pipeline¶
pipeline
Package¶
This pipeline
module includes the following workflows:
qipipe.pipeline.qipipeline
: the soup-to-nuts pipeline to stage, mask, register and model new imagesqipipe.pipeline.staging
: executes the staging workflow to detect new images, group them by volume, import them into XNAT and prepare them for TCIA importqipipe.pipeline.mask
: creates a mask to subtract extraneous tissue from the input imagesqipipe.pipeline.registration
: masks the target tissue and corrects motion artifactsqipipe.pipeline.modeling
: performs pharmokinetic modeling
mask
¶
modeling
¶
pipeline_error
¶
-
exception
qipipe.pipeline.pipeline_error.
PipelineError
¶ Bases:
exceptions.Exception
The common pipeline error class.
qipipeline
¶
registration
¶
roi
¶
staging
¶
workflow_base
¶
-
class
qipipe.pipeline.workflow_base.
WorkflowBase
(name, **opts)¶ Bases:
object
The WorkflowBase class is the base class for the qipipe workflow wrapper classes.
If the distributable flag is set, then the execution is distributed using the Nipype plug-in specified in the configuration plug_in parameter.
The workflow plug-in arguments and node inputs can be specified in a
qiutil.ast_config.ASTConfig
file. The configuration directory order consist of the order consist of the search locations in low-to-high precedence order consist of the following:- the qipipe module
conf
directory - the config_dir initialization keyword option
The common configuration is loaded from the
default.cfg
file or in the directory locations. The workflow-specific configuration file name is the lower-case name of theWorkflowBase
subclass with.cfg
extension, e.g.registration.cfg
forqipipe.workflow.registration.RegistrationWorkflow
. The configuration settings are then loaded from the common configuration files followed by the workflow-specific configuration files.Initializes this workflow wrapper object. The parent option obviates the other options.
Parameters: - name – the module name
- opts – the following keyword arguments:
- project – the
project
- parent – the parent workflow for a child workflow
- base_dir – the
base_dir
- config_dir – the optional workflow node
configuration
file location or dictionary - dry_run – the
dry_run
flag - distributable – the
distributable
flag
Raises: PipelineError – if there is neither a project nor a parent argument
-
INTERFACE_PREFIX_PAT
= <_sre.SRE_Pattern object>¶ Regexp matcher for an interface module.
Example:
>>> from qipipe.pipeline.workflow_base import WorkflowBase >>> WorkflowBase.INTERFACE_PREFIX_PAT.match('nipype.interfaces.ants.util.AverageImages').groups() ('nipype.',)
-
MODULE_PREFIX_PAT
= <_sre.SRE_Pattern object>¶ Regexp matcher for a module prefix.
Example:
>>> from qipipe.pipeline.workflow_base import WorkflowBase >>> WorkflowBase.MODULE_PREFIX_PAT.match('ants.util.AverageImages').groups() ('ants.', 'ants.', 'util.', 'AverageImages') >>> WorkflowBase.MODULE_PREFIX_PAT.match('AverageImages') None
-
__init__
(name, **opts)¶ Initializes this workflow wrapper object. The parent option obviates the other options.
Parameters: - name – the module name
- opts – the following keyword arguments:
- project – the
project
- parent – the parent workflow for a child workflow
- base_dir – the
base_dir
- config_dir – the optional workflow node
configuration
file location or dictionary - dry_run – the
dry_run
flag - distributable – the
distributable
flag
Raises: PipelineError – if there is neither a project nor a parent argument
-
base_dir
= None¶ The workflow execution directory (default a new temp directory).
-
config_dir
= None¶ The workflow node inputs configuration directory.
-
configuration
= None¶ The workflow node inputs configuration.
-
depict_workflow
(workflow)¶ Diagrams the given workflow graph. The diagram is written to the name
.dot.png
in the workflow base directory.:param workflow the workflow to diagram
-
dry_run
= None¶ Flag indicating whether to prepare but not run the workflow.
-
is_distributable
= None¶ Flag indicating whether to submit jobs to a cluster.
-
logger
= None¶ This workflow’s logger.
-
project
= None¶ The XNAT project name.
- the qipipe module