interfaces¶

`interfaces` Package¶

The interfaces module includes the custom Nipype interface classes. As a convenience, this interfaces module imports all of the non-proprietary interface classes. The proprietary interface class qipipe.interfaces.fastfit.Fastfit must be imported separately from the qipipe.interfaces.fastfit module, e.g.:

from qipipe.interfaces.fastfit import Fastfit

Importing fastfit in an environment that does not provide the fastfit application will raise an ImportError.

`compress`¶

`convert_bolero_mask`¶

OHSU - This module wraps the proprietary OHSU AIRC bolero_mask_conv utility. bolero_mask_conv converts a proprietary OHSU format mask file into a NIfTI mask file.

class qipipe.interfaces.convert_bolero_mask.ConvertBoleroMask(**inputs)¶

Bases: nipype.interfaces.base.CommandLine

Interface to the proprietary OHSU AIRC bolero_mask_conv utility.

__init__(**inputs)¶

`copy`¶

class qipipe.interfaces.copy.Copy(from_file=None, **inputs)¶

Bases: nipype.interfaces.base.BaseInterface

The Copy interface copies a file to a destination directory.

`dce_to_r1`¶

OHSU - This module wraps the proprietary OHSU AIRC dce_to_r1 utility.

class qipipe.interfaces.dce_to_r1.DceToR1(**inputs)¶

Bases: nipype.interfaces.base.CommandLine

Convert a T1-weighted DCE time series of signal intensities to a series of R1 values.

__init__(**inputs)¶

qipipe.interfaces.dce_to_r1.MASK_FILE_NAME = 'valid_mask.nii.gz'¶: The dce_to_r1 output mask file base name.

qipipe.interfaces.dce_to_r1.OUTPUT_FILE_NAME = 'r1_series.nii.gz'¶: The dce_to_r1 output R1 file base name.

`fastfit`¶

OHSU - This module wraps the proprietary OHSU AIRC fastfit software. fastfit optimizes the input pharmacokinetic model.

Note

this interface is adapted from the OHSU AIRC cluster file /usr/global/scripts/fastfit_iface.py.

class qipipe.interfaces.fastfit.Fastfit(**inputs)¶

Bases: nipype.interfaces.base.CommandLine

Interface to the fastfit software package.

__init__(**inputs)¶

output_spec¶: alias of DynamicTraitedSpec

`fix_dicom`¶

class qipipe.interfaces.fix_dicom.FixDicom(from_file=None, **inputs)¶

Bases: nipype.interfaces.base.BaseInterface

The FixDicom interface wraps the qipipe.staging.fix_dicom.fix_dicom_headers() function.

`group_dicom`¶

`interface_error`¶

`lookup`¶

class qipipe.interfaces.lookup.Lookup(from_file=None, **inputs)¶

Bases: nipype.interfaces.io.IOBase

The Lookup Interface wraps a dictionary look-up.

Example:

>>> from qipipe.interfaces import Lookup
>>> lookup = Lookup(key='a', dictionary=dict(a=1, b=2))
>>> result = lookup.run()
>>> result.outputs.value
1

`map_ctp`¶

Maps the DICOM Patient IDs to the CTP Patient IDs.

class qipipe.interfaces.map_ctp.MapCTP(from_file=None, **inputs)¶

Bases: nipype.interfaces.base.BaseInterface

The MapCTP interface wraps the qipipe.interfaces.map_ctp.map_ctp() method.

`move`¶

class qipipe.interfaces.move.Move(from_file=None, **inputs)¶

Bases: nipype.interfaces.base.BaseInterface

The Move interface moves a file to a destination using shutil.move. Unlike shutil.move, the dest parent directory is created if it does not yet exist (like mkdir -p).

`mri_volcluster`¶

class qipipe.interfaces.mri_volcluster.MriVolCluster(command=None, **inputs)¶

Bases: nipype.interfaces.base.CommandLine

MriVolCluster encapsulates the FSL mri_volcluster command.

`preview`¶

class qipipe.interfaces.preview.Preview(from_file=None, **inputs)¶

Bases: nipype.interfaces.base.BaseInterface

Preview creates a JPEG image from an input DICOM image.

`reorder_bolero_mask`¶

This module reorders the OHSU AIRC bolero_mask_conv result to conform with the time series x and y order.

class qipipe.interfaces.reorder_bolero_mask.ReorderBoleroMask(from_file=None, **inputs)¶

Bases: nipype.interfaces.base.BaseInterface

Interface to the ROI reordering utility.

`sticky_identity`¶

class qipipe.interfaces.sticky_identity.StickyIdentityInterface(fields=None, mandatory_inputs=True, **inputs)¶

Bases: nipype.interfaces.io.IOBase

The StickyIdentityInterface interface class is a copy of the Nipype IdentityInterface. Since Nipype over-zealously elides IdentityInterface nodes from the execution graph, IdentityInterface cannot be used to capture workflow output nor to constrain execution order, as in the examples below. StickyIdentityInterface is an IdentityInterface look-alike that preserves the node connection in the execution graph.

Example:

>> from qipipe.interfaces import StickyIdentityInterface
>> gate = Node(StickyIdentityInterface(fields=['a', 'b']))
>> workflow.connect(upstream1, 'a', gate, 'a')
>> workflow.connect(upstream2, 'b', gate, 'b')
>> workflow.connect(gate, 'a', downstream, 'a')

In this example, the gate node starts after both upstream1 and upstream2 finish. Consequently, the downstream node starts only after both upstream1 and upstream2 finish. This execution precedence constraint does not hold if gate were an IdentityInterface.

Example:

>> from qipipe.interfaces import StickyIdentityInterface
>> output_spec = Node(StickyIdentityInterface(fields=['a']))
>> workflow.connect(upstream, 'a', output_spec, 'a')
>> upstream.inputs.a = 1
>> # The magic incantation to get a Nipype workflow output.
>> wf_res = workflow.run()
>> output_res = next(n for n in wf_res.nodes()
...                  if n.name == 'output_spec')
>> output_res.inputs.get()['a']
1
>> # But, oddly:
>> output_res.outputs.get()['a']  # bad!
<undefined>

Note

a better solution is to set a preserve flag on IdentityInterface. If this solution is implemented by Nipype, then this StickyIdentityInterface class will be deprecated.

__init__(fields=None, mandatory_inputs=True, **inputs)¶

input_spec¶: alias of DynamicTraitedSpec

output_spec¶: alias of DynamicTraitedSpec

`touch`¶

class qipipe.interfaces.touch.Touch(from_file=None, **inputs)¶

Bases: nipype.interfaces.base.BaseInterface

The Touch interface emulates the Unix touch command. This interface is useful for stubbing out processing nodes during workflow development.

`uncompress`¶

`unpack`¶

class qipipe.interfaces.unpack.Unpack(input_name, output_names, mandatory_inputs=True, **inputs)¶

Bases: nipype.interfaces.io.IOBase

The Unpack Interface converts a list input field to one output field per list item.

Example:

>>> from qipipe.interfaces.unpack import Unpack
>>> unpack = Unpack(input_name='list', output_names=['a', 'b'], list=[1, 2])
>>> result = unpack.run()
>>> result.outputs.a
1
>>> result.outputs.b
2

Parameters:	input_name – the input list field name output_names – the output field names mandatory_inputs – a flag indicating whether every input field is required inputs – the input field name => value bindings

__init__(input_name, output_names, mandatory_inputs=True, **inputs)¶

Parameters:	input_name – the input list field name output_names – the output field names mandatory_inputs – a flag indicating whether every input field is required inputs – the input field name => value bindings

input_spec¶: alias of DynamicTraitedSpec

output_spec¶: alias of DynamicTraitedSpec

`update_qiprofile`¶

class qipipe.interfaces.update_qiprofile.UpdateQIProfile(from_file=None, **inputs)¶

Bases: nipype.interfaces.base.BaseInterface

The UpdateQIProfile Nipype interface updates the Imaging Profile database.

`xnat_copy`¶

class qipipe.interfaces.xnat_copy.XNATCopy(command=None, **inputs)¶

Bases: nipype.interfaces.base.CommandLine

The XNATCopy Nipype interface wraps the cpxnat command.

input_spec¶: alias of XNATCopyInputSpec

class qipipe.interfaces.xnat_copy.XNATCopyInputSpec(**kwargs)¶

Bases: nipype.interfaces.base.CommandLineInputSpec

The input spec with arguments in the following order: * options * the input files, for an upload * the XNAT object path * the destination directory, for a download

Initialize handlers and inputs

`xnat_download`¶

qipipe.interfaces.xnat_download.CONTAINER_OPTS = ['container_type', 'scan', 'reconstruction', 'assessor']¶: The download input container options.

class qipipe.interfaces.xnat_download.XNATDownload(from_file=None, **inputs)¶

Bases: nipype.interfaces.base.BaseInterface

The XNATDownload Nipype interface wraps the qixnat.facade.XNAT.download() method.

Note

only one XNAT operation can run at a time.

Examples:

>>> # Download the scan NIfTI files.
>>> from qipipe.interfaces import XNATDownload
>>> XNATDownload(project='QIN', subject='Breast003',
...     session='Session02', scan=1, resource='NIFTI',
...     dest='data').run()

>>> # Download the scan DICOM files.
>>> from qipipe.interfaces import XNATDownload
>>> XNATDownload(project='QIN', subject='Breast003',
...     session='Session02', scan=1, resource='DICOM',
...     dest='data').run()

>>> # Download the registration reg_H3pIz4s images.
>>> from qipipe.interfaces import XNATDownload
>>> XNATDownload(project='QIN', subject='Breast003',
...     session='Session02', resource='reg_H3pIz4',
...     dest='data').run()

`xnat_find`¶

class qipipe.interfaces.xnat_find.XNATFind(**inputs)¶

Bases: nipype.interfaces.base.BaseInterface

The XNATFind Nipype interface wraps the qixnat.facade.XNAT find_one and find_or_create methods.

Note

concurrent XNAT operations can fail. See the qipipe.pipeline.staging.StagingWorkflow note.

__init__(**inputs)¶

`xnat_upload`¶

class qipipe.interfaces.xnat_upload.XNATUpload(from_file=None, **inputs)¶

Bases: nipype.interfaces.base.BaseInterface

The XNATUpload Nipype interface wraps the qixnat.facade.XNAT.upload() method.

interfaces¶

interfaces Package¶

compress¶

convert_bolero_mask¶

copy¶

dce_to_r1¶

fastfit¶

fix_dicom¶

group_dicom¶

interface_error¶

lookup¶

map_ctp¶

move¶

mri_volcluster¶

preview¶

reorder_bolero_mask¶

sticky_identity¶

touch¶

uncompress¶

unpack¶

update_qiprofile¶

xnat_copy¶

xnat_download¶

xnat_find¶

xnat_upload¶

`interfaces` Package¶

`compress`¶

`convert_bolero_mask`¶

`copy`¶

`dce_to_r1`¶

`fastfit`¶

`fix_dicom`¶

`group_dicom`¶

`interface_error`¶

`lookup`¶

`map_ctp`¶

`move`¶

`mri_volcluster`¶

`preview`¶

`reorder_bolero_mask`¶

`sticky_identity`¶

`touch`¶

`uncompress`¶

`unpack`¶

`update_qiprofile`¶

`xnat_copy`¶

`xnat_download`¶

`xnat_find`¶

`xnat_upload`¶