Python nipype.MapNode类代码示例

def test_serial_input(tmpdir):
    tmpdir.chdir()
    wd = os.getcwd()
    from nipype import MapNode, Function, Workflow

    def func1(in1):
        return in1
    n1 = MapNode(Function(input_names=['in1'],
                          output_names=['out'],
                          function=func1),
                 iterfield=['in1'],
                 name='n1')
    n1.inputs.in1 = [1, 2, 3]

    w1 = Workflow(name='test')
    w1.base_dir = wd
    w1.add_nodes([n1])
    # set local check
    w1.config['execution'] = {'stop_on_first_crash': 'true',
                              'local_hash_check': 'true',
                              'crashdump_dir': wd,
                              'poll_sleep_duration': 2}

    # test output of num_subnodes method when serial is default (False)
    assert n1.num_subnodes() == len(n1.inputs.in1)

    # test running the workflow on default conditions
    w1.run(plugin='MultiProc')

    # test output of num_subnodes method when serial is True
    n1._serial = True
    assert n1.num_subnodes() == 1

    # test running the workflow on serial conditions
    w1.run(plugin='MultiProc')

def test_serial_input():
    cwd = os.getcwd()
    wd = mkdtemp()
    os.chdir(wd)
    from nipype import MapNode, Function, Workflow
    def func1(in1):
        return in1
    n1 = MapNode(Function(input_names=['in1'],
                          output_names=['out'],
                          function=func1),
                 iterfield=['in1'],
                 name='n1')
    n1.inputs.in1 = [1,2,3]


    w1 = Workflow(name='test')
    w1.base_dir = wd
    w1.add_nodes([n1])
    # set local check
    w1.config['execution'] = {'stop_on_first_crash': 'true',
                              'local_hash_check': 'true',
                              'crashdump_dir': wd}

    # test output of num_subnodes method when serial is default (False)
    yield assert_equal, n1.num_subnodes(), len(n1.inputs.in1)

    # test running the workflow on default conditions
    error_raised = False
    try:
        w1.run(plugin='MultiProc')
    except Exception, e:
        pe.logger.info('Exception: %s' % str(e))
        error_raised = True

def test_mapnode_nested():
    cwd = os.getcwd()
    wd = mkdtemp()
    os.chdir(wd)
    from nipype import MapNode, Function
    def func1(in1):
        return in1 + 1
    n1 = MapNode(Function(input_names=['in1'],
                          output_names=['out'],
                          function=func1),
                 iterfield=['in1'],
                 nested=True,
                 name='n1')
    n1.inputs.in1 = [[1,[2]],3,[4,5]]
    n1.run()
    print n1.get_output('out')
    yield assert_equal, n1.get_output('out'), [[2,[3]],4,[5,6]]

    n2 = MapNode(Function(input_names=['in1'],
                          output_names=['out'],
                          function=func1),
                 iterfield=['in1'],
                 nested=False,
                 name='n1')
    n2.inputs.in1 = [[1,[2]],3,[4,5]]
    error_raised = False
    try:
        n2.run()
    except Exception, e:
        pe.logger.info('Exception: %s' % str(e))
        error_raised = True

def test_mapnode_iterfield_type(x_inp, f_exp):
    from nipype import MapNode, Function
    def double_func(x):
        return 2 * x
    double = Function(["x"], ["f_x"], double_func)

    double_node = MapNode(double, name="double", iterfield=["x"])
    double_node.inputs.x = x_inp

    res  = double_node.run()
    assert res.outputs.f_x == f_exp

def test_mapnode_nested(tmpdir):
    tmpdir.chdir()
    from nipype import MapNode, Function

    def func1(in1):
        return in1 + 1
    n1 = MapNode(Function(input_names=['in1'],
                          output_names=['out'],
                          function=func1),
                 iterfield=['in1'],
                 nested=True,
                 name='n1')
    n1.inputs.in1 = [[1, [2]], 3, [4, 5]]
    n1.run()
    print(n1.get_output('out'))
    assert n1.get_output('out') == [[2, [3]], 4, [5, 6]]

    n2 = MapNode(Function(input_names=['in1'],
                          output_names=['out'],
                          function=func1),
                 iterfield=['in1'],
                 nested=False,
                 name='n1')
    n2.inputs.in1 = [[1, [2]], 3, [4, 5]]

    with pytest.raises(Exception) as excinfo:
        n2.run()
    assert "can only concatenate list" in str(excinfo.value)

def test_mapnode_expansion(tmpdir):
    tmpdir.chdir()
    from nipype import MapNode, Function

    def func1(in1):
        return in1 + 1

    mapnode = MapNode(Function(function=func1),
                      iterfield='in1',
                      name='mapnode',
                      n_procs=2,
                      mem_gb=2)
    mapnode.inputs.in1 = [1, 2]

    for idx, node in mapnode._make_nodes():
        for attr in ('overwrite', 'run_without_submitting', 'plugin_args'):
            assert getattr(node, attr) == getattr(mapnode, attr)
        for attr in ('_n_procs', '_mem_gb'):
            assert (getattr(node, attr) ==
                    getattr(mapnode, attr))

def run_bet(T1_image, workdir):
    """Run freesurfer, convert to nidm and extract stats
    """
    from nipype import fsl
    from nipype import MapNode

    strip = MapNode(fsl.BET(), iterfield=['in_file'], name='skullstripper')
    strip.inputs.in_file = T1_image
    strip.inputs.mesh = True
    strip.inputs.mask = True
    strip.base_dir = workdir

    bet_results = strip.run()
    provgraph = bet_results.provenance[0]
    for bundle in bet_results.provenance[1:]:
        provgraph.add_bundle(bundle)

    vol = MapNode(fsl.ImageStats(op_string='-V'), iterfield=['in_file'],
                  name='volumeextractor')
    vol.inputs.in_file = bet_results.outputs.out_file
    vol.base_dir = workdir
    vol_results = vol.run()
    for bundle in vol_results.provenance:
        provgraph.add_bundle(bundle)

    return provgraph, provgraph.rdf()

def create_workflow(files,
                    target_file,
                    subject_id,
                    TR,
                    slice_times,
                    norm_threshold=1,
                    num_components=5,
                    vol_fwhm=None,
                    surf_fwhm=None,
                    lowpass_freq=-1,
                    highpass_freq=-1,
                    subjects_dir=None,
                    sink_directory=os.getcwd(),
                    target_subject=['fsaverage3', 'fsaverage4'],
                    name='resting'):

    wf = Workflow(name=name)

    # Rename files in case they are named identically
    name_unique = MapNode(Rename(format_string='rest_%(run)02d'),
                          iterfield=['in_file', 'run'],
                          name='rename')
    name_unique.inputs.keep_ext = True
    name_unique.inputs.run = list(range(1, len(files) + 1))
    name_unique.inputs.in_file = files

    realign = Node(nipy.SpaceTimeRealigner(), name="spacetime_realign")
    realign.inputs.slice_times = slice_times
    realign.inputs.tr = TR
    realign.inputs.slice_info = 2
    realign.plugin_args = {'sbatch_args': '-c%d' % 4}

    # Compute TSNR on realigned data regressing polynomials up to order 2
    tsnr = MapNode(TSNR(regress_poly=2), iterfield=['in_file'], name='tsnr')
    wf.connect(realign, "out_file", tsnr, "in_file")

    # Compute the median image across runs
    calc_median = Node(Function(input_names=['in_files'],
                                output_names=['median_file'],
                                function=median,
                                imports=imports),
                       name='median')
    wf.connect(tsnr, 'detrended_file', calc_median, 'in_files')

    """Segment and Register
    """

    registration = create_reg_workflow(name='registration')
    wf.connect(calc_median, 'median_file', registration, 'inputspec.mean_image')
    registration.inputs.inputspec.subject_id = subject_id
    registration.inputs.inputspec.subjects_dir = subjects_dir
    registration.inputs.inputspec.target_image = target_file

    """Quantify TSNR in each freesurfer ROI
    """

    get_roi_tsnr = MapNode(fs.SegStats(default_color_table=True),
                           iterfield=['in_file'], name='get_aparc_tsnr')
    get_roi_tsnr.inputs.avgwf_txt_file = True
    wf.connect(tsnr, 'tsnr_file', get_roi_tsnr, 'in_file')
    wf.connect(registration, 'outputspec.aparc', get_roi_tsnr, 'segmentation_file')

    """Use :class:`nipype.algorithms.rapidart` to determine which of the
    images in the functional series are outliers based on deviations in
    intensity or movement.
    """

    art = Node(interface=ArtifactDetect(), name="art")
    art.inputs.use_differences = [True, True]
    art.inputs.use_norm = True
    art.inputs.norm_threshold = norm_threshold
    art.inputs.zintensity_threshold = 9
    art.inputs.mask_type = 'spm_global'
    art.inputs.parameter_source = 'NiPy'

    """Here we are connecting all the nodes together. Notice that we add the merge node only if you choose
    to use 4D. Also `get_vox_dims` function is passed along the input volume of normalise to set the optimal
    voxel sizes.
    """

    wf.connect([(name_unique, realign, [('out_file', 'in_file')]),
                (realign, art, [('out_file', 'realigned_files')]),
                (realign, art, [('par_file', 'realignment_parameters')]),
                ])

    def selectindex(files, idx):
        import numpy as np
        from nipype.utils.filemanip import filename_to_list, list_to_filename
        return list_to_filename(np.array(filename_to_list(files))[idx].tolist())

    mask = Node(fsl.BET(), name='getmask')
    mask.inputs.mask = True
    wf.connect(calc_median, 'median_file', mask, 'in_file')
    # get segmentation in normalized functional space

    def merge_files(in1, in2):
        out_files = filename_to_list(in1)
        out_files.extend(filename_to_list(in2))
        return out_files

#.........这里部分代码省略.........

def create_workflow(files,
                    subject_id,
                    n_vol=0,
                    despike=True,
                    TR=None,
                    slice_times=None,
                    slice_thickness=None,
                    fieldmap_images=[],
                    norm_threshold=1,
                    num_components=6,
                    vol_fwhm=None,
                    surf_fwhm=None,
                    lowpass_freq=-1,
                    highpass_freq=-1,
                    sink_directory=os.getcwd(),
                    FM_TEdiff=2.46,
                    FM_sigma=2,
                    FM_echo_spacing=.7,
                    target_subject=['fsaverage3', 'fsaverage4'],
                    name='resting'):

    wf = Workflow(name=name)

    # Skip starting volumes
    remove_vol = MapNode(fsl.ExtractROI(t_min=n_vol, t_size=-1),
                         iterfield=['in_file'],
                         name="remove_volumes")
    remove_vol.inputs.in_file = files

    # Run AFNI's despike. This is always run, however, whether this is fed to
    # realign depends on the input configuration
    despiker = MapNode(afni.Despike(outputtype='NIFTI_GZ'),
                       iterfield=['in_file'],
                       name='despike')
    #despiker.plugin_args = {'qsub_args': '-l nodes=1:ppn='}

    wf.connect(remove_vol, 'roi_file', despiker, 'in_file')

    # Run Nipy joint slice timing and realignment algorithm
    realign = Node(nipy.SpaceTimeRealigner(), name='realign')
    realign.inputs.tr = TR
    realign.inputs.slice_times = slice_times
    realign.inputs.slice_info = 2

    if despike:
        wf.connect(despiker, 'out_file', realign, 'in_file')
    else:
        wf.connect(remove_vol, 'roi_file', realign, 'in_file')

    # Comute TSNR on realigned data regressing polynomials upto order 2
    tsnr = MapNode(TSNR(regress_poly=2), iterfield=['in_file'], name='tsnr')
    wf.connect(realign, 'out_file', tsnr, 'in_file')

    # Compute the median image across runs
    calc_median = Node(Function(input_names=['in_files'],
                                output_names=['median_file'],
                                function=median,
                                imports=imports),
                       name='median')
    wf.connect(tsnr, 'detrended_file', calc_median, 'in_files')

    # Coregister the median to the surface
    register = Node(freesurfer.BBRegister(),
                    name='bbregister')
    register.inputs.subject_id = subject_id
    register.inputs.init = 'fsl'
    register.inputs.contrast_type = 't2'
    register.inputs.out_fsl_file = True
    register.inputs.epi_mask = True

    # Compute fieldmaps and unwarp using them
    if fieldmap_images:
        fieldmap = Node(interface=EPIDeWarp(), name='fieldmap_unwarp')
        fieldmap.inputs.tediff = FM_TEdiff
        fieldmap.inputs.esp = FM_echo_spacing
        fieldmap.inputs.sigma = FM_sigma
        fieldmap.inputs.mag_file = fieldmap_images[0]
        fieldmap.inputs.dph_file = fieldmap_images[1]
        wf.connect(calc_median, 'median_file', fieldmap, 'exf_file')

        dewarper = MapNode(interface=fsl.FUGUE(), iterfield=['in_file'],
                           name='dewarper')
        wf.connect(tsnr, 'detrended_file', dewarper, 'in_file')
        wf.connect(fieldmap, 'exf_mask', dewarper, 'mask_file')
        wf.connect(fieldmap, 'vsm_file', dewarper, 'shift_in_file')
        wf.connect(fieldmap, 'exfdw', register, 'source_file')
    else:
        wf.connect(calc_median, 'median_file', register, 'source_file')

    # Get the subject's freesurfer source directory
    fssource = Node(FreeSurferSource(),
                    name='fssource')
    fssource.inputs.subject_id = subject_id
    fssource.inputs.subjects_dir = os.environ['SUBJECTS_DIR']

    # Extract wm+csf, brain masks by eroding freesurfer lables and then
    # transform the masks into the space of the median
    wmcsf = Node(freesurfer.Binarize(), name='wmcsfmask')
    mask = wmcsf.clone('anatmask')
    wmcsftransform = Node(freesurfer.ApplyVolTransform(inverse=True,
#.........这里部分代码省略.........

def create_timeseries_model_workflow(name="model", exp_info=None):

    # Default experiment parameters for generating graph inamge, testing, etc.
    if exp_info is None:
        exp_info = default_experiment_parameters()

    # Define constant inputs
    inputs = ["design_file", "realign_file", "artifact_file", "timeseries"]

    # Possibly add the regressor file to the inputs
    if exp_info["regressor_file"] is not None:
        inputs.append("regressor_file")

    # Define the workflow inputs
    inputnode = Node(IdentityInterface(inputs), "inputs")

    # Set up the experimental design
    modelsetup = MapNode(Function(["exp_info",
                                   "design_file",
                                   "realign_file",
                                   "artifact_file",
                                   "regressor_file",
                                   "run"],
                                  ["design_matrix_file",
                                   "contrast_file",
                                   "design_matrix_pkl",
                                   "report"],
                                  setup_model,
                                  imports),
                          ["realign_file", "artifact_file", "run"],
                          "modelsetup")
    modelsetup.inputs.exp_info = exp_info
    if exp_info["regressor_file"] is None:
        modelsetup.inputs.regressor_file = None

    # Use film_gls to estimate the timeseries model
    modelestimate = MapNode(fsl.FILMGLS(smooth_autocorr=True,
                                        mask_size=5,
                                        threshold=1000),
                            ["design_file", "in_file"],
                            "modelestimate")

    # Run the contrast estimation routine
    contrastestimate = MapNode(fsl.ContrastMgr(),
                               ["tcon_file",
                                "dof_file",
                                "corrections",
                                "param_estimates",
                                "sigmasquareds"],
                               "contrastestimate")

    calcrsquared = MapNode(Function(["design_matrix_pkl",
                                     "timeseries",
                                     "pe_files"],
                                    ["r2_files",
                                     "ss_files"],
                                    compute_rsquareds,
                                    imports),
                           ["design_matrix_pkl",
                            "timeseries",
                            "pe_files"],
                           "calcrsquared")
    calcrsquared.plugin_args = dict(qsub_args="-l h_vmem=8G")

    # Save the experiment info for this run
    dumpjson = MapNode(Function(["exp_info", "timeseries"], ["json_file"],
                                dump_exp_info, imports),
                    "timeseries",
                    "dumpjson")
    dumpjson.inputs.exp_info = exp_info

    # Report on the results of the model
    modelreport = MapNode(Function(["timeseries",
                                    "sigmasquareds_file",
                                    "zstat_files",
                                    "r2_files"],
                                   ["report"],
                                   report_model,
                                   imports),
                          ["timeseries", "sigmasquareds_file",
                           "zstat_files", "r2_files"],
                          "modelreport")

    # Define the workflow outputs
    outputnode = Node(IdentityInterface(["results",
                                         "copes",
                                         "varcopes",
                                         "zstats",
                                         "r2_files",
                                         "ss_files",
                                         "report",
                                         "design_mat",
                                         "contrast_mat",
                                         "design_pkl",
                                         "design_report",
                                         "json_file"]),
                      "outputs")

    # Define the workflow and connect the nodes
    model = Workflow(name=name)
#.........这里部分代码省略.........

def create_timeseries_model_workflow(name="model", exp_info=None):

    # Default experiment parameters for generating graph image, testing, etc.
    if exp_info is None:
        exp_info = lyman.default_experiment_parameters()

    # Define constant inputs
    inputs = ["realign_file", "artifact_file", "timeseries"]

    # Possibly add the design and regressor files to the inputs
    if exp_info["design_name"] is not None:
        inputs.append("design_file")
    if exp_info["regressor_file"] is not None:
        inputs.append("regressor_file")

    # Define the workflow inputs
    inputnode = Node(IdentityInterface(inputs), "inputs")

    # Set up the experimental design
    modelsetup = MapNode(ModelSetup(exp_info=exp_info),
                         ["timeseries", "realign_file", "artifact_file"],
                         "modelsetup")

    # For some nodes, make it possible to request extra memory
    mem_request = {"qsub_args": "-l h_vmem=%dG" % exp_info["memory_request"]}

    # Use film_gls to estimate the timeseries model
    modelestimate = MapNode(fsl.FILMGLS(smooth_autocorr=True,
                                        mask_size=5,
                                        threshold=100),
                            ["design_file", "in_file"],
                            "modelestimate")
    modelestimate.plugin_args = mem_request

    # Run the contrast estimation routine
    contrastestimate = MapNode(fsl.ContrastMgr(),
                               ["tcon_file",
                                "dof_file",
                                "corrections",
                                "param_estimates",
                                "sigmasquareds"],
                               "contrastestimate")
    contrastestimate.plugin_args = mem_request

    # Compute summary statistics about the model fit
    modelsummary = MapNode(ModelSummary(),
                           ["design_matrix_pkl",
                            "timeseries",
                            "pe_files"],
                           "modelsummary")
    modelsummary.plugin_args = mem_request

    # Save the experiment info for this run
    # Save the experiment info for this run
    saveparams = MapNode(SaveParameters(exp_info=exp_info),
                         "in_file", "saveparams")

    # Report on the results of the model
    # Note: see below for a conditional iterfield
    modelreport = MapNode(ModelReport(),
                          ["timeseries", "sigmasquareds_file",
                           "tsnr_file", "r2_files"],
                          "modelreport")

    # Define the workflow outputs
    outputnode = Node(IdentityInterface(["results",
                                         "copes",
                                         "varcopes",
                                         "zstats",
                                         "r2_files",
                                         "ss_files",
                                         "tsnr_file",
                                         "report",
                                         "design_mat",
                                         "contrast_mat",
                                         "design_pkl",
                                         "design_report",
                                         "json_file"]),
                      "outputs")

    # Define the workflow and connect the nodes
    model = Workflow(name=name)
    model.connect([
        (inputnode, modelsetup,
            [("realign_file", "realign_file"),
             ("artifact_file", "artifact_file"),
             ("timeseries", "timeseries")]),
        (inputnode, modelestimate,
            [("timeseries", "in_file")]),
        (inputnode, saveparams,
            [("timeseries", "in_file")]),
        (modelsetup, modelestimate,
            [("design_matrix_file", "design_file")]),
        (modelestimate, contrastestimate,
            [("dof_file", "dof_file"),
             ("corrections", "corrections"),
             ("param_estimates", "param_estimates"),
             ("sigmasquareds", "sigmasquareds")]),
        (modelsetup, contrastestimate,
            [("contrast_file", "tcon_file")]),
#.........这里部分代码省略.........