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Waveform.c
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Waveform.c
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#include "Waveform.h"
#include <math.h>
#include <stdlib.h>
// TODO We should probably scale the retrace length according to
// zoomFactor * width_or_height
static const uint32_t X_RETRACE_LEN = 128;
// Generate 1D (undershoot + trace + retrace).
// The trace part spans voltage scanStart to scanEnd.
void GenerateXGalvoWaveform(int32_t effectiveScanLen, int32_t retraceLen,
int32_t undershootLen, double scanStart,
double scanEnd, double *waveform) {
double scanAmplitude = scanEnd - scanStart;
double step = scanAmplitude / effectiveScanLen;
int32_t linearLen = undershootLen + effectiveScanLen;
// Generate the linear scan curve
double undershootStart = scanStart - undershootLen * step;
for (int i = 0; i < linearLen; ++i) {
waveform[i] = undershootStart + step * i;
}
// Generate the rescan curve
// Slope at start end end are both equal to the linear scan
if (retraceLen > 0) {
SplineInterpolate(retraceLen, scanEnd, undershootStart, step, step,
waveform + linearLen);
}
}
// Generate Y waveform for one frame
void GenerateYGalvoWaveform(int32_t linesPerFrame, int32_t retraceLen,
size_t xLength, double scanStart, double scanEnd,
double *waveform) {
double scanAmplitude = scanEnd - scanStart;
double step = scanAmplitude / linesPerFrame;
// Generate staircase for one frame
for (int j = 0; j < linesPerFrame; ++j) {
for (unsigned i = 0; i < xLength; ++i) {
waveform[i + j * xLength] = scanStart + step * j;
// stop at last x retrace
if ((j >= linesPerFrame - 1) && (i >= xLength - X_RETRACE_LEN)) {
break;
}
}
}
// Generate the rescan curve at end of frame
if (X_RETRACE_LEN > 0) {
SplineInterpolate(X_RETRACE_LEN, scanEnd, scanStart, 0, 0,
waveform + (linesPerFrame * xLength) -
X_RETRACE_LEN);
}
}
// n = number of elements
// slope in units of per element
void SplineInterpolate(int32_t n, double yFirst, double yLast,
double slopeFirst, double slopeLast, double *result) {
double m = n;
double mm = m * m;
double mmm = m * m * m;
double c[4];
c[0] = slopeFirst / mm + 2.0 * yFirst / mmm + slopeLast / mm -
2.0 * yLast / mmm;
c[1] = 3.0 * yLast / mm - slopeLast / m - 2.0 * slopeFirst / m -
3.0 * yFirst / mm;
c[2] = slopeFirst;
c[3] = yFirst;
for (int32_t x = 0; x < n; x++) {
result[x] = c[0] * x * x * x + c[1] * x * x + c[2] * x + c[3];
}
}
/* Line clock pattern for NI DAQ to output from one of its digital IOs */
OScDev_RichError *GenerateLineClock(const struct WaveformParams *parameters,
uint8_t *lineClock) {
uint32_t lineDelay = parameters->undershoot;
uint32_t width = parameters->width;
uint32_t height = parameters->height;
uint32_t x_length = lineDelay + width + X_RETRACE_LEN;
for (uint32_t j = 0; j < height; j++)
for (uint32_t i = 0; i < x_length; i++)
lineClock[i + j * x_length] =
((i >= lineDelay) && (i < lineDelay + width)) ? 1 : 0;
return OScDev_RichError_OK;
}
// High voltage right after a line acquisition is done
// like a line clock of reversed polarity
// specially for B&H FLIM application
OScDev_RichError *
GenerateFLIMLineClock(const struct WaveformParams *parameters,
uint8_t *lineClockFLIM) {
uint32_t lineDelay = parameters->undershoot;
uint32_t width = parameters->width;
uint32_t height = parameters->height;
uint32_t x_length = lineDelay + width + X_RETRACE_LEN;
for (uint32_t j = 0; j < height; j++)
for (uint32_t i = 0; i < x_length; i++)
lineClockFLIM[i + j * x_length] = (i >= lineDelay + width) ? 1 : 0;
return OScDev_RichError_OK;
}
// Frame clock for B&H FLIM
// High voltage at the end of the frame
OScDev_RichError *
GenerateFLIMFrameClock(const struct WaveformParams *parameters,
uint8_t *frameClockFLIM) {
uint32_t lineDelay = parameters->undershoot;
uint32_t width = parameters->width;
uint32_t height = parameters->height;
uint32_t x_length = lineDelay + width + X_RETRACE_LEN;
for (uint32_t j = 0; j < height; ++j)
for (uint32_t i = 0; i < x_length; ++i)
frameClockFLIM[i + j * x_length] =
((j == height - 1) && (i > lineDelay + width)) ? 1 : 0;
return OScDev_RichError_OK;
}
int32_t GetLineWaveformSize(const struct WaveformParams *parameters) {
return parameters->undershoot + parameters->width + X_RETRACE_LEN;
}
int32_t GetClockWaveformSize(const struct WaveformParams *parameters) {
uint32_t elementsPerLine = GetLineWaveformSize(parameters);
uint32_t height = parameters->height;
return elementsPerLine * height;
}
int32_t GetScannerWaveformSize(const struct WaveformParams *parameters) {
uint32_t elementsPerLine = GetLineWaveformSize(parameters);
uint32_t height = parameters->height;
uint32_t yLen = height;
return elementsPerLine * yLen; // including y retrace portion
}
int32_t
GetScannerWaveformSizeAfterLastPixel(const struct WaveformParams *parameters) {
return X_RETRACE_LEN;
}
int32_t GetParkWaveformSize(const struct WaveformParams *parameters) {
uint32_t elementsPerLine = X_RETRACE_LEN;
return elementsPerLine;
}
/*
Generate X and Y waveforms in analog format (voltage) for a whole frame scan
Format: X|Y in a 1D array for NI DAQ to simultaneously output in two channels
Analog voltage range (-0.5V, 0.5V) at zoom 1
Including Y retrace waveform that moves the slow galvo back to its starting
position
*/
OScDev_RichError *
GenerateGalvoWaveformFrame(const struct WaveformParams *parameters,
double *xyWaveformFrame) {
uint32_t pixelsPerLine = parameters->width; // ROI size
uint32_t linesPerFrame = parameters->height;
uint32_t resolution = parameters->resolution;
double zoom = parameters->zoom;
uint32_t undershoot = parameters->undershoot;
uint32_t xOffset = parameters->xOffset; // ROI offset
uint32_t yOffset = parameters->yOffset;
double galvoOffsetX = parameters->galvoOffsetX; // Adjustment Offset
double galvoOffsetY = parameters->galvoOffsetY;
// Voltage ranges of the ROI
double xStart = (-0.5 * resolution + xOffset) / (zoom * resolution);
double yStart = (-0.5 * resolution + yOffset) / (zoom * resolution);
double xEnd = xStart + pixelsPerLine / (zoom * resolution);
double yEnd = yStart + linesPerFrame / (zoom * resolution);
size_t xLength = undershoot + pixelsPerLine + X_RETRACE_LEN;
size_t yLength = linesPerFrame;
double *xWaveform = (double *)malloc(sizeof(double) * xLength);
double *yWaveform =
(double *)malloc(sizeof(double) * (yLength * xLength)); // change size
GenerateXGalvoWaveform(pixelsPerLine, X_RETRACE_LEN, undershoot, xStart,
xEnd, xWaveform);
GenerateYGalvoWaveform(linesPerFrame, X_RETRACE_LEN, xLength, yStart, yEnd,
yWaveform);
// convert to optical degree assuming 10V equal to 30 optical degree
// TODO We shouldn't make such an assumption! Also I think the variable
// names are the other way around ("inDegree" means "in volts" here).
double offsetXinDegree = galvoOffsetX / 3.0;
double offsetYinDegree = galvoOffsetY / 3.0;
// effective scan waveform for a whole frame
for (unsigned j = 0; j < yLength; ++j) {
for (unsigned i = 0; i < xLength; ++i) {
// first half is X waveform,
// x line scan repeated yLength times (sawteeth)
// galvo x stays at starting position after one frame is scanned
xyWaveformFrame[i + j * xLength] = xWaveform[i] + offsetXinDegree;
// xyWaveformFrame[i + j*xLength] = xWaveform[i];
// second half is Y waveform
// at each x (fast) scan line, y value is constant
// effectively y retrace takes (Y_RETRACE_LENGTH * xLength) steps
xyWaveformFrame[i + j * xLength + yLength * xLength] =
yWaveform[i + j * xLength] + offsetYinDegree;
}
}
// TODO When we are scanning multiple frames, the Y retrace can be
// simultaneous with the last line's X retrace. (Spline interpolate
// with zero slope at each end of retrace.)
// TODO Simpler to use interleaved x,y format?
free(xWaveform);
free(yWaveform);
return OScDev_RichError_OK;
}
// Generate waveform from parking to start before one frame
OScDev_RichError *
GenerateGalvoUnparkWaveform(const struct WaveformParams *parameters,
double *xyWaveformFrame) {
uint32_t resolution = parameters->resolution;
double zoom = parameters->zoom;
uint32_t xOffset = parameters->xOffset; // ROI offset
uint32_t yOffset = parameters->yOffset;
double galvoOffsetX = parameters->galvoOffsetX; // Adjustment Offset
double galvoOffsetY = parameters->galvoOffsetY;
int32_t undershoot = parameters->undershoot;
int32_t xPark = parameters->xPark;
int32_t yPark = parameters->yPark;
double xParkVoltage = parameters->prevXParkVoltage;
double yParkVoltage = parameters->prevYParkVoltage;
// Voltage ranges of the ROI
double xStart = xParkVoltage;
double yStart = yParkVoltage;
double xEnd =
(-0.5 * resolution + xOffset - undershoot) / (zoom * resolution);
double yEnd = (-0.5 * resolution + yOffset) / (zoom * resolution);
size_t length = X_RETRACE_LEN;
double *xWaveform = (double *)malloc(sizeof(double) * length);
double *yWaveform = (double *)malloc(sizeof(double) * length);
SplineInterpolate((int32_t)length, xStart, xEnd, 0, 0, xWaveform);
SplineInterpolate((int32_t)length, yStart, yEnd, 0, 0, yWaveform);
double offsetXinDegree = galvoOffsetX / 3.0;
double offsetYinDegree = galvoOffsetY / 3.0;
// effective scan waveform for a whole frame
for (unsigned i = 0; i < length; ++i) {
// first half is X waveform,
// x line scan repeated yLength times (sawteeth)
xyWaveformFrame[i] = xWaveform[i] + offsetXinDegree;
// second half is Y waveform
xyWaveformFrame[i + length] = yWaveform[i] + offsetYinDegree;
}
free(xWaveform);
free(yWaveform);
return OScDev_RichError_OK;
}
// Generate waveform from start to parking after one frame
OScDev_RichError *
GenerateGalvoParkWaveform(const struct WaveformParams *parameters,
double *xyWaveformFrame) {
uint32_t resolution = parameters->resolution;
double zoom = parameters->zoom;
uint32_t xOffset = parameters->xOffset; // ROI offset
uint32_t yOffset = parameters->yOffset;
double galvoOffsetX = parameters->galvoOffsetX; // Adjustment Offset
double galvoOffsetY = parameters->galvoOffsetY;
int32_t undershoot = parameters->undershoot;
int32_t xPark = parameters->xPark;
int32_t yPark = parameters->yPark;
// Voltage ranges of the ROI
double xStart =
(-0.5 * resolution + xOffset - undershoot) / (zoom * resolution);
double yStart = (-0.5 * resolution + yOffset) / (zoom * resolution);
double xEnd = (-0.5 * resolution + xPark) / (zoom * resolution);
double yEnd = (-0.5 * resolution + yPark) / (zoom * resolution);
size_t length = X_RETRACE_LEN;
double *xWaveform = (double *)malloc(sizeof(double) * length);
double *yWaveform = (double *)malloc(sizeof(double) * length);
SplineInterpolate((int32_t)length, xStart, xEnd, 0, 0, xWaveform);
SplineInterpolate((int32_t)length, yStart, yEnd, 0, 0, yWaveform);
double offsetXinDegree = galvoOffsetX / 3.0;
double offsetYinDegree = galvoOffsetY / 3.0;
// effective scan waveform for a whole frame
for (unsigned i = 0; i < length; ++i) {
// first half is X waveform,
// x line scan repeated yLength times (sawteeth)
// galvo x stays at starting position after one frame is scanned
xyWaveformFrame[i] = xWaveform[i] + offsetXinDegree;
// xyWaveformFrame[i + j*xLength] = xWaveform[i];
// second half is Y waveform
xyWaveformFrame[i + length] = yWaveform[i] + offsetYinDegree;
}
free(xWaveform);
free(yWaveform);
return OScDev_RichError_OK;
}