megadetector 5.0.27__py3-none-any.whl → 5.0.29__py3-none-any.whl

megadetector/data_management/importers/zamba_results_to_md_results.py

@@ -1,180 +0,0 @@
-"""
-
- zamba_results_to_md_results.py
-
- Convert a labels.csv file produced by Zamba Cloud to a MD results file suitable
- for import into Timelapse.
-
- Columns are expected to be:
-
- video_uuid (not used)
- original_filename (assumed to be a relative path name)
- top_k_label,top_k_probability, for k = 1..N
- [category name 1],[category name 2],...
- corrected_label
-
- Because the MD results file fundamentally stores detections, what we'll
- actually do is create bogus detections that fill the entire image.
-
- There is no special handling of empty/blank categories; because these results are
- based on a classifier, rather than a detector (where "blank" would be the absence of
- all other categories), "blank" can be queried in Timelapse just like any other class.
-
-"""
-
-#%% Imports and constants
-
-import pandas as pd
-import json
-
-
-#%% Main function
-
-def zamba_results_to_md_results(input_file,output_file=None):
-    """
-    Converts the .csv file [input_file] to the MD-formatted .json file [output_file].
-    
-    If [output_file] is None, '.json' will be appended to the input file.
-    """
-    
-    if output_file is None:
-        output_file = input_file + '.json'
-
-    df = pd.read_csv(input_file)
-    
-    expected_columns = ('video_uuid','corrected_label','original_filename')
-    for s in expected_columns:
-        assert s in df.columns,\
-            'Expected column {} not found, are you sure this is a Zamba results .csv file?'.format(
-                s)
-            
-    # How many results are included per file?
-    assert 'top_1_probability' in df.columns and 'top_1_label' in df.columns
-    top_k = 2
-    while(True):
-        p_string = 'top_' + str(top_k) + '_probability'
-        label_string = 'top_' + str(top_k) + '_label'
-        
-        if p_string in df.columns:
-            assert label_string in df.columns,\
-                'Oops, {} is a column but {} is not'.format(
-                    p_string,label_string)
-            top_k += 1
-            continue
-        else:
-            assert label_string not in df.columns,\
-                'Oops, {} is a column but {} is not'.format(
-                    label_string,p_string)
-            top_k -= 1
-            break
-            
-    print('Found {} probability column pairs'.format(top_k))
-    
-    # Category names start after the fixed columns and the probability columns
-    category_names = []
-    column_names = list(df.columns)
-    first_category_name_index = 0
-    while('top_' in column_names[first_category_name_index] or \
-          column_names[first_category_name_index] in expected_columns):
-        first_category_name_index += 1
-        
-    i_column = first_category_name_index
-    while( (i_column < len(column_names)) and (column_names[i_column] != 'corrected_label') ):
-        category_names.append(column_names[i_column])
-        i_column += 1
-        
-    print('Found {} categories:\n'.format(len(category_names)))
-    
-    for s in category_names:
-        print(s)
-    
-    info = {}
-    info['format_version'] = '1.3'
-    info['detector'] = 'Zamba Cloud'
-    info['classifier'] = 'Zamba Cloud'    
-    
-    detection_category_id_to_name = {}
-    for category_id,category_name in enumerate(category_names):
-        detection_category_id_to_name[str(category_id)] = category_name
-    detection_category_name_to_id = {v: k for k, v in detection_category_id_to_name.items()}
-    
-    images = []
-    
-    # i_row = 0; row = df.iloc[i_row]
-    for i_row,row in df.iterrows():
-        
-        im = {}
-        images.append(im)
-        im['file'] = row['original_filename']
-        
-        detections = []
-        
-        # k = 1
-        for k in range(1,top_k+1):
-            label = row['top_{}_label'.format(k)]
-            confidence = row['top_{}_probability'.format(k)]
-            det = {}
-            det['category'] = detection_category_name_to_id[label]
-            det['conf'] = confidence
-            det['bbox'] = [0,0,1.0,1.0]
-            detections.append(det)
-            
-        im['detections'] = detections
-        
-    # ...for each row
-    
-    results = {}
-    results['info'] = info
-    results['detection_categories'] = detection_category_id_to_name
-    results['images'] = images
-    
-    with open(output_file,'w') as f:
-        json.dump(results,f,indent=1)
-        
-# ...zamba_results_to_md_results(...)
-        
-
-#%% Interactive driver
-
-if False:
-
-    pass
-
-    #%%
-    
-    input_file = r"G:\temp\labels-job-b95a4b76-e332-4e17-ab40-03469392d36a-2023-11-04_16-28-50.060130.csv"
-    output_file = None
-    zamba_results_to_md_results(input_file,output_file)
-    
-
-#%% Command-line driver
-
-import sys,argparse
-
-def main():
-
-    parser = argparse.ArgumentParser(
-        description='Convert a Zamba-formatted .csv results file to a MD-formatted .json results file')
-    
-    parser.add_argument(
-        'input_file',
-        type=str,
-        help='input .csv file')
-    
-    parser.add_argument(
-        '--output_file',
-        type=str,
-        default=None,
-        help='output .json file (defaults to input file appended with ".json")')
-    
-    if len(sys.argv[1:]) == 0:
-        parser.print_help()
-        parser.exit()
-
-    args = parser.parse_args()
-
-    zamba_results_to_md_results(args.input_file,args.output_file)
-    
-if __name__ == '__main__':
-    main()
-    

megadetector/data_management/lila/add_locations_to_island_camera_traps.py

@@ -1,101 +0,0 @@
-"""
-
-add_locations_to_island_camera_traps.py
-
-The Island Conservation Camera Traps dataset had unique camera identifiers embedded
-in filenames, but not in the proper metadata fields.  This script copies that information
-to metadata.
-
-"""
-
-#%% Imports and constants
-
-import os
-import json
-from tqdm import tqdm
-
-input_fn = os.path.expanduser('~/lila/metadata/island_conservation.json')
-output_fn = os.path.expanduser('~/tmp/island_conservation.json')
-preview_folder = os.path.expanduser('~/tmp/island_conservation_preview')
-image_directory = os.path.expanduser('~/data/icct/public/')
-
-
-#%% Prevent imports during testing
-
-if False:
-
-    #%% Read input file
-    
-    with open(input_fn,'r') as f:
-        d = json.load(f)
-        
-    d['info']
-    d['info']['version'] = '1.01'
-    
-    
-    #%% Find locations
-    
-    images = d['images']
-    
-    locations = set()
-    
-    for i_image,im in tqdm(enumerate(images),total=len(images)):
-        tokens_fn = im['file_name'].split('/')
-        tokens_id = im['id'].split('_')
-        assert tokens_fn[0] == tokens_id[0]
-        assert tokens_fn[1] == tokens_id[1]
-        location = tokens_fn[0] + '_' + tokens_fn[1]
-        im['location'] = location
-        locations.add(location)
-    
-    locations = sorted(list(locations))
-        
-    for s in locations:
-        print(s)
-        
-        
-    #%% Write output file
-    
-    with open(output_fn,'w') as f:
-        json.dump(d,f,indent=1)
-        
-    
-    #%% Validate .json files
-    
-    from megadetector.data_management.databases import integrity_check_json_db
-    
-    options = integrity_check_json_db.IntegrityCheckOptions()
-    options.baseDir = image_directory
-    options.bCheckImageSizes = False
-    options.bCheckImageExistence = True
-    options.bFindUnusedImages = True
-    
-    sorted_categories, data, error_info = integrity_check_json_db.integrity_check_json_db(output_fn, options)
-    
-    
-    #%% Preview labels
-    
-    from megadetector.visualization import visualize_db
-    
-    viz_options = visualize_db.DbVizOptions()
-    viz_options.num_to_visualize = 2000
-    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.classes_to_exclude = ['test']
-    html_output_file, image_db = visualize_db.visualize_db(db_path=output_fn,
-                                                             output_dir=preview_folder,
-                                                             image_base_dir=image_directory,
-                                                             options=viz_options)
-    
-    from megadetector.utils import path_utils
-    path_utils.open_file(html_output_file)
-    
-    
-    #%% Zip output file
-    
-    from megadetector.utils.path_utils import zip_file
-    
-    zip_file(output_fn, verbose=True)
-    assert os.path.isfile(output_fn + '.zip')

megadetector/data_management/lila/add_locations_to_nacti.py

@@ -1,151 +0,0 @@
-"""
-
-add_locations_to_nacti.py
-
-As of 10.2023, NACTI metadata only has very coarse location information (e.g. "Florida"),
-but camera IDs are embedded in filenames.  This script pulls that information from filenames
-and adds it to metadata.
-
-"""
-
-#%% Imports and constants
-
-import os
-import json
-import shutil
-
-from tqdm import tqdm
-from collections import defaultdict
-
-input_file = r'd:\lila\nacti\nacti_metadata.json.1.13\nacti_metadata.json'
-output_file = r'g:\temp\nacti_metadata.1.14.json'
-
-
-#%% Prevent execution during testing
-
-if False:
-
-    #%% Read metadata
-    
-    with open(input_file,'r') as f:
-        d = json.load(f)
-        
-    assert d['info']['version'] == 1.13
-    
-    
-    #%% Map images to locations (according to the metadata)
-    
-    file_name_to_original_location = {}
-    
-    # im = dataset_labels['images'][0]
-    for im in tqdm(d['images']):
-        file_name_to_original_location[im['file_name']] = im['location']
-    
-    original_locations = set(file_name_to_original_location.values())
-    
-    print('Found {} locations in the original metadata:'.format(len(original_locations)))
-    for loc in original_locations:
-        print('[{}]'.format(loc))
-    
-    
-    #%% Map images to new locations
-    
-    def path_to_location(relative_path):
-        
-        relative_path = relative_path.replace('\\','/')
-        if relative_path in file_name_to_original_location:
-            location_name = file_name_to_original_location[relative_path]
-            if location_name == 'San Juan Mntns, Colorado':
-                # "part0/sub000/2010_Unit150_Ivan097_img0003.jpg"
-                tokens = relative_path.split('/')[-1].split('_')
-                assert tokens[1].startswith('Unit')
-                location_name = 'sanjuan_{}_{}_{}'.format(tokens[0],tokens[1],tokens[2])
-            elif location_name == 'Lebec, California':
-                # "part0/sub035/CA-03_08_13_2015_CA-03_0009738.jpg"
-                tokens = relative_path.split('/')[-1].split('_')
-                assert tokens[0].startswith('CA-') or tokens[0].startswith('TAG-')
-                location_name = 'lebec_{}'.format(tokens[0])   
-            elif location_name == 'Archbold, FL':
-                # "part1/sub110/FL-01_01_25_2016_FL-01_0040421.jpg"
-                tokens = relative_path.split('/')[-1].split('_')
-                assert tokens[0].startswith('FL-')
-                location_name = 'archbold_{}'.format(tokens[0])   
-            else:
-                assert location_name == ''
-                tokens = relative_path.split('/')[-1].split('_')
-                if tokens[0].startswith('CA-') or tokens[0].startswith('TAG-') or tokens[0].startswith('FL-'):
-                    location_name = '{}'.format(tokens[0])
-                
-        else:
-            
-            location_name = 'unknown'    
-        
-        # print('Returning location {} for file {}'.format(location_name,relative_path))          
-    
-        return location_name
-    
-    file_name_to_updated_location = {}
-    updated_location_to_count = defaultdict(int)
-    for im in tqdm(d['images']):
-        
-        updated_location = path_to_location(im['file_name'])
-        file_name_to_updated_location[im['file_name']] = updated_location
-        updated_location_to_count[updated_location] += 1
-    
-    updated_location_to_count = {k: v for k, v in sorted(updated_location_to_count.items(), 
-                             key=lambda item: item[1],
-                             reverse=True)}
-    
-    updated_locations = set(file_name_to_updated_location.values())
-    
-    print('Found {} updated locations in the original metadata:'.format(len(updated_locations)))
-    for loc in updated_location_to_count:
-        print('{}: {}'.format(loc,updated_location_to_count[loc]))
-    
-    
-    #%% Re-write metadata
-    
-    for im in d['images']:
-        im['location'] = file_name_to_updated_location[im['file_name']]
-    d['info']['version'] = 1.14
-    
-    with open(output_file,'w') as f:
-        json.dump(d,f,indent=1)
-        
-    
-    #%% For each location, sample some random images to make sure they look consistent
-    
-    input_base = r'd:\lila\nacti-unzipped'
-    assert os.path.isdir(input_base)
-    
-    location_to_images = defaultdict(list)
-    
-    for im in d['images']:
-        location_to_images[im['location']].append(im)
-        
-    n_to_sample = 10
-    import random
-    random.seed(0)
-    sampling_folder_base = r'g:\temp\nacti_samples'
-    
-    for location in tqdm(location_to_images):
-        
-        images_this_location = location_to_images[location]
-        if len(images_this_location) > n_to_sample:
-            images_this_location = random.sample(images_this_location,n_to_sample)
-            
-        for i_image,im in enumerate(images_this_location):
-            
-            fn_relative = im['file_name']
-            source_fn_abs = os.path.join(input_base,fn_relative)
-            assert os.path.isfile(source_fn_abs)
-            ext = os.path.splitext(fn_relative)[1]            
-            target_fn_abs = os.path.join(sampling_folder_base,'{}/{}'.format(
-                location,'image_{}{}'.format(str(i_image).zfill(2),ext)))
-            os.makedirs(os.path.dirname(target_fn_abs),exist_ok=True)
-            shutil.copyfile(source_fn_abs,target_fn_abs)
-            
-        # ...for each image
-        
-    # ...for each location
-                

megadetector-5.0.27.dist-info/RECORD

@@ -1,208 +0,0 @@
-megadetector/api/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-megadetector/api/batch_processing/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-megadetector/api/batch_processing/api_core/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-megadetector/api/batch_processing/api_core/server.py,sha256=-g6hfaSp7dUaT-2-bUSXkLE-MJnig3gZ3W_GbNkoAE0,11618
-megadetector/api/batch_processing/api_core/server_api_config.py,sha256=AjmLStXYoMMwxZJSephYROEprcSkG5RPlOr7Zho9xLk,3277
-megadetector/api/batch_processing/api_core/server_app_config.py,sha256=tQCFsFv0wJCegHfnu-Za3okdXwEd4U522hiM0YGNkMY,1860
-megadetector/api/batch_processing/api_core/server_batch_job_manager.py,sha256=K7fMFBJA8Z1SkA4eBM-nymcq7VQjwZ6ZRaNnNKFlat8,10324
-megadetector/api/batch_processing/api_core/server_job_status_table.py,sha256=P621Df7RTTKqW8VlxnCqkBtIO4Ko5bSS6WbU0ETzPGY,5984
-megadetector/api/batch_processing/api_core/server_orchestration.py,sha256=LYHABzhOvP0NrM1VIjI6Vwb95YZ5xjQ52mUJW8oIOQ0,17003
-megadetector/api/batch_processing/api_core/server_utils.py,sha256=uJvnW50lSE_LnRtEyrFI2dbVSecmGudaRhUH6NcAx1M,3100
-megadetector/api/batch_processing/api_core/batch_service/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-megadetector/api/batch_processing/api_core/batch_service/score.py,sha256=_hjUBIe0s9wmpmQwwDg-fd7tJMCn8735zJcgF15mTFo,17354
-megadetector/api/batch_processing/api_core_support/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-megadetector/api/batch_processing/api_core_support/aggregate_results_manually.py,sha256=pPLRVb54kMzcndiRQx0JGna3v9cSX__hBc_7PZ8NFEU,2274
-megadetector/api/batch_processing/api_support/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-megadetector/api/batch_processing/api_support/summarize_daily_activity.py,sha256=5H3DyXtdIW5uCp09Fbu9Tdf0hgfNKYnzv7v8Q7CPsDc,5382
-megadetector/api/batch_processing/data_preparation/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-megadetector/api/batch_processing/integration/digiKam/setup.py,sha256=7P1X3JYrBDXmLUeLRrzxNfDkL5lo-pY8nXsp9Cz8rOI,203
-megadetector/api/batch_processing/integration/digiKam/xmp_integration.py,sha256=zk5s7dD-FIkNnRxECT-0TAuBw7R__Or5_ft7Ha3iqMM,17774
-megadetector/api/batch_processing/integration/eMammal/test_scripts/config_template.py,sha256=UnvrgaFRBu59MuVUJa2WpG8ebcOJWcNeZEx6GWuYLzc,73
-megadetector/api/batch_processing/integration/eMammal/test_scripts/push_annotations_to_emammal.py,sha256=keqru1Ktbrj6J6TBEUm3e5N0Ps_0G2X4u4YVavWvDiU,3576
-megadetector/api/batch_processing/integration/eMammal/test_scripts/select_images_for_testing.py,sha256=OYMu97p8vprSv03QcnS6aSxPBocn9sgaozfUqq_JpyM,1369
-megadetector/api/synchronous/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-megadetector/api/synchronous/api_core/animal_detection_api/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-megadetector/api/synchronous/api_core/animal_detection_api/api_backend.py,sha256=g4HvPJ1bynLPzL79yta0GtWunxb8RjCADF56_YbYCsA,4955
-megadetector/api/synchronous/api_core/animal_detection_api/api_frontend.py,sha256=f16J7OBN87Tv0vVIIpXlyyVDeT6qYXDe5Kpr5XGqhdQ,10233
-megadetector/api/synchronous/api_core/animal_detection_api/config.py,sha256=05fVcLx0KK3wWFi62Mr-m_soewVn81qqeObUh-a2mrA,982
-megadetector/api/synchronous/api_core/tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-megadetector/api/synchronous/api_core/tests/load_test.py,sha256=bxyk3Oufl0V79vRsCPeRtWlE2o2KRtVgiqs7TSyP-iU,3277
-megadetector/classification/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-megadetector/classification/aggregate_classifier_probs.py,sha256=gj6PBCe12Z05r3FbOHXuNJHPWyIogoQJvt4kFzApOqg,3429
-megadetector/classification/analyze_failed_images.py,sha256=boY5MupCWEceHHpiJ4au7Rhz8bzmABlTz2B5w08V2qQ,8446
-megadetector/classification/cache_batchapi_outputs.py,sha256=PvbQZYjskIUlzqQl3TDs0bptqCS37rmU14Ix9a5TPRE,6308
-megadetector/classification/create_classification_dataset.py,sha256=bxj3SRyARQfP2ohRT7zEdge_hfs8iBnDETGQWcvNBuI,25467
-megadetector/classification/crop_detections.py,sha256=gFqUch8iapeqlgSU7VSDBB3LgetyyfX5xU3lI9o4Ulk,20438
-megadetector/classification/csv_to_json.py,sha256=hXxUqM92e9AtZVk_BkkjHNi2gMkXHpwmDnYv_uplLxA,5889
-megadetector/classification/detect_and_crop.py,sha256=1rdR9uEURwNO6CAPdRuOc3SmiBLNMwYPUYcMaV3mLWI,37029
-megadetector/classification/evaluate_model.py,sha256=ed6LrBo-U49Q_0tbaEExVZI3GOdA1BVUnc01WwCDUzU,19320
-megadetector/classification/identify_mislabeled_candidates.py,sha256=zOWHmWeaiOpM9c0s1uHOKgxJSHyJJR-oAM4R6f1c7T0,5032
-megadetector/classification/json_to_azcopy_list.py,sha256=146gUlCOMw5oaiZzNR2z0q1-gn6q56hkxIfY4lMiPVE,1670
-megadetector/classification/json_validator.py,sha256=uLHWs9X1r_Hi5Gq7zqpQYl6mDc_7M2KAnbmU5Hu_EXs,26553
-megadetector/classification/map_classification_categories.py,sha256=2vAfbVnVtyq38SuHpdo3H_kjt8ZGc6FUOyl50VxHjMM,10679
-megadetector/classification/merge_classification_detection_output.py,sha256=rDYj6vEQT78nP3bsbrnyAGgHTJ3yxQFYIVQtpdWJxDw,20015
-megadetector/classification/prepare_classification_script.py,sha256=zE8j3wi8YJBkEnuqkIb-SK8xoEnAu-XtlkSiO8-zpdQ,6510
-megadetector/classification/prepare_classification_script_mc.py,sha256=zQV6Vlr0cQxPrFLNk33RlPKAFPA4VuhlHsz-FtAIWv4,7190
-megadetector/classification/run_classifier.py,sha256=8PtkQzCUceOyoYxMfriJzA9ZLz_-YAd3OEr2865i3SM,9339
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