-
Notifications
You must be signed in to change notification settings - Fork 229
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Include StudyInstanceUID and SeriesInstanceUID in filename
- Loading branch information
1 parent
b536b6b
commit 3f2d477
Showing
9 changed files
with
267 additions
and
7 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,214 @@ | ||
| #include "nii_foreign.h" | ||
| #include "nifti1.h" | ||
| #include "nifti1_io_core.h" | ||
|
|
||
| #include <sys/types.h> | ||
| #include <stdio.h> | ||
| #include <stdlib.h> | ||
| #include <stdint.h> | ||
| #include <stdbool.h> | ||
| #include "print.h" | ||
|
|
||
| #ifndef Float32 | ||
| #define Float32 float | ||
| #endif | ||
| #ifndef uint32 | ||
| #define uint32 uint32_t | ||
| #endif | ||
|
|
||
|
|
||
|
|
||
| /*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 | ||
| */ | ||
|
|
||
| //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; | ||
| } | ||
|
|
||
|
|
||
|
|
||
| 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"); | ||
|
|
||
| return ret; | ||
| }// open_foreign() | ||
|
|
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,16 @@ | ||
| //Attempt to open non-DICOM image | ||
|
|
||
| #ifndef _NII_FOREIGN_ | ||
| #define _NII_FOREIGN_ | ||
|
|
||
| #ifdef __cplusplus | ||
| extern "C" { | ||
| #endif | ||
|
|
||
| int open_foreign (const char *fn); | ||
|
|
||
| #ifdef __cplusplus | ||
| } | ||
| #endif | ||
|
|
||
| #endif |