Python matlab.MatlabCommand类代码示例

    def _run_interface(self, runtime):
        from nipype.interfaces.matlab import MatlabCommand
        def islist(i):
            if not isinstance(i,list):
                i = [str(i)]
                return i
            else:
                I = []
                for l in i:
                    if not l.endswith('.par'):
                        I.append(str(l))
                    else:
                        shutil.copy2(l,l+'.txt')
                        I.append(l+'.txt')
                return I

        info = {}
        info["functional_files"] = islist(self.inputs.functional_files)
        info["structural_files"] = islist(self.inputs.structural_files)
        info["csf_mask"] = islist(self.inputs.csf_mask)
        info["white_mask"] = islist(self.inputs.white_mask)
        info["grey_mask"] = islist(self.inputs.grey_mask)
        info["TR"] = float(self.inputs.tr)
        info["realignment_parameters"] = islist(self.inputs.realignment_parameters)
        info["outliers"] = islist(self.inputs.outliers)
        info["norm_components"] = islist(self.inputs.norm_components)
        info["filename"] = '%s/conn_%s.mat'%(os.getcwd(),self.inputs.project_name)
        info["n_subjects"] = int(self.inputs.n_subjects)
        conn_inputs = os.path.abspath('inputs_to_conn.mat')
        sio.savemat(conn_inputs, {"in":info})
        print "saved conn_inputs.mat file"
        script="""load %s; batch=bips_load_conn(in); conn_batch(batch)"""%conn_inputs
        mlab = MatlabCommand(script=script, mfile=True)
        result = mlab.run()
        return result.runtime

    def _run_interface(self, runtime):
        d = dict(worldmat=self.inputs.worldmat,
        src=self.inputs.src,
        trg=self.inputs.trg,
        output_file=self.inputs.output_file)
        #this is your MATLAB code template
        script = Template("""worldmat = '$worldmat';
        src = '$src';
        trg = '$trg';
        output_file = '$output_file'
        worldmat2flirtmap(worldmat, src, trg, output_file);
        exit;
        """).substitute(d)

        # mfile = True  will create an .m file with your script and executed.
        # Alternatively
        # mfile can be set to False which will cause the matlab code to be
        # passed
        # as a commandline argument to the matlab executable
        # (without creating any files).
        # This, however, is less reliable and harder to debug
        # (code will be reduced to
        # a single line and stripped of any comments).

        mlab = MatlabCommand(script=script, mfile=True)
        result = mlab.run()
        return result.runtime

	def _run_interface(self, runtime):
		from nipype.interfaces.spm.base import scans_for_fname,scans_for_fnames
		from nipype.utils.filemanip import filename_to_list,list_to_filename

		# setup parameters
		input_dir = "."
		in_files = "{"
		asl_first = str(self.inputs.first_image_type)
		TR = str(self.inputs.TR)
		# convert images to cell array string in matlab
		for f in sorted(scans_for_fnames(filename_to_list(self.inputs.in_files))):
			in_files += "'"+f+"',\n"
			input_dir = os.path.dirname(f)
		in_files = in_files[:-2]+"}"
		self.input_dir = input_dir

		d = dict(in_files=in_files,in_dir=input_dir,first_image_type=asl_first,TR =TR)
		myscript = Template("""
		warning('off','all');
		cd('$in_dir');
		input = char($in_files);
		asl_script(input,$first_image_type,0,$TR);
		exit;
		""").substitute(d)
		mlab = MatlabCommand(script=myscript,matlab_cmd="matlab -nodesktop -nosplash",mfile=True)
		result = mlab.run()
		return result.runtime

	def _run_interface(self, runtime):
	
		d = dict(in_file=self.inputs.in_file,mask_file=self.inputs.mask_file,out_file=self.inputs.out_file)

		script = Template("""addpath('/home/sharad/fcon1000/lib/');in_file = '$in_file';mask_file = '$mask_file';out_file = '$out_file';reho(in_file,mask_file,out_file);exit;""").substitute(d)

		mlab = MatlabCommand(script=script, mfile=True)	
		result = mlab.run()
		return result.runtime

    def _run_interface(self, runtime):
        d = dict(in_file=self.inputs.in_file,
        out_folder=self.inputs.out_folder,
        subject_id=self.inputs.subject_id)
        #this is your MATLAB code template
        script = Template("""
        	cd '$out_folder'
        	WaveletDespike('$in_file','$subject_id')""").substitute(d)

        mlab = MatlabCommand(script=script, mfile=True)
        result = mlab.run()
        return result.runtime

 def _matlab_cmd_update(self):
     # MatlabCommand has to be created here,
     # because matlab_cmb is not a proper input
     # and can be set only during init
     self.mlab = MatlabCommand(matlab_cmd=self.inputs.matlab_cmd,
                                   mfile=self.inputs.mfile,
                                   paths=self.inputs.paths)
     self.mlab.inputs.script_file = 'pyscript_%s.m' % \
     self.__class__.__name__.split('.')[-1].lower()

    def version( matlab_cmd = None ):
        """Returns the path to the SPM directory in the Matlab path
        If path not found, returns None.

        Parameters
        ----------
        matlab_cmd : String specifying default matlab command

            default None, will look for environment variable MATLABCMD
            and use if found, otherwise falls back on MatlabCommand
            default of 'matlab -nodesktop -nosplash'

        Returns
        -------
        spm_path : string representing path to SPM directory

            returns None of path not found
        """
        if matlab_cmd is None:
            try:
                matlab_cmd = os.environ['MATLABCMD']
            except:
                matlab_cmd = 'matlab -nodesktop -nosplash'
        mlab = MatlabCommand(matlab_cmd = matlab_cmd)
        mlab.inputs.script = """
        if isempty(which('spm')),
        throw(MException('SPMCheck:NotFound','SPM not in matlab path'));
        end;
        spm_path = spm('dir');
        [name, version] = spm('ver');
        fprintf(1, 'NIPYPE path:%s|name:%s|release:%s', spm_path, name, version);
        exit;
        """
        mlab.inputs.mfile = False
        try:
            out = mlab.run()
        except (IOError,RuntimeError), e:
            # if no Matlab at all -- exception could be raised
            # No Matlab -- no spm
            logger.debug(str(e))
            return None

    def version( matlab_cmd = None ):
        """Returns the path to the SPM directory in the Matlab path
        If path not found, returns None.

        Parameters
        ----------
        matlab_cmd : String specifying default matlab command
        
            default None, will look for environment variable MATLABCMD
            and use if found, otherwise falls back on MatlabCommand
            default of 'matlab -nodesktop -nosplash'

        Returns
        -------
        spm_path : string representing path to SPM directory

            returns None of path not found
        """
        if matlab_cmd is None:
            try:
                matlab_cmd = os.environ['MATLABCMD']
            except:
                matlab_cmd = 'matlab -nodesktop -nosplash'
        mlab = MatlabCommand(matlab_cmd = matlab_cmd)
        mlab.inputs.script_file = 'spminfo'
        mlab.inputs.script = """
        if isempty(which('spm')),
        throw(MException('SPMCheck:NotFound','SPM not in matlab path'));
        end;
        spm_path = spm('dir');
        fprintf(1, 'NIPYPE  %s', spm_path);
        """
        out = mlab.run()
        if out.runtime.returncode == 0:
            spm_path = sd._strip_header(out.runtime.stdout)
        else:
            logger.debug(out.runtime.stderr)
            return None
        return spm_path

def test_MatlabCommand_inputs():
    input_map = dict(args=dict(argstr='%s',
    ),
    environ=dict(nohash=True,
    usedefault=True,
    ),
    ignore_exception=dict(nohash=True,
    usedefault=True,
    ),
    logfile=dict(argstr='-logfile %s',
    ),
    mfile=dict(usedefault=True,
    ),
    nodesktop=dict(argstr='-nodesktop',
    nohash=True,
    usedefault=True,
    ),
    nosplash=dict(argstr='-nosplash',
    nohash=True,
    usedefault=True,
    ),
    paths=dict(),
    postscript=dict(usedefault=True,
    ),
    prescript=dict(usedefault=True,
    ),
    script=dict(argstr='-r "%s;exit"',
    mandatory=True,
    position=-1,
    ),
    script_file=dict(usedefault=True,
    ),
    single_comp_thread=dict(argstr='-singleCompThread',
    nohash=True,
    ),
    terminal_output=dict(mandatory=True,
    nohash=True,
    ),
    uses_mcr=dict(nohash=True,
    xor=['nodesktop', 'nosplash', 'single_comp_thread'],
    ),
    )
    inputs = MatlabCommand.input_spec()

    for key, metadata in input_map.items():
        for metakey, value in metadata.items():
            yield assert_equal, getattr(inputs.traits()[key], metakey), value

from os.path import join as opj
from nipype.interfaces.afni import Despike
from nipype.interfaces.freesurfer import (BBRegister, ApplyVolTransform,
                                          Binarize, MRIConvert, FSCommand)
from nipype.interfaces.spm import (SliceTiming, Realign, Smooth, Level1Design,
                                   EstimateModel, EstimateContrast)
from nipype.interfaces.utility import Function, IdentityInterface
from nipype.interfaces.io import FreeSurferSource, SelectFiles, DataSink
from nipype.algorithms.rapidart import ArtifactDetect
from nipype.algorithms.misc import TSNR, Gunzip
from nipype.algorithms.modelgen import SpecifySPMModel
from nipype.pipeline.engine import Workflow, Node, MapNode

# MATLAB - Specify path to current SPM and the MATLAB's default mode
from nipype.interfaces.matlab import MatlabCommand
MatlabCommand.set_default_paths('/usr/local/MATLAB/R2014a/toolbox/spm12')
MatlabCommand.set_default_matlab_cmd("matlab -nodesktop -nosplash")

# FreeSurfer - Specify the location of the freesurfer folder
fs_dir = '~/nipype_tutorial/freesurfer'
FSCommand.set_default_subjects_dir(fs_dir)


###
# Specify variables
experiment_dir = '~/nipype_tutorial'          # location of experiment folder
subject_list = ['sub001', 'sub002', 'sub003',
                'sub004', 'sub005', 'sub006',
                'sub007', 'sub008', 'sub009',
                'sub010']                     # list of subject identifiers
output_dir = 'output_fMRI_example_1st'        # name of 1st-level output folder

class SPMCommand(BaseInterface):
    """Extends `BaseInterface` class to implement SPM specific interfaces.

    WARNING: Pseudo prototype class, meant to be subclassed
    """
    input_spec = SPMCommandInputSpec

    _jobtype = 'basetype'
    _jobname = 'basename'

    _matlab_cmd = None
    _paths = None
    _use_mcr = None

    def __init__(self, **inputs):
        super(SPMCommand, self).__init__(**inputs)
        self.inputs.on_trait_change(self._matlab_cmd_update, ['matlab_cmd',
                                                              'mfile',
                                                              'paths',
                                                              'use_mcr'])
        self._check_mlab_inputs()
        self._matlab_cmd_update()

    @classmethod
    def set_mlab_paths(cls, matlab_cmd=None, paths = None, use_mcr=None):
        cls._matlab_cmd = matlab_cmd
        cls._paths = paths
        cls._use_mcr = use_mcr

    def _matlab_cmd_update(self):
        # MatlabCommand has to be created here,
        # because matlab_cmb is not a proper input
        # and can be set only during init
        self.mlab = MatlabCommand(matlab_cmd=self.inputs.matlab_cmd,
                                  mfile=self.inputs.mfile,
                                  paths=self.inputs.paths,
                                  uses_mcr=self.inputs.use_mcr)
        self.mlab.inputs.script_file = 'pyscript_%s.m' % \
        self.__class__.__name__.split('.')[-1].lower()

    @property
    def jobtype(self):
        return self._jobtype

    @property
    def jobname(self):
        return self._jobname

    def _check_mlab_inputs(self):
        if not isdefined(self.inputs.matlab_cmd) and self._matlab_cmd:
            self.inputs.matlab_cmd = self._matlab_cmd
        if not isdefined(self.inputs.paths) and self._paths:
            self.inputs.paths = self._paths
        if not isdefined(self.inputs.use_mcr) and self._use_mcr:
            self.inputs.use_mcr = self._use_mcr

    def _run_interface(self, runtime):
        """Executes the SPM function using MATLAB."""
        self.mlab.inputs.script = self._make_matlab_command(deepcopy(self._parse_inputs()))
        results = self.mlab.run()
        runtime.returncode = results.runtime.returncode
        if self.mlab.inputs.uses_mcr:
            if 'Skipped' in results.runtime.stdout:
                self.raise_exception(runtime)
        runtime.stdout = results.runtime.stdout
        runtime.stderr = results.runtime.stderr
        runtime.merged = results.runtime.merged
        return runtime

    def _list_outputs(self):
        """Determine the expected outputs based on inputs."""

        raise NotImplementedError


    def _format_arg(self, opt, spec, val):
        """Convert input to appropriate format for SPM."""

        return val

    def _parse_inputs(self, skip=()):
        spmdict = {}
        metadata=dict(field=lambda t : t is not None)
        for name, spec in self.inputs.traits(**metadata).items():
            if skip and name in skip:
                continue
            value = getattr(self.inputs, name)
            if not isdefined(value):
                continue
            field = spec.field
            if '.' in field:
                fields = field.split('.')
                dictref = spmdict
                for f in fields[:-1]:
                    if f not in dictref.keys():
                        dictref[f] = {}
                    dictref = dictref[f]
                dictref[fields[-1]] = self._format_arg(name, spec, value)
            else:
                spmdict[field] = self._format_arg(name, spec, value)
#.........这里部分代码省略.........

    def _run_interface(self, runtime):
        in_files = self.inputs.in_files
        data_dir = op.join(os.getcwd(),'origdata')
        if not op.exists(data_dir):
            os.makedirs(data_dir)
        all_names = []
        print 'Multiple ({n}) input images detected! Copying to {d}...'.format(n=len(self.inputs.in_files), d=data_dir)
        for in_file in self.inputs.in_files:
            path, name, ext = split_filename(in_file)
            shutil.copyfile(in_file, op.join(data_dir, name) + ext)
            if ext == '.img':
                shutil.copyfile(op.join(path, name) + '.hdr', op.join(data_dir, name) + '.hdr')
            elif ext == '.hdr':
                shutil.copyfile(op.join(path, name) + '.img', op.join(data_dir, name) + '.img')
            all_names.append(name)
        print 'Copied!'

        input_files_as_str = op.join(data_dir, os.path.commonprefix(all_names) + '*' + ext)
        number_of_components = self.inputs.desired_number_of_components
        output_dir = os.getcwd()
        prefix = self.inputs.prefix
        d = dict(output_dir=output_dir, prefix=prefix, number_of_components=number_of_components, in_files=input_files_as_str)
        variables = Template("""

        %% After entering the parameters, use icatb_batch_file_run(inputFile);

        modalityType = 'fMRI';
        which_analysis = 1;
        perfType = 1;
        keyword_designMatrix = 'no';
        dataSelectionMethod = 4;
        input_data_file_patterns = {'$in_files'};
        dummy_scans = 0;
        outputDir = '$output_dir';
        prefix = '$prefix';
        maskFile = [];
        group_pca_type = 'subject specific';
        backReconType = 'gica';

        %% Data Pre-processing options
        % 1 - Remove mean per time point
        % 2 - Remove mean per voxel
        % 3 - Intensity normalization
        % 4 - Variance normalization
        preproc_type = 3;
        pcaType = 1;
        pca_opts.stack_data = 'yes';
        pca_opts.precision = 'single';
        pca_opts.tolerance = 1e-4;
        pca_opts.max_iter = 1000;
        numReductionSteps = 2;
        doEstimation = 0;
        estimation_opts.PC1 = 'mean';
        estimation_opts.PC2 = 'mean';
        estimation_opts.PC3 = 'mean';

        numOfPC1 = $number_of_components;
        numOfPC2 = $number_of_components;
        numOfPC3 = 0;

        %% Scale the Results. Options are 0, 1, 2, 3 and 4
        % 0 - Don't scale
        % 1 - Scale to Percent signal change
        % 2 - Scale to Z scores
        % 3 - Normalize spatial maps using the maximum intensity value and multiply timecourses using the maximum intensity value
        % 4 - Scale timecourses using the maximum intensity value and spatial maps using the standard deviation of timecourses
        scaleType = 0;
        algoType = 1;
        refFunNames = {'Sn(1) right*bf(1)', 'Sn(1) left*bf(1)'};
        refFiles = {which('ref_default_mode.nii'), which('ref_left_visuomotor.nii'), which('ref_right_visuomotor.nii')};
        %% ICA Options - Name by value pairs in a cell array. Options will vary depending on the algorithm. See icatb_icaOptions for more details. Some options are shown below.
        %% Infomax -  {'posact', 'off', 'sphering', 'on', 'bias', 'on', 'extended', 0}
        %% FastICA - {'approach', 'symm', 'g', 'tanh', 'stabilization', 'on'}
        icaOptions =  {'posact', 'off', 'sphering', 'on', 'bias', 'on', 'extended', 0};
        """).substitute(d)

        file = open('input_batch.m', 'w')
        file.writelines(variables)
        file.close()

        script = """param_file = icatb_read_batch_file('input_batch.m');
        load(param_file);
        global FUNCTIONAL_DATA_FILTER;
        global ZIP_IMAGE_FILES;
        FUNCTIONAL_DATA_FILTER = '*.nii';
        ZIP_IMAGE_FILES = 'No';
        icatb_runAnalysis(sesInfo, 1);"""

        result = MatlabCommand(script=script, mfile=True, prescript=[''], postscript=[''])
        r = result.run()
        return runtime

    def _run_interface(self, runtime):
        data_dir = op.abspath('./denoise/components')
        if not os.path.exists(data_dir):
            os.makedirs(data_dir)

        in_files = self.inputs.in_files
        if len(self.inputs.in_files) > 1:
            print 'Multiple ({n}) input images detected! Copying to {d}...'.format(n=len(self.inputs.in_files), d=data_dir)
            for in_file in self.inputs.in_files:
                path, name, ext = split_filename(in_file)
                shutil.copyfile(in_file, op.join(data_dir, name) + ext)
                if ext == '.img':
                    shutil.copyfile(op.join(path, name) + '.hdr',
                                    op.join(data_dir, name) + '.hdr')
                elif ext == '.hdr':
                    shutil.copyfile(op.join(path, name) + '.img',
                                    op.join(data_dir, name) + '.img')
            print 'Copied!'
            in_files = self.inputs.in_files

        elif isdefined(self.inputs.in_file4d):
            print 'Single four-dimensional image selected. Splitting and copying to {d}'.format(d=data_dir)
            in_files = nb.four_to_three(self.inputs.in_file4d)
            for in_file in in_files:
                path, name, ext = split_filename(in_file)
                shutil.copyfile(in_file, op.join(data_dir, name) + ext)
            print 'Copied!'

        else:
            print 'Single functional image provided. Ending...'
            in_files = self.inputs.in_files

        nComponents = len(in_files)
        path, name, ext = split_filename(self.inputs.time_course_image)
        shutil.copyfile(self.inputs.time_course_image,
                        op.join(data_dir, name) + ext)

        if ext == '.img':
            shutil.copyfile(op.join(path, name) + '.hdr',
                            op.join(data_dir, name) + '.hdr')
        elif ext == '.hdr':
            shutil.copyfile(op.join(path, name) + '.img',
                            op.join(data_dir, name) + '.img')

        data_dir = op.abspath('./denoise')
        path, name, ext = split_filename(self.inputs.ica_mask_image)
        shutil.copyfile(self.inputs.ica_mask_image,
                        op.join(data_dir, name) + ext)
        if ext == '.img':
            shutil.copyfile(op.join(path, name) + '.hdr',
                            op.join(data_dir, name) + '.hdr')
        elif ext == '.hdr':
            shutil.copyfile(op.join(path, name) + '.img',
                            op.join(data_dir, name) + '.img')
        mask_file = op.join(data_dir, name)
        repetition_time = self.inputs.repetition_time
        neuronal_image = op.abspath(self.inputs.out_neuronal_image)
        non_neuronal_image = op.abspath(self.inputs.out_non_neuronal_image)
        coma_rest_lib_path = op.abspath(self.inputs.coma_rest_lib_path)
        d = dict(
            data_dir=data_dir, mask_name=mask_file, nComponents=nComponents, Tr=repetition_time,
            nameNeuronal=neuronal_image, nameNonNeuronal=non_neuronal_image, coma_rest_lib_path=coma_rest_lib_path)
        script = Template("""
        restlib_path = '$coma_rest_lib_path';
        setup_restlib_paths(restlib_path)
        dataDir = '$data_dir';
        maskName = '$mask_name';
        nCompo = $nComponents;
        Tr = $Tr;
        nameNeuronalData = '$nameNeuronal';
        nameNonNeuronalData = '$nameNonNeuronal';
        denoiseImage(dataDir,maskName,nCompo,Tr,nameNeuronalData,nameNonNeuronalData, restlib_path);
        """).substitute(d)
        result = MatlabCommand(script=script, mfile=True,
                               prescript=[''], postscript=[''])
        r = result.run()
        print 'Neuronal component image saved as {n}'.format(n=neuronal_image)
        print 'Non-neuronal component image saved as {n}'.format(n=non_neuronal_image)
        return runtime

import os
import socket
from nipype.interfaces.matlab import MatlabCommand

if socket.gethostname() == 'malin':
    os.environ['MATLABCMD'] = "/opt/matlab/R2015b/bin/matlab -nodesktop -nosplash"
    MatlabCommand.set_default_paths('/opt/matlab/R2015b/toolbox/spm12')
    MatlabCommand.set_default_matlab_cmd("/opt/matlab/R2015b/bin/matlab -nodesktop -nosplash")
    TPM = '/opt/matlab/R2015b/toolbox/spm12/tpm/TPM.nii'
    # os.environ['MATLABCMD'] = "/opt/matlab/R2012a/bin/matlab -nodesktop -nosplash"
    # MatlabCommand.set_default_paths('/opt/matlab/R2012a/toolbox/spm12')
    # MatlabCommand.set_default_matlab_cmd("/opt/matlab/R2012a/bin/matlab -nodesktop -nosplash")
elif socket.gethostname() == 'cala':
    os.environ['MATLABCMD'] = "/opt/matlab/64bit/R2015a/bin/matlab -nodesktop -nosplash"
    MatlabCommand.set_default_paths('/opt/matlab/64bit/R2015a/toolbox/spm12')
    MatlabCommand.set_default_matlab_cmd("/opt/matlab/64bit/R2015a/bin/matlab -nodesktop -nosplash")
    TPM = '/opt/matlab/64bit/R2015a/toolbox/spm12/tpm/TPM.nii'

def display_crash_files(crashfile, rerun=False):
    from nipype.utils.filemanip import loadcrash
    crash_data = loadcrash(crashfile)
    node = crash_data['node']
    tb = crash_data['traceback']
    print("\n")
    print("File: %s"%crashfile)
    print("Node: %s"%node)
    if node.base_dir:
        print("Working directory: %s" % node.output_dir())
    else:
        print("Node crashed before execution")
    print("\n")

from nipype.interfaces.fsl.epi import ApplyTOPUP, TOPUP
from nipype.interfaces.freesurfer import Resample, Binarize, MRIConvert
from nipype.algorithms.confounds import CompCor
from nipype.interfaces.afni.preprocess import Bandpass
from nipype.interfaces.afni.utils import AFNItoNIFTI
from nipype.interfaces.ants import ApplyTransforms, Registration
from nipype.algorithms.misc import Gunzip
from pandas import DataFrame, Series

#set output file type for FSL to NIFTI
from nipype.interfaces.fsl.preprocess import FSLCommand
FSLCommand.set_default_output_type('NIFTI')

# MATLAB setup - Specify path to current SPM and the MATLAB's default mode
from nipype.interfaces.matlab import MatlabCommand
MatlabCommand.set_default_paths('~/spm12')
MatlabCommand.set_default_matlab_cmd("matlab -nodesktop -nosplash")

# Set study variables
setup='sherlock'
sample='6mo' #6mo or newborn
sequence='spiral'#spiral or mux6

if setup=='sherlock':
    studyhome = '/oak/stanford/groups/iang/BABIES_data/BABIES_rest'
    raw_data = studyhome + '/subjDir/all'
    output_dir = studyhome + '/processed/preproc'
    workflow_dir = studyhome + '/workflows'
elif setup=='Cat':
    studyhome = '/Users/catcamacho/Box/SNAP/BABIES/BABIES_rest'
    raw_data = studyhome + '/rest_raw'