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

megadetector/detection/run_inference_with_yolov5_val.py

@@ -0,0 +1,1087 @@
+"""
+
+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.
+
+"""
+
+#%% Imports
+
+import os
+import sys
+import uuid
+import glob
+import tempfile
+import shutil
+import json
+import copy
+
+from tqdm import tqdm
+
+from megadetector.utils import path_utils
+from megadetector.utils import process_utils
+from megadetector.utils import string_utils
+
+from megadetector.utils.ct_utils import is_iterable, split_list_into_fixed_size_chunks
+from megadetector.utils.path_utils import path_is_abs
+from megadetector.data_management import yolo_output_to_md_output
+from megadetector.detection.run_detector import try_download_known_detector
+from megadetector.postprocessing.combine_api_outputs import combine_api_output_files
+
+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.
+    """
+    
+    def __init__(self):
+        
+        ## Required-ish ##
+        
+        #: Folder of images to process (can be None if image_filename_list contains absolute paths)
+        self.input_folder = None
+        
+        #: If this is None, [input_folder] can't be None, we'll process all images in [input_folder].
+        #:            
+        #: If this is not None, and [input_folder] is not None, this should be a list of relative image 
+        #: paths within [input_folder] to process, or a .txt or .json file containing a list of 
+        #: relative image paths.
+        #:
+        #: If this is not None, and [input_folder] is None, this should be a list of absolute image
+        #: paths, or a .txt or .json file containing a list of absolute image paths.            
+        self.image_filename_list = None
+        
+        #: Model filename (ending in .pt), or a well-known model name (e.g. "MDV5A")
+        self.model_filename = None
+        
+        #: .json output file, in MD results format
+        self.output_file = None
+        
+        
+        ## Optional ##
+        
+        #: Required for older YOLOv5 inference, not for newer ulytralytics/YOLOv8 inference
+        self.yolo_working_folder = None
+        
+        #: Currently 'yolov5' and 'ultralytics' are supported, and really these are proxies for
+        #: "the yolov5 repo" and "the ultralytics repo".
+        self.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".
+        self.image_size = default_image_size_with_augmentation
+        
+        #: Detections below this threshold will not be included in the output file
+        self.conf_thres = '0.001'
+        
+        #: Batch size... has no impact on results, but may create memory issues if you set
+        #: this to large values
+        self.batch_size = 1
+        
+        #: Device string: typically '0' for GPU 0, '1' for GPU 1, etc., or 'cpu'
+        self.device_string = '0'
+        
+        #: Should we enable test-time augmentation?
+        self.augment = True
+        
+        #: Should we enable half-precision inference?
+        self.half_precision_enabled = None
+        
+        #: Where should we stash the temporary symlinks (or copies) used to give unique identifiers to image 
+        # files?
+        #:
+        #: If this is None, we'll create a folder in system temp space.
+        self.symlink_folder = None
+        
+        #: Should we use symlinks to give unique identifiers to image files (vs. copies)?
+        self.use_symlinks = True
+        
+        #: How should we guarantee that YOLO IDs (base filenames) are unique?  Choices are:
+        #:
+        #: * 'verify': assume image IDs are unique, but verify and error if they're not
+        #: * 'links': create symlinks (or copies, depending on use_symlinks) to enforce uniqueness
+        #: * 'auto': check whether IDs are unique, create links if necessary
+        self.unique_id_strategy = 'links'
+        
+        #: Temporary folder to stash intermediate YOLO results.
+        #:
+        #: If this is None, we'll create a folder in system temp space.    
+        self.yolo_results_folder = None
+        
+        #: Should we remove the symlink folder when we're done?
+        self.remove_symlink_folder = True
+        
+        #: Should we remove the intermediate results folder when we're done?
+        self.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.
+        self.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'.
+        self.overwrite_handling = 'skip'
+        
+        #: If True, we'll do a dry run that lets you preview the YOLO val command, without
+        #: actually running it.
+        self.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.
+        self.treat_copy_failures_as_warnings = False
+        
+        #: Save YOLO console output
+        self.save_yolo_debug_output = False
+        
+        #: Whether to search for images recursively within [input_folder]
+        #:
+        #: Ignored if a list of files is provided.
+        self.recursive = True
+        
+        #: Maximum number of images to run in a single chunk
+        self.checkpoint_frequency = None
+        
+    # ...def __init__()
+    
+# ...YoloInferenceOptions()
+
+
+#%% Support functions
+
+def _clean_up_temporary_folders(options,
+                                symlink_folder,yolo_results_folder,
+                                symlink_folder_is_temp_folder,yolo_folder_is_temp_folder):
+    """
+    Remove temporary symlink/results folders, unless the caller requested that we leave them in place.
+    """
+    
+    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))
+
+    
+#%% 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
+    
+    default_options = YoloInferenceOptions()
+    
+    for k in options.__dict__.keys():
+        if k not in default_options.__dict__:
+            print('Warning: unexpected variable {} in options object'.format(k))
+            
+    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)
+                
+    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)
+    
+    assert (options.input_folder is not None) or (options.image_filename_list is not None), \
+        'You must specify a folder and/or a file list'
+        
+    if options.input_folder is not None:
+        assert os.path.isdir(options.input_folder), 'Could not find input folder {}'.format(
+            options.input_folder)
+    
+    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)
+    
+    if options.input_folder is not None:
+        options.input_folder = options.input_folder.replace('\\','/')
+        
+
+    ##%% 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
+    
+    image_files_relative = None
+    image_files_absolute = None
+    
+    if options.image_filename_list is None:
+        assert options.input_folder is not None and os.path.isdir(options.input_folder), \
+            'Could not find input folder {}'.format(options.input_folder)
+        image_files_relative = path_utils.find_images(options.input_folder,
+                                                      recursive=options.recursive,
+                                                      return_relative_paths=True,
+                                                      convert_slashes=True)
+        image_files_absolute = [os.path.join(options.input_folder,fn) for \
+                                fn in image_files_relative]
+    else:
+        
+        if is_iterable(options.image_filename_list):
+            
+            image_files_relative = options.image_filename_list
+            
+        else:
+            assert isinstance(options.image_filename_list,str), \
+                'Unrecognized image filename list object type: {}'.format(options.image_filename_list)
+            assert os.path.isfile(options.image_filename_list), \
+                'Could not find image filename list file: {}'.format(options.image_filename_list)
+            ext = os.path.splitext(options.image_filename_list).lower()
+            assert ext in ('.json','.txt'), \
+                'Unrecognized image filename list file extension: {}'.format(options.image_filename_list)
+            if ext == '.json':
+                with open(options.image_filename_list,'r') as f:
+                    image_files_relative = json.load(f)
+                    assert is_iterable(image_files_relative)
+            else:
+                assert ext == '.txt'
+                with open(options.image_filename_list,'r') as f:
+                    image_files_relative = f.readlines()
+                    image_files_relative = [s.strip() for s in image_files_relative]
+        
+        # ...whether the image filename list was supplied as list vs. a filename
+        
+        if options.input_folder is None:
+            image_files_absolute = image_files_relative
+        else:
+            # The list should be relative filenames
+            for fn in image_files_relative:
+                assert not path_is_abs(fn), \
+                    'When providing a folder and a list, paths in the list should be relative'
+                
+            image_files_absolute = \
+                [os.path.join(options.input_folder,fn) for fn in image_files_relative]
+        for fn in image_files_absolute:
+            assert os.path.isfile(fn), 'Could not find image file {}'.format(fn)
+    
+    # ...whether the caller supplied a list of filenames
+    
+    image_files_absolute = [fn.replace('\\','/') for fn in image_files_absolute]
+    del image_files_relative
+    
+    
+    ##%% Recurse if necessary to handle checkpoints
+    
+    if options.checkpoint_frequency is not None and options.checkpoint_frequency > 0:
+        
+        chunks = split_list_into_fixed_size_chunks(image_files_absolute,options.checkpoint_frequency)
+        
+        chunk_output_files = []
+        
+        # i_chunk = 0; chunk_files_abs = chunks[i_chunk]
+        for i_chunk,chunk_files_abs in enumerate(chunks):
+            
+            print('Processing {} images from chunk {} of {}'.format(
+                len(chunk_files_abs),i_chunk,len(chunks)))
+    
+            chunk_options = copy.deepcopy(options)
+            
+            # Run each chunk without checkpointing
+            chunk_options.checkpoint_frequency = None
+            
+            if options.input_folder is not None:
+                chunk_files_relative = \
+                    [os.path.relpath(fn,options.input_folder) for fn in chunk_files_abs]
+                chunk_options.image_filename_list = chunk_files_relative
+            else:
+                chunk_options.image_filename_list = chunk_files_abs
+                
+            chunk_options.image_filename_list = \
+                [fn.replace('\\','/') for fn in chunk_options.image_filename_list]
+                
+            chunk_string = 'chunk_{}'.format(str(i_chunk).zfill(5))
+            chunk_options.yolo_results_folder = yolo_results_folder + '_' + chunk_string
+            chunk_options.symlink_folder = symlink_folder + '_' + chunk_string
+            
+            # Put the output file in the parent job's scratch folder
+            chunk_output_file = os.path.join(yolo_results_folder,chunk_string + '_results_md_format.json')
+            chunk_output_files.append(chunk_output_file)
+            chunk_options.output_file = chunk_output_file
+            
+            if os.path.isfile(chunk_output_file):
+                
+                print('Chunk output file {} exists, checking completeness'.format(chunk_output_file))
+                
+                with open(chunk_output_file,'r') as f:
+                    chunk_results = json.load(f)
+                images_in_this_chunk_results_file = [im['file'] for im in chunk_results['images']]                    
+                assert len(images_in_this_chunk_results_file) == len(chunk_options.image_filename_list), \
+                    'Expected {} images in chunk results file {}, found {}, possibly this is left over from a previous job?'.format(
+                        len(chunk_options.image_filename_list),chunk_output_file,
+                        len(images_in_this_chunk_results_file))
+                for fn in images_in_this_chunk_results_file:
+                    assert fn in chunk_options.image_filename_list, \
+                        'Unexpected image {} in chunk results file {}, possibly this is left over from a previous job?'.format(
+                            fn,chunk_output_file)
+                
+                print('Chunk output file {} exists and is complete, skipping this chunk'.format(
+                    chunk_output_file))
+                
+            # ...if the outptut file exists
+            
+            else:
+                
+                run_inference_with_yolo_val(chunk_options)
+                
+            # ...if we do/don't have to run this chunk
+            
+            assert os.path.isfile(chunk_options.output_file)
+            
+        # ...for each chunk
+    
+        # Merge
+        _ = combine_api_output_files(input_files=chunk_output_files,
+                                 output_file=options.output_file,
+                                 require_uniqueness=True,
+                                 verbose=True)
+        
+        # Validate
+        with open(options.output_file,'r') as f:
+            combined_results = json.load(f)
+        assert len(combined_results['images']) == len(image_files_absolute), \
+            'Expected {} images in merged output file, found {}'.format(
+                len(image_files_absolute),len(combined_results['images']))
+        
+        # Clean up
+        _clean_up_temporary_folders(options,
+                                    symlink_folder,yolo_results_folder,
+                                    symlink_folder_is_temp_folder,yolo_folder_is_temp_folder)
+        
+        return
+    
+    # ...if we need to make recursive calls for file chunks
+    
+    
+    ##%% Create symlinks (or copy images) to give a unique ID to each image
+    
+    # Maps YOLO image IDs (base filename without extension as it will appear in YOLO .json output)
+    # to the *original full path* for each image (not the symlink path).
+    image_id_to_file = {}  
+    
+    # Maps YOLO image IDs (base filename without extension as it will appear in YOLO .json output)
+    # to errors, including errors that happen before we run the model at all (e.g. file access errors).
+    image_id_to_error = {}
+    
+    create_links = True
+    
+    if options.unique_id_strategy == 'links':
+        
+        create_links = True
+        
+    else:
+        
+        assert options.unique_id_strategy in ('auto','verify'), \
+            'Unknown unique ID strategy {}'.format(options.unique_id_strategy)
+            
+        image_ids_are_unique = True
+        
+        for i_image,image_fn in tqdm(enumerate(image_files_absolute),total=len(image_files_absolute)):        
+            
+            image_id = os.path.splitext(os.path.basename(image_fn))[0]
+            
+            # Is this image ID unique?
+            if image_id in image_id_to_file:
+                if options.unique_id_strategy == 'verify':
+                    raise ValueError('"verify" specified for image uniqueness, but ' +
+                                     'image ID {} occurs more than once:\n\n{}\n\n{}'.format(
+                                         image_id,image_fn,image_id_to_file[image_id]))
+                else:
+                    assert options.unique_id_strategy == 'auto'
+                    image_ids_are_unique = False
+                    image_id_to_file = {}
+                    break
+                
+            image_id_to_file[image_id] = image_fn
+        
+        # ...for each image
+        
+        if image_ids_are_unique:
+            
+            print('"{}" specified for image uniqueness and images are unique, skipping links'.format(
+                options.unique_id_strategy))
+            assert len(image_id_to_file) == len(image_files_absolute)
+            create_links = False
+            
+        else:
+            
+            assert options.unique_id_strategy == 'auto'
+            create_links = True
+            link_type = 'copies'
+            if options.use_symlinks:
+                link_type = 'links'
+            print('"auto" specified for image uniqueness and images are not unique, defaulting to {}'.format(
+                link_type))
+            
+    # ...which unique ID strategy?
+    
+    if create_links:
+        
+        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))
+            
+        link_full_paths = []
+        
+        # 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]
+            
+            # YOLO .json output identifies images by the base filename without the extension
+            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)
+            link_full_paths.append(symlink_full_path)
+            
+            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
+            
+            # ...except
+            
+        # ...for each image
+                
+    # ...if we need to create links/copies
+
+    
+    ##%% 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')
+    yolo_image_list_file = os.path.join(yolo_results_folder,'images.txt')
+    
+    
+    with open(yolo_image_list_file,'w') as f:
+        
+        if create_links:
+            image_files_to_write = link_full_paths
+        else:
+            image_files_to_write = image_files_absolute
+            
+        for fn_abs in image_files_to_write:
+            # At least in YOLOv5 val (need to verify for YOLOv8 val), filenames in this 
+            # text file are treated as relative to the text file itself if they start with
+            # "./", otherwise they're treated as absolute paths.  Since we don't want to put this
+            # text file in the image folder, we'll use absolute paths.
+            # fn_relative = os.path.relpath(fn_abs,options.input_folder)
+            # f.write(fn_relative + '\n')
+            f.write(fn_abs + '\n')
+    
+    if create_links:
+        inference_folder = symlink_folder_inner
+    else:
+        # This doesn't matter, but it has to be a valid path
+        inference_folder = options.yolo_results_folder
+        
+    with open(yolo_dataset_file,'w') as f:
+        
+        f.write('path: {}\n'.format(inference_folder))        
+        # These need to be valid paths, even if you're not using them, and "." is always safe
+        f.write('train: .\n')
+        f.write('val: .\n')
+        f.write('test: {}\n'.format(yolo_image_list_file))
+        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()
+        return
+    
+    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, 'Unexpected image ID {}'.format(image_id)
+        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]
+
+    # Map YOLO image IDs to paths
+    image_id_to_relative_path = {}
+    for image_id in image_id_to_file:
+        fn = image_id_to_file[image_id].replace('\\','/')
+        assert path_is_abs(fn)
+        if options.input_folder is not None:
+            assert os.path.isdir(options.input_folder)
+            assert options.input_folder in fn, 'Internal error: base folder {} not in file {}'.format(
+                options.input_folder,fn)
+            relative_path = os.path.relpath(fn,options.input_folder)
+        else:
+            # 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
+        
+    # Are we working with a base folder?
+    if options.input_folder is not None:
+        assert os.path.isdir(options.input_folder)
+        image_base = options.input_folder
+    else:
+        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
+    
+    _clean_up_temporary_folders(options,
+                                symlink_folder,yolo_results_folder,
+                                symlink_folder_is_temp_folder,yolo_folder_is_temp_folder)
+        
+# ...def run_inference_with_yolo_val()
+
+
+#%% Command-line driver
+
+import argparse
+from megadetector.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')
+    parser.add_argument(
+        'output_file',type=str,
+        help='.json file where output will be written')
+    
+    parser.add_argument(
+        '--image_filename_list',type=str,default=None,
+        help='.json or .txt file containing a list of relative image filenames within [input_folder]')
+    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.yaml 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('--unique_id_strategy', default=options.unique_id_strategy, type=str,
+        help='how should we ensure that unique filenames are passed to the YOLO val script, ' + \
+             'can be "verify", "auto", or "links", see options class docs for details (default {})'.format(
+                 options.unique_id_strategy))
+    parser.add_argument(
+        '--symlink_folder', default=None, type=str,
+        help='temporary folder for symlinks (defaults to a folder in the system temp dir)')
+    parser.add_argument(
+        '--yolo_results_folder', default=None, 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(
+        '--checkpoint_frequency', default=options.checkpoint_frequency, type=int,
+        help='break the job into chunks with no more than this many images (default {})'.format(
+            options.checkpoint_frequency))    
+    
+    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
+        del options.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)        
+    
+    del options.nonrecursive
+    del options.no_remove_symlink_folder
+    del options.no_remove_yolo_results_folder
+    del options.no_use_symlinks
+    del options.augment_enabled
+        
+    print(options.__dict__)
+    
+    run_inference_with_yolo_val(options)    
+
+if __name__ == '__main__':
+    main()
+
+
+#%% Interactive driver
+
+if False:
+
+    #%% Run inference on a folder
+    
+    input_folder = r'g:\temp\tegu-val-mini'.replace('\\','/')
+    model_filename = r'g:\temp\usgs-tegus-yolov5x-231003-b8-img1280-e3002-best.pt'
+    output_folder = r'g:\temp\tegu-scratch'
+    yolo_working_folder = r'c:\git\yolov5-tegus'
+    dataset_file = r'g:\temp\dataset.yaml'
+    
+    # This only impacts the output file name, it's not passed to the inference functio
+    job_name = 'yolo-inference-test'
+    
+    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(
+        job_name,model_name))
+    
+    options = YoloInferenceOptions()
+    
+    options.yolo_working_folder = yolo_working_folder
+    options.input_folder = input_folder
+    options.output_file = output_file
+    
+    pass_image_filename_list = False    
+    pass_relative_paths = True
+    
+    if pass_image_filename_list:
+        if pass_relative_paths:
+            options.image_filename_list =  [
+                r"val#american_cardinal#american_cardinal#CaCa#31W.01_C83#2017-2019#C90 and C83_31W.01#(05) 18AUG17 - 05SEP17 FTC AEG#MFDC1949_000065.JPG",
+                r"val#american_cardinal#american_cardinal#CaCa#31W.01_C83#2017-2019#C90 and C83_31W.01#(04) 27JUL17 - 18AUG17 FTC AEG#MFDC1902_000064.JPG"
+            ]   
+        else:
+            options.image_filename_list =  [
+                r"g:/temp/tegu-val-mini/val#american_cardinal#american_cardinal#CaCa#31W.01_C83#2017-2019#C90 and C83_31W.01#(05) 18AUG17 - 05SEP17 FTC AEG#MFDC1949_000065.JPG",
+                r"g:/temp/tegu-val-mini/val#american_cardinal#american_cardinal#CaCa#31W.01_C83#2017-2019#C90 and C83_31W.01#(04) 27JUL17 - 18AUG17 FTC AEG#MFDC1902_000064.JPG"
+            ]
+    else:
+        options.image_filename_list = None    
+    
+    options.yolo_category_id_to_name = dataset_file
+    options.augment = False
+    options.conf_thres = '0.001'
+    options.batch_size = 1
+    options.device_string = '0'
+    options.unique_id_strategy = 'auto'
+    options.overwrite_handling = 'overwrite'
+
+    if options.augment:
+        options.image_size = round(1280 * 1.3)
+    else:
+        options.image_size = 1280
+    
+    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_symlink_folder = True
+    options.remove_yolo_results_folder = True
+    
+    options.checkpoint_frequency = 5
+    
+    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} ' + \
+          f' --yolo_dataset_file {options.yolo_category_id_to_name} ' + \
+          f' --unique_id_strategy {options.unique_id_strategy} --overwrite_handling {options.overwrite_handling}'
+      
+    if not options.remove_symlink_folder:
+        cmd += ' --no_remove_symlink_folder'
+    if not options.remove_yolo_results_folder: 
+        cmd += ' --no_remove_yolo_results_folder'
+    if options.checkpoint_frequency is not None:
+        cmd += f' --checkpoint_frequency {options.checkpoint_frequency}'
+    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)
+