The Biozentrum Micrograph Data Processing Program

MENU of Commands

Command Description ----------------------------------------------------------- AA -- angular average AB -- angular back interpolation AC -- average contour AD -- angular addition AF -- angular forward Fourier transform AI -- angular interpolation AK -- projection stack correlate AM -- angular modulus AO -- alter output/input files AR -- angular reverse Fourier transform AS -- arbitary section AT -- attach a buffer file AU -- autocorrelation AV -- average adjacent pixels BD -- binary dump BF -- Bessel forward transform: D(Z,k) transform BG -- background processing BK -- Brookhaven magnetic tape read program BP -- backprojection reconstruction BR -- Bessel reverse transform: D(Z,k) transform BT -- build transform CF -- compressed forward Fourier transform CG -- generate CGM files CM -- contour manipulation CN -- change number CO -- contour output CR -- center regression CS -- center search CV -- calculate volume and area CW -- cosine wave (model wave) CY -- cylindrical section DC -- `discretize' array DK -- deconvolve 3-D array DM -- modify display colour table DO -- digital output numerically DP -- display on printer DS -- de-shadow 3-D image DT -- detach a buffer file DV -- display visually DY -- dyad axis symmetrization DZ -- digitize an image using the Eikonix ED -- edit array EI -- enhance image element EL -- extract layerline EO -- enter order ER -- erase display screen ES -- extract section ET -- extract tile FC -- filter center FD -- float down (helices) FF -- forward Fourier transform FH -- filter helix FI -- format interchange FL -- filter FR -- reverse Fourier transform FS -- find statistics FT -- float array F3 -- 3-D forward Fourier transform GA -- generate array (model image) GB -- grab an image from a TV screen (Gould only). GC -- generate coefficients GF -- general filtering program GH -- generate helix (model image) GI -- general interpolation GN -- generate noise (model image) GP -- generate projection (model image) GR -- compute gradient of image GS -- generate scan G3 -- generate 3-d array from a stack HE -- requests HELP from MDPP HI -- histogram equalize HR -- helical reconstruction programs IB -- input buffer IC -- incore IE -- if error switch IL -- interpolate layerline IN -- integrate IO -- input/output IS -- integrate surface IT -- input tape IV -- invert image IX -- input external environment JF -- jump to flag JI -- correct image `jitter' KA -- correspondance analysis: data preparation KN -- contour manipulation KP -- pick-point option of correspondance analysis KR -- alter array dimensions KZ -- alter job-step indicator LB -- library of `.BMD' files LC -- layerline correlation LG -- illuminate (light) a surface LI -- linear interpolation (computer "Markham") LP -- layerline plot/regression LR -- layerline transform regeneration LS -- layerline rescale MB -- manipulate binary image MC -- move center in polar of Fourier transform MD -- modulus MM -- maximum and minimum MS -- merge scan MT -- message to terminal (background only) MV -- play a movie loop MW -- make Wiener filter NR -- normalize OB -- output buffer OD -- on disc OO -- output order PA -- patch PD -- positive definite PF -- pad-float PH -- output to tape for photowrite PJ -- project 2D image onto a line with vernier sampling PK -- pack PL -- plotter package PO -- printer order PP -- pre-process(complex image rescaling) PR -- prepare for Fourier-Bessel transform PS -- plot scan PZ -- pause for terminal input P3 -- pack a 2-d array into a 3-d array PT -- protect file (nonfunctional?, but should bring back!) QC -- sequence gel QS -- list the contents of a stack RD -- read input file RE -- return to foreground operation RF -- radial filter RH -- read header RN -- rename (subtitle) RO -- rotate image RS -- restore RV -- replace value RW -- Read/Write Apollo transfer file R3 -- reverse 3-D Fourier transform SA -- stack add SC -- search and correlate projections SD -- compute a surface display from a 3-d image SE -- symmetrize and extend projections SF -- surface relief reconstruction SG -- subtract gradient SI -- superimpose arrays SL -- slice density levels of pixels SM -- smear SP -- spool output file to printer SQ -- alter FFT indexing (skew diffraction pattern) SO -- smooth SR -- stack preparation ('stack ready') SS -- sub-array display ST -- statistics SU -- sum two pictures SV -- save image file SX -- sort array by a row SW -- spawn a line to the CLI SZ -- Generate Sixel output from an image TA -- transfer amplitudes TC -- translate center TF -- transfer function TM -- trim TP -- total power TR -- terminate MDPP TS -- transfer to curvilinear coordinates TY -- type TZ -- program test-bed command (user's own test function) UA -- unit-cell average UB -- unbend lattice UP -- unpack VA -- Vectorize array VD -- Visual display tool VF -- verify file title VL -- verify layerline VP -- video project VS -- vertical section VW -- view moving zoomed window of image or FT WA -- warp image WF -- bring window to foreground XC -- cross-correlation XK -- external command XL -- exact layerline extraction XM -- change MDPP default setup parameters XP -- execute procedure XX -- external exchange ZI -- 'zap' image onto the screen ZU -- zero unit ZW -- sent MDPP to sleep for specified time ZZ -- job step reentry point after error

** -- comment: written to output file ++ -- comment: ignored anywhere on input +@ -- confirm input +* -- screen input re-direct: text following is a default line. +- -- comment: output to screen only

GENERAL

These are special commands to request specific services from MDPP or the CLI for the machine you are using.

Control Characters for VMS SMG$ UI:


<Cntl-B>	--	Pop up the Broadcast window. 
<Cntl-C>	--	Terminate ongoing process (after all input is complete)
<Cntl-E>	--	Expand the image at the cursor 
<Cntl-G>	--	Toggel the use of the graphics mouse 
<Cntl-P>	--	Pause for 4 seconds 
<Cntl-V>	--	View the work window 
<Cntl-W>	--	Re-paint the screen 
<Cntl-X>	--	Break-out Spawn 
<Cntl-Y>	--	Force job termination (neatly!)  
<Cntl-Z>	--	Abandon command (at a request for parameter input)

Note:: These command work with the screen management options of MDP. Only <Cntl-C> and <Cntl-Z> work in line-mode: in line mode <Cntl-Y> causes MDP to abort rather than to shut down neatly.

Control Characters for the simple UI (UNIX only):


<Cntl-\> 	-	Terminate ongoing process (after all input is complete)
<Cntl-D> 	-	Abandon command (at a request for parameter input)
<Cntl-C>	-	Force job termination (neatly!)

Control Characters for the simple UI (VMS only):


<Cntl-C> 	-	Terminate ongoing process (after all input is complete)
<Cntl-Z> 	-	Abandon command (at a request for parameter input)
<Cntl-Y>	-	Force job termination (neatly!)

Control Commands:


?	--	Gets HELP for that command segment (if available)	 
??	--	Gets HELP for that command.	
HELP	--	Requests HELP on a command	
MENU	--	Prints this file	
PROC	--	invokes the procedure driver (same as `XP')
XXXX	--	"XXXX" is any command, three letters or more, entered 
                at the terminal (e.g. DIR <string>, PUR <string>, DEL <string> etc).
                All such lines are SPAWNED to the CLI for processing.

UTILITIES

These are standalone programs which are run to perform useful operations for the enlighted user. HELP is available for all of them.


KERMIT	  --	A terminal emulator and file transfer program.  
LATTICE	  --	Program to assist in the indexation of plane lattices 
LZCMP	  --	Compresses files: useful for on-line achiving of images.  
LZDCM	  --	Decompresses a file compressed with LZCMP
SCREW	  --	Program to aid indexation of helices.
TAPEDIT	  --	Copies tape-to-tape on two drives selecting files to copy
TAPEREAD  --	Reads an IBM tape to disc
TAPESPC	  --	Positions a tape after a given number of files.
TAPEWRITE --	Writes an unlabled tape in IBM format from files specified.
TPO	  --	Scans a tape and lists the file characteristics and errors.

MENU of Commands

GENERAL

Control Commands:

UTILITIES

OTHER DOCUMENTATION