/usr/bin/mincpik is in minc-tools 2.3.00+dfsg-1.1+b1.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 | #! /usr/bin/env perl
#
# Copyright 2009
# Andrew Janke - a.janke@gmail.com
# The University of Queensland
#
# Permission to use, copy, modify, and distribute this software and its
# documentation for any purpose and without fee is hereby granted,
# provided that the above copyright notice appear in all copies. The
# author and the University make no representations about the
# suitability of this software for any purpose. It is provided "as is"
# without express or implied warranty.
use strict;
use warnings "all";
use Getopt::Long;
use Pod::Usage;
use File::Basename;
use File::Temp qw/ tempdir /;
my($Help, $Usage, $me, @opt_table, $tmpdir, %opt);
my(@args, $args, $infile, $outfile, %ordering, $CODE);
# permutation 'matrix' for differing views
%ordering = (
'zspace' => ['yspace', 'xspace'],
'yspace' => ['zspace', 'xspace'],
'xspace' => ['zspace', 'yspace'],
);
$me = &basename($0);
%opt = (
'help' => 0,
'man' => 0,
'verbose' => 0,
'clobber' => 0,
'fake' => 0,
'scale' => 2,
'width' => undef,
'bitdepth' => 8,
'range' => undef,
'image_range' => undef,
'auto_range' => 0,
'lookup' => undef,
'slice' => undef,
'dirs' => ['zspace'],
'triplanar' => 0,
'tilesize' => 250,
'title' => 0,
'title_text' => undef,
'title_size' => 16,
'sagittal_offset' => undef,
'sagittal_offset_perc' => undef,
'orientation' => 'vertical',
'anot_bar' => undef,
);
# Check arguments
&GetOptions(
'help|?' => \$opt{'help'},
'man' => \$opt{'man'},
'version' => sub { &print_version_info },
'v|verbose' => \$opt{'verbose'},
'c|clobber' => \$opt{'clobber'},
'f|fake' => \$opt{'fake'},
'scale=i' => \$opt{'scale'},
'width=i' => \$opt{'width'},
'depth=i' => \$opt{'bitdepth'},
'title' => \$opt{'title'},
'title_text=s' => \$opt{'title_text'},
'title_size=i' => \$opt{'title_size'},
'anot_bar=s' => \$opt{'anot_bar'},
# Image range and lookup table options
'range=f{2}' => \@{$opt{'range'}},
'image_range=f{2}' => \@{$opt{'image_range'}},
'auto_range' => \$opt{'auto_range'},
'lookup=s' => \$opt{'lookup'},
# Slicing options
's|slice=i' => \$opt{'slice'},
'z|axial|transverse' => sub { $opt{'dirs'} = ['zspace']; },
'y|coronal' => sub { $opt{'dirs'} = ['yspace']; },
'x|sagittal' => sub { $opt{'dirs'} = ['xspace']; },
# triplanar options
't|triplanar' => \$opt{'triplanar'},
'tilesize=i' => \$opt{'tilesize'},
'sagittal_offset=i' => \$opt{'sagittal_offset'},
'sagittal_offset_perc=i' => \$opt{'sagittal_offset_perc'},
'vertical' => \$opt{'orientation'},
'horizontal' => \$opt{'orientation'},
) or pod2usage(-verbose => 1) && exit;
# handle -man, -help or missing args
pod2usage(-verbose => 1) if $opt{'help'};
pod2usage(-exitstatus => 0, -verbose => 2) if $opt{'man'};
pod2usage(-verbose => 0) && exit if ($#ARGV != 1);
# Check arguments
#&Getopt::Tabular::SetHelp ($Help, $Usage);
#&GetOptions (\@opt_table, \@ARGV) || exit 1;
#die $Usage if ($#ARGV < 0);
# create temporary directory
$tmpdir = &tempdir( "$me-XXXXXXXX", TMPDIR => 1, CLEANUP => 1 );
# set up file names and do a few checks
$infile = $ARGV[0];
$outfile = (defined($ARGV[1])) ? $ARGV[1] : 'PNG:-';
die "$me: Couldn't find $infile\n\n" if (!-e $infile);
if($outfile ne 'PNG:-' && -e $outfile && !$opt{'clobber'}){
die "\n$me: $outfile exists, use -clobber to overwrite\n\n";
}
if($opt{'bitdepth'} != 16 && $opt{bitdepth} != 8) {
die "\n$me: Invalid bitdepth specified - $opt{bitdepth} instead of 8 or 16\n\n";
}
# sanity check
if($opt{'auto_range'} && @{$opt{'image_range'}}){
die "\n$me: only specify one of -auto_range and -image_range (not both)\n\n";
}
# warn about -slice and -triplanar
if(defined($opt{'slice'}) && $opt{'triplanar'}){
warn "\n$me: you probably don't want to use both -triplanar and -slice\n\n";
}
# warn about -sagittal_offset and -sagittal_offset_perc
if(defined($opt{'sagittal_offset'}) && $opt{'sagittal_offset_perc'}){
warn "\n$me: only use one of -sagittal_offset -sagittal_offset_perc\n\n";
}
# set up directions for triplanar
if($opt{'triplanar'}){
$opt{'dirs'} = ['zspace', 'xspace', 'yspace'];
}
my ($space, $n_slices, $convert_infile, $imgfile,
@extract_args, @convert_args,
$img_x, $img_y,
$img_step_x, $img_step_y,
$img_length_x, $img_length_y,
$dim_names, $pipe_args, $dimorder,
@mont_files);
# find the 5% to 95% PcT image range if -auto_range
if($opt{'auto_range'}){
my $buf;
print STDERR "Getting range of $infile\n" if $opt{'verbose'};
chomp($buf = `mincstats -quiet -pctT 5 $infile`);
$buf *= 1.0;
@{$opt{'image_range'}}[0] = $buf;
chomp($buf = `mincstats -quiet -pctT 95 $infile`);
$buf *= 1.0;
@{$opt{'image_range'}}[1] = $buf;
# a bit of output
if($opt{'verbose'}){
print STDERR "Using image range of [@{$opt{image_range}}[0]:@{$opt{image_range}}[1]]\n";
}
}
# foreach slicing direction
foreach $space (@{$opt{'dirs'}}){
print STDERR "Doing direction $space\n" if $opt{'verbose'};
my($slice);
$CODE = "GRAY";
# set up the imgfile depending on triplanar and -title
if($opt{'triplanar'}){
$imgfile = "$tmpdir/trip-$space.png";
push(@mont_files, $imgfile);
}
elsif($opt{'title'}){
$imgfile = "$tmpdir/image.png";
}
else{
$imgfile = $outfile;
}
# Get the info we need
$args = "mincinfo ".
"-dimlength $space ".
"-dimlength $ordering{$space}[0] ".
"-dimlength $ordering{$space}[1] ".
"-attvalue $ordering{$space}[0]:step ".
"-attvalue $ordering{$space}[1]:step ".
"-dimnames ".
$infile;
($n_slices, $img_x, $img_y, $img_step_x, $img_step_y, $dim_names) = split("\n", `$args`);
if(defined($opt{'width'})){
$opt{'scale'} = $opt{'width'}/abs($img_step_y * $img_y);
print STDERR "Auto-scaling width factor: $opt{'scale'}\n" if $opt{'verbose'};
}
$img_length_x = abs(int($img_step_x * $img_x * $opt{'scale'}));
$img_length_y = abs(int($img_step_y * $img_y * $opt{'scale'}));
# figure out the slice to get
$slice = (!defined($opt{'slice'})) ? int($n_slices/2) : $opt{'slice'};
# do the sagittal offset (only one of these should be done)
if($space eq 'xspace'){
# slice offset
if(defined($opt{'sagittal_offset'})){
$slice += $opt{'sagittal_offset'};
}
# perc offset
if(defined($opt{'sagittal_offset_perc'})){
$slice += int($n_slices * $opt{'sagittal_offset_perc'} / 100);
}
}
# check we didn't step of the edge
if($slice >= $n_slices || $slice < 0){
die "Slice $slice out of range (0-" . ($n_slices-1) . ")\n\n";
}
# check if we have a vector_dimension already
if($dim_names =~ m/vector_dimension/){
$CODE = 'RGB';
}
# take only the first timepoint if we have a time dimension
my @time_res_args = ();
if($dim_names =~ m/time/){
@time_res_args = ('-dimrange', "time=0,0");
}
# do the reshaping
$dimorder = join(',', $space, @{$ordering{$space}});
if($CODE eq 'RGB'){
$dimorder .= ',vector_dimension';
}
@args = ('mincreshape', '-clobber', '-quiet',
'-normalize',
'+direction',
'-dimsize', "$space=-1",
'-dimsize', "$ordering{$space}[0]=-1",
'-dimsize', "$ordering{$space}[1]=-1",
'-dimorder', $dimorder,
'-dimrange', "$space=$slice,1",
@time_res_args,
$infile, "$tmpdir/reshaped.mnc");
if(scalar(@{$opt{'range'}}) != 0){
push(@args, '-valid_range', @{$opt{'range'}}[0], @{$opt{'range'}}[1]);
}
if(scalar(@{$opt{'image_range'}}) != 0){
push(@args, '-image_range', @{$opt{'image_range'}}[0], @{$opt{'image_range'}}[1]);
}
&do_cmd(@args);
# do the lookup if required
$convert_infile = "$tmpdir/reshaped.mnc";
if($opt{'lookup'}){
if($CODE eq 'RGB'){
warn "$me: Input is vector-valued already. No colour lookup done.\n";
}
else{
$convert_infile = "$tmpdir/lookup.mnc";
$CODE = 'RGB';
&do_cmd('minclookup', '-clobber', '-quiet',
split(' ', $opt{'lookup'}),
"$tmpdir/reshaped.mnc", $convert_infile);
}
}
# set up mincextract command
@extract_args = ('mincextract', $convert_infile,
'-normalize',
($opt{'bitdepth'} == 16) ? ('-short', '-unsigned') : '-byte');
# set up convert arguments
# a flip is 'normal' due to the difference between mnc and most image co-ordinates
@convert_args = ('convert',
'-depth', $opt{'bitdepth'},
'-flip',
'-size', $img_y . 'x' . $img_x,
'-geometry', $img_length_y . 'x' . $img_length_x . '!',
"$CODE:-", $imgfile);
# check if we are big or little endian for convert's MSB wierdity
$pipe_args = '|';
if($opt{'bitdepth'} == 16){
if(unpack("c",substr(pack("s",1),0,1))){
warn "$me: LSB machine, swapping bytes with dd and crossing fingers\n";
$pipe_args .= ' dd conv=swab | ';
}
}
&do_cmd(join(' ', @extract_args, $pipe_args, @convert_args));
}
# do the triplanar if requested
if($opt{'triplanar'}){
my @orient_args;
if($opt{'title'}){
$imgfile = "$tmpdir/mont.png";
}
else{
$imgfile = $outfile;
}
if($opt{'orientation'} eq 'vertical'){
@orient_args = ('-tile', ('1x' . ($#mont_files + 1)));
}
else{ # $opt{orientation} eq 'horizontal'
@orient_args = ('-tile', (($#mont_files + 1) . 'x1'));
}
# do the montage
&do_cmd('montage',
@orient_args,
'-background', 'grey10',
'-geometry', "$opt{tilesize}x$opt{tilesize}+1+1",
@mont_files, $imgfile);
}
# Add the title
if($opt{'title'}){
# set up the title text
if(!defined($opt{'title_text'})){
$opt{'title_text'} = &basename($infile);
$opt{'title_text'} =~ s/\.mnc$//;
}
# This really does not work all that well (but should), go figure
# &do_cmd('convert', '-box', 'black',
# '-font', '7x13',
# '-fill', 'white',
# '-draw', "text 4,12 \"$opt{'title_text'}\"",
# $imgfile, $outfile);
#
# use montage instead
&do_cmd('montage',
'-geometry', '100x100%',
'-background', 'black',
'-fill', 'white',
'-label', $opt{'title_text'},
'-pointsize', $opt{'title_size'},
$imgfile, $outfile);
}
# create the annotated bar if required
if(defined($opt{'anot_bar'})){
my($min, $max, $pcode,
$q0, $q1, $q2, $q3, $q4, $bh, $bw, $bb, $ob,
$textbump, $i, @buf);
# set up a few constants
$textbump = 3;
$pcode = '%6g';
# text border, other border, height, width
$bb = 50;
$ob = 25;
$bh = $img_length_y - ($ob*2);
$bw = int($bh/10);
# get range if not defined
if(!defined($opt{'image_range'}[0])){
print STDERR "Getting image range\n" if $opt{'verbose'};
@buf = split(/\n/, `mincstats -min -max -quiet $infile`);
@{$opt{'image_range'}}[0] = $buf[0] * 1.0;
@{$opt{'image_range'}}[1] = $buf[1] * 1.0;
}
$min = @{$opt{'image_range'}}[0];
$max = @{$opt{'image_range'}}[1];
# set up the datafile
my(@data) = undef;
my($packstring) = '';
for($i=0; $i<$bh; $i++){
$data[$i] = $i;
$packstring .= 'f';
}
open(FH, ">$tmpdir/tmp-float.raw");
for($i=0; $i<$bw; $i++){
syswrite(FH, pack($packstring, @data));
}
close(FH);
# make minc file
&do_cmd('rawtominc', '-clobber',
'-float',
'-input', "$tmpdir/tmp-float.raw",
'-xstep', 1, '-ystep', 1, '-zstep', 1,
'-xstart', 0, '-ystart', 0, '-zstart', 0,
'-dimorder', 'xspace,yspace,zspace',
"$tmpdir/bar.mnc", $bw, $bh, 1);
# make .miff bar image (whoa... recursion!)
&do_cmd('mincpik', '-clobber',
'-scale', 1,
(defined($opt{'lookup'})) ? ('-lookup', $opt{'lookup'}) : (),
"$tmpdir/bar.mnc", "$tmpdir/bar.png");
# set up the text
$q0 = sprintf($pcode, $min);
$q1 = sprintf($pcode, (($max-$min) * 0.25) + $min);
$q2 = sprintf($pcode, (($max-$min) * 0.5) + $min);
$q3 = sprintf($pcode, (($max-$min) * 0.75) + $min);
$q4 = sprintf($pcode, $max);
# create the bar itself via convert
&do_cmd('convert',
'-bordercolor', 'white',
'-border', $bb,
# color for all the decorations
'-fill', 'black',
# bar border
'-draw', "line " . join(',', $bb, $bb, ($bb+$bw), $bb ),
'-draw', "line " . join(',', $bb, ($bb+$bh), ($bb+$bw), ($bb+$bh)),
'-draw', "line " . join(',', $bb, $bb, $bb, ($bb+$bh)),
'-draw', "line " . join(',', ($bb+$bw), $bb, ($bb+$bw), ($bb+$bh)),
# 3 ticks at 1/4, 1/2 and 3/4
'-draw', "line " . join(',', ($bb+($bw*3/4)), ($bb+($bh*1/4)), ($bb+$bw), ($bb+($bh*1/4))),
'-draw', "line " . join(',', ($bb+($bw*3/4)), ($bb+($bh*2/4)), ($bb+$bw), ($bb+($bh*2/4))),
'-draw', "line " . join(',', ($bb+($bw*3/4)), ($bb+($bh*3/4)), ($bb+$bw), ($bb+($bh*3/4))),
# text
'-draw', 'text ' . ($bb+$bw) . ',' . ($bb+($bh*0/4)+$textbump) . " '$q4'",
'-draw', 'text ' . ($bb+$bw) . ',' . ($bb+($bh*1/4)+$textbump) . " '$q3'",
'-draw', 'text ' . ($bb+$bw) . ',' . ($bb+($bh*2/4)+$textbump) . " '$q2'",
'-draw', 'text ' . ($bb+$bw) . ',' . ($bb+($bh*3/4)+$textbump) . " '$q1'",
'-draw', 'text ' . ($bb+$bw) . ',' . ($bb+($bh*4/4)+$textbump) . " '$q0'",
# finally crop of the extra border
'-crop', (($bb*2)+$bw-($bb-$ob)) . "x" . (($bb*2)+$bh-$bb) . "+" . ($bb-$ob) . "+" . ($bb-$ob),
"$tmpdir/bar.png", $opt{'anot_bar'});
}
sub do_cmd {
print STDERR "@_\n" if $opt{'verbose'};
if(!$opt{'fake'}){
system(@_) == 0 or die "\n$me: Failed executing @_\n\n";
}
}
# print version information
sub print_version_info {
my $PACKAGE = 'minc-tools';
my $VERSION = '2.3.00';
my $PACKAGE_BUGREPORT = 'a.janke@gmail.com';
print STDOUT "\n$PACKAGE version $VERSION\n".
"Comments to $PACKAGE_BUGREPORT\n\n";
exit 0;
}
__END__
=head1 NAME
B<mincpik> - generate images from minc files
=head1 SYNOPSIS
B<mincpik> [options] <infile>.mnc [<image.type>]
mincpik generates image files from MINC volumes using the Imagemagick
convert utility. Use -help or -man for more information and examples
=head1 DESCRIPTION
B<mincpik> generates image files from MINC volumes using the Imagemagick
B<convert> utility. For a complete list of output file types see the
B<convert> man pages.
EXAMPLES:
To display a default view, axial (z) slicing, middle slice
using display. (display is part of the Imagemagick package)
mincpik infile.mnc PNG:- | display -
To generate a PNG file of the 15th coronal slice
mincpik -slice 15 -coronal infile.mnc outfile.png
To generate a JPG file using the hotmetal lookup table
with the image range 0 to 100
mincpik -lookup '-hotmetal' -image_range 0 100 infile.mnc outfile.jpg
ImageMagick: http://www.wizards.dupont.com/cristy/ImageMagick.html
NB: ImageMagick should be compiled without 16-bit quanta.
Currently if there is a time dimension in the file the image will
only produced from the first time point
Problems or comments should be sent to: a.janke\@gmail.com
=head1 OPTIONS
=over 4
=item B<-v>, B<--verbose>
Be noisy when doing things
=item B<--version>
Print version number and exit
=item B<-?>, B<--help>
Dump some quick help output
=item B<--man>
Dump a man page
=item B<-c> B<--clobber>
overwrite the output file if it exists already
=item B<-f> B<--fake>
do a dry run, (echo cmds only). This is usually used in combination with -verbose to echo commands only
=item B<--scale>
scaling factor for resulting image, by default images are output
at twice their original resolution
=item B<--width>
autoscale the resulting image to have a fixed image width (in pixels)
=item B<--depth>
bitdepth for resulting image 8 or 16 (MSB machines only!)
=item B<--title>
add a title to the resulting image, if just this option is specified the text used for the title is the name of the input image file.
=item B<--title_text>
use the input string for the title [default: input-filename]. This option must be used in conjunction with -title
=item B<--title_size>
font point size for the title
=item B<--anot_bar>
create an annotated bar to match the image (use height of the output image)
=back
=head2 Image range and lookup table options
=over 4
=item B<--range>
valid range of values for MINC file
=item B<--image_range>
range of image values to use for pixel intensity
=item B<--auto_range>
automatically determine image range using a 5 and 95% PcT. (histogram)
=item B<--lookup>
arguments to pass to minclookup
=back
=head2 Slicing options
=over 4
=item B<-s> B<--slice>
slice number to get. (note this is in voxel co-ordinates)
=item B<-z> B<--axial> B<--transverse>
get an axial/transverse (z) slice
=item B<-y> B<--coronal>
get a coronal (y) slice
=item B<-x> B<--sagittal>
get a sagital (x) slice
=back
=head2 Triplanar options
=over 4
=item B<-t> B<--triplanar>
create a triplanar view of the input file
=item B<--tilesize>
pixel size for each image in a triplanar
=item B<--sagittal_offset>
offset the sagittal slice from the centre
=item B<--sagittal_offset_perc>
offset the sagittal slice by a percentage from the centre
=item B<--vertical>
create a vertical triplanar view (Default)
=item B<--horizontal>
create a horizontal triplanar view
=back
=head1 SEE ALSO
convert(1) mincextract(1) display(1)
=head1 AUTHOR
Andrew Janke - a.janke@gmail.com
=head1 COPYRIGHTS
Copyright 2012 by Andrew L Janke
=cut
|