ST | ; set header values operation |
BAD000 | ; bad input file |
B | ; put new values into specified locations in the header |
24,25 | ; header locations to be changed |
0,1 | ; appropriate values for these header locations in images |
For SPIDER releases before 06/01/97 this method will only work in interactive mode, not in batch mode
resource settings in your .Xdefaults file:
e.g. Web*background : green Web*foreground : red Web*useSchemes: all (The "useSchemes" option selects SGI's color coordinated settings for standard Window Manager controlled colors) or with command line options: -bg Background-color -bd Border-color -fg Foreground-color e.g. web -bg green DAT web -bg purple -fg red DAT
After the end of the batch, the files SEL001.DAT through SEL150.DAT will
exist and they will contain the selected windows.
You can test for values of decw$server_default_visual_class, and specify
values for the different heads: (put following in above file)
if decw$server_default_visual_class="3,4,0",
head 1=3=8-bit pseudocolor
head 2=4=24-bit truecolor
head 3=0=staticgrey
One user had success by just adding:
decw$server_default_visual_class="3,4,0",
to: SYS$COMMON:[000000.SYSMGR]DECW$PRIVATE_SERVER_SETUP.COM
;b01.cpr -- procedure to import images from GATAN to SPIDER
x10=1 ; (set counter)
do lb1 i=1,7 ; (DO-LOOP over the number of micrographs)
cp from raw ; (Copy command)
(16) ; (how many bits)
mic/micx10 ; (input file name, indexed by counter)
(1024 1024) ; (input file dimensions)
(8) ; (skip header bytes)
(1) ; (most significant byte)
n ; (do not fold negatives)
mic/spix10 ; (output file name, indexed by conter)
x10=x10+1 ; (increment counter)
lb1 ; (end of DO-LOOP)
en ; (end of batch)
Start WEB,
Display the image on the screen using option "Image" from the COMMANDS menu,
Select option "Pixel" from the COMMANDS menu,
-- this allows you to pick points (for examples the centers of the
particles you wish to select) and deposit their coordinates in a document
file.
"Pixel" popup menue: you should select "document file option", and
specify the initial number to be used in the first document file name
(default is 0). You should ask for "Show marker" since in that case
the system will put a little circle in each position where you do
a selection. After "accept", each click on the displayed image will result
in the pixel coordinate being deposited in the document file under a
key that keeps count of the particles you select.
After you are done, click the right button and the "Pixel" option of
WEB will terminate.
Now create a SPIDER batch file that will read the coordinates of the
selected particles from the document file and window the data
accordingly into individual files. For example, if you want to create
windowed files of size (100,100) from a document file containing
coordinates of 150 particles, you would use the following sequence:
; B01.RIB Window particles (this is a comment line. Use it to identify
; the name and purpose of this batch file)
DO LB1 I=1,150 ; (run do-loop up to label LB1 from 1 to 150)
UD IC,I,X10,X11 ; (unsave doc "in-core" at key I, put coos into X10, X11)
DOC001 ; (name of document file)
X20=X10-50 ; calculate the top left coordinates from the center coos
X21=X11-50
WI ; (window)
RAW001 ; (name of input file)
SEL00I ; (indexed name of output files)
(100,100) ; (dimensions of output files)
X20,X21 ; (top left coordinates of selected windows)
LB1 ; (end of do-loop)
EN ; (end of batch)
Run SPIDER (in this example with project code "RIB") and start
batch file by entering "@B01" at the "OPERATION:" prompt.
(By using command "MD" with "TR ON",
you can follow the progress of the
batch program on the screen)
CP FROM RAW ; (Copy command)
8 ; (how many bits)
imgin ; (input file name)
512 512 ; (input file dimensions)
1024 ; (skip header bytes)
imgout ; (output file name)