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/*=========================================================================
Program: GDCM (Grassroots DICOM). A DICOM library
Copyright (c) 2006-2011 Mathieu Malaterre
All rights reserved.
See Copyright.txt or http://gdcm.sourceforge.net/Copyright.html for details.
This software is distributed WITHOUT ANY WARRANTY; without even
the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
PURPOSE. See the above copyright notice for more information.
=========================================================================*/
#include "gdcmCleaner.h"
#include "gdcmFilename.h"
#include "gdcmReader.h"
#include "gdcmSmartPointer.h"
#include "gdcmSystem.h"
#include "gdcmTesting.h"
#include "gdcmWriter.h"
namespace gdcm {
template <typename T>
static const DataSet &GetNestedDataSet(const DataSet &ds, const T &path) {
const DataElement &de = ds.GetDataElement(path);
SmartPointer<SequenceOfItems> sqi = de.GetValueAsSQ();
assert(sqi && sqi->GetNumberOfItems() == 1);
const Item &item = sqi->GetItem(1);
const DataSet &subds = item.GetNestedDataSet();
return subds;
}
template <typename T>
static bool IsTagIn(const DataSet &ds, const T &pt) {
return ds.FindDataElement(pt);
}
template <typename T1, typename T2>
static bool IsTagIn(const DataSet &ds, const T1 &path, const T2 &pt) {
const DataSet &subds = GetNestedDataSet(ds, path);
return subds.FindDataElement(pt);
}
template <typename T>
static bool IsTagEmpty(const DataSet &ds, const T &pt) {
if (!ds.FindDataElement(pt)) return false;
const DataElement &de = ds.GetDataElement(pt);
return de.IsEmpty();
}
template <typename T1, typename T2>
static bool IsTagEmpty(const DataSet &ds, const T1 &path, const T2 &pt) {
const DataSet &subds = GetNestedDataSet(ds, path);
if (!subds.FindDataElement(pt)) return false;
const DataElement &de = subds.GetDataElement(pt);
return de.IsEmpty();
}
} // namespace gdcm
struct TestCleaner4Impl {
virtual ~TestCleaner4Impl() = default;
virtual bool check_before(gdcm::DataSet &ds) = 0;
virtual bool check_after(gdcm::DataSet &ds, bool preservePatientName) = 0;
int run(std::string const &filename, std::string const &outfilename,
bool useDPath, bool preservePatientName = false) {
using namespace gdcm;
// Setup DPath
DPath dpath1, dpath2;
if (useDPath) {
}
// first pass
{
Reader reader;
reader.SetFileName(filename.c_str());
if (!reader.Read()) {
std::cerr << "Could not read: " << filename << std::endl;
return 1;
}
File &file = reader.GetFile();
DataSet &ds = file.GetDataSet();
if (!check_before(ds)) {
std::cerr << "Test not setup correctly" << std::endl;
return 1;
}
Cleaner cleaner;
cleaner.SetFile(file);
cleaner.RemoveAllGroupLength(false);
if (preservePatientName) {
DPath dpath;
dpath.ConstructFromString("\\0010,0010");
cleaner.Preserve(dpath);
}
if (useDPath) {
if (!cleaner.Empty(dpath1)) {
return 1;
}
} else {
if (!cleaner.Empty(VR(VR::PN))) {
return 1;
}
}
if (!cleaner.Clean()) {
return 1;
}
Writer writer;
writer.SetFileName(outfilename.c_str());
writer.SetFile(cleaner.GetFile());
#if 0
gdcm::FileMetaInformation::SetSourceApplicationEntityTitle("gdcmconv");
file.GetHeader().Clear();
writer.SetCheckFileMetaInformation(true);
#endif
if (!writer.Write()) {
std::cerr << "Failed to write: " << outfilename << std::endl;
return 1;
}
}
// re-read, written out:
{
Reader reader;
reader.SetFileName(outfilename.c_str());
if (!reader.Read()) {
std::cerr << "Could not read: " << outfilename << std::endl;
return 1;
}
File &file = reader.GetFile();
DataSet &ds = file.GetDataSet();
if (!check_after(ds, preservePatientName)) {
std::cerr << "At least one tag was not empty" << std::endl;
return 1;
}
}
return 0;
}
};
struct TestCleaner4Impl1 : public TestCleaner4Impl {
bool check_before(gdcm::DataSet &ds) override {
const gdcm::Tag t1(0x0008, 0x0090); //
const gdcm::Tag t2(0x0008, 0x1050); //
const gdcm::Tag t3(0x0008, 0x1070); //
const gdcm::Tag t4(0x0010, 0x0010); //
{
const bool b1 = IsTagIn(ds, t1);
const bool b2 = IsTagIn(ds, t2);
const bool b3 = IsTagIn(ds, t3);
const bool b4 = IsTagIn(ds, t4);
if (!b1 || !b2 || !b3 || !b4) {
return false;
}
}
{
const bool b1 = IsTagEmpty(ds, t1);
const bool b2 = IsTagEmpty(ds, t2);
const bool b3 = IsTagEmpty(ds, t3);
const bool b4 = IsTagEmpty(ds, t4);
if (b1 || b2 || b3 || b4) {
return false;
}
}
return true;
}
bool check_after(gdcm::DataSet &ds, bool /*preservePatientName*/) override {
const gdcm::Tag t1(0x0008, 0x0090); //
const gdcm::Tag t2(0x0008, 0x1050); //
const gdcm::Tag t3(0x0008, 0x1070); //
const gdcm::Tag t4(0x0010, 0x0010); //
const bool b1 = IsTagEmpty(ds, t1);
const bool b2 = IsTagEmpty(ds, t2);
const bool b3 = IsTagEmpty(ds, t3);
const bool b4 = IsTagEmpty(ds, t4);
if (!b1 || !b2 || !b3 || !b4) {
return false;
}
return true;
}
};
struct TestCleaner4Impl2 : public TestCleaner4Impl {
bool check_before(gdcm::DataSet &ds) override {
const gdcm::Tag t1(0x0008, 0x0090); // PN 6 EU^^^^
const gdcm::Tag t2(0x0008, 0x1050); // PN 4 ^^^^
const gdcm::Tag t3(0x0008, 0x1060); // PN 16 DR.H.DOOLITTLER
const gdcm::Tag t4(0x0008, 0x1070); // PN 4 CNA
const gdcm::Tag t5(0x0010, 0x0010); // PN 16 ABCDEF^GHIJK^^MR
const gdcm::Tag t6(0x0032, 0x1032); // PN 10 EMERG-UNIT
{
const bool b1 = IsTagIn(ds, t1);
const bool b2 = IsTagIn(ds, t2);
const bool b3 = IsTagIn(ds, t3);
const bool b4 = IsTagIn(ds, t4);
const bool b5 = IsTagIn(ds, t5);
const bool b6 = IsTagIn(ds, t6);
if (!b1 || !b2 || !b3 || !b4 || !b5 || !b6) {
return false;
}
}
{
const bool b1 = IsTagEmpty(ds, t1);
const bool b2 = IsTagEmpty(ds, t2);
const bool b3 = IsTagEmpty(ds, t3);
const bool b4 = IsTagEmpty(ds, t4);
const bool b5 = IsTagEmpty(ds, t5);
const bool b6 = IsTagEmpty(ds, t6);
if (b1 || b2 || b3 || b4 || b5 || b6) {
return false;
}
}
return true;
}
bool check_after(gdcm::DataSet &ds, bool /*preservePatientName*/) override {
const gdcm::Tag t1(0x0008, 0x0090); // PN 6 EU^^^^
const gdcm::Tag t2(0x0008, 0x1050); // PN 4 ^^^^
const gdcm::Tag t3(0x0008, 0x1060); // PN 16 DR.H.DOOLITTLER
const gdcm::Tag t4(0x0008, 0x1070); // PN 4 CNA
const gdcm::Tag t5(0x0010, 0x0010); // PN 16 ABCDEF^GHIJK^^MR
const gdcm::Tag t6(0x0032, 0x1032); // PN 10 EMERG-UNIT
const bool b1 = IsTagEmpty(ds, t1);
const bool b2 = IsTagEmpty(ds, t2);
const bool b3 = IsTagEmpty(ds, t3);
const bool b4 = IsTagEmpty(ds, t4);
const bool b5 = IsTagEmpty(ds, t5);
const bool b6 = IsTagEmpty(ds, t6);
if (!b1 || !b2 || !b3 || !b4 || !b5 || !b6) {
return false;
}
return true;
}
};
struct TestCleaner4Impl3 : public TestCleaner4Impl {
bool check_before(gdcm::DataSet &ds) override {
const gdcm::Tag t1(0x0008, 0x0090); //
const gdcm::Tag t2(0x0008, 0x1070); //
const gdcm::Tag t3(0x0010, 0x0010); //
const gdcm::PrivateTag path1(0x2001, 0x00, "Philips Imaging DD 129");
const gdcm::Tag t4(0x0070, 0x0084); //
const gdcm::PrivateTag pt5(0x2005, 0x91, "Philips MR Imaging DD 004"); //
{
const bool b1 = IsTagIn(ds, t1);
const bool b2 = IsTagIn(ds, t2);
const bool b3 = IsTagIn(ds, t3);
const bool b4 = IsTagIn(ds, path1, t4);
const bool b5 = IsTagIn(ds, pt5);
if (!b1 || !b2 || !b3 || !b4 || !b5) {
return false;
}
}
{
const bool b1 = IsTagEmpty(ds, t1);
const bool b2 = IsTagEmpty(ds, t2);
const bool b3 = IsTagEmpty(ds, t3);
const bool b4 = IsTagEmpty(ds, path1, t4);
const bool b5 = IsTagEmpty(ds, pt5);
if (!b1 || !b2 || b3 || b4 || !b5) {
return false;
}
}
return true;
}
bool check_after(gdcm::DataSet &ds, bool /*preservePatientName*/) override {
const gdcm::Tag t1(0x0008, 0x0090); //
const gdcm::Tag t2(0x0008, 0x1070); //
const gdcm::Tag t3(0x0010, 0x0010); //
const gdcm::PrivateTag path1(0x2001, 0x00, "Philips Imaging DD 129");
const gdcm::Tag t4(0x0070, 0x0084); //
const gdcm::PrivateTag pt5(0x2005, 0x91, "Philips MR Imaging DD 004"); //
const bool b1 = IsTagEmpty(ds, t1);
const bool b2 = IsTagEmpty(ds, t2);
const bool b3 = IsTagEmpty(ds, t3);
const bool b4 = IsTagEmpty(ds, path1, t4);
const bool b5 = IsTagEmpty(ds, pt5);
if (!b1 || !b2 || !b3 || !b4 || !b5) {
return false;
}
return true;
}
};
struct TestCleaner4Impl4 : public TestCleaner4Impl {
bool check_before(gdcm::DataSet &ds) override {
const gdcm::Tag t1(0x0008, 0x0090); //
const gdcm::Tag t2(0x0008, 0x1070); //
const gdcm::Tag t3(0x0010, 0x0010); //
const gdcm::PrivateTag path1(0xe1, 0x39, "ELSCINT1");
const gdcm::Tag t4(0x0008, 0x0090); //
const gdcm::Tag t5(0x0032, 0x1032); //
{
const bool b1 = IsTagIn(ds, t1);
const bool b2 = IsTagIn(ds, t2);
const bool b3 = IsTagIn(ds, t3);
const bool b4 = IsTagIn(ds, path1, t4);
const bool b5 = IsTagIn(ds, path1, t5);
if (!b1 || !b2 || !b3 || !b4 || !b5) {
return false;
}
}
{
const bool b1 = IsTagEmpty(ds, t1);
const bool b2 = IsTagEmpty(ds, t2);
const bool b3 = IsTagEmpty(ds, t3);
const bool b4 = IsTagEmpty(ds, path1, t4);
const bool b5 = IsTagEmpty(ds, path1, t5);
if (!b1 || b2 || b3 || !b4 || !b5) {
return false;
}
}
return true;
}
bool check_after(gdcm::DataSet &ds, bool preservePatientName) override {
const gdcm::Tag t1(0x0008, 0x0090); //
const gdcm::Tag t2(0x0008, 0x1070); //
const gdcm::Tag t3(0x0010, 0x0010); //
const gdcm::PrivateTag path1(0xe1, 0x39, "ELSCINT1");
const gdcm::Tag t4(0x0008, 0x0090); //
const gdcm::Tag t5(0x0032, 0x1032); //
const bool b1 = IsTagEmpty(ds, t1);
const bool b2 = IsTagEmpty(ds, t2);
const bool b3 =
preservePatientName ? !IsTagEmpty(ds, t3) : IsTagEmpty(ds, t3);
const bool b4 = IsTagEmpty(ds, path1, t4);
const bool b5 = IsTagEmpty(ds, path1, t5);
if (!b1 || !b2 || !b3 || !b4 || !b5) {
assert(0);
return false;
}
return true;
}
};
int TestCleaner4(int, char *[]) {
using namespace gdcm;
const char *directory = gdcm::Testing::GetDataRoot();
std::string sfilename1 =
std::string(directory) + "/GE_DLX-8-MONO2-Multiframe.dcm"; // implicit
const char *filename1 = sfilename1.c_str();
std::string sfilename2 =
std::string(directory) + "/JPEGInvalidSecondFrag.dcm"; // OB => PN
const char *filename2 = sfilename2.c_str();
std::string sfilename3 =
std::string(directory) + "/undefined_length_un_vr.dcm"; // => nested
const char *filename3 = sfilename3.c_str();
std::string sfilename4 =
std::string(directory) + "/MAROTECH_CT_JP2Lossy.dcm"; // => nested
const char *filename4 = sfilename4.c_str();
// Create directory first:
const char subdir[] = "TestCleaner4";
std::string tmpdir = Testing::GetTempDirectory(subdir);
if (!System::FileIsDirectory(tmpdir.c_str())) {
System::MakeDirectory(tmpdir.c_str());
}
std::string outfilename1 = Testing::GetTempFilename(filename1, subdir);
std::string outfilename2 = Testing::GetTempFilename(filename2, subdir);
std::string outfilename3 = Testing::GetTempFilename(filename3, subdir);
std::string outfilename4 = Testing::GetTempFilename(filename4, subdir);
TestCleaner4Impl1 testCleaner1;
TestCleaner4Impl2 testCleaner2;
TestCleaner4Impl3 testCleaner3;
TestCleaner4Impl4 testCleaner4;
int res1 = testCleaner1.run(filename1, outfilename1, false);
int res2 = testCleaner2.run(filename2, outfilename2, false);
int res3 = testCleaner3.run(filename3, outfilename3, false);
int res4 = testCleaner4.run(filename4, outfilename4, false, false);
int res5 = testCleaner4.run(filename4, outfilename4, false, true);
return res1 + res2 + res3 + res4 + res5;
}
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