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feat(pstate): Integrate apply-presentation-state-to-image with itk::w…
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…asm::Pipeline

Modify the apply-presentation-state-to-image (dcmp2pgm) operation to make it
work with itk::wasm::Pipeline.
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@jadh4v
jadh4v committed Oct 27, 2022
1 parent 7b0712f commit 1c49353
Showing 1 changed file with 99 additions and 98 deletions.
197 changes: 99 additions & 98 deletions src/io/internal/pipelines/dicom/apply-presentation-state-to-image.cxx
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Original file line number Diff line number Diff line change
Expand Up @@ -42,6 +42,8 @@

#include "itkPipeline.h"
#include "itkOutputTextStream.h"
#include "itkOutputImage.h"
#include "itkImportImageFilter.h"

#include "dcmtk/config/osconfig.h" /* make sure OS specific configuration is included first */

Expand All @@ -56,6 +58,8 @@
#include "dcmtk/ofstd/ofconapp.h"
#include "dcmtk/dcmdata/dcuid.h" /* for dcmtk version name */

#include <cstring>

#ifdef WITH_ZLIB
#include "itk_zlib.h" /* for zlibVersion() */
#endif
Expand All @@ -68,7 +72,7 @@ static char rcsid[] = "$dcmtk: " OFFIS_CONSOLE_APPLICATION " v"
OFFIS_DCMTK_VERSION " " OFFIS_DCMTK_RELEASEDATE " $";


static void dumpPresentationState(DVPresentationState &ps)
static void dumpPresentationState(STD_NAMESPACE ostream &out, DVPresentationState &ps)
{
size_t i, j, max;
const char *c;
Expand Down Expand Up @@ -426,6 +430,7 @@ static void dumpPresentationState(DVPresentationState &ps)
}

oss << OFStringStream_ends;
out << oss.str();
OFSTRINGSTREAM_GETSTR(oss, res)
OFLOG_INFO(dcmp2pgmLogger, res);
OFSTRINGSTREAM_FREESTR(res)
Expand All @@ -434,79 +439,66 @@ static void dumpPresentationState(DVPresentationState &ps)

int main(int argc, char *argv[])
{
OFBool opt_dump_pstate = OFFalse; /* default: do not dump presentation state */
itk::wasm::Pipeline pipeline("apply-presentation-state-to-image", "Apply a presentation state to a given DICOM image and render output as pgm bitmap or dicom file.", argc, argv);
// Inputs
std::string imageIn;
pipeline.add_option("image-in", imageIn, "Input DICOM file")->required()->check(CLI::ExistingFile)->type_name("INPUT_BINARY_FILE");

// Outputs
// Metadata output regarding overlays
itk::wasm::OutputTextStream pstateOutStream;
pipeline.add_option("presentation-state-out-stream", pstateOutStream, "Output overlay information")->type_name("OUTPUT_TEXT_STREAM");
// Processed output image
constexpr unsigned int Dimension = 2;
using PixelType = unsigned char;
using ImageType = itk::Image<PixelType, Dimension>;
using OutputImageType = itk::wasm::OutputImage<ImageType>;
OutputImageType outputImage;
pipeline.add_option("output-image", outputImage, "Output image")->type_name("OUTPUT_IMAGE");

// Parameters
// addGroup "processing options:"
std::string pstateFile;
pipeline.add_option("--presentation-state-file", pstateFile, "[f]ilename: string, process using presentation state file")->required()->check(CLI::ExistingFile)->type_name("INPUT_BINARY_FILE");
std::string configFile;
pipeline.add_option("--config-file", configFile, "[f]ilename: string, process using settings from configuration file");
// process a specific frame within the input dicom:
int frame = 1;
pipeline.add_option("--frame", frame, "[f]rame: integer, process using image frame f (default: 1)");

// addGroup "output format:"
bool pstateOutput{true};
pipeline.add_flag("--presentation-state-output", pstateOutput, "get presentation state information in text stream (default: ON).");
bool bitmapOutput{true};
pipeline.add_flag("--bitmap-output", bitmapOutput, "get resulting image as bitmap output stream (default: ON).");

bool outputFormatPGM{true};
pipeline.add_flag("--pgm", outputFormatPGM, "save image as PGM (default)");
bool outputFormatDICOM{false};
pipeline.add_flag("--dicom", outputFormatDICOM, "save image as DICOM secondary capture");

/* evaluate command line */
ITK_WASM_PARSE(pipeline);

// OFBool opt_dump_pstate = OFFalse; /* default: do not dump presentation state */
OFBool opt_dicom_mode = OFFalse; /* default: create PGM, not DICOM SC */
OFCmdUnsignedInt opt_frame = 1; /* default: first frame */
OFCmdUnsignedInt opt_frame = frame; /* default: first frame */
const char *opt_pstName = NULL; /* pstate read file name */
const char *opt_imgName = NULL; /* image read file name */
const char *opt_imgName = imageIn.c_str(); /* image read file name */
const char *opt_pgmName = NULL; /* pgm save file name */
const char *opt_savName = NULL; /* pstate save file name */
const char *opt_cfgName = NULL; /* config read file name */

OFConsoleApplication app(OFFIS_CONSOLE_APPLICATION, "Read DICOM image and presentation state and render bitmap", rcsid);
OFCommandLine cmd;
cmd.setOptionColumns(LONGCOL, SHORTCOL);
cmd.setParamColumn(LONGCOL + SHORTCOL + 2);

cmd.addParam("dcmfile-in", "input DICOM image");
cmd.addParam("bitmap-out", "output DICOM image or PGM bitmap", OFCmdParam::PM_Optional);

cmd.addGroup("general options:");
cmd.addOption("--help", "-h", "print this help text and exit", OFCommandLine::AF_Exclusive);
cmd.addOption("--version", "print version information and exit", OFCommandLine::AF_Exclusive);
OFLog::addOptions(cmd);

cmd.addGroup("processing options:");
cmd.addOption("--pstate", "-p", 1, "[f]ilename: string",
"process using presentation state file");
cmd.addOption("--config", "-c", 1, "[f]ilename: string",
"process using settings from configuration file");
cmd.addOption("--frame", "-f", 1, "[f]rame: integer",
"process using image frame f (default: 1)");

cmd.addGroup("output format:");
cmd.addOption("--pgm", "-D", "save image as PGM (default)");
cmd.addOption("--dicom", "+D", "save image as DICOM secondary capture");

cmd.addGroup("output options:");
cmd.addOption("--save-pstate", "+S", 1, "[f]ilename: string",
"save presentation state to file");
/* evaluate command line */
prepareCmdLineArgs(argc, argv, OFFIS_CONSOLE_APPLICATION);
if (app.parseCommandLine(cmd, argc, argv))
/* command line parameters and options */
if (!pstateOutput && !bitmapOutput)
{
/* check exclusive options first */
if (cmd.hasExclusiveOption())
{
if (cmd.findOption("--version"))
{
app.printHeader(OFTrue /*print host identifier*/);
COUT << OFendl << "External libraries used:";
#ifdef WITH_ZLIB
COUT << OFendl << "- ZLIB, Version " << zlibVersion() << OFendl;
#else
COUT << " none" << OFendl;
#endif
return 0;
}
}

/* command line parameters and options */
cmd.getParam(1, opt_imgName);
if (cmd.getParamCount() > 1)
cmd.getParam(2, opt_pgmName);

OFLog::configureFromCommandLine(cmd, app);
OFLOG_FATAL(dcmp2pgmLogger, "No output form requested. Specify either --presentation-state-output, --bitmap-output or both.");
}

opt_dump_pstate = dcmp2pgmLogger.isEnabledFor(OFLogger::INFO_LOG_LEVEL);
if(!pstateFile.empty()) opt_pstName = pstateFile.c_str();
if(!configFile.empty()) opt_cfgName = configFile.c_str();

if (cmd.findOption("--pstate")) app.checkValue(cmd.getValue(opt_pstName));
if (cmd.findOption("--config")) app.checkValue(cmd.getValue(opt_cfgName));
if (cmd.findOption("--frame")) app.checkValue(cmd.getValueAndCheckMin(opt_frame, 1));
if (cmd.findOption("--pgm")) opt_dicom_mode = OFFalse;
if (cmd.findOption("--dicom")) opt_dicom_mode = OFTrue;
if (cmd.findOption("--save-pstate")) app.checkValue(cmd.getValue(opt_savName));
}
if (outputFormatPGM) opt_dicom_mode = OFFalse;
if (outputFormatDICOM) opt_dicom_mode = OFTrue;

/* print resource identifier */
OFLOG_DEBUG(dcmp2pgmLogger, rcsid << OFendl);
Expand All @@ -528,61 +520,70 @@ int main(int argc, char *argv[])
OFLOG_DEBUG(dcmp2pgmLogger, "reading DICOM image file: " << opt_imgName);
status = dvi.loadImage(opt_imgName);
} else {
OFLOG_DEBUG(dcmp2pgmLogger, "reading DICOM pstate file: " << opt_pstName);
OFLOG_DEBUG(dcmp2pgmLogger, "reading DICOM presentation-state file: " << opt_pstName);
OFLOG_DEBUG(dcmp2pgmLogger, "reading DICOM image file: " << opt_imgName);
status = dvi.loadPState(opt_pstName, opt_imgName);
}

if (status == EC_Normal)
{
if (opt_dump_pstate) dumpPresentationState(dvi.getCurrentPState());
if (opt_pgmName != NULL)
if (pstateOutput) dumpPresentationState(pstateOutStream.Get(), dvi.getCurrentPState());
if (bitmapOutput)
{
const void *pixelData = NULL;
unsigned long width = 0;
unsigned long height = 0;
OFLOG_DEBUG(dcmp2pgmLogger, "creating pixel data");
if ((opt_frame > 0) && (dvi.getCurrentPState().selectImageFrameNumber(opt_frame) != EC_Normal))
OFLOG_ERROR(dcmp2pgmLogger, "cannot select frame " << opt_frame);

std::array<double, 2> pixelSpacing{0.0, 0.0};
if (EC_Normal != dvi.getCurrentPState().getDisplayedAreaPresentationPixelSpacing(pixelSpacing[0], pixelSpacing[1]))
OFLOG_ERROR(dcmp2pgmLogger, "cannot read pixel spacing from presentation state.");

if ((dvi.getCurrentPState().getPixelData(pixelData, width, height) == EC_Normal) && (pixelData != NULL))
{
if (opt_dicom_mode)
{
double pixelAspectRatio = dvi.getCurrentPState().getPrintBitmapPixelAspectRatio(); // works for rotated images
OFLOG_DEBUG(dcmp2pgmLogger, "writing DICOM SC file: " << opt_pgmName);
if (EC_Normal != dvi.saveDICOMImage(opt_pgmName, pixelData, width, height, pixelAspectRatio))
{
OFLOG_ERROR(dcmp2pgmLogger, "error during creation of DICOM file");
}
} else {
FILE *outfile = fopen(opt_pgmName, "wb");
if (outfile)
{
OFLOG_DEBUG(dcmp2pgmLogger, "writing PGM file: " << opt_pgmName);
fprintf(outfile, "P5\n%ld %ld 255\n", width, height);
if (fwrite(pixelData, OFstatic_cast(size_t, width), OFstatic_cast(size_t, height), outfile) != OFstatic_cast(size_t, height))
OFLOG_FATAL(dcmp2pgmLogger, "Can't write output data to file.");
fclose(outfile);
} else {
OFLOG_FATAL(dcmp2pgmLogger, "Can't create output file.");
return 10;
}
OFLOG_ERROR(dcmp2pgmLogger, "DICOM output format is currently not supported.");
}
else
{
using ImportFilterType = itk::ImportImageFilter<PixelType, Dimension>;
auto importFilter = ImportFilterType::New();
ImportFilterType::SizeType size;
size[0] = width;
size[1] = height;

ImportFilterType::IndexType start;
start.Fill(0);

ImportFilterType::RegionType region;
region.SetIndex(start);
region.SetSize(size);
importFilter->SetRegion(region);

const itk::SpacePrecisionType origin[Dimension] = { 0.0, 0.0 };
importFilter->SetOrigin(origin);
const itk::SpacePrecisionType spacing[Dimension] = { pixelSpacing[0], pixelSpacing[1] };
importFilter->SetSpacing(spacing);
const unsigned int numberOfPixels = size[0] * size[1];
importFilter->SetImportPointer((PixelType*)pixelData, numberOfPixels, false);
importFilter->Update();

// set as output image
outputImage.Set(importFilter->GetOutput());
}
} else {
OFLOG_FATAL(dcmp2pgmLogger, "Can't create output data.");
return 10;
}
}
if (opt_savName != NULL)
{
OFLOG_DEBUG(dcmp2pgmLogger, "writing pstate file: " << opt_savName);
if (dvi.savePState(opt_savName, OFFalse) != EC_Normal)
else
{
OFLOG_FATAL(dcmp2pgmLogger, "Can't write pstate file.");
OFLOG_FATAL(dcmp2pgmLogger, "Can't create output data.");
return 10;
}
}
} else {
}
else
{
OFLOG_FATAL(dcmp2pgmLogger, "Can't open input file(s).");
return 10;
}
Expand Down

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