14319867210

Committed 07 Apr 2025 09:29PM UTC coverage: 12.911% (-0.4%) from 13.308%

Build # 14319867210

Build Type

push

github

Committed by

paulmthompson

Commit Message

can load multi channel digital events

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0 of 89 new or added lines in 6 files covered. (0.0%)

5 existing lines in 2 files now uncovered.

208 of 1611 relevant lines covered (12.91%)

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4.18

/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 "Masks/Mask_Data_Loader.hpp"
#include "Media/Video_Data_Loader.hpp"
#include "Points/Point_Data_Loader.hpp"

#include "loaders/CSV_Loaders.hpp"
#include "loaders/binary_loaders.hpp"
#include "transforms/data_transforms.hpp"

#include "TimeFrame.hpp"

#include "utils/container.hpp"
#include "utils/glob.hpp"
#include "utils/hdf5_mask_load.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;
}

std::vector<std::vector<float>> read_ragged_hdf5(std::string const & filepath, std::string const & key) {
    auto myvector = load_ragged_array<float>(filepath, key);
    return myvector;
}

std::vector<int> read_array_hdf5(std::string const & filepath, std::string const & key) {
    auto myvector = load_array<int>(filepath, key);
    return myvector;
}

enum class DataType {
    Video,
    Points,
    Mask,
    Line,
    Analog,
    DigitalEvent,
    DigitalInterval,
    Tensor,
    Time,
    Unknown
};

DataType stringToDataType(std::string const & data_type_str) {
    if (data_type_str == "video") return DataType::Video;
    if (data_type_str == "points") return DataType::Points;
    if (data_type_str == "mask") return DataType::Mask;
    if (data_type_str == "line") return DataType::Line;
    if (data_type_str == "analog") return DataType::Analog;
    if (data_type_str == "digital_event") return DataType::DigitalEvent;
    if (data_type_str == "digital_interval") return DataType::DigitalInterval;
    if (data_type_str == "tensor") return DataType::Tensor;
    if (data_type_str == "time") return DataType::Time;
    return 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"];
        DataType const data_type = stringToDataType(data_type_str);
        if (data_type == 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 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 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 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));
                            std::string const output_name = name + "_area";
                            dm->setData<AnalogTimeSeries>(output_name, area_data);
                        }
                    }
                }
                break;
            }
            case 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 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 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 DataType::DigitalInterval: {

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

                break;
            }
            case 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 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;
}

std::string 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 "MediaData";
        } else if (std::holds_alternative<std::shared_ptr<PointData>>(it->second)) {
            return "PointData";
        } else if (std::holds_alternative<std::shared_ptr<LineData>>(it->second)) {
            return "LineData";
        } else if (std::holds_alternative<std::shared_ptr<MaskData>>(it->second)) {
            return "MaskData";
        } else if (std::holds_alternative<std::shared_ptr<AnalogTimeSeries>>(it->second)) {
            return "AnalogTimeSeries";
        } else if (std::holds_alternative<std::shared_ptr<DigitalEventSeries>>(it->second)) {
            return "DigitalEventSeries";
        } else if (std::holds_alternative<std::shared_ptr<DigitalIntervalSeries>>(it->second)) {
            return "DigitalIntervalSeries";
        } else if (std::holds_alternative<std::shared_ptr<TensorData>>(it->second)) {
            return "TensorData";
        }
        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 "Masks/Mask_Data_Loader.hpp"
16	#include "Media/Video_Data_Loader.hpp"
17	#include "Points/Point_Data_Loader.hpp"
18
19	#include "loaders/CSV_Loaders.hpp"
20	#include "loaders/binary_loaders.hpp"
21	#include "transforms/data_transforms.hpp"
22
23	#include "TimeFrame.hpp"
24
25	#include "utils/container.hpp"
26	#include "utils/glob.hpp"
27	#include "utils/hdf5_mask_load.hpp"
28
29	#include "nlohmann/json.hpp"
30	#include "utils/string_manip.hpp"
31
32	#include <filesystem>
33	#include <fstream>
34	#include <iostream>
35	#include <optional>
36	#include <regex>
37
38	using namespace nlohmann;
39
40	DataManager::DataManager() {	2✔
41	_times["time"] = std::make_shared<TimeFrame>();	6✔
42	_data["media"] = std::make_shared<MediaData>();	6✔
43
44	setTimeFrame("media", "time");	10✔
45	_output_path = std::filesystem::current_path();	2✔
46	}	2✔
47
48	void DataManager::setTimeFrame(std::string const & data_key, std::string const & time_key) {	2✔
49	//Check that data_key is in _data
50	if (_data.find(data_key) == _data.end()) {	2✔
51	std::cerr << "Data key not found in DataManager: " << data_key << std::endl;	×
52	return;	×
53	}
54
55	//Check that time_key is in _times
56	if (_times.find(time_key) == _times.end()) {	2✔
57	std::cerr << "Time key not found in DataManager: " << time_key << std::endl;	×
58	return;	×
59	}
60
61	_time_frames[data_key] = time_key;	2✔
62	}
63
64	std::vector<std::vector<float>> read_ragged_hdf5(std::string const & filepath, std::string const & key) {	×
65	auto myvector = load_ragged_array<float>(filepath, key);	×
66	return myvector;	×
67	}
68
69	std::vector<int> read_array_hdf5(std::string const & filepath, std::string const & key) {	×
70	auto myvector = load_array<int>(filepath, key);	×
71	return myvector;	×
72	}
73
74	enum class DataType {
75	Video,
76	Points,
77	Mask,
78	Line,
79	Analog,
80	DigitalEvent,
81	DigitalInterval,
82	Tensor,
83	Time,
84	Unknown
85	};
86
87	DataType stringToDataType(std::string const & data_type_str) {	×
88	if (data_type_str == "video") return DataType::Video;	×
89	if (data_type_str == "points") return DataType::Points;	×
90	if (data_type_str == "mask") return DataType::Mask;	×
91	if (data_type_str == "line") return DataType::Line;	×
92	if (data_type_str == "analog") return DataType::Analog;	×
93	if (data_type_str == "digital_event") return DataType::DigitalEvent;	×
94	if (data_type_str == "digital_interval") return DataType::DigitalInterval;	×
95	if (data_type_str == "tensor") return DataType::Tensor;	×
96	if (data_type_str == "time") return DataType::Time;	×
97	return DataType::Unknown;	×
98	}
99
100	std::optional<std::string> processFilePath(	×
101	std::string const & file_path,
102	std::filesystem::path const & base_path) {
103	std::filesystem::path full_path = file_path;	×
104
105	// Check for wildcard character
106	if (file_path.find('*') != std::string::npos) {	×
107	// Convert wildcard pattern to regex
108	std::string const pattern = std::regex_replace(full_path.string(), std::regex("\\"), ".");	×
109	std::regex const regex_pattern(pattern);	×
110
111	// Iterate through the directory to find matching files
112	for (auto const & entry: std::filesystem::directory_iterator(base_path)) {	×
113	std::cout << "Checking " << entry.path().string() << " with full path " << full_path << std::endl;	×
114	if (std::regex_match(entry.path().string(), regex_pattern)) {	×
115	std::cout << "Loading file " << entry.path().string() << std::endl;	×
116	return entry.path().string();	×
117	}
118	}	×
119	return std::nullopt;	×
120	} else {	×
121	// Check if the file path is relative
122	if (!std::filesystem::path(file_path).is_absolute()) {	×
123	full_path = base_path / file_path;	×
124	}
125	// Check for the presence of the file
126	if (std::filesystem::exists(full_path)) {	×
127	std::cout << "Loading file " << full_path.string() << std::endl;	×
128	return full_path.string();	×
129	} else {
130	return std::nullopt;	×
131	}
132	}
133	}	×
134
135	bool checkRequiredFields(json const & item, std::vector<std::string> const & requiredFields) {	×
136	for (auto const & field: requiredFields) {	×
137	if (!item.contains(field)) {	×
138	std::cerr << "Error: Missing required field \"" << field << "\" in JSON item." << std::endl;	×
139	return false;	×
140	}
141	}
142	return true;	×
143	}
144
145	int DataManager::addCallbackToData(std::string const & key, ObserverCallback callback) {	×
146
147	int id = -1;	×
148
149	if (_data.find(key) != _data.end()) {	×
150	auto data = _data[key];	×
151
152	id = std::visit([callback](auto & x) {	×
153	return x.get()->addObserver(callback);	×
154	},
155	data);
156	}	×
157
158	return id;	×
159	}
160
161	void DataManager::removeCallbackFromData(std::string const & key, int callback_id) {	×
162	if (_data.find(key) != _data.end()) {	×
163	auto data = _data[key];	×
164
165	std::visit([callback_id](auto & x) {	×
166	x.get()->removeObserver(callback_id);	×
167	},	×
168	data);
169	}	×
170	}	×
171
172	void checkOptionalFields(json const & item, std::vector<std::string> const & optionalFields) {	×
173	for (auto const & field: optionalFields) {	×
174	if (!item.contains(field)) {	×
175	std::cout << "Warning: Optional field \"" << field << "\" is missing in JSON item." << std::endl;	×
176	}
177	}
178	}	×
179
180	std::vector<DataInfo> load_data_from_json_config(DataManager * dm, std::string const & json_filepath) {	×
181	std::vector<DataInfo> data_info_list;	×
182	// Open JSON file
183	std::ifstream ifs(json_filepath);	×
184	if (!ifs.is_open()) {	×
185	std::cerr << "Failed to open JSON file: " << json_filepath << std::endl;	×
186	return data_info_list;	×
187	}
188
189	// Parse JSON
190	json j;	×
191	ifs >> j;	×
192
193	// get base path of filepath
194	std::filesystem::path const base_path = std::filesystem::path(json_filepath).parent_path();	×
195
196	// Iterate through JSON array
197	for (auto const & item: j) {	×
198
199	if (!checkRequiredFields(item, {"data_type", "name", "filepath"})) {	×
200	continue;// Exit if any required field is missing	×
201	}
202
203	std::string const data_type_str = item["data_type"];	×
204	DataType const data_type = stringToDataType(data_type_str);	×
205	if (data_type == DataType::Unknown) {	×
206	std::cout << "Unknown data type: " << data_type_str << std::endl;	×
207	continue;	×
208	}
209
210	std::string const name = item["name"];	×
211
212	auto file_exists = processFilePath(item["filepath"], base_path);	×
213	if (!file_exists) {	×
214	std::cerr << "File does not exist: " << item["filepath"] << std::endl;	×
215	continue;	×
216	}
217
218	std::string const file_path = file_exists.value();	×
219
220	switch (data_type) {	×
221	case DataType::Video: {	×
222	// Create VideoData object
223	auto video_data = load_video_into_VideoData(file_path);	×
224
225	// Add VideoData to DataManager
226	dm->setMedia(video_data);	×
227
228	data_info_list.push_back({name, "VideoData", ""});	×
229	break;	×
230	}	×
231	case DataType::Points: {	×
232
233	auto point_data = load_into_PointData(file_path, item);	×
234
235	dm->setData<PointData>(name, point_data);	×
236
237	std::string const color = item.value("color", "#0000FF");	×
238	data_info_list.push_back({name, "PointData", color});	×
239	break;	×
240	}	×
241	case DataType::Mask: {	×
242
243	auto mask_data = load_into_MaskData(file_path, item);	×
244
245	std::string const color = item.value("color", "0000FF");	×
246	dm->setData<MaskData>(name, mask_data);	×
247
248	data_info_list.push_back({name, "MaskData", color});	×
249
250	if (item.contains("operations")) {	×
251
252	for (auto const & operation: item["operations"]) {	×
253
254	std::string const operation_type = operation["type"];	×
255
256	if (operation_type == "area") {	×
257	std::cout << "Calculating area for mask: " << name << std::endl;	×
258	auto area_data = area(dm->getData<MaskData>(name));	×
259	std::string const output_name = name + "_area";	×
260	dm->setData<AnalogTimeSeries>(output_name, area_data);	×
261	}	×
262	}	×
263	}
264	break;	×
265	}	×
266	case DataType::Line: {	×
267
268	auto line_map = load_line_csv(file_path);	×
269
270	//Get the whisker name from the filename using filesystem
271	auto whisker_filename = std::filesystem::path(file_path).filename().string();	×
272
273	//Remove .csv suffix from filename
274	auto whisker_name = remove_extension(whisker_filename);	×
275
276	dm->setData<LineData>(whisker_name, std::make_shared<LineData>(line_map));	×
277
278	std::string const color = item.value("color", "0000FF");	×
279
280	data_info_list.push_back({name, "LineData", color});	×
281
282	break;	×
283	}	×
284	case DataType::Analog: {	×
285
286	auto analog_time_series = load_into_AnalogTimeSeries(file_path, item);	×
287
288	for (int channel = 0; channel < analog_time_series.size(); channel++) {	×
289	std::string const channel_name = name + "_" + std::to_string(channel);	×
290
291	dm->setData<AnalogTimeSeries>(channel_name, analog_time_series[channel]);	×
292
293	if (item.contains("clock")) {	×
294	std::string const clock = item["clock"];	×
295	dm->setTimeFrame(channel_name, clock);	×
296	}	×
297	}	×
298	break;	×
299	}	×
300	case DataType::DigitalEvent: {	×
301
302	auto digital_event_series = load_into_DigitalEventSeries(file_path, item);	×
303
NEW 304	for (int channel = 0; channel < digital_event_series.size(); channel++) {	×
NEW 305	std::string const channel_name = name + "_" + std::to_string(channel);	×
306
NEW 307	dm->setData<DigitalEventSeries>(channel_name, digital_event_series[channel]);	×
308
NEW 309	if (item.contains("clock")) {	×
NEW 310	std::string const clock = item["clock"];	×
NEW 311	dm->setTimeFrame(channel_name, clock);	×
NEW 312	}	×
NEW 313	}	×
314	break;	×
315	}	×
316	case DataType::DigitalInterval: {	×
317
318	auto digital_interval_series = load_into_DigitalIntervalSeries(file_path, item);	×
319	dm->setData<DigitalIntervalSeries>(name, digital_interval_series);	×
320
321	break;	×
322	}	×
323	case DataType::Tensor: {	×
324
325	if (item["format"] == "numpy") {	×
326
327	TensorData tensor_data;	×
328	loadNpyToTensorData(file_path, tensor_data);	×
329
330	dm->setData<TensorData>(name, std::make_shared<TensorData>(tensor_data));	×
331
332	} else {	×
333	std::cout << "Format " << item["format"] << " not found for " << name << std::endl;	×
334	}
335	break;	×
336	}
337	case DataType::Time: {	×
338
339	if (item["format"] == "uint16") {	×
340
341	int const channel = item["channel"];	×
342	std::string const transition = item["transition"];	×
343
NEW 344	int const header_size = item.value("header_size", 0);	×
345
NEW 346	auto opts = Loader::BinaryAnalogOptions{.file_path = file_path,	×
NEW 347	.header_size_bytes = static_cast<size_t>(header_size)};	×
UNCOV 348	auto data = readBinaryFile<uint16_t>(opts);	×
349
350	auto digital_data = Loader::extractDigitalData(data, channel);	×
351	auto events = Loader::extractEvents(digital_data, transition);	×
352
353	// convert to int with std::transform
354	std::vector<int> events_int;	×
355	events_int.reserve(events.size());	×
356	for (auto e: events) {	×
357	events_int.push_back(static_cast<int>(e));	×
358	}
359	std::cout << "Loaded " << events_int.size() << " events for " << name << std::endl;	×
360
361	auto timeframe = std::make_shared<TimeFrame>(events_int);	×
362	dm->setTime(name, timeframe);	×
363	}	×
364
365	if (item["format"] == "uint16_length") {	×
366
NEW 367	int const header_size = item.value("header_size", 0);	×
368
NEW 369	auto opts = Loader::BinaryAnalogOptions{.file_path = file_path,	×
NEW 370	.header_size_bytes = static_cast<size_t>(header_size)};	×
UNCOV 371	auto data = readBinaryFile<uint16_t>(opts);	×
372
373	std::vector<int> t(data.size());	×
374	std::iota(std::begin(t), std::end(t), 0);	×
375
376	std::cout << "Total of " << t.size() << " timestamps for " << name << std::endl;	×
377
378	auto timeframe = std::make_shared<TimeFrame>(t);	×
379	dm->setTime(name, timeframe);	×
380	}	×
381	break;	×
382	}
383	default:	×
384	std::cout << "Unsupported data type: " << data_type_str << std::endl;	×
385	continue;	×
386	}	×
387	if (item.contains("clock")) {	×
388	std::string const clock = item["clock"];	×
389	std::cout << "Setting time for " << name << " to " << clock << std::endl;	×
390	dm->setTimeFrame(name, clock);	×
391	}	×
392	}	×
393
394	return data_info_list;
395	}	×
396
397	std::string DataManager::getType(std::string const & key) const {	×
398	auto it = _data.find(key);	×
399	if (it != _data.end()) {	×
400	if (std::holds_alternative<std::shared_ptr<MediaData>>(it->second)) {	×
401	return "MediaData";	×
402	} else if (std::holds_alternative<std::shared_ptr<PointData>>(it->second)) {	×
403	return "PointData";	×
404	} else if (std::holds_alternative<std::shared_ptr<LineData>>(it->second)) {	×
405	return "LineData";	×
406	} else if (std::holds_alternative<std::shared_ptr<MaskData>>(it->second)) {	×
407	return "MaskData";	×
408	} else if (std::holds_alternative<std::shared_ptr<AnalogTimeSeries>>(it->second)) {	×
409	return "AnalogTimeSeries";	×
410	} else if (std::holds_alternative<std::shared_ptr<DigitalEventSeries>>(it->second)) {	×
411	return "DigitalEventSeries";	×
412	} else if (std::holds_alternative<std::shared_ptr<DigitalIntervalSeries>>(it->second)) {	×
413	return "DigitalIntervalSeries";	×
414	} else if (std::holds_alternative<std::shared_ptr<TensorData>>(it->second)) {	×
415	return "TensorData";	×
416	}
417	return "Unknown";	×
418	}
419	}

paulmthompson / WhiskerToolbox / 14319867210

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