megadetector 5.0.10__py3-none-any.whl → 5.0.11__py3-none-any.whl

data_management/databases/combine_coco_camera_traps_files.py

@@ -1,206 +0,0 @@
-"""
-
-combine_coco_camera_traps_files.py
-
-Merges two or more .json files in COCO Camera Traps format, optionally
-writing the results to another .json file.
-
-- Concatenates image lists, erroring if images are not unique.
-- Errors on unrecognized fields.
-- Checks compatibility in info structs, within reason.
-
-*Example command-line invocation*
-    
-combine_coco_camera_traps_files input1.json input2.json ... inputN.json output.json
-
-"""
-
-#%% Constants and imports
-
-import argparse
-import json
-import sys
-
-
-#%% Merge functions
-
-def combine_cct_files(input_files, output_file=None, require_uniqueness=True,
-                      filename_prefixes=None):                             
-    """
-    Merges the list of COCO Camera Traps files [input_files] into a single
-    dictionary, optionally writing the result to [output_file].
-
-    Args:
-        input_files (list): paths to CCT .json files
-        output_file (str, optional): path to write merged .json file
-        require_uniqueness (bool): whether to require that the images in
-            each input_dict be unique
-    
-    Returns:
-        dict: the merged COCO-formatted .json dict
-    """
-    
-    input_dicts = []
-    print('Loading input files')
-    for fn in input_files:
-        with open(fn, 'r', encoding='utf-8') as f:
-            d = json.load(f)
-            if filename_prefixes is not None:
-                assert fn in filename_prefixes
-                d['filename_prefix'] = filename_prefixes[fn]
-            input_dicts.append(d)
-
-    print('Merging results')
-    merged_dict = combine_cct_dictionaries(
-        input_dicts, require_uniqueness=require_uniqueness)
-
-    print('Writing output')
-    if output_file is not None:
-        with open(output_file, 'w') as f:
-            json.dump(merged_dict, f, indent=1)
-
-    return merged_dict
-
-
-def combine_cct_dictionaries(input_dicts, require_uniqueness=True):                                    
-    """
-    Merges the list of COCO Camera Traps dictionaries [input_dicts].  See module header
-    comment for details on merge rules.
-
-    Args:
-        input_dicts: list of CCT dicts
-        require_uniqueness: bool, whether to require that the images in
-            each input_dict be unique
-
-    Returns: 
-        dict: the merged COCO-formatted .json dict
-    """
-    
-    filename_to_image = {}
-    all_annotations = []
-    info = None
-    
-    category_name_to_id = {}
-    category_name_to_id['empty'] = 0
-    next_category_id = 1
-    
-    known_fields = ['info', 'categories', 'annotations','images','filename_prefix']
-
-    # i_input_dict = 0; input_dict = input_dicts[i_input_dict]
-    for i_input_dict,input_dict in enumerate(input_dicts):
-
-        filename_prefix = ''
-        if ('filename_prefix' in input_dict.keys()):
-            filename_prefix = input_dict['filename_prefix']
-        
-        for k in input_dict.keys():
-            if k not in known_fields:
-                raise ValueError(f'Unrecognized CCT field: {k}')
-
-        # We will prepend an index to every ID to guarantee uniqueness
-        index_string = 'ds' + str(i_input_dict).zfill(3) + '_'
-        
-        old_cat_id_to_new_cat_id = {}
-        
-        # Map detection categories from the original data set into the merged data set
-        for original_category in input_dict['categories']:
-        
-            original_cat_id = original_category['id']
-            cat_name = original_category['name']
-            if cat_name in category_name_to_id:
-                new_cat_id = category_name_to_id[cat_name]
-            else:
-                new_cat_id = next_category_id
-                next_category_id += 1
-                category_name_to_id[cat_name] = new_cat_id
-                
-            if original_cat_id in old_cat_id_to_new_cat_id:
-                assert old_cat_id_to_new_cat_id[original_cat_id] == new_cat_id
-            else:
-                old_cat_id_to_new_cat_id[original_cat_id] = new_cat_id
-            
-        # ...for each category
-        
-        
-        # Merge original image list into the merged data set
-        for im in input_dict['images']:
-            
-            if 'seq_id' in im:
-                im['seq_id'] = index_string + im['seq_id']
-            if 'location' in im:
-                im['location'] = index_string + im['location']
-                
-            im_file = filename_prefix + im['file_name']
-            im['file_name'] = im_file
-            if require_uniqueness:
-                assert im_file not in filename_to_image, f'Duplicate image: {im_file}'                
-            else:
-                if im_file in filename_to_image:
-                    print('Redundant image {}'.format(im_file))
-            
-            # Create a unique ID
-            im['id'] = index_string + im['id']
-            filename_to_image[im_file] = im
-
-        # ...for each image
-                  
-        
-        # Same for annotations
-        for ann in input_dict['annotations']:
-            
-            ann['image_id'] = index_string + ann['image_id']
-            ann['id'] = index_string + ann['id']
-            assert ann['category_id'] in old_cat_id_to_new_cat_id
-            ann['category_id'] = old_cat_id_to_new_cat_id[ann['category_id']]
-            
-        # ...for each annotation
-        
-        all_annotations.extend(input_dict['annotations'])
-        
-        # Merge info dicts, don't check completion time fields
-        if info is None:
-            import copy            
-            info = copy.deepcopy(input_dict['info'])
-            info['original_info'] = [input_dict['info']]
-        else:
-            info['original_info'].append(input_dict['info'])
-            
-    # ...for each dictionary
-
-    # Convert merged image dictionaries to a sorted list
-    sorted_images = sorted(filename_to_image.values(), key=lambda im: im['file_name'])
-
-    all_categories = [{'id':category_name_to_id[cat_name],'name':cat_name} for\
-                      cat_name in category_name_to_id.keys()]
-    
-    merged_dict = {'info': info,
-                   'categories': all_categories,
-                   'images': sorted_images,
-                   'annotations': all_annotations}
-    
-    return merged_dict
-
-# ...combine_cct_dictionaries(...)
-
-
-#%% Command-line driver
-
-def main():
-    
-    parser = argparse.ArgumentParser()
-    parser.add_argument(
-        'input_paths', nargs='+',
-        help='List of input .json files')
-    parser.add_argument(
-        'output_path',
-        help='Output .json file')
-
-    if len(sys.argv[1:]) == 0:
-        parser.print_help()
-        parser.exit()
-        
-    args = parser.parse_args()
-    combine_cct_files(args.input_paths, args.output_path)
-
-if __name__ == '__main__':
-    main()

data_management/databases/integrity_check_json_db.py

@@ -1,477 +0,0 @@
-"""
-
-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 multiprocessing.pool import ThreadPool
-from operator import itemgetter
-from tqdm import tqdm
-
-from md_visualization.visualization_utils import open_image
-from md_utils import ct_utils
-
-
-#%% Classes and environment
-
-class IntegrityCheckOptions:
-    """
-    Options for integrity_check_json_db()
-    """
-    
-    #: Image path; the filenames in the .json file should be relative to this folder
-    baseDir = ''
-    
-    #: Should we validate the image sizes?
-    bCheckImageSizes = False
-    
-    #: Should we check that all the images in the .json file exist on disk?
-    bCheckImageExistence = False
-    
-    #: Should we search [baseDir] for images that are not used in the .json file?
-    bFindUnusedImages = False
-    
-    #: Should we require that all images in the .json file have a 'location' field?
-    bRequireLocation = True
-    
-    #: For debugging, limit the number of images we'll process
-    iMaxNumImages = -1
-    
-    #: Number of threads to use for parallelization, set to <= 1 to disable parallelization
-    nThreads = 10
-    
-    #: Enable additional debug output
-    verbose = True
-    
-    
-# This is used in a medium-hacky way to share modified options across threads
-defaultOptions = IntegrityCheckOptions()
-
-
-#%% 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:
-        bool: whether this image passes validation
-    """
-
-    if options is None:        
-        options = defaultOptions
-    
-    assert options.bCheckImageExistence
-    
-    filePath = os.path.join(options.baseDir,image['file_name'])
-    if not os.path.isfile(filePath):
-        # print('Image path {} does not exist'.format(filePath))
-        return False
-    
-    if options.bCheckImageSizes:
-        if not ('height' in image and 'width' in image):
-            print('Missing image size in {}'.format(filePath))
-            return False
-
-        # width, height = Image.open(filePath).size
-        pil_im = open_image(filePath)
-        width,height = pil_im.size
-        if (not (width == image['width'] and height == image['height'])):
-            print('Size mismatch for image {}: {} (reported {},{}, actual {},{})'.format(
-                    image['id'], filePath, image['width'], image['height'], width, height))
-            return False
-        
-    return True
-
-  
-def integrity_check_json_db(jsonFile, 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:
-        jsonFile (str): filename to validate, or an already-loaded dict
-    
-    Returns:
-        tuple: tuple containing:
-            - sortedCategories (dict): list of categories used in [jsonFile], sorted by frequency
-            - data (dict): the data loaded from [jsonFile]
-            - errorInfo (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 = ''
-        
-    baseDir = options.baseDir
-    
-    
-    ##%% Read .json file if necessary, integrity-check fields
-    
-    if isinstance(jsonFile,dict):
-        
-        data = jsonFile
-        
-    elif isinstance(jsonFile,str):
-        
-        assert os.path.isfile(jsonFile), '.json file {} does not exist'.format(jsonFile)
-    
-        if options.verbose:
-            print('Reading .json {} with base dir [{}]...'.format(
-                    jsonFile,baseDir))
-        
-        with open(jsonFile,'r') as f:
-            data = json.load(f) 
-            
-    else:
-        
-        raise ValueError('Illegal value for jsonFile')
-            
-    images = data['images']
-    annotations = data['annotations']
-    categories = data['categories']
-    # info = data['info']
-    assert 'info' in data, 'No info struct in database'
-    
-    if len(baseDir) > 0:        
-        assert os.path.isdir(baseDir), 'Base directory {} does not exist'.format(baseDir)
-        
-        
-    ##%% Build dictionaries, checking ID uniqueness and internal validity as we go
-    
-    imageIdToImage = {}
-    annIdToAnn = {}
-    catIdToCat = {}
-    catNameToCat = {}
-    imageLocationSet = 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']))
-        
-        catId = cat['id']
-        catName = cat['name']
-        
-        # Confirm ID uniqueness
-        assert catId not in catIdToCat, 'Category ID {} is used more than once'.format(catId)
-        catIdToCat[catId] = cat
-        cat['_count'] = 0
-        
-        assert catName not in catNameToCat, 'Category name {} is used more than once'.format(catName)
-        catNameToCat[catName] = cat        
-        
-    # ...for each category
-        
-    if options.verbose:
-        print('\nChecking images...')
-    
-    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]
-        
-    imagePathsInJson = 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'] = os.path.normpath(image['file_name'])
-                
-        imagePathsInJson.add(image['file_name'])
-        
-        assert isinstance(image['file_name'],str), 'Illegal image filename type'
-        assert isinstance(image['id'],str), 'Illegal image ID type'
-        
-        imageId = image['id']        
-        
-        # Confirm ID uniqueness
-        assert imageId not in imageIdToImage, 'Duplicate image ID {}'.format(imageId)
-        
-        imageIdToImage[imageId] = 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)
-            imageLocationSet.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'
-        
-    unusedFiles = []
-                
-    # Are we checking for unused images?
-    if (len(baseDir) > 0) and options.bFindUnusedImages:    
-        
-        if options.verbose:
-            print('\nEnumerating images...')
-        
-        # Recursively enumerate images
-        imagePaths = []
-        for root, dirs, files in os.walk(baseDir):
-            for file in files:
-                if file.lower().endswith(('.jpeg', '.jpg', '.png')):
-                    relDir = os.path.relpath(root, baseDir)
-                    relFile = os.path.join(relDir,file)
-                    relFile = os.path.normpath(relFile)
-                    if len(relFile) > 2 and \
-                        (relFile[0:2] == './' or relFile[0:2] == '.\\'):                     
-                            relFile = relFile[2:]
-                    imagePaths.append(relFile)
-          
-        for p in imagePaths:
-            if p not in imagePathsInJson:
-                # print('Image {} is unused'.format(p))
-                unusedFiles.append(p)
-                
-    validationErrors = []
-    
-    # Are we checking file existence and/or image size?
-    if options.bCheckImageSizes or options.bCheckImageExistence:
-        
-        if len(baseDir) == 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:
-            pool = ThreadPool(options.nThreads)
-            # results = pool.imap_unordered(lambda x: fetch_url(x,nImages), indexedUrlList)
-            defaultOptions.baseDir = options.baseDir
-            defaultOptions.bCheckImageSizes = options.bCheckImageSizes
-            defaultOptions.bCheckImageExistence = options.bCheckImageExistence
-            results = tqdm(pool.imap(_check_image_existence_and_size, images), total=len(images))
-        else:
-            results = []
-            for im in tqdm(images):
-                results.append(_check_image_existence_and_size(im,options))
-                
-        for iImage,r in enumerate(results):
-            if not r:            
-                validationErrors.append(os.path.join(options.baseDir,images[iImage]['file_name']))
-                            
-    # ...for each image
-    
-    if options.verbose:
-        print('{} validation errors (of {})'.format(len(validationErrors),len(images)))
-        print('Checking annotations...')
-    
-    nBoxes = 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
-        
-        assert isinstance(ann['id'],str), 'Illegal annotation ID type'
-        assert isinstance(ann['category_id'],int), 'Illegal annotation category ID type'
-        assert isinstance(ann['image_id'],str), 'Illegal annotation image ID type'
-        
-        if 'bbox' in ann:
-            nBoxes += 1
-            
-        annId = ann['id']        
-        
-        # Confirm ID uniqueness
-        assert annId not in annIdToAnn
-        annIdToAnn[annId] = ann
-    
-        # Confirm validity
-        assert ann['category_id'] in catIdToCat, \
-            'Category {} not found in category list'.format(ann['category_id'])
-        assert ann['image_id'] in imageIdToImage, \
-          'Image ID {} referred to by annotation {}, not available'.format(
-            ann['image_id'],ann['id'])
-    
-        imageIdToImage[ann['image_id']]['_count'] += 1
-        catIdToCat[ann['category_id']]['_count'] +=1 
-        
-    # ...for each annotation
-    
-    sortedCategories = sorted(categories, key=itemgetter('_count'), reverse=True)
-    
-    
-    ##%% Print statistics
-    
-    if options.verbose:
-    
-        # Find un-annotated images and multi-annotation images
-        nUnannotated = 0
-        nMultiAnnotated = 0
-        
-        for image in images:
-            if image['_count'] == 0:
-                nUnannotated += 1
-            elif image['_count'] > 1:
-                nMultiAnnotated += 1
-                
-        print('Found {} unannotated images, {} images with multiple annotations'.format(
-                nUnannotated,nMultiAnnotated))
-        
-        if (len(baseDir) > 0) and options.bFindUnusedImages:
-            print('Found {} unused image files'.format(len(unusedFiles)))
-            
-        nUnusedCategories = 0
-        
-        # Find unused categories
-        for cat in categories:
-            if cat['_count'] == 0:
-                print('Unused category: {}'.format(cat['name']))
-                nUnusedCategories += 1
-        
-        print('Found {} unused categories'.format(nUnusedCategories))
-                
-        sequenceString = 'no sequence info'
-        if len(sequences) > 0:
-            sequenceString = '{} sequences'.format(len(sequences))
-            
-        print('\nDB contains {} images, {} annotations, {} bboxes, {} categories, {}\n'.format(
-                len(images),len(annotations),nBoxes,len(categories),sequenceString))
-    
-        if len(imageLocationSet) > 0:
-            print('DB contains images from {} locations\n'.format(len(imageLocationSet)))
-                
-        print('Categories and annotation (not image) counts:\n')
-        
-        for cat in sortedCategories:
-            print('{:6} {}'.format(cat['_count'],cat['name']))
-        
-        print('')
-    
-    errorInfo = {}
-    errorInfo['unusedFiles'] = unusedFiles
-    errorInfo['validationErrors'] = validationErrors
-    
-    return sortedCategories, data, errorInfo
-
-# ...def integrity_check_json_db()
-    
-
-#%% Command-line driver
-    
-def main():
-        
-    parser = argparse.ArgumentParser()
-    parser.add_argument('jsonFile')
-    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.jsonFile,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:
-        
-        sortedCategories,data,_ = integrity_check_json_db(json_file, options)