Digital Micrograph Scripting

Digital Micrograph Scripting 

Vincent Richard 

GATAN France, Division de Roper Scientific. vrichard@gatan.com 

1 

Journées du Cercle des Microscopistes JEOL Physique, 1 et 2 décembre 2009

DM Scripting – WHY ? – AND WHY NOT ? 


Where to go from here? 

The help-documentation of DM is a the starting point and the only “official” documentation. It is 

listing most of the available commands. (You launch the documentation by pressing F1 within DM.) 

•The DM script database hosted at HTTP://www.felmi-zfe.at has lots of scripts both as simple 

examples and as useful tools shared by other DM users. An exhaustive list of DM script functions 

and procedures can be found in this website 

• At HTTP://lists.asu.edu/archives/dmsug.html you can sign up a mailing list about DM scripting. 

Please also check the archives of the list prior to sending your questions. The answer might already 

be there! 


Script examples 

Image Filters Diffraction / FFT Other examples 

Tilt series 


Install scripts in DM 

Use the menu File…/ Install Script… 

Menu 

Librarie 

Plug in 

The scripts are now stored in the preference files of 

DM (DigitalMicrographCF.8.prf) , could be launched 

from custom menu. 

The scripts are now stored in the preference files of 

DM (DigitalMicrographCF.8.prf) and are 

automatically loaded on launching DM. 

To deinstall scripts or functions, use the menu 

File…/Remove Script… , then select the library you 

want to deinstall and press “Remove”. 


Compile scripts in Plug-In with Package Creator 

1) Launch Package Creator script 

2) Regroup the scripts in one directory 

3) Select them in Package creator windows 

4) Create the Plug-In : .gtk 

5) It will automatically create and save in : 

C:\ProgramFiles\Gatan\DigitalMicrograph\ 

PlugIns 

6) The Command will be display in the 

Tomography menu 



Scripting Window 


First scripting window – GMS 1.8.0 


First script 

• While a script is running, no other tasks can be performed in DM. The mouse cursor becomes an hourglass. 

After the script finishes, the mouse cursor becomes an arrow again. 

•A running script can be interrupted by pressing the keys Ctrl and Break simultaneously. 

• The following script command prints output to the results window: result(string) where string can be a 

variable or any text within quotes, e.g.: result(“Hello word!\n”) prints to the results window: Hello world! 

The two characters \n add a line break. 

Write in the results window : 

// This is the first line of my script! Just a comment. 

// The purpose of the script is to demonstrate the RESULT command. 

result("My name is Vincent Richard") 

result("\n\n\n\n") 

result("And who are you?") // I will always comment my scripts! 


Images as number arrays 


Directly addressing images 


Directly addressing images areas 


Useful commands for image evaluation 


Script example: pixel by pixel operation 

Calculate the relative thickness map t/λ by script from 

unfiltered and Zero loss images : 


tert () – a powerful command 

This script creates a binary mask from image B 

Each point, where < 10000 counts, becomes 1, 

each other point 0. 

ShowImage (tert( t( B < 10000 , 0 , 1 )) 


warp () – another powerful command 


Variables (numbers and strings) 


A third type of variables : images type 


Image related commands 


Condition in script 


WHILE loops 


FOR Loops 


Writing a function 


Functions: arguments and optional arguments 


Functions: image arguments 


How to create a customized dialog 

Example : View / Focus / acquire dialog box 

Window size and position 

Name of the Button 

Name of the function 

Buttons positions 


How to perform a task on all open images 


How to open/save a file 


“ChooseMenuItem command” 

This command allows you to launch a functions or a script present in Digital Micrograph menu. 

Syntaxe : ChooseMenuitem(“menu“ ,“submenu“ ,“function") 

Example : this following function will acquire a live image in view mode 

= 


Hardware control by scripts 

Microscope control ->setup -> test : Common microscope functions: 


Hardware control by scripts 

List of universal commands (works for any TEM): 

> EMGetMagnification( number mag ) 

> EMImageShift( dac, dac ) 

> EMBeamShift( dac, dac ) 

> EMChangeFocus( dac ) 

> EMChangeTilt( dac,dac ) 

> EMGetBrightness() 

> EMSetBrightness( dac ) 

> EMGetSpotSize() 

> EMSetSpotSize( dac ) 

> EMGetStageX() 

> EMSetStageX( um ) 

> EMGetStageY() 

> EMSetStageY( um ) 

> EMGetStageZ() 

> EMSetStageZ( um ) 

> EMGetStageAlpha() 

> EMSetStageAlpha( deg ) 

Example : function to set alpha stage to 30° 


JEOL COM microscope control by scripts 

MICROSCOPES DE TYPE 2100/1400/2200 use the universal commands : 

EMGet(or)SetCommand (dac,dac) 

Or 

Specific JEOL commands can be used like screen commands 

JEOLCOM_SetScreen( 0 ) set fluorescent to 0° 

JEOLCOM_SetScreen(1) set fluorescent to 7° 

JEOLCOM_SetScreen( 2 ) 

set fluorescent to 90° 

Or for JEOL 2200FS filter : Jeolcom_getslitwith(). Script example (deflector change button) : 


Serial JEOL microscope control by scripts 

JEM 2010 /2011/3010/3011/2010F/1010/1011/1200EXII/2000EX/FXI 

Jeolcommand is the Digital Micrograph command to sent an order to the 

microscope : 

Reply=jeolcommand(« command », »ok ») 

Serial commands examples : 

gmove (x,y) 

move x/y stage 

Objf x OL value change 

gtilt (alpha,beta) move alpha/beta stage 

Bright x CL3 value (brightness) change 

gmovez (z) 

move z 

Dfc n,x,y 

deflector n change of x,y values 

Htset 

Change HT 

Gun 1 n=0 

SCRSET 2 

Screen up 

Gun 2 n=1 

SCRSET 0 

Screen down 

Cla 1 n=5 

SPOTDN 

Spot size down 

Cla 2 n=6 

. 

Pla n=11 

All microscope commands available are listed in the JEOL microscope manual. 


JEOL Serial microscope script examples 

By Michel Ribardière

Digital Micrograph Scripting

You also want an ePaper? Increase the reach of your titles

Delete template?

Save as template?