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Include StudyInstanceUID and SeriesInstanceUID in filename
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| Original file line number | Diff line number | Diff line change |
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| #include "nii_foreign.h" | ||
| #include "nifti1.h" | ||
| #include "nifti1_io_core.h" | ||
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| #include <sys/types.h> | ||
| #include <stdio.h> | ||
| #include <stdlib.h> | ||
| #include <stdint.h> | ||
| #include <stdbool.h> | ||
| #include "print.h" | ||
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| #ifndef Float32 | ||
| #define Float32 float | ||
| #endif | ||
| #ifndef uint32 | ||
| #define uint32 uint32_t | ||
| #endif | ||
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| /*nii_readEcat7 2017 by Chris Rorden, BSD license | ||
| http://www.turkupetcentre.net/software/libdoc/libtpcimgio/ecat7_8h_source.html#l00060 | ||
| http://www.turkupetcentre.net/software/libdoc/libtpcimgio/ecat7r_8c_source.html#l00717 | ||
| http://xmedcon.sourcearchive.com/documentation/0.10.7-1build1/ecat7_8h_source.html | ||
| https://github.com/BIC-MNI/minc-tools/tree/master/conversion/ecattominc | ||
| https://github.com/nipy/nibabel/blob/ec4567fb09b4472c5a4bb9a13dbcc9eb0a63d875/nibabel/ecat.py | ||
| */ | ||
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| //TO DO: | ||
| // currently only reads first 3D volume: for multiple volumes we need to handle num_frames num_bed_pos | ||
| // SForm and QForm copy SPM and do not account for slice angulation or orientation | ||
| int nii_readEcat7(const char * fname, struct nifti_1_header *nhdr, bool * swapEndian) { | ||
| //data type | ||
| #define ECAT7_BYTE 1 | ||
| #define ECAT7_VAXI2 2 | ||
| #define ECAT7_VAXI4 3 | ||
| #define ECAT7_VAXR4 4 | ||
| #define ECAT7_IEEER4 5 | ||
| #define ECAT7_SUNI2 6 | ||
| #define ECAT7_SUNI4 7 | ||
| //file types | ||
| //#define ECAT7_UNKNOWN 0 | ||
| #define ECAT7_2DSCAN 1 | ||
| #define ECAT7_IMAGE16 2 | ||
| #define ECAT7_ATTEN 3 | ||
| #define ECAT7_2DNORM 4 | ||
| #define ECAT7_POLARMAP 5 | ||
| #define ECAT7_VOLUME8 6 | ||
| #define ECAT7_VOLUME16 7 | ||
| #define ECAT7_PROJ 8 | ||
| #define ECAT7_PROJ16 9 | ||
| #define ECAT7_IMAGE8 10 | ||
| #define ECAT7_3DSCAN 11 | ||
| #define ECAT7_3DSCAN8 12 | ||
| #define ECAT7_3DNORM 13 | ||
| #define ECAT7_3DSCANFIT 14 | ||
| typedef struct __attribute__((packed)) { | ||
| char magic[14],original_filename[32]; | ||
| uint16_t sw_version, system_type, file_type; | ||
| char serial_number[10]; | ||
| uint32 scan_start_time; | ||
| char isotope_name[8]; | ||
| Float32 isotope_halflife; | ||
| char radiopharmaceutical[32]; | ||
| Float32 gantry_tilt, gantry_rotation, bed_elevation, intrinsic_tilt; | ||
| int16_t wobble_speed, transm_source_type; | ||
| Float32 distance_scanned, transaxial_fov; | ||
| uint16_t angular_compression, coin_samp_mode, axial_samp_mode; | ||
| Float32 ecat_calibration_factor; | ||
| uint16_t calibration_unitS, calibration_units_type, compression_code; | ||
| char study_type[12], patient_id[16], patient_name[32], patient_sex, patient_dexterity; | ||
| Float32 patient_age, patient_height, patient_weight; | ||
| uint32 patient_birth_date; | ||
| char physician_name[32], operator_name[32], study_description[32]; | ||
| uint16_t acquisition_type, patient_orientation; | ||
| char facility_name[20]; | ||
| uint16_t num_planes, num_frames, num_gates, num_bed_pos; | ||
| Float32 init_bed_position; | ||
| Float32 bed_position[15]; | ||
| Float32 plane_separation; | ||
| uint16_t lwr_sctr_thres, lwr_true_thres, upr_true_thres; | ||
| char user_process_code[10]; | ||
| uint16_t acquisition_mode; | ||
| Float32 bin_size, branching_fraction; | ||
| uint32 dose_start_time; | ||
| Float32 dosage, well_counter_corr_factor; | ||
| char data_units[32]; | ||
| uint16_t septa_state; | ||
| char fill[12]; | ||
| } ecat_main_hdr; | ||
| typedef struct __attribute__((packed)) { | ||
| int16_t data_type, num_dimensions, x_dimension, y_dimension, z_dimension; | ||
| Float32 x_offset, y_offset, z_offset, recon_zoom, scale_factor; | ||
| int16_t image_min, image_max; | ||
| Float32 x_pixel_size, y_pixel_size, z_pixel_size; | ||
| int32_t frame_duration, frame_start_time; | ||
| int16_t filter_code; | ||
| Float32 x_resolution, y_resolution, z_resolution, num_r_elements, num_angles, z_rotation_angle, decay_corr_fctr; | ||
| int32_t processing_code, gate_duration, r_wave_offset, num_accepted_beats; | ||
| Float32 filter_cutoff_frequenc, filter_resolution, filter_ramp_slope; | ||
| int16_t filter_order; | ||
| Float32 filter_scatter_fraction, filter_scatter_slope; | ||
| char annotation[40]; | ||
| Float32 mtx[9], rfilter_cutoff, rfilter_resolution; | ||
| int16_t rfilter_code, rfilter_order; | ||
| Float32 zfilter_cutoff, zfilter_resolution; | ||
| int16_t zfilter_code, zfilter_order; | ||
| Float32 mtx_1_4, mtx_2_4, mtx_3_4; | ||
| int16_t scatter_type, recon_type, recon_views, fill_cti[87], fill_user[49]; | ||
| } ecat_img_hdr; | ||
| typedef struct __attribute__((packed)) { | ||
| int32_t hdr[4], | ||
| r01[4],r02[4],r03[4],r04[4],r05[4],r06[4],r07[4],r08[4],r09[4],r10[4], | ||
| r11[4],r12[4],r13[4],r14[4],r15[4],r16[4],r17[4],r18[4],r19[4],r20[4], | ||
| r21[4],r22[4],r23[4],r24[4],r25[4],r26[4],r27[4],r28[4],r29[4],r30[4], | ||
| r31[4]; | ||
| } ecat_list_hdr; | ||
| * swapEndian = false; | ||
| size_t n; | ||
| FILE *f; | ||
| ecat_main_hdr mhdr; | ||
| f = fopen(fname, "rb"); | ||
| if (f) | ||
| n = fread(&mhdr, sizeof(mhdr), 1, f); | ||
| if(!f || n!=1) { | ||
| printf("Problem reading ECAT7 file!\n"); | ||
| fclose(f); | ||
| return EXIT_FAILURE; | ||
| } | ||
| if ((mhdr.magic[0] != 'M') || (mhdr.magic[1] != 'A') || (mhdr.magic[2] != 'T') | ||
| || (mhdr.magic[3] != 'R') || (mhdr.magic[4] != 'I') || (mhdr.magic[5] != 'X') ) { | ||
| printf("Signature not 'MATRIX' (ECAT7)\n"); | ||
| fclose(f); | ||
| return EXIT_FAILURE; | ||
| } | ||
| * swapEndian = mhdr.file_type > 255; | ||
| if (*swapEndian) { | ||
| nifti_swap_2bytes(1, &mhdr.sw_version); | ||
| nifti_swap_2bytes(1, &mhdr.file_type); | ||
| nifti_swap_2bytes(1, &mhdr.num_frames); | ||
| nifti_swap_4bytes(1, &mhdr.ecat_calibration_factor); | ||
| } | ||
| if ((mhdr.file_type < ECAT7_2DSCAN) || (mhdr.file_type > ECAT7_3DSCANFIT)) { | ||
| printf("Unknown ECAT file type %d\n", mhdr.file_type); | ||
| fclose(f); | ||
| return EXIT_FAILURE; | ||
| } | ||
| if ((mhdr.num_frames > 1) || (mhdr.num_bed_pos > 1)) //to do: multi-volume files | ||
| printf("Only reading first volume from ECAT file with %d frames and %d bed positions\n", mhdr.num_frames, mhdr.num_bed_pos); | ||
| //read list matrix | ||
| fseek(f, 512, SEEK_SET); | ||
| ecat_list_hdr lhdr; | ||
| fread(&lhdr, sizeof(lhdr), 1, f); | ||
| if (*swapEndian) { | ||
| nifti_swap_4bytes(128, &lhdr.hdr[0]); | ||
| } | ||
| //offset to first image | ||
| int img1_StartBytes = lhdr.r01[1] * 512; | ||
| //load image header for first image | ||
| fseek(f, img1_StartBytes - 512, SEEK_SET); //image header is block immediately before image | ||
| ecat_img_hdr ihdr; | ||
| fread(&ihdr, sizeof(ihdr), 1, f); | ||
| if (*swapEndian) { | ||
| nifti_swap_2bytes(5, &ihdr.data_type); | ||
| nifti_swap_4bytes(7, &ihdr.x_resolution); | ||
| nifti_swap_4bytes(3, &ihdr.x_pixel_size); | ||
| } | ||
| if ((ihdr.data_type != ECAT7_BYTE) && (ihdr.data_type != ECAT7_SUNI2) && (ihdr.data_type != ECAT7_SUNI4)) { | ||
| printf("Unknown or unsupported ECAT data type %d\n", ihdr.data_type); | ||
| fclose(f); | ||
| return EXIT_FAILURE; | ||
| } | ||
| //cm -> mm | ||
| ihdr.x_pixel_size *= 10.0; | ||
| ihdr.y_pixel_size *= 10.0; | ||
| ihdr.z_pixel_size *= 10.0; | ||
| fclose(f); | ||
| nhdr->dim[0]=3;//3D | ||
| nhdr->dim[1]=ihdr.x_dimension; | ||
| nhdr->dim[2]=ihdr.y_dimension; | ||
| nhdr->dim[3]=ihdr.z_dimension; //slices per volume | ||
| nhdr->dim[4]=1; //volumes | ||
| nhdr->pixdim[1]=ihdr.x_pixel_size; | ||
| nhdr->pixdim[2]=ihdr.y_pixel_size; | ||
| nhdr->pixdim[3]=ihdr.z_pixel_size; //TO DO: slice gap? | ||
| nhdr->datatype = DT_INT16; | ||
| if (ihdr.data_type == ECAT7_BYTE) nhdr->datatype = DT_UINT8; | ||
| if (ihdr.data_type == ECAT7_SUNI4) nhdr->datatype = DT_INT32; | ||
| nhdr->vox_offset = img1_StartBytes; | ||
| nhdr->sform_code = NIFTI_XFORM_UNKNOWN; //NIFTI_XFORM_SCANNER_ANAT; | ||
| nhdr->scl_slope = ihdr.scale_factor * mhdr.ecat_calibration_factor; | ||
| //direct clone of spm_ecat2nifti: seems off by one (indexed from zero) | ||
| vec3 start = setVec3((ihdr.x_dimension-2.0)/2.0*ihdr.x_pixel_size, (ihdr.y_dimension-2.0)/2.0*ihdr.y_pixel_size, (ihdr.z_dimension-2.0)/2.0*ihdr.z_pixel_size); | ||
| nhdr->srow_x[0]=-nhdr->pixdim[1];nhdr->srow_x[1]=0.0f;nhdr->srow_x[2]=0.0f;nhdr->srow_x[3]=start.v[0]; | ||
| nhdr->srow_y[0]=0.0f;nhdr->srow_y[1]=-nhdr->pixdim[2];nhdr->srow_y[2]=0.0f;nhdr->srow_y[3]=start.v[1]; | ||
| nhdr->srow_z[0]=0.0f;nhdr->srow_z[1]=0.0f;nhdr->srow_z[2]=-nhdr->pixdim[3];nhdr->srow_z[3]=start.v[2]; | ||
| fclose(f); | ||
| //convertForeignToNifti(nhdr); | ||
| return EXIT_SUCCESS; | ||
| } | ||
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| int open_foreign (const char *fn){ | ||
| printf("--> %s\n", fn); | ||
| struct nifti_1_header nhdr; | ||
| bool swapEndian; | ||
| int ret = nii_readEcat7(fn, &nhdr, &swapEndian); | ||
| if (ret == EXIT_SUCCESS) | ||
| printf("!\n"); | ||
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| return ret; | ||
| }// open_foreign() | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,16 @@ | ||
| //Attempt to open non-DICOM image | ||
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| #ifndef _NII_FOREIGN_ | ||
| #define _NII_FOREIGN_ | ||
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| #ifdef __cplusplus | ||
| extern "C" { | ||
| #endif | ||
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| int open_foreign (const char *fn); | ||
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| #ifdef __cplusplus | ||
| } | ||
| #endif | ||
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| #endif |