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BioradHeader.h
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BioradHeader.h
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/*=========================================================================
Program: OsiriX
Copyright (c) OsiriX Team
All rights reserved.
Distributed under GNU - GPL
See http://homepage.mac.com/rossetantoine/osirix/copyright for details.
This software is distributed WITHOUT ANY WARRANTY; without even
the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
PURPOSE.
=========================================================================*/
#define BIORAD_HEADER_LENGTH 76
#define BIORAD_NOTE_LENGTH 96
#define BIORAD_NOTE_TEXT_LENGTH 80
struct BioradHeader{
short int nx,ny,npic;
int unused0;
int notesAvailable;
short int byte_format;
char unused1[38];
short int magicNumber;
char unused2[20];
} __attribute__((__packed__));
struct BioradNote
{
// short displayLevel;
// int moreNotes; // 0 if this is the last note, else there is another note
// int unused;
// short noteType;
char unsused[16];
/* Note type := 1 for live collection note,
:= 2 for note including file name,
:= 3 if note for multiplier file,
:= 4, 5, etc.,; additional descriptive notes */
char noteText[BIORAD_NOTE_LENGTH];
} __attribute__((__packed__));
/*
Bio-Rad(TM) .PIC Image File Information
(taken from: "Introductory Edited Version 1.0", issue 1/12/93.)
(Location of Image Calibration Parameters in Comos 6.03 and MPL .PIC files)
The general structure of Bio-Rad .PIC files is as follows:
HEADER (76 bytes)
Image data (#1)
.
.
Image data (#npic)
NOTE (#1)
. ; NOTES are optional.
.
NOTE (#notes)
RGB LUT (color Look Up Table)
Header Information:
The header of Bio-Rad .PIC files is fixed in size, and is 76 bytes.
------------------------------------------------------------------------------
'C' Definition byte size Information
(bytes)
------------------------------------------------------------------------------
int nx, ny; 0 2*2 image width and height in pixels
int npic; 4 2 number of images in file
int ramp1_min, ramp1_max; 6 2*2 LUT1 ramp min. and max.
NOTE *notes; 10 4 no notes=0; has notes=non zero
BOOL byte_format; 14 2 bytes=TRUE(1); words=FALSE(0)
int n; 16 2 image number within file
char name[32]; 18 32 file name
int merged; 50 2 merged format
unsigned color1; 52 2 LUT1 color status
unsigned file_id; 54 2 valid .PIC file=12345
int ramp2_min, ramp2_max; 56 2*2 LUT2 ramp min. and max.
unsigned color2; 60 2 LUT2 color status
BOOL edited; 62 2 image has been edited=TRUE(1)
int _lens; 64 2 Integer part of lens magnification
float mag_factor; 66 4 4 byte real mag. factor (old ver.)
unsigned dummy[3]; 70 6 NOT USED (old ver.=real lens mag.)
------------------------------------------------------------------------------
Additional information about the HEADER structure:
Bytes Description Details
------------------------------------------------------------------------------
0-9 nx, ny, npic, ramp1_min, ramp1_max; (all are 2-byte integers)
10-13 notes NOTES are present in the file, otherwise there are
none. NOTES follow immediately after image data at
the end of the file. Each note os 96 bytes long.
14-15 byte_format Read as a 2 byte integer. If this is set to 1, then
each pixel is 8-bits; otherwise pixels are 16-bits.
16-17 n Only used in COMOS/SOM when the file is loaded into
memory.
18-49 name The name of the file (without path); zero terminated.
50-51 merged see Note 1.
52-53 colour1
54-55 file_id Read as a 2 byte integer. Aways set to 12345.
Just a check that the file is in Bio-Rad .PIC format.
56-59 ramp2_min/max Read as 2 byte integers.
60-61 color2 Read as a 2 byte integer.
62-63 edited Not used in disk files.
64-65 int_lens Read as a 2 byte integer.
Integer part of the objective lens used.
66-69 mag_factor Read as a 4-byte real.
mag. factor=(float)(dispbox.dy*2)/(float)(512.0*scandata.ly)
where: dispbox.dy = the width of the image.
scandata.ly = the width of the scan region.
the pixel size in microns can be calculated as follows:
pixel size = scale_factor/lens/mag_factor
where: lens = the objective lens used as a floating pt. number
scale_factor = the scaling number setup for the system
on which the image was collected.
70-75 dummy[3] Last 6 bytes not used in current version of disk file
format. (older versions stored a 4 byte real lens mag
here.)
------------------------------------------------------------------------------
Note 1 : Values stored in bytes 50-51 :
0 : Merge off
1 : 4-bit merge
2 : Alternate 8-bit merge
3 : Alternate columns merge
4 : Alternate rows merge
5 : Maximum pixel intensity merge
6 : 256 colour optimised merge with RGB LUT saved at the end
of each merge.
7 : As 6 except that RGB LUT saved after all the notes.
Information about NOTE structure and the RGB LUT are not included in this
file. Please see the Bio-Rad manual for more information.
==============================================================================
Info added by Geert Meesen from MRC-600 and MRC-1024 Manuals.
-------------------------------------------------------------
Note Structure :
Bytes Description Details
------------------------------------------------------------------------------
0-1 Display level of this note
2-5 =0 if this is the last note, else there is another note (32 bit integer)
10-11 Note type := 1 for live collection note,
:= 2 for note including file name,
:= 3 if note for multiplier file,
:= 4, 5, etc.,; additional descriptive notes
16-95 Text of note (80 bytes)
=============================================================================
Info added by Geert Meesen from personal experiments.
------------------------------------------------------------
- Until now I only have experience with 8-bit images from the MRC-1024 confocal microscope.
The newer microscopes (Radiance 2000, for example) are capable of generating 16 bit images,
I think. I have access to such a microscope and will try to find out later. For now it
should be possible to look at the byte-word flag in the header.
- I have experience with two types of images :
--- One slice in the Z-direction, 3 channels of recording. This type is stored as a three-slice image
with the 3 channels in consecutive layers. (Single-Slice)
--- Different Z slices with only one channel. (Z-stack)
- The header should contain some info about the pixel-size, but until now I was not really
able to interpret this info. It's easier to extract the info from the notes at the end.
You can find 3 notes saying something like (from AUPCE.NOT, a Z-stack file)
AXIS_2 001 0.000000e+00 2.999667e-01 microns
AXIS_3 001 0.000000e+00 2.999667e-01 microns
AXIS_4 001 0.000000e+00 1.000000e+00 microns
AXIS_9 011 0.000000e+00 1.000000e+00 RGB channel
These lines give the pixelsize for the X (axis_2), Y (axis_3) and Z (axis_4) axis in the units mentioned. I don't
know if this unit is always 'microns'.
For a Single-Slice images you get ( from AB003A.NOT, a Single-Slice image) :
AXIS_2 001 0.000000e+00 1.799800e+00 microns
AXIS_3 001 0.000000e+00 1.799800e+00 microns
AXIS_4 011 0.000000e+00 1.000000e+00 RGB channel
It seems that AXIS_4 is used for indicating an RGB channel image.
*/