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preprocessing_rsfmri/utils.py

+import nibabel.gifti as ng
+from os import system
+
+# ***** GIFTI ******************************************************************
+def gii_convert_to_texture(gii_f, out_gii_f=None, meta=None, verbose=0):
+    """ Change intent of first data array and create a new Gifti """
+    # TODO: verify the that description is good and function is general
+    orig_gii = ng.read(gii_f)
+
+    data = orig_gii.darrays[len(orig_gii.darrays) - 1].data[0]
+    darray = ng.GiftiDataArray(data=data, intent='NIFTI_INTENT_ESTIMATE')
+    gii = ng.GiftiImage(darrays=[darray])
+
+    if meta:
+        gii.meta = ng.GiftiMetaData().from_dict(meta)
+
+    out_f = out_gii_f if out_gii_f else gii_f
+    ng.write(gii, out_f)
+
+    if verbose > 0:
+        print("Texture saved at: {}".format(out_f))
+
+
+# ***** Freesurfer *************************************************************
+def project_epi(fs_subdir, sub, nii_file, filename, gii_dir,
+                tgt_subject, hem_list=['lh', 'rh'], sfwhm=0):
+    """
+        Project one Nifti file (3D image) to surface saved as Gifti file.
+
+        Projection is done for left and right
+        :param fs_subdir: FreeSurfer subjects directory
+        :param sub: Subject name
+        :param nii_file: Splitted .nii directory
+        :param gii_dir: Output directory
+        :param gii_sfx: Gifti files suffix (add to the hemisphere name)
+        :param tgt_subject: Name of target subject
+        :param hem_list: Hemispheres (default: left and right)
+        :param sfwhm: Surface smoothing (default = 0mm)
+    """
+    for hem in hem_list:
+        gii_file = "{}/{}.{}.gii".format(gii_dir, filename, hem)
+
+        cmd = '$FREESURFER_HOME/bin/mri_vol2surf --src {} --o {} ' \
+              '--out_type gii --regheader {} --hemi {} '\
+              '--projfrac-avg 0 1 0.1 --surf-fwhm {:d} --sd {} ' \
+              '--trgsubject {}'.format(
+               nii_file, gii_file, sub, hem, sfwhm, fs_subdir, tgt_subject)
+        system(cmd)
+
+# ***** SHELL ******************************************************************
+def run(cmd, verbose=True, execute=True):
+    """ Print and run a shell command """
+    if verbose:
+        print(cmd)
+
+    if execute:
+        system(cmd)
+
+
+# ***** SPM ********************************************************************
+def spm_run_batch(batch, variables, display=True, n_jobs=-1):
+    """ Run the SPM batch script file in Matlab
+
+        :param variables: Variables set in matlab
+        :param batch: SPM Batch file (.m)
+        :param display: Open Matlab's GUI if is True. (Default: True)
+        :param n_jobs: Set the max number of jobs in Matlab (default: maximum)
+        :return: Nothing
+    """
+
+    m_script = matlab_define(variables)
+    if n_jobs > -1:
+        m_script += ' LASTN = maxNumCompThreads({:d});'.format(n_jobs)
+    m_script += "spm fmri; run('{}');".format(batch)
+    m_script += "spm_jobman('run',matlabbatch); clear variables;"
+
+    matlab_run_script(m_script, display=display, exit_after=True)
+
+
+# ***** MATLAB *****************************************************************
+
+def run_script_matlab(script, var, display=True ):
+    m_script = matlab_define(var)
+    m_script += "run('{}');".format(script)
+    matlab_run_script(m_script, display=display, exit_after=True)
+
+def matlab_run_script(mat_script, exit_after=True, display=True):
+    """ Start matlab throught the terminal and run the given script
+
+        :param mat_script: Matlab script.
+        :param exit_after: (opt.) Add the matlab exit command at the end of the
+                            script. Default: False.
+        :param display: Open Matlab's GUI if is True. (Default: True)
+        :return: Nothing
+    """
+    if exit_after is True:
+        mat_script += " exit();"
+
+    cmd = "matlab "
+    if display is False:
+        cmd += "-nodisplay "
+    cmd += '-r "{}"'.format(mat_script)
+    run(cmd)
+
+
+def matlab_val(val):
+    """ Return val formatted for Matlab """
+    if type(val) == str:
+        var = "'" + val + "'"
+    elif type(val) == dict:
+        var = matlab_format_dict(val)
+    elif type(val) == bool:
+        var = int(val)
+    elif type(val) == list:
+        if len(val) == 0:
+            var = '[]'
+        elif type(val[0]) == str or type(val[0]) == list:
+            var = matlab_format_str_array(val)
+        else:
+            var = matlab_format_array(val)
+    else:
+        var = val
+    return var
+
+
+def matlab_format_array(array):
+    """ Return Matlab array that define an array """
+    m_tab = "["
+    for val in array:
+        m_tab += "{} ".format(matlab_val(val))
+    if m_tab[:-2] == ", ":
+        m_tab = m_tab[:-2]
+    m_tab += "]"
+    return m_tab
+
+
+def matlab_format_str_array(array):
+    """ Return Matlab script that define an array of strings """
+    m_tab = "{"
+    for val in array:
+        m_tab += "{}, ".format(matlab_val(val))
+    if m_tab[:-2] == ", ":
+        m_tab = m_tab[:-2]
+    m_tab += "}"
+    return m_tab
+
+
+def matlab_format_dict(data):
+    """ Return Matlab script that define a dictionnary as cells """
+    m_dict = "{"
+    for k in data.keys():
+        m_dict += "struct('key', '{}', 'val', {}), ".format(
+            k, matlab_format_array(data[k]))
+    m_dict += "}"
+    return m_dict
+
+
+def matlab_define(variables):
+    """ Return Matlab script that define all variables
+
+    :param variables: dictionnary of variables (names as keys)
+    """
+    m_script = ""
+    for v_name in variables.keys():
+        m_script += "{}={}; ".format(v_name, matlab_val(variables[v_name]))
+    return m_script
+
+
+
+
+