megadetector 5.0.28__py3-none-any.whl → 5.0.29__py3-none-any.whl

megadetector/data_management/importers/idfg_iwildcam_lila_prep.py

@@ -1,294 +0,0 @@
-"""
-
- idfg_iwildcam_lila_prep.py
-
- Adding class labels (from the private test .csv) to the iWildCam 2019 IDFG 
- test set, in preparation for release on LILA.
-
- This version works with the public iWildCam release images.
-
-"""
-
-#%% ############ Take one, from iWildCam .json files ############ 
-
-#%% Imports and constants
-
-import uuid
-import json
-import os
-from tqdm import tqdm
-
-base_folder = r'h:\iWildCam_2019_IDFG'
-input_json = os.path.join(base_folder,'iWildCam_2019_IDFG_info.json')
-input_csv = os.path.join(base_folder,'IDFG_eval_public_v_private.csv')
-output_json = os.path.join(base_folder,'idaho_camera_traps.json')
-
-assert os.path.isfile(input_json)
-assert os.path.isfile(input_csv)
-
-
-#%% Read input files
-
-with open(input_json,'r') as f:
-    input_data = json.load(f)
-
-with open(input_csv,'r') as f:
-    private_csv_lines = f.readlines()
-
-private_csv_lines = [s.strip() for s in private_csv_lines]
-    
-# Remove the header line    
-assert private_csv_lines[0] == 'Id,Category,Usage'
-private_csv_lines = private_csv_lines[1:]
-
-print('Read {} annotations for {} images'.format(len(private_csv_lines),len(input_data['images'])))
-
-assert len(private_csv_lines) == len(input_data['images'])
-n_images = len(input_data['images'])
-
-
-#%% Parse annotations
-
-image_id_to_category_ids = {}
-for line in tqdm(private_csv_lines):
-    
-    # Lines look like:
-    #
-    # b005e5b2-2c0b-11e9-bcad-06f1011196c4,1,Private
-    
-    tokens = line.split(',')
-    assert len(tokens) == 3
-    assert tokens[2] in ['Private','Public']
-    image_id_to_category_ids[tokens[0]] = int(tokens[1])
-    
-assert len(image_id_to_category_ids) == n_images
-
-
-#%% Minor cleanup re: images
-
-for im in tqdm(input_data['images']):
-    image_id = im['id']
-    im['file_name'] = im['file_name'].replace('iWildCam_IDFG_images/','')
-    assert isinstance(im['location'],int)
-    im['location'] = str(im['location'])
-    
-
-#%% Create annotations
-
-annotations = []
-
-for image_id in tqdm(image_id_to_category_ids):
-    category_id = image_id_to_category_ids[image_id]
-    ann = {}
-    ann['id'] = str(uuid.uuid1())
-    ann['image_id'] = image_id
-    ann['category_id'] = category_id
-    annotations.append(ann)
-    
-
-#%% Prepare info
-
-info = input_data['info']
-info['contributor'] = 'Images acquired by the Idaho Department of Fish and Game, dataset curated by Sara Beery'
-info['description'] = 'Idaho Camera traps'
-info['version'] = '2021.07.19'
-
-
-#%% Minor adjustments to categories
-
-input_categories = input_data['categories']
-
-category_id_to_name = {cat['id']:cat['name'] for cat in input_categories}
-category_name_to_id = {cat['name']:cat['id'] for cat in input_categories}
-assert category_id_to_name[0] == 'empty'
-
-category_names_to_counts = {}
-for category in input_categories:
-    category_names_to_counts[category['name']] = 0
-    
-for ann in annotations:
-    category_id = ann['category_id']
-    category_name = category_id_to_name[category_id]
-    category_names_to_counts[category_name] = category_names_to_counts[category_name] + 1
-    
-categories = []
-
-for category_name in category_names_to_counts:
-    count = category_names_to_counts[category_name]    
-    
-    # Remove unused categories
-    if count == 0:
-        continue
-    
-    category_id = category_name_to_id[category_name]
-    
-    # Name adjustments
-    if category_name == 'prongs':
-        category_name = 'pronghorn'
-    
-    categories.append({'id':category_id,'name':category_name})
-    
-    
-#%% Create output
-
-output_data = {}
-output_data['images'] = input_data['images']
-output_data['annotations'] = annotations
-output_data['categories'] = categories
-output_data['info'] = info
-
-
-#%% Write output
-
-with open(output_json,'w') as f:
-    json.dump(output_data,f,indent=2)
-    
-
-#%% Validate .json file
-
-from megadetector.data_management.databases import integrity_check_json_db
-
-options = integrity_check_json_db.IntegrityCheckOptions()
-options.baseDir = os.path.join(base_folder,'images'); assert os.path.isdir(options.baseDir)
-options.bCheckImageSizes = False
-options.bCheckImageExistence = False
-options.bFindUnusedImages = False
-
-_, _, _ = integrity_check_json_db.integrity_check_json_db(output_json, options)
-
-
-#%% Preview labels
-
-from megadetector.visualization import visualize_db
-
-viz_options = visualize_db.DbVizOptions()
-viz_options.num_to_visualize = 100
-viz_options.trim_to_images_with_bboxes = False
-viz_options.add_search_links = False
-viz_options.sort_by_filename = False
-viz_options.parallelize_rendering = True
-viz_options.include_filename_links = True
-
-# viz_options.classes_to_exclude = ['test']
-html_output_file, _ = visualize_db.visualize_db(db_path=output_json,
-                                                         output_dir=os.path.join(
-                                                         base_folder,'preview'),
-                                                         image_base_dir=os.path.join(base_folder,'images'),
-                                                         options=viz_options)
-os.startfile(html_output_file)
-
-
-#%% ############ Take two, from pre-iWildCam .json files created from IDFG .csv files ############ 
-
-#%% Imports and constants
-
-import json
-import os
-
-base_folder = r'h:\idaho-camera-traps'
-input_json_sl = os.path.join(base_folder,'iWildCam_IDFG.json')
-input_json = os.path.join(base_folder,'iWildCam_IDFG_ml.json')
-output_json = os.path.join(base_folder,'idaho_camera_traps.json')
-remote_image_base_dir = r'z:\idfg'
-
-assert os.path.isfile(input_json)
-
-
-#%% One-time line break addition
-
-if not os.path.isfile(input_json):
-    
-    sl_json = input_json_sl
-    ml_json = input_json
-    
-    with open(sl_json,'r') as f:
-        d = json.load(f)
-    with open(ml_json,'w') as f:
-        json.dump(d,f,indent=2)
-        
-        
-#%% Read input files
-
-with open(input_json,'r') as f:
-    input_data = json.load(f)
-
-print('Read {} annotations for {} images'.format(len(input_data['annotations']),len(input_data['images'])))
-
-n_images = len(input_data['images'])
-
-
-#%% Prepare info
-
-info = {}
-info['contributor'] = 'Images acquired by the Idaho Department of Fish and Game, dataset curated by Sara Beery'
-info['description'] = 'Idaho Camera traps'
-info['version'] = '2021.07.19'
-
-
-#%% Minor adjustments to categories
-
-input_categories = input_data['categories']
-output_categories = []
-
-for c in input_categories:
-    category_name = c['name']
-    category_id = c['id']
-    if category_name == 'prong':
-        category_name = 'pronghorn'
-    category_name = category_name.lower()
-    output_categories.append({'name':category_name,'id':category_id})
-
-
-#%% Minor adjustments to annotations
-
-for ann in input_data['annotations']:
-    ann['id'] = str(ann['id'])
-
-
-#%% Create output
-
-output_data = {}
-output_data['images'] = input_data['images']
-output_data['annotations'] = input_data['annotations']
-output_data['categories'] = output_categories
-output_data['info'] = info
-
-
-#%% Write output
-
-with open(output_json,'w') as f:
-    json.dump(output_data,f,indent=2)
-    
-
-#%% Validate .json file
-
-from megadetector.data_management.databases import integrity_check_json_db
-
-options = integrity_check_json_db.IntegrityCheckOptions()
-options.baseDir = remote_image_base_dir
-options.bCheckImageSizes = False
-options.bCheckImageExistence = False
-options.bFindUnusedImages = False
-
-_, _, _ = integrity_check_json_db.integrity_check_json_db(output_json, options)
-
-
-#%% Preview labels
-
-from megadetector.visualization import visualize_db
-
-viz_options = visualize_db.DbVizOptions()
-viz_options.num_to_visualize = 100
-viz_options.trim_to_images_with_bboxes = False
-viz_options.add_search_links = False
-viz_options.sort_by_filename = False
-viz_options.parallelize_rendering = True
-viz_options.include_filename_links = True
-
-# viz_options.classes_to_exclude = ['test']
-html_output_file, _ = visualize_db.visualize_db(db_path=output_json,
-                                                         output_dir=os.path.join(
-                                                         base_folder,'preview'),
-                                                         image_base_dir=remote_image_base_dir,
-                                                         options=viz_options)
-os.startfile(html_output_file)

megadetector/data_management/importers/import_desert_lion_conservation_camera_traps.py

@@ -1,387 +0,0 @@
-"""
-
-import_desert_lion_conservation_camera_traps.py
-
-Prepare the Desert Lion Conservation Camera Traps dataset for release on LILA.
-
-"""
-
-#%% Imports and constants
-
-import os
-import json
-
-input_base_folder = r'i:/data/desert-lion'
-assert os.path.isdir(input_base_folder)
-
-# md_results_file = r'i:/data/desert-lion/desert-lion-camera-traps-2024-07-14-v5a.0.0_detections-all.json'
-md_results_file = r'i:/data/desert-lion/desert-lion-camera-traps-2024-07-14-v5a.0.0_detections.json'
-assert os.path.isfile(md_results_file)
-
-export_base = os.path.join(input_base_folder,'annotated-imgs')
-assert os.path.isdir(export_base)
-
-preview_dir = r'g:\temp\desert-lion-viz'
-output_file = os.path.join(input_base_folder,'desert_lion_camera_traps.json')
-output_zipfile = os.path.join(input_base_folder,'desert-lion-camera-traps-images.zip')
-
-exif_cache_file_post_exif_removal = os.path.join(input_base_folder,'exif_data_post_exif_removal.json')
-exif_cache_file = os.path.join(input_base_folder,'exif_data.json')
-
-
-#%% Find images and videos
-
-from megadetector.detection.video_utils import find_videos
-from megadetector.utils.path_utils import find_images
-
-video_files = find_videos(input_base_folder,recursive=True,return_relative_paths=True,convert_slashes=True)
-image_files = find_images(input_base_folder,recursive=True,return_relative_paths=True,convert_slashes=True)
-
-n_annotated_imgs = len([fn for fn in image_files if 'annotated-imgs' in fn])
-print('Found {} images ({} in the annotated-imgs folder), {} videos'.format(
-    len(image_files),n_annotated_imgs,len(video_files)))
-
-
-#%% Read EXIF data
-
-from megadetector.data_management.read_exif import read_exif_from_folder, ReadExifOptions
-
-exif_options = ReadExifOptions()
-exif_options.n_workers = 10
-
-if os.path.isfile(exif_cache_file):
-    print('EXIF cache {} exists, skipping EXIF read'.format(exif_cache_file))
-    with open(exif_cache_file,'r') as f:
-        exif_data = json.load(f)    
-else:
-    exif_data = read_exif_from_folder(input_folder=input_base_folder,
-                                      output_file=exif_cache_file,
-                                      options=exif_options,
-                                      filenames=None,
-                                      recursive=True)
-
-assert len(exif_data) == len(image_files)
-
-
-#%% Remove EXIF data
-
-from megadetector.data_management.remove_exif import remove_exif
-remove_exif(input_base_folder,recursive=True,n_processes=1)
-
-
-#%% Read EXIF data again
-
-exif_data_post_exif_removal = read_exif_from_folder(input_folder=input_base_folder,
-                                                    output_file=exif_cache_file_post_exif_removal,
-                                                    options=exif_options,
-                                                    filenames=None,
-                                                    recursive=True)
-
-
-#%% Make sure no lat/lon data is present
-
-from tqdm import tqdm
-
-for i_image,im in enumerate(tqdm(exif_data_post_exif_removal)):
-    tags = im['exif_tags']
-    if tags is None:
-        continue
-    for k in tags:
-        assert 'gps' not in str(k).lower()
-
-
-#%% Look for images that contain humans
-
-with open(md_results_file,'r') as f:
-    md_results = json.load(f)
-
-assert len(md_results['images']) == len(image_files)
-
-human_threshold = 0.1
-human_categories = ['2','3']
-
-candidate_human_images = set()
-failed_images = set()
-
-# i_image = 0; im = md_results['images'][0]
-for i_image,im in tqdm(enumerate(md_results['images']),total=len(md_results['images'])):
-
-    if 'failure' in im:
-        failed_images.add(im['file'])
-        continue
-    
-    for det in im['detections']:
-        if det['category'] in human_categories and det['conf'] >= human_threshold:
-            candidate_human_images.add(im['file'])
-            break
-        
-    # ...for each detection
-    
-# ...for each image    
-
-print('Found {} failed images and {} candidate human images'.format(
-    len(failed_images),len(candidate_human_images)))
-
-
-#%% Copy failed images and human images to a temporary folder for review
-
-review_folder_base = r'g:/temp/review_images'
-os.makedirs(review_folder_base,exist_ok=True)
-
-images_to_review = failed_images.union(candidate_human_images)
-images_to_review = sorted(list(images_to_review))
-
-source_file_to_target_file = {}
-
-# fn_relative = images_to_review[0]
-for fn_relative in images_to_review:
-    assert '\\' not in fn_relative
-    fn_abs_source = input_base_folder + '/' + fn_relative
-    assert os.path.isfile(fn_abs_source)
-    fn_abs_dest = review_folder_base + '/' + fn_relative.replace('/','_')
-    source_file_to_target_file[fn_abs_source] = fn_abs_dest
-
-from megadetector.utils.path_utils import parallel_copy_files
-
-parallel_copy_files(input_file_to_output_file=source_file_to_target_file,
-                    max_workers=16, 
-                    use_threads=True,
-                    overwrite=False,verbose=False)
-
-
-#%% Copy videos to a temporary folder for review
-
-review_folder_base = r'g:/temp/review_videos'
-os.makedirs(review_folder_base,exist_ok=True)
-
-source_file_to_target_file = {}
-
-# fn_relative = video_files[0]
-for fn_relative in video_files:
-    assert '\\' not in fn_relative
-    fn_abs_source = input_base_folder + '/' + fn_relative
-    assert os.path.isfile(fn_abs_source)
-    fn_abs_dest = review_folder_base + '/' + fn_relative.replace('/','_')
-    source_file_to_target_file[fn_abs_source] = fn_abs_dest
-
-from megadetector.utils.path_utils import parallel_copy_files
-
-parallel_copy_files(input_file_to_output_file=source_file_to_target_file,
-                    max_workers=16, 
-                    use_threads=True,
-                    overwrite=False,verbose=False)
-
-
-#%% Track removed images
-
-removed_images = [
-    "annotated-imgs\panthera leo\Camera Trap\Events\X73Okngwe\2013\02\PvL_seq_41468415-4518-44d6-acac-2113b442f723\PICT0190.JPG",
-    "annotated-imgs\panthera leo\Camera Trap\Hoanib\FldPln_Arch\211011\PvL_seq_5a9c6379-6980-4ab8-903a-b3bcba2ad21b\PICT0039.JPG",
-    "annotated-imgs\panthera leo\Camera Trap\Hoanib\FldPln_Arch\211011\PvL_seq_5a9c6379-6980-4ab8-903a-b3bcba2ad21b\PICT0037.JPG",
-    "annotated-imgs\panthera leo\Camera Trap\Hoanib\FldPln_Arch\211011\PvL_seq_5a9c6379-6980-4ab8-903a-b3bcba2ad21b\PICT0038.JPG",
-    "annotated-imgs\panthera leo\Camera Trap\2015\09\PvL_seq_da9c9ab1-74a2-485e-b6e7-3827b0c2a2f0\20150924-RCX_0835.JPG",
-    "annotated-imgs\panthera leo\Camera Trap\2015\09\PvL_seq_b0c1c6c5-474e-4844-a66c-e2bf5513d47a\20150924-RCX_0841.JPG",
-    "annotated-imgs\oryx gazella\Camera Trap\Video_Clips\Leylands\CDY_0003.AVI"
-]
-
-removed_images = [fn.replace('\\','/') for fn in removed_images]
-
-
-#%% Map filenames to datetimes
-
-filename_to_datetime = {}
-n_valid_datetimes = 0
-
-# im = exif_data[0]
-for im in tqdm(exif_data):
-    if im['exif_tags'] is None or len(im['exif_tags']) == 0:
-        filename_to_datetime[im['file_name']] = None
-        continue
-    dt = im['exif_tags']['DateTime']
-    assert len(dt) == 19
-    filename_to_datetime[im['file_name']] = dt
-    n_valid_datetimes += 1
-
-print('\nFound datetime information for {} of {} images'.format(
-    n_valid_datetimes,len(exif_data)))    
-
-
-#%% Convert "annotated_imgs" folder to COCO Camera Traps
-
-from megadetector.utils.path_utils import recursive_file_list
-
-species_name_to_category_id = {}
-
-filenames_relative = \
-    recursive_file_list(export_base,return_relative_paths=True,recursive=True,convert_slashes=True)
-    
-short_species_names = ['aves','cn-owls','cn-francolins','cn-raptors',
-                       'columbidae','equus zebra hartmannae','numididae',
-                       'pteroclidae']
-
-images = []
-annotations = []
-n_datetimes = 0
-
-for fn in filenames_relative:
-    
-    assert fn.lower().endswith('.jpg') or fn.lower().endswith('.avi') or fn.lower().endswith('.json')
-    
-    if fn.lower().endswith('.json'):
-        continue
-
-    tokens = fn.split('/')
-    species_name = tokens[0]
-    assert species_name in short_species_names or len(species_name.split(' ')) == 2
-    
-    if species_name not in species_name_to_category_id:
-        category_id = len(species_name_to_category_id)
-        species_name_to_category_id[species_name] = category_id
-    else:
-        category_id = species_name_to_category_id[species_name]
-                
-    im = {}
-    im['id'] = fn
-    im['file_name'] = fn
-    im['location'] = 'unknown'
-    
-    fn_for_datetime_lookup = 'annotated-imgs/' + fn
-    if (fn_for_datetime_lookup in filename_to_datetime) and \
-        (filename_to_datetime[fn_for_datetime_lookup] is not None):
-        im['datetime'] = filename_to_datetime[fn_for_datetime_lookup]
-        n_datetimes += 1
-
-    ann = {}
-    ann['image_id'] = im['id']
-    ann['id'] = im['id'] + ':ann_00'
-    ann['sequence_level_annotation'] = False
-    ann['category_id'] = category_id
-    
-    images.append(im)
-    annotations.append(ann)
-    
-# ...for each filename
-
-categories = []
-for species_name in species_name_to_category_id:
-    category = {}
-    category['name'] = species_name
-    category['id'] = species_name_to_category_id[species_name]
-    categories.append(category)
-
-info = {}
-info['version'] = '2024.07.15_00'
-info['description'] = 'Desert Lion Camera Traps'
-
-d = {}
-d['info'] = info
-d['images'] = images
-d['annotations'] = annotations
-d['categories'] = categories
-
-with open(output_file,'w') as f:
-    json.dump(d,f,indent=1)
-
-
-#%% Integrity check
-
-from megadetector.data_management.databases.integrity_check_json_db import \
-    IntegrityCheckOptions, integrity_check_json_db
-    
-integrity_check_options = IntegrityCheckOptions()
-
-integrity_check_options.baseDir = export_base
-integrity_check_options.bCheckImageExistence = True
-integrity_check_options.bRequireLocation = True
-integrity_check_options.nThreads = 10
-integrity_check_options.verbose = True
-integrity_check_options.allowIntIDs = False
-
-integrity_check_results = integrity_check_json_db(output_file,integrity_check_options)
-
-
-#%% Preview    
-
-from megadetector.visualization.visualize_db \
-    import DbVizOptions, visualize_db
-    
-viz_options = DbVizOptions()
-viz_options.num_to_visualize = 2500
-
-html_output_file,_ = visualize_db(output_file, preview_dir, export_base, options=viz_options)
-
-from megadetector.utils.path_utils import open_file
-open_file(html_output_file)
-
-
-#%% Make MD results paths line up with the output
-
-md_results_remapped_file = md_results_file.replace('-all','')
-assert md_results_remapped_file != md_results_file
-
-with open(output_file,'r') as f:
-    d = json.load(f)
-    
-image_filenames = [im['file_name'] for im in d['images']]
-image_filenames_set = set(image_filenames)
-
-with open(md_results_file,'r') as f:
-    md_results = json.load(f)
-
-md_results_images_remapped = []
-
-# im = md_results['images'][0]
-for im in md_results['images']:
-    assert im['file'].startswith('annotated-imgs/') or im['file'].startswith('bboxes/')
-    if im['file'].startswith('bboxes/'):
-        continue
-    im['file'] = im['file'].replace('annotated-imgs/','')
-    md_results_images_remapped.append(im)
-    
-print('Keeping {} of {} images in MD results'.format(
-    len(md_results_images_remapped),len(md_results['images'])))
-
-d['images'] = md_results_images_remapped
-
-with open(md_results_remapped_file,'w') as f:
-    json.dump(d,f,indent=1)
-
-
-#%% Zip MD results and COCO file
-
-from megadetector.utils.path_utils import zip_file
-
-zip_file(input_fn=md_results_remapped_file, output_fn=None, overwrite=True, verbose=True, compresslevel=9)
-zip_file(input_fn=output_file, output_fn=None, overwrite=True, verbose=True, compresslevel=9)
-
-
-#%% Zip images
-
-from megadetector.utils.path_utils import zip_folder
-
-zip_folder(input_folder=export_base, output_fn=output_zipfile, overwrite=True, verbose=True, compresslevel=0)
-
-
-#%% Copy lion images to a folder for thumbnail selection
-
-review_folder_base = r'g:/temp/thumbnail-candidates'
-os.makedirs(review_folder_base,exist_ok=True)
-
-source_file_to_target_file = {}
-
-# fn_relative = image_files[0]
-for fn_relative in image_files:
-    assert '\\' not in fn_relative
-    if '/lion/' not in fn_relative and '/panthera leo/' not in fn_relative:
-        continue
-    fn_abs_source = input_base_folder + '/' + fn_relative
-    assert os.path.isfile(fn_abs_source)
-    fn_abs_dest = review_folder_base + '/' + fn_relative.replace('/','_')
-    source_file_to_target_file[fn_abs_source] = fn_abs_dest
-
-from megadetector.utils.path_utils import parallel_copy_files
-
-parallel_copy_files(input_file_to_output_file=source_file_to_target_file,
-                    max_workers=16, 
-                    use_threads=True,
-                    overwrite=False,verbose=False)