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FAQ

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== Running workflows ==
=== How can I run a workflow using the command line? ===
=== How can I run a workflow using the command line? ===
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<code>python vistrails.py -l -b path_to_vistrails_file -w pipeline </code>
<code>python vistrails.py -l -b path_to_vistrails_file -w pipeline </code>
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Where ''pipeline'' is a version number or a tag.
 
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=== How can I save an image from the spreadsheet? ===
 
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While having the focus on a spreadsheet cell press "Ctrl" (on Windows) and select the camera to take a snapshot. The system will prompt you for the location and file name where it should be saved. The other icons can be used for saving multiple images that can be used for generating an animation on demand.
 
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===Is it possible to save the complete state of the spreadsheet?===
 
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===How can I integrate my own program into VisTrails?===
 
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The easiest way is to create a package. Writing a package is often very simple, here are instructions on how to do it: [[UsersGuideVisTrailsPackages]]
 
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=== Given a VTK visualization, how can I generate a webpage from it? ===
 
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Check out the html pipeline in offscreen.xml.
 
=== Using the command line, we'd like to execute a workflow multiple times, with slightly different parameters, and create a series of output files. Is this possible?===
=== Using the command line, we'd like to execute a workflow multiple times, with slightly different parameters, and create a series of output files. Is this possible?===
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Refer to the package documentation for details. The one inconvenient step is that currently there's no automated way to describe what is the missing package. We're working on this feature for future releases.
Refer to the package documentation for details. The one inconvenient step is that currently there's no automated way to describe what is the missing package. We're working on this feature for future releases.
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== Spreadsheet ==
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Where ''pipeline'' is a version number or a tag.
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=== How can I save an image from the spreadsheet? ===
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While having the focus on a spreadsheet cell press "Ctrl" (on Windows) and select the camera to take a snapshot. The system will prompt you for the location and file name where it should be saved. The other icons can be used for saving multiple images that can be used for generating an animation on demand.
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===Is it possible to save the complete state of the spreadsheet?===
=== Can I view multiple sheets at the same time? ===
=== Can I view multiple sheets at the same time? ===
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By default, an unoccupied cell on the active sheet will be chosen to display the result. However, you can specify exactly in the pipeline where a spreadsheet cell will be placed by using CellLocation and SheetReference. CellLocation specifies the location (row and column) of a cell when connecting to a spreadsheet cell (VTKCell, ImageViewerCell, ...). Similarly, a SheetReference module (when connecting to a CellLocation) will specify which sheet the cell will be put on given its name, minimum row size and minimum column size. There is an example of this in examples/vtk.xml (select the version below Double Renderer).
By default, an unoccupied cell on the active sheet will be chosen to display the result. However, you can specify exactly in the pipeline where a spreadsheet cell will be placed by using CellLocation and SheetReference. CellLocation specifies the location (row and column) of a cell when connecting to a spreadsheet cell (VTKCell, ImageViewerCell, ...). Similarly, a SheetReference module (when connecting to a CellLocation) will specify which sheet the cell will be put on given its name, minimum row size and minimum column size. There is an example of this in examples/vtk.xml (select the version below Double Renderer).
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== Integrating your software into VisTrails ==
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===How can I integrate my own program into VisTrails?===
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The easiest way is to create a package. Writing a package is often very simple, here are instructions on how to do it: [[UsersGuideVisTrailsPackages]]
=== How do modules deal with multiple inputs in a same port? ===
=== How do modules deal with multiple inputs in a same port? ===
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If on your module you need multiple inputs connected to a single port, use the 'forceGetInputListFromPort' method. It will return a list of all the data items coming through the port. The VTK package uses this feature, so look there for usage examples (packages/vtk/base_widget.py)
If on your module you need multiple inputs connected to a single port, use the 'forceGetInputListFromPort' method. It will return a list of all the data items coming through the port. The VTK package uses this feature, so look there for usage examples (packages/vtk/base_widget.py)
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== VTK ==
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=== Given a VTK visualization, how can I generate a webpage from it? ===
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Check out the html pipeline in offscreen.xml.
=== I'm trying to use VTK, but there doesn't seem to be any output. What is wrong? ===
=== I'm trying to use VTK, but there doesn't seem to be any output. What is wrong? ===
To use VTK on VisTrails, you need a slightly different way of connecting the renderer modules. Instead of using the standard RenderWindow/RenderWindowInteractor infrastructure, you simply connect the renderer to a VTKCell. The examples directory in the distribution has several VTK examples that illustrate.
To use VTK on VisTrails, you need a slightly different way of connecting the renderer modules. Instead of using the standard RenderWindow/RenderWindowInteractor infrastructure, you simply connect the renderer to a VTKCell. The examples directory in the distribution has several VTK examples that illustrate.

Revision as of 09:27, 10 May 2007

Also check our Known Issues page for troubleshooting.


Contents

Running workflows

How can I run a workflow using the command line?

Call vistrails using the following options:

python vistrails.py -l -b path_to_vistrails_file -w pipeline

Using the command line, we'd like to execute a workflow multiple times, with slightly different parameters, and create a series of output files. Is this possible?

Starting in rev 444, we can change parameters that have an alias through the command line.

For example, offscreen pipeline in offscreen.xml always creates the file called image.png. If you want generate it with a different filename:

python vistrails.py -l -b ../examples/offscreen.xml -w offscreen -a"filename=other.png"

filename in the example above is the alias name assigned to the parameter in the value method inside the String module. When running a pipeline from the command line, VisTrails will try to start the spreadsheet automatically if the pipeline requires it. For example, this other execution will also start the spreadsheet:

python vistrails.py -l -b ../examples/head.xml -w aliases -a"isovalue=30,Diffuse_Color_R=0.8,Diffuse_Color_G=0.4,Diffuse_Color_B=0.2"

I can load a vistrail, and the version tree shows up fine. However, no pipelines appear when I click on a version. What gives?

The most likely reason is that the vistrail uses a package that is not registered with VisTrails. You need to identify the needed package and add it to your .vistrails/startup.py. A single line like the following should be enough:

addPackage('enter_package_name_here')

Some packages might need more information. For example:

addPackage('afront', executable_path='/path/to/afront')

Refer to the package documentation for details. The one inconvenient step is that currently there's no automated way to describe what is the missing package. We're working on this feature for future releases.

Spreadsheet

Where pipeline is a version number or a tag.

How can I save an image from the spreadsheet?

While having the focus on a spreadsheet cell press "Ctrl" (on Windows) and select the camera to take a snapshot. The system will prompt you for the location and file name where it should be saved. The other icons can be used for saving multiple images that can be used for generating an animation on demand.

Is it possible to save the complete state of the spreadsheet?

Can I view multiple sheets at the same time?

Yes. Each sheet on the spreadsheet can be displayed as a dock widget separated from the main spreadsheet window by dragging its tab name out of the tab bar at the bottom of the spreadsheet.

Then, how can I put back a separated sheet?

A sheet can be docked back to the main window by dragging it back to the tab bar or double-click on its title bar.

How can I order sheets on the spreadsheet?

This can be done by dragging the sheet name on the bottom top bar and drop it to the right place.

Can I control where a cell will be placed on the spreadsheet window?

By default, an unoccupied cell on the active sheet will be chosen to display the result. However, you can specify exactly in the pipeline where a spreadsheet cell will be placed by using CellLocation and SheetReference. CellLocation specifies the location (row and column) of a cell when connecting to a spreadsheet cell (VTKCell, ImageViewerCell, ...). Similarly, a SheetReference module (when connecting to a CellLocation) will specify which sheet the cell will be put on given its name, minimum row size and minimum column size. There is an example of this in examples/vtk.xml (select the version below Double Renderer).

Integrating your software into VisTrails

How can I integrate my own program into VisTrails?

The easiest way is to create a package. Writing a package is often very simple, here are instructions on how to do it: UsersGuideVisTrailsPackages

How do modules deal with multiple inputs in a same port?

(And should that even be allowed?)

For compatibility reasons, we do need to allow multiple connections to an input port. However, most package developers should never have to use this, and so we do our best to hide it. the default behavior for getting inputs from a port, then, is to always return a single input.

If on your module you need multiple inputs connected to a single port, use the 'forceGetInputListFromPort' method. It will return a list of all the data items coming through the port. The VTK package uses this feature, so look there for usage examples (packages/vtk/base_widget.py)

VTK

Given a VTK visualization, how can I generate a webpage from it?

Check out the html pipeline in offscreen.xml.

I'm trying to use VTK, but there doesn't seem to be any output. What is wrong?

To use VTK on VisTrails, you need a slightly different way of connecting the renderer modules. Instead of using the standard RenderWindow/RenderWindowInteractor infrastructure, you simply connect the renderer to a VTKCell. The examples directory in the distribution has several VTK examples that illustrate.

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