15939366926

Committed 28 Jun 2025 01:59AM UTC coverage: 71.74% (+0.1%) from 71.62%

Build # 15939366926

Build Type

push

github

Committed by

paulmthompson

Commit Message

convert mask data over to strong typed time

Run Details

208 of 218 new or added lines in 16 files covered. (95.41%)

42 existing lines in 3 files now uncovered.

11340 of 15807 relevant lines covered (71.74%)

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0.0

/src/WhiskerToolbox/DataManager/Masks/IO/Image/Mask_Data_Image.cpp

#include "Mask_Data_Image.hpp"

#include "Masks/Mask_Data.hpp"
#include "Masks/masks.hpp"
#include "Points/points.hpp"
#include "utils/string_manip.hpp"

#include <opencv2/imgcodecs.hpp>
#include <opencv2/opencv.hpp>

#include <algorithm>
#include <filesystem>
#include <iostream>
#include <regex>
#include <vector>

std::shared_ptr<MaskData> load(ImageMaskLoaderOptions const & opts) {
    auto mask_data = std::make_shared<MaskData>();

    // Validate directory
    if (!std::filesystem::exists(opts.directory_path) || !std::filesystem::is_directory(opts.directory_path)) {
        std::cerr << "Error: Directory does not exist: " << opts.directory_path << std::endl;
        return mask_data;
    }

    // Get list of image files matching the pattern
    std::vector<std::filesystem::path> image_files;
    std::string pattern = opts.file_pattern;

    // Convert wildcard pattern to regex
    std::string regex_pattern = std::regex_replace(pattern, std::regex("\\*"), ".*");
    std::regex file_regex(regex_pattern, std::regex_constants::icase);

    for (auto const & entry: std::filesystem::directory_iterator(opts.directory_path)) {
        if (entry.is_regular_file()) {
            std::string filename = entry.path().filename().string();
            if (std::regex_match(filename, file_regex)) {
                image_files.push_back(entry.path());
            }
        }
    }

    if (image_files.empty()) {
        std::cerr << "Warning: No image files found matching pattern '" << opts.file_pattern
                  << "' in directory: " << opts.directory_path << std::endl;
        return mask_data;
    }

    // Sort files to ensure consistent ordering
    std::sort(image_files.begin(), image_files.end());

    int files_loaded = 0;
    int files_skipped = 0;

    std::cout << "Loading mask images from directory: " << opts.directory_path << std::endl;
    std::cout << "Found " << image_files.size() << " image files matching pattern: " << opts.file_pattern << std::endl;

    for (auto const & file_path: image_files) {
        std::string filename = file_path.filename().string();
        std::string stem = file_path.stem().string();// Remove extension

        // Remove prefix if specified
        if (!opts.filename_prefix.empty()) {
            if (stem.find(opts.filename_prefix) != 0) {
                std::cerr << "Warning: File '" << filename
                          << "' does not start with expected prefix '" << opts.filename_prefix << "'" << std::endl;
                files_skipped++;
                continue;
            }
            stem = stem.substr(opts.filename_prefix.length());// Remove prefix
        }

        // Parse frame number
        int frame_number;
        try {
            frame_number = std::stoi(stem);
        } catch (std::exception const & e) {
            std::cerr << "Warning: Could not parse frame number from filename: " << filename << std::endl;
            files_skipped++;
            continue;
        }

        // Load the image using OpenCV
        cv::Mat image = cv::imread(file_path.string(), cv::IMREAD_GRAYSCALE);
        if (image.empty()) {
            std::cerr << "Warning: Could not load image: " << file_path.string() << std::endl;
            files_skipped++;
            continue;
        }

        // Extract mask points from image
        std::vector<Point2D<uint32_t>> mask_points;
        int const width = image.cols;
        int const height = image.rows;

        for (int y = 0; y < height; ++y) {
            for (int x = 0; x < width; ++x) {
                // Get pixel intensity (0-255)
                uint8_t pixel_value = image.at<uint8_t>(y, x);

                // Apply threshold and inversion logic
                bool is_mask_pixel;
                if (opts.invert_mask) {
                    is_mask_pixel = pixel_value < opts.threshold_value;
                } else {
                    is_mask_pixel = pixel_value >= opts.threshold_value;
                }

                if (is_mask_pixel) {
                    //mask_points.emplace_back(static_cast<float>(x), static_cast<float>(y)); // This fails on mac
                    mask_points.push_back(Point2D<uint32_t>{static_cast<uint32_t>(x), static_cast<uint32_t>(y)});
                }
            }
        }

        // Add mask to data if we have points
        if (!mask_points.empty()) {
            mask_data->addAtTime(TimeFrameIndex(static_cast<size_t>(frame_number)), std::move(mask_points), false);
            files_loaded++;
        } else {
            std::cout << "Warning: No mask pixels found in image: " << filename << std::endl;
            files_skipped++;
        }
    }

    // Notify observers once at the end
    if (files_loaded > 0) {
        mask_data->notifyObservers();
    }

    std::cout << "Image mask loading complete: " << files_loaded << " files loaded";
    if (files_skipped > 0) {
        std::cout << ", " << files_skipped << " files skipped";
    }
    std::cout << std::endl;

    return mask_data;
}

void save(MaskData const * mask_data, ImageMaskSaverOptions const & opts) {
    if (!mask_data) {
        std::cerr << "Error: MaskData pointer is null" << std::endl;
        return;
    }

    // Create output directory if it doesn't exist
    if (!std::filesystem::exists(opts.parent_dir)) {
        std::filesystem::create_directories(opts.parent_dir);
        std::cout << "Created directory: " << opts.parent_dir << std::endl;
    }

    int files_saved = 0;
    int files_skipped = 0;

    auto mask_data_size = mask_data->getImageSize();

    std::cout << "Saving mask images to directory: " << opts.parent_dir << std::endl;

    // Iterate through all masks with their timestamps
    for (auto const & time_mask_pair: mask_data->getAllAsRange()) {
        auto time = time_mask_pair.time;
        std::vector<Mask2D> const & masks = time_mask_pair.masks;

        if (masks.empty()) {
            files_skipped++;
            continue;
        }

        // Create output image with desired dimensions
        cv::Mat output_img = cv::Mat::zeros(opts.image_height, opts.image_width, CV_8UC1);
        output_img.setTo(opts.background_value);

        // Resize each mask and draw it on the output image
        ImageSize dest_size{opts.image_width, opts.image_height};
        for (Mask2D const & mask: masks) {
            // Resize the mask using our new resize function
            Mask2D resized_mask = resize_mask(mask, mask_data_size, dest_size);

            // Draw the resized mask on the output image
            for (Point2D<uint32_t> const & point: resized_mask) {
                int x = static_cast<int>(point.x);
                int y = static_cast<int>(point.y);

                // Check bounds (should already be valid after resize, but be safe)
                if (x >= 0 && x < opts.image_width && y >= 0 && y < opts.image_height) {
                    output_img.at<uint8_t>(y, x) = static_cast<uint8_t>(opts.mask_value);
                }
            }
        }

        // Generate filename using the pad_frame_id utility
        std::string filename;
        if (!opts.filename_prefix.empty()) {
            filename = opts.filename_prefix;
        }

        // Add zero-padded frame number
        filename += pad_frame_id(time.getValue(), opts.frame_number_padding);

        // Add extension based on format
        std::string extension = "." + opts.image_format;
        std::transform(extension.begin(), extension.end(), extension.begin(), ::tolower);
        filename += extension;

        // Full path
        std::filesystem::path full_path = std::filesystem::path(opts.parent_dir) / filename;

        // Check if file exists and handle according to overwrite setting
        if (std::filesystem::exists(full_path) && !opts.overwrite_existing) {
            std::cout << "Skipping existing file: " << full_path.string() << std::endl;
            files_skipped++;
            continue;
        }

        // Save the image using OpenCV
        if (cv::imwrite(full_path.string(), output_img)) {
            files_saved++;
            if (std::filesystem::exists(full_path) && opts.overwrite_existing) {
                std::cout << "Overwritten existing file: " << full_path.string() << std::endl;
            }
        } else {
            std::cerr << "Warning: Failed to save image: " << full_path.string() << std::endl;
            files_skipped++;
        }
    }

    std::cout << "Image mask saving complete: " << files_saved << " files saved";
    if (files_skipped > 0) {
        std::cout << ", " << files_skipped << " files skipped";
    }
    std::cout << std::endl;
}

1	#include "Mask_Data_Image.hpp"
2
3	#include "Masks/Mask_Data.hpp"
4	#include "Masks/masks.hpp"
5	#include "Points/points.hpp"
6	#include "utils/string_manip.hpp"
7
8	#include <opencv2/imgcodecs.hpp>
9	#include <opencv2/opencv.hpp>
10
11	#include <algorithm>
12	#include <filesystem>
13	#include <iostream>
14	#include <regex>
15	#include <vector>
16
17	std::shared_ptr<MaskData> load(ImageMaskLoaderOptions const & opts) {	×
18	auto mask_data = std::make_shared<MaskData>();	×
19
20	// Validate directory
21	if (!std::filesystem::exists(opts.directory_path) \|\| !std::filesystem::is_directory(opts.directory_path)) {	×
22	std::cerr << "Error: Directory does not exist: " << opts.directory_path << std::endl;	×
23	return mask_data;	×
24	}
25
26	// Get list of image files matching the pattern
27	std::vector<std::filesystem::path> image_files;	×
28	std::string pattern = opts.file_pattern;	×
29
30	// Convert wildcard pattern to regex
31	std::string regex_pattern = std::regex_replace(pattern, std::regex("\\"), ".");	×
32	std::regex file_regex(regex_pattern, std::regex_constants::icase);	×
33
34	for (auto const & entry: std::filesystem::directory_iterator(opts.directory_path)) {	×
35	if (entry.is_regular_file()) {	×
36	std::string filename = entry.path().filename().string();	×
37	if (std::regex_match(filename, file_regex)) {	×
38	image_files.push_back(entry.path());	×
39	}
40	}	×
41	}	×
42
43	if (image_files.empty()) {	×
44	std::cerr << "Warning: No image files found matching pattern '" << opts.file_pattern	×
45	<< "' in directory: " << opts.directory_path << std::endl;	×
46	return mask_data;	×
47	}
48
49	// Sort files to ensure consistent ordering
50	std::sort(image_files.begin(), image_files.end());	×
51
52	int files_loaded = 0;	×
53	int files_skipped = 0;	×
54
55	std::cout << "Loading mask images from directory: " << opts.directory_path << std::endl;	×
56	std::cout << "Found " << image_files.size() << " image files matching pattern: " << opts.file_pattern << std::endl;	×
57
58	for (auto const & file_path: image_files) {	×
59	std::string filename = file_path.filename().string();	×
60	std::string stem = file_path.stem().string();// Remove extension	×
61
62	// Remove prefix if specified
63	if (!opts.filename_prefix.empty()) {	×
64	if (stem.find(opts.filename_prefix) != 0) {	×
65	std::cerr << "Warning: File '" << filename
66	<< "' does not start with expected prefix '" << opts.filename_prefix << "'" << std::endl;	×
67	files_skipped++;	×
68	continue;	×
69	}
70	stem = stem.substr(opts.filename_prefix.length());// Remove prefix	×
71	}
72
73	// Parse frame number
74	int frame_number;
75	try {
76	frame_number = std::stoi(stem);	×
77	} catch (std::exception const & e) {	×
78	std::cerr << "Warning: Could not parse frame number from filename: " << filename << std::endl;	×
79	files_skipped++;	×
80	continue;	×
81	}	×
82
83	// Load the image using OpenCV
84	cv::Mat image = cv::imread(file_path.string(), cv::IMREAD_GRAYSCALE);	×
85	if (image.empty()) {	×
86	std::cerr << "Warning: Could not load image: " << file_path.string() << std::endl;	×
87	files_skipped++;	×
88	continue;	×
89	}
90
91	// Extract mask points from image
92	std::vector<Point2D<uint32_t>> mask_points;	×
93	int const width = image.cols;	×
94	int const height = image.rows;	×
95
96	for (int y = 0; y < height; ++y) {	×
97	for (int x = 0; x < width; ++x) {	×
98	// Get pixel intensity (0-255)
99	uint8_t pixel_value = image.at<uint8_t>(y, x);	×
100
101	// Apply threshold and inversion logic
102	bool is_mask_pixel;
103	if (opts.invert_mask) {	×
104	is_mask_pixel = pixel_value < opts.threshold_value;	×
105	} else {
106	is_mask_pixel = pixel_value >= opts.threshold_value;	×
107	}
108
109	if (is_mask_pixel) {	×
110	//mask_points.emplace_back(static_cast<float>(x), static_cast<float>(y)); // This fails on mac
111	mask_points.push_back(Point2D<uint32_t>{static_cast<uint32_t>(x), static_cast<uint32_t>(y)});	×
112	}
113	}
114	}
115
116	// Add mask to data if we have points
117	if (!mask_points.empty()) {	×
NEW 118	mask_data->addAtTime(TimeFrameIndex(static_cast<size_t>(frame_number)), std::move(mask_points), false);	×
119	files_loaded++;	×
120	} else {
121	std::cout << "Warning: No mask pixels found in image: " << filename << std::endl;	×
122	files_skipped++;	×
123	}
124	}	×
125
126	// Notify observers once at the end
127	if (files_loaded > 0) {	×
128	mask_data->notifyObservers();	×
129	}
130
131	std::cout << "Image mask loading complete: " << files_loaded << " files loaded";	×
132	if (files_skipped > 0) {	×
133	std::cout << ", " << files_skipped << " files skipped";	×
134	}
135	std::cout << std::endl;	×
136
137	return mask_data;	×
138	}	×
139
140	void save(MaskData const * mask_data, ImageMaskSaverOptions const & opts) {	×
141	if (!mask_data) {	×
142	std::cerr << "Error: MaskData pointer is null" << std::endl;	×
143	return;	×
144	}
145
146	// Create output directory if it doesn't exist
147	if (!std::filesystem::exists(opts.parent_dir)) {	×
148	std::filesystem::create_directories(opts.parent_dir);	×
149	std::cout << "Created directory: " << opts.parent_dir << std::endl;	×
150	}
151
152	int files_saved = 0;	×
153	int files_skipped = 0;	×
154
155	auto mask_data_size = mask_data->getImageSize();	×
156
157	std::cout << "Saving mask images to directory: " << opts.parent_dir << std::endl;	×
158
159	// Iterate through all masks with their timestamps
160	for (auto const & time_mask_pair: mask_data->getAllAsRange()) {	×
NEW 161	auto time = time_mask_pair.time;	×
162	std::vector<Mask2D> const & masks = time_mask_pair.masks;	×
163
164	if (masks.empty()) {	×
165	files_skipped++;	×
166	continue;	×
167	}
168
169	// Create output image with desired dimensions
170	cv::Mat output_img = cv::Mat::zeros(opts.image_height, opts.image_width, CV_8UC1);	×
171	output_img.setTo(opts.background_value);	×
172
173	// Resize each mask and draw it on the output image
174	ImageSize dest_size{opts.image_width, opts.image_height};	×
175	for (Mask2D const & mask: masks) {	×
176	// Resize the mask using our new resize function
177	Mask2D resized_mask = resize_mask(mask, mask_data_size, dest_size);	×
178
179	// Draw the resized mask on the output image
180	for (Point2D<uint32_t> const & point: resized_mask) {	×
181	int x = static_cast<int>(point.x);	×
182	int y = static_cast<int>(point.y);	×
183
184	// Check bounds (should already be valid after resize, but be safe)
185	if (x >= 0 && x < opts.image_width && y >= 0 && y < opts.image_height) {	×
186	output_img.at<uint8_t>(y, x) = static_cast<uint8_t>(opts.mask_value);	×
187	}
188	}
189	}	×
190
191	// Generate filename using the pad_frame_id utility
192	std::string filename;	×
193	if (!opts.filename_prefix.empty()) {	×
194	filename = opts.filename_prefix;	×
195	}
196
197	// Add zero-padded frame number
NEW 198	filename += pad_frame_id(time.getValue(), opts.frame_number_padding);	×
199
200	// Add extension based on format
201	std::string extension = "." + opts.image_format;	×
202	std::transform(extension.begin(), extension.end(), extension.begin(), ::tolower);	×
203	filename += extension;	×
204
205	// Full path
206	std::filesystem::path full_path = std::filesystem::path(opts.parent_dir) / filename;	×
207
208	// Check if file exists and handle according to overwrite setting
209	if (std::filesystem::exists(full_path) && !opts.overwrite_existing) {	×
210	std::cout << "Skipping existing file: " << full_path.string() << std::endl;	×
211	files_skipped++;	×
212	continue;	×
213	}
214
215	// Save the image using OpenCV
216	if (cv::imwrite(full_path.string(), output_img)) {	×
217	files_saved++;	×
218	if (std::filesystem::exists(full_path) && opts.overwrite_existing) {	×
219	std::cout << "Overwritten existing file: " << full_path.string() << std::endl;	×
220	}
221	} else {
222	std::cerr << "Warning: Failed to save image: " << full_path.string() << std::endl;	×
223	files_skipped++;	×
224	}
225	}	×
226
227	std::cout << "Image mask saving complete: " << files_saved << " files saved";	×
228	if (files_skipped > 0) {	×
229	std::cout << ", " << files_skipped << " files skipped";	×
230	}
231	std::cout << std::endl;	×
232	}

paulmthompson / WhiskerToolbox / 15939366926

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