SPIDER: CP FROM PE (Copy Perkin Elmer disk file to SPIDER format)

CP FROM PE - Copy Perkin Elmer disk file to SPIDER format

(3/09/99)

PURPOSE: Converts Perkin Elmer densitometer disk files to SPIDER image files. Operation was previously named "TR DISK".

USAGE

.OPERATION: CP FROM PE

.SCAN INPUT FILE: IMAGE0001

[Enter file name. Each image scanned by the densitometer is contained in two files. Both have the name of the identification specified in SCANSALOT with 4 digits added to it. Example: If the identification was "IMAGE", then you need to have two files: IMAGE0001.IMG and IMAGE0001.HDR in the same directory. This program looks up in IMAGE0001.HDR to find the file dimensions and the scanning direction. This information is then used to convert IMAGE0001.IMG into a SPIDER image file.]

.OUTPUT FILE: SPI001
[Enter output file name (use SPIDER conventions).]

.(D)ENSITY, (T)RANSMISSION: D
[If image was digitzed in density mode, enter "D" , otherwise enter "T" and the program will convert the transmission values into densities.]

If "T" was answered, the system asks:

.ENTER GAIN FACTOR: 5
[Default value is 1. If the micrdensitometer was calibrated according to the description in the manual (1988), the gain value is 5.]

.REDUCTION FACTOR (0 IF NO RED.): 4
[Enter integer reduction factor. The program averages over aXa pixels (a=reduction factor). If you do not want to have any reduction, enter 1.]

NOTES

This operation converts only files that were originally written onto disk by the PDS software. If file was originally written to tape by the PDS software, use 'COPY FROM TR" for conversion.
The output file will occupy twice as much disk space as the input file.
After scanning if you somehow corrupt your .HDR file you can retreive your image by modifying any other .HDR file (it is an ASCII file) and substituting the known X and Y dimensions. If you do not know the dimensions divide the size of the file by 2 and the answer is the product of the X and Y dimension. i.e. a 4451 X and 3502 Y will give you a file that has the size of 31174804.
File extensions are uppercase: .HDR and .IMG.
The Perkin Elmer header file (".HDR") is a standard ASCII text file and thus can be printed, edited, etc..