megadetector 10.0.15__py3-none-any.whl

megadetector/data_management/databases/integrity_check_json_db.py

@@ -0,0 +1,563 @@
+"""
+
+integrity_check_json_db.py
+
+Does some integrity-checking and computes basic statistics on a COCO Camera Traps .json file, specifically:
+
+* Verifies that required fields are present and have the right types
+* Verifies that annotations refer to valid images
+* Verifies that annotations refer to valid categories
+* Verifies that image, category, and annotation IDs are unique
+* Optionally checks file existence
+* Finds un-annotated images
+* Finds unused categories
+* Prints a list of categories sorted by count
+
+"""
+
+#%% Constants and environment
+
+import argparse
+import json
+import os
+import sys
+
+from functools import partial
+from multiprocessing.pool import Pool, ThreadPool
+from operator import itemgetter
+from tqdm import tqdm
+
+from megadetector.visualization.visualization_utils import open_image
+from megadetector.utils import ct_utils
+from megadetector.utils.path_utils import find_images
+
+
+#%% Classes and environment
+
+class IntegrityCheckOptions:
+    """
+    Options for integrity_check_json_db()
+    """
+
+    def __init__(self):
+
+        #: Image path; the filenames in the .json file should be relative to this folder
+        self.baseDir = ''
+
+        #: Should we validate the image sizes?
+        self.bCheckImageSizes = False
+
+        #: Should we check that all the images in the .json file exist on disk?
+        self.bCheckImageExistence = False
+
+        #: Should we search [baseDir] for images that are not used in the .json file?
+        self.bFindUnusedImages = False
+
+        #: Should we require that all images in the .json file have a 'location' field?
+        self.bRequireLocation = True
+
+        #: For debugging, limit the number of images we'll process
+        self.iMaxNumImages = -1
+
+        #: Number of threads to use for parallelization, set to <= 1 to disable parallelization
+        self.nThreads = 10
+
+        #: Whether to use threads (rather than processes for parallelization)
+        self.parallelizeWithThreads = True
+
+        #: Enable additional debug output
+        self.verbose = True
+
+        #: Allow integer-valued image and annotation IDs (COCO uses this, CCT files use strings)
+        self.allowIntIDs = False
+
+        #: If True, error if the 'info' field is not present
+        self.requireInfo = False
+
+        #: Validate that boxes have positive width/height values, can be 'error',
+        #: 'warning', or None
+        self.validateBoxes = None
+
+
+#%% Functions
+
+def _check_image_existence_and_size(image,options=None):
+    """
+    Validate the image represented in the CCT image dict [image], which should have fields:
+
+    * file_name
+    * width
+    * height
+
+    Args:
+        image (dict): image to validate
+        options (IntegrityCheckOptions): parameters impacting validation
+
+    Returns:
+        str: None if this image passes validation, otherwise an error string
+    """
+
+    if options is None:
+        options = IntegrityCheckOptions()
+
+    assert options.bCheckImageExistence
+
+    file_path = os.path.join(options.baseDir,image['file_name'])
+    if not os.path.isfile(file_path):
+        s = 'Image path {} does not exist'.format(file_path)
+        return s
+
+    if options.bCheckImageSizes:
+        if not ('height' in image and 'width' in image):
+            s = 'Missing image size in {}'.format(file_path)
+            return s
+
+        # width, height = Image.open(file_path).size
+        try:
+            pil_im = open_image(file_path)
+            width,height = pil_im.size
+            pil_im.close()
+        except Exception as e:
+            s = 'Error opening {}: {}'.format(file_path,str(e))
+            return s
+        if (not (width == image['width'] and height == image['height'])):
+            s = 'Size mismatch for image {}: {} (reported {},{}, actual {},{})'.format(
+                    image['id'], file_path, image['width'], image['height'], width, height)
+            return s
+
+    return None
+
+
+def integrity_check_json_db(json_file, options=None):
+    """
+    Does some integrity-checking and computes basic statistics on a COCO Camera Traps .json file; see
+    module header comment for a list of the validation steps.
+
+    Args:
+        json_file (str): filename to validate, or an already-loaded dict
+        options (IntegrityCheckOptions, optional): see IntegrityCheckOptions
+
+    Returns:
+        tuple: tuple containing:
+            - sorted_categories (dict): list of categories used in [json_file], sorted by frequency
+            - data (dict): the data loaded from [json_file]
+            - error_info (dict): specific validation errors
+    """
+
+    if options is None:
+        options = IntegrityCheckOptions()
+
+    if options.bCheckImageSizes:
+        options.bCheckImageExistence = True
+
+    if options.verbose:
+        print(options.__dict__)
+
+    if options.baseDir is None:
+        options.baseDir = ''
+
+    base_dir = options.baseDir
+
+
+    ##%% Read .json file if necessary, integrity-check fields
+
+    if isinstance(json_file,dict):
+
+        data = json_file
+
+    elif isinstance(json_file,str):
+
+        assert os.path.isfile(json_file), '.json file {} does not exist'.format(json_file)
+
+        if options.verbose:
+            print('Reading .json {} with base dir [{}]...'.format(
+                    json_file,base_dir))
+
+        with open(json_file,'r') as f:
+            data = json.load(f)
+
+    else:
+
+        raise ValueError('Illegal value for json_file')
+
+    images = data['images']
+    annotations = data['annotations']
+    categories = data['categories']
+
+    if options.requireInfo:
+        assert 'info' in data, 'No info struct in database'
+
+    if len(base_dir) > 0:
+        assert os.path.isdir(base_dir), \
+            'Base directory {} does not exist'.format(base_dir)
+
+
+    ##%% Build dictionaries, checking ID uniqueness and internal validity as we go
+
+    image_id_to_image = {}
+    ann_id_to_ann = {}
+    category_id_to_category = {}
+    category_name_to_category = {}
+    image_location_set = set()
+
+    if options.verbose:
+        print('Checking categories...')
+
+    for cat in tqdm(categories):
+
+        # Confirm that required fields are present
+        assert 'name' in cat
+        assert 'id' in cat
+
+        assert isinstance(cat['id'],int), \
+            'Illegal category ID type: [{}]'.format(str(cat['id']))
+        assert isinstance(cat['name'],str), \
+            'Illegal category name type [{}]'.format(str(cat['name']))
+
+        category_id = cat['id']
+        category_name = cat['name']
+
+        # Confirm ID uniqueness
+        assert category_id not in category_id_to_category, \
+            'Category ID {} is used more than once'.format(category_id)
+        category_id_to_category[category_id] = cat
+        cat['_count'] = 0
+
+        assert category_name not in category_name_to_category, \
+            'Category name {} is used more than once'.format(category_name)
+        category_name_to_category[category_name] = cat
+
+    # ...for each category
+
+    if options.verbose:
+        print('\nChecking image records...')
+
+    if options.iMaxNumImages > 0 and len(images) > options.iMaxNumImages:
+
+        if options.verbose:
+            print('Trimming image list to {}'.format(options.iMaxNumImages))
+        images = images[0:options.iMaxNumImages]
+
+    image_paths_in_json = set()
+
+    sequences = set()
+
+    # image = images[0]
+    for image in tqdm(images):
+
+        image['_count'] = 0
+
+        # Confirm that required fields are present
+        assert 'file_name' in image
+        assert 'id' in image
+
+        image['file_name'] = image['file_name'].replace('\\','/')
+
+        image_paths_in_json.add(image['file_name'])
+
+        assert isinstance(image['file_name'],str), 'Illegal image filename type'
+
+        if options.allowIntIDs:
+            assert isinstance(image['id'],str) or isinstance(image['id'],int), \
+                'Illegal image ID type'
+        else:
+            assert isinstance(image['id'],str), 'Illegal image ID type'
+
+        image_id = image['id']
+
+        # Confirm ID uniqueness
+        assert image_id not in image_id_to_image, 'Duplicate image ID {}'.format(image_id)
+
+        image_id_to_image[image_id] = image
+
+        if 'height' in image:
+            assert 'width' in image, 'Image with height but no width: {}'.format(image['id'])
+
+        if 'width' in image:
+            assert 'height' in image, 'Image with width but no height: {}'.format(image['id'])
+
+        if options.bRequireLocation:
+            assert 'location' in image, 'No location available for: {}'.format(image['id'])
+
+        if 'location' in image:
+            # We previously supported ints here; this should be strings now
+            # assert isinstance(image['location'], str) or isinstance(image['location'], int), \
+            #  'Illegal image location type'
+            assert isinstance(image['location'], str)
+            image_location_set.add(image['location'])
+
+        if 'seq_id' in image:
+            sequences.add(image['seq_id'])
+
+        assert not ('sequence_id' in image or 'sequence' in image), 'Illegal sequence identifier'
+
+    unused_files = []
+
+    image_paths_relative = None
+
+    # Are we checking for unused images?
+    if (len(base_dir) > 0) and options.bFindUnusedImages:
+
+        if options.verbose:
+            print('\nEnumerating images...')
+
+        image_paths_relative = find_images(base_dir,return_relative_paths=True,recursive=True)
+
+        for fn_relative in image_paths_relative:
+            if fn_relative not in image_paths_in_json:
+                unused_files.append(fn_relative)
+
+    # List of (filename,error_string) tuples
+    validation_errors = []
+
+    # If we're checking image existence but not image size, we don't need to read the images
+    if options.bCheckImageExistence and not options.bCheckImageSizes:
+
+        if image_paths_relative is None:
+            image_paths_relative = find_images(base_dir,return_relative_paths=True,recursive=True)
+
+        image_paths_relative_set = set(image_paths_relative)
+
+        for im in images:
+            if im['file_name'] not in image_paths_relative_set:
+                validation_errors.append((im['file_name'],'not found in relative path list'))
+
+    # If we're checking image size, we need to read the images
+    if options.bCheckImageSizes:
+
+        if len(base_dir) == 0:
+            print('Warning: checking image sizes without a base directory, assuming "."')
+
+        if options.verbose:
+            print('Checking image existence and/or image sizes...')
+
+        if options.nThreads is not None and options.nThreads > 1:
+
+            if options.parallelizeWithThreads:
+                worker_string = 'threads'
+            else:
+                worker_string = 'processes'
+
+            if options.verbose:
+                print('Starting a pool of {} {}'.format(options.nThreads,worker_string))
+            if options.parallelizeWithThreads:
+                pool = ThreadPool(options.nThreads)
+            else:
+                pool = Pool(options.nThreads)
+            try:
+                results = list(tqdm(pool.imap(
+                    partial(_check_image_existence_and_size,options=options), images),
+                    total=len(images)))
+            finally:
+                pool.close()
+                pool.join()
+                print('Pool closed and joined for image size checks')
+        else:
+            results = []
+            for im in tqdm(images):
+                results.append(_check_image_existence_and_size(im,options))
+
+        for i_image,result in enumerate(results):
+            if result is not None:
+                validation_errors.append((images[i_image]['file_name'],result))
+
+    # ...for each image
+
+    if options.verbose:
+        print('{} validation errors (of {})'.format(len(validation_errors),len(images)))
+        print('Checking annotations...')
+
+    n_boxes = 0
+
+    for ann in tqdm(annotations):
+
+        # Confirm that required fields are present
+        assert 'image_id' in ann
+        assert 'id' in ann
+        assert 'category_id' in ann
+
+        if options.allowIntIDs:
+            assert isinstance(ann['id'],str) or isinstance(ann['id'],int), \
+                'Illegal annotation ID type'
+            assert isinstance(ann['image_id'],str) or isinstance(ann['image_id'],int), \
+                'Illegal annotation image ID type'
+        else:
+            assert isinstance(ann['id'],str), 'Illegal annotation ID type'
+            assert isinstance(ann['image_id'],str), 'Illegal annotation image ID type'
+
+        assert isinstance(ann['category_id'],int), 'Illegal annotation category ID type'
+
+        if 'bbox' in ann:
+            n_boxes += 1
+
+        ann_id = ann['id']
+        image_id = ann['image_id']
+
+        if ('bbox' in ann) and (options.validateBoxes is not None):
+
+            assert options.validateBoxes in ('error','warning'), \
+                'Illegal value {} for validateBoxes'.format(options.validateBoxes)
+
+            annotation_string = str(ann['bbox'])
+
+            # We'll allow aribtrary metadata to be tacked on to the end of boxes
+            s = ''
+            if len(ann['bbox']) < 4:
+                s += 'Annotation error: illegal bounding box in annotation {} for image {}: {}\n'.format(
+                        ann_id,image_id,annotation_string)
+            if ann['bbox'][2] < 0:
+                s += 'Annotation error: negative width in annotation {} for image {}: {}\n'.format(
+                        ann_id,image_id,annotation_string)
+            if ann['bbox'][3] < 0:
+                s += 'Annotation error: negative height in annotation {} for image {}: {}\n'.format(
+                        ann_id,image_id,annotation_string)
+            if len(s) > 0:
+                if options.validateBoxes == 'error':
+                    raise ValueError(s)
+                else:
+                    print('Warning: {}'.format(s))
+                    im = image_id_to_image[image_id]
+                    validation_errors.append((im['file_name'],s))
+
+        # ...if we're supposed to validate boxes
+
+        # Confirm ID uniqueness
+        assert ann_id not in ann_id_to_ann, \
+            'Duplicate annotation ID {}'.format(ann_id)
+
+        ann_id_to_ann[ann_id] = ann
+
+        # Confirm validity
+        assert ann['category_id'] in category_id_to_category, \
+            'Category {} not found in category list'.format(ann['category_id'])
+        assert ann['image_id'] in image_id_to_image, \
+          'Image ID {} referred to by annotation {}, not available'.format(
+            ann['image_id'],ann['id'])
+
+        image_id_to_image[ann['image_id']]['_count'] += 1
+        category_id_to_category[ann['category_id']]['_count'] +=1
+
+    # ...for each annotation
+
+    sorted_categories = sorted(categories, key=itemgetter('_count'), reverse=True)
+
+
+    ##%% Print statistics
+
+    if options.verbose:
+
+        # Find un-annotated images and multi-annotation images
+        n_unannotated = 0
+        n_multi_annotated = 0
+
+        for image in images:
+            if image['_count'] == 0:
+                n_unannotated += 1
+            elif image['_count'] > 1:
+                n_multi_annotated += 1
+
+        print('\nFound {} unannotated images, {} images with multiple annotations'.format(
+                n_unannotated,n_multi_annotated))
+
+        if (len(base_dir) > 0) and options.bFindUnusedImages:
+            print('Found {} unused image files'.format(len(unused_files)))
+
+        n_unused_categories = 0
+
+        # Find unused categories
+        for cat in categories:
+            if cat['_count'] == 0:
+                print('Unused category: {}'.format(cat['name']))
+                n_unused_categories += 1
+
+        print('Found {} unused categories'.format(n_unused_categories))
+
+        sequence_string = 'no sequence info'
+        if len(sequences) > 0:
+            sequence_string = '{} sequences'.format(len(sequences))
+
+        print('\nDB contains {} images, {} annotations, {} bboxes, {} categories, {}\n'.format(
+                len(images),len(annotations),n_boxes,len(categories),sequence_string))
+
+        if len(image_location_set) > 0:
+            print('DB contains images from {} locations\n'.format(len(image_location_set)))
+
+        print('Categories and annotation (not image) counts:\n')
+
+        for cat in sorted_categories:
+            print('{:6} {}'.format(cat['_count'],cat['name']))
+
+        print('')
+
+    error_info = {}
+    error_info['unused_files'] = unused_files
+    error_info['validation_errors'] = validation_errors
+
+    return sorted_categories, data, error_info
+
+# ...def integrity_check_json_db()
+
+
+#%% Command-line driver
+
+def main(): # noqa
+
+    parser = argparse.ArgumentParser()
+    parser.add_argument('json_file',type=str,
+                        help='COCO-formatted .json file to validate')
+    parser.add_argument('--bCheckImageSizes', action='store_true',
+                        help='Validate image size, requires baseDir to be specified. ' + \
+                             'Implies existence checking.')
+    parser.add_argument('--bCheckImageExistence', action='store_true',
+                        help='Validate image existence, requires baseDir to be specified')
+    parser.add_argument('--bFindUnusedImages', action='store_true',
+                        help='Check for images in baseDir that aren\'t in the database, ' + \
+                             'requires baseDir to be specified')
+    parser.add_argument('--baseDir', action='store', type=str, default='',
+                        help='Base directory for images')
+    parser.add_argument('--bAllowNoLocation', action='store_true',
+                        help='Disable errors when no location is specified for an image')
+    parser.add_argument('--iMaxNumImages', action='store', type=int, default=-1,
+                        help='Cap on total number of images to check')
+    parser.add_argument('--nThreads', action='store', type=int, default=10,
+                        help='Number of threads (only relevant when verifying image ' + \
+                             'sizes and/or existence)')
+
+    if len(sys.argv[1:])==0:
+        parser.print_help()
+        parser.exit()
+
+    args = parser.parse_args()
+    args.bRequireLocation = (not args.bAllowNoLocation)
+    options = IntegrityCheckOptions()
+    ct_utils.args_to_object(args, options)
+    integrity_check_json_db(args.json_file,options)
+
+if __name__ == '__main__':
+    main()
+
+
+#%% Interactive driver(s)
+
+if False:
+
+    #%%
+
+    """
+    python integrity_check_json_db.py ~/data/ena24.json --baseDir ~/data/ENA24 --bAllowNoLocation
+    """
+
+    # Integrity-check .json files for LILA
+    json_files = [os.path.expanduser('~/data/ena24.json')]
+
+    options = IntegrityCheckOptions()
+    options.baseDir = os.path.expanduser('~/data/ENA24')
+    options.bCheckImageSizes = False
+    options.bFindUnusedImages = True
+    options.bRequireLocation = False
+
+    # options.iMaxNumImages = 10
+
+    for json_file in json_files:
+
+        sorted_categories,data,_ = integrity_check_json_db(json_file, options)