1 /*****************************************************************************
5 ** Purpose: Interface to CTN Dicom classes
6 ** Programmer: Kevin Rosenberg
7 ** Date Started: March 2001
9 ** This is part of the CTSim program
10 ** Copyright (c) 1983-2001 Kevin Rosenberg
14 ** This program is free software; you can redistribute it and/or modify
15 ** it under the terms of the GNU General Public License (version 2) as
16 ** published by the Free Software Foundation.
18 ** This program is distributed in the hope that it will be useful,
19 ** but WITHOUT ANY WARRANTY; without even the implied warranty of
20 ** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
21 ** GNU General Public License for more details.
23 ** You should have received a copy of the GNU General Public License
24 ** along with this program; if not, write to the Free Software
25 ** Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
26 ******************************************************************************/
35 #include "imagefile.h"
36 #include "projections.h"
39 DicomImporter::DicomImporter (const char* const pszFile)
40 : m_strFilename(pszFile), m_bFail(false), m_iContents(DICOM_CONTENTS_INVALID),
41 m_pImageFile(NULL), m_pProjections(NULL), m_pFile(NULL)
43 unsigned long lOptions = DCM_ORDERLITTLEENDIAN | DCM_FORMATCONVERSION;
46 CONDITION cond = DCM_OpenFile (pszFile, lOptions, &m_pFile);
47 if (cond != DCM_NORMAL) {
50 CONDITION cond2 = COND_TopCondition (&cond, textbuf, sizeof(textbuf));
51 cond2 = DCM_NORMAL; // testing
52 if (cond2 != DCM_NORMAL) {
53 m_strFailMessage = "DCM_OpenFile failure: ";
54 m_strFailMessage += m_strFilename;
56 m_strFailMessage = textbuf;
61 unsigned short iNRows, iNCols, iBitsAllocated, iBitsStored, iHighBit, iPixRep;
62 DCM_ELEMENT aElemRequired[] = {
63 {DCM_IMGROWS, DCM_US, "", 1, sizeof(iNRows),
64 {reinterpret_cast<char*>(&iNRows)}},
65 {DCM_IMGCOLUMNS, DCM_US, "", 1, sizeof(iNCols),
66 {reinterpret_cast<char*>(&iNCols)}},
67 {DCM_IMGBITSALLOCATED, DCM_US, "", 1, sizeof(iBitsAllocated),
68 {reinterpret_cast<char*>(&iBitsAllocated)}},
69 {DCM_IMGBITSSTORED, DCM_US, "", 1, sizeof(iBitsStored),
70 {reinterpret_cast<char*>(&iBitsStored)}},
71 {DCM_IMGHIGHBIT, DCM_US, "", 1, sizeof(iHighBit),
72 {reinterpret_cast<char*>(&iHighBit)}},
73 {DCM_IMGPIXELREPRESENTATION, DCM_US, "", 1, sizeof(iPixRep),
74 {reinterpret_cast<char*>(&iPixRep)}},
76 int nElemRequired = sizeof (aElemRequired) / sizeof(DCM_ELEMENT);
78 if (DCM_ParseObject (&m_pFile, aElemRequired, nElemRequired, NULL, 0, NULL) == DCM_NORMAL) {
79 loadImage (iNRows, iNCols, iBitsAllocated, iBitsStored, iHighBit, iPixRep);
83 DCM_TAG somatomTag = DCM_MAKETAG(TAG_GROUP_SOMATOM, TAG_MEMBER_SOMATOM_DATA);
84 if (DCM_GetElementSize (&m_pFile, somatomTag, &lRtnLength) == DCM_NORMAL)
89 DicomImporter::loadImage(unsigned short iNRows, unsigned short iNCols, unsigned short iBitsAllocated,
90 unsigned short iBitsStored, unsigned short iHighBit, unsigned short iPixRep)
93 unsigned short iSamplesPerPixel, iPlanarConfig;
95 DCM_ELEMENT elemPlanarConfig =
96 {DCM_IMGPLANARCONFIGURATION, DCM_US, "", 1, sizeof(iPlanarConfig),
97 {reinterpret_cast<char*>(&iPlanarConfig)}};
98 DCM_ELEMENT elemSamplesPerPixel =
99 {DCM_IMGSAMPLESPERPIXEL, DCM_US, "", 1,
100 sizeof(iSamplesPerPixel), {reinterpret_cast<char*>(&iSamplesPerPixel)}};
102 if (DCM_ParseObject (&m_pFile, &elemSamplesPerPixel, 1, NULL, 0, NULL) != DCM_NORMAL)
103 iSamplesPerPixel = 1; // default value
105 if (iSamplesPerPixel > 1) {
107 if (DCM_GetElementValue (&m_pFile, &elemPlanarConfig, &lRtnLength, &ctx) != DCM_NORMAL) {
109 m_strFailMessage = "Planar Configuration not specified when iSamplesPerPixel > 1";
113 char szRescaleSlope[17];
114 char szRescaleIntercept[17];
115 double dRescaleSlope = 1;
116 double dRescaleIntercept = 0;
117 DCM_ELEMENT elemRescaleSlope =
118 {DCM_IMGRESCALESLOPE, DCM_DS, "", 1, strlen(szRescaleSlope),
120 DCM_ELEMENT elemRescaleIntercept =
121 {DCM_IMGRESCALEINTERCEPT, DCM_DS, "", 1, strlen(szRescaleIntercept),
122 {szRescaleIntercept}};
123 if (DCM_ParseObject (&m_pFile, &elemRescaleSlope, 1, NULL, 0, NULL) == DCM_NORMAL) {
124 if (sscanf (szRescaleSlope, "%lf", &dRescaleSlope) != 1)
125 sys_error (ERR_SEVERE, "Error parsing rescale slope");
127 if (DCM_ParseObject (&m_pFile, &elemRescaleIntercept, 1, NULL, 0, NULL) == DCM_NORMAL) {
128 if (sscanf (szRescaleIntercept, "%lf", &dRescaleIntercept) != 1)
129 sys_error (ERR_SEVERE, "Error parsing rescale intercept");
132 DCM_ELEMENT elemPixelData = {DCM_PXLPIXELDATA, DCM_OT, "", 1, 0, {NULL}};
133 // Get the actual pixel data (the only other required element)
134 if (DCM_GetElementSize (&m_pFile, elemPixelData.tag, &lRtnLength) != DCM_NORMAL) {
136 m_strFailMessage = "Can't get pixel data size";
140 // Check the size of the pixel data to make sure we have the correct amount...
141 unsigned long lRealLength = lRtnLength;
142 unsigned long lCheckLengthInBytes = iNRows * iNCols * iSamplesPerPixel;
143 if (iBitsAllocated == 16)
144 lCheckLengthInBytes *= 2;
145 if (lCheckLengthInBytes > lRealLength) {
147 m_strFailMessage = "Too little pixel data supplied";
150 // Now allocate the memory to hold the pixel data and get it from the DICOM file...
152 unsigned char* pRawPixels = new unsigned char [lCheckLengthInBytes];
153 elemPixelData.length = lCheckLengthInBytes;
154 elemPixelData.d.ot = pRawPixels;
157 CONDITION cond = DCM_GetElementValue (&m_pFile, &elemPixelData, &lRtnLength, &ctx);
158 if ((cond != DCM_NORMAL) && (cond != DCM_GETINCOMPLETE)) {
160 m_strFailMessage = "Can't read pixel data";
164 if ((lCheckLengthInBytes < lRealLength) && (cond != DCM_GETINCOMPLETE)) {
166 m_strFailMessage = "Should have gooten incomplete message reading pixel data";
171 m_pImageFile = new ImageFile (iNCols, iNRows);
172 ImageFileArray v = m_pImageFile->getArray();
173 double dScale = 1 << iBitsStored;
174 unsigned int iMaskLength = iBitsStored;
177 unsigned int iMask = (1 << iMaskLength) - 1;
178 for (int iy = 0; iy < iNRows; iy++) {
179 for (int ix = 0; ix < iNCols; ix++) {
180 if (iBitsAllocated == 8) {
181 unsigned char cV = pRawPixels[iy * iNRows + ix];
182 v[ix][iy] = (cV & iMask) / dScale;
183 } else if (iBitsAllocated == 16) {
184 unsigned long lBase = (iy * iNRows + ix) * 2;
185 unsigned char cV1 = pRawPixels[lBase];
186 unsigned char cV2 = pRawPixels[lBase+1] & iMask;
187 int iV = cV1 + (cV2 << 8);
188 v[ix][iNRows - 1 - iy] = iV * dRescaleSlope + dRescaleIntercept;
192 m_iContents = DICOM_CONTENTS_IMAGE;
196 DicomImporter::loadProjections()
201 unsigned short iNViews, iNDets;
202 DCM_ELEMENT aElemRequired[] = {
203 {DCM_IMGROWS, DCM_US, "", 1, sizeof(iNViews),
204 {reinterpret_cast<char*>(&iNViews)}},
205 {DCM_IMGCOLUMNS, DCM_US, "", 1, sizeof(iNDets),
206 {reinterpret_cast<char*>(&iNDets)}},
208 int nElemRequired = sizeof (aElemRequired) / sizeof(DCM_ELEMENT);
210 if (DCM_ParseObject (&m_pFile, aElemRequired, nElemRequired, NULL, 0, NULL) != DCM_NORMAL) {
212 m_strFailMessage = "Unable to read header for projections";
216 DCM_TAG somatomTag = DCM_MAKETAG(TAG_GROUP_SOMATOM, TAG_MEMBER_SOMATOM_DATA);
217 DCM_ELEMENT elemProjections = {somatomTag, DCM_UN, "", 1, 0, {NULL}};
218 if (DCM_GetElementSize (&m_pFile, elemProjections.tag, &lRtnLength) != DCM_NORMAL) {
220 m_strFailMessage = "Can't find projection data";
224 unsigned char* pRawProjections = new unsigned char [lRtnLength];
225 elemProjections.length = lRtnLength;
226 elemProjections.d.ot = pRawProjections;
229 CONDITION cond = DCM_GetElementValue (&m_pFile, &elemProjections, &lRtnLength, &ctx);
230 if ((cond != DCM_NORMAL) && (cond != DCM_GETINCOMPLETE)) {
232 m_strFailMessage = "Can't read projections data";
233 delete pRawProjections;
236 m_iContents = DICOM_CONTENTS_PROJECTIONS;
237 m_pProjections = new Projections;
238 if (! m_pProjections->initFromSomatomAR_STAR (iNViews, iNDets, pRawProjections, lRtnLength)) {
240 m_strFailMessage = "Error converting raw projection data";
241 delete m_pProjections;
242 m_pProjections = NULL;
245 delete pRawProjections;
249 DicomImporter::~DicomImporter()
252 DCM_CloseObject (&m_pFile);
256 DicomExporter::DicomExporter (ImageFile* pImageFile)
257 : m_pImageFile(pImageFile), m_pObject(NULL)
262 m_strFailMessage = "Initialized DicomExported with NULL imagefile";
265 m_bFail = ! createDicomObject();
268 DicomExporter::~DicomExporter ()
271 DCM_CloseObject (&m_pObject);
275 DicomExporter::writeFile (const char* const pszFilename)
280 m_strFilename = pszFilename;
282 CONDITION cond = DCM_WriteFile (&m_pObject, DCM_ORDERLITTLEENDIAN, pszFilename);
283 if (cond != DCM_NORMAL) {
285 m_strFailMessage = "Error writing DICOM file ";
286 m_strFailMessage += pszFilename;
294 DicomExporter::createDicomObject()
296 CONDITION cond = DCM_CreateObject (&m_pObject, 0);
297 if (cond != DCM_NORMAL) {
299 m_strFailMessage = "Error creating DICOM object";
304 m_pImageFile->getMinMax (dMin, dMax);
305 double dWidth = dMax - dMin;
308 double dScale = 65535. / dWidth;
310 double dRescaleIntercept = dMin;
311 double dRescaleSlope = 1 / dScale;
312 char szRescaleIntercept[17];
313 char szRescaleSlope[17];
314 snprintf (szRescaleIntercept, sizeof(szRescaleIntercept), "%e", dRescaleIntercept);
315 snprintf (szRescaleSlope, sizeof(szRescaleIntercept), "%e", dRescaleSlope);
317 char szCTSimRoot[] = "1.2.826.0.1.3680043.2.284.";
318 char szModality[] = "CT";
319 char szSOPClassUID[65] = "1.2.840.10008.5.4.1.1.2";
320 char szImgPhotometricInterp[] = "MONOCHROME2";
321 char szPixelSpacing[33] = "0\\0";
322 char szRelImageOrientationPatient[100] = "1\\0\\0\\0\\1\\0";
323 char szRelImagePositionPatient[49] = "0\\0\\0";
324 char szAcqKvp[] = "0";
325 char szRelAcquisitionNumber[] = "1";
326 char szRelImageNumber[] = "1";
327 char szIDSOPInstanceUID[65] = "";
328 char szIDManufacturer[] = "CTSim";
329 char szRelPositionRefIndicator[] = "0";
330 char szRelFrameOfReferenceUID[65] = "";
331 char szRelSeriesNumber[] = "1";
332 char szIDAccessionNumber[] = "0";
333 char szRelStudyID[] = "1";
334 char szIDReferringPhysician[] = "NONE";
335 char szIDStudyTime[] = "000000.0";
336 char szIDStudyDate[] = "00000000";
337 char szRelStudyInstanceUID[65] = "";
338 char szPatSex[] = "O";
339 char szPatBirthdate[] = "0000000";
340 char szPatID[] = "NONE";
341 char szPatName[] = "NONE";
342 char szIDImageType[] = "ORIGINAL";
343 char szIDManufacturerModel[65] = "";
345 std::ostringstream osPatComments;
346 m_pImageFile->printLabelsBrief (osPatComments);
347 size_t sizePatComments = osPatComments.str().length();
348 char* pszPatComments = new char [sizePatComments+1];
349 strncpy (pszPatComments, osPatComments.str().c_str(), sizePatComments);
351 snprintf (szIDSOPInstanceUID, sizeof(szIDSOPInstanceUID), "%s.2.1.6.1", szCTSimRoot);
352 snprintf (szRelStudyInstanceUID, sizeof(szRelStudyInstanceUID), "%s.2.1.6.1.1", szCTSimRoot);
353 snprintf (szRelFrameOfReferenceUID, sizeof(szRelFrameOfReferenceUID), "%s.99", szCTSimRoot);
355 snprintf (szIDManufacturerModel, sizeof(szIDManufacturerModel), "VERSION %s", VERSION);
357 snprintf (szPixelSpacing, sizeof(szPixelSpacing), "%e\\%e", m_pImageFile->axisIncrementX(), m_pImageFile->axisIncrementY());
358 double minX, maxX, minY, maxY;
359 if (m_pImageFile->getAxisExtent(minX, maxX, minY, maxY)) {
360 minX += m_pImageFile->axisIncrementX() / 2;
361 minY += m_pImageFile->axisIncrementY() / 2;
362 snprintf(szRelImagePositionPatient, sizeof(szRelImagePositionPatient), "%e\\%e\\0", minX, minY);
365 unsigned short iNRows = m_pImageFile->ny();
366 unsigned short iNCols = m_pImageFile->nx();
367 unsigned short iBitsAllocated = 16;
368 unsigned short iBitsStored = 16;
369 unsigned short iHighBit = 15;
370 unsigned short iPixRep = 0;
371 unsigned short iSamplesPerPixel = 1;
372 DCM_ELEMENT aElemRequired[] = {
373 {DCM_IMGROWS, DCM_US, "", 1, sizeof(iNRows),
374 {reinterpret_cast<char*>(&iNRows)}},
375 {DCM_IMGCOLUMNS, DCM_US, "", 1, sizeof(iNCols),
376 {reinterpret_cast<char*>(&iNCols)}},
377 {DCM_IMGBITSALLOCATED, DCM_US, "", 1, sizeof(iBitsAllocated),
378 {reinterpret_cast<char*>(&iBitsAllocated)}},
379 {DCM_IMGBITSSTORED, DCM_US, "", 1, sizeof(iBitsStored),
380 {reinterpret_cast<char*>(&iBitsStored)}},
381 {DCM_IMGHIGHBIT, DCM_US, "", 1, sizeof(iHighBit),
382 {reinterpret_cast<char*>(&iHighBit)}},
383 {DCM_IMGPIXELREPRESENTATION, DCM_US, "", 1, sizeof(iPixRep),
384 {reinterpret_cast<char*>(&iPixRep)}},
385 {DCM_IMGSAMPLESPERPIXEL, DCM_US, "", 1, sizeof(iSamplesPerPixel),
386 {reinterpret_cast<char*>(&iSamplesPerPixel)}},
387 {DCM_IMGRESCALESLOPE, DCM_DS, "", 1, strlen(szRescaleSlope),
389 {DCM_IMGRESCALEINTERCEPT, DCM_DS, "", 1, strlen(szRescaleIntercept),
390 {szRescaleIntercept}},
391 {DCM_IMGPHOTOMETRICINTERP, DCM_CS, "", 1, strlen(szImgPhotometricInterp),
392 {szImgPhotometricInterp}},
393 {DCM_IMGPIXELSPACING, DCM_DS, "", 1, strlen(szPixelSpacing),
395 {DCM_RELIMAGEORIENTATIONPATIENT, DCM_DS, "", 1,
396 strlen(szRelImageOrientationPatient), {szRelImageOrientationPatient}},
397 {DCM_RELIMAGEPOSITIONPATIENT, DCM_DS, "", 1,
398 strlen(szRelImagePositionPatient), {szRelImagePositionPatient}},
399 {DCM_ACQKVP, DCM_DS, "", 1, strlen(szAcqKvp), {szAcqKvp}},
400 {DCM_RELACQUISITIONNUMBER, DCM_IS, "", 1, strlen(szRelAcquisitionNumber),
401 {szRelAcquisitionNumber}},
402 {DCM_ACQSLICETHICKNESS, DCM_DS, "", 1, strlen(szRelAcquisitionNumber),
403 {szRelAcquisitionNumber}},
404 {DCM_RELIMAGENUMBER, DCM_IS, "", 1, strlen(szRelImageNumber),
406 {DCM_IDSOPINSTANCEUID, DCM_UI, "", 1, strlen(szIDSOPInstanceUID),
407 {szIDSOPInstanceUID}},
408 {DCM_IDMANUFACTURER, DCM_LO, "", 1, strlen(szIDManufacturer),
410 {DCM_RELPOSITIONREFINDICATOR, DCM_LO, "", 1,
411 strlen(szRelPositionRefIndicator), {szRelPositionRefIndicator}},
412 {DCM_RELFRAMEOFREFERENCEUID, DCM_UI, "", 1,
413 strlen(szRelFrameOfReferenceUID), {szRelFrameOfReferenceUID}},
414 {DCM_RELSERIESNUMBER, DCM_IS, "", 1, strlen(szRelSeriesNumber),
415 {szRelSeriesNumber}},
416 {DCM_RELSERIESINSTANCEUID, DCM_UI, "", 1, strlen(szIDAccessionNumber),
417 {szIDAccessionNumber}},
418 {DCM_IDACCESSIONNUMBER, DCM_SH, "", 1, strlen(szIDAccessionNumber),
419 {szIDAccessionNumber}},
420 {DCM_RELSTUDYID, DCM_SH, "", 1, strlen(szRelStudyID), {szRelStudyID}},
421 {DCM_IDREFERRINGPHYSICIAN, DCM_PN, "", 1, strlen(szIDReferringPhysician),
422 {szIDReferringPhysician}},
423 {DCM_IDSTUDYTIME, DCM_TM, "", 1, strlen(szIDStudyTime), {szIDStudyTime}},
424 {DCM_IDSTUDYDATE, DCM_DA, "", 1, strlen(szIDStudyDate), {szIDStudyDate}},
425 {DCM_RELSTUDYINSTANCEUID, DCM_UI, "", 1, strlen(szRelStudyInstanceUID),
426 {szRelStudyInstanceUID}},
427 {DCM_PATSEX, DCM_CS, "", 1, strlen(szPatSex), {szPatSex}},
428 {DCM_PATBIRTHDATE, DCM_DA, "", 1, strlen(szPatBirthdate), {szPatBirthdate}},
429 {DCM_PATID, DCM_LO, "", 1, strlen(szPatID), {szPatID}},
430 {DCM_PATNAME, DCM_PN, "", 1, strlen(szPatName), {szPatName}},
431 {DCM_IDIMAGETYPE, DCM_CS, "", 1, strlen(szIDImageType), {szIDImageType}},
432 {DCM_IDMODALITY, DCM_CS, "", 1, strlen(szModality), {szModality}},
433 {DCM_IDSOPCLASSUID, DCM_UI, "", 1, strlen(szSOPClassUID), {szSOPClassUID}},
434 {DCM_IDMANUFACTURERMODEL, DCM_LO, "", 1, strlen(szIDManufacturerModel),
435 {szIDManufacturerModel}},
436 {DCM_PATCOMMENTS, DCM_LT, "", 1, strlen(pszPatComments), {pszPatComments}},
438 int nElemRequired = sizeof (aElemRequired) / sizeof(DCM_ELEMENT);
441 cond = DCM_ModifyElements (&m_pObject, aElemRequired, nElemRequired, NULL, 0, &iUpdateCount);
443 DCM_ELEMENT elemPixelData = {DCM_PXLPIXELDATA, DCM_OT, "", 1, 0, {NULL}};
445 unsigned long lRealLength = 2 * m_pImageFile->nx() * m_pImageFile->ny();
447 unsigned char* pRawPixels = new unsigned char [lRealLength];
448 elemPixelData.length = lRealLength;
449 elemPixelData.d.ot = pRawPixels;
451 ImageFileArray v = m_pImageFile->getArray();
452 for (int iy = 0; iy < iNRows; iy++) {
453 for (int ix = 0; ix < iNCols; ix++) {
454 unsigned long lBase = (iy * iNRows + ix) * 2;
455 unsigned int iValue = nearest<int>(dScale * (v[ix][iNRows - 1 - iy] - dMin));
456 pRawPixels[lBase] = iValue & 0xFF;
457 pRawPixels[lBase+1] = (iValue & 0xFF00) >> 8;
460 cond = DCM_ModifyElements (&m_pObject, &elemPixelData, 1, NULL, 0, &iUpdateCount);
463 delete pszPatComments;
465 if (cond != DCM_NORMAL || iUpdateCount != 1) {
467 m_strFailMessage = "Error modifying pixel data";
474 #endif // HAVE_CTN_DICOM