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

detection/run_inference_with_yolov5_val.py

@@ -1,917 +0,0 @@
-"""
-
-run_inference_with_yolov5_val.py
-
-Runs a folder of images through MegaDetector (or another YOLOv5/YOLOv8 model) with YOLO's
-val.py, converting the output to the standard MD format.  The reasons this script exists,
-as an alternative to the standard run_detector_batch.py are:
-    
-* This script provides access to YOLO's test-time augmentation tools.
-* This script serves a reference implementation: by any reasonable definition, YOLOv5's
-  val.py produces the "correct" result for any image, since it matches what was used in 
-  training.
-* This script works for any Ultralytics detection model, including YOLOv8 models  
-
-YOLOv5's val.py uses each file's base name as a unique identifier, which doesn't work 
-when you have typical camera trap images like:
-
-* a/b/c/RECONYX0001.JPG
-* d/e/f/RECONYX0001.JPG
-
-...both of which would just be "RECONYX0001.JPG".  So this script jumps through a bunch of 
-hoops to put a symlinks in a flat folder, run YOLOv5 on that folder, and map the results back 
-to the real files.
-
-If you are running a YOLOv5 model, this script currently requires the caller to supply the path
-where a working YOLOv5 install lives, and assumes that the current conda environment is all set up for 
-YOLOv5.  If you are running a YOLOv8 model, the folder doesn't matter, but it assumes that ultralytics
-tools are available in the current environment.
-
-By default, this script uses symlinks to format the input images in a way that YOLO's 
-val.py likes, as per above.  This requires admin privileges on Windows... actually technically this 
-only requires permissions to create symbolic links, but I've never seen a case where someone has
-that permission and *doesn't* have admin privileges.  If you are running this script on
-Windows and you don't have admin privileges, use --no_use_symlinks, which will make copies of images,
-rather than using symlinks.
-
-TODO:
-
-* Multiple GPU support
-* Checkpointing
-* Support alternative class names at the command line (currently defaults to MD classes,
-  though other class names can be supplied programmatically)
-
-"""
-
-#%% Imports
-
-import os
-import sys
-import uuid
-import glob
-import tempfile
-import shutil
-import json
-
-from tqdm import tqdm
-
-from md_utils import path_utils
-from md_utils import process_utils
-from md_utils import string_utils
-from data_management import yolo_output_to_md_output
-from detection.run_detector import try_download_known_detector
-
-default_image_size_with_augmentation = int(1280 * 1.3)
-default_image_size_with_no_augmentation = 1280
-
-
-#%% Options class
-
-class YoloInferenceOptions:
-    """
-    Parameters that control the behavior of run_inference_with_yolov5_val(), including 
-    the input/output filenames.
-    """
-    
-    ## Required ##
-    
-    #: Folder of images to process
-    input_folder = None
-    
-    #: Model filename (ending in .pt), or a well-known model name (e.g. "MDV5A")
-    model_filename = None
-    
-    #: .json output file, in MD results format
-    output_file = None
-    
-    
-    ## Optional ##
-    
-    #: Required for older YOLOv5 inference, not for newer ulytralytics/YOLOv8 inference
-    yolo_working_folder = None
-    
-    #: Currently 'yolov5' and 'ultralytics' are supported, and really these are proxies for
-    #: "the yolov5 repo" and "the ultralytics repo".
-    model_type = 'yolov5' 
-
-    #: Image size to use; this is a single int, which in ultralytics's terminology means
-    #: "scale the long side of the image to this size, and preserve aspect ratio".
-    image_size = default_image_size_with_augmentation
-    
-    #: Detections below this threshold will not be included in the output file
-    conf_thres = '0.001'
-    
-    #: Batch size... has no impact on results, but may create memory issues if you set
-    #: this to large values
-    batch_size = 1
-    
-    #: Device string: typically '0' for GPU 0, '1' for GPU 1, etc., or 'cpu'
-    device_string = '0'
-    
-    #: Should we enable test-time augmentation?
-    augment = True
-    
-    #: Should we enable half-precision inference?
-    half_precision_enabled = None
-    
-    #: Where should we stash the temporary symlinks used to give unique identifiers to image files?
-    #:
-    #: If this is None, we'll create a folder in system temp space.
-    symlink_folder = None
-    
-    #: Should we use symlinks to give unique identifiers to image files (vs. copies)?
-    use_symlinks = True
-    
-    #: Temporary folder to stash intermediate YOLO results.
-    #:
-    #: If this is None, we'll create a folder in system temp space.    
-    yolo_results_folder = None
-    
-    #: Should we remove the symlink folder when we're done?
-    remove_symlink_folder = True
-    
-    #: Should we remove the intermediate results folder when we're done?
-    remove_yolo_results_folder = True
-    
-    #: These are deliberately offset from the standard MD categories; YOLOv5
-    #: needs categories IDs to start at 0.
-    #:
-    #: This can also be a string that points to a YOLO dataset.yaml file.
-    yolo_category_id_to_name = {0:'animal',1:'person',2:'vehicle'}
-    
-    #: What should we do if the output file already exists?
-    #:
-    #: Can be 'error', 'skip', or 'overwrite'.
-    overwrite_handling = 'skip'
-    
-    #: If True, we'll do a dry run that lets you preview the YOLO val command, without
-    #: actually running it.
-    preview_yolo_command_only = False
-    
-    #: By default, if any errors occur while we're copying images or creating symlinks, it's
-    #: game over.  If this is True, those errors become warnings, and we plow ahead.
-    treat_copy_failures_as_warnings = False
-    
-    #: Save YOLO console output
-    save_yolo_debug_output = False
-    
-    #: Whether to search for images recursively within [input_folder]
-    recursive = True
-            
-    
-# ...YoloInferenceOptions()
-
-    
-#%% Main function
-
-def run_inference_with_yolo_val(options):
-    """
-    Runs a folder of images through MegaDetector (or another YOLOv5/YOLOv8 model) with YOLO's
-    val.py, converting the output to the standard MD format.
-    
-    Args: 
-        options (YoloInferenceOptions): all the parameters used to control this process,
-            including filenames; see YoloInferenceOptions for details            
-    """
-    
-    ##%% Input and path handling
-    
-    if options.model_type == 'yolov8':
-        
-        print('Warning: model type "yolov8" supplied, "ultralytics" is the preferred model type string for YOLOv8 models')
-        options.model_type = 'ultralytics'
-        
-    if (options.model_type == 'yolov5') and ('yolov8' in options.model_filename.lower()):
-        print('\n\n*** Warning: model type set as "yolov5", but your model filename contains "yolov8"... did you mean to use --model_type yolov8?" ***\n\n')        
-    
-    if options.yolo_working_folder is None:
-        assert options.model_type == 'ultralytics', \
-            'A working folder is required to run YOLOv5 val.py'
-    else:
-        assert os.path.isdir(options.yolo_working_folder), \
-            'Could not find working folder {}'.format(options.yolo_working_folder)
-                
-    assert os.path.isdir(options.input_folder) or os.path.isfile(options.input_folder), \
-        'Could not find input {}'.format(options.input_folder)
-    
-    if options.half_precision_enabled is not None:
-        assert options.half_precision_enabled in (0,1), \
-            'Invalid value {} for --half_precision_enabled (should be 0 or 1)'.format(
-                options.half_precision_enabled)
-            
-    # If the model filename is a known model string (e.g. "MDv5A", download the model if necessary)
-    model_filename = try_download_known_detector(options.model_filename)
-    
-    assert os.path.isfile(model_filename), \
-        'Could not find model file {}'.format(model_filename)
-    
-    if os.path.exists(options.output_file):
-        if options.overwrite_handling == 'skip':
-            print('Warning: output file {} exists, skipping'.format(options.output_file))
-            return
-        elif options.overwrite_handling == 'overwrite':
-            print('Warning: output file {} exists, overwriting'.format(options.output_file))
-        elif options.overwrite_handling == 'error':
-            raise ValueError('Output file {} exists'.format(options.output_file))
-        else:
-            raise ValueError('Unknown output handling method {}'.format(options.overwrite_handling))
-            
-    os.makedirs(os.path.dirname(options.output_file),exist_ok=True)
-    
-    
-    ##%% Other input handling
-    
-    if isinstance(options.yolo_category_id_to_name,str):
-        assert os.path.isfile(options.yolo_category_id_to_name)
-        yolo_dataset_file = options.yolo_category_id_to_name
-        options.yolo_category_id_to_name = \
-            yolo_output_to_md_output.read_classes_from_yolo_dataset_file(yolo_dataset_file)
-        print('Loaded {} category mappings from {}'.format(
-            len(options.yolo_category_id_to_name),yolo_dataset_file))
-
-    temporary_folder = None
-    symlink_folder_is_temp_folder = False
-    yolo_folder_is_temp_folder = False
-    
-    job_id = str(uuid.uuid1())
-    
-    def get_job_temporary_folder(tf):
-        if tf is not None:
-            return tf
-        tempdir_base = tempfile.gettempdir()
-        tf = os.path.join(tempdir_base,'md_to_yolo','md_to_yolo_' + job_id)
-        os.makedirs(tf,exist_ok=True)
-        return tf
-        
-    symlink_folder = options.symlink_folder
-    yolo_results_folder = options.yolo_results_folder
-    
-    if symlink_folder is None:
-        temporary_folder = get_job_temporary_folder(temporary_folder)
-        symlink_folder = os.path.join(temporary_folder,'symlinks')
-        symlink_folder_is_temp_folder = True
-    
-    if yolo_results_folder is None:
-        temporary_folder = get_job_temporary_folder(temporary_folder)
-        yolo_results_folder = os.path.join(temporary_folder,'yolo_results')
-        yolo_folder_is_temp_folder = True
-        
-    # Attach a GUID to the symlink folder, regardless of whether we created it
-    symlink_folder_inner = os.path.join(symlink_folder,job_id)
-    
-    os.makedirs(symlink_folder_inner,exist_ok=True)
-    os.makedirs(yolo_results_folder,exist_ok=True)
-    
-
-    ##%% Enumerate images
-    
-    if os.path.isdir(options.input_folder):
-        image_files_absolute = path_utils.find_images(options.input_folder,recursive=options.recursive)
-    else:
-        assert os.path.isfile(options.input_folder)
-        with open(options.input_folder,'r') as f:            
-            image_files_absolute = json.load(f)
-            assert isinstance(image_files_absolute,list)
-            for fn in image_files_absolute:
-                assert os.path.isfile(fn), 'Could not find image file {}'.format(fn)
-    
-    
-    ##%% Create symlinks to give a unique ID to each image
-    
-    image_id_to_file = {}  
-    image_id_to_error = {}
-    
-    if options.use_symlinks:
-        print('Creating {} symlinks in {}'.format(len(image_files_absolute),symlink_folder_inner))
-    else:
-        print('Symlinks disabled, copying {} images to {}'.format(len(image_files_absolute),symlink_folder_inner))
-        
-    # i_image = 0; image_fn = image_files_absolute[i_image]
-    for i_image,image_fn in tqdm(enumerate(image_files_absolute),total=len(image_files_absolute)):
-        
-        ext = os.path.splitext(image_fn)[1]
-        
-        image_id = str(i_image).zfill(10)
-        image_id_to_file[image_id] = image_fn
-        symlink_name = image_id + ext
-        symlink_full_path = os.path.join(symlink_folder_inner,symlink_name)
-        
-        try:
-            if options.use_symlinks:
-                path_utils.safe_create_link(image_fn,symlink_full_path)
-            else:
-                shutil.copyfile(image_fn,symlink_full_path)
-        except Exception as e:
-            error_string = str(e)
-            image_id_to_error[image_id] = error_string
-            # Always break if the user is trying to create symlinks on Windows without
-            # permission, 100% of images will always fail in this case.
-            if ('a required privilege is not held by the client' in error_string.lower()) or \
-               (not options.treat_copy_failures_as_warnings):
-                   print('\nError copying/creating link for input file {}: {}'.format(
-                       image_fn,error_string))
-                   
-                   raise
-            else:
-                print('Warning: error copying/creating link for input file {}: {}'.format(
-                    image_fn,error_string))
-                continue
-        
-    # ...for each image
-
-
-    ##%% Create the dataset file if necessary
-    
-    # This may have been passed in as a string, but at this point, we should have
-    # loaded the dataset file.
-    assert isinstance(options.yolo_category_id_to_name,dict)
-    
-    # Category IDs need to be continuous integers starting at 0
-    category_ids = sorted(list(options.yolo_category_id_to_name.keys()))
-    assert category_ids[0] == 0
-    assert len(category_ids) == 1 + category_ids[-1]
-    
-    yolo_dataset_file = os.path.join(yolo_results_folder,'dataset.yaml')
-    
-    with open(yolo_dataset_file,'w') as f:
-        f.write('path: {}\n'.format(symlink_folder_inner))
-        f.write('train: .\n')
-        f.write('val: .\n')
-        f.write('test: .\n')
-        f.write('\n')
-        f.write('nc: {}\n'.format(len(options.yolo_category_id_to_name)))
-        f.write('\n')
-        f.write('names:\n')
-        for category_id in category_ids:
-            assert isinstance(category_id,int)
-            f.write('  {}: {}\n'.format(category_id,
-                                        options.yolo_category_id_to_name[category_id]))
-
-
-    ##%% Prepare Python command or YOLO CLI command
-    
-    image_size_string = str(round(options.image_size))
-    
-    if options.model_type == 'yolov5':
-        
-        cmd = 'python val.py --task test --data "{}"'.format(yolo_dataset_file)
-        cmd += ' --weights "{}"'.format(model_filename)
-        cmd += ' --batch-size {} --imgsz {} --conf-thres {}'.format(
-            options.batch_size,image_size_string,options.conf_thres)
-        cmd += ' --device "{}" --save-json'.format(options.device_string)
-        cmd += ' --project "{}" --name "{}" --exist-ok'.format(yolo_results_folder,'yolo_results')
-        
-        if options.augment:
-            cmd += ' --augment'
-                
-        # --half is a store_true argument for YOLOv5's val.py
-        if (options.half_precision_enabled is not None) and (options.half_precision_enabled == 1):
-            cmd += ' --half'
-        
-        # Sometimes useful for debugging
-        # cmd += ' --save_conf --save_txt'
-        
-    elif options.model_type == 'ultralytics':
-                
-        if options.augment:
-            augment_string = 'augment'
-        else:
-            augment_string = ''
-            
-        cmd = 'yolo val {} model="{}" imgsz={} batch={} data="{}" project="{}" name="{}" device="{}"'.\
-            format(augment_string,model_filename,image_size_string,options.batch_size,
-                   yolo_dataset_file,yolo_results_folder,'yolo_results',options.device_string)
-        cmd += ' save_json exist_ok'
-        
-        if (options.half_precision_enabled is not None):
-            if options.half_precision_enabled == 1:
-                cmd += ' --half=True'
-            else:
-                assert options.half_precision_enabled == 0
-                cmd += ' --half=False'
-        
-        # Sometimes useful for debugging
-        # cmd += ' save_conf save_txt'
-            
-    else:
-        
-        raise ValueError('Unrecognized model type {}'.format(options.model_type))
-        
-    # print(cmd); import clipboard; clipboard.copy(cmd)
-
-    
-    ##%% Run YOLO command
-    
-    if options.yolo_working_folder is not None:
-        current_dir = os.getcwd()
-        os.chdir(options.yolo_working_folder)
-
-    print('Running YOLO inference command:\n{}\n'.format(cmd))
-    
-    if options.preview_yolo_command_only:
-        
-        if options.remove_symlink_folder:
-            try:
-                print('Removing YOLO symlink folder {}'.format(symlink_folder))
-                shutil.rmtree(symlink_folder)
-            except Exception:
-                print('Warning: error removing symlink folder {}'.format(symlink_folder))
-                pass
-        if options.remove_yolo_results_folder:
-            try:
-                print('Removing YOLO results folder {}'.format(yolo_results_folder))
-                shutil.rmtree(yolo_results_folder)
-            except Exception:
-                print('Warning: error removing YOLO results folder {}'.format(yolo_results_folder))
-                pass
-        
-        sys.exit()
-    
-    execution_result = process_utils.execute_and_print(cmd,encoding='utf-8',verbose=True)
-    assert execution_result['status'] == 0, 'Error running {}'.format(options.model_type)
-    yolo_console_output = execution_result['output']
-      
-    if options.save_yolo_debug_output:
-        with open(os.path.join(yolo_results_folder,'yolo_console_output.txt'),'w') as f:
-            for s in yolo_console_output:
-                f.write(s + '\n')
-        with open(os.path.join(yolo_results_folder,'image_id_to_file.json'),'w') as f:
-            json.dump(image_id_to_file,f,indent=1)
-        with open(os.path.join(yolo_results_folder,'image_id_to_error.json'),'w') as f:
-            json.dump(image_id_to_error,f,indent=1)
-                
-        
-    # YOLO console output contains lots of ANSI escape codes, remove them for easier parsing
-    yolo_console_output = [string_utils.remove_ansi_codes(s) for s in yolo_console_output]
-    
-    # Find errors that occurred during the initial corruption check; these will not be included in the
-    # output.  Errors that occur during inference will be handled separately.
-    yolo_read_failures = []
-    
-    for line in yolo_console_output:
-        # Lines look like:
-        #
-        # For ultralytics val:
-        #
-        # val: WARNING ⚠️ /a/b/c/d.jpg: ignoring corrupt image/label: [Errno 13] Permission denied: '/a/b/c/d.jpg'
-        # line = "val: WARNING ⚠️ /a/b/c/d.jpg: ignoring corrupt image/label: [Errno 13] Permission denied: '/a/b/c/d.jpg'"
-        #
-        # For yolov5 val.py:
-        #
-        # test: WARNING: a/b/c/d.jpg: ignoring corrupt image/label: cannot identify image file '/a/b/c/d.jpg'
-        # line = "test: WARNING: a/b/c/d.jpg: ignoring corrupt image/label: cannot identify image file '/a/b/c/d.jpg'"
-        if 'cannot identify image file' in line:
-            tokens = line.split('cannot identify image file')
-            image_name = tokens[-1].strip()
-            assert image_name[0] == "'" and image_name [-1] == "'"
-            image_name = image_name[1:-1]
-            yolo_read_failures.append(image_name)            
-        elif 'ignoring corrupt image/label' in line:
-            assert 'WARNING' in line
-            if '⚠️' in line:
-                assert line.startswith('val'), \
-                    'Unrecognized line in YOLO output: {}'.format(line)
-                tokens = line.split('ignoring corrupt image/label')
-                image_name = tokens[0].split('⚠️')[-1].strip()
-            else:
-                assert line.startswith('test'), \
-                    'Unrecognized line in YOLO output: {}'.format(line)
-                tokens = line.split('ignoring corrupt image/label')
-                image_name = tokens[0].split('WARNING:')[-1].strip()
-            assert image_name.endswith(':')
-            image_name = image_name[0:-1]
-            yolo_read_failures.append(image_name)
-                    
-    # image_file = yolo_read_failures[0]
-    for image_file in yolo_read_failures:
-        image_id = os.path.splitext(os.path.basename(image_file))[0]
-        assert image_id in image_id_to_file
-        if image_id not in image_id_to_error:
-            image_id_to_error[image_id] = 'YOLO read failure'
-    
-    if options.yolo_working_folder is not None:
-        os.chdir(current_dir)
-        
-    
-    ##%% Convert results to MD format
-    
-    json_files = glob.glob(yolo_results_folder + '/yolo_results/*.json')
-    assert len(json_files) == 1    
-    yolo_json_file = json_files[0]
-
-    image_id_to_relative_path = {}
-    for image_id in image_id_to_file:
-        fn = image_id_to_file[image_id]
-        if os.path.isdir(options.input_folder):
-            assert options.input_folder in fn
-            relative_path = os.path.relpath(fn,options.input_folder)
-        else:
-            assert os.path.isfile(options.input_folder)
-            # We'll use the absolute path as a relative path, and pass '/'
-            # as the base path in this case.
-            relative_path = fn
-        image_id_to_relative_path[image_id] = relative_path
-        
-    if os.path.isdir(options.input_folder):
-        image_base = options.input_folder
-    else:
-        assert os.path.isfile(options.input_folder)
-        image_base = '/'
-        
-    yolo_output_to_md_output.yolo_json_output_to_md_output(
-        yolo_json_file=yolo_json_file,
-        image_folder=image_base,
-        output_file=options.output_file,
-        yolo_category_id_to_name=options.yolo_category_id_to_name,
-        detector_name=os.path.basename(model_filename),
-        image_id_to_relative_path=image_id_to_relative_path,
-        image_id_to_error=image_id_to_error)
-
-
-    ##%% Clean up
-    
-    if options.remove_symlink_folder:
-        shutil.rmtree(symlink_folder)
-    elif symlink_folder_is_temp_folder:
-        print('Warning: using temporary symlink folder {}, but not removing it'.format(
-            symlink_folder))
-        
-    if options.remove_yolo_results_folder:
-        shutil.rmtree(yolo_results_folder)
-    elif yolo_folder_is_temp_folder:
-        print('Warning: using temporary YOLO results folder {}, but not removing it'.format(
-            yolo_results_folder))
-            
-# ...def run_inference_with_yolo_val()
-
-
-#%% Command-line driver
-
-import argparse
-from md_utils.ct_utils import args_to_object
-
-def main():
-    
-    options = YoloInferenceOptions()
-    
-    parser = argparse.ArgumentParser()
-    parser.add_argument(
-        'model_filename',type=str,
-        help='model file name')
-    parser.add_argument(
-        'input_folder',type=str,
-        help='folder on which to recursively run the model, or a .json list of filenames')
-    parser.add_argument(
-        'output_file',type=str,
-        help='.json file where output will be written')
-    
-    parser.add_argument(
-        '--yolo_working_folder',type=str,default=None,
-        help='folder in which to execute val.py (not necessary for YOLOv8 inference)')
-    parser.add_argument(
-        '--image_size', default=None, type=int,
-        help='image size for model execution (default {} when augmentation is enabled, else {})'.format(
-            default_image_size_with_augmentation,default_image_size_with_no_augmentation))
-    parser.add_argument(
-        '--conf_thres', default=options.conf_thres, type=float,
-        help='confidence threshold for including detections in the output file (default {})'.format(
-            options.conf_thres))
-    parser.add_argument(
-        '--batch_size', default=options.batch_size, type=int,
-        help='inference batch size (default {})'.format(options.batch_size))
-    parser.add_argument(
-        '--half_precision_enabled', default=None, type=int,
-        help='use half-precision-inference (1 or 0) (default is the underlying model\'s default, probably full for YOLOv8 and half for YOLOv5')
-    parser.add_argument(
-        '--device_string', default=options.device_string, type=str,
-        help='CUDA device specifier, typically "0" or "1" for CUDA devices, "mps" for M1/M2 devices, or "cpu" (default {})'.format(options.device_string))
-    parser.add_argument(
-        '--overwrite_handling', default=options.overwrite_handling, type=str,
-        help='action to take if the output file exists (skip, error, overwrite) (default {})'.format(
-            options.overwrite_handling))
-    parser.add_argument(
-        '--yolo_dataset_file', default=None, type=str,
-        help='YOLOv5 dataset.yml file from which we should load category information ' + \
-            '(otherwise defaults to MD categories)')
-    parser.add_argument(
-        '--model_type', default=options.model_type, type=str,
-        help='Model type ("yolov5" or "ultralytics" ("yolov8" behaves the same as "ultralytics")) (default {})'.format(options.model_type))
-
-    parser.add_argument(
-        '--symlink_folder', type=str,
-        help='temporary folder for symlinks (defaults to a folder in the system temp dir)')
-    parser.add_argument(
-        '--yolo_results_folder', type=str,
-        help='temporary folder for YOLO intermediate output (defaults to a folder in the system temp dir)')
-    parser.add_argument(
-        '--no_use_symlinks', action='store_true',
-        help='copy files instead of creating symlinks when preparing the yolo input folder')
-    parser.add_argument(
-        '--no_remove_symlink_folder', action='store_true',
-        help='don\'t remove the temporary folder full of symlinks')
-    parser.add_argument(
-        '--no_remove_yolo_results_folder', action='store_true',
-        help='don\'t remove the temporary folder full of YOLO intermediate files')
-    parser.add_argument(
-        '--save_yolo_debug_output', action='store_true',
-        help='write yolo console output to a text file in the results folder, along with additional debug files')
-    
-    parser.add_argument(
-        '--nonrecursive', action='store_true',
-        help='Disable recursive folder processing')
-    
-    parser.add_argument(
-        '--preview_yolo_command_only', action='store_true',
-        help='don\'t run inference, just preview the YOLO inference command (still creates symlinks)')
-    
-    if options.augment:
-        default_augment_enabled = 1
-    else:
-        default_augment_enabled = 0
-            
-    parser.add_argument(
-        '--augment_enabled', default=default_augment_enabled, type=int,
-        help='enable/disable augmentation (default {})'.format(default_augment_enabled))
-        
-    if len(sys.argv[1:]) == 0:
-        parser.print_help()
-        parser.exit()
-
-    args = parser.parse_args()
-        
-    # If the caller hasn't specified an image size, choose one based on whether augmentation
-    # is enabled.
-    if args.image_size is None:        
-        assert args.augment_enabled in (0,1), \
-            'Illegal augment_enabled value {}'.format(args.augment_enabled)
-        if args.augment_enabled == 1:
-            args.image_size = default_image_size_with_augmentation
-        else:
-            args.image_size = default_image_size_with_no_augmentation
-        augment_enabled_string = 'enabled'
-        if not args.augment_enabled:
-            augment_enabled_string = 'disabled'
-        print('Augmentation is {}, using default image size {}'.format(
-            augment_enabled_string,args.image_size))
-        
-    args_to_object(args, options)
-    
-    if args.yolo_dataset_file is not None:
-        options.yolo_category_id_to_name = args.yolo_dataset_file
-        
-    options.recursive = (not options.nonrecursive)
-    options.remove_symlink_folder = (not options.no_remove_symlink_folder)
-    options.remove_yolo_results_folder = (not options.no_remove_yolo_results_folder)
-    options.use_symlinks = (not options.no_use_symlinks)
-    options.augment = (options.augment_enabled > 0)        
-            
-    print(options.__dict__)
-    
-    run_inference_with_yolo_val(options)    
-
-if __name__ == '__main__':
-    main()
-
-
-#%% Scrap
-
-if False:
-
-    #%% Test driver (folder)
-    
-    project_name = 'KRU-test-corrupted'
-    input_folder = os.path.expanduser(f'~/data/{project_name}')
-    output_folder = os.path.expanduser(f'~/tmp/{project_name}')
-    model_filename = os.path.expanduser('~/models/camera_traps/megadetector/md_v5.0.0/md_v5a.0.0.pt')
-    yolo_working_folder = os.path.expanduser('~/git/yolov5')
-    model_name = os.path.splitext(os.path.basename(model_filename))[0]
-    
-    symlink_folder = os.path.join(output_folder,'symlinks')
-    yolo_results_folder = os.path.join(output_folder,'yolo_results')
-    
-    output_file = os.path.join(output_folder,'{}_{}-md_format.json'.format(
-        project_name,model_name))
-    
-    options = YoloInferenceOptions()
-    
-    options.yolo_working_folder = yolo_working_folder
-    
-    options.output_file = output_file
-    
-    options.augment = False
-    options.conf_thres = '0.001'
-    options.batch_size = 1
-    options.device_string = '0'
-
-    if options.augment:
-        options.image_size = round(1280 * 1.3)
-    else:
-        options.image_size = 1280
-    
-    options.input_folder = input_folder
-    options.model_filename = model_filename
-    
-    options.yolo_results_folder = yolo_results_folder # os.path.join(output_folder + 'yolo_results')        
-    options.symlink_folder = symlink_folder # os.path.join(output_folder,'symlinks')
-    options.use_symlinks = False
-    
-    options.remove_temporary_symlink_folder = False
-    options.remove_yolo_results_file = False
-    
-    cmd = f'python run_inference_with_yolov5_val.py {model_filename} {input_folder} ' + \
-          f'{output_file} --yolo_working_folder {yolo_working_folder} ' + \
-          f' --image_size {options.image_size} --conf_thres {options.conf_thres} ' + \
-          f' --batch_size {options.batch_size} ' + \
-          f' --symlink_folder {options.symlink_folder} --yolo_results_folder {options.yolo_results_folder} ' + \
-          ' --no_remove_symlink_folder --no_remove_yolo_results_folder'
-      
-    if not options.use_symlinks:
-        cmd += ' --no_use_symlinks'
-    if not options.augment:
-        cmd += ' --augment_enabled 0'
-        
-    print(cmd)
-    execute_in_python = False
-    if execute_in_python:
-        run_inference_with_yolo_val(options)
-    else:
-        import clipboard; clipboard.copy(cmd)
-    
-    
-    #%% Test driver (folder) (YOLOv8 model)
-    
-    project_name = 'yolov8-inference-test'
-    input_folder = os.path.expanduser('~/data/usgs-kissel-training-resized/val')
-    dataset_file = os.path.expanduser('~/data/usgs-kissel-training-yolo/dataset.yaml')
-    output_folder = os.path.expanduser(f'~/tmp/{project_name}')
-    model_filename = os.path.expanduser(
-        '~/models/usgs-tegus/usgs-tegus-yolov8x-2023.10.25-b-1-img640-e200-best.pt')
-    model_name = os.path.splitext(os.path.basename(model_filename))[0]
-    
-    assert os.path.isdir(input_folder)
-    assert os.path.isfile(dataset_file)
-    assert os.path.isfile(model_filename)    
-    
-    symlink_folder = os.path.join(output_folder,'symlinks')
-    yolo_results_folder = os.path.join(output_folder,'yolo_results')
-    
-    output_file = os.path.join(output_folder,'{}_{}-md_format.json'.format(
-        project_name,model_name))
-    
-    options = YoloInferenceOptions()
-    
-    options.model_type = 'yolov8'    
-    options.yolo_category_id_to_name = dataset_file    
-    options.yolo_working_folder = None    
-    options.output_file = output_file
-    
-    options.augment = False
-    options.conf_thres = '0.001'
-    options.batch_size = 1
-    options.device_string = '0'
-
-    if options.augment:
-        options.image_size = round(640 * 1.3)
-    else:
-        options.image_size = 640
-    
-    options.input_folder = input_folder
-    options.model_filename = model_filename
-    
-    options.yolo_results_folder = yolo_results_folder 
-    options.symlink_folder = symlink_folder
-    options.use_symlinks = False
-    
-    options.remove_temporary_symlink_folder = False
-    options.remove_yolo_results_file = False
-    
-    cmd = f'python run_inference_with_yolov5_val.py {model_filename} ' + \
-          f'{input_folder} {output_file}' + \
-          f' --image_size {options.image_size} --conf_thres {options.conf_thres} ' + \
-          f' --batch_size {options.batch_size} --symlink_folder {options.symlink_folder} ' + \
-          f'--yolo_results_folder {options.yolo_results_folder} --model_type {options.model_type}' + \
-          f' --yolo_dataset_file {options.yolo_category_id_to_name}' + \
-          ' --no_remove_symlink_folder --no_remove_yolo_results_folder'
-      
-    if not options.use_symlinks:
-        cmd += ' --no_use_symlinks'
-    if not options.augment:
-        cmd += ' --augment_enabled 0'
-        
-    print(cmd)
-    execute_in_python = False
-    if execute_in_python:
-        run_inference_with_yolo_val(options)
-    else:
-        import clipboard; clipboard.copy(cmd)
-    
-    
-    #%% Preview results
-    
-    postprocessing_output_folder = os.path.join(output_folder,'yolo-val-preview')
-    md_json_file = options.output_file
-    
-    from api.batch_processing.postprocessing.postprocess_batch_results import (
-        PostProcessingOptions, process_batch_results)
-    
-    with open(md_json_file,'r') as f:
-        d = json.load(f)
-    
-    base_task_name = os.path.basename(md_json_file)
-    
-    pp_options = PostProcessingOptions()
-    pp_options.image_base_dir = input_folder
-    pp_options.include_almost_detections = True
-    pp_options.num_images_to_sample = None
-    pp_options.confidence_threshold = 0.1
-    pp_options.almost_detection_confidence_threshold = pp_options.confidence_threshold - 0.025
-    pp_options.ground_truth_json_file = None
-    pp_options.separate_detections_by_category = True
-    # pp_options.sample_seed = 0
-    
-    pp_options.parallelize_rendering = True
-    pp_options.parallelize_rendering_n_cores = 16
-    pp_options.parallelize_rendering_with_threads = False
-    
-    output_base = os.path.join(postprocessing_output_folder,
-        base_task_name + '_{:.3f}'.format(pp_options.confidence_threshold))
-    
-    os.makedirs(output_base, exist_ok=True)
-    print('Processing to {}'.format(output_base))
-    
-    pp_options.api_output_file = md_json_file
-    pp_options.output_dir = output_base
-    ppresults = process_batch_results(pp_options)
-    html_output_file = ppresults.output_html_file
-    
-    path_utils.open_file(html_output_file)
-    
-    # ...for each prediction file
-    
-    
-    #%% Compare results
-    
-    import itertools
-    
-    from api.batch_processing.postprocessing.compare_batch_results import (
-        BatchComparisonOptions,PairwiseBatchComparisonOptions,compare_batch_results)
-    
-    options = BatchComparisonOptions()
-    
-    organization_name = ''
-    project_name = ''
-    
-    options.job_name = f'{organization_name}-comparison'
-    options.output_folder = os.path.join(output_folder,'model_comparison')
-    options.image_folder = input_folder
-    
-    options.pairwise_options = []
-    
-    filenames = [
-        f'/home/user/tmp/{project_name}/{project_name}_md_v5a.0.0-md_format.json',
-        f'/home/user/postprocessing/{organization_name}/{organization_name}-2023-04-06-v5a.0.0/combined_api_outputs/{organization_name}-2023-04-06-v5a.0.0_detections.json',
-        f'/home/user/postprocessing/{organization_name}/{organization_name}-2023-04-06-v5b.0.0/combined_api_outputs/{organization_name}-2023-04-06-v5b.0.0_detections.json'
-        ]
-    
-    descriptions = ['YOLO w/augment','MDv5a','MDv5b']
-    
-    if False:
-        results = []
-        
-        for fn in filenames:
-            with open(fn,'r') as f:
-                d = json.load(f)
-            results.append(d)
-        
-    detection_thresholds = [0.1,0.1,0.1]
-    
-    assert len(detection_thresholds) == len(filenames)
-    
-    rendering_thresholds = [(x*0.6666) for x in detection_thresholds]
-    
-    # Choose all pairwise combinations of the files in [filenames]
-    for i, j in itertools.combinations(list(range(0,len(filenames))),2):
-            
-        pairwise_options = PairwiseBatchComparisonOptions()
-        
-        pairwise_options.results_filename_a = filenames[i]
-        pairwise_options.results_filename_b = filenames[j]
-        
-        pairwise_options.results_description_a = descriptions[i]
-        pairwise_options.results_description_b = descriptions[j]
-        
-        pairwise_options.rendering_confidence_threshold_a = rendering_thresholds[i]
-        pairwise_options.rendering_confidence_threshold_b = rendering_thresholds[j]
-        
-        pairwise_options.detection_thresholds_a = {'animal':detection_thresholds[i],
-                                                   'person':detection_thresholds[i],
-                                                   'vehicle':detection_thresholds[i]}
-        pairwise_options.detection_thresholds_b = {'animal':detection_thresholds[j],
-                                                   'person':detection_thresholds[j],
-                                                   'vehicle':detection_thresholds[j]}
-        options.pairwise_options.append(pairwise_options)
-    
-    results = compare_batch_results(options)
-    
-    from md_utils.path_utils import open_file
-    open_file(results.html_output_file)