medcon - MedCon C project for conversion of medical images

Local MedCon C library ( libmdc.a )

#include "medcon.h"

-----------------------------------------------------------------------
Important Global Variables
-----------------------------------------------------------------------

char prefix[MDC_MAX_PREFIX+1];          /* prefix for new filenames */

/* command-line input data */ char *mdc_arg_files[]; /* pointers to input files */ int mdc_arg_convs[]; /* conversions selected */ int mdc_arg_total[]; /* total files & conversions*/

/* options set at command-line */ Int8 MDC_INFO; /* print image info */ Int8 MDC_INTERACTIVE; /* interactive read */ Int8 MDC_CONVERT; /* do conversion */ Int8 MDC_EXTRACT; /* extract images */ Int8 MDC_PIXELS; /* print pixel values */ Int8 MDC_SKIP_PREVIEW; /* skip first preview image*/ Int8 MDC_DICOM_MOSAIC; /* support mosaic files */ Int8 MDC_TRUE_GAP; /* spacing true gap/overlap */ Int8 MDC_DEBUG; /* show debug info */ Int8 MDC_ANLZ_REV; /* analyze reverse images */ Int8 MDC_ANLZ_SPM; /* analyze for SPM */ Int8 MDC_GIF_OPTIONS; /* define gif options */ Int8 MDC_COLOR_MAP; /* gray colormap selected */ Int8 MDC_MAKE_GRAY; /* remap color to gray */ Int8 MDC_DITHER_COLOR; /* dither color reduction */ Int8 MDC_FORCE_INT; /* force writing BIT?_? pixs*/ Int8 MDC_NEGATIVE; /* preserve negative pixels */ Int8 MDC_QUANTIFY; /* preserve quantification */ Int8 MDC_CALIBRATE; /* preserve calibration */ Int8 MDC_VERBOSE; /* verbose mode */ Int8 MDC_NORM_OVER_FRAMES /* normalize over frames */ /* 'QUANTIFY' & 'CALIBRATE' may NOT be ON at the same time! */

----------------------------------------------------------------------- Important Defines -----------------------------------------------------------------------

/* representation of supported formats */
#define MDC_FRMT_NONE    0              /* unsupported format       */
#define MDC_FRMT_RAW     1              /* Read  Interactive        */
                                        /* Write RAW Binary         */
#define MDC_FRMT_ASCII   2              /* Write RAW Ascii          */
#define MDC_FRMT_GIF     3              /* GIF89a or GIF87a         */
#define MDC_FRMT_ACR     4              /* Acr/Nema 2.0 (Papyrus)   */
#define MDC_FRMT_INW     5              /* INW (RUG)                */
#define MDC_FRMT_ECAT6   6              /* Siemens/CTI ECAT 6.4     */
#define MDC_FRMT_ECAT7   7              /* Siemens/CTI ECAT 7.2     */
#define MDC_FRMT_INTF    8              /* Interfile v3.3           */
#define MDC_FRMT_ANLZ    9              /* Analyze                  */
#define MDC_FRMT_DICM   10              /* DICOM 3.0                */
#define MDC_FRMT_PNG    11              /* PNG                      */
#define MDC_FRMT_CONC   12              /* Concorde uPet            */

#define MDC_MAX_FMTS 13 /* total + 1 */

/* supported color maps */ #define MDC_MAP_PRESENT 0 /* 256 RGB colormap */ #define MDC_MAP_GRAY 1 /* grayscale colormap */ #define MDC_MAP_INVERTED 2 /* inverted colormap */ #define MDC_MAP_RAINBOW 3 /* rainbow colormap */ #define MDC_MAP_COMBINED 4 /* combined colormap */ #define MDC_MAP_HOTMETAL 5 /* hotmetal colormap */ #define MDC_MAP_LOADED 6 /* extern LUT loaded */

----------------------------------------------------------------------- Important Definitions -----------------------------------------------------------------------

typedef struct Gated_Data_t { Int8 gspect_nesting; /* gated spect nesting */ float nr_projections; /* number of projections */ float extent_rotation; /* extent of rotation */ float study_duration; /* study duration (ms) */ float image_duration; /* image duration (ms) */ float time_per_proj; /* time per proj (ms) */ float window_low; /* lower limit (ms) */ float window_high; /* higher limit (ms) */ float cycles_observed; /* cardiac cycles observed */ float cycles_acquired; /* cardiac cycles acquired */

} GATED_DATA;

typedef struct Acquisition_Data_t {

Int16 rotation_direction; /* direction of rotation */ Int16 detector_motion; /* type detector motion */ float angle_start; /* start angle (interfile) */ float angle_step; /* angular step */ float scan_arc; /* angular range */

} ACQ_DATA;

typedef struct Dynamic_Data_t {

Uint32 nr_of_slices; /* images in time frame */ float time_frame_start; /* start time frame (ms) */ float time_frame_delay; /* delay this frame (ms) */ float time_frame_duration; /* duration frame (ms) */ float delay_slices; /* delay each slice (ms) */

} DYNAMIC_DATA;

typedef struct Bed_Data_t { float hoffset; /* horizontal position (mm) */ float voffset; /* vertical position (mm) */ } BED_DATA;

typedef struct Image_Data_t {

/* ** general data ** */ Uint32 width,height; /* image dimension */ Int16 bits,type; /* bits/pixel & datatype */ Uint16 flags; /* extra flag */ double min, max; /* min/max pixelvalue */ double qmin, qmax; /* quantified min/max */ double fmin, fmax; /* min/max in whole frame */ double qfmin, qfmax; /* in whole frame (quant) */

float rescale_slope; /* rescale slope */ /* P */ float rescale_intercept; /* rescale intercept */ /* P */

Uint32 frame_number; /* part of frame (1-based) */ /* P */ float slice_start; /* start of slicd (ms) */ /* P */ Uint8 *buf; /* pointer to raw image */ long location; /* data start in file */

/* ** internal items ** */ Int8 rescaled; /* rescaled YES or NO */ double rescaled_min; /* new rescaled max */ double rescaled_max; /* new rescaled min */ double rescaled_fctr; /* new rescale fctr */

/* ** ecat64 items ** */ Int16 quant_units; /* quantification units */ Int16 calibr_units; /* calibration units */ float quant_scale; /* quantification scale */ float calibr_fctr; /* calibration factor */ float pixel_xsize; /* pixel size X (mm) */ float pixel_ysize; /* pixel size Y (mm) */ Uint32 frame_number; /* part of frame # (1-based) */ float slice_width; /* slice width (mm) */ float slice_start; /* start of slice (ms) */ float recon_scale; /* recon magnification */

/* ** Acr/Nema items ** */ char image_mod[3]; /* images modality */ float image_pos_dev[3]; /* image pos. device (mm) */ float image_orient_dev[6]; /* image orient device (mm) */ float image_pos_pat[3]; /* image pos. patient (mm) */ float image_orient_dev[6]; /* image orient patient (mm) */ float slice_spacing; /* space btw centres (mm) */ float ct_zoom_fctr; /* CT image zoom factor */

unsigned char *plugb; /* like to attach here? */

} IMG_DATA;

typedef struct File_Info_t {

FILE *ifp; /* pointer to input file */ FILE *ifp_raw; /* pointer to raw input file*/ FILE *ofp; /* pointer to output file */ FILE *ofp_raw; /* pointer to raw output file*/ char ipath[MAX_PATH]; /* path to input file */ char opath[MAX_PATH]; /* path to output file */ char *idir; /* dir to input file */ char *odir; /* dir to output file */ char *ifname; /* name of input file */ char *ofname; /* name of output file */ int iformat; /* format of input file */ int oformat; /* format of output file */ Int8 rawconv; /* FRMT_RAW | FRMT_ASCII */ Int8 endian; /* endian type of file */ Int8 compression; /* file compression */ Int8 truncated; /* truncated ? */ Int8 diff_type; /* images with diff type */ Int8 diff_size; /* images with diff size */ Uint32 number; /* total number of images */ /* P */ Uint32 mwidth, mheight; /* global max dimensions */ Uint16 bits, type; /* global bits & datatype */ Int16 dim[8]; /* [0] = # of dimensions */ /* [1] = X-dim (pixels) */ /* [2] = Y-dim (pixels) */ /* [3] = Z-dim (planes) */ /* [4] = (frames) */ /* [5] = (gates) */ /* [6] = (beds) */ /* ... */ /* values must be 1-based */

float pixdim[8]; /* [0] = # of dimensions */ /* [1] = X-dim (mm) */ /* [2] = Y-dim (mm) */ /* [3] = Z-dim (mm) */ /* [4] = time (ms) */ /* ... */

double glmin, glmax; /* global min/max value */ double qglmin, qglmax; /* quantified min/max */

Int8 pat_slice_orient /* combined flag */ char pat_pos[MDC_MAXSTR]; /* patient position */ char pat_orient[MDC_MAXSTR]; /* patient orientation */ char patient_sex[MDC_MAXSTR]; /* sex of patient */ char patient_name[MDC_MAXSTR]; /* name of patient */ char patient_id[MDC_MAXSTR]; /* id of patient */ char patient_dob[MDC_MAXSTR]; /* birth of patient YYYYMMDD */ float patient_weight; /* weight of patient (kg) */ char study_descr[MDC_MAXSTR]; /* study description */ char study_id[MDC_MAXSTR]; /* study id */ Int16 study_date_day; /* day of study */ Int16 study_date_month; /* month of study */ Int16 study_date_year; /* year of study */ Int16 study_time_hour; /* hour of study */ Int16 study_time_minute; /* minute of study */ Int16 study_time_second; /* second of study */ Int16 nr_series; /* number of series */ Int16 nr_acquisition; /* number of acquisition */ Int16 nr_instance; /* number of instance (image)*/ Int16 acquisition_type; /* acquisition type */ Int16 planar; /* planar of tomo ? */ Int16 decay_corrected; /* decay corrected ? */ Int16 flood_corrected; /* flood corrected ? */

Int16 reconstructed; /* reconstructed ? */ char recon_method[MDC_MAXSTR]; /* reconstruction method */

char institution[MDC_MAXSTR]; /* name of institution */ char manufacturer[MDC_MAXSTR]; /* name of manufacturer */ char series_descr[MDC_MAXSTR]; /* series description */ char radiopharma[MDC_MAXSTR]; /* radiopharmaceutical */ char filter_type[MDC_MAXSTR]; /* filter type */ char organ_code[MDC_MAXSTR]; /* organ */ char isotope_code[MDC_MAXSTR]; /* isotope */ float isotope_halflife; /* isotope halflife (sec) */ float injected_dose; /* amount injected (MBq) */ float gantry_tilt; /* gantry tilt */

Uint8 map; /* indexed 256 colormap */ Uint8 palette[768]; /* global palette */ char *comment; /* whatever comment */ Uint32 comm_length; /* length of comment */

Uint32 gatednr; /* number of gated entries */ GATED_DATA *gdata; /* array of GATED_DATA */

Uint32 acqnr; /* number acq. data entries */ ACQ_DATA *acqdata; /* array of ACQ_DATA entries */

Uint32 dynnr; /* number of time frames */ DYNAMIC_DATA *dyndata; /* array of DYNAMIC_DATA */

Uint32 bednr; /* number bed data entries */ BED_DATA *beddata; /* array of BED_DATA entries */

IMG_DATA *image; /* array of IMG_DATA images */

MOD_INFO *mod; /* modalities specific info */

unsigned char *pluga; /* want to attach stuff? */

} FILEINFO;

------------------------------------------------------------------------ Important Functions ------------------------------------------------------------------------

void MdcInit              (void);
void MdcFinish            (void);

int MdcHandleArgs ( FILEINFO *fi,int argc,char *argv[],int MAXFILES ); void MdcPrintUsage ( char *pgrname );

int MdcOpenFile ( FILEINFO *fi, char *path ); int MdcReadFile ( FILEINFO *fi, int filenr, char *(*ReadFile)(FILEINFO *fi) ); int MdcWriteFile ( FILEINFO *fi, int format, int prefixnr, char *(*WriteFile)(FILEINFO *fi) );

void MdcInitFI ( FILEINFO *fi, char *path ); void MdcFreeIDs ( FILEINFO *fi ); void MdcCleanUpFI ( FILEINFO *fi ); void MdcResetIDs ( FILEINFO *fi ); void MdcPrintFI ( FILEINFO *fi ); void MdcCloseFile ( FILEINFO *fi ); void MdcSplitPath ( char path[], char **dir, char **fname ); int MdcGetFrmt ( FILEINFO *fi );

void MdcGetColorMap ( int map, Uint8 palette[] ); char *MdcImagesPixelFiddle( FILEINFO *fi);

void MdcPrntMesg ( char *fmt, ... ); void MdcPrntWarn ( char *fmt, ... ); void MdcPrntErr ( int code, char *fmt, ... );

char *MdcReadGIF ( FILEINFO *fi ); char *MdcReadACR ( FILEINFO *fi ); char *MdcReadINW ( FILEINFO *fi ); char *MdcReadECAT6 ( FILEINFO *fi ); char *MdcReadECAT7 ( FILEINFO *fi ); char *MdcReadINTF ( FILEINFO *fi ); char *MdcReadANLZ ( FILEINFO *fi ); char *MdcReadRAW ( FILEINFO *fi ); char *MdcReadDICM ( FILEINFO *fi ); char *MdcReadPNG ( FILEINFO *fi ); char *MdcReadCONC ( FILEINFO *fi );

char *MdcWriteRAW ( FILEINFO *fi ); char *MdcWriteGIF ( FILEINFO *fi ); char *MdcWriteACR ( FILEINFO *fi ); char *MdcWriteINW ( FILEINFO *fi ); char *MdcWriteECAT6 ( FILEINFO *fi ); char *MdcWriteINTF ( FILEINFO *fi ); char *MdcWriteANLZ ( FILEINFO *fi ); char *MdcWriteDICM ( FILEINFO *fi ); char *MdcWritePNG ( FILEINFO *fi ); char *MdcWriteCONC ( FILEINFO *fi );

The MedCon library is intended for easy use of read/write routines for the various medical image formats. Our main test format is Ecat 6.4. The FILEINFO structure holds all the interesting data and pointers to the images. A fast introduction ...

MdcInit(), MdcFinish()

The very first and very last function to call when using this library. Currently changes occur to the signal handler for floating point exceptions and the program's locale.

MdcHandleArgs()

Parser for the command-line arguments. Last function argument determines the maximum of input files allowed. The absolute maximum is MDC_MAX_FILES defined in the library.

MdcPrintUsage()

Prints possible MedCon command-line options and terminates the program.

MdcOpenFile()

Initializes FILEINFO struct and opens the file with or without decompression.

MdcReadFile()

Reads the (decompressed) file with format autodetection or by trying a fallback format, initializes a (grayscale) colormap and does the obligated pixel handling. The last argument enables the use of an external read function.

MdcWriteFile()

Writes a file in the supplied format. Last argument is a number used in the prefix of the output filename. Give a negative value when a personal prefix was prepared. The last argument enables the use of an external write function.

MdcCloseFile()

Closes the file and sets the pointer to NULL.

MdcInitFI()

Initializes the FILEINFO structure.

MdcFreeIDs()

Cleans the IMG_DATA structures by freeing all allocated memory.

MdcCleanUpFI()

Cleans the FILEINFO structure. The routine makes use of FreeIDs().

MdcResetIDs()

Resets the IMG_DATA structures. This is necessary after each conversion.

MdcPrintFI()

Prints the content of the FILEINFO structure. Useful for debug purposes.

MdcSplitPath()

Splits the path in a string pointer to directory and filename.

MdcGetFrmt()

Checks the format of the file. For the return value, see the representation of the supported formats under the section `Important Defines'. With the INTERACTIVE variable ON, the function returns F_RAW; see also ReadRaw().

MdcGetColorMap()

Fills a 256 byte RGB palette with the requested grayscale colormap.

MdcImagesPixelFiddle()

Performs all the pixel by pixel processes such as swapping bytes, make positive values, quantification, rescaling, filling the FILEINFO structure with global & image variables and check some important parameters. This function is required after a file was read!

MdcPrntMesg()

Prints a message. Argument is a variable parameter list.

MdcPrntWarn()

Prints a warning. Argument is a variable parameter list.

MdcPrntErr()

Prints an error and quits the program. The first argument is the error code.

MdcReadRAW() - MdcWriteRAW()

Reads files of an unknown format interactively and writes raw image arrays with out headers. ReadInterActive() is an alias for MdcReadRAW().

MdcReadGIF() - MdcWriteGIF()

Reads GIF87a & GIF89a, writes annimated GIF89a files.

MdcReadACR() - MdcWriteACR()

Reads and writes Acr/Nema files.

MdcReadINW() - MdcWriteINW()

Reads and writes RUG INW files.

MdcReadECAT6(), MdcReadECAT7() - MdcWriteECAT6()

Reads ECAT 6 (resp. 7). Writes ECAT 6.4 files.

MdcReadINTF() - MdcWriteINTF()

Reads and writes Interfile 3.3 files.

MdcReadANLZ() - MdcWriteANLZ()

Reads and writes Analyze (SPM) files.

MdcReadDICM() - MdcWriteDICM()

Reads DICOM files. Writes DICOM files.

MdcReadPNG() - MdcWritePNG()

Reads PNG files. Writes PNG files.

MdcReadCONC() - MdcWriteCONC()

Reads and writes Concorde microPET.

A sample C-source code to show the usage of the functions. Please, look into the project source code for more details.

-----------------------------------------------------------------------

/* filename: testit.c */

#include <stdio.h>

#include "medcon.h"

#undef VERSION /* prevent any conflict */ #define VERSION "TestIt v2.3"

void NewPrefix(int n) { sprintf(prefix,"my%02d-",n); /* max of 5 chars */ }

int main(int argc, char *argv[]) { FILEINFO fi; int *total = mdc_arg_total; /* total arguments of files & conversions */ int *convs = mdc_arg_convs; /* counter for each conversion format */ char **files = mdc_arg_files; /* array of pointers to input filenames */ int f, c; /* some counters */ int t=0; /* counter for the output name prefix */ int convert, err=MDC_OK; /* some variables */

/* check arguments */ if (argc < 2) { printf("%s - %s\n",VERSION,MdcGetLibLongVersion()); MdcPrintUsage(argv[0]); }

/* init library */ MdcInit();

/* handle arguments, last one determines max inputfiles */ if (MdcHandleArgs(&fi,argc,argv,MDC_MAX_FILES) != MDC_OK) MdcPrintUsage(argv[0]);

/* check output/conversion formats */ if (total[MDC_CONVS] == 0) { printf("\n%s: ERROR : No output format specified\n\n",argv[0]); return(MDC_BAD_CODE); }

/* do the stuff for each input file */ for (f=0; f<total[MDC_FILES]; f++) {

if ((err = MdcOpenFile(&fi, files[f])) != MDC_OK) return(err);

if ((err = MdcReadFile(&fi, f+1, NULL)) != MDC_OK) return(err);

/* do the conversions */ if (total[MDC_CONVS] > 0) {

/* go through conversion formats */ for (c=1; c<MDC_MAX_FRMTS; c++) { convert = convs[c]; /* write output format when selected */ while (convert -- > 0) { if ((err = MdcWriteFile(&fi, c, t++, NULL)) != MDC_OK) { MdcCleanUpFI(&fi); return(err); } } } } /* clean up FILEINFO struct */ MdcCleanUpFI(&fi); }

/* finish library */ MdcFinish();

return(err);

} -----------------------------------------------------------------------

Example `Makefile' for compiling `testit.c':

-----------------------------------------------------------------------
# filename: Makefile
CC = gcc
CCOPTS = -Wall -g
CFLAGS = $(CCOPTS)

INCS = `xmedcon-config --cflags` LIBS = `xmedcon-config --libs`

testit: testit.c $(CC) $(CFLAGS) $(INCS) -o testit testit.c $(LIBS)

# don't forget a <tab> before $(CC). You can lose this with copy/paste -----------------------------------------------------------------------

tab(@); l l. /usr/local/xmedcon/include/@Directory with header files.. /usr/local/xmedcon/lib/@Directory with libraries. /usr/local/xmedcon/bin/@Directory with executables. /usr/local/xmedcon/man/@Directory with man-pages. /usr/local/xmedcon/etc/@Directory with rcfiles.

medcon(1), xmedcon(1), xmedcon-config(1)

m-acr(4), m-anlz(4), m-gif(4), m-intf(4), m-ecat(4), m-inw(4)

(X)MedCon project was written by Erik Nolf (eNlf) for the PET-Centre at Ghent University (Belgium).

tab(=); lB l lB l. e-mail:=enlf-at-users.sourceforge.net=www:=http://xmedcon.sourceforge.net