Update headless-related docs for Jaunch

Author: ctrueden

_pages/learn/headless.md

@@ -10,38 +10,33 @@ However, it acquired [macro](/scripting/macro) capabilities, a [batch mode](/scr
 
 Naturally, users want to execute such [macros](/scripting/macro) or [scripts](/scripting) in environments such as clusters where there is no graphical user interface available.
 
-# `--headless` mode
+## `--headless` mode
 
 To address all of these needs, [ImageJ2](/software/imagej2) provides the capability to execute ImageJ plugins, macros and scripts in headless mode. This feature uses bytecode manipulation to patch ImageJ's behavior at runtime, making it possible to start ImageJ in batch mode without instantiating GUI components.
 
 **Shortcoming:** There are plugins which are even more bound to a GUI than
 ImageJ is. Naturally, these plugins will still try to instantiate GUI
 elements when being called in headless mode, failing.
 
-## Running scripts in headless mode
+### Running scripts in headless mode
 
 Please see the [headless scripting guide](/scripting/headless).
 
-## Running macros in headless mode
+### Running macros in headless mode
 
-To run a *macro* in headless mode via a command prompt, first open a command prompt in the Fiji.app or ImageJ directory where the .exe (on windows) of ImageJ resides.  Then use the following syntax, with the `-macro` command line argument along with the `--headless` option, as follows:
+To run a *macro* in headless mode via a command prompt, first open a command prompt in the directory where a Fiji installation resides. Then use the following syntax, with the `-macro` command line argument along with the `--headless` option, as follows:
 
 ```shell
-ImageJ --headless --console -macro path-to-Macro.ijm
+./fiji --headless -macro path-to-Macro.ijm
 ```
-The `--console` flag is optional, it only ensures that print statements and error messages are shown in the command prompt.    
-However, **it also has a side effect of preventing the command prompt from "returning" after execution**, in effect giving the impression that the code is hanging. This is especially not desirable if calling ImageJ from an external program : the external program would just wait indefinitly for the execution to terminate.   
-**An external program can still access the printed statements without the `--console` flag**, by redirecting the standard/error output of the process (ImageJ.exe).  
-
-If you omit the `--headless` flag, the GUI will open and the macro will be executed.  
+If you omit the `--headless` flag, the GUI will open and the macro will be executed.
 
 If the macro resides in ImageJ's macro directory, it is possible to specify the macro name instead of the actual file path. The file extension is always very recommended but for backwards compatibility, it is not strictly required *only* when specifying the macro name instead of a path.
 
-
 You can even pass parameters to the macro; e.g.:
 
 ```shell
-./ImageJ-win64.exe --headless --console -macro ./RunBatch.ijm 'folder=../folder1 parameters=a.properties output=../samples/Output'
+./fiji --headless -macro ./RunBatch.ijm 'folder=../folder1 parameters=a.properties output=../samples/Output'
 ```
 
 In that case, the RunBatch.ijm file should be something like:
@@ -59,11 +54,10 @@ the `getArgument()` is used to grab the parameter string itself, and it is then
 
 {% include notice icon="warning" content='Please note that you will not be able to use [script parameters](/scripting/parameters) with `-macro`. Follow instructions in [Scripting Headless](/scripting/headless) instead.' %}
 
-Some ImageJ commands relying on the GUI do not work in headless mode such as : 
-- `selectWindow("name")`, use `selectImage(title)` instead for images  
+Some commands relying on the GUI do not work in headless mode such as:
+- `selectWindow("name")`, use `selectImage(title)` instead for images
 - `Table.Rename("oldTitle", "newTitle")`
 
-
 {% capture historical-note %}
 Headless support was originally a branch in [ImageJA](/libs/imageja); it worked
 by putting rewritten versions of three core ImageJ classes into a file called
@@ -79,8 +73,7 @@ launching ImageJ from the command line.
 {% endcapture %}
 {% include aside title="Historical note" content=historical-note %}
 
-
-# Why is `--headless` needed?
+## Why is `--headless` needed?
 
 Java *does* support a headless mode via the `java.awt.headless` property; setting this property to `true` enables it.
 
@@ -90,16 +83,17 @@ Since ImageJ was devised as a desktop application, everything -- including macro
 
 On macOS, there is no problem: Aqua provides GUI-independent text rendering (mapping to the actual display using anti-aliasing). There, running in headless mode allows instantiating GUI elements such as the menu bar.
 
-# Other solutions
-## Xvfb virtual desktop
+## Other solutions
+
+### Xvfb virtual desktop
 
 Another method is to have a virtual desktop, e.g. {% include wikipedia title='Xvfb' text='Xvfb'%}. This will allow ImageJ to start with a virtualised graphical desktop.
 
 **Advantage:** No run-time patching is required.
 
 **Shortcomings:** It is slower than it needs to be because of the overhead of starting the GUI, it is harder to configure, and plugins might get stuck because they wait for user input which never comes.
 
-### Examples
+#### Examples
 
 Here are a couple of simple examples.
 
@@ -109,7 +103,7 @@ Passing direct arguments:
 $ cat hello.js
 importClass(Packages.ij.IJ);
 IJ.log("hello " + arguments[0]);
-$ xvfb-run -a $IMAGEJ_DIR/ImageJ-linux64 hello.js Emerson
+$ xvfb-run -a $FIJI_DIR/fiji hello.js Emerson
 hello Emerson
 ```
 
@@ -120,7 +114,7 @@ $ cat hello-with-params.js
 // @String name
 importClass(Packages.ij.IJ);
 IJ.log("hello " + name);
-$ xvfb-run -a $IMAGEJ_DIR/ImageJ-linux64 --ij2 --headless --run hello-with-params.js 'name="Emerson"'
+$ xvfb-run -a $FIJI_DIR/fiji --ij2 --headless --run hello-with-params.js 'name="Emerson"'
 hello Emerson
 ```
 
@@ -143,6 +137,6 @@ wait # waits until all 'program' processes are finished
 
 See also [this post on the ImageJ mailing list](https://list.nih.gov/cgi-bin/wa.exe?A2=IMAGEJ;5ace1ed0.1508).
 
-## Rewriting as scripts or plugins
+### Rewriting as scripts or plugins
 
 The most robust method is to rewrite macros as scripts that do not require interaction with the GUI to begin with. Unfortunately, this is the most involved solution, too, since it usually takes some time to convert macros.

_pages/plugins/bigstitcher/headless.md

@@ -96,6 +96,6 @@ to process another dataset with a different number of tiles headlessly:
 
 After saving the macro, it can be run from any Terminal by starting Fiji in [Headless](/learn/headless) mode and passing the macro as well as a parameter string.
 
-`   /path/to/fiji/ImageJ-linux64 --headless --console -macro /path/to/macro/bigStitcherBatch.ijm "/path/to/data 2 3"`
+`   /path/to/Fiji/fiji --headless -macro /path/to/macro/bigStitcherBatch.ijm "/path/to/data 2 3"`
 
 Go back to the [main page](/plugins/bigstitcher#documentation)

_pages/scripting/headless.md

@@ -9,13 +9,13 @@ project: /software/imagej2
 To start ImageJ2 headless mode, run (with the launcher appropriate for your system substituted):
 
 ```ssh
-./ImageJ-linux64 --headless
+./fiji --headless
 ```
 
 By default, when ImageJ2 runs headlessly it acts like a one-off program: it will only perform the requested operations, then quit. To run a script headlessly, use:
 
 ```ssh
-./ImageJ-linux64 --headless --run path/to/script [key1=value1,key2=value2,...]
+./fiji --headless --run path/to/script [key1=value1,key2=value2,...]
 ```
 
 {% include notice icon="warning" content='In many cases, it is necessary to enclose the entire list of key/value pairs in single quotes, to avoid shell expansion. See the following examples.' %}
@@ -33,21 +33,21 @@ print('Hello ' + name)
 we could run this script with the command on [Linux](/platforms/linux):
 
 ```ssh
-./ImageJ-linux64 --headless --run hello.py 'name="Mr Kraken"'
+./fiji --headless --run hello.py 'name="Mr Kraken"'
 ```
 
 Note that the `name` parameter must be enclosed in double quotes, since it is a string literal.
 
 On [Windows](/platforms/windows) systems, single/double quotes might be inverted though, such that strings are enclosed in single quotes while the list of argument as well as the path to the py script are in double quotes.
 
 ```ssh
-ImageJ-win64.exe --headless --run "PathTo/hello.py" "name='Mr Kraken'"
+fiji --headless --run "PathTo/hello.py" "name='Mr Kraken'"
 ```
 
 On [macOS](/platforms/macos) systems, the command can run in with the same quoting as on Linux:
 
 ```ssh
-./ImageJ-macosx --headless --run hello.py 'name="Mr Kracken"'
+./fiji --headless --run hello.py 'name="Mr Kracken"'
 ```
 
 ## Multiple parameters
@@ -63,37 +63,37 @@ print('Hello ' + name1 + " and " + name2)
 then these are filled by using a comma-separated list of parameter pairs—e.g.:
 
 ```ssh
-./ImageJ-linux64 --headless --run hello.py 'name1="Mr",name2="Mrs Kraken"'
+./fiji --headless --run hello.py 'name1="Mr",name2="Mrs Kraken"'
 ```
 
 Similarly for Windows (again respect single/double quotes) or macOS,
 
 ```ssh
-ImageJ-win64.exe --headless --run "PathTo/hello.py" "name1='Mr', name2='Kraken'"
-./ImageJ-macosx --headless --run hello.py 'name1="Mr",name2="Mrs Kraken"'
+.\fiji --headless --run "PathTo/hello.py" "name1='Mr', name2='Kraken'"
+.\fiji --headless --run hello.py 'name1="Mr",name2="Mrs Kraken"'
 ```
 
 ## Controlling the Updater
 
 To prevent unnecessary server connections to update sites in headless mode you can set the `imagej.updater.disableAutocheck` java parameter `true`:
 
 ```ssh
-./ImageJ-linux64 -Dimagej.updater.disableAutocheck=true -- --headless --run hello.py 'name="Mr Kraken"'
+./fiji -Dimagej.updater.disableAutocheck=true -- --headless --run hello.py 'name="Mr Kraken"'
 ```
 
 Often headless mode is used to run many scripts in parallel that could result in huge numbers of server connections. Setting this parameter will prevent this issue. This parameter does not persist between launches and must be included every time server connections to update sites should be prevented.
 
 If desired, the updater can be controlled in headless mode using the following commands to add an update site and update ImageJ.
 
 ```ssh
-./ImageJ-linux64 --update add-update-site BAR https://sites.imagej.net/Tiago/
-./ImageJ-linux64 --headless --update update
+./fiji --update add-update-site BAR https://sites.imagej.net/Tiago/
+./fiji --update update
 ```
 
 You can also add multiple update sites in a single command line:
 
 ```ssh
-./ImageJ-win64.exe --update add-update-sites "BAR" "https://sites.imagej.net/Tiago/" "IJPB-plugins" "https://sites.imagej.net/IJPB-plugins/"
+./fiji --update add-update-sites "BAR" "https://sites.imagej.net/Tiago/" "IJPB-plugins" "https://sites.imagej.net/IJPB-plugins/"
 ```
 
 Go to the updater section to get the [complete list of available commands](/plugins/updater).