Python PipelineDevelopperView.show方法代码示例

# 需要导入模块: from capsul.qt_gui.widgets import PipelineDevelopperView [as 别名]
# 或者: from capsul.qt_gui.widgets.PipelineDevelopperView import show [as 别名]
    def test_simple_run(self):
        """ Method to test a simple 1 cpu call with the scheduler.
        """
        # Configure the environment
        study_config = StudyConfig(
            modules=[],
            use_smart_caching=True,
            output_directory=self.outdir,
            number_of_cpus=1,
            generate_logging=True,
            use_scheduler=True)

        # Create pipeline
        pipeline = get_process_instance(self.pipeline_name)
        pipeline.date_in_filename = True

        # Set pipeline input parameters
        dicom_dataset = get_sample_data("dicom")
        dcmfolder = os.path.join(self.outdir, "dicom")
        if not os.path.isdir(dcmfolder):
            os.makedirs(dcmfolder)
        shutil.copy(dicom_dataset.barre, os.path.join(dcmfolder, "heart.dcm"))
        pipeline.source_dir = dcmfolder

        # View pipeline
        if 0:
            from capsul.qt_gui.widgets import PipelineDevelopperView
            from PySide import QtGui
            app = QtGui.QApplication(sys.argv)
            view1 = PipelineDevelopperView(pipeline)
            view1.show()
            app.exec_()

        # Execute the pipeline in the configured study
        study_config.run(pipeline)

# 需要导入模块: from capsul.qt_gui.widgets import PipelineDevelopperView [as 别名]
# 或者: from capsul.qt_gui.widgets.PipelineDevelopperView import show [as 别名]
class ActivationInspectorApp(Application):
    """ ActiovationInspector Application.
    """
    # Load some meta informations
    from capsul.info import __version__ as _version
    from capsul.info import NAME as _application_name
    from capsul.info import ORGANISATION as _organisation_name

    def __init__(self, pipeline_path, record_file=None, *args, **kwargs):
        """ Method to initialize the ActivationInspectorApp class.

        Parameters
        ----------
        pipeline_path: str (mandatory)
            the name of the pipeline we want to load.
        record_file: str (optional)
            a file where the pipeline activation steps are stored.
        """
        # Inhetritance
        super(ActivationInspectorApp, self).__init__(*args, **kwargs)

        # Load the pipeline
        self.pipeline = get_process_instance(pipeline_path)

        # Initialize the application
        self.record_file = record_file
        self.window = None
        self.init_window()

    def init_window(self):
        """ Method to initialize the main window.
        """
        # First set some meta informations
        self.setApplicationName(self._application_name)
        self.setOrganizationName(self._organisation_name)
        self.setApplicationVersion(self._version)

        # Get the user interface description from capsul resources
        ui_file = os.path.join(
            os.path.dirname(__file__), "activation_inspector.ui")
        #ui_file = os.path.join(resources.__path__[0], "activation_inspector.ui")

        # Create and show the activation/pipeline/controller windows
        self.pipeline_window = PipelineDevelopperView(self.pipeline)
        self.controller_window = ScrollControllerWidget(self.pipeline,live=True)
        self.activation_window = ActivationInspector(
            self.pipeline, ui_file, self.record_file,
            developper_view=self.pipeline_window)
        self.pipeline_window.show()
        self.activation_window.show()
        self.controller_window.show()

        return True

# 需要导入模块: from capsul.qt_gui.widgets import PipelineDevelopperView [as 别名]
# 或者: from capsul.qt_gui.widgets.PipelineDevelopperView import show [as 别名]
            except: pass
            try:
                os.unlink(output_name)
            except: pass


def test():
    """ Function to execute unitest
    """
    suite = unittest.TestLoader().loadTestsFromTestCase(TestPipelineWithTemp)
    runtime = unittest.TextTestRunner(verbosity=2).run(suite)
    return runtime.wasSuccessful()


if __name__ == "__main__":
    print "RETURNCODE: ", test()

    if 1:
        import sys
        from soma.qt_gui.qt_backend import QtGui
        from capsul.qt_gui.widgets import PipelineDevelopperView

        app = QtGui.QApplication(sys.argv)
        pipeline = MyPipeline()
        pipeline.input_image = '/data/file.txt'
        pipeline.output_image = '/data/output_file.txt'
        view1 = PipelineDevelopperView(pipeline)
        view1.show()
        app.exec_()
        del view1

# 需要导入模块: from capsul.qt_gui.widgets import PipelineDevelopperView [as 别名]
# 或者: from capsul.qt_gui.widgets.PipelineDevelopperView import show [as 别名]
def pilot_bet(enable_display=False):
    """ 
    BET
    ===

    Brain extraction with FSL. 

    Start to import required modules:
    """
    import os
    from mmutils.toy_datasets import get_sample_data
    from capsul.study_config import StudyConfig
    from capsul.process import get_process_instance

    """
    Study configuration
    -------------------

    We first define the working directory and guarantee this folder exists on
    the file system:
    """
    working_dir = "/volatile/nsap/catalogue/pclinfmri/fsl_bet"
    if not os.path.isdir(working_dir):
        os.makedirs(working_dir)

    """
    And then define the study configuration:
    """
    study_config = StudyConfig(
        modules=["MatlabConfig", "SPMConfig", "FSLConfig", "NipypeConfig"],
        use_smart_caching=False,
        fsl_config="/etc/fsl/4.1/fsl.sh",
        use_fsl=True,
        output_directory=working_dir,
        number_of_cpus=1,
        generate_logging=True,
        use_scheduler=True)

    """
    Load the toy dataset
    --------------------

    To do so, we use the get_sample_data function to download the toy
    dataset on the local file system (here localizer data):
    """
    toy_dataset = get_sample_data("localizer")

    """
    The toy_dataset is an Enum structure with some specific elements of
    interest:

        * fmri: the functional volume.
        * anat: the structural volume.
        * TR: the repetition time.

    Processing definition
    ---------------------

    First create the
    :ref:`slice timing pipeline <clinfmri.preproc.FslBet>` that
    define the different step of the processings:
    """
    pipeline = get_process_instance("clinfmri.utils.fsl_bet.xml")
    print pipeline.get_input_spec()

    """
    It is possible to display the pipeline.
    """
    if enable_display:
        import sys
        from PySide import QtGui
        from capsul.qt_gui.widgets import PipelineDevelopperView

        app = QtGui.QApplication(sys.argv)
        view = PipelineDevelopperView(pipeline)
        view.show()
        app.exec_()

    """
    Now we need now to parametrize this pipeline:
    """
    pipeline.input_image_file = toy_dataset.anat
    pipeline.generate_binary_mask = True
    pipeline.bet_threshold = 0.5

    """
    The pipeline is now ready to be run:
    """
    study_config.run(pipeline, executer_qc_nodes=False, verbose=1)

    """
    Results
    -------

    Finally, we print the pipeline outputs:
    """
    print("\nOUTPUTS\n")
    for trait_name, trait_value in pipeline.get_outputs().items():
        print("{0}: {1}".format(trait_name, trait_value))

# 需要导入模块: from capsul.qt_gui.widgets import PipelineDevelopperView [as 别名]
# 或者: from capsul.qt_gui.widgets.PipelineDevelopperView import show [as 别名]
def pilot_new_segment(enable_display=False):
    """ 
    New Segment
    ===========

    Unifed SPM segmentation: segments, bias corrects and spatially normalises. 

    Start to import required modules:
    """
    import os
    from mmutils.toy_datasets import get_sample_data
    from capsul.study_config import StudyConfig
    from capsul.process import get_process_instance

    """
    Study configuration
    -------------------

    We first define the working directory and guarantee this folder exists on
    the file system:
    """
    working_dir = "/volatile/nsap/catalogue/pclinfmri/spm_newsegment"
    if not os.path.isdir(working_dir):
        os.makedirs(working_dir)

    """
    And then define the study configuration:
    """
    study_config = StudyConfig(
        modules=["MatlabConfig", "SPMConfig", "FSLConfig", "NipypeConfig"],
        use_smart_caching=False,
        matlab_exec="/neurospin/local/bin/matlab",
        use_matlab=True,
        spm_directory="/i2bm/local/spm8",
        use_spm=True,
        output_directory=working_dir,
        number_of_cpus=1,
        generate_logging=True,
        use_scheduler=True)

    """
    Load the toy dataset
    --------------------

    To do so, we use the get_sample_data function to download the toy
    dataset on the local file system (here localizer data):
    """
    toy_dataset = get_sample_data("localizer")
    template_dataset = get_sample_data("mni_1mm")

    """
    The toy_dataset is an Enum structure with some specific elements of
    interest:

        * fmri: the functional volume.
        * anat: the structural volume.
        * TR: the repetition time.

    Processing definition
    ---------------------

    First create the
    :ref:`slice timing pipeline <clinfmri.utils.SpmNewSegment>`
    that define the different step of the processings:
    """
    pipeline = get_process_instance("clinfmri.utils.spm_new_segment.xml")
    print pipeline.get_input_spec()

    """
    It is possible to display the pipeline.
    """
    if enable_display:
        import sys
        from PySide import QtGui
        from capsul.qt_gui.widgets import PipelineDevelopperView

        app = QtGui.QApplication(sys.argv)
        view = PipelineDevelopperView(pipeline)
        view.show()
        app.exec_()

    """
    Now we need now to parametrize this pipeline:
    """
    pipeline.channel_files = [toy_dataset.mean]
    pipeline.reference_volume = template_dataset.brain

    """
    The pipeline is now ready to be run:
    """
    study_config.run(pipeline, executer_qc_nodes=False, verbose=1)

    """
    Results
    -------

    Finally, we print the pipeline outputs:
    """
    print("\nOUTPUTS\n")
    for trait_name, trait_value in pipeline.get_outputs().items():
#.........这里部分代码省略.........

# 需要导入模块: from capsul.qt_gui.widgets import PipelineDevelopperView [as 别名]
# 或者: from capsul.qt_gui.widgets.PipelineDevelopperView import show [as 别名]
def pilot_qa_fmri():
    """
    Imports
    -------

    This code needs 'capsul' and 'mmutils' package in order to instanciate and
    execute the pipeline and to get a toy dataset.
    These packages are available in the 'neurospin' source list or in pypi.
    """
    # Capsul import
    from capsul.study_config.study_config import StudyConfig
    from capsul.process.loader import get_process_instance

    # Mmutils import
    from mmutils.toy_datasets import get_sample_data

    """
    Parameters
    ----------

    The 'pipeline_name' parameter contains the location of the pipeline XML
    description that will perform the DICOMs conversion, and the 'outdir' the
    location of the pipeline's results: in this case a temporary directory.
    """

    pipeline_name = "mmqa.fmri.fmri_quality_assurance_bbox.xml"
    outdir = tempfile.mkdtemp()

    """
    Capsul configuration
    --------------------

    A 'StudyConfig' has to be instantiated in order to execute the pipeline
    properly. It enables us to define the results directory through the
    'output_directory' attribute, the number of CPUs to be used through the
    'number_of_cpus' attributes, and to specify that we want a log of the
    processing step through the 'generate_logging'. The 'use_scheduler'
    must be set to True if more than 1 CPU is used.
    """
    study_config = StudyConfig(
        number_of_cpus=1,
        generate_logging=True,
        use_scheduler=True,
        output_directory=outdir)
    """
    Get the toy dataset
    -------------------

    The toy dataset is composed of a functional image that is downloaded
    if it is necessary throught the 'get_sample_data' function and exported
    locally.
    """

    localizer_dataset = get_sample_data("localizer_extra")

    """
    Pipeline definition
    -------------------

    The pipeline XML description is first imported throught the
    'get_process_instance' method, and the resulting pipeline instance is
    parametrized: in this example we decided to set the date in the converted
    file name and we set two DICOM directories to be converted in Nifti
    format.
    """

    pipeline = get_process_instance(pipeline_name)
    pipeline.image_file = localizer_dataset.fmri
    pipeline.repetition_time = 2.0
    pipeline.exclude_volume = []
    pipeline.roi_size = 21
    pipeline.score_file = os.path.join(outdir, "scores.json")

    """
    Pipeline representation
    -----------------------

    By executing this block of code, a pipeline representation can be
    displayed. This representation is composed of boxes connected to each
    other.
    """
    if 0:
        from capsul.qt_gui.widgets import PipelineDevelopperView
        from PySide import QtGui
        app = QtGui.QApplication(sys.argv)
        view1 = PipelineDevelopperView(pipeline)
        view1.show()
        app.exec_()

    """
    Pipeline execution
    ------------------

    Finally the pipeline is eecuted in the defined 'study_config'.
    """
    study_config.run(pipeline)

    """
    Access the result
    -----------------
#.........这里部分代码省略.........

# 需要导入模块: from capsul.qt_gui.widgets import PipelineDevelopperView [as 别名]
# 或者: from capsul.qt_gui.widgets.PipelineDevelopperView import show [as 别名]
Processing definition: create the <clinfmri.preproc.FmriPreproc> that
define the different step of the processings.
"""
pipeline = get_process_instance("clinfmri.preproc.fmri_preproc.xml")

"""
It is possible to display the pipeline.
"""
if args.display:
    import sys
    from PySide import QtGui
    from capsul.qt_gui.widgets import PipelineDevelopperView

    app = QtGui.QApplication(sys.argv)
    view = PipelineDevelopperView(pipeline)
    view.show()
    app.exec_()

"""
Now to parametrize the pipeline pipeline.
"""
pipeline.fmri_file = funcfile
pipeline.realign_register_to_mean = True
pipeline.select_slicer = args.timings
pipeline.select_normalization = args.normalization
pipeline.force_repetition_time = args.repetition_time
pipeline.force_slice_orders = args.slice_order
pipeline.realign_wrap = [0, 1, 0]
pipeline.realign_write_wrap = [0, 1, 0]
pipeline.ref_slice = args.ref_slice
if args.template is not None:

# 需要导入模块: from capsul.qt_gui.widgets import PipelineDevelopperView [as 别名]
# 或者: from capsul.qt_gui.widgets.PipelineDevelopperView import show [as 别名]
def pilot_dcm2nii():
    """
    Imports
    -------

    This code needs 'capsul' and 'mmutils' package in order to instanciate and
    execute the pipeline and to get a toy dataset.
    These packages are available in the 'neurospin' source list or in pypi.
    """
    import os
    import sys
    import shutil
    import tempfile
    from capsul.study_config.study_config import StudyConfig
    from capsul.process.loader import get_process_instance
    from mmutils.toy_datasets import get_sample_data

    """
    Parameters
    ----------

    The 'pipeline_name' parameter contains the location of the pipeline XML
    description that will perform the DICOMs conversion, and the 'outdir' the
    location of the pipeline's results: in this case a temporary directory.
    """
    pipeline_name = "dcmio.dcmconverter.dcm_to_nii.xml"
    outdir = tempfile.mkdtemp()

    """
    Capsul configuration
    --------------------

    A 'StudyConfig' has to be instantiated in order to execute the pipeline
    properly. It enables us to define the results directory through the
    'output_directory' attribute, the number of CPUs to be used through the
    'number_of_cpus' attributes, and to specify that we want a log of the
    processing step through the 'generate_logging'. The 'use_scheduler'
    must be set to True if more than 1 CPU is used.
    """
    study_config = StudyConfig(
        modules=[],
        output_directory=outdir,
        number_of_cpus=1,
        generate_logging=True,
        use_scheduler=True)

    """
    Get the toy dataset
    -------------------

    The toy dataset is composed of a 3D heart dicom image that is downloaded
    if it is necessary throught the 'get_sample_data' function and exported
    locally in a 'heart.dcm' file.
    """
    dicom_dataset = get_sample_data("dicom")
    dcmfolder = os.path.join(outdir, "dicom")
    if not os.path.isdir(dcmfolder):
        os.makedirs(dcmfolder)
    shutil.copy(dicom_dataset.barre, os.path.join(dcmfolder, "heart.dcm"))

    """
    Pipeline definition
    -------------------

    The pipeline XML description is first imported throught the
    'get_process_instance' method, and the resulting pipeline instance is
    parametrized: in this example we decided to set the date in the converted
    file name and we set two DICOM directories to be converted in Nifti
    format.
    """
    pipeline = get_process_instance(pipeline_name)
    pipeline.date_in_filename = True
    pipeline.dicom_directories = [dcmfolder, dcmfolder]
    pipeline.additional_informations = [[("Provided by", "[email protected]")],
                                        [("Provided by", "[email protected]"),
                                         ("TR", "1500")]]

    pipeline.dcm_tags = [("TR", [("0x0018", "0x0080")]),
                         ("TE", [("0x0018", "0x0081")])]

    """
    Pipeline representation
    -----------------------

    By executing this block of code, a pipeline representation can be
    displayed. This representation is composed of boxes connected to each
    other.
    """
    if 0:
        from capsul.qt_gui.widgets import PipelineDevelopperView
        from PySide import QtGui
        app = QtGui.QApplication(sys.argv)
        view1 = PipelineDevelopperView(pipeline)
        view1.show()
        app.exec_()

    """
    Pipeline execution
    ------------------

#.........这里部分代码省略.........

# 需要导入模块: from capsul.qt_gui.widgets import PipelineDevelopperView [as 别名]
# 或者: from capsul.qt_gui.widgets.PipelineDevelopperView import show [as 别名]
def pilot_preproc_spm_fmri(enable_display=False):
    """
    FMRI preprocessings
    ===================

    Preprocessing with the SPM slice timing and a normalization to a given
    template.

    Start to import required modules:
    """
    import os
    from mmutils.toy_datasets import get_sample_data
    from capsul.study_config import StudyConfig
    from capsul.api import get_process_instance

    """
    Study configuration
    -------------------

    We first define the working directory and guarantee this folder exists on
    the file system:
    """
    working_dir = "/volatile/nsap/catalogue/pclinfmri/fmri_preproc_spm_fmri"
    if not os.path.isdir(working_dir):
        os.makedirs(working_dir)

    """
    Then define the study configuration:
    """
    study_config = StudyConfig(
        modules=["MatlabConfig", "SPMConfig", "FSLConfig", "NipypeConfig"],
        use_smart_caching=False,
        fsl_config="/etc/fsl/4.1/fsl.sh",
        use_fsl=True,
        matlab_exec="/neurospin/local/bin/matlab",
        use_matlab=True,
        spm_directory="/i2bm/local/spm8",
        use_spm=True,
        output_directory=working_dir,
        number_of_cpus=1,
        generate_logging=True,
        use_scheduler=True,)

    """
    Load the toy dataset
    --------------------

    To do so, we use the get_sample_data function to download the toy
    dataset on the local file system (here localizer data):
    """
    toy_dataset = get_sample_data("localizer")
    template_dataset = get_sample_data("mni_1mm")

    """
    The toy_dataset is an Enum structure with some specific elements of
    interest:

        * fmri: the functional volume.
        * anat: the structural volume.
        * TR: the repetition time.

    Processing definition
    ---------------------

    First create the
    :ref:`slice timing pipeline <clinfmri.preproc.FmriPreproc>` that
    define the different step of the processings:
    """
    pipeline = get_process_instance("clinfmri.preproc.converted_fmri_preproc")
    print pipeline.get_input_spec()

    """
    Now we need now to parametrize this pipeline:
    """
    pipeline.fmri_file = toy_dataset.fmri
    pipeline.structural_file = toy_dataset.anat
    pipeline.realign_register_to_mean = True
    pipeline.select_slicer = "spm"
    pipeline.select_normalization = "fmri"
    pipeline.template_file = template_dataset.brain
    pipeline.force_repetition_time = toy_dataset.TR
    pipeline.force_slice_orders = [index + 1 for index in range(40)]

    """
    It is possible to display the pipeline.
    """
    if enable_display:
        import sys
        from PySide import QtGui
        from capsul.qt_gui.widgets import PipelineDevelopperView

        app = QtGui.QApplication(sys.argv)
        view = PipelineDevelopperView(pipeline)
        view.show()
        app.exec_()

    """
    The pipeline is now ready to be run:
    """
    study_config.run(pipeline, executer_qc_nodes=False, verbose=1)
#.........这里部分代码省略.........

# 需要导入模块: from capsul.qt_gui.widgets import PipelineDevelopperView [as 别名]
# 或者: from capsul.qt_gui.widgets.PipelineDevelopperView import show [as 别名]
def pilot_gdti_estimation():
    """
    Generalized diffusion tensor estimation
    =======================================
    """
    # System import
    import os
    import sys
    import datetime
    import PySide.QtGui as QtGui

    # CAPSUL import
    from capsul.qt_gui.widgets import PipelineDevelopperView
    from capsul.study_config.study_config import StudyConfig
    from capsul.process.loader import get_process_instance

    """
    Study configuration
    -------------------

    We first define the working directory and guarantee this folder exists on
    the file system:
    """
    working_dir = "/volatile/nsap/clindmri/gdti"
    if not os.path.isdir(working_dir):
        os.makedirs(working_dir)

    """
    And then define the study configuration (here we activate the smart
    caching module that will be able to remember which process has already been
    processed):
    """
    study_config = StudyConfig(
        modules=["SmartCachingConfig"],
        use_smart_caching=True,   
        output_directory=working_dir)

    # Create pipeline
    start_time = datetime.datetime.now()
    print "Start Pipeline Creation", start_time
    pipeline = get_process_instance("clindmri.estimation.gdti.xml")
    print "Done in {0} seconds.".format(datetime.datetime.now() - start_time)

    # View pipeline
    if 0:
        app = QtGui.QApplication(sys.argv)
        view1 = PipelineDevelopperView(pipeline)
        view1.show()
        app.exec_()
        del view1

    # Set pipeline input parameters
    pipeline.dfile = "/volatile/imagen/dmritest/000000022453/DTI/000000022453s011a1001.nii.gz"
    pipeline.bvalfile = "/volatile/imagen/dmritest/000000022453/DTI/000000022453s011a1001.bval"
    pipeline.bvecfile = "/volatile/imagen/dmritest/000000022453/DTI/000000022453s011a1001.bvec"
    pipeline.order = 2
    pipeline.odf = False
    print "Done in {0} seconds.".format(datetime.datetime.now() - start_time)

    # Execute the pipeline in the configured study
    study_config.run(pipeline, verbose=1)

# 需要导入模块: from capsul.qt_gui.widgets import PipelineDevelopperView [as 别名]
# 或者: from capsul.qt_gui.widgets.PipelineDevelopperView import show [as 别名]
def pilot_fsl_preproc():
    """
    FSL preprocessings
    ==================
    """
    # System import
    import os
    import sys
    import datetime
    import PySide.QtGui as QtGui

    # CAPSUL import
    from capsul.qt_gui.widgets import PipelineDevelopperView
    from capsul.study_config.study_config import StudyConfig
    from capsul.process.loader import get_process_instance

    """
    Study configuration
    -------------------

    We first define the working directory and guarantee this folder exists on
    the file system:
    """
    working_dir = "/volatile/nsap/clindmri/fslpreproc"
    if not os.path.isdir(working_dir):
        os.makedirs(working_dir)

    """
    And then define the study configuration (here we activate the smart
    caching module that will be able to remember which process has already been
    processed):
    """
    study_config = StudyConfig(
        modules=["SmartCachingConfig", "FSLConfig", "MatlabConfig",
                 "SPMConfig", "NipypeConfig"],
        use_smart_caching=True,
        fsl_config="/etc/fsl/4.1/fsl.sh",
        use_fsl=True,        
        output_directory=working_dir)

    # Create pipeline
    start_time = datetime.datetime.now()
    print "Start Pipeline Creation", start_time
    pipeline = get_process_instance("clindmri.preproc.fsl_preproc.xml")
    print "Done in {0} seconds.".format(datetime.datetime.now() - start_time)

    # View pipeline
    if 0:
        app = QtGui.QApplication(sys.argv)
        view1 = PipelineDevelopperView(pipeline)
        view1.show()
        app.exec_()
        del view1

    # Set pipeline input parameters
    pipeline.dfile = "/volatile/imagen/dmritest/000000022453/DTI/000000022453s011a1001.nii.gz"
    pipeline.bvalfile = "/volatile/imagen/dmritest/000000022453/DTI/000000022453s011a1001.bval"
    pipeline.bvecfile = "/volatile/imagen/dmritest/000000022453/DTI/000000022453s011a1001.bvec"
    print "Done in {0} seconds.".format(datetime.datetime.now() - start_time)

    #print pipeline.nodes["eddy"].process._nipype_interface.inputs
    print pipeline.nodes["eddy"].process._nipype_interface.cmdline

    # Execute the pipeline in the configured study
    study_config.run(pipeline, verbose=1)