NAME
medcon - MedCon C project for conversion of medical imagesLIBRARY
Local MedCon C library ( libmdc.a )
SYNOPSIS
#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! */
/* 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 Static_Data_t { char label[MDC_MAXSTR]; /* label name of image */ float total_counts; /* total counts in image */ float image_duration; /* duration of image (ms) */ Int16 start_time_hour; /* start time hour */ Int16 start_time_minute; /* start time minute */ Int16 start_time_second; /* start time second */ } STATIC_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 slice (ms) */ /* P */ Uint8 *buf; /* pointer to raw image */ long load_location; /* load 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 */ double rescaled_slope; /* new rescaled slope */ double rescaled_intercept; /* new rescaled intercept */ /* ** ecat64 items ** */ Int16 quant_units; /* quantification units */ Int16 calibr_units; /* calibration units */ float quant_scale; /* quantification scale */ float calibr_fctr; /* calibration factor */ float intercept; /* scale intercept */ float pixel_xsize; /* pixel size X (mm) */ float pixel_ysize; /* pixel size Y (mm) */ float slice_width; /* slice width (mm) */ float recon_scale; /* recon magnification */ /* ** Acr/Nema items ** */ 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 */ /* ** Miscellaneous ** STATIC_DATA *sdata; /* extra static entries */ 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 */ Int8 diff_scale; /* images with diff rescale? */ 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 contrast_remapped; /* contrast remap applied? */ float window_centre; /* contrast window centre */ float window_width; /* contrast window width */ Int8 slice_projection; /* projection of images */ 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 dose_time_hour; /* hour of dose start */ Int16 dose_time_minute; /* minute of dose start */ Int16 dose_time_second; /* second of dose start */ 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;
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 *MdcReadNIFTI ( 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 ); char *MdcWriteNIFTI ( FILEINFO *fi );
DESCRIPTION
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.
- MdcReadNIFTI() - MdcWriteNIFTI()
- Reads and writes NIH's NIfTI files.
EXAMPLE
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
-----------------------------------------------------------------------
FILES
| /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. |
SEE ALSO
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)
AUTHOR
(X)MedCon project was originally written by Erik Nolf (eNlf) for the former PET-Centre at Ghent University (Belgium).
| e-mail: | enlf-at-users.sourceforge.net | www: | http://xmedcon.sourceforge.net |