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

api/batch_processing/postprocessing/merge_detections.py

@@ -1,401 +0,0 @@
-"""
-
-merge_detections.py
-
-Merge high-confidence detections from one or more results files into another 
-file.  Typically used to combine results from MDv5b and/or MDv4 into a "primary"
-results file from MDv5a.
-
-Detection categories must be the same in both files; if you want to first remap
-one file's category mapping to be the same as another's, see remap_detection_categories.
-
-If you want to literally merge two .json files, see combine_api_outputs.py.
-
-"""
-
-#%% Constants and imports
-
-import argparse
-import sys
-import json
-import os
-
-from tqdm import tqdm
-
-from md_utils.ct_utils import get_iou
-
-
-#%% Structs
-
-class MergeDetectionsOptions:
-    
-    def __init__(self):
-        
-        self.max_detection_size = 1.01
-        self.min_detection_size = 0
-        self.source_confidence_thresholds = [0.05]
-        
-        # Don't bother merging into target images if there is a similar detection
-        # above this threshold (or if there is *any* detection above this threshold,
-        # and merge_empty_only is True)
-        self.target_confidence_threshold = 0.2
-        
-        # If you want to merge only certain categories, specify one
-        # (but not both) of these.  These are category IDs, not names.
-        self.categories_to_include = None
-        self.categories_to_exclude = None
-
-        # Only merge detections into images that have *no* detections in the 
-        # target results file.
-        self.merge_empty_only = False
-        
-        self.iou_threshold = 0.65
-        
-        self.overwrite = False
-
-
-#%% Main function
-
-def merge_detections(source_files,target_file,output_file,options=None):
-    """
-    Merge high-confidence detections from one or more results files into another 
-    file.   Typically used to combine results from MDv5b and/or MDv4 into a "primary"
-    results file from MDv5a.
-    
-    [source_files] (a list of files or a single filename) specifies the set of 
-    results files that will be merged into [target_file].  The difference between a 
-    "source file" and the "target file" is that if no merging is necessary, either because
-    two boxes are nearly identical or because merge_only_empty is True and the target
-    file already has above-threshold detection for an image+category, the output file gets
-    the results of the "target" file.  I.e., the "target" file wins all ties.
-    
-    The results are written to [output_file].
-
-    """
-    
-    if isinstance(source_files,str):
-        source_files = [source_files]    
-        
-    if options is None:
-        options = MergeDetectionsOptions()    
-        
-    if (not options.overwrite) and (os.path.isfile(output_file)):
-        print('File {} exists, bypassing merge'.format(output_file))
-        return
-    
-    assert not ((options.categories_to_exclude is not None) and \
-                (options.categories_to_include is not None)), \
-                'categories_to_include and categories_to_exclude are mutually exclusive'
-    
-    if options.categories_to_exclude is not None:
-        options.categories_to_exclude = [int(c) for c in options.categories_to_exclude]
-        
-    if options.categories_to_include is not None:
-        options.categories_to_include = [int(c) for c in options.categories_to_include]
-        
-    assert len(source_files) == len(options.source_confidence_thresholds), \
-        '{} source files provided, but {} source confidence thresholds provided'.format(
-            len(source_files),len(options.source_confidence_thresholds))
-    
-    for fn in source_files:
-        assert os.path.isfile(fn), 'Could not find source file {}'.format(fn)
-    
-    assert os.path.isfile(target_file)
-    
-    os.makedirs(os.path.dirname(output_file),exist_ok=True)
-    
-    with open(target_file,'r') as f:
-        output_data = json.load(f)
-
-    print('Loaded results for {} images'.format(len(output_data['images'])))
-    
-    fn_to_image = {}
-    
-    # im = output_data['images'][0]
-    for im in output_data['images']:
-        fn_to_image[im['file']] = im
-    
-    if 'detections_transferred_from' not in output_data['info']:
-        output_data['info']['detections_transferred_from'] = []
-
-    if 'detector' not in output_data['info']:
-        output_data['info']['detector'] = 'MDv4 (assumed)'
-        
-    detection_categories_raw = output_data['detection_categories'].keys()
-    
-    # Determine whether we should be processing all categories, or just a subset
-    # of categories.
-    detection_categories = []
-
-    if options.categories_to_exclude is not None:    
-        for c in detection_categories_raw:
-            if int(c) not in options.categories_to_exclude:
-                detection_categories.append(c)
-            else:
-                print('Excluding category {}'.format(c))
-    elif options.categories_to_include is not None:
-        for c in detection_categories_raw:
-            if int(c) in options.categories_to_include:
-                print('Including category {}'.format(c))
-                detection_categories.append(c)
-    else:
-        detection_categories = detection_categories_raw
-    
-    # i_source_file = 0; source_file = source_files[i_source_file]
-    for i_source_file,source_file in enumerate(source_files):
-    
-        print('Processing detections from file {}'.format(source_file))
-        
-        with open(source_file,'r') as f:
-            source_data = json.load(f)
-        
-        if 'detector' in source_data['info']:
-            source_detector_name = source_data['info']['detector']
-        else:
-            source_detector_name = os.path.basename(source_file)
-        
-        output_data['info']['detections_transferred_from'].append(os.path.basename(source_file))
-        output_data['info']['detector'] = output_data['info']['detector'] + ' + ' + source_detector_name
-        
-        assert source_data['detection_categories'] == output_data['detection_categories'], \
-            'Cannot merge files with different detection category maps'
-        
-        source_confidence_threshold = options.source_confidence_thresholds[i_source_file]
-        
-        # source_im = source_data['images'][0]
-        for source_im in tqdm(source_data['images']):
-            
-            image_filename = source_im['file']            
-            
-            assert image_filename in fn_to_image, 'Image {} not in target image set'.format(image_filename)
-            target_im = fn_to_image[image_filename]
-            
-            if 'detections' not in source_im or source_im['detections'] is None:
-                continue
-            
-            if 'detections' not in target_im or target_im['detections'] is None:
-                continue
-                    
-            source_detections_this_image = source_im['detections']
-            target_detections_this_image = target_im['detections']
-              
-            detections_to_transfer = []
-            
-            # detection_category = list(detection_categories)[0]
-            for detection_category in detection_categories:
-                
-                target_detections_this_category = \
-                    [det for det in target_detections_this_image if det['category'] == \
-                     detection_category]
-                
-                max_target_confidence_this_category = 0.0
-                
-                if len(target_detections_this_category) > 0:
-                    max_target_confidence_this_category = max([det['conf'] for \
-                      det in target_detections_this_category])
-                
-                # If we have a valid detection in the target file, and we're only merging
-                # into images that have no detections at all, we don't need to review the individual
-                # detections in the source file.
-                if options.merge_empty_only and \
-                    (max_target_confidence_this_category >= options.target_confidence_threshold):
-                    continue
-                
-                source_detections_this_category_raw = [det for det in \
-                  source_detections_this_image if det['category'] == detection_category]
-                
-                # Boxes are x/y/w/h
-                # source_sizes = [det['bbox'][2]*det['bbox'][3] for det in source_detections_this_category_raw]
-                
-                # Only look at source boxes within the size range
-                source_detections_this_category_filtered = [
-                    det for det in source_detections_this_category_raw if \
-                        (det['bbox'][2]*det['bbox'][3] <= options.max_detection_size) and \
-                        (det['bbox'][2]*det['bbox'][3] >= options.min_detection_size) \
-                        ]
-                           
-                # det = source_detections_this_category_filtered[0]
-                for det in source_detections_this_category_filtered:
-                    
-                    if det['conf'] >= source_confidence_threshold:
-
-                        # Check only whole images
-                        if options.merge_empty_only:
-                            
-                            # We verified this above, asserting here for clarity
-                            assert max_target_confidence_this_category < options.target_confidence_threshold
-                            det['transferred_from'] = source_detector_name
-                            detections_to_transfer.append(det)
-
-                        # Check individual detections                       
-                        else:
-                            
-                            # Does this source detection match any existing above-threshold
-                            # target category detections?
-                            matches_existing_box = False
-                            
-                            # target_detection = target_detections_this_category[0]
-                            for target_detection in target_detections_this_category:
-                                
-                                if (target_detection['conf'] >= options.target_confidence_threshold) \
-                                   and \
-                                   (get_iou(det['bbox'],target_detection['bbox']) >= options.iou_threshold):
-                                    matches_existing_box = True
-                                    break
-                                
-                            if (not matches_existing_box):
-                                det['transferred_from'] = source_detector_name
-                                detections_to_transfer.append(det)
-                    
-                    # ...if this source detection is above the confidence threshold
-                    
-                # ...for each source detection within category                            
-                                    
-            # ...for each detection category
-            
-            if len(detections_to_transfer) > 0:
-                
-                # print('Adding {} detections to image {}'.format(len(detections_to_transfer),image_filename))
-                detections = fn_to_image[image_filename]['detections']                
-                detections.extend(detections_to_transfer)
-
-                # Update the max_detection_conf field (if present)
-                if 'max_detection_conf' in fn_to_image[image_filename]:
-                    fn_to_image[image_filename]['max_detection_conf'] = \
-                        max([d['conf'] for d in detections])
-            
-            # ...if we have any detections to transfer
-            
-        # ...for each image
-        
-    # ...for each source file        
-    
-    with open(output_file,'w') as f:
-        json.dump(output_data,f,indent=1)
-    
-    print('Saved merged results to {}'.format(output_file))
-
-
-#%% Command-line driver
-
-def main():
-    
-    default_options = MergeDetectionsOptions()
-    
-    parser = argparse.ArgumentParser(
-        description='Merge detections from one or more MegaDetector results files into an existing reuslts file')
-    parser.add_argument(
-        'source_files',
-        nargs="+",
-        help='Path to source .json file(s) to merge from')
-    parser.add_argument(
-        'target_file',
-        help='Path to a .json file to merge detections into')
-    parser.add_argument(
-        'output_file',
-        help='Path to output .json results file')
-    parser.add_argument(
-        '--max_detection_size',
-        type=float,
-        default=default_options.max_detection_size,
-        help='Ignore detections with an area larger than this (as a fraction of ' + \
-             'image size) (default {})'.format(
-             default_options.max_detection_size))
-    parser.add_argument(
-        '--min_detection_size',
-        default=default_options.min_detection_size,
-        type=float,
-        help='Ignore detections with an area smaller than this (as a fraction of ' + \
-              'image size) (default {})'.format(
-              default_options.min_detection_size))
-    parser.add_argument(
-        '--source_confidence_thresholds',
-        nargs="+",
-        type=float,
-        default=default_options.source_confidence_thresholds,
-        help='List of thresholds for each source file (default {}). '.format(
-            default_options.source_confidence_thresholds) + \
-            'Merge only if the source file\'s detection confidence is higher than its ' + \
-            'corresponding threshold.  Should be the same length as the number of source files.')
-    parser.add_argument(
-        '--target_confidence_threshold',
-        type=float,
-        default=default_options.target_confidence_threshold,
-        help='Don\'t merge if target file\'s detection confidence is already higher ' + \
-             'than this (default {}). '.format(
-             default_options.target_confidence_threshold))
-    parser.add_argument(
-        '--categories_to_include',
-        type=int,
-        nargs="+",
-        default=None,
-        help='List of numeric detection category IDs to include')
-    parser.add_argument(
-        '--categories_to_exclude',
-        type=int,
-        nargs="+",
-        default=None,
-        help='List of numeric detection categories to include')
-    parser.add_argument(
-        '--merge_empty_only',
-        action='store_true',
-        help='Ignore individual detections and only merge images for which the target ' + \
-             'file contains no detections')   
-    parser.add_argument(
-        '--iou_threshold',
-        type=float,
-        default=default_options.iou_threshold,
-        help='Sets the minimum IoU for a source detection to be considered the same as ' + \
-             'a target detection (default {})'.format(default_options.iou_threshold))
-
-    if len(sys.argv[1:]) == 0:
-        parser.print_help()
-        parser.exit()
-
-    args = parser.parse_args()
-
-    options = MergeDetectionsOptions()
-    options.max_detection_size = args.max_detection_size
-    options.min_detection_size = args.min_detection_size
-    options.source_confidence_thresholds = args.source_confidence_thresholds
-    options.target_confidence_threshold = args.target_confidence_threshold
-    options.categories_to_include = args.categories_to_include
-    options.categories_to_exclude = args.categories_to_exclude
-    options.merge_empty_only = args.merge_empty_only
-    options.iou_threshold = args.iou_threshold
-    
-    merge_detections(args.source_files, args.target_file, args.output_file, options)
-
-
-#%% Test driver
-
-if False:
-    
-    #%%
-    
-    options = MergeDetectionsOptions()
-    options.max_detection_size = 0.1
-    options.target_confidence_threshold = 0.3
-    options.categories_to_include = [1]
-    source_files = ['/home/user/postprocessing/iwildcam/iwildcam-mdv4-2022-05-01/combined_api_outputs/iwildcam-mdv4-2022-05-01_detections.json']
-    options.source_confidence_thresholds = [0.8]
-    target_file = '/home/user/postprocessing/iwildcam/iwildcam-mdv5-camcocoinat-2022-05-02/combined_api_outputs/iwildcam-mdv5-camcocoinat-2022-05-02_detections.json'
-    output_file = '/home/user/postprocessing/iwildcam/merged-detections/mdv4_mdv5-camcocoinat-2022-05-02.json'
-    merge_detections(source_files, target_file, output_file, options)
-    
-    options = MergeDetectionsOptions()
-    options.max_detection_size = 0.1
-    options.target_confidence_threshold = 0.3
-    options.categories_to_include = [1]
-    source_files = [
-        '/home/user/postprocessing/iwildcam/iwildcam-mdv4-2022-05-01/combined_api_outputs/iwildcam-mdv4-2022-05-01_detections.json',
-        '/home/user/postprocessing/iwildcam/iwildcam-mdv5-camonly-2022-05-02/combined_api_outputs/iwildcam-mdv5-camonly-2022-05-02_detections.json',
-        ]
-    options.source_confidence_thresholds = [0.8,0.5]
-    target_file = '/home/user/postprocessing/iwildcam/iwildcam-mdv5-camcocoinat-2022-05-02/combined_api_outputs/iwildcam-mdv5-camcocoinat-2022-05-02_detections.json'
-    output_file = '/home/user/postprocessing/iwildcam/merged-detections/mdv4_mdv5-camonly_mdv5-camcocoinat-2022-05-02.json'
-    merge_detections(source_files, target_file, output_file, options)
-    
-if __name__ == '__main__':
-    main()
-