Python Parser.parse方法代码示例

# 需要导入模块: from msct_parser import Parser [as 别名]
# 或者: from msct_parser.Parser import parse [as 别名]
def get_data_or_scalar(argument, data_in):
    """
    Get data from list of file names (scenario 1) or scalar (scenario 2)
    :param argument: list of file names of scalar
    :param data_in: if argument is scalar, use data to get shape
    :return: 3d or 4d numpy array
    """
    if argument.replace('.', '').isdigit():  # so that it recognize float as digits too
        # build data2 with same shape as data
        data_out = data_in[:, :, :] * 0 + float(argument)
    else:
        # parse file name and check integrity
        parser2 = Parser(__file__)
        parser2.add_option(name='-i', type_value=[[','], 'file'])
        list_fname = parser2.parse(['-i', argument]).get('-i')
        data_out = get_data(list_fname)
    return data_out

# 需要导入模块: from msct_parser import Parser [as 别名]
# 或者: from msct_parser.Parser import parse [as 别名]
                      description="reference volume for label removing.",
                      mandatory=False)
    parser.add_option(name="-c",
                      type_value="int",
                      description="cross radius in mm (default=5mm).",
                      mandatory=False)
    parser.add_option(name="-d",
                      type_value=None,
                      description="dilatation bool for cross generation ('-c' option).",
                      mandatory=False)
    parser.add_option(name="-v",
                      type_value="multiple_choice",
                      description="verbose. Default=" + str(param_default.verbose),
                      mandatory=False,
                      example=['0', '1'])
    arguments = parser.parse(sys.argv[1:])

    input_filename = arguments["-i"]
    process_type = arguments["-t"]
    input_fname_output = None
    input_fname_ref = None
    input_cross_radius = 5
    input_dilate = False
    input_coordinates = None
    input_verbose = '1'
    input_fname_output = arguments["-o"]
    if "-r" in arguments:
        input_fname_ref = arguments["-r"]
    if "-x" in arguments:
        input_coordinates = arguments["-x"]
    if "-c" in arguments:

# 需要导入模块: from msct_parser import Parser [as 别名]
# 或者: from msct_parser.Parser import parse [as 别名]
def main():

    # get default parameters
    step1 = Paramreg(step='1', type='seg', algo='slicereg', metric='MeanSquares', iter='10')
    step2 = Paramreg(step='2', type='im', algo='syn', metric='MI', iter='3')
    # step1 = Paramreg()
    paramreg = ParamregMultiStep([step1, step2])

    # step1 = Paramreg_step(step='1', type='seg', algo='bsplinesyn', metric='MeanSquares', iter='10', shrink='1', smooth='0', gradStep='0.5')
    # step2 = Paramreg_step(step='2', type='im', algo='syn', metric='MI', iter='10', shrink='1', smooth='0', gradStep='0.5')
    # paramreg = ParamregMultiStep([step1, step2])

    # Initialize the parser
    parser = Parser(__file__)
    parser.usage.set_description('Register anatomical image to the template.')
    parser.add_option(name="-i",
                      type_value="file",
                      description="Anatomical image.",
                      mandatory=True,
                      example="anat.nii.gz")
    parser.add_option(name="-s",
                      type_value="file",
                      description="Spinal cord segmentation.",
                      mandatory=True,
                      example="anat_seg.nii.gz")
    parser.add_option(name="-l",
                      type_value="file",
                      description="Labels. See: http://sourceforge.net/p/spinalcordtoolbox/wiki/create_labels/",
                      mandatory=True,
                      default_value='',
                      example="anat_labels.nii.gz")
    parser.add_option(name="-t",
                      type_value="folder",
                      description="Path to MNI-Poly-AMU template.",
                      mandatory=False,
                      default_value=param.path_template)
    parser.add_option(name="-p",
                      type_value=[[':'], 'str'],
                      description="""Parameters for registration (see sct_register_multimodal). Default:\n--\nstep=1\ntype="""+paramreg.steps['1'].type+"""\nalgo="""+paramreg.steps['1'].algo+"""\nmetric="""+paramreg.steps['1'].metric+"""\npoly="""+paramreg.steps['1'].poly+"""\n--\nstep=2\ntype="""+paramreg.steps['2'].type+"""\nalgo="""+paramreg.steps['2'].algo+"""\nmetric="""+paramreg.steps['2'].metric+"""\niter="""+paramreg.steps['2'].iter+"""\nshrink="""+paramreg.steps['2'].shrink+"""\nsmooth="""+paramreg.steps['2'].smooth+"""\ngradStep="""+paramreg.steps['2'].gradStep+"""\n--""",
                      mandatory=False,
                      example="step=2,type=seg,algo=bsplinesyn,metric=MeanSquares,iter=5,shrink=2:step=3,type=im,algo=syn,metric=MI,iter=5,shrink=1,gradStep=0.3")
    parser.add_option(name="-r",
                      type_value="multiple_choice",
                      description="""Remove temporary files.""",
                      mandatory=False,
                      default_value='1',
                      example=['0', '1'])
    parser.add_option(name="-v",
                      type_value="multiple_choice",
                      description="""Verbose. 0: nothing. 1: basic. 2: extended.""",
                      mandatory=False,
                      default_value=param.verbose,
                      example=['0', '1', '2'])
    if param.debug:
        print '\n*** WARNING: DEBUG MODE ON ***\n'
        fname_data = '/Users/julien/data/temp/sct_example_data/t2/t2.nii.gz'
        fname_landmarks = '/Users/julien/data/temp/sct_example_data/t2/labels.nii.gz'
        fname_seg = '/Users/julien/data/temp/sct_example_data/t2/t2_seg.nii.gz'
        path_template = param.path_template
        remove_temp_files = 0
        verbose = 2
        # speed = 'superfast'
        #param_reg = '2,BSplineSyN,0.6,MeanSquares'
    else:
        arguments = parser.parse(sys.argv[1:])

        # get arguments
        fname_data = arguments['-i']
        fname_seg = arguments['-s']
        fname_landmarks = arguments['-l']
        path_template = arguments['-t']
        remove_temp_files = int(arguments['-r'])
        verbose = int(arguments['-v'])
        if '-p' in arguments:
            paramreg_user = arguments['-p']
            # update registration parameters
            for paramStep in paramreg_user:
                paramreg.addStep(paramStep)

    # initialize other parameters
    file_template = param.file_template
    file_template_label = param.file_template_label
    file_template_seg = param.file_template_seg
    output_type = param.output_type
    zsubsample = param.zsubsample
    # smoothing_sigma = param.smoothing_sigma

    # start timer
    start_time = time.time()

    # get absolute path - TO DO: remove! NEVER USE ABSOLUTE PATH...
    path_template = os.path.abspath(path_template)

    # get fname of the template + template objects
    fname_template = sct.slash_at_the_end(path_template, 1)+file_template
    fname_template_label = sct.slash_at_the_end(path_template, 1)+file_template_label
    fname_template_seg = sct.slash_at_the_end(path_template, 1)+file_template_seg

    # check file existence
    sct.printv('\nCheck template files...')
#.........这里部分代码省略.........

# 需要导入模块: from msct_parser import Parser [as 别名]
# 或者: from msct_parser.Parser import parse [as 别名]
def main():

    # Initialization
    fname_output = ''
    fname_mask = param.fname_mask
    fname_src_seg = ''
    fsloutput = 'export FSLOUTPUTTYPE=NIFTI; '  # for faster processing, all outputs are in NIFTI'

    start_time = time.time()
    # get path of the toolbox
    status, path_sct = commands.getstatusoutput('echo $SCT_DIR')

    # get default registration parameters
    # step1 = Paramreg(step='1', type='im', algo='syn', metric='MI', iter='5', shrink='1', smooth='0', gradStep='0.5')
    step0 = Paramreg(step='0', type='im', algo='syn', metric='MI', iter='0', shrink='1', smooth='0', gradStep='0.5')  # only used to put src into dest space
    step1 = Paramreg()
    paramreg = ParamregMultiStep([step0, step1])

    # Initialize the parser
    parser = Parser(__file__)
    parser.usage.set_description('This program co-registers two 3D volumes. The deformation is non-rigid and is '
                                 'constrained along Z direction (i.e., axial plane). Hence, this function assumes '
                                 'that orientation of the destination image is axial (RPI). If you need to register '
                                 'two volumes with large deformations and/or different contrasts, it is recommended to '
                                 'input spinal cord segmentations (binary mask) in order to achieve maximum robustness.'
                                 ' The program outputs a warping field that can be used to register other images to the'
                                 ' destination image. To apply the warping field to another image, use '
                                 'sct_apply_transfo')
    parser.add_option(name="-i",
                      type_value="file",
                      description="Image source.",
                      mandatory=True,
                      example="src.nii.gz")
    parser.add_option(name="-d",
                      type_value="file",
                      description="Image destination.",
                      mandatory=True,
                      example="dest.nii.gz")
    parser.add_option(name="-iseg",
                      type_value="file",
                      description="Segmentation source.",
                      mandatory=False,
                      example="src_seg.nii.gz")
    parser.add_option(name="-dseg",
                      type_value="file",
                      description="Segmentation destination.",
                      mandatory=False,
                      example="dest_seg.nii.gz")
    parser.add_option(name="-m",
                      type_value="file",
                      description="Binary mask to improve accuracy over region of interest.",
                      mandatory=False,
                      example="mask.nii.gz")
    parser.add_option(name="-o",
                      type_value="file_output",
                      description="Name of output file.",
                      mandatory=False,
                      example="src_reg.nii.gz")
    parser.add_option(name="-p",
                      type_value=[[':'],'str'],
                      description="""Parameters for registration. Separate arguments with ",". Separate steps with ":".\nstep: <int> Step number (starts at 1).\ntype: {im,seg} type of data used for registration.\nalgo: {slicereg,rigid,affine,syn,bsplinesyn}. Default="""+paramreg.steps['1'].algo+"""\n  For info about slicereg, see here: goo.gl/Sj3ZeU\nmetric: {CC,MI,MeanSquares}. Default="""+paramreg.steps['1'].metric+"""\niter: <int> Number of iterations. Default="""+paramreg.steps['1'].iter+"""\nshrink: <int> Shrink factor (only for SyN). Default="""+paramreg.steps['1'].shrink+"""\nsmooth: <int> Smooth factor (only for SyN). Default="""+paramreg.steps['1'].smooth+"""\ngradStep: <float> Gradient step (only for SyN). Default="""+paramreg.steps['1'].gradStep+"""\npoly: <int> Polynomial degree (only for slicereg). Default="""+paramreg.steps['1'].poly,
                      mandatory=False,
                      example="step=1,type=seg,algo=slicereg,metric=MeanSquares:step=2,type=im,algo=syn,metric=MI,iter=5,shrink=2")
    parser.add_option(name="-z",
                      type_value="int",
                      description="""size of z-padding to enable deformation at edges when using SyN.""",
                      mandatory=False,
                      default_value=param.padding)
    parser.add_option(name="-x",
                      type_value="multiple_choice",
                      description="""Final interpolation.""",
                      mandatory=False,
                      default_value='linear',
                      example=['nn', 'linear', 'spline'])
    parser.add_option(name="-r",
                      type_value="multiple_choice",
                      description="""Remove temporary files.""",
                      mandatory=False,
                      default_value='1',
                      example=['0', '1'])
    parser.add_option(name="-v",
                      type_value="multiple_choice",
                      description="""Verbose.""",
                      mandatory=False,
                      default_value='1',
                      example=['0', '1', '2'])
    arguments = parser.parse(sys.argv[1:])

    # get arguments
    fname_src = arguments['-i']
    fname_dest = arguments['-d']
    if '-iseg' in arguments:
        fname_src_seg = arguments['-iseg']
    if '-dseg' in arguments:
        fname_dest_seg = arguments['-dseg']
    if '-o' in arguments:
        fname_output = arguments['-o']
    if "-m" in arguments:
        fname_mask = arguments['-m']
    padding = arguments['-z']
#.........这里部分代码省略.........

# 需要导入模块: from msct_parser import Parser [as 别名]
# 或者: from msct_parser.Parser import parse [as 别名]
def main():

    # get default parameters
    step1 = Paramreg(step='1', type='seg', algo='slicereg', metric='MeanSquares', iter='10')
    step2 = Paramreg(step='2', type='im', algo='syn', metric='MI', iter='3')
    # step1 = Paramreg()
    paramreg = ParamregMultiStep([step1, step2])

    # step1 = Paramreg_step(step='1', type='seg', algo='bsplinesyn', metric='MeanSquares', iter='10', shrink='1', smooth='0', gradStep='0.5')
    # step2 = Paramreg_step(step='2', type='im', algo='syn', metric='MI', iter='10', shrink='1', smooth='0', gradStep='0.5')
    # paramreg = ParamregMultiStep([step1, step2])

    # Initialize the parser
    parser = Parser(__file__)
    parser.usage.set_description('Register anatomical image to the template.')
    parser.add_option(name="-i",
                      type_value="file",
                      description="Anatomical image.",
                      mandatory=True,
                      example="anat.nii.gz")
    parser.add_option(name="-s",
                      type_value="file",
                      description="Spinal cord segmentation.",
                      mandatory=True,
                      example="anat_seg.nii.gz")
    parser.add_option(name="-l",
                      type_value="file",
                      description="Labels. See: http://sourceforge.net/p/spinalcordtoolbox/wiki/create_labels/",
                      mandatory=True,
                      default_value='',
                      example="anat_labels.nii.gz")
    parser.add_option(name="-t",
                      type_value="folder",
                      description="Path to MNI-Poly-AMU template.",
                      mandatory=False,
                      default_value=param.path_template)
    parser.add_option(name="-p",
                      type_value=[[':'], 'str'],
                      description="""Parameters for registration (see sct_register_multimodal). Default:\n--\nstep=1\ntype="""+paramreg.steps['1'].type+"""\nalgo="""+paramreg.steps['1'].algo+"""\nmetric="""+paramreg.steps['1'].metric+"""\npoly="""+paramreg.steps['1'].poly+"""\n--\nstep=2\ntype="""+paramreg.steps['2'].type+"""\nalgo="""+paramreg.steps['2'].algo+"""\nmetric="""+paramreg.steps['2'].metric+"""\niter="""+paramreg.steps['2'].iter+"""\nshrink="""+paramreg.steps['2'].shrink+"""\nsmooth="""+paramreg.steps['2'].smooth+"""\ngradStep="""+paramreg.steps['2'].gradStep+"""\n--""",
                      mandatory=False,
                      example="step=2,type=seg,algo=bsplinesyn,metric=MeanSquares,iter=5,shrink=2:step=3,type=im,algo=syn,metric=MI,iter=5,shrink=1,gradStep=0.3")
    parser.add_option(name="-r",
                      type_value="multiple_choice",
                      description="""Remove temporary files.""",
                      mandatory=False,
                      default_value='1',
                      example=['0', '1'])
    parser.add_option(name="-v",
                      type_value="multiple_choice",
                      description="""Verbose. 0: nothing. 1: basic. 2: extended.""",
                      mandatory=False,
                      default_value=param.verbose,
                      example=['0', '1', '2'])
    if param.debug:
        print '\n*** WARNING: DEBUG MODE ON ***\n'
        fname_data = '/Users/julien/data/temp/sct_example_data/t2/t2.nii.gz'
        fname_landmarks = '/Users/julien/data/temp/sct_example_data/t2/labels.nii.gz'
        fname_seg = '/Users/julien/data/temp/sct_example_data/t2/t2_seg.nii.gz'
        path_template = param.path_template
        remove_temp_files = 0
        verbose = 2
        # speed = 'superfast'
        #param_reg = '2,BSplineSyN,0.6,MeanSquares'
    else:
        arguments = parser.parse(sys.argv[1:])

        # get arguments
        fname_data = arguments['-i']
        fname_seg = arguments['-s']
        fname_landmarks = arguments['-l']
        path_template = arguments['-t']
        remove_temp_files = int(arguments['-r'])
        verbose = int(arguments['-v'])
        if '-p' in arguments:
            paramreg_user = arguments['-p']
            # update registration parameters
            for paramStep in paramreg_user:
                paramreg.addStep(paramStep)

    # initialize other parameters
    file_template = param.file_template
    file_template_label = param.file_template_label
    file_template_seg = param.file_template_seg
    output_type = param.output_type
    zsubsample = param.zsubsample
    # smoothing_sigma = param.smoothing_sigma

    # start timer
    start_time = time.time()

    # get absolute path - TO DO: remove! NEVER USE ABSOLUTE PATH...
    path_template = os.path.abspath(path_template)

    # get fname of the template + template objects
    fname_template = sct.slash_at_the_end(path_template, 1)+file_template
    fname_template_label = sct.slash_at_the_end(path_template, 1)+file_template_label
    fname_template_seg = sct.slash_at_the_end(path_template, 1)+file_template_seg

    # check file existence
    sct.printv('\nCheck template files...')
#.........这里部分代码省略.........

# 需要导入模块: from msct_parser import Parser [as 别名]
# 或者: from msct_parser.Parser import parse [as 别名]
def main():

    # Initialization
    fsloutputdir = 'export FSLOUTPUTTYPE=NIFTI_GZ; '
    file_ordering = 'alternate'
    start_time = time.time()

    # Initialize the parser
    parser = Parser(__file__)
    parser.usage.set_description('Convert dcm2nii using nin sequence from J. Finsterbusch. '
                                 'Requires the software dcm2nii (from mricron).')
    parser.add_option(name="-i",
                      type_value="folder",
                      description="Path to dicom data.",
                      mandatory=True,
                      example="data/my_data")
    parser.add_option(name="-ord",
                      type_value="multiple_choice",
                      description="""File ordering: \nalternate: spine,brain,spine,brain... (with custom coil)\nbloc: spine,spine... brain,brain... (with head-neck coil)\n""",
                      mandatory=False,
                      default_value='bloc',
                      example=['alternate', 'bloc'])
    parser.add_option(name="-r",
                      type_value="multiple_choice",
                      description="""Remove temporary files.""",
                      mandatory=False,
                      default_value='1',
                      example=['0', '1'])
    parser.add_option(name="-v",
                      type_value="multiple_choice",
                      description="""Verbose.""",
                      mandatory=False,
                      default_value='1',
                      example=['0', '1', '2'])

    arguments = parser.parse(sys.argv[1:])

    # get arguments
    path_data = arguments['-i']
    if '-ord' in arguments:
        file_ordering = arguments['-ord']
    remove_temp_files = int(arguments['-r'])
    verbose = int(arguments['-v'])

    path_tmp = sct.tmp_create(basename="nin_convert_dcm2nii", verbose=verbose)

    # go to temporary folder
    curdir = os.getcwd()
    os.chdir(path_tmp)

    # list DICOM files
    file_data_list = os.listdir(path_data)

    # create another temp folder for conversion
    sct.run('mkdir tmp', verbose)

    # loop across files
    file_nii = []
    i = 0
    for i_file in file_data_list:
        # convert dicom to nifti and put in temporary folder
        status, output = sct.run('dcm2nii -o tmp/ -v n '+os.path.join(path_data, i_file), verbose)
        # change file name
        file_nii.append('data_'+str(i).zfill(4)+'.nii.gz')
        sct.run('mv tmp/*.nii.gz '+file_nii[i])
        # increment file index
        i = i+1

    # Merge data
    nb_files = len(file_data_list)
    if file_ordering == 'alternate':
        sct.run(fsloutputdir+'fslmerge -t data_spine '+' '.join([file_nii[i] for i in range(0, nb_files, 2)]))
        sct.run(fsloutputdir+'fslmerge -t data_brain '+' '.join([file_nii[i] for i in range(1, nb_files, 2)]))
    if file_ordering == 'bloc':
        sct.run(fsloutputdir+'fslmerge -t data_spine '+' '.join([file_nii[i] for i in range(0, nb_files/2)]))
        sct.run(fsloutputdir+'fslmerge -t data_brain '+' '.join([file_nii[i] for i in range(nb_files/2+1, nb_files)]))

    # come back
    os.chdir(curdir)

    # Generate output files
    sct.printv('\nGenerate output files...', verbose)
    fname_data_spine = sct.generate_output_file(os.path.join(path_tmp, 'data_spine.nii.gz'), 'data_spine.nii.gz', verbose)
    fname_data_brain = sct.generate_output_file(os.path.join(path_tmp, 'data_brain.nii.gz'), 'data_brain.nii.gz', verbose)

    # Delete temporary files
    if remove_temp_files:
        sct.printv('\nRemove temporary files...', verbose)
        sct.run('rm -rf '+path_tmp, verbose)

    elapsed_time = time.time() - start_time
    sct.printv('\nFinished! Elapsed time: '+str(int(round(elapsed_time)))+'s', verbose)
    sct.printv('\nTo view results, type:', verbose)
    sct.printv('fslview data_spine &', verbose, 'info')
    sct.printv('fslview data_brain &\n', verbose, 'info')