Fix mangled imagej.nih.gov links

My search-and-replace was too eager; there are
places where '/ij' should not have been changed.

Author: ctrueden

_pages/learn/user-guides.md

@@ -7,7 +7,7 @@ nav-links: true
 <div style="display: table">
 
 <div style="text-align:center;" markdown="1">
-<a href="https://imagej.nih.govhttps://imagej.nih.gov/ij/docs/guide"><img src="/media/books/imagej-user-guide.jpg" width="247" height="350"></a>\\
+<a href="https://imagej.nih.gov/ij/docs/guide"><img src="/media/books/imagej-user-guide.jpg" width="247" height="350"></a>\\
 The [ImageJ User Guide](https://imagej.nih.gov/ij/docs/guide/) provides a
 thorough description of ImageJ's built-in functions.
 </div>

_pages/plugins/bunwarpj.md

@@ -315,7 +315,7 @@ Notice here that the input and output file names must include the path, since th
 
 For instance, to see the program help we can call the program from the command line (where $IJDIR is the directory where ImageJ is installed) like this in Linux:
 
-`java -Xmx512m -cp $IJDIRhttps://imagej.nih.gov/ij.jar:$IJDIR/plugins/bUnwarpJ_.jar bunwarpj.bUnwarpJ_ -help`
+`java -Xmx512m -cp $IJDIR/ij.jar:$IJDIR/plugins/bUnwarpJ_.jar bunwarpj.bUnwarpJ_ -help`
 
 For the rest of the options, follow the help instructions.
 

_pages/plugins/miji.md

@@ -45,7 +45,7 @@ run("Command", "key1=7 key2 key3=[C:\\Documents and Settings\\Fiji\\Test.png]");
 
 The first parameter to the `run()` method is the menu item's label which identifies the plugin to run (in this example, the label would read: *Command*).
 
-The second parameter is a String containing values the user specified via an [ImageJ dialog](http://jenkins.imagej.net/job/ImageJ1-javadoc/javadochttps://imagej.nih.gov/ij/gui/GenericDialog.html). Every value is identified by a label, and except for checkboxes (such as `key2` in the example above), they have values. If the values contain spaces, you need to enclose the value in square brackets (such as `key3` in the example above).
+The second parameter is a String containing values the user specified via an [ImageJ dialog](http://jenkins.imagej.net/job/ImageJ1-javadoc/javadoc/ij/gui/GenericDialog.html). Every value is identified by a label, and except for checkboxes (such as `key2` in the example above), they have values. If the values contain spaces, you need to enclose the value in square brackets (such as `key3` in the example above).
 
 Note that the backslash is a so-called *escape character*, i.e. it can be used to insert special characters such as line breaks or tabs. To insert a plain backslash, it has to be repeated therefore (as in the `key3` value: `C:\\Documents and Settings` becomes `C:\\\\Documents and Settings`).
 

_pages/plugins/morpholibj.md

@@ -697,15 +697,15 @@ At the end of the script a dialog is shown to smooth the surfaces at will. Each
 
 ## Documentation
 
-Each [released version of MorphoLibJ](https://github.comhttps://imagej.nih.gov/ijpb/MorphoLibJ/releases) comes with a [User Manual in PDF format](https://github.comhttps://imagej.nih.gov/ijpb/MorphoLibJ/releases/download/v1.4.0/MorphoLibJ-manual-v1.4.0.pdf).
+Each [released version of MorphoLibJ](https://github.com/ijpb/MorphoLibJ/releases) comes with a [User Manual in PDF format](https://github.com/ijpb/MorphoLibJ/releases/download/v1.4.0/MorphoLibJ-manual-v1.4.0.pdf).
 
-The main source code directory is on GitHub under [src/main/java/inrahttps://imagej.nih.gov/ijpb](http://github.comhttps://imagej.nih.gov/ijpb/MorphoLibJ/tree/master/src/main/java/inrahttps://imagej.nih.gov/ijpb).
+The main source code directory is on GitHub under [src/main/java/inra/ijpb](http://github.com/ijpb/MorphoLibJ/tree/master/src/main/java/inra/ijpb).
 
-You can browse the [javadoc](http:/https://imagej.nih.gov/ijpb.github.io/MorphoLibJ/javadoc/) for more information about its API.
+You can browse the [javadoc](http://ijpb.github.io/MorphoLibJ/javadoc/) for more information about its API.
 
 ## Installation
 
--   In [ImageJ 1.x](/software/imagej1), download the [latest released jar](https://github.comhttps://imagej.nih.gov/ijpb/MorphoLibJ/releases) into the *plugins* folder.
+-   In [ImageJ 1.x](/software/imagej1), download the [latest released jar](https://github.com/ijpb/MorphoLibJ/releases) into the *plugins* folder.
 -   In [ImageJ2](/software/imagej2) (including [Fiji](/software/fiji)), you just need to [ add](/update-sites/following#add-update-sites) the IJPB-plugins site to your list of update sites:
     1.  Select {% include bc path='Help | Update...'%} from the menu to start the [updater](/plugins/updater).
     2.  Click on *Manage update sites*. This brings up a dialog where you can activate additional update sites.

_pages/plugins/multi-stack-montage.md

@@ -70,7 +70,7 @@ You can have a look at this minimal plugin that runs StackMontage.
         public void run(String arg) {
 
             // Make some nice images
-            ImagePlus imp = IJ.openImage("https://imagej.net/ij/images/confocal-series.zip");
+            ImagePlus imp = IJ.openImage("https://imagej.nih.gov/ij/images/confocal-series.zip");
             String imageName = imp.getTitle();
 
             // Recolor them

_pages/plugins/nanotrackj.md

@@ -12,7 +12,7 @@ categories: [Uncategorized]
 {% capture maintainer%}
 {% include person id='thorstenwagner' %},
 {% endcapture %}
-{% include info-box software='ImageJFiji' name='NanoTrackJ' author=author maintainer=maintainer filename='nanotrackj.jar [\[1](https://github.com/thorstenwagnerhttps://imagej.nih.gov/ij-nanotrackj/releases/latest) \]' source='Github [\[2](https://github.com/thorstenwagnerhttps://imagej.nih.gov/ij-nanotrackj) \]' latest-version='v1.0.3 (22 Feb 2016)' status='active' %}
+{% include info-box software='ImageJFiji' name='NanoTrackJ' author=author maintainer=maintainer filename='nanotrackj.jar [\[1](https://github.com/thorstenwagner/ij-nanotrackj/releases/latest) \]' source='Github [\[2](https://github.com/thorstenwagner/ij-nanotrackj) \]' latest-version='v1.0.3 (22 Feb 2016)' status='active' %}
 
 ## General
 
@@ -78,7 +78,7 @@ If the plugin finishes analyzing it opens histogram plots for the size distribut
 
 ## Simulation
 
-If you like to check NanoTrackJ by Monte-Carlo simulation, you may use our [simulation macros](https://github.com/thorstenwagnerhttps://imagej.nih.gov/ij-nanotrackj/tree/master/scripts/simulation).
+If you like to check NanoTrackJ by Monte-Carlo simulation, you may use our [simulation macros](https://github.com/thorstenwagner/ij-nanotrackj/tree/master/scripts/simulation).
 
 PartSimDC.ijm: This macro allows you to simulate particle by specifying their diffusion coefficient.
 

_pages/plugins/robust-clump-splitting.md

@@ -12,7 +12,7 @@ categories: [Uncategorized]
 {% capture maintainer%}
 {% include person id='LouiseBloch' %}, {% include person id='thorstenwagner' %}
 {% endcapture %}
-{% include info-box software='Fiji' name='Robust Clump Splitting' author=author maintainer=maintainer filename='ij\_robust\_split.jar \[\]' source='Github https://github.com/thorstenwagnerhttps://imagej.nih.gov/ij-robust-split' latest-version='v1.0.0 (04 Sep 2016)' status='active' %}
+{% include info-box software='Fiji' name='Robust Clump Splitting' author=author maintainer=maintainer filename='ij\_robust\_split.jar \[\]' source='Github https://github.com/thorstenwagner/ij-robust-split' latest-version='v1.0.0 (04 Sep 2016)' status='active' %}
 
 ## Purpose
 
@@ -28,7 +28,7 @@ and
 
 The plugin provides an alternative to the ImageJ "build-in"-[watershed](https://imagej.nih.gov/ij/docs/guide/146-29.html#sub:Watershed)-plugin. It does not perform better results on regular round clumps. Especially for big clumps with image disturbances and many holes in the clump the results of the watershed plugins are much more robust and it does not depends on so many parameters. For elongated indididual objects, the plugin can produce better results than the watershed.
 
-It depends on the [IJ-Blob](/pluginshttps://imagej.nih.gov/ij-blob) library, the [Vecmath](https://github.com/hharrison/vecmath) library, the [LIBSVM](https://www.csie.ntu.edu.tw/~cjlin/libsvm/) library and the [JavaML](http://java-ml.sourceforge.net/) library.
+It depends on the [IJ-Blob](/plugins/ij-blob) library, the [Vecmath](https://github.com/hharrison/vecmath) library, the [LIBSVM](https://www.csie.ntu.edu.tw/~cjlin/libsvm/) library and the [JavaML](http://java-ml.sourceforge.net/) library.
 
 ## Plugin usage
 
@@ -168,7 +168,7 @@ As already mentioned the main algorithm follows the publication of *Kumar et al.
 
 # Installation
 
-If you use ImageJ just copy ij\_robust\_split.jar in your plugins folder and copy the [IJ-Blob](/pluginshttps://imagej.nih.gov/ij-blob), [Vecmath](https://github.com/hharrison/vecmath), the [LIBSVM](https://www.csie.ntu.edu.tw/~cjlin/libsvm/) and the [JavaML](http://java-ml.sourceforge.net/) jars into the plugins/jars folder.
+If you use ImageJ just copy ij\_robust\_split.jar in your plugins folder and copy the [IJ-Blob](/plugins/ij-blob), [Vecmath](https://github.com/hharrison/vecmath), the [LIBSVM](https://www.csie.ntu.edu.tw/~cjlin/libsvm/) and the [JavaML](http://java-ml.sourceforge.net/) jars into the plugins/jars folder.
 
 # How to cite
 

_pages/plugins/tws/index.md

@@ -102,7 +102,7 @@ Here we can load the data (in [Weka](http://www.cs.waikato.ac.nz/ml/weka/) forma
 
 #### Save data
 
-With this button we can save the current trace information into a data file that we can handle later with the plugin or the Weka Explorer itself. The plugin will save the feature vectors derived from the pixels belonging to each trace into an [ARFF](http://weka.wikispaces.com/ARFF+%28stable+version%29) file at a location chosen by the user. Notice the traces (regions of interests selected by the user) are not saved but only their corresponding feature vectors. To save the ROIs, you can simply use the \[https://imagej.nih.gov/ijhttps://imagej.nih.gov/ij/docs/guide/146-30.html#sub:ROI-Manager... ROI Manager\].
+With this button we can save the current trace information into a data file that we can handle later with the plugin or the Weka Explorer itself. The plugin will save the feature vectors derived from the pixels belonging to each trace into an [ARFF](http://weka.wikispaces.com/ARFF+%28stable+version%29) file at a location chosen by the user. Notice the traces (regions of interests selected by the user) are not saved but only their corresponding feature vectors. To save the ROIs, you can simply use the \[https://imagej.nih.gov/ij/docs/guide/146-30.html#sub:ROI-Manager... ROI Manager\].
 
 #### Create new class
 

_pages/scripting/clojure.md

@@ -27,7 +27,7 @@ See [Scripting Help](/scripting) for details on keybindings and how to use the i
 A minimal, complete clojure example:
 
     (import '(ij IJ))
-    (def gold (IJ/openImage "https://imagej.nih.govhttps://imagej.nih.gov/ij/images/AuPbSn40.jpg"))
+    (def gold (IJ/openImage "https://imagej.nih.gov/ij/images/AuPbSn40.jpg"))
     (.show gold)
 
 To create scripts, just save them as .clj text files (with an underscore in the name) in any folder or subfolder of Fiji's plugins folder, and run {% include bc path='Plugins|Scripting|Refresh Clojure Scripts'%} to update the menus (it's done automatically at start up as well).
@@ -299,13 +299,13 @@ Above, note the dot '.' after Random, which indicates we are calling the constru
 
 ImageJ has three basic objects:
 
--   The <b>[ImagePlus](https://imagej.nih.gov/ij/developer/apihttps://imagej.nih.gov/ij/ImagePlus.html)</b>, which wraps the ImageProcessor and contains properties and pointers to the ROI (region of interest) and the ImageWindow that may be displaying the image.
--   The <b>[ImageProcessor](https://imagej.nih.gov/ij/developer/apihttps://imagej.nih.gov/ij/process/ImageProcessor.html)</b>, which is an abstract class enabling the high-level manipulation of and access to pixels. Its subclasses each wraps a different kind of data type:
+-   The <b>[ImagePlus](https://imagej.nih.gov/ij/developer/api/ij/ImagePlus.html)</b>, which wraps the ImageProcessor and contains properties and pointers to the ROI (region of interest) and the ImageWindow that may be displaying the image.
+-   The <b>[ImageProcessor](https://imagej.nih.gov/ij/developer/api/ij/process/ImageProcessor.html)</b>, which is an abstract class enabling the high-level manipulation of and access to pixels. Its subclasses each wraps a different kind of data type:
     -   ByteProcessor - byte\[\]
     -   ShortProcessor - short\[\]
     -   FloatProcessor - float\[\]
     -   ColorProcessor - int\[\] (byte-packed ARGB, but Alpha channel is ignored)
--   The <b>[ImageStack](https://imagej.nih.gov/ij/developer/apihttps://imagej.nih.gov/ij/ImageStack.html)</b> which contains unfortunately not an array of ImageProcessor, but an Object\[\] containing an homogeneous list of equal length byte\[\], or float\[\], etc.
+-   The <b>[ImageStack](https://imagej.nih.gov/ij/developer/api/ij/ImageStack.html)</b> which contains unfortunately not an array of ImageProcessor, but an Object\[\] containing an homogeneous list of equal length byte\[\], or float\[\], etc.
 
 For extensive documentation, see the [Anatomy of an ImageJ image](http://albert.rierol.net/imagej_programming_tutorials.html#ImageJ%20programming%20basics) ImageJ programming basics tutorial.
 
@@ -362,7 +362,7 @@ An alternative way would be to simply duplicate the processor of imp-1, and then
 
 ### Resizing an ImageStack
 
-This one is harder, because an ImageStack is just a wrapper for Object\[\] list of pixel arrays. ImageJ though provides a mid-level resizing method, via the [CanvasResizer](https://imagej.nih.gov/ij/developer/apihttps://imagej.nih.gov/ij/plugin/CanvasResizer.html) class:
+This one is harder, because an ImageStack is just a wrapper for Object\[\] list of pixel arrays. ImageJ though provides a mid-level resizing method, via the [CanvasResizer](https://imagej.nih.gov/ij/developer/api/ij/plugin/CanvasResizer.html) class:
 
     (import '(ij.plugin CanvasResizer)
             '(ij IJ ImagePlus))
@@ -1125,7 +1125,7 @@ To compile the clojure code to .class files, you need:
 For example:
 
     $ mkdir classes
-    $ java -cp .:../..https://imagej.nih.gov/ij.jar:../../jars/clojure.jar:./classes/:./fj/tests/process/ clojure.lang.Repl
+    $ java -cp .:../../ij.jar:../../jars/clojure.jar:./classes/:./fj/tests/process/ clojure.lang.Repl
 
 `user=> (compile 'fj.tests.process.FloatProcessorPlus)`  
 `fj.tests.process.FloatProcessorPlus`  
@@ -1156,7 +1156,7 @@ The example clojure code:
     ; ...
     ; $ cd ../../../
     ; $ mkdir classes
-    ; $ java -cp ../..https://imagej.nih.gov/ij.jar:../../jars/clojure.jar:./classes/:.:./fj/tests/process/ clojure.lang.Repl
+    ; $ java -cp ../../ij.jar:../../jars/clojure.jar:./classes/:.:./fj/tests/process/ clojure.lang.Repl
     ; user=> (compile 'fj.tests.process.FloatProcessorPlus)
     ; fj.tests.process.FloatProcessorPlus
     ; user=>
@@ -1165,7 +1165,7 @@ The example clojure code:
     ; structure in the ./classes/ folder.
     ;
     ; Then run like any other java class with a static public void main method:
-    ; $ java -cp .:../..https://imagej.nih.gov/ij.jar:../../jars/clojure.jar:./classes fj.tests.process.FloatProcessorPlus
+    ; $ java -cp .:../../ij.jar:../../jars/clojure.jar:./classes fj.tests.process.FloatProcessorPlus
     ;
 
     (ns fj.tests.process.FloatProcessorPlus

_pages/scripting/generic-dialog.md

@@ -73,7 +73,7 @@ Dialog.addChoice("Type:", newArray("8-bit", "16-bit", "32-bit", "RGB"));
 Dialog.addCheckbox("Ramp", true);
 
 // One can add a Help button that opens a webpage
-Dialog.addHelp("https://imagej.nethttps://imagej.nih.gov/ij/macros/DialogDemo.txt");
+Dialog.addHelp("https://imagej.nih.gov/ij/macros/DialogDemo.txt");
 
 // Finally show the GUI, once all parameters have been added
 Dialog.show();