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

api/synchronous/api_core/animal_detection_api/detection/run_inference_with_yolov5_val.py

@@ -1,581 +0,0 @@
-########
-# 
-# run_inference_with_yolov5_val.py
-#
-# Runs a folder of images through MegaDetector (or another YOLOv5 model) with YOLOv5's 
-# val.py, converting the output to the standard MD format.  The main goal is to leverage
-# YOLO's test-time augmentation tools.
-#
-# 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
-#
-# ...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.
-#
-# Currently requires the user to supply the path where a working YOLOv5 install lives,
-# and assumes that the current conda environment is all set up for YOLOv5.
-#
-# By default, this script uses symlinks to format the input images in a way that YOLOv5's 
-# val.py likes.  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.
-#
-# 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 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 data_management import yolo_output_to_md_output
-
-
-#%% Options class
-
-class YoloInferenceOptions:
-        
-    ## Required ##
-    
-    input_folder = None
-    model_filename = None
-    yolo_working_folder = None
-    output_file = None
-
-    ## Optional ##
-    
-    image_size = 1280 * 1.3
-    conf_thres = '0.001'
-    batch_size = 1
-    device_string = '0'
-    augment = True
-
-    symlink_folder = None
-    use_symlinks = True
-    
-    yolo_results_folder = None
-    
-    remove_symlink_folder = True
-    remove_yolo_results_folder = True
-    
-    # These are deliberately offset from the standard MD categories; YOLOv5
-    # needs categories IDs to start at 0.
-    yolo_category_id_to_name = {0:'animal',1:'person',2:'vehicle'}
-    
-    # 'error','skip','overwrite'
-    overwrite_handling = 'skip'
-            
-    
-#%% Main function
-
-def run_inference_with_yolo_val(options):
-
-    ##%% Path handling
-    
-    assert os.path.isdir(options.input_folder) or os.path.isfile(options.input_folder), \
-        'Could not find input {}'.format(options.input_folder)
-    assert os.path.isdir(options.yolo_working_folder), \
-        'Could not find working folder {}'.format(options.yolo_working_folder)
-    assert os.path.isfile(options.model_filename), \
-        'Could not find model file {}'.format(options.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)
-    
-    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=True)
-    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:
-            image_id_to_error[image_id] = str(e)
-            print('Warning: error copying/creating link for input file {}: {}'.format(
-                image_fn,str(e)))
-            continue
-        
-    # ...for each image
-
-
-    ##%% Create the dataset file
-    
-    # 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]
-    
-    dataset_file = os.path.join(yolo_results_folder,'dataset.yaml')
-    
-    with open(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 YOLOv5 command
-    
-    image_size_string = str(round(options.image_size))
-    cmd = 'python val.py --data "{}"'.format(dataset_file)
-    cmd += ' --weights "{}"'.format(options.model_filename)
-    cmd += ' --batch-size {} --imgsz {} --conf-thres {} --task test'.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'
-    
-
-    ##%% Run YOLOv5 command
-    
-    current_dir = os.getcwd()
-    os.chdir(options.yolo_working_folder)    
-    execution_result = process_utils.execute_and_print(cmd)
-    assert execution_result['status'] == 0, 'Error running YOLOv5'
-    yolo_console_output = execution_result['output']
-    
-    yolo_read_failures = []
-    for line in yolo_console_output:
-        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)            
-            
-    # 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] = 'YOLOv5 read failure'
-    
-    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(options.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,sys
-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,
-        help='folder in which to execute val.py')
-    
-    parser.add_argument(
-        '--image_size', default=options.image_size, type=int,
-        help='image size for model execution (default {})'.format(
-            options.image_size))
-    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(
-        '--device_string', default=options.device_string, type=str,
-        help='CUDA device specifier, e.g. "0" 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(
-        '--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')
-    
-    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()
-    
-    args_to_object(args, options)
-    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:
-    
-    #%% Run from a set of options
-    
-    options = YoloInferenceOptions()
-
-    args = {'augment': 1, 'batch_size': 1, 'conf_thres': 0.005, 'device_string': '1', 'image_size': 1664.0, 'input_folder': '/home/user/postprocessing/usgs-kissel/usgs-kissel-2023-09-11-aug-v5a.0.0/chunk031.json', 'model_filename': '/home/user/models/camera_traps/megadetector/md_v5.0.0/md_v5a.0.0.pt', 'output_file': '/home/user/postprocessing/usgs-kissel/usgs-kissel-2023-09-11-aug-v5a.0.0/chunk031_results.json', 'overwrite_handling': 'skip', 'symlink_folder': '/home/user/postprocessing/usgs-kissel/usgs-kissel-2023-09-11-aug-v5a.0.0/symlinks/symlinks_031', 'yolo_results_folder': '/home/user/postprocessing/usgs-kissel/usgs-kissel-2023-09-11-aug-v5a.0.0/yolo_results/yolo_results_031', 'yolo_working_folder': '/home/user/git/yolov5', 'remove_symlink_folder': True, 'remove_yolo_results_folder': True, 'use_symlinks': False, 'augment': True}
-    
-    for k in args:
-        setattr(options, k, args[k])
-
-
-    #%% 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} {output_file} {yolo_working_folder} ' + \
-          f' --image_size {options.image_size} --conf_thres {options.conf_thres} --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)
-    
-    
-    #%% 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)