imshow(input_img, cmap='gray')28 ax[0].set_title("Input", fontsize=20)29 ax[0].grid(False)30 ax[0].set_xlabel("PSNR: {:.4f}\nSSIM: {:.4f}\n".format(save_cfg['org_psnr'], save_cfg['org_ssim']), fontsize=20)31 ax[1].imshow(pred_img, cmap='gray')32 ax[1].set_title("Prediction", fontsize=20)33 ax[1].grid(False)34 ax[1].set_xlabel("PSNR: {:.4f}\nSSIM: {:.4f}\n".format(save_cfg['pred_psnr'], save_cfg['pred_ssim']), fontsize=20)35 ax[2].imshow(target_img, cmap='gray')36 ax[2].set_title("Target", fontsize=20)37 ax[2].grid(False)38 fig.savefig(os.path.join(save_cfg['save_path'], 'result_{}.png'.format(save_cfg['name'])))39 plt.close()40def plot_save_ct(input_img, pred_img, target_img, save_cfg):41 input_img = torch.clamp(input_img, min=0, max=1.)42 pred_img = torch.clamp(pred_img, min=0, max=1.)43 target_img = torch.clamp(target_img, min=0, max=1.)44 if len(input_img) == 3:45 input_img = input_img.squeeze().permute(1, 2, 0).cpu().numpy()46 pred_img = pred_img.squeeze().permute(1, 2, 0).cpu().numpy()47 target_img = target_img.squeeze().permute(1, 2, 0).cpu().numpy()48 else:49 input_img = input_img.squeeze().cpu().numpy()50 pred_img = pred_img.squeeze().cpu().numpy()51 target_img = target_img.squeeze().cpu().numpy()52 input_img = trunc_denorm(input_img, trunc_max=240, trunc_min=-160)53 pred_img = trunc_denorm(pred_img, trunc_max=240, trunc_min=-160)54 target_img = trunc_denorm(target_img, trunc_max=240, trunc_min=-160)55 fig, ax = plt.subplots(1, 3, figsize=(30, 10))56 fig.suptitle(save_cfg['name'], fontsize=20)57 ax[0].imshow(input_img, cmap='gray')58 ax[0].set_title("Input", fontsize=20)59 ax[0].grid(False)60 ax[0].set_xlabel("PSNR: {:.4f}\nSSIM: {:.4f}\n".format(save_cfg['org_psnr'], save_cfg['org_ssim']), fontsize=20)61 ax[1].imshow(pred_img, cmap='gray')62 ax[1].set_title("Prediction", fontsize=20)63 ax[1].grid(False)64 ax[1].set_xlabel("PSNR: {:.4f}\nSSIM: {:.4f}\n".format(save_cfg['pred_psnr'], save_cfg['pred_ssim']), fontsize=20)65 ax[2].imshow(target_img, cmap='gray')66 ax[2].set_title("Target", fontsize=20)67 ax[2].grid(False)68 fig.savefig(os.path.join(save_cfg['save_path'], 'plot_{}.png'.format(save_cfg['name'])))69 plt.close()70def save_single_slice(pred_img, save_cfg):71 pred_img = torch.clamp(pred_img, min=0, max=1.)72 if len(pred_img) == 3:73 pred_img = pred_img.squeeze().permute(1, 2, 0).cpu().numpy()74 else:75 pred_img = pred_img.squeeze().cpu().numpy()76 pred_img = trunc_denorm(pred_img) + 102477 pred_img = ((pred_img / 4096) * 65535).astype(np.uint16)78 imageio.imwrite(os.path.join(save_cfg['save_path'], 'single_{}.png'.format(save_cfg['name'])), pred_img)79def trunc_denorm(image, trunc_max=3072.0, trunc_min=-1024.0, norm_range_max=3072.0, norm_range_min=-1024.0):80 image = denormalize(image, norm_range_max, norm_range_min)81 image = trunc(image, trunc_max, trunc_min)82 return image83def denormalize(image, norm_range_max=3072.0, norm_range_min=-1024.0):84 image = image * (norm_range_max - norm_range_min) + norm_range_min85 return image86def trunc(image, trunc_max, trunc_min):87 image[image <= trunc_min] = trunc_min88 image[image >= trunc_max] = trunc_max89 return image90def save_nifti(arrays, save_cfg, params):91 nifti_org = sorted(glob.glob(os.path.join(params.data_dir, params.subject, '*.nii.gz')))92 image_org = sitk.ReadImage(nifti_org[0])93 images = sitk.GetImageFromArray(arrays)94 images.CopyInformation(image_org)...
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