BSL is a 2-D interactive data manipulation package for image data. The program is has a wide range of applications even if some of the instructions and options are specific to X-ray applications. BSL developed by J.Bordas and G.Mant and was based on the OTOKO package sharing the same data format and interface style. This allows data to be reduced to 1-D in BSL and then imported into OTOKO for further processing. The program is now available for all major hardware platforms (Sun, HP, DEC, and SG) in two varieties bsltek and bsl. The former runs on character based terminals and the latter on X windows based workstations. This manual is based on contributions from the original authors, R.Rule (ICI, Runcorn) and I.Dobbie (Kings College).
The interface is based upon a set of 3 letter instructions, that are preceded with either a dot (e.g. .MUC to multiply an image by a constant). Most input is then taken from the keyboard, although some functions require the selection of coordinates using either the keyboard cursors or the mouse. BSL prompts for filenames with the question:
Enter filename (X99999.XXX[/]) or <ctrl-D>
By entering either <ctrl-d>, ^d or ^D will terminate the prompt without any file input. Nearly all BSL functions can be applied to either:
a) a single frame file or a single frame from multi-frame file.
Enter filename (X99999.XXX[/]) or <ctrl-D>: s58026.tmp
In this case only time frame 26 in the file S58001.TMP will be processed.
b) several time frames from one file
Enter filename (X99999.XXX[/]) or <ctrl-D>:
s58000.tmp
Enter [1] positional [2] calibrational data or aux[3] [1]:
1
Total number of frames 256
Enter first and last frame, increment or <ctrl-D>:
26,38,2
Memory 1 first and last frame 26 3 incr 2
Enter first and last channel of output [1,256]:
<return>
In this case all channels of frames 26,28,30,32,34,36 and 38 of the binary file S58001.TMP will be processed. Another way of obtaining the same result is by giving the name of the first frame followed by a slash (/).
Enter filename (X99999.XXX[/]) or <ctrl-D>:
s58026.tmp/
Enter last file number, increment or <ctrl-D>:
58036,2
Enter first and last channel of output [1,256]:
<return>
NOTE that the only way to access the contents of binary files other than the SAXS files, is to enter the header file name (e.g. S58000.TMP) and answer the first question with the required choice of file. If a frame number (the last three digits) is non-zero (e.g. S58002.TMP) then the SAXS binary file is always assumed.
c) one time frame from several files in a sequence
Enter filename (X99999.XXX[/]) or <ctrl-D>:
s58000.tmp/
Enter last file number, increment or <ctrl-D>:
59000,1000
Enter memory [1]: <return>
Total number of frames: 256
Enter first and last frame, increment or <ctrl-D>:
25
Memory 1 first and last frame 25 25 incr 1
Enter first and last channel of output [1,256]:
<return>
In this case all channels of frame 25 of file S58001.TMP and of file S59001.TMP will be processed.
When a command has been executed on a given data file, the output filename is usually given the same extension as the command itself; i.e. after a .DIN command, the output file is Xnn000.DIN.
A full list of commands and a brief description of their operation is provided for the present version:
.ADC Add a constant to a selected range in spectrum. .ADD Weighted addition of two images. .ADN Add and normalise image using a calibration file. .ARG Display image on X-window terminal .ASF Add/subtract a single file/raster to an image. .AVE Average a series of images .BAK Background subtraction of an image .CHG Change a selected value in an image .CIN Circular integration and integration .CNV Convolve two files .CON Generate a contour map .CUT Cut part of an image into a smaller image .DGL Deglitch an image .DIC Divide a selected region of an image by a constant .DIN Divide and normalise image using a calibration file. .DIS Display image on X-window terminal .DIV Weighted division of two images .DSF Divide an image by a single file/raster. .DUP Duplicate and or remove frames of an image. .EXP Exponentiate data values. .FFT Perform 2-D fourier transform on an image .GAU Generate a 2-D gaussian function .HOR Perform a horizontal integration in a selected region. .IFT Calculate the inverse fourier transform. .INT Integrate through selected region of image. .IPO Transform image from polar to cartesian coordinates. .ITP Interpolate a 2-D iamge .LOG Calculate natural or base10 log of image. .LZR Create postscript output file of image. .MAX Calculate minimum & maximum values of an image. .MIR Mirror the four quadrants of an image. .MSF Multiply an image by a single file/raster. .MSK Display an image & create a bit mask of selected areas. .MUC Multiply a selected region of an image by a constant. .MUL Weighted multiplication of two images. .MUN Multiply and normalise image using a calibration file. .PAK Pack an image into smaller dimensions by averaging. .POL Transform image from cartesian to polar cordinates .POW Raises image to specified power. .PRT Print values of data on lineprinter or terminal. .RAD Create circles around a centre point. .REM Duplicate and or remove frames of an image. .REP Replace a single raster or rasters in an image. .RIN Radial scan and integration .RMP Remap an image to a given set of remapping points. .ROT Rotate an image. .SEC Perform sector integration. .SHF Shift an image in x and/or y directions. .SUM Sum a series of images. .SUN Subtract and normalise image using a calibration file. .SUR Surface plot (isometric projection) .VER Perform a vertical integration in a selected region. .WIN Create a contrast transfer function in 2D from 1D file. .ZER Set all negative values in an image equal to 0.0.
A set of standard files consists of:
* Header file * One or more binary files.
Data from the NCD experimental stations appears with filenames of the type
Xnn000.mdd Header file Xnn001.mdd SAXS data Xnn002.mdd Calibration data Xnn003.mdd WAXS data
where the first letter refers to the experimental session and the next two digits to the number of the individual experiment. The number increases by one after each experiment until the 100th experiment after which the number returns to zero. This Xnn format can be used to identify any experiment in a session.
The next three digits refer to the type of information contained in the file. The 000 file is the header file and is in ASCII or readable form. It contains information such as the sample title, the number of frames in the file, the names of the intensity and calibration data files. The 001 file contains the raw SAXS data in binary (unreadable) format. The 002 file contains calibration information, again in binary format and finally, the 003 file contains the raw WAXS data also in binary format.
The mdd gives the date on which the data was recorded. The first digit being the duodecimal month and the other digits the date:
Xnn000.807 7th August Xnn000.A24 24th October
The name of a header file is of the form Xnn000.XXX where X is any alphanumeric character and n is any digit. e.g. M74000.TMP. This header file is always written in ASCII and contains the following information:
* line 1. Header with up to 80 alphanumeric characters. * line 2. Header with up to 80 alphanumeric characters. * line 3. Integer indicators for the first binary file indicator(1) = number of pixels. indicator(2) = number of rasters indicator(3) = number of time frames indicator(4) = indicator(5) = indicator(6) = indicator(7) = indicator(8) = indicator(9) = indicator(10) = 1, except for the last binary file, when it is zero
* line 4. File name of the binary file
The lines 3 and 4 should be repeated for subsequent binary files. The panel below shows an example of a header file with two binary files.
SRS Data recorded on Wed Mar 8 23:54:33 1995
Collagen
512 512 1 0 0 0 0 0 0 1
1 4 1 0 0 0 0 0 0 0
C01002.308
The binary files contain the data, in Fortran terms, as direct access, unformatted, fixed length records (frames) containing REAL*4 values and as a stream of 4 byte floats in C terminology. The floating point format, as recorded by the Daresbury data acquisition system, is IEEE format based on "big endian" machines. The contentsof these files are organised as indicated by the header file.
There are some advantages and some disadvantages for this simple flat file format. The files are easy to process and writing conversion routines from one format to another is relatively simple. The fact that there is no header etc. in the actual file means that the number of frames, and even the frame size can be deduced simply from the file size. Mislabelled files can often be rectified from this alone (1x 512*512 frame is 1MB, or 1048576 bytes). The lack of any information in the actual data file means that several files are needed which can lead to confusion and difficulties if the ASCII header is lost. This can often be rectified reasonable easily by constructing a new ASCII header in a text editor.
It is worth noting that the binary data file is written in native byte order. This can lead to problems when transferring from a big-endian to a little-endian machine. There is a program to deal with the conversion,
In progress
