/*!
* Writes the header for unit [iunit] to file with the minimum, maximum and mean
* density values in [dmin], [dmax], and [dmean]. A single title can be supplied in
* an 80-byte array, [label], and will be treated according to the value of [labFlag]: ^
* 0: [label] becomes the only title ^
* 1: [label] is added at the end of existing titles, replacing the last one if there
* are already 10 titles ^
* 2: [label] is added as the first title and others are shifted up ^
* -1 or anything else: do not add a title ^
* Returns -1 for various internal errors or 1 for an error writing the header.
* Fortran wrappers iiuWriteHeader and iwrhdr (a void).
*/
int iiuWriteHeader(int iunit, int *label, int labFlag, float dmin, float dmax,
float dmean)
{
int doExit = iiuGetExitOnError();
int i;
MrcHeader *hdr = iiuMrcHeader(iunit, "iiuWriteHeader", doExit, 2);
if (!hdr)
return -1;
if (labFlag == 0) {
iiuAltLabels(iunit, label, 1);
} else if (labFlag == 1) {
hdr->nlabl = B3DMIN(hdr->nlabl + 1, MRC_NLABELS);
memcpy(hdr->labels[hdr->nlabl - 1], label, MRC_LABEL_SIZE);
fixTitlePadding(hdr->labels[hdr->nlabl - 1]);
} else if (labFlag == 2) {
hdr->nlabl = B3DMIN(hdr->nlabl + 1, MRC_NLABELS);
for (i = hdr->nlabl - 1; i > 0; i--)
memcpy(hdr->labels[i], hdr->labels[i - 1], MRC_LABEL_SIZE);
memcpy(hdr->labels[0], label, MRC_LABEL_SIZE);
fixTitlePadding(hdr->labels[0]);
}
hdr->amin = dmin;
hdr->amax = dmax;
hdr->amean = dmean;
if (mrc_head_write(hdr->fp, hdr)) {
if (doExit)
exit(1);
return 1;
}
return 0;
}
// Set the drawing state and dialog to the start or end of the given movie segment
void mvImageSetMovieEndState(int startEnd, MovieSegment &segment)
{
MovieTerminus *term = &segment.start;
int maxSlices = B3DMIN(Imodv->vi->zsize, MAX_SLICES);
if (startEnd == IMODV_MOVIE_END_STATE)
term = &segment.end;
if (mvImageSetMovieDrawState(segment))
return;
// Otherwise set the image position and copy all the data over
sImageTrans = term->imgTransparency;
ivwSetLocation(Imodv->vi, term->imgXcenter - 1, term->imgYcenter - 1,
term->imgZcenter - 1);
sNumSlices = B3DMIN(term->imgSlices, maxSlices);
// Update the dialog as needed
if (sDia) {
// Set this to prevent Y/Z swapping of sizes in the update
sLastYsize = Imodv->vi->ysize;
sDia->updateCoords();
sDia->mSliders->setValue(IIS_SLICES, sNumSlices);
sDia->mSliders->setValue(IIS_TRANSPARENCY, sImageTrans);
}
}
/*!
* Extracts a square matrix of size [dim] from the slice [sin], centered
* around position [x], [y] and places the result into the array [mat].
*/
void mrc_slice_mat_getimat(Islice *sin, int x, int y, int dim,
float *mat)
{
int xs, ys, xe, ye;
int i, j, ic, jc;
xs = x - (dim / 2);
xe = xs + dim;
ys = y - (dim / 2);
ye = ys + dim;
if (xs >= 0 && xe < sin->xsize && ys >= 0 && ye < sin->ysize) {
for(j = ys; j < ye; j++)
for(i = xs; i < xe; i++)
mat[(i-xs )+ dim * (j-ys)] = sliceGetPixelMagnitude(sin, i, j);
} else {
/* If any pixels are out of bounds, replicate from inside pixels */
for(j = ys; j < ye; j++)
for(i = xs; i < xe; i++) {
ic = B3DMAX(0, B3DMIN(sin->xsize - 1, i));
jc = B3DMAX(0, B3DMIN(sin->ysize - 1, j));
mat[(i-xs )+ dim * (j-ys)] = sliceGetPixelMagnitude(sin, ic, jc);
}
}
}
void ContourCopy::update()
{
int minVal, maxVal, curVal;
ImodView *vw = sData.vw;
// For each operation that uses spin box, set up min and max value
// and adjust the current value if necessary
switch(sData.copyOperation){
case COPY_TO_OBJECT:
minVal = 1;
maxVal = vw->imod->objsize;
sData.objectNumber = B3DMAX(1, B3DMIN(maxVal, sData.objectNumber));
curVal = sData.objectNumber;
break;
case COPY_TO_SECTION:
minVal = 1;
maxVal = vw->zsize;
sData.sectionNumber = B3DMAX(1, B3DMIN(maxVal, sData.sectionNumber));
curVal = sData.sectionNumber;
break;
case COPY_TO_TIME:
minVal = 1;
maxVal = vw->numTimes;
sData.timeIndex = B3DMAX(1, B3DMIN(maxVal, sData.timeIndex));
curVal = sData.timeIndex;
break;
case COPY_TO_NEXT_SECTION:
case COPY_TO_PREV_SECTION:
case COPY_TO_CURRENT:
default:
minVal = 0;
maxVal = 0;
curVal = 0;
break;
}
// Set up spin box limits and value and enable it if meaningful
diaSetSpinMMVal(mToSpinBox, minVal, maxVal, curVal);
mToSpinBox->setSpecialValueText(minVal ? "" : " ");
mToSpinBox->setEnabled(minVal > 0);
mEllipseBox->setEnabled(sData.copyOperation == COPY_TO_OBJECT);
// Enable the time radio button if appropriate
if (vw->numTimes)
mTimeRadio->setEnabled(sData.copyOperation == COPY_TO_TIME);
}
/*
* Ruueads a file of tilt angles whose name is in angleFile, and which must
* have at least nzz lines. angleSign should be 1., or -1. to invert the
* sign of the angles. Minimum and maximum angles are returned in minAngle
* and maxAngle. The return value is the array of tilt angles.
*/
float *readTiltAngles(const char *angleFile, int nzz, float angleSign,
float &minAngle, float &maxAngle)
{
char angleStr[MAX_LINE];
FILE *fpAngle;
int k, err;
float currAngle;
float *tiltAngles = (float *)malloc(nzz * sizeof(float));
minAngle = 10000.;
maxAngle = -10000.;
if (!tiltAngles)
exitError("Allocating array for tilt angles");
if ((fpAngle = fopen(angleFile, "r")) == 0)
exitError("Opening tilt angle file %s", angleFile);
for (k = 0; k < nzz; k++) {
do {
err = fgetline(fpAngle, angleStr, MAX_LINE);
} while (err == 0);
if (err == -1 || err == -2)
exitError("%seading tilt angle file %s\n",
err == -1 ? "R" : "End of file while r", angleFile);
sscanf(angleStr, "%f", &currAngle);
currAngle *= angleSign;
minAngle = B3DMIN(minAngle, currAngle);
maxAngle = B3DMAX(maxAngle, currAngle);
tiltAngles[k] = currAngle;
}
fclose(fpAngle);
return tiltAngles;
}
/*!
* Computes the minimum [DMIN], maximum [dmax], mean [avg], and standard deviation [SD]
* from data in [array], dimensioned [nx] by [ny], for X indices from [ix0] to [ix1] and
* Y indices from [iy0] to [iy1], inclusive (numbered from 0 when calling from C). It
* also returns the sum in [sumDbl] and sum of squares in [sumSqDl].
*/
void arrayMinMaxMeanSd(float *array, int nx, int ny, int ix0, int ix1, int iy0, int iy1,
float *dmin, float *dmax, double *sumDbl, double *sumSqDbl,
float *avg, float *SD)
{
float den;
float *arrTmp;
double sumTmp, sumTmpSq;
int ix, iy;
*sumDbl = 0.;
*sumSqDbl = 0.;
*dmin = 1.e37;
*dmax = -1.e37;
for (iy = iy0; iy <= iy1; iy++) {
sumTmp = 0.;;
sumTmpSq = 0.;
arrTmp = array + (size_t)iy * nx + ix0;
for (ix = ix0; ix <= ix1; ix++) {
den = *arrTmp++;
sumTmp = sumTmp + den;
sumTmpSq = sumTmpSq + den * den;
*dmin = B3DMIN(*dmin, den);
*dmax = B3DMAX(*dmax, den);
}
*sumDbl += sumTmp;
*sumSqDbl += sumTmpSq;
}
sumsToAvgSDdbl(*sumDbl, *sumSqDbl, ix1 + 1 - ix0, iy1 + 1 - iy0, avg, SD);
}
/*
* Compute the limits of usable data in one dimension for calling from the interp function
*/
static void interpLimits(int na, int nb, float cen, float trans, double scale,
float *aOff, int *bSize, int *bOff)
{
float bcStart, bcEnd;
int bdStart, bdEnd;
/* Get starting and ending continuous coordinates in b from corners of a and limit
them to edges of first and last pixel */
bcStart = -cen / scale + nb / 2. + trans;
bcEnd = (na - cen) / scale + nb / 2. + trans;
bcStart = B3DMAX(0., bcStart);
bcEnd = B3DMIN(nb, bcEnd);
/* Get discrete coordinates of the nearest whole pixel by rounding up on the start and
down on the end, then get the offset and size from them */
bdStart = (int)ceil(bcStart - 0.001);
bdEnd = (int)floor(bcEnd + 0.001) - 1;
*bOff = bdStart;
*aOff = scale * (bdStart - nb / 2. - trans) + cen;
/* Make sure this is not negative; roundoff errors can give negative values */
*aOff = B3DMAX(0., *aOff);
*bSize = bdEnd + 1 - bdStart;
/* Make sure the output size will pass the test below too */
if (*bSize * scale + *aOff > na)
(*bSize)--;
}
// Compute starting and ending draw coordinates from center coordinate, desired
// size and maximum size, shifting center if necessary
static void setCoordLimits(int cur, int maxSize, int drawSize,
int &str, int &end)
{
str = cur - drawSize / 2;
str = B3DMAX(1, str);
end = B3DMIN(str + drawSize, maxSize - 1);
str = B3DMAX(1, end - drawSize);
}
void SliceCache::clearAndSetSize(int dim, int hyper, int tSize)
{
int fftXdim, i, j, rIndex;
double freqInc;
numXtiles = mHeader.nx / (tSize / 2) - 1;
mNumYtiles = mHeader.ny / (tSize / 2) - 1;
mPsArraySize = numXtiles * mNumYtiles * mPsDim;
mMaxSliceNum = mMaxCacheSize * 1024 * 1024 / (mPsArraySize * sizeof(float));
for (i = 0; i < (int)mCachedPS.size(); i++) {
free(mCachedPS[i]);
free(mCachedTileDone[i]);
free(mCachedMeans[i]);
}
if (mTile)
free(mTile);
mTile = (float *)malloc(tSize * (tSize + 2) * sizeof(float));
if (mTileToPsInd)
free(mTileToPsInd);
mTileToPsInd = (int *)malloc(tSize * (tSize + 2) * sizeof(int));
if (!mTile || !mTileToPsInd)
exitError("Allocating memory for mTile or PS index");
// Compute the index for each component of FFT and the counts in each bin
mTileSize = tSize;
mNDim = dim;
mHyperRes = hyper;
fftXdim = (mTileSize + 2) / 2;
freqInc = 1. / ((mNDim - 1) * hyper);
for (i = 0; i < mPsDim; i++)
mFreqCount[i] = 0;
for (i = 0; i < fftXdim - 1; i++) {
for (j = 0; j < fftXdim; j++) {
// Here make bins with integer truncation
rIndex = (int)(sqrt((double)(i * i + j * j)) / (fftXdim - 1) / freqInc);
rIndex = B3DMIN(rIndex, mPsDim - 1);
mTileToPsInd[i * fftXdim + j] = rIndex;
mFreqCount[rIndex] += 2;
}
}
/*for (i = 0; i < mPsDim; i++)
printf("%d\n", mFreqCount[i]); */
// Clear cache components
mCachedPS.clear();
mCachedMeans.clear();
mCachedTileDone.clear();
mSliceAngles.clear();
mCachedSliceMap.clear();
mOldestIdx = -1;
if (debugLevel >= 2)
printf("cacheSize is set to %d \n", mMaxSliceNum);
}
/*!
* Sets the labels for unit [iunit] from the array in [labels], which should have the
* 80 characters for [numLabels] labels packed contiguously. The labels may be
* null-terminated; the null and following bytes will be filled with spaces.
* Fortran wrappers iiuAltLabels and iallab.
*/
void iiuAltLabels(int iunit, int *labels, int numLabels)
{
MrcHeader *hdr = iiuMrcHeader(iunit, "iiuAltLabels", 1, 0);
int i;
hdr->nlabl = B3DMIN(MRC_NLABELS, numLabels);
for (i = 0; i < hdr->nlabl; i++) {
memcpy(hdr->labels[i], labels + 20 * i, MRC_LABEL_SIZE);
fixTitlePadding(hdr->labels[i]);
}
for (i = hdr->nlabl; i < MRC_NLABELS; i++)
memset(hdr->labels[i], 0, MRC_LABEL_SIZE + 1);
}
// Set ancillary parameters to the state for a movie segment
int mvImageSetMovieDrawState(MovieSegment &segment)
{
if (!segment.imgAxisFlags) {
// If there is no image drawing, turn off Imodv flag and then, if there is currently,
// take the update route to updating this module
Imodv->texMap = 0;
if (sFlags)
mvImageUpdate(Imodv);
return 1;
}
sFlags = segment.imgAxisFlags;
Imodv->texMap = 1;
sWhiteLevel = segment.imgWhiteLevel;
sBlackLevel = segment.imgBlackLevel;
sFalsecolor = segment.imgFalseColor;
makeColorMap();
sXdrawSize = B3DMIN(segment.imgXsize, Imodv->vi->xsize);
sYdrawSize = B3DMIN(segment.imgYsize, Imodv->vi->ysize);
sZdrawSize = B3DMIN(segment.imgZsize, Imodv->vi->zsize);
// Update the dialog as needed
if (sDia) {
sDia->mSliders->setValue(IIS_X_SIZE, sXdrawSize);
sDia->mSliders->setValue(IIS_Y_SIZE, sYdrawSize);
sDia->mSliders->setValue(IIS_Z_SIZE, sZdrawSize);
diaSetChecked(sDia->mViewXBox, (sFlags & IMODV_DRAW_CX) != 0);
diaSetChecked(sDia->mViewYBox, (sFlags & IMODV_DRAW_CY) != 0);
diaSetChecked(sDia->mViewZBox, (sFlags & IMODV_DRAW_CZ) != 0);
sDia->mSliders->setValue(IIS_BLACK, sBlackLevel);
sDia->mSliders->setValue(IIS_WHITE, sWhiteLevel);
diaSetChecked(sDia->mFalseBox, sFalsecolor != 0);
}
return 0;
}
/*
* Does common initial tasks for a montage snapshot: allocates the arrays,
* (returns true for an error), and saves and adjusts the scale bar data
*/
bool utilStartMontSnap(int winx, int winy, int xFullSize, int yFullSize,
float factor, ScaleBar &barSaved, int &numChunks,
unsigned char **framePix, unsigned char ***fullPix,
unsigned char ***linePtrs)
{
int iy, maxLines, line, ch, ndo;
int chunkMax = 10000000; // This was needed to get to 2.9 GB on WinXP
ScaleBar *barReal = scaleBarGetParams();
maxLines = B3DMAX(1, chunkMax / (4 * xFullSize));
numChunks = (yFullSize + maxLines - 1) / maxLines;
*fullPix = (unsigned char **)malloc(numChunks * sizeof (unsigned char *));
if (!*fullPix)
return true;
for (ch = 0; ch < numChunks; ch++)
(*fullPix)[ch] = NULL;
*linePtrs = NULL;
*framePix = NULL;
*framePix = (unsigned char *)malloc(4 * winx * winy);
*linePtrs = (unsigned char **)malloc(yFullSize * sizeof(unsigned char *));
if (!*framePix || !*linePtrs) {
utilFreeMontSnapArrays(*fullPix, numChunks, *framePix, *linePtrs);
return true;
}
line = 0;
for (ch = 0; ch < numChunks; ch++) {
ndo = B3DMIN(yFullSize - line, maxLines);
(*fullPix)[ch] = (unsigned char *)malloc(ndo * 4 * xFullSize);
if (!(*fullPix)[ch]) {
imodPrintStderr("Failed on chunk %d, after %u\n", ch, (unsigned int)ch * ndo * 4 * xFullSize);
utilFreeMontSnapArrays(*fullPix, numChunks, *framePix, *linePtrs);
return true;
}
for (iy = 0; iy < ndo; iy++)
(*linePtrs)[iy+line] = (*fullPix)[ch] + 4 * xFullSize * iy;
line += ndo;
}
// Save and modify scale bar directives
barSaved = *barReal;
barReal->minLength = B3DNINT(factor * barReal->minLength);
barReal->thickness = B3DNINT(factor * barReal->thickness);
barReal->indentX = B3DNINT(factor * barReal->indentX);
barReal->indentY = B3DNINT(factor * barReal->indentY);
return false;
}
// Return the limits of what is being drawn in X and Y
bool mvImageSubsetLimits(double &zoom, float &zoomUpLimit, float &zoomDownLimit,
int &ixStart, int &iyStart, int &nxUse, int &nyUse)
{
int ixCur, iyCur, izCur, xend, yend;
ImodvApp *a = Imodv;
if (ImodvClosed || !a->texMap || !sFlags || sXdrawSize <= 0)
return false;
zoomUpLimit = sPyrZoomUpLimit;
zoomDownLimit = sPyrZoomDownLimit;
zoom = 0.5 * B3DMIN(a->winx, a->winy) / a->imod->view->rad;
ivwGetLocation(a->vi, &ixCur, &iyCur, &izCur);
setCoordLimits(ixCur, a->vi->xsize, sXdrawSize, ixStart, xend);
setCoordLimits(iyCur, a->vi->ysize, sYdrawSize, iyStart, yend);
nxUse = xend + 1 - ixStart;
nyUse = yend + 1 - iyStart;
return true;
}
/*
* Finds the next section in the current object with a contour, given curz is
* the current Z and dir is 1 to go forward or -1 to go back
*/
int utilNextSecWithCont(ImodView *vi, Iobj *obj, int curz, int dir)
{
int diff, co, contz;
int newz = curz;
Icont *cont;
if (!obj)
return newz;
newz = -1;
for (co = 0; co < obj->contsize; co++) {
cont = &obj->cont[co];
if (!cont->psize)
continue;
contz = B3DNINT(cont->pts[0].z);
contz = B3DMAX(0, B3DMIN(contz, vi->zsize - 1));
diff = dir * (contz - curz);
if (diff > 0 && (newz < 0 || diff < dir * (newz - curz)))
newz = contz;
}
return newz >= 0 ? newz : curz;
}
/*!
* Computes the minimum [DMIN], maximum [dmax], and mean [dmean] from data in [array],
* dimensioned [nx] by [ny], for X indices from [ix0] to [ix1] and Y indices from [iy0]
* to [iy1], inclusive (numbered from 0 when calling from C).
*/
void arrayMinMaxMean(float *array, int nx, int ny, int ix0, int ix1, int iy0, int iy1,
float *dmin, float *dmax, float *dmean)
{
float den, sumTmp;
float *arrTmp;
double sumDbl;
int ix, iy;
sumDbl = 0.;
*dmin = 1.e37;
*dmax = -1.e37;
for (iy = iy0; iy <= iy1; iy++) {
sumTmp = 0.;;
arrTmp = array + (size_t)iy * nx + ix0;
for (ix = ix0; ix <= ix1; ix++) {
den = *arrTmp++;
sumTmp = sumTmp + den;
*dmin = B3DMIN(*dmin, den);
*dmax = B3DMAX(*dmax, den);
}
sumDbl += sumTmp;
}
*dmean = sumDbl / ((double)(ix1 + 1 - ix0) * (iy1 + 1 - iy0));
}
static void plax_draw_text(b3dInt32 thickness,
b3dInt32 iysize,
b3dInt32 cindex,
b3dInt32 x, b3dInt32 y,
b3dInt32 strsize, char *string)
{
static int lastbold;
int width, height, align, maxWidth, maxHeight;
int ysize = (int)(iysize * TEXT_SIZE_SCALE);
int ifbold = 0;
char *cstring = f2cString(string, strsize);
if (!cstring)
return;
#ifdef PLAX_DEBUG
printf("draw text %d %d %d %d %d %s\n", thickness, iysize, cindex, x, y,
cstring);
#endif
if (thickness > 1)
ifbold = 1;
ysize = plax_scale(ysize);
if (ysize <= 1)
ysize = 1;
if (sLastSize != ysize || lastbold != ifbold) {
//QFont newFont("courier", ysize);
QFont newFont;
newFont.setPointSize(ysize);
newFont.setStyleHint(QFont::TypeWriter);
newFont.setItalic(false);
newFont.setBold(ifbold != 0);
sPainter->setFont(newFont);
}
lastbold = ifbold;
sLastSize = ysize;
plax_transform(&x, &y);
plax_set_pen(cindex, 0);
if (sNextTextAlign % 10) {
maxWidth = 2 * B3DMIN(x, sPlaxWidth - x);
maxHeight = 2 * B3DMIN(y - 1, sPlaxHeight - y - 1);
switch (sNextTextAlign % 10) {
case 1: // Top center
align = Qt::AlignHCenter | Qt::AlignTop;
width = B3DMIN(maxWidth, sPlaxWidth / 2);
height = B3DMIN(sPlaxHeight - 1 - y, sPlaxHeight / 2);
x -= width / 2;
break;
case 2: // right center
align = Qt::AlignVCenter | Qt::AlignRight;
width = B3DMIN(x - 1, sPlaxWidth / 2);
height = B3DMIN(maxHeight, sPlaxHeight / 2);
x -= width;
y -= height / 2;
break;
case 3: // Bottom center
align = Qt::AlignHCenter | Qt::AlignBottom;
width = B3DMIN(maxWidth, sPlaxWidth / 2);
height = B3DMIN(y - 1, sPlaxHeight / 2);
x -= width / 2;
y -= height;
break;
case 4: // left center
align = Qt::AlignVCenter | Qt::AlignLeft;
width = B3DMIN(sPlaxWidth - x - 1, sPlaxWidth / 2);
height = B3DMIN(maxHeight, sPlaxHeight / 2);
y -= height / 2;
break;
default: // all centered
align = Qt::AlignVCenter | Qt::AlignHCenter;
height = B3DMIN(maxHeight, sPlaxHeight / 2);
width = B3DMIN(maxWidth, sPlaxWidth / 2);
x -= width / 2;
y -= height / 2;
break;
}
if (sNextTextAlign >= 10)
align |= Qt::TextWordWrap;
sPainter->drawText(x, y, width, height, align, QString(cstring));
//printf("%d %d %d %d %d %s\n", x,y, width, height, align,cstring);
sNextTextAlign = 0;
} else {
//printf("%d %d %s\n", x,y, cstring);
sPainter->drawText(x, y, QString(cstring));
}
fflush(stdout);
free(cstring);
}
static void fillPatchFromTiles(std::vector<FastSegment> &segments,
std::vector<int> &startInds, int ushort,
unsigned char *bmap, int fillXsize, int istart, int iend,
int jstart, int jend)
{
int u, v, j, i, iseg, numSeg, segEnd, nextToFill, uvind, segStart;
FastSegment *segp;
unsigned char *imdata;
unsigned short *usimdata;
unsigned char pix;
for (j = jstart; j < jend; j++) {
v = j - jstart;
numSeg = startInds[j + 1] - startInds[j];
nextToFill = istart;
for (iseg = startInds[j]; iseg < startInds[j + 1]; iseg++) {
segp = &(segments[iseg]);
// If segment starts past the end, done with segments
if (segp->XorY >= iend)
break;
// If segment ends before the start, skip it
if (segp->XorY + segp->length <= istart)
continue;
// If segment starts past next place to fill, need to fill with 0's
if (segp->XorY > nextToFill) {
for (i = nextToFill; i < segp->XorY; i++) {
u = i - istart;
FILLDATA(0);
}
}
// Fill with segment data
segEnd = B3DMIN(segp->XorY + segp->length, iend);
segStart = B3DMAX(segp->XorY, istart);
imdata = segp->line + segp->stride * (segStart - segp->XorY);
if (ushort) {
usimdata = (unsigned short *)imdata;
for (i = segStart; i < segEnd; i++) {
u = i - istart;
pix = bmap[*usimdata];
usimdata += segp->stride;
FILLDATA(pix);
}
} else {
for (i = segStart; i < segEnd; i++) {
u = i - istart;
pix = *imdata;
imdata += segp->stride;
FILLDATA(pix);
}
}
nextToFill = segEnd;
}
// Fill past end
for (i = nextToFill; i < iend; i++) {
u = i - istart;
FILLDATA(0);
}
}
}
// The call from within the openGL calling routines to draw the image
void imodvDrawImage(ImodvApp *a, int drawTrans)
{
Ipoint lowerLeft, lowerRight, upperRight, upperLeft, clamp;
int tstep;
int ixCur, iyCur, izCur;
int xsize, ysize, zsize;
int xstr, xend, ystr, yend, zstr, zend, fillXsize;
unsigned char **idata;
b3dUInt16 **usidata;
unsigned char pix;
int i, j, ypatch, jend, xpatch, zpatch, iend, xconst;
int u, v, uvind;
int iz, idir, numSave, baseXstr, baseXsize, baseYstr, baseYsize;
int cacheSum, curtime, cacheInd = -1;
float clampEnd;
int pyrXYscale = 1, pyrZscale = 1;
float pyrXoffset = 0., pyrYoffset = 0., pyrZoffset = 0.;
double zoom;
unsigned char **imdata;
b3dUInt16 **usimdata;
unsigned char *bmap = NULL;
bool flipped, invertX, invertY, invertZ;
Imat *mat;
Ipoint inp, outp;
std::vector<FastSegment> segments;
std::vector<int> startInds;
QTime drawTime;
drawTime.start();
sWallLoad = sWallDraw = 0.;
xsize = a->vi->xsize;
ysize = a->vi->ysize;
zsize = a->vi->zsize;
if (sDia)
sDia->updateCoords();
if (!sFlags)
return;
if (a->vi->pyrCache != NULL) {
zoom = 0.5 * B3DMIN(a->winx, a->winy) / a->imod->view->rad;
cacheInd = a->vi->pyrCache->pickBestCache(zoom, sPyrZoomUpLimit, sPyrZoomDownLimit,
pyrXYscale);
imodTrace('t', "zoom = %.3f, cache %d, scale %d", zoom, cacheInd, pyrXYscale);
}
ivwGetLocation(a->vi, &ixCur, &iyCur, &izCur);
ivwGetTime(a->vi, &curtime);
if (!sCmapInit || (a->vi->colormapImage &&
(izCur != cmapZ || curtime != cmapTime))) {
makeColorMap();
cmapTime = curtime;
cmapZ = izCur;
}
if (sXdrawSize < 0) {
sXdrawSize = xsize;
sYdrawSize = ysize;
sZdrawSize = zsize;
}
// If doing stereo pairs, draw the pair as long as the step up stays in the
// same set of images for an area
if (a->imageStereo && a->stereo < 0) {
iz = izCur + a->imageDeltaZ;
if (izCur % a->imagesPerArea < iz % a->imagesPerArea)
izCur = iz;
}
// Get data pointers if doing X or Y planes
if ((sFlags & (IMODV_DRAW_CX | IMODV_DRAW_CY)) && cacheInd < 0 &&
!(a->imageStereo && a->stereo)) {
if (ivwSetupFastAccess(a->vi, &imdata, 0, &cacheSum))
return;
flipped = (!a->vi->vmSize || a->vi->fullCacheFlipped) &&
a->vi->li->axis == 2;
usimdata = (b3dUInt16 **)imdata;
}
if (a->vi->ushortStore) {
bmap = ivwUShortInRangeToByteMap(a->vi);
if (!bmap)
return;
}
// If doing multiple slices, need to find direction in which to do them
invertX = invertY = invertZ = false;
if (a->vi->colormapImage && sNumSlices > 1) {
sNumSlices = 1;
if (sDia)
sDia->mSliders->setValue(IIS_SLICES, sNumSlices);
}
numSave = sNumSlices;
if (a->imageStereo && a->stereo)
sNumSlices = 1;
if (sNumSlices > 1) {
mat = imodMatNew(3);
imodMatRot(mat, (double)a->imod->view->rot.z, b3dZ);
imodMatRot(mat, (double)a->imod->view->rot.y, b3dY);
imodMatRot(mat, (double)a->imod->view->rot.x, b3dX);
inp.x = 1.;
inp.y = inp.z = 0.0f;
imodMatTransform(mat, &inp, &outp);
invertX = outp.z < 0.;
inp.x = 0.;
inp.y = 1.;
imodMatTransform(mat, &inp, &outp);
invertY = outp.z < 0.;
inp.y = 0.;
inp.z = 1.;
imodMatTransform(mat, &inp, &outp);
invertZ = outp.z < 0.;
imodMatDelete(mat);
}
if (!sTexImageSize && initTexMapping())
return;
tstep = sTexImageSize - 2;
clampEnd = (tstep + 1.) / (tstep + 2.);
// This used to be 1 with RGB data being passed in
glPixelStorei(GL_UNPACK_ALIGNMENT, 4);
glEnable(GL_TEXTURE_2D);
/* Draw Current Z image. */
if (sFlags & IMODV_DRAW_CZ) {
// Get the limits for the 3 axes. In every section, xstr, xend etc are the full image
// starting and ending coordinates in actual X, Y, and Z diections.
setSliceLimits(izCur, zsize, invertZ, drawTrans, zstr, zend, idir);
setCoordLimits(ixCur, xsize, sXdrawSize, xstr, xend);
setCoordLimits(iyCur, ysize, sYdrawSize, ystr, yend);
baseXstr = xstr;
baseXsize = xend + 1 - xstr;
baseYstr = ystr;
baseYsize = yend + 1 - ystr;
// When displaying a lower resolution cache, this converts all of the limits to
// loaded coordinates in that cache
adjustLimitsForTiles(a, cacheInd, idir, xstr, xend, ystr, yend, zstr, zend,
pyrXoffset, pyrYoffset, pyrZoffset, pyrZscale);
// Outer loop is on the coordinate that varies through multiple slices if any
for (iz = zstr; idir * (zend - iz) >= 0 ; iz += idir) {
setAlpha(iz, zstr, zend, idir);
lowerLeft.z = lowerRight.z = upperRight.z = upperLeft.z = iz * pyrZscale +
pyrZoffset;
// Load the area if this is the central Z value, and set up access to the tiles
if (cacheInd >= 0) {
if (iz == B3DNINT((izCur - pyrZoffset) / pyrZscale))
a->vi->pyrCache->loadTilesContainingArea(cacheInd, baseXstr, baseYstr,
baseXsize, baseYsize, iz);
if (a->vi->pyrCache->fastPlaneAccess(cacheInd, iz, b3dZ, segments, startInds))
continue;
} else {
// Or get the Z section
idata = ivwGetZSection(a->vi, iz);
if (!idata)
continue;
usidata = (b3dUInt16 **)idata;
}
// Loop on patches in Y, for each patch get limits to fill and set corners
// ypatch is the starting coordinate and jend is the ending one
for (ypatch = ystr; ypatch < yend; ypatch += tstep){
clamp.y = clampEnd;
jend = ypatch + tstep;
if (jend > yend) {
jend = yend;
clamp.y = (yend + 1. - ypatch) / (tstep + 2.);
}
lowerRight.y = lowerLeft.y = ypatch * pyrXYscale + pyrYoffset;
upperLeft.y = upperRight.y = jend * pyrXYscale + pyrYoffset;
// Loop on patches in X, for each patch get limits to fill and set corners
// xpatch is the starting coordinate and iend is the ending one
for (xpatch = xstr; xpatch < xend; xpatch += tstep){
clamp.x = clampEnd;
iend = xpatch + tstep;
if (iend > xend) {
iend = xend;
clamp.x = (xend + 1. - xpatch) / (tstep + 2.);
}
upperLeft.x = lowerLeft.x = xpatch * pyrXYscale + pyrXoffset;
upperRight.x = lowerRight.x = iend * pyrXYscale + pyrXoffset;
fillXsize = 2 + iend - xpatch;
// Fill the data for one patch then draw the patch
// each patch is filled to one more than its limits to allow interpolation
// u and v are the coordinates in the plane being filled
if (cacheInd >= 0) {
fillPatchFromTiles(segments, startInds, a->vi->ushortStore, bmap, fillXsize,
xpatch-1, iend+1, ypatch-1, jend+1);
} else if (a->vi->ushortStore) {
for (j = ypatch-1; j < jend+1; j++) {
v = (j - (ypatch-1));
for (i = xpatch-1; i < iend+1; i++) {
u = i - (xpatch-1);
pix = bmap[usidata[j][i]];
FILLDATA(pix);
}
}
} else {
for (j = ypatch-1; j < jend+1; j++) {
v = (j - (ypatch-1));
for (i = xpatch-1; i < iend+1; i++) {
u = i - (xpatch-1);
pix = idata[j][i];
FILLDATA(pix);
}
}
}
imodvDrawTImage(&lowerLeft, &lowerRight, &upperRight, &upperLeft, &clamp,
(unsigned char *)sTdata, fillXsize, 2 + jend - ypatch);
}
}
}
}
glDisable(GL_BLEND);
/* Draw Current X image. */
if ((sFlags & IMODV_DRAW_CX) &&
!(a->stereo && a->imageStereo)) {
setSliceLimits(ixCur, xsize, invertX, drawTrans, xstr, xend, idir);
setCoordLimits(iyCur, ysize, sYdrawSize, ystr, yend);
setCoordLimits(izCur, zsize, sZdrawSize, zstr, zend);
adjustLimitsForTiles(a, cacheInd, idir, xstr, xend, ystr, yend, zstr, zend,
pyrXoffset, pyrYoffset, pyrZoffset, pyrZscale);
// Outer loop on X
for (xpatch = xstr; idir * (xend - xpatch) >= 0 ; xpatch += idir) {
setAlpha(xpatch, xstr, xend, idir);
lowerLeft.x = lowerRight.x = upperRight.x = upperLeft.x = xpatch * pyrXYscale +
pyrXoffset;
if (cacheInd >= 0) {
if (a->vi->pyrCache->fastPlaneAccess(cacheInd, xpatch, b3dX, segments, startInds))
continue;
}
// Next loop on Z patches
for (zpatch = zstr; zpatch < zend; zpatch += tstep){
clamp.y = clampEnd;
jend = zpatch + tstep;
if (jend > zend) {
jend = zend;
clamp.y = (zend + 1. - zpatch) / (tstep + 2.);
}
lowerRight.z = lowerLeft.z = zpatch * pyrZscale + pyrZoffset;
upperLeft.z = upperRight.z = jend * pyrZscale + pyrZoffset;
// Loop on Y patches
for (ypatch = ystr; ypatch < yend; ypatch += tstep){
clamp.x = clampEnd;
iend = ypatch + tstep;
if (iend > yend) {
iend = yend;
clamp.x = (yend + 1. - ypatch) / (tstep + 2.);
}
upperLeft.y = lowerLeft.y = ypatch * pyrXYscale + pyrYoffset;
upperRight.y = lowerRight.y = iend * pyrXYscale + pyrYoffset;
fillXsize = 2 + iend - ypatch;
if (cacheInd >= 0) {
fillPatchFromTiles(segments, startInds, a->vi->ushortStore, bmap, fillXsize,
ypatch-1, iend+1, zpatch-1, jend+1);
// Handle cases of flipped or not with different loops to put test
// on presence of data in the outer loop
} else if (flipped) {
for (i = ypatch-1; i < iend+1; i++) {
u = i - (ypatch-1);
if (imdata[i]) {
// Invert Z when accessing cache for flipped data
xconst = xpatch + (zsize - 1) * xsize;
if (a->vi->ushortStore) {
for (j = zpatch-1; j < jend+1; j++) {
v = j - (zpatch-1);
pix = bmap[usimdata[i][xconst - j * xsize]];
FILLDATA(pix);
}
} else {
for (j = zpatch-1; j < jend+1; j++) {
v = j - (zpatch-1);
pix = imdata[i][xconst - j * xsize];
FILLDATA(pix);
}
}
} else {
for (j = zpatch-1; j < jend+1; j++) {
v = j - (zpatch-1);
FILLDATA(0);
}
}
}
} else {
for (j = zpatch-1; j < jend+1; j++) {
v = j - (zpatch-1);
if (imdata[j]) {
if (a->vi->ushortStore) {
for (i = ypatch-1; i < iend+1; i++) {
u = i - (ypatch-1);
pix = bmap[usimdata[j][xpatch + (i * xsize)]];
FILLDATA(pix);
}
} else {
for (i = ypatch-1; i < iend+1; i++) {
u = i - (ypatch-1);
pix = imdata[j][xpatch + (i * xsize)];
FILLDATA(pix);
}
}
} else {
for (i = ypatch-1; i < iend+1; i++) {
u = i - (ypatch-1);
FILLDATA(0);
}
}
}
}
imodvDrawTImage(&lowerLeft, &lowerRight, &upperRight, &upperLeft, &clamp,
(unsigned char *)sTdata, fillXsize, 2 + jend - zpatch);
}
}
}
}
glDisable(GL_BLEND);
/* Draw Current Y image. */
if ((sFlags & IMODV_DRAW_CY) &&
!(a->stereo && a->imageStereo)) {
setSliceLimits(iyCur, ysize, invertY, drawTrans, ystr, yend, idir);
setCoordLimits(ixCur, xsize, sXdrawSize, xstr, xend);
setCoordLimits(izCur, zsize, sZdrawSize, zstr, zend);
adjustLimitsForTiles(a, cacheInd, idir, xstr, xend, ystr, yend, zstr, zend, pyrXoffset,
pyrYoffset, pyrZoffset, pyrZscale);
// Outer loop on Y
for (ypatch = ystr; idir * (yend - ypatch) >= 0 ; ypatch += idir) {
setAlpha(ypatch, ystr, yend, idir);
lowerLeft.y = lowerRight.y = upperRight.y = upperLeft.y = ypatch * pyrXYscale +
pyrYoffset;
if (cacheInd >= 0) {
if (a->vi->pyrCache->fastPlaneAccess(cacheInd, ypatch, b3dY, segments, startInds))
continue;
}
// Loop on patches in Z
for (zpatch = zstr; zpatch < zend; zpatch += tstep) {
clamp.y = clampEnd;
jend = zpatch + tstep;
if (jend > zend) {
jend = zend;
clamp.y = (zend + 1. - zpatch) / (tstep + 2.);
}
lowerRight.z = lowerLeft.z = zpatch * pyrZscale + pyrZoffset;
upperLeft.z = upperRight.z = jend * pyrZscale + pyrZoffset;
// Loop on patches in X
for (xpatch = xstr; xpatch < xend; xpatch += tstep) {
clamp.x = clampEnd;
iend = xpatch + tstep;
if (iend > xend) {
iend = xend;
clamp.x = (xend + 1. - xpatch) / (tstep + 2.);
}
upperLeft.x = lowerLeft.x = xpatch * pyrXYscale + pyrXoffset;
upperRight.x = lowerRight.x = iend * pyrXYscale + pyrXoffset;
fillXsize = 2 + iend - xpatch;
if (cacheInd >= 0) {
fillPatchFromTiles(segments, startInds, a->vi->ushortStore, bmap, fillXsize,
xpatch-1, iend+1, zpatch-1, jend+1);
} else {
// This one is easier, one outer loop and flipped, non-flipped, or
// no data cases for inner loop
for (j = zpatch-1; j < jend+1; j++) {
v = j - (zpatch-1);
if (flipped && imdata[ypatch]) {
xconst = (zsize - 1 - j) * xsize;
if (a->vi->ushortStore) {
for (i = xpatch-1; i < iend+1; i++) {
u = i - (xpatch-1);
pix = bmap[usimdata[ypatch][i + xconst]];
FILLDATA(pix);
}
} else {
for (i = xpatch-1; i < iend+1; i++) {
u = i - (xpatch-1);
pix = imdata[ypatch][i + xconst];
FILLDATA(pix);
}
}
} else if (!flipped && imdata[j]) {
if (a->vi->ushortStore) {
for (i = xpatch-1; i < iend+1; i++) {
u = i - (xpatch-1);
pix = bmap[usimdata[j][i + (ypatch * xsize)]];
FILLDATA(pix);
}
} else {
for (i = xpatch-1; i < iend+1; i++) {
u = i - (xpatch-1);
pix = imdata[j][i + (ypatch * xsize)];
FILLDATA(pix);
}
}
} else {
for (i = xpatch-1; i < iend+1; i++) {
u = i - (xpatch-1);
FILLDATA(0);
}
}
}
}
imodvDrawTImage(&lowerLeft, &lowerRight, &upperRight, &upperLeft, &clamp,
(unsigned char *)sTdata, fillXsize, 2 + jend - zpatch);
}
}
}
}
B3DFREE(bmap);
glDisable(GL_BLEND);
//glFlush();
glDisable(GL_TEXTURE_2D);
sNumSlices = numSave;
if (imodDebug('v'))
imodPrintStderr("Draw time %d load %.2f draw %.2f\n", drawTime.elapsed(),
sWallLoad * 1000., sWallDraw * 1000.);
}
// Read an image as raw or byte data
static int ReadSection(ImodImageFile *inFile, char *buf, int byte)
{
int ysize = inFile->ny;
int i, pixel, y, maxind;
float slope = inFile->slope;
float offset = inFile->offset;
int outmin = 0;
int outmax = 255;
int xmin, xmax, ymin, ymax;
unsigned char *obuf;
float *fbuf;
unsigned char *bdata;
unsigned char map[256];
QRgb *rgbdata;
QRgb rgbval;
QImage *image;
QImage image2;
unsigned char *map2 = NULL;
QVector<QRgb> colorTable;
if (inFile->axis == 2)
return -1;
if (byte && (inFile->format != IIFORMAT_LUMINANCE))
return -1;
if (!inFile->header && iiReopen(inFile))
return -1;
image = (QImage *)inFile->header;
// Convert a 16-bpp image to 32
if (image->depth() == 16) {
image2 = image->convertToFormat(QImage::Format_RGB32);
if (image2.isNull())
return -1;
image = &image2;
}
colorTable = image->colorTable();
/* set the dimensions to read in */
xmin = inFile->llx;
ymin = inFile->lly;
if (inFile->urx < 0)
xmax = inFile->nx-1;
else
xmax = inFile->urx;
if (inFile->ury < 0)
ymax = inFile->ny-1;
else
ymax = inFile->ury;
if (byte) {
// Get a map for scaling the bytes, then get composite map to go from
// pixel indexes to scaled value;
map2 = get_byte_map(slope, offset, outmin, outmax, 0);
maxind = B3DMAX(0, colorTable.size() - 1);
for (i = 0; i < 256; i++) {
pixel = qRed(colorTable[B3DMIN(i, maxind)]);
map[i] = map2[pixel];
}
}
// Loop on the lines to get data
obuf = (unsigned char *)buf;
fbuf = (float *)buf;
for (y = ymin; y <= ymax; y++) {
bdata = image->scanLine(ysize - 1 - y);
// Bytes: just map the index values
if (byte == 1) {
for (i = xmin; i <= xmax; i++)
*obuf++ = map[bdata[i]];
} else if (byte == 2) {
for (i = xmin; i <= xmax; i++)
*fbuf++ = bdata[i];
// 8 bit RGB: look up in color table
} else if (image->depth() == 8) {
for (i = xmin; i <= xmax; i++) {
rgbval = colorTable[bdata[i]];
*obuf++ = qRed(rgbval);
*obuf++ = qGreen(rgbval);
*obuf++ = qBlue(rgbval);
}
// 32-bit: convert scan line pointer to rgb, get components
} else {
rgbdata = (QRgb *)bdata;
for (i = xmin; i <= xmax; i++) {
rgbval = rgbdata[i];
*obuf++ = qRed(rgbval);
*obuf++ = qGreen(rgbval);
*obuf++ = qBlue(rgbval);
}
}
}
return 0;
}
// A new size comes in. Compute a new rad value to keep scale constant, set window size
// accounting for the menu bar
void ImodvWindow::newResizerSize(int sizeX, int sizeY)
{
ImodvApp *a = Imodv;
a->imod->view->rad *= ((float)B3DMIN(sizeX, sizeY)) / B3DMIN(a->winx, a->winy);
a->mainWin->resize(sizeX, sizeY + a->mainWin->height() - a->winy);
}
int main( int argc, char *argv[])
{
int i, ind, col, maxValType;
FILE *fout;
Imod *mod;
int npatch = 0;
int numValues[MAX_VALUE_COLS], valueIDs[MAX_VALUE_COLS];
int ix, iy, iz;
int colForVal1 = 1;
float dx, dy, dz;
float value, maxVal[MAX_VALUE_COLS];
int ob, co, listInd, listStart, numCols;
Ipoint *pts;
char format[MAX_VALUE_COLS][10];
int colToTypeMap[MAX_VALUE_COLS];
setExitPrefix("ERROR: imod2patch - ");
if (argc < 3){
if (argc != 1)
printf("ERROR: imod2patch - wrong # of arguments\n");
printf("imod2patch usage:\n");
printf("imod2patch [-v col] imod_model patch_file\n");
exit(1);
}
for (ind = 0; ind < MAX_VALUE_COLS; ind++) {
numValues[ind] = 0;
valueIDs[ind] = 0;
colToTypeMap[ind] = -1;
maxVal[ind] = -1.e37;
}
i = 1;
if (!strcmp(argv[i], "-v")) {
i++;
colForVal1 = atoi(argv[i++]);
}
mod = imodRead(argv[i]);
if (!mod)
exitError("Reading model %s\n", argv[i]);
if (imodBackupFile(argv[++i]))
exitError("Renaming existing output file to %s\n", argv[i]);
fout = fopen(argv[i], "w");
if (!fout)
exitError("Could not open %s\n", argv[i]);
/* Count up patches and values and find max of values */
for (ob = 0; ob < mod->objsize; ob++) {
listInd = 0;
for (co = 0; co < mod->obj[ob].contsize; co++) {
listStart = listInd;
if (mod->obj[ob].cont[co].psize >= 2) {
npatch++;
for (ind = 0; ind < MAX_VALUE_COLS; ind++) {
listInd = listStart;
if (istoreFindValue(mod->obj[ob].store, co, GEN_STORE_VALUE1 + 2 * ind, &value,
&listInd)) {
maxVal[ind] = B3DMAX(maxVal[ind], value);
numValues[ind]++;
}
}
}
}
}
/* printf("numval %d %d %d %f %f %f\n", numValues[0], numValues[1], numValues[2],
maxVal[0], maxVal[1], maxVal[2]); */
/* Get the value ID's if any and convert an entered ID to a type #. Also set format
for output based on maximum value */
maxValType = -1;
numCols = 0;
for (ind = 0; ind < MAX_VALUE_COLS; ind++) {
strcpy(format[ind], "%10.4f");
if (numValues[ind]) {
numCols++;
maxValType = ind;
if (maxVal[ind] > 10.1)
strcpy(format[ind], "%10.2f");
else if (maxVal[ind] > 1.01)
strcpy(format[ind], "%10.3f");
}
}
for (ind = 0; ind < B3DMIN(maxValType + 1, mod->obj[0].extra[IOBJ_EXSIZE - 1]); ind++)
valueIDs[ind] = mod->obj[0].extra[IOBJ_EXSIZE - 2 - ind];
/*printf("# vla ID %d %d %d %d\n", maxValType, valueIDs[0],valueIDs[1],valueIDs[2]);*/
/* Error checks on the column for value 1 */
if (colForVal1 < 1 || colForVal1 > numCols) {
if (numCols)
exitError("The column for general value type must be between 1 and %d", numCols);
exitError("There are no general values stored in the model");
}
colForVal1--;
/* Set up map from column to value type index */
if (numValues[0])
colToTypeMap[colForVal1] = 0;
col = 0;
for (ind = 1; ind <= maxValType; ind++) {
if (numValues[ind]) {
if (!colToTypeMap[col])
col++;
colToTypeMap[col++] = ind;
}
}
/*printf("%d %d %d %d\n", numCols, colToTypeMap[0], colToTypeMap[1], colToTypeMap[2]);*/
/* Output the header line */
fprintf(fout, "%d edited positions", npatch);
if (mod->obj[0].extra[IOBJ_EXSIZE - 1] > 0)
for (col = 0; col < numCols; col++)
fprintf(fout, " %d", valueIDs[colToTypeMap[col]]);
fprintf(fout, "\n");
for (ob = 0; ob < mod->objsize; ob++) {
listInd = 0;
for (co = 0; co < mod->obj[ob].contsize; co++) {
listStart = listInd;
if (mod->obj[ob].cont[co].psize >= 2) {
pts = mod->obj[ob].cont[co].pts;
ix = pts[0].x + 0.5;
iy = pts[0].y + 0.5;
iz = pts[0].z + 0.5;
dx = (pts[1].x - pts[0].x) / mod->pixsize;
dy = (pts[1].y - pts[0].y) / mod->pixsize;
dz = (pts[1].z - pts[0].z) / mod->pixsize;
if (mod->flags & IMODF_FLIPYZ)
fprintf(fout, "%6d %5d %5d %8.2f %8.2f %8.2f",
ix, iz, iy, dx, dz, dy);
else
fprintf(fout, "%6d %5d %5d %8.2f %8.2f %8.2f",
ix, iy, iz, dx, dy, dz);
for (col = 0; col < numCols; col++) {
ind = colToTypeMap[col];
if (numValues[ind]) {
listInd = listStart;
value = 0.;
istoreFindValue(mod->obj[ob].store, co, GEN_STORE_VALUE1 + 2 * ind, &value,
&listInd);
fprintf(fout, format[ind], value);
}
}
fprintf(fout, "\n");
}
}
}
fclose(fout);
exit(0);
}
/*
* Sets up variables for defining the input size and center, and section lists
* for the 2D processing case, and also sets ox, oy,oz and output mode.
*/
void set_input_options(ClipOptions *opt, MrcHeader *hin)
{
int i, zst, znd, ozst;
if (opt->nofsecs == IP_DEFAULT){
opt->nofsecs = hin->nz;
opt->secs = (int *)malloc(sizeof(int) * hin->nz);
for (i = 0; i < hin->nz; i++)
opt->secs[i] = i;
}
if (opt->dim == 3){
if (opt->iz == IP_DEFAULT){
opt->iz = hin->nz;
}
if (opt->cz == IP_DEFAULT){
opt->cz = hin->nz * 0.5f;
}
/* If there is no output entry, make it be same as input; but if there is,
and it is smaller output, trim input to that size */
if (opt->oz == IP_DEFAULT)
opt->oz = opt->iz;
else if (opt->iz > opt->oz)
opt->iz = opt->oz;
/* Set up a section list for the case where something is treated as
2d without -2d being given */
if (opt->nofsecs != IP_DEFAULT)
free(opt->secs);
zst = (int)floor(opt->cz - opt->iz / 2.);
znd = B3DMAX(B3DMIN(zst + opt->iz - 1, hin->nz - 1), 0);
zst = B3DMAX(B3DMIN(zst, hin->nz - 1), 0);
opt->nofsecs = znd + 1 - zst;
opt->secs = (int *)malloc(sizeof(int) * opt->nofsecs);
for (i = zst; i <= znd; i++)
opt->secs[i - zst] = i;
/* If requested output is larger than this output set, keep track of
blank slices to put out before and after */
if (opt->oz != IP_DEFAULT && opt->oz > opt->nofsecs) {
ozst = (int)floor(opt->cz - opt->oz / 2.);
opt->outBefore = B3DMAX(0, zst - ozst);
opt->outAfter = opt->oz - opt->nofsecs - opt->outBefore;
if (opt->outAfter < 0) {
opt->outBefore += opt->outAfter;
opt->outAfter = 0;
}
}
} else {
/* 2D case: use section list size for default output size */
if (opt->oz == IP_DEFAULT)
opt->oz = opt->nofsecs;
}
/* Convert starting, ending X or Y to ix/cx entries - main routine already
checked for conflict */
if (opt->x != IP_DEFAULT) {
opt->x2 = B3DMAX(opt->x, opt->x2);
opt->cx = (opt->x + opt->x2 + 1) / 2.;
opt->ix = opt->x2 + 1 - opt->x;
}
if (opt->ix == IP_DEFAULT)
opt->ix = hin->nx;
if ((int)opt->cx == IP_DEFAULT)
opt->cx = hin->nx * 0.5f;
if (opt->ox == IP_DEFAULT) {
opt->ox = opt->ix;
if (opt->process == IP_UNPACK)
opt->ox *= 2;
} else {
if (!opt->ocanresize){
show_warning("clip - Process can't change output size.");
opt->ox = opt->ix;
}
}
if (opt->y != IP_DEFAULT) {
opt->y2 = B3DMAX(opt->y, opt->y2);
opt->cy = (opt->y + opt->y2 + 1) / 2.;
opt->iy = opt->y2 + 1 - opt->y;
}
if (opt->iy == IP_DEFAULT)
opt->iy = hin->ny;
if ((int)opt->cy == IP_DEFAULT)
opt->cy = hin->ny * 0.5f;
if (opt->oy == IP_DEFAULT)
opt->oy = opt->iy;
else{
if (!opt->ocanresize){
show_warning("clip - Process can't change output size.");
opt->oy = opt->iy;
}
}
if (opt->pad == IP_DEFAULT)
opt->pad = hin->amean;
if (opt->mode == IP_DEFAULT)
opt->mode = hin->mode;
}
/*
* Write one slice to output file
* kSec is the index of the sections being processed,
* zWrite is address of z value at which to write, maintained here
* freeSlice 1 indicates to free the slice when done
*/
int clipWriteSlice(Islice *slice, MrcHeader *hout, ClipOptions *opt, int kSec,
int *zWrite, int freeSlice)
{
Islice *ps = NULL;
Islice *s;
int z;
int blankBefore = 0;
int blankAfter = 0;
/* Ignore if output size is smaller than # being processed */
if (kSec < (opt->nofsecs - opt->oz) / 2 ||
kSec >= (opt->nofsecs - opt->oz) / 2 + opt->oz) {
if (freeSlice)
sliceFree(slice);
return 0;
}
/* determine if blank slices need to be written before or after this slice */
if (opt->oz > opt->nofsecs) {
if (!kSec) {
if (opt->outBefore == IP_DEFAULT)
blankBefore = (opt->oz - opt->nofsecs) / 2;
else
blankBefore = opt->outBefore;
}
if (kSec == opt->nofsecs - 1) {
if (opt->outAfter == IP_DEFAULT)
blankAfter = opt->oz - opt->nofsecs - (opt->oz - opt->nofsecs) / 2;
else
blankAfter = opt->outAfter;
}
if (blankBefore || blankAfter) {
ps = clipBlankSlice(hout, opt);
if (!ps)
return -1;
}
}
/* Write blank slices before */
for (z = 0; z < blankBefore; z++)
if (mrc_write_slice((void *)ps->data.b, hout->fp, hout, (*zWrite)++, 'z'))
return -1;
/* convert slice to output mode if needed */
if (slice->mode != opt->mode && sliceNewMode(slice, opt->mode) < 0)
return -1;
/* Resize slice if necessary */
s = slice;
if (opt->ox != slice->xsize || opt->oy != slice->ysize) {
slice->mean = opt->pad;
s = mrc_slice_resize(slice, opt->ox, opt->oy);
if (!s) {
fprintf(stderr, "clipWriteSlice: error resizing slice.\n");
return(-1);
}
}
/* maintain min & max, add to mean unless overwriting */
sliceMMM(s);
hout->amin = B3DMIN(hout->amin, s->min);
hout->amax = B3DMAX(hout->amax, s->max);
if (opt->add2file != IP_APPEND_OVERWRITE)
hout->amean += (s->mean + (blankBefore + blankAfter) * opt->pad) /
hout->nz;
/* Write slice, free slices as needed */
if (mrc_write_slice((void *)s->data.b, hout->fp, hout, (*zWrite)++, 'z'))
return -1;
if (opt->ox != slice->xsize || opt->oy != slice->ysize)
sliceFree(s);
if (freeSlice)
sliceFree(slice);
/* Write blank slices after */
for (z = 0; z < blankAfter; z++)
if (mrc_write_slice((void *)ps->data.b, hout->fp, hout, (*zWrite)++, 'z'))
return -1;
if (ps)
sliceFree(ps);
return 0;
}
int main( int argc, char *argv[] )
{
int i = 0;
FILE *fin, *fout;
struct MRCheader hdata, hout;
struct MRCheader *hptr;
unsigned char *buf;
int bsize, csize, dsize;
int inside = 0;
int ntaper = DEFAULT_TAPER;
int taperEntered = 0;
Islice slice;
int zmin = -1, zmax = -1;
int secofs;
char *progname = imodProgName(argv[0]);
setStandardExitPrefix(progname);
if (argc < 2){
fprintf(stderr,
"%s version %s\n", progname, VERSION_NAME);
imodCopyright();
mrctaper_help(progname);
exit(3);
}
for (i = 1; i < argc; i++) {
if (argv[i][0] == '-') {
switch (argv[i][1]) {
case 'i':
inside = 1;
break;
case 't':
taperEntered = 1;
if (argv[i][2] != 0x00)
sscanf(argv[i], "-t%d", &ntaper);
else
sscanf(argv[++i], "%d", &ntaper);
break;
case 'z':
if (argv[i][2] != 0x00)
sscanf(argv[i], "-z%d%*c%d", &zmin, &zmax);
else
sscanf(argv[++i], "%d%*c%d", &zmin, &zmax);
break;
default:
printf("ERROR: %s - illegal option\n", progname);
mrctaper_help(progname);
exit(1);
break;
}
} else
break;
}
if (i < (argc - 2) || i == argc){
mrctaper_help(progname);
exit(3);
}
if (ntaper < 1 || ntaper > 127)
exitError("Taper must be between 1 and 127.");
if (i < argc - 1)
fin = iiFOpen(argv[i++], "rb");
else
fin = iiFOpen(argv[i++], "rb+");
if (fin == NULL)
exitError("Opening %s.", argv[i - 1]);
if (mrc_head_read(fin, &hdata))
exitError("Can't Read Input File Header.");
if (sliceModeIfReal(hdata.mode) < 0)
exitError("Can operate only on byte, integer and real data.");
if (!taperEntered) {
ntaper = (hdata.nx + hdata.ny) / 200;
ntaper = B3DMIN(127, B3DMAX(DEFAULT_TAPER, ntaper));
printf("Tapering over %d pixels\n", ntaper);
}
if (zmin == -1 && zmax == -1) {
zmin = 0;
zmax = hdata.nz - 1;
} else {
if (zmin < 0)
zmin = 0;
if (zmax >= hdata.nz)
zmax = hdata.nz - 1;
}
if (i < argc) {
fout = iiFOpen(argv[i], "wb");
if (fout == NULL)
exitError("Opening %s.", argv[i]);
hout = hdata;
hout.fp = fout;
/* DNM: eliminate extra header info in the output, and mark it as not swapped */
mrcInitOutputHeader(&hout);
hptr = &hout;
hout.nz = zmax + 1 - zmin;
hout.mz = hout.nz;
hout.zlen = hout.nz;
secofs = zmin;
} else {
if (b3dOutputFileType() == IIFILE_TIFF)
exitError("Cannot write to an existing TIFF file.");
hptr = &hdata;
fout = fin;
secofs = 0;
}
mrc_getdcsize(hdata.mode, &dsize, &csize);
bsize = hdata.nx * hdata.ny;
buf = (unsigned char *)malloc(dsize * csize * bsize);
if (!buf)
exitError("Couldn't get memory for slice.");
sliceInit(&slice, hdata.nx, hdata.ny, hdata.mode, buf);
for (i = zmin; i <= zmax; i++) {
printf("\rDoing section #%4d", i);
fflush(stdout);
if (mrc_read_slice(buf, fin, &hdata, i, 'Z'))
exitError("Reading section %d.", i);
if (sliceTaperAtFill(&slice, ntaper, inside))
exitError("Can't get memory for taper operation.");
if (mrc_write_slice(buf, fout, hptr, i - secofs, 'Z'))
exitError("Writing section %d.", i);
}
puts("\nDone!");
mrc_head_label(hptr, "mrctaper: Image tapered down to fill value at edges");
mrc_head_write(fout, hptr);
iiFClose(fout);
return(0);
}
/* Write the data volume with potential padding */
int grap_volume_write(Istack *v, MrcHeader *hout, ClipOptions *opt)
{
FILE *fp = hout->fp;
int zs, ks, z;
int k;
float min, max, mean, zscale;
Islice *s, *ps = NULL;
int labels;
if (opt->mode == IP_DEFAULT)
opt->mode = v->vol[0]->mode;
if (opt->ox == IP_DEFAULT)
opt->ox = v->vol[0]->xsize;
if (opt->oy == IP_DEFAULT)
opt->oy = v->vol[0]->ysize;
if (opt->oz == IP_DEFAULT)
opt->oz = v->zsize;
if (v->vol[0]->mode != opt->mode)
for(k = 0; k < v->zsize; k++){
sliceNewMode(v->vol[k], opt->mode);
}
/* calculate min, max, mean of volume. */
sliceMMM(v->vol[0]);
min = v->vol[0]->min;
max = v->vol[0]->max;
mean = v->vol[0]->mean;
for(k = 1; k < v->zsize; k++){
sliceMMM(v->vol[k]);
min = B3DMIN(min, v->vol[k]->min);
max = B3DMAX(max, v->vol[k]->max);
mean += v->vol[k]->mean;
}
mean /= (float)v->zsize;
/* DNM 6/26/02: do not make a new header if appending or overwriting! */
switch(opt->add2file){
case IP_APPEND_OVERWRITE:
ks = opt->isec;
hout->nz = ks + opt->oz;
opt->ox = hout->nx;
opt->oy = hout->ny;
if (hout->mode != v->vol[0]->mode){
fprintf(stderr,
"overwriting requires data modes to be the same.\n");
return(-1);
}
/* DNM 6/26/02: fix min and max, also fix mz and zlen */
/* DNM 9/13/02: oops, had xlen instead of zlen */
/* todo: recalc mmm. This is a start but not much */
hout->amin = B3DMIN(min, hout->amin);
hout->amax = B3DMAX(max, hout->amax);
zscale = hout->zlen / hout->mz;
hout->mz = hout->nz;
hout->zlen = hout->mz * zscale;
break;
case IP_APPEND_ADD:
ks = hout->nz;
hout->nz = hout->nz + opt->oz;
opt->ox = hout->nx;
opt->oy = hout->ny;
if (hout->mode != v->vol[0]->mode){
fprintf(stderr, "inserting requires data modes to be the same.\n");
return(-1);
}
hout->amin = B3DMIN(min, hout->amin);
hout->amax = B3DMAX(max, hout->amax);
hout->amean = ((hout->amean * ks) + (mean * opt->oz)) / hout->nz;
zscale = hout->zlen / hout->mz;
hout->mz = hout->nz;
hout->zlen = hout->mz * zscale;
break;
case IP_APPEND_FALSE:
/* New file: reinitialize header but preserve the labels, set
min/max/mean */
labels = hout->nlabl;
mrc_head_new(hout, opt->ox, opt->oy, opt->oz, v->vol[0]->mode);
hout->nlabl = labels;
hout->amin = min;
hout->amax = max;
hout->amean = mean;
ks = 0;
}
if (opt->pad == IP_DEFAULT)
opt->pad = hout->amean;
if (mrc_head_write(fp, hout))
return -1;
zs = (v->zsize - opt->oz) / 2;
for (k = ks, z = zs; k < hout->nz; k++, z++) {
/* printf("%d %d\n", k, z);*/
/* Write blank slice outside z range */
if ((z < 0) || (z >= v->zsize)) {
if (!ps) {
ps = clipBlankSlice(hout, opt);
if (!ps)
return -1;
}
if (mrc_write_slice((void *)ps->data.b, fp, hout, k, 'z'))
return (-1);
} else {
/* Resize slice only if necessary */
s = v->vol[z];
if (opt->ox != v->vol[0]->xsize || opt->oy != v->vol[0]->ysize) {
v->vol[z]->mean = opt->pad;
s = mrc_slice_resize(v->vol[z], opt->ox, opt->oy);
if (!s){
fprintf(stderr, "volume_write: error resizing slice.\n");
return(-1);
}
}
if (mrc_write_slice((void *)s->data.b, fp, hout, k, 'z'))
return (-1);
if (opt->ox != v->vol[0]->xsize || opt->oy != v->vol[0]->ysize)
sliceFree(s);
}
}
if (ps)
sliceFree(ps);
return(0);
}
/* Really fill the slice data for one slice */
void TumblerWindow::fillASlice(TumblerStruct *xtum)
{
unsigned short *sdata;
short *ndata = xtum->count->data.s;
int xysize = xtum->slice->xsize * xtum->slice->ysize;
int n;
float xs, ys, zs, xt, yt, zt;
float x, y, z;
float xsx, xsy, xsz;
float ysx, ysy, ysz;
float zsx, zsy, zsz;
float xtz, ytz, ztz;
int isize, jsize;
int ksize, xsize, ysize, zsize;
int xi, yi, zi;
int i, j, k;
float zoomfac;
int xmin,ymin,zmin,xmax,ymax,zmax;
int val;
float dx, dy, dz;
float x1, x2, y1, y2, z1, z2;
float a, b, c, d, e, f;
int pxi, nxi, pyi, nyi, pzi, nzi, cindex;
int maxval = xtum->maxval;
int minval = xtum->minval;
float dsum;
int nsum, shortcut, izoom, ilimshort, jlimshort, ishort, fillval, nmax;
float zoom = xtum->zoom;
unsigned char *bmap = NULL;
sdata = (unsigned short *)xtum->slice->data.s;
if (xtum->slice->xsize <= 0)
return;
if (xtum->slice->ysize <= 0)
return;
if (xtum->vi->ushortStore) {
bmap = ivwUShortInRangeToByteMap(xtum->vi);
if (!bmap)
return;
}
zoomfac = xtum->highres ? zoom : 1.0;
xmin = xtum->cx - xtum->nx/2;
if (xmin < 0) xmin = 0;
ymin = xtum->cy - xtum->ny/2;
if (ymin < 0) ymin = 0;
zmin = xtum->cz - xtum->nz/2;
if (zmin < 0) zmin = 0;
xmax = xtum->cx + xtum->nx/2;
if (xmax >= xtum->vi->xsize)
xmax = xtum->vi->xsize - 1;
ymax = xtum->cy + xtum->ny/2;
if (ymax >= xtum->vi->ysize)
ymax = xtum->vi->ysize - 1;
zmax = xtum->cz + xtum->nz/2;
if (zmax >= xtum->vi->zsize)
zmax = xtum->vi->zsize - 1;
isize = xtum->slice->xsize;
jsize = xtum->slice->ysize;
ksize = xtum->ms;
xsize = xtum->vi->xsize;
ysize = xtum->vi->ysize;
zsize = xtum->vi->zsize;
xsx = xtum->xstep.x/zoomfac;
xsy = xtum->xstep.y/zoomfac;
xsz = xtum->xstep.z/zoomfac;
ysx = xtum->ystep.x/zoomfac;
ysy = xtum->ystep.y/zoomfac;
ysz = xtum->ystep.z/zoomfac;
/* Steps in Z are independent of highres */
zsx = xtum->zstep.x;
zsy = xtum->zstep.y;
zsz = xtum->zstep.z;
/* DNM 4/29/04: rewrote for compactness and clarity */
xs = xtum->cx - 0.5f * (xsx * isize + ysx * jsize + zsx * xtum->ms);
ys = xtum->cy - 0.5f * (xsy * isize + ysy * jsize + zsy * xtum->ms);
zs = xtum->cz - 0.5f * (xsz * isize + ysz * jsize + zsz * xtum->ms);
/* imodPrintStderr("xyzs %f %f %f\n", xs, ys, zs); */
x = xs; y = ys; z = zs;
shortcut = 0;
izoom = (int)zoom;
if (xtum->highres && (zoom == izoom) && (zoom > 1.0)) {
shortcut = 1;
ilimshort = izoom * ((isize - 1) / izoom - 1);
jlimshort = izoom * ((jsize - 1) / izoom - 1);
} else
izoom = 1;
for(n = 0; n < xysize; n++) {
sdata[n] = 0;
ndata[n] = 0;
}
for(k = 0; k < ksize; k++){
xtz = x; ytz = y; ztz = z;
for(j = 0, n = 0; j < jsize; j++){
xt = x; yt = y; zt = z;
cindex = j * isize;
for(i = 0; i < isize; i++){
/* DNM 2/25/03: eliminate floor as in slicer */
xi = (int)x;
yi = (int)y;
zi = (int)(z + 0.5);
if ((xi >= xmin) && (xi <= xmax) &&
(yi >= ymin) && (yi <= ymax) &&
(zi >= zmin) && (zi <= zmax)
){
val = (*ivwFastGetValue)(xi, yi, zi);
if (xtum->highres) {
dx = x - xi - 0.5;
dy = y - yi - 0.5;
dz = z - zi;
pxi = xi - 1;
nxi = xi + 1;
pyi = yi - 1;
nyi = yi + 1;
pzi = zi - 1;
nzi = zi + 1;
if (pxi < 0) pxi = 0;
if (nxi >= xsize) nxi = xi;
if (pyi < 0) pyi = 0;
if (nyi >= ysize) nyi = yi;
if (pzi < 0) pzi = 0;
if (nzi >= zsize) nzi = zi;
x1 = (*ivwFastGetValue)(pxi, yi, zi);
x2 = (*ivwFastGetValue)(nxi, yi, zi);
y1 = (*ivwFastGetValue)( xi, pyi, zi);
y2 = (*ivwFastGetValue)( xi, nyi, zi);
z1 = (*ivwFastGetValue)( xi, yi, pzi);
z2 = (*ivwFastGetValue)( xi, yi, nzi);
a = (x1 + x2) * 0.5f - (float)val;
b = (y1 + y2) * 0.5f - (float)val;
c = (z1 + z2) * 0.5f - (float)val;
d = (x2 - x1) * 0.5f;
e = (y2 - y1) * 0.5f;
f = (z2 - z1) * 0.5f;
val = (int) ((a * dx * dx) + (b * dy * dy) + (c * dz * dz)
+ (d * dx) + (e * dy) + (f * dz) + (float)val + 0.5);
}
if (bmap)
val = bmap[B3DMAX(0, B3DMIN(65535, val))];
if (val > maxval)
val = maxval;
if (val < minval)
val = minval;
sdata[cindex + i] += (unsigned short)val;
ndata[cindex + i]++;
}
x += xsx;
y += xsy;
z += xsz;
/* If taking short cut, advance the source position to get to next
unzoomed pixel position */
if (shortcut != 0 && ((i >= izoom && j % izoom == 0) ||
(i >= izoom - 1 && j % izoom != 0))
&& i < ilimshort && j >= izoom && j < jlimshort) {
ishort = izoom - 1;
if (j % izoom)
ishort = ilimshort - izoom;
x += xsx * ishort;
y += xsy * ishort;
z += xsz * ishort;
i += ishort;
}
}
x = xt + ysx;
y = yt + ysy;
z = zt + ysz;
}
x = xtz + zsx;
y = ytz + zsy;
z = ztz + zsz;
}
nmax = 0;
nsum = 0;
dsum = 0.;
for (n = 0; n < xysize; n++) {
if (nmax < ndata[n])
nmax = ndata[n];
nsum += ndata[n];
dsum += sdata[n];
}
fillval = (int)(dsum / nsum + 0.5);
for(n = 0; n < xysize; n++)
sdata[n] += (nmax - ndata[n]) * fillval;
xtum->fillval = fillval * nmax;
if (shortcut)
slicerCubicFillin(sdata, isize, jsize, izoom, ilimshort, jlimshort, 0, 65535, 0);
B3DFREE(bmap);
}
/*!
* Fills [mat] with the coefficients of a Gaussian kernel with standard deviation
* [sigma]. The size of the kernel is set to 3 for [sigma] up to 1., 5 for [sigma]
* up to 2., etc., up to the size given by [limit]. The size is returned in [dim].
* The coefficients are scaled to sum to 1.
*/
void scaledGaussianKernel(float *mat, int *dim, int limit, float sigma)
{
*dim = 2 * (int)ceil((double)sigma) + 1;
*dim = B3DMIN(limit, *dim);
sliceGaussianKernel(mat, *dim, sigma);
}
/* Draw one of the image arrays in a subarea of the window */
void TumblerWindow::drawSubArea(TumblerStruct *xtum, unsigned short *sdata,
int llx, int urx)
{
float scale, offset;
unsigned int i, xysize;
unsigned char *data;
b3dUInt16 *usdata;
float tf, tmax, tmin;
int xo, yo;
int zoom = xtum->zoom;
xysize = xtum->slice->xsize * xtum->slice->ysize;
data = xtum->bwslice->data.b;
usdata = xtum->bwslice->data.us;
scaleData(xtum, sdata);
tmax = 255.0f;
tmin = 0.0f;
scale = xtum->scale;
offset = xtum->offset;
/* DNM: scale for depth 8 only if not rgba */
if (App->depth == 8 && !App->rgba){
scale *= xtum->vi->rampsize/256.0f;
tmax = xtum->vi->rampbase + xtum->vi->rampsize;
tmin = xtum->vi->rampbase;
for(i = 0; i < xysize; i++){
tf = ((sdata[i] + offset) * scale) + xtum->vi->rampbase;
if (tf < tmin) tf = tmin;
if (tf > tmax) tf = tmax;
data[i] = (unsigned char)tf;
}
} else if (xtum->vi->ushortStore) {
tmax = 65535.;
scale *= 256.;
for (i = 0; i < xysize; i++) {
tf = (sdata[i] + offset) * scale;
usdata[i] = (b3dUInt16)B3DMAX(tmin, B3DMIN(tmax, tf));
}
} else {
for(i = 0; i < xysize; i++){
tf = (sdata[i] + offset) * scale;
data[i] = (unsigned char)B3DMAX(tmin, B3DMIN(tmax, tf));
}
}
if (xtum->highres)
zoom = 1;
/* DNM 1/20/02: add slice argument to graphics calls; make it -1 to
prevent image re-use */
b3dDrawGreyScalePixelsSubArea
(xtum->image, ivwMakeLinePointers(xtum->vi, data, xtum->slice->xsize,
xtum->slice->ysize, xtum->vi->rawImageStore),
xtum->slice->xsize, xtum->slice->ysize,
0, 0, llx, 0, urx, xtum->height,
xtum->vi->rampbase, zoom,
&xo, &yo, -1);
}
/*!
* Converts the data in slice [s] from its current mode to [mode], allocating
* a new data array as needed. Complex values are converted to others by
* taking the magnitude. Values are converted to complex modes by setting the
* real component to the value, and the imaginary component to 0. RGB values
* are converted by taking a weighted sum of components. When converting to a
* mode with integer or byte values, the data are truncated to fit within the
* range of the new mode. Returns the new mode or -1 for error.
*/
int sliceNewMode(Islice *s, int mode)
{
Islice *ns;
Ival val;
int i, j;
int default_copy = 0;
int limit_val = 0;
float minval, maxval;
if (!s)
return(-1);
if (s->mode == mode)
return(mode);
ns = sliceCreate(s->xsize, s->ysize, mode);
/* Set up limiting values */
if (mode == MRC_MODE_BYTE || mode == MRC_MODE_RGB) {
limit_val = 1;
minval = 0.;
maxval = 255;
} else if (mode == MRC_MODE_SHORT) {
limit_val = 1;
minval = -32768.;
maxval = 32767.;
} else if (mode == MRC_MODE_USHORT) {
limit_val = 1;
minval = 0.;
maxval = 65535.;
}
if (!ns)
return(-1);
switch(s->mode){
case MRC_MODE_BYTE:
case MRC_MODE_SHORT:
case MRC_MODE_USHORT:
case MRC_MODE_FLOAT:
switch(mode){
case MRC_MODE_BYTE:
case MRC_MODE_SHORT:
case MRC_MODE_USHORT:
case MRC_MODE_FLOAT:
default_copy = 1;
break;
case MRC_MODE_COMPLEX_FLOAT:
case MRC_MODE_COMPLEX_SHORT:
val[1] = 0;
default_copy = 1;
break;
case MRC_MODE_RGB:
for(j = 0; j < s->ysize; j++)
for(i = 0; i < s->xsize; i++){
sliceGetVal(s, i, j, val);
if (limit_val)
val[0] = B3DMIN(maxval, B3DMAX(minval, val[0]));
val[2] = val[1] = val[0];
slicePutVal(ns, i, j, val);
}
break;
default:
default_copy = 1;
break;
}
break;
case MRC_MODE_COMPLEX_FLOAT:
case MRC_MODE_COMPLEX_SHORT:
switch(mode){
case MRC_MODE_BYTE:
case MRC_MODE_SHORT:
case MRC_MODE_USHORT:
case MRC_MODE_FLOAT:
for(j = 0; j < s->ysize; j++)
for(i = 0; i < s->xsize; i++){
sliceGetVal(s, i, j, val);
val[0] = (float)sqrt(val[0] * val[0] + val[1] * val[1]);
if (limit_val)
val[0] = B3DMIN(maxval, B3DMAX(minval, val[0]));
slicePutVal(ns, i, j, val);
}
break;
case MRC_MODE_COMPLEX_FLOAT:
case MRC_MODE_COMPLEX_SHORT:
default_copy = 1;
break;
case MRC_MODE_RGB:
for(j = 0; j < s->ysize; j++)
for(i = 0; i < s->xsize; i++){
sliceGetVal(s, i, j, val);
val[0] = (float)sqrt(val[0] * val[0] + val[1] * val[1]);
if (limit_val)
val[0] = B3DMIN(maxval, B3DMAX(minval, val[0]));
val[2] = val[1] = val[0];
slicePutVal(ns, i, j, val);
}
break;
}
break;
case MRC_MODE_RGB:
switch(mode){
case MRC_MODE_BYTE:
case MRC_MODE_SHORT:
case MRC_MODE_USHORT:
case MRC_MODE_FLOAT:
for(j = 0; j < s->ysize; j++)
for(i = 0; i < s->xsize; i++){
sliceGetVal(s, i, j, val);
val[0] = (val[0] * 0.3f) +
(val[1] * 0.59f) + (val[2] * 0.11f);
if (limit_val)
val[0] = B3DMIN(maxval, B3DMAX(minval, val[0]));
slicePutVal(ns, i, j, val);
}
break;
case MRC_MODE_COMPLEX_FLOAT:
case MRC_MODE_COMPLEX_SHORT:
for(j = 0; j < s->ysize; j++)
for(i = 0; i < s->xsize; i++){
sliceGetVal(s, i, j, val);
val[0] = (val[0] * 0.3f) +
(val[1] * 0.59f) + (val[2] * 0.11f);
val[1] = 0;
slicePutVal(ns, i, j, val);
}
break;
default:
default_copy = 1;
break;
}
break;
default:
default_copy = 1;
break;
}
if (default_copy){
for(j = 0; j < s->ysize; j++)
for(i = 0; i < s->xsize; i++){
sliceGetVal(s, i, j, val);
if (limit_val)
val[0] = B3DMIN(maxval, B3DMAX(minval, val[0]));
slicePutVal(ns, i, j, val);
}
}
free(s->data.b);
/* 2/3/07: switch from copying ns to s to just setting data and mode */
s->data.b = ns->data.b;
s->mode = mode;
free(ns);
return(mode);
}
/*
* Main entry
*/
int main( int argc, char *argv[])
{
Imod *imod;
Iobj *obj;
Ipoint point;
Istore store;
FILE *infp;
char line[1024];
int open = 0, zsort = 0, scat = 0, numPerCont = 0, fromZero = 0, zFromZero = 0;
int err, nvals, nread, ob, co, lineNum, after, needcont, i, numOffset, linelen;
int numPts = 0, numConts = 0, numObjs = 0;
int sphere = 0, circle = 0;
float tst1, tst2, xx, yy, zz, value;
float zOffset = 0.;
int numColors = 0;
int numNames = 0;
int hasValues = 0;
int contValues = 0;
int *red, *green, *blue;
int directScale = 0;
float xscale = 1., yscale = 1., zscale = 1., xtrans = 0., ytrans = 0., ztrans = 0.;
char **names = NULL;
char *progname = imodProgName(argv[0]);
char *filename, *imagename;
MrcHeader hdata;
IrefImage *ref;
FILE *fpimage = NULL;
char *errString;
int numOptArgs, numNonOptArgs;
/* Fallbacks from ../manpages/autodoc2man 2 1 point2model */
int numOptions = 16;
const char *options[] = {
"input:InputFile:FN:", "output:OutputFile:FN:", "open:OpenContours:B:",
"scat:ScatteredPoints:B:", "number:PointsPerContour:I:", "planar:PlanarContours:B:",
"zero:NumberedFromZero:B:", "zcoord:ZCoordinatesFromZero:B:",
"values:ValuesInLastColumn:I:", "circle:CircleSize:I:", "sphere:SphereRadius:I:",
"color:ColorOfObject:ITM:", "name:NameOfObject:CHM:",
"image:ImageForCoordinates:FN:", "pixel:PixelSpacingOfImage:FT:",
"origin:OriginOfImage:FT:"
};
/* Startup with fallback */
PipReadOrParseOptions(argc, argv, options, numOptions, progname,
2, 1, 1, &numOptArgs, &numNonOptArgs, imodUsageHeader);
/* Get input and output files */
if (PipGetInOutFile("InputFile", 0, &filename))
exitError("No input file specified");
infp = fopen(filename, "r");
if (!infp)
exitError("Error opening input file %s", filename);
free(filename);
if (PipGetInOutFile("OutputFile", 1, &filename))
exitError("No output file specified");
if (!PipGetString("ImageForCoordinates", &imagename)) {
fpimage = fopen(imagename, "rb");
if (!fpimage)
exitError("Could not open image file for coordinates: %s", imagename);
if (mrc_head_read(fpimage, &hdata))
exitError("Reading header from %s", imagename);
free(imagename);
}
directScale = 2 - PipGetThreeFloats("PixelSpacingOfImage", &xscale, &yscale, &zscale)
- PipGetThreeFloats("OriginOfImage", &xtrans, &ytrans, &ztrans);
if (directScale && fpimage)
exitError("You cannot use -image together with -pixel or -origin");
err = PipGetInteger("PointsPerContour", &numPerCont);
err = PipGetInteger("SphereRadius", &sphere);
err = PipGetInteger("CircleSize", &circle);
err = PipGetBoolean("OpenContours", &open);
err = PipGetBoolean("ScatteredPoints", &scat);
err = PipGetBoolean("PlanarContours", &zsort);
err = PipGetInteger("ValuesInLastColumn", &hasValues);
err = PipGetBoolean("ZCoordinatesFromZero", &zFromZero);
if (zFromZero)
zOffset = 0.5;
B3DCLAMP(hasValues, -1, 1);
if (hasValues < 0) {
hasValues = 1;
contValues = 1;
}
err = PipGetBoolean("NumberedFromZero", &fromZero);
numOffset = 1 - fromZero;
if (numPerCont < 0)
exitError("Number of points per contour must be positive or zero");
if (open + scat > 1)
exitError("Only one of -open or -scat may be entered");
// Get colors
err = PipNumberOfEntries("ColorOfObject", &numColors);
if (numColors) {
red = (int *)malloc(numColors * sizeof(int));
green = (int *)malloc(numColors * sizeof(int));
blue = (int *)malloc(numColors * sizeof(int));
if (!red || !green || !blue)
exitError("Allocating memory for colors");
for (co = 0; co < numColors; co++)
err = PipGetThreeIntegers("ColorOfObject", &red[co], &green[co],
&blue[co]);
}
// Get names
err = PipNumberOfEntries("NameOfObject", &numNames);
if (numNames) {
names = (char **)malloc(numNames * sizeof(char *));
if (!names)
exitError("Allocating memory for names");
for (co = 0; co < numNames; co++)
err = PipGetString("NameOfObject", &names[co]);
}
PipDone();
// Read first line of file, figure out how many values
if (fgetline(infp, line, 1024) <= 0)
exitError("Reading beginning of file");
nvals = sscanf(line, "%f %f %f %f %f %f", &tst1, &tst2, &xx, &yy, &zz, &value);
nvals -= hasValues;
if (nvals < 3)
exitError("There must be at least %d values per line", 3 + hasValues);
nvals = B3DMIN(nvals, 5);
if (numPerCont && nvals > 3) {
exitError("The point file has contour numbers and the -number option "
"cannot be used");
}
if (zsort && nvals > 3)
exitError("The point file has contour numbers and the -planar option "
"cannot be used");
rewind(infp);
imod = imodNew();
if (!imod)
exitError("Failed to get model structure");
// Set the image reference scaling
if (fpimage) {
imodSetRefImage(imod, &hdata);
fclose(fpimage);
} else if (directScale) {
imod->refImage = (IrefImage *)malloc(sizeof(IrefImage));
if (!imod->refImage)
exitError("Allocating IrefImage structure");
ref = imod->refImage;
ref->ctrans.x = xtrans;
ref->ctrans.y = ytrans;
ref->ctrans.z = ztrans;
ref->cscale.x = xscale;
ref->cscale.y = yscale;
ref->cscale.z = zscale;
ref->oscale.x = ref->oscale.y = ref->oscale.z = 1.;
ref->orot.x = ref->orot.y = ref->orot.z = 0.;
ref->crot.x = ref->crot.y = ref->crot.z = 0.;
ref->otrans.x = ref->otrans.y = ref->otrans.z = 0.;
}
ob = 0;
co = 0;
lineNum = 0;
imod->xmax = 0.;
imod->ymax = 0.;
imod->zmax = 0.;
store.type = GEN_STORE_VALUE1;
store.flags = GEN_STORE_FLOAT << 2;
// To do: error check contour and object #'s, and they are numbered from 1.
while (1) {
// get line, done on EOF, skip blank line
linelen = fgetline(infp, line, 1024);
if (linelen < 0)
break;
if (linelen == 0)
continue;
if (nvals == 3) {
nread = sscanf(line, "%f %f %f %f", &xx, &yy, &zz, &value);
} else if (nvals == 4) {
nread = sscanf(line, "%d %f %f %f %f", &co, &xx, &yy, &zz, &value);
co -= numOffset;
} else {
nread = sscanf(line, "%d %d %f %f %f %f", &ob, &co, &xx, &yy, &zz, &value);
co -= numOffset;
ob -= numOffset;
}
zz -= zOffset;
lineNum++;
// Skip line with no values
if (nread <= 0)
continue;
if (B3DMIN(5 + hasValues, nread) != nvals + hasValues &&
!(contValues && nread == nvals))
exitError("Every line should have %d entries; line %d has %d",
nvals + hasValues, lineNum, nread);
if (ob < 0 || co < 0)
exitError("Illegal object or contour number (object %d, contour %d at line %d",
ob + numOffset, co + numOffset, lineNum);
// Add objects if needed to get to the current object
if (ob >= imod->objsize) {
for (i = imod->objsize; i <= ob; i++) {
if (imodNewObject(imod))
exitError("Failed to add object to model");
if (open)
imod->obj[i].flags |= IMOD_OBJFLAG_OPEN;
if (scat)
imod->obj[i].flags |= IMOD_OBJFLAG_SCAT | IMOD_OBJFLAG_OPEN;
numObjs++;
imod->obj[i].pdrawsize = B3DMAX(0, sphere);
if (circle > 0) {
imod->obj[i].symsize = circle;
imod->obj[i].symbol = IOBJ_SYM_CIRCLE;
}
if (i < numColors) {
imod->obj[i].red = red[i] / 255.;
imod->obj[i].green = green[i] / 255.;
imod->obj[i].blue = blue[i] / 255.;
}
if (i < numNames) {
strncpy(imod->obj[i].name, names[i], IOBJ_STRSIZE - 1);
imod->obj[i].name[IOBJ_STRSIZE - 1] = 0x00;
}
}
}
// Determine if a contour is needed: either the contour number is too high
// or the number limit is reached or there is a change in Z
needcont = 0;
obj = &imod->obj[ob];
if (co >= obj->contsize)
needcont = 1;
else if ((numPerCont && obj->cont[co].psize >= numPerCont) ||
(zsort && B3DNINT(obj->cont[co].pts[0].z) != B3DNINT(zz))) {
co++;
needcont = 1;
}
if (needcont) {
imodSetIndex(imod, ob, -1, -1);
for (i = obj->contsize; i<= co; i++) {
if (imodNewContour(imod))
exitError("Failed to add contour to model");
numConts++;
}
}
point.x = xx;
point.y = yy;
point.z = zz;
imod->xmax = B3DMAX(imod->xmax, B3DNINT(xx + 10.));
imod->ymax = B3DMAX(imod->ymax, B3DNINT(yy + 10.));
imod->zmax = B3DMAX(imod->zmax, B3DNINT(zz + 1.));
if (!imodPointAppend(&obj->cont[co], &point))
exitError("Failed to add point to contour");
numPts++;
// take care of value for contour or point, only add one per contour
if (hasValues) {
store.value.f = value;
err = 0;
if (contValues && istoreLookup(obj->store, co, &after) < 0) {
if (nread < nvals + 1)
exitError("The first point for a contour must have a value entry; line %d "
"has only %d entries", lineNum, nread);
store.index.i = co;
err = istoreInsert(&obj->store, &store);
} else {
store.index.i = obj->cont[co].psize - 1;
err = istoreInsert(&obj->cont[co].store, &store);
}
if (err)
exitError("Failed to add general value");
}
}
// Get the object min/max values set up
if (hasValues) {
for (ob = 0; ob < imod->objsize; ob++) {
if (imod->obj[ob].contsize && istoreFindAddMinMax1(&imod->obj[ob]))
exitError("Adding min/max values to object");
}
}
// Attach image file's size as the max values
if (fpimage) {
imod->xmax = hdata.nx;
imod->ymax = hdata.ny;
imod->zmax = hdata.nz;
}
fclose(infp);
if (imodBackupFile(filename))
printf("Warning: %s - Failed to make old version of %s be a backup file\n",
progname, filename);
imod->file = fopen(filename, "wb");
if (!imod->file)
exitError("Opening new model file %s", filename);
if (imodWriteFile(imod))
exitError("Writing model file %s", filename);
free(filename);
printf("Model created with %d objects, %d contours, %d points\n", numObjs,
numConts, numPts);
exit(0);
}
