Python CommandLine.run方法代码示例

# 需要导入模块: from nipype.interfaces.base import CommandLine [as 别名]
# 或者: from nipype.interfaces.base.CommandLine import run [as 别名]
def geodesic_depth(command, surface_file):
    """
    Measure "travel depth" of each vertex in a surface mesh.
    (Calls Joachim Giard's C++ code)

    Parameters
    ----------
    command : travel depth C++ executable command
    surface_file : ``vtk file``

    Returns
    -------
    depth_file: string
        vtk file with geodesic depth per vertex of mesh

    """
    import os
    from nipype.interfaces.base import CommandLine

    depth_file = os.path.join(os.getcwd(),
                 os.path.splitext(os.path.basename(surface_file))[0] + '.geodesic_depth.vtk')
    cli = CommandLine(command = command)
    cli.inputs.args = ' '.join([surface_file, depth_file])
    cli.cmdline
    cli.run()

    if not os.path.exists(depth_file):
        raise(IOError(depth_file + " not found"))

    return depth_file

# 需要导入模块: from nipype.interfaces.base import CommandLine [as 别名]
# 或者: from nipype.interfaces.base.CommandLine import run [as 别名]
def dicom2nrrd(dicomdir, out_prefix, out_suffix):
    import os
    from nipype.interfaces.base import CommandLine
    cmd = CommandLine('DWIConvert --inputDicomDirectory %s --outputVolume %s/%s/%s%s.nrrd' % (dicomdir, experiment_dir,out_prefix,out_prefix,out_suffix))
    print "DICOM->NRRD:" + cmd.cmd
    cmd.run()
    return os.path.abspath('%s/%s/%s%s.nrrd' % (experiment_dir,out_prefix,out_prefix,out_suffix))

# 需要导入模块: from nipype.interfaces.base import CommandLine [as 别名]
# 或者: from nipype.interfaces.base.CommandLine import run [as 别名]
def DICOM2animatedGIF_sidebyside(dcmdir_l, dcmdir_r, outputpath, slice_i, suffix):

    dcmio = DicomIO.DicomIO()
    dwidcm_l = dcmio.ReadDICOM_frames(dcmdir_l)
    dwidcm_r = dcmio.ReadDICOM_frames(dcmdir_r)
    # Write all frames of slice into set of png files
    for frame_i in range(len(dwidcm_l)):
        slice_l = dwidcm_l[frame_i][slice_i].pixel_array.T
        slice_r = dwidcm_r[frame_i][slice_i].pixel_array.T
        dimx = slice_l.shape[0]
        dimy = slice_l.shape[1]
        newImg1 = PIL.Image.new('L', (dimx*2, dimy))
        pixels1 = newImg1.load()
        for i in range (0, dimx):
            for j in range (0, dimy):
                pixels1[i, j] = float(slice_l[i, j])
                pixels1[dimx+i, j] = float(slice_r[i, j])
        #pixels1[i, j] = float(slice[i, j]) * dwidcm[frame_i][slice_i].RescaleSlope + dwidcm[frame_i][slice_i].RescaleIntercept
        newImg1.save((outputpath + '_' + ('%02d' % frame_i) + '.png'),'PNG')
    cmd = CommandLine('convert -delay 25 -loop 0 %s_*.png %s_%s.gif' % (outputpath, outputpath, suffix))
    cmd.run()
    for frame_i in range(len(dwidcm_l)):
        os.remove((outputpath + '_' + ('%02d' % frame_i) + '.png'))
    print "convert (ImageMagick):" + cmd.cmd
    return (outputpath + '.gif')

# 需要导入模块: from nipype.interfaces.base import CommandLine [as 别名]
# 或者: from nipype.interfaces.base.CommandLine import run [as 别名]
def area(command, surface_file):
    """
    Measure area of each vertex in a surface mesh.
    (Calls Joachim Giard's C++ code)

    Parameters
    ----------
    command : string
        Voronoi-based surface area C++ executable command
    surface_file : string
        vtk file with surface mesh

    Returns
    -------
    area_file: string
        vtk file with surface area per vertex of mesh

    """
    import os
    from nipype.interfaces.base import CommandLine

    area_file = os.path.join(os.getcwd(),
                os.path.splitext(os.path.basename(surface_file))[0] + '.area.vtk')
    cli = CommandLine(command = command)
    cli.inputs.args = ' '.join([surface_file, area_file])
    cli.cmdline
    cli.run()

    if not os.path.exists(area_file):
        raise(IOError(area_file + " not found"))

    return area_file

# 需要导入模块: from nipype.interfaces.base import CommandLine [as 别名]
# 或者: from nipype.interfaces.base.CommandLine import run [as 别名]
def make_cerebellum(aseg):
      cwd = os.getcwd()
      pth, nme = os.path.split(aseg)
      os.chdir(pth)
      cl = CommandLine('fslmaths %s -thr 47 -uthr 47 right_cerebellum'% (aseg))
      cout = cl.run()
      
      if not cout.runtime.returncode == 0:
            os.chdir(cwd)
            print 'Unable to create  right cerebellum for %s'%(aseg)
            return None

      cl2 = CommandLine('fslmaths %s -thr 8 -uthr 8 left_cerebellum'% (aseg))
      cout2 = cl2.run()

      if not cout2.runtime.returncode == 0:
            os.chdir(cwd)
            print 'Unable to create  left cerebellum for %s'%(aseg)
            return None

      cl3 = CommandLine('fslmaths left_cerebellum -add right_cerebellum -bin grey_cerebellum')
      cout3 = cl3.run()
      if not cout3.runtime.returncode == 0:
            print 'Unable to create whole cerebellum for %s'%(aseg)
            print cout3.runtime.stderr
            print cout3.runtime.stdout
            return None
      
      cmd = 'rm right_cerebellum.* left_cerebellum.*'
      cl4 = CommandLine(cmd)
      cout4 = cl4.run()
      os.chdir(cwd)
      cerebellum = glob('%s/grey_cerebellum.*'%(pth))
      return cerebellum[0]

# 需要导入模块: from nipype.interfaces.base import CommandLine [as 别名]
# 或者: from nipype.interfaces.base.CommandLine import run [as 别名]
def elastix(input_file, target_file, mask_file, output_prefix, output_sub_prefix, param_rigid, param_BSpline):
    from os.path import abspath as opap
    from nipype.interfaces.base import CommandLine
    from nipype.utils.filemanip import split_filename
    import shutil
    import glob
    import os

    out_dir = experiment_dir + os.sep + output_prefix + os.sep + output_sub_prefix
    # Create output directory if it does not exist
    if os.path.exists(out_dir):
        print "rmtree: " + out_dir
        shutil.rmtree(out_dir)
    print "creating: " + out_dir
    os.makedirs(out_dir)

    cmd = CommandLine(
        (
            "/Users/eija/Documents/SW/Elastix/elastix_sources_v4.7/bin/bin/elastix -f %s -m %s -out %s -p %s -p %s -threads 8"
        )
        % (target_file, input_file, out_dir, param_rigid, param_BSpline)
    )

    print "elastix: " + cmd.cmd
    cmd.run()
    resultfiles = glob.glob(out_dir + os.sep + "result.*.tiff")
    return resultfiles

# 需要导入模块: from nipype.interfaces.base import CommandLine [as 别名]
# 或者: from nipype.interfaces.base.CommandLine import run [as 别名]
def area(command, surface_file, verbose=False):
    """
    Measure area of each vertex in a surface mesh.
    (Calls Joachim Giard's C++ code)

    Parameters
    ----------
    command : string
        Voronoi-based surface area C++ executable command
    surface_file : string
        vtk file with surface mesh
    verbose : bool
        print statements?

    Returns
    -------
    area_file: string
        vtk file with surface area per vertex of mesh

    Examples
    --------
    >>> import os
    >>> import numpy as np
    >>> from mindboggle.shapes.surface_shapes import area
    >>> from mindboggle.mio.vtks import read_scalars
    >>> from mindboggle.mio.fetch_data import prep_tests
    >>> urls, fetch_data = prep_tests()
    >>> surface_file = fetch_data(urls['left_pial'], '', '.vtk')
    >>> verbose = False
    >>> ccode_path = os.environ['vtk_cpp_tools']
    >>> command = os.path.join(ccode_path, 'area', 'PointAreaMain')
    >>> area_file = area(command, surface_file, verbose)
    >>> scalars, name = read_scalars(area_file)
    >>> np.allclose(scalars[0:8],
    ...             [0.48270401731, 0.39661528543, 0.57813454792, 0.70574099571,
    ...              0.84318527207, 0.57642554119, 0.66942016035, 0.70629953593])
    True

    """
    import os
    from nipype.interfaces.base import CommandLine

    basename = os.path.splitext(os.path.basename(surface_file))[0]
    area_file = os.path.join(os.getcwd(), basename + '.area.vtk')
    args = ' '.join([surface_file, area_file])

    if verbose:
        print("{0} {1}".format(command, args))

    cli = CommandLine(command=command)
    cli.inputs.args = args
    cli.terminal_output = 'file'
    cli.run()

    if not os.path.exists(area_file):
        raise IOError(area_file + " not found")

    return area_file

# 需要导入模块: from nipype.interfaces.base import CommandLine [as 别名]
# 或者: from nipype.interfaces.base.CommandLine import run [as 别名]
def travel_depth(command, surface_file, verbose=False):
    """
    Measure "travel depth" of each vertex in a surface mesh.
    (Calls Joachim Giard's C++ code)

    Parameters
    ----------
    command : string
        travel depth C++ executable command
    surface_file : string
        vtk file
    verbose : bool
        print statements?

    Returns
    -------
    depth_file: string
        vtk file with travel depth per vertex of mesh

    Examples
    --------
    >>> import os
    >>> import numpy as np
    >>> from mindboggle.shapes.surface_shapes import travel_depth
    >>> from mindboggle.mio.vtks import read_scalars
    >>> from mindboggle.mio.fetch_data import prep_tests
    >>> urls, fetch_data = prep_tests()
    >>> surface_file = fetch_data(urls['left_pial'], '', '.vtk')
    >>> verbose = False
    >>> ccode_path = os.environ['vtk_cpp_tools']
    >>> command = os.path.join(ccode_path, 'travel_depth', 'TravelDepthMain')
    >>> depth_file = travel_depth(command, surface_file, verbose)
    >>> scalars, name = read_scalars(depth_file)
    >>> print(np.array_str(np.array(scalars[0:8]), precision=5,
    ...     suppress_small=True))
    [ 0.02026  0.06009  0.12859  0.04564  0.00774  0.05284  0.05354  0.01316]

    """
    import os
    from nipype.interfaces.base import CommandLine

    basename = os.path.splitext(os.path.basename(surface_file))[0]
    depth_file = os.path.join(os.getcwd(), basename + '.travel_depth.vtk')
    args = ' '.join([surface_file, depth_file])

    if verbose:
        print("{0} {1}".format(command, args))

    cli = CommandLine(command=command)
    cli.inputs.args = args
    cli.cmdline
    cli.run()

    if not os.path.exists(depth_file):
        raise IOError(depth_file + " not found")

    return depth_file

# 需要导入模块: from nipype.interfaces.base import CommandLine [as 别名]
# 或者: from nipype.interfaces.base.CommandLine import run [as 别名]
def unzip(infile):
    gunzipfile, gz = os.path.splitext(infile)
    if not 'gz' in gz:
        #when running gunzip on file when
        return infile
    else:
       c3 = CommandLine('gunzip %s'%(infile))
       c3.run()
       return gunzipfile

# 需要导入模块: from nipype.interfaces.base import CommandLine [as 别名]
# 或者: from nipype.interfaces.base.CommandLine import run [as 别名]
def gznii2nii(in_file):
    import os
    import shutil

    fileName, fileExtension = os.path.splitext(in_file)
    cmd = CommandLine('gunzip -f -k %s.nii.gz' % (fileName))
    print "gunzip NII.GZ:" + cmd.cmd
    cmd.run()
    return os.path.abspath('%s.nii' % (fileName))

# 需要导入模块: from nipype.interfaces.base import CommandLine [as 别名]
# 或者: from nipype.interfaces.base.CommandLine import run [as 别名]
def travel_depth(command, surface_file, verbose=False):
    """
    Measure "travel depth" of each vertex in a surface mesh.
    (Calls Joachim Giard's C++ code)

    Parameters
    ----------
    command : string
        travel depth C++ executable command
    surface_file : string
        vtk file
    verbose : bool
        print statements?

    Returns
    -------
    depth_file: string
        vtk file with travel depth per vertex of mesh

    Examples
    --------
    >>> import os
    >>> import numpy as np
    >>> from mindboggle.shapes.surface_shapes import travel_depth
    >>> from mindboggle.mio.vtks import read_scalars
    >>> from mindboggle.mio.fetch_data import prep_tests
    >>> urls, fetch_data = prep_tests()
    >>> surface_file = fetch_data(urls['left_pial'], '', '.vtk')
    >>> verbose = False
    >>> ccode_path = os.environ['vtk_cpp_tools']
    >>> command = os.path.join(ccode_path, 'travel_depth', 'TravelDepthMain')
    >>> depth_file = travel_depth(command, surface_file, verbose)
    >>> scalars, name = read_scalars(depth_file)
    >>> np.allclose(scalars[0:8], [0.020259869839, 0.06009166489, 0.12858575442, 0.045639221313, 0.007742772964, 0.052839111255, 0.053538904296, 0.013158746337])
    True

    """
    import os
    from nipype.interfaces.base import CommandLine

    basename = os.path.splitext(os.path.basename(surface_file))[0]
    depth_file = os.path.join(os.getcwd(), basename + '.travel_depth.vtk')
    args = ' '.join([surface_file, depth_file])

    if verbose:
        print("{0} {1}".format(command, args))

    cli = CommandLine(command=command)
    cli.inputs.args = args
    cli.terminal_output = 'file'
    cli.run()

    if not os.path.exists(depth_file):
        raise IOError(depth_file + " not found")

    return depth_file

# 需要导入模块: from nipype.interfaces.base import CommandLine [as 别名]
# 或者: from nipype.interfaces.base.CommandLine import run [as 别名]
def nii2nrrd(filename_nii, filename_bval, filename_bvec, out_prefix, out_suffix):
    import os
    import shutil

    from nipype.interfaces.base import CommandLine
    basename = experiment_dir + os.sep + out_prefix + os.sep + out_prefix + out_suffix
    cmd = CommandLine('./DWIConvert --inputVolume %s --outputVolume %s.nrrd --conversionMode FSLToNrrd --inputBValues %s --inputBVectors %s' % (filename_nii, basename, filename_bval, filename_bvec))
    print "NII->NRRD:" + cmd.cmd
    cmd.run()
    return os.path.abspath('%s.nrrd' % (basename))

# 需要导入模块: from nipype.interfaces.base import CommandLine [as 别名]
# 或者: from nipype.interfaces.base.CommandLine import run [as 别名]
 def gunzip(file):
     import os
     os.mkdir("./out")
     from nipype.interfaces.base import CommandLine
     c = CommandLine(command="tar zxvf %s"%file)
     c.run()
     from nipype.utils.filemanip import split_filename
     _,base,_  = split_filename(file)
     
     return os.path.abspath(base)

# 需要导入模块: from nipype.interfaces.base import CommandLine [as 别名]
# 或者: from nipype.interfaces.base.CommandLine import run [as 别名]
def geodesic_depth(command, surface_file, verbose=False):
    """
    Estimate geodesic depth of each vertex in a surface mesh.
    (Calls Joachim Giard's C++ code)

    Parameters
    ----------
    command : travel depth C++ executable command
    surface_file : ``vtk file``
    verbose : bool
        print statements?

    Returns
    -------
    depth_file: string
        vtk file with geodesic depth per vertex of mesh

    Examples
    --------
    >>> import os
    >>> import numpy as np
    >>> from mindboggle.shapes.surface_shapes import geodesic_depth
    >>> from mindboggle.mio.vtks import read_scalars
    >>> from mindboggle.mio.fetch_data import prep_tests
    >>> urls, fetch_data = prep_tests()
    >>> surface_file = fetch_data(urls['left_pial'], '', '.vtk')
    >>> verbose = False
    >>> ccode_path = os.environ['vtk_cpp_tools']
    >>> command = os.path.join(ccode_path, 'geodesic_depth', 'GeodesicDepthMain')
    >>> depth_file = geodesic_depth(command, surface_file, verbose)
    >>> scalars, name = read_scalars(depth_file)
    >>> [np.float("{0:.{1}f}".format(x, 5)) for x in scalars[0:8]]
    [0.02026, 0.06009, 0.12859, 0.04564, 0.00774, 0.05284, 0.05354, 0.01316]

    """
    import os
    from nipype.interfaces.base import CommandLine

    basename = os.path.splitext(os.path.basename(surface_file))[0]
    depth_file = os.path.join(os.getcwd(), basename + '.geodesic_depth.vtk')
    args = ' '.join([surface_file, depth_file])

    if verbose:
        print("{0} {1}".format(command, args))

    cli = CommandLine(command=command)
    cli.inputs.args = args
    cli.cmdline
    cli.run()

    if not os.path.exists(depth_file):
        raise IOError(depth_file + " not found")

    return depth_file

# 需要导入模块: from nipype.interfaces.base import CommandLine [as 别名]
# 或者: from nipype.interfaces.base.CommandLine import run [as 别名]
def dtiprep(in_file, output_prefix):
    from glob import glob
    import os
    from nipype.interfaces.base import CommandLine
    cmd = CommandLine('DTIPrepExec -c -d -f %s -n %s/%s_notes.txt -p %s -w %s/%s.nrrd' % ((experiment_dir + '/' + output_prefix),(experiment_dir + '/' + output_prefix),output_prefix,DTIprep_protocol,experiment_dir,output_prefix))
    print "DTIPREP:" + cmd.cmd
    cmd.run()
    qcfile = experiment_dir + '/' + output_prefix + '/' + output_prefix + '_QCed.nrrd'
    xmlfile = experiment_dir + '/' + output_prefix + '/' + output_prefix + '_XMLQCResult.xml'
    sumfile = experiment_dir + '/' + output_prefix + '/' + output_prefix + '_QCReport.txt'
    return qcfile, xmlfile, sumfile