Changes as defined by MLAB-6185 (#130)

* Changes as defined by MLAB-6185

* Resolved merge mistakes

* Resolved comments

Author: sahehb

mevislab.github.io/content/introduction/introduction.md

@@ -147,13 +147,13 @@ Each module has a context menu, providing the following options:
 
 ![Context Menu of a module](images/tutorials/introduction/ModuleContextMenu.png "Context Menu of a module")
 
-* **Show Internal Network:** [Macro modules](glossary/#macro-module) provide an entry to open the internal network. You can see what happens inside a macro module. The internal network may also contain other macro modules.
-* **Show Window:** If a module does not provide a User Interface, you will see the automatic panel showing the module's name. Modules may additionally have one or more windows that can be opened. You can also open the Scripting Console of a module to integrate Python.
+* **Show Internal Network:** [Macro modules](glossary/#macro-module) provide an entry to open the internal network. You can see what happens inside a macro module. The internal network may also contain other macro modules. Changes in the internal network are applied to the currently running instance of your module but not saved permanently.
+* **Show Window:** If a module does not provide a User Interface, you will see the automatic panel, showing the module's name. Modules may additionally have one or more windows that can be opened. You can also open the Scripting Console of a module to integrate Python.
 * **Instance Name:** You can edit or copy the instance name. Renaming can be useful if the same module appears more than once in one network and/or if you want to access and distinguish the modules in your Python script. 
 * **Help:** The menu entry Help provides access to the Module Help pages and to an example network where the module is used. This example network often helps to understand which additional modules can be added to create your desired effect.
 * **Extras:** Automated tests written for the specific module can be executed here. You can also run this module in a separate process.
 * **Reload Definition:** In the case you are currently working on a module, you may need to reload the definition so that your changes are applied on the module (for example, attached Python scripts).
-* **Related Files:** Related files allows a quick access to the modules *.script* or *.py* files. The files are automatically opened in [MATE](glossary/#mevislab-mate) for editing.
+* **Related Files:** Related files allows a quick access to the modules *.script* or *.py* files. The files are automatically opened in [MATE](glossary/#mevislab-mate) for editing. Changes to the *.mlab* file are applied permanently for your module.
 * **Show Enclosing Folder:** This entry opens the directory where your module is stored.
 * **Grouping:** Multiple modules can be clustered and the groups can be named. This adds clarity to the structure of your network. In addition to that, grouped modules can be converted to local or global macro modules easily.
 

mevislab.github.io/content/tutorials/basicmechanisms.md

@@ -165,15 +165,15 @@ It is also possible to use the pre-defined module `SynchroView2D` to accomplish
 
 ### Grouping Modules {#TutorialGroupingModules}
 
-A contour filter can be created based on our previously created network. To finalize the filter, add the modules `Arithmetic2` and `Morphology` to your workspace and connect the modules as shown below. Double-click the module `Arithmetic2` to open its panel. Change the field *Function* of the module `Arithmetic2` to use the function *subtract* in the panel of the module. The contour filter is done now. You can inspect each processing step using the Output Inspector by clicking on the input and output connectors of the respective modules. The final results can be displayed using the viewer modules. If necessary, adjust the contrast by pressing the right mouse button and moving the cursor.
+A contour filter can be created based on our previously created network. To finalize the filter, add the modules `Arithmetic2` and `Morphology` to your workspace and connect the modules as shown below. Double-click {{< mousebutton "left" >}} the module `Arithmetic2` to open its panel. Change the field *Function* of the module `Arithmetic2` to use the function *subtract* in the panel of the module. The contour filter is done now. You can inspect each processing step using the Output Inspector by clicking on the input and output connectors of the respective modules. The final results can be displayed using the viewer modules. If necessary, adjust the contrast by pressing the right arrow key and moving the cursor.
 
 ![Grouping modules](images/tutorials/basicmechanics/BM_17.png "Grouping modules")
 
-If you'd like to know more about specific modules, search for help. You can do this by right-clicking the module and select help, which offers an example network and further information about the selected module in particular.
+If you'd like to know more about specific modules, search for help. You can do this by right-clicking {{< mousebutton "right" >}} the module and select help, which offers an example network and further information about the selected module in particular.
 
 ![Module Help](images/tutorials/basicmechanics/BM_18.png "Module Help")
 
-To be able to better distinguish the image processing pipeline, you can encapsulate it in a group: Select the three modules, for example, by dragging a selection rectangle around them. Then right-click the selection to open the context menu and select {{< menuitem "Add to New Group" >}}.
+To be able to better distinguish the image processing pipeline, you can encapsulate it in a group: Select the three modules, for example by dragging a selection rectangle around them. Then right-click {{< mousebutton "right" >}} the selection to open the context menu and select {{< menuitem "Add to New Group" >}}.
 
 ![Add modules to new group](images/tutorials/basicmechanics/BM_19.png "Add to new group")
 
@@ -199,15 +199,17 @@ You have probably already noticed how the modules differ in color. Each color re
   * Green modules are OpenInventor modules: they enable visual 3D scene graphs. 
   * The brown modules are called macro modules. Macro modules encapsulate a whole network in a single module. 
 
-To condense our filter into one single module, we will now be creating a macro module out of it. To do that, right-click on the group title and select *Convert To Local Macro*. Name your new macro module and finish. You just created a local macro module. Local macros can only be used from networks in the same or any parent directory.
+To condense our filter into one single module, we will now be creating a macro module out of it. To do that, right-click {{< mousebutton "right" >}} on the group title and select *Convert To Local Macro*. Name your new macro module and finish. You just created a local macro module. Local macros can only be used from networks in the same or any parent directory.
 
 ![Convert to local macro](images/tutorials/basicmechanics/BM_21.png "Convert to local macro")
 ![Your first local macro](images/tutorials/basicmechanics/BM_22.png "Your first local macro")
 
-Right-click the macro module and select *Show Internal Network* to inspect and change the internal network. You can change the properties of the new macro module by changing the properties in the internal network. You can, for example, right-click the module `Convolution` and change the kernel. These changes will be preserved.
+Right-click the macro module and select *Show Internal Network* to inspect and change the internal network. You can change the properties of the new macro module by changing the properties in the internal network. You can, for example, right-click {{< mousebutton "right" >}} the module `Convolution` and change the kernel. These changes will be applied for the currently running instance.
 
 ![Internal Network of your local macro](images/tutorials/basicmechanics/BM_23.png "Internal Network of your local macro")
 
+If you want to change the permanent behavior or the module, right-click {{< mousebutton "right" >}} and select {{< menuitem "Related Files" "Filter.mlab" >}}. The network file of the module opens. Changes applied to this file are saved permanently.
+
 {{< youtube "VmK6qx-vKWk">}}
 
 {{<alert class="info" caption="Extra Infos">}}
@@ -224,6 +226,6 @@ More information on macro modules can be found {{< docuLinks "/Resources/Documen
 * Parameters of each module can be changed in the Module Inspector or Automatic Panel of the module.
 * Parameter connections can be established to synchronize the values of these parameters.
 * Modules can be clustered. Clustered modules can be encapsulated into local or global macro modules.
-* Macro modules encapsulate networks. Internal networks can be shown and modified. Any changes of the internal network are applied to the macro module.
+* Macro modules encapsulate networks. Internal networks can be shown and modified. Any changes of the internal network are applied to the macro module on-the-fly, changes in the *.mlab* file change the permanent behavior of your module.
 
 {{< networkfile "examples/basic_mechanisms/contour_filter/ContourFilter.zip" >}}

mevislab.github.io/content/tutorials/basicmechanisms/macromodules/scriptingexample2.md

@@ -85,11 +85,7 @@ Window {
 
 ### Edit Viewer Settings in the Panel
 
-You may want to change the design setting of the right viewer. This is
-still possible via the internal network of the macro module. Open the
-internal network either via the context menu or using the middle mouse
-button {{< mousebutton "middle" >}} and click on the module. After that, open the Automatic Panel of
-the module `SoExaminerViewer` via context menu {{< menuitem "Show Windows" "Automatic Panel" >}} and change the field *decoration* to *False*. Keep in mind, as we did not create CSOs by now, the right viewer stays black.
+You may want to change the design setting of the right viewer. This is possible via the network file of the macro module. Open the context menu {{< mousebutton "right" >}} and select {{< menuitem "Related Files" "IsoCSOs.mlab" >}} on the module. In the network file, open the Automatic Panel of the module `SoExaminerViewer` via context menu {{< menuitem "Show Windows" "Automatic Panel" >}} and change the field *decoration* to *False*. Keep in mind, as we did not create CSOs by now, the right viewer stays black.
 
 ![Change viewer settings](images/tutorials/basicmechanics/ChangeViewerSettings.png "Change viewer settings")
 
@@ -98,11 +94,7 @@ the module `SoExaminerViewer` via context menu {{< menuitem "Show Windows" "Auto
 ### Selection of Images
 
 Next, we like to add the option to browse through the folders and select
-the image, we like to create CSOs from. This functionality is already given in the internal network in the module `LocalImage`. We can copy this functionality from `LocalImage` and add this option to the panel above both viewers. But, how should we know, which field name we
-reference to? To find this out, open the
-internal network of your macro module. Now you are able to open the panel of
-the module `LocalImage`. Right-click {{< mousebutton "right" >}} the desired field: In this case, right-click the label
-*Name:*. Select *Copy Name*, to copy the internal name of this field.
+the image, we like to create CSOs from. This functionality is already present in the internal network in the module `LocalImage`. We can copy this functionality from `LocalImage` and add this option to the panel above both viewers. But, how should we know which field name we reference to? To find this out, open the network file of your macro module again. Now you are able to open the panel of the module `LocalImage`. Right-click {{< mousebutton "right" >}} the desired field: In this case, right-click the label *Name:*. Select *Copy Name* to copy the internal name of this field.
 
 ![Copy the field name](images/tutorials/basicmechanics/GUI_Exp_09.png "Copy the field name")
 
@@ -239,7 +231,7 @@ can do this in the following way:
 
     ![Scripting Assistant](images/tutorials/basicmechanics/GUI_Exp_15.png "Scripting Assistant")
 
-2. Enable a functionality that allows us to notice the id of the CSO we are currently hovering over with our mouse. For this open the internal network of our macro module. We will use the module `SoView2DCSOExtensibleEditor`. Open its panel and select the tab *Advanced*. You can check a box to enable *Update CSO id under mouse*. If you now hover over a CSO, you can see its id in the panel. We can save the internal network to save this functionality, but we can also solve our problem via scripting. The Scripting Assistant translated our action into code, which we can use.
+2. Enable a functionality that allows us to notice the id of the CSO we are currently hovering over with our mouse. For this open the network file of our macro module. We will use the module `SoView2DCSOExtensibleEditor`. Open its panel and select the tab *Advanced*. You can check a box to enable *Update CSO id under mouse*. If you now hover over a CSO, you can see its id in the panel. We can save the network to save this functionality, but we can also solve our problem via scripting. The Scripting Assistant translated our action into code, which we can use.
 
     ![Enabling CSO id identification](images/tutorials/basicmechanics/GUI_Exp_16.png "Enabling CSO id identification")
 

mevislab.github.io/content/tutorials/basicmechanisms/macromodules/viewerexample.md

@@ -53,7 +53,7 @@ MeVisLab reloads its internal database and you can open a new tab. Search for yo
 In the case you double-click {{< mousebutton "left" >}} your module now, you will see the *Automatic Panel* only showing the name of your module, because we did not add any own *Window* until now.
 
 ### Develop Your User Interface
-Before adding your own UI, open the internal network of your macro module via right-click {{< mousebutton "right" >}} and {{< menuitem "Show Internal Network" >}}. Open the panel of your `ImageLoad` module and set *filename* to an empty string (clear). This is necessary for later.
+Before adding your own UI, open the internal network of your macro module via right-click {{< mousebutton "right" >}} and {{< menuitem "Related Files" "MyViewerApplication.mlab" >}}. Open the panel of your `ImageLoad` module and set *filename* to an empty string (clear). This is necessary for later.
 
 Now, right-click on your *MyViewerApplication* and select {{< menuitem "Related Files" "MyViewerApplication.script" >}}
 

mevislab.github.io/content/tutorials/summary/summary6.md

@@ -68,7 +68,7 @@ You can also update your Python files for new or updated requirements. In this e
 If you want to write an additional Python test case, you can also do that.
 
 ## Summary
-* Your application can be updated by modifying the macro module and/or internal network of your application
+* Your application can be updated by modifying the macro module and/or network file of your application
 * Any changes will be applied to your installable executable in the next step
 
 {{< networkfile "examples/summary/TutorialSummaryUpdated.zip" >}}

mevislab.github.io/content/tutorials/thirdparty/pytorch/pytorchexample3.md

@@ -149,7 +149,7 @@ def releaseCamera(_):
 You should now have the complete functionality of the [Example 2: Face Detection with OpenCV](tutorials/thirdparty/opencv/thirdpartyexample2 "Example 2: Face Detection with OpenCV").
 
 ### Adapt the network
-For *PyTorch*, we require some additional modules in our network. Open the internal network of your module and add another `PythonImage` module. Connect a `Resample3D` and an `ImagePropertyConvert` module.
+For *PyTorch*, we require some additional modules in our network. Open the network file via right-click {{< mousebutton "right" >}} and selecting {{< menuitem "Related Files" "PyTorchSegmentationExample.mlab" >}} of your module and add another `PythonImage` module. Connect a `Resample3D` and an `ImagePropertyConvert` module.
 
 In `Resample3D` module, define the *Image Size* 693, 520, 1. Change *VoxelSize* for all dimensions to 1.
 
@@ -163,7 +163,7 @@ Then add a `SoView2DOverlayMPR` module and connect it to the `ImagePropertyConve
 
 ![SoView2DOverlayMPR](images/tutorials/thirdparty/pytorch_example3_8.png "SoView2DOverlayMPR")
 
-Save the internal network.
+Save the network file.
 
 ### Remove OpenCV specific code
 We want to use PyTorch for segmentation, therefore you need to add all necessary imports.