[Gdcm-hackers] gdcm-git:Grassroots DICOM branch release updated. 2cda327ea622a1905506e0be6c5086fdc0
Cross-platform DICOM implementation
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[Gdcm-hackers] gdcm-git:Grassroots DICOM branch release updated. 2cda327ea622a1905506e0be6c5086fdc06e31d9
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From: Mathieu M. <ma...@us...> - 2022-09-23 13:35:10
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- Log -----------------------------------------------------------------
https://sourceforge.net/p/gdcm/gdcm/ci/2cda327ea622a1905506e0be6c5086fdc06e31d9/
commit 2cda327ea622a1905506e0be6c5086fdc06e31d9
Author: Mathieu Malaterre <mat...@gm...>
Date: Fri Sep 23 06:32:15 2022 -0700
Add hints
diff --git a/Utilities/gdcmext/csa.c b/Utilities/gdcmext/csa.c
index 0b7db9054..e0a0eb40c 100644
--- a/Utilities/gdcmext/csa.c
+++ b/Utilities/gdcmext/csa.c
@@ -160,6 +160,7 @@ static bool read_magic(struct app *self) {
assert(0);
return false;
}
+ assert(n > 0 && n < 128);
self->nelements = n;
self->csa_type = magic;
return true;
@@ -227,11 +228,19 @@ static bool read_info(struct app *self, struct csa_info *i) {
// vr
s = fread_mirror(i->vr, sizeof *i->vr, sizeof i->vr / sizeof *i->vr, self);
ERROR_RETURN(s, 4);
+ {
+ const char *s = i->vr;
+ assert(s[0] >= 'A' && s[0] <= 'Z');
+ assert(s[1] >= 'A' && s[1] <= 'Z');
+ assert(s[2] == 0);
+ if (self->csa_type == SV10) assert(s[3] == 0);
+ }
// syngodt (signed)
s = fread_mirror(&i->syngodt, sizeof i->syngodt, 1, self);
ERROR_RETURN(s, 1);
// numer of items
s = fread_mirror(&i->nitems, sizeof i->nitems, 1, self);
+ if (self->csa_type == SV10) assert(i->nitems % 6 == 0);
ERROR_RETURN(s, 1);
{
uint32_t unused;
diff --git a/Utilities/gdcmext/mec_mr3.c b/Utilities/gdcmext/mec_mr3.c
index ff30adcc2..98700e9f7 100644
--- a/Utilities/gdcmext/mec_mr3.c
+++ b/Utilities/gdcmext/mec_mr3.c
@@ -400,6 +400,7 @@ static bool mec_mr3_scrub(void *output, const void *input, size_t len) {
if (s != 1 || nitems == 0) {
good = false;
}
+ assert(nitems < 512);
if (good && nitems <= MAGIC_NUM_ELEMENTS) {
// special case to handle last groups
remain = nitems;
https://sourceforge.net/p/gdcm/gdcm/ci/259e8d3fb4bcf93b2603f1c75d797bd5d2ab7e9e/
commit 259e8d3fb4bcf93b2603f1c75d797bd5d2ab7e9e
Author: Mathieu Malaterre <mat...@gm...>
Date: Fri Sep 23 02:48:01 2022 -0700
Check a pseudo magic value
diff --git a/Source/MediaStorageAndFileFormat/gdcmCleaner.cxx b/Source/MediaStorageAndFileFormat/gdcmCleaner.cxx
index 03912d1dd..437154750 100644
--- a/Source/MediaStorageAndFileFormat/gdcmCleaner.cxx
+++ b/Source/MediaStorageAndFileFormat/gdcmCleaner.cxx
@@ -18,8 +18,8 @@
#include "gdcmDataSetHelper.h"
#include "gdcmDicts.h"
#include "gdcmEvent.h"
-#include "gdcmMEC_MR3.h"
#include "gdcmGlobal.h"
+#include "gdcmMEC_MR3.h"
#include "gdcmext/csa.h"
#include "gdcmext/mec_mr3.h"
@@ -643,7 +643,8 @@ struct Cleaner::impl {
static const PrivateTag &pmtf2 = gdcm::MEC_MR3::GetToshibaMECMR3Tag();
static const PrivateTag &pmtf3 = gdcm::MEC_MR3::GetCanonMECMR3Tag();
- if (pt == csa1 || pt == csa2 || pt == mec_mr3 || pt == pmtf1 || pt == pmtf2 || pt == pmtf3) {
+ if (pt == csa1 || pt == csa2 || pt == mec_mr3 || pt == pmtf1 ||
+ pt == pmtf2 || pt == pmtf3) {
scrub_privatetags.insert(pt);
return true;
}
@@ -798,6 +799,17 @@ static bool CleanMEC_MR3(DataSet &ds, const DataElement &de) {
clean.SetVR(de.GetVR());
std::vector<char> v;
v.resize(bv->GetLength());
+ {
+ // check a pseudo magic value here:
+ uint32_t magic = 0xffff;
+ if (bv->GetLength() > 4) {
+ memcpy(&magic, bv->GetPointer(), sizeof magic);
+ }
+ if (magic > 512) {
+ gdcmDebugMacro("Cannot handle MEC_MR3");
+ return true;
+ }
+ }
if (mec_mr3_memcpy(&v[0], bv->GetPointer(), bv->GetLength())) {
clean.SetByteValue(&v[0], v.size());
ds.Replace(clean);
@@ -814,7 +826,9 @@ static bool CleanPMTF(DataSet &ds, const DataElement &de) {
const char *input = bv->GetPointer();
const size_t len = bv->GetLength();
- bool success = true;
+ gdcm::Cleaner cleaner;
+ gdcm::File &file = cleaner.GetFile();
+ gdcm::DataSet &revds = file.GetDataSet();
try {
std::istringstream is;
{
@@ -826,13 +840,16 @@ static bool CleanPMTF(DataSet &ds, const DataElement &de) {
// FIXME gdcm::Cleaner will by default change defined length SQ into undef
// length...there is a risk of incompatibily with vendor
- gdcm::Cleaner cleaner;
- gdcm::File &file = cleaner.GetFile();
gdcm::FileMetaInformation &fmi = file.GetHeader();
fmi.SetDataSetTransferSyntax(gdcm::TransferSyntax::ExplicitVRLittleEndian);
- gdcm::DataSet &revds = file.GetDataSet();
revds.Read<gdcm::ExplicitDataElement, gdcm::SwapperNoOp>(is);
+ } catch (...) {
+ gdcmDebugMacro("Unhanded file format");
+ return true;
+ }
+ bool success = true;
+ try {
gdcm::VR vr = VR::PN;
cleaner.Empty(vr);
if (!cleaner.Clean()) {
@@ -1051,7 +1068,8 @@ bool Cleaner::impl::ProcessDataSet(Subject &subject, File &file, DataSet &ds,
static const PrivateTag &csa1 = CSAHeader::GetCSAImageHeaderInfoTag();
static const PrivateTag &csa2 = CSAHeader::GetCSASeriesHeaderInfoTag();
const PrivateTag mec_mr3(0x700d, 0x08, "TOSHIBA_MEC_MR3");
- static const PrivateTag &pmtf1 = gdcm::MEC_MR3::GetPMTFInformationDataTag();
+ static const PrivateTag &pmtf1 =
+ gdcm::MEC_MR3::GetPMTFInformationDataTag();
static const PrivateTag &pmtf2 = gdcm::MEC_MR3::GetToshibaMECMR3Tag();
static const PrivateTag &pmtf3 = gdcm::MEC_MR3::GetCanonMECMR3Tag();
https://sourceforge.net/p/gdcm/gdcm/ci/4bde268028b84eca9db2229518d9ead3c9544252/
commit 4bde268028b84eca9db2229518d9ead3c9544252
Author: Mathieu Malaterre <mat...@gm...>
Date: Fri Sep 23 02:46:00 2022 -0700
Add extra check
diff --git a/Source/DataStructureAndEncodingDefinition/gdcmCSAHeader.cxx b/Source/DataStructureAndEncodingDefinition/gdcmCSAHeader.cxx
index 247c831ed..5b8880667 100644
--- a/Source/DataStructureAndEncodingDefinition/gdcmCSAHeader.cxx
+++ b/Source/DataStructureAndEncodingDefinition/gdcmCSAHeader.cxx
@@ -1116,6 +1116,7 @@ bool CSAHeader::LoadFromDataElement(DataElement const &de)
ss.read((char*)&nitems, sizeof(nitems));
SwapperNoOp::SwapArray(&nitems,1);
csael.SetNoOfItems( nitems );
+ if( InternalType == SV10) { assert( nitems % 6 == 0 );}
//std::cout << "NoOfItems " << nitems << ", ";
uint32_t xx;
ss.read((char*)&xx, sizeof(xx));
https://sourceforge.net/p/gdcm/gdcm/ci/686b253b4fbee579ef51139b78ae457f5697fa36/
commit 686b253b4fbee579ef51139b78ae457f5697fa36
Author: Mathieu Malaterre <mat...@gm...>
Date: Fri Sep 16 00:52:19 2022 -0700
fix siemens attribute
they are bogus in official DCS...sigh
diff --git a/Source/DataDictionary/gdcmPrivateDefaultDicts.cxx b/Source/DataDictionary/gdcmPrivateDefaultDicts.cxx
index 22a9d10d3..35648870d 100644
--- a/Source/DataDictionary/gdcmPrivateDefaultDicts.cxx
+++ b/Source/DataDictionary/gdcmPrivateDefaultDicts.cxx
@@ -2965,6 +2965,7 @@ static const DICT_ENTRY DICOMV3DataDict [] = {
{0x07a1,0x0050,"ELSCINT1",VR::US,VM::VM1,"Tamar Site Id",false },
{0x07a1,0x0056,"ELSCINT1",VR::US,VM::VM1,"?",false },
{0x07a1,0x0058,"ELSCINT1",VR::CS,VM::VM1,"?",false },
+ {0x07a1,0x005a,"ELSCINT1",VR::CS,VM::VM1,"?",false },
{0x07a1,0x005d,"ELSCINT1",VR::DT,VM::VM1,"?",false },
{0x07a1,0x005f,"ELSCINT1",VR::CS,VM::VM1,"?",false },
{0x07a1,0x0070,"ELSCINT1",VR::SH,VM::VM1,"?patient name?",false },
@@ -10423,11 +10424,12 @@ static const DICT_ENTRY DICOMV3DataDict [] = {
{0x0009,0x0075,"SIENET",VR::LO,VM::VM1,"?",false },
{0x0091,0x0020,"SIENET",VR::PN,VM::VM1_n,"Patient Name",false },
{0x0095,0x0001,"SIENET",VR::LO,VM::VM1,"Examination Folder ID",false },
- {0x0095,0x0004,"SIENET",VR::UL,VM::VM1,"Folder Reported Status",false },
+ {0x0095,0x0004,"SIENET",VR::SL,VM::VM1,"Folder Reported Status",false },
{0x0095,0x0005,"SIENET",VR::LO,VM::VM1,"Folder Reporting Radiologist",false },
{0x0095,0x0007,"SIENET",VR::LO,VM::VM1,"SIENET ISA PLA",false },
- {0x0095,0x000c,"SIENET",VR::UL,VM::VM1,"Folder Rebuild Status",false },
+ {0x0095,0x000c,"SIENET",VR::SL,VM::VM1,"Folder Rebuild Status",false },
{0x0095,0x0020,"SIENET",VR::UN,VM::VM1,"?",false },
+ {0x0095,0x00fb,"SIENET",VR::ST,VM::VM1,"?",false },
{0x0099,0x0002,"SIENET",VR::UL,VM::VM1,"Key Images",false },
{0x0099,0x0005,"SIENET",VR::SL,VM::VM1,"Image Number",false },
{0x0009,0x0010,"SPI",VR::LO,VM::VM1,"Comments",false },
diff --git a/Source/DataDictionary/privatedicts.xml b/Source/DataDictionary/privatedicts.xml
index e0c434370..036c2018c 100644
--- a/Source/DataDictionary/privatedicts.xml
+++ b/Source/DataDictionary/privatedicts.xml
@@ -2517,6 +2517,7 @@
<entry owner="ELSCINT1" group="07a1" element="xx43" vr="IS" vm="1" name="?"/>
<entry owner="ELSCINT1" group="07a1" element="xx50" vr="US" vm="1" name="Tamar Site Id"/>
<entry owner="ELSCINT1" group="07a1" element="xx56" vr="US" vm="1" name="?"/>
+ <entry owner="ELSCINT1" group="07a1" element="xx5a" vr="CS" vm="1" name="?"/>
<entry owner="ELSCINT1" group="07a1" element="xx75" vr="LO" vm="2" name="?"/>
<entry owner="ELSCINT1" group="07a1" element="xx85" vr="UL" vm="1" name="Tamar Translate Flags"/>
<entry owner="ELSCINT1" group="07a1" element="xx9f" vr="CS" vm="1" name="?"/>
@@ -9286,11 +9287,12 @@
<entry owner="SIENET" group="0009" element="xx75" vr="LO" vm="1" name="?"/>
<entry owner="SIENET" group="0091" element="xx20" vr="PN" vm="1-n" name="Patient Name"/>
<entry owner="SIENET" group="0095" element="xx01" vr="LO" vm="1" name="Examination Folder ID"/>
- <entry owner="SIENET" group="0095" element="xx04" vr="UL" vm="1" name="Folder Reported Status"/>
+ <entry owner="SIENET" group="0095" element="xx04" vr="SL" vm="1" name="Folder Reported Status"/>
<entry owner="SIENET" group="0095" element="xx05" vr="LO" vm="1" name="Folder Reporting Radiologist"/>
<entry owner="SIENET" group="0095" element="xx07" vr="LO" vm="1" name="SIENET ISA PLA"/>
- <entry owner="SIENET" group="0095" element="xx0c" vr="UL" vm="1" name="Folder Rebuild Status"/>
+ <entry owner="SIENET" group="0095" element="xx0c" vr="SL" vm="1" name="Folder Rebuild Status"/>
<entry owner="SIENET" group="0095" element="xx20" vr="UN" vm="1" name="?"/>
+ <entry owner="SIENET" group="0095" element="xxfb" vr="ST" vm="1" name="?"/>
<entry owner="SIENET" group="0099" element="xx02" vr="UL" vm="1" name="Key Images"/>
<entry owner="SIENET" group="0099" element="xx05" vr="SL" vm="1" name="Image Number"/>
<entry owner="SPI" group="0009" element="xx10" vr="LO" vm="1" name="Comments"/>
https://sourceforge.net/p/gdcm/gdcm/ci/4759862de35850f4c7fb1ef9c0be84ed0cfc5ac9/
commit 4759862de35850f4c7fb1ef9c0be84ed0cfc5ac9
Author: Mathieu Malaterre <mat...@gm...>
Date: Fri Sep 16 00:52:12 2022 -0700
add debug
diff --git a/Applications/Cxx/gdcmdump.cxx b/Applications/Cxx/gdcmdump.cxx
index b781f2c8c..db9299a2d 100644
--- a/Applications/Cxx/gdcmdump.cxx
+++ b/Applications/Cxx/gdcmdump.cxx
@@ -1074,7 +1074,9 @@ static int PrintCSABase64Impl(gdcm::CSAHeader &csa, std::string const & csaname
return 1;
}
gdcm::Printer p;
+ //gdcm::DictPrinter p;
p.SetFile( file );
+ //p.SetColor( 1 );
std::cout << "--" << csaname << "--" << std::endl;
p.Print(std::cout);
}
https://sourceforge.net/p/gdcm/gdcm/ci/828ab57c6da3e888983e357535bffb5d0ce02115/
commit 828ab57c6da3e888983e357535bffb5d0ce02115
Author: Mathieu Malaterre <mat...@gm...>
Date: Thu Sep 15 23:38:16 2022 -0700
Add SIEMENS MR FMRI
diff --git a/Source/DataDictionary/gdcmPrivateDefaultDicts.cxx b/Source/DataDictionary/gdcmPrivateDefaultDicts.cxx
index a83bc0bc4..22a9d10d3 100644
--- a/Source/DataDictionary/gdcmPrivateDefaultDicts.cxx
+++ b/Source/DataDictionary/gdcmPrivateDefaultDicts.cxx
@@ -38,6 +38,29 @@ using DICT_ENTRY = struct
};
static const DICT_ENTRY DICOMV3DataDict [] = {
+ {0x0021,0x0010,"SIEMENS MR FMRI",VR::SQ,VM::VM1,"?",false },
+ {0x0021,0x0011,"SIEMENS MR FMRI",VR::LO,VM::VM1,"?",false },
+ {0x0021,0x0012,"SIEMENS MR FMRI",VR::SQ,VM::VM1,"?",false },
+ {0x0021,0x0013,"SIEMENS MR FMRI",VR::US,VM::VM1,"?",false },
+ {0x0021,0x0014,"SIEMENS MR FMRI",VR::SQ,VM::VM1,"?",false },
+ {0x0021,0x0015,"SIEMENS MR FMRI",VR::US,VM::VM1,"?",false },
+ {0x0021,0x0016,"SIEMENS MR FMRI",VR::LO,VM::VM1,"?",false },
+ {0x0021,0x0017,"SIEMENS MR FMRI",VR::US,VM::VM1,"?",false },
+ {0x0021,0x0018,"SIEMENS MR FMRI",VR::UL,VM::VM1,"?",false },
+ {0x0021,0x0019,"SIEMENS MR FMRI",VR::FL,VM::VM1,"?",false },
+ {0x0021,0x0031,"SIEMENS MR FMRI",VR::SQ,VM::VM1,"?",false },
+ {0x0021,0x0040,"SIEMENS MR FMRI",VR::SQ,VM::VM1,"?",false },
+ {0x0021,0x0041,"SIEMENS MR FMRI",VR::LO,VM::VM1,"?",false },
+ {0x0021,0x0042,"SIEMENS MR FMRI",VR::SQ,VM::VM1,"?",false },
+ {0x0021,0x0043,"SIEMENS MR FMRI",VR::LO,VM::VM1,"?",false },
+ {0x0021,0x0044,"SIEMENS MR FMRI",VR::US,VM::VM1,"?",false },
+ {0x0021,0x0045,"SIEMENS MR FMRI",VR::LO,VM::VM1_n,"?",false },
+ {0x0021,0x0046,"SIEMENS MR FMRI",VR::SQ,VM::VM1,"?",false },
+ {0x0021,0x0047,"SIEMENS MR FMRI",VR::UL,VM::VM1,"?",false },
+ {0x0021,0x0048,"SIEMENS MR FMRI",VR::LO,VM::VM1,"?",false },
+ {0x0021,0x0049,"SIEMENS MR FMRI",VR::FD,VM::VM1,"?",false },
+ {0x0021,0x004a,"SIEMENS MR FMRI",VR::FD,VM::VM1_n,"?",false },
+ {0x0021,0x004b,"SIEMENS MR FMRI",VR::FL,VM::VM1,"?",false },
{0x0009,0x0002,"CANON_MEC_MR3^10",VR::SH,VM::VM1,"?",false },
{0x0011,0x0003,"CANON_MEC_MR3^10",VR::US,VM::VM1,"?",false },
{0x0011,0x0004,"CANON_MEC_MR3^10",VR::SQ,VM::VM1,"?",false },
diff --git a/Source/DataDictionary/privatedicts.xml b/Source/DataDictionary/privatedicts.xml
index bd5abc996..e0c434370 100644
--- a/Source/DataDictionary/privatedicts.xml
+++ b/Source/DataDictionary/privatedicts.xml
@@ -11,6 +11,29 @@
PURPOSE. See the above copyright notice for more information.
-->
<dict>
+<entry group="0021" element="0010" vr="SQ" vm="1" name="?" owner="SIEMENS MR FMRI"/>
+<entry group="0021" element="0011" vr="LO" vm="1" name="?" owner="SIEMENS MR FMRI"/>
+<entry group="0021" element="0012" vr="SQ" vm="1" name="?" owner="SIEMENS MR FMRI"/>
+<entry group="0021" element="0013" vr="US" vm="1" name="?" owner="SIEMENS MR FMRI"/>
+<entry group="0021" element="0014" vr="SQ" vm="1" name="?" owner="SIEMENS MR FMRI"/>
+<entry group="0021" element="0015" vr="US" vm="1" name="?" owner="SIEMENS MR FMRI"/>
+<entry group="0021" element="0016" vr="LO" vm="1" name="?" owner="SIEMENS MR FMRI"/>
+<entry group="0021" element="0017" vr="US" vm="1" name="?" owner="SIEMENS MR FMRI"/>
+<entry group="0021" element="0018" vr="UL" vm="1" name="?" owner="SIEMENS MR FMRI"/>
+<entry group="0021" element="0019" vr="FL" vm="1" name="?" owner="SIEMENS MR FMRI"/>
+<entry group="0021" element="0031" vr="SQ" vm="1" name="?" owner="SIEMENS MR FMRI"/>
+<entry group="0021" element="0040" vr="SQ" vm="1" name="?" owner="SIEMENS MR FMRI"/>
+<entry group="0021" element="0041" vr="LO" vm="1" name="?" owner="SIEMENS MR FMRI"/>
+<entry group="0021" element="0042" vr="SQ" vm="1" name="?" owner="SIEMENS MR FMRI"/>
+<entry group="0021" element="0043" vr="LO" vm="1" name="?" owner="SIEMENS MR FMRI"/>
+<entry group="0021" element="0044" vr="US" vm="1" name="?" owner="SIEMENS MR FMRI"/>
+<entry group="0021" element="0045" vr="LO" vm="1-n" name="?" owner="SIEMENS MR FMRI"/>
+<entry group="0021" element="0046" vr="SQ" vm="1" name="?" owner="SIEMENS MR FMRI"/>
+<entry group="0021" element="0047" vr="UL" vm="1" name="?" owner="SIEMENS MR FMRI"/>
+<entry group="0021" element="0048" vr="LO" vm="1" name="?" owner="SIEMENS MR FMRI"/>
+<entry group="0021" element="0049" vr="FD" vm="1" name="?" owner="SIEMENS MR FMRI"/>
+<entry group="0021" element="004a" vr="FD" vm="1-n" name="?" owner="SIEMENS MR FMRI"/>
+<entry group="0021" element="004b" vr="FL" vm="1" name="?" owner="SIEMENS MR FMRI"/>
<entry group="0009" element="0002" vr="SH" vm="1" name="?" owner="CANON_MEC_MR3^10"/>
<entry group="0011" element="0003" vr="US" vm="1" name="?" owner="CANON_MEC_MR3^10"/>
<entry group="0011" element="0004" vr="SQ" vm="1" name="?" owner="CANON_MEC_MR3^10"/>
https://sourceforge.net/p/gdcm/gdcm/ci/421985cd1c97348f5ac822c778fc04d2cbd5eb0b/
commit 421985cd1c97348f5ac822c778fc04d2cbd5eb0b
Author: Mathieu Malaterre <mat...@gm...>
Date: Thu Sep 15 08:26:09 2022 -0700
implement csa64 mode
diff --git a/Applications/Cxx/gdcmdump.cxx b/Applications/Cxx/gdcmdump.cxx
index 0a6e3b5ed..b781f2c8c 100644
--- a/Applications/Cxx/gdcmdump.cxx
+++ b/Applications/Cxx/gdcmdump.cxx
@@ -1040,26 +1040,14 @@ static int PrintPDB(const std::string & filename, bool verbose)
return ret;
}
-static int PrintCSABase64(const std::string & filename, const char * name)
+static int PrintCSABase64Impl(gdcm::CSAHeader &csa, std::string const & csaname )
{
- gdcm::Reader reader;
- reader.SetFileName( filename.c_str() );
- if( !reader.Read() )
- {
- std::cerr << "Failed to read: " << filename << std::endl;
- return 1;
- }
- const gdcm::DataSet& ds = reader.GetFile().GetDataSet();
-
- gdcm::CSAHeader csa;
- const gdcm::PrivateTag &t1 = csa.GetCSAImageHeaderInfoTag();
- if( !ds.FindDataElement( t1 ) ) return 1;
- csa.LoadFromDataElement( ds.GetDataElement( t1 ) );
-
+ const char *name = csaname.c_str();
if( csa.FindCSAElementByName(name) )
{
const gdcm::CSAElement & el = csa.GetCSAElementByName(name);
- if( el.IsEmpty() ) return 1;
+ // this is not error if empty:
+ if( el.IsEmpty() ) return 0;
const gdcm::ByteValue* bv = el.GetByteValue();
std::string str( bv->GetPointer(), bv->GetLength() );
str.erase(std::remove(str.begin(), str.end(), '\n'), str.end());
@@ -1087,11 +1075,45 @@ static int PrintCSABase64(const std::string & filename, const char * name)
}
gdcm::Printer p;
p.SetFile( file );
+ std::cout << "--" << csaname << "--" << std::endl;
p.Print(std::cout);
}
return 0;
}
+static int PrintCSABase64(const std::string & filename, std::vector<std::string> const & csanames )
+{
+ gdcm::Reader reader;
+ reader.SetFileName( filename.c_str() );
+ if( !reader.Read() )
+ {
+ std::cerr << "Failed to read: " << filename << std::endl;
+ return 1;
+ }
+ const gdcm::DataSet& ds = reader.GetFile().GetDataSet();
+
+ int ret = 0;
+
+ gdcm::CSAHeader csa;
+ const gdcm::PrivateTag &t1 = csa.GetCSAImageHeaderInfoTag();
+ if( !ds.FindDataElement( t1 ) ) return 1;
+ csa.LoadFromDataElement( ds.GetDataElement( t1 ) );
+ for( std::vector<std::string>::const_iterator it = csanames.begin();
+ it != csanames.end(); ++it ) {
+ ret += PrintCSABase64Impl(csa, *it );
+ }
+
+ const gdcm::PrivateTag &t2 = csa.GetCSASeriesHeaderInfoTag();
+ if( !ds.FindDataElement( t2 ) ) return 1;
+ csa.LoadFromDataElement( ds.GetDataElement( t2 ) );
+ for( std::vector<std::string>::const_iterator it = csanames.begin();
+ it != csanames.end(); ++it ) {
+ ret += PrintCSABase64Impl(csa, *it );
+ }
+
+ return ret;
+}
+
static int PrintCSA(const std::string & filename)
{
gdcm::Reader reader;
@@ -1271,6 +1293,7 @@ static void PrintHelp()
std::cout << " -C --csa print SIEMENS CSA Header (0029,[12]0,SIEMENS CSA HEADER)." << std::endl;
std::cout << " --csa-asl print decoded SIEMENS CSA MR_ASL (base64)." << std::endl;
std::cout << " --csa-diffusion print decoded SIEMENS CSA MRDiffusion (base64)." << std::endl;
+ std::cout << " --csa64 print decoded SIEMENS CSA FMRI/MR_ASL/MRDiffusion... (base64)." << std::endl;
std::cout << " --mrprotocol print SIEMENS CSA MrProtocol only (within ASCCONV BEGIN/END)." << std::endl;
std::cout << " or Phoenix Meta Protocol (0021,19,SIEMENS MR SDS 01)." << std::endl;
std::cout << " -P --pdb print GEMS Protocol Data Block (0025,1b,GEMS_SERS_01)." << std::endl;
@@ -1312,6 +1335,7 @@ int main (int argc, char *argv[])
int printmedcom = 0; // MedCom History Information
int printcsaasl = 0;
int printcsadiffusion = 0;
+ int printcsa64 = 0;
int printpdb = 0;
int printelscint = 0;
int printvepro = 0;
@@ -1363,6 +1387,7 @@ int main (int argc, char *argv[])
{"ct3", 0, &printct3, 1},
{"csa-asl", 0, &printcsaasl, 1},
{"csa-diffusion", 0, &printcsadiffusion, 1},
+ {"csa64", 0, &printcsa64, 1},
{"mrprotocol", 0, &printmrprotocol, 1},
{"pmtf", 0, &printpmtf, 1},
{"mecmr3", 0, &printpmtf, 1},
@@ -1539,16 +1564,26 @@ int main (int argc, char *argv[])
std::cerr << "Not handled for now" << std::endl;
}
- const char * csaname = nullptr;
+ std::vector<std::string> csanames;
if( printcsaasl )
{
printcsabase64 = 1;
- csaname = "MR_ASL";
+ csanames.push_back( "MR_ASL" );
}
else if( printcsadiffusion )
{
printcsabase64 = 1;
- csaname = "MRDiffusion";
+ csanames.push_back( "MRDiffusion" );
+ }
+ else if( printcsa64 )
+ {
+ printcsabase64 = 1;
+ // keep me sorted
+ csanames.push_back( "FmriAcquisitionDescriptionSequence" );
+ csanames.push_back( "FmriConditionsDataSequence" );
+ csanames.push_back( "FmriResultSequence" );
+ csanames.push_back( "MR_ASL" );
+ csanames.push_back( "MRDiffusion" );
}
// else
@@ -1615,7 +1650,7 @@ int main (int argc, char *argv[])
}
else if( printcsabase64 )
{
- res += PrintCSABase64(*it, csaname);
+ res += PrintCSABase64(*it, csanames);
}
else if( dump )
{
@@ -1682,7 +1717,7 @@ int main (int argc, char *argv[])
}
else if( printcsabase64 )
{
- res += PrintCSABase64(filename, csaname);
+ res += PrintCSABase64(filename, csanames);
}
else if( dump )
{
https://sourceforge.net/p/gdcm/gdcm/ci/89ecad08052d1e5e4745cf2fc8b3a2b3bf8db62c/
commit 89ecad08052d1e5e4745cf2fc8b3a2b3bf8db62c
Author: Mathieu Malaterre <mat...@gm...>
Date: Wed Sep 14 05:00:07 2022 -0700
hande missing case
diff --git a/Utilities/gdcmext/csa.c b/Utilities/gdcmext/csa.c
index ffee00f91..0b7db9054 100644
--- a/Utilities/gdcmext/csa.c
+++ b/Utilities/gdcmext/csa.c
@@ -251,7 +251,7 @@ static bool read_data(struct app *self, struct csa_item_data *d) {
uint32_t unused;
s = fread_mirror(&unused, sizeof unused, 1, self);
ERROR_RETURN(s, 1);
- assert(unused == d->len || unused == 0x4d);
+ assert(unused == d->len || unused == 0x4d || unused == 0xcd);
}
if (d->len != 0) {
https://sourceforge.net/p/gdcm/gdcm/ci/fd53ea07cebc38cebec2a7ef03c9ddf94acc9061/
commit fd53ea07cebc38cebec2a7ef03c9ddf94acc9061
Author: Mathieu Malaterre <mat...@gm...>
Date: Wed Sep 14 04:58:06 2022 -0700
Fix VM
diff --git a/Source/DataDictionary/gdcmPrivateDefaultDicts.cxx b/Source/DataDictionary/gdcmPrivateDefaultDicts.cxx
index 647d5d0d9..a83bc0bc4 100644
--- a/Source/DataDictionary/gdcmPrivateDefaultDicts.cxx
+++ b/Source/DataDictionary/gdcmPrivateDefaultDicts.cxx
@@ -1232,7 +1232,7 @@ static const DICT_ENTRY DICOMV3DataDict [] = {
{0x0021,0x005a,"SIEMENS MR SDS 01",VR::CS,VM::VM1,"?Sequence Variant 1?",false},
{0x0021,0x005b,"SIEMENS MR SDI 02",VR::FD,VM::VM3,"Image Position (Patient)",false},
{0x0021,0x005b,"SIEMENS MR SDS 01",VR::CS,VM::VM1_n,"?Sequence Variant 2?",false},
- {0x0021,0x005c,"SIEMENS MR SDS 01",VR::CS,VM::VM1,"MTR flag. MT => ON",false},
+ {0x0021,0x005c,"SIEMENS MR SDS 01",VR::CS,VM::VM1_n,"MTR flag. MT => ON",false},
{0x0021,0x005d,"SIEMENS MR SDS 01",VR::SL,VM::VM1,"??",false},
{0x0021,0x005e,"SIEMENS MR SDI 02",VR::IS,VM::VM1,"?FrameIndex?",false},
{0x0021,0x005e,"SIEMENS MR SDS 01",VR::LO,VM::VM1,"?",false},
-----------------------------------------------------------------------
Summary of changes:
Applications/Cxx/gdcmdump.cxx | 79 ++++++++++++++++------
Source/DataDictionary/gdcmPrivateDefaultDicts.cxx | 31 ++++++++-
Source/DataDictionary/privatedicts.xml | 29 +++++++-
.../gdcmCSAHeader.cxx | 1 +
Source/MediaStorageAndFileFormat/gdcmCleaner.cxx | 32 +++++++--
Utilities/gdcmext/csa.c | 11 ++-
Utilities/gdcmext/mec_mr3.c | 1 +
7 files changed, 150 insertions(+), 34 deletions(-)
hooks/post-receive
--
Grassroots DICOM
|
