A Macro Example

The example shows how variables and macros may be defined to allow a sequence of operations to be defined for one file and easily adapted to apply to other files. The example shows how regions of input files may be defined and corrected for spatial distortion, provided of course that the spatial distortion has been previously defined (See Section 16, Page ). This example should be easy to modify for other sequences of operations which need to be repeated.

Two variables are defined, #IN for the input file and #OUT for the output file to contain the corrected image. The START MACRO command is used to open a macro, and within the macro the variables #IN and #OUT are used instead of the real files names. The STOP MACRO command closes the macro. Prior to using the macro, the variables are re-defined to different file names. (The text has been created by FIT2D using the OPEN LOG command to create a listing of terminal I/O, see Section 15.63, Page ).

First the variables for the input and output files are defined:

Main menu: ENTER COMMAND [VARIABLE]:variable
ENTER VARIABLE NAME [#IN]:#IN
ENTER VARIABLE VALUE [test.dat]:lyso1.gel
Main menu: ENTER COMMAND [INPUT DATA]:variable
ENTER VARIABLE NAME [#IN]:#OUT
ENTER VARIABLE VALUE [lyso1.gel]:lyso1.cor

Now the macro is created using the variables rather than the direct file names:

Main menu: ENTER COMMAND [INPUT DATA]:start macro
FILE NAME [fit2d.mac]:lyso.mac
Main menu: ENTER COMMAND [SET CURVE STYLES]:input
FILE FORMAT [IMAGEQUANT]:imagequant
DATA FILE NAME [test.dat]:#IN
LEFT-HAND PIXEL OF IMAGE REGION [1]:
LOWER PIXEL OF IMAGE REGION [1]:
RIGHT-HAND PIXEL OF IMAGE REGION (Range: 1 to 1152) [1152]:
UPPER PIXEL OF IMAGE REGION (Range: 1 to 1482) [1482]:
INFO: Full image size =      1152 *      1482 pixels
Main menu: ENTER COMMAND [IMAGE]:reg
X-MINIMUM VALUE (Range: 0.0 to 1152.00) [.50000]:10
Y-MINIMUM VALUE (Range: 0.0 to 1482.00) [.50000]:90
X-MAXIMUM VALUE (Range: 10.0000 to 1152.00) [1151.50]:1120
Y-MAXIMUM VALUE (Range: 90.0000 to 1482.00) [1481.50]:1410
Main menu: ENTER COMMAND [IMAGE]:calibrat
Calibration sub-menu: ENTER COMMAND [SPATIAL CORRECTION]:input
Name of file for spatial distortion interpolation function
FILE NAME [176.spline]:176.spline
Calibration sub-menu: ENTER COMMAND [SPATIAL CORRECTION]:
INFO: The corrected pixel dimension in X is     176.4269 microns
INFO: The corrected pixel dimension in Y is     175.8364 microns
INFO: Number of rows re-binned =    100 (  7%)

(Here some program information output has been missed out.)

INFO: Number of rows re-binned =   1300 ( 98%)
INFO: Time for re-binning =        57.68 seconds
Calibration sub-menu: ENTER COMMAND [EXIT]:
DESTROY DYNAMIC ARRAYS [NO]:
Main menu: ENTER COMMAND [EXCHANGE]:
Main menu: ENTER COMMAND [IMAGE]:out
FILE FORMAT [FIT2D STANDARD FORMAT]:dump
DUMP FILE NAME [fit2d.dump]:#OUT
INFO: Data region is   1152 *   1482 pixels
RECORD LENGTH (BYTES) (Range: 1 to 6000) [2304]:
FIRST RECORD FOR OUTPUT (Range: 1 to 100000) [1]:
BIG ENDIAN FORMAT INTEGERS [NO]:y
INFO: Data minimum value =    .0000000E+00
INFO: Data maximum value =    .5378928E+09
LOWER LIMIT OF RANGE (Range: -1.700E+38 to 5.379E+08) [0.0]:
UPPER LIMIT OF RANGE (Range: 0.0 to 1.700E+38) [5.379E+08]:
Main menu: ENTER COMMAND [INPUT DATA]:stop

The first image has been, input corrected, and output. In doing this, we have saved the entered operations as a macro. Now the variables can be re-defined to refer to new input and output files:

Main menu: ENTER COMMAND [EXIT]:variable
ENTER VARIABLE NAME [#OUT]:
ENTER DATA TYPE OF VARIABLE:string
ENTER VARIABLE VALUE [lyso1.cor]:lyso2.cor
Main menu: ENTER COMMAND [INPUT DATA]:varia
ENTER VARIABLE NAME [#OUT]:#IN
ENTER DATA TYPE OF VARIABLE:s
ENTER VARIABLE VALUE [lyso2.cor]:lyso2.gel

Now the command macro is used to run the previously created macro file. The same variables are used, but now they refer to different files:

Main menu: ENTER COMMAND [INPUT DATA]:macro
FILE NAME [lyso.mac]:lyso.mac
Main menu: ENTER COMMAND [IMAGE]:INPUT DATA
FILE FORMAT [IMAGEQUANT]:IMAGEQUANT
DATA FILE NAME [grid1.gel]:#IN
LEFT-HAND PIXEL OF IMAGE REGION [1]:
LOWER PIXEL OF IMAGE REGION [1]:
RIGHT-HAND PIXEL OF IMAGE REGION (Range: 1 to 1152) [1152]:
UPPER PIXEL OF IMAGE REGION (Range: 1 to 1482) [1482]:
INFO: Full image size =      1152 *      1482 pixels
Main menu: ENTER COMMAND [IMAGE]:REGION
X-MINIMUM VALUE (Range: 0.0 to 1152.00) [.50000]:1.0000000E+01
Y-MINIMUM VALUE (Range: 0.0 to 1482.00) [.50000]:9.0000000E+01
X-MAXIMUM VALUE (Range: 10.0000 to 1152.00) [1151.50]:1.1200000E+03
Y-MAXIMUM VALUE (Range: 90.0000 to 1482.00) [1481.50]:1.4100000E+03
Main menu: ENTER COMMAND [IMAGE]:CALIBRATION
Calibration sub-menu: ENTER COMMAND [SPATIAL CORRECTION]:INPUT SPATIAL
Name of file for spatial distortion interpolation function
FILE NAME [176.spline]:176.spline
Calibration sub-menu: ENTER COMMAND [SPATIAL CORRECTION]:SPATIAL CORR
INFO: The corrected pixel dimension in X is     176.4269 microns
INFO: The corrected pixel dimension in Y is     175.8364 microns
INFO: Number of rows re-binned =    100 (  7%)

(Here some program information output has been missed out.)

INFO: Number of rows re-binned =   1300 ( 98%)
INFO: Time for re-binning =        56.05 seconds
Calibration sub-menu: ENTER COMMAND [EXIT]:EXIT
DESTROY DYNAMIC ARRAYS [NO]:NO
Main menu: ENTER COMMAND [EXCHANGE]:EXCHANGE
Main menu: ENTER COMMAND [IMAGE]:OUTPUT DATA
FILE FORMAT [FIT2D STANDARD FORMAT]:DUMP
DUMP FILE NAME [fit2d.dump]:#OUT
INFO: Data region is   1152 *   1482 pixels
RECORD LENGTH (BYTES) (Range: 1 to 6000) [2304]:
FIRST RECORD FOR OUTPUT (Range: 1 to 100000) [1]:
BIG ENDIAN FORMAT INTEGERS [NO]:YES
INFO: Data minimum value =    .0000000E+00
INFO: Data maximum value =    .1259027E+10
LOWER LIMIT OF RANGE (Range: -1.700E+38 to 1.259E+09) [0.0]:
UPPER LIMIT OF RANGE (Range: 0.0 to 1.700E+38) [1.259E+09]: