megadetector 5.0.11__py3-none-any.whl → 5.0.13__py3-none-any.whl

megadetector/visualization/visualize_detector_output.py

@@ -0,0 +1,405 @@
+"""
+
+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 functools import partial
+from tqdm import tqdm
+
+from megadetector.data_management.annotations.annotation_constants import detector_bbox_category_id_to_name
+from megadetector.visualization import visualization_utils as vis_utils
+from megadetector.utils.ct_utils import get_max_conf
+from megadetector.utils import write_html_image_list
+from megadetector.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 megadetector.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 megadetector.utils.path_utils import open_file
+    open_file(html_output_file)

{megadetector-5.0.11.dist-info → megadetector-5.0.13.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: megadetector
-Version: 5.0.11
+Version: 5.0.13
 Summary: MegaDetector is an AI model that helps conservation folks spend less time doing boring things with camera trap images.
 Author-email: Your friendly neighborhood MegaDetector team <cameratraps@lila.science>
 Maintainer-email: Your friendly neighborhood MegaDetector team <cameratraps@lila.science>
@@ -114,7 +114,7 @@ print('Found {} detections above threshold'.format(len(detections_above_threshol
 
 ```
 from megadetector.detection.run_detector_batch import \
-    load_and_run_detector_batch,write_results_to_file
+    load_and_run_detector_batch, write_results_to_file
 from megadetector.utils import path_utils
 import os
 

megadetector-5.0.13.dist-info/RECORD

@@ -0,0 +1,201 @@
+megadetector/api/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+megadetector/api/batch_processing/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+megadetector/api/batch_processing/api_core/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+megadetector/api/batch_processing/api_core/server.py,sha256=-g6hfaSp7dUaT-2-bUSXkLE-MJnig3gZ3W_GbNkoAE0,11618
+megadetector/api/batch_processing/api_core/server_api_config.py,sha256=AjmLStXYoMMwxZJSephYROEprcSkG5RPlOr7Zho9xLk,3277
+megadetector/api/batch_processing/api_core/server_app_config.py,sha256=tQCFsFv0wJCegHfnu-Za3okdXwEd4U522hiM0YGNkMY,1860
+megadetector/api/batch_processing/api_core/server_batch_job_manager.py,sha256=K7fMFBJA8Z1SkA4eBM-nymcq7VQjwZ6ZRaNnNKFlat8,10324
+megadetector/api/batch_processing/api_core/server_job_status_table.py,sha256=P621Df7RTTKqW8VlxnCqkBtIO4Ko5bSS6WbU0ETzPGY,5984
+megadetector/api/batch_processing/api_core/server_orchestration.py,sha256=LYHABzhOvP0NrM1VIjI6Vwb95YZ5xjQ52mUJW8oIOQ0,17003
+megadetector/api/batch_processing/api_core/server_utils.py,sha256=uJvnW50lSE_LnRtEyrFI2dbVSecmGudaRhUH6NcAx1M,3100
+megadetector/api/batch_processing/api_core/batch_service/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+megadetector/api/batch_processing/api_core/batch_service/score.py,sha256=_hjUBIe0s9wmpmQwwDg-fd7tJMCn8735zJcgF15mTFo,17354
+megadetector/api/batch_processing/api_core_support/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+megadetector/api/batch_processing/api_core_support/aggregate_results_manually.py,sha256=pPLRVb54kMzcndiRQx0JGna3v9cSX__hBc_7PZ8NFEU,2274
+megadetector/api/batch_processing/api_support/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+megadetector/api/batch_processing/api_support/summarize_daily_activity.py,sha256=5H3DyXtdIW5uCp09Fbu9Tdf0hgfNKYnzv7v8Q7CPsDc,5382
+megadetector/api/batch_processing/data_preparation/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+megadetector/api/batch_processing/integration/digiKam/setup.py,sha256=7P1X3JYrBDXmLUeLRrzxNfDkL5lo-pY8nXsp9Cz8rOI,203
+megadetector/api/batch_processing/integration/digiKam/xmp_integration.py,sha256=zk5s7dD-FIkNnRxECT-0TAuBw7R__Or5_ft7Ha3iqMM,17774
+megadetector/api/batch_processing/integration/eMammal/test_scripts/config_template.py,sha256=UnvrgaFRBu59MuVUJa2WpG8ebcOJWcNeZEx6GWuYLzc,73
+megadetector/api/batch_processing/integration/eMammal/test_scripts/push_annotations_to_emammal.py,sha256=keqru1Ktbrj6J6TBEUm3e5N0Ps_0G2X4u4YVavWvDiU,3576
+megadetector/api/batch_processing/integration/eMammal/test_scripts/select_images_for_testing.py,sha256=OYMu97p8vprSv03QcnS6aSxPBocn9sgaozfUqq_JpyM,1369
+megadetector/api/synchronous/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+megadetector/api/synchronous/api_core/animal_detection_api/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+megadetector/api/synchronous/api_core/animal_detection_api/api_backend.py,sha256=6fo9k1byFZdxeHzov-qNFD1ZMClXPIG-BBUlZlbHoMw,4929
+megadetector/api/synchronous/api_core/animal_detection_api/api_frontend.py,sha256=f16J7OBN87Tv0vVIIpXlyyVDeT6qYXDe5Kpr5XGqhdQ,10233
+megadetector/api/synchronous/api_core/animal_detection_api/config.py,sha256=05fVcLx0KK3wWFi62Mr-m_soewVn81qqeObUh-a2mrA,982
+megadetector/api/synchronous/api_core/tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+megadetector/api/synchronous/api_core/tests/load_test.py,sha256=bxyk3Oufl0V79vRsCPeRtWlE2o2KRtVgiqs7TSyP-iU,3277
+megadetector/classification/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+megadetector/classification/aggregate_classifier_probs.py,sha256=gj6PBCe12Z05r3FbOHXuNJHPWyIogoQJvt4kFzApOqg,3429
+megadetector/classification/analyze_failed_images.py,sha256=boY5MupCWEceHHpiJ4au7Rhz8bzmABlTz2B5w08V2qQ,8446
+megadetector/classification/cache_batchapi_outputs.py,sha256=PvbQZYjskIUlzqQl3TDs0bptqCS37rmU14Ix9a5TPRE,6308
+megadetector/classification/create_classification_dataset.py,sha256=bxj3SRyARQfP2ohRT7zEdge_hfs8iBnDETGQWcvNBuI,25467
+megadetector/classification/crop_detections.py,sha256=gFqUch8iapeqlgSU7VSDBB3LgetyyfX5xU3lI9o4Ulk,20438
+megadetector/classification/csv_to_json.py,sha256=hXxUqM92e9AtZVk_BkkjHNi2gMkXHpwmDnYv_uplLxA,5889
+megadetector/classification/detect_and_crop.py,sha256=1rdR9uEURwNO6CAPdRuOc3SmiBLNMwYPUYcMaV3mLWI,37029
+megadetector/classification/evaluate_model.py,sha256=ed6LrBo-U49Q_0tbaEExVZI3GOdA1BVUnc01WwCDUzU,19320
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