14913265839

Committed 08 May 2025 06:17PM UTC coverage: 20.55% (-0.2%) from 20.758%

Build # 14913265839

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push

github

Committed by

paulmthompson

Commit Message

use datatype return from data manager.

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78 existing lines in 1 file now uncovered.

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3.91

/src/WhiskerToolbox/DataManager/DataManager.cpp


#include "DataManager.hpp"
#include "AnalogTimeSeries/Analog_Time_Series.hpp"
#include "DigitalTimeSeries/Digital_Event_Series.hpp"
#include "DigitalTimeSeries/Digital_Interval_Series.hpp"
#include "Lines/Line_Data.hpp"
#include "Masks/Mask_Data.hpp"
#include "Media/Video_Data.hpp"
#include "Points/Point_Data.hpp"
#include "Tensors/Tensor_Data.hpp"

#include "AnalogTimeSeries/Analog_Time_Series_Loader.hpp"
#include "DigitalTimeSeries/Digital_Event_Series_Loader.hpp"
#include "DigitalTimeSeries/Digital_Interval_Series_Loader.hpp"
#include "Lines/IO/CSV/Line_Data_CSV.hpp"
#include "Masks/IO/HDF5/Mask_Data_HDF5.hpp"
#include "Media/Video_Data_Loader.hpp"
#include "Points/IO/CSV/Point_Data_CSV.hpp"

#include "loaders/binary_loaders.hpp"
#include "transforms/data_transforms.hpp"
#include "transforms/Masks/mask_area.hpp"

#include "TimeFrame.hpp"

#include "nlohmann/json.hpp"
#include "utils/string_manip.hpp"

#include <filesystem>
#include <fstream>
#include <iostream>
#include <optional>
#include <regex>

using namespace nlohmann;

DataManager::DataManager() {
    _times["time"] = std::make_shared<TimeFrame>();
    _data["media"] = std::make_shared<MediaData>();

    setTimeFrame("media", "time");
    _output_path = std::filesystem::current_path();
}

void DataManager::setTimeFrame(std::string const & data_key, std::string const & time_key) {
    //Check that data_key is in _data
    if (_data.find(data_key) == _data.end()) {
        std::cerr << "Data key not found in DataManager: " << data_key << std::endl;
        return;
    }

    //Check that time_key is in _times
    if (_times.find(time_key) == _times.end()) {
        std::cerr << "Time key not found in DataManager: " << time_key << std::endl;
        return;
    }

    _time_frames[data_key] = time_key;
}

DM_DataType stringToDataType(std::string const & data_type_str) {
    if (data_type_str == "video") return DM_DataType::Video;
    if (data_type_str == "points") return DM_DataType::Points;
    if (data_type_str == "mask") return DM_DataType::Mask;
    if (data_type_str == "line") return DM_DataType::Line;
    if (data_type_str == "analog") return DM_DataType::Analog;
    if (data_type_str == "digital_event") return DM_DataType::DigitalEvent;
    if (data_type_str == "digital_interval") return DM_DataType::DigitalInterval;
    if (data_type_str == "tensor") return DM_DataType::Tensor;
    if (data_type_str == "time") return DM_DataType::Time;
    return DM_DataType::Unknown;
}

std::optional<std::string> processFilePath(
        std::string const & file_path,
        std::filesystem::path const & base_path) {
    std::filesystem::path full_path = file_path;

    // Check for wildcard character
    if (file_path.find('*') != std::string::npos) {
        // Convert wildcard pattern to regex
        std::string const pattern = std::regex_replace(full_path.string(), std::regex("\\*"), ".*");
        std::regex const regex_pattern(pattern);

        // Iterate through the directory to find matching files
        for (auto const & entry: std::filesystem::directory_iterator(base_path)) {
            std::cout << "Checking " << entry.path().string() << " with full path " << full_path << std::endl;
            if (std::regex_match(entry.path().string(), regex_pattern)) {
                std::cout << "Loading file " << entry.path().string() << std::endl;
                return entry.path().string();
            }
        }
        return std::nullopt;
    } else {
        // Check if the file path is relative
        if (!std::filesystem::path(file_path).is_absolute()) {
            full_path = base_path / file_path;
        }
        // Check for the presence of the file
        if (std::filesystem::exists(full_path)) {
            std::cout << "Loading file " << full_path.string() << std::endl;
            return full_path.string();
        } else {
            return std::nullopt;
        }
    }
}

bool checkRequiredFields(json const & item, std::vector<std::string> const & requiredFields) {
    for (auto const & field: requiredFields) {
        if (!item.contains(field)) {
            std::cerr << "Error: Missing required field \"" << field << "\" in JSON item." << std::endl;
            return false;
        }
    }
    return true;
}

int DataManager::addCallbackToData(std::string const & key, ObserverCallback callback) {

    int id = -1;

    if (_data.find(key) != _data.end()) {
        auto data = _data[key];

        id = std::visit([callback](auto & x) {
            return x.get()->addObserver(callback);
        },
                        data);
    }

    return id;
}

void DataManager::removeCallbackFromData(std::string const & key, int callback_id) {
    if (_data.find(key) != _data.end()) {
        auto data = _data[key];

        std::visit([callback_id](auto & x) {
            x.get()->removeObserver(callback_id);
        },
                   data);
    }
}

void checkOptionalFields(json const & item, std::vector<std::string> const & optionalFields) {
    for (auto const & field: optionalFields) {
        if (!item.contains(field)) {
            std::cout << "Warning: Optional field \"" << field << "\" is missing in JSON item." << std::endl;
        }
    }
}

std::vector<DataInfo> load_data_from_json_config(DataManager * dm, std::string const & json_filepath) {
    std::vector<DataInfo> data_info_list;
    // Open JSON file
    std::ifstream ifs(json_filepath);
    if (!ifs.is_open()) {
        std::cerr << "Failed to open JSON file: " << json_filepath << std::endl;
        return data_info_list;
    }

    // Parse JSON
    json j;
    ifs >> j;

    // get base path of filepath
    std::filesystem::path const base_path = std::filesystem::path(json_filepath).parent_path();

    // Iterate through JSON array
    for (auto const & item: j) {

        if (!checkRequiredFields(item, {"data_type", "name", "filepath"})) {
            continue;// Exit if any required field is missing
        }

        std::string const data_type_str = item["data_type"];
        auto const data_type = stringToDataType(data_type_str);
        if (data_type == DM_DataType::Unknown) {
            std::cout << "Unknown data type: " << data_type_str << std::endl;
            continue;
        }

        std::string const name = item["name"];

        auto file_exists = processFilePath(item["filepath"], base_path);
        if (!file_exists) {
            std::cerr << "File does not exist: " << item["filepath"] << std::endl;
            continue;
        }

        std::string const file_path = file_exists.value();

        switch (data_type) {
            case DM_DataType::Video: {
                // Create VideoData object
                auto video_data = load_video_into_VideoData(file_path);

                // Add VideoData to DataManager
                dm->setMedia(video_data);

                data_info_list.push_back({name, "VideoData", ""});
                break;
            }
            case DM_DataType::Points: {

                auto point_data = load_into_PointData(file_path, item);

                dm->setData<PointData>(name, point_data);

                std::string const color = item.value("color", "#0000FF");
                data_info_list.push_back({name, "PointData", color});
                break;
            }
            case DM_DataType::Mask: {

                auto mask_data = load_into_MaskData(file_path, item);

                std::string const color = item.value("color", "0000FF");
                dm->setData<MaskData>(name, mask_data);

                data_info_list.push_back({name, "MaskData", color});

                if (item.contains("operations")) {

                    for (auto const & operation: item["operations"]) {

                        std::string const operation_type = operation["type"];

                        if (operation_type == "area") {
                            std::cout << "Calculating area for mask: " << name << std::endl;
                            auto area_data = area(dm->getData<MaskData>(name).get());
                            std::string const output_name = name + "_area";
                            dm->setData<AnalogTimeSeries>(output_name, area_data);
                        }
                    }
                }
                break;
            }
            case DM_DataType::Line: {

                auto line_map = load_line_csv(file_path);

                //Get the whisker name from the filename using filesystem
                auto whisker_filename = std::filesystem::path(file_path).filename().string();

                //Remove .csv suffix from filename
                auto whisker_name = remove_extension(whisker_filename);

                dm->setData<LineData>(whisker_name, std::make_shared<LineData>(line_map));

                std::string const color = item.value("color", "0000FF");

                data_info_list.push_back({name, "LineData", color});

                break;
            }
            case DM_DataType::Analog: {

                auto analog_time_series = load_into_AnalogTimeSeries(file_path, item);

                for (int channel = 0; channel < analog_time_series.size(); channel++) {
                    std::string const channel_name = name + "_" + std::to_string(channel);

                    dm->setData<AnalogTimeSeries>(channel_name, analog_time_series[channel]);

                    if (item.contains("clock")) {
                        std::string const clock = item["clock"];
                        dm->setTimeFrame(channel_name, clock);
                    }
                }
                break;
            }
            case DM_DataType::DigitalEvent: {

                auto digital_event_series = load_into_DigitalEventSeries(file_path, item);

                for (int channel = 0; channel < digital_event_series.size(); channel++) {
                    std::string const channel_name = name + "_" + std::to_string(channel);

                    dm->setData<DigitalEventSeries>(channel_name, digital_event_series[channel]);

                    if (item.contains("clock")) {
                        std::string const clock = item["clock"];
                        dm->setTimeFrame(channel_name, clock);
                    }
                }
                break;
            }
            case DM_DataType::DigitalInterval: {

                auto digital_interval_series = load_into_DigitalIntervalSeries(file_path, item);
                dm->setData<DigitalIntervalSeries>(name, digital_interval_series);

                break;
            }
            case DM_DataType::Tensor: {

                if (item["format"] == "numpy") {

                    TensorData tensor_data;
                    loadNpyToTensorData(file_path, tensor_data);

                    dm->setData<TensorData>(name, std::make_shared<TensorData>(tensor_data));

                } else {
                    std::cout << "Format " << item["format"] << " not found for " << name << std::endl;
                }
                break;
            }
            case DM_DataType::Time: {

                if (item["format"] == "uint16") {

                    int const channel = item["channel"];
                    std::string const transition = item["transition"];

                    int const header_size = item.value("header_size", 0);

                    auto opts = Loader::BinaryAnalogOptions{.file_path = file_path,
                                                            .header_size_bytes = static_cast<size_t>(header_size)};
                    auto data = readBinaryFile<uint16_t>(opts);

                    auto digital_data = Loader::extractDigitalData(data, channel);
                    auto events = Loader::extractEvents(digital_data, transition);

                    // convert to int with std::transform
                    std::vector<int> events_int;
                    events_int.reserve(events.size());
                    for (auto e: events) {
                        events_int.push_back(static_cast<int>(e));
                    }
                    std::cout << "Loaded " << events_int.size() << " events for " << name << std::endl;

                    auto timeframe = std::make_shared<TimeFrame>(events_int);
                    dm->setTime(name, timeframe);
                }

                if (item["format"] == "uint16_length") {

                    int const header_size = item.value("header_size", 0);

                    auto opts = Loader::BinaryAnalogOptions{.file_path = file_path,
                                                            .header_size_bytes = static_cast<size_t>(header_size)};
                    auto data = readBinaryFile<uint16_t>(opts);

                    std::vector<int> t(data.size());
                    std::iota(std::begin(t), std::end(t), 0);

                    std::cout << "Total of " << t.size() << " timestamps for " << name << std::endl;

                    auto timeframe = std::make_shared<TimeFrame>(t);
                    dm->setTime(name, timeframe);
                }
                break;
            }
            default:
                std::cout << "Unsupported data type: " << data_type_str << std::endl;
                continue;
        }
        if (item.contains("clock")) {
            std::string const clock = item["clock"];
            std::cout << "Setting time for " << name << " to " << clock << std::endl;
            dm->setTimeFrame(name, clock);
        }
    }

    return data_info_list;
}

DM_DataType DataManager::getType(std::string const & key) const {
    auto it = _data.find(key);
    if (it != _data.end()) {
        if (std::holds_alternative<std::shared_ptr<MediaData>>(it->second)) {
            return DM_DataType::Video;
        } else if (std::holds_alternative<std::shared_ptr<PointData>>(it->second)) {
            return DM_DataType::Points;
        } else if (std::holds_alternative<std::shared_ptr<LineData>>(it->second)) {
            return DM_DataType::Line;
        } else if (std::holds_alternative<std::shared_ptr<MaskData>>(it->second)) {
            return DM_DataType::Mask;
        } else if (std::holds_alternative<std::shared_ptr<AnalogTimeSeries>>(it->second)) {
            return DM_DataType::Analog;
        } else if (std::holds_alternative<std::shared_ptr<DigitalEventSeries>>(it->second)) {
            return DM_DataType::DigitalEvent;
        } else if (std::holds_alternative<std::shared_ptr<DigitalIntervalSeries>>(it->second)) {
            return DM_DataType::DigitalInterval;
        } else if (std::holds_alternative<std::shared_ptr<TensorData>>(it->second)) {
            return DM_DataType::Tensor;
        }
        return DM_DataType::Unknown;
    }
    return DM_DataType::Unknown;
}

std::string convert_data_type_to_string(DM_DataType type) {
    switch (type) {
        case DM_DataType::Video:
            return "video";
        case DM_DataType::Points:
            return "points";
        case DM_DataType::Mask:
            return "mask";
        case DM_DataType::Line:
            return "line";
        case DM_DataType::Analog:
            return "analog";
        case DM_DataType::DigitalEvent:
            return "digital_event";
        case DM_DataType::DigitalInterval:
            return "digital_interval";
        case DM_DataType::Tensor:
            return "tensor";
        case DM_DataType::Time:
            return "time";
        default:
            return "unknown";
    }
}

1
2	#include "DataManager.hpp"
3	#include "AnalogTimeSeries/Analog_Time_Series.hpp"
4	#include "DigitalTimeSeries/Digital_Event_Series.hpp"
5	#include "DigitalTimeSeries/Digital_Interval_Series.hpp"
6	#include "Lines/Line_Data.hpp"
7	#include "Masks/Mask_Data.hpp"
8	#include "Media/Video_Data.hpp"
9	#include "Points/Point_Data.hpp"
10	#include "Tensors/Tensor_Data.hpp"
11
12	#include "AnalogTimeSeries/Analog_Time_Series_Loader.hpp"
13	#include "DigitalTimeSeries/Digital_Event_Series_Loader.hpp"
14	#include "DigitalTimeSeries/Digital_Interval_Series_Loader.hpp"
15	#include "Lines/IO/CSV/Line_Data_CSV.hpp"
16	#include "Masks/IO/HDF5/Mask_Data_HDF5.hpp"
17	#include "Media/Video_Data_Loader.hpp"
18	#include "Points/IO/CSV/Point_Data_CSV.hpp"
19
20	#include "loaders/binary_loaders.hpp"
21	#include "transforms/data_transforms.hpp"
22	#include "transforms/Masks/mask_area.hpp"
23
24	#include "TimeFrame.hpp"
25
26	#include "nlohmann/json.hpp"
27	#include "utils/string_manip.hpp"
28
29	#include <filesystem>
30	#include <fstream>
31	#include <iostream>
32	#include <optional>
33	#include <regex>
34
35	using namespace nlohmann;
36
37	DataManager::DataManager() {	2✔
38	_times["time"] = std::make_shared<TimeFrame>();	6✔
39	_data["media"] = std::make_shared<MediaData>();	6✔
40
41	setTimeFrame("media", "time");	10✔
42	_output_path = std::filesystem::current_path();	2✔
43	}	2✔
44
45	void DataManager::setTimeFrame(std::string const & data_key, std::string const & time_key) {	2✔
46	//Check that data_key is in _data
47	if (_data.find(data_key) == _data.end()) {	2✔
48	std::cerr << "Data key not found in DataManager: " << data_key << std::endl;	×
49	return;	×
50	}
51
52	//Check that time_key is in _times
53	if (_times.find(time_key) == _times.end()) {	2✔
54	std::cerr << "Time key not found in DataManager: " << time_key << std::endl;	×
55	return;	×
56	}
57
58	_time_frames[data_key] = time_key;	2✔
59	}
60
NEW 61	DM_DataType stringToDataType(std::string const & data_type_str) {	×
NEW 62	if (data_type_str == "video") return DM_DataType::Video;	×
NEW 63	if (data_type_str == "points") return DM_DataType::Points;	×
NEW 64	if (data_type_str == "mask") return DM_DataType::Mask;	×
NEW 65	if (data_type_str == "line") return DM_DataType::Line;	×
NEW 66	if (data_type_str == "analog") return DM_DataType::Analog;	×
NEW 67	if (data_type_str == "digital_event") return DM_DataType::DigitalEvent;	×
NEW 68	if (data_type_str == "digital_interval") return DM_DataType::DigitalInterval;	×
NEW 69	if (data_type_str == "tensor") return DM_DataType::Tensor;	×
NEW 70	if (data_type_str == "time") return DM_DataType::Time;	×
NEW 71	return DM_DataType::Unknown;	×
72	}
73
74	std::optional<std::string> processFilePath(	×
75	std::string const & file_path,
76	std::filesystem::path const & base_path) {
77	std::filesystem::path full_path = file_path;	×
78
79	// Check for wildcard character
80	if (file_path.find('*') != std::string::npos) {	×
81	// Convert wildcard pattern to regex
82	std::string const pattern = std::regex_replace(full_path.string(), std::regex("\\"), ".");	×
83	std::regex const regex_pattern(pattern);	×
84
85	// Iterate through the directory to find matching files
UNCOV 86	for (auto const & entry: std::filesystem::directory_iterator(base_path)) {	×
87	std::cout << "Checking " << entry.path().string() << " with full path " << full_path << std::endl;	×
UNCOV 88	if (std::regex_match(entry.path().string(), regex_pattern)) {	×
UNCOV 89	std::cout << "Loading file " << entry.path().string() << std::endl;	×
90	return entry.path().string();	×
91	}
UNCOV 92	}	×
93	return std::nullopt;	×
UNCOV 94	} else {	×
95	// Check if the file path is relative
96	if (!std::filesystem::path(file_path).is_absolute()) {	×
UNCOV 97	full_path = base_path / file_path;	×
98	}
99	// Check for the presence of the file
100	if (std::filesystem::exists(full_path)) {	×
101	std::cout << "Loading file " << full_path.string() << std::endl;	×
102	return full_path.string();	×
103	} else {
UNCOV 104	return std::nullopt;	×
105	}
106	}
107	}	×
108
109	bool checkRequiredFields(json const & item, std::vector<std::string> const & requiredFields) {	×
110	for (auto const & field: requiredFields) {	×
UNCOV 111	if (!item.contains(field)) {	×
UNCOV 112	std::cerr << "Error: Missing required field \"" << field << "\" in JSON item." << std::endl;	×
113	return false;	×
114	}
115	}
UNCOV 116	return true;	×
117	}
118
UNCOV 119	int DataManager::addCallbackToData(std::string const & key, ObserverCallback callback) {	×
120
UNCOV 121	int id = -1;	×
122
123	if (_data.find(key) != _data.end()) {	×
124	auto data = _data[key];	×
125
126	id = std::visit([callback](auto & x) {	×
UNCOV 127	return x.get()->addObserver(callback);	×
128	},
129	data);
UNCOV 130	}	×
131
132	return id;	×
133	}
134
UNCOV 135	void DataManager::removeCallbackFromData(std::string const & key, int callback_id) {	×
136	if (_data.find(key) != _data.end()) {	×
137	auto data = _data[key];	×
138
139	std::visit([callback_id](auto & x) {	×
140	x.get()->removeObserver(callback_id);	×
UNCOV 141	},	×
142	data);
143	}	×
UNCOV 144	}	×
145
UNCOV 146	void checkOptionalFields(json const & item, std::vector<std::string> const & optionalFields) {	×
UNCOV 147	for (auto const & field: optionalFields) {	×
148	if (!item.contains(field)) {	×
149	std::cout << "Warning: Optional field \"" << field << "\" is missing in JSON item." << std::endl;	×
150	}
151	}
152	}	×
153
154	std::vector<DataInfo> load_data_from_json_config(DataManager * dm, std::string const & json_filepath) {	×
UNCOV 155	std::vector<DataInfo> data_info_list;	×
156	// Open JSON file
157	std::ifstream ifs(json_filepath);	×
UNCOV 158	if (!ifs.is_open()) {	×
159	std::cerr << "Failed to open JSON file: " << json_filepath << std::endl;	×
160	return data_info_list;	×
161	}
162
163	// Parse JSON
UNCOV 164	json j;	×
165	ifs >> j;	×
166
167	// get base path of filepath
168	std::filesystem::path const base_path = std::filesystem::path(json_filepath).parent_path();	×
169
170	// Iterate through JSON array
171	for (auto const & item: j) {	×
172
173	if (!checkRequiredFields(item, {"data_type", "name", "filepath"})) {	×
UNCOV 174	continue;// Exit if any required field is missing	×
175	}
176
177	std::string const data_type_str = item["data_type"];	×
178	auto const data_type = stringToDataType(data_type_str);	×
NEW 179	if (data_type == DM_DataType::Unknown) {	×
UNCOV 180	std::cout << "Unknown data type: " << data_type_str << std::endl;	×
181	continue;	×
182	}
183
184	std::string const name = item["name"];	×
185
186	auto file_exists = processFilePath(item["filepath"], base_path);	×
187	if (!file_exists) {	×
UNCOV 188	std::cerr << "File does not exist: " << item["filepath"] << std::endl;	×
UNCOV 189	continue;	×
190	}
191
192	std::string const file_path = file_exists.value();	×
193
194	switch (data_type) {	×
NEW 195	case DM_DataType::Video: {	×
196	// Create VideoData object
197	auto video_data = load_video_into_VideoData(file_path);	×
198
199	// Add VideoData to DataManager
200	dm->setMedia(video_data);	×
201
202	data_info_list.push_back({name, "VideoData", ""});	×
UNCOV 203	break;	×
UNCOV 204	}	×
NEW 205	case DM_DataType::Points: {	×
206
207	auto point_data = load_into_PointData(file_path, item);	×
208
UNCOV 209	dm->setData<PointData>(name, point_data);	×
210
UNCOV 211	std::string const color = item.value("color", "#0000FF");	×
UNCOV 212	data_info_list.push_back({name, "PointData", color});	×
213	break;	×
UNCOV 214	}	×
NEW 215	case DM_DataType::Mask: {	×
216
217	auto mask_data = load_into_MaskData(file_path, item);	×
218
UNCOV 219	std::string const color = item.value("color", "0000FF");	×
220	dm->setData<MaskData>(name, mask_data);	×
221
222	data_info_list.push_back({name, "MaskData", color});	×
223
224	if (item.contains("operations")) {	×
225
226	for (auto const & operation: item["operations"]) {	×
227
228	std::string const operation_type = operation["type"];	×
229
230	if (operation_type == "area") {	×
UNCOV 231	std::cout << "Calculating area for mask: " << name << std::endl;	×
232	auto area_data = area(dm->getData<MaskData>(name).get());	×
233	std::string const output_name = name + "_area";	×
UNCOV 234	dm->setData<AnalogTimeSeries>(output_name, area_data);	×
235	}	×
UNCOV 236	}	×
237	}
UNCOV 238	break;	×
239	}	×
NEW 240	case DM_DataType::Line: {	×
241
UNCOV 242	auto line_map = load_line_csv(file_path);	×
243
244	//Get the whisker name from the filename using filesystem
245	auto whisker_filename = std::filesystem::path(file_path).filename().string();	×
246
247	//Remove .csv suffix from filename
248	auto whisker_name = remove_extension(whisker_filename);	×
249
UNCOV 250	dm->setData<LineData>(whisker_name, std::make_shared<LineData>(line_map));	×
251
252	std::string const color = item.value("color", "0000FF");	×
253
UNCOV 254	data_info_list.push_back({name, "LineData", color});	×
255
UNCOV 256	break;	×
UNCOV 257	}	×
NEW 258	case DM_DataType::Analog: {	×
259
UNCOV 260	auto analog_time_series = load_into_AnalogTimeSeries(file_path, item);	×
261
UNCOV 262	for (int channel = 0; channel < analog_time_series.size(); channel++) {	×
263	std::string const channel_name = name + "_" + std::to_string(channel);	×
264
265	dm->setData<AnalogTimeSeries>(channel_name, analog_time_series[channel]);	×
266
267	if (item.contains("clock")) {	×
UNCOV 268	std::string const clock = item["clock"];	×
269	dm->setTimeFrame(channel_name, clock);	×
270	}	×
271	}	×
UNCOV 272	break;	×
273	}	×
NEW 274	case DM_DataType::DigitalEvent: {	×
275
276	auto digital_event_series = load_into_DigitalEventSeries(file_path, item);	×
277
278	for (int channel = 0; channel < digital_event_series.size(); channel++) {	×
UNCOV 279	std::string const channel_name = name + "_" + std::to_string(channel);	×
280
281	dm->setData<DigitalEventSeries>(channel_name, digital_event_series[channel]);	×
282
283	if (item.contains("clock")) {	×
284	std::string const clock = item["clock"];	×
285	dm->setTimeFrame(channel_name, clock);	×
286	}	×
287	}	×
UNCOV 288	break;	×
289	}	×
NEW 290	case DM_DataType::DigitalInterval: {	×
291
292	auto digital_interval_series = load_into_DigitalIntervalSeries(file_path, item);	×
UNCOV 293	dm->setData<DigitalIntervalSeries>(name, digital_interval_series);	×
294
UNCOV 295	break;	×
296	}	×
NEW 297	case DM_DataType::Tensor: {	×
298
299	if (item["format"] == "numpy") {	×
300
301	TensorData tensor_data;	×
302	loadNpyToTensorData(file_path, tensor_data);	×
303
UNCOV 304	dm->setData<TensorData>(name, std::make_shared<TensorData>(tensor_data));	×
305
306	} else {	×
UNCOV 307	std::cout << "Format " << item["format"] << " not found for " << name << std::endl;	×
308	}
309	break;	×
310	}
NEW 311	case DM_DataType::Time: {	×
312
UNCOV 313	if (item["format"] == "uint16") {	×
314
315	int const channel = item["channel"];	×
UNCOV 316	std::string const transition = item["transition"];	×
317
UNCOV 318	int const header_size = item.value("header_size", 0);	×
319
320	auto opts = Loader::BinaryAnalogOptions{.file_path = file_path,	×
UNCOV 321	.header_size_bytes = static_cast<size_t>(header_size)};	×
322	auto data = readBinaryFile<uint16_t>(opts);	×
323
324	auto digital_data = Loader::extractDigitalData(data, channel);	×
UNCOV 325	auto events = Loader::extractEvents(digital_data, transition);	×
326
327	// convert to int with std::transform
328	std::vector<int> events_int;	×
329	events_int.reserve(events.size());	×
UNCOV 330	for (auto e: events) {	×
331	events_int.push_back(static_cast<int>(e));	×
332	}
333	std::cout << "Loaded " << events_int.size() << " events for " << name << std::endl;	×
334
335	auto timeframe = std::make_shared<TimeFrame>(events_int);	×
UNCOV 336	dm->setTime(name, timeframe);	×
337	}	×
338
UNCOV 339	if (item["format"] == "uint16_length") {	×
340
341	int const header_size = item.value("header_size", 0);	×
342
343	auto opts = Loader::BinaryAnalogOptions{.file_path = file_path,	×
344	.header_size_bytes = static_cast<size_t>(header_size)};	×
UNCOV 345	auto data = readBinaryFile<uint16_t>(opts);	×
346
UNCOV 347	std::vector<int> t(data.size());	×
348	std::iota(std::begin(t), std::end(t), 0);	×
349
350	std::cout << "Total of " << t.size() << " timestamps for " << name << std::endl;	×
351
352	auto timeframe = std::make_shared<TimeFrame>(t);	×
UNCOV 353	dm->setTime(name, timeframe);	×
354	}	×
UNCOV 355	break;	×
356	}
357	default:	×
358	std::cout << "Unsupported data type: " << data_type_str << std::endl;	×
UNCOV 359	continue;	×
360	}	×
361	if (item.contains("clock")) {	×
UNCOV 362	std::string const clock = item["clock"];	×
363	std::cout << "Setting time for " << name << " to " << clock << std::endl;	×
UNCOV 364	dm->setTimeFrame(name, clock);	×
365	}	×
366	}	×
367
368	return data_info_list;
UNCOV 369	}	×
370
NEW 371	DM_DataType DataManager::getType(std::string const & key) const {	×
372	auto it = _data.find(key);	×
373	if (it != _data.end()) {	×
374	if (std::holds_alternative<std::shared_ptr<MediaData>>(it->second)) {	×
NEW 375	return DM_DataType::Video;	×
376	} else if (std::holds_alternative<std::shared_ptr<PointData>>(it->second)) {	×
NEW 377	return DM_DataType::Points;	×
378	} else if (std::holds_alternative<std::shared_ptr<LineData>>(it->second)) {	×
NEW 379	return DM_DataType::Line;	×
UNCOV 380	} else if (std::holds_alternative<std::shared_ptr<MaskData>>(it->second)) {	×
NEW 381	return DM_DataType::Mask;	×
382	} else if (std::holds_alternative<std::shared_ptr<AnalogTimeSeries>>(it->second)) {	×
NEW 383	return DM_DataType::Analog;	×
384	} else if (std::holds_alternative<std::shared_ptr<DigitalEventSeries>>(it->second)) {	×
NEW 385	return DM_DataType::DigitalEvent;	×
386	} else if (std::holds_alternative<std::shared_ptr<DigitalIntervalSeries>>(it->second)) {	×
NEW 387	return DM_DataType::DigitalInterval;	×
388	} else if (std::holds_alternative<std::shared_ptr<TensorData>>(it->second)) {	×
NEW 389	return DM_DataType::Tensor;	×
390	}
NEW 391	return DM_DataType::Unknown;	×
392	}
NEW 393	return DM_DataType::Unknown;	×
394	}
395
NEW 396	std::string convert_data_type_to_string(DM_DataType type) {	×
397	switch (type) {	×
NEW 398	case DM_DataType::Video:	×
399	return "video";	×
NEW 400	case DM_DataType::Points:	×
401	return "points";	×
NEW 402	case DM_DataType::Mask:	×
UNCOV 403	return "mask";	×
NEW 404	case DM_DataType::Line:	×
UNCOV 405	return "line";	×
NEW 406	case DM_DataType::Analog:	×
UNCOV 407	return "analog";	×
NEW 408	case DM_DataType::DigitalEvent:	×
UNCOV 409	return "digital_event";	×
NEW 410	case DM_DataType::DigitalInterval:	×
UNCOV 411	return "digital_interval";	×
NEW 412	case DM_DataType::Tensor:	×
UNCOV 413	return "tensor";	×
NEW 414	case DM_DataType::Time:	×
UNCOV 415	return "time";	×
UNCOV 416	default:	×
UNCOV 417	return "unknown";	×
418	}
419	}

paulmthompson / WhiskerToolbox / 14913265839

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