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Because no specification of this file format was available for the development of uocte, the file format was reverse engineered for interoperability. The information on this page therefore is incomplete and may be incorrect. It only serves to document which parts of the data are interpreted by uocte and which assumptions it makes concerning interpretation.
High-Level Structure
Topcon is one binary, little endian file that contains both measured data and metadata. Its extension is fda and its high-level structure is a header followed by named chunks:
u8[4] "FOCT" u8[3] "FDA" or "FAA", denoting "macula" or "external" fixation u32 "0x2", may be version information u32 "0x3e8", may be version information while true u8 chunk_name_size if chunk_name_size == 0 eof else u8[chunk_name_size] chunk_name u32 chunk_size u8[chunk_size] chunk_data
The chunk names start with @. They also seem to occur always in the same order, although some chunks are optional. The following list of chunks is sorted by the typical order in which they occur within the file. Strings, including chunk names, are not zero-terminated and ISO8859-1 coded. All images' origins are at the lower left.
@FDA_FILE_INFO u32 "0x2" u32 "0x3e8" u8[32] "8.0.1.20198"
@HW_INFO_03 u8[16] model name u8[16] serial number u8[32] (zeros) u8[16] version u16 build year u16 build month u16 build day u16 build hour u16 build minute u16 build second u8[8] (zeros) u8[5][16] version numbers
@PATIENT_INFO_02 u8[32] patient id u8[32] patient given name u8[32] patient surname u8[8] (zeros) u8 3 or 1, in the latter case birth date is valid u16 birth year u16 birth month u16 birth day u8[504] mostly zeros
@CAPTURE_INFO_02 u16 x u16[52] (zeros) u16 aquisition year u16 aquisition month u16 aquisition day u16 aquisition hour u16 aquisition minute u16 aquisition second
@IMG_JPEG u8 type u32 ? u32 ? u32 width u32 height u32 num_slices u32 "0xa02" for i in 1..num_slices int32 size u8[size] greyscale tomogram slice image, j2k coded
These are the values for type found in the wild:
0a line scan2a rectangular volume scan3a cylindrical volume scan7a 7 line scan (horitontal or vertical)11two 5 line scans put into one 10 slice volume
@PARAM_SCAN_04 u16[6] ? f64 tomogram x dimension in mm f64 tomogram z dimension in mm f64 tomogram y resolution in µm f64[2] ? u8[?] ?
@IMG_TRC_02 u32 width u32 height u32 bits per pixel u32 num_slices ("0x2") u8 "0x1" for i in 1..num_slices u32 size u8[size] greyscale fundus image, j2k coded
There are always two images, but these are identical. uocte uses the last image as a fundus image.
@PARAM_TRC u16[2] ?
@IMG_FUNDUS (present if @CAPTURE_INFO_02.x & 0x200 != 0) u32 width u32 height u32 bits per pixel u32 num_slices ("0x1") u32 "0xa02" for i in 1..num_slices u32 size u8[size] BGR fundus image, j2c coded
Note that the blue and red channel are swapped.
@PARAM_OBS_02 (present if @CAPTURE_INFO_02.x & 0x200 != 0) u16 "0x1" u16[2] 2x "0xffff" u8[12] "D7000" (camera model "Kodak ...") u8[24] "JPEG Fine" u16 "0x300" u16 "0x1" u16 "0x0" u8[24] "Color Temparature" u16 "0x2014" u8[12] (zeros) f32 ?
@IMG_MOT_COMP_03 (present if @IMG_JPEG.type == "0x2") u8 "0x0" u32 width u32 height u32 bits per pixel ("0x10") u32 num_slices ("0x9") u16[num_slices][height][width] raw volume image
@IMG_PROJECTION (present if @IMG_JPEG.type == "0x2") u32 width u32 height u32 bits per pixel ("0x8") u32 0x1000002 u32 size u8[size] greyscale maximum intensity projection of tomogram volume, j2k coded
@REGIST_INFO u8 "0x0" u32[2] ? u32[4] bounding box in fundus pixels (minx, miny, maxx, maxy) or (centerx, centery, radius, 0) u8[32] "8.0.1.20198" u32[4] bounding boy in trc pixels (minx, miny, maxx, maxy) or (centerx, centery, radius, 0) f64[4] 4x "0.5" u8[48] (zeros)
@ALIGN_INFO u16 "0x0" u32 num_slices u32[3] (zeros) u32 ? u32 ? u8[32] "8.0.1.22004"
@CONTOUR_INFO u8[20] id u16 type u32 width u32 height u32 size if type == "0x0" u16[height][width] contour depth in tomogram volume pixels else if type == "0x100" f64[height][width] contour depth in tomogram volume pixels u8[32] "8.0.1.20198"
This chunk may appear multiple times with different values for id. Contour depth is measured from the top of the tomogram slice images rather than the bottom. If type is 0x0, id is typically RETINA_# or FLA_#, when it is 0x100, id is typically CORNEA_#.
@FAST_Q2_INFO f32[6] various quality statistics u8[20] (zeros)
@THUMBNAIL u32 size u8[size] raw RGB BMP-coded thumbnail image
@GLA_LITTMANN_01 u32[11] (zeros) u32 "0xffff" u32 "0x1"
@PATIENTEXT_INFO u8[128] (zeros)
@EFFECTIVE_SCAN_RANGE u32[4] fundus bounding box (minx, miny, maxx, maxy) u32[4] trc bounding box (minx, miny, maxx, maxy)
Note that unlike in @REGIST_INFO these bounding boxes are always rectangular. They do not always match the ranges given in @REGIST_INFO.
@MAIN_MODULE u8[128] "3DOCT-2000.exe" u16[4] version ("0x8", "0x0", "0x1", "0x5616") u8[128] (zeros)
@RESULT_CORNEA_CURVE (present if @IMG_JPEG.type == "0x3") u8[20] id u32 width u32 height u8[32] "8.0.1.21781" f64[height] ? f64[height][width] contour data
@ANTERIOR_CALIB_INFO (present if fixation is external) u8[16] "2.1.0" f64[84] ?
@RESULT_CORNEA_THICKNESS (present if @IMG_JPEG.type == "0x3") u8[32] "8.0.1.21781" u8[20] id u32 width u32 height f64[height][width] contour data
@REPORT_INFO u8[7] (zeros)
Not yet found in the data is the subjects sex and the laterality.
Updated