void read(int argc, char **argv)
{
parser.setCommandLine(argc, argv);
int general_section = parser.addSection("General options");
fn1 = parser.getOption("--i1", "1st input STAR file ");
fn2 = parser.getOption("--i2", "2nd input STAR file ");
fn_both = parser.getOption("--both", "Output STAR file with entries from both input STAR files ", "");
fn_only1 = parser.getOption("--only1", "Output STAR file with entries that only occur in the 1st input STAR files ", "");
fn_only2 = parser.getOption("--only2", "Output STAR file with entries that only occur in the 2nd input STAR files ", "");
fn_label1 = parser.getOption("--label1", "1st metadata label for the comparison (may be string, int or DOUBLE)", "");
fn_label2 = parser.getOption("--label2", "2nd metadata label for the comparison (DOUBLE only) for 2D/3D-distance)", "");
fn_label3 = parser.getOption("--label3", "3rd metadata label for the comparison (DOUBLE only) for 3D-distance)", "");
eps = textToFloat(parser.getOption("--max_dist", "Maximum distance to consider a match (for int and DOUBLE only)", "0."));
// Check for errors in the command-line option
if (parser.checkForErrors())
REPORT_ERROR("Errors encountered on the command line, exiting...");
}
void read(int argc, char **argv)
{
parser.setCommandLine(argc, argv);
int general_section = parser.addSection("General options");
fn_star = parser.getOption("--i", "Input STAR file with the images (as rlnImageName) to be saved in a stack");
fn_root = parser.getOption("--o", "Output rootname","output");
do_spider = parser.checkOption("--spider_format", "Write out in SPIDER stack format (by default MRC stack format)");
do_split_per_micrograph = parser.checkOption("--split_per_micrograph", "Write out separate stacks for each micrograph (needs rlnMicrographName in STAR file)");
do_apply_trans = parser.checkOption("--apply_transformation", "Apply the inplane-transformations (needs _rlnOriginX/Y and _rlnAnglePsi in STAR file)");
fn_ext = (do_spider) ? ".spi" : ".mrcs";
// Check for errors in the command-line option
if (parser.checkForErrors())
REPORT_ERROR("Errors encountered on the command line, exiting...");
}
void read(int argc, char **argv)
{
parser.setCommandLine(argc, argv);
int general_section = parser.addSection("General Options");
fn_unt = parser.getOption("--u", "STAR file with the untilted xy-coordinates");
fn_til = parser.getOption("--t", "STAR file with the untilted xy-coordinates");
size = textToInteger(parser.getOption("--size", "Largest dimension of the micrograph (in pixels), e.g. 4096"));
dim = textToInteger(parser.getOption("--dim", "Dimension of boxed particles (for EMAN .box files in pixels)", "200"));
acc = textToFloat(parser.getOption("--acc", "Allowed accuracy (in pixels), e.g. half the particle diameter"));
tilt = textToFloat(parser.getOption("--tilt", "Fix tilt angle (in degrees)", "99999."));
rot = textToFloat(parser.getOption("--rot", "Fix direction of the tilt axis (in degrees), 0 = along y, 90 = along x", "99999."));
do_opt = !parser.checkOption("--dont_opt", "Skip optimization of the transformation matrix");
mind2 = ROUND(acc * acc);
int angle_section = parser.addSection("Specified tilt axis and translational search ranges");
tilt0 = textToFloat(parser.getOption("--tilt0", "Minimum tilt angle (in degrees)","0."));
tiltF = textToFloat(parser.getOption("--tiltF", "Maximum tilt angle (in degrees)","99999."));
if (tiltF == 99999.) tiltF = tilt0;
tiltStep = textToFloat(parser.getOption("--tiltStep", "Tilt angle step size (in degrees)","1."));
rot0 = textToFloat(parser.getOption("--rot0", "Minimum rot angle (in degrees)","0."));
rotF = textToFloat(parser.getOption("--rotF", "Maximum rot angle (in degrees)","99999."));
if (rotF == 99999.) rotF = rot0;
rotStep = textToFloat(parser.getOption("--rotStep", "Rot angle step size (in degrees)","1."));
x0 = textToInteger(parser.getOption("--x0", "Minimum X offset (pixels)","-99999"));
xF = textToInteger(parser.getOption("--xF", "Maximum X offset (pixels)","99999"));
xStep = textToInteger(parser.getOption("--xStep", "X offset step size (pixels)","-1"));
y0 = textToInteger(parser.getOption("--y0", "Minimum Y offset (pixels)","-99999"));
yF = textToInteger(parser.getOption("--yF", "Maximum Y offset (pixels)","99999"));
yStep = textToInteger(parser.getOption("--yStep", "Y offset step size (pixels)","-1"));
// Check for errors in the command-line option
if (parser.checkForErrors())
REPORT_ERROR("Errors encountered on the command line, exiting...");
// If tilt and rot were given: do not search those
if (tilt != 99999.)
{
tilt0 = tiltF = tilt;
tiltStep = 1.;
}
if (rot != 99999.)
{
rot0 = rotF = rot;
rotStep = 1.;
}
// By default search the entire micrograph
x0 = XMIPP_MAX(x0, -size);
xF = XMIPP_MIN(xF, size);
// By default use a xStep of one third the accuracy
if (xStep < 0)
xStep = acc / 3;
// By default treat y search in the same way as the x-search
if (y0 == -99999)
y0 = x0;
if (yF == 99999)
yF = xF;
if (yStep < 0)
yStep = xStep;
// Done reading, now fill p_unt and p_til
MDunt.read(fn_unt);
MDtil.read(fn_til);
// Check for the correct labels
if (!MDunt.containsLabel(EMDL_IMAGE_COORD_X) || !MDunt.containsLabel(EMDL_IMAGE_COORD_Y))
REPORT_ERROR("ERROR: Untilted STAR file does not contain the rlnCoordinateX or Y labels");
if (!MDtil.containsLabel(EMDL_IMAGE_COORD_X) || !MDtil.containsLabel(EMDL_IMAGE_COORD_Y))
REPORT_ERROR("ERROR: Tilted STAR file does not contain the rlnCoordinateX or Y labels");
double x, y;
p_unt.clear();
FOR_ALL_OBJECTS_IN_METADATA_TABLE(MDunt)
{
MDunt.getValue(EMDL_IMAGE_COORD_X, x);
MDunt.getValue(EMDL_IMAGE_COORD_Y, y);
p_unt.push_back((int)x);
p_unt.push_back((int)y);
}
p_til.clear();
FOR_ALL_OBJECTS_IN_METADATA_TABLE(MDtil)
{
MDtil.getValue(EMDL_IMAGE_COORD_X, x);
MDtil.getValue(EMDL_IMAGE_COORD_Y, y);
p_til.push_back((int)x);
p_til.push_back((int)y);
}
// Initialize best transformation params
best_x = best_y = 9999;
best_rot = best_tilt = 9999.;
}
void usage()
{
parser.writeUsage(std::cerr);
}
void read(int argc, char **argv)
{
parser.setCommandLine(argc, argv);
int general_section = parser.addSection("General options");
fn_unt = parser.getOption("--u", "Input STAR file with untilted particles");
fn_til = parser.getOption("--t", "Input STAR file with tilted particles");
fn_eps = parser.getOption("--o", "Output EPS file ", "tiltpair.eps");
fn_sym = parser.getOption("--sym", "Symmetry point group", "C1");
exp_tilt = textToFloat(parser.getOption("--exp_tilt", "Choose symmetry operator that gives tilt angle closest to this value", "0."));
exp_beta = textToFloat(parser.getOption("--exp_beta", "Choose symmetry operator that gives beta angle closest to this value", "0."));
dist_from_alpha = textToFloat(parser.getOption("--dist_from_alpha", "Direction (alpha angle) of tilt axis from which to calculate distance", "0."));
dist_from_tilt = textToFloat(parser.getOption("--dist_from_tilt", "Tilt angle from which to calculate distance", "0."));
plot_max_tilt = textToFloat(parser.getOption("--max_tilt", "Maximum tilt angle to plot in the EPS file", "90."));
plot_spot_radius = textToInteger(parser.getOption("--spot_radius", "Radius in pixels of the spots in the tiltpair plot", "3"));
// Check for errors in the command-line option
if (parser.checkForErrors())
REPORT_ERROR("Errors encountered on the command line, exiting...");
}