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Imagej / Fiji Short Introduction Into Macro and Plugin Programming ZOI Friday Seminar Introduction GUI Macro Language Plugin Programming Conclusions Resources ImageJ / Fiji Short Introduction into Macro and Plugin Programming ZOI Friday seminar B. Kov´aˇr Department of Image Processing Institute of Information Theory and Automation 21. ´unora 2014 Introduction GUI Macro Language Plugin Programming Conclusions Resources Contents 1 Introduction 2 GUI 3 Macro Language 4 Plugin Programming 5 Conclusions Introduction GUI Macro Language Plugin Programming Conclusions Resources ImageJ: successor of a software from the National Institutes of Health called NIH Image (Pascal-based, Mac only, early 90's) • Public Domain { source code available, • Java based { Win, Mac, Linux, ::: , • Macros & plug-ins, • Huge potential, very active community, • Technical design limitations (15 yrs. old design), • ) ImageJ v2 ImageJ requires a Java runtime installed, can update itself and is shipped with small, generic set of Plugins and Macros... ImageJ basically can do everything, it's just sometimes very hard to find out how... Introduction GUI Macro Language Plugin Programming Conclusions Resources Fiji { FijiisjustImageJ { "ImageJ (batteries included)" • FiJi is an ImageJ distribution intended for Life sciences, • Huge set of Plugins, • Powerful update mechanism, • Extensive documentation, tutorials, etc., • But: shares ImageJ's limitations. Introduction GUI Macro Language Plugin Programming Conclusions Resources ImageJ • Generic image processing framework - unfocused FiJi • Aimed for Life Sciences, • Emphasis on Registration, Segmentation & Volume Data, • Community development effort, • Quality mechanisms for plugins, • Support for more additional languages: Python, Ruby, Scala ..., • Script editor to develop plugins and macros. Introduction GUI Macro Language Plugin Programming Conclusions Resources Contents 1 Introduction 2 GUI 3 Macro Language 4 Plugin Programming 5 Conclusions Introduction GUI Macro Language Plugin Programming Conclusions Resources The main window has three parts: 1 Menu bar 2 Tools 3 Status line • ImageJ & Java version • Memory architecture & current usage • Pixel positions and intensities while hovering on images • Descriptions of toolbar entries • ... Introduction GUI Macro Language Plugin Programming Conclusions Resources Contents 1 Introduction 2 GUI 3 Macro Language 4 Plugin Programming 5 Conclusions Introduction GUI Macro Language Plugin Programming Conclusions Resources Macros can be used to • automate repetitive tasks • document what you did • share common procedures • provide consistency in your analysis • scripting languages (build-in, javascript, python, . ) A Macro is a program that automates a series of ImageJ commands. ImageJ has a dedicated programming language for this. Introduction GUI Macro Language Plugin Programming Conclusions Resources Introduction GUI Macro Language GettingPlugin Programming StartedConclusions Resources The obligatory “Hello World” code: The obligatory "Hello World"code: macro "hello" { print("Hello World!"); } Running this opens a new window “Log” showing the message: → print() is useful for debugging Niko Ehrenfeuchter 6 ImageJ / FiJi workshop Imaging Core Facility Introduction GUI Macro Language Plugin Programming Conclusions Resources Variables &Variables Strings & Strings The most important concept: a named piece of memory! The most• importantName and concept: value a named piece of memory! – Name and value –•ValueValue can can be benumeric numeric or text or text –•CanCan be be used used in arithmetic in arithmetic expressions expressions or string or combinations string combinations – Variables & Strings x = 2; y = 3; Self-references in expressions: result = x * x + y + y; amount = amountVariables * 2; & Strings namecounter = "Bob"; = counter + 1; msg = "Those days are over, " + name; Self-referencesprint(msg); in expressions: Short-handamount for increment:= amount * 2; counter = counter + 1; Niko Ehrenfeuchter 7 counter++; ImageJ / FiJi workshop Imaging Core Facility Short-hand for increment: counter++; Niko Ehrenfeuchter 8 ImageJ / FiJi workshop Imaging Core Facility Niko Ehrenfeuchter 8 ImageJ / FiJi workshop Imaging Core Facility Introduction GUI Macro Language Plugin Programming Conclusions Resources Parameter input by user getNumber() can be usedParameter to request a numericalinput by input user by the user, getString() for text. getNumber() can be used to request a numerical input by the user: macro "input_print_out_calc" { a = getNumber("a?", 10); b = getNumber("b?", 5); c = a*b; print("\\Clear"); print(c); } Note: if no number is entered, no assignment will take place. getString() for text: a = getString("b?", 5); Niko Ehrenfeuchter 9 ImageJ / FiJi workshop Imaging Core Facility Introduction GUI Macro Language Plugin Programming Conclusions Resources Running ImageJ commands Crucial element for macros: run ImageJ commands 1 Almost all commands can be run from macros 2 A few Plugins are not macro-ready Most convenient way to find the corresponding macro commands is to use the built-in Macro Recorder: Introduction GUI Macro Language Plugin Programming Conclusions Resources Batch processing To apply a macro or multiple macro commands to many files, you could add file-accessing and looping commands or use the Batch Process tool. Introduction GUI Macro Language Plugin Programming Conclusions Resources Looping Looping Loops areLoops required are required to iterate to a iterate certain a part certain of our part macro. of our macro. macro "loop1" { msg = getString("message to loop?", "default"); for(i=0; i<5; i+=1) { print(i + ": " + msg); } } Niko Ehrenfeuchter 12 ImageJ / FiJi workshop Imaging Core Facility Introduction GUI Macro Language Plugin Programming Conclusions Resources Stack-processingStack-processing with loops with loops One very powerful application of loops is stack processing since manyOne ImageJvery powerful commands application work of loops just onis stack a single processing slice. since To work many on all slicesImageJ the \nSlices" commands and work \setSlice" just on a single commands slice. To are work used: on all slices the “nSlices” and “setSlice” commands are used: macro "Measure Avg Intensity Stack" { frames=nSlices; run("Set Measurements...", " mean redirect=None decimal=4"); run("Clear Results"); for(i=0; i<frames; i++) { currentslice=i+1; setSlice(currentslice); run("Measure"); } } Niko Ehrenfeuchter 13 ImageJ / FiJi workshop Imaging Core Facility Introduction GUI Macro Language Plugin Programming Conclusions Resources Conditional statements If{else statements can be used to run a certain part only if one or more conditions are met. Note the "=="in the condition (a comparison operator),Conditional this is different from statements a single "="(assignment). Other comparison operators are: < , <= , > , >If–else= , ! =statements can be used to run a certain part only if one or more conditions are met: num = getNumber("Number:", 3); if (num == 3) { print(num + ": default value"); } else { print(num + ": value changed"); } Note the “==” in the condition (a comparison operator), this is different from a single “=” (assignment). Other comparison operators are: < , <= , > , >= , != Niko Ehrenfeuchter 14 ImageJ / FiJi workshop Imaging Core Facility Introduction GUI Macro Language Plugin Programming Conclusions Resources User-defined functions User-defined functions WhenWhen macrosmacros becomebecome moremore sophisticated,sophisticated, it is is very very likely likely that that some parts somewill parts appear will multiple appear times. multiple These times. parts These should parts be shouldplaced bein separate placed in separatefunctions functions to avoid redundancy to avoid redundancy and improve and readability: improve readability: User-defined functions function CheckStack() { if (nSlices==1) { When macros become more sophisticated, it is veryexit("Image likely that is somenot a partsstack"); } will appear multiple times. These parts should be placed in separate macro “threshold check” { } functions to avoid redundancy and improve readability: CheckStack(); CheckThreshold(); function CheckThreshold() { getThreshold(lower, upper); getThreshold(lower, upper); } if ((lower==-1) && (upper==-1)) { function CheckStack() { exit("Must be thresholded"); if (nSlices==1) { } exit("Image is not a stack"); } } macro “threshold check” { } CheckStack(); CheckThreshold(); function CheckThreshold() { getThreshold(lower, upper); getThreshold(lower, upper); Niko Ehrenfeuchter 15 } ImageJ / FiJi workshop if ((lower==-1) && (upper==-1)) { Imaging Core Facility exit("Must be thresholded"); } } Niko Ehrenfeuchter 15 ImageJ / FiJi workshop Imaging Core Facility Return values Introduction GUI Macro Language Plugin Programming Conclusions Resources If your function does some calculation, you need a way to hand back the Return valuesresult to the code that called the function: Return values If your function does some calculation, you need a way to hand If your function does some calculation, youback need the result a way to the to codehand that back called the the function: result to the code that called the function: macro “function add” { function ReturnAdd(n, m) { a = 1; p = n + m; b = 2; return p; result = ReturnAdd(a, b); } print(result); } macro “function add” { function ReturnAdd(n, m) { a = 1; p = n + m; b = 2; return p; result = ReturnAdd(a, b); } print(result); } Niko Ehrenfeuchter 16 ImageJ / FiJi workshop Imaging Core Facility Niko Ehrenfeuchter 16 ImageJ / FiJi workshop Imaging Core Facility Introduction GUI Macro Language Plugin Programming
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