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
|
/*
Copyright 2008 Brain Research Institute, Melbourne, Australia
Written by J-Donald Tournier, 27/06/08.
This file is part of MRtrix.
MRtrix is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
MRtrix is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with MRtrix. If not, see <http://www.gnu.org/licenses/>.
02-10-2008 J-Donald Tournier <d.tournier@brain.org.au>
* extra sanity check to make sure that each element fits within the file.
31-10-2008 J-Donald Tournier <d.tournier@brain.org.au>
* only attempt to read a "truncated format" DICOM file if the extension is ".dcm"
18-12-2008 J-Donald Tournier <d.tournier@brain.org.au>
* printout of DICOM group & element is now in hexadecimal
17-03-2009 J-Donald Tournier <d.tournier@brain.org.au>
* modify to allow use of either TR1 unordered map or SGI hash_map for the DICOM dictionary
09-09-2009 J-Donald Tournier <d.tournier@brain.org.au>
* include <cstdio> to allow compilation on Fedora 11
03-03-2010 J-Donald Tournier <d.tournier@brain.org.au>
* fix bug in handling of IS sequences
16-08-2010 J-Donald Tournier <d.tournier@brain.org.au>
* fix bug in handling of big-endian files
*/
#include <cstdio>
#include <glibmm/stringutils.h>
#include "file/dicom/element.h"
#include "get_set.h"
namespace MR {
namespace File {
namespace Dicom {
void Element::set (const String& filename)
{
group = element = VR = 0;
size = 0;
start = data = next = NULL;
is_BE = previous_BO_was_BE = false;
sequence.clear();
fmap.init (filename);
if (fmap.size() < 256)
throw Exception ("\"" + fmap.name() + "\" is too small to be a valid DICOM file", 3);
fmap.map();
next = (guint8*) fmap.address();
if (memcmp (next + 128, "DICM", 4)) {
is_explicit = false;
debug ("DICOM magic number not found in file \"" + fmap.name() + "\" - trying truncated format");
if (!Glib::str_has_suffix (fmap.name(), ".dcm"))
throw Exception ("file \"" + fmap.name() + "\" does not have the DICOM magic number or the .dcm extension - assuming not DICOM");
}
else next += 132;
try { set_explicit_encoding(); }
catch (Exception) {
fmap.unmap();
throw Exception ("\"" + fmap.name() + "\" is not a valid DICOM file", 3);
}
}
void Element::set_explicit_encoding ()
{
if (read_GR_EL()) throw Exception ("\"" + fmap.name() + "\" is too small to be DICOM", 3);
is_explicit = true;
next = start;
VR = ByteOrder::BE (*((guint16*) (start+4)));
if ((VR == VR_OB) | (VR == VR_OW) | (VR == VR_OF) | (VR == VR_SQ) |
(VR == VR_UN) | (VR == VR_AE) | (VR == VR_AS) | (VR == VR_AT) |
(VR == VR_CS) | (VR == VR_DA) | (VR == VR_DS) | (VR == VR_DT) |
(VR == VR_FD) | (VR == VR_FL) | (VR == VR_IS) | (VR == VR_LO) |
(VR == VR_LT) | (VR == VR_PN) | (VR == VR_SH) | (VR == VR_SL) |
(VR == VR_SS) | (VR == VR_ST) | (VR == VR_TM) | (VR == VR_UI) |
(VR == VR_UL) | (VR == VR_US) | (VR == VR_UT)) return;
debug ("using implicit DICOM encoding");
is_explicit = false;
}
bool Element::read_GR_EL ()
{
group = element = VR = 0;
size = 0;
start = next;
data = next = NULL;
if (start < (guint8*) fmap.address()) throw Exception ("invalid DICOM element", 3);
if (start + 8 > (guint8*) fmap.address() + fmap.size()) return (true);
is_BE = previous_BO_was_BE;
group = get<guint16> (start, is_BE);
if (group == GROUP_BYTE_ORDER_SWAPPED) {
if (!is_BE)
throw Exception ("invalid DICOM group ID " + str (group) + " in file \"" + fmap.name() + "\"", 3);
is_BE = false;
group = GROUP_BYTE_ORDER;
}
element = get<guint16> (start+2, is_BE);
return (false);
}
bool Element::read ()
{
if (read_GR_EL()) return (false);
data = start + 8;
if ((is_explicit && group != GROUP_SEQUENCE) || group == GROUP_BYTE_ORDER) {
// explicit encoding:
VR = ByteOrder::BE (*((guint16*) (start+4)));
if (VR == VR_OB || VR == VR_OW || VR == VR_OF || VR == VR_SQ || VR == VR_UN || VR == VR_UT) {
size = get<guint32> (start+8, is_BE);
data += 4;
}
else size = get<guint16> (start+6, is_BE);
}
else {
// implicit encoding:
String name = tag_name();
if (!name.size()) {
if (group%2 == 0)
debug ("WARNING: unknown DICOM tag (" + str (group) + ", " + str (element)
+ ") with implicit encoding in file \"" + fmap.name() + "\"");
VR = VR_UN;
}
else {
gchar t[] = { name[0], name[1] };
VR = ByteOrder::BE (*((guint16*) t));
}
size = get<guint32> (start+4, is_BE);
}
next = data;
if (size == LENGTH_UNDEFINED) {
if (VR != VR_SQ && !(group == GROUP_SEQUENCE && element == ELEMENT_SEQUENCE_ITEM))
throw Exception ("undefined length used for DICOM tag " + ( tag_name().size() ? tag_name().substr (2) : "" )
+ " (" + str (group) + ", " + str (element)
+ ") in file \"" + fmap.name() + "\"", 3);
}
else if (next+size > (guint8*) fmap.address() + fmap.size())
throw Exception ("file \"" + fmap.name() + "\" is too small to contain DICOM elements specified", 3);
else if (size%2)
throw Exception ("odd length (" + str (size) + ") used for DICOM tag " + ( tag_name().size() ? tag_name().substr (2) : "" )
+ " (" + str (group) + ", " + str (element) + ") in file \"" + fmap.name() + "", 3);
else if (VR != VR_SQ && ( group != GROUP_SEQUENCE || element != ELEMENT_SEQUENCE_ITEM ) )
next += size;
if (sequence.size())
if ((sequence.back().end && data > sequence.back().end) ||
(group == GROUP_SEQUENCE && element == ELEMENT_SEQUENCE_DELIMITATION_ITEM))
sequence.pop_back();
if (VR == VR_SQ) {
if (size == LENGTH_UNDEFINED)
sequence.push_back (Sequence (group, element, NULL));
else
sequence.push_back (Sequence (group, element, data + size));
}
switch (group) {
case GROUP_BYTE_ORDER:
switch (element) {
case ELEMENT_TRANSFER_SYNTAX_UID:
if (strncmp ((const gchar*) data, "1.2.840.10008.1.2.1", size) == 0) {
is_BE = previous_BO_was_BE = false; // explicit VR Little Endian
is_explicit = true;
}
else if (strncmp ((const gchar*) data, "1.2.840.10008.1.2.2", size) == 0) {
is_BE = previous_BO_was_BE = true; // Explicit VR Big Endian
is_explicit = true;
}
else if (strncmp ((const gchar*) data, "1.2.840.10008.1.2", size) == 0) {
is_BE = previous_BO_was_BE = false; // Implicit VR Little Endian
is_explicit = false;
}
else if (strncmp ((const gchar*) data, "1.2.840.10008.1.2.1.99", size) == 0) {
throw Exception ("DICOM deflated explicit VR little endian transfer syntax not supported");
}
else error ("unknown DICOM transfer syntax: \"" + String ((const gchar*) data, size)
+ "\" in file \"" + fmap.name() + "\" - ignored");
break;
}
break;
}
return (true);
}
ElementType Element::type () const
{
if (!VR) return (INVALID);
if (VR == VR_FD || VR == VR_FL) return (FLOAT);
if (VR == VR_SL || VR == VR_SS) return (INT);
if (VR == VR_UL || VR == VR_US) return (UINT);
if (VR == VR_SQ) return (SEQ);
if (VR == VR_AE || VR == VR_AS || VR == VR_CS || VR == VR_DA ||
VR == VR_DS || VR == VR_DT || VR == VR_IS || VR == VR_LO ||
VR == VR_LT || VR == VR_PN || VR == VR_SH || VR == VR_ST ||
VR == VR_TM || VR == VR_UI || VR == VR_UT || VR == VR_AT) return (STRING);
return (OTHER);
}
std::vector<gint32> Element::get_int () const
{
std::vector<gint32> V;
if (VR == VR_SL)
for (const guint8* p = data; p < data + size; p += sizeof (gint32))
V.push_back (get<gint32> (p, is_BE));
else if (VR == VR_SS)
for (const guint8* p = data; p < data + size; p += sizeof (gint16))
V.push_back (get<gint16> (p, is_BE));
else if (VR == VR_IS) {
std::vector<String> strings (split (String ((const gchar*) data, size), "\\", false));
V.resize (strings.size());
for (guint n = 0; n < V.size(); n++) V[n] = to<gint32> (strings[n]);
}
return (V);
}
std::vector<guint32> Element::get_uint () const
{
std::vector<guint32> V;
if (VR == VR_UL)
for (const guint8* p = data; p < data + size; p += sizeof (guint32))
V.push_back (get<guint32> (p, is_BE));
else if (VR == VR_US)
for (const guint8* p = data; p < data + size; p += sizeof (guint16))
V.push_back (get<guint16> (p, is_BE));
else if (VR == VR_IS) {
std::vector<String> strings (split (String ((const gchar*) data, size), "\\", false));
V.resize (strings.size());
for (guint n = 0; n < V.size(); n++) V[n] = to<guint32> (strings[n]);
}
return (V);
}
std::vector<double> Element::get_float () const
{
std::vector<double> V;
if (VR == VR_FD)
for (const guint8* p = data; p < data + size; p += sizeof (float64))
V.push_back (get<float64> (p, is_BE));
else if (VR == VR_FL)
for (const guint8* p = data; p < data + size; p += sizeof (float32))
V.push_back (get<float32> (p, is_BE));
else if (VR == VR_DS) {
std::vector<String> strings (split (String ((const gchar*) data, size), "\\", false));
V.resize (strings.size());
for (guint n = 0; n < V.size(); n++) V[n] = to<double> (strings[n]);
}
return (V);
}
std::vector<String> Element::get_string () const
{
if (VR == VR_AT) {
std::vector<String> strings;
strings.push_back (printf ("%02X %02X", get<guint16> (data, is_BE), get<guint16> (data+2, is_BE)));
return strings;
}
std::vector<String> strings (split (String ((const gchar*) data, size), "\\", false));
for (std::vector<String>::iterator i = strings.begin(); i != strings.end(); ++i) {
*i = strip (*i);
replace (*i, '^', ' ');
}
return (strings);
}
namespace {
template <class T> inline void print_vec (const std::vector<T>& V)
{ for (guint n = 0; n < V.size(); n++) fprintf (stdout, "%s ", str (V[n]).c_str()); }
}
void Element::print() const
{
String name = tag_name();
fprintf (stdout, " [DCM] %*s : ", int(2*level()), ( name.size() ? name.substr(2).c_str() : "unknown" ));
switch (type()) {
case INT: print_vec (get_int()); break;
case UINT: print_vec (get_int()); break;
case FLOAT: print_vec (get_int()); break;
case STRING:
if (group == GROUP_DATA && element == ELEMENT_DATA) fprintf (stdout, "(data)");
else print_vec (get_int());
break;
case SEQ: fprintf (stdout, "(sequence)"); break;
default: fprintf (stdout, "unknown data type");
}
if (group%2) fprintf (stdout, " [ PRIVATE ]\n");
else fprintf (stdout, "\n");
}
std::ostream& operator<< (std::ostream& stream, const Element& item)
{
const String& name (item.tag_name());
stream << "[DCM] ";
guint indent = item.level() + ( item.VR == VR_SQ ? 0 : 1 );
for (guint i = 0; i < indent; i++)
stream << " ";
if (item.VR == VR_SQ)
stream << "+ ";
else if (item.group == GROUP_SEQUENCE && item.element == ELEMENT_SEQUENCE_ITEM)
stream << "- ";
else
stream << " ";
stream << printf ("%02X %02X ", item.group, item.element)
+ ((const gchar*) &item.VR)[1] + ((const gchar*) &item.VR)[0] + " "
+ str ( item.size == LENGTH_UNDEFINED ? 0 : item.size ) + " "
+ str (item.offset (item.start)) + " " + ( name.size() ? name.substr (2) : "unknown" ) + " ";
switch (item.type()) {
case INT: stream << item.get_int(); break;
case UINT: stream << item.get_uint(); break;
case FLOAT: stream << item.get_float(); break;
case STRING:
if (item.group == GROUP_DATA && item.element == ELEMENT_DATA) stream << "(data)";
else stream << item.get_string();
break;
case SEQ:
break;
default:
if (item.group != GROUP_SEQUENCE || item.element != ELEMENT_SEQUENCE_ITEM)
stream << "unknown data type";
}
if (item.group%2) stream << " [ PRIVATE ]";
return (stream);
}
}
}
}
|