Digital Micrograph Scripting

Transcription

1 Digital Micrograph Scripting Vincent Richard GATAN France, Division de Roper Scientific. 1

2 DM Scripting WHY? AND WHY NOT?

3 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 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 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!

4 Script examples Image Filters Diffraction / FFT Other examples Tilt series

5 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.

6 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

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8 Scripting Window

9 First scripting window GMS 1.8.0

10 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!

11 Images as number arrays

12 Directly addressing images

13 Directly addressing images areas

14 Useful commands for image evaluation

15 Script example: pixel by pixel operation Calculate the relative thickness map t/λ by script from unfiltered and Zero loss images :

16 tert () a powerful command This script creates a binary mask from image B Each point, where < counts, becomes 1, each other point 0. ShowImage (tert( t( B < 10000, 0, 1 ))

17 warp () another powerful command

18 Variables (numbers and strings)

19 A third type of variables : images type

20 Image related commands

21 Condition in script

22 WHILE loops

23 FOR Loops

24 Writing a function

25 Functions: arguments and optional arguments

26 Functions: image arguments

27 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

28 How to perform a task on all open images

29 How to open/save a file

30 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 =

31 Hardware control by scripts Microscope control ->setup -> test : Common microscope functions:

32 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

33 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) :

34 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.

35 JEOL Serial microscope script examples By Michel Ribardière