the required
initialisation files. In addition you will need to write an xml
settings file (this can be done by modifying one of the existing examples).
To start the digitiser you need to open the digitiser.xul file in a browser
window. This can be done either by typing in the url for the file or by
opening it using the File>Open menu of your browser.
If you type in the url to open digitiser.xul you can also specify the location of the xml settings file after a "?" as shown above. The location can be set using either an absolute path or a path relative to the digitiser.xul file location.
If no xml file is specified in the url a dialog will pop up, asking you to select the location of your xml settings file.
This file is required as it tells where all the image and data files are located as well as defining various other settings. More information on the contents of this file is given below.
Loading the settings file directly from the url is very useful if you are working with the same settings file a lot. You can bookmark the url and load up your files just by accessing your bookmarked link.
By exploring the Non axial vocal tract digitise example
you can learn how to use the digitiser to load up different image slices and then add data points on the surface of each slice. In this example the images are from MRI scans of the vocal tract and include a co-planar sagittal set as well as slices which were generated normal to the tract path. The slices normal to the tract path are not co-planar (ie the slices are not all stacked on top of each other but are at various different angles).
At the core of the digitser interface are two scene viewers, one for digitising in a 2D plane and one for viewing the data in 3D.
The 2D digitise scene viewer
The left hand scene viewer shows a 2D image of the current selected image slice. Clicking in this scene will create points on this slice.
Changing the view to focus on a particular area can be done using the Ctrl key and the mouse.
- To move your view point
- Hold down the Ctrl key and the middle mouse button while moving the mouse.
- To zoom in or out
- Hold down the Ctrl key and the right mouse button while moving the mouse.
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To select and load up a particular image slice you can use any combination of the following controls.
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| The slice drop down list is a sorted list of all available image slices. The previous and next buttons allow you to quickly swap between adjacent image slices.
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Once a slice is loaded up in the 2D digitise window nodes can be created, edited, deleted and saved by using the controls summarised below.
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The Group drop down list is used to select which group created nodes will be added to. To add nodes to a different group change the selection and then create them. Note that when groups are saved the nodes from each group will be written to the appropriate group files (which are specified in the xml settings file).
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Check the Create nodes check box to create nodes. Clicking on the 2d digitise scene will then create a node. When a point is created it is drawn
in red to indicate it is selected. If you can not see a point try zooming in as your point glyph may be too small to see. (You can change the glyph size in your xml settings file).
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Check the Edit nodes check box to edit the position of any selected nodes. You must select a node before editing it, so if you wish to change your selection, check the Select nodes check box, otherwise you will only be able to edit the currently selected node(s). Once a node is selected you can edit its position by dragging it with the mouse to a new one. It can be useful to uncheck the Create nodes check box when editing, to ensure you do not accidently create new nodes while trying to select existing ones.
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Check the Select nodes check box to select nodes. Clicking on a node will then select it. To select more than one node hold down the shift key while clicking. Each node you click on will be added to the selection. Note that it is only possible to delete or edit nodes if they are selected.
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Click the Delete selected button to delete and selected nodes.
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The save drop down menu is used to save nodes. There are three possibilities which will pop up when the menu is clicked:
- Save
- Save all the nodes to the default exnode database file that is specified in the xml settings file.
- Save As
- Open a file chooser dialog so that the user can choose a file name and the location of the file to save all the nodes to.
- Save Groups
- Save the nodes in each group to their appropriate group file names (as specified in the xml settings file).
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Dpending on your computer and system set up the brightness and contrast controls may or may not be available. If they will not work with your computer they will be disabled and displayed as greyed out.
| The Brightness slider adjusts the brightness of both scene viewers.
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| The Contrast slider adjusts the contrast of both scene viewers.
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The right hand 3D scene viewer shows the position of all the data points digitised so far with the option of viewing 1 or 2 slices as well.
Changing the view to focus on a particular area can be done using the mouse.
- To rotate your view point
- Hold down the Ctrl key and the left mouse button while moving the mouse.
- To translate your view point
- Hold down the Ctrl key and the middle mouse button while moving the mouse.
- To zoom in or out
- Hold down the Ctrl key and the right moused button while moving the mouse.
The Filter pipeline drop down list allows the user to select from various image processing pipelines. Each pipeline consists of one or more filters chained together, so that the output of the previous filter is fed as the input into the next filter. Applyings filters can make it easier to identify anatomical boundaries.
When a particular pipeline is selected the current image slice is taken and fed through the various filters using the default filter settings. This produces a filtered output image which is then displayed. It can take several seconds to calculate the output image for a given slice so be aware of this when changing slices. When a pipeline is loaded up buttons will be displayed next to the pipeline name, indicating the order of filters used for that pipeline (running from left to right). An example of this is shown below:
Settings for an individual filter can be edited by clicking on the filter button, which will then bring up a settings dialog. If no settings are required the button will be greyed out, indicating there is no dialog. Help for how a filter works and what the settings do can be accessed from the settings dialog for that filter.
The settings file is a text file that uses various tags to set required and optional values. It can be edited using any text editor. The easiest way to create a settings file is to take an existing one and modify it for your needs.
VocalTractDigitiseSettings.xml is a simple example of a settings file. It contains comments which describe all the xml tags used in the file.
A more complicated settings file is required for the
Non axial vocal tract example. This is because this example demonstrates the use of non axially aligned slices. Each slice set positioned at an angle requires its own sliceSet tag so there are many more slice sets specified.
The NonAxialVocalTractDigitiseSettings.xml file shows how to define these slice sets.
Open up the list of installed extensions (Tools->Add ons or Tools->Extensions). Check your list to see if there is an entry for Zinc. If there is, right click on the zinc entry and select "About ZINC". An about dialog should open and after a few seconds a 3D model of the torso should load up. Check that you can rotate the torso by using the mouse buttons.
It is possible your current version of Zinc is conflicting with a previously installed version of MozCmgui or Zinc. You will need to uninstall the existing versions. Open up the list of installed extensions (Tools->Add ons or Tools->Extensions). Then use either of the following methods
- Left click on each Zinc/MozCmgui entry and then click on the uninstall button.
or
- Right click on each Zinc/MozCmgui entry and then select uninstall from the drop down menu.
You will need to restart firefox for your changes to take effect. Once restarted, check the list of installed extensions to make sure they have been removed and then reinstall the desired version of Zinc.
You have either forgotten to install the Zinc extension, or have installed the wrong version. Click on the tools menu and then select Add-ons (or Extensions) to see whether you have Zinc installed. It should also tell you which version is installed. If you need to install Zinc for the first time or install a newer version see the instructions for Installing Zinc .
If you are running the example off the website you must enable a particular security setting for the digitiser to be able to open the settings file. Enter the following url into your browser: about:config . This will bring up a configuration page. Scroll down to the setting signed.applets.code_base_principal_support (near the bottom), double click it and set its value to true.
Another possible reason you will not be asked for a settings file is if your profile settings are confused. If you have logged into a 64 bit machine with the same profile you use for a 32 bit machine and have installed the appropriate versions of Zinc on both machines your profile will confuse firefox. Uninstall Zinc from one of the machines and it should work.
See the answer to the previous question.
Depending on which version of zinc you are using, you may run into problems if you try and read in a database file on a linux machine which has been manually edited on a windows machine. Editing on a windows machine can result in extra carriage return characters being inserted, as windows and linux machines handle line endings differently.
Note that you may have edited the database file without even realizing it. Some zip programs will insert extra carriage returns when you unzip a file on a windows machine. This has caught several people out in the past, when transferring files between operating systems.
The problem can be hard to spot as the database file will look fine if opened in a text editor as the extra carriage return characters are invisible.
If your database file is not loading under linux, it is likely due to the presence of these window style carraige return characters. You can strip the extra carriage returns out and your database file should work again. There are many ways to do this and several
are suggested here .
There are two possible causes of this problem. The most likely cause is that
the digitiser can not find your image files because you have given it an incorrect file path to your image directory. Check your xml settings file and look at the filepath attribute of your sliceset. It must be set to the location of your image files.
If you are using a relative file path note that it is
relative to your xml settings file.
If you are using an absolute file path you can test whether
your path is correct by typing it as a url into your browser.
If your location is correct the browser will display
a listing of the contents of your directory. Note when using
absolute file paths is is a very good idea
to include the protocol , ie whether to use
http:// or file://. If you omit the protocol
the digitiser will do its best to assume the correct protocol
but i may make the wrong assumption. An example of setting
your file path using the absolute method is given below:
filePath="file:///home/pbie003/cmiss/examples/a/digitise/cmiss_input/images"
Note the triple slash.
The second possible cause is that you may have used the reserved name "database" as the group name in one of your group tags from your xml settings file. Do NOT use database as a group name, as the digitiser uses this name for other purposes.
Either the default location you have specified in your xml settings file does not exist, or it does exist and the files are being saved but to somewhere you don't expect. Check your xml settings file and look at the filename attribute of your database element. It must be set to the location of your database file (where nodes are loaded from at start up and saved to). If the file does not exist but the path to it does than selecting "Save nodes to file" will create a new database file for you. To avoid confusion use an absolute path rather than a relative path. This will ensure your database file is located where you think it is. Note you should not begin your file path with file:// as the file path MUST be on your local machine so there is no need to differentiate between file:// and http:// .
Either the default location you have specified in your xml settings file does not exist, or it does exist and the files are being saved but to somewhere you don't expect. Check your xml settings file and look at the groupFilename attribute of your group element. It must be set to the location of your exdata file for that group (where nodes will be written to on a group export). If the file does not exist but the path to it does than selecting "Export nodes to group files" will create a new exdata file for you. To avoid confusion use an absolute path rather than a relative path. This will ensure your exdata files are located where you think it is. Note you should not begin your file path with file:// as the file path MUST be on your local machine so there is no need to differentiate between file:// and http:// .
Some combinations of older versions of Zinc and the digitiser will crash your browser if you use the digitiser and then hit
your browsers' back or refresh button. One solution is to make sure you only use the most
up to date version of both the Zinc plug in and the digitister.
Alternatively when you finish using the digitiser either close the window, hit the home button or type in a new url.
Peter Bier
Last modified: Mon Mar 30 18:50:09 PDT 2009
