postprocess_batch_results.py

"""

postprocess_batch_results.py

Given a .json or .csv file containing MD results, do one or more of the following:

* Sample detections/non-detections and render to HTML (when ground truth isn't
  available) (this is 99.9% of what this module is for)
* Evaluate detector precision/recall, optionally rendering results (requires
  ground truth)
* Sample true/false positives/negatives and render to HTML (requires ground
  truth)

Ground truth, if available, must be in COCO Camera Traps format:
    
https://github.com/agentmorris/MegaDetector/blob/main/megadetector/data_management/README.md#coco-camera-traps-format

"""

#%% Constants and imports

import argparse
import collections
import copy
import errno
import io
import os
import sys
import time
import uuid
import warnings
import random

from enum import IntEnum
from multiprocessing.pool import ThreadPool
from multiprocessing.pool import Pool
from functools import partial

import matplotlib.pyplot as plt
import numpy as np
import humanfriendly
import pandas as pd

from sklearn.metrics import precision_recall_curve, confusion_matrix, average_precision_score
from tqdm import tqdm

from megadetector.visualization import visualization_utils as vis_utils
from megadetector.visualization import plot_utils
from megadetector.utils.write_html_image_list import write_html_image_list
from megadetector.utils import path_utils
from megadetector.utils.ct_utils import args_to_object, sets_overlap
from megadetector.data_management.cct_json_utils import (CameraTrapJsonUtils, IndexedJsonDb)
from megadetector.postprocessing.load_api_results import load_api_results
from megadetector.detection.run_detector import get_typical_confidence_threshold_from_results

warnings.filterwarnings('ignore', '(Possibly )?corrupt EXIF data', UserWarning)


#%% Options

DEFAULT_NEGATIVE_CLASSES = ['empty']
DEFAULT_UNKNOWN_CLASSES = ['unknown', 'unlabeled', 'ambiguous']

# Make sure there is no overlap between the two sets, because this will cause
# issues in the code
assert not sets_overlap(DEFAULT_NEGATIVE_CLASSES, DEFAULT_UNKNOWN_CLASSES), (
        'Default negative and unknown classes cannot overlap.')


class PostProcessingOptions:
    """
    Options used to parameterize process_batch_results().
    """
    
    def __init__(self):
        
        ### Required inputs
    
        #: MD results .json file to process
        self.md_results_file = ''
        
        #: Folder to which we should write HTML output
        self.output_dir = ''
    
        ### Options
    
        #: Folder where images live (filenames in [md_results_file] should be relative to this folder)
        self.image_base_dir = '.'
    
        ## These apply only when we're doing ground-truth comparisons
        
        #: Optional .json file containing ground truth information
        self.ground_truth_json_file = ''
    
        #: List of classes we'll treat as negative (defaults to "empty", typically includes 
        #: classes like "blank", "misfire", etc.).
        #:
        #: Include the token "#NO_LABELS#" to indicate that an image with no annotations
        #: should be considered empty.
        self.negative_classes = DEFAULT_NEGATIVE_CLASSES
        
        #: List of classes we'll treat as neither positive nor negative (defaults to 
        #: "unknown", typically includes classes like "unidentifiable").
        self.unlabeled_classes = DEFAULT_UNKNOWN_CLASSES
    
        #: List of output sets that we should count, but not render images for.
        #:
        #: Typically used to preview sets with lots of empties, where you don't want to
        #: subset but also don't want to render 100,000 empty images.
        #:
        #: detections, non_detections
        #: detections_animal, detections_person, detections_vehicle
        self.rendering_bypass_sets = []
    
        #: If this is None, choose a confidence threshold based on the detector version.
        #:
        #: This can either be a float or a dictionary mapping category names (not IDs) to 
        #: thresholds.  The category "default" can be used to specify thresholds for 
        #: other categories.  Currently the use of a dict here is not supported when 
        #: ground truth is supplied.
        self.confidence_threshold = None
        
        #: Confidence threshold to apply to classification (not detection) results
        #:
        #: Only a float is supported here (unlike the "confidence_threshold" parameter, which
        #: can be a dict).    
        self.classification_confidence_threshold = 0.5
    
        #: Used for summary statistics only
        self.target_recall = 0.9
    
        #: Number of images to sample, -1 for "all images"
        self.num_images_to_sample = 500
    
        #: Random seed for sampling, or None
        self.sample_seed = 0 # None
    
        #: Image width for images in the HTML output
        self.viz_target_width = 800
    
        #: Line width (in pixels) for rendering detections
        self.line_thickness = 4
        
        #: Box expansion (in pixels) for rendering detections
        self.box_expansion = 0
    
        #: Job name to include in big letters in the output HTML
        self.job_name_string = None
        
        #: Model version string to include in the output HTML
        self.model_version_string = None
        
        #: Sort order for the output, should be one of "filename", "confidence", or "random"
        self.html_sort_order = 'filename'
       
        #: If True, images in the output HTML will be links back to the original images
        self.link_images_to_originals = True
        
        #: Optionally separate detections into categories (animal/vehicle/human)
        #: 
        #: Currently only supported when ground truth is unavailable
        self.separate_detections_by_category = True
    
        #: Optionally replace one or more strings in filenames with other strings;
        #: useful for taking a set of results generated for one folder structure
        #: and applying them to a slightly different folder structure.
        self.api_output_filename_replacements = {}
        
        #: Optionally replace one or more strings in filenames with other strings;
        #: useful for taking a set of results generated for one folder structure
        #: and applying them to a slightly different folder structure.
        self.ground_truth_filename_replacements = {}
    
        #: Allow bypassing API output loading when operating on previously-loaded
        #: results.  If present, this is a Pandas DataFrame.  Almost never useful.
        self.api_detection_results = None
        
        #: Allow bypassing API output loading when operating on previously-loaded
        #: results.  If present, this is a str --> obj dict.  Almost never useful.
        self.api_other_fields = None
    
        #: Should we also split out a separate report about the detections that were
        #: just below our main confidence threshold?
        #:
        #: Currently only supported when ground truth is unavailable.
        self.include_almost_detections = False
        
        #: Only a float is supported here (unlike the "confidence_threshold" parameter, which
        #: can be a dict).
        self.almost_detection_confidence_threshold = None
    
        #: Enable/disable rendering parallelization    
        self.parallelize_rendering = False
        
        #: Number of threads/processes to use for rendering parallelization
        self.parallelize_rendering_n_cores = 25
        
        #: Whether to use threads (True) or processes (False) for rendering parallelization
        self.parallelize_rendering_with_threads = True
        
        #: When classification results are present, should be sort alphabetically by class name (False)
        #: or in descending order by frequency (True)?
        self.sort_classification_results_by_count = False
        
        #: Should we split individual pages up into smaller pages if there are more than
        #: N images?
        self.max_figures_per_html_file = None
        
        #: Footer text for the index page
        # self.footer_text = '<br/><p style="font-size:80%;">Preview page created with the <a href="{}">MegaDetector Python package</a>.</p>'.\
        #    format('https://megadetector.readthedocs.io')
        self.footer_text = ''

    # ...__init__()
    
# ...PostProcessingOptions


class PostProcessingResults:
    """
    Return format from process_batch_results
    """
    
    def __init__(self):
        
        #: HTML file to which preview information was written
        self.output_html_file = ''
        
        #: Pandas Dataframe containing detection results
        self.api_detection_results = None
        
        #: str --> obj dictionary containing other information loaded from the results file
        self.api_other_fields = None


##%% Helper classes and functions

class DetectionStatus(IntEnum):
    """
    Flags used to mark images as positive or negative for P/R analysis
    (according to ground truth and/or detector output)
        
    :meta private:
    """
    
    DS_NEGATIVE = 0
    DS_POSITIVE = 1

    # Anything greater than this isn't clearly positive or negative
    DS_MAX_DEFINITIVE_VALUE = DS_POSITIVE

    # image has annotations suggesting both negative and positive
    DS_AMBIGUOUS = 2

    # image is not annotated or is annotated with 'unknown', 'unlabeled', ETC.
    DS_UNKNOWN = 3

    # image has not yet been assigned a state
    DS_UNASSIGNED = 4

    # In some analyses, we add an additional class that lets us look at
    # detections just below our main confidence threshold
    DS_ALMOST = 5


def _mark_detection_status(indexed_db,
                           negative_classes=DEFAULT_NEGATIVE_CLASSES,
                           unknown_classes=DEFAULT_UNKNOWN_CLASSES):
    """
    For each image in indexed_db.db['images'], add a '_detection_status' field
    to indicate whether to treat this image as positive, negative, ambiguous,
    or unknown.

    Makes modifications in-place.

    returns (n_negative, n_positive, n_unknown, n_ambiguous)
    """
    
    negative_classes = set(negative_classes)
    unknown_classes = set(unknown_classes)

    # count the # of images with each type of DetectionStatus
    n_unknown = 0
    n_ambiguous = 0
    n_positive = 0
    n_negative = 0

    print('Preparing ground-truth annotations')
    for im in tqdm(indexed_db.db['images']):

        image_id = im['id']
        annotations = indexed_db.image_id_to_annotations[image_id]
        categories = [ann['category_id'] for ann in annotations]
        category_names = set(indexed_db.cat_id_to_name[cat] for cat in categories)

        # Check whether this image has:
        # - unknown / unassigned-type labels
        # - negative-type labels
        # - positive labels (i.e., labels that are neither unknown nor negative)
        has_unknown_labels = sets_overlap(category_names, unknown_classes)
        has_negative_labels = sets_overlap(category_names, negative_classes)
        has_positive_labels = 0 < len(category_names - (unknown_classes | negative_classes))
        # assert has_unknown_labels is False, '{} has unknown labels'.format(annotations)

        # If there are no image annotations...
        if len(categories) == 0:
                        
            if '#NO_LABELS#' in negative_classes:
                n_negative += 1
                im['_detection_status'] = DetectionStatus.DS_NEGATIVE
            else:
                n_unknown += 1
                im['_detection_status'] = DetectionStatus.DS_UNKNOWN

            # n_negative += 1
            # im['_detection_status'] = DetectionStatus.DS_NEGATIVE

        # If the image has more than one type of labels, it's ambiguous
        # note: bools are automatically converted to 0/1, so we can sum
        elif (has_unknown_labels + has_negative_labels + has_positive_labels) > 1:
            n_ambiguous += 1
            im['_detection_status'] = DetectionStatus.DS_AMBIGUOUS

        # After the check above, we can be sure it's only one of positive,
        # negative, or unknown.
        #
        # Important: do not merge the following 'unknown' branch with the first
        # 'unknown' branch above, where we tested 'if len(categories) == 0'
        #
        # If the image has only unknown labels
        elif has_unknown_labels:
            n_unknown += 1
            im['_detection_status'] = DetectionStatus.DS_UNKNOWN

        # If the image has only negative labels
        elif has_negative_labels:
            n_negative += 1
            im['_detection_status'] = DetectionStatus.DS_NEGATIVE

        # If the images has only positive labels
        elif has_positive_labels:
            n_positive += 1
            im['_detection_status'] = DetectionStatus.DS_POSITIVE

            # Annotate the category, if it is unambiguous
            if len(category_names) == 1:
                im['_unambiguous_category'] = list(category_names)[0]

        else:
            raise Exception('Invalid detection state')

    # ...for each image

    return n_negative, n_positive, n_unknown, n_ambiguous

# ..._mark_detection_status()


def is_sas_url(s) -> bool:
    """
    Placeholder for a more robust way to verify that a link is a SAS URL.
    99.999% of the time this will suffice for what we're using it for right now.
    
    :meta private:
    """
    
    return (s.startswith(('http://', 'https://')) and ('core.windows.net' in s)
            and ('?' in s))


def relative_sas_url(folder_url, relative_path):
    """
    Given a container-level or folder-level SAS URL, create a SAS URL to the
    specified relative path.
    
    :meta private:
    """
    
    relative_path = relative_path.replace('%','%25')
    relative_path = relative_path.replace('#','%23')
    relative_path = relative_path.replace(' ','%20')

    if not is_sas_url(folder_url):
        return None
    tokens = folder_url.split('?')
    assert len(tokens) == 2
    if not tokens[0].endswith('/'):
        tokens[0] = tokens[0] + '/'
    if relative_path.startswith('/'):
        relative_path = relative_path[1:]
    return tokens[0] + relative_path + '?' + tokens[1]


def _render_bounding_boxes(
        image_base_dir,
        image_relative_path,
        display_name,
        detections,
        res,
        ground_truth_boxes=None,
        detection_categories=None,
        classification_categories=None,
        options=None):
    """
    Renders detection bounding boxes on a single image.
    
    This is an internal function; if you want tools for rendering boxes on images, see 
    visualization.visualization_utils.

    The source image is:

        image_base_dir / image_relative_path

    The target image is, for example:

        [options.output_dir] / 
        ['detections' or 'non_detections'] / 
        [filename with slashes turned into tildes]

    "res" is a result type, e.g. "detections", "non-detections"; this determines the
    output folder for the rendered image.
    
    Only very preliminary support is provided for ground truth box rendering.
    
    Returns the html info struct for this image in the format that's used for
    write_html_image_list.
    
    :meta private:
    """

    if options is None:
        options = PostProcessingOptions()

    # Leaving code in place for reading from blob storage, may support this
    # in the future.
    """
    stream = io.BytesIO()
    _ = blob_service.get_blob_to_stream(container_name, image_id, stream)
    # resize is to display them in this notebook or in the HTML more quickly
    image = Image.open(stream).resize(viz_size)
    """

    image_full_path = None
    
    if res in options.rendering_bypass_sets:

        sample_name = res + '_' + path_utils.flatten_path(image_relative_path)

    else:

        if is_sas_url(image_base_dir):
            image_full_path = relative_sas_url(image_base_dir, image_relative_path)
        else:
            image_full_path = os.path.join(image_base_dir, image_relative_path)

        # os.path.isfile() is slow when mounting remote directories; much faster
        # to just try/except on the image open.
        try:
            image = vis_utils.open_image(image_full_path)
        except:
            print('Warning: could not open image file {}'.format(image_full_path))
            image = None
            # return ''
        
        # Render images to a flat folder
        sample_name = res + '_' + path_utils.flatten_path(image_relative_path)
        fullpath = os.path.join(options.output_dir, res, sample_name)

        if image is not None:
            
            original_size = image.size
            
            if options.viz_target_width is not None:
                image = vis_utils.resize_image(image, options.viz_target_width)
    
            if ground_truth_boxes is not None and len(ground_truth_boxes) > 0:
                
                # Create class labels like "gt_1" or "gt_27"
                gt_classes = [0] * len(ground_truth_boxes)
                label_map = {0:'ground truth'}
                # for i_box,box in enumerate(ground_truth_boxes):
                #    gt_classes.append('_' + str(box[-1]))
                vis_utils.render_db_bounding_boxes(ground_truth_boxes, gt_classes, image,
                                                   original_size=original_size,label_map=label_map,
                                                   thickness=4,expansion=4)
        
            # render_detection_bounding_boxes expects either a float or a dict mapping
            # category IDs to names.
            if isinstance(options.confidence_threshold,float):
                rendering_confidence_threshold = options.confidence_threshold
            else:
                category_ids = set()
                for d in detections:
                    category_ids.add(d['category'])
                rendering_confidence_threshold = {}
                for category_id in category_ids:
                    rendering_confidence_threshold[category_id] = \
                        _get_threshold_for_category_id(category_id, options, detection_categories)
                
            vis_utils.render_detection_bounding_boxes(
                detections, image,
                label_map=detection_categories,
                classification_label_map=classification_categories,
                confidence_threshold=rendering_confidence_threshold,
                thickness=options.line_thickness,
                expansion=options.box_expansion)
    
            try:
                image.save(fullpath)
            except OSError as e:
                # errno.ENAMETOOLONG doesn't get thrown properly on Windows, so
                # we awkwardly check against a hard-coded limit
                if (e.errno == errno.ENAMETOOLONG) or (len(fullpath) >= 259):
                    extension = os.path.splitext(sample_name)[1]
                    sample_name = res + '_' + str(uuid.uuid4()) + extension
                    image.save(os.path.join(options.output_dir, res, sample_name))
                else:
                    raise

    # Use slashes regardless of os
    file_name = '{}/{}'.format(res,sample_name)

    info = {
        'filename': file_name,
        'title': display_name,
        'textStyle':\
         'font-family:verdana,arial,calibri;font-size:80%;text-align:left;margin-top:20;margin-bottom:5'
    }
    
    # Optionally add links back to the original images
    if options.link_images_to_originals and (image_full_path is not None):
                
        # Handling special characters in links has been pushed down into
        # write_html_image_list
        #
        # link_target = image_full_path.replace('\\','/')
        # link_target  = urllib.parse.quote(link_target)
        link_target = image_full_path
        info['linkTarget'] = link_target 
        
    return info

# ..._render_bounding_boxes


def _prepare_html_subpages(images_html, output_dir, options=None):
    """
    Write out a series of html image lists, e.g. the "detections" or "non-detections"
    pages.

    image_html is a dictionary mapping an html page name (e.g. "detections_animal") to 
    a list of image structs friendly to write_html_image_list.
    
    Returns a dictionary mapping category names to image counts.
    """
    
    if options is None:
        options = PostProcessingOptions()

    # Count items in each category
    image_counts = {}
    for res, array in images_html.items():
        image_counts[res] = len(array)

    # Optionally sort by filename before writing to html
    if options.html_sort_order == 'filename':
        images_html_sorted = {}
        for res, array in images_html.items():
            sorted_array = sorted(array, key=lambda x: x['filename'])
            images_html_sorted[res] = sorted_array
        images_html = images_html_sorted
    
    # Optionally sort by confidence before writing to html
    elif options.html_sort_order == 'confidence':
        images_html_sorted = {}
        for res, array in images_html.items():
            
            if not all(['max_conf' in d for d in array]):
                print("Warning: some elements in the {} page don't have confidence values, can't sort by confidence".format(res))
            else:
                sorted_array = sorted(array, key=lambda x: x['max_conf'], reverse=True)
                images_html_sorted[res] = sorted_array
                images_html = images_html_sorted
        
    else:
        assert options.html_sort_order == 'random',\
            'Unrecognized sort order {}'.format(options.html_sort_order)
        images_html_sorted = {}
        for res, array in images_html.items():
            sorted_array = random.sample(array,len(array))
            images_html_sorted[res] = sorted_array
        images_html = images_html_sorted
        
    # Write the individual HTML files
    for res, array in images_html.items():
        
        html_image_list_options = {}    
        html_image_list_options['maxFiguresPerHtmlFile'] = options.max_figures_per_html_file
        html_image_list_options['headerHtml'] = '<h1>{}</h1>'.format(res.upper())
        html_image_list_options['pageTitle'] = '{}'.format(res.lower())
        
        # Don't write empty pages
        if len(array) == 0:
            continue
        else:
            write_html_image_list(
                filename=os.path.join(output_dir, '{}.html'.format(res)),
                images=array,
                options=html_image_list_options)

    return image_counts

# ..._prepare_html_subpages()


def _get_threshold_for_category_name(category_name,options):
    """
    Determines the confidence threshold we should use for a specific category name.
    """
    
    if isinstance(options.confidence_threshold,float):
        return options.confidence_threshold
    else:
        assert isinstance(options.confidence_threshold,dict), \
            'confidence_threshold must either be a float or a dict'
                           
    if category_name in options.confidence_threshold:
        
        return options.confidence_threshold[category_name]
    
    else:
        assert 'default' in options.confidence_threshold, \
            'category {} not in confidence_threshold dict, and no default supplied'.format(
                category_name)
        return options.confidence_threshold['default']

    
def _get_threshold_for_category_id(category_id,options,detection_categories):
    """
    Determines the confidence threshold we should use for a specific category ID.
    
    [detection_categories] is a dict mapping category IDs to names.
    """
    
    if isinstance(options.confidence_threshold,float):        
        return options.confidence_threshold
    
    assert category_id in detection_categories, \
        'Invalid category ID {}'.format(category_id)
        
    category_name = detection_categories[category_id]
    
    return _get_threshold_for_category_name(category_name,options)
    
    
def _get_positive_categories(detections,options,detection_categories):
    """
    Gets a sorted list of unique categories (as string IDs) above the threshold for this image
    
    [detection_categories] is a dict mapping category IDs to names.
    """
    
    positive_categories = set()
    for d in detections:
        threshold = _get_threshold_for_category_id(d['category'], options, detection_categories)
        if d['conf'] >= threshold:
            positive_categories.add(d['category'])
    return sorted(positive_categories)


def _has_positive_detection(detections,options,detection_categories):
    """
    Determines whether any positive detections are present in the detection list
    [detections].
    """    
    
    found_positive_detection = False
    for d in detections:
        threshold = _get_threshold_for_category_id(d['category'], options, detection_categories)
        if d['conf'] >= threshold:
            found_positive_detection = True
            break
    return found_positive_detection
        

def _render_image_no_gt(file_info,detection_categories_to_results_name,
                       detection_categories,classification_categories,
                       options):
    """
    Renders an image (with no ground truth information)
    
    Returns a list of rendering structs, where the first item is a category (e.g. "detections_animal"), 
    and  the second is a dict of information needed for rendering.  E.g.:
        
    [['detections_animal', 
    {
     'filename': 'detections_animal/detections_animal_blah~01060415.JPG', 
     'title': '<b>Result type</b>: detections_animal, 
               <b>Image</b>: blah\\01060415.JPG,
               <b>Max conf</b>: 0.897',
      'textStyle': 'font-family:verdana,arial,calibri;font-size:80%;text-align:left;margin-top:20;margin-bottom:5',
      'linkTarget': 'full_path_to_%5C01060415.JPG'
    }]]
     
    When no classification data is present, this list will always be length-1.  When
    classification data is present, an image may appear in multiple categories.
    
    Populates the 'max_conf' field of the first element of the list.
    
    Returns None if there are any errors.
    """
    
    image_relative_path = file_info[0]
    max_conf = file_info[1]
    detections = file_info[2]

    # Determine whether any positive detections are present (using a threshold that
    # may vary by category)
    found_positive_detection = _has_positive_detection(detections,options,detection_categories)
        
    detection_status = DetectionStatus.DS_UNASSIGNED
    if found_positive_detection:
        detection_status = DetectionStatus.DS_POSITIVE
    else:
        if options.include_almost_detections:
            if max_conf >= options.almost_detection_confidence_threshold:
                detection_status = DetectionStatus.DS_ALMOST
            else:
                detection_status = DetectionStatus.DS_NEGATIVE
        else:
            detection_status = DetectionStatus.DS_NEGATIVE

    if detection_status == DetectionStatus.DS_POSITIVE:
        if options.separate_detections_by_category:
            positive_categories = tuple(_get_positive_categories(detections,options,detection_categories))
            if positive_categories not in detection_categories_to_results_name:
                raise ValueError('Error: {} not in category mapping (file {})'.format(
                    str(positive_categories),image_relative_path))
            res = detection_categories_to_results_name[positive_categories]
        else:
            res = 'detections'

    elif detection_status == DetectionStatus.DS_NEGATIVE:
        res = 'non_detections'
    else:
        assert detection_status == DetectionStatus.DS_ALMOST
        res = 'almost_detections'

    display_name = '<b>Result type</b>: {}, <b>Image</b>: {}, <b>Max conf</b>: {:0.3f}'.format(
        res, image_relative_path, max_conf)

    rendering_options = copy.copy(options)
    if detection_status == DetectionStatus.DS_ALMOST:
        rendering_options.confidence_threshold = \
            rendering_options.almost_detection_confidence_threshold
            
    rendered_image_html_info = _render_bounding_boxes(
        image_base_dir=options.image_base_dir,
        image_relative_path=image_relative_path,
        display_name=display_name,
        detections=detections,
        res=res,
        ground_truth_boxes=None,
        detection_categories=detection_categories,
        classification_categories=classification_categories,
        options=rendering_options)

    image_result = None

    if len(rendered_image_html_info) > 0:

        image_result = [[res, rendered_image_html_info]]
        classes_rendered_this_image = set()
        max_conf = 0
        
        for det in detections:
            
            if det['conf'] > max_conf:
                max_conf = det['conf']

            if ('classifications' in det) and (len(det['classifications']) > 0):

                # This is a list of [class,confidence] pairs, sorted by confidence
                classifications = det['classifications']
                top1_class_id = classifications[0][0]
                top1_class_name = classification_categories[top1_class_id]
                top1_class_score = classifications[0][1]

                # If we either don't have a confidence threshold, or we've met our
                # confidence threshold
                if (options.classification_confidence_threshold < 0) or \
                    (top1_class_score >= options.classification_confidence_threshold):
                    class_string = 'class_{}'.format(top1_class_name)                    
                else:
                    class_string = 'class_unreliable'
                
                if class_string not in classes_rendered_this_image:
                    image_result.append([class_string,
                                         rendered_image_html_info])
                    classes_rendered_this_image.add(class_string)

            # ...if this detection has classification info

        # ...for each detection

        image_result[0][1]['max_conf'] = max_conf
        
    # ...if we got valid rendering info back from _render_bounding_boxes()
    
    return image_result

# ...def _render_image_no_gt()
    

def _render_image_with_gt(file_info,ground_truth_indexed_db,
                         detection_categories,classification_categories,options):
    """
    Render an image with ground truth information.  See _render_image_no_gt for return
    data format.
    """
    
    image_relative_path = file_info[0]
    max_conf = file_info[1]
    detections = file_info[2]

    # This should already have been normalized to either '/' or '\'

    image_id = ground_truth_indexed_db.filename_to_id.get(image_relative_path, None)
    if image_id is None:
        print('Warning: couldn''t find ground truth for image {}'.format(image_relative_path))
        return None

    image = ground_truth_indexed_db.image_id_to_image[image_id]
    annotations = ground_truth_indexed_db.image_id_to_annotations[image_id]

    ground_truth_boxes = []
    for ann in annotations:
        if 'bbox' in ann:
            ground_truth_box = [x for x in ann['bbox']]
            ground_truth_box.append(ann['category_id'])
            ground_truth_boxes.append(ground_truth_box)
    
    gt_status = image['_detection_status']

    gt_presence = bool(gt_status)

    gt_classes = CameraTrapJsonUtils.annotations_to_class_names(
        annotations, ground_truth_indexed_db.cat_id_to_name)
    gt_class_summary = ','.join(gt_classes)

    if gt_status > DetectionStatus.DS_MAX_DEFINITIVE_VALUE:
        print(f'Skipping image {image_id}, does not have a definitive '
              f'ground truth status (status: {gt_status}, classes: {gt_class_summary})')
        return None

    detected = _has_positive_detection(detections, options, detection_categories)

    if gt_presence and detected:
        if '_classification_accuracy' not in image.keys():
            res = 'tp'
        elif np.isclose(1, image['_classification_accuracy']):
            res = 'tpc'
        else:
            res = 'tpi'
    elif not gt_presence and detected:
        res = 'fp'
    elif gt_presence and not detected:
        res = 'fn'
    else:
        res = 'tn'

    display_name = '<b>Result type</b>: {}, <b>Presence</b>: {}, <b>Class</b>: {}, <b>Max conf</b>: {:0.3f}%, <b>Image</b>: {}'.format(
        res.upper(), str(gt_presence), gt_class_summary,
        max_conf * 100, image_relative_path)

    rendered_image_html_info = _render_bounding_boxes(
        image_base_dir=options.image_base_dir,
        image_relative_path=image_relative_path,
        display_name=display_name,
        detections=detections,
        res=res,
        ground_truth_boxes=ground_truth_boxes,
        detection_categories=detection_categories,
        classification_categories=classification_categories,
        options=options)

    image_result = None
    if len(rendered_image_html_info) > 0:
        image_result = [[res, rendered_image_html_info]]
        for gt_class in gt_classes:
            image_result.append(['class_{}'.format(gt_class), rendered_image_html_info])

    return image_result

# ...def _render_image_with_gt()

    
#%% Main function

def process_batch_results(options):
    """
    Given a .json or .csv file containing MD results, do one or more of the following:

    * Sample detections/non-detections and render to HTML (when ground truth isn't
      available) (this is 99.9% of what this module is for)
    * Evaluate detector precision/recall, optionally rendering results (requires
      ground truth)
    * Sample true/false positives/negatives and render to HTML (requires ground
      truth)

    Ground truth, if available, must be in COCO Camera Traps format:
        
    https://github.com/agentmorris/MegaDetector/blob/main/megadetector/data_management/README.md#coco-camera-traps-format

    Args:
        options (PostProcessingOptions): everything we need to render a preview/analysis for
            this set of results; see the PostProcessingOptions class for details.
           
    Returns:
        PostProcessingResults: information about the results/preview, most importantly the 
        HTML filename of the output.  See the PostProcessingResults class for details.
    """
    ppresults = PostProcessingResults()

    ##%% Expand some options for convenience

    output_dir = options.output_dir


    ##%% Prepare output dir

    os.makedirs(output_dir, exist_ok=True)


    ##%% Load ground truth if available

    ground_truth_indexed_db = None

    if (options.ground_truth_json_file is not None) and (len(options.ground_truth_json_file) > 0):
        assert (options.confidence_threshold is None) or (isinstance(options.confidence_threshold,float)), \
            'Variable confidence thresholds are not supported when supplying ground truth'
            
    if (options.ground_truth_json_file is not None) and (len(options.ground_truth_json_file) > 0):

        if options.separate_detections_by_category:
            print("Warning: I don't know how to separate categories yet when doing " + \
                  "a P/R analysis, disabling category separation")
            options.separate_detections_by_category = False

        ground_truth_indexed_db = IndexedJsonDb(
            options.ground_truth_json_file, b_normalize_paths=True,
            filename_replacements=options.ground_truth_filename_replacements)

        # Mark images in the ground truth as positive or negative
        n_negative, n_positive, n_unknown, n_ambiguous = _mark_detection_status(
            ground_truth_indexed_db, negative_classes=options.negative_classes,
            unknown_classes=options.unlabeled_classes)
        print(f'Finished loading and indexing ground truth: {n_negative} '
              f'negative, {n_positive} positive, {n_unknown} unknown, '
              f'{n_ambiguous} ambiguous')

        if n_positive == 0:
            print('\n*** Warning: no positives found in ground truth, analysis won\'t be very meaningful ***\n')
        if n_negative == 0:
            print('\n*** Warning: no negatives found in ground truth, analysis won\'t be very meaningful ***\n')
        if n_ambiguous > 0:
            print('\n*** Warning: {} images with ambiguous positive/negative status found in ground truth ***\n'.format(
                n_ambiguous))

    ##%% Load detection (and possibly classification) results

    # If the caller hasn't supplied results, load them
    if options.api_detection_results is None:
        detections_df, other_fields = load_api_results(
            options.md_results_file, force_forward_slashes=True,
            filename_replacements=options.api_output_filename_replacements)
        ppresults.api_detection_results = detections_df
        ppresults.api_other_fields = other_fields        

    else:
        print('Bypassing detection results loading...')
        assert options.api_other_fields is not None
        detections_df = options.api_detection_results
        other_fields = options.api_other_fields

    # Determine confidence thresholds if necessary
    
    if options.confidence_threshold is None:
        options.confidence_threshold = \
            get_typical_confidence_threshold_from_results(other_fields)
        print('Choosing default confidence threshold of {} based on MD version'.format(
            options.confidence_threshold))    
            
    if options.almost_detection_confidence_threshold is None and options.include_almost_detections:
        assert isinstance(options.confidence_threshold,float), \
            'If you are using a dictionary of confidence thresholds and almost-detections are enabled, ' + \
            'you need to supply a threshold for almost detections.'
        options.almost_detection_confidence_threshold = options.confidence_threshold - 0.05
        if options.almost_detection_confidence_threshold < 0:
            options.almost_detection_confidence_threshold = 0
            
    # Remove rows with inference failures (typically due to corrupt images)
    n_failures = 0
    if 'failure' in detections_df.columns:
        n_failures = detections_df['failure'].count()
        print('Ignoring {} failed images'.format(n_failures))
        # Explicitly forcing a copy() operation here to suppress "trying to be set
        # on a copy" warnings (and associated risks) below.
        detections_df = detections_df[detections_df['failure'].isna()].copy()
        
    assert other_fields is not None

    detection_categories = other_fields['detection_categories']
    
    # Convert keys and values to lowercase
    classification_categories = other_fields.get('classification_categories', {})
    if classification_categories is not None:
        classification_categories = {
            k.lower(): v.lower()
            for k, v in classification_categories.items()
        }

    # Count detections and almost-detections for reporting purposes
    n_positives = 0
    n_almosts = 0
    
    for i_row,row in tqdm(detections_df.iterrows(),total=len(detections_df)):
        
        detections = row['detections']
        max_conf = row['max_detection_conf']
        if _has_positive_detection(detections, options, detection_categories):
            n_positives += 1
        elif (options.almost_detection_confidence_threshold is not None) and \
             (max_conf >= options.almost_detection_confidence_threshold):
            n_almosts += 1        
        
    print(f'Finished loading and preprocessing {len(detections_df)} rows '
          f'from detector output, predicted {n_positives} positives.')

    if options.include_almost_detections:
        print('...and {} almost-positives'.format(n_almosts))


    ##%% Find descriptive metadata to include at the top of the page

    if options.job_name_string is not None:
        job_name_string = options.job_name_string
    else:
        # This is rare; it only happens during debugging when the caller
        # is supplying already-loaded MD results.
        if options.md_results_file is None:
            job_name_string = 'unknown'
        else:
            job_name_string = os.path.basename(options.md_results_file)
    
    if options.model_version_string is not None:
        model_version_string = options.model_version_string
    else:
        
        if 'info' not in other_fields or 'detector' not in other_fields['info']:
            print('No model metadata supplied, assuming MDv4')
            model_version_string = 'MDv4 (assumed)'
        else:            
            model_version_string = other_fields['info']['detector']
    
        
    ##%% If we have ground truth, remove images we can't match to ground truth

    if ground_truth_indexed_db is not None:

        b_match = detections_df['file'].isin(
            ground_truth_indexed_db.filename_to_id)
        print(f'Confirmed filename matches to ground truth for {sum(b_match)} '
              f'of {len(detections_df)} files')

        detections_df = detections_df[b_match]
        detector_files = detections_df['file'].tolist()

        assert len(detector_files) > 0, (
            'No detection files available, possible path issue?')

        print('Trimmed detection results to {} files'.format(len(detector_files)))


    ##%% (Optionally) sample from the full set of images

    images_to_visualize = detections_df

    if options.num_images_to_sample is not None and options.num_images_to_sample > 0:
        images_to_visualize = images_to_visualize.sample(
            n=min(options.num_images_to_sample, len(images_to_visualize)),
            random_state=options.sample_seed)

    output_html_file = ''

    style_header = """<head>    
        <title>Detection results preview</title>
        <style type="text/css">
        a { text-decoration: none; }
        body { font-family: segoe ui, calibri, "trebuchet ms", verdana, arial, sans-serif; }
        div.contentdiv { margin-left: 20px; }
        </style>
        </head>"""


    ##%% Fork here depending on whether or not ground truth is available

    # If we have ground truth, we'll compute precision/recall and sample tp/fp/tn/fn.
    #
    # Otherwise we'll just visualize detections/non-detections.

    if ground_truth_indexed_db is not None:

        ##%% Detection evaluation: compute precision/recall

        # numpy array of maximum confidence values
        p_detection = detections_df['max_detection_conf'].values
        n_detection_values = len(p_detection)

        # numpy array of bools (0.0/1.0), and -1 as null value
        gt_detections = np.zeros(n_detection_values, dtype=float)

        n_positive = 0
        n_negative = 0
        
        for i_detection, fn in enumerate(detector_files):
            
            image_id = ground_truth_indexed_db.filename_to_id[fn]
            image = ground_truth_indexed_db.image_id_to_image[image_id]
            detection_status = image['_detection_status']

            if detection_status == DetectionStatus.DS_NEGATIVE:
                gt_detections[i_detection] = 0.0
                n_negative += 1
            elif detection_status == DetectionStatus.DS_POSITIVE:
                gt_detections[i_detection] = 1.0
                n_positive += 1
            else:
                gt_detections[i_detection] = -1.0

        print('Of {} ground truth values, found {} positives and {} negatives'.format(
            len(detections_df),n_positive,n_negative))
        
        # Don't include ambiguous/unknown ground truth in precision/recall analysis
        b_valid_ground_truth = gt_detections >= 0.0

        p_detection_pr = p_detection[b_valid_ground_truth]
        gt_detections_pr = (gt_detections[b_valid_ground_truth] == 1.)

        print('Including {} of {} values in p/r analysis'.format(np.sum(b_valid_ground_truth),
              len(b_valid_ground_truth)))

        precisions, recalls, thresholds = precision_recall_curve(gt_detections_pr, p_detection_pr)

        # For completeness, include the result at a confidence threshold of 1.0
        thresholds = np.append(thresholds, [1.0])

        precisions_recalls = pd.DataFrame(data={
            'confidence_threshold': thresholds,
            'precision': precisions,
            'recall': recalls
        })

        # Compute and print summary statistics
        average_precision = average_precision_score(gt_detections_pr, p_detection_pr)
        print('Average precision: {:.1%}'.format(average_precision))

        # Thresholds go up throughout precisions/recalls/thresholds; find the last
        # value where recall is at or above target.  That's our precision @ target recall.
        
        i_above_target_recall = (np.where(recalls >= options.target_recall))
        
        # np.where returns a tuple of arrays, but in this syntax where we're 
        # comparing an array with a scalar, there will only be one element.
        assert len (i_above_target_recall) == 1
        
        # Convert back to a list
        i_above_target_recall = i_above_target_recall[0].tolist()
        
        if len(i_above_target_recall) == 0:
            precision_at_target_recall = 0.0
        else:
            precision_at_target_recall = precisions[i_above_target_recall[-1]]
        print('Precision at {:.1%} recall: {:.1%}'.format(options.target_recall,
                                                          precision_at_target_recall))

        cm_predictions = np.array(p_detection_pr) > options.confidence_threshold
        cm = confusion_matrix(gt_detections_pr, cm_predictions, labels=[False,True])

        # Flatten the confusion matrix
        tn, fp, fn, tp = cm.ravel()

        precision_at_confidence_threshold = tp / (tp + fp)
        recall_at_confidence_threshold = tp / (tp + fn)
        f1 = 2.0 * (precision_at_confidence_threshold * recall_at_confidence_threshold) / \
            (precision_at_confidence_threshold + recall_at_confidence_threshold)

        print('At a confidence threshold of {:.1%}, precision={:.1%}, recall={:.1%}, f1={:.1%}'.format(
                options.confidence_threshold, precision_at_confidence_threshold,
                recall_at_confidence_threshold, f1))

        ##%% Collect classification results, if they exist

        classifier_accuracies = []

        # Mapping of classnames to idx for the confusion matrix.
        #
        # The lambda is actually kind of a hack, because we use assume that
        # the following code does not reassign classname_to_idx
        classname_to_idx = collections.defaultdict(lambda: len(classname_to_idx))

        # Confusion matrix as defaultdict of defaultdict
        #
        # Rows / first index is ground truth, columns / second index is predicted category
        classifier_cm = collections.defaultdict(lambda: collections.defaultdict(lambda: 0))

        # i_detection = 0; fn = detector_files[i_detection]; print(fn)
        assert len(detector_files) == len(detections_df)
        for i_detection, fn in enumerate(detector_files):

            image_id = ground_truth_indexed_db.filename_to_id[fn]
            image = ground_truth_indexed_db.image_id_to_image[image_id]
            detections = detections_df['detections'].iloc[i_detection]
            pred_class_ids = [det['classifications'][0][0] \
                for det in detections if 'classifications' in det.keys()]
            pred_classnames = [classification_categories[pd] for pd in pred_class_ids]

            # If this image has classification predictions, and an unambiguous class
            # annotated, and is a positive image...
            if len(pred_classnames) > 0 \
                    and '_unambiguous_category' in image.keys() \
                    and image['_detection_status'] == DetectionStatus.DS_POSITIVE:

                # The unambiguous category, we make this a set for easier handling afterward
                gt_categories = set([image['_unambiguous_category']])
                pred_categories = set(pred_classnames)

                # Compute the accuracy as intersection of union,
                # i.e. (# of categories in both prediction and GT)
                #      divided by (# of categories in either prediction or GT
                #
                # In case of only one GT category, the result will be 1.0, if
                # prediction is one category and this category matches GT
                #
                # It is 1.0/(# of predicted top-1 categories), if the GT is
                # one of the predicted top-1 categories.
                #
                # It is 0.0, if none of the predicted categories is correct

                classifier_accuracies.append(
                    len(gt_categories & pred_categories)
                    / len(gt_categories | pred_categories)
                )
                image['_classification_accuracy'] = classifier_accuracies[-1]

                # Distribute this accuracy across all predicted categories in the
                # confusion matrix
                assert len(gt_categories) == 1
                gt_class_idx = classname_to_idx[list(gt_categories)[0]]
                for pred_category in pred_categories:
                    pred_class_idx = classname_to_idx[pred_category]
                    classifier_cm[gt_class_idx][pred_class_idx] += 1

        # ...for each file in the detection results

        # If we have classification results
        if len(classifier_accuracies) > 0:

            # Build confusion matrix as array from classifier_cm
            all_class_ids = sorted(classname_to_idx.values())
            classifier_cm_array = np.array(
                [[classifier_cm[r_idx][c_idx] for c_idx in all_class_ids] for \
                 r_idx in all_class_ids], dtype=float)
            classifier_cm_array /= (classifier_cm_array.sum(axis=1, keepdims=True) + 1e-7)

            # Print some statistics
            print('Finished computation of {} classification results'.format(
                len(classifier_accuracies)))
            print('Mean accuracy: {}'.format(np.mean(classifier_accuracies)))

            # Prepare confusion matrix output

            # Get confusion matrix as string
            sio = io.StringIO()
            np.savetxt(sio, classifier_cm_array * 100, fmt='%5.1f')
            cm_str = sio.getvalue()
            # Get fixed-size classname for each idx
            idx_to_classname = {v:k for k,v in classname_to_idx.items()}
            classname_list = [idx_to_classname[idx] for idx in sorted(classname_to_idx.values())]
            classname_headers = ['{:<5}'.format(cname[:5]) for cname in classname_list]

            # Prepend class name on each line and add to the top
            cm_str_lines = [' ' * 16 + ' '.join(classname_headers)]
            cm_str_lines += ['{:>15}'.format(cn[:15]) + ' ' + cm_line for cn, cm_line in \
                             zip(classname_list, cm_str.splitlines())]

            # Print formatted confusion matrix
            if False:
                # Actually don't, this gets really messy in all but the widest consoles
                print('Confusion matrix: ')
                print(*cm_str_lines, sep='\n')

            # Plot confusion matrix

            # To manually add more space at bottom: plt.rcParams['figure.subplot.bottom'] = 0.1
            #
            # Add 0.5 to figsize for every class. For two classes, this will result in
            # fig = plt.figure(figsize=[4,4])
            fig = plot_utils.plot_confusion_matrix(
                classifier_cm_array,
                classname_list,
                normalize=False,
                title='Confusion matrix',
                cmap=plt.cm.Blues,
                vmax=1.0,
                use_colorbar=True,
                y_label=True)
            cm_figure_relative_filename = 'confusion_matrix.png'
            cm_figure_filename = os.path.join(output_dir, cm_figure_relative_filename)
            plt.savefig(cm_figure_filename)
            plt.close(fig)

        # ...if we have classification results


        ##%% Render output

        # Write p/r table to .csv file in output directory
        pr_table_filename = os.path.join(output_dir, 'prec_recall.csv')
        precisions_recalls.to_csv(pr_table_filename, index=False)

        # Write precision/recall plot to .png file in output directory
        t = 'Precision-Recall curve: AP={:0.1%}, P@{:0.1%}={:0.1%}'.format(
            average_precision, options.target_recall, precision_at_target_recall)
        fig = plot_utils.plot_precision_recall_curve(precisions, recalls, t)
        
        pr_figure_relative_filename = 'prec_recall.png'
        pr_figure_filename = os.path.join(output_dir, pr_figure_relative_filename)
        fig.savefig(pr_figure_filename)
        plt.close(fig)


        ##%% Sampling

        # Sample true/false positives/negatives with correct/incorrect top-1
        # classification and render to html

        # Accumulate html image structs (in the format expected by write_html_image_lists)
        # for each category, e.g. 'tp', 'fp', ..., 'class_bird', ...
        images_html = collections.defaultdict(list)
        
        # Add default entries by accessing them for the first time
        [images_html[res] for res in ['tp', 'tpc', 'tpi', 'fp', 'tn', 'fn']]
        for res in images_html.keys():
            os.makedirs(os.path.join(output_dir, res), exist_ok=True)

        image_count = len(images_to_visualize)

        # Each element will be a list of 2-tuples, with elements [collection name,html info struct]
        rendering_results = []

        # Each element will be a three-tuple with elements file,max_conf,detections
        files_to_render = []

        # Assemble the information we need for rendering, so we can parallelize without
        # dealing with Pandas
        # i_row = 0; row = images_to_visualize.iloc[0]
        for _, row in images_to_visualize.iterrows():

            # Filenames should already have been normalized to either '/' or '\'
            files_to_render.append([row['file'], row['max_detection_conf'], row['detections']])

        start_time = time.time()
        if options.parallelize_rendering:
            if options.parallelize_rendering_n_cores is None:                
                if options.parallelize_rendering_with_threads:
                    pool = ThreadPool()
                else:
                    pool = Pool()
            else:
                if options.parallelize_rendering_with_threads:
                    pool = ThreadPool(options.parallelize_rendering_n_cores)
                    worker_string = 'threads'
                else:
                    pool = Pool(options.parallelize_rendering_n_cores)
                    worker_string = 'processes'
                print('Rendering images with {} {}'.format(options.parallelize_rendering_n_cores,
                                                           worker_string))
                
            rendering_results = list(tqdm(pool.imap(
                partial(_render_image_with_gt,
                        ground_truth_indexed_db=ground_truth_indexed_db,
                        detection_categories=detection_categories,
                        classification_categories=classification_categories,
                        options=options), 
                files_to_render), total=len(files_to_render)))
        else:
            for file_info in tqdm(files_to_render):
                rendering_results.append(_render_image_with_gt(
                    file_info,ground_truth_indexed_db,
                    detection_categories,classification_categories,
                    options=options))
        elapsed = time.time() - start_time

        # Map all the rendering results in the list rendering_results into the
        # dictionary images_html, which maps category names to lists of results
        image_rendered_count = 0
        for rendering_result in rendering_results:
            if rendering_result is None:
                continue
            image_rendered_count += 1
            for assignment in rendering_result:
                images_html[assignment[0]].append(assignment[1])

        # Prepare the individual html image files
        image_counts = _prepare_html_subpages(images_html, output_dir, options)

        print('{} images rendered (of {})'.format(image_rendered_count,image_count))

        # Write index.html
        all_tp_count = image_counts['tp'] + image_counts['tpc'] + image_counts['tpi']
        total_count = all_tp_count + image_counts['tn'] + image_counts['fp'] + image_counts['fn']

        classification_detection_results = """&nbsp;&nbsp;&nbsp;&nbsp;<a href="tpc.html">with all correct top-1 predictions (TPC)</a> ({})<br/>
           &nbsp;&nbsp;&nbsp;&nbsp;<a href="tpi.html">with one or more incorrect top-1 prediction (TPI)</a> ({})<br/>
           &nbsp;&nbsp;&nbsp;&nbsp;<a href="tp.html">without classification evaluation</a><sup>*</sup> ({})<br/>""".format(
            image_counts['tpc'],
            image_counts['tpi'],
            image_counts['tp']
        )

        confidence_threshold_string = ''
        if isinstance(options.confidence_threshold,float):
            confidence_threshold_string = '{:.2%}'.format(options.confidence_threshold)
        else:
            confidence_threshold_string = str(options.confidence_threshold)
        
        index_page = """<html>        
        {}
        <body>
        <h2>Evaluation</h2>

        <h3>Job metadata</h3>
        
        <div class="contentdiv">
        <p>Job name: {}<br/>
        <p>Model version: {}</p>
        </div>
        
        <h3>Sample images</h3>
        <div class="contentdiv">
        <p>A sample of {} images, annotated with detections above confidence {}.</p>
        <a href="tp.html">True positives (TP)</a> ({}) ({:0.1%})<br/>
        CLASSIFICATION_PLACEHOLDER_1
        <a href="tn.html">True negatives (TN)</a> ({}) ({:0.1%})<br/>
        <a href="fp.html">False positives (FP)</a> ({}) ({:0.1%})<br/>
        <a href="fn.html">False negatives (FN)</a> ({}) ({:0.1%})<br/>
        CLASSIFICATION_PLACEHOLDER_2
        </div>
        """.format(
            style_header,job_name_string,model_version_string,
            image_count, confidence_threshold_string,
            all_tp_count, all_tp_count/total_count,
            image_counts['tn'], image_counts['tn']/total_count,
            image_counts['fp'], image_counts['fp']/total_count,
            image_counts['fn'], image_counts['fn']/total_count
        )

        index_page += """
            <h3>Detection results</h3>
            <div class="contentdiv">
            <p>At a confidence threshold of {}, precision={:0.1%}, recall={:0.1%}</p>
            <p><strong>Precision/recall summary for all {} images</strong></p><img src="{}"><br/>
            </div>
            """.format(
                confidence_threshold_string, precision_at_confidence_threshold, recall_at_confidence_threshold,
                len(detections_df), pr_figure_relative_filename
           )

        if len(classifier_accuracies) > 0:
            index_page = index_page.replace('CLASSIFICATION_PLACEHOLDER_1',classification_detection_results)
            index_page = index_page.replace('CLASSIFICATION_PLACEHOLDER_2',"""<p><sup>*</sup>We do not evaluate the classification result of images
                if the classification information is missing, if the image contains
                categories like &lsquo;empty&rsquo; or &lsquo;human&rsquo;, or if the image has multiple
                classification labels.</p>""")
        else:
            index_page = index_page.replace('CLASSIFICATION_PLACEHOLDER_1','')
            index_page = index_page.replace('CLASSIFICATION_PLACEHOLDER_2','')

        if len(classifier_accuracies) > 0:
            index_page += """
                <h3>Classification results</h3>
                <div class="contentdiv">
                <p>Classification accuracy: {:.2%}<br>
                The accuracy is computed only for images with exactly one classification label.
                The accuracy of an image is computed as 1/(number of unique detected top-1 classes),
                i.e. if the model detects multiple boxes with different top-1 classes, then the accuracy
                decreases and the image is put into 'TPI'.</p>
                <p>Confusion matrix:</p>
                <p><img src="{}"></p>
                <div style='font-family:monospace;display:block;'>{}</div>
                </div>
                """.format(
                    np.mean(classifier_accuracies),
                    cm_figure_relative_filename,
                    "<br>".join(cm_str_lines).replace(' ', '&nbsp;')
                )

        # Show links to each GT class
        #
        # We could do this without classification results; currently we don't.
        if len(classname_to_idx) > 0:

            index_page += '<h3>Images of specific classes</h3><br/><div class="contentdiv">'
            # Add links to all available classes
            for cname in sorted(classname_to_idx.keys()):
                index_page += '<a href="class_{0}.html">{0}</a> ({1})<br>'.format(
                    cname,
                    len(images_html['class_{}'.format(cname)]))
            index_page += '</div>'

        # Close body and html tags
        index_page += '{}</body></html>'.format(options.footer_text)
        output_html_file = os.path.join(output_dir, 'index.html')
        with open(output_html_file, 'w') as f:
            f.write(index_page)

        print('Finished writing html to {}'.format(output_html_file))

    # ...for each image


    ##%% Otherwise, if we don't have ground truth...

    else:

        ##%% Sample detections/non-detections

        # Accumulate html image structs (in the format expected by write_html_image_list)
        # for each category
        images_html = collections.defaultdict(list)
        
        # Add default entries by accessing them for the first time

        # Maps sorted tuples of detection category IDs (string ints) - e.g. ("1"), ("1", "4", "7") - to 
        # result set names, e.g. "detections_human", "detections_cat_truck".
        detection_categories_to_results_name = {}
        
        # Keep track of which categories are single-class (e.g. "animal") and which are
        # combinations (e.g. "animal_vehicle")
        detection_categories_to_category_count = {}
        
        # For the creation of a "non-detections" category
        images_html['non_detections']
        detection_categories_to_category_count['non_detections'] = 0
        
        
        if not options.separate_detections_by_category:
            # For the creation of a "detections" category
            images_html['detections']
            detection_categories_to_category_count['detections'] = 0            
        else:
            # Add a set of results for each category and combination of categories, e.g.
            # "detections_animal_vehicle".  When we're using this script for non-MegaDetector
            # results, this can generate lots of categories, e.g. detections_bear_bird_cat_dog_pig.
            # We'll keep that huge set of combinations in this map, but we'll only write
            # out links for the ones that are non-empty.            
            used_combinations = set()
            
            # row = images_to_visualize.iloc[0]
            for i_row, row in images_to_visualize.iterrows():
                detections_this_row = row['detections']
                above_threshold_category_ids_this_row = set()
                for detection in detections_this_row:
                    threshold = _get_threshold_for_category_id(detection['category'], options, detection_categories)
                    if detection['conf'] >= threshold:
                        above_threshold_category_ids_this_row.add(detection['category'])
                if len(above_threshold_category_ids_this_row) == 0:
                    continue
                sorted_categories_this_row = tuple(sorted(above_threshold_category_ids_this_row))
                used_combinations.add(sorted_categories_this_row)
            
            for sorted_subset in used_combinations:
                assert len(sorted_subset) > 0
                results_name = 'detections'
                for category_id in sorted_subset:
                    results_name = results_name + '_' + detection_categories[category_id]
                images_html[results_name]
                detection_categories_to_results_name[sorted_subset] = results_name
                detection_categories_to_category_count[results_name] = len(sorted_subset)                

        if options.include_almost_detections:
            images_html['almost_detections']
            detection_categories_to_category_count['almost_detections'] = 0

        # Create output directories
        for res in images_html.keys():
            os.makedirs(os.path.join(output_dir, res), exist_ok=True)

        image_count = len(images_to_visualize)
        
        # Each element will be a list of 2-tuples, with elements [collection name,html info struct]
        rendering_results = []

        # list of 3-tuples with elements (file, max_conf, detections)
        files_to_render = []

        # Assemble the information we need for rendering, so we can parallelize without
        # dealing with Pandas
        # i_row = 0; row = images_to_visualize.iloc[0]
        for _, row in images_to_visualize.iterrows():

            assert isinstance(row['detections'],list)
            
            # Filenames should already have been normalized to either '/' or '\'
            files_to_render.append([row['file'],
                                    row['max_detection_conf'],
                                    row['detections']])

        start_time = time.time()
        if options.parallelize_rendering:
            
            if options.parallelize_rendering_n_cores is None:                
                if options.parallelize_rendering_with_threads:
                    pool = ThreadPool()
                else:
                    pool = Pool()
            else:
                if options.parallelize_rendering_with_threads:
                    pool = ThreadPool(options.parallelize_rendering_n_cores)
                    worker_string = 'threads'
                else:
                    pool = Pool(options.parallelize_rendering_n_cores)
                    worker_string = 'processes'
                print('Rendering images with {} {}'.format(options.parallelize_rendering_n_cores,
                                                           worker_string))
                
            # _render_image_no_gt(file_info,detection_categories_to_results_name,
            # detection_categories,classification_categories)

            rendering_results = list(tqdm(pool.imap(
                partial(_render_image_no_gt, 
                        detection_categories_to_results_name=detection_categories_to_results_name,
                        detection_categories=detection_categories,
                        classification_categories=classification_categories,
                        options=options),
                        files_to_render), total=len(files_to_render)))
        else:
            for file_info in tqdm(files_to_render):
                rendering_result = _render_image_no_gt(file_info,
                                                       detection_categories_to_results_name,
                                                       detection_categories,
                                                       classification_categories,
                                                       options=options)
                rendering_results.append(rendering_result)
                
        elapsed = time.time() - start_time        
        
        # Do we have classification results in addition to detection results?
        has_classification_info = False
        
        # Map all the rendering results in the list rendering_results into the
        # dictionary images_html
        image_rendered_count = 0
        for rendering_result in rendering_results:
            if rendering_result is None:
                continue
            image_rendered_count += 1
            for assignment in rendering_result:
                if 'class' in assignment[0]:
                    has_classification_info = True
                images_html[assignment[0]].append(assignment[1])

        # Prepare the individual html image files
        image_counts = _prepare_html_subpages(images_html, output_dir, options)
        
        if image_rendered_count == 0:
            seconds_per_image = 0.0
        else:
            seconds_per_image = elapsed/image_rendered_count

        print('Rendered {} images (of {}) in {} ({} per image)'.format(image_rendered_count,
              image_count,humanfriendly.format_timespan(elapsed),
              humanfriendly.format_timespan(seconds_per_image)))

        # Write index.html

        # We can't just sum these, because image_counts includes images in both their
        # detection and classification classes
        # total_images = sum(image_counts.values())
        total_images = 0
        for k in image_counts.keys():
            v = image_counts[k]
            if has_classification_info and k.startswith('class_'):
                continue
            total_images += v

        if total_images != image_count:
            print('Warning, missing images: image_count is {}, total_images is {}'.format(total_images,image_count))
        
        almost_detection_string = ''
        if options.include_almost_detections:
            almost_detection_string = ' (&ldquo;almost detection&rdquo; threshold at {:.1%})'.format(
                options.almost_detection_confidence_threshold)

        confidence_threshold_string = ''
        if isinstance(options.confidence_threshold,float):
            confidence_threshold_string = '{:.2%}'.format(options.confidence_threshold)
        else:
            confidence_threshold_string = str(options.confidence_threshold)
            
        index_page = """<html>\n{}\n<body>\n
        <h2>Visualization of results for {}</h2>\n
        <p>A sample of {} images (of {} total)FAILURE_PLACEHOLDER, annotated with detections above confidence {}{}.</p>\n
        
        <div class="contentdiv">
        <p>Model version: {}</p>
        </div>
        
        <h3>Sample images</h3>\n
        <div class="contentdiv">\n""".format(
            style_header, job_name_string, image_count, len(detections_df), confidence_threshold_string,
            almost_detection_string, model_version_string)

        failure_string = ''
        if n_failures is not None:
            failure_string = ' ({} failures)'.format(n_failures)        
        index_page = index_page.replace('FAILURE_PLACEHOLDER',failure_string)
        
        def result_set_name_to_friendly_name(result_set_name):
            friendly_name = ''
            friendly_name = result_set_name.replace('_','-')
            if friendly_name.startswith('detections-'):
                friendly_name = friendly_name.replace('detections-', 'detections: ')
            friendly_name = friendly_name.capitalize()
            return friendly_name

        sorted_result_set_names = sorted(list(images_html.keys()))
        
        result_set_name_to_count = {}
        for result_set_name in sorted_result_set_names:
            image_count = image_counts[result_set_name]
            result_set_name_to_count[result_set_name] = image_count
        sorted_result_set_names = sorted(sorted_result_set_names,
                                         key=lambda x: result_set_name_to_count[x],
                                         reverse=True)
            
        for result_set_name in sorted_result_set_names:

            # Don't print classification classes here; we'll do that later with a slightly
            # different structure
            if has_classification_info and result_set_name.lower().startswith('class_'):
                continue

            filename = result_set_name + '.html'
            label = result_set_name_to_friendly_name(result_set_name)
            image_count = image_counts[result_set_name]
            
            # Don't include line items for empty multi-category pages
            if image_count == 0 and \
                detection_categories_to_category_count[result_set_name] > 1:
                    continue
            
            if total_images == 0:
                image_fraction = -1
            else:
                image_fraction = image_count / total_images
                
            # Write the line item for this category, including a link only if the
            # category is non-empty
            if image_count == 0:
                index_page += '{} ({}, {:.1%})<br/>\n'.format(
                    label,image_count,image_fraction)
            else:
                index_page += '<a href="{}">{}</a> ({}, {:.1%})<br/>\n'.format(
                    filename,label,image_count,image_fraction)

        index_page += '</div>\n'

        if has_classification_info:
            index_page += '<h3>Images of detected classes</h3>'
            index_page += '<p>The same image might appear under multiple classes ' + \
                'if multiple species were detected.</p>\n'
            index_page += '<p>Classifications with confidence less than {:.1%} confidence are considered "unreliable".</p>\n'.format(
                options.classification_confidence_threshold)
            index_page += '<div class="contentdiv">\n'

            # Add links to all available classes
            class_names = sorted(classification_categories.values())
            if 'class_unreliable' in images_html.keys():
                class_names.append('unreliable')

            if options.sort_classification_results_by_count:
                class_name_to_count = {}                
                for cname in class_names:
                    ccount = len(images_html['class_{}'.format(cname)])
                    class_name_to_count[cname] = ccount
                class_names = sorted(class_names,key=lambda x: class_name_to_count[x],reverse=True)                
                    
            for cname in class_names:
                ccount = len(images_html['class_{}'.format(cname)])
                if ccount > 0:
                    index_page += '<a href="class_{}.html">{}</a> ({})<br/>\n'.format(
                        cname, cname.lower(), ccount)
            index_page += '</div>\n'

        index_page += '{}</body></html>'.format(options.footer_text)
        output_html_file = os.path.join(output_dir, 'index.html')
        with open(output_html_file, 'w') as f:
            f.write(index_page)

        print('Finished writing html to {}'.format(output_html_file))

        # os.startfile(output_html_file)

    # ...if we do/don't have ground truth

    ppresults.output_html_file = output_html_file
    return ppresults

# ...process_batch_results


#%% Interactive driver(s)

if False:

    #%%

    base_dir = r'g:\temp'
    options = PostProcessingOptions()
    options.image_base_dir = base_dir
    options.output_dir = os.path.join(base_dir, 'preview')
    options.md_results_file = os.path.join(base_dir, 'results.json')
    options.confidence_threshold = {'person':0.5,'animal':0.5,'vehicle':0.01}
    options.include_almost_detections = True
    options.almost_detection_confidence_threshold = 0.001

    ppresults = process_batch_results(options)
    # from megadetector.utils.path_utils import open_file; open_file(ppresults.output_html_file)


#%% Command-line driver

def main():
    
    options = PostProcessingOptions()

    parser = argparse.ArgumentParser()
    parser.add_argument(
        'md_results_file',
        help='path to .json file containing MegaDetector results')
    parser.add_argument(
        'output_dir',
        help='base directory for output')
    parser.add_argument(
        '--image_base_dir', default=options.image_base_dir,
        help='base directory for images (optional, can compute statistics '
             'without images)')
    parser.add_argument(
        '--ground_truth_json_file', default=options.ground_truth_json_file,
        help='ground truth labels (optional, can render detections without '
             'ground truth), in the COCO Camera Traps format')
    parser.add_argument(
        '--confidence_threshold', type=float,
        default=options.confidence_threshold,
        help='Confidence threshold for statistics and visualization')
    parser.add_argument(
        '--almost_detection_confidence_threshold', type=float,
        default=options.almost_detection_confidence_threshold,
        help='Almost-detection confidence threshold for statistics and visualization')
    parser.add_argument(
        '--target_recall', type=float, default=options.target_recall,
        help='Target recall (for statistics only)')
    parser.add_argument(
        '--num_images_to_sample', type=int,
        default=options.num_images_to_sample,
        help='number of images to visualize, -1 for all images (default: 500)')
    parser.add_argument(
        '--viz_target_width', type=int, default=options.viz_target_width,
        help='Output image width')
    parser.add_argument(
        '--include_almost_detections', action='store_true',
        help='Include a separate category for images just above a second confidence threshold')
    parser.add_argument(
        '--html_sort_order', type=str, default='filename',
        help='Sort order for output pages, should be one of [filename,confidence,random] (defaults to filename)')
    parser.add_argument(
        '--sort_by_confidence', action='store_true',
        help='Sort output in decreasing order by confidence (defaults to sorting by filename)')
    parser.add_argument(
        '--n_cores', type=int, default=1,
        help='Number of threads to use for rendering (default: 1)')
    parser.add_argument(
        '--parallelize_rendering_with_processes', 
        action='store_true',
        help='Should we use processes (instead of threads) for parallelization?')
    parser.add_argument(
        '--no_separate_detections_by_category', 
        action='store_true',
        help='Collapse all categories into just "detections" and "non-detections"')    
    parser.add_argument(
        '--open_output_file', 
        action='store_true',
        help='Open the HTML output file when finished')    
    parser.add_argument(
        '--max_figures_per_html_file', 
        type=int, default=None,
        help='Maximum number of images to put on a single HTML page')
    
    if len(sys.argv[1:]) == 0:
        parser.print_help()
        parser.exit()

    args = parser.parse_args()
    
    if args.n_cores != 1:
        assert (args.n_cores > 1), 'Illegal number of cores: {}'.format(args.n_cores)
        if args.parallelize_rendering_with_processes:
            args.parallelize_rendering_with_threads = False
        args.parallelize_rendering = True
        args.parallelize_rendering_n_cores = args.n_cores        

    args_to_object(args, options)    

    if args.no_separate_detections_by_category:
        options.separate_detections_by_category = False
    
    ppresults = process_batch_results(options)
    
    if options.open_output_file:
        path_utils.open_file(ppresults.output_html_file)

if __name__ == '__main__':
    main()