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

megadetector/postprocessing/merge_detections.py

@@ -0,0 +1,412 @@
+"""
+
+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 megadetector.utils.ct_utils import get_iou
+
+
+#%% Structs
+
+class MergeDetectionsOptions:
+    
+    def __init__(self):
+        
+        #: Maximum detection size to include in the merged output
+        self.max_detection_size = 1.01
+        
+        #: Minimum detection size to include in the merged output
+        self.min_detection_size = 0
+        
+        #: Exclude detections whose confidence in the source file(s) is less
+        #: than this.  Should have the same length as the number of source files.
+        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
+        
+        #: If you want to merge only certain categories, specify one
+        #: (but not both) of these.  These are category IDs, not names.
+        self.categories_to_exclude = None
+
+        #: Only merge detections into images that have *no* detections in the 
+        #: target results file.
+        self.merge_empty_only = False
+        
+        #: IoU threshold above which two detections are considered the same
+        self.iou_threshold = 0.65
+        
+        #: Error if this is False and the output file exists
+        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()
+