megadetector 5.0.28__py3-none-any.whl → 10.0.0__py3-none-any.whl

megadetector/data_management/importers/auckland_doc_test_to_json.py

@@ -1,373 +0,0 @@
-"""
-
- auckland_doc_test_to_json.py
-
- Convert Auckland DOC data set to COCO camera traps format.  This was
- for a testing data set where a .csv file was provided with class
- information.
-
-"""
-
-#%% Constants and imports
-
-import json
-import os
-import uuid
-import pandas as pd
-import datetime
-import ntpath
-import re
-import numpy as np
-
-from tqdm import tqdm
-
-from megadetector.visualization import visualize_db
-from megadetector.data_management.databases import integrity_check_json_db
-from megadetector.utils.path_utils import find_images
-
-input_base_dir = r'e:\auckland-test\2_Testing'
-
-input_metadata_file = r'G:\auckland-doc\Maukahuka - Auckland Island - Cat camera data Master April 2019 - DOC-5924483.xlsx'
-
-# Filenames will be stored in the output .json relative to this base dir
-output_base_dir = r'g:\auckland-doc'
-output_json_filename = os.path.join(output_base_dir, 'auckland-doc-test.json')
-
-assert os.path.isdir(input_base_dir)
-os.makedirs(output_base_dir,exist_ok=True)
-
-output_encoding = 'utf-8'
-read_image_sizes = True
-
-info = {}
-info['year'] = 2020
-info['version'] = '1.0'
-info['description'] = 'Auckaland DOC Camera Traps (test)'
-info['contributor'] = 'Auckland DOC'
-info['date_created'] = str(datetime.date.today())
-
-
-#%% Enumerate files
-
-print('Enumerating files from {}'.format(input_base_dir))
-absolute_image_paths = find_images(input_base_dir, recursive=True)
-print('Enumerated {} images'.format(len(absolute_image_paths)))
-
-relative_image_paths = []
-for fn in absolute_image_paths:
-    relative_image_paths.append(os.path.relpath(fn,input_base_dir).replace('\\','/'))
-
-relative_image_paths_set = set(relative_image_paths)
-
-assert len(relative_image_paths_set) == len(relative_image_paths)
-
-
-#%% Create unique identifier for each image
-
-# The ground truth doesn't have full paths in it; create unique identifiers for each image 
-# based on the camera name and filename.
-# 
-# We store file identifiers as cameraname_filename.
-file_identifier_to_relative_paths = {}
-camera_names = set()
-
-# relative_path = relative_image_paths[0]
-for relative_path in relative_image_paths:
-    
-    # Example relative paths
-    #
-    # Summer_Trial_2019/A1_1_42_SD114_20190210/AucklandIsland_A1_1_42_SD114_20190210_01300001.jpg
-    # Winter_Trial_2019/Installation/10_F4/10_F4_tmp_201908210001.JPG
-    fn = ntpath.basename(relative_path)    
-    
-    # Find the camera name
-    tokens = relative_path.split('/')
-    
-    if tokens[1] == 'Installation' or 'Rebait' in tokens[1]:
-        camera_name = tokens[2]
-    
-    else:
-        # E..g. "A1_1_42_SD114_20190210" in the above example
-        camera_token = tokens[1]
-        camera_name = None
-        m = re.search('^(.+)_SD',camera_token)
-        if m:
-            camera_name = m.group(1)
-        else:
-            # For camera tokens like C1_5_D_190207
-            m = re.search('^(.+_.+_.+)',camera_token)
-            camera_name = m.group(1)
-    
-    assert camera_name
-    camera_names.add(camera_name)
-    
-    file_identifier = camera_name + '_' + fn
-    if file_identifier not in file_identifier_to_relative_paths:
-        file_identifier_to_relative_paths[file_identifier] = [relative_path]
-    else:
-        file_identifier_to_relative_paths[file_identifier].append(relative_path)
-    
-print('Found {} unique camera names'.format(len(camera_names)))
-      
-      
-#%% Load input data
-
-input_metadata = pd.read_excel(input_metadata_file)
-
-print('Read {} columns and {} rows from metadata file'.format(len(input_metadata.columns),
-      len(input_metadata)))
-
-# The spreadsheet has a space after "Camera"
-input_metadata = input_metadata.rename(columns={'Camera ':'Camera'})
-    
-
-#%% Assemble dictionaries
-
-image_id_to_image = {}
-category_name_to_category = {}
-annotations = []
-
-# Force the empty category to be ID 0
-empty_category = {}
-empty_category['name'] = 'empty'
-empty_category['id'] = 0
-category_name_to_category['empty'] = empty_category
-
-rows_not_found_in_folder = []
-rows_ambiguous = []
-rows_no_filename = []
-rows_no_annotation = []
-
-image_id_to_rows = {}
-
-next_id = 1
-
-category_names = ['cat','mouse','unknown','human','pig','sealion','penguin','dog','openadjusted']
-
-# array([nan, 'Blackbird', 'Bellbird', 'Tomtit', 'Song thrush', 'Pippit',
-#       'Pippet', '?', 'Dunnock', 'Song thursh', 'Kakariki', 'Tui', ' ',
-#       'Silvereye', 'NZ Pipit', 'Blackbird and Dunnock', 'Unknown',
-#       'Pipit', 'Songthrush'], dtype=object)
-
-def bird_name_to_category_name(bird_name):
-    bird_name = bird_name.lower().strip().replace(' ','_').replace('song_thursh','song_thrush')
-    bird_name = bird_name.replace('pippet','pipt').replace('pippit','pipit').replace('nz_pipit','pipit')
-    if bird_name == '?' or bird_name == '' or bird_name == 'unknown':
-        category_name = 'unknown_bird'
-    else:
-        category_name = bird_name
-    return category_name
-    
-bird_names = input_metadata.Bird_ID.unique()
-for bird_name in bird_names:
-    if isinstance(bird_name,float):
-        continue
-    category_name = bird_name_to_category_name(bird_name)
-    if category_name not in category_names:
-        category_names.append(category_name)
-        
-for category_name in category_names:
-    cat = {}
-    cat['name'] = category_name
-    cat['id'] = next_id
-    next_id = next_id +1
-    category_name_to_category[category_name] = cat
-    
-def create_annotation(image_id,category_name,count):
-    assert isinstance(image_id,str)
-    assert isinstance(category_name,str)
-    assert isinstance(count,int) or isinstance(count,float)
-    if isinstance(count,float):
-        count = int(count)
-    ann = {}    
-    ann['id'] = str(uuid.uuid1())
-    ann['image_id'] = image_id
-    category = category_name_to_category[category_name]
-    category_id = category['id']
-    ann['category_id'] = category_id
-    ann['count'] = count
-    return ann
-    
-# i_row = 0; row = input_metadata.iloc[i_row]
-for i_row,row in tqdm(input_metadata.iterrows(),total=len(input_metadata)):
-
-    # E.g.: AucklandIsland_A1_1_42_SD114_20190210_01300009.jpg
-    filename = row['File']
-    if isinstance(filename,float):
-        rows_no_filename.append(i_row)
-        continue
-    
-    camera_name = row['Camera']
-    file_identifier = camera_name + '_' + filename
-    if not file_identifier in file_identifier_to_relative_paths:
-        rows_not_found_in_folder.append(i_row)
-        continue        
-
-    relative_paths_this_file_id = file_identifier_to_relative_paths[file_identifier]
-    
-    if len(relative_paths_this_file_id) == 1:
-        relative_path = relative_paths_this_file_id[0]
-    else:
-        
-        # We have multiple files matching this identifier, can we uniquely resolve this
-        # to one of those files based on the camera ID?
-        matches = [s for s in relative_paths_this_file_id if camera_name in s]
-        assert len(matches) > 0
-        if len(matches) > 1:
-            rows_ambiguous.append(i_row)
-            continue
-        relative_path = matches[0]
-
-    assert filename.endswith('.jpg') or filename.endswith('.JPG')
-    image_id = filename.lower().replace('.jpg','')
-
-    if image_id in image_id_to_rows:
-        image_id_to_rows[image_id].append(i_row)
-        continue
-        
-    image_id_to_rows[image_id] = [i_row]
-        
-    im = {}
-    im['id'] = image_id 
-    im['file_name'] = relative_path
-    im['datetime'] = str(row['Date and time'])
-    im['camera'] = row['Camera']
-    im['sd_card'] = row['SD_Card']
-    im['sd_change'] = row['SD_Change']
-    im['comments'] = row['Comments']
-    
-    image_id_to_image[im['id']] = im
-    
-    # create_annotation(image_id,category_name,count)
-    
-    # 'SD_Change', 'Cat', 'Mouse', 'Bird', 'Bird_ID', 'False_trig', 'Unknown',
-    # 'Human', 'Collared_cat', 'Cat_ID', 'Pig', 'Sea_lion', 'Open_adjusted',
-    # 'Penguin', 'Dog', 'Comments', 'Unnamed: 22']
-    
-    # Each of these categories is handled a little differently...
-    
-    annotations_this_image = []
-    if (not np.isnan(row['Cat'])):
-        assert np.isnan(row['Collared_cat'] )
-        annotations_this_image.append(create_annotation(im['id'],'cat',row['Cat']))
-    
-    if (not np.isnan(row['Collared_cat'])):
-        assert np.isnan(row['Cat'] )
-        annotations_this_image.append(create_annotation(im['id'],'cat',row['Collared_cat']))
-    
-    if (not np.isnan(row['Bird'])):
-        if isinstance(row['Bird_ID'],str):
-            category_name = bird_name_to_category_name(row['Bird_ID'])
-        else:
-            assert np.isnan(row['Bird_ID'])            
-            category_name = 'unknown_bird'
-        annotations_this_image.append(create_annotation(im['id'],category_name,row['Bird']))
-    
-    if (not np.isnan(row['False_trig'])):
-        annotations_this_image.append(create_annotation(im['id'],'empty',-1))
-    
-    # These are straightforward
-    for s in ['Mouse','Unknown','Pig','Human','Sea_lion','Penguin','Dog','Open_adjusted']:
-        if isinstance(row[s],float) or isinstance(row[s],int):
-            if not np.isnan(row[s]):
-                 annotations_this_image.append(create_annotation(im['id'],s.lower().replace('_',''),row[s]))
-        elif isinstance(row[s],str):
-            print('File {}, label {}, value {}'.format(filename,s,row[s]))
-        else:
-            raise ValueError('Error handling count value {}'.format(row[s]))
-        
-    if len(annotations_this_image) > 1:
-        print('Multiple annotations for filename {}'.format(filename))
-       
-    if len(annotations_this_image) == 0:
-        rows_no_annotation.append(i_row)
-        
-    annotations.extend(annotations_this_image)
-
-# ...for each image
-
-
-#%% Summarize errors
-
-print('Of {} rows:\n'.format(len(input_metadata)))
-
-print('{} images not found in folder'.format(len(rows_not_found_in_folder)))
-print('{} images ambiguously mapped'.format(len(rows_ambiguous)))
-print('{} images no filename'.format(len(rows_no_filename)))
-print('{} images no annotation'.format(len(rows_no_annotation)))
-print('{} images handled successfully, {} total annotations'.format(len(image_id_to_image),len(annotations)))
-    
-
-#%% Write output .json
-
-images = list(image_id_to_image.values())
-categories = list(category_name_to_category.values())
-
-data = {}
-data['info'] = info
-data['images'] = images
-data['annotations'] = annotations
-data['categories'] = categories
-
-json.dump(data, open(output_json_filename, 'w'), indent=1)
-print('Finished writing json to {}'.format(output_json_filename))
-
-
-#%% Validate .json file
-
-options = integrity_check_json_db.IntegrityCheckOptions()
-options.baseDir = input_base_dir
-options.bCheckImageSizes = False
-options.bCheckImageExistence = False
-options.bFindUnusedImages = False
-
-sortedCategories, data, _ = integrity_check_json_db.integrity_check_json_db(output_json_filename, options)
-
-
-#%% Preview labels
-
-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 = ['empty']
-html_output_file, image_db = visualize_db.visualize_db(db_path=output_json_filename,
-                                                         output_dir=os.path.join(
-                                                         output_base_dir, 'preview'),
-                                                         image_base_dir=input_base_dir,
-                                                         options=viz_options)
-os.startfile(html_output_file)
-
-
-#%% Precision-recall analysis
-
-from megadetector.postprocessing.postprocess_batch_results import PostProcessingOptions
-from megadetector.postprocessing.postprocess_batch_results import process_batch_results
-
-api_output_file = r'g:\auckland-doc\auckland-doc_20200801\combined_api_outputs\auckland-doc_202008012020.08.01_reformatMaukahuka_Auckland_Island2_TestingSummer_Trial_2019_detections.filtered_rde_0.60_0.85_5_0.05.json'
-postprocessing_output_folder = r'G:\auckland-doc\auckland-doc_20200801\postprocessing'
-image_base = r'E:\auckland-test\2_Testing'
-ground_truth_json_file = output_json_filename
-
-output_base = os.path.join(postprocessing_output_folder,'pr_analysis')
-os.makedirs(output_base,exist_ok=True)
-
-options = PostProcessingOptions()
-options.unlabeled_classes.append('openadjusted')
-options.image_base_dir = image_base
-options.parallelize_rendering = True
-options.include_almost_detections = True
-options.num_images_to_sample = 2500
-options.confidence_threshold = 0.75
-options.almost_detection_confidence_threshold = 0.7
-options.ground_truth_json_file = ground_truth_json_file
-options.allow_missing_images = True
-options.ground_truth_filename_replacements = {} 
-options.api_output_filename_replacements = {'2020.08.01_reformat\\Maukahuka_Auckland_Island\\2_Testing\\':''}
-options.api_output_file = api_output_file
-options.output_dir = output_base
-ppresults = process_batch_results(options)
-os.startfile(ppresults.output_html_file)
-

megadetector/data_management/importers/auckland_doc_to_json.py

@@ -1,201 +0,0 @@
-"""
-
- auckland_doc_to_json.py
-
- Convert Auckland DOC data set to COCO camera traps format.  This was
- for a training data set where class names were encoded in path names.
-
-"""
-
-#%% Constants and imports
-
-import json
-import os
-import uuid
-import datetime
-
-from tqdm import tqdm
-
-from megadetector.visualization import visualize_db
-from megadetector.data_management.databases import integrity_check_json_db
-from megadetector.utils.path_utils import find_images, split_path, insert_before_extension
-
-# Filenames will be stored in the output .json relative to this base dir
-input_base_dir = 'y:\\'
-output_base_dir = r'f:\auckland-doc'
-output_json_filename = os.path.join(output_base_dir, 'auckland-doc-Maukahuka_Auckland_Island.json')
-
-assert os.path.isdir(input_base_dir)
-os.makedirs(output_base_dir,exist_ok=True)
-
-output_encoding = 'utf-8'
-read_image_sizes = True
-
-info = {}
-info['year'] = 2019
-info['version'] = '1.0'
-info['description'] = 'Auckaland DOC Camera Traps'
-info['contributor'] = 'Auckland DOC'
-info['date_created'] = str(datetime.date.today())
-
-
-#%% Enumerate files
-
-print('Enumerating files from {}'.format(input_base_dir))
-image_files = find_images(input_base_dir, bRecursive=True)
-print('Enumerated {} images'.format(len(image_files)))
-
-
-#%% Assemble dictionaries
-
-images = []
-image_id_to_image = {}
-annotations = []
-categories = []
-
-category_name_to_category = {}
-category_id_to_category = {}
-
-# Force the empty category to be ID 0
-empty_category = {}
-empty_category['name'] = 'empty'
-empty_category['id'] = 0
-category_id_to_category[0] = empty_category
-categories.append(empty_category)
-next_id = 1
-
-behaviors = set()
-
-# fn = image_files[0]; print(fn)
-for fn in tqdm(image_files):
-
-    # Typically y:\Maukahuka_Auckland_Island\1_Training\Winter_Trial_2019\cat\cat\eat\20190903_IDdY_34_E3_tmp_201908240051.JPG
-    relative_path = os.path.relpath(fn,input_base_dir)
-    tokens = split_path(fn)
-    assert tokens[1] == 'Maukahuka_Auckland_Island'
-    
-    trainval_split = tokens[2]
-    assert trainval_split in ['1_Training','2_Testing']
-    
-    # This data set has two top-level folders, "1_Training" (which has class names encoded
-    # in paths) and "2_Testing" (which has no class information).
-    if trainval_split == '2_Testing':
-        category_name = 'test'
-    else:
-        category_name = tokens[-3]
-        if category_name.startswith('2_'):
-            category_name = category_name.replace('2_', '')
-        category_name = category_name.lower().strip()
-
-    if category_name not in category_name_to_category:        
-
-        category_id = next_id
-        next_id += 1
-        category = {}
-        category['id'] = category_id
-        category['name'] = category_name
-        category['count'] = 0
-        categories.append(category)
-        category_name_to_category[category_name] = category
-        category_id_to_category[category_id] = category
-
-    else:
-        
-        category = category_name_to_category[category_name]
-        
-    category_id = category['id']
-    
-    category['count'] += 1
-    behavior = None
-    if (category_name) != 'test':
-        behavior = fn.split('\\')[-2]
-        behaviors.add(behavior)            
-
-    im = {}
-    im['id'] = str(uuid.uuid1())
-    im['file_name'] = relative_path
-    image_id_to_image[im['id']] = im
-    
-    images.append(im)
-    
-    ann = {}
-    
-    ann['id'] = str(uuid.uuid1())
-    ann['image_id'] = im['id']
-    ann['category_id'] = category_id
-    if behavior is not None:
-        ann['behavior'] = behavior
-    annotations.append(ann)
-
-# ...for each image
-    
-
-#%% Write output .json
-
-data = {}
-data['info'] = info
-data['images'] = images
-data['annotations'] = annotations
-data['categories'] = categories
-
-json.dump(data, open(output_json_filename, 'w'), indent=2)
-print('Finished writing json to {}'.format(output_json_filename))
-
-
-#%% Write train/test .jsons
-
-train_images = []; test_images = []
-train_annotations = []; test_annotations = []
-
-for ann in tqdm(annotations):
-    category_id = ann['category_id']
-    image_id = ann['image_id']
-    category_name = category_id_to_category[category_id]['name']
-    im = image_id_to_image[image_id]
-    if category_name == 'test':
-        test_images.append(im)
-        test_annotations.append(ann)
-    else:
-        train_images.append(im)
-        train_annotations.append(ann)
-
-train_fn = insert_before_extension(output_json_filename,'train')
-test_fn = insert_before_extension(output_json_filename,'test')
-
-data['images'] = train_images
-data['annotations'] = train_annotations
-json.dump(data, open(train_fn, 'w'), indent=2)
-
-data['images'] = test_images
-data['annotations'] = test_annotations
-json.dump(data, open(test_fn, 'w'), indent=2)
-
-    
-#%% Validate .json files
-
-options = integrity_check_json_db.IntegrityCheckOptions()
-options.baseDir = input_base_dir
-options.bCheckImageSizes = False
-options.bCheckImageExistence = True
-options.bFindUnusedImages = True
-
-sorted_categories, data, _ = integrity_check_json_db.integrity_check_json_db(output_json_filename, options)
-sorted_categories, data, _ = integrity_check_json_db.integrity_check_json_db(train_fn, options)
-sorted_categories, data, _ = integrity_check_json_db.integrity_check_json_db(test_fn, options)
-
-
-#%% Preview labels
-
-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_json_filename,
-                                                         output_dir=os.path.join(
-                                                         output_base_dir, 'preview'),
-                                                         image_base_dir=input_base_dir,
-                                                         options=viz_options)
-os.startfile(html_output_file)