Importing files from local storage in PSLab Android application

This blog demonstrates how a user can import log files from local storage to the PSLab Android application for various instruments and play them. This functionality is really useful as users can share their log files and import them in their app. This blog mostly consists of my work in the PSLab Android repository.

How to access local storage files?

We here use the concept of implicit intent to access the local storage of the device and then generate the file from the received data URI.

Implicit intents differ from explicit intents in a way that, they don’t give exact class or activity to be initialized through the intent, instead they provide the action to be performed and the class or activities are selected implicitly from the required action

The code block is shown below. 

private void selectFile() {
        Intent intent = new Intent(Intent.ACTION_GET_CONTENT);
        intent.setType("*/*");
        startActivityForResult(intent, 100);
}

Here the Intent.ACTION_GET_CONTENT defines implicit intent. This intent opens the activity related to the action of GETTING CONTENT. The type of content is specified in the Intent.setType(<TYPE>). Since here the type is set to “*/*”, it will open all types of files. If we want only images we can set Type to “images”.

startActivityForResult(intent, <REQUEST_CODE>) starts the file selection activity. 

How to generate a file from received URI?

Once the user selects a file from the file selection activity we can generate the selected file from the data passed in the callback function of startActivityForResult(). The data intent passed as a parameter to onActivityResult() callback contains data for the selected file. We can retrieve path, name, etc details of the selected file from this data intent. The code block for the same is given below.

@Override
    protected void onActivityResult(int requestCode, int resultCode, @Nullable Intent data) {
        if (requestCode == 100) {
            if (resultCode == RESULT_OK) {
                Uri uri = data.getData();
                String path = uri.getPath();
                path = path.replace("/root_path/", "/");
                File file = new File(path);
                getFileData(file);
            }
            else Toast.makeText(this, this.getResources().getString(R.string.no_file_selected), Toast.LENGTH_SHORT).show();
        }
    }

Here we check for the requestCode, which we passed when calling the startActivityForResult() function. We further check if the result is valid and then generate the file from the file path we received in the data Intent. Once we get the path we can get the selected file using the following lines of code:

String path = uri.getPath();
path = path.replace("/root_path/", "/");
File file = new File(path);

How to get Data from the file?

Once the file is generated, it is passed to a function getFileData(File file) to get data in the file to add to the logs of the selected device.  The main part of the getFileData function is given below.

FileInputStream is = new FileInputStream(file);
BufferedReader reader = new BufferedReader(new InputStreamReader(is));
String line = reader.readLine();
int i = 0;
long block = 0, time = 0;
while (line != null) {
   if (i != 0) {
        String[] data = line.split(",");
        try {
              time += 1000;
              BaroData baroData = new BaroData(time, block, Float.valueOf(data[2]),                              Double.valueOf(data[3]), Double.valueOf(data[4]));
              realm.beginTransaction();
              realm.copyToRealm(baroData);
              realm.commitTransaction();
            } catch (Exception e) {
       Toast.makeText(this, getResources().getString(R.string.incorrect_import_format), Toast.LENGTH_SHORT).show();
           }
    }
    i++;
    line = reader.readLine();

Here we read the file line by line and convert the CSV data into the object of the selected device. And then this data is added to app storage using the realm. As shown in the code block above, we are parsing the data to the BarometerData class instances. We split each line by “,” and then use each field as input to the constructor of the BarometerData class. Once we create the instances of the class, we add them to the realm, so the imported file is saved in the realm and now we can access it easily from DataLoggerActivity.

The following images demonstrate the functionality of Import log 

Step 1: Select Import Log menu from 


(Figure 1: Import Log menu)

Step 2: Select the file to be imported from the local storage 


(Figure 2: Files to import from Local storage)

Step 3: Play the imported log from the DataLoggerActivity


(Figure 3: Imported logged data in DataLoggerActivity)

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Tags: PSLab, Android, GSoC 19, ImportLog, Intents, Implicit Intent

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Examples of how AsyncTask is used in PSLab Android App

In this blog, we will look at a very useful and important feature provided by Android – AsyncTask and more importantly how AsyncTasks have been put to use for various functionalities throughout the PSLab Android Project

What are Threads?

Threads are basically paths of sequential execution within a process. In a way, threads are lightweight processes. A process may contain more than one threads and all these threads are executed in parallel. Such a method is called “Multithreading”. Multithreading is very useful when some long tasks need to be executed in the background while other tasks continue to execute in the foreground.

Android has the main UI thread which works continuously and interacts with a user to display text, images, listen for click and touch, receive keyboard inputs and many more. This thread needs to run without any interruption to have a seamless user experience.

When AsyncTask comes into the picture?

AsyncTask enables proper and easy use of the UI thread. This class allows you to perform background operations and publish results on the UI thread without having to manipulate threads and/or handlers.  

In PSLab Android application, we communicate with PSLab hardware through I/O(USB) interface. We connect the PSLab board with the mobile and request and wait for data such as voltage values and signal samples and once the data is received we display it as per requirements. Now clearly we can’t run this whole process on the main thread because it might take a long time to finish and because of that other UI tasks would be delayed which eventually degrade the user experience. So, to overcome this situation, we use AsyncTasks to handle communication with PSLab hardware.

Methods of AsyncTask  

AsyncTask is an Abstract class and must be subclassed to use. Following are the methods of the AsyncTask:

  • onPreExecute()
    • Used to set up the class before the actual execution
  • doInBackground(Params…)
    • This method must be overridden to use AsyncTask. This method contains the main part of the task to be executed. Like the network call etc.
    • The result from this method  is passed as a parameter to onPostExecute() method
  • onProgressUpdate(Progress…)
    • This method is used to display the progress of the AsyncTask
  • onPostExecute(Result)
    • Called when the task is finished and receives the results from the doInBackground() method

There are 3 generic types passed to the definition of the AsyncTask while inheriting. The three types in order are 

  1. Params: Used to pass some parameters to doInBackground(Params…) method of the Task 
  2. Progress: Defines the units in which the progress needs to be displayed/
  3. Result : Defines the data type to be returned from onInBackground() and receive as a parameter in the onPostExecute(Result) method

Example of the usage of the AsyncClass is as under : 

private class SampleTask extends AsyncTask<Params, Progress, Result> {
     @Override
     protected Result doInBackground(Params... params) {
          // The main code goes here
          return result;
     }
     @Override 
     protected void onProgressUpdate(Progress... progress) {
          // display the progress
     }
     @Override 
     protected void onPostExecute(Result result) {
         // display the result
     }
}

We can create an instance of this class as under and execute it.

SampleTask sampleTask = new SampleTask();
sampleTask.execute(params)

We can cancel a running class by calling the task.cancel() function

sampleTask.cancel()

AsyncTask in PSLab Android Application

As mentioned earlier some task which takes a lot of time, can’t be executed on the main thread. Hence in such cases AsyncTask is used. We will look into some examples where AsyncTask has been put to use in PSLab Android Application

Delete All Logs: 

In the DataLoggerActivity, user has an option to delete all the logs that have been saved on the local storage. Now there might be a lot number of log files that needs to be deleted. Hence it is better to use AsyncTask for these. The code snippet for this is below,

private class DeleteAllTask extends AsyncTask<Void, Void, Void> {
        @Override
        protected Void doInBackground(Void... voids) {
            Realm realm = Realm.getDefaultInstance();
            for (SensorDataBlock data : realm.where(SensorDataBlock.class)
                    .findAll()) {
                File logDirectory = new File(
                        Environment.getExternalStorageDirectory().getAbsolutePath() +
                                File.separator + CSVLogger.CSV_DIRECTORY +
                                File.separator + data.getSensorType() +
                                File.separator + CSVLogger.FILE_NAME_FORMAT.format(data.getBlock()) + ".csv");
                logDirectory.delete();
                realm.beginTransaction();
                realm.where(SensorDataBlock.class)
                        .equalTo("block", data.getBlock())
                        .findFirst().deleteFromRealm();
                realm.commitTransaction();
            }
            realm.close();
            return null;
        }
        @Override
        protected void onPostExecute(Void aVoid) {
            deleteAllProgressBar.setVisibility(View.GONE);
            if (LocalDataLog.with().getAllSensorBlocks().size() <= 0) {
                blankView.setVisibility(View.VISIBLE);
            }
        }
    }

As can be seen we look for all the stored logs, and then delete each file one after another in doInBackground() . Once all the files are deleted, onPostExecute() is called, where we make the progress bar disappear. So, this how AsyncTask is used to implement deleteAllFiles feature.

Capture Task and Fourier Transform Output of Signals in Oscilloscope.

To display the generated signal in the oscilloscope, we call captureTraces() and fetchTraces functions from the ScienceLab class. Now, both these functions communicate with the PSLab Board, request for data, receives the data, manipulates it into desired format and then display the signal on the Oscilloscope screen. Now clearly we can’t afford to run such a process on the main thread. So we use AsyncTask to handle it. 

In the Oscilloscope, there is a feature to see the fourier transform output of the signal generated by the oscilloscope. Now to generate the Fourier Transform Output of the signal, we use Fast Fourier Transform method. The time complexity of  FFT (Fast Fourier Transform) is O(Nlog(N)), where N is the number of samples of the input signal. Now even if FFT is fast, we can risk to run this function on the main Thread. So once again we get help from AsyncTask.
Both of these functionalities are included in same AsyncTask Class called captureTask  A snippet for this task can be seen below,

public class CaptureTask extends AsyncTask<String, Void, Void> {
        private ArrayList<ArrayList<Entry>> entries = new ArrayList<>();
        private ArrayList<ArrayList<Entry>> curveFitEntries = new ArrayList<>();
        private Integer noOfChannels;
        private String[] paramsChannels;
        private String channel;
        @Override
        protected Void doInBackground(String... channels) {
            paramsChannels = channels;
            noOfChannels = channels.length;
            try {
                double[] xData;
                double[] yData;
                ArrayList<String[]> yDataString = new ArrayList<>();
                String[] xDataString = null;
                maxAmp = 0;
                for (int i = 0; i < noOfChannels; i++) {
                    entries.add(new ArrayList<>());
                    channel = channels[i];
                    HashMap<String, double[]> data;
                    if (triggerChannel.equals(channel))
                        scienceLab.configureTrigger(channelIndexMap.get(channel), channel, trigger, null, null);
                    scienceLab.captureTraces(1, samples, timeGap, channel, isTriggerSelected, null);
                    data = scienceLab.fetchTrace(1);

In this part of the capture Task class, we use the captureTrace() and fetchTrace() function to get the signal samples and then store them into the data variable. Below is the part where we use call the fft() for the input signal.

if (isFourierTransformSelected) {
     Complex[] yComplex = new Complex[yData.length];
     for (int j = 0; j < yData.length; j++) {
              yComplex[j] = Complex.valueOf(yData[j]);
     }
     fftOut = fft(yComplex);
}

This is a very simple part where we just call the Fast Fourier Transfer function is the user has selected to see the fourier transform output. The implementation of the Fourier function can be seen below,

 public Complex[] fft(Complex[] input) {
        Complex[] x = input;
        int n = x.length;
        if (n == 1) return new Complex[]{x[0]}; // if only single element, return as it is
        if (n % 2 != 0) {
            x = Arrays.copyOfRange(x, 0, x.length - 1);
        //No of samples should be even for this function to run, so i case of odd samples we remove the last element. This doesn’t affect the output significantly
        }
        Complex[] halfArray = new Complex[n / 2];
        for (int k = 0; k < n / 2; k++) {
            halfArray[k] = x[2 * k]; // Array of input terms at even places
        }
        Complex[] q = fft(halfArray); // recursive call for even terms
        for (int k = 0; k < n / 2; k++) {
            halfArray[k] = x[2 * k + 1]; // Array of terms at odd places
        }
        Complex[] r = fft(halfArray); // recursive call for odd terms
        Complex[] y = new Complex[n]; // Array of final output
        for (int k = 0; k < n / 2; k++) {
            double kth = -2 * k * Math.PI / n;
            Complex wk = new Complex(Math.cos(kth), Math.sin(kth)); // “kernel” for kth term is the output (based on nth root of unity)
            if (r[k] == null) {
                r[k] = new Complex(1); // exception handling
            }
            if (q[k] == null) {
                q[k] = new Complex(1); // exception handling
            }
            y[k] = q[k].add(wk.multiply(r[k])); // kth term will be addition of odd and even terms
            y[k + n / 2] = q[k].subtract(wk.multiply(r[k])); // (k + n/2)th term will be subtraction of odd and even terms
        }
        return y; // rsultant array
    }

This is a classic implementation of Fast Fourier Transform. We divide the samples of input into odd and even placed terms and call the same function recursively until there is only one term left. After that we use nth (n being the number of samples) complex root of  unity, we combine the results of odd termed fft() and even termed fft() to get the final output. Since at each iteration we are breaking the input into half it will run for O(logN) time and to merge the odd and even termed output we run a loop in each iteration on the O(N). So the total complexity would be O(NlogN), and since it might take longer to compute the fourier transform for large input we require it to be inside the AsyncTask and not on the main thread.

There are many other functionalities throughout the app, where AsyncTask has been used. In a nutshell, AsyncTask is a very useful method to handle longer tasks off the main thread. 

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Tags: PSLab, Android, GSoC 19, AsyncTask, Threading

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How to use and implement Save Wave Configs feature in Pocket Science Lab Wave Generator

What is a Wave Generator?

A Wave Generator is one of the most important features of PSLab. It is used to generate different kinds of waves like, sine, triangular, square, PWM. Wave generator UI is as under:

  (Figure 1 : Wave Generator Analog Mode UI)
  (Figure 2 : Wave Generator Digital Mode UI)

As can be seen the Screenshot above user is provided with options to set Frequency, Phase, Duty of different waves and once configurations are set user can either output the waves in Oscilloscope or can compare different waves in Logic Analyzer.

What is Save Wave Configs Feature?


        (Figure 3 : Wave Generator Control Buttons (View,Save,Mode))

In this feature, the user is given a ”Save” button to use this feature. 

The reason to add this feature is that, sometimes we need to perform the same experiment multiple times, is such scenarios if we have to set wave configurations everytime, it will become boring and there will be chances of errors. Hence using the save configs feature, user can currently set configurations in the Local Storage and can use it anytime later. 

Further since the Wave Configurations are saved on Local Storage as .CSV file, a user can save configs and can share the file with others so others can as well set their device to same configurations. The saved Wave Configurations can be seen in the DataLogger Activity and opening a saved log would take the user to Wave Generator Activity where all the configs will be set as per the saved log.

A sample CSV of the log data can be seen below.


(Figure 4: Wave Configs CSV file)

How is Save Configs Feature Implemented

The implementation of this feature is quite simple. There is a class named WaveData.  With the parameters of Mode(Square or PWM), Wave name, Shape, Freq, Phase and Duty. Whenever the user clicks the save configs button, the saveWaveConfigs()  function is called. This function fetches set values of different fields and creates realm objects and also write them to csv file as shown above. Once the realm objects are created, this log can be seen in the Data Logger Activity. The code to generate the realm object for the wave configs (that is the implementation of the function saveWaveConfig()) is given below.

public void saveWaveConfig(View view) {
        long block = System.currentTimeMillis();
        csvLogger.prepareLogFile();
          csvLogger.writeMetaData(getResources().getString(R.string.wave_generator));
        long timestamp;
        double lat, lon;
        String data = "Timestamp,DateTime,Mode,Wave,Shape,Freq,Phase,Duty,lat,lon\n";
        recordSensorDataBlockID(new SensorDataBlock(block, getResources().getString(R.string.wave_generator)));

So till now in the function, we create a header string for the data to be stored in the csv file. We create a block from the current system time. This block will be used to save all the realm object for this function, so all the objects created at this instance will be grouped as a single log entry in DataLoggerActivity.

double freq1 = (double) (WaveGeneratorCommon.wave.get(WaveConst.WAVE1).get(WaveConst.FREQUENCY));
double freq2 = (double) WaveGeneratorCommon.wave.get(WaveConst.WAVE2).get(WaveConst.FREQUENCY);
double phase = (double) WaveGeneratorCommon.wave.get(WaveConst.WAVE2).get(WaveConst.PHASE);

String waveType1 = WaveGeneratorCommon.wave.get(WaveConst.WAVE1).get(WaveConst.WAVETYPE) == SIN ? "sine" : "tria";
String waveType2 = WaveGeneratorCommon.wave.get(WaveConst.WAVE2).get(WaveConst.WAVETYPE) == SIN ? "sine" : "tria";

timestamp = System.currentTimeMillis();
String timeData = timestamp + "," + CSVLogger.FILE_NAME_FORMAT.format(new Date(timestamp));
String locationData = lat + "," + lon;

Next, in the function we get currently set Frequency for both analog waves and phase in the variables. We also store the selected wave shape for each of the waves. Since each entry in the csv file is required to have a timestamp and a location stamp,here we create common stamps of both types and will append it to each entry further in the function. 

if (scienceLab.isConnected()) {
            if (digital_mode == WaveConst.SQUARE) {
                data += timeData + ",Square,Wave1," + waveType1 + "," + String.valueOf(freq1) + ",0,0," + locationData + "\n"; //wave1
                recordSensorData(new WaveGeneratorData(timestamp, block, "Square", "Wave1", waveType1, String.valueOf(freq1), "0", "0", lat, lon));
                data += timeData + ",Square,Wave2," + waveType2 + "," + String.valueOf(freq2) + "," + String.valueOf(phase) + ",0," + locationData + "\n";//wave2
                recordSensorData(new WaveGeneratorData(timestamp + 1, block, "Square", "Wave2", waveType2, String.valueOf(freq2), String.valueOf(phase), "0", lat, lon));

Here we check whether the currently selected mode is Analog(Square) or Digital (PWM). Above code snippet is for the SQUARE mode block. We create WaveGeneratorData object for both SI1 and SI2 waves based on the parameters we stored earlier. We also append the data to a string, data.  Which we will later use to write the log into a csv file.

else {
   double freqSqr1 = (double) WaveGeneratorCommon.wave.get(WaveConst.SQR1).get(WaveConst.FREQUENCY);
   double dutySqr1 = (double) WaveGeneratorCommon.wave.get(WaveConst.SQR1).get(WaveConst.DUTY) / 100;
   double dutySqr2 = ((double) WaveGeneratorCommon.wave.get(WaveConst.SQR2).get(WaveConst.DUTY)) / 100;
   double phaseSqr2 = (double) WaveGeneratorCommon.wave.get(WaveConst.SQR2).get(WaveConst.PHASE) / 360;
   double dutySqr3 = ((double) WaveGeneratorCommon.wave.get(WaveConst.SQR3).get(WaveConst.DUTY)) / 100;
   double phaseSqr3 = (double) WaveGeneratorCommon.wave.get(WaveConst.SQR3).get(WaveConst.PHASE) / 360;
   double dutySqr4 = ((double) WaveGeneratorCommon.wave.get(WaveConst.SQR4).get(WaveConst.DUTY)) / 100;
   double phaseSqr4 = (double) WaveGeneratorCommon.wave.get(WaveConst.SQR4).get(WaveConst.PHASE) / 360;

 data += timeData + ",PWM,Sq1,PWM," + String.valueOf(freqSqr1) + ",0," + String.valueOf(dutySqr1) + "," + locationData + "\n";

 recordSensorData(new WaveGeneratorData(timestamp, block, "PWM", "Sq1", "PWM", String.valueOf(freqSqr1), "0", String.valueOf(dutySqr1), lat, lon));
}

The above code snippet shows a block of the condition when the selected mode is PWM. Here we store the set values of Freq, Phase and Duty for each SQ1, SQ2, SQ3 and SQ4 waves into variables. Once we store the values we create WaveGeneratorData objects for each of the waves and also append the data to the data string to write to the csv. The code above includes details only for SQ1, but exact same procedure is followed for SQ2, SQ3, and SQ4. One we have all the data appended to the string we call the following function to write the data to csv file. 

 csvLogger.writeCSVFile(data);

We can see that this function basically stores the current set values of different params into a WaveData object. For each of the waveforms in selected mode (analog/digital), a new instance of WaveData object is created and stored into realm.

When the user opens one of the logs, setReceivedData() function is called in WaveGeneratorActivity. This function iterates on the received realm objects and based on the attributes of each object the data is set in the UI automatically. The implementation of this function is given below, 

public void setReceivedData() {
        for (WaveGeneratorData data : recordedWaveData) {
            Log.d("data", data.toString());
            if (data.getMode().equals(MODE_SQUARE)) {
                WaveGeneratorCommon.mode_selected = WaveConst.SQUARE;
                switch (data.getWave()) {
                    case "Wave1":
                        if (data.getShape().equals("sine")) {
                            WaveGeneratorCommon.wave.get(WaveConst.WAVE1).put(WaveConst.WAVETYPE, SIN);
                        } else {
                            WaveGeneratorCommon.wave.get(WaveConst.WAVE1).put(WaveConst.WAVETYPE, TRIANGULAR);
                        }
                        WaveGeneratorCommon.wave.get(WaveConst.WAVE1).put(WaveConst.FREQUENCY, Double.valueOf(data.getFreq()).intValue());
                        break;
                }
                enableInitialState();
            } 

This function iterates over the received WaveGeneratorData objects. For each object we check what is the mode of the waveData. The above code snippet is used when the mode is SQUARE. We get the waveType from the object, and since for SQUARE mode there are only 2 types : Wave1 and Wave2, we set the attributes for each wave as we get them from the objects using WaveGeneratorCommon

else if (data.getMode().equals(MODE_PWM)) {
                WaveGeneratorCommon.mode_selected = WaveConst.PWM;
                switch (data.getWave()) {
                    case "Sq1":
                        WaveGeneratorCommon.wave.get(WaveConst.SQR1).put(WaveConst.FREQUENCY, Double.valueOf(data.getFreq()).intValue());
                        WaveGeneratorCommon.wave.get(WaveConst.SQR1).put(WaveConst.DUTY, ((Double) (Double.valueOf(data.getDuty()) * 100)).intValue());
                        break;
                }
                enableInitialStatePWM();
            }
        }

Same as before if the mode of the object is PWM, there will be 4 cases : SQ1, SQ2, SQ3 and SQ4. And depending on the data stored in the received objects.

In a nutshell this features enables to save and reuse wave configuration with ease. 

A small video to explain the whole functionality of this feature can be found here. 

References

Write to a file in Android

Code Repository

PSLab Android

Tags

PSLab, Wave Generator, SaveConfig, Android, GSoC 19

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