megadetector 5.0.11__py3-none-any.whl → 5.0.12__py3-none-any.whl

megadetector/postprocessing/render_detection_confusion_matrix.py

@@ -0,0 +1,660 @@
+"""
+
+render_detection_confusion_matrix.py
+
+Given a CCT-formatted ground truth file and a MegaDetector-formatted results file,
+render an HTML confusion matrix.  Typically used for multi-class detectors.  Currently
+assumes a single class per image.
+
+"""
+
+#%% Imports and constants
+
+import os
+import json
+
+import matplotlib.pyplot as plt
+import numpy as np
+
+from tqdm import tqdm
+from collections import defaultdict
+from functools import partial
+
+from megadetector.utils.path_utils import find_images
+from megadetector.utils.path_utils import flatten_path
+from megadetector.utils.write_html_image_list import write_html_image_list
+from megadetector.visualization import visualization_utils as vis_utils
+from megadetector.visualization import plot_utils
+
+from multiprocessing.pool import ThreadPool
+from multiprocessing.pool import Pool
+
+
+#%% Support functions
+
+def _image_to_output_file(im,preview_images_folder):
+    """
+    Produces a clean filename from im (if [im] is a str) or im['file'] (if [im] is a dict).
+    """
+    
+    if isinstance(im,str):
+        filename_relative = im
+    else:
+        filename_relative = im['file']
+        
+    fn_clean = flatten_path(filename_relative).replace(' ','_')
+    return os.path.join(preview_images_folder,fn_clean)
+
+
+def _render_image(im,render_image_constants):
+    """
+    Internal function for rendering a single image to the confusion matrix preview folder.
+    """
+    
+    filename_to_ground_truth_im = render_image_constants['filename_to_ground_truth_im']
+    image_folder = render_image_constants['image_folder']
+    preview_images_folder = render_image_constants['preview_images_folder']
+    force_render_images = render_image_constants['force_render_images']
+    results_category_id_to_name = render_image_constants['results_category_id_to_name']
+    rendering_confidence_thresholds = render_image_constants['rendering_confidence_thresholds']
+    target_image_size = render_image_constants['target_image_size']
+    
+    assert im['file'] in filename_to_ground_truth_im
+    
+    output_file = _image_to_output_file(im,preview_images_folder)
+    if os.path.isfile(output_file) and not force_render_images:
+        return output_file
+    
+    input_file = os.path.join(image_folder,im['file'])
+    assert os.path.isfile(input_file)
+                          
+    detections_to_render = []
+    
+    for det in im['detections']:
+        category_name = results_category_id_to_name[det['category']]
+        detection_threshold = rendering_confidence_thresholds['default']
+        if category_name in rendering_confidence_thresholds:
+            detection_threshold = rendering_confidence_thresholds[category_name]
+        if det['conf'] > detection_threshold:
+            detections_to_render.append(det)
+        
+    vis_utils.draw_bounding_boxes_on_file(input_file, output_file, detections_to_render,
+                                          detector_label_map=results_category_id_to_name,
+                                          label_font_size=20,target_size=target_image_size)
+    
+    return output_file
+
+
+#%% Main function
+
+def render_detection_confusion_matrix(ground_truth_file,
+                                      results_file,
+                                      image_folder,
+                                      preview_folder,
+                                      force_render_images=False, 
+                                      confidence_thresholds=None,
+                                      rendering_confidence_thresholds=None,
+                                      target_image_size=(1280,-1),
+                                      parallelize_rendering=True,
+                                      parallelize_rendering_n_cores=None,
+                                      parallelize_rendering_with_threads=False,
+                                      job_name='unknown',
+                                      model_file=None,
+                                      empty_category_name='empty',
+                                      html_image_list_options=None):
+    """    
+    Given a CCT-formatted ground truth file and a MegaDetector-formatted results file,
+    render an HTML confusion matrix in [preview_folder.  Typically used for multi-class detectors. 
+    Currently assumes a single class per image.
+    
+    confidence_thresholds and rendering_confidence_thresholds are dictionaries mapping
+    class names to thresholds.  "default" is a special token that will be used for all
+    classes not otherwise assigned thresholds.
+    
+    Args:
+        ground_truth_file (str): the CCT-formatted .json file with ground truth information
+        results_file (str): the MegaDetector results .json file
+        image_folder (str): the folder where images live; filenames in [ground_truth_file] and
+            [results_file] should be relative to this folder.
+        preview_folder (str): the output folder, i.e. the folder in which we'll create our nifty
+            HTML stuff.
+        force_rendering_images (bool, optional): if False, skips images that already exist
+        confidence_thresholds (dict, optional): a dictionary mapping class names to thresholds;
+            all classes not explicitly named here will use the threshold for the "default" category.
+        rendering_thresholds (dict, optional): a dictionary mapping class names to thresholds;
+            all classes not explicitly named here will use the threshold for the "default" category.
+        target_image_size (tuple, optional): output image size, as a pair of ints (width,height).  If one 
+            value is -1 and the other is not, aspect ratio is preserved.  If both are -1, the original image
+            sizes are preserved.
+        parallelize_rendering (bool, optional): enable (default) or disable parallelization when rendering
+        parallelize_rendering_n_core (int, optional): number of threads or processes to use for rendering, only
+            used if parallelize_rendering is True
+        parallelize_rendering_with_threads: whether to use threads (True) or processes (False) when rendering,
+            only used if parallelize_rendering is True
+        job_name (str, optional): job name to include in big letters in the output file
+        model_file (str, optional) model filename to include in HTML output
+        empty_category_name (str, optional): special category name that we should treat as empty, typically
+            "empty"
+        html_image_list_options (dict, optional): options listed passed along to write_html_image_list; 
+            see write_html_image_list for documentation.            
+    """
+    
+    ##%% Argument and path handling
+    
+    preview_images_folder = os.path.join(preview_folder,'images')
+    os.makedirs(preview_images_folder,exist_ok=True)
+
+    if confidence_thresholds is None:
+        confidence_thresholds = {'default':0.5}
+    if rendering_confidence_thresholds is None:
+        rendering_confidence_thresholds = {'default':0.4}
+    
+
+    ##%% Load ground truth 
+        
+    with open(ground_truth_file,'r') as f:
+        ground_truth_data_cct = json.load(f)
+    
+    filename_to_ground_truth_im = {}
+    for im in ground_truth_data_cct['images']:
+        assert im['file_name'] not in filename_to_ground_truth_im
+        filename_to_ground_truth_im[im['file_name']] = im
+    
+    
+    ##%% Confirm that the ground truth images are present in the image folder
+    
+    ground_truth_images = find_images(image_folder,return_relative_paths=True,recursive=True)
+    assert len(ground_truth_images) == len(ground_truth_data_cct['images'])
+    del ground_truth_images
+    
+    
+    ##%% Map images to categories
+    
+    # gt_image_id_to_image = {im['id']:im for im in ground_truth_data_cct['images']}
+    gt_image_id_to_annotations = defaultdict(list)
+    
+    ground_truth_category_id_to_name = {}
+    for c in ground_truth_data_cct['categories']:
+        ground_truth_category_id_to_name[c['id']] = c['name']
+    
+    # Add the empty category if necessary
+    if empty_category_name not in ground_truth_category_id_to_name.values():
+        empty_category_id = max(ground_truth_category_id_to_name.keys())+1
+        ground_truth_category_id_to_name[empty_category_id] = empty_category_name
+        
+    ground_truth_category_names = sorted(list(ground_truth_category_id_to_name.values()))
+        
+    for ann in ground_truth_data_cct['annotations']:
+        gt_image_id_to_annotations[ann['image_id']].append(ann)
+        
+    gt_filename_to_category_names = defaultdict(set)
+    
+    for im in ground_truth_data_cct['images']:
+        annotations_this_image = gt_image_id_to_annotations[im['id']]
+        for ann in annotations_this_image:
+            category_name = ground_truth_category_id_to_name[ann['category_id']]
+            gt_filename_to_category_names[im['file_name']].add(category_name)
+            
+    for filename in gt_filename_to_category_names:
+        
+        category_names_this_file = gt_filename_to_category_names[filename]
+        
+        # The empty category should be exclusive
+        if empty_category_name in category_names_this_file:
+            assert len(category_names_this_file) == 1, \
+              'Empty category assigned along with another category for {}'.format(filename)
+        assert len(category_names_this_file) > 0, \
+            'No ground truth category assigned to {}'.format(filename)
+    
+        
+    ##%% Load results
+    
+    with open(results_file,'r') as f:
+        md_formatted_results = json.load(f)
+    
+    results_category_id_to_name = md_formatted_results['detection_categories']
+    
+    
+    ##%% Render images with detections    
+    
+    render_image_constants = {}
+    render_image_constants['filename_to_ground_truth_im'] = filename_to_ground_truth_im
+    render_image_constants['image_folder'] = image_folder
+    render_image_constants['preview_images_folder'] = preview_images_folder
+    render_image_constants['force_render_images'] = force_render_images
+    render_image_constants['results_category_id_to_name'] = results_category_id_to_name
+    render_image_constants['rendering_confidence_thresholds'] = rendering_confidence_thresholds
+    render_image_constants['target_image_size'] = target_image_size    
+    
+    if parallelize_rendering:
+
+        if parallelize_rendering_n_cores is None:                
+            if parallelize_rendering_with_threads:
+                pool = ThreadPool()
+            else:
+                pool = Pool()
+        else:
+            if parallelize_rendering_with_threads:
+                pool = ThreadPool(parallelize_rendering_n_cores)
+                worker_string = 'threads'
+            else:
+                pool = Pool(parallelize_rendering_n_cores)
+                worker_string = 'processes'
+            print('Rendering images with {} {}'.format(parallelize_rendering_n_cores,
+                                                       worker_string))
+            
+        _ = list(tqdm(pool.imap(partial(_render_image,render_image_constants=render_image_constants),
+                                md_formatted_results['images']),
+                                total=len(md_formatted_results['images'])))        
+    
+    else:
+        
+        # im = md_formatted_results['images'][0]
+        for im in tqdm(md_formatted_results['images']):    
+            _render_image(im,render_image_constants)
+    
+    
+    ##%% Map images to predicted categories, and vice-versa
+    
+    filename_to_predicted_categories = defaultdict(set)
+    predicted_category_name_to_filenames = defaultdict(set)
+    
+    # im = md_formatted_results['images'][0]
+    for im in tqdm(md_formatted_results['images']):
+        
+        assert im['file'] in filename_to_ground_truth_im
+        
+        # det = im['detections'][0]
+        for det in im['detections']:
+            category_name = results_category_id_to_name[det['category']]
+            detection_threshold = confidence_thresholds['default']
+            if category_name in confidence_thresholds:
+                detection_threshold = confidence_thresholds[category_name]
+            if det['conf'] > detection_threshold:
+                filename_to_predicted_categories[im['file']].add(category_name)
+                predicted_category_name_to_filenames[category_name].add(im['file'])
+                
+        # ...for each detection
+    
+    # ...for each image
+    
+    
+    ##%% Create TP/TN/FP/FN lists
+    
+    category_name_to_image_lists = {}
+    
+    sub_page_tokens = ['fn','tn','fp','tp']
+    
+    for category_name in ground_truth_category_names:
+        
+        category_name_to_image_lists[category_name] = {}
+        for sub_page_token in sub_page_tokens:
+            category_name_to_image_lists[category_name][sub_page_token] = []
+        
+    # filename = next(iter(gt_filename_to_category_names))
+    for filename in gt_filename_to_category_names.keys():
+        
+        ground_truth_categories_this_image = gt_filename_to_category_names[filename]
+        predicted_categories_this_image = filename_to_predicted_categories[filename]
+        
+        for category_name in ground_truth_category_names:
+            
+            assignment = None
+            
+            if category_name == empty_category_name:
+                # If this is an empty image
+                if category_name in ground_truth_categories_this_image:
+                    assert len(ground_truth_categories_this_image) == 1
+                    if len(predicted_categories_this_image) == 0:
+                        assignment = 'tp'
+                    else:
+                        assignment = 'fn'
+                # If this not an empty image
+                else:
+                    if len(predicted_categories_this_image) == 0:
+                        assignment = 'fp'
+                    else:
+                        assignment = 'tn'
+                    
+            else:
+                if category_name in ground_truth_categories_this_image:
+                    if category_name in predicted_categories_this_image:
+                        assignment = 'tp'
+                    else:
+                        assignment = 'fn'
+                else:
+                    if category_name in predicted_categories_this_image:
+                        assignment = 'fp'
+                    else:
+                        assignment = 'tn'        
+                            
+            category_name_to_image_lists[category_name][assignment].append(filename)
+                        
+    # ...for each filename
+    
+    
+    ##%% Create confusion matrix
+    
+    gt_category_name_to_category_index = {}
+    
+    for i_category,category_name in enumerate(ground_truth_category_names):
+        gt_category_name_to_category_index[category_name] = i_category
+    
+    n_categories = len(gt_category_name_to_category_index)    
+    
+    # indexed as [true,predicted]
+    confusion_matrix = np.zeros(shape=(n_categories,n_categories),dtype=int)
+    
+    filename_to_results_im = {im['file']:im for im in md_formatted_results['images']}
+    
+    true_predicted_to_file_list = defaultdict(list)
+    
+    # filename = next(iter(gt_filename_to_category_names.keys()))
+    for filename in gt_filename_to_category_names.keys():
+        
+        ground_truth_categories_this_image = gt_filename_to_category_names[filename]
+        assert len(ground_truth_categories_this_image) == 1
+        ground_truth_category_name = next(iter(ground_truth_categories_this_image))
+        
+        results_im = filename_to_results_im[filename]
+        
+        # If there were no detections at all, call this image empty
+        if len(results_im['detections']) == 0:
+            predicted_category_name = empty_category_name
+        # Otherwise look for above-threshold detections
+        else:            
+            results_category_name_to_confidence = defaultdict(int)
+            for det in results_im['detections']:
+                category_name = results_category_id_to_name[det['category']]
+                detection_threshold = confidence_thresholds['default']
+                if category_name in confidence_thresholds:
+                    detection_threshold = confidence_thresholds[category_name]
+                if det['conf'] > detection_threshold:
+                    results_category_name_to_confidence[category_name] = max(
+                        results_category_name_to_confidence[category_name],det['conf'])
+                # If there were no detections above threshold
+                if len(results_category_name_to_confidence) == 0:
+                    predicted_category_name = empty_category_name
+                else:
+                    predicted_category_name = max(results_category_name_to_confidence,
+                        key=results_category_name_to_confidence.get)
+        
+        ground_truth_category_index = gt_category_name_to_category_index[ground_truth_category_name]
+        predicted_category_index = gt_category_name_to_category_index[predicted_category_name]
+        
+        true_predicted_token = ground_truth_category_name + '_' + predicted_category_name
+        true_predicted_to_file_list[true_predicted_token].append(filename)
+        
+        confusion_matrix[ground_truth_category_index,predicted_category_index] += 1
+    
+    # ...for each file
+    
+    plt.ioff()    
+    
+    fig_h = 3 + 0.3 * n_categories
+    fig_w = fig_h
+    fig = plt.figure(figsize=(fig_w, fig_h),tight_layout=True)
+        
+    plot_utils.plot_confusion_matrix(
+        matrix=confusion_matrix,
+        classes=ground_truth_category_names,
+        normalize=False,
+        title='Confusion matrix',
+        cmap=plt.cm.Blues,
+        vmax=1.0,
+        use_colorbar=False,
+        y_label=True,
+        fig=fig)
+    
+    cm_figure_fn_relative = 'confusion_matrix.png'
+    cm_figure_fn_abs = os.path.join(preview_folder, cm_figure_fn_relative)
+    # fig.show()
+    fig.savefig(cm_figure_fn_abs,dpi=100)
+    plt.close(fig)
+    
+    # open_file(cm_figure_fn_abs)
+    
+    
+    ##%% Create HTML confusion matrix
+    
+    html_confusion_matrix = '<table class="result-table">\n'
+    html_confusion_matrix += '<tr>\n'
+    html_confusion_matrix += '<td>{}</td>\n'.format('True category')
+    for category_name in ground_truth_category_names:
+        html_confusion_matrix += '<td>{}</td>\n'.format('&nbsp;')
+    html_confusion_matrix += '</tr>\n'
+    
+    for true_category in ground_truth_category_names:
+        
+        html_confusion_matrix += '<tr>\n'
+        html_confusion_matrix += '<td>{}</td>\n'.format(true_category)
+        
+        for predicted_category in ground_truth_category_names:
+            
+            true_predicted_token = true_category + '_' + predicted_category
+            image_list = true_predicted_to_file_list[true_predicted_token]
+            if len(image_list) == 0:
+                td_content = '0'
+            else:
+                if html_image_list_options is None:
+                    html_image_list_options = {}
+                title_string = 'true: {}, predicted {}'.format(
+                    true_category,predicted_category)
+                html_image_list_options['headerHtml'] = '<h1>{}</h1>'.format(title_string)
+                
+                html_image_info_list = []
+                
+                for image_filename_relative in image_list:
+                    html_image_info = {}
+                    detections = filename_to_results_im[image_filename_relative]['detections']
+                    if len(detections) == 0:
+                        max_conf = 0
+                    else:
+                        max_conf = max([d['conf'] for d in detections])
+                    
+                    title = '<b>Image</b>: {}, <b>Max conf</b>: {:0.3f}'.format(
+                        image_filename_relative, max_conf)
+                    image_link = 'images/' + os.path.basename(
+                        _image_to_output_file(image_filename_relative,preview_images_folder))
+                    html_image_info = {
+                        'filename': image_link,
+                        'title': title,
+                        'textStyle':\
+                         'font-family:verdana,arial,calibri;font-size:80%;' + \
+                             'text-align:left;margin-top:20;margin-bottom:5'
+                    }                
+                    
+                    html_image_info_list.append(html_image_info)
+                
+                target_html_file_relative = true_predicted_token + '.html'
+                target_html_file_abs = os.path.join(preview_folder,target_html_file_relative)
+                write_html_image_list(
+                    filename=target_html_file_abs,
+                    images=html_image_info_list,
+                    options=html_image_list_options)
+                
+                td_content = '<a href="{}">{}</a>'.format(target_html_file_relative,
+                                                          len(image_list))
+            
+            html_confusion_matrix += '<td>{}</td>\n'.format(td_content)
+        
+        # ...for each predicted category
+        
+        html_confusion_matrix += '</tr>\n'
+        
+    # ...for each true category    
+    
+    html_confusion_matrix += '<tr>\n'
+    html_confusion_matrix += '<td>&nbsp;</td>\n'
+    
+    for category_name in ground_truth_category_names:
+        html_confusion_matrix += '<td class="rotate"><p style="margin-left:20px;">{}</p></td>\n'.format(
+            category_name)
+    html_confusion_matrix += '</tr>\n'
+    
+    html_confusion_matrix += '</table>'
+    
+        
+    ##%% Create HTML sub-pages and HTML table
+    
+    html_table = '<table class="result-table">\n'
+    
+    html_table += '<tr>\n'
+    html_table += '<td>{}</td>\n'.format('True category')
+    for sub_page_token in sub_page_tokens:
+        html_table += '<td>{}</td>'.format(sub_page_token)
+    html_table += '</tr>\n'
+        
+    filename_to_results_im = {im['file']:im for im in md_formatted_results['images']}
+    
+    sub_page_token_to_page_name = {
+        'fp':'false positives',
+        'tp':'true positives',
+        'fn':'false negatives',
+        'tn':'true negatives'
+    }
+    
+    # category_name = ground_truth_category_names[0]
+    for category_name in ground_truth_category_names:
+        
+        html_table += '<tr>\n'
+        
+        html_table += '<td>{}</td>\n'.format(category_name)
+        
+        # sub_page_token = sub_page_tokens[0]
+        for sub_page_token in sub_page_tokens:
+            
+            html_table += '<td>\n'
+            
+            image_list = category_name_to_image_lists[category_name][sub_page_token]
+            
+            if len(image_list) == 0:
+                
+                html_table += '0\n'
+                
+            else:
+                
+                html_image_list_options = {}
+                title_string = '{}: {}'.format(category_name,sub_page_token_to_page_name[sub_page_token])
+                html_image_list_options['headerHtml'] = '<h1>{}</h1>'.format(title_string)
+                
+                target_html_file_relative = '{}_{}.html'.format(category_name,sub_page_token)
+                target_html_file_abs = os.path.join(preview_folder,target_html_file_relative)
+                
+                html_image_info_list = []
+                
+                # image_filename_relative = image_list[0]
+                for image_filename_relative in image_list:
+                    
+                    source_file = os.path.join(image_folder,image_filename_relative)
+                    assert os.path.isfile(source_file)
+                    
+                    html_image_info = {}
+                    detections = filename_to_results_im[image_filename_relative]['detections']
+                    if len(detections) == 0:
+                        max_conf = 0
+                    else:
+                        max_conf = max([d['conf'] for d in detections])
+                    
+                    title = '<b>Image</b>: {}, <b>Max conf</b>: {:0.3f}'.format(
+                        image_filename_relative, max_conf)
+                    image_link = 'images/' + os.path.basename(
+                        _image_to_output_file(image_filename_relative,preview_images_folder))
+                    html_image_info = {
+                        'filename': image_link,
+                        'title': title,
+                        'linkTarget': source_file,
+                        'textStyle':\
+                         'font-family:verdana,arial,calibri;font-size:80%;' + \
+                             'text-align:left;margin-top:20;margin-bottom:5'
+                    }                
+                    
+                    html_image_info_list.append(html_image_info)
+                    
+                # ...for each image
+                    
+                write_html_image_list(
+                    filename=target_html_file_abs,
+                    images=html_image_info_list,
+                    options=html_image_list_options)
+    
+                html_table += '<a href="{}">{}</a>\n'.format(target_html_file_relative,len(image_list))
+            
+            html_table += '</td>\n'
+    
+        # ...for each sub-page
+            
+        html_table += '</tr>\n'
+    
+    # ...for each category
+        
+    html_table += '</table>'        
+    
+    html = '<html>\n'
+    
+    style_header = """<head>
+        <style type="text/css">
+        a { text-decoration: none; }
+        body { font-family: segoe ui, calibri, "trebuchet ms", verdana, arial, sans-serif; }
+        div.contentdiv { margin-left: 20px; }
+        table.result-table { border:1px solid black; border-collapse: collapse; margin-left:50px;}
+        td,th { padding:10px; }
+        .rotate {    
+          padding:0px;
+          writing-mode:vertical-lr;
+          -webkit-transform: rotate(-180deg);        
+          -moz-transform: rotate(-180deg);            
+          -ms-transform: rotate(-180deg);         
+          -o-transform: rotate(-180deg);         
+          transform: rotate(-180deg);
+        }
+        </style>
+        </head>"""
+        
+    html += style_header + '\n'
+    
+    html += '<body>\n'
+    
+    html += '<h1>Results summary for {}</h1>\n'.format(job_name)
+    
+    if model_file is not None and len(model_file) > 0:
+        html += '<p><b>Model file</b>: {}</p>'.format(os.path.basename(model_file))
+    
+    html += '<p><b>Confidence thresholds</b></p>'
+    
+    for c in confidence_thresholds.keys():
+        html += '<p style="margin-left:15px;">{}: {}</p>'.format(c,confidence_thresholds[c])
+    
+    html += '<h2>Confusion matrix</h2>\n'
+    
+    html += '<p>...assuming a single category per image.</p>\n'
+    
+    html += '<img src="{}"/>\n'.format(cm_figure_fn_relative)
+    
+    html += '<h2>Confusion matrix (with links)</h2>\n'
+    
+    html += '<p>...assuming a single category per image.</p>\n'
+    
+    html += html_confusion_matrix
+    
+    html += '<h2>Per-class statistics</h2>\n'
+    
+    html += html_table
+    
+    html += '</body>\n'
+    html += '<html>\n'
+    
+    target_html_file = os.path.join(preview_folder,'index.html')
+    
+    with open(target_html_file,'w') as f:
+        f.write(html)
+    
+    
+    ##%% Prepare return data
+    
+    confusion_matrix_info = {}
+    confusion_matrix_info['html_file'] = target_html_file
+    
+    return confusion_matrix_info
+
+# ...render_detection_confusion_matrix(...)