megadetector 5.0.11__py3-none-any.whl → 5.0.12__py3-none-any.whl

megadetector/data_management/yolo_to_coco.py

@@ -0,0 +1,676 @@
+"""
+
+yolo_to_coco.py
+
+Converts a folder of YOLO-formatted annotation files to a COCO-formatted dataset. 
+
+"""
+
+#%% Imports and constants
+
+import json
+import os
+
+from multiprocessing.pool import ThreadPool
+from multiprocessing.pool import Pool
+from functools import partial
+
+from tqdm import tqdm
+
+from megadetector.utils.path_utils import find_images
+from megadetector.utils.path_utils import recursive_file_list
+from megadetector.utils.path_utils import find_image_strings
+from megadetector.utils.ct_utils import invert_dictionary
+from megadetector.visualization.visualization_utils import open_image
+from megadetector.data_management.yolo_output_to_md_output import read_classes_from_yolo_dataset_file
+
+
+#%% Support functions
+
+def _filename_to_image_id(fn):
+    """
+    Image IDs can't have spaces in them, replae spaces with underscores
+    """
+    return fn.replace(' ','_')
+
+
+def _process_image(fn_abs,input_folder,category_id_to_name):
+    """
+    Internal support function for processing one image's labels.
+    """
+    
+    # Create the image object for this image
+    fn_relative = os.path.relpath(fn_abs,input_folder)
+    image_id = _filename_to_image_id(fn_relative)
+    
+    # This is done in a separate loop now
+    #
+    # assert image_id not in image_ids, \
+    #    'Oops, you have hit a very esoteric case where you have the same filename ' + \
+    #    'with both spaces and underscores, this is not currently handled.'
+    # image_ids.add(image_id)
+    
+    im = {}
+    im['file_name'] = fn_relative    
+    im['id'] = image_id
+    
+    annotations_this_image = []
+    
+    try:        
+        pil_im = open_image(fn_abs)
+        im_width, im_height = pil_im.size
+        im['width'] = im_width
+        im['height'] = im_height
+        im['error'] = None
+    except Exception as e:
+        print('Warning: error reading {}:\n{}'.format(fn_relative,str(e)))
+        im['width'] = -1
+        im['height'] = -1
+        im['error'] = str(e)
+        return (im,annotations_this_image)
+        
+    # Is there an annotation file for this image?
+    annotation_file = os.path.splitext(fn_abs)[0] + '.txt'
+    if not os.path.isfile(annotation_file):
+        annotation_file = os.path.splitext(fn_abs)[0] + '.TXT'
+    
+    if os.path.isfile(annotation_file):
+        
+        with open(annotation_file,'r') as f:
+            lines = f.readlines()
+        lines = [s.strip() for s in lines]
+        
+        # s = lines[0]
+        annotation_number = 0
+        
+        for s in lines:
+            
+            if len(s.strip()) == 0:
+                continue
+            
+            tokens = s.split()
+            assert len(tokens) == 5
+            category_id = int(tokens[0])
+            assert category_id in category_id_to_name, \
+                'Unrecognized category ID {} in annotation file {}'.format(
+                    category_id,annotation_file)
+            ann = {}
+            ann['id'] = im['id'] + '_' + str(annotation_number)
+            ann['image_id'] = im['id']
+            ann['category_id'] = category_id
+            ann['sequence_level_annotation'] = False
+            
+            # COCO: [x_min, y_min, width, height] in absolute coordinates
+            # YOLO: [class, x_center, y_center, width, height] in normalized coordinates
+            
+            yolo_bbox = [float(x) for x in tokens[1:]]
+            
+            normalized_x_center = yolo_bbox[0]
+            normalized_y_center = yolo_bbox[1]
+            normalized_width = yolo_bbox[2]
+            normalized_height = yolo_bbox[3]
+            
+            absolute_x_center = normalized_x_center * im_width 
+            absolute_y_center = normalized_y_center * im_height
+            absolute_width = normalized_width * im_width
+            absolute_height = normalized_height * im_height
+            absolute_x_min = absolute_x_center - absolute_width / 2
+            absolute_y_min = absolute_y_center - absolute_height / 2
+            
+            coco_bbox = [absolute_x_min, absolute_y_min, absolute_width, absolute_height]
+            
+            ann['bbox'] = coco_bbox
+            annotation_number += 1
+            
+            annotations_this_image.append(ann)                
+            
+        # ...for each annotation 
+        
+    # ...if this image has annotations
+    
+    return (im,annotations_this_image)
+
+# ...def _process_image(...)
+
+
+def load_yolo_class_list(class_name_file):
+    """
+    Loads a dictionary mapping zero-indexed IDs to class names from the text/yaml file
+    [class_name_file].    
+    
+    Args:
+        class_name_file (str or list): this can be:
+            - a .yaml or .yaml file in YOLO's dataset.yaml format
+            - a .txt or .data file containing a flat list of class names
+            - a list of class names
+            
+    Returns:
+        dict: A dict mapping zero-indexed integer IDs to class names
+    """
+    
+    # class_name_file can also be a list of class names
+    if isinstance(class_name_file,list):
+        category_id_to_name = {}
+        for i_name,name in enumerate(class_name_file):
+            category_id_to_name[i_name] = name
+        return category_id_to_name
+            
+    ext = os.path.splitext(class_name_file)[1][1:]
+    assert ext in ('yml','txt','yaml','data'), 'Unrecognized class name file type {}'.format(
+        class_name_file)
+    
+    if ext in ('txt','data'):
+        
+        with open(class_name_file,'r') as f:
+            lines = f.readlines()
+        assert len(lines) > 0, 'Empty class name file {}'.format(class_name_file)
+        class_names = [s.strip() for s in lines]
+        assert len(lines[0]) > 0, 'Empty class name file {} (empty first line)'.format(class_name_file)
+        
+        # Blank lines should only appear at the end
+        b_found_blank = False
+        for s in lines:
+            if len(s) == 0:
+                b_found_blank = True
+            elif b_found_blank:
+                raise ValueError('Invalid class name file {}, non-blank line after the last blank line'.format(
+                    class_name_file))
+    
+        category_id_to_name = {}        
+        for i_category_id,category_name in enumerate(class_names):
+            assert len(category_name) > 0
+            category_id_to_name[i_category_id] = category_name
+            
+    else:
+        
+        assert ext in ('yml','yaml')
+        category_id_to_name = read_classes_from_yolo_dataset_file(class_name_file)
+        
+    return category_id_to_name
+
+# ...load_yolo_class_list(...)
+
+
+def validate_label_file(label_file,category_id_to_name=None,verbose=False):
+    """"
+    Verifies that [label_file] is a valid YOLO label file.  Does not check the extension.
+    
+    Args:
+        label_file (str): the .txt file to validate
+        category_id_to_name (dict, optional): a dict mapping integer category IDs to names;
+            if this is not None, this function errors if the file uses a category that's not
+            in this dict
+        verbose (bool, optional): enable additional debug console output
+    
+    Returns:
+        dict: a dict with keys 'file' (the same as [label_file]) and 'errors' (a list of 
+        errors (if any) that we found in this file)
+    """
+    
+    label_result = {}
+    label_result['file'] = label_file
+    label_result['errors'] = []
+    
+    try:
+        with open(label_file,'r') as f:
+            lines = f.readlines()
+    except Exception as e:
+        label_result['errors'].append('Read error: {}'.format(str(e)))
+        return label_result
+    
+    # i_line 0; line = lines[i_line]
+    for i_line,line in enumerate(lines):
+        s = line.strip()
+        if len(s) == 0 or s[0] == '#':
+            continue
+        
+        try:
+        
+            tokens = s.split()
+            assert len(tokens) == 5, '{} tokens'.format(len(tokens))                
+            
+            if category_id_to_name is not None:
+                category_id = int(tokens[0])
+                assert category_id in category_id_to_name, \
+                    'Unrecognized category ID {}'.format(category_id)
+        
+            yolo_bbox = [float(x) for x in tokens[1:]]
+            
+        except Exception as e:
+            label_result['errors'].append('Token error at line {}: {}'.format(i_line,str(e)))
+            continue
+                            
+        normalized_x_center = yolo_bbox[0]
+        normalized_y_center = yolo_bbox[1]
+        normalized_width = yolo_bbox[2]
+        normalized_height = yolo_bbox[3]
+        
+        normalized_x_min = normalized_x_center - normalized_width / 2.0
+        normalized_x_max = normalized_x_center + normalized_width / 2.0
+        normalized_y_min = normalized_y_center - normalized_height / 2.0
+        normalized_y_max = normalized_y_center + normalized_height / 2.0
+        
+        if normalized_x_min < 0 or normalized_y_min < 0 or \
+            normalized_x_max > 1 or normalized_y_max > 1:
+            label_result['errors'].append('Invalid bounding box: {} {} {} {}'.format(
+                normalized_x_min,normalized_y_min,normalized_x_max,normalized_y_max))
+        
+    # ...for each line
+    
+    if verbose:
+        if len(label_result['errors']) > 0:
+            print('Errors for {}:'.format(label_file))
+            for error in label_result['errors']:
+                print(error)
+                
+    return label_result
+    
+# ...def validate_label_file(...)
+
+    
+def validate_yolo_dataset(input_folder, class_name_file, n_workers=1, pool_type='thread', verbose=False):
+    """
+    Verifies all the labels in a YOLO dataset folder.  
+    
+    Looks for:
+        
+    * Image files without label files
+    * Text files without image files
+    * Illegal classes in label files
+    * Invalid boxes in label files
+
+    Args:
+        input_folder (str): the YOLO dataset folder to validate
+        class_name_file (str or list): a list of classes, a flat text file, or a yolo 
+            dataset.yml/.yaml file.  If it's a dataset.yml file, that file should point to 
+            input_folder as the base folder, though this is not explicitly checked.
+        n_workers (int, optional): number of concurrent workers, set to <= 1 to disable
+            parallelization
+        pool_type (str, optional): 'thread' or 'process', worker type to use for parallelization;
+            not used if [n_workers] <= 1
+        verbose (bool, optional): enable additional debug console output
+    
+    Returns:
+        dict: validation results, as a dict with fields:        
+        
+        - image_files_without_label_files (list)
+        - label_files_without_image_files (list)
+        - label_results (list of dicts with field 'filename', 'errors') (list)
+    """
+    
+    # Validate arguments
+    assert os.path.isdir(input_folder), 'Could not find input folder {}'.format(input_folder)
+    if n_workers > 1:
+        assert pool_type in ('thread','process'), 'Illegal pool type {}'.format(pool_type)
+        
+    category_id_to_name = load_yolo_class_list(class_name_file)
+    
+    print('Enumerating files in {}'.format(input_folder))
+    
+    all_files = recursive_file_list(input_folder,recursive=True,return_relative_paths=False,
+                                    convert_slashes=True)
+    label_files = [fn for fn in all_files if fn.endswith('.txt')]
+    image_files = find_image_strings(all_files)
+    print('Found {} images files and {} label files in {}'.format(
+        len(image_files),len(label_files),input_folder))
+    
+    label_files_set = set(label_files)
+    
+    image_files_without_extension = set()
+    for fn in image_files:
+        image_file_without_extension = os.path.splitext(fn)[0]
+        assert image_file_without_extension not in image_files_without_extension, \
+            'Duplicate image file, likely with different extensions: {}'.format(fn)
+        image_files_without_extension.add(image_file_without_extension)
+        
+    print('Looking for missing image/label files')
+    
+    image_files_without_label_files = []
+    label_files_without_images = []
+    
+    for image_file in tqdm(image_files):
+        expected_label_file = os.path.splitext(image_file)[0] + '.txt'
+        if expected_label_file not in label_files_set:
+            image_files_without_label_files.append(image_file)
+            
+    for label_file in tqdm(label_files):
+        expected_image_file_without_extension = os.path.splitext(label_file)[0]
+        if expected_image_file_without_extension not in image_files_without_extension:
+            label_files_without_images.append(label_file)
+            
+    print('Found {} image files without labels, {} labels without images'.format(
+        len(image_files_without_label_files),len(label_files_without_images)))
+
+    print('Validating label files')
+    
+    if n_workers <= 1:
+        
+        label_results = []        
+        for fn_abs in tqdm(label_files):                
+            label_results.append(validate_label_file(fn_abs,
+                                                      category_id_to_name=category_id_to_name,
+                                                      verbose=verbose))
+            
+    else:
+        
+        assert pool_type in ('process','thread'), 'Illegal pool type {}'.format(pool_type)
+        
+        if pool_type == 'thread':
+            pool = ThreadPool(n_workers)
+        else:
+            pool = Pool(n_workers)
+        
+        print('Starting a {} pool of {} workers'.format(pool_type,n_workers))
+        
+        p = partial(validate_label_file,
+                    category_id_to_name=category_id_to_name,
+                    verbose=verbose)
+        label_results = list(tqdm(pool.imap(p, label_files),
+                                  total=len(label_files)))        
+    
+    assert len(label_results) == len(label_files)
+    
+    validation_results = {}
+    validation_results['image_files_without_label_files'] = image_files_without_label_files
+    validation_results['label_files_without_images'] = label_files_without_images
+    validation_results['label_results'] = label_results
+    
+    return validation_results
+    
+# ...validate_yolo_dataset(...)    
+
+
+#%% Main conversion function
+
+def yolo_to_coco(input_folder,
+                 class_name_file,
+                 output_file=None,
+                 empty_image_handling='no_annotations',
+                 empty_image_category_name='empty',
+                 error_image_handling='no_annotations',
+                 allow_images_without_label_files=True,
+                 n_workers=1,
+                 pool_type='thread',
+                 recursive=True,
+                 exclude_string=None,
+                 include_string=None):
+    """
+    Converts a YOLO-formatted dataset to a COCO-formatted dataset.
+    
+    All images will be assigned an "error" value, usually None.    
+    
+    Args:
+        input_folder (str): the YOLO dataset folder to validate
+        class_name_file (str or list): a list of classes, a flat text file, or a yolo 
+            dataset.yml/.yaml file.  If it's a dataset.yml file, that file should point to 
+            input_folder as the base folder, though this is not explicitly checked.
+        output_file (str, optional): .json file to which we should write COCO .json data
+        empty_image_handling (str, optional): how to handle images with no boxes; whether
+            this includes images with no .txt files depending on the value of 
+            [allow_images_without_label_files].  Can be:
+                
+            - 'no_annotations': include the image in the image list, with no annotations
+            - 'empty_annotations': include the image in the image list, and add an annotation without
+              any bounding boxes, using a category called [empty_image_category_name].
+            - 'skip': don't include the image in the image list
+            - 'error': there shouldn't be any empty images            
+        error_image_handling (str, optional): how to handle images that don't load properly; can
+            be:
+            
+            - 'skip': don't include the image at all
+            - 'no_annotations': include with no annotations
+            
+        n_workers (int, optional): number of concurrent workers, set to <= 1 to disable
+            parallelization
+        pool_type (str, optional): 'thread' or 'process', worker type to use for parallelization;
+            not used if [n_workers] <= 1
+        recursive (bool, optional): whether to recurse into [input_folder]
+        exclude_string (str, optional): exclude any images whose filename contains a string
+        include_string (str, optional): include only images whose filename contains a string
+    
+    Returns:
+        dict: COCO-formatted data, the same as what's written to [output_file]
+    """
+    
+    ## Validate input
+    
+    assert os.path.isdir(input_folder)
+    assert os.path.isfile(class_name_file)
+    
+    assert empty_image_handling in \
+        ('no_annotations','empty_annotations','skip','error'), \
+            'Unrecognized empty image handling spec: {}'.format(empty_image_handling)
+     
+            
+    ## Read class names
+    
+    category_id_to_name = load_yolo_class_list(class_name_file)
+    
+    
+    # Find or create the empty image category, if necessary
+    empty_category_id = None
+    
+    if (empty_image_handling == 'empty_annotations'):
+        category_name_to_id = invert_dictionary(category_id_to_name)
+        if empty_image_category_name in category_name_to_id:
+            empty_category_id = category_name_to_id[empty_image_category_name]
+            print('Using existing empty image category with name {}, ID {}'.format(
+                empty_image_category_name,empty_category_id))            
+        else:
+            empty_category_id = len(category_id_to_name)
+            print('Adding an empty category with name {}, ID {}'.format(
+                empty_image_category_name,empty_category_id))
+            category_id_to_name[empty_category_id] = empty_image_category_name
+            
+            
+    ## Enumerate images
+    
+    print('Enumerating images...')
+    
+    image_files_abs = find_images(input_folder,recursive=recursive,convert_slashes=True)
+
+    n_files_original = len(image_files_abs)
+    
+    # Optionally include/exclude images matching specific strings
+    if exclude_string is not None:
+        image_files_abs = [fn for fn in image_files_abs if exclude_string not in fn]
+    if include_string is not None:
+        image_files_abs = [fn for fn in image_files_abs if include_string in fn]
+    
+    if len(image_files_abs) != n_files_original or exclude_string is not None or include_string is not None:
+        n_excluded = n_files_original - len(image_files_abs)
+        print('Excluded {} of {} images based on filenames'.format(n_excluded,n_files_original))
+        
+    categories = []
+    
+    for category_id in category_id_to_name:
+        categories.append({'id':category_id,'name':category_id_to_name[category_id]})
+        
+    info = {}
+    info['version'] = '1.0'
+    info['description'] = 'Converted from YOLO format'
+    
+    image_ids = set()
+    
+    
+    ## If we're expected to have labels for every image, check before we process all the images
+    
+    if not allow_images_without_label_files:
+        print('Verifying that label files exist')
+        for image_file_abs in tqdm(image_files_abs):
+            label_file_abs = os.path.splitext(image_file_abs)[0] + '.txt'
+            assert os.path.isfile(label_file_abs), \
+                'No annotation file for {}'.format(image_file_abs)
+    
+    
+    ## Initial loop to make sure image IDs will be unique
+    
+    print('Validating image IDs...')
+    
+    for fn_abs in tqdm(image_files_abs):
+        
+        fn_relative = os.path.relpath(fn_abs,input_folder)
+        image_id = _filename_to_image_id(fn_relative)
+        assert image_id not in image_ids, \
+            'Oops, you have hit a very esoteric case where you have the same filename ' + \
+            'with both spaces and underscores, this is not currently handled.'
+        image_ids.add(image_id)
+    
+    
+    ## Main loop to process labels
+    
+    print('Processing labels...')
+    
+    if n_workers <= 1:
+        
+        image_results = []        
+        for fn_abs in tqdm(image_files_abs):                
+            image_results.append(_process_image(fn_abs,input_folder,category_id_to_name))
+            
+    else:
+        
+        assert pool_type in ('process','thread'), 'Illegal pool type {}'.format(pool_type)
+        
+        if pool_type == 'thread':
+            pool = ThreadPool(n_workers)
+        else:
+            pool = Pool(n_workers)
+        
+        print('Starting a {} pool of {} workers'.format(pool_type,n_workers))
+        
+        p = partial(_process_image,input_folder=input_folder,
+                    category_id_to_name=category_id_to_name)
+        image_results = list(tqdm(pool.imap(p, image_files_abs),
+                                  total=len(image_files_abs)))
+                
+    
+    assert len(image_results) == len(image_files_abs)
+    
+    
+    ## Re-assembly of results into a COCO dict
+    
+    print('Assembling labels...')
+    
+    images = []
+    annotations = []
+    
+    for image_result in tqdm(image_results):
+    
+        im = image_result[0]
+        annotations_this_image = image_result[1]
+           
+        # If we have annotations for this image
+        if len(annotations_this_image) > 0:
+            assert im['error'] is None
+            images.append(im)
+            for ann in annotations_this_image:
+                annotations.append(ann)
+                
+        # If this image failed to read
+        elif im['error'] is not None:
+            
+            if error_image_handling == 'skip':
+                pass
+            elif error_image_handling == 'no_annotations':
+                images.append(im)            
+                
+        # If this image read successfully, but there are no annotations
+        else:
+            
+            if empty_image_handling == 'skip':
+                pass
+            elif empty_image_handling == 'no_annotations':
+                images.append(im)
+            elif empty_image_handling == 'empty_annotations':
+                assert empty_category_id  is not None
+                ann = {}
+                ann['id'] = im['id'] + '_0'
+                ann['image_id'] = im['id']
+                ann['category_id'] = empty_category_id
+                ann['sequence_level_annotation'] = False
+                # This would also be a reasonable thing to do, but it's not the convention
+                # we're adopting.
+                # ann['bbox'] = [0,0,0,0]
+                annotations.append(ann)
+                images.append(im)        
+        
+    # ...for each image result
+    
+    print('Read {} annotations for {} images'.format(len(annotations),
+                                                     len(images)))
+    
+    d = {}
+    d['images'] = images
+    d['annotations'] = annotations
+    d['categories'] = categories
+    d['info'] = info
+
+    if output_file is not None:
+        print('Writing to {}'.format(output_file))
+        with open(output_file,'w') as f:
+            json.dump(d,f,indent=1)
+
+    return d
+
+# ...def yolo_to_coco()
+
+
+#%% Interactive driver
+
+if False:
+    
+    pass
+
+    #%% Convert YOLO folders to COCO
+    
+    preview_folder = '/home/user/data/noaa-fish/val-coco-conversion-preview'
+    input_folder = '/home/user/data/noaa-fish/val'
+    output_file = '/home/user/data/noaa-fish/val.json'
+    class_name_file = '/home/user/data/noaa-fish/AllImagesWithAnnotations/classes.txt'
+
+    d = yolo_to_coco(input_folder,class_name_file,output_file)
+        
+    input_folder = '/home/user/data/noaa-fish/train'
+    output_file = '/home/user/data/noaa-fish/train.json'
+    class_name_file = '/home/user/data/noaa-fish/AllImagesWithAnnotations/classes.txt'
+
+    d = yolo_to_coco(input_folder,class_name_file,output_file)
+    
+    
+    #%% Check DB integrity
+
+    from megadetector.data_management.databases import integrity_check_json_db
+
+    options = integrity_check_json_db.IntegrityCheckOptions()
+    options.baseDir = input_folder
+    options.bCheckImageSizes = False
+    options.bCheckImageExistence = True
+    options.bFindUnusedImages = True
+
+    _, _, _ = integrity_check_json_db.integrity_check_json_db(output_file, options)
+
+
+    #%% Preview some images
+
+    from megadetector.visualization import visualize_db
+
+    viz_options = visualize_db.DbVizOptions()
+    viz_options.num_to_visualize = None
+    viz_options.trim_to_images_with_bboxes = False
+    viz_options.add_search_links = False
+    viz_options.sort_by_filename = False
+    viz_options.parallelize_rendering = True
+    viz_options.include_filename_links = True
+
+    html_output_file, _ = visualize_db.visualize_db(db_path=output_file,
+                                                        output_dir=preview_folder,
+                                                        image_base_dir=input_folder,
+                                                        options=viz_options)
+    
+    from megadetector.utils.path_utils import open_file
+    open_file(html_output_file)
+
+
+#%% Command-line driver
+
+# TODO