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feat(axivity6): support for Axivity 6 (gyroscope data) #42

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merged 5 commits into from
Jul 24, 2024
Merged

feat(axivity6): support for Axivity 6 (gyroscope data) #42

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321fd1a
Extract acc and gyroscope cols from Ax6 cwa file
Jul 16, 2024
5a87606
fix(geneactive): trim whitespace when parsing header
chanshing Jul 10, 2024
20900d0
refactor(calibrate_gravity): skip if error already below threshold
chanshing Jul 10, 2024
59b7800
refactor(calibrate_gravity): improve error threshold check: >= instea…
chanshing Jul 10, 2024
8901863
refactor(reader): handle empty files gracefully
chanshing Jul 10, 2024
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178 changes: 147 additions & 31 deletions src/actipy/AxivityReader.java
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Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,8 @@ public class AxivityReader {
private static final int BLOCKSIZE = 512;

// Specification of items to be written
private static final Map<String, String> ITEM_NAMES_AND_TYPES;
private static final Map<String, String> ITEM_NAMES_AND_TYPES_AX3;
private static final Map<String, String> ITEM_NAMES_AND_TYPES_AX6;
static{
Map<String, String> itemNamesAndTypes = new LinkedHashMap<String, String>();
itemNamesAndTypes.put("time", "Datetime");
Expand All @@ -32,7 +33,20 @@ public class AxivityReader {
itemNamesAndTypes.put("z", "Float");
itemNamesAndTypes.put("temperature", "Float");
itemNamesAndTypes.put("light", "Float");
ITEM_NAMES_AND_TYPES = Collections.unmodifiableMap(itemNamesAndTypes);
ITEM_NAMES_AND_TYPES_AX3 = Collections.unmodifiableMap(itemNamesAndTypes);
}
static{
Map<String, String> itemNamesAndTypes = new LinkedHashMap<String, String>();
itemNamesAndTypes.put("time", "Datetime");
itemNamesAndTypes.put("x", "Float");
itemNamesAndTypes.put("y", "Float");
itemNamesAndTypes.put("z", "Float");
itemNamesAndTypes.put("gyro_x", "Float");
itemNamesAndTypes.put("gyro_y", "Float");
itemNamesAndTypes.put("gyro_z", "Float");
itemNamesAndTypes.put("temperature", "Float");
itemNamesAndTypes.put("light", "Float");
ITEM_NAMES_AND_TYPES_AX6 = Collections.unmodifiableMap(itemNamesAndTypes);
}

public static void main(String[] args) {
Expand Down Expand Up @@ -63,8 +77,11 @@ public static void main(String[] args) {
System.exit(1);
}

boolean hasGyro = detectGyro(accFile);
Map<String, String> item_names_and_types = hasGyro ? ITEM_NAMES_AND_TYPES_AX6 : ITEM_NAMES_AND_TYPES_AX3;

String outData = outDir + File.separator + "data.npy";
NpyWriter writer = new NpyWriter(outData, ITEM_NAMES_AND_TYPES);
NpyWriter writer = new NpyWriter(outData, item_names_and_types);

BlockParser blockParser = new BlockParser(writer);

Expand Down Expand Up @@ -128,6 +145,33 @@ public static void main(String[] args) {
}


// Check if the accFile has a gyroscope columns
private static boolean detectGyro(String accFile) {
boolean hasGyro = false;
try (FileInputStream accStream = new FileInputStream(accFile);
FileChannel accChannel = accStream.getChannel()) {

ByteBuffer block = ByteBuffer.allocate(BLOCKSIZE);
while (accChannel.read(block) != -1) {
block.flip();
block.order(ByteOrder.LITTLE_ENDIAN);
String header = "" + (char) block.get() + (char) block.get();
if (header.equals("AX")) {
int numAxesBPS = block.get(25) & 0xff;
hasGyro = ((numAxesBPS >> 4) & 0x0f) >= 6;
break;
}
block.clear();
}
} catch (IOException e) {
System.err.println("ERROR: Failed to read the file header.");
e.printStackTrace();
System.exit(1);
}
return hasGyro;
}


private static class BlockParser {

float sampleRate = -1;
Expand Down Expand Up @@ -177,6 +221,18 @@ public void parse(ByteBuffer block) {
float offsetStart = 0;
float freq = 0;
short checkSum = 0;
int numAxes = 0;
int accelAxis = -1;
int gyroAxis = -1;
int accelUnit = 256; // default 1g = 256
int gyroRange = 2000; // default 32768 = 2000dps
int rawLight = getUnsignedShort(block, 18);

accelUnit = 1 << (8 + ((rawLight >>> 13) & 0x07));
if (((rawLight >> 10) & 0x07) != 0) {
gyroRange = 8000 / (1 << ((rawLight >>> 10) & 0x07));
}
float gyroUnit = (gyroRange != 0) ? (32768.0f / gyroRange) : 0;

// Figure out sample rate (freq)
if (rateCode == 0) {
Expand Down Expand Up @@ -211,14 +267,31 @@ public void parse(ByteBuffer block) {
lastBlockTime = blockEndTime;

// calculate num bytes per sample...
byte bytesPerSample = 4;
int bytesPerSample = 0;
numAxes = (numAxesBPS >> 4) & 0x0f;

if ((numAxesBPS & 0x0f) == 2) {
bytesPerSample = 2 * numAxes; // 3*16-bit
} else if ((numAxesBPS & 0x0f) == 0) {
bytesPerSample = 4; // 3*10-bit + 2
}
short expectedCount = (short)((bytesPerSample != 0) ? 480 / bytesPerSample : 0);

int NUM_AXES_PER_SAMPLE = 3;
if ((numAxesBPS & 0x0f) == 2) {
bytesPerSample = 6; // 3*16-bit
} else if ((numAxesBPS & 0x0f) == 0) {
bytesPerSample = 4; // 3*10-bit + 2
}

numAxes = (numAxesBPS >> 4) & 0x0f;
if (numAxes >= 6) {
gyroAxis = 0;
accelAxis = 3;
} else if (numAxes >= 3) {
accelAxis = 0;
}

// Limit values
int maxSamples = 480 / bytesPerSample; //80 or 120 samples/block
if (sampleCount > maxSamples) { sampleCount = maxSamples; }
Expand All @@ -228,37 +301,46 @@ public void parse(ByteBuffer block) {

// raw reading values
double t = 0;
long value = 0; // x/y/z vals
float x = 0.0f;
float y = 0.0f;
float z = 0.0f;
short[] sampleValues = new short[sampleCount * numAxes];

for (int i = 0; i < sampleCount; i++) {

if (bytesPerSample == 4) {
value = getUnsignedInt(block, 30 + 4 * i);
// Sign-extend 10-bit values, adjust for exponents
x = (float) ((short) (0xffffffc0 & (value << 6)) >> (6 - ((value >> 30) & 0x03)));
y = (float) ((short) (0xffffffc0 & (value >> 4)) >> (6 - ((value >> 30) & 0x03)));
z = (float) ((short) (0xffffffc0 & (value >> 14)) >> (6 - ((value >> 30) & 0x03)));
} else if (bytesPerSample == 6) {
x = (float) block.getShort(30 + 2 * NUM_AXES_PER_SAMPLE * i + 0);
y = (float) block.getShort(30 + 2 * NUM_AXES_PER_SAMPLE * i + 2);
z = (float) block.getShort(30 + 2 * NUM_AXES_PER_SAMPLE * i + 4);
} else {
x = 0;
y = 0;
z = 0;
if (bytesPerSample == 4) {
long value = getUnsignedInt(block, 30 + 4 * i);
sampleValues[i * numAxes + 0] = (short)((short)(0xffffffc0 & (value << 6)) >> (6 - ((value >> 30) & 0x03))); // Sign-extend 10-bit value, adjust for exponent
sampleValues[i * numAxes + 1] = (short)((short)(0xffffffc0 & (value >> 4)) >> (6 - ((value >> 30) & 0x03))); // Sign-extend 10-bit value, adjust for exponent
sampleValues[i * numAxes + 2] = (short)((short)(0xffffffc0 & (value >> 14)) >> (6 - ((value >> 30) & 0x03))); // Sign-extend 10-bit value, adjust for exponent
} else if (bytesPerSample >= 0) {
for (int j = 0; j < numAxes; j++) {
sampleValues[i * numAxes + j] = block.getShort(30 + (2 * numAxes * i) + (2 * j));
}
} else {
for (int j = 0; j < numAxes; j++) {
sampleValues[i * numAxes + j] = 0;
}
}

x /= 256; // to gravity
y /= 256;
z /= 256;

t = blockStartTime + (double)i * (blockEndTime - blockStartTime) / sampleCount;
t *= 1000; // secs to millis

writer.write(toItems(TimeUnit.MILLISECONDS.toNanos((long) t), x, y, z, temperature, light));
float ax = 0, ay = 0, az = 0;
if (accelAxis >= 0) {
ax = (float)sampleValues[numAxes * i + accelAxis + 0] / accelUnit;
ay = (float)sampleValues[numAxes * i + accelAxis + 1] / accelUnit;
az = (float)sampleValues[numAxes * i + accelAxis + 2] / accelUnit;
}

float gx = 0, gy = 0, gz = 0;
if (gyroAxis >= 0) {
gx = (float)sampleValues[numAxes * i + gyroAxis + 0] / gyroUnit;
gy = (float)sampleValues[numAxes * i + gyroAxis + 1] / gyroUnit;
gz = (float)sampleValues[numAxes * i + gyroAxis + 2] / gyroUnit;
}

if (gyroAxis >= 0) {
writer.write(toItems(TimeUnit.MILLISECONDS.toNanos((long) t), ax, ay, az, gx, gy, gz, temperature, light));
} else {
writer.write(toItems(TimeUnit.MILLISECONDS.toNanos((long) t), ax, ay, az, temperature, light));
}

}

Expand Down Expand Up @@ -313,7 +395,9 @@ private static int getUnsignedShort(ByteBuffer bb, int position) {
}


private static Map<String, Object> toItems(long t, float x, float y, float z, float temperature, float light) {
private static Map<String, Object> toItems(
long t, float x, float y, float z,
float temperature, float light) {
Map<String, Object> items = new HashMap<String, Object>();
items.put("time", t);
items.put("x", x);
Expand All @@ -325,9 +409,41 @@ private static Map<String, Object> toItems(long t, float x, float y, float z, fl
}


private static Map<String, Object> toItems(long t, double x, double y, double z, double temperature, float light) {
return toItems(t, (float) x, (float) y, (float) z, (float) temperature, (float) light);
private static Map<String, Object> toItems(
long t, float x, float y, float z,
float gyro_x, float gyro_y, float gyro_z,
float temperature, float light) {
Map<String, Object> items = new HashMap<String, Object>();
items.put("time", t);
items.put("x", x);
items.put("y", y);
items.put("z", z);
items.put("gyro_x", gyro_x);
items.put("gyro_y", gyro_y);
items.put("gyro_z", gyro_z);
items.put("temperature", temperature);
items.put("light", light);
return items;
}


private static Map<String, Object> toItems(
long t, double x, double y, double z,
double temperature, float light) {
return toItems(
t, (float) x, (float) y, (float) z,
(float) temperature, (float) light);
}


private static Map<String, Object> toItems(
long t, double x, double y, double z,
double gyro_x, double gyro_y, double gyro_z,
double temperature, float light) {
return toItems(
t, (float) x, (float) y, (float) z,
(float) gyro_x, (float) gyro_y, (float) gyro_z,
(float) temperature, (float) light);
}

}
18 changes: 9 additions & 9 deletions src/actipy/GENEActivReader.java
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Original file line number Diff line number Diff line change
Expand Up @@ -218,17 +218,17 @@ private static int parseBinFileHeader(
}
// read axes calibration lines for gain and offset values
// data like -> x gain:25548 \n x offset:574 ... Volts:300 \n Lux:800
gainVals[0] = Double.parseDouble(readLine(reader).split(":")[1]); // xGain
offsetVals[0] = Integer.parseInt(readLine(reader).split(":")[1]); // xOffset
gainVals[1] = Double.parseDouble(readLine(reader).split(":")[1]); // y
offsetVals[1] = Integer.parseInt(readLine(reader).split(":")[1]); // y
gainVals[2] = Double.parseDouble(readLine(reader).split(":")[1]); // z
offsetVals[2] = Integer.parseInt(readLine(reader).split(":")[1]); // z
int volts = Integer.parseInt(readLine(reader).split(":")[1]); // volts
int lux = Integer.parseInt(readLine(reader).split(":")[1]); // lux
gainVals[0] = Double.parseDouble(readLine(reader).split(":")[1].trim()); // xGain
offsetVals[0] = Integer.parseInt(readLine(reader).split(":")[1].trim()); // xOffset
gainVals[1] = Double.parseDouble(readLine(reader).split(":")[1].trim()); // y
offsetVals[1] = Integer.parseInt(readLine(reader).split(":")[1].trim()); // y
gainVals[2] = Double.parseDouble(readLine(reader).split(":")[1].trim()); // z
offsetVals[2] = Integer.parseInt(readLine(reader).split(":")[1].trim()); // z
int volts = Integer.parseInt(readLine(reader).split(":")[1].trim()); // volts
int lux = Integer.parseInt(readLine(reader).split(":")[1].trim()); // lux
readLine(reader); // 9 blank
readLine(reader); // 10 memory status header
int numBlocksTotal = Integer.parseInt(readLine(reader).split(":")[1]); // 11
int numBlocksTotal = Integer.parseInt(readLine(reader).split(":")[1].trim()); // 11

// ignore remaining header lines in bin file
for (int i = 0; i < fileHeaderSize - linesToAxesCalibration - 11; i++) {
Expand Down
12 changes: 9 additions & 3 deletions src/actipy/processing.py
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Original file line number Diff line number Diff line change
Expand Up @@ -315,13 +315,19 @@ def calibrate_gravity(data, calib_cube=0.3, calib_min_samples=50, window='10s',

# Check that we have sufficiently uniformly distributed points:
# need at least one point outside each face of the cube
if (np.max(xyz, axis=0) < calib_cube).any() \
or (np.min(xyz, axis=0) > -calib_cube).any():
if (np.max(xyz, axis=0) < calib_cube).any() or (np.min(xyz, axis=0) > -calib_cube).any():
info['CalibOK'] = 0
info['CalibErrorAfter(mg)'] = init_err * 1000

return data, info

# If initial error is already below threshold, skip and return
if init_err < ERR_TOL:
info['CalibOK'] = 1
info['CalibErrorAfter(mg)'] = init_err * 1000

return data, info

for it in range(MAXITER):

# Weighting. Outliers are zeroed out
Expand Down Expand Up @@ -369,7 +375,7 @@ def calibrate_gravity(data, calib_cube=0.3, calib_min_samples=50, window='10s',

info['CalibErrorAfter(mg)'] = best_err * 1000

if (best_err > ERR_TOL) or (it + 1 == MAXITER):
if (best_err >= ERR_TOL) or (it + 1 >= MAXITER):
info['CalibOK'] = 0

return data, info
Expand Down
14 changes: 14 additions & 0 deletions src/actipy/reader.py
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Original file line number Diff line number Diff line change
Expand Up @@ -61,6 +61,10 @@ def read_device(input_file,

sample_rate = info['SampleRate']

if len(data) == 0:
print("File is empty. No data to process.")
return data, info

if lowpass_hz not in (None, False):
timer.start("Lowpass filter...")
data, info_lowpass = P.lowpass(data, sample_rate, lowpass_hz)
Expand Down Expand Up @@ -198,6 +202,16 @@ def _read_device(input_file, verbose=True):
data = {c: np.asarray(data_mmap[c]) for c in data_mmap.dtype.names}
data = pd.DataFrame(data, copy=False)

if len(data) == 0:
info['NumTicks'] = 0
info['StartTime'] = None
info['EndTime'] = None
info['WearTime(days)'] = 0
info['NumInterrupts'] = 0
data.set_index('time', inplace=True)
timer.stop()
return data, info

# Check for non-increasing timestamps. This is rare but can happen with
# buggy devices. TODO: Parser should do this.
errs = (data['time'].diff() <= pd.Timedelta(0)).sum()
Expand Down
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