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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,4 @@ | ||
| #!/bin/sh | ||
| /*/. 2>/dev/null; exec "$(dirname "$0")"/../fiji "$0" "$@" # exec with fiji */ | ||
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| fiji.Headless.main(new String[0]); |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,56 @@ | ||
| // This macro imports a saved ImageJ results table, | ||
| // or any tab or comma-separated data file. | ||
|
|
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| lineseparator = "\n"; | ||
| cellseparator = ",\t"; | ||
|
|
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| // copies the whole table to an array of lines | ||
| lines=split(File.openAsString(""), lineseparator); | ||
| if (lines.length==0) return; | ||
| path = File.directory + File.name; | ||
|
|
||
| // get the columns headers | ||
| labels=split(lines[0], cellseparator); | ||
| if (labels.length==1) | ||
| exit("This is not a tab or comma delimited text file."); | ||
| if (labels[0]==" ") | ||
| k=1; // it is an ImageJ Results table, skip first column | ||
| else | ||
| k=0; // it is not a Results table, load all columns | ||
|
|
||
| // is this a Results table? | ||
| if (k==1 || lines.length<2) | ||
| {importResults(); exit;} | ||
| items = split(lines[1]); | ||
| nonNumeric = false; | ||
| for (i=0; i<items.length; i++) | ||
| if (isNaN(parseFloat(items[i]))) nonNumeric=true; | ||
| if (nonNumeric) | ||
| importTable(); | ||
| else | ||
| importResults(); | ||
| exit; | ||
|
|
||
| function importResults() { | ||
| for (j=k; j<labels.length; j++) | ||
| setResult(labels[j],0,0); | ||
| run("Clear Results"); | ||
| if (k==1) | ||
| call("ij.plugin.filter.Analyzer.setDefaultHeadings"); | ||
| for (i=1; i<lines.length; i++) { | ||
| items=split(lines[i], cellseparator); | ||
| for (j=k; j<items.length; j++) | ||
| setResult(labels[j],i-1,items[j]); | ||
| } | ||
| updateResults(); | ||
| } | ||
|
|
||
| function importTable() { | ||
| name = "["+File.name+"]"; | ||
| if (!isOpen(File.name)) | ||
| run("New... ", "name="+name+" type=Table"); | ||
| f = name; | ||
| print(f, "\\Headings:"+lines[0]); | ||
| for (i=1; i<lines.length; i++) | ||
| print(f, lines[i]); | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,260 @@ | ||
| // "StartupMacros" | ||
| // The macros and macro tools in this file ("StartupMacros.txt") are | ||
| // automatically installed in the Plugins>Macros submenu and | ||
| // in the tool bar when ImageJ starts up. | ||
|
|
||
| // About the drawing tools. | ||
| // | ||
| // This is a set of drawing tools similar to the pencil, paintbrush, | ||
| // eraser and flood fill (paint bucket) tools in NIH Image. The | ||
| // pencil and paintbrush draw in the current foreground color | ||
| // and the eraser draws in the current background color. The | ||
| // flood fill tool fills the selected area using the foreground color. | ||
| // Hold down the alt key to have the pencil and paintbrush draw | ||
| // using the background color or to have the flood fill tool fill | ||
| // using the background color. Set the foreground and background | ||
| // colors by double-clicking on the flood fill tool or on the eye | ||
| // dropper tool. Double-click on the pencil, paintbrush or eraser | ||
| // tool to set the drawing width for that tool. | ||
| // | ||
| // Icons contributed by Tony Collins. | ||
|
|
||
| // Global variables | ||
| var pencilWidth=1, eraserWidth=10, leftClick=16, alt=8; | ||
| var brushWidth = 10; //call("ij.Prefs.get", "startup.brush", "10"); | ||
| var floodType = "8-connected"; //call("ij.Prefs.get", "startup.flood", "8-connected"); | ||
|
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||
| // The macro named "AutoRunAndHide" runs when ImageJ starts | ||
| // and the file containing it is not displayed when ImageJ opens it. | ||
|
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| // macro "AutoRunAndHide" {} | ||
|
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||
| function UseHEFT { | ||
| requires("1.38f"); | ||
| state = call("ij.io.Opener.getOpenUsingPlugins"); | ||
| if (state=="false") { | ||
| setOption("OpenUsingPlugins", true); | ||
| showStatus("TRUE (images opened by HandleExtraFileTypes)"); | ||
| } else { | ||
| setOption("OpenUsingPlugins", false); | ||
| showStatus("FALSE (images opened by ImageJ)"); | ||
| } | ||
| } | ||
|
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| UseHEFT(); | ||
|
|
||
| // The macro named "AutoRun" runs when ImageJ starts. | ||
|
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| //macro "AutoRun" {} | ||
|
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|
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| var pmCmds = newMenu("Popup Menu", | ||
| newArray("Help...", "Rename...", "Duplicate...", "Original Scale", | ||
| "Paste Control...", "-", "Record...", "Capture Screen ", "Monitor Memory...", | ||
| "Find Commands...", "Control Panel...", "Startup Macros...", "Search...")); | ||
|
|
||
| macro "Popup Menu" { | ||
| cmd = getArgument(); | ||
| if (cmd=="Help...") | ||
| showMessage("About Popup Menu", | ||
| "To customize this menu, edit the line that starts with\n\"var pmCmds\" in ImageJ/macros/StartupMacros.txt."); | ||
| else | ||
| run(cmd); | ||
| } | ||
|
|
||
| macro "Abort Macro or Plugin (or press Esc key) Action Tool - CbooP51b1f5fbbf5f1b15510T5c10X" { | ||
| setKeyDown("Esc"); | ||
| } | ||
|
|
||
| var xx = requires138b(); // check version at install | ||
| function requires138b() {requires("1.38b"); return 0; } | ||
|
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||
| var dCmds = newMenu("Developer Menu Tool", | ||
| newArray("ImageJ Website","News", "Documentation", "ImageJ Wiki", "Resources", "Macro Language", "Macros", | ||
| "Macro Functions", "Startup Macros...", "Plugins", "Source Code", "Mailing List Archives", "-", "Record...", | ||
| "Capture Screen ", "Monitor Memory...", "List Commands...", "Control Panel...", "Search...", "Debug Mode")); | ||
|
|
||
| macro "Developer Menu Tool - C037T0b11DT7b09eTcb09v" { | ||
| cmd = getArgument(); | ||
| if (cmd=="ImageJ Website") | ||
| run("URL...", "url=http://rsbweb.nih.gov/ij/"); | ||
| else if (cmd=="News") | ||
| run("URL...", "url=http://rsbweb.nih.gov/ij/notes.html"); | ||
| else if (cmd=="Documentation") | ||
| run("URL...", "url=http://rsbweb.nih.gov/ij/docs/"); | ||
| else if (cmd=="ImageJ Wiki") | ||
| run("URL...", "url=http://imagejdocu.tudor.lu/imagej-documentation-wiki/"); | ||
| else if (cmd=="Resources") | ||
| run("URL...", "url=http://rsbweb.nih.gov/ij/developer/"); | ||
| else if (cmd=="Macro Language") | ||
| run("URL...", "url=http://rsbweb.nih.gov/ij/developer/macro/macros.html"); | ||
| else if (cmd=="Macros") | ||
| run("URL...", "url=http://rsbweb.nih.gov/ij/macros/"); | ||
| else if (cmd=="Macro Functions") | ||
| run("URL...", "url=http://rsbweb.nih.gov/ij/developer/macro/functions.html"); | ||
| else if (cmd=="Plugins") | ||
| run("URL...", "url=http://rsbweb.nih.gov/ij/plugins/"); | ||
| else if (cmd=="Source Code") | ||
| run("URL...", "url=http://rsbweb.nih.gov/ij/developer/source/"); | ||
| else if (cmd=="Mailing List Archives") | ||
| run("URL...", "url=https://list.nih.gov/archives/imagej.html"); | ||
| else if (cmd=="Debug Mode") | ||
| setOption("DebugMode", true); | ||
| else if (cmd!="-") | ||
| run(cmd); | ||
| } | ||
|
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||
| var sCmds = newMenu("Stacks Menu Tool", | ||
| newArray("Add Slice", "Delete Slice", "Next Slice [>]", "Previous Slice [<]", "Set Slice...", "-", | ||
| "Convert Images to Stack", "Convert Stack to Images", "Make Montage...", "Reslice [/]...", "Z Project...", | ||
| "3D Project...", "Plot Z-axis Profile", "-", "Start Animation", "Stop Animation", "Animation Options...", | ||
| "-", "MRI Stack (528K)")); | ||
| macro "Stacks Menu Tool - C037T0b11ST8b09tTcb09k" { | ||
| cmd = getArgument(); | ||
| if (cmd!="-") run(cmd); | ||
| } | ||
|
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||
| var luts = getLutMenu(); | ||
| var lCmds = newMenu("LUT Menu Tool", luts); | ||
| macro "LUT Menu Tool - C037T0b11LT6b09UTcb09T" { | ||
| cmd = getArgument(); | ||
| if (cmd!="-") run(cmd); | ||
| } | ||
| function getLutMenu() { | ||
| list = getLutList(); | ||
| menu = newArray(16+list.length); | ||
| menu[0] = "Invert LUT"; menu[1] = "Apply LUT"; menu[2] = "-"; | ||
| menu[3] = "Fire"; menu[4] = "Grays"; menu[5] = "Ice"; | ||
| menu[6] = "Spectrum"; menu[7] = "3-3-2 RGB"; menu[8] = "Red"; | ||
| menu[9] = "Green"; menu[10] = "Blue"; menu[11] = "Cyan"; | ||
| menu[12] = "Magenta"; menu[13] = "Yellow"; menu[14] = "Red/Green"; | ||
| menu[15] = "-"; | ||
| for (i=0; i<list.length; i++) | ||
| menu[i+16] = list[i]; | ||
| return menu; | ||
| } | ||
|
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||
| function getLutList() { | ||
| lutdir = getDirectory("luts"); | ||
| list = newArray("No LUTs in /ImageJ/luts"); | ||
| if (!File.exists(lutdir)) | ||
| return list; | ||
| rawlist = getFileList(lutdir); | ||
| if (rawlist.length==0) | ||
| return list; | ||
| count = 0; | ||
| for (i=0; i< rawlist.length; i++) | ||
| if (endsWith(rawlist[i], ".lut")) count++; | ||
| if (count==0) | ||
| return list; | ||
| list = newArray(count); | ||
| index = 0; | ||
| for (i=0; i< rawlist.length; i++) { | ||
| if (endsWith(rawlist[i], ".lut")) | ||
| list[index++] = substring(rawlist[i], 0, lengthOf(rawlist[i])-4); | ||
| } | ||
| return list; | ||
| } | ||
|
|
||
| macro "Pencil Tool - C037L494fL4990L90b0Lc1c3L82a4Lb58bL7c4fDb4L5a5dL6b6cD7b" { | ||
| getCursorLoc(x, y, z, flags); | ||
| if (flags&alt!=0) | ||
| setColorToBackgound(); | ||
| draw(pencilWidth); | ||
| } | ||
|
|
||
| macro "Paintbrush Tool - C037La077Ld098L6859L4a2fL2f4fL3f99L5e9bL9b98L6888L5e8dL888c" { | ||
| getCursorLoc(x, y, z, flags); | ||
| if (flags&alt!=0) | ||
| setColorToBackgound(); | ||
| draw(brushWidth); | ||
| } | ||
|
|
||
| macro "Flood Fill Tool -C037B21P085373b75d0L4d1aL3135L4050L6166D57D77D68La5adLb6bcD09D94" { | ||
| requires("1.34j"); | ||
| setupUndo(); | ||
| getCursorLoc(x, y, z, flags); | ||
| if (flags&alt!=0) setColorToBackgound(); | ||
| floodFill(x, y, floodType); | ||
| } | ||
|
|
||
| function draw(width) { | ||
| requires("1.32g"); | ||
| setupUndo(); | ||
| getCursorLoc(x, y, z, flags); | ||
| setLineWidth(width); | ||
| moveTo(x,y); | ||
| x2=-1; y2=-1; | ||
| while (true) { | ||
| getCursorLoc(x, y, z, flags); | ||
| if (flags&leftClick==0) exit(); | ||
| if (x!=x2 || y!=y2) | ||
| lineTo(x,y); | ||
| x2=x; y2 =y; | ||
| wait(10); | ||
| } | ||
| } | ||
|
|
||
| function setColorToBackgound() { | ||
| savep = getPixel(0, 0); | ||
| makeRectangle(0, 0, 1, 1); | ||
| run("Clear"); | ||
| background = getPixel(0, 0); | ||
| run("Select None"); | ||
| setPixel(0, 0, savep); | ||
| setColor(background); | ||
| } | ||
|
|
||
| // Runs when the user double-clicks on the pencil tool icon | ||
| macro 'Pencil Tool Options...' { | ||
| pencilWidth = getNumber("Pencil Width (pixels):", pencilWidth); | ||
| } | ||
|
|
||
| // Runs when the user double-clicks on the paint brush tool icon | ||
| macro 'Paintbrush Tool Options...' { | ||
| brushWidth = getNumber("Brush Width (pixels):", brushWidth); | ||
| call("ij.Prefs.set", "startup.brush", brushWidth); | ||
| } | ||
|
|
||
| // Runs when the user double-clicks on the flood fill tool icon | ||
| macro 'Flood Fill Tool Options...' { | ||
| Dialog.create("Flood Fill Tool"); | ||
| Dialog.addChoice("Flood Type:", newArray("4-connected", "8-connected"), floodType); | ||
| Dialog.show(); | ||
| floodType = Dialog.getChoice(); | ||
| call("ij.Prefs.set", "startup.flood", floodType); | ||
| } | ||
|
|
||
| macro "Set Drawing Color..."{ | ||
| run("Color Picker..."); | ||
| } | ||
|
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||
| macro "-" {} //menu divider | ||
|
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||
| macro "About Startup Macros..." { | ||
| title = "About Startup Macros"; | ||
| id = "[" + title + "]"; | ||
| if (isOpen(title)) | ||
| print(id, "\\Update"); | ||
| else | ||
| run("Text Window...", "name=" + id + " width=65 height=8"); | ||
| print(id, "Macros, such as this one, contained in a file named 'StartupMacros.txt',\n" | ||
| + "located in the 'macros' folder inside the Fiji folder, are automatically\n" | ||
| + "installed in the Plugins>Macros menu when Fiji starts.\n" | ||
| + "\n" | ||
| + "More information is available at:\n" | ||
| + "<http://rsb.info.nih.gov/ij/developer/macro/macros.html>"); | ||
| } | ||
|
|
||
| macro "Save As JPEG... [j]" { | ||
| quality = call("ij.plugin.JpegWriter.getQuality"); | ||
| quality = getNumber("JPEG quality (0-100):", quality); | ||
| run("Input/Output...", "jpeg="+quality); | ||
| saveAs("Jpeg"); | ||
| } | ||
|
|
||
| macro "Save Inverted FITS" { | ||
| run("Flip Vertically"); | ||
| run("FITS...", ""); | ||
| run("Flip Vertically"); | ||
| } |
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