megadetector 5.0.9__py3-none-any.whl → 5.0.11__py3-none-any.whl

md_visualization/visualize_detector_output.py

@@ -1,406 +0,0 @@
-"""
-
-visualize_detector_output.py
-
-Render images with bounding boxes annotated on them to a folder, based on a
-detector output result file (.json), optionally writing an HTML index file.
-
-"""
-
-#%% Imports
-
-import argparse
-import json
-import os
-import random
-import sys
-from multiprocessing.pool import ThreadPool
-from multiprocessing.pool import Pool
-from typing import List
-from functools import partial
-
-from tqdm import tqdm
-
-from data_management.annotations.annotation_constants import detector_bbox_category_id_to_name
-from md_visualization import visualization_utils as vis_utils
-from md_utils.ct_utils import get_max_conf
-from md_utils import write_html_image_list
-from detection.run_detector import get_typical_confidence_threshold_from_results
-
-
-#%% Constants
-
-# This will only be used if a category mapping is not available in the results file.
-DEFAULT_DETECTOR_LABEL_MAP = {
-    str(k): v for k, v in detector_bbox_category_id_to_name.items()
-}
-
-
-#%% Support functions
-
-def _render_image(entry,
-                 detector_label_map,classification_label_map,
-                 confidence_threshold,classification_confidence_threshold,
-                 render_detections_only,preserve_path_structure,out_dir,images_dir,
-                 output_image_width):
-    """
-    Internal function for rendering a single image.
-    """
-    
-    rendering_result = {'failed_image':False,'missing_image':False,
-                        'skipped_image':False,'annotated_image_path':None,
-                        'max_conf':None,'file':entry['file']}
-    
-    image_id = entry['file']
-
-    if 'failure' in entry and entry['failure'] is not None:
-        rendering_result['failed_image'] = True
-        return rendering_result
-
-    assert 'detections' in entry and entry['detections'] is not None
-    
-    max_conf = get_max_conf(entry)
-    rendering_result['max_conf'] = max_conf
-    
-    if (max_conf < confidence_threshold) and render_detections_only:
-        rendering_result['skipped_image'] = True
-        return rendering_result
-    
-    image_obj = os.path.join(images_dir, image_id)
-    if not os.path.exists(image_obj):
-        print(f'Image {image_id} not found in images_dir')
-        rendering_result['missing_image'] = True
-        return rendering_result
-
-    # If output_image_width is -1 or None, this will just return the original image
-    image = vis_utils.resize_image(
-        vis_utils.open_image(image_obj), output_image_width)
-
-    vis_utils.render_detection_bounding_boxes(
-        entry['detections'], image, 
-        label_map=detector_label_map,
-        classification_label_map=classification_label_map,
-        confidence_threshold=confidence_threshold,
-        classification_confidence_threshold=classification_confidence_threshold)
-
-    if not preserve_path_structure:
-        for char in ['/', '\\', ':']:
-            image_id = image_id.replace(char, '~')
-        annotated_img_path = os.path.join(out_dir, f'anno_{image_id}')
-    else:
-        assert not os.path.isabs(image_id), "Can't preserve paths when operating on absolute paths"
-        annotated_img_path = os.path.join(out_dir, image_id)
-        os.makedirs(os.path.dirname(annotated_img_path),exist_ok=True)
-        
-    image.save(annotated_img_path)
-    rendering_result['annotated_image_path'] = annotated_img_path        
-
-    return rendering_result
-
-
-#%% Main function
-
-def visualize_detector_output(detector_output_path,
-                              out_dir,
-                              images_dir,
-                              confidence_threshold=0.15,
-                              sample=-1,
-                              output_image_width=700,
-                              random_seed=None,
-                              render_detections_only=False,
-                              classification_confidence_threshold=0.1,
-                              html_output_file=None,
-                              html_output_options=None,
-                              preserve_path_structure=False,
-                              parallelize_rendering=False,
-                              parallelize_rendering_n_cores=10,
-                              parallelize_rendering_with_threads=True):
-    
-    """
-    Draws bounding boxes on images given the output of a detector.
-
-    Args:
-        detector_output_path (str): path to detector output .json file
-        out_dir (str): path to directory for saving annotated images
-        images_dir (str): folder where the images live; filenames in 
-            [detector_output_path] should be relative to [image_dir]
-        confidence_threshold (float, optional): threshold above which detections will be rendered
-        sample (int, optional): maximum number of images to render, -1 for all
-        output_image_width (int, optional): width in pixels to resize images for display,
-            preserving aspect ration; set to -1 to use original image width
-        random_seed (int, optional): seed to use for choosing images when sample != -1
-        render_detections_only (bool): only render images with above-threshold detections
-        classification_confidence_threshold (float, optional): only show classifications
-            above this threshold; does not impact whether images are rendered, only whether
-            classification labels (not detection categories) are displayed
-        html_output_file (str, optional): output path for an HTML index file (not written
-            if None)
-        html_output_options (dict, optional): HTML formatting options; see write_html_image_list 
-            for details
-        preserve_path_structure (bool, optional): if False (default), writes images to unique
-            names in a flat structure in the output folder; if True, preserves relative paths
-            within the output folder
-        parallelize_rendering (bool, optional): whether to use concurrent workers for rendering
-        parallelize_rendering_n_cores (int, optional): number of concurrent workers to use 
-            (ignored if parallelize_rendering is False)
-        parallelize_rendering_with_threads (bool, optional): determines whether we use
-            threads (True) or processes (False) for parallelization (ignored if parallelize_rendering 
-            is False)
-
-    Returns:
-        list: list of paths to annotated images
-    """
-    
-    assert os.path.exists(detector_output_path), \
-        'Detector output file does not exist at {}'.format(detector_output_path)
-
-    assert os.path.isdir(images_dir), \
-        'Image folder {} is not available'.format(images_dir)
-
-    os.makedirs(out_dir, exist_ok=True)
-
-
-    ##%% Load detector output
-
-    with open(detector_output_path) as f:
-        detector_output = json.load(f)
-    assert 'images' in detector_output, (
-        'Detector output file should be a json with an "images" field.')
-    images = detector_output['images']
-    
-    if confidence_threshold is None:
-        confidence_threshold = get_typical_confidence_threshold_from_results(detector_output)
-        
-    assert confidence_threshold >= 0 and confidence_threshold <= 1, (
-        f'Confidence threshold {confidence_threshold} is invalid, must be in (0, 1).')
-    
-    if 'detection_categories' in detector_output:
-        print('Using custom label mapping')
-        detector_label_map = detector_output['detection_categories']
-    else:
-        detector_label_map = DEFAULT_DETECTOR_LABEL_MAP
-
-    num_images = len(images)
-    print(f'Detector output file contains {num_images} entries.')
-
-    if sample > 0:
-        assert num_images >= sample, (
-            f'Sample size {sample} greater than number of entries '
-            f'({num_images}) in detector result.')
-
-        if random_seed is not None:
-            images = sorted(images, key=lambda x: x['file'])
-            random.seed(random_seed)
-
-        random.shuffle(images)
-        images = sorted(images[:sample], key=lambda x: x['file'])
-        print(f'Sampled {len(images)} entries from the detector output file.')
-
-
-    ##%% Load images, annotate them and save
-
-    print('Rendering detections above a confidence threshold of {}'.format(
-        confidence_threshold))
-    
-    classification_label_map = None
-    
-    if 'classification_categories' in detector_output:
-        classification_label_map = detector_output['classification_categories']
-        
-    rendering_results = []
-    
-    if parallelize_rendering:
-        
-        if parallelize_rendering_with_threads:
-            worker_string = 'threads'
-        else:
-            worker_string = 'processes'
-            
-        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)
-            else:
-                pool = Pool(parallelize_rendering_n_cores)
-            print('Rendering images with {} {}'.format(parallelize_rendering_n_cores,
-                                                       worker_string))            
-        rendering_results = list(tqdm(pool.imap(
-                                 partial(_render_image,detector_label_map=detector_label_map,
-                                         classification_label_map=classification_label_map,
-                                         confidence_threshold=confidence_threshold,
-                                         classification_confidence_threshold=classification_confidence_threshold,
-                                         render_detections_only=render_detections_only,
-                                         preserve_path_structure=preserve_path_structure,
-                                         out_dir=out_dir,
-                                         images_dir=images_dir,
-                                         output_image_width=output_image_width),
-                                 images), total=len(images)))
-        
-    else:
-                
-        for entry in tqdm(images):
-            
-            rendering_result = _render_image(entry,detector_label_map,classification_label_map,
-                                            confidence_threshold,classification_confidence_threshold,
-                                            render_detections_only,preserve_path_structure,out_dir,
-                                            images_dir,output_image_width)
-            rendering_results.append(rendering_result)
-        
-    # ...for each image
-    
-    failed_images = [r for r in rendering_results if r['failed_image']]
-    missing_images = [r for r in rendering_results if r['missing_image']]
-    skipped_images = [r for r in rendering_results if r['skipped_image']]
-    
-    print('Skipped {} failed images (of {})'.format(len(failed_images),len(images)))
-    print('Skipped {} missing images (of {})'.format(len(missing_images),len(images)))
-    print('Skipped {} below-threshold images (of {})'.format(len(skipped_images),len(images)))
-    
-    print(f'Rendered detection results to {out_dir}')
-
-    annotated_image_paths = [r['annotated_image_path'] for r in rendering_results if \
-                             r['annotated_image_path'] is not None]
-    
-    if html_output_file is not None:
-        
-        html_dir = os.path.dirname(html_output_file)
-        
-        html_image_info = []
-        
-        for r in rendering_results:
-            d = {}
-            annotated_image_path_relative = os.path.relpath(r['annotated_image_path'],html_dir)
-            d['filename'] = annotated_image_path_relative
-            d['textStyle'] = \
-             'font-family:verdana,arial,calibri;font-size:80%;' + \
-                 'text-align:left;margin-top:20;margin-bottom:5'
-            d['title'] = '{} (max conf: {})'.format(r['file'],r['max_conf'])
-            html_image_info.append(d)
-            
-        _ = write_html_image_list.write_html_image_list(html_output_file,html_image_info,
-                                                    options=html_output_options)
-        
-    return annotated_image_paths
-
-
-#%% Command-line driver
-
-def main():
-    
-    parser = argparse.ArgumentParser(
-        formatter_class=argparse.ArgumentDefaultsHelpFormatter,
-        description='Annotate the bounding boxes predicted by a detector above '
-                    'some confidence threshold, and save the annotated images.')
-    parser.add_argument(
-        'detector_output_path', type=str,
-        help='Path to json output file of the detector')
-    parser.add_argument(
-        'out_dir', type=str,
-        help='Path to directory where the annotated images will be saved. '
-             'The directory will be created if it does not exist.')
-    parser.add_argument(
-        '-c', '--confidence', type=float, default=0.15,
-        help='Value between 0 and 1, indicating the confidence threshold '
-             'above which to visualize bounding boxes')
-    parser.add_argument(
-        '-i', '--images_dir', type=str, default=None,
-        help='Path to a local directory where images are stored. This '
-             'serves as the root directory for image paths in '
-             'detector_output_path.')
-    parser.add_argument(
-        '-n', '--sample', type=int, default=-1,
-        help='Number of images to be annotated and rendered. Set to -1 '
-             '(default) to annotate all images in the detector output file. '
-             'There may be fewer images if some are not found in images_dir.')
-    parser.add_argument(
-        '-w', '--output_image_width', type=int, default=700,
-        help='Integer, desired width in pixels of the output annotated images. '
-             'Use -1 to not resize. Default: 700.')
-    parser.add_argument(
-        '-r', '--random_seed', type=int, default=None,
-        help='Integer, for deterministic order of image sampling')
-    parser.add_argument(
-        '-html', '--html_output_file', type=str, default=None,
-        help='Filename to which we should write an HTML image index (off by default)')
-    parser.add_argument(
-        '--open_html_output_file', action='store_true',
-        help='Open the .html output file when done')
-    parser.add_argument(
-        '-do', '--detections_only', action='store_true',
-        help='Only render images with above-threshold detections (by default, '
-             'both empty and non-empty images are rendered).')
-    parser.add_argument(
-        '-pps', '--preserve_path_structure', action='store_true',
-        help='Preserve relative image paths (otherwise flattens and assigns unique file names)')
-
-    if len(sys.argv[1:]) == 0:
-        parser.print_help()
-        parser.exit()
-
-    args = parser.parse_args()
-    visualize_detector_output(
-        detector_output_path=args.detector_output_path,
-        out_dir=args.out_dir,
-        confidence_threshold=args.confidence,
-        images_dir=args.images_dir,
-        sample=args.sample,
-        output_image_width=args.output_image_width,
-        random_seed=args.random_seed,
-        render_detections_only=args.detections_only,
-        preserve_path_structure=args.preserve_path_structure,
-        html_output_file=args.html_output_file)
-
-    if args.html_output_file is not None and args.open_html_output_file:
-        from md_utils.path_utils import open_file
-        open_file(args.html_output_file)
-
-if __name__ == '__main__':
-    main()
-
-
-#%% Interactive driver
-
-if False:
-    
-    pass
-
-    #%%
-    
-    detector_output_path = os.path.expanduser('~/postprocessing/bellevue-camera-traps/bellevue-camera-traps-2023-12-05-v5a.0.0/combined_api_outputs/bellevue-camera-traps-2023-12-05-v5a.0.0_detections.json')
-    out_dir = r'g:\temp\preview'
-    images_dir = r'g:\camera_traps\camera_trap_images'
-    confidence_threshold = 0.15
-    sample = 50
-    output_image_width = 700
-    random_seed = 1
-    render_detections_only = True
-    classification_confidence_threshold = 0.1
-    html_output_file = os.path.join(out_dir,'index.html')
-    html_output_options = None
-    preserve_path_structure = False
-    parallelize_rendering = True
-    parallelize_rendering_n_cores = 10
-    parallelize_rendering_with_threads = False
-
-    _ = visualize_detector_output(detector_output_path,
-                              out_dir,
-                              images_dir,
-                              confidence_threshold,
-                              sample,
-                              output_image_width,
-                              random_seed,
-                              render_detections_only,
-                              classification_confidence_threshold,
-                              html_output_file,
-                              html_output_options,
-                              preserve_path_structure,
-                              parallelize_rendering,
-                              parallelize_rendering_n_cores,
-                              parallelize_rendering_with_threads)
-    
-    from md_utils.path_utils import open_file
-    open_file(html_output_file)

megadetector-5.0.9.dist-info/RECORD

@@ -1,224 +0,0 @@
-api/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-api/batch_processing/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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-api/batch_processing/postprocessing/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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-api/batch_processing/postprocessing/repeat_detection_elimination/remove_repeat_detections.py,sha256=I4HgQm8X2atupmVE2adAOrxxjK-ScKnoAY3M95sJsgU,2836
-api/batch_processing/postprocessing/repeat_detection_elimination/repeat_detections_core.py,sha256=ot6FW7hIWgp_TS_2LGYchNrP_1vAR7HxKN64SnwxIb4,66477
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megadetector-5.0.9.dist-info/top_level.txt

@@ -1,8 +0,0 @@
-api
-classification
-data_management
-detection
-docs
-md_utils
-md_visualization
-taxonomy_mapping