diff --git a/.MATLABDriveTag b/.MATLABDriveTag deleted file mode 100644 index 84059a2..0000000 --- a/.MATLABDriveTag +++ /dev/null @@ -1 +0,0 @@ -3496f669-9381-4974-bb7c-5cc1ddcb05d4 \ No newline at end of file diff --git a/pgmatlab/.Rhistory b/.Rhistory similarity index 100% rename from pgmatlab/.Rhistory rename to .Rhistory diff --git a/.github/workflows/build-package.yml b/.github/workflows/build-package.yml new file mode 100644 index 0000000..9b5a851 --- /dev/null +++ b/.github/workflows/build-package.yml @@ -0,0 +1,36 @@ +# This workflow will automatically create a ZIP file +# of the distribution files, and add them to a GitHub +# release. It only runs, on creation of the GitHub +# release. + +name: Build Package + +on: + release: + types: [published] + +permissions: + contents: write + +jobs: + build: + runs-on: ubuntu-latest + + steps: + - name: Checkout code + uses: actions/checkout@v4 + + - name: Zip code to distribute + run: | + zip -r "pgmatlab-${{ github.event.release.tag_name }}.zip" pgmatlab/* LICENSE README.md + + - name: Upload code to distribute + uses: actions/upload-artifact@v4 + with: + name: dist-files + path: "pgmatlab-${{ github.event.release.tag_name }}.zip" + + - name: Append distribution code to release + uses: softprops/action-gh-release@v2 + with: + files: "pgmatlab-${{ github.event.release.tag_name }}.zip" \ No newline at end of file diff --git a/.github/workflows/build-toolbox.yml b/.github/workflows/build-toolbox.yml new file mode 100644 index 0000000..82066ca --- /dev/null +++ b/.github/workflows/build-toolbox.yml @@ -0,0 +1,35 @@ +name: Build MATLAB Toolbox + +on: + release: + types: [published] + +jobs: + build: + runs-on: ubuntu-latest + steps: + - name: Checkout repository + uses: actions/checkout@v3 + + - name: Set MATLAB version + uses: matlab-actions/setup-matlab@v2.1.2 + with: + release: 'R2025a' + + - name: Determine toolbox version + id: version + run: | + # Remove leading 'v' from git tag + echo "VERSION=${{ github.event.release.tag_name }}" >> $GITHUB_ENV + + - name: Build toolbox + run: | + matlab -batch " + opts = matlab.addons.toolbox.ToolboxOptions('pgmatlab_toolbox.prj'); + opts.ToolboxVersion = getenv('VERSION'); + matlab.addons.toolbox.packageToolbox(opts, sprintf('pgmatlab_%s.mltbx', getenv('VERSION')));" + + - name: Attach to GitHub release + uses: softprops/action-gh-release@v2 + with: + files: "pgmatlab_*.mltbx" \ No newline at end of file diff --git a/.github/workflows/matlab-testing.yml b/.github/workflows/matlab-testing.yml new file mode 100644 index 0000000..469bc5d --- /dev/null +++ b/.github/workflows/matlab-testing.yml @@ -0,0 +1,38 @@ +name: MATLAB Testing + +# Controls when the workflow will run +on: + # Triggers the workflow on push or pull request events but only for the "main" branch + push: + branches: [ "v2", "main" ] + pull_request: + branches: [ "v2", "main" ] + + # Allows you to run this workflow manually from the Actions tab + workflow_dispatch: + +# A workflow run is made up of one or more jobs that can run sequentially or in parallel +jobs: + # This workflow contains a single job called "build" + build: + # The type of runner that the job will run on + runs-on: ${{ matrix.os }} + strategy: + matrix: + matlab-version: [r2020a, r2021a, r2022a, r2023a, r2025a] + os: [ubuntu-latest, windows-latest, macos-latest] + + + steps: + - name: Check out repository + uses: actions/checkout@v4 + + - name: Set up MATLAB + uses: matlab-actions/setup-matlab@v2.1.2 + with: + version: ${{ matrix.matlab-version }} + + - name: Run MATLAB Tests + uses: matlab-actions/run-tests@v2.1.2 + with: + select-by-folder: tests \ No newline at end of file diff --git a/.gitignore b/.gitignore index e77c42a..e511779 100644 --- a/.gitignore +++ b/.gitignore @@ -11,3 +11,4 @@ pgmatlab/Array/.MATLABDriveTag .MATLABDriveTag pgmatlab/.MATLABDriveTag pgmatlab/Array/.MATLABDriveTag +*.mltbx \ No newline at end of file diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md new file mode 100644 index 0000000..4c6c6ee --- /dev/null +++ b/CONTRIBUTING.md @@ -0,0 +1,237 @@ +# Contributing Guidelines + +PAMGuardMatlab is an open-source project. Whilst out license does not require it, we welcome you to contribute any changes you make back to the original repository. + +## Getting Started + +If you're planning on making contributions to PAMGuardMatlab, we highly recommend that you fork the repository, and then clone it into your machine. In the MATLAB editor, on the left sidebar, click on the 'Project' button then select [pgmatlab.prj](pgmatlab.prj) in the root of your cloned repository. This will automatically set-up the development environment, including the MATLAB path. + +## Testing + +There is a comprehensive testing suite located in the [tests](tests) folder. To run these tests, run the following commands. + +```commandline +cd tests; +runtests; +``` + +If you add new functionality to PAMGuardMatlab, please ensure you write appropriate unit tests in the testing suite. + +> If you find that the changes you have made are failing existing tests (due to an existing bug in the program or the testing suite), you are welcome to change the testing suite. + +## Making a Pull Request + +Once you are satisfied with your tested changes, you should make a pull request, linking an issue and with a detailed commit history (if there is one), changelog, and details and any new tests written. + +The GitHub repository will automatically run the unit tests in MacOS, Linux, and Windows - and you can see this by viewing your pull request. + +## Creating a New Release + +Stable code is maintained through new releases. This allows users to download a lightweight copy of the code without development tools such as tests. + +Upon the creation of a release, the following CI action is executed (allow 30-60 seconds for this to complete): + +- The user-facing code (README.md, LICENCE, pgmatlab/*) is put in an archive and attached to the release. + +Releases should be semantically named and tagged like so. These tags are dynamically inserted in the tarball and wheel uploaded to PyPI. + +- V1.2.3 + - Tag: v1.2.3 +- V1.2.3 Beta 1 + - Tag: v1.2.3-b1 +- V1.2.3 Alpha 1 + - Tag: v1.2.3-a1 + +## Structure + +All the source code is found in the [pgmatlab/+pgmatlab](pgmatlab/+pgmatlab/) folder. + +Folders use the plus (+) prefix to be treated as a 'package' (where [+pgmatlab](pgmatlab/+pgmatlab/) is the root). By adding [pgmatlab/](pgmatlab/) only the namespace `pgmatlab` is added to the MATLAB path. All classes and functions are accessible through sub-packages, such as: `pgmatlab.utils.millisToDateNum()`. We have temporarily kept three legacy entry points in the root source code folder to allow existing users to continue using the updated code. + +PAMGuardMatlab has three main sub-packages: + +1. [+core](pgmatlab/+pgmatlab/+core/): contains classes for reading chunks from data files. + +2. [+db](pgmatlab/+pgmatlab/+db/): contains functions for interacting with the database (legacy). + +3. [+utils](pgmatlab/+pgmatlab/+utils/): contains functions +for utilities used by the rest of the library. + +## Adding New Modules + +The object-oriented structure of PAMGuardMatlab allows you to easily create new modules by extending the base classes. This section provides templates and instructions for creating new module types. + +### Creating a New Module Class + +To create a new module, you need to extend the `StandardModule` class and implement the required abstract methods. + +#### Template for a New Module + +Create a new file in `pgmatlab/+pgmatlab/+core/+modules/` with the following template: + +```matlab +classdef YourModuleName < pgmatlab.core.standard.StandardModule + properties (Access = public) + objectType = 'Your Object Type'; % Set this to match PAMGuard's object type + end + + methods + function obj = YourModuleName() + % Constructor - set custom header/footer classes if needed + obj.header = @pgmatlab.core.standard.StandardModuleHeader; + obj.footer = @pgmatlab.core.standard.StandardModuleFooter; + obj.background = -1; % Set to a background class if needed + end + + function [data, selState] = readImpl(obj, fid, data, fileInfo, length, identifier, selState) + % Read module-specific data from the binary file + % This is where you implement the actual data reading logic + + % Example: Read some custom fields + data.customField1 = fread(fid, 1, 'int32'); + data.customField2 = fread(fid, 1, 'double'); + + % Additional processing can be done here + + % Return selState (1 = keep, 0 = skip, 2 = stop if sorted) + selState = 1; + end + + function [data, selState] = readBackgroundImpl(obj, fid, data, fileInfo, length, identifier, selState) + % Optional: Implement background data reading if your module has background data + % Leave empty if no background data + end + end +end +``` + +#### Creating Custom Header Classes + +If your module requires a custom header format, create a class extending `StandardModuleHeader`: + +```matlab +classdef YourModuleHeader < pgmatlab.core.standard.StandardModuleHeader + methods + function data = readImpl(obj, fid, data, fileInfo, length, identifier) + % Call parent implementation first + data = readImpl@pgmatlab.core.standard.StandardModuleHeader(obj, fid, data, fileInfo, length, identifier); + + % Read custom header fields + data.customHeaderField = fread(fid, 1, 'int32'); + + % Process additional header data as needed + end + end +end +``` + +#### Creating Custom Footer Classes + +Similarly, for custom footers, extend `StandardModuleFooter`: + +```matlab +classdef YourModuleFooter < pgmatlab.core.standard.StandardModuleFooter + methods + function data = readImpl(obj, fid, data, fileInfo, length, identifier) + % Call parent implementation first + data = readImpl@pgmatlab.core.standard.StandardModuleFooter(obj, fid, data, fileInfo, length, identifier); + + % Read custom footer fields + data.customFooterField = fread(fid, 1, 'int32'); + end + end +end +``` + +#### Creating Custom Background Classes + +For modules with background data, extend `StandardBackground`: + +```matlab +classdef YourModuleBackground < pgmatlab.core.standard.StandardBackground + properties (Access = public) + objectType = 'Your Background Object Type'; + end + + methods + function [data, selState] = readImpl(obj, fid, data, fileInfo, length, identifier, selState) + % Read background-specific data + data.backgroundField1 = fread(fid, 1, 'double'); + data.backgroundField2 = fread(fid, [1, 10], 'int16'); + + selState = 1; + end + end +end +``` + +### Registering Your Module + +After creating your module class, you need to register it in the main loading function. Add your module to the switch statement in `loadPamguardBinaryFile.m`: + +```matlab +% In the file header case (-1) switch statement: +case 'Your Module Type' + switch fileInfo.fileHeader.streamName + case 'Your Stream Name' + moduleObj = pgmatlab.core.modules.YourModuleName(); + % Add additional stream cases if needed + end +``` + +The module type should match the string used by PAMGuard's module (found in the Java code), and the stream name should match the data stream name used by your PAMGuard module. + +### Testing Your Module + +1. Create test data using your PAMGuard module +2. Add test cases to the appropriate test file in the `tests/` folder +3. Run the tests to ensure your module loads data correctly: + +```matlab +cd tests; +runtests('YourModuleTest'); +``` + +### Example: Complete Module Implementation + +Here's a complete example of a simple module: + +```matlab +classdef ExampleModule < pgmatlab.core.standard.StandardModule + properties (Access = public) + objectType = 'Example Detection'; + end + + methods + function obj = ExampleModule() + obj.header = @pgmatlab.core.standard.StandardModuleHeader; + obj.footer = @pgmatlab.core.standard.StandardModuleFooter; + obj.background = -1; + end + + function [data, selState] = readImpl(obj, fid, data, fileInfo, length, identifier, selState) + % Read example-specific fields + data.detectionType = fread(fid, 1, 'int32'); + data.confidence = fread(fid, 1, 'double'); + data.frequency = fread(fid, 1, 'double'); + + % Validate data + if data.confidence < 0 || data.confidence > 1 + warning('Invalid confidence value: %f', data.confidence); + end + + selState = 1; + end + end +end +``` + +Then register it in `loadPamguardBinaryFile.m`: + +```matlab +case 'Example Detector' + switch fileInfo.fileHeader.streamName + case 'Example Detections' + moduleObj = pgmatlab.core.modules.ExampleModule(); + end +``` \ No newline at end of file diff --git a/README.md b/README.md index 923e2bb..66f0c40 100644 --- a/README.md +++ b/README.md @@ -1,120 +1,308 @@ # PAMGuardMatlab -[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.16979862.svg)](https://doi.org/10.5281/zenodo.16979862) +[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.17641583.svg)](https://doi.org/10.5281/zenodo.17641583) -PAMGuard binary files contains detections such as clicks, whistle contours, deep learning detections, noise, long term spectral averages etc. Binary files provide an efficient and very fast data management system but are not human readable. The `PAMGuard-MATLAB` library is a set of functions that allows the importing of PAMGuard binary files directly into MATLAB. -### Installation +A MATLAB library for loading [PAMGuard binary files](https://www.pamguard.org/olhelp/utilities/BinaryStore/docs/binarystore_overview.html) containing acoustic detection data including clicks, whistle contours, deep learning detections, noise measurements, and spectral data. PAMGuard binary files provide efficient data storage and fast access, but are not human-readable. This library allows you to import PAMGuard binary data directly into MATLAB. -`PAMGuard-MATLAB` needs to be downloaded from here (or via a git client e.g. the integrated one in MATLAB) and added to you MATLAB path +## Installation -### Tutorial +1. Go to [GitHub Releases](https://github.com/PAMGuard/PAMGuardMatlab/releases) +2. Download the latest `pgmatlab-{version}.zip` file +3. Extract the ZIP file to your desired location +4. Add the extracted `pgmatlab` folder to your MATLAB path: -The core function of this library is `loadPamguardBinaryFile`. This loads any PAMGuard binary file, automatically figures out what type of data it contains and then imports the data into a struct with relevant field names. Usage is straightforward, simply point the function to the correct file. +```matlab +addpath('path/to/extracted/pgmatlab'); +``` +You only need to add the one pgmatlab folder to your path to use the main PAMGuard binary file functions. +However, if you're using any of the utility and database functions directly within your own code, +you'll need to either import the namespaces, import individual functions from within the namespaces, +or put the full namespace path in every function call: + ```matlab -binaryfile= './Files/SomeBinaryFile.pgdf' -[binarydata, fileinfo]= loadPamguardBinaryFile(myBinaryFile) +import pgmatlab.utils.*; % import PAMGuard utils functions +import pgmatlab.db.*; % import PAMGuard database functions ``` -`fileinfo` contains information about the binary file e.g. when it was created, what version of PAMGuard was used to process the data. `binarydata` is a struct with relevant field names. Some of these field names are consistent across different types of detections e.g. millis, date, UID and others are unique to the particular detection. +## Quick Start -An example of the fields from a click detection are: +Load a single binary file: -**millis:** the start time of the click in milliseconds; this number can be -converted to a date/time with millisecond accuracy. +```matlab +[data, fileInfo] = loadPamguardBinaryFile('path/to/file.pgdf'); +``` -**date:** the start time of the click in MATLAB datenum format. Use datastr(date) -to show a time string. +Load multiple files from a folder: -**UID:** a unique serial number for the -detection. Within a processed dataset no other detection will have this number. +```matlab +data = loadPamguardBinaryFolder('path/to/folder', '*.pgdf'); +``` -**startSample:** The first sample of this click- often used for -finer scale time delay measurements. Samples refers to the number of samples in -total the sound card has taken since processing begun. +Load specific data points across multiple files: -**channelMap:** The channel map for this click. One number which -represents which channels this click detection is from: To get the true -channels use the *getChannels(channelMap)* function. +```matlab +fileNames = {'file1.pgdf', 'file2.pgdf'}; +uids = [500001, 500002]; +eventData = loadPamguardMultiFile('path/to/folder', fileNames, uids); +``` -**triggerMap:** which channel triggered the detection. +## Core Functions -**type:** Classification type. Must use database or settings to see what species -this refers to. +### `loadPamguardBinaryFile` -**duration:** Duration of this click detection in samples. +The primary function for loading individual PAMGuard binary files. Automatically detects the data type and imports it into a structured format. -**nChan:** Number of channels the -detection was made on. +**Syntax:** +```matlab +[data, fileInfo, selState] = loadPamguardBinaryFile(filename, ...) +[data, fileInfo] = loadPamguardBinaryFile(filename, ...) +data = loadPamguardBinaryFile(filename, ...) +``` -**wave:** Waveform data for each channel. +**Parameters:** +- `filename` - Path to the binary file +- Optional name-value pairs: + - `'timerange', [startTime, endTime]` - Load data within time range + - `'uidrange', [startUID, endUID]` - Load data within UID range + - `'uidlist', [uid1, uid2, ...]` - Load specific UIDs + - `'channel', channelMap` - Load data from specific channels + - `'filter', @filterFunction` - Apply custom filter function + - `'sorted', true/false` - Optimize for sorted data (default: false) -There are a few additional options for `loadPamguardBinaryFile`. +**Examples:** -Time ranges to load can be defined. +Load entire file: +```matlab +[data, fileInfo] = loadPamguardBinaryFile('detections.pgdf'); +``` +Load specific time range: ```matlab -timerange = [datenum('2020-03-19 20:00:00', 'yyyy-mm-dd HH:MM:SS'),... - datenum('2020-03-19 21:00:00', 'yyyy-mm-dd HH:MM:SS')]; -[binarydata, fileinfo]= loadPamguardBinaryFile(myBinaryFile, 'timerange', timerange) +startTime = datenum(2023,1,15,10,0,0); +endTime = datenum(2023,1,15,11,0,0); +[data, fileInfo] = loadPamguardBinaryFile('detections.pgdf', ... + 'timerange', [startTime, endTime], 'sorted', true); ``` -UID's are unique serial numbers for each detection. They are sequential and users can define values to load via. +Load specific UIDs: +```matlab +[data, fileInfo] = loadPamguardBinaryFile('detections.pgdf', ... + 'uidlist', [500001, 500005, 500010]); +``` +Apply custom filter: ```matlab -uids = 3456:8679; -[binarydata, fileinfo]= loadPamguardBinaryFile(myBinaryFile, 'uidlist', uids) +function keep = myFilter(detection) + keep = detection.amplitude > 0.5; % Keep high amplitude detections +end + +[data, fileInfo] = loadPamguardBinaryFile('detections.pgdf', ... + 'filter', @myFilter); ``` -Some files can have multiple channel groups. Each channel group can contain one or more channels of data. To load detections with a specific channel map use. +### `loadPamguardBinaryFolder` + +Load multiple binary files from a folder using file pattern matching. +**Syntax:** ```matlab -channel = 3; %channel map -[binarydata, fileinfo]= loadPamguardBinaryFile(myBinaryFile, 'channel', channel) +[allData, allBackground, fileInfos] = loadPamguardBinaryFolder(dir, fileMask, verbose, filterfun, ...) +[allData, allBackground] = loadPamguardBinaryFolder(dir, fileMask, verbose, filterfun, ...) +allData = loadPamguardBinaryFolder(dir, fileMask, verbose, filterfun, ...) ``` -If you don't know the bitmap then you can create it using a list of channels via +**Parameters:** +- `dir` - Directory containing binary files +- `fileMask` - File pattern (e.g., '*.pgdf', 'WhistlesMoans_*.pgdf') +- `verbose` - Progress logging interval (0 = no logging) +- `filterfun` - Filter function or 0 for no filtering +- Additional name-value pairs as in `loadPamguardBinaryFile` + +**Examples:** + +Load all click detections: +```matlab +clickData = loadPamguardBinaryFolder('./Data', 'Click_*.pgdf', 1, 0); +``` +Load whistle data with filtering: ```matlab -function [channelMap] = makeChannelList(channels) -%MAKECHANNELLIST Make a channel bitmap from list. -% [CHANNELMAP] = MAKECHANNELLIST(CHANNELS) makes a channel bitmap from a -% list of channels. Noted channel numbers are from zero, not one. +whistleData = loadPamguardBinaryFolder('./Data', 'WhistlesMoans_*.pgdf', ... + 0, @myFilter, 'channel', 1); +``` -channelMap=0; -for i=1:length(channels) - channelMap = channelMap + bitsll(1,channels(i)); -end +### `loadPamguardMultiFile` + +Load specific data points from multiple files, useful for event-based analysis. + +**Syntax:** +```matlab +eventData = loadPamguardMultiFile(dir, fileNames, UIDs, verbose) ``` -Finally, there is an option to define a custom filter for data using +**Parameters:** +- `dir` - Directory containing the files +- `fileNames` - Cell array of filenames +- `UIDs` - Array of UIDs to load (parallel to fileNames) +- `verbose` - Progress logging (optional, default: 0) + +**Example:** +Load specific detections from multiple files: ```matlab -myfilter = @myfilterfunction; +files = {'clicks_20230115_100000.pgdf', 'clicks_20230115_110000.pgdf'}; +uids = [500001, 500123]; +eventData = loadPamguardMultiFile('./Data', files, uids, 1); +``` + + + +## Supported Modules + +PAMGuardMatlab supports the following PAMGuard modules: + +**Detectors:** +- Click Detector +- Whistle and Moan Detector +- GPL Detector +- Right Whale Edge Detector + +**Classifiers:** +- Deep Learning Classifier + +**Processing Modules:** +- AIS Processing +- Clip Generator +- DIFAR Processing +- Long Term Spectral Average (LTSA) +- Noise Band Monitor +- Noise Monitor + +**Plugins:** +- Sperm Whale IPI +- Gemini Threshold Detector + +## Performance Tips + +1. **Use sorted flag** when loading time/UID ranges from chronologically ordered files +2. **Specify file masks** when loading folders to avoid processing unnecessary files +3. **Use filters** to reduce memory usage for large datasets +4. **Load specific channels** rather than all channels when possible -[binarydata, fileinfo]= loadPamguardBinaryFile(myBinaryFile, 'filter', myfilter); +## Utility Functions -function [passed] = myfilterfunction(dataunit) - passed=false; - if (length(dataunit.wave)>100) - passed =true; +To use the functions in +utils you will need to import that folder in every +function that uses this library +```matlab +import pgmatlab.utils.* +``` + +### Channel Map Functions + +Convert channel lists to bitmaps: +```matlab +function channelMap = makeChannelMap(channels) + channelMap = 0; + for i = 1:length(channels) + channelMap = channelMap + bitshift(1, channels(i)); end end ``` -### Load a folder of data +Extract channels from bitmap: +```matlab +import pgmatlab.utils.* +channels = getChannels(channelMap); +``` -There is a convenience function to load a folder of binary files. Folders contain a mix of data from different detections in PAMGuard and so the load folder function requires a `filemask` input to define which type of data to import. Below shows an example to load a folder of whistle contours. +### Time Conversion +Convert milliseconds to MATLAB datenum: ```matlab -binaryfolder= './Files/SomeBinaryFolder' -filemask='WhistlesMoans_*.pgdf'; -whistles = loadPAMGuardBinaryFolder(binaryfolder,filemask); +matlabTime = pgmatlab.utils.millisToDateNum(milliseconds); ``` -To load different types of detections change the `filemask` variable to a filename identifier that is unique to the detection type. +## Database Functions + +To use the functions in +db you will need to import that folder in every +function that uses this library +```matlab +import pgmatlab.db.* +``` + +This folder contains an ad-hoc set of database functions written to support our own research. They +are not directly associated with reading binary files, but can be a useful companion to +the binary file functions. + +### Getting a database connection + +If you're using the PAMGuard sqlite database, Matlab provide a built in function to open sqlite +database files +```matlab +conn = sqlite(dbfile,mode) +``` +However, we've found that queries using connections from the sqlite function fail when any columms +contain null data. Therefore, to read data from a PAMGuard database, we recommend using our own +function +```matlab +import pgmatlab.db.* +conn = sqlitedatabase(dbfile) +``` +which uses a different library that supports null data. + +**HOWEVER !!!** + +We've also found that the the sqlite function is slightly better at writing data than +sqlitedatabase. In particular, when writing TIMESTAMPS to a databsae, sqlitedatabase seems +to convert times to long integer times in milliseconds, whereas a database opened with the sqlite +function will write them correctly in a human readable date format. -### Compatibility +So yes: Use sqlitedatabase to read from a PAMGuard database, and sqlite to write to one. -PAMGuard-MATLAB should be compatible with Pamguard v2.00.15 and earlier. +### Database Timestamp conversion + +Timestamps are usually returned in a String or char array format. Use the dbdate2datenum function +to convert these data to Matlab dates + +```matlab +import pgmatlab.utils.* +import pgmatlab.db.* +dbFile = './mydata/somedatabse.sqlite3'; +conn = sqlitedatabase(dbFile); +data = conn.fetch('SELECT * FROM Sometableorother'); +matlabDates = dbdate2datenum(data.UTC); +``` + +Although Matlab now supports a more advanced date handling functions using datetime arrays, +we've found that the performance of these is poor and are currently sticking with the simple +numeric dates, which are the number of days that have elapsed since '00-Jan-0000'. + + +## Compatibility + +- Compatible with PAMGuard v2.00.15 and later +- Requires MATLAB R2016b or later +- Supports Windows, macOS, and Linux + +## Contributing + +Contributions are welcome! See [contributing.md](contributing.md) for development guidelines, including: + +- How to set up the development environment +- Testing procedures +- How to add support for new PAMGuard modules +- Pull request guidelines + +## License + +See [LICENSE](LICENSE) file for details. + +## Citation + +If you use PAMGuardMatlab in your research, please cite: + +``` +PAMGuardMatlab (2024). Zenodo. DOI: 10.5281/zenodo.16979862 +``` diff --git a/pgmatlab.prj b/pgmatlab.prj new file mode 100644 index 0000000..6b95f98 --- /dev/null +++ b/pgmatlab.prj @@ -0,0 +1,2 @@ + + diff --git a/pgmatlab/+pgmatlab/+core/+annotations/@BeamFormer/BeamFormer.m b/pgmatlab/+pgmatlab/+core/+annotations/@BeamFormer/BeamFormer.m new file mode 100644 index 0000000..2a6baa8 --- /dev/null +++ b/pgmatlab/+pgmatlab/+core/+annotations/@BeamFormer/BeamFormer.m @@ -0,0 +1,18 @@ + +classdef BeamFormer < pgmatlab.core.standard.StandardAnnotation + properties + name = "BeamFormer" + end + methods + function obj = BeamFormer(); end + function [data, selState] = read(obj, fid, data, fileInfo, anLength, anVersion); + [data, selState] = read@pgmatlab.core.standard.StandardAnnotation(obj, fid, data, fileInfo, anLength, anVersion); + + data.hydrophones = fread(fid, 1, 'uint32'); + data.arrayType = fread(fid, 1, 'int16'); + data.localisationContent = fread( fid, 1, 'uint32'); + data.nAngles = fread(fid, 1, 'int16'); + data.angles = fread(fid, data.nAngles, 'float32'); + end + end +end \ No newline at end of file diff --git a/pgmatlab/+pgmatlab/+core/+annotations/@Bearing/Bearing.m b/pgmatlab/+pgmatlab/+core/+annotations/@Bearing/Bearing.m new file mode 100644 index 0000000..bb6e287 --- /dev/null +++ b/pgmatlab/+pgmatlab/+core/+annotations/@Bearing/Bearing.m @@ -0,0 +1,26 @@ + +classdef Bearing < pgmatlab.core.standard.StandardAnnotation + properties + name = "Bearing" + end + methods + function obj = Bearing(); end + function [data, selState] = read(obj, fid, data, fileInfo, anLength, anVersion) + [data, selState] = read@pgmatlab.core.standard.StandardAnnotation(obj, fid, data, fileInfo, anLength, anVersion); + + data.algorithmName = pgmatlab.utils.readJavaUTFString(fid); + data.version = anVersion; + data.hydrophones = fread(fid, 1, 'uint32'); + data.arrayType = fread(fid, 1, 'int16'); + data.localisationContent = fread( fid, 1, 'uint32'); + data.nAngles = fread(fid, 1, 'int16'); + data.angles = fread(fid, data.nAngles, 'float32'); + data.nErrors = fread(fid, 1, 'int16'); + data.errors = fread(fid, data.nErrors, 'float32'); + if (anVersion >= 2) + nAng = fread(fid, 1, 'int16'); + data.refAngles = fread(fid, nAng, 'float32') + end + end + end +end \ No newline at end of file diff --git a/pgmatlab/+pgmatlab/+core/+annotations/@ClickClsFr/ClickClsFr.m b/pgmatlab/+pgmatlab/+core/+annotations/@ClickClsFr/ClickClsFr.m new file mode 100644 index 0000000..11cc848 --- /dev/null +++ b/pgmatlab/+pgmatlab/+core/+annotations/@ClickClsFr/ClickClsFr.m @@ -0,0 +1,16 @@ +classdef ClickClsFr < pgmatlab.core.standard.StandardAnnotation + properties + name = "ClickClsFr" + end + methods + function obj = ClickClsFr(); end + function [data, selState] = read(obj, fid, data, fileInfo, anLength, anVersion); + [data, selState] = read@pgmatlab.core.standard.StandardAnnotation(obj, fid, data, fileInfo, anLength, anVersion); + nclassifications = fread(fid, 1, 'int16'); + for i = 1:nclassifications + data.classify_set(i) = fread(fid, 1, 'int16'); + end + end + end +end + diff --git a/pgmatlab/+pgmatlab/+core/+annotations/@DL/DL.m b/pgmatlab/+pgmatlab/+core/+annotations/@DL/DL.m new file mode 100644 index 0000000..1405877 --- /dev/null +++ b/pgmatlab/+pgmatlab/+core/+annotations/@DL/DL.m @@ -0,0 +1,65 @@ +classdef DL < pgmatlab.core.standard.StandardAnnotation + properties + name = 'dlclassification'; + end + + methods (Access = private) + function modeldata = readModelData(~, fid) + + modeltype = fread(fid, 1, 'char'); % bye in Java + + isbinary = fread(fid, 1, 'char'); % bye in Java + isbinary = isbinary~=0; % boolean is stored as byte in Java + scale = fread(fid, 1, 'float'); % the scale for prediciton results - short in Java + nspecies = fread(fid, 1, 'int16'); % the scale for prediciton results - short in Java + + % read prediciton results + tempdata=-1*ones(length(nspecies),1); + for j=1:nspecies + tempdata(j) = fread(fid, 1, 'int16')/scale; + end + + % get the class name IDs + nclass = fread(fid, 1, 'int16'); % the number of class names.classnames + classnames=-1*ones(length(nclass),1); + for j=1:nclass + classnames(j) = fread(fid, 1, 'int16'); + end + + switch (modeltype) + + case 0 % generic deep learning annotation + modeldata.predictions = tempdata; + modeldata.classID = classnames; + modeldata.isbinary = isbinary; + modeldata.type = modeltype; + case 1 % Sound Spot classifier. + % Sound spot + modeldata.predictions = tempdata; + modeldata.classID = classnames; + modeldata.isbinary = isbinary; + modeldata.type = modeltype; + + case 2 % dummy result + modeldata.predictions = []; + modeldata.type = 'dummy'; + end + end + end + + methods + function obj = DL(); end + function [data, selState] = read(obj, fid, data, fileInfo, anLength, anVersion) + + nummodels = fread(fid, 1, 'int16'); % short in Java + + % disp(['Num models: ' num2str(nummodels)]) + % read the data from each model. + % data = zeros(1, nummodels); + for i=1:nummodels + data(i) = obj.readModelData(fid); + end + end + end +end + diff --git a/pgmatlab/+pgmatlab/+core/+annotations/@MatchCls/MatchCls.m b/pgmatlab/+pgmatlab/+core/+annotations/@MatchCls/MatchCls.m new file mode 100644 index 0000000..052960f --- /dev/null +++ b/pgmatlab/+pgmatlab/+core/+annotations/@MatchCls/MatchCls.m @@ -0,0 +1,54 @@ +classdef MatchCls < pgmatlab.core.standard.StandardAnnotation + properties + name = 'MatchCls'; + end + methods + function obj = MatchCls(); end + function [data, selState] = read(obj, fid, data, fileInfo, anLength, anVersion) + [data, selState] = read@pgmatlab.core.standard.StandardAnnotation(obj, fid, data, fileInfo, anLength, anVersion); + + if (anVersion==1) + %the threshold value. This is used to classify the clicks. + threshold = fread(fid, 1, 'double'); + + %the maximum correlation between the match template and the click + matchcorr = fread(fid, 1, 'double'); + + %the max correlation value between the reject template and the click. + rejectcorr = fread(fid, 1, 'double'); + + data = [threshold matchcorr rejectcorr]; + + end + + % new version with multiple templates. + if (anVersion==2) + %read the number of templates there are + ntemplates = fread(fid, 1, 'int16'); % short in Java + + n=1; + data=zeros(ntemplates,3); % pre allocate the data array, + for i=1:ntemplates + + %the threshold value. This is used to classify the clicks. + threshold = fread(fid, 1, 'double'); + + %the maximum correlation between the match template and the click + matchcorr = fread(fid, 1, 'double'); + + %the max correlation value between the reject template and the click. + rejectcorr = fread(fid, 1, 'double'); + + data(n,1) = threshold; + data(n,2) = matchcorr; + data(n,3) = rejectcorr; + n=n+1; + + end + end + end + end +end + + + diff --git a/pgmatlab/+pgmatlab/+core/+annotations/@RWUDP/RWUDP.m b/pgmatlab/+pgmatlab/+core/+annotations/@RWUDP/RWUDP.m new file mode 100644 index 0000000..9d4ceca --- /dev/null +++ b/pgmatlab/+pgmatlab/+core/+annotations/@RWUDP/RWUDP.m @@ -0,0 +1,18 @@ +classdef RWUDP < pgmatlab.core.standard.StandardAnnotation + properties + name = 'RWUDP'; + end + methods + function obj = RWUDP(); end + function [data, selState] = read(obj, fid, data, fileInfo, anLength, anVersion) + [data, selState] = read@pgmatlab.core.standard.StandardAnnotation(obj, fid, data, fileInfo, anLength, anVersion); + + data.label = pgmatlab.utils.readJavaUTFString(fid); + data.method = pgmatlab.utils.readJavaUTFString(fid); + data.score = fread(fid, 1, 'float32'); + end + end +end + + + diff --git a/pgmatlab/+pgmatlab/+core/+annotations/@TDBL/TDBL.m b/pgmatlab/+pgmatlab/+core/+annotations/@TDBL/TDBL.m new file mode 100644 index 0000000..0f9bdcc --- /dev/null +++ b/pgmatlab/+pgmatlab/+core/+annotations/@TDBL/TDBL.m @@ -0,0 +1,16 @@ +classdef TDBL < pgmatlab.core.standard.StandardAnnotation + properties + name = 'TDBL'; + end + methods + function obj = TDBL(); end + function [data, selState] = read(obj, fid, data, fileInfo, anLength, anVersion) + [data, selState] = read@pgmatlab.core.standard.StandardAnnotation(obj, fid, data, fileInfo, anLength, anVersion); + + nAngles = fread(fid, 1, 'int16'); + data.angles = fread(fid, nAngles, 'float32'); + nErrors = fread(fid, 1, 'int16'); + data.angleErrors = fread(fid, nErrors, 'float32'); + end + end +end diff --git a/pgmatlab/+pgmatlab/+core/+annotations/@TM/TM.m b/pgmatlab/+pgmatlab/+core/+annotations/@TM/TM.m new file mode 100644 index 0000000..d30f4f9 --- /dev/null +++ b/pgmatlab/+pgmatlab/+core/+annotations/@TM/TM.m @@ -0,0 +1,22 @@ +classdef TM < pgmatlab.core.standard.StandardAnnotation + properties + name = 'TargetMotion'; + end + methods + function obj = TM(); end + function [data, selState] = read(obj, fid, data, fileInfo, anLength, anVersion) + [data, selState] = read@pgmatlab.core.standard.StandardAnnotation(obj, fid, data, fileInfo, anLength, anVersion); + + data.model = pgmatlab.utils.readJavaUTFString(fid); + data.nLocations = fread(fid, 1, 'int16'); + data.hydrophones = fread(fid, 1, 'uint32'); + for i = 1:data.nLocations + loc.latitude = fread(fid, 1, 'float64'); + loc.longitude = fread(fid, 1, 'float64'); + loc.height = fread(fid, 1, 'float32'); + loc.error = pgmatlab.utils.readJavaUTFString(fid); + data.loc(i) = loc; + end + end + end +end diff --git a/pgmatlab/+pgmatlab/+core/+annotations/@UserForm/UserForm.m b/pgmatlab/+pgmatlab/+core/+annotations/@UserForm/UserForm.m new file mode 100644 index 0000000..2b2356b --- /dev/null +++ b/pgmatlab/+pgmatlab/+core/+annotations/@UserForm/UserForm.m @@ -0,0 +1,16 @@ +classdef UserForm < pgmatlab.core.standard.StandardAnnotation + properties + name = 'USerForm'; + end + methods + function obj = UserForm(); end + function [data, selState] = read(obj, fid, data, fileInfo, anLength, anVersion) + [data, selState] = read@pgmatlab.core.standard.StandardAnnotation(obj, fid, data, fileInfo, anLength, anVersion); + + % this is not quite right... + % txtLen = anLength-length(anId)-2-2; + % data = fread(fid, txtLen, 'char')'; + % data = char(data); + end + end +end diff --git a/pgmatlab/+pgmatlab/+core/+modules/+classifiers/@DeepLearningClassifierDetections/DeepLearningClassifierDetections.m b/pgmatlab/+pgmatlab/+core/+modules/+classifiers/@DeepLearningClassifierDetections/DeepLearningClassifierDetections.m new file mode 100644 index 0000000..56b74d1 --- /dev/null +++ b/pgmatlab/+pgmatlab/+core/+modules/+classifiers/@DeepLearningClassifierDetections/DeepLearningClassifierDetections.m @@ -0,0 +1,15 @@ +classdef DeepLearningClassifierDetections < pgmatlab.core.standard.StandardModule + properties + objectType = 1; + end + methods + function obj = DeepLearningClassifierDetections(); end + function [data, selState] = readImpl(~, fid, data, fileInfo, length, identifier, selState); + + data.nChan = fread(fid, 1, 'int16'); + data.nSamps = fread(fid, 1, 'int32'); + data.scale = 1/fread(fid, 1, 'float'); + data.wave = fread(fid, [data.nSamps,data.nChan], 'int8')/ data.scale; + end + end +end \ No newline at end of file diff --git a/pgmatlab/+pgmatlab/+core/+modules/+classifiers/@DeepLearningClassifierModels/DeepLearningClassifierModels.m b/pgmatlab/+pgmatlab/+core/+modules/+classifiers/@DeepLearningClassifierModels/DeepLearningClassifierModels.m new file mode 100644 index 0000000..0ed4a67 --- /dev/null +++ b/pgmatlab/+pgmatlab/+core/+modules/+classifiers/@DeepLearningClassifierModels/DeepLearningClassifierModels.m @@ -0,0 +1,30 @@ +classdef DeepLearningClassifierModels < pgmatlab.core.standard.StandardModule + properties + objectType = 0; + end + methods + function obj = DeepLearningClassifierModels(); end + function [data, selState] = readImpl(~, fid, data, fileInfo, length, identifier, selState); + + data.type = fread(fid, 1, 'int8'); + data.isbinary = fread(fid, 1, 'uint8=>logical'); + scale = fread(fid, 1, 'float32'); + nSpecies = fread(fid, 1, 'int16'); + + %read the predictions + for i=1:nSpecies + pred(i) = fread(fid, 1, 'int16')/scale; + end + data.predictions = pred; + + %number of output classes + nclass = fread(fid, 1, 'int16'); + + if (nclass>0) + for i=1:nclass + fread(fid, 1, 'int16'); + end + end + end + end +end \ No newline at end of file diff --git a/pgmatlab/+pgmatlab/+core/+modules/+detectors/@Click/Click.m b/pgmatlab/+pgmatlab/+core/+modules/+detectors/@Click/Click.m new file mode 100644 index 0000000..0ab68fb --- /dev/null +++ b/pgmatlab/+pgmatlab/+core/+modules/+detectors/@Click/Click.m @@ -0,0 +1,59 @@ +classdef Click < pgmatlab.core.standard.StandardModule + properties + objectType = 1000; + end + methods + function obj = Click(); + obj.footer = @pgmatlab.core.modules.detectors.ClickFooter; + obj.background = @pgmatlab.core.modules.detectors.ClickBackground; + end + function [data, selState] = readImpl(~, fid, data, fileInfo, length, identifier, selState); + if (fileInfo.moduleHeader.version<=3) + data.startSample = fread(fid, 1, 'int64'); + data.channelMap = fread(fid, 1, 'int32'); + end + + data.triggerMap = fread(fid, 1, 'int32'); + data.type = fread(fid, 1, 'int16'); + if (fileInfo.moduleHeader.version >= 2) + data.flags = fread(fid, 1, 'int32'); + else + data.flags = 0; + end + + if (fileInfo.moduleHeader.version <= 3) + nDelays = fread(fid, 1, 'int16'); + if (nDelays) + data.delays = fread(fid, nDelays, 'float'); + else + data.delays=[]; + end + end + + nAngles = fread(fid, 1, 'int16'); + if (nAngles) + data.angles = fread(fid, nAngles, 'float'); + else + data.angles = []; + end + + + if (fileInfo.moduleHeader.version >= 3) + nAngleErrors = fread(fid, 1, 'int16'); + data.angleErrors = fread(fid, nAngleErrors, 'float'); + else + data.angleErrors = []; + end + + if (fileInfo.moduleHeader.version <= 3) + data.duration = fread(fid, 1, 'uint16'); + else + data.duration = data.sampleDuration; % duplicate the value to maintain backwards compatibility + end + + data.nChan = pgmatlab.utils.countChannels(data.channelMap); + maxVal = fread(fid, 1, 'float'); + data.wave = fread(fid, [data.duration,data.nChan], 'int8') * maxVal / 127; + end + end +end \ No newline at end of file diff --git a/pgmatlab/+pgmatlab/+core/+modules/+detectors/@ClickBackground/ClickBackground.m b/pgmatlab/+pgmatlab/+core/+modules/+detectors/@ClickBackground/ClickBackground.m new file mode 100644 index 0000000..a38f012 --- /dev/null +++ b/pgmatlab/+pgmatlab/+core/+modules/+detectors/@ClickBackground/ClickBackground.m @@ -0,0 +1,9 @@ +classdef ClickBackground < pgmatlab.core.standard.StandardBackground + methods + function obj = ClickBackground(); end + function [data, selState] = readImpl(~, fid, data, fileInfo, length, identifier, selState); + data.noiseLen = fread(fid, 1, 'int16'); + data.backGround = fread(fid, data.noiseLen, 'float32'); + end + end +end \ No newline at end of file diff --git a/pgmatlab/+pgmatlab/+core/+modules/+detectors/@ClickFooter/ClickFooter.m b/pgmatlab/+pgmatlab/+core/+modules/+detectors/@ClickFooter/ClickFooter.m new file mode 100644 index 0000000..6860085 --- /dev/null +++ b/pgmatlab/+pgmatlab/+core/+modules/+detectors/@ClickFooter/ClickFooter.m @@ -0,0 +1,11 @@ +classdef ClickFooter < pgmatlab.core.standard.StandardModuleFooter + methods + function obj = ClickFooter(); end + function data = readImpl(obj, fid, data, fileInfo, length, identifier); + if (data.binaryLength ~= 0) + data.typesCountLength = fread(fid, 1, 'int16'); + data.typesCount = fread(fid, data.typesCountLength, 'int32'); + end + end + end +end \ No newline at end of file diff --git a/pgmatlab/+pgmatlab/+core/+modules/+detectors/@ClickTrigger/ClickTrigger.m b/pgmatlab/+pgmatlab/+core/+modules/+detectors/@ClickTrigger/ClickTrigger.m new file mode 100644 index 0000000..d5ea53b --- /dev/null +++ b/pgmatlab/+pgmatlab/+core/+modules/+detectors/@ClickTrigger/ClickTrigger.m @@ -0,0 +1,20 @@ +classdef ClickTrigger < pgmatlab.core.standard.StandardModule + properties + objectType = 0; + end + methods + function obj = ClickTrigger() + obj.header = @pgmatlab.core.modules.detectors.ClickTriggerHeader; + end + function [data, selState] = readImpl(~, fid, data, fileInfo, length, identifier, selState); + + nChan = pgmatlab.utils.countChannels(data.channelMap); + scale = fread(fid, 1, 'float32'); + data.rawLevels = fread(fid, nChan, 'int16') / scale; + cal = fileInfo.moduleHeader.calibration; + if ~isempty(cal) + data.absLevelsdB = 20*log10(data.rawLevels) + cal; + end + end + end +end \ No newline at end of file diff --git a/pgmatlab/+pgmatlab/+core/+modules/+detectors/@ClickTriggerHeader/ClickTriggerHeader.m b/pgmatlab/+pgmatlab/+core/+modules/+detectors/@ClickTriggerHeader/ClickTriggerHeader.m new file mode 100644 index 0000000..e12648e --- /dev/null +++ b/pgmatlab/+pgmatlab/+core/+modules/+detectors/@ClickTriggerHeader/ClickTriggerHeader.m @@ -0,0 +1,14 @@ +classdef ClickTriggerHeader < pgmatlab.core.standard.StandardModuleHeader + methods + function obj = ClickTriggerHeader(); end + function [data, selState] = readImpl(~, fid, data, fileInfo, length, identifier); + if (data.binaryLength~=0) + data.channelMap = fread(fid, 1, 'int32'); + nChan = pgmatlab.utils.countChannels(data.channelMap); + data.calibration = fread(fid, nChan, 'float32'); + else + data.calibration = []; + end + end + end +end \ No newline at end of file diff --git a/pgmatlab/+pgmatlab/+core/+modules/+detectors/@GPL/GPL.m b/pgmatlab/+pgmatlab/+core/+modules/+detectors/@GPL/GPL.m new file mode 100644 index 0000000..d9f7c7c --- /dev/null +++ b/pgmatlab/+pgmatlab/+core/+modules/+detectors/@GPL/GPL.m @@ -0,0 +1,32 @@ +classdef GPL < pgmatlab.core.standard.StandardModule + properties + objectType = []; + end + methods + function obj = GPL(); + obj.background = @pgmatlab.core.modules.detectors.SpectralBackground; + end + function [data, selState] = readImpl(~, fid, data, fileInfo, length, identifier, selState); + data.timeRes = fread(fid, 1, 'float32'); + data.freqRes = fread(fid, 1, 'float32'); + data.area = fread(fid, 1, 'int16'); + bitDepth = fread(fid, 1, 'int8'); + if (bitDepth == 8) + pType = 'uint8'; + else + pType = 'uint16'; + end + points = zeros(2,data.area,pType); + excess = zeros(1,data.area,'single'); + energy = zeros(1,data.area,'single'); + for i = 1:data.area + points(:,i) = fread(fid, 2, pType); + excess(i) = fread(fid, 1, 'float32'); + energy(i) = fread(fid, 1, 'float32'); + end + data.points = points; + data.excess = excess; + data.energy = energy; + end + end +end \ No newline at end of file diff --git a/pgmatlab/+pgmatlab/+core/+modules/+detectors/@RWEdge/RWEdge.m b/pgmatlab/+pgmatlab/+core/+modules/+detectors/@RWEdge/RWEdge.m new file mode 100644 index 0000000..04b04cd --- /dev/null +++ b/pgmatlab/+pgmatlab/+core/+modules/+detectors/@RWEdge/RWEdge.m @@ -0,0 +1,35 @@ +classdef RWEdge < pgmatlab.core.standard.StandardModule + properties + objectType = 0; + end + methods + function obj = RWEdge(); end + function [data, selState] = readImpl(~, fid, data, fileInfo, length, identifier, selState); + + isBuoy = (fileInfo.fileHeader.fileFormat == 0); + if (fileInfo.moduleHeader.version== 0 || isBuoy) + data.startSample = fread(fid, 1, 'int64'); + data.channelMap = fread(fid, 1, 'int32'); + end + + data.type = fread(fid, 1, 'int16'); + data.signal = fread(fid, 1, 'float'); + data.noise = fread(fid, 1, 'float'); + data.nSlices = fread(fid, 1, 'int16'); + + data.times = zeros(1, data.nSlices); + data.sliceNums = zeros(1, data.nSlices); + data.loFreqs = zeros(1, data.nSlices); + data.peakFreqs = zeros(1, data.nSlices); + data.hiFreqs = zeros(1, data.nSlices); + data.peakAmps = zeros(1, data.nSlices); + for i = 1:data.nSlices + data.sliceNums(i) = fread(fid, 1, 'int16'); + data.loFreqs(i) = fread(fid, 1, 'int16'); + data.peakFreqs(i) = fread(fid, 1, 'int16'); + data.hiFreqs(i) = fread(fid, 1, 'int16'); + data.peakAmps(i) = fread(fid, 1, 'float'); + end + end + end +end \ No newline at end of file diff --git a/pgmatlab/+pgmatlab/+core/+modules/+detectors/@SpectralBackground/SpectralBackground.m b/pgmatlab/+pgmatlab/+core/+modules/+detectors/@SpectralBackground/SpectralBackground.m new file mode 100644 index 0000000..c586ce4 --- /dev/null +++ b/pgmatlab/+pgmatlab/+core/+modules/+detectors/@SpectralBackground/SpectralBackground.m @@ -0,0 +1,10 @@ +classdef SpectralBackground < pgmatlab.core.standard.StandardBackground + methods + function obj = SpectralBackground(); end + function [data, selState] = readImpl(~, fid, data, fileInfo, length, identifier, selState); + data.firstBin = fread(fid, 1, 'int32'); + data.noiseLen = fread(fid, 1, 'int32'); + data.backGround = fread(fid, data.noiseLen, 'float32'); + end + end +end \ No newline at end of file diff --git a/pgmatlab/+pgmatlab/+core/+modules/+detectors/@WhistleAndMoan/WhistleAndMoan.m b/pgmatlab/+pgmatlab/+core/+modules/+detectors/@WhistleAndMoan/WhistleAndMoan.m new file mode 100644 index 0000000..8b411d8 --- /dev/null +++ b/pgmatlab/+pgmatlab/+core/+modules/+detectors/@WhistleAndMoan/WhistleAndMoan.m @@ -0,0 +1,48 @@ +classdef WhistleAndMoan < pgmatlab.core.standard.StandardModule + properties + objectType = 2000; + end + methods + function obj = WhistleAndMoan() + obj.header = @pgmatlab.core.modules.detectors.WhistleAndMoanHeader; + obj.background = @pgmatlab.core.modules.detectors.SpectralBackground; + end + function [data, selState] = readImpl(~, fid, data, fileInfo, length, identifier, selState); + if (fileInfo.moduleHeader.version<=1) + data.startSample = fread(fid, 1, 'int64'); + data.channelMap = fread(fid, 1, 'int32'); + end + + data.nSlices = fread(fid, 1, 'int16'); + + if (fileInfo.moduleHeader.version >= 1) + data.amplitude = fread(fid, 1, 'int16') / 100; + end + + if (fileInfo.moduleHeader.version == 1) + data.nDelays = fread(fid, 1, 'int8'); + data.delays = fread(fid, data.nDelays, 'int16'); % need to scale this still !!!! + if ~isempty(fileInfo.moduleHeader) + data.delays = data.delays / fileInfo.moduleHeader.delayScale; + end + end + + data.sliceData = []; + data.contour = zeros(1,data.nSlices); + data.contWidth = zeros(1,data.nSlices); + for i = 1:data.nSlices + aSlice.sliceNumber = fread(fid, 1, 'int32'); + aSlice.nPeaks = fread(fid, 1, 'int8'); + aSlice.peakData = zeros(4, aSlice.nPeaks); + for p = 1:aSlice.nPeaks + sss = fread(fid, 4, 'int16'); + aSlice.peakData(:,p) = sss; + end + data.sliceData{i} = aSlice; + data.contour(i) = aSlice.peakData(2,1); + data.contWidth(i) = aSlice.peakData(3,1) - aSlice.peakData(1,1) + 1; + end + data.meanWidth = mean(data.contWidth); + end + end +end \ No newline at end of file diff --git a/pgmatlab/+pgmatlab/+core/+modules/+detectors/@WhistleAndMoanHeader/WhistleAndMoanHeader.m b/pgmatlab/+pgmatlab/+core/+modules/+detectors/@WhistleAndMoanHeader/WhistleAndMoanHeader.m new file mode 100644 index 0000000..5d11c8e --- /dev/null +++ b/pgmatlab/+pgmatlab/+core/+modules/+detectors/@WhistleAndMoanHeader/WhistleAndMoanHeader.m @@ -0,0 +1,10 @@ +classdef WhistleAndMoanHeader < pgmatlab.core.standard.StandardModuleHeader + methods + function obj = WhistleAndMoanHeader(); end + function [data, selState] = readImpl(~, fid, data, fileInfo, length, identifier); + if (data.binaryLength~=0 && data.version>=1) + data.delayScale = fread(fid, 1, 'int32'); + end + end + end +end \ No newline at end of file diff --git a/pgmatlab/+pgmatlab/+core/+modules/+plugins/@GeminiThreshold/GeminiThreshold.m b/pgmatlab/+pgmatlab/+core/+modules/+plugins/@GeminiThreshold/GeminiThreshold.m new file mode 100644 index 0000000..c1810ee --- /dev/null +++ b/pgmatlab/+pgmatlab/+core/+modules/+plugins/@GeminiThreshold/GeminiThreshold.m @@ -0,0 +1,52 @@ + + +classdef GeminiThreshold < pgmatlab.core.standard.StandardModule + properties + objectType = 0; + end + methods + function obj = GeminiThreshold(); + obj.background = @pgmatlab.core.modules.plugins.GeminiThresholdBackground; + end + function [data, selState] = readImpl(~, fid, data, fileInfo, length, identifier, selState); + + data.nPoints = fread(fid, 1, 'int32'); + data.nSonar = fread(fid, 1, 'int8'); + data.sonarIds = fread(fid, data.nSonar, 'int16'); + dum = fread(fid,3,'float32'); + data.straightLength = dum(1); + data.wobblyLength = dum(2); + data.meanOccupancy = dum(3); + data.timeMillis = zeros(1, data.nPoints); + data.sonarId = zeros(1, data.nPoints); + data.minBearing = zeros(1, data.nPoints); + data.maxBearing = zeros(1, data.nPoints); + data.peakBearing = zeros(1, data.nPoints); + data.minRange = zeros(1, data.nPoints); + data.maxRange = zeros(1, data.nPoints); + data.peakRange = zeros(1, data.nPoints); + data.objSize = zeros(1, data.nPoints); + data.occupancy = zeros(1, data.nPoints); + data.aveValue = zeros(1, data.nPoints); + data.totValue = zeros(1, data.nPoints); + data.maxValue = zeros(1, data.nPoints); + for i = 1:data.nPoints + data.timeMillis(i) = fread(fid, 1, 'int64'); + data.sonarId(i) = fread(fid, 1, 'int16'); + fDum = fread(fid,8,'float32'); + data.minBearing(i) = fDum(1); + data.maxBearing(i) = fDum(2); + data.peakBearing(i) = fDum(3); + data.minRange(i) = fDum(4); + data.maxRange(i) = fDum(5); + data.peakRange(i) = fDum(6); + data.objSize(i) = fDum(7); + data.occupancy(i) = fDum(8); + data.aveValue(i) = fread(fid, 1, 'int16'); + data.totValue(i) = fread(fid, 1, 'int32'); + data.maxValue(i) = fread(fid, 1, 'int16'); + end + data.dates = pgmatlab.utils.millisToDateNum(data.timeMillis); + end + end +end \ No newline at end of file diff --git a/pgmatlab/+pgmatlab/+core/+modules/+plugins/@GeminiThresholdBackground/GeminiThresholdBackground.m b/pgmatlab/+pgmatlab/+core/+modules/+plugins/@GeminiThresholdBackground/GeminiThresholdBackground.m new file mode 100644 index 0000000..72b951e --- /dev/null +++ b/pgmatlab/+pgmatlab/+core/+modules/+plugins/@GeminiThresholdBackground/GeminiThresholdBackground.m @@ -0,0 +1,105 @@ + + +classdef GeminiThresholdBackground < pgmatlab.core.standard.StandardBackground + methods (Static) + function glf = readTritechGLFRecord(fid, fileInfo) %#ok<*INUSD> + endy = 'ieee-le'; + + glf.id1 = fread(fid, 1, 'uint16', endy); + glf.efef = dec2hex(fread(fid, 1, 'uint16', endy)); + glf.imageVersion = fread(fid, 1, 'uint16', endy); + glf.startRange = fread(fid, 1, 'uint32', endy); + glf.endRange = fread(fid, 1, 'uint32', endy); + glf.rangeCompression = fread(fid, 1, 'uint16', endy); + glf.startBearing = fread(fid, 1, 'uint32', endy); + glf.endBearing = fread(fid, 1, 'uint32', endy); + if (glf.imageVersion == 3) + skip = fread(fid, 1, 'uint16', endy); %#ok<*NASGU> + end + % disp("I GOT HERE 1"); + nBearing = glf.endBearing-glf.startBearing; + nRange = glf.endRange-glf.startRange; + packedSize = fread(fid, 1, 'uint32', endy); + zipped = uint8(fread(fid, packedSize, 'uint8', endy))'; + fullLen = nRange*nBearing; + % disp(glf.imageVersion); + try + % from https://uk.mathworks.com/matlabcentral/answers/313672-java-class-inflater-call-from-matlab-command-window + output = java.io.ByteArrayOutputStream(); + unzipper = java.util.zip.Inflater; + outstrm = java.util.zip.InflaterOutputStream(output,unzipper); + outstrm.write(zipped); + unzipper.finished; + outstrm.flush + outstrm.close(); + % output to ByteArray + unzipped = output.toByteArray(); + catch errr + error = true; + return; + end + + % it seems that I wasn't flushing properly when writing the zipped data, so + % the records are short and we're getting fewer measures back than + % intended. Need to modify range data accordingly or it's all gonna go a + % bit weird. + if (length(unzipped) < fullLen) + % fprintf('expLen %d, gotLen %d, inputlen %d, ratio %3.4f\n', fullLen, length(unzipped),packedSize, length(unzipped)/fullLen); + nRange = floor(length(unzipped)/nBearing); + glf.endRange = nRange; + unzipped = unzipped(1:(nRange*nBearing)); + end + + % then reshape it before adding to the glf record + % and deal with negatives ! + shortData = int16(unzipped); + isNeg = find(shortData < 0); + shortData(isNeg) = shortData(isNeg)+256; + glf.imageData = reshape(shortData, nBearing, nRange); + + % now continue and get the rest of the stuff out of the record. + glf.bearingTable = fread(fid, nBearing, 'double', endy); + glf.stateFlags = fread(fid, 1, 'uint32', endy); + glf.modulationFrequency = fread(fid, 1, 'uint32', endy); + glf.beamformAperture = fread(fid, 1, 'float32', endy); + glf.txTime = fread(fid, 1, 'double', endy); + glf.pingFlags = fread(fid, 1, 'uint16', endy); + glf.sosAtXd = fread(fid, 1, 'float32', endy); + glf.percentGain = fread(fid, 1, 'uint16', endy); + glf.chirp = fread(fid, 1, 'uint8', endy); + glf.sonarType = fread(fid, 1, 'uint8', endy); + glf.platform = fread(fid, 1, 'uint8', endy); + glf.oneSpare = fread(fid, 1, 'uint8', endy); + glf.dede = dec2hex(fread(fid, 1, 'uint16', endy)); + + glf.maxRange = glf.endRange * glf.sosAtXd/2. / glf.modulationFrequency; + + + % finally, need to convert the times, which are some funny double number, + % into something sensible such as millis or Matlab datenum. + % cDate is ref's to 1980 in secs, Matlab is days since '00-Jan-0000' + tOffs = 723181; % datenum(1980,0,1,0,0,0) + secsPerDay = 3600*24; + glf.txDate = (glf.txTime / secsPerDay) + tOffs; + end + function head = readTritechHeader(fid, fileInfo) + endy = 'ieee-le'; + head.m_idChar = fread(fid, 1, 'uint8', endy); + head.m_version = fread(fid, 1, 'uint8', endy); + head.m_length = fread(fid, 1, 'uint32', endy); + head.m_timestamp = fread(fid, 1, 'double', endy); + head.m_dataType = fread(fid, 1, 'uint8', endy); + head.tm_deviceId = fread(fid, 1, 'uint16', endy); + head.m_node_ID = fread(fid, 1, 'uint16', endy); + head.spare = fread(fid, 1, 'uint16'); + end + end + + methods + function obj = GeminiThresholdBackground(); end + function [data, selState] = readImpl(~, fid, data, fileInfo, length, identifier, selState); + data.head = pgmatlab.core.modules.plugins.GeminiThresholdBackground.readTritechHeader(fid, fileInfo); + data.glf = pgmatlab.core.modules.plugins.GeminiThresholdBackground.readTritechGLFRecord(fid, fileInfo); + end + end +end \ No newline at end of file diff --git a/pgmatlab/+pgmatlab/+core/+modules/+plugins/@SpermWhaleIPI/SpermWhaleIPI.m b/pgmatlab/+pgmatlab/+core/+modules/+plugins/@SpermWhaleIPI/SpermWhaleIPI.m new file mode 100644 index 0000000..3a05f0f --- /dev/null +++ b/pgmatlab/+pgmatlab/+core/+modules/+plugins/@SpermWhaleIPI/SpermWhaleIPI.m @@ -0,0 +1,19 @@ +classdef SpermWhaleIPI < pgmatlab.core.standard.StandardModule + properties + objectType = 0; + end + methods + function obj = SpermWhaleIPI(); end + function [data, selState] = readImpl(~, fid, data, fileInfo, length, identifier, selState); + + data.parentUID = fread(fid, 1, 'int64'); % 8 + data.ipi = fread(fid,1,'float'); % 4 + data.ipiAmplitude = fread(fid,1,'float'); % 4 + data.sampleRate = fread(fid,1,'float'); % 4 + data.maxVal = fread(fid,1,'float'); % 4 + data.echoLen = fread(fid, 1, 'int32'); % 4 + data.echoData = fread(fid, data.echoLen, 'int16')... + * data.maxVal / 32767; % len * 2 + end + end +end \ No newline at end of file diff --git a/pgmatlab/+pgmatlab/+core/+modules/+processing/@AIS/AIS.m b/pgmatlab/+pgmatlab/+core/+modules/+processing/@AIS/AIS.m new file mode 100644 index 0000000..842a071 --- /dev/null +++ b/pgmatlab/+pgmatlab/+core/+modules/+processing/@AIS/AIS.m @@ -0,0 +1,16 @@ +classdef AIS < pgmatlab.core.standard.StandardModule + properties + objectType = 0; + end + methods + function obj = AIS(); end + function [data, selState] = readImpl(~, fid, data, fileInfo, length, identifier, selState); + data.mmsiNumber = fread(fid, 1, 'int32'); + data.fillBits = fread(fid, 1, 'int16'); + [strVal, strLen] = pgmatlab.utils.readJavaUTFString(fid); %#ok + data.charData = strVal; + [strVal, strLen] = pgmatlab.utils.readJavaUTFString(fid); %#ok + data.aisChannel = strVal; + end + end +end \ No newline at end of file diff --git a/pgmatlab/+pgmatlab/+core/+modules/+processing/@ClipGenerator/ClipGenerator.m b/pgmatlab/+pgmatlab/+core/+modules/+processing/@ClipGenerator/ClipGenerator.m new file mode 100644 index 0000000..4cef901 --- /dev/null +++ b/pgmatlab/+pgmatlab/+core/+modules/+processing/@ClipGenerator/ClipGenerator.m @@ -0,0 +1,36 @@ +classdef ClipGenerator < pgmatlab.core.standard.StandardModule + properties + objectType = [1 2]; + end + methods + function obj = ClipGenerator(); end + function [data, selState] = readImpl(~, fid, data, fileInfo, length, identifier, selState); + + if (fileInfo.moduleHeader.version <= 1) + data.startSample = fread(fid, 1, 'int64'); + data.channelMap = fread(fid, 1, 'int32'); + end + + data.triggerMillis = fread(fid, 1, 'int64'); + + if (fileInfo.moduleHeader.version <= 1) + data.sampleDuration = fread(fid, 1, 'int32'); + end + + data.filename = pgmatlab.utils.readJavaUTFString(fid); + data.triggerName = pgmatlab.utils.readJavaUTFString(fid); + if (fileInfo.moduleHeader.version >= 3) + data.triggerUID = fread(fid, 1, 'int64'); + end + + % check if the object type = 2. If it is, there must be wav data at + % the end of this object + if (data.identifier==2) + data.nChan = fread(fid, 1, 'int16'); + data.nSamps = fread(fid, 1, 'int32'); + data.scale = 1/fread(fid, 1, 'float'); + data.wave = fread(fid, [data.nSamps,data.nChan], 'int8') * data.scale; + end + end + end +end \ No newline at end of file diff --git a/pgmatlab/+pgmatlab/+core/+modules/+processing/@DbHt/DbHt.m b/pgmatlab/+pgmatlab/+core/+modules/+processing/@DbHt/DbHt.m new file mode 100644 index 0000000..5e5ad0a --- /dev/null +++ b/pgmatlab/+pgmatlab/+core/+modules/+processing/@DbHt/DbHt.m @@ -0,0 +1,19 @@ +classdef DbHt < pgmatlab.core.standard.StandardModule + properties + objectType = 1; + end + methods + function obj = DbHt(); end + function [data, selState] = readImpl(~, fid, data, fileInfo, length, identifier, selState); + + if (fileInfo.moduleHeader.version <= 1) + data.startSample = fread(fid, 1, 'int64'); + data.channelMap = fread(fid, 1, 'int32'); + end + + data.rms = fread(fid, 1, 'int16')/100; + data.zeroPeak = fread(fid, 1, 'int16')/100; + data.peakPeak = fread(fid, 1, 'int16')/100; + end + end +end \ No newline at end of file diff --git a/pgmatlab/+pgmatlab/+core/+modules/+processing/@Difar/Difar.m b/pgmatlab/+pgmatlab/+core/+modules/+processing/@Difar/Difar.m new file mode 100644 index 0000000..fe68f2d --- /dev/null +++ b/pgmatlab/+pgmatlab/+core/+modules/+processing/@Difar/Difar.m @@ -0,0 +1,74 @@ +classdef Difar < pgmatlab.core.standard.StandardModule + properties + objectType = 0; + end + methods + function obj = Difar(); end + function [data, selState] = readImpl(~, fid, data, fileInfo, length, identifier, selState); + + if (fileInfo.moduleHeader.version <= 1) + data.startSample = fread(fid, 1, 'int64'); + end + + data.clipStart = fread(fid, 1, 'int64'); + + if (fileInfo.moduleHeader.version <= 1) + data.channelMap = fread(fid, 1, 'int32'); + end + + data.displaySampleRate = fread(fid, 1, 'float'); + data.demuxedLength = fread(fid, 1, 'int32'); + + if (fileInfo.moduleHeader.version <= 1) + minFreq = fread(fid,1,'float'); + maxFreq = fread(fid,1,'float'); + data.freqLimits = [minFreq maxFreq]; + end + + data.amplitude = fread(fid, 1, 'float'); + data.gain = fread(fid, 1, 'float'); + data.selAngle = fread(fid, 1, 'float'); + data.selFreq = fread(fid, 1, 'float'); + data.speciesCode = pgmatlab.utils.readJavaUTFString(fid); + + if (fileInfo.moduleHeader.version >= 1) + data.trackedGroup = pgmatlab.utils.readJavaUTFString(fid); + end + + data.maxVal = fread(fid, 1, 'float'); + + if (data.demuxedLength==0) + data.demuxData = 0; + else + data.demuxData = fread(fid, [data.demuxedLength,3], 'int16') * data.maxVal / 32767; + end + + data.numMatches = fread(fid, 1, 'int16'); + if (data.numMatches > 0) + data.latitude = fread(fid, 1, 'float'); + data.longitude = fread(fid, 1, 'float'); + + if (fileInfo.moduleHeader.version >= 1) + errorX = fread(fid,1,'float'); + errorY = fread(fid,1,'float'); + data.errors = [errorX errorY 0]; + end + + for i=1:data.numMatches-1 + data.matchChan(i) = fread(fid, 1, 'int16'); + data.matchTime(i) = fread(fid, 1, 'int64'); + end + else + data.latitude = 0; + data.longitude = 0; + + if (fileInfo.moduleHeader.version >= 1) + data.errors = [0 0 0]; + end + + data.matchChan(1) = 0; + data.matchTime(1) = 0; + end + end + end +end \ No newline at end of file diff --git a/pgmatlab/+pgmatlab/+core/+modules/+processing/@IshmaelData/IshmaelData.m b/pgmatlab/+pgmatlab/+core/+modules/+processing/@IshmaelData/IshmaelData.m new file mode 100644 index 0000000..1a7b7e9 --- /dev/null +++ b/pgmatlab/+pgmatlab/+core/+modules/+processing/@IshmaelData/IshmaelData.m @@ -0,0 +1,22 @@ +classdef IshmaelData < pgmatlab.core.standard.StandardModule + properties + objectType = []; + end + methods + function obj = IshmaelData(); end + function [data, selState] = readImpl(~, fid, data, fileInfo, length, identifier, selState); + + nDet = fread(fid, 1, 'int32'); + nDet2 = 2; + if fileInfo.moduleHeader.version >= 2 + nDet2 = fread(fid, 1, 'int32'); + end + data.data = zeros(nDet,nDet2); + for i = 1:nDet + for i2 = 1:nDet2 + data.data(i,i2) = fread(fid, 1, 'double'); + end + end + end + end +end \ No newline at end of file diff --git a/pgmatlab/+pgmatlab/+core/+modules/+processing/@IshmaelDetections/IshmaelDetections.m b/pgmatlab/+pgmatlab/+core/+modules/+processing/@IshmaelDetections/IshmaelDetections.m new file mode 100644 index 0000000..9eb49cb --- /dev/null +++ b/pgmatlab/+pgmatlab/+core/+modules/+processing/@IshmaelDetections/IshmaelDetections.m @@ -0,0 +1,10 @@ +classdef IshmaelDetections < pgmatlab.core.standard.StandardModule + properties + objectType = []; + end + methods + function obj = IshmaelDetections(); end + function [data, selState] = readImpl(~, fid, data, fileInfo, length, identifier, selState); + end + end +end \ No newline at end of file diff --git a/pgmatlab/+pgmatlab/+core/+modules/+processing/@LongTermSpectralAverage/LongTermSpectralAverage.m b/pgmatlab/+pgmatlab/+core/+modules/+processing/@LongTermSpectralAverage/LongTermSpectralAverage.m new file mode 100644 index 0000000..7d8666f --- /dev/null +++ b/pgmatlab/+pgmatlab/+core/+modules/+processing/@LongTermSpectralAverage/LongTermSpectralAverage.m @@ -0,0 +1,45 @@ +classdef LongTermSpectralAverage < pgmatlab.core.standard.StandardModule + properties(Access = private) + a = 127.*2./log(32767); + b = -127; + end + properties + objectType = 1; + end + methods + function obj = LongTermSpectralAverage(); + obj.header = @pgmatlab.core.modules.processing.LongTermSpectralAverageHeader; + end + function [data, selState] = readImpl(obj, fid, data, fileInfo, length, identifier, selState); + + if (fileInfo.moduleHeader.version<=1) + data.startSample = fread(fid, 1, 'int64'); + end + + if (fileInfo.moduleHeader.version==0) + data.duration = fread(fid, 1, 'int64'); + end + + if (fileInfo.moduleHeader.version<=1) + data.channelMap = fread(fid, 1, 'int32'); + end + + data.endMillis = fread(fid, 1, 'int64'); + data.endDate = pgmatlab.utils.millisToDateNum(data.endMillis); + data.nFFT = fread(fid, 1, 'int32'); + data.maxVal = fread(fid, 1, 'float'); + + % version 0 scaled the data linearly to 16 bit + if (fileInfo.moduleHeader.version==0) + data.byteData = fread(fid, fileInfo.moduleHeader.fftLength/2, 'int16'); + data.data = data.byteData / 32767. * data.maxVal; + + % after version 0, the data was first scaled to 16 bit and then + % converted to a log so that it could be saved as an 8 bit. + else + data.byteData = fread(fid, fileInfo.moduleHeader.fftLength/2, 'int8'); + data.data = exp((data.byteData-obj.b)/obj.a)*data.maxVal / 32767; + end + end + end +end \ No newline at end of file diff --git a/pgmatlab/+pgmatlab/+core/+modules/+processing/@LongTermSpectralAverageHeader/LongTermSpectralAverageHeader.m b/pgmatlab/+pgmatlab/+core/+modules/+processing/@LongTermSpectralAverageHeader/LongTermSpectralAverageHeader.m new file mode 100644 index 0000000..e3e118e --- /dev/null +++ b/pgmatlab/+pgmatlab/+core/+modules/+processing/@LongTermSpectralAverageHeader/LongTermSpectralAverageHeader.m @@ -0,0 +1,13 @@ +classdef LongTermSpectralAverageHeader < pgmatlab.core.standard.StandardModuleHeader + methods + function obj = LongTermSpectralAverageHeader(); end + function [data, selState] = readImpl(~, fid, data, fileInfo, length, identifier); + + if (data.binaryLength ~= 0) + data.fftLength = fread(fid, 1, 'int32'); + data.fftHop = fread(fid, 1, 'int32'); + data.intervalSeconds = fread(fid, 1, 'int32'); + end + end + end +end \ No newline at end of file diff --git a/pgmatlab/+pgmatlab/+core/+modules/+processing/@NoiseBand/NoiseBand.m b/pgmatlab/+pgmatlab/+core/+modules/+processing/@NoiseBand/NoiseBand.m new file mode 100644 index 0000000..90c64fa --- /dev/null +++ b/pgmatlab/+pgmatlab/+core/+modules/+processing/@NoiseBand/NoiseBand.m @@ -0,0 +1,24 @@ +classdef NoiseBand < pgmatlab.core.standard.StandardModule + properties + objectType = 1; + end + methods + function obj = NoiseBand(); end + function [data, selState] = readImpl(~, fid, data, fileInfo, length, identifier, selState); + + if (fileInfo.moduleHeader.version<=2) + data.startSample = fread(fid, 1, 'int64'); + data.channelMap = fread(fid, 1, 'int32'); + end + + data.rms = fread(fid, 1, 'int16')/100.; + data.zeroPeak = fread(fid, 1, 'int16')/100.; + data.peakPeak = fread(fid, 1, 'int16')/100.; + + if (fileInfo.moduleHeader.version>=2) + data.sel = fread(fid, 1, 'int16')/100.; + data.selSecs = fread(fid, 1, 'int16'); + end + end + end +end \ No newline at end of file diff --git a/pgmatlab/+pgmatlab/+core/+modules/+processing/@NoiseMonitor/NoiseMonitor.m b/pgmatlab/+pgmatlab/+core/+modules/+processing/@NoiseMonitor/NoiseMonitor.m new file mode 100644 index 0000000..026053a --- /dev/null +++ b/pgmatlab/+pgmatlab/+core/+modules/+processing/@NoiseMonitor/NoiseMonitor.m @@ -0,0 +1,28 @@ +classdef NoiseMonitor < pgmatlab.core.standard.StandardModule + properties + objectType = 1; + end + methods + function obj = NoiseMonitor(); + obj.header = @pgmatlab.core.modules.processing.NoiseMonitorHeader; + end + function [data, selState] = readImpl(~, fid, data, fileInfo, length, identifier, selState); + + data.iChan = fread(fid, 1, 'int16'); + data.nBands = fread(fid, 1, 'int16'); + + if (fileInfo.moduleHeader.version>=1) + data.nMeasures = fread(fid, 1, 'int16'); + else + data.nMeasures = 4; + end + + if (fileInfo.moduleHeader.version<=1) + n = fread(fid, data.nBands*data.nMeasures, 'float'); + else + n = fread(fid, data.nBands*data.nMeasures, 'int16') / 100.; + end + data.noise = reshape(n, data.nMeasures, data.nBands); + end + end +end \ No newline at end of file diff --git a/pgmatlab/+pgmatlab/+core/+modules/+processing/@NoiseMonitorHeader/NoiseMonitorHeader.m b/pgmatlab/+pgmatlab/+core/+modules/+processing/@NoiseMonitorHeader/NoiseMonitorHeader.m new file mode 100644 index 0000000..17e9bb1 --- /dev/null +++ b/pgmatlab/+pgmatlab/+core/+modules/+processing/@NoiseMonitorHeader/NoiseMonitorHeader.m @@ -0,0 +1,14 @@ +classdef NoiseMonitorHeader < pgmatlab.core.standard.StandardModuleHeader + methods + function obj = NoiseMonitorHeader(); end + function [data, selState] = readImpl(~, fid, data, fileInfo, length, identifier); + + if (data.binaryLength~=0) + data.nBands = fread(fid, 1, 'int16'); + data.statsTypes = fread(fid, 1, 'int16'); + data.loEdges = fread(fid, data.nBands, 'float'); + data.hiEdges = fread(fid, data.nBands, 'float'); + end + end + end +end \ No newline at end of file diff --git a/pgmatlab/+pgmatlab/+core/+standard/@BaseChunk/BaseChunk.m b/pgmatlab/+pgmatlab/+core/+standard/@BaseChunk/BaseChunk.m new file mode 100644 index 0000000..f995348 --- /dev/null +++ b/pgmatlab/+pgmatlab/+core/+standard/@BaseChunk/BaseChunk.m @@ -0,0 +1,10 @@ + + +classdef BaseChunk + methods + function obj = BaseChunk(); end + function [data, selState] = read(obj, fid, data, fileInfo, length, identifier); %#ok + selState = 1; + end + end +end diff --git a/pgmatlab/+pgmatlab/+core/+standard/@StandardAnnotation/StandardAnnotation.m b/pgmatlab/+pgmatlab/+core/+standard/@StandardAnnotation/StandardAnnotation.m new file mode 100644 index 0000000..64a5182 --- /dev/null +++ b/pgmatlab/+pgmatlab/+core/+standard/@StandardAnnotation/StandardAnnotation.m @@ -0,0 +1,13 @@ +% StandardAnnotation.m +classdef StandardAnnotation < pgmatlab.core.standard.BaseChunk + properties (Abstract) + name; + end + methods + function obj = StandardAnnotation(); end + %function [data, selState] = read(obj, fid, fileInfo, anLength, anVersion) + function [data, selState] = read(obj, fid, data, fileInfo, anLength, anVersion) + [data, selState] = read@pgmatlab.core.standard.BaseChunk(obj, fid, data, fileInfo, anLength, anVersion); + end + end +end diff --git a/pgmatlab/+pgmatlab/+core/+standard/@StandardBackground/StandardBackground.m b/pgmatlab/+pgmatlab/+core/+standard/@StandardBackground/StandardBackground.m new file mode 100644 index 0000000..4d7e089 --- /dev/null +++ b/pgmatlab/+pgmatlab/+core/+standard/@StandardBackground/StandardBackground.m @@ -0,0 +1,10 @@ +% StandarFileHeader.m + +classdef StandardBackground < pgmatlab.core.standard.BaseChunk + methods + function obj = StandardBackground(); end + function [data, selState] = read(obj, fid, data, fileInfo, length, identifier, selState) + [data, selState] = obj.readImpl(fid, data, fileInfo, length, identifier, selState); + end + end +end diff --git a/pgmatlab/+pgmatlab/+core/+standard/@StandardFileFooter/StandardFileFooter.m b/pgmatlab/+pgmatlab/+core/+standard/@StandardFileFooter/StandardFileFooter.m new file mode 100644 index 0000000..58fb151 --- /dev/null +++ b/pgmatlab/+pgmatlab/+core/+standard/@StandardFileFooter/StandardFileFooter.m @@ -0,0 +1,24 @@ +% StandarFileFooter.m + +classdef StandardFileFooter < pgmatlab.core.standard.BaseChunk + methods + function obj = StandardFileFooter(); end + function [data, selState] = read(obj, fid, data, fileInfo, length, identifier) + import pgmatlab.*; + [data, selState] = read@pgmatlab.core.standard.BaseChunk(obj, fid, data, fileInfo, length, identifier); + version = fileInfo.fileHeader.version; + data.length = length; + data.identifier = identifier; + data.nObjects = fread(fid, 1, 'int32'); + data.dataDate = pgmatlab.utils.millisToDateNum(fread(fid, 1, 'int64')); + data.analysisDate = pgmatlab.utils.millisToDateNum(fread(fid, 1, 'int64')); + data.endSample = fread(fid, 1, 'int64'); + if (version>=3) + data.lowestUID = fread(fid, 1, 'int64'); + data.highestUID = fread(fid, 1, 'int64'); + end + data.fileLength = fread(fid, 1, 'int64'); + data.endReason = fread(fid, 1, 'int32'); + end + end +end diff --git a/pgmatlab/+pgmatlab/+core/+standard/@StandardFileHeader/StandardFileHeader.m b/pgmatlab/+pgmatlab/+core/+standard/@StandardFileHeader/StandardFileHeader.m new file mode 100644 index 0000000..7c701d6 --- /dev/null +++ b/pgmatlab/+pgmatlab/+core/+standard/@StandardFileHeader/StandardFileHeader.m @@ -0,0 +1,28 @@ +% StandarFileHeader.m + +classdef StandardFileHeader < pgmatlab.core.standard.BaseChunk + methods + function obj = StandardFileHeader(); end + function [data, selState] = read(obj, fid, data, fileInfo, length, identifier) + [data, selState] = read@pgmatlab.core.standard.BaseChunk(obj, fid, data, fileInfo, length, identifier); + data.length = length; + data.identifier = identifier; + data.fileFormat = fread(fid, 1, 'int32'); + data.pamguard = char(fread(fid, 12, 'uchar')'); + data.version = pgmatlab.utils.readJavaUTFString(fid); + data.branch = pgmatlab.utils.readJavaUTFString(fid); + data.dataDate = pgmatlab.utils.millisToDateNum(fread(fid, 1, 'int64')); + data.analysisDate = pgmatlab.utils.millisToDateNum(fread(fid, 1, 'int64')); + data.startSample = fread(fid, 1, 'int64'); + data.moduleType = pgmatlab.utils.readJavaUTFString(fid); + data.moduleName = pgmatlab.utils.readJavaUTFString(fid); + data.streamName = pgmatlab.utils.readJavaUTFString(fid); + data.extraInfoLen = fread(fid, 1, 'int32'); + % TODO: extra info is not always expected + % data.extraInfo = []; + if (data.extraInfoLen > 0) + data.extraInfo = fread(fid, data.extraInfoLen, 'int8'); + end + end + end +end diff --git a/pgmatlab/+pgmatlab/+core/+standard/@StandardModule/StandardModule.m b/pgmatlab/+pgmatlab/+core/+standard/@StandardModule/StandardModule.m new file mode 100644 index 0000000..2fc420c --- /dev/null +++ b/pgmatlab/+pgmatlab/+core/+standard/@StandardModule/StandardModule.m @@ -0,0 +1,254 @@ +% StandardModule.m +% +% Reads in standard module data. Extends BaseChunk. +% As it only reads in standard data, this class +% should be extended for specific modules. + +classdef StandardModule < pgmatlab.core.standard.BaseChunk + properties (Abstract) + objectType; + end + properties (Access = public) + header = @pgmatlab.core.standard.StandardModuleHeader; + footer = @pgmatlab.core.standard.StandardModuleFooter; + background = -1; + end + + methods (Abstract) + % Method readImpl 'read implementation', to be concretely implemented + % with module-specific data to read + [data, selState] = readImpl(~, fid, data, fileInfo, length, identifier, selState); + end + + methods + function [data, selState] = readBackgroundImpl(~, fid, data, fileInfo, length, identifier, selState); end + end + + methods (Access = public, Sealed) + function obj = StandardModule(); end + function [data, selState] = read(obj, fid, data, fileInfo, length, identifier, timeRange, uidRange, uidList, channelMap) + import pgmatlab.*; + isBackground = identifier == -6; + + selState = 1; + data.identifier = identifier; + fileVersion = fileInfo.fileHeader.fileFormat; + + + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + %%%%%% READ STANDARD MODULE DATA %%%%%% + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + + persistent flags; + if isempty(flags) + flags = struct; + flags.TIMEMILLIS = hex2dec('1'); + flags.TIMENANOS = hex2dec('2'); + flags.CHANNELMAP = hex2dec('4'); + flags.UID = hex2dec('8'); + flags.STARTSAMPLE = hex2dec('10'); + flags.SAMPLEDURATION = hex2dec('20'); + flags.FREQUENCYLIMITS = hex2dec('40'); + flags.MILLISDURATION = hex2dec('80'); + flags.TIMEDELAYSSECS = hex2dec('100'); + flags.HASBINARYANNOTATIONS = hex2dec('200'); + flags.HASSEQUENCEMAP = hex2dec('400'); + flags.HASNOISE = hex2dec('800'); + flags.HASSIGNAL = hex2dec('1000'); + flags.HASSIGNALEXCESS = hex2dec('2000'); + end + + % CHECK: THIS IS LEGACY CODE AND NOT IMPLEMENTED IN PYPAMGUARD + % if ~isBackground & isfield(fileInfo, 'objectType') + % if (any(data.identifier==fileInfo.objectType)) + % % do nothing here - couldn't figure out a clean way of checking if + % % number wasn't in array + % else + % disp(['Error - Object Identifier does not match ' fileInfo.fileHeader.moduleType ' type. Aborting data read.']); + % fseek(fid, nextObj, 'bof'); + % return; + % end + % end + + data.millis = fread(fid, 1, 'int64'); + % set date, to maintain backwards compatibility + data.date = pgmatlab.utils.millisToDateNum(data.millis); + + % TIMERANGE FILTER + if (data.date < timeRange(1)) + selState = 0; + return; + elseif (data.date > timeRange(2)) + selState = 2; + return; + end + + % read flagBitmap (since version 3) + if (fileVersion >= 3) + data.flagBitmap = fread(fid, 1, 'int16'); + else + data.flagBitmap = 0; + end + + % TODO: check version 2 logic here. + if (fileVersion == 2 || (bitand(data.flagBitmap, flags.TIMENANOS) ~= 0) ) + data.timeNanos = fread(fid, 1, 'int64'); + end + if (fileVersion == 2 || (bitand(data.flagBitmap, flags.CHANNELMAP) ~= 0) ) + data.channelMap = fread(fid, 1, 'int32'); + % Filter by channel + if channelMap > 0 && channelMap ~= data.channelMap + selState = 0; + return; + end + end + + % what's going on here? == UID? + if (bitand(data.flagBitmap, flags.UID) == flags.UID) + data.UID = fread(fid, 1, 'int64'); + % UIDRANGE FILTER + if (data.UID < uidRange(1)) + selState = 0; + return; + elseif (data.UID > uidRange(2)) + selState = 2; + return; + end + + % UIDLIST filter + if ~isempty(uidList) + inList = sum(uidList == data.UID) > 0; + if ~inList + selState = 0; + return; + end + end + end + + if (bitand(data.flagBitmap, flags.STARTSAMPLE) ~= 0) + data.startSample = fread(fid, 1, 'int64'); + end + + if (bitand(data.flagBitmap, flags.SAMPLEDURATION) ~= 0) + data.sampleDuration = fread(fid, 1, 'int32'); + end + + if (bitand(data.flagBitmap, flags.FREQUENCYLIMITS) ~= 0) + minFreq = fread(fid, 1, 'float'); + maxFreq = fread(fid, 1, 'float'); + data.freqLimits = [minFreq maxFreq]; + end + + if (bitand(data.flagBitmap, flags.MILLISDURATION) ~= 0) + data.millisDuration = fread(fid, 1, 'float'); + end + + if (bitand(data.flagBitmap, flags.TIMEDELAYSSECS) ~= 0) + data.numTimeDelays = fread(fid, 1, 'int16'); + td=zeros(1, data.numTimeDelays); + for i = 1:data.numTimeDelays + td(i)=fread(fid, 1, 'float'); + end + data.timeDelays=td; + end + + if (bitand(data.flagBitmap, flags.HASSEQUENCEMAP) ~= 0) + data.sequenceMap = fread(fid, 1, 'int32'); + end + + if (bitand(data.flagBitmap, flags.HASNOISE) ~= 0) + data.noise = fread(fid, 1, 'float32'); + end + + if (bitand(data.flagBitmap, flags.HASSIGNAL) ~= 0) + data.signal = fread(fid, 1, 'float32'); + end + + if (bitand(data.flagBitmap, flags.HASSIGNALEXCESS) ~= 0) + data.signalExcess = fread(fid, 1, 'float32'); + end + + + + % read standard module data (each module has this) + + + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + %%%%%% READ MODULE-SPECIFIC DATA %%%%%% + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + + % [data, selState] = StandardModule.readStandardModuleData(fid, data, fileInfo, length, identifier); + % read length of module specific data (if 0, escape) + dataLength = fread(fid, 1, 'int32'); + if (dataLength == 0) + return; end + if isBackground + % read module-specific background data + [data, selState] = obj.background().read(fid, data, fileInfo, length, identifier, selState); + else + % read module-specific data + [data, selState] = obj.readImpl(fid, data, fileInfo, length, identifier, selState); + end + + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + %%%%%%%% READ ANNOTATION DATA %%%%%%%% + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + + data.annotations = []; + + if (bitand(data.flagBitmap, flags.HASBINARYANNOTATIONS) ~= 0) + anStartPos = ftell(fid); + anTotLength = fread(fid, 1, 'int16'); + anTotCount = fread(fid, 1, 'int16'); + + for i = 1:anTotCount + filePos = ftell(fid); + anLength = fread(fid, 1, 'int16')-2; % this length does not include itself + anId = pgmatlab.utils.readJavaUTFString(fid); + anVersion = fread(fid, 1, 'int16'); + + anObj = -1; + switch (anId) + case 'Beer' + anObj = pgmatlab.core.annotations.BeamFormer(); + case 'Bearing' + anObj = pgmatlab.core.annotations.Bearing(); + case 'TMAN' + anObj = pgmatlab.core.annotations.TM(); + case 'TDBL' + anObj = pgmatlab.core.annotations.TDBL(); + case 'ClickClasssifier_1' + anObj = pgmatlab.core.annotations.ClickClsFr(); + case 'Matched_Clk_Clsfr' + anObj = pgmatlab.core.annotations.MatchCls(); + case 'BCLS' + anObj = pgmatlab.core.annotations.RWUDP(); + case {'DLRE', 'Delt'} + anObj = pgmatlab.core.annotations.DL(); + case {'Uson', 'USON'} + anObj = pgmatlab.core.annotations.UserForm(); + otherwise + fprintf('Unknown anotation type "%s" length %d version %d in file\n', ... + anId, anLength, anVersion); + fseek(fid, filePos + anLength, 'bof'); + end + if ~isempty(anObj) + % Assign the result of anObj() to a dynamic field of anData.annotations + d = anObj.read(fid, data, fileInfo, anLength, anVersion); + data.annotations.(anObj.name) = d; + end + anEndPos = ftell(fid); + if (anEndPos ~= filePos + anLength) + disp('Possible annotation read size error in file') + fseek(fid, filePos + anLength, 'bof'); + anEndPos = ftell(fid); + end + end + if (anEndPos ~= anStartPos + anTotLength) + fseek(fid, anStartPos + anTotLength, 'bof'); + end + end + end + + end +end diff --git a/pgmatlab/+pgmatlab/+core/+standard/@StandardModuleFooter/StandardModuleFooter.m b/pgmatlab/+pgmatlab/+core/+standard/@StandardModuleFooter/StandardModuleFooter.m new file mode 100644 index 0000000..07aa2bc --- /dev/null +++ b/pgmatlab/+pgmatlab/+core/+standard/@StandardModuleFooter/StandardModuleFooter.m @@ -0,0 +1,18 @@ +% StandardModuleFooter.m + +classdef StandardModuleFooter < pgmatlab.core.standard.BaseChunk + methods + function obj = StandardModuleFooter(); end + function data = readImpl(obj, fid, data, fileInfo, length, identifier); end + function data = read(obj, fid, data, fileInfo, length, identifier) + import pgmatlab.*; + data.length = length; + data.identifier = identifier; + data.binaryLength = fread(fid, 1, 'int32'); + data = obj.readImpl(fid, data, fileInfo, data.binaryLength, identifier); + end + end +end + + + diff --git a/pgmatlab/+pgmatlab/+core/+standard/@StandardModuleHeader/StandardModuleHeader.m b/pgmatlab/+pgmatlab/+core/+standard/@StandardModuleHeader/StandardModuleHeader.m new file mode 100644 index 0000000..802f5ac --- /dev/null +++ b/pgmatlab/+pgmatlab/+core/+standard/@StandardModuleHeader/StandardModuleHeader.m @@ -0,0 +1,18 @@ +% StandardModuleHeader.m + +classdef StandardModuleHeader < pgmatlab.core.standard.BaseChunk + methods + function obj = StandardModuleHeader(); end + function data = readImpl(obj, fid, data, fileInfo, length, identifier); end + function data = read(obj, fid, data, fileInfo, length, identifier) + data.length = length; + data.identifier = identifier; + data.version = fread(fid, 1, 'int32'); + data.binaryLength = fread(fid, 1, 'int32'); + data = obj.readImpl(fid, data, fileInfo, length, identifier); + end + end +end + + + diff --git a/pgmatlab/importloggertable.m b/pgmatlab/+pgmatlab/+db/+logger/importloggertable.m similarity index 100% rename from pgmatlab/importloggertable.m rename to pgmatlab/+pgmatlab/+db/+logger/importloggertable.m diff --git a/pgmatlab/importudftable.m b/pgmatlab/+pgmatlab/+db/+logger/importudftable.m similarity index 100% rename from pgmatlab/importudftable.m rename to pgmatlab/+pgmatlab/+db/+logger/importudftable.m diff --git a/pgmatlab/lookuptableformat.m b/pgmatlab/+pgmatlab/+db/+logger/lookuptableformat.m similarity index 100% rename from pgmatlab/lookuptableformat.m rename to pgmatlab/+pgmatlab/+db/+logger/lookuptableformat.m diff --git a/pgmatlab/udftableformat.m b/pgmatlab/+pgmatlab/+db/+logger/udftableformat.m similarity index 100% rename from pgmatlab/udftableformat.m rename to pgmatlab/+pgmatlab/+db/+logger/udftableformat.m diff --git a/pgmatlab/+pgmatlab/+db/addColumn.m b/pgmatlab/+pgmatlab/+db/addColumn.m new file mode 100644 index 0000000..bbdd849 --- /dev/null +++ b/pgmatlab/+pgmatlab/+db/addColumn.m @@ -0,0 +1,8 @@ +function e = addColumn(con, tableName, columnName, format); +%addColumn - adda column to a database table +% +% Syntax: +% e = addColumn(con, tableName, columnName, format); +cmd = sprintf('ALTER TABLE %s ADD COLUMN %s %s', tableName, columnName, format); +exec(con, cmd); +e = pgmatlab.db.columnExists(con, tableName, columnName); \ No newline at end of file diff --git a/pgmatlab/+pgmatlab/+db/checkColumn.m b/pgmatlab/+pgmatlab/+db/checkColumn.m new file mode 100644 index 0000000..a1ab2c8 --- /dev/null +++ b/pgmatlab/+pgmatlab/+db/checkColumn.m @@ -0,0 +1,13 @@ +function e = checkColumn(con, tableName, columnName, format); +% function e = checkColumn(con, tableName, columnName, format) +% checks a database table column, adding it if it doesn't exist. +e = pgmatlab.db.columnExists(con,tableName, columnName); +if e + return +end +tableName = pgmatlab.utils.charArray(tableName); +columnName = pgmatlab.utils.charArray(columnName); +format = pgmatlab.utils.charArray(columnName); +cmd = sprintf('ALTER TABLE %s ADD COLUMN %s %s', tableName, columnName, format); +ans = exec(con, cmd); +e = pgmatlab.db.columnExists(con, tableName, columnName); \ No newline at end of file diff --git a/pgmatlab/+pgmatlab/+db/checkTable.m b/pgmatlab/+pgmatlab/+db/checkTable.m new file mode 100644 index 0000000..dd0972f --- /dev/null +++ b/pgmatlab/+pgmatlab/+db/checkTable.m @@ -0,0 +1,52 @@ +function e = checkTable(con, tableName, create, colNames, colTypes) +% checkTable - Check a database table. +% +% Syntax: +% e = checkTable(con, tableName, create, colNames, colTypes) +% +% con - database connection +% tableName - database table name (char array) +% create - flag to create the table with a single Id primary key in case it doesn't exist. +% colNames - a list of column names to add to the table +% colTypes - a list of column types to add to the table +% +% Examples: +% e = checkTable(con, tableName) +% Returns true if the table exists within the given database connection +% +% e = checkTable(con, tableName, true) +% Creates the table if it doesn't exist, and adds a single column Id set +% to be a primary key. Returns true if the table then exists. +% +% e = checkTable(con, tableName, true, {'UTC', 'Duration', 'Comment'}, {'TIMESTAMP', 'DOUBLE', 'CHAR(50)'}) +% Creates the table if it doesn't exist, adds a single column Id set +% to be a primary key and three other columns in the given format. Returns true if the table then exists. +% colNames and colTypes must be cell arrays of the same lengths. + +if nargin < 3 + create = false; +end + +e = 0; +tableName = pgmatlab.utils.charArray(tableName); +if pgmatlab.db.tableExists(con, tableName) + e = 1; +end +if e == 0 && create + c = sprintf('CREATE TABLE %s (\"Id\" COUNTER NOT NULL, Primary Key (Id))', tableName); + q = exec(con, c); + e = pgmatlab.db.tableExists(con, tableName); +end +if nargin >= 5 + colNames = pgmatlab.utils.charArray(colNames); + colTypes = pgmatlab.utils.charArray(colTypes); + nCol = numel(colNames); + for i = 1:nCol + c = pgmatlab.db.checkColumn(con, tableName, colNames{i}, colTypes{i}); + if c == 0 + e = 0; + end + end +end + + diff --git a/pgmatlab/+pgmatlab/+db/checksqlitefuncs.m b/pgmatlab/+pgmatlab/+db/checksqlitefuncs.m new file mode 100644 index 0000000..bab3017 --- /dev/null +++ b/pgmatlab/+pgmatlab/+db/checksqlitefuncs.m @@ -0,0 +1,19 @@ +% check some functionality works with both the Matlab built in sqlite +% function and also with my own sqlitedatabase function + +dbName = 'C:\ProjectData\RobRiver\Y4_2023_2024_offline\RobRiver_Yr4_annotationsReproc240303.sqlite3' +tableName = 'Auto_Seal' +colName = 'UID' +con = sqlite(dbName) +pgmatlab.db.tableExists(con, tableName) + +% pStr = sprintf('PRAGMA table_Info(''%s'')', tableName); +% con.fetch(pStr) + +sq = sprintf('SELECT * FROM sqlite_master where name=''%s''', tableName); +con.fetch(sq) + +pgmatlab.db.columnExists(con, tableName, colName) + +close(con) + diff --git a/pgmatlab/clearcolumn.m b/pgmatlab/+pgmatlab/+db/clearcolumn.m similarity index 100% rename from pgmatlab/clearcolumn.m rename to pgmatlab/+pgmatlab/+db/clearcolumn.m diff --git a/pgmatlab/columnExists.m b/pgmatlab/+pgmatlab/+db/columnExists.m similarity index 100% rename from pgmatlab/columnExists.m rename to pgmatlab/+pgmatlab/+db/columnExists.m diff --git a/pgmatlab/getmaxcolvalue.m b/pgmatlab/+pgmatlab/+db/getmaxcolvalue.m similarity index 100% rename from pgmatlab/getmaxcolvalue.m rename to pgmatlab/+pgmatlab/+db/getmaxcolvalue.m diff --git a/pgmatlab/getmaxid.m b/pgmatlab/+pgmatlab/+db/getmaxid.m similarity index 100% rename from pgmatlab/getmaxid.m rename to pgmatlab/+pgmatlab/+db/getmaxid.m diff --git a/pgmatlab/sqlite-jdbc-3.45.3.0.jar b/pgmatlab/+pgmatlab/+db/sqlite-jdbc-3.45.3.0.jar similarity index 100% rename from pgmatlab/sqlite-jdbc-3.45.3.0.jar rename to pgmatlab/+pgmatlab/+db/sqlite-jdbc-3.45.3.0.jar diff --git a/pgmatlab/+pgmatlab/+db/sqlitedatabase.m b/pgmatlab/+pgmatlab/+db/sqlitedatabase.m new file mode 100644 index 0000000..1b71aa3 --- /dev/null +++ b/pgmatlab/+pgmatlab/+db/sqlitedatabase.m @@ -0,0 +1,64 @@ +function con = sqlitedatabase(fn, create) +% function con = sqlitedatabase(fn) +% Directly open a SQLite database for use in Matlab. +% fn: the path (filename) of a SQLite database file. +% create: if true, create an empty database. If false, return null +% + +% to use this function you will need to first download the sqlite-jdbc +% interface version sqlite-jdbc-3.36.0.jar or later. This is currently +% available from https://github.com/xerial/sqlite-jdbc/releases. +% You wil then need to add the jar file to your Matlab Java class path +% or put it in a folder somewhere in your 'normal' Matlab path and +% it will be loaded dynamically as needed. +% persistent waswarned; +% if isempty(waswarned) +% waswarned = 1; +% disp(' ************************ OBSOLETE FUNCTION ************************'); +% disp(' * You''re probably better off using the in built sqlite function *' ); +% disp(' * to open sqlite database files. This one is OK for reading, but *'); +% disp(' * does not write timestamps to the database in the correct format *'); +% disp(' *******************************************************************'); +% end +if nargin == 0 + error('You must specify a database file name'); +end +if nargin == 1 + create = false; +end +if (~create) + % check the file exists + dd = dir(fn); + if (numel(dd) == 0) + error('You must specify a path to an existing databse or set create to true to make a blank database'); + end +end + +% declare the driver and protocl needed to open the database. +driver = 'org.sqlite.JDBC'; +protocol = 'jdbc:sqlite:'; + +% these lines can be removed if the driver class is already +% added permanently to your class path. +% need to see if the class is available, in which case +% we won't need to load it. +% javarmpath(driver) +try + javaObjectEDT(driver) +catch + % if an exception was thrown, try to load the library. + % this will always happen the first time the function is called. + % driverClassPath = 'sqlite-jdbc-3.36.0.jar'; + % 3.45.3.0 is the current PAMGuard version as of V2.02.17, August 2025 + % driverClassPath = 'sqlite-jdbc-3.45.3.0.jar'; + driverClassPath = '+pgmatlab/+db/sqlite-jdbc-3.45.3.0.jar'; + jarFile = which(driverClassPath); + javaaddpath(jarFile); +end + +% check dbName is char, not string +if isstring(fn) + fn = char(fn); +end +% now open the database. +con = database('','','',driver, [protocol fn]); \ No newline at end of file diff --git a/pgmatlab/tableExists.m b/pgmatlab/+pgmatlab/+db/tableExists.m similarity index 100% rename from pgmatlab/tableExists.m rename to pgmatlab/+pgmatlab/+db/tableExists.m diff --git a/pgmatlab/+pgmatlab/+db/unpackLocaliserError.m b/pgmatlab/+pgmatlab/+db/unpackLocaliserError.m new file mode 100644 index 0000000..c84ee31 --- /dev/null +++ b/pgmatlab/+pgmatlab/+db/unpackLocaliserError.m @@ -0,0 +1,70 @@ +function [error, unpacked] = unpackLocaliserError(errorString) +% function error = unpackError(errorString) +% unpack an error string from the PAMGuard 3D localiser. These are in a +% json like format but without all the json headers. +if iscell(errorString) + % handle multiple strings + n = numel(errorString); + for i = n:-1:1 + e = pgmatlab.db.unpackLocaliserError(errorString{i}); + if ~isempty(e) + error(i) = e; + else +% error(i) = 0; + end + + end +else + % call gets here for a single string. + try + error = jsondecode(errorString); + catch + error = []; + end +end + +if nargout < 2 + return +end +% now further transofrm the errors into cartesian coordinates. + +% take the errors and try to get a meanish / total error out of them. +totErrors = zeros(1,numel(errorString))*NaN; +radialError = zeros(1,numel(errorString))*NaN; +xyError = zeros(1,numel(errorString))*NaN; +vError = zeros(1,numel(errorString))*NaN; +allEangles = zeros(3,numel(errorString))*NaN; +for i = 1:numel(error) + e = error(i); + eVal = e.ERRORS; + if numel(e.ANGLES) == 3 + allEangles(:,i) = e.ANGLES; + end + if isempty(eVal) + xyError(i) = NaN; + radialError(i) = NaN; + totErrors(i) = NaN; + continue; + end + if numel(eVal) == 6 + et = 0; + for ii = 1:3 + ei = sqrt(eVal(ii)*eVal(ii+3)); + et = et + ei^2; + end +% er = sqrt(eVal(1)*eVal(4)); + er = max(eVal([1 4])); + % er = eVal(1); + et = sqrt(et); + else + et = sqrt(sum(eVal.^2)); + er = eVal(2); + end + xyError(i) = cos(e.ANGLES(2))*er; + vError(i) = sin(e.ANGLES(2))*er; + radialError(i) = er; + totErrors(i) = et; +end +unpacked.xyError = xyError; +unpacked.radialError = radialError; +unpacked.totErrors = totErrors; \ No newline at end of file diff --git a/pgmatlab/+pgmatlab/+db/writespecannotationdata.m b/pgmatlab/+pgmatlab/+db/writespecannotationdata.m new file mode 100644 index 0000000..e7f7c97 --- /dev/null +++ b/pgmatlab/+pgmatlab/+db/writespecannotationdata.m @@ -0,0 +1,62 @@ +function n = writespectrogramannotationdata(dbName, tableName, data, exColNames, exColTypes) +% a nice one stop function to write data into a +% PAMGuard spectrogram annotations table. Well, not nice, but at least +% reusable. +colNames = {'Id', 'UID', 'UTC', 'UTCMilliseconds', 'PCLocalTime', 'PCTime', 'ChannelBitmap',... + 'SequenceBitmap', 'Duration', 'f1', 'f2'}; +colTypes = {'INTEGER NOT NULL', 'INTEGER', 'TIMESTAMP', 'INTEGER', 'TIMESTAMP', 'TIMESTAMP', 'INTEGER',... + 'INTEGER', 'DOUBLE', 'DOUBLE', 'DOUBLE'}; +if nargin >= 5 + colNames = [colNames, exColNames]; + colTypes = [colTypes, exColTypes]; +end +con = sqlite(dbName); +pgmatlab.db.checkTable(con, tableName, true, colNames, colTypes); + +maxId = pgmatlab.db.getmaxcolvalue(con, tableName, 'Id'); +maxUID = pgmatlab.db.getmaxcolvalue(con, tableName, 'UID'); +if isempty(maxId) + maxId = 0; +end +if isempty(maxUID) + maxUID = 0; +end + +close(con) + +% now put data into a table and insert. Data must either be a structure +% or a table in the correct format. +if istable(data) + tableData = data; +elseif isstruct(data) + cData = cell(numel(data), numel(colNames)); + for i = 1:numel(data) + maxId = maxId + 1; + maxUID = maxUID + 1; + cData{i,1} = maxId; + cData{i,2} = maxUID; + if isnumeric(data(i).UTC); + cData{i,3} = pgmatlab.utils.datenum2dbdate(data(i).UTC, '', true); + else + cData{i,3} = data(i).UTC; + end + cData{i,4} = 0; + cData{i,5} = cData{i,3}; + cData{i,6} = pgmatlab.utils.datenum2dbdate(now(), '', true); + cData{i,7} = data(i).ChannelBitmap; + cData{i,8} = cData{i,7}; + cData{i,9} = data(i).Duration; + cData{i,10} = data(i).f1; + cData{i,11} = data(i).f2; + if nargin >= 5 + for j = 1:numel(exColNames) + cData{i,11+j} = getfield(data(i), exColNames{j}); + end + end + end + tableData = cell2table(cData, 'VariableNames',colNames); +end +con = sqlite(dbName); +con.sqlwrite(tableName, tableData); +close(con); +end diff --git a/pgmatlab/Array/threadinglocaliser.m b/pgmatlab/+pgmatlab/+utils/+Array/threadinglocaliser.m similarity index 100% rename from pgmatlab/Array/threadinglocaliser.m rename to pgmatlab/+pgmatlab/+utils/+Array/threadinglocaliser.m diff --git a/pgmatlab/Array/threadinglocalisertest.m b/pgmatlab/+pgmatlab/+utils/+Array/threadinglocalisertest.m similarity index 100% rename from pgmatlab/Array/threadinglocalisertest.m rename to pgmatlab/+pgmatlab/+utils/+Array/threadinglocalisertest.m diff --git a/pgmatlab/+pgmatlab/+utils/charArray.m b/pgmatlab/+pgmatlab/+utils/charArray.m new file mode 100644 index 0000000..de795e0 --- /dev/null +++ b/pgmatlab/+pgmatlab/+utils/charArray.m @@ -0,0 +1,29 @@ +function c = charArray(in) + %pgmatlab.utils.CHARARRAY - convert a string to a byte array, or cell + % of strings to a cell array of char arrays. Can pass in a mix of + % strings and char arrays. + % + % Example 1: + % >>> res = pgmatlab.utils.charArray({"v1", 'v2', {'v3', "v4"}}; + % This produces {'v1', 'v2', {'v3', 'v4'}} + % + % Example 2: + % >>> res = pgmatlab.utils.charArray([]) + % This produces {} + % + % Example 3: + % >>> res = pgmatlab.utils.charArray({}) + % This produces {} + % + + if (iscell(in)) + % Preallocate space for c + c{numel(in)} = -1; + for i = 1:numel(in) + c{i} = pgmatlab.utils.charArray(in{i}); + end + return; + end + c = char(in); + return; +end \ No newline at end of file diff --git a/pgmatlab/+pgmatlab/+utils/checkArrayAllocation.m b/pgmatlab/+pgmatlab/+utils/checkArrayAllocation.m new file mode 100644 index 0000000..06bd062 --- /dev/null +++ b/pgmatlab/+pgmatlab/+utils/checkArrayAllocation.m @@ -0,0 +1,19 @@ +% Check the array allocation. This gets called every time data are read and +% will extend the array by approximately the sqrt of the arrays own length +% if required. Preallocation acheived by sticking a sample object at a high +% data index so that array up to that point gets filled with nulls. +function array = checkArrayAllocation(array, reqLength, sampleObject) +if isempty(array) + currentLength = 0; + clear array; +else + currentLength = numel(array); +end +if (currentLength >= reqLength) + return; +end +allocStep = round(sqrt(reqLength)); +allocStep = max(10, min(allocStep, 10000)); +array(reqLength + allocStep) = sampleObject; +return; +end diff --git a/pgmatlab/countChannels.m b/pgmatlab/+pgmatlab/+utils/countChannels.m similarity index 100% rename from pgmatlab/countChannels.m rename to pgmatlab/+pgmatlab/+utils/countChannels.m diff --git a/pgmatlab/+pgmatlab/+utils/dateNumToMillis.m b/pgmatlab/+pgmatlab/+utils/dateNumToMillis.m new file mode 100644 index 0000000..bad833c --- /dev/null +++ b/pgmatlab/+pgmatlab/+utils/dateNumToMillis.m @@ -0,0 +1,9 @@ +function millis = dateNumToMillis(datenum) +%dateNumToMillis - convert a matlab date (days since 00-Jan-0000) to a time +%in Java milliseconds (milliseconds since 00-Jan-1970) +% +% Syntax: +% javamillis = dateNumToMillis(matlabdatenum) + +millis = (datenum-719529)*86400000; +% datenum = double(millis)/86400000.0+719529; \ No newline at end of file diff --git a/pgmatlab/datenum2dbdate.m b/pgmatlab/+pgmatlab/+utils/datenum2dbdate.m similarity index 100% rename from pgmatlab/datenum2dbdate.m rename to pgmatlab/+pgmatlab/+utils/datenum2dbdate.m diff --git a/pgmatlab/+pgmatlab/+utils/dbdate2datenum.m b/pgmatlab/+pgmatlab/+utils/dbdate2datenum.m new file mode 100644 index 0000000..6f7f20f --- /dev/null +++ b/pgmatlab/+pgmatlab/+utils/dbdate2datenum.m @@ -0,0 +1,66 @@ +function [dn, millis] = dbdate2datenum(dbdate) +%dbdate2datenum convert string format dates returned by a database to +%Matlab datenums +% +% Syntax: +% [dn, millis] = dbdate2datenum(dbdate) +% dndate can ne a single char array or string, or can be a cell array of +% char arrays or of string, e.g. a columns of a table returned from a +% database query. + +if (numel(dbdate) == 0) + dn = []; + millis = []; + return; +end +dbdate=convertStringsToChars(dbdate); + +% function dn = dbdate2datenum(dbdate) +% converts a YYYY-MM-DD HH:MM:SS.ms datestring returned from a database +% into a datenum (standard Matlab time) +if iscell(dbdate) + n = length(dbdate); + dn = zeros(size(dbdate)); + millis = zeros(size(dbdate)); + for i = 1:n + [aDate, ms] = pgmatlab.utils.dbdate2datenum(dbdate{i}); + dn(i) = aDate; + millis(i) = ms; + end + return; +end +if size(dbdate,1) > 1 + % this will happen if it's an array of UTC times read from a table. + n = size(dbdate, 1); +if isstring(dbdate) + dbdate = char(dbdate); + dn = zeros(n,1); + millis = zeros(n,1); + for i = 1:n + try + [aDate, ms] = pgmatlab.utils.dbdate2datenum(dbdate(i,:)); + dn(i) = aDate; + millis(i) = ms; + catch + disp('crap date'); + dbdate(i,:) + end + end + return; +end +end +dbdate = deblank(dbdate); +dbdate = strrep(dbdate,'''',''); +% dbdate will be in the format YYYY-MM-DD HH:MM:SS.ms which matlab doesn't understand ! +YY = str2num(dbdate(1:4)); +MM = str2num(dbdate(6:7)); +DD = str2num(dbdate(9:10)); +HH = str2num(dbdate(12:13)); +M = str2num(dbdate(15:16)); +SS = str2num(dbdate(18:19)); +MS = 0; +if length(dbdate) > 20; + MS = str2num(dbdate(20:length(dbdate))); % this is read with the . so is fractional seconds +end +dn = datenum(YY,MM,DD,HH,M,SS) + MS/24/3600; +millis = MS*1000; diff --git a/pgmatlab/dirsub.m b/pgmatlab/+pgmatlab/+utils/dirsub.m similarity index 100% rename from pgmatlab/dirsub.m rename to pgmatlab/+pgmatlab/+utils/dirsub.m diff --git a/pgmatlab/+pgmatlab/+utils/findBinaryFile.m b/pgmatlab/+pgmatlab/+utils/findBinaryFile.m new file mode 100644 index 0000000..1e0a664 --- /dev/null +++ b/pgmatlab/+pgmatlab/+utils/findBinaryFile.m @@ -0,0 +1,45 @@ +function filePath = findBinaryFile(root, mask, file) +root = pgmatlab.utils.charArray(root); +mask = pgmatlab.utils.charArray(mask); +file = pgmatlab.utils.charArray(file); +% find a file in the root, and mask with a given name. +% will make a master list once, then reuse it to find the +% right file. +persistent lastRoot lastMask; +persistent masterList namesOnly shortenedNames; +if needFullSearch(lastRoot, lastMask, root, mask) + maxNameLen = 80; % problem in database limiting names to 80 characters + masterList = pgmatlab.utils.dirsub(root, mask); + namesOnly = cell(1,numel(masterList)); + shortenedNames = cell(1,numel(masterList)); + for i = 1:numel(masterList) + fn = masterList(i).name; + fp = masterList(i).folder; + namesOnly{i} = fn(length(fp)+2:end); + shortenedNames{i} = namesOnly{i}; + if length(shortenedNames{i}) > maxNameLen + shortenedNames{i} = shortenedNames{i}(end-(maxNameLen-1):end); + end + end + lastRoot = root; + lastMask = mask; +end +filePath = []; +wants = find(strcmp(namesOnly, file)); +if (numel(wants) == 0) + wants = find(strcmp(shortenedNames, file)); +end +if numel(wants) ~= 1 + return +else + filePath = masterList(wants).name; +end + +end +function full =needFullSearch(lastRoot, lastMask, root, mask) +if isempty(lastRoot) || isempty(lastMask) + full = true; + return; +end +full = ~(strcmp(lastRoot, root) && strcmp(lastMask, mask)); +end \ No newline at end of file diff --git a/pgmatlab/+pgmatlab/+utils/findBinaryFileForDate.m b/pgmatlab/+pgmatlab/+utils/findBinaryFileForDate.m new file mode 100644 index 0000000..610e03b --- /dev/null +++ b/pgmatlab/+pgmatlab/+utils/findBinaryFileForDate.m @@ -0,0 +1,79 @@ +function filePath = findBinaryFileForDate(root, mask, dates, verbose) +root = pgmatlab.utils.charArray(root); +mask = pgmatlab.utils.charArray(mask); +% find a file in the root that has data in the dates range. if necessary +% dates may be a vector and multiple files may be returned. +if nargin < 4 + verbose = 0; +end +if numel(dates) > 1 + filePath = cell(size(dates)); + mt = zeros(size(dates)); + for i = 1:numel(dates) + filePath{i} = pgmatlab.findBinaryFileForDate(root, mask, dates(i), verbose); + mt(i) = isempty(filePath{i}); + end + % remove nulls + filePath = filePath(find(mt==0)); + + return +end +% from here it's only a single date. +% need to catalog all the times of all the pgdx files. +persistent lastRoot lastMask; +persistent masterList namesOnly shortenedNames dataStarts dataEnds; +if needFullSearch(lastRoot, lastMask, root, mask) + maxNameLen = 80; % problem in database limiting names to 80 characters + if (verbose) + fprintf('Searching folder %s for files type %s\n', root, mask); + end + masterList = pgmatlab.utils.dirsub(root, mask); + namesOnly = cell(1,numel(masterList)); + shortenedNames = cell(1,numel(masterList)); + dataStarts = zeros(1,numel(masterList)); + dataEnds = zeros(1,numel(masterList)); + for i = 1:numel(masterList) + if (verbose) + if mod(i,100) == 0 + fprintf('Extracting times from file %d of %d: %s\n', ... + i, numel(masterList), masterList(i).name); + end + end + xFile = strrep(masterList(i).name, '.pgdf', '.pgdx'); + xFile = strrep(xFile, '.pgnf', '.pgdx'); + [~, fileInfo] = pgmatlab.loadPamguardBinaryFile(xFile); + try + dataStarts(i) = fileInfo.fileHeader.dataDate; + dataEnds(i) = fileInfo.fileFooter.dataDate; + catch + fprintf('Error in file %s\n', xFile); + end + end + + for i = 1:numel(masterList) + fn = masterList(i).name; + fp = masterList(i).folder; + namesOnly{i} = fn(length(fp)+2:end); + shortenedNames{i} = namesOnly{i}; + if length(shortenedNames{i}) > maxNameLen + shortenedNames{i} = shortenedNames{i}(end-(maxNameLen-1):end); + end + end + lastRoot = root; + lastMask = mask; +end +filePath = []; +% find files in the right date range. +wants = find(dates>=dataStarts & dates <=dataEnds); +if numel(wants) + filePath = masterList(wants).name; +end + +end +function full =needFullSearch(lastRoot, lastMask, root, mask) +if isempty(lastRoot) || isempty(lastMask) + full = true; + return; +end +full = ~(strcmp(lastRoot, root) && strcmp(lastMask, mask)); +end \ No newline at end of file diff --git a/pgmatlab/getChannels.m b/pgmatlab/+pgmatlab/+utils/getChannels.m similarity index 100% rename from pgmatlab/getChannels.m rename to pgmatlab/+pgmatlab/+utils/getChannels.m diff --git a/pgmatlab/+pgmatlab/+utils/millisToDateNum.m b/pgmatlab/+pgmatlab/+utils/millisToDateNum.m new file mode 100644 index 0000000..ad48e5e --- /dev/null +++ b/pgmatlab/+pgmatlab/+utils/millisToDateNum.m @@ -0,0 +1,8 @@ +function datenum = millisToDateNum(millis) +%dateNumToMillis - convert a time in Java milliseconds (millis since 1970) +%into a Matlab date (days since 00-Jan-0000) +% +% Syntax: +% matlabdate = millisToDateNum(javamillis) + +datenum = double(millis)/double(86400000.0)+double(719529); \ No newline at end of file diff --git a/pgmatlab/passalldata.m b/pgmatlab/+pgmatlab/+utils/passalldata.m similarity index 100% rename from pgmatlab/passalldata.m rename to pgmatlab/+pgmatlab/+utils/passalldata.m diff --git a/pgmatlab/+pgmatlab/+utils/readJavaUTFString.m b/pgmatlab/+pgmatlab/+utils/readJavaUTFString.m new file mode 100644 index 0000000..d1753c1 --- /dev/null +++ b/pgmatlab/+pgmatlab/+utils/readJavaUTFString.m @@ -0,0 +1,7 @@ +function [str len] = readJavaUTFString(file); +% function [str len] = pgmatlab.utils.readJavaUTFString(file); +% read a string written in Java UTF-8 format from a file. +% The first two bytes are the length of the string, then +% it's the string. +len = fread(file, 1, 'int16'); +str = char(fread(file, len, 'uchar')'); \ No newline at end of file diff --git a/pgmatlab/+pgmatlab/loadPamguardBinaryFile.m b/pgmatlab/+pgmatlab/loadPamguardBinaryFile.m new file mode 100644 index 0000000..04b0d87 --- /dev/null +++ b/pgmatlab/+pgmatlab/loadPamguardBinaryFile.m @@ -0,0 +1,378 @@ +function [dataSet, fileInfo, selState] = loadPamguardBinaryFile(fileName, varargin) +%PGMATLAB.LOADPAMGUARDBINARYFILE - Load a PAMGuard Binary File into memory. +% Produces a 1x2 vector with structs of the data set and file information. +% +% Syntax +% [dataSet, fileInfo] = PGMATLAB.LOADPAMGUARDBINARYFILE(fileName, varargin) +% dataSet = PGMATLAB.LOADPAMGUARDBINARYFILE(fileName, varargin) +% +% varargin can be one or more of the following options: +% +% 'timerange', TIME_RANGE: Specify the time range to load data from. +% TIME_RANGE is a 1x2 vector of the form [START_TIME, END_TIME]. +% +% 'uidrange', UID_RANGE: Specify the UID range to load data from. +% UID_RANGE is a 1x2 vector of the form [START_UID, END_UID]. +% +% 'uidlist', UID_LIST: Specify a list of UIDs to load data from. +% UID_LIST is a vector of UIDs. +% +% 'filter', FILTER_FUN: Specify a filter function to apply to the data. +% FILTER_FUN is a function handle that takes the data as input and +% returns a selection state (0 = skip, 1 = keep, 2 = stop, if data +% is ordered). +% +% 'channel', CHANNEL_MAP: Specify a channel map to apply to the data. +% CHANNEL_MAP a bitmap of the channels to load. +% +% 'sorted', SORTED: Specify whether the data is sorted. SORTED is a +% logical value (1 true or 0 false). It serves to speed up execution +% if the data exceeds the upper bound of a range filter. This applies +% if 'timerange' and/or 'uidrange' are provided. Setting SORTED to 1 +% when using these range filters can cause unexpected behaviour if the +% data being filtered on is not actually sorted. Defaults to 0 (false). +% +% Example 1: load an entire binary file +% >>> [d,f] = pgmatlab.loadPamguardBinaryFile("./data.pgdf") +% +% Example 2: load a specific time range (indicating sorted data) +% >>> startTime = datenum(2017,10,21,0,25,0); +% >>> endTime = datenum(2017,10,21,0,26,0); +% >>> [d,f] = pgmatlab.loadPamguardBinaryFile("./data.pgdf", 'timerange', [startTime endTime], 'sorted', 1) +% +% Example 3: load a specific UID range +% >>> [d,f] = pgmatlab.loadPamguardBinaryFile("./data.pgdf", 'uidrange', [1000345 1000345]) +% +% Example 4: load a specific list of UIDs +% >>> [d,f] = pgmatlab.loadPamguardBinaryFile("./data.pgdf", 'uidlist', [1000345 1000347 1000348]) +% +% Example 5: load a specific channel map +% >>> [d,f] = pgmatlab.loadPamguardBinaryFile("./data.pgdf", 'channel', [0 1]) +% +% Example 6: load a specific channel map +% >>> [d,f] = pgmatlab.loadPamguardBinaryFile("./data.pgdf", 'sorted', true) +% +% Example 7: filter based on an un-sorted parameter +% >>> function selState = myFilter(data) +% % remove all data where type ~= 0 +% if data.type == 1 +% selState = 1; % keep +% else +% selState = 0; % skip +% end +% >>> end +% >>> [d,f] = pgmatlab.loadPamguardBinaryFile("./data.pgdf", 'filter', @myFilter) +% +% Example 8: filter based on a sorted parameter +% >>> function selState = myFilter(data) +% % remove all data where type ~= 0 +% if data.type == 1 +% selState = 1; % keep +% else +% selState = 2; % stop +% end +% >>> end +% >>> [d,f] = pgmatlab.loadPamguardBinaryFile("./data.pgdf", 'filter', @myFilter, 'sorted', 1) +% +% See also PGMATLAB.LOADPAMGUARDBINARYFOLDER, PGMATLAB.LOADPAMGUARDMULTIFILE. +% + +import pgmatlab.utils.*; +import pgmatlab.core.annotations.*; +import pgmatlab.core.modules.*; +import pgmatlab.core.standard.*; + +dataSet = []; +fileInfo = []; +nBackground = 0; +timeRange = [-Inf +Inf]; +uidRange = [-Inf +Inf]; +uidList = []; +iArg = 0; +sorted = 0; +filterfun = @pgmatlab.utils.passalldata; +channelmap=-1; +while iArg < numel(varargin) + iArg = iArg + 1; + switch(varargin{iArg}) + case 'timerange' + iArg = iArg + 1; + % timeRange = pgmatlab.utils.dateNumToMillis(varargin{iArg}); + timeRange = varargin{iArg}; + case 'uidrange' + iArg = iArg + 1; + uidRange = varargin{iArg}; + case 'uidlist' + iArg = iArg + 1; + uidList = sort(varargin{iArg}); + case 'filter' + iArg = iArg + 1; + filterfun = varargin{iArg}; + case 'channel' + iArg = iArg + 1; + channelmap = varargin{iArg}; + case 'sorted' + iArg = iArg + 1; + sorted = varargin{iArg}; + end +end +selState = 0; +% open binary file and read data +nData = 0; +try + fid = fopen(fileName, 'r', 'ieee-be.l64'); + + % initialize variables + prevPos = -1; + background = []; + + moduleObj = -1; + + + % main loop + while (1) + + % if for some reason we're stuck at one byte, warn the user and + % abort + pos = ftell(fid); + if (pos == prevPos) + disp(fprintf('File stuck at byte %d', pos)); + break; + end + prevPos = pos; + + % read in the length of the object and the type. + [length, nL] = fread(fid, 1, 'int32'); + [identifier, nT] = fread(fid, 1, 'int32'); + if (nL == 0 || nT == 0), break; end + nextPos = ftell(fid) - 8 + length; + switch identifier + + % Case 1: File Header. Read in the file header, and then set + % the function handles depending on what type of data the + % binary file holds. The module type is typically specified in + % the package class that extends PamControlledUnit, and is a + % string unique to that module. + case -1 + fileInfo.fileHeader = pgmatlab.core.standard.StandardFileHeader().read(fid, [], fileInfo, length, identifier); + + switch fileInfo.fileHeader.moduleType + + % AIS Processing Module + case 'AIS Processing' + moduleObj = pgmatlab.core.modules.processing.AIS(); + + % Clip Generator Module + case 'Clip Generator' + moduleObj = pgmatlab.core.modules.processing.ClipGenerator(); + + % DbHt Module + case 'DbHt' + moduleObj = pgmatlab.core.modules.processing.DbHt(); + + % % Difar Module + case 'DIFAR Processing' + moduleObj = pgmatlab.core.modules.processing.Difar(); + + % Ishmael Data & Detections + case {'Energy Sum Detector','Spectrogram Correlation Detector','Matched Filter Detector'} + switch fileInfo.fileHeader.streamName + case 'Ishmael Peak Data' + moduleObj = pgmatlab.core.modules.processing.IshmaelData(); + % TODO: specify objectType + case 'Ishmael Detections' + moduleObj = pgmatlab.core.modules.processing.IshmaelDetections(); + % TODO: specify objectType + end + + % LTSA Module + case 'LTSA' + moduleObj = pgmatlab.core.modules.processing.LongTermSpectralAverage(); + + % Filtered Noise Measurement Module (Noise One Band) + case 'NoiseBand' + moduleObj = pgmatlab.core.modules.processing.NoiseBand(); + + % Noise Monitor Module and Noise Band Monitor Module + % Note: The two modules have different types, but both + % use noiseMonitor.NoiseBinaryDataSource class to save + % data + case {'Noise Monitor', 'Noise Band'} + moduleObj = pgmatlab.core.modules.processing.NoiseMonitor(); + + % Deep learning module + case 'Deep Learning Classifier' + switch fileInfo.fileHeader.streamName + case {'DL_detection', 'DL detection'} + moduleObj = pgmatlab.core.modules.classifiers.DeepLearningClassifierDetections(); + case {'DL_Model_Data', 'DL Model Data'} + moduleObj = pgmatlab.core.modules.classifiers.DeepLearningClassifierModels(); + end + + % Click Detector or Soundtrap Click Detector Module + case {'Click Detector', 'SoundTrap Click Detector'} + switch fileInfo.fileHeader.streamName + case 'Clicks' + moduleObj = pgmatlab.core.modules.detectors.Click(); + case 'Trigger Background' + moduleObj = pgmatlab.core.modules.detectors.ClickTrigger(); + end + + case 'GPL Detector' + switch fileInfo.fileHeader.streamName + case 'GPL Detections' + moduleObj = pgmatlab.core.modules.detectors.GPL(); + end + + % Right Whale Edge Detector Module + case 'RW Edge Detector' + moduleObj = pgmatlab.core.modules.detectors.RWEdge(); + disp('Right Whale Edge Detector binary file detected'); + disp('Note that the low, high and peak frequencies are actually'); + disp('saved as FFT slices. In order to convert values to Hz, they'); + disp('must be multiplied by (sampleRate/fftLength)'); + + % Whistle And Moans Module + case 'WhistlesMoans' + moduleObj = pgmatlab.core.modules.detectors.WhistleAndMoan(); + + % Ipi module + case 'Ipi module' + moduleObj = pgmatlab.core.modules.plugins.SpermWhaleIPI(); + + case 'Gemini Threshold Detector' + moduleObj = pgmatlab.core.modules.plugins.GeminiThreshold(); + + % Note: PamRawDataBlock has it's own Binary Store (RawDataBinarySource), + % but it is created by multiple different processes so doesn't have one + % particular type, and may have a type shared with a different binary + % store (e.g. the DbHt module creates both a DbHtDataSource and a + % RawDataBinarySource, and they will both have type 'DbHt'). + % The comments in the class indicate that the binary store should never + % be used for raw data and that the sole purpose of the class is to + % enable sending raw data over the network. If this is ever changed + % and raw data is allowed to be stored in the binary files, we will + % have to come up with a way of determining where the raw data came + % from besides querying the type. + + otherwise + disp(['Don''t recognize type ' fileInfo.fileHeader.moduleType '. Aborting load']); + break; + end + + + case -2 + % Case 2: File Footer. The file version should have been set + % when we read the file header. If the file header is empty, + % something has gone wrong so warn the user and exit + if (isempty(fileInfo.fileHeader)) + disp('Error: found file footer before file header. Aborting load'); + break; + end + fileInfo.fileFooter = pgmatlab.core.standard.StandardFileFooter().read(fid, [], fileInfo, length, identifier); + case -3 + % Case 3: Module Header. The correct function handle should + % have been set when we read the file header. If the file + % header is empty, something has gone wrong so warn the user + % and exit + if (isempty(fileInfo.fileHeader)) + disp('Error: found module header before file header. Aborting load'); + break; + end + fileInfo.moduleHeader = moduleObj.header().read(fid, [], fileInfo, length, identifier); + + case -4 + % Case 4: Module Footer. The correct function handle should + % have been set when we read the file header. If the file + % header is empty, something has gone wrong so warn the user + % and exit + if (isempty(fileInfo.fileHeader)) + disp('Error: found module footer before headers. Aborting load'); + break; + end + fileInfo.moduleFooter = moduleObj.footer().read(fid, [], fileInfo, length, identifier); + case -5 + % Case 5: Datagram. Skip it for now. + fseek(fid, length - 8, 'cof'); + + otherwise + % Case 6: Data/Background. The correct moduleObj should have been + % set when we read in the file header. If the file header is + % empty, something has gone wrong so warn the user and exit + + if (isempty(fileInfo.fileHeader) || isempty(fileInfo.moduleHeader)) + disp('Error: found data before headers. Aborting load'); + end + + isBackground = identifier == -6; + dataPoint = struct(); + + try + [dataPoint, selState] = moduleObj.read(fid, dataPoint, fileInfo, length, identifier, timeRange, uidRange, uidList, channelmap); + catch mError + disp(['Error reading ' fileInfo.fileHeader.moduleType ' data object. Data read:']); + disp(dataPoint); + disp(getReport(mError)); + end + + % Allow custom filters to be applied + if selState == 1 + selState = filterfun(dataPoint); + end + + % If the selState is 2 (STOP) and the data is sorted then + % stop reading the file. If the data is not sorted, then + % selState 0 (SKIP) and 2 (STOP) both mean 'SKIP'. If + % selState is 1 (KEEP), we keep the data point. + if (selState == 2 && sorted) + break; + elseif (selState ~= 1) + if (~sorted) + selState = 0; + end + fseek(fid, nextPos - ftell(fid), 'cof'); + continue; + end + + % add to the data or background variables accordingly + if isBackground + nBackground = nBackground + 1; + background = pgmatlab.utils.checkArrayAllocation(background, nBackground, dataPoint); + background(nBackground) = dataPoint; + else + nData = nData + 1; + dataSet = pgmatlab.utils.checkArrayAllocation(dataSet, nData, dataPoint); + dataSet(nData) = dataPoint; + end + + % reconcile file position with what we expect + if ftell(fid) ~= nextPos + fprintf('Error in file position: %d bytes\n', ftell(fid)-nextPos); + fseek(fid, nextPos - ftell(fid), 'cof'); + end + end + end + % due to preallocation it's likely the array is now far too large so + % shrink it back to the correct size. + dataSet = dataSet(1:nData); + background = background(1:nBackground); +catch mError + disp('Error reading file'); + disp(getReport(mError)); +end + +if nBackground > 0 + fileInfo.background = background; +end + +if ~isempty(moduleObj.objectType) + fileInfo.objectType = moduleObj.objectType; +end + +% close the file and return to the calling function +try + fclose(fid); +catch +end +return; +end diff --git a/pgmatlab/+pgmatlab/loadPamguardBinaryFolder.m b/pgmatlab/+pgmatlab/loadPamguardBinaryFolder.m new file mode 100644 index 0000000..b50834b --- /dev/null +++ b/pgmatlab/+pgmatlab/loadPamguardBinaryFolder.m @@ -0,0 +1,159 @@ +function [allData, allBackground, fileInfos] = loadPamguardBinaryFolder(dir, fileMask, verbose, varargin) +%PGMATLAB.LOADPAMGUARDBINARYFOLDER - Load many PAMGuard Binary Files into memory from a folder (and subfol +% ders). +% +% Produces a 1x3 vector with the datasets, backgrounds, and fileInfos +% from all of the files in the folder. +% +% Syntax: +% [allData, allBackground, fileInfos] = PGMATLAB.LOADPAMGUARDBINARYFOLDER(dir, fileMask, verbose, varargin) +% [allData, allBackground] = PGMATLAB.LOADPAMGUARDBINARYFOLDER(dir, fileMask, verbose, varargin) +% allData = PGMATLAB.LOADPAMGUARDBINARYFOLDER(dir, fileMask, verbose, varargin) +% +% - dir (string, required) is the root directory of the binary data files to be read. +% +% - fileMask (string, required) is a file mask used to select the files in dir (e.g. "*.pgdf"). +% +% - verbose (integer, default 0) if a non-zero number n then every n files prints a progress log. +% To avoid logging set verbose to 0. +% +% - varargin (optional) can be one or more of the following options, used to filter data: +% +% 'timerange', TIME_RANGE (default ALL): Specify the time range to load data from. +% TIME_RANGE is a 1x2 vector of the form [START_TIME, END_TIME]. +% +% 'uidrange', UID_RANGE (default ALL): Specify the UID range to load data from. +% UID_RANGE is a 1x2 vector of the form [START_UID, END_UID]. +% +% 'uidlist', UID_LIST (default ALL): Specify a list of UIDs to load data from. +% UID_LIST is a vector of UIDs. +% +% 'channel', CHANNEL_MAP (default ALL): Specify a channel map to apply to the data. +% CHANNEL_MAP a bitmap of the channels to load. +% +% 'filter', FILTER_FUN: Specify a filter function to apply to the data. +% FILTER_FUN is a function handle that takes the data as input and +% returns a selection state (0 = skip, 1 = keep, 2 = stop, if data +% is ordered). +% +% 'sorted', SORTED (default 0): Specify whether the data is sorted. SORTED is a +% logical value (1 true or 0 false). It serves to speed up execution +% if the data exceeds the upper bound of a range filter. This applies +% if 'timerange' and/or 'uidrange' are provided. Setting SORTED to 1 +% when using these range filters can cause unexpected behaviour if the +% data being filtered on is not actually sorted. Defaults to 0 (false). +% SORTED also requires files to be alphanumerically sorted in the folder +% bring read. +% +% Example 1: load an entire folder of binary files +% >>> [d,b,f] = pgmatlab.loadPamguardBinaryFolder("./Data"); +% +% Example 2: load an entire folder of binary files with a filterfun +% >>> function selState = myFilter(data) +% % remove all data where type ~= 1 +% if data.type == 1 +% selState = 1; % keep +% else +% selState = 0; % skip +% end +% >>> end +% >>> [d,b,f] = pgmatlab.loadPamguardBinaryFolder("./Data", "*.pgdf", 1, @myFilter) +% +% Example 3: load an entire folder of binary files within a specific time range (indicating sorted data); +% >>> startTime = datenum(2017,10,21,0,25,0); +% >>> endTime = datenum(2017,10,21,0,26,0); +% >>> [d,b,f] = pgmatlab.loadPamguardBinaryFile("./Data.pgdf", "*.pgdf", 1, @pgmatlab.utils.passalldata, "timerange", [startTime endTime], "sorted", 1) +% +% For more examples on how to use varargin to specify filters, check out help PGMATLAB.LOADPAMGUARDBINARYFILE. +% +% See also PGMATLAB.LOADPAMGUARDBINARYFILE, PGMATLAB.LOADPAMGUARDBINARYFOLDER. +% + +% Set default verbosity +if (nargin < 3) + verbose = 0; +end + +% Set default varargin variable +iArg = length(varargin); +if iArg == 0 + varargin = {}; +end + +% % Manually add filter to the varargin. This is to +% % support legacy code, and should be discouraged. +% if nargin < 4 || (nargin >= 4 && ~filterfun) +% filterfun = @pgmatlab.utils.passalldata; +% end +% varargin{iArg + 1} = "filter"; +% varargin{iArg + 2} = filterfun; + +allData = []; +nData = 0; +allBackground = []; +nBackground = 0; + +allFiles = pgmatlab.utils.dirsub(dir, fileMask); +fileInfos = []; +nFileInfos = 0; + +for i = 1:numel(allFiles) + % Which file is going to be loaded + [fDir, fName, fEnd] = fileparts(allFiles(i).name); + fileName = [fName fEnd]; + + % Print log message based on verbosity + if verbose + if mod(i, verbose) == 0 + fprintf('Loading %d/%d (%d) %s%s (%s)\n', i, numel(allFiles), numel(allData), fName, fEnd, fDir); + end + end + + % Load binary file data + [data, fileInfo, selState] = pgmatlab.loadPamguardBinaryFile(allFiles(i).name, varargin{:}); + + % Populate allData array is necessary + if ~isempty(data) + for j = 1:numel(data) + data(j).clickNumber = j; % DEPRACATED: use uid instead of clickNumber to track specific nodes + data(j).fileName = fileName; + end + allData = [pgmatlab.utils.checkArrayAllocation(allData, nData + length(data), data(1)) data]; + nData = nData + length(data); + end + + % Populate allBackground array if necessary + if isfield(fileInfo, 'background') && nargout >= 2 + allBackground = [pgmatlab.utils.checkArrayAllocation(allBackground, nBackground + length(fileInfo.background), -1) fileInfo.background]; + nBackground = nBackground + length(fileInfo.background); + end + + % Populate fileInfo array if necessary + if nargout >= 3 + fileInfos = pgmatlab.utils.checkArrayAllocation(fileInfos, numel(allFiles), fileInfo); + fileInfos(i) = fileInfo; + nFileInfos = nFileInfos + 1; + end + + % Selection state of 2 means the data has surpassed the upper + % boundary of a particular range (usually time or uid). This + % means that we can stop searching files. + if selState == 2 + break; + end +end + +% Ensure addData, allBackground and fileInfos are the +% correct size. Due to preallocation, they are likely +% to have exceeded the expected length. +if nData > 0 + allData = allData(1:nData); +end +if nBackground > 0 + allBackground = allBackground(1:nBackground); +end +if nFileInfos >0 + fileInfos = fileInfos(1:nFileInfos); +end \ No newline at end of file diff --git a/pgmatlab/+pgmatlab/loadPamguardMultiFile.m b/pgmatlab/+pgmatlab/loadPamguardMultiFile.m new file mode 100644 index 0000000..4712f83 --- /dev/null +++ b/pgmatlab/+pgmatlab/loadPamguardMultiFile.m @@ -0,0 +1,107 @@ +function eventData = loadPamguardMultiFile(dir, fileNames, UIDs, verbose) +%PGMATLAB.LOADPAMGUARDMULTIFILE - Load multiple P +% AMGuard Binary Files into memory filtering by certain UIDs in certain +% files. +% +% This can be used to get binary file data for data associated with PAMGuard +% events. In other words, PGMATLAB.LOADPAMGUARDMULTIFILE is a bulk-load +% function with file-specific UID filters. +% +% Produces an array of data points which correspond to the UID filters from +% multiple binary files. +% +% Syntax: +% eventData = PGMATLAB.LOADPAMGUARDMULTIFILE(dir, fileNames, UIDs, verbose); +% +% - dir (string, required): the root directory in which to search for +% PAMGuard binary files (.pgdf). +% +% - fileNames (cell {}) and UIDs (array []): two parallel arrays specifying +% specific UIDs in each file to load into eventData. See Examples for +% more information on how these arrays interact with each other. These +% arrays must have the same number of elements. +% +% - verbose (integer, default 0): if a non-zero number n then every n +% files prints a progress log. To avoid logging set verbose to 0. +% +% Example 1: Load sample event +% fileNames = {'file1.pgdf', 'file2.pgdf'}; +% uids = [500001, 500002]; +% pgmatlab.loadPamguardMultiFile('./path/to/dir', fileNames, uids); +% +% Example 2: Load sample event with logging verbosity +% fileNames = {'file1.pgdf', 'file2.pgdf'}; +% uids = [500001, 500002]; +% pgmatlab.loadPamguardMultiFile('./path/to/dir', fileNames, uids, 1); +% + +dir = pgmatlab.utils.charArray(dir); +fileNames = pgmatlab.utils.charArray(fileNames); +if iscell(UIDs) + UIDs = cell2mat(UIDs); +end + +eventData = []; +nEvents = 0; +if nargin < 4 + verbose = 0; +end + +if numel(fileNames) ~= numel(UIDs) + error('fileNames and UIDs must have the same number of elements.'); +end + +% find the files we need using the findBinaryFile function. +% unique file list +unFiles = unique(fileNames); +for i = 1:numel(unFiles) + if (verbose) + fileName = unFiles{i}; + if length(dir) < length(fileName) + fileName = fileName(length(dir):end); + end + fprintf('Loading file %s %d of %d\n', fileName, i, numel(unFiles)); + end + + filePath = pgmatlab.utils.findBinaryFile(dir,'*.pgdf',unFiles{i}); + % Ensure the file exists + if ~exist(filePath, 'file') + fprintf(' - Unable to find file %s\n', unFiles{i}); + continue; + end + + % list of clicks in a particular file + mask = strcmp(fileNames, unFiles{i}); + fileUIDs = UIDs(mask); + + fileData = pgmatlab.loadPamguardBinaryFile(filePath, 'uidlist', fileUIDs); + + % Do some validation checks. Warn user if no (or not enough) data is found. + if isempty(fileData) + fprintf(' - No data found for file "%s" matching UIDs [%s]\n', unFiles{i}, sprintf('%d, ', fileUIDs)); + continue; + end + if length(fileData) ~= length(fileUIDs) + fprintf(' - Only %d/%d data points found for file "%s" matching UIDs [%s]\n', length(fileData), length(fileUIDs), unFiles{i}, sprintf('%d, ', fileUIDs)); + end + + % Add the file information to all data loaded. + [~,fName,fEnd] = fileparts(filePath); + fileName = [fName fEnd]; + for d = 1:numel(fileData) + fileData(d).binaryFile = fileName; + end + + % Preallocate eventData (performance) + if isempty(eventData) + eventData = fileData; + else + eventData = pgmatlab.utils.checkArrayAllocation(eventData, numel(eventData) + numel(fileData), fileData(1)); + eventData(end-numel(fileData)+1:end) = fileData; + end + nEvents = nEvents + numel(fileData); +end +% Cut short preallocated eventData to the correct size +eventData = eventData(1:nEvents); +end \ No newline at end of file diff --git a/pgmatlab/.MATLABDriveTag b/pgmatlab/.MATLABDriveTag deleted file mode 100644 index df9fcd4..0000000 --- a/pgmatlab/.MATLABDriveTag +++ /dev/null @@ -1 +0,0 @@ -ee53bc03-ef5e-44bc-aea4-8fae1e2a0b9f \ No newline at end of file diff --git a/pgmatlab/Array/.MATLABDriveTag b/pgmatlab/Array/.MATLABDriveTag deleted file mode 100644 index 656b51a..0000000 --- a/pgmatlab/Array/.MATLABDriveTag +++ /dev/null @@ -1 +0,0 @@ -c4dd0a9d-e15d-496f-91ff-d9ff561a4fa0 \ No newline at end of file diff --git a/pgmatlab/loadPamguardBinaryFile.m b/pgmatlab/loadPamguardBinaryFile.m index c8029de..85f408c 100644 --- a/pgmatlab/loadPamguardBinaryFile.m +++ b/pgmatlab/loadPamguardBinaryFile.m @@ -1,380 +1,17 @@ -function [dataSet, fileInfo] = loadPamguardBinaryFile(fileName, varargin) -% Program to load a Pamguard binary file -% [dataSet, fileInfo] = loadPamguardBinaryFile(fileName, varargin) -% flleName is the full path to a PAMGuard pgdf file. -% varargin can be a number of paired parameters. -% 'timerange' must be followed by a two element data rage -% 'uidrange' must be followed by a two element UID range +function [data, fileInfo, selState] = loadPamguardBinaryFile(filename, varargin) +%LOADPAMGUARDBINARYFILE - Load a PAMGuard Binary File into memory. % -% clicks = -% loadPamguardBinaryFile('C:/MyData/Click_Detector_Click_Detector_Clicks_20171021_002421.pgdf') -% will load all data from the data file -% Click_Detector_Click_Detector_Clicks_20171021_002421.pgdf into a Matlab -% structure. +% This is a depracated function for pgmatlab v1. To access the latest +% code, use the function pgmatlab.loadPamguardBinaryFile. % -% startdate = datenum(2017,10,21,0,25,0) -% enddate = datenum(2017,10,21,0,26,0) -% clicks = -% loadPamguardBinaryFile('C:/MyData/Click_Detector_Click_Detector_Clicks_20171021_002421.pgdf', 'timerange', [startdate enddate]) -% will load clicks between 00:25 and 00:26 on 21 October 2017. -% -% clicks = -% loadPamguardBinaryFile('C:/MyData/Click_Detector_Click_Detector_Clicks_20171021_002421.pgdf', -% 'uidrange', [1000345 1000345]) will load a single click with UID 1000345 -% into memory. -% -% clicks = -% loadPamguardBinaryFile('C:/MyData/Click_Detector_Click_Detector_Clicks_20171021_002421.pgdf', -% 'uidlist', [1000345 1000347 ...]) will load a list of specific UID's into -% memory. -% -% [dataSet, fileInfo] = loadPamguardBinaryFile( ... ) -% will return an optional fileInfo structure containing header and footer -% information from the file which includes information such as the data -% start and end times. -dataSet = []; -fileInfo = []; -nBackground = 0; -timeRange = [-Inf +Inf]; -uidRange = [-Inf +Inf]; -uidList = []; -iArg = 0; -sorted = 0; -filterfun = @passalldata; -channelmap=-1; -while iArg < numel(varargin) - iArg = iArg + 1; - switch(varargin{iArg}) - case 'timerange' - iArg = iArg + 1; -% timeRange = dateNumToMillis(varargin{iArg}); - timeRange = varargin{iArg}; - case 'uidrange' - iArg = iArg + 1; - uidRange = varargin{iArg}; - case 'uidlist' - iArg = iArg + 1; - uidList = sort(varargin{iArg}); - case 'filter' - iArg = iArg + 1; - filterfun = varargin{iArg}; - case 'channel' - iArg = iArg + 1; - channelmap = varargin{iArg}; - case 'sorted' - iArg = iArg + 1; - sorted = varargin{iArg}; - end -end -selState = 0; -% open binary file and read data -nData = 0; -try - fid = fopen(fileName, 'r', 'ieee-be.l64'); - - % initialize variables - prevPos = -1; - dataSet=[]; - clear fileInfo; - fileInfo.readModuleHeader=@readStdModuleHeader; - fileInfo.readModuleFooter=@readStdModuleFooter; - - % main loop - while (1) - - % if for some reason we're stuck at one byte, warn the user and - % abort - pos = ftell(fid); - if (pos == prevPos) - disp(fprintf('File stuck at byte %d', pos)); - break; - end - prevPos = pos; - - % read in the length of the object and the type. Move the file - % pointer back to the beginning of the length variable, and switch - % on the type. If we couldn't read nextLen or nextType, assume - % that means we've hit the end of the file and break out of loop - [nextLen, nL] = fread(fid, 1, 'int32'); - [nextType, nT] = fread(fid, 1, 'int32'); -% if (nextType < 0) -% nextType -% end - if (nL == 0 || nT == 0) - break; - end - fseek(fid, -8, 'cof'); - switch nextType - - % Case 1: File Header. Read in the file header, and then set - % the function handles depending on what type of data the - % binary file holds. The module type is typically specified in - % the package class that extends PamControlledUnit, and is a - % string unique to that module. - case -1 - fileInfo.fileHeader = readFileHeader(fid); - % disp(fileInfo.fileHeader.moduleType); - switch fileInfo.fileHeader.moduleType - - % AIS Processing Module - case 'AIS Processing' - fileInfo.objectType=0; - fileInfo.readModuleData=@readAISData; - - % Click Detector or Soundtrap Click Detector Module - case {'Click Detector', 'SoundTrap Click Detector'} - switch fileInfo.fileHeader.streamName - case 'Clicks' - fileInfo.objectType=1000; - fileInfo.readModuleData=@readClickData; - fileInfo.readModuleFooter=@readClickFooter; - fileInfo.readBackgroundData = @readClickBackground; - case 'Trigger Background' - fileInfo.objectType=0; - fileInfo.readModuleData=@readClickTriggerData; - fileInfo.readModuleHeader=@readClickTriggerHeader; - end - % Clip Generator Module - case 'Clip Generator' - fileInfo.objectType=[1 2]; - fileInfo.readModuleData=@readClipData; - - %Deep learning module - case 'Deep Learning Classifier' - disp(['Deep learning stream: ' fileInfo.fileHeader.streamName]) - switch fileInfo.fileHeader.streamName - case {'DL_detection', 'DL detection'} - fileInfo.objectType=1; - fileInfo.readModuleData=@readDLDetData; - case {'DL_Model_Data', 'DL Model Data'} - fileInfo.objectType=0; - fileInfo.readModuleData=@readDLModelData; - end - - - % DbHt Module - % NOT TESTED YET - case 'DbHt' - fileInfo.objectType=1; - fileInfo.readModuleData=@readDbHtData; - - % Difar Module - case 'DIFAR Processing' - fileInfo.objectType=0; - fileInfo.readModuleData=@readDifarData; - - % LTSA Module - case 'LTSA' - fileInfo.objectType=1; - fileInfo.readModuleHeader=@readLTSAHeader; - fileInfo.readModuleData=@readLTSAData; - - % Noise Monitor Module and Noise Band Monitor Module - % Note: The two modules have different types, but both - % use noiseMonitor.NoiseBinaryDataSource class to save - % data - case {'Noise Monitor', 'Noise Band'} - fileInfo.objectType=1; - fileInfo.readModuleHeader=@readNoiseMonHeader; - fileInfo.readModuleData=@readNoiseMonData; - - % Filtered Noise Measurement Module (Noise One Band) - case 'NoiseBand' - fileInfo.objectType=1; - fileInfo.readModuleData=@readNoiseBandData; - case 'GPL Detector' - switch fileInfo.fileHeader.streamName - case 'GPL Detections' - fileInfo.readModuleData = @readGPLDetections; - fileInfo.readBackgroundData = @readSpectralBackground; - end - % Right Whale Edge Detector Module - case 'RW Edge Detector' - fileInfo.objectType=0; - fileInfo.readModuleData=@readRWEDetectorData; - disp('Right Whale Edge Detector binary file detected'); - disp('Note that the low, high and peak frequencies are actually'); - disp('saved as FFT slices. In order to convert values to Hz, they'); - disp('must be multiplied by (sampleRate/fftLength)'); - - % Whistle And Moans Module - case 'WhistlesMoans' - fileInfo.objectType=2000; - fileInfo.readModuleHeader=@readWMDHeader; - fileInfo.readModuleData=@readWMDData; - fileInfo.readBackgroundData = @readSpectralBackground; - - case {'Energy Sum Detector','Spectrogram Correlation Detector','Matched Filter Detector'} - switch fileInfo.fileHeader.streamName - % Ishmael detector data - case 'Ishmael Peak Data' - fileInfo.readModuleData=@readIshmaelData; - - % Ismael detections - case 'Ishmael Detections' - fileInfo.readModuleData=@readIshmaelDetection; - end - - % Ipi module - case 'Ipi module' - fileInfo.objectType=0; - fileInfo.readModuleData=@readIpiData; - - case 'Gemini Threshold Detector' - fileInfo.objectType = 0; - fileInfo.readModuleData=@readTritechTrack; - fileInfo.readBackgroundData = @readTritechBackground; - - % Note: PamRawDataBlock has it's own Binary Store (RawDataBinarySource), - % but it is created by multiple different processes so doesn't have one - % particular type, and may have a type shared with a different binary - % store (e.g. the DbHt module creates both a DbHtDataSource and a - % RawDataBinarySource, and they will both have type 'DbHt'). - % The comments in the class indicate that the binary store should never - % be used for raw data and that the sole purpose of the class is to - % enable sending raw data over the network. If this is ever changed - % and raw data is allowed to be stored in the binary files, we will - % have to come up with a way of determining where the raw data came - % from besides querying the type. - - otherwise - disp(['Don''t recognize type ' fileInfo.fileHeader.moduleType '. Aborting load']); - break; - end - - % Case 2: File Footer. The file version should have been set - % when we read the file header. If the file header is empty, - % something has gone wrong so warn the user and exit - case -2 - if (isempty(fileInfo.fileHeader)) - disp('Error: found file footer before file header. Aborting load'); - break; - end - fileInfo.fileFooter = readFileFooterInfo(fid, fileInfo.fileHeader.fileFormat); - - % Case 3: Module Header. The correct function handle should - % have been set when we read the file header. If the file - % header is empty, something has gone wrong so warn the user - % and exit - case -3 - if (isempty(fileInfo.fileHeader)) - disp('Error: found module header before file header. Aborting load'); - break; - end - fileInfo.moduleHeader = fileInfo.readModuleHeader(fid); - - % Case 4: Module Footer. The correct function handle should - % have been set when we read the file header. If the file - % header is empty, something has gone wrong so warn the user - % and exit - case -4 - if (isempty(fileInfo.fileHeader)) - disp('Error: found module footer before file header. Aborting load'); - break; - end - fileInfo.moduleFooter = fileInfo.readModuleFooter(fid); - - % Case 5: Data. The correct function handle should have been - % set when we read in the file header. If the file header is - % empty, something has gone wrong so warn the user and exit - case -5 - % datagram data Skip it for now. - fseek(fid, nextLen, 'cof'); - otherwise - - if (isempty(fileInfo.fileHeader)) - disp('Error: found data before file header. Aborting load'); - end - - [dataPoint, selState] = readPamData(fid, fileInfo, timeRange, uidRange, uidList); - - % see if it's in the specified list of wanted UID's - if ~isempty(uidList) - - try - dataUID = dataPoint.UID; - % if dataUID > uidList(end) - % break; - % end - - selState = sum(dataUID == uidList); - catch - - end - end - if channelmap>0 && channelmap~=dataPoint.channelMap - selState = 0; - end - - if selState == 1 - selState = filterfun(dataPoint); - end - if (selState == 0 || (selState == 2 && ~sorted)) - fseek(fid, prevPos+nextLen, 'bof'); - continue; - elseif (selState == 2 && sorted) - break; - end - - newP = ftell(fid); - pErr = newP - (prevPos+nextLen); - if pErr ~= 0 - fprintf('Error in file position: %d bytes\n', pErr); - fseek(fid, -pErr, 'cof'); - end - - if nextType == -6 - nBackground = nBackground + 1; - backgroundData(nBackground) = dataPoint; - continue; - end - - - % Preallocation. Acheived by adding new data points beyond - % the end of the existing array, then shortening the array - % before it is returned to the user. - nData = nData + 1; - dataSet = checkArrayAllocation(dataSet, nData, dataPoint); - dataSet(nData) = dataPoint; - -% dataSet = [dataSet dataPoint]; - end - end - % due to preallocation it's likely the array is now far too large so - % shrink it back to the correct size. - dataSet = dataSet(1:nData); -catch mError - disp('Error reading file'); - disp(getReport(mError)); -end -if nBackground > 0 - fileInfo.background = backgroundData; -end -% close the file and return to the calling function -try -fclose(fid); -catch -end -return; -end +% Syntax: +% [data, fileInfo, selState] = LOADPAMGUARDBINARYFILE(filename, varargin) +% [data, fileInfo] = LOADPAMGUARDBINARYFILE(filename, varargin) +% data = LOADPAMGUARDBINARYFILE(filename, varargin) +% +% See also PGMATLAB.LOADPAMGUARDBINARYFILE, LOADPAMGUARDBINARYFOLDER, LOADPAMGUARDMULTIFILE. +warning("loadPamguardBinaryFile is deprecated. Use pgmatlab.loadPamguardBinaryFile instead."); +[data, fileInfo, selState] = pgmatlab.loadPamguardBinaryFile(filename, varargin{:}); -% Check the array allocation. This gets called every time data are read and -% will extend the array by approximately the sqrt of the arrays own length -% if required. Preallocation acheived by sticking a sample object at a high -% data index so that array up to that point gets filled with nulls. -function array = checkArrayAllocation(array, reqLength, sampleObject) -if isempty(array) - currentLength = 0; - clear array; -else - currentLength = numel(array); -end -if (currentLength >= reqLength) - return; -end -allocStep = round(sqrt(reqLength)); -allocStep = max(10, min(allocStep, 10000)); -array(reqLength + allocStep) = sampleObject; -return; -end +end \ No newline at end of file diff --git a/pgmatlab/loadPamguardBinaryFolder.m b/pgmatlab/loadPamguardBinaryFolder.m index 9dc66e8..e6c1e5c 100644 --- a/pgmatlab/loadPamguardBinaryFolder.m +++ b/pgmatlab/loadPamguardBinaryFolder.m @@ -1,49 +1,31 @@ -function [data background fileInfos] = loadPamguardBinaryFolder(dir, fileMask, verbose, filterfun) -% load all data from a folder and it's sub folders -% data = loadPamguardBinaryFolder(dir, fileMask, verbose) loads all data from -% the folder dir where files satisfy the fileMask. All files must -% contain data of the same format so mask must specify a particular type -% of data file, e.g. clicks*.pgdf. If verbose is a non-zero number 'n' then -% every n files a progress message will be printed on the temrinal. +function [allData, allBackground, fileInfos] = loadPamguardBinaryFolder(dir, fileMask, verbose, filterfun) +%LOADPAMGUARDBINARYFOLDER - Load many PAMGuard Binary Files into memory from a folder (and subfolders). % -% e.g. allclicks = loadPAMFolder('C:/Mydata', 'Click_Detector_*.pgdf', 5); +% This is a depracated function for pgmatlab v1. To access the latest +% code, use the function pgmatlab.loadPamguardBinaryFolder. Read full +% documentation, as the function signature has changed. % -if (nargin < 3) +% Syntax: +% [allData, allBackground, fileInfos] = LOADPAMGUARDBINARYFOLDER(dir, fileMask, verbose, filterfun) +% [allData, allBackground] = LOADPAMGUARDBINARYFOLDER(dir, fileMask, verbose, filterfun) +% allData = LOADPAMGUARDBINARYFOLDER(dir, fileMask, verbose, filterfun) +% +% See also PGMATLAB.LOADPAMGUARDBINARYFOLDER, PGMATLAB.LOADPAMGUARDBINARYFILE, PGMATLAB.LOADPAMGUARDMULTIFILE. + +% Handle optional arguments +if nargin < 3 verbose = 0; end + if nargin < 4 - filterfun = @passalldata; + filterfun = 0; end -data = []; -background = []; -d = dirsub(dir, fileMask); -for i = 1:numel(d) - if verbose - if mod(i, verbose) == 0 - fprintf('Loading %d/%d (%d) %s\n', i, numel(d), numel(data), d(i).name); - end - end - [fRoot, fName, fEnd] = fileparts(d(i).name); - fileNameOnly = [fName fEnd]; - [dat fInf] = loadPamguardBinaryFile(d(i).name, 'filter', filterfun); - if ~isempty(dat) - % need to add bookkeeping data to dat so that we know which file - % each click comes from and also know which click it is within the - % file. - for iDat = 1:numel(dat) - dat(iDat).clickNumber = iDat; - dat(iDat).fileName = fileNameOnly; - end - data = [data dat]; - end - if isfield(fInf, 'background') - background = [background fInf.background]; - end - if nargout >= 3 - if i == 1 - fileInfos(numel(d)) = fInf; % allocate entire array - end - fileInfos(i) = fInf; - end + +warning("loadPamguardBinaryFolder is deprecated. Use pgmatlab.loadPamguardBinaryFolder instead. Read full documentation, as the function signature has changed."); + +if isa(filterfun, "function_handle") + [allData, allBackground, fileInfos] = pgmatlab.loadPamguardBinaryFolder(dir, fileMask, verbose, 'filter', filterfun); +else + [allData, allBackground, fileInfos] = pgmatlab.loadPamguardBinaryFolder(dir, fileMask, verbose); end - \ No newline at end of file +end \ No newline at end of file diff --git a/pgmatlab/loadPamguardMultiFile.m b/pgmatlab/loadPamguardMultiFile.m index 1d92a03..0ec65bf 100644 --- a/pgmatlab/loadPamguardMultiFile.m +++ b/pgmatlab/loadPamguardMultiFile.m @@ -1,53 +1,21 @@ -function eventData = loadPamguardMultiFile(dataDir, fileNames, itemUID, verbose) -% function to load all data from an event even if spread over multiple -% files. This can be used to get binary file data for data associated with -% PAMGuard 'events' marked out using the click detector or the 'Detection -% Grouper'. From the database query, for each event make a list of the -% fileNames and the UID's of individual datas, then this function will call -% loadPamguardBinaryFile(...) for each of one or more files associated with -% the event and merge all the data into one array of structure. +function eventData = loadPamguardMultiFile(dir, fileNames, UIDs, verbose) +%LOADPAMGUARDMULTIFILE - Load multiple PAMGuard Binary Files into memory filtering by certain UIDs in certain files. % -% inputs are root data folder, cell array of binary file names and click -% numbers +% This is a depracated function for pgmatlab v1. To access the latest +% code, use the function pgmatlab.loadPamguardMultiFile. % -% eventData = loadPamguardMultiFile(dataDir, fileNames, itemUID) -% 'dataDir': root folder for binary data -% 'fileNames': list of file names for each item of interest (generally read from database) -% 'itemUID': list of UID's of wanted data. Shoule be same length as array of file names -% -% returns binary data from multiple files. +% Syntax: +% eventData = LOADPAMGUARDMULTIFILE(dir, fileNames, UIDs, verbose) +% +% See also PGMATLAB.LOADPAMGUARDMULTIFILE, PGMATLAB.LOADPAMGUARDBINARYFILE, PGMATLAB.LOADPAMGUARDBINARYFOLDER. + +warning("loadPamguardMultiFile is deprecated. Use pgmatlab.loadPamguardMultiFile instead."); -eventData = []; +% Handle optional arguments if nargin < 4 verbose = 0; end -% find the files we need using the findBinaryFile function. -% unique file list -unFiles = unique(fileNames); -for i = 1:numel(unFiles) % loop over the different files - - if (verbose) - fileName = unFiles{i}; - if length(dataDir) < length(fileName) - fileName = fileName(length(dataDir):end); - end - fprintf('Loading file %s %d of %d\n', fileName, i, numel(unFiles)); - end - - filePath = findBinaryFile(dataDir,'*.pgdf',unFiles{i}); - - % list of clicks in a particular file - fileUIDs = itemUID(find(strcmp(fileNames, unFiles{i}))); - - fileData = loadPamguardBinaryFile(filePath, 'uidlist', fileUIDs); - % add the file information to all data loaded. - [~,fName,fEnd] = fileparts(filePath); - fileName = [fName fEnd]; - for d = 1:numel(fileData) - fileData(d).binaryFile = fileName; - end - - eventData = [eventData fileData]; -end +eventData = pgmatlab.loadPamguardMultiFile(dir, fileNames, UIDs, verbose); +end \ No newline at end of file diff --git a/resources/pgmatlab-logo.png b/resources/pgmatlab-logo.png new file mode 100644 index 0000000..22fb8e1 Binary files /dev/null and b/resources/pgmatlab-logo.png differ diff --git a/resources/project/-i5CiiJthkzqFJL8FHGU2qUdrQ4/N24do7FmnXUTmI4jiYSdZFNDTo0d.xml b/resources/project/-i5CiiJthkzqFJL8FHGU2qUdrQ4/N24do7FmnXUTmI4jiYSdZFNDTo0d.xml new file mode 100644 index 0000000..4356a6a --- /dev/null +++ b/resources/project/-i5CiiJthkzqFJL8FHGU2qUdrQ4/N24do7FmnXUTmI4jiYSdZFNDTo0d.xml @@ -0,0 +1,2 @@ + + \ No newline at end of file diff --git a/resources/project/-i5CiiJthkzqFJL8FHGU2qUdrQ4/N24do7FmnXUTmI4jiYSdZFNDTo0p.xml b/resources/project/-i5CiiJthkzqFJL8FHGU2qUdrQ4/N24do7FmnXUTmI4jiYSdZFNDTo0p.xml new file mode 100644 index 0000000..01cb34e --- /dev/null +++ b/resources/project/-i5CiiJthkzqFJL8FHGU2qUdrQ4/N24do7FmnXUTmI4jiYSdZFNDTo0p.xml @@ -0,0 +1,2 @@ + + \ No newline at end of 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diff --git a/resources/project/00EIX37DyA_CbKJH9yEDrF6Y8ns/2a1Q608c32XZfL4zh3sL7_cWVXUd.xml b/resources/project/00EIX37DyA_CbKJH9yEDrF6Y8ns/2a1Q608c32XZfL4zh3sL7_cWVXUd.xml new file mode 100644 index 0000000..4356a6a --- /dev/null +++ b/resources/project/00EIX37DyA_CbKJH9yEDrF6Y8ns/2a1Q608c32XZfL4zh3sL7_cWVXUd.xml @@ -0,0 +1,2 @@ + + \ No newline at end of file diff --git a/resources/project/00EIX37DyA_CbKJH9yEDrF6Y8ns/2a1Q608c32XZfL4zh3sL7_cWVXUp.xml b/resources/project/00EIX37DyA_CbKJH9yEDrF6Y8ns/2a1Q608c32XZfL4zh3sL7_cWVXUp.xml new file mode 100644 index 0000000..274de9f --- /dev/null +++ b/resources/project/00EIX37DyA_CbKJH9yEDrF6Y8ns/2a1Q608c32XZfL4zh3sL7_cWVXUp.xml @@ -0,0 +1,2 @@ + + \ No newline at end of file diff --git a/resources/project/00EIX37DyA_CbKJH9yEDrF6Y8ns/AT9o4BPb49qYUPSNvx0SM9aoGLAd.xml b/resources/project/00EIX37DyA_CbKJH9yEDrF6Y8ns/AT9o4BPb49qYUPSNvx0SM9aoGLAd.xml new file mode 100644 index 0000000..4356a6a --- /dev/null +++ b/resources/project/00EIX37DyA_CbKJH9yEDrF6Y8ns/AT9o4BPb49qYUPSNvx0SM9aoGLAd.xml @@ -0,0 +1,2 @@ + + \ No newline at end of file diff --git a/resources/project/00EIX37DyA_CbKJH9yEDrF6Y8ns/AT9o4BPb49qYUPSNvx0SM9aoGLAp.xml b/resources/project/00EIX37DyA_CbKJH9yEDrF6Y8ns/AT9o4BPb49qYUPSNvx0SM9aoGLAp.xml new file mode 100644 index 0000000..5c24086 --- /dev/null +++ b/resources/project/00EIX37DyA_CbKJH9yEDrF6Y8ns/AT9o4BPb49qYUPSNvx0SM9aoGLAp.xml @@ -0,0 +1,2 @@ + + \ No newline at end of file diff --git a/resources/project/00EIX37DyA_CbKJH9yEDrF6Y8ns/d8u7Zre2q3HiK5fcd3h_7wsKJkAd.xml b/resources/project/00EIX37DyA_CbKJH9yEDrF6Y8ns/d8u7Zre2q3HiK5fcd3h_7wsKJkAd.xml new file mode 100644 index 0000000..4356a6a --- /dev/null +++ b/resources/project/00EIX37DyA_CbKJH9yEDrF6Y8ns/d8u7Zre2q3HiK5fcd3h_7wsKJkAd.xml @@ -0,0 +1,2 @@ + + \ No newline at end of file diff --git a/resources/project/00EIX37DyA_CbKJH9yEDrF6Y8ns/d8u7Zre2q3HiK5fcd3h_7wsKJkAp.xml 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diff --git a/resources/project/00EIX37DyA_CbKJH9yEDrF6Y8ns/ke48wZA2YxIzn3v5vrnf99LqbEYd.xml b/resources/project/00EIX37DyA_CbKJH9yEDrF6Y8ns/ke48wZA2YxIzn3v5vrnf99LqbEYd.xml new file mode 100644 index 0000000..4356a6a --- /dev/null +++ b/resources/project/00EIX37DyA_CbKJH9yEDrF6Y8ns/ke48wZA2YxIzn3v5vrnf99LqbEYd.xml @@ -0,0 +1,2 @@ + + \ No newline at end of file diff --git a/resources/project/00EIX37DyA_CbKJH9yEDrF6Y8ns/ke48wZA2YxIzn3v5vrnf99LqbEYp.xml b/resources/project/00EIX37DyA_CbKJH9yEDrF6Y8ns/ke48wZA2YxIzn3v5vrnf99LqbEYp.xml new file mode 100644 index 0000000..f12fe52 --- /dev/null +++ b/resources/project/00EIX37DyA_CbKJH9yEDrF6Y8ns/ke48wZA2YxIzn3v5vrnf99LqbEYp.xml @@ -0,0 +1,2 @@ + + \ No newline at end of file diff --git a/resources/project/00EIX37DyA_CbKJH9yEDrF6Y8ns/lrPbbhm4s70prEhLj2U5_gpkizUd.xml b/resources/project/00EIX37DyA_CbKJH9yEDrF6Y8ns/lrPbbhm4s70prEhLj2U5_gpkizUd.xml new file mode 100644 index 0000000..4356a6a --- /dev/null +++ b/resources/project/00EIX37DyA_CbKJH9yEDrF6Y8ns/lrPbbhm4s70prEhLj2U5_gpkizUd.xml @@ -0,0 +1,2 @@ + + \ No newline at end of file diff --git a/resources/project/00EIX37DyA_CbKJH9yEDrF6Y8ns/lrPbbhm4s70prEhLj2U5_gpkizUp.xml b/resources/project/00EIX37DyA_CbKJH9yEDrF6Y8ns/lrPbbhm4s70prEhLj2U5_gpkizUp.xml new file mode 100644 index 0000000..cbee8e2 --- /dev/null +++ b/resources/project/00EIX37DyA_CbKJH9yEDrF6Y8ns/lrPbbhm4s70prEhLj2U5_gpkizUp.xml @@ -0,0 +1,2 @@ + + \ No newline at end of file diff --git a/resources/project/00EIX37DyA_CbKJH9yEDrF6Y8ns/oFB9IUOq4iQgOhupbKN0Lu6r_t8d.xml b/resources/project/00EIX37DyA_CbKJH9yEDrF6Y8ns/oFB9IUOq4iQgOhupbKN0Lu6r_t8d.xml new file mode 100644 index 0000000..4356a6a --- /dev/null +++ b/resources/project/00EIX37DyA_CbKJH9yEDrF6Y8ns/oFB9IUOq4iQgOhupbKN0Lu6r_t8d.xml @@ -0,0 +1,2 @@ + + \ No newline at end of file diff --git a/resources/project/00EIX37DyA_CbKJH9yEDrF6Y8ns/oFB9IUOq4iQgOhupbKN0Lu6r_t8p.xml 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diff --git a/resources/project/00EIX37DyA_CbKJH9yEDrF6Y8ns/v9VUCXOs3f_1u6SHw1-ICFBpaZ4d.xml b/resources/project/00EIX37DyA_CbKJH9yEDrF6Y8ns/v9VUCXOs3f_1u6SHw1-ICFBpaZ4d.xml new file mode 100644 index 0000000..4356a6a --- /dev/null +++ b/resources/project/00EIX37DyA_CbKJH9yEDrF6Y8ns/v9VUCXOs3f_1u6SHw1-ICFBpaZ4d.xml @@ -0,0 +1,2 @@ + + \ No newline at end of file diff --git a/resources/project/00EIX37DyA_CbKJH9yEDrF6Y8ns/v9VUCXOs3f_1u6SHw1-ICFBpaZ4p.xml b/resources/project/00EIX37DyA_CbKJH9yEDrF6Y8ns/v9VUCXOs3f_1u6SHw1-ICFBpaZ4p.xml new file mode 100644 index 0000000..65a114a --- /dev/null +++ b/resources/project/00EIX37DyA_CbKJH9yEDrF6Y8ns/v9VUCXOs3f_1u6SHw1-ICFBpaZ4p.xml @@ -0,0 +1,2 @@ + + \ No newline at end of file diff --git a/resources/project/00EIX37DyA_CbKJH9yEDrF6Y8ns/vmjbHl25tTgLvKhScF_qF-MAUv4d.xml b/resources/project/00EIX37DyA_CbKJH9yEDrF6Y8ns/vmjbHl25tTgLvKhScF_qF-MAUv4d.xml new file mode 100644 index 0000000..4356a6a --- /dev/null +++ b/resources/project/00EIX37DyA_CbKJH9yEDrF6Y8ns/vmjbHl25tTgLvKhScF_qF-MAUv4d.xml @@ -0,0 +1,2 @@ + + \ No newline at end of file diff --git a/resources/project/00EIX37DyA_CbKJH9yEDrF6Y8ns/vmjbHl25tTgLvKhScF_qF-MAUv4p.xml b/resources/project/00EIX37DyA_CbKJH9yEDrF6Y8ns/vmjbHl25tTgLvKhScF_qF-MAUv4p.xml new file mode 100644 index 0000000..29c16a8 --- /dev/null +++ b/resources/project/00EIX37DyA_CbKJH9yEDrF6Y8ns/vmjbHl25tTgLvKhScF_qF-MAUv4p.xml @@ -0,0 +1,2 @@ + + \ No newline at end of file diff --git a/resources/project/0IJR_-GHKzclpP23ENDUUIttpv8/0oQx25bskqGkeABJz4-2BAP8UX4d.xml b/resources/project/0IJR_-GHKzclpP23ENDUUIttpv8/0oQx25bskqGkeABJz4-2BAP8UX4d.xml new file mode 100644 index 0000000..4356a6a --- /dev/null +++ b/resources/project/0IJR_-GHKzclpP23ENDUUIttpv8/0oQx25bskqGkeABJz4-2BAP8UX4d.xml @@ -0,0 +1,2 @@ + + \ No newline at end of file diff --git a/resources/project/0IJR_-GHKzclpP23ENDUUIttpv8/0oQx25bskqGkeABJz4-2BAP8UX4p.xml 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a/testing-resources/v1.0.1code/Array/threadinglocaliser.m b/testing-resources/v1.0.1code/Array/threadinglocaliser.m new file mode 100644 index 0000000..d58bab5 --- /dev/null +++ b/testing-resources/v1.0.1code/Array/threadinglocaliser.m @@ -0,0 +1,121 @@ +function [arrayPos, shipPos, shipIndex, arrayIndex] = threadinglocaliser(gpsData, arrayLength, time) +% function arrayPos = threadinglocaliser(gpsData, arrayLength, time) +% +% calculate the likely array position based on a set of vessel gps datas +% read in from the database, a distance astern of the gps receiver and a +% time. Return will be a structure containing the latitude, longitude and +% heading of the array at that moment in time. +if nargin == 0 + % convenience fude to make it call the test function without me + % having to keep flipping to a different editor tab + threadinglocalisertest() + return +end +global gpsDate +arrayPos = []; +shipPos = []; +arrayIndex = []; +shipIndex = []; +if numel(time) > 1 + % will have to call this function individually for every different time + % for it to work. + for i = 1:numel(time) + [aPos, sPos, sIndex, aIndex] = threadinglocaliser(gpsData, arrayLength, time(i)); + arrayPos = catstruct(arrayPos, aPos); + shipPos = catstruct(shipPos, sPos); + arrayIndex = [arrayIndex aIndex]; + shipIndex = [shipIndex, sIndex]; + end + return +end +% need to extract the times from the gpsData +gpsDate = dbdate2datenum(gpsData.UTC); +% now find the GPS position closest in time to our current position +[shipTime shipIndex] = min(abs(time-gpsDate)); +shipTime = gpsDate(shipIndex); +% fprintf('wanted %s, ship gps %s\n', datestr(time, 31), datestr(shipTime, 31)); +% really want the Gps before, so we really know where we are +if (shipTime > time) + shipIndex = shipIndex-1; + shipTime = gpsDate(shipIndex); +end +nextShipTime = gpsDate(shipIndex+1); % time of the gps point after the one we want. +shipPos = interpolateGpsTime(gpsData, shipIndex, shipIndex+1, time); +% now work backwards along the array for the appropriate distance. +distanceBack = arrayLength - latlongdistance(shipPos.Latitude, shipPos.Longitude, ... + gpsData.Latitude(shipIndex), gpsData.Longitude(shipIndex)); +arrayIndex = shipIndex; +d = 0; +while distanceBack > 0 + arrayIndex = arrayIndex - 1; + if (arrayIndex <= 0) + break + end + d = latlongdistance(gpsData.Latitude(arrayIndex+1), gpsData.Longitude(arrayIndex+1),... + gpsData.Latitude(arrayIndex), gpsData.Longitude(arrayIndex)); + if (d > distanceBack) + break; + end + distanceBack = distanceBack-d; +end + arrayIndex = arrayIndex + 0; +% should now have pIndex pointing at the gps data BEFORE where the +% hydrophone is so do a final interpolation based on distance. +% distance back should still be >= 0 +if (d == 0) + x1 = 1; + x2 = 0; +else + x2 = distanceBack/d; + x1 = 1-x2; +end +arrayPos = interpolateGps(gpsData, arrayIndex, arrayIndex+1, x1, x2); + +end + + +function g = interpolateGpsTime(gpsData, ind1, ind2, time) +global gpsDate +% interpolate between two gps points based on time. +% assume that ind1 and ind2 refer to points before and after the +% time we want. +dt1 = time-gpsDate(ind1); +dt2 = gpsDate(ind2)-time; +if (dt1+dt2 == 0) + x1 = 1; + x2 = 0; +else + x1 = dt2/(dt1+dt2); + x2 = dt1/(dt1+dt2); +end +g = interpolateGps(gpsData, ind1, ind1, x1, x2); +end +function g = interpolateGps(gpsData, ind1, ind2, x1, x2) +% interpolate between gps points based on x1 = fraction of first to use +% and x2 = fraction of second to use. x1+x2 = 1 ! +g.Latitude = gpsData.Latitude(ind1)*x1+gpsData.Latitude(ind2)*x2; +g.Longitude = gpsData.Longitude(ind1)*x1+gpsData.Longitude(ind2)*x2; +g.Speed = gpsData.Speed(ind1)*x1 + gpsData.Speed(ind2)*x2; +fNames = fields(gpsData); +if sum(strcmp(fNames,'Heading')) + g.Heading = interpolateAngle(gpsData.Heading(ind1), gpsData.Heading(ind2), x1, x2); +end +if sum(strcmp(fNames,'TrueHeading')) + g.TrueHeading = interpolateAngle(gpsData.TrueHeading(ind1), gpsData.TrueHeading(ind2), x1, x2); +end +if sum(strcmp(fNames,'MagneticHeading')) + g.MagneticHeading = interpolateAngle(gpsData.MagneticHeading(ind1), gpsData.MagneticHeading(ind2), x1, x2); +end + +end + +function h = interpolateAngle(head1, head2, x1, x2) +% interpolate between two angles, noting that they may be either side of +% zero, i.e. the mean angle of 359 and 1 is 0, not 180 ! +x = sind(head1)*x1+sind(head2)*x2; +y = cosd(head1)*x1+cosd(head2)*x2; +h = atan2d(x,y); +if h < 0 + h = h + 360; +end +end \ No newline at end of file diff --git a/testing-resources/v1.0.1code/Array/threadinglocalisertest.m b/testing-resources/v1.0.1code/Array/threadinglocalisertest.m new file mode 100644 index 0000000..a4d1fe3 --- /dev/null +++ b/testing-resources/v1.0.1code/Array/threadinglocalisertest.m @@ -0,0 +1,59 @@ +dbName = 'C:\OBSERVE_SURVEY\Survey#2\OBSERVE#2Offline.sqlite3'; +phoneLength = 100; % hydrophone length in metres. +date = datenum(2015,8,28,12,0,0); % the date we want a position for +% read in data for a few minutes either side ... +oneSecond = 1/(24*3600); +% test for several positions, seconds apart ... +date = date + [0:20]*oneSecond; + +% get gps data from 10 minutes before to one minute after our first and +% last times. +dateRange = [min(date)-oneSecond*600 max(date)+oneSecond*60]; +% read in some gps data +qStr = sprintf('SELECT * FROM gpsData WHERE UTC BETWEEN %s AND %s AND Id>0 ORDER BY UTC', ... + datenum2dbdate(dateRange(1),''''), datenum2dbdate(dateRange(2),'''')); +% qStr = 'SELECT * FROM gpsData WHERE Id>0 ORDER BY UTC' +setdbprefs('datareturnformat', 'structure'); +con = sqlitedatabase(dbName); +q =exec(con, qStr); +q = fetch(q); +gpsData = q.Data; +close(con); + + +[hPos, shipPos, shipInd, arrayInd] = threadinglocaliser(gpsData, phoneLength, date); + +figure(1) +clf +plot(gpsData.Longitude, gpsData.Latitude) +axis equal +hold on +plot(shipPos.Longitude, shipPos.Latitude, 'ob'); +plot(hPos.Longitude, hPos.Latitude, 'or'); +% set(gca, 'ylim', minmax(hPos.Latitude)) + +figure(2) +clf +% plot in metres +refLat = shipPos.Latitude(1); +refLong = shipPos.Longitude(1); +[~, x, y] = latlongdistance(refLat, refLong, gpsData.Latitude, gpsData.Longitude); +plot(x, y, '-k') +hold on +plot(x, y, '.') +axis equal; +[~, x, y] = latlongdistance(refLat, refLong, shipPos.Latitude, shipPos.Longitude); +plot(x, y, 'ob') +[~, x, y] = latlongdistance(refLat, refLong, hPos.Latitude, hPos.Longitude); +plot(x, y, 'or') +% now draw on all the headings of all the hydrophone points to see if +% they are realistic or not +head = hPos.Heading; +hLen = 2; +for i = 1:numel(head) + dx = sind(head(i))*hLen; + dy = cosd(head(i))*hLen; + line(x(i)+[0 dx], y(i)+[0 dy], 'color', 'r'); +end + +% set(gca, 'ylim', minmax(y) + [-2 2]) \ No newline at end of file diff --git a/pgmatlab/addColumn.m b/testing-resources/v1.0.1code/addColumn.m similarity index 100% rename from pgmatlab/addColumn.m rename to testing-resources/v1.0.1code/addColumn.m diff --git a/pgmatlab/checkColumn.m b/testing-resources/v1.0.1code/checkColumn.m similarity index 100% rename from pgmatlab/checkColumn.m rename to testing-resources/v1.0.1code/checkColumn.m diff --git a/pgmatlab/checkTable.m b/testing-resources/v1.0.1code/checkTable.m similarity index 100% rename from pgmatlab/checkTable.m rename to testing-resources/v1.0.1code/checkTable.m diff --git a/pgmatlab/checksqlitefuncs.m b/testing-resources/v1.0.1code/checksqlitefuncs.m similarity index 100% rename from pgmatlab/checksqlitefuncs.m rename to testing-resources/v1.0.1code/checksqlitefuncs.m diff --git a/testing-resources/v1.0.1code/clearcolumn.m b/testing-resources/v1.0.1code/clearcolumn.m new file mode 100644 index 0000000..b24125c --- /dev/null +++ b/testing-resources/v1.0.1code/clearcolumn.m @@ -0,0 +1,4 @@ +function clearcolumn(con, table, col) +% function clearcolumn(con, table, col) +wh = sprintf('where %s is not null', col); +update(con, table, {col}, {'null'}, wh); \ No newline at end of file diff --git a/testing-resources/v1.0.1code/columnExists.m b/testing-resources/v1.0.1code/columnExists.m new file mode 100644 index 0000000..01096ac --- /dev/null +++ b/testing-resources/v1.0.1code/columnExists.m @@ -0,0 +1,47 @@ +function e = columnExists(con, tableName, columnName) +% function e = columnExists(con, tableName, columnName) +% check to see if a column exists in a database table +% +% con: database connection +% tableName: database table name +% columnName: database column name +% +% returns 1 (true) if the column exists, 0 (false) otherwise. +e = 0; +%% This method worked and may still work for ODBC database connections. +try + dbmeta = dmd(con); +% t = tables(dbmeta,''); + colNames = columns(dbmeta, con.DefaultCatalog, '', tableName); + e = sum(strcmp(lower(columnName), lower(colNames))); + return +catch +end +%% This method works for connections established with the sqlitedatabase function +%% and for connections using the Matlab sqlite connection function +try + sq = sprintf('SELECT sql FROM sqlite_master where name=''%s''', tableName); + tableData = con.fetch(sq); + if size(tableData,1) == 0 + return; + end + search = ['"' columnName '"']; + has = strfind(tableData.sql, search); + if isempty(has) + e = 0; + return; + end + if iscell(has) + has = has{1}; + if isempty(has) + e = 0; + return; + end + end + dat = has(1); + e = ~isempty(dat); + return +catch er +end +er +error('Unable to perform column checks for this type of database'); \ No newline at end of file diff --git a/testing-resources/v1.0.1code/countChannels.m b/testing-resources/v1.0.1code/countChannels.m new file mode 100644 index 0000000..3337034 --- /dev/null +++ b/testing-resources/v1.0.1code/countChannels.m @@ -0,0 +1,19 @@ +function nC = countChannels(channelMap) +% function nC = countChannels(channelMap) +% count the numebr of set bits in the channel map + +%this function is called alot but many times folk will be anlalysing one +%channel data. This speeds up one channel a lot +if channelMap==1 + nC=1; + return; +end + +nC = 0; +j = 1; +for i = 1:32 + if (bitand(channelMap, j)) + nC = nC + 1; + end + j = j * 2; +end \ No newline at end of file diff --git a/pgmatlab/dateNumToMillis.m b/testing-resources/v1.0.1code/dateNumToMillis.m similarity index 100% rename from pgmatlab/dateNumToMillis.m rename to testing-resources/v1.0.1code/dateNumToMillis.m diff --git a/testing-resources/v1.0.1code/datenum2dbdate.m b/testing-resources/v1.0.1code/datenum2dbdate.m new file mode 100644 index 0000000..d365761 --- /dev/null +++ b/testing-resources/v1.0.1code/datenum2dbdate.m @@ -0,0 +1,13 @@ +function ds = datenum2dbdate(dn, delimChar, millis) +if nargin < 2 + delimChar = '#'; +end +if nargin < 3 + millis = false; +end +% converts a datenum to the #mm/dd/yyyy hh:mm:ss# format required by SQL. +if millis +ds = [delimChar datestr(dn, 'yyyy-mm-dd HH:MM:SS.FFF') delimChar]; +else +ds = [delimChar datestr(dn, 31) delimChar]; +end \ No newline at end of file diff --git a/pgmatlab/dbdate2datenum.m b/testing-resources/v1.0.1code/dbdate2datenum.m similarity index 100% rename from pgmatlab/dbdate2datenum.m rename to testing-resources/v1.0.1code/dbdate2datenum.m diff --git a/testing-resources/v1.0.1code/dirsub.m b/testing-resources/v1.0.1code/dirsub.m new file mode 100644 index 0000000..9360563 --- /dev/null +++ b/testing-resources/v1.0.1code/dirsub.m @@ -0,0 +1,43 @@ +function files = dirsub(rootFolder, mask) +% function files = dirsub(rootFolder, mask) +% lists all files in the top level folder and all sub folders thereof. +files = []; +if nargin < 1 + rootFolder = '.'; +end +if nargin < 2 + mask = '*.*'; +end +files = searchFolder(rootFolder, mask); +end + +function files = searchFolder(aFolder, mask) + % first do the fiels in this folder which match the mask. + % check there is no / or \ on the end of afolder + %disp(['Search folder ' aFolder]); + files = []; + lastChar = aFolder(end); + if strcmp(lastChar, '/') || strcmp(lastChar, '\') + aFolder = aFolder([1:end-1]); + end + files = dir(fullfile(aFolder , mask)); + for i = 1:length(files) + files(i).name = fullfile(aFolder, files(i).name); + end + + % now check out sub folders + all = dir(aFolder); + for i = 1:length(all) + aFile = fullfile(aFolder, all(i).name); + if ~isfolder(aFile) + continue; + end + if strcmp(all(i).name(1),'.') + continue; + end + moreFiles = searchFolder(aFile, mask); + for f = 1:length(moreFiles) + files(end+1) = moreFiles(f); + end + end +end diff --git a/pgmatlab/findBinaryFile.m b/testing-resources/v1.0.1code/findBinaryFile.m similarity index 100% rename from pgmatlab/findBinaryFile.m rename to testing-resources/v1.0.1code/findBinaryFile.m diff --git a/pgmatlab/findBinaryFileForDate.m b/testing-resources/v1.0.1code/findBinaryFileForDate.m similarity index 100% rename from pgmatlab/findBinaryFileForDate.m rename to testing-resources/v1.0.1code/findBinaryFileForDate.m diff --git a/testing-resources/v1.0.1code/getChannels.m b/testing-resources/v1.0.1code/getChannels.m new file mode 100644 index 0000000..a19c415 --- /dev/null +++ b/testing-resources/v1.0.1code/getChannels.m @@ -0,0 +1,17 @@ +function [ nC ] = getChannels( channelMap ) +% GETCHANNELS - returns an array of channel numbers (starting at 0) for a +% channel bitmap. +nC =[]; +j = 1; +for i = 1:32 + if (bitand(channelMap, j)) + nC = [nC ,i-1]; + end + j = j * 2; +end + +if (isempty(nC)) + nC=[0]; +end +end + diff --git a/testing-resources/v1.0.1code/getmaxcolvalue.m b/testing-resources/v1.0.1code/getmaxcolvalue.m new file mode 100644 index 0000000..09c8c1e --- /dev/null +++ b/testing-resources/v1.0.1code/getmaxcolvalue.m @@ -0,0 +1,14 @@ +function m = getmaxcolvalue(con, tableName, colName) +% get maximum integer value of a column. Return [] if the table is empty +m = []; +try % sqlite database throws up if no data. + qStr = sprintf('SELECT MAX(%s) FROM %s', colName, tableName); + dat = con.fetch(qStr); + if height(dat) == 1 + m = table2array(dat(1,1)); + end + if isnan(m) + m = []; + end +catch +end diff --git a/testing-resources/v1.0.1code/getmaxid.m b/testing-resources/v1.0.1code/getmaxid.m new file mode 100644 index 0000000..f152501 --- /dev/null +++ b/testing-resources/v1.0.1code/getmaxid.m @@ -0,0 +1,19 @@ +function mid = getMaxId(con, tableName, idName) +% get the current max id for a database table. +if nargin < 3 + idName = 'Id'; +end +mid = 0; +mQuery = sprintf('SELECT max(%s) as MaxId FROM %s', idName, tableName); +try + data = con.fetch(mQuery); + if height(data) > 0 + mid = data.MaxId(1); + if isnan(mid) + mid = 0; + end + end +catch + mid = 0; +end +end \ No newline at end of file diff --git a/testing-resources/v1.0.1code/importloggertable.m b/testing-resources/v1.0.1code/importloggertable.m new file mode 100644 index 0000000..db7f7d8 --- /dev/null +++ b/testing-resources/v1.0.1code/importloggertable.m @@ -0,0 +1,44 @@ +% import an old logger lookup table to a PAMGUArd sqlite database. + +xlsFile = 'C:\PAMGuardTest\Goniometer\xlsforms\Lookup.xlsx' +dbName = 'C:\PAMGuardTest\Goniometer\GoniometerTest.sqlite3' + +con = sqlite(dbName); +[colNames, colTypes, createStmt] = lookuptableformat(); + +tableData = readtable(xlsFile) +h = size(tableData,1); +for i = 1:h + tableData.Id(i) = i; +end + +tableName = 'Lookup' + +changes(1,:) = {'Order', 'DisplayOrder'}; +changes(2,:) = {'Text', 'ItemText'}; +changes(3,:) = {'Colour', 'FillColour'} +changes(4,:) = {'Selectable', 'isSelectable'}; + +xlsCols = tableData.Properties.VariableNames; +keep = ones(1,numel(xlsCols)); +for i = 1:numel(xlsCols) + f = find(strcmp(xlsCols{i}, changes(:,:))); + if ~isempty(f) + xlsCols{i} = changes{f,2}; + end + % and check it's still a column we want + f = find(strcmp(xlsCols{i},colNames)); + if isempty(f) + keep(i) = 0; + fprintf('Don''t keep xls column %s\n', xlsCols{i}) + end +end +tableData.Properties.VariableNames = xlsCols; +outData = tableData(:,find(keep)) + +con.exec('DELETE FROM Lookup'); +con.sqlwrite(tableName, outData); + +con.exec('UPDATE Lookup SET BorderColour = FillColour') + +close(con); \ No newline at end of file diff --git a/testing-resources/v1.0.1code/importudftable.m b/testing-resources/v1.0.1code/importudftable.m new file mode 100644 index 0000000..8e1593a --- /dev/null +++ b/testing-resources/v1.0.1code/importudftable.m @@ -0,0 +1,112 @@ +% convert a set of udf table from access to sqlite. +% tables were first exported as excel files. +sqDb = 'C:\PAMGuardTest\Goniometer\GoniometerTest.sqlite3' + +con = sqlite(sqDb); +[colNames, colTypes, createStmt] = udftableformat(); + +changes(1,:) = {'NMEAString', 'NMEA_String'}; +changes(2,:) = {'NMEAPosition', 'NMEA_Position'}; +changes(3,:) = {'ADCChannel', 'ADC_Channel'}; +changes(4,:) = {'ADCGain', 'ADC_Gain'}; +changes(5,:) = {'AnalogMultiply', 'Analog_Multiply'}; +changes(6,:) = {'AnalogAdd', 'Analog_Add'}; +changes(7,:) = {'AutoClear', 'Autoclear'}; +changes(8,:) = {'SendControlName', 'Send_Control_Name'}; +changes(9,:) = {'ControlOnSubform', 'Control_on_Subform'}; +changes(10,:) = {'GetControlData', 'Get_Control_Data'}; +changes(11,:) = {'Order', 'dumOrder'}; +changes(12,:) = {'Default', 'dumDefault'}; + +root = 'C:\PAMGuardTest\Goniometer\xlsforms\'; +forms = dir([root '*.xlsx']) + +for i = 1:numel(forms) + xlsFile = fullfile(forms(i).folder, forms(i).name) + xlsData = readtable(xlsFile) + nRow = height(xlsData); + for ir = 1:nRow + xlsData.Id(ir) = ir; + end + xlsCols = xlsData.Properties.VariableNames; + for x = 1:size(changes,1) + f = find(strcmp(xlsCols,changes{x,1})); + xlsCols{f} = changes{x,2}; + end + xlsData.Properties.VariableNames = xlsCols; + + for x = 1:numel(xlsCols) + f = find(strcmp(colNames, xlsCols{x})); + if numel(f) ~= 1 + fprintf('unable to find excel column ''%s'' in table\n', xlsCols{x}) + end + end + + [~, tableName] = fileparts(xlsFile) + tableName = strrep(tableName,' ', ''); + tableName = ['"' tableName '"']; + createLine = strrep(createStmt, 'SAMPLETABLE', ['' tableName '']); + try + con.exec(['DROP Table ' tableName '']) + catch + end + con.exec(createLine) + con.exec(sprintf('ALTER TABLE %s ADD COLUMN "dumOrder" INTEGER', tableName)); + con.exec(sprintf('ALTER TABLE %s ADD COLUMN "dumDefault" CHAR(50)', tableName)); + % now need to dealwith null data, which the connectin is crap at + for ir = 1:nRow + aRow = xlsData(ir,:); + isnull = columnisnull(aRow); + % get a single row out of the table + rowTable = xlsData(ir,find(~isnull)); + rowTable = fixBooleans(rowTable); + % rowTable = rowTable(1,[2:end]); + con.sqlwrite(tableName, rowTable); + end + stmt = sprintf('UPDATE %s SET "Order" = "dumOrder"', tableName); + con.exec(stmt); + con.exec(sprintf('ALTER TABLE %s DROP COLUMN "dumOrder"', tableName)); + stmt = sprintf('UPDATE %s SET "Default" = "dumDefault"', tableName); + con.exec(stmt); + con.exec(sprintf('ALTER TABLE %s DROP COLUMN "dumDefault"', tableName)); + + % break +end + +close(con) + +function row = fixBooleans(row) +w = size(row,2); +for i = 1:w + bit = row{1,i}; + if (islogical(i)) + end +end +end + +function isnull = columnisnull(data) +w = size(data,2); +isnull = zeros(1,w); +names = data.Properties.VariableNames +for i = 1:w + bit = data{1,i}; + if iscell(bit) + bit = bit{1}; + end + if isnumeric(bit) + if isnan(bit) + isnull(i) = 1; + end + end + if ischar(bit) + if length(bit) == 0 + isnull(i) = 1; + end + end + if isstring(bit) + if length(bit) == 0 + isnull(i) = 1; + end + end +end +end \ No newline at end of file diff --git a/pgmatlab/loadAllWhistles.m b/testing-resources/v1.0.1code/loadAllWhistles.m similarity index 100% rename from pgmatlab/loadAllWhistles.m rename to testing-resources/v1.0.1code/loadAllWhistles.m diff --git a/pgmatlab/loadClickFile.m b/testing-resources/v1.0.1code/loadClickFile.m similarity index 100% rename from pgmatlab/loadClickFile.m rename to testing-resources/v1.0.1code/loadClickFile.m diff --git a/pgmatlab/loadClickFolder.m b/testing-resources/v1.0.1code/loadClickFolder.m similarity index 100% rename from pgmatlab/loadClickFolder.m rename to testing-resources/v1.0.1code/loadClickFolder.m diff --git a/pgmatlab/loadEventClicks.m b/testing-resources/v1.0.1code/loadEventClicks.m similarity index 100% rename from pgmatlab/loadEventClicks.m rename to testing-resources/v1.0.1code/loadEventClicks.m diff --git a/pgmatlab/loadFolder.m b/testing-resources/v1.0.1code/loadFolder.m similarity index 100% rename from pgmatlab/loadFolder.m rename to testing-resources/v1.0.1code/loadFolder.m diff --git a/pgmatlab/loadPAMFolder.m b/testing-resources/v1.0.1code/loadPAMFolder.m similarity index 100% rename from pgmatlab/loadPAMFolder.m rename to testing-resources/v1.0.1code/loadPAMFolder.m diff --git a/testing-resources/v1.0.1code/loadPamguardBinaryFile.m b/testing-resources/v1.0.1code/loadPamguardBinaryFile.m new file mode 100644 index 0000000..c8029de --- /dev/null +++ b/testing-resources/v1.0.1code/loadPamguardBinaryFile.m @@ -0,0 +1,380 @@ +function [dataSet, fileInfo] = loadPamguardBinaryFile(fileName, varargin) +% Program to load a Pamguard binary file +% [dataSet, fileInfo] = loadPamguardBinaryFile(fileName, varargin) +% flleName is the full path to a PAMGuard pgdf file. +% varargin can be a number of paired parameters. +% 'timerange' must be followed by a two element data rage +% 'uidrange' must be followed by a two element UID range +% +% clicks = +% loadPamguardBinaryFile('C:/MyData/Click_Detector_Click_Detector_Clicks_20171021_002421.pgdf') +% will load all data from the data file +% Click_Detector_Click_Detector_Clicks_20171021_002421.pgdf into a Matlab +% structure. +% +% startdate = datenum(2017,10,21,0,25,0) +% enddate = datenum(2017,10,21,0,26,0) +% clicks = +% loadPamguardBinaryFile('C:/MyData/Click_Detector_Click_Detector_Clicks_20171021_002421.pgdf', 'timerange', [startdate enddate]) +% will load clicks between 00:25 and 00:26 on 21 October 2017. +% +% clicks = +% loadPamguardBinaryFile('C:/MyData/Click_Detector_Click_Detector_Clicks_20171021_002421.pgdf', +% 'uidrange', [1000345 1000345]) will load a single click with UID 1000345 +% into memory. +% +% clicks = +% loadPamguardBinaryFile('C:/MyData/Click_Detector_Click_Detector_Clicks_20171021_002421.pgdf', +% 'uidlist', [1000345 1000347 ...]) will load a list of specific UID's into +% memory. +% +% [dataSet, fileInfo] = loadPamguardBinaryFile( ... ) +% will return an optional fileInfo structure containing header and footer +% information from the file which includes information such as the data +% start and end times. +dataSet = []; +fileInfo = []; +nBackground = 0; +timeRange = [-Inf +Inf]; +uidRange = [-Inf +Inf]; +uidList = []; +iArg = 0; +sorted = 0; +filterfun = @passalldata; +channelmap=-1; +while iArg < numel(varargin) + iArg = iArg + 1; + switch(varargin{iArg}) + case 'timerange' + iArg = iArg + 1; +% timeRange = dateNumToMillis(varargin{iArg}); + timeRange = varargin{iArg}; + case 'uidrange' + iArg = iArg + 1; + uidRange = varargin{iArg}; + case 'uidlist' + iArg = iArg + 1; + uidList = sort(varargin{iArg}); + case 'filter' + iArg = iArg + 1; + filterfun = varargin{iArg}; + case 'channel' + iArg = iArg + 1; + channelmap = varargin{iArg}; + case 'sorted' + iArg = iArg + 1; + sorted = varargin{iArg}; + end +end +selState = 0; +% open binary file and read data +nData = 0; +try + fid = fopen(fileName, 'r', 'ieee-be.l64'); + + % initialize variables + prevPos = -1; + dataSet=[]; + clear fileInfo; + fileInfo.readModuleHeader=@readStdModuleHeader; + fileInfo.readModuleFooter=@readStdModuleFooter; + + % main loop + while (1) + + % if for some reason we're stuck at one byte, warn the user and + % abort + pos = ftell(fid); + if (pos == prevPos) + disp(fprintf('File stuck at byte %d', pos)); + break; + end + prevPos = pos; + + % read in the length of the object and the type. Move the file + % pointer back to the beginning of the length variable, and switch + % on the type. If we couldn't read nextLen or nextType, assume + % that means we've hit the end of the file and break out of loop + [nextLen, nL] = fread(fid, 1, 'int32'); + [nextType, nT] = fread(fid, 1, 'int32'); +% if (nextType < 0) +% nextType +% end + if (nL == 0 || nT == 0) + break; + end + fseek(fid, -8, 'cof'); + switch nextType + + % Case 1: File Header. Read in the file header, and then set + % the function handles depending on what type of data the + % binary file holds. The module type is typically specified in + % the package class that extends PamControlledUnit, and is a + % string unique to that module. + case -1 + fileInfo.fileHeader = readFileHeader(fid); + % disp(fileInfo.fileHeader.moduleType); + switch fileInfo.fileHeader.moduleType + + % AIS Processing Module + case 'AIS Processing' + fileInfo.objectType=0; + fileInfo.readModuleData=@readAISData; + + % Click Detector or Soundtrap Click Detector Module + case {'Click Detector', 'SoundTrap Click Detector'} + switch fileInfo.fileHeader.streamName + case 'Clicks' + fileInfo.objectType=1000; + fileInfo.readModuleData=@readClickData; + fileInfo.readModuleFooter=@readClickFooter; + fileInfo.readBackgroundData = @readClickBackground; + case 'Trigger Background' + fileInfo.objectType=0; + fileInfo.readModuleData=@readClickTriggerData; + fileInfo.readModuleHeader=@readClickTriggerHeader; + end + % Clip Generator Module + case 'Clip Generator' + fileInfo.objectType=[1 2]; + fileInfo.readModuleData=@readClipData; + + %Deep learning module + case 'Deep Learning Classifier' + disp(['Deep learning stream: ' fileInfo.fileHeader.streamName]) + switch fileInfo.fileHeader.streamName + case {'DL_detection', 'DL detection'} + fileInfo.objectType=1; + fileInfo.readModuleData=@readDLDetData; + case {'DL_Model_Data', 'DL Model Data'} + fileInfo.objectType=0; + fileInfo.readModuleData=@readDLModelData; + end + + + % DbHt Module + % NOT TESTED YET + case 'DbHt' + fileInfo.objectType=1; + fileInfo.readModuleData=@readDbHtData; + + % Difar Module + case 'DIFAR Processing' + fileInfo.objectType=0; + fileInfo.readModuleData=@readDifarData; + + % LTSA Module + case 'LTSA' + fileInfo.objectType=1; + fileInfo.readModuleHeader=@readLTSAHeader; + fileInfo.readModuleData=@readLTSAData; + + % Noise Monitor Module and Noise Band Monitor Module + % Note: The two modules have different types, but both + % use noiseMonitor.NoiseBinaryDataSource class to save + % data + case {'Noise Monitor', 'Noise Band'} + fileInfo.objectType=1; + fileInfo.readModuleHeader=@readNoiseMonHeader; + fileInfo.readModuleData=@readNoiseMonData; + + % Filtered Noise Measurement Module (Noise One Band) + case 'NoiseBand' + fileInfo.objectType=1; + fileInfo.readModuleData=@readNoiseBandData; + case 'GPL Detector' + switch fileInfo.fileHeader.streamName + case 'GPL Detections' + fileInfo.readModuleData = @readGPLDetections; + fileInfo.readBackgroundData = @readSpectralBackground; + end + % Right Whale Edge Detector Module + case 'RW Edge Detector' + fileInfo.objectType=0; + fileInfo.readModuleData=@readRWEDetectorData; + disp('Right Whale Edge Detector binary file detected'); + disp('Note that the low, high and peak frequencies are actually'); + disp('saved as FFT slices. In order to convert values to Hz, they'); + disp('must be multiplied by (sampleRate/fftLength)'); + + % Whistle And Moans Module + case 'WhistlesMoans' + fileInfo.objectType=2000; + fileInfo.readModuleHeader=@readWMDHeader; + fileInfo.readModuleData=@readWMDData; + fileInfo.readBackgroundData = @readSpectralBackground; + + case {'Energy Sum Detector','Spectrogram Correlation Detector','Matched Filter Detector'} + switch fileInfo.fileHeader.streamName + % Ishmael detector data + case 'Ishmael Peak Data' + fileInfo.readModuleData=@readIshmaelData; + + % Ismael detections + case 'Ishmael Detections' + fileInfo.readModuleData=@readIshmaelDetection; + end + + % Ipi module + case 'Ipi module' + fileInfo.objectType=0; + fileInfo.readModuleData=@readIpiData; + + case 'Gemini Threshold Detector' + fileInfo.objectType = 0; + fileInfo.readModuleData=@readTritechTrack; + fileInfo.readBackgroundData = @readTritechBackground; + + % Note: PamRawDataBlock has it's own Binary Store (RawDataBinarySource), + % but it is created by multiple different processes so doesn't have one + % particular type, and may have a type shared with a different binary + % store (e.g. the DbHt module creates both a DbHtDataSource and a + % RawDataBinarySource, and they will both have type 'DbHt'). + % The comments in the class indicate that the binary store should never + % be used for raw data and that the sole purpose of the class is to + % enable sending raw data over the network. If this is ever changed + % and raw data is allowed to be stored in the binary files, we will + % have to come up with a way of determining where the raw data came + % from besides querying the type. + + otherwise + disp(['Don''t recognize type ' fileInfo.fileHeader.moduleType '. Aborting load']); + break; + end + + % Case 2: File Footer. The file version should have been set + % when we read the file header. If the file header is empty, + % something has gone wrong so warn the user and exit + case -2 + if (isempty(fileInfo.fileHeader)) + disp('Error: found file footer before file header. Aborting load'); + break; + end + fileInfo.fileFooter = readFileFooterInfo(fid, fileInfo.fileHeader.fileFormat); + + % Case 3: Module Header. The correct function handle should + % have been set when we read the file header. If the file + % header is empty, something has gone wrong so warn the user + % and exit + case -3 + if (isempty(fileInfo.fileHeader)) + disp('Error: found module header before file header. Aborting load'); + break; + end + fileInfo.moduleHeader = fileInfo.readModuleHeader(fid); + + % Case 4: Module Footer. The correct function handle should + % have been set when we read the file header. If the file + % header is empty, something has gone wrong so warn the user + % and exit + case -4 + if (isempty(fileInfo.fileHeader)) + disp('Error: found module footer before file header. Aborting load'); + break; + end + fileInfo.moduleFooter = fileInfo.readModuleFooter(fid); + + % Case 5: Data. The correct function handle should have been + % set when we read in the file header. If the file header is + % empty, something has gone wrong so warn the user and exit + case -5 + % datagram data Skip it for now. + fseek(fid, nextLen, 'cof'); + otherwise + + if (isempty(fileInfo.fileHeader)) + disp('Error: found data before file header. Aborting load'); + end + + [dataPoint, selState] = readPamData(fid, fileInfo, timeRange, uidRange, uidList); + + % see if it's in the specified list of wanted UID's + if ~isempty(uidList) + + try + dataUID = dataPoint.UID; + % if dataUID > uidList(end) + % break; + % end + + selState = sum(dataUID == uidList); + catch + + end + end + if channelmap>0 && channelmap~=dataPoint.channelMap + selState = 0; + end + + if selState == 1 + selState = filterfun(dataPoint); + end + if (selState == 0 || (selState == 2 && ~sorted)) + fseek(fid, prevPos+nextLen, 'bof'); + continue; + elseif (selState == 2 && sorted) + break; + end + + newP = ftell(fid); + pErr = newP - (prevPos+nextLen); + if pErr ~= 0 + fprintf('Error in file position: %d bytes\n', pErr); + fseek(fid, -pErr, 'cof'); + end + + if nextType == -6 + nBackground = nBackground + 1; + backgroundData(nBackground) = dataPoint; + continue; + end + + + % Preallocation. Acheived by adding new data points beyond + % the end of the existing array, then shortening the array + % before it is returned to the user. + nData = nData + 1; + dataSet = checkArrayAllocation(dataSet, nData, dataPoint); + dataSet(nData) = dataPoint; + +% dataSet = [dataSet dataPoint]; + end + end + % due to preallocation it's likely the array is now far too large so + % shrink it back to the correct size. + dataSet = dataSet(1:nData); +catch mError + disp('Error reading file'); + disp(getReport(mError)); +end +if nBackground > 0 + fileInfo.background = backgroundData; +end +% close the file and return to the calling function +try +fclose(fid); +catch +end +return; +end + + +% Check the array allocation. This gets called every time data are read and +% will extend the array by approximately the sqrt of the arrays own length +% if required. Preallocation acheived by sticking a sample object at a high +% data index so that array up to that point gets filled with nulls. +function array = checkArrayAllocation(array, reqLength, sampleObject) +if isempty(array) + currentLength = 0; + clear array; +else + currentLength = numel(array); +end +if (currentLength >= reqLength) + return; +end +allocStep = round(sqrt(reqLength)); +allocStep = max(10, min(allocStep, 10000)); +array(reqLength + allocStep) = sampleObject; +return; +end diff --git a/testing-resources/v1.0.1code/loadPamguardBinaryFolder.m b/testing-resources/v1.0.1code/loadPamguardBinaryFolder.m new file mode 100644 index 0000000..9dc66e8 --- /dev/null +++ b/testing-resources/v1.0.1code/loadPamguardBinaryFolder.m @@ -0,0 +1,49 @@ +function [data background fileInfos] = loadPamguardBinaryFolder(dir, fileMask, verbose, filterfun) +% load all data from a folder and it's sub folders +% data = loadPamguardBinaryFolder(dir, fileMask, verbose) loads all data from +% the folder dir where files satisfy the fileMask. All files must +% contain data of the same format so mask must specify a particular type +% of data file, e.g. clicks*.pgdf. If verbose is a non-zero number 'n' then +% every n files a progress message will be printed on the temrinal. +% +% e.g. allclicks = loadPAMFolder('C:/Mydata', 'Click_Detector_*.pgdf', 5); +% +if (nargin < 3) + verbose = 0; +end +if nargin < 4 + filterfun = @passalldata; +end +data = []; +background = []; +d = dirsub(dir, fileMask); +for i = 1:numel(d) + if verbose + if mod(i, verbose) == 0 + fprintf('Loading %d/%d (%d) %s\n', i, numel(d), numel(data), d(i).name); + end + end + [fRoot, fName, fEnd] = fileparts(d(i).name); + fileNameOnly = [fName fEnd]; + [dat fInf] = loadPamguardBinaryFile(d(i).name, 'filter', filterfun); + if ~isempty(dat) + % need to add bookkeeping data to dat so that we know which file + % each click comes from and also know which click it is within the + % file. + for iDat = 1:numel(dat) + dat(iDat).clickNumber = iDat; + dat(iDat).fileName = fileNameOnly; + end + data = [data dat]; + end + if isfield(fInf, 'background') + background = [background fInf.background]; + end + if nargout >= 3 + if i == 1 + fileInfos(numel(d)) = fInf; % allocate entire array + end + fileInfos(i) = fInf; + end +end + \ No newline at end of file diff --git a/testing-resources/v1.0.1code/loadPamguardMultiFile.m b/testing-resources/v1.0.1code/loadPamguardMultiFile.m new file mode 100644 index 0000000..1d92a03 --- /dev/null +++ b/testing-resources/v1.0.1code/loadPamguardMultiFile.m @@ -0,0 +1,53 @@ +function eventData = loadPamguardMultiFile(dataDir, fileNames, itemUID, verbose) +% function to load all data from an event even if spread over multiple +% files. This can be used to get binary file data for data associated with +% PAMGuard 'events' marked out using the click detector or the 'Detection +% Grouper'. From the database query, for each event make a list of the +% fileNames and the UID's of individual datas, then this function will call +% loadPamguardBinaryFile(...) for each of one or more files associated with +% the event and merge all the data into one array of structure. +% +% inputs are root data folder, cell array of binary file names and click +% numbers +% +% eventData = loadPamguardMultiFile(dataDir, fileNames, itemUID) +% 'dataDir': root folder for binary data +% 'fileNames': list of file names for each item of interest (generally read from database) +% 'itemUID': list of UID's of wanted data. Shoule be same length as array of file names +% +% returns binary data from multiple files. + +eventData = []; +if nargin < 4 + verbose = 0; +end + +% find the files we need using the findBinaryFile function. +% unique file list +unFiles = unique(fileNames); +for i = 1:numel(unFiles) % loop over the different files + + if (verbose) + fileName = unFiles{i}; + if length(dataDir) < length(fileName) + fileName = fileName(length(dataDir):end); + end + fprintf('Loading file %s %d of %d\n', fileName, i, numel(unFiles)); + end + + filePath = findBinaryFile(dataDir,'*.pgdf',unFiles{i}); + + % list of clicks in a particular file + fileUIDs = itemUID(find(strcmp(fileNames, unFiles{i}))); + + fileData = loadPamguardBinaryFile(filePath, 'uidlist', fileUIDs); + % add the file information to all data loaded. + [~,fName,fEnd] = fileparts(filePath); + fileName = [fName fEnd]; + for d = 1:numel(fileData) + fileData(d).binaryFile = fileName; + end + + eventData = [eventData fileData]; +end + diff --git a/pgmatlab/loadWhistleFile.m b/testing-resources/v1.0.1code/loadWhistleFile.m similarity index 100% rename from pgmatlab/loadWhistleFile.m rename to testing-resources/v1.0.1code/loadWhistleFile.m diff --git a/testing-resources/v1.0.1code/lookuptableformat.m b/testing-resources/v1.0.1code/lookuptableformat.m new file mode 100644 index 0000000..2a538f3 --- /dev/null +++ b/testing-resources/v1.0.1code/lookuptableformat.m @@ -0,0 +1,21 @@ +function [colNames, colTypes, createStmt] = lookuptableformat() +% get the format of a standard PAMGuard lookup table. + +% these lines were run once on an existing database to get the +% table formats, a result was then copied manually as createStmt +% con = sqlite('C:\PAMGuardTest\Goniometer\GoniometerTest.sqlite3') +% tablesTable = con.fetch('select * from sqlite_master') +% close(con) + +createStmt = ['CREATE TABLE Lookup ("Id" INTEGER NOT NULL, "Topic" CHAR(50), ' ... + '"DisplayOrder" INTEGER, "Code" CHAR(12), "ItemText" CHAR(50), "isSelectable" BIT, ' ... + '"FillColour" CHAR(20), "BorderColour" CHAR(20), "Symbol" CHAR(2), PRIMARY KEY ("Id") )']; + +quotes = strfind(createStmt, '"'); +commas = strfind(createStmt, ','); +nCol = numel(quotes)/2-1; +for i = 1:nCol + j = i-1; + colNames{i} = createStmt(quotes(j*2+1)+1:quotes(j*2+2)-1); + colTypes{i} = createStmt(quotes(j*2+2)+2:commas(i)-1); +end \ No newline at end of file diff --git a/pgmatlab/millisToDateNum.m b/testing-resources/v1.0.1code/millisToDateNum.m similarity index 100% rename from pgmatlab/millisToDateNum.m rename to testing-resources/v1.0.1code/millisToDateNum.m diff --git a/testing-resources/v1.0.1code/passalldata.m b/testing-resources/v1.0.1code/passalldata.m new file mode 100644 index 0000000..82b04bf --- /dev/null +++ b/testing-resources/v1.0.1code/passalldata.m @@ -0,0 +1,2 @@ +function pass = passalldata(dataUnit) +pass = 1; \ No newline at end of file diff --git a/pgmatlab/readAISData.m b/testing-resources/v1.0.1code/readAISData.m similarity index 100% rename from pgmatlab/readAISData.m rename to testing-resources/v1.0.1code/readAISData.m diff --git a/pgmatlab/readBeamFormerAnnotation.m b/testing-resources/v1.0.1code/readBeamFormerAnnotation.m similarity index 100% rename from pgmatlab/readBeamFormerAnnotation.m rename to testing-resources/v1.0.1code/readBeamFormerAnnotation.m diff --git a/pgmatlab/readBearingAnnotation.m b/testing-resources/v1.0.1code/readBearingAnnotation.m similarity index 100% rename from pgmatlab/readBearingAnnotation.m rename to testing-resources/v1.0.1code/readBearingAnnotation.m diff --git a/pgmatlab/readClickBackground.m b/testing-resources/v1.0.1code/readClickBackground.m similarity index 100% rename from pgmatlab/readClickBackground.m rename to testing-resources/v1.0.1code/readClickBackground.m diff --git a/pgmatlab/readClickClsfrAnotation.m b/testing-resources/v1.0.1code/readClickClsfrAnotation.m similarity index 100% rename from pgmatlab/readClickClsfrAnotation.m rename to testing-resources/v1.0.1code/readClickClsfrAnotation.m diff --git a/pgmatlab/readClickData.m b/testing-resources/v1.0.1code/readClickData.m similarity index 100% rename from pgmatlab/readClickData.m rename to testing-resources/v1.0.1code/readClickData.m diff --git a/pgmatlab/readClickFooter.m b/testing-resources/v1.0.1code/readClickFooter.m similarity index 100% rename from pgmatlab/readClickFooter.m rename to testing-resources/v1.0.1code/readClickFooter.m diff --git a/pgmatlab/readClickTriggerData.m b/testing-resources/v1.0.1code/readClickTriggerData.m similarity index 100% rename from pgmatlab/readClickTriggerData.m rename to testing-resources/v1.0.1code/readClickTriggerData.m diff --git a/pgmatlab/readClickTriggerHeader.m b/testing-resources/v1.0.1code/readClickTriggerHeader.m similarity index 100% rename from pgmatlab/readClickTriggerHeader.m rename to testing-resources/v1.0.1code/readClickTriggerHeader.m diff --git a/pgmatlab/readClipData.m b/testing-resources/v1.0.1code/readClipData.m similarity index 100% rename from pgmatlab/readClipData.m rename to testing-resources/v1.0.1code/readClipData.m diff --git a/pgmatlab/readDLAnnotation.m b/testing-resources/v1.0.1code/readDLAnnotation.m similarity index 100% rename from pgmatlab/readDLAnnotation.m rename to testing-resources/v1.0.1code/readDLAnnotation.m diff --git a/pgmatlab/readDLDetData.m b/testing-resources/v1.0.1code/readDLDetData.m similarity index 100% rename from pgmatlab/readDLDetData.m rename to testing-resources/v1.0.1code/readDLDetData.m diff --git a/pgmatlab/readDLModelData.m b/testing-resources/v1.0.1code/readDLModelData.m similarity index 100% rename from pgmatlab/readDLModelData.m rename to testing-resources/v1.0.1code/readDLModelData.m diff --git a/pgmatlab/readDbHtData.m b/testing-resources/v1.0.1code/readDbHtData.m similarity index 100% rename from pgmatlab/readDbHtData.m rename to testing-resources/v1.0.1code/readDbHtData.m diff --git a/pgmatlab/readDifarData.m b/testing-resources/v1.0.1code/readDifarData.m similarity index 100% rename from pgmatlab/readDifarData.m rename to testing-resources/v1.0.1code/readDifarData.m diff --git a/pgmatlab/readFileFooterInfo.m b/testing-resources/v1.0.1code/readFileFooterInfo.m similarity index 100% rename from pgmatlab/readFileFooterInfo.m rename to testing-resources/v1.0.1code/readFileFooterInfo.m diff --git a/pgmatlab/readFileHeader.m b/testing-resources/v1.0.1code/readFileHeader.m similarity index 100% rename from pgmatlab/readFileHeader.m rename to testing-resources/v1.0.1code/readFileHeader.m diff --git a/pgmatlab/readGPLDetections.m b/testing-resources/v1.0.1code/readGPLDetections.m similarity index 100% rename from pgmatlab/readGPLDetections.m rename to testing-resources/v1.0.1code/readGPLDetections.m diff --git a/pgmatlab/readIpiData.m b/testing-resources/v1.0.1code/readIpiData.m similarity index 100% rename from pgmatlab/readIpiData.m rename to testing-resources/v1.0.1code/readIpiData.m diff --git a/pgmatlab/readIshmaelData.m b/testing-resources/v1.0.1code/readIshmaelData.m similarity index 100% rename from pgmatlab/readIshmaelData.m rename to testing-resources/v1.0.1code/readIshmaelData.m diff --git a/pgmatlab/readIshmaelDetection.m b/testing-resources/v1.0.1code/readIshmaelDetection.m similarity index 100% rename from pgmatlab/readIshmaelDetection.m rename to testing-resources/v1.0.1code/readIshmaelDetection.m diff --git a/pgmatlab/readJavaUTFString.m b/testing-resources/v1.0.1code/readJavaUTFString.m similarity index 100% rename from pgmatlab/readJavaUTFString.m rename to testing-resources/v1.0.1code/readJavaUTFString.m diff --git a/pgmatlab/readLTSAData.m b/testing-resources/v1.0.1code/readLTSAData.m similarity index 100% rename from pgmatlab/readLTSAData.m rename to testing-resources/v1.0.1code/readLTSAData.m diff --git a/pgmatlab/readLTSAHeader.m b/testing-resources/v1.0.1code/readLTSAHeader.m similarity index 100% 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a/pgmatlab/readPamData.m b/testing-resources/v1.0.1code/readPamData.m similarity index 100% rename from pgmatlab/readPamData.m rename to testing-resources/v1.0.1code/readPamData.m diff --git a/pgmatlab/readRWEDetectorData.m b/testing-resources/v1.0.1code/readRWEDetectorData.m similarity index 100% rename from pgmatlab/readRWEDetectorData.m rename to testing-resources/v1.0.1code/readRWEDetectorData.m diff --git a/pgmatlab/readRWUDPAnnotation.m b/testing-resources/v1.0.1code/readRWUDPAnnotation.m similarity index 100% rename from pgmatlab/readRWUDPAnnotation.m rename to testing-resources/v1.0.1code/readRWUDPAnnotation.m diff --git a/pgmatlab/readSpectralBackground.m b/testing-resources/v1.0.1code/readSpectralBackground.m similarity index 100% rename from pgmatlab/readSpectralBackground.m rename to testing-resources/v1.0.1code/readSpectralBackground.m diff --git a/pgmatlab/readStdModuleFooter.m b/testing-resources/v1.0.1code/readStdModuleFooter.m similarity index 100% rename from pgmatlab/readStdModuleFooter.m rename to testing-resources/v1.0.1code/readStdModuleFooter.m diff --git a/pgmatlab/readStdModuleHeader.m b/testing-resources/v1.0.1code/readStdModuleHeader.m similarity index 100% rename from pgmatlab/readStdModuleHeader.m rename to testing-resources/v1.0.1code/readStdModuleHeader.m diff --git a/pgmatlab/readTDBLAnnotation.m b/testing-resources/v1.0.1code/readTDBLAnnotation.m similarity index 100% rename from pgmatlab/readTDBLAnnotation.m rename to testing-resources/v1.0.1code/readTDBLAnnotation.m diff --git a/pgmatlab/readTMAnnotation.m b/testing-resources/v1.0.1code/readTMAnnotation.m similarity index 100% rename from pgmatlab/readTMAnnotation.m rename to testing-resources/v1.0.1code/readTMAnnotation.m diff --git a/pgmatlab/readTritechBackground.m b/testing-resources/v1.0.1code/readTritechBackground.m similarity index 100% rename from pgmatlab/readTritechBackground.m rename to testing-resources/v1.0.1code/readTritechBackground.m diff --git a/pgmatlab/readTritechGLFRecord.m b/testing-resources/v1.0.1code/readTritechGLFRecord.m similarity index 100% rename from pgmatlab/readTritechGLFRecord.m rename to testing-resources/v1.0.1code/readTritechGLFRecord.m diff --git a/pgmatlab/readTritechHeader.m b/testing-resources/v1.0.1code/readTritechHeader.m similarity index 100% rename from pgmatlab/readTritechHeader.m rename to testing-resources/v1.0.1code/readTritechHeader.m diff --git a/pgmatlab/readTritechTrack.m b/testing-resources/v1.0.1code/readTritechTrack.m similarity index 100% rename from pgmatlab/readTritechTrack.m rename to testing-resources/v1.0.1code/readTritechTrack.m diff --git a/pgmatlab/readUserFormAnnotation.m b/testing-resources/v1.0.1code/readUserFormAnnotation.m similarity index 100% rename from pgmatlab/readUserFormAnnotation.m rename to testing-resources/v1.0.1code/readUserFormAnnotation.m diff --git a/pgmatlab/readWMDData.m b/testing-resources/v1.0.1code/readWMDData.m similarity index 100% rename from pgmatlab/readWMDData.m rename to testing-resources/v1.0.1code/readWMDData.m diff --git a/pgmatlab/readWMDHeader.m b/testing-resources/v1.0.1code/readWMDHeader.m similarity index 100% rename from pgmatlab/readWMDHeader.m rename to testing-resources/v1.0.1code/readWMDHeader.m diff --git a/pgmatlab/sqlite-jdbc-3.36.0.jar b/testing-resources/v1.0.1code/sqlite-jdbc-3.36.0.jar similarity index 100% rename from pgmatlab/sqlite-jdbc-3.36.0.jar rename to testing-resources/v1.0.1code/sqlite-jdbc-3.36.0.jar diff --git a/testing-resources/v1.0.1code/sqlite-jdbc-3.45.3.0.jar b/testing-resources/v1.0.1code/sqlite-jdbc-3.45.3.0.jar new file mode 100644 index 0000000..4debbd4 Binary files /dev/null and b/testing-resources/v1.0.1code/sqlite-jdbc-3.45.3.0.jar differ diff --git a/pgmatlab/sqlitedatabase.m b/testing-resources/v1.0.1code/sqlitedatabase.m similarity index 100% rename from pgmatlab/sqlitedatabase.m rename to testing-resources/v1.0.1code/sqlitedatabase.m diff --git a/testing-resources/v1.0.1code/tableExists.m b/testing-resources/v1.0.1code/tableExists.m new file mode 100644 index 0000000..4e61f81 --- /dev/null +++ b/testing-resources/v1.0.1code/tableExists.m @@ -0,0 +1,27 @@ +function e = tableExists(con, tableName) +% function e = tableExists(con, tableName) +% return true if the table exists in connection con +e = 0; +%% ODBC Method +try + dbmeta = dmd(con, 'tables'); + t = tables(dbmeta,''); + n = size(t,1); + for i = 1:n + tt = t{i,1}; + if strcmp(lower(tt),lower(tableName)) == 1 + e = 1; + return; + end + end + return +catch +end +%% SQLITE Method +try + sq = sprintf('SELECT * FROM sqlite_master where name=''%s''', tableName); + tableData = con.fetch(sq); + e = size(tableData,1) > 0; + return +catch +end \ No newline at end of file diff --git a/testing-resources/v1.0.1code/udftableformat.m b/testing-resources/v1.0.1code/udftableformat.m new file mode 100644 index 0000000..7cfe2dd --- /dev/null +++ b/testing-resources/v1.0.1code/udftableformat.m @@ -0,0 +1,29 @@ +function [colNames, colTypes, createStmt] = udftableformat() +% get the names and types of udf table columns + +% % con = sqlitedatabase('C:\PAMGuardTest\Goniometer\GoniometerTest.sqlite3') +% % tablesTable = con.fetch('select * from sqlite_master') +% % % tables(con) +% % % dbmeta = dmd(con); +% % % % t = tables(dbmeta,''); +% % % colNames = columns(dbmeta, con.DefaultCatalog, '', 'UDF_Sample'); +% % +% % +% % close(con); +createStmt = ['CREATE TABLE SAMPLETABLE ("Id" INTEGER NOT NULL, "Order" INTEGER, "Type" CHAR(50), ' ... + '"Title" CHAR(50), "PostTitle" CHAR(50), "DbTitle" CHAR(50), "Length" INTEGER, "Topic" CHAR(50), ' ... + '"NMEA_Module" CHAR(50), "NMEA_String" CHAR(50), "NMEA_Position" INTEGER, "Required" BOOLEAN, ' ... + '"AutoUpdate" INTEGER, "Autoclear" BOOLEAN, "ForceGps" BOOLEAN, "Hint" CHAR(100), "ADC_Channel" INTEGER, ' ... + '"ADC_Gain" REAL, "Analog_Multiply" REAL, "Analog_Add" REAL, "Plot" BOOLEAN, "Height" INTEGER, "Colour" CHAR(20), ' ... + '"MinValue" REAL, "MaxValue" REAL, "ReadOnly" BOOLEAN, "Send_Control_Name" CHAR(50), "Control_on_Subform" CHAR(50), ' ... + '"Get_Control_Data" CHAR(50), "Default" CHAR(50), PRIMARY KEY ("Id") )'] +% pull a list of names and types out of that. +quotes = strfind(createStmt, '"'); +commas = strfind(createStmt, ','); +nCol = numel(quotes)/2-1; +for i = 1:nCol + j = i-1; + colNames{i} = createStmt(quotes(j*2+1)+1:quotes(j*2+2)-1); + colTypes{i} = createStmt(quotes(j*2+2)+2:commas(i)-1); +end + diff --git a/pgmatlab/unpackLocaliserError.m b/testing-resources/v1.0.1code/unpackLocaliserError.m similarity index 100% rename from pgmatlab/unpackLocaliserError.m rename to testing-resources/v1.0.1code/unpackLocaliserError.m diff --git a/pgmatlab/writespecannotationdata.m b/testing-resources/v1.0.1code/writespecannotationdata.m similarity index 100% rename from pgmatlab/writespecannotationdata.m rename to testing-resources/v1.0.1code/writespecannotationdata.m diff --git a/tests/+testUtils/README.md b/tests/+testUtils/README.md new file mode 100644 index 0000000..43caff5 --- /dev/null +++ b/tests/+testUtils/README.md @@ -0,0 +1 @@ +Some helper functions for writing new tests. \ No newline at end of file diff --git a/tests/+testUtils/generateRecursivePaths.m b/tests/+testUtils/generateRecursivePaths.m new file mode 100644 index 0000000..28e27b6 --- /dev/null +++ b/tests/+testUtils/generateRecursivePaths.m @@ -0,0 +1,18 @@ +% dir_to_search = './data/detectors'; + +dir_to_search = './data/'; + +files = dir(fullfile(dir_to_search, '**/*.pgdf')); +file_paths = fullfile({files.folder}, {files.name}); + +% Convert to a cell array of strings +file_paths_cell = cellfun(@(x) ['''', x, ''''], file_paths, 'UniformOutput', false); + +% Join the cell array into a single string +file_paths_str = sprintf('%s, ', file_paths_cell{:}); + +% Remove the trailing comma and space +file_paths_str = file_paths_str(1:end-2); + +% Print the result +fprintf('{%s};\n', file_paths_str); \ No newline at end of file diff --git a/tests/+testUtils/myFilter.m b/tests/+testUtils/myFilter.m new file mode 100644 index 0000000..86585b4 --- /dev/null +++ b/tests/+testUtils/myFilter.m @@ -0,0 +1,10 @@ +function selState = myFilter(data) + % remove all data where type ~= 0 + if data.UID == 5000004 + selState = 0; % skip + elseif data.UID >= 5000005 + selState = 2; % stop + else + selState = 1; % keep + end +end \ No newline at end of file diff --git a/tests/LegacyTests.m b/tests/LegacyTests.m new file mode 100644 index 0000000..4371d5f --- /dev/null +++ b/tests/LegacyTests.m @@ -0,0 +1,198 @@ +% test the outputs of pgmatlab code with legacy code to ensure +% consistent interface and data. + +classdef LegacyTests < matlab.unittest.TestCase + properties + testsFolder = 'tests'; % inside root + resourcesFolder = 'testing-resources'; % inside root + dataFolder = 'data'; % inside resources + legacyFolder = 'v1.0.1code'; % inside resources + codeFolder = 'src'; % inside root + + rootDir; + testsDir; + resourcesDir; + dataDir; + legacyDir; + codeDir; + end + + properties (TestParameter) + % NOTE: the 'sorted' parameter was added in v2 to speed up filtering on sorted date. It defaults to 0 + % to ensure backwards compatibility with pgmaptlab v1. + + filters = { + struct(); + struct('uidrange', [1,10], 'sorted', 1); + struct('uidrange', [5000001,5000009], 'sorted', 1); + struct('uidrange', [1 500006], 'sorted', 0) + struct('uidlist', [500001], 'uidrange', [1 500006], 'sorted', 0) + struct('uidlist', [500001], 'uidrange', [1 500006], 'channel', 1, 'sorted', 0) + struct('channel', 4); + struct('channel', 1); + struct('uidlist', [500001]); + struct('uidlist', [500001], 'uidrange', [1 100000]); + struct('filter', @testUtils.myFilter) + struct('uidlist', [5000003, 5000004, 5000005, 5000006], 'filter', @testUtils.myFilter) + struct('uidlist', [5000003, 5000004, 5000005, 5000006], 'filter', @testUtils.myFilter, 'sorted', 1) + } + + filePath = { + struct('path', "processing/ais/ais_v1_test1.pgdf"); + struct('path', "classifiers/deeplearningclassifier/deeplearningclassifier_v2_test1_detections.pgdf"); + struct('path', "classifiers/deeplearningclassifier/deeplearningclassifier_v2_test1_models.pgdf"); + struct('path', "detectors/click/click_v4_test2.pgdf"); + struct('path', "detectors/click/click_v4_test3.pgdf"); + struct('path', "detectors/clicktriggerbackground/clicktriggerbackground_v0_test1.pgdf"); + struct('path', "detectors/gpl/gpl_v2_test1.pgdf"); + struct('path', "detectors/gpl/gpl_v2_test2.pgdf"); + struct('path', "detectors/rwedge/RW_Edge_Detector_Right_Whale_Edge_Detector_Edges_20090328_230139.pgdf"); + struct('path', "detectors/whistleandmoan/whistleandmoan_v2_test1.pgdf"); + struct('path', "plugins/geminithreshold/geminithreshold_test1.pgdf"); + struct('path', "plugins/spermwhaleipi/spermwhaleipi_v1_test1.pgdf"); + struct('path', "processing/clipgenerator/clipgenerator_v3_test1.pgdf"); + struct('path', "processing/clipgenerator/clipgenerator_v3_test2.pgdf"); + struct('path', "processing/dbht/dbht_v2_test1.pgdf"); + struct('path', "processing/difar/difar_v2_test1.pgdf"); + struct('path', "processing/difar/difar_v2_test2.pgdf"); + struct('path', "processing/difar/difar_v2_test3.pgdf"); + struct('path', "processing/ishmael/ishmaeldetections_energysum_v2_test1.pgdf"); + struct('path', "processing/ishmael/ishmaeldetections_energysum_v2_test2.pgdf"); + struct('path', "processing/ishmael/ishmaeldetections_energysum_v2_test3.pgdf"); + struct('path', "processing/ishmael/ishmaeldetections_matchedfilter_v2_test1.pgdf"); + struct('path', "processing/ishmael/ishmaeldetections_matchedfilter_v2_test2.pgdf"); + struct('path', "processing/ishmael/ishmaeldetections_spectrogramcorrelation_v2_test1.pgdf"); + struct('path', "processing/ishmael/ishmaeldetections_spectrogramcorrelation_v2_test2.pgdf"); + struct('path', "processing/longtermspectralaverage/longtermspectralaverage_v2_test1.pgdf"); + struct('path', "processing/noiseband/noiseband_v3_test1.pgdf"); + struct('path', "processing/noiseband/noisebandnoise_v3_test1.pgdf"); + struct('path', "processing/noiseband/noisebandpulses_v3_test1.pgdf"); + struct('path', "processing/noisemonitor/noisemonitor_v2_test1.pgdf"); + struct('path', "processing/ais/ais_v1_test1.pgdx"); + struct('path', "classifiers/deeplearningclassifier/deeplearningclassifier_v2_test1_detections.pgdx"); + struct('path', "classifiers/deeplearningclassifier/deeplearningclassifier_v2_test1_models.pgdx"); + struct('path', "detectors/click/click_v4_test1.pgdx"); + struct('path', "detectors/click/click_v4_test2.pgdx"); + struct('path', "detectors/click/click_v4_test3.pgdx"); + struct('path', "detectors/clicktriggerbackground/clicktriggerbackground_v0_test1.pgdx"); + struct('path', "detectors/gpl/gpl_v2_test1.pgdx"); + struct('path', "detectors/gpl/gpl_v2_test2.pgdx"); + struct('path', "detectors/rwedge/RW_Edge_Detector_Right_Whale_Edge_Detector_Edges_20090328_230139.pgdx"); + struct('path', "detectors/whistleandmoan/whistleandmoan_v2_test1.pgdx"); + struct('path', "plugins/geminithreshold/geminithreshold_test1.pgdx"); + struct('path', "plugins/spermwhaleipi/spermwhaleipi_v1_test1.pgdx"); + struct('path', "processing/clipgenerator/clipgenerator_v3_test1.pgdx"); + struct('path', "processing/clipgenerator/clipgenerator_v3_test2.pgdx"); + struct('path', "processing/dbht/dbht_v2_test1.pgdx"); + struct('path', "processing/difar/difar_v2_test1.pgdx"); + struct('path', "processing/difar/difar_v2_test2.pgdx"); + struct('path', "processing/difar/difar_v2_test3.pgdx"); + struct('path', "processing/ishmael/ishmaeldetections_energysum_v2_test1.pgdx"); + struct('path', "processing/ishmael/ishmaeldetections_energysum_v2_test2.pgdx"); + struct('path', "processing/ishmael/ishmaeldetections_energysum_v2_test3.pgdx"); + struct('path', "processing/ishmael/ishmaeldetections_matchedfilter_v2_test1.pgdx"); + struct('path', "processing/ishmael/ishmaeldetections_matchedfilter_v2_test2.pgdx"); + struct('path', "processing/ishmael/ishmaeldetections_spectrogramcorrelation_v2_test1.pgdx"); + struct('path', "processing/ishmael/ishmaeldetections_spectrogramcorrelation_v2_test2.pgdx"); + struct('path', "processing/longtermspectralaverage/longtermspectralaverage_v2_test1.pgdx"); + struct('path', "processing/noiseband/noiseband_v3_test1.pgdx"); + struct('path', "processing/noiseband/noisebandnoise_v3_test1.pgdx"); + struct('path', "processing/noiseband/noisebandpulses_v3_test1.pgdx"); + struct('path', "processing/noisemonitor/noisemonitor_v2_test1.pgdx"); + struct('path', "detectors/click/click_v4_test1.pgnf"); + struct('path', "detectors/click/click_v4_test2.pgnf"); + struct('path', "detectors/click/click_v4_test3.pgnf"); + struct('path', "detectors/gpl/gpl_v2_test1.pgnf"); + struct('path', "detectors/gpl/gpl_v2_test2.pgnf"); + struct('path', "detectors/whistleandmoan/whistleandmoan_v2_test1.pgnf"); + struct('path', "plugins/geminithreshold/geminithreshold_test1.pgnf")' + }; + end + methods + function obj = LegacyTests() + obj.testsDir = pwd; % assumes running tests from within testsDir + obj.rootDir = fileparts(obj.testsDir); % one level up (into root) + obj.resourcesDir = fullfile(obj.rootDir, obj.resourcesFolder); + obj.dataDir = fullfile(obj.resourcesDir, obj.dataFolder); + obj.legacyDir = fullfile(obj.resourcesDir, obj.legacyFolder); + obj.codeDir = fullfile(obj.rootDir, obj.codeFolder); + + disp("RUNNING TESTS WITH THE FOLLOWING CONFIGURATION") + disp("Test Directory: " + obj.testsDir); + disp("Root Directory: " + obj.rootDir); + disp("Data Directory: " + obj.dataDir); + disp("Legacy Directory: " + obj.legacyDir); + disp("Code Directory: " + obj.codeDir); + end + function [data, fileInfo, time] = runCur(obj, filename, vin) + % rmpath(obj.legacyDir); + addpath(genpath(obj.codeDir)); + tic; + [data, fileInfo] = pgmatlab.loadPamguardBinaryFile(filename, vin{:}); + time = toc; + end + function [data, fileInfo, time] = runOld(obj, filename, vin) + % rmpath(obj.codeDir); + addpath(obj.legacyDir); + tic + [data, fileInfo] = loadPamguardBinaryFile(filename, vin{:}); + time = toc; + end + end + + + methods(Test) + function testFile(testCase, filePath, filters) + fp = filePath.path; + + iArg = 1; + vin = {}; + + fields = fieldnames(filters); + vin_str = ""; + + for i = 1:length(fields) + fieldName = fields{i}; + if ~strcmp(fieldName, 'path') % exclude the 'path' field + vin{iArg} = fieldName; + vin{iArg+1} = filters.(fieldName); + iArg = iArg + 2; + if strcmp(fieldName, "filter") + vin_str = vin_str + " " + fieldName + " customFunc"; + else + vin_str = vin_str + " " + fieldName + " " + num2str(filters.(fieldName)); + end + end + end + + relFilePath = fullfile(testCase.dataDir, fp); + fprintf('Testing %s\n', relFilePath); + disp(vin_str); + + [newData, newFileInfo, newTime] = testCase.runCur(relFilePath, vin); + + [oldData, oldFileInfo, oldTime] = testCase.runOld(relFilePath, vin); + + testCase.verifyEqual(newData, oldData); + fields_to_remove = {'readModuleHeader', 'readModuleFooter', 'readBackgroundData', 'readModuleData'}; + for i = 1:length(fields_to_remove) + if isfield(oldFileInfo, fields_to_remove{i}) + oldFileInfo = rmfield(oldFileInfo, fields_to_remove{i}); + end + end + testCase.verifyEqual(newFileInfo, oldFileInfo); + + % Get file size + fileSize = dir(relFilePath); + fileSize = fileSize.bytes; + + % % Write results to CSV file + fid = fopen('results.csv', 'a'); + if ftell(fid) == 0 % check if file is empty + fprintf(fid, 'File Path,Filters,File Size (bytes),New Time (s),Old Time (s)\n'); + end + fprintf(fid, '%s,%s,%d,%f,%f\n', relFilePath, vin_str, fileSize, newTime, oldTime); + fclose(fid); + end + end +end \ No newline at end of file diff --git a/tests/README.md b/tests/README.md new file mode 100644 index 0000000..50df57f --- /dev/null +++ b/tests/README.md @@ -0,0 +1,13 @@ +The legacy tests compare the outputs of up-to-date pgmatlab code with +the stable outputs from v1 (as at 25/08/2025). It is limited to testing +only modules that were available in v1. To test new modules that are +created at a later date, please write new unit tests. + +Run the code by executing `runtests` from the tests/ directory of the repository. An example of this in action, starting in the root of the repository is shown below. + +```matlab +cd tests; +runtests +``` + +Check out the main README file for more information about pgmatlab. \ No newline at end of file diff --git a/toolbox.ignore b/toolbox.ignore new file mode 100644 index 0000000..66eb30e --- /dev/null +++ b/toolbox.ignore @@ -0,0 +1,40 @@ +% List the files in your toolbox folder to exclude from packaging. Specify the +% file path as a path relative to the toolbox folder. +% List only one exclude per line. +% +% For example: +% +% Exclude a specific file in the toolbox folder: +% file1.svn +% +% Exclude a specific file in a subfolder of the toolbox folder: +% example/file1.svn +% +% Exclude all files in a subfolder of the toolbox folder: +% example/* +% +% Exclude all files with a certain name in all subfolders of the toolbox folder: +% **/file1.svn +% +%Exclude all files matching a pattern in all subfolders of the toolbox folder: +% **/*.bak +% +% Exclude all top level files and folders beginning with the character "%": +% \%example/%file.svn +% +**/resources/project/**/* +resources +**/*.prj +**/*.prj.bak +**/.git/**/* +**/.svn/**/* +**/.buildtool/**/* +**/*.asv +testing-resources +tests +.git +.github +.gitattributes +.gitignore +src/+pgmatlab/+db +dist \ No newline at end of file