Fastr User Reference

fastr.toollist

A ToolManager containing all versions of all Tools loaded into the FASTR environment. The ToolManager can be indexed using the Tool id string or a tool id string and a version. For example if you have two versions (4.5 and 4.8) of a tool called Elastix:

>>> fastr.toollist['elastix.Elastix']
Tool Elastix v4.8 (Elastix Registration)
                           Inputs                              |             Outputs
--------------------------------------------------------------------------------------------------
fixed_image       (ITKImageFile)                               |  directory (Directory)
moving_image      (ITKImageFile)                               |  transform (ElastixTransformFile)
parameters        (ElastixParameterFile)                       |  log_file  (ElastixLogFile)
fixed_mask        (ITKImageFile)                               |
moving_mask       (ITKImageFile)                               |
initial_transform (ElastixTransformFile)                       |
priority          (__Elastix_4.8_interface__priority__Enum__)  |
threads           (Int)                                        |

>>> fastr.toollist['elastix.Elastix', '4.5']
Tool Elastix v4.5 (Elastix Registration)
                           Inputs                              |             Outputs
--------------------------------------------------------------------------------------------------
fixed_image       (ITKImageFile)                               |  directory (Directory)
moving_image      (ITKImageFile)                               |  transform (ElastixTransformFile)
parameters        (ElastixParameterFile)                       |  log_file  (ElastixLogFile)
fixed_mask        (ITKImageFile)                               |
moving_mask       (ITKImageFile)                               |
initial_transform (ElastixTransformFile)                       |
priority          (__Elastix_4.5_interface__priority__Enum__)  |
threads           (Int)                                        |
fastr.typelist

A dictionary containing all types loaded into the FASTR environment. The keys are the typenames and the values are the classes.

class fastr.Network(id_='unnamed_network', version=None, filename=None)[source]

The NetworkRun contains the entire Run state for a Network execution. It has a working copy of the network, but also includes all temporary data required for the execution. These objects are meant to be single use.

Add a Link to the Network. Make sure the link is in the link list and the link parent is set to this Network

Parameters:

link (Link) – link to add

Raises:
add_node(node)[source]

Add a Node to the Network. Make sure the node is in the node list and the node parent is set to this Network

Parameters:node (Node) – node to add
Raises:FastrTypeError – if node is incorrectly typed

Create a link between two Nodes and add it to the current Network.

Parameters:
  • source (BaseOutput) – the output that is the source of the link
  • target (BaseInput) – the input that is the target of the link
  • id (str) – the id of the link
Returns:

the created link

Type:

Link

create_node(tool, id_=None, stepid=None, cores=None, memory=None, walltime=None, nodegroup=None)[source]

Create a Node in this Network. The Node will be automatically added to the Network.

Parameters:
  • tool (Tool) – The Tool to base the Node on
  • id (str) – The id of the node to be created
  • stepid (str) – The stepid to add the created node to
  • nodegroup (str) – The group the node belongs to, this can be important for FlowNodes and such, as they will have matching dimension names.
Returns:

the newly created node

Return type:

Node

create_sink(datatype, id_=None, stepid=None)[source]

Create a SinkNode in this Network. The Node will be automatically added to the Network.

Parameters:
  • datatype (BaseDataType) – The DataType of the sink node
  • id (str) – The id of the sink node to be created
  • stepid (str) – The stepid to add the created sink node to
Returns:

the newly created sink node

Return type:

SinkNode

create_source(datatype, id_=None, stepid=None, nodegroup=None, sourcegroup=None)[source]

Create a SourceNode in this Network. The Node will be automatically added to the Network.

Parameters:
  • datatype (BaseDataType) – The DataType of the source source_node
  • id (str) – The id of the source source_node to be created
  • stepid (str) – The stepid to add the created source source_node to
  • nodegroup (str) – The group the node belongs to, this can be important for FlowNodes and such, as they will have matching dimension names.
  • sourcegroup (str) – DEPRECATED! The nodegroup this SourceNode will be added to
Returns:

the newly created source source_node

Return type:

SourceNode

draw_network(name='network_layout', img_format='svg', draw_dimension=False, expand_macro=False)[source]

Output a dot file and try to convert it to an image file.

Parameters:img_format (str) – extension of the image format to convert to
Returns:path of the image created or None if failed
Return type:str or None

Class for linking outputs (BaseOutput) to inputs (BaseInput)

Examples:

>>> import fastr
>>> network = fastr.Network()
>>> link1 = network.create_link( n1.ouputs['out1'], n2.inputs['in2'] )

link2 = Link()
link2.source = n1.ouputs['out1']
link2.target = n2.inputs['in2']
source

The source BaseOutput of the Link. Setting the source will automatically register the Link with the source BaseOutput. Updating source will also make sure the Link is unregistered with the previous source.

Raises:FastrTypeError – if assigning a non BaseOutput
target

The target BaseInput of the Link. Setting the target will automatically register the Link with the target BaseInput. Updating target will also make sure the Link is unregistered with the previous target.

Raises:FastrTypeError – if assigning a non BaseInput