[Gdcm-hackers] gdcm-git:Grassroots DICOM branch release updated. 10ca9d3468a95d1b6d9786c5693d59c215
Cross-platform DICOM implementation
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[Gdcm-hackers] gdcm-git:Grassroots DICOM branch release updated. 10ca9d3468a95d1b6d9786c5693d59c21510a4e3
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From: Mathieu M. <ma...@us...> - 2022-11-15 07:53:26
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https://sourceforge.net/p/gdcm/gdcm/ci/10ca9d3468a95d1b6d9786c5693d59c21510a4e3/
commit 10ca9d3468a95d1b6d9786c5693d59c21510a4e3
Author: Mathieu Malaterre <mat...@gm...>
Date: Mon Nov 14 23:52:48 2022 -0800
Make code future proof with possibly new extension
diff --git a/Source/MediaStorageAndFileFormat/gdcmCleaner.cxx b/Source/MediaStorageAndFileFormat/gdcmCleaner.cxx
index f7131b57f..5f185dd90 100644
--- a/Source/MediaStorageAndFileFormat/gdcmCleaner.cxx
+++ b/Source/MediaStorageAndFileFormat/gdcmCleaner.cxx
@@ -754,8 +754,8 @@ enum CSAImageHeaderType {
static const char *CSAImageHeaderTypeStrings[]{ //
"HG IRECORD", //
"IMAGE NUM 4", //
- "IMAGE_MR", //
- "NUC_FLOOD", //
+ "MR", //
+ "NUC FLOOD", //
"PET NUM 4", //
"SOM 5"};
@@ -856,7 +856,7 @@ static inline bool bs_is_signature_end(const ByteValue *bv, const char *str) {
return false;
}
-bool isSV10Legacy(const ByteValue *bv) {
+static inline bool isSV10Legacy(const ByteValue *bv) {
// 4 bytes aligned:
if (bv->GetLength() % 4 == 0) {
uint32_t n;
@@ -877,60 +877,19 @@ static bool CleanCSAImage(DataSet &ds, const DataElement &de) {
if (!bv) return true;
CSAImageHeaderType image_type = IMAGE_UNK;
+ std::string ref;
{
const PrivateTag ihtTag(0x0029, 0x08, "SIEMENS CSA HEADER");
- std::string ref;
image_type = GetCSAType<CSAImageHeaderType>(ref, ds, ihtTag,
CSAImageHeaderTypeStrings);
- // handle unknown cases first:
- if (image_type == IMAGE_UNK) {
- // not implemented, assume no PHI for now:
- gdcmDebugMacro("NotImplemented CSA: " << ref);
- return true;
- }
- }
-
- bool isSV104321 = false;
- CSAImageHeaderType image_guesstype = IMAGE_UNK;
- static const char sv10[] = "SV10\4\3\2\1"; // 8
- static const char ini2[] = "label:=Standar"; // 14
- static const char end[] = "END! "; // 10
- if (is_signature(bv, sv10) || isSV10Legacy(bv)) {
- assert(image_type == IMAGE_NUM_4 // MR Image Storage / NUMARIS/4
- || image_type ==
- PET_NUM_4 // Positron Emission Tomography Image Storage
- || image_type == IMAGE_MR); // Enhanced SR Storage
- image_guesstype = image_type;
- isSV104321 = true;
- } else if (bs_is_signature(bv, sv10)) {
- assert(image_type == IMAGE_NUM_4 // MR Image Storage / NUMARIS/4
- || image_type ==
- PET_NUM_4 // Positron Emission Tomography Image Storage
- || image_type == IMAGE_MR); // Enhanced SR Storage
- image_guesstype = image_type;
- gdcmWarningMacro("Found byte-swapped SV10");
- } else if (is_signature(bv, ini2) || bs_is_signature(bv, ini2)) {
- // some kind of INI style structured with base64 thumbnail (zlib)
- image_guesstype = HG_IRECORD;
- } else if (is_signature_end(bv, end) || bs_is_signature_end(bv, end)) {
- image_guesstype = SOM_5;
- } else {
- const bool zero = isAllZero(bv->GetPointer(), bv->GetLength());
- if (zero) {
- gdcmWarningMacro("Zero out SV10");
- image_guesstype = image_type;
- }
}
+ static const char sv10[] = "SV10\4\3\2\1"; // 8
- // this is an implementation error must return error
- if (image_guesstype == IMAGE_UNK || image_guesstype != image_type) {
- gdcmErrorMacro("Implementation error CSA: " << image_type);
- return false;
- }
-
- // else
- assert(image_guesstype == image_type);
- if (isSV104321) {
+ // easy case: recognized keywords:
+ if (image_type == IMAGE_NUM_4 // MR Image Storage / NUMARIS/4
+ || image_type == PET_NUM_4 // Positron Emission Tomography Image Storage
+ || image_type == IMAGE_MR) // Enhanced SR Storage
+ {
DataElement clean(de.GetTag());
clean.SetVR(de.GetVR());
std::vector<char> v;
@@ -940,13 +899,23 @@ static bool CleanCSAImage(DataSet &ds, const DataElement &de) {
ds.Replace(clean);
return true;
}
- gdcmErrorMacro("Failure to call CleanCSA");
+ // we failed to clean CSA, let's check possible well known errors
+ if (bs_is_signature(bv, sv10)) {
+ gdcmWarningMacro("Found byte-swapped SV10. Skipping.");
+ return true;
+ } else if (isAllZero(bv->GetPointer(), bv->GetLength())) {
+ gdcmDebugMacro("Zero-out CSA header");
+ return true;
+ }
+ gdcmErrorMacro("Failure to call CleanCSAImage");
return false;
- } else {
- gdcmDebugMacro("Scrubbing is no-op for "
- << CSAImageHeaderTypeStrings[image_type]);
- return true;
}
+ // else
+ // add a dummy check for SV10 signature
+ if (is_signature(bv, sv10)) {
+ gdcmWarningMacro("Please report. SV10 Header found for new type: " << ref);
+ }
+ return true;
}
static bool CleanCSASeries(DataSet &ds, const DataElement &de) {
@@ -955,61 +924,16 @@ static bool CleanCSASeries(DataSet &ds, const DataElement &de) {
if (!bv) return true;
CSASeriesHeaderType series_type = SERIES_UNK;
+ std::string ref;
{
const PrivateTag shtTag(0x0029, 0x18, "SIEMENS CSA HEADER");
- std::string ref;
series_type = GetCSAType<CSASeriesHeaderType>(ref, ds, shtTag,
CSASeriesHeaderTypeStrings);
- // handle unknown cases first:
- if (series_type == SERIES_UNK) {
- // not implemented, assume no PHI for now:
- gdcmWarningMacro("NotImplemented CSA: " << ref);
- return true;
- }
}
+ static const char sv10[] = "SV10\4\3\2\1"; // 8
- bool isSV104321 = false;
- CSASeriesHeaderType series_guesstype = SERIES_UNK;
- static const char sv10[] = "SV10\4\3\2\1"; // 8
- static const char xml_root[] = "<?xml version=\"1.0\" ?>"; // 22
- static const char pds_com[] = "<pds><com>"; // 10
- static const char som7dev[] = "ORIGINALSERIES"; // 14
- if (is_signature(bv, sv10) || isSV10Legacy(bv)) {
- assert(series_type == PT ||
- series_type == SERIES_MR); // Enhanced SR Storage
- series_guesstype = series_type;
- isSV104321 = true;
- } else if (bs_is_signature(bv, sv10)) {
- assert(series_type == PT ||
- series_type == SERIES_MR); // Enhanced SR Storage
- series_guesstype = series_type;
- gdcmWarningMacro("Found byte-swapped SV10");
- } else if (is_signature(bv, xml_root) || bs_is_signature(bv, xml_root)) {
- // ParameterBlock case:
- series_guesstype = ParameterBlock;
- } else if (is_signature(bv, pds_com) || bs_is_signature(bv, pds_com)) {
- // PET_REPLAY_PARAM case:
- series_guesstype = PET_REPLAY_PARAM;
- } else if (is_signature(bv, som7dev) || bs_is_signature(bv, som7dev)) {
- // SOM 7 DEV
- series_guesstype = SOM_7_DEV;
- } else {
- const bool zero = isAllZero(bv->GetPointer(), bv->GetLength());
- if (zero) {
- gdcmWarningMacro("Zero out SV10");
- series_guesstype = series_type;
- }
- }
-
- // this is an implementation error must return error
- if (series_guesstype == SERIES_UNK || series_guesstype != series_type) {
- gdcmErrorMacro("Implementation error CSA: " << series_type);
- return false;
- }
-
- // else
- assert(series_guesstype == series_type);
- if (isSV104321) {
+ // easy case: recognized keywords:
+ if (series_type == PT || series_type == SERIES_MR) {
DataElement clean(de.GetTag());
clean.SetVR(de.GetVR());
std::vector<char> v;
@@ -1019,66 +943,24 @@ static bool CleanCSASeries(DataSet &ds, const DataElement &de) {
ds.Replace(clean);
return true;
}
- gdcmErrorMacro("Failure to call CleanCSA");
+ // we failed to clean CSA, let's check possible well known errors
+ if (bs_is_signature(bv, sv10)) {
+ gdcmWarningMacro("Found byte-swapped SV10. Skipping.");
+ return true;
+ } else if (isAllZero(bv->GetPointer(), bv->GetLength())) {
+ gdcmDebugMacro("Zero-out CSA header");
+ return true;
+ }
+ gdcmErrorMacro("Failure to call CleanCSASeries");
return false;
- } else {
- gdcmDebugMacro("Scrubbing is no-op for "
- << CSASeriesHeaderTypeStrings[series_type]);
- return true;
- }
-}
-
-static bool CleanCSA(DataSet &ds, const DataElement &de) {
- const ByteValue *bv = de.GetByteValue();
- // fast path:
- if (!bv) return true;
- static const char vs01[] = "VS01";
- // bogus big-endian conversion
- if (bv->GetLength() >= 4 && memcmp(bv->GetPointer(), vs01, 4) == 0) {
- // technically there is digital trash, but since it is written in
- // byte-swap mode, it cannot be detected easily.
- return true;
- }
- static const char pds_com[] = "<pds><com>";
- // PET_REPLAY_PARAM case:
- if (bv->GetLength() >= 10 && memcmp(bv->GetPointer(), pds_com, 10) == 0) {
- return true;
- }
- static const char psd_ocm[] = "p<sd<>oc>m";
- // byte-swap PET_REPLAY_PARAM case:
- if (bv->GetLength() >= 10 && memcmp(bv->GetPointer(), psd_ocm, 10) == 0) {
- return true;
}
- // ANGIOHEAD case. This is a DICOM Explicit with a odd ending:
- static const char end[] = "END! ";
- // const char *debug = bv->GetPointer() + bv->GetLength() - 10;
- // size_t d = strlen(end);
- // int i1 = memcmp(bv->GetPointer() + bv->GetLength() - 10, end, 10) ;
- // int i2 = memcmp(debug, end, 10) ;
- if (bv->GetLength() >= 10 &&
- memcmp(bv->GetPointer() + bv->GetLength() - 10, end, 10) == 0) {
- return true;
- }
- // byte-swapped ANGIOHEAD
- static const char ned[] = "NE!D ";
- if (bv->GetLength() >= 10 &&
- memcmp(bv->GetPointer() + bv->GetLength() - 10, ned, 10) == 0) {
- return true;
- }
- const bool zero = isAllZero(bv->GetPointer(), bv->GetLength());
- if (zero) return true;
-
- DataElement clean(de.GetTag());
- clean.SetVR(de.GetVR());
- std::vector<char> v;
- v.resize(bv->GetLength());
- if (csa_memcpy(&v[0], bv->GetPointer(), bv->GetLength())) {
- clean.SetByteValue(&v[0], v.size());
- ds.Replace(clean);
- return true;
+ // else
+ // add a dummy check for SV10 signature
+ if (is_signature(bv, sv10)) {
+ gdcmWarningMacro("SV10 Header found for new type: " << ref);
+ assert(0);
}
- gdcmErrorMacro("Failure to call CleanCSA");
- return false;
+ return true;
}
static bool CleanMEC_MR3(DataSet &ds, const DataElement &de) {
https://sourceforge.net/p/gdcm/gdcm/ci/13780759a34cf25afc3b5e0917397941f5112fd3/
commit 13780759a34cf25afc3b5e0917397941f5112fd3
Author: Mathieu Malaterre <mat...@gm...>
Date: Mon Nov 14 23:52:33 2022 -0800
Simlify code logic
diff --git a/Utilities/gdcmext/csa.c b/Utilities/gdcmext/csa.c
index e0a0eb40c..ad95a6eca 100644
--- a/Utilities/gdcmext/csa.c
+++ b/Utilities/gdcmext/csa.c
@@ -148,19 +148,9 @@ static bool read_magic(struct app *self) {
} else if (n < 0x100 && unused == 0x4d) { // 'M'
// SIEMENS_Sonata-16-MONO2-Value_Multiplicity.dcm
magic = NOMAGIC;
- } else if (n == 0x7364703c && unused == 0x6f633c3e) { // aka '<pds><co'
- // 'PET_REPLAY_PARAM'
- assert(0);
- return false;
- } else if (n == 0x31305356 && unused == 0x2010403) { // aka 'VS01' ...
- // technically could be reserved; should not happen in the wild
- assert(0);
- return false;
} else {
- assert(0);
return false;
}
- assert(n > 0 && n < 128);
self->nelements = n;
self->csa_type = magic;
return true;
https://sourceforge.net/p/gdcm/gdcm/ci/8fe824c39bc18ffe57c5b6c1305b87463b4e2d99/
commit 8fe824c39bc18ffe57c5b6c1305b87463b4e2d99
Author: Mathieu Malaterre <mat...@gm...>
Date: Mon Nov 14 07:49:40 2022 -0800
Reduce verbosity for now
diff --git a/Source/DataStructureAndEncodingDefinition/gdcmPrivateTag.cxx b/Source/DataStructureAndEncodingDefinition/gdcmPrivateTag.cxx
index 809ecab2a..00d457a29 100644
--- a/Source/DataStructureAndEncodingDefinition/gdcmPrivateTag.cxx
+++ b/Source/DataStructureAndEncodingDefinition/gdcmPrivateTag.cxx
@@ -32,7 +32,8 @@ namespace gdcm_ns
|| group % 2 == 0
/*|| strlen(owner.c_str()) == 0*/ ) // can't use owner.empty()
{
- gdcmDebugMacro( "Problem reading Private Tag: " << str );
+ // comment out the following since too verbose
+ //gdcmDebugMacro( "Problem reading Private Tag: " << str );
return false;
}
SetGroup( (uint16_t)group );
diff --git a/Source/DataStructureAndEncodingDefinition/gdcmTag.cxx b/Source/DataStructureAndEncodingDefinition/gdcmTag.cxx
index b55879fd9..a4f5d40f2 100644
--- a/Source/DataStructureAndEncodingDefinition/gdcmTag.cxx
+++ b/Source/DataStructureAndEncodingDefinition/gdcmTag.cxx
@@ -23,7 +23,7 @@ namespace gdcm
unsigned int group = 0, element = 0;
if( !str || sscanf(str, "%04x,%04x", &group , &element) != 2 )
{
- gdcmDebugMacro( "Problem reading Tag: " << str );
+ //gdcmDebugMacro( "Problem reading Tag: " << str );
return false;
}
SetGroup( (uint16_t)group );
https://sourceforge.net/p/gdcm/gdcm/ci/c897cb249306c6530a1e0ad16e798b945bbaeca9/
commit c897cb249306c6530a1e0ad16e798b945bbaeca9
Author: Mathieu Malaterre <mat...@gm...>
Date: Mon Nov 14 07:48:49 2022 -0800
Another round of fix for siemens/csa
diff --git a/Source/MediaStorageAndFileFormat/gdcmCleaner.cxx b/Source/MediaStorageAndFileFormat/gdcmCleaner.cxx
index e2e658e86..f7131b57f 100644
--- a/Source/MediaStorageAndFileFormat/gdcmCleaner.cxx
+++ b/Source/MediaStorageAndFileFormat/gdcmCleaner.cxx
@@ -751,12 +751,13 @@ enum CSAImageHeaderType {
SOM_5, // SOM 5
};
-static const char *CSAImageHeaderTypeStrings[]{
- "HG IRECORD", //
- "IMAGE NUM 4", //
- "IMAGE_MR", "NUC_FLOOD", "PET_NUM_4", "SOM_5",
- nullptr // sentinel
-};
+static const char *CSAImageHeaderTypeStrings[]{ //
+ "HG IRECORD", //
+ "IMAGE NUM 4", //
+ "IMAGE_MR", //
+ "NUC_FLOOD", //
+ "PET NUM 4", //
+ "SOM 5"};
enum CSASeriesHeaderType {
SERIES_UNK = -1,
@@ -778,7 +779,7 @@ static const char *CSASeriesHeaderTypeStrings[]{
};
template <typename T, int N>
-static T GetCSAType(CSComp &ref, const DataSet &ds, const PrivateTag &pt,
+static T GetCSAType(std::string &ref, const DataSet &ds, const PrivateTag &pt,
const char *(&array)[N]) {
T series_type = (T)-1; // UNK
ref = "";
@@ -786,7 +787,7 @@ static T GetCSAType(CSComp &ref, const DataSet &ds, const PrivateTag &pt,
const gdcm::DataElement &de1 = ds.GetDataElement(pt);
Element<VR::CS, VM::VM1> el = {};
el.SetFromDataElement(de1);
- ref = el.GetValue();
+ ref = el.GetValue().Trim();
for (int i = 0; i < N; i++) {
if (strcmp(array[i], ref.c_str()) == 0) {
series_type = (T)(i);
@@ -796,6 +797,80 @@ static T GetCSAType(CSComp &ref, const DataSet &ds, const PrivateTag &pt,
return series_type;
}
+// byte-swapped memcmp implementation:
+static inline int bs_memcmp(const void *s1, const void *s2, size_t n) {
+ size_t i;
+ const unsigned char *us1 = (const unsigned char *)s1;
+ const unsigned char *us2 = (const unsigned char *)s2;
+ assert(n % 2 == 0);
+
+ for (i = 0; i < n; i += 2, us1 += 2, us2 += 2) {
+ if (*us1 < *(us2 + 1)) {
+ return -1;
+ } else if (*us1 > *(us2 + 1)) {
+ return 1;
+ }
+
+ if (*(us1 + 1) < *us2) {
+ return -1;
+ } else if (*(us1 + 1) > *us2) {
+ return 1;
+ }
+ }
+ return 0;
+}
+
+static inline bool is_signature(const ByteValue *bv, const char *str) {
+ const size_t len = strlen(str);
+ if (bv->GetLength() >= len && memcmp(bv->GetPointer(), str, len) == 0) {
+ return true;
+ }
+ return false;
+}
+
+static inline bool bs_is_signature(const ByteValue *bv, const char *str) {
+ const size_t len = strlen(str);
+ if (bv->GetLength() >= len && bs_memcmp(bv->GetPointer(), str, len) == 0) {
+ return true;
+ }
+ return false;
+}
+
+static inline bool is_signature_end(const ByteValue *bv, const char *str) {
+ const size_t len = strlen(str);
+ if (bv->GetLength() >= len &&
+ memcmp(bv->GetPointer() + bv->GetLength() - len, str, len) == 0) {
+ return true;
+ }
+
+ return false;
+}
+
+static inline bool bs_is_signature_end(const ByteValue *bv, const char *str) {
+ const size_t len = strlen(str);
+ if (bv->GetLength() >= len &&
+ bs_memcmp(bv->GetPointer() + bv->GetLength() - len, str, len) == 0) {
+ return true;
+ }
+
+ return false;
+}
+
+bool isSV10Legacy(const ByteValue *bv) {
+ // 4 bytes aligned:
+ if (bv->GetLength() % 4 == 0) {
+ uint32_t n;
+ uint32_t unused;
+ if (bv->GetLength() >= 8) {
+ const char *buffer = bv->GetPointer();
+ memcpy(&n, buffer, 4);
+ memcpy(&unused, buffer + 4, 4);
+ if (n < 0x100 && unused == 0x4d) return true;
+ }
+ }
+ return false;
+}
+
static bool CleanCSAImage(DataSet &ds, const DataElement &de) {
const ByteValue *bv = de.GetByteValue();
// fast path:
@@ -804,7 +879,7 @@ static bool CleanCSAImage(DataSet &ds, const DataElement &de) {
CSAImageHeaderType image_type = IMAGE_UNK;
{
const PrivateTag ihtTag(0x0029, 0x08, "SIEMENS CSA HEADER");
- CSComp ref;
+ std::string ref;
image_type = GetCSAType<CSAImageHeaderType>(ref, ds, ihtTag,
CSAImageHeaderTypeStrings);
// handle unknown cases first:
@@ -815,11 +890,38 @@ static bool CleanCSAImage(DataSet &ds, const DataElement &de) {
}
}
+ bool isSV104321 = false;
CSAImageHeaderType image_guesstype = IMAGE_UNK;
- static const char xml_root[] = "<?xml version=\"1.0\" ?>";
- // ParameterBlock case:
- if (bv->GetLength() >= 22 && memcmp(bv->GetPointer(), xml_root, 22) == 0) {
+ static const char sv10[] = "SV10\4\3\2\1"; // 8
+ static const char ini2[] = "label:=Standar"; // 14
+ static const char end[] = "END! "; // 10
+ if (is_signature(bv, sv10) || isSV10Legacy(bv)) {
+ assert(image_type == IMAGE_NUM_4 // MR Image Storage / NUMARIS/4
+ || image_type ==
+ PET_NUM_4 // Positron Emission Tomography Image Storage
+ || image_type == IMAGE_MR); // Enhanced SR Storage
+ image_guesstype = image_type;
+ isSV104321 = true;
+ } else if (bs_is_signature(bv, sv10)) {
+ assert(image_type == IMAGE_NUM_4 // MR Image Storage / NUMARIS/4
+ || image_type ==
+ PET_NUM_4 // Positron Emission Tomography Image Storage
+ || image_type == IMAGE_MR); // Enhanced SR Storage
+ image_guesstype = image_type;
+ gdcmWarningMacro("Found byte-swapped SV10");
+ } else if (is_signature(bv, ini2) || bs_is_signature(bv, ini2)) {
+ // some kind of INI style structured with base64 thumbnail (zlib)
+ image_guesstype = HG_IRECORD;
+ } else if (is_signature_end(bv, end) || bs_is_signature_end(bv, end)) {
+ image_guesstype = SOM_5;
+ } else {
+ const bool zero = isAllZero(bv->GetPointer(), bv->GetLength());
+ if (zero) {
+ gdcmWarningMacro("Zero out SV10");
+ image_guesstype = image_type;
+ }
}
+
// this is an implementation error must return error
if (image_guesstype == IMAGE_UNK || image_guesstype != image_type) {
gdcmErrorMacro("Implementation error CSA: " << image_type);
@@ -828,7 +930,7 @@ static bool CleanCSAImage(DataSet &ds, const DataElement &de) {
// else
assert(image_guesstype == image_type);
- if (image_type == IMAGE_MR) {
+ if (isSV104321) {
DataElement clean(de.GetTag());
clean.SetVR(de.GetVR());
std::vector<char> v;
@@ -841,7 +943,8 @@ static bool CleanCSAImage(DataSet &ds, const DataElement &de) {
gdcmErrorMacro("Failure to call CleanCSA");
return false;
} else {
- gdcmDebugMacro("Scrubbing is no-op for " << image_type);
+ gdcmDebugMacro("Scrubbing is no-op for "
+ << CSAImageHeaderTypeStrings[image_type]);
return true;
}
}
@@ -854,23 +957,50 @@ static bool CleanCSASeries(DataSet &ds, const DataElement &de) {
CSASeriesHeaderType series_type = SERIES_UNK;
{
const PrivateTag shtTag(0x0029, 0x18, "SIEMENS CSA HEADER");
- CSComp ref;
+ std::string ref;
series_type = GetCSAType<CSASeriesHeaderType>(ref, ds, shtTag,
CSASeriesHeaderTypeStrings);
// handle unknown cases first:
if (series_type == SERIES_UNK) {
// not implemented, assume no PHI for now:
- gdcmDebugMacro("NotImplemented CSA: " << ref);
+ gdcmWarningMacro("NotImplemented CSA: " << ref);
return true;
}
}
+ bool isSV104321 = false;
CSASeriesHeaderType series_guesstype = SERIES_UNK;
- static const char xml_root[] = "<?xml version=\"1.0\" ?>";
- // ParameterBlock case:
- if (bv->GetLength() >= 22 && memcmp(bv->GetPointer(), xml_root, 22) == 0) {
+ static const char sv10[] = "SV10\4\3\2\1"; // 8
+ static const char xml_root[] = "<?xml version=\"1.0\" ?>"; // 22
+ static const char pds_com[] = "<pds><com>"; // 10
+ static const char som7dev[] = "ORIGINALSERIES"; // 14
+ if (is_signature(bv, sv10) || isSV10Legacy(bv)) {
+ assert(series_type == PT ||
+ series_type == SERIES_MR); // Enhanced SR Storage
+ series_guesstype = series_type;
+ isSV104321 = true;
+ } else if (bs_is_signature(bv, sv10)) {
+ assert(series_type == PT ||
+ series_type == SERIES_MR); // Enhanced SR Storage
+ series_guesstype = series_type;
+ gdcmWarningMacro("Found byte-swapped SV10");
+ } else if (is_signature(bv, xml_root) || bs_is_signature(bv, xml_root)) {
+ // ParameterBlock case:
series_guesstype = ParameterBlock;
+ } else if (is_signature(bv, pds_com) || bs_is_signature(bv, pds_com)) {
+ // PET_REPLAY_PARAM case:
+ series_guesstype = PET_REPLAY_PARAM;
+ } else if (is_signature(bv, som7dev) || bs_is_signature(bv, som7dev)) {
+ // SOM 7 DEV
+ series_guesstype = SOM_7_DEV;
+ } else {
+ const bool zero = isAllZero(bv->GetPointer(), bv->GetLength());
+ if (zero) {
+ gdcmWarningMacro("Zero out SV10");
+ series_guesstype = series_type;
+ }
}
+
// this is an implementation error must return error
if (series_guesstype == SERIES_UNK || series_guesstype != series_type) {
gdcmErrorMacro("Implementation error CSA: " << series_type);
@@ -879,7 +1009,7 @@ static bool CleanCSASeries(DataSet &ds, const DataElement &de) {
// else
assert(series_guesstype == series_type);
- if (series_type == SERIES_MR) {
+ if (isSV104321) {
DataElement clean(de.GetTag());
clean.SetVR(de.GetVR());
std::vector<char> v;
@@ -892,7 +1022,8 @@ static bool CleanCSASeries(DataSet &ds, const DataElement &de) {
gdcmErrorMacro("Failure to call CleanCSA");
return false;
} else {
- gdcmDebugMacro("Scrubbing is no-op for " << series_type);
+ gdcmDebugMacro("Scrubbing is no-op for "
+ << CSASeriesHeaderTypeStrings[series_type]);
return true;
}
}
https://sourceforge.net/p/gdcm/gdcm/ci/84c8c3c058cce1a65f3b263fa44a8ab2e5ae179f/
commit 84c8c3c058cce1a65f3b263fa44a8ab2e5ae179f
Author: Mathieu Malaterre <mat...@gm...>
Date: Mon Nov 14 05:20:28 2022 -0800
Rework the SIEMENS/CSA handling
diff --git a/Source/MediaStorageAndFileFormat/gdcmCleaner.cxx b/Source/MediaStorageAndFileFormat/gdcmCleaner.cxx
index 437154750..e2e658e86 100644
--- a/Source/MediaStorageAndFileFormat/gdcmCleaner.cxx
+++ b/Source/MediaStorageAndFileFormat/gdcmCleaner.cxx
@@ -741,6 +741,162 @@ static bool isAllZero(const char *buffer, size_t len) {
return true;
}
+enum CSAImageHeaderType {
+ IMAGE_UNK = -1,
+ HG_IRECORD = 0, // HG IRECORD,
+ IMAGE_NUM_4, // IMAGE NUM 4 ,
+ IMAGE_MR,
+ NUC_FLOOD,
+ PET_NUM_4,
+ SOM_5, // SOM 5
+};
+
+static const char *CSAImageHeaderTypeStrings[]{
+ "HG IRECORD", //
+ "IMAGE NUM 4", //
+ "IMAGE_MR", "NUC_FLOOD", "PET_NUM_4", "SOM_5",
+ nullptr // sentinel
+};
+
+enum CSASeriesHeaderType {
+ SERIES_UNK = -1,
+ HG_RECORD_SERIES = 0, // HG RECORD SERIES,
+ SERIES_MR,
+ ParameterBlock,
+ PET_REPLAY_PARAM,
+ PT,
+ SOM_7_DEV, // SOM 7 DEV
+};
+
+static const char *CSASeriesHeaderTypeStrings[]{
+ "HG RECORD SERIES", // HG_RECORD_SERIES
+ "MR", // SERIES_MR
+ "ParameterBlock", // ParameterBlock
+ "PET_REPLAY_PARAM", //
+ "PT", //
+ "SOM 7 DEV", // SOM_7_DEV
+};
+
+template <typename T, int N>
+static T GetCSAType(CSComp &ref, const DataSet &ds, const PrivateTag &pt,
+ const char *(&array)[N]) {
+ T series_type = (T)-1; // UNK
+ ref = "";
+ if (ds.FindDataElement(pt)) {
+ const gdcm::DataElement &de1 = ds.GetDataElement(pt);
+ Element<VR::CS, VM::VM1> el = {};
+ el.SetFromDataElement(de1);
+ ref = el.GetValue();
+ for (int i = 0; i < N; i++) {
+ if (strcmp(array[i], ref.c_str()) == 0) {
+ series_type = (T)(i);
+ }
+ }
+ }
+ return series_type;
+}
+
+static bool CleanCSAImage(DataSet &ds, const DataElement &de) {
+ const ByteValue *bv = de.GetByteValue();
+ // fast path:
+ if (!bv) return true;
+
+ CSAImageHeaderType image_type = IMAGE_UNK;
+ {
+ const PrivateTag ihtTag(0x0029, 0x08, "SIEMENS CSA HEADER");
+ CSComp ref;
+ image_type = GetCSAType<CSAImageHeaderType>(ref, ds, ihtTag,
+ CSAImageHeaderTypeStrings);
+ // handle unknown cases first:
+ if (image_type == IMAGE_UNK) {
+ // not implemented, assume no PHI for now:
+ gdcmDebugMacro("NotImplemented CSA: " << ref);
+ return true;
+ }
+ }
+
+ CSAImageHeaderType image_guesstype = IMAGE_UNK;
+ static const char xml_root[] = "<?xml version=\"1.0\" ?>";
+ // ParameterBlock case:
+ if (bv->GetLength() >= 22 && memcmp(bv->GetPointer(), xml_root, 22) == 0) {
+ }
+ // this is an implementation error must return error
+ if (image_guesstype == IMAGE_UNK || image_guesstype != image_type) {
+ gdcmErrorMacro("Implementation error CSA: " << image_type);
+ return false;
+ }
+
+ // else
+ assert(image_guesstype == image_type);
+ if (image_type == IMAGE_MR) {
+ DataElement clean(de.GetTag());
+ clean.SetVR(de.GetVR());
+ std::vector<char> v;
+ v.resize(bv->GetLength());
+ if (csa_memcpy(&v[0], bv->GetPointer(), bv->GetLength())) {
+ clean.SetByteValue(&v[0], v.size());
+ ds.Replace(clean);
+ return true;
+ }
+ gdcmErrorMacro("Failure to call CleanCSA");
+ return false;
+ } else {
+ gdcmDebugMacro("Scrubbing is no-op for " << image_type);
+ return true;
+ }
+}
+
+static bool CleanCSASeries(DataSet &ds, const DataElement &de) {
+ const ByteValue *bv = de.GetByteValue();
+ // fast path:
+ if (!bv) return true;
+
+ CSASeriesHeaderType series_type = SERIES_UNK;
+ {
+ const PrivateTag shtTag(0x0029, 0x18, "SIEMENS CSA HEADER");
+ CSComp ref;
+ series_type = GetCSAType<CSASeriesHeaderType>(ref, ds, shtTag,
+ CSASeriesHeaderTypeStrings);
+ // handle unknown cases first:
+ if (series_type == SERIES_UNK) {
+ // not implemented, assume no PHI for now:
+ gdcmDebugMacro("NotImplemented CSA: " << ref);
+ return true;
+ }
+ }
+
+ CSASeriesHeaderType series_guesstype = SERIES_UNK;
+ static const char xml_root[] = "<?xml version=\"1.0\" ?>";
+ // ParameterBlock case:
+ if (bv->GetLength() >= 22 && memcmp(bv->GetPointer(), xml_root, 22) == 0) {
+ series_guesstype = ParameterBlock;
+ }
+ // this is an implementation error must return error
+ if (series_guesstype == SERIES_UNK || series_guesstype != series_type) {
+ gdcmErrorMacro("Implementation error CSA: " << series_type);
+ return false;
+ }
+
+ // else
+ assert(series_guesstype == series_type);
+ if (series_type == SERIES_MR) {
+ DataElement clean(de.GetTag());
+ clean.SetVR(de.GetVR());
+ std::vector<char> v;
+ v.resize(bv->GetLength());
+ if (csa_memcpy(&v[0], bv->GetPointer(), bv->GetLength())) {
+ clean.SetByteValue(&v[0], v.size());
+ ds.Replace(clean);
+ return true;
+ }
+ gdcmErrorMacro("Failure to call CleanCSA");
+ return false;
+ } else {
+ gdcmDebugMacro("Scrubbing is no-op for " << series_type);
+ return true;
+ }
+}
+
static bool CleanCSA(DataSet &ds, const DataElement &de) {
const ByteValue *bv = de.GetByteValue();
// fast path:
@@ -748,8 +904,8 @@ static bool CleanCSA(DataSet &ds, const DataElement &de) {
static const char vs01[] = "VS01";
// bogus big-endian conversion
if (bv->GetLength() >= 4 && memcmp(bv->GetPointer(), vs01, 4) == 0) {
- // technically there is digital trash, but since it is written in byte-swap
- // mode, it cannot be detected easily.
+ // technically there is digital trash, but since it is written in
+ // byte-swap mode, it cannot be detected easily.
return true;
}
static const char pds_com[] = "<pds><com>";
@@ -764,6 +920,10 @@ static bool CleanCSA(DataSet &ds, const DataElement &de) {
}
// ANGIOHEAD case. This is a DICOM Explicit with a odd ending:
static const char end[] = "END! ";
+ // const char *debug = bv->GetPointer() + bv->GetLength() - 10;
+ // size_t d = strlen(end);
+ // int i1 = memcmp(bv->GetPointer() + bv->GetLength() - 10, end, 10) ;
+ // int i2 = memcmp(debug, end, 10) ;
if (bv->GetLength() >= 10 &&
memcmp(bv->GetPointer() + bv->GetLength() - 10, end, 10) == 0) {
return true;
@@ -965,8 +1125,8 @@ Cleaner::impl::ACTION Cleaner::impl::ComputeAction(
if (!empty_vrs.empty() || !remove_vrs.empty()) {
VR vr = de.GetVR();
assert(ref_dict_vr != VR::INVALID);
- // be careful with vr handling since we must always prefer the one from the
- // dict in case of attribute written as 'OB' but dict states 'PN':
+ // be careful with vr handling since we must always prefer the one from
+ // the dict in case of attribute written as 'OB' but dict states 'PN':
if (ref_dict_vr != VR::UN /*&& ref_dict_vr != VR::INVALID*/) {
// we want to clean VR==PN; but this is a problem for implicit transfer
// syntax, so let's be nice to the user and prefer dict_vr. however for
@@ -1048,7 +1208,8 @@ bool Cleaner::impl::ProcessDataSet(Subject &subject, File &file, DataSet &ds,
// SmartPointer<SequenceOfItems> sqi = de.GetValueAsSQ();
if (!de.IsEmpty()) {
gdcmWarningMacro(
- "Please report. Dictionary states this should be a SQ. But we "
+ "Please report. Dictionary states this should be a SQ. But "
+ "we "
"failed to load it as such. Passing-through as-is"
<< de);
}
@@ -1074,10 +1235,10 @@ bool Cleaner::impl::ProcessDataSet(Subject &subject, File &file, DataSet &ds,
static const PrivateTag &pmtf3 = gdcm::MEC_MR3::GetCanonMECMR3Tag();
if (pt == csa1) {
- const bool ret = CleanCSA(ds, de);
+ const bool ret = CleanCSAImage(ds, de);
if (!ret) return false;
} else if (pt == csa2) {
- const bool ret = CleanCSA(ds, de);
+ const bool ret = CleanCSASeries(ds, de);
if (!ret) return false;
} else if (pt == mec_mr3) {
const bool ret = CleanMEC_MR3(ds, de);
-----------------------------------------------------------------------
Summary of changes:
.../gdcmPrivateTag.cxx | 3 +-
.../DataStructureAndEncodingDefinition/gdcmTag.cxx | 2 +-
Source/MediaStorageAndFileFormat/gdcmCleaner.cxx | 254 +++++++++++++++++----
Utilities/gdcmext/csa.c | 10 -
4 files changed, 217 insertions(+), 52 deletions(-)
hooks/post-receive
--
Grassroots DICOM
|
