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

megadetector/data_management/wi_download_csv_to_coco.py

@@ -0,0 +1,247 @@
+"""
+
+wi_download_csv_to_coco.py
+
+Converts a .csv file from a Wildlife Insights project export to a COCO camera traps .json file.
+
+Currently assumes that common names are unique identifiers, which is convenient but unreliable.
+
+"""
+
+#%% Imports and constants
+
+import os
+import json
+import pandas as pd
+
+from tqdm import tqdm
+from collections import defaultdict
+
+from megadetector.visualization import visualization_utils as vis_utils
+from megadetector.utils.ct_utils import isnan
+
+wi_extra_annotation_columns = \
+    ('is_blank','identified_by','wi_taxon_id','class','order','family','genus','species','uncertainty',
+             'number_of_objects','age','sex','animal_recognizable','individual_id','individual_animal_notes',
+             'behavior','highlighted','markings')
+
+wi_extra_image_columns = ('project_id','deployment_id')
+
+def _make_location_id(project_id,deployment_id):    
+    return 'project_' + str(project_id) + '_deployment_' + deployment_id
+
+default_category_remappings = {
+    'Homo Species':'Human',
+    'Human-Camera Trapper':'Human',
+    'No CV Result':'Unknown'
+}
+
+
+#%% Main function
+
+def wi_download_csv_to_coco(csv_file_in,
+                            coco_file_out=None,
+                            image_folder=None,
+                            validate_images=False,
+                            gs_prefix=None,
+                            verbose=True,
+                            category_remappings=default_category_remappings):
+    """
+    Converts a .csv file from a Wildlife Insights project export to a COCO 
+    Camera Traps .json file.
+    
+    Args:
+        csv_file_in (str): the downloaded .csv file we should convert to COCO
+        coco_file_out (str, optional): the .json file we should write; if [coco_file_out] is None, 
+            uses [csv_file_in].json
+        image_folder (str, optional): the folder where images live, only relevant if 
+            [validate_images] is True
+        validate_images (bool, optional): whether to check images for corruption and load
+            image sizes; if this is True, [image_folder] must be a valid folder
+        gs_prefix (str, optional): a string to remove from GS URLs to convert to path names... 
+            for example, if your gs:// URLs look like:
+    
+            `gs://11234134_xyz/deployment/55554/dfadfasdfs.jpg`
+    
+            ...and you specify gs_prefix='11234134_xyz/deployment/', the filenames in
+            the .json file will look like:
+        
+            `55554/dfadfasdfs.jpg`
+        verbose (bool, optional): enable additional debug console output
+        category_remappings (dict, optional): str --> str dict that maps any number of
+            WI category names to output category names; for example defaults to mapping
+            "Homo Species" to "Human", but leaves 99.99% of categories unchanged.        
+            
+    Returns: 
+        dict: COCO-formatted data, identical to what's written to [coco_file_out]
+    """
+    
+    ##%% Create COCO dictionaries
+    
+    category_name_to_id = {}
+    category_name_to_id['empty'] = 0
+    
+    df = pd.read_csv(csv_file_in)
+    
+    print('Read {} rows from {}'.format(len(df),csv_file_in))
+    
+    image_id_to_image = {}
+    image_id_to_annotations = defaultdict(list)
+    
+    # i_row = 0; row = df.iloc[i_row]
+    for i_row,row in df.iterrows():
+        
+        image_id = row['image_id']
+        
+        if image_id not in image_id_to_image:
+            
+            im = {}
+            image_id_to_image[image_id] = im
+            
+            im['id'] = image_id
+            
+            gs_url = row['location']
+            assert gs_url.startswith('gs://')
+            
+            file_name = gs_url.replace('gs://','')
+            if gs_prefix is not None:
+                file_name = file_name.replace(gs_prefix,'')
+                
+            location_id = _make_location_id(row['project_id'],row['deployment_id'])
+            im['file_name'] = file_name
+            im['location'] = location_id
+            im['datetime'] = row['timestamp']
+            
+            im['wi_image_info'] = {}
+            for s in wi_extra_image_columns:
+                im['wi_image_info'][s] = str(row[s])
+            
+        else:
+            
+            im = image_id_to_image[image_id]
+            assert im['datetime'] == row['timestamp']
+            location_id = _make_location_id(row['project_id'],row['deployment_id'])
+            assert im['location'] == location_id
+            
+        category_name = row['common_name']
+        if category_remappings is not None and category_name in category_remappings:
+            category_name = category_remappings[category_name]
+            
+        if category_name == 'Blank':
+            category_name = 'empty'
+            assert row['is_blank'] == 1
+        else:
+            assert row['is_blank'] == 0
+        assert isinstance(category_name,str)
+        if category_name in category_name_to_id:
+            category_id = category_name_to_id[category_name]
+        else:
+            category_id = len(category_name_to_id)
+            category_name_to_id[category_name] = category_id
+        
+        ann = {}
+        ann['image_id'] = image_id
+        annotations_this_image = image_id_to_annotations[image_id]
+        annotation_number = len(annotations_this_image)
+        ann['id'] = image_id + '_' + str(annotation_number).zfill(2)        
+        ann['category_id'] = category_id
+        annotations_this_image.append(ann)
+        
+        extra_info = {}
+        for s in wi_extra_annotation_columns:            
+            v = row[s]
+            if not isnan(v):
+                extra_info[s] = v
+        ann['wi_extra_info'] = extra_info
+        
+    # ...for each row
+    
+    images = list(image_id_to_image.values())
+    categories = []
+    for category_name in category_name_to_id:
+        category_id = category_name_to_id[category_name]
+        categories.append({'id':category_id,'name':category_name})
+    annotations = []
+    for image_id in image_id_to_annotations:
+        annotations_this_image = image_id_to_annotations[image_id]
+        for ann in annotations_this_image:
+            annotations.append(ann)
+    info = {'version':'1.00','description':'converted from WI export'}
+    info['source_file'] = csv_file_in
+    coco_data = {}
+    coco_data['info'] = info
+    coco_data['images'] = images
+    coco_data['annotations'] = annotations
+    coco_data['categories'] = categories
+    
+    
+    ##%% Validate images, add sizes        
+    
+    if validate_images:
+        
+        print('Validating images')
+        
+        assert os.path.isdir(image_folder), \
+            'Must specify a valid image folder if you specify validate_images=True'
+        
+        # TODO: trivially parallelizable
+        #    
+        # im = images[0]
+        for im in tqdm(images):
+            file_name_relative = im['file_name']
+            file_name_abs = os.path.join(image_folder,file_name_relative)
+            assert os.path.isfile(file_name_abs)
+                
+            im['corrupt'] = False
+            try:
+                pil_im = vis_utils.load_image(file_name_abs)
+            except Exception:
+                im['corrupt'] = True
+            if not im['corrupt']:
+                im['width'] = pil_im.width
+                im['height'] = pil_im.height
+    
+    
+    ##%% Write output json
+        
+    if coco_file_out is None:        
+        coco_file_out = csv_file_in + '.json'
+        
+    with open(coco_file_out,'w') as f:
+        json.dump(coco_data,f,indent=1)
+
+
+    ##%% Validate output
+    
+    from megadetector.data_management.databases.integrity_check_json_db import \
+        IntegrityCheckOptions,integrity_check_json_db
+    options = IntegrityCheckOptions()
+    options.baseDir = image_folder
+    options.bCheckImageExistence = True
+    options.verbose = verbose
+    _ = integrity_check_json_db(coco_file_out,options)
+    
+    return coco_data
+
+# ...def wi_download_csv_to_coco(...)    
+
+
+#%% Interactive driver
+
+if False:
+    
+    #%%
+    
+    base_folder = r'a/b/c'
+    csv_file_in = os.path.join(base_folder,'images.csv')
+    coco_file_out = None
+    gs_prefix = 'a_b_c_main/'
+    image_folder = os.path.join(base_folder,'images')
+    validate_images = False
+    verbose = True
+    category_remappings = default_category_remappings
+
+
+#%% Command-line driver
+
+# TODO

megadetector/data_management/yolo_output_to_md_output.py

@@ -0,0 +1,446 @@
+"""
+
+yolo_output_to_md_output.py
+
+Converts the output of YOLOv5's detect.py or val.py to the MD API output format.
+
+**Converting .txt files**
+
+detect.py writes a .txt file per image, in YOLO training format.  Converting from this
+format does not currently support recursive results, since detect.py doesn't save filenames
+in a way that allows easy inference of folder names.  Requires access to the input
+images, because the YOLO format uses the *absence* of a results file to indicate that
+no detections are present.
+
+YOLOv5 output has one text file per image, like so:
+
+0 0.0141693 0.469758 0.0283385 0.131552 0.761428 
+
+That's [class, x_center, y_center, width_of_box, height_of_box, confidence]
+
+val.py can write in this format as well, using the --save-txt argument.
+
+In both cases, a confidence value is only written to each line if you include the --save-conf
+argument.  Confidence values are required by this conversion script.
+
+
+**Converting .json files**
+
+val.py can also write a .json file in COCO-ish format.  It's "COCO-ish" because it's
+just the "images" portion of a COCO .json file.
+
+Converting from this format also requires access to the original images, since the format
+written by YOLOv5 uses absolute coordinates, but MD results are in relative coordinates.
+
+"""
+
+#%% Imports and constants
+
+import json
+import csv
+import os
+import re
+
+from collections import defaultdict
+from tqdm import tqdm
+
+from megadetector.utils import path_utils
+from megadetector.utils import ct_utils
+from megadetector.visualization import visualization_utils as vis_utils
+from megadetector.detection.run_detector import CONF_DIGITS, COORD_DIGITS
+
+
+#%% Support functions
+
+def read_classes_from_yolo_dataset_file(fn):
+    """
+    Reads a dictionary mapping integer class IDs to class names from a YOLOv5/YOLOv8
+    dataset.yaml file or a .json file.  A .json file should contain a dictionary mapping
+    integer category IDs to string category names.
+    
+    Args:
+        fn (str): YOLOv5/YOLOv8 dataset file with a .yml or .yaml extension, or a .json file 
+            mapping integer category IDs to category names.
+            
+    Returns:
+        dict: a mapping from integer category IDs to category names
+    """
+        
+    if fn.endswith('.yml') or fn.endswith('.yaml'):
+        
+        with open(fn,'r') as f:
+            lines = f.readlines()
+                
+        category_id_to_name = {}
+        pat = '\d+:.+'
+        for s in lines:
+            if re.search(pat,s) is not None:
+                tokens = s.split(':')
+                assert len(tokens) == 2, 'Invalid token in category file {}'.format(fn)
+                category_id_to_name[int(tokens[0].strip())] = tokens[1].strip()
+                
+    elif fn.endswith('.json'):
+        
+        with open(fn,'r') as f:
+            d_in = json.load(f)
+            category_id_to_name = {}
+            for k in d_in.keys():
+                category_id_to_name[int(k)] = d_in[k]
+        
+    else:
+        
+        raise ValueError('Unrecognized category file type: {}'.format(fn))
+        
+    assert len(category_id_to_name) > 0, 'Failed to read class mappings from {}'.format(fn)
+    
+    return category_id_to_name
+    
+
+def yolo_json_output_to_md_output(yolo_json_file, 
+                                  image_folder,
+                                  output_file, 
+                                  yolo_category_id_to_name,                              
+                                  detector_name='unknown',
+                                  image_id_to_relative_path=None,
+                                  offset_yolo_class_ids=True,
+                                  truncate_to_standard_md_precision=True,
+                                  image_id_to_error=None,
+                                  convert_slashes=True):
+    """
+    Converts a YOLOv5/YOLOv8 .json file to MD .json format.
+    
+    Args:
+        
+        yolo_json_file (str): the .json file to convert from YOLOv5 format to MD output format
+        image_folder (str): the .json file contains relative path names, this is the path base
+        yolo_category_id_to_name (str or dict): the .json results file contains only numeric 
+            identifiers for categories, but we want names and numbers for the output format; 
+            yolo_category_id_to_name provides that mapping either as a dict or as a YOLOv5 
+            dataset.yaml file.
+        detector_name (str, optional): a string that gets put in the output file, not otherwise 
+            used within this function
+        image_id_to_relative_path (dict, optional): YOLOv5 .json uses only basenames (e.g. 
+            abc1234.JPG); by default these will be appended to the input path to create pathnames.
+            If you have a flat folder, this is fine.  If you want to map base names to relative paths in
+            a more complicated way, use this parameter.   
+        offset_yolo_class_ids (bool, optional): YOLOv5 class IDs always start at zero; if you want to 
+            make the output classes start at 1, set offset_yolo_class_ids to True.    
+        truncate_to_standard_md_precision (bool, optional): YOLOv5 .json includes lots of 
+            (not-super-meaningful) precision, set this to truncate to COORD_DIGITS and CONF_DIGITS.
+        image_id_to_error (dict, optional): if you want to include image IDs in the output file for which 
+            you couldn't prepare the input file in the first place due to errors, include them here.
+        convert_slashes (bool, optional): force all slashes to be forward slashes in the output file
+    """    
+        
+    assert os.path.isfile(yolo_json_file), \
+        'Could not find YOLO .json file {}'.format(yolo_json_file)
+    assert os.path.isdir(image_folder), \
+        'Could not find image folder {}'.format(image_folder)
+      
+    if image_id_to_error is None:
+        image_id_to_error = {}
+            
+    print('Converting {} to MD format and writing results to {}'.format(
+        yolo_json_file,output_file))
+    
+    if isinstance(yolo_category_id_to_name,str):
+        assert os.path.isfile(yolo_category_id_to_name), \
+            'YOLO category mapping specified as a string, but file does not exist: {}'.format(
+                yolo_category_id_to_name)
+        yolo_category_id_to_name = read_classes_from_yolo_dataset_file(yolo_category_id_to_name)
+    
+    if image_id_to_relative_path is None:
+        
+        image_files = path_utils.find_images(image_folder,recursive=True)
+        image_files = [os.path.relpath(fn,image_folder) for fn in image_files]
+        
+        # YOLOv5 identifies images in .json output by ID, which is the filename without
+        # extension.  If a mapping is not provided, these need to be unique.
+        image_id_to_relative_path = {}
+        
+        for fn in image_files:
+            image_id = os.path.splitext(os.path.basename(fn))[0]
+            if image_id in image_id_to_relative_path:
+                print('Error: image ID {} refers to:\n{}\n{}'.format(
+                    image_id,image_id_to_relative_path[image_id],fn))
+                raise ValueError('Duplicate image ID {}'.format(image_id))
+            image_id_to_relative_path[image_id] = fn
+
+    image_files_relative = sorted(list(image_id_to_relative_path.values()))
+    
+    image_file_relative_to_image_id = {}
+    for image_id in image_id_to_relative_path:
+        relative_path = image_id_to_relative_path[image_id]
+        assert relative_path not in image_file_relative_to_image_id, \
+            'Duplication image IDs in YOLO output conversion for image {}'.format(relative_path)
+        image_file_relative_to_image_id[relative_path] = image_id
+        
+    with open(yolo_json_file,'r') as f:
+        detections = json.load(f)
+    assert isinstance(detections,list)
+    
+    image_id_to_detections = defaultdict(list)
+    
+    int_formatted_image_ids = False
+    
+    # det = detections[0]
+    for det in detections:
+        
+        # This could be a string, but if the YOLOv5 inference script sees that the strings
+        # are really ints, it converts to ints.
+        image_id = det['image_id']
+        image_id_to_detections[image_id].append(det)
+        if isinstance(image_id,int):
+            int_formatted_image_ids = True
+    
+    # If there are any ints present, everything should be ints
+    if int_formatted_image_ids:
+        for det in detections:
+            assert isinstance(det['image_id'],int), \
+                'Found mixed int and string image IDs'
+        
+        # Convert the keys in image_id_to_error to ints
+        #
+        # This should error if we're given non-int-friendly IDs        
+        int_formatted_image_id_to_error = {}        
+        for image_id in image_id_to_error:
+            int_formatted_image_id_to_error[int(image_id)] = \
+                image_id_to_error[image_id]
+        image_id_to_error = int_formatted_image_id_to_error        
+           
+    # ...if image IDs are formatted as integers in YOLO output
+    
+    # In a modified version of val.py, we use negative category IDs to indicate an error
+    # that happened during inference (typically truncated images with valid headers,
+    # so corruption was not detected during val.py's initial corruption check pass.
+    for det in detections:
+        if det['category_id'] < 0:
+            assert 'error' in det, 'Negative category ID present with no error string'
+            error_string = det['error']
+            print('Caught inference-time failure {} for image {}'.format(error_string,det['image_id']))
+            image_id_to_error[det['image_id']] = error_string
+            
+    output_images = []
+    
+    # image_file_relative = image_files_relative[10]
+    for image_file_relative in tqdm(image_files_relative):
+        
+        im = {}
+        im['file'] = image_file_relative
+        if convert_slashes:
+            im['file'] = im['file'].replace('\\','/')
+        
+        image_id = image_file_relative_to_image_id[image_file_relative]
+        if int_formatted_image_ids:
+            image_id = int(image_id)
+        if image_id in image_id_to_error:
+            im['failure'] = str(image_id_to_error[image_id])
+            output_images.append(im)
+            continue
+        elif image_id not in image_id_to_detections:
+            detections = []
+        else:
+            detections = image_id_to_detections[image_id]
+        
+        image_full_path = os.path.join(image_folder,image_file_relative)
+        try:
+            pil_im = vis_utils.open_image(image_full_path)
+        except Exception as e:
+            s = str(e).replace('\n',' ')
+            print('Warning: error opening image {}: {}, outputting as a failure'.format(image_full_path,s))
+            im['failure'] = 'Conversion error: {}'.format(s)
+            output_images.append(im)
+            continue
+        
+        im['detections'] = []
+        
+        image_w = pil_im.size[0]
+        image_h = pil_im.size[1]
+        
+        # det = detections[0]
+        for det in detections:
+            
+            output_det = {}
+            
+            yolo_cat_id = int(det['category_id'])
+            if offset_yolo_class_ids:
+                yolo_cat_id += 1
+            output_det['category'] = str(int(yolo_cat_id))
+            conf = det['score']
+            if truncate_to_standard_md_precision:
+                conf = ct_utils.truncate_float(conf,CONF_DIGITS)
+            output_det['conf'] = conf
+            input_bbox = det['bbox']
+            
+            # YOLO's COCO .json is not *that* COCO-like, but it is COCO-like in
+            # that the boxes are already [xmin/ymin/w/h]
+            box_xmin_absolute = input_bbox[0]
+            box_ymin_absolute = input_bbox[1]
+            box_width_absolute = input_bbox[2]
+            box_height_absolute = input_bbox[3]
+            
+            box_xmin_relative = box_xmin_absolute / image_w
+            box_ymin_relative = box_ymin_absolute / image_h
+            box_width_relative = box_width_absolute / image_w
+            box_height_relative = box_height_absolute / image_h
+            
+            output_bbox = [box_xmin_relative,box_ymin_relative,
+                           box_width_relative,box_height_relative]
+            
+            if truncate_to_standard_md_precision:
+                output_bbox = ct_utils.truncate_float_array(output_bbox,COORD_DIGITS)
+                
+            output_det['bbox'] = output_bbox
+            im['detections'].append(output_det)
+            
+        # ...for each detection            
+                
+        output_images.append(im)
+        
+    # ...for each image file
+    
+    d = {}
+    d['images'] = output_images
+    d['info'] = {'format_version':1.3,'detector':detector_name}
+    d['detection_categories'] = {}
+        
+    for cat_id in yolo_category_id_to_name:
+        yolo_cat_id = int(cat_id)
+        if offset_yolo_class_ids:
+            yolo_cat_id += 1
+        d['detection_categories'][str(yolo_cat_id)] = yolo_category_id_to_name[cat_id]
+    
+    with open(output_file,'w') as f:
+        json.dump(d,f,indent=1)
+            
+# ...def yolo_json_output_to_md_output(...)
+    
+
+def yolo_txt_output_to_md_output(input_results_folder, 
+                                 image_folder,
+                                 output_file, 
+                                 detector_tag=None):
+    """
+    Converts a folder of YOLO-output .txt files to MD .json format.
+    
+    Less finished than the .json conversion function; this .txt conversion assumes 
+    a hard-coded mapping representing the standard MD categories (in MD indexing, 
+    1/2/3=animal/person/vehicle; in YOLO indexing, 0/1/2=animal/person/vehicle).
+    
+    Args:
+        input_results_folder (str): the folder containing YOLO-output .txt files
+        image_folder (str): the folder where images live, may be the same as
+            [input_results_folder]
+        output_file (str): the MD-formatted .json file to which we should write
+            results
+        detector_tag (str, optional): string to put in the 'detector' field in the
+            output file            
+    """
+    
+    assert os.path.isdir(input_results_folder)
+    assert os.path.isdir(image_folder)
+    
+    ## Enumerate results files and image files
+    
+    yolo_results_files = os.listdir(input_results_folder)
+    yolo_results_files = [f for f in yolo_results_files if f.lower().endswith('.txt')]
+    # print('Found {} results files'.format(len(yolo_results_files)))
+    
+    image_files = path_utils.find_images(image_folder,recursive=False)
+    image_files_relative = [os.path.basename(f) for f in image_files]
+    # print('Found {} images'.format(len(image_files)))
+            
+    image_files_relative_no_extension = [os.path.splitext(f)[0] for f in image_files_relative]
+    
+    ## Make sure that every results file corresponds to an image
+    
+    for f in yolo_results_files:
+        result_no_extension = os.path.splitext(f)[0]
+        assert result_no_extension in image_files_relative_no_extension
+    
+    ## Build MD output data
+    
+    # Map 0-indexed YOLO categories to 1-indexed MD categories
+    yolo_cat_map = { 0: 1, 1: 2, 2: 3 }
+    
+    images_entries = []
+
+    # image_fn = image_files_relative[0]
+    for image_fn in image_files_relative:
+        
+        image_name, ext = os.path.splitext(image_fn)        
+        label_fn = image_name + '.txt'
+        label_path = os.path.join(input_results_folder, label_fn)
+            
+        detections = []
+        
+        if not os.path.exists(label_path):
+            # This is assumed to be an image with no detections
+            pass
+        else:
+            with open(label_path, newline='') as f:
+                reader = csv.reader(f, delimiter=' ')
+                for row in reader:
+                    category = yolo_cat_map[int(row[0])]    
+                    api_box = ct_utils.convert_yolo_to_xywh([float(row[1]), float(row[2]), 
+                                                             float(row[3]), float(row[4])])
+    
+                    conf = ct_utils.truncate_float(float(row[5]), precision=4)
+                    
+                    detections.append({
+                        'category': str(category),
+                        'conf': conf,
+                        'bbox': ct_utils.truncate_float_array(api_box, precision=4)
+                    })
+                
+        images_entries.append({
+            'file': image_fn,
+            'detections': detections
+        })
+    
+    # ...for each image
+    
+    ## Save output file
+    
+    detector_string = 'converted_from_yolo_format'
+    
+    if detector_tag is not None:
+        detector_string = detector_tag
+        
+    output_content = {
+        'info': {
+            'detector': detector_string,
+            'detector_metadata': {},
+            'format_version': '1.3'
+        },
+        'detection_categories': {
+            '1': 'animal',
+            '2': 'person',
+            '3': 'vehicle'
+        },
+        'images': images_entries
+    }
+    
+    with open(output_file,'w') as f:
+        json.dump(output_content,f,indent=1)
+    
+# ...def yolo_txt_output_to_md_output(...)
+
+
+#%% Interactive driver
+
+if False:
+    
+    pass
+
+    #%%    
+    
+    input_results_folder = os.path.expanduser('~/tmp/model-version-experiments/pt-test-kru/exp/labels')
+    image_folder = os.path.expanduser('~/data/KRU-test')
+    output_file = os.path.expanduser('~/data/mdv5a-yolo-pt-kru.json')    
+    yolo_txt_output_to_md_output(input_results_folder,image_folder,output_file)
+
+
+#%% Command-line driver
+
+# TODO