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[u'Component.export(folder=None, format=None, save_std=False, only_free=True)', u':module: hyperspy.component', u'', u'Plot the value of the parameters of the model', u'', u':Parameters:', u'', u'    **folder** : str or None', u'', u'        The path to the folder where the file will be saved. If', u'        `None` the', u'        current folder is used by default.', u'', u'    **format** : str', u'', u'        The format to which the data will be exported. It must be', u'        the', u'        extension of any format supported by HyperSpy. If None, the', u'        default', u'        format for exporting as defined in the `Preferences` will be', u'         used.', u'', u'    **save_std** : bool', u'', u'        If True, also the standard deviation will be saved.', u'', u'    **only_free** : bool', u'', u'        If True, only the value of the parameters that are free will', u'         be', u'        exported.', u'', u'.. rubric:: Notes', u'', u'The name of the files will be determined by each the Component', u'and', u'each Parameter name attributes. Therefore, it is possible to', u'customise', u'the file names modify the name attributes.']:20: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy/hyperspy/component.py:docstring of hyperspy.component.Component.export:7: WARNING: Definition list ends without a blank line; unexpected unindent.
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/home/fjd29/Python/hyperspy/hyperspy/component.py:docstring of hyperspy.component.Parameter:18: ERROR: Malformed table.
Column span alignment problem in table line 5.

=====================  ========  ==========
    bmin, bmax: float            
                                 Lower and upper bounds of the parameter value.
        twin_function  function  
                                 Function that, if selt.twin is not None, takes self.twin.value
                                 as its only argument and returns a float or array that is
                                 returned when getting Parameter.value
twin_inverse_function  function  
                                 The inverse of twin_function. If it is None then it is not
                                 possible to set the value of the parameter twin by setting
                                 the value of the current parameter.
=====================  ========  ==========
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Parameters
---------
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Parameters
---------
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[u"MVATools.export_bss_results(comp_ids=None, folder=None, calibrate=True, multiple_files=None, save_figures=False, factor_prefix='bss_factor', factor_format=None, loading_prefix='bss_loading', loading_format=None, comp_label=None, cmap=<matplotlib.colors.LinearSegmentedColormap object at 0x7fd6e8869b50>, same_window=False, no_nans=True, per_row=3, save_figures_format='png')", u':module: hyperspy.signal', u'', u'Export results from ICA to any of the supported formats.', u'', u':Parameters:', u'', u'    **comp_ids** : None, int, or list of ints', u'', u'        if None, returns all components/loadings.', u'        if int, returns components/loadings with ids from 0 to given', u'         int.', u'        if list of ints, returns components/loadings with ids in', u'        iven list.', u'', u'    **folder** : str or None', u'', u'        The path to the folder where the file will be saved. If', u'        `None` the', u'        current folder is used by default.', u'', u'    **factor_prefix** : string', u'', u'        The prefix that any exported filenames for', u'        factors/components', u'        begin with', u'', u'    **factor_format** : string', u'', u'        The extension of the format that you wish to save to.', u'        Determines', u'        the kind of output.', u'            - For image formats (tif, png, jpg, etc.), plots are', u'            created', u'              using the plotting flags as below, and saved at', u'              600 dpi.', u'              One plot per factor is saved.', u'            - For multidimensional formats (rpl, hdf5), arrays are', u'            saved', u'              in single files.  All factors are contained in the one', u'              file.', u'            - For spectral formats (msa), each factor is saved to a', u'              separate file.', u'', u'    **loading_prefix** : string', u'', u'        The prefix that any exported filenames for', u'        factors/components', u'        begin with', u'', u'    **loading_format** : string', u'', u'        The extension of the format that you wish to save to.', u'', u'    **multiple_files** : Bool', u'', u'        If True, on exporting a file per factor and per loading', u'        will be', u'        created. Otherwise only two files will be created, one', u'        for the', u'        factors and another for the loadings. The default value', u'        can be', u'        chosen in the preferences.', u'', u'    **save_figures** : Bool', u'', u'        If True the same figures that are obtained when using the', u'        plot', u'        methods will be saved with 600 dpi resolution', u'', u'    **Plotting options (for save_figures = True ONLY)** : ', u'', u'    **----------------------------------------------** : ', u'', u'    **calibrate** : bool', u'', u'        if True, calibrates plots where calibration is available', u'        from', u'        the axes_manager.  If False, plots are in pixels/channels.', u'', u'    **same_window** : bool', u'', u'        if True, plots each factor to the same window.', u'', u'    **comp_label** : string', u'', u'        the label that is either the plot title (if plotting in', u'        separate windows) or the label in the legend (if plotting', u'        in the', u'        same window)', u'', u'    **cmap** : The colormap used for the factor image, or for peak', u'', u'        characteristics, the colormap used for the scatter plot of', u'        some peak characteristic.', u'', u'    **per_row** : int, the number of plots in each row, when the', u'', u'    **same_window** : ', u'', u'        parameter is True.', u'', u'    **save_figures_format** : str', u'', u'        The image format extension.', u'', u'.. seealso::', u'', u'    :obj:`get_bss_factors`, :obj:`get_bss_loadings.`']:11: ERROR: Unexpected indentation.
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[u"MVATools.export_bss_results(comp_ids=None, folder=None, calibrate=True, multiple_files=None, save_figures=False, factor_prefix='bss_factor', factor_format=None, loading_prefix='bss_loading', loading_format=None, comp_label=None, cmap=<matplotlib.colors.LinearSegmentedColormap object at 0x7fd6e8869b50>, same_window=False, no_nans=True, per_row=3, save_figures_format='png')", u':module: hyperspy.signal', u'', u'Export results from ICA to any of the supported formats.', u'', u':Parameters:', u'', u'    **comp_ids** : None, int, or list of ints', u'', u'        if None, returns all components/loadings.', u'        if int, returns components/loadings with ids from 0 to given', u'         int.', u'        if list of ints, returns components/loadings with ids in', u'        iven list.', u'', u'    **folder** : str or None', u'', u'        The path to the folder where the file will be saved. If', u'        `None` the', u'        current folder is used by default.', u'', u'    **factor_prefix** : string', u'', u'        The prefix that any exported filenames for', u'        factors/components', u'        begin with', u'', u'    **factor_format** : string', u'', u'        The extension of the format that you wish to save to.', u'        Determines', u'        the kind of output.', u'            - For image formats (tif, png, jpg, etc.), plots are', u'            created', u'              using the plotting flags as below, and saved at', u'              600 dpi.', u'              One plot per factor is saved.', u'            - For multidimensional formats (rpl, hdf5), arrays are', u'            saved', u'              in single files.  All factors are contained in the one', u'              file.', u'            - For spectral formats (msa), each factor is saved to a', u'              separate file.', u'', u'    **loading_prefix** : string', u'', u'        The prefix that any exported filenames for', u'        factors/components', u'        begin with', u'', u'    **loading_format** : string', u'', u'        The extension of the format that you wish to save to.', u'', u'    **multiple_files** : Bool', u'', u'        If True, on exporting a file per factor and per loading', u'        will be', u'        created. Otherwise only two files will be created, one', u'        for the', u'        factors and another for the loadings. The default value', u'        can be', u'        chosen in the preferences.', u'', u'    **save_figures** : Bool', u'', u'        If True the same figures that are obtained when using the', u'        plot', u'        methods will be saved with 600 dpi resolution', u'', u'    **Plotting options (for save_figures = True ONLY)** : ', u'', u'    **----------------------------------------------** : ', u'', u'    **calibrate** : bool', u'', u'        if True, calibrates plots where calibration is available', u'        from', u'        the axes_manager.  If False, plots are in pixels/channels.', u'', u'    **same_window** : bool', u'', u'        if True, plots each factor to the same window.', u'', u'    **comp_label** : string', u'', u'        the label that is either the plot title (if plotting in', u'        separate windows) or the label in the legend (if plotting', u'        in the', u'        same window)', u'', u'    **cmap** : The colormap used for the factor image, or for peak', u'', u'        characteristics, the colormap used for the scatter plot of', u'        some peak characteristic.', u'', u'    **per_row** : int, the number of plots in each row, when the', u'', u'    **same_window** : ', u'', u'        parameter is True.', u'', u'    **save_figures_format** : str', u'', u'        The image format extension.', u'', u'.. seealso::', u'', u'    :obj:`get_bss_factors`, :obj:`get_bss_loadings.`']:32: ERROR: Unexpected indentation.
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/home/fjd29/Python/hyperspy/hyperspy/signal.py:docstring of hyperspy.signal.MVATools.export_bss_results:34: WARNING: Definition list ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy/hyperspy/signal.py:docstring of hyperspy.signal.MVATools.export_bss_results:35: WARNING: Bullet list ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy/hyperspy/signal.py:docstring of hyperspy.signal.MVATools.export_bss_results:38: WARNING: Definition list ends without a blank line; unexpected unindent.
[u"MVATools.export_decomposition_results(comp_ids=None, folder=None, calibrate=True, factor_prefix='factor', factor_format=None, loading_prefix='loading', loading_format=None, comp_label=None, cmap=<matplotlib.colors.LinearSegmentedColormap object at 0x7fd6e8869b50>, same_window=False, multiple_files=None, no_nans=True, per_row=3, save_figures=False, save_figures_format='png')", u':module: hyperspy.signal', u'', u'Export results from a decomposition to any of the supported', u'formats.', u'', u':Parameters:', u'', u'    **comp_ids** : None, int, or list of ints', u'', u'        if None, returns all components/loadings.', u'        if int, returns components/loadings with ids from 0 to', u'        given int.', u'        if list of ints, returns components/loadings with ids in', u'        given list.', u'', u'    **folder** : str or None', u'', u'        The path to the folder where the file will be saved.', u'        If `None` the', u'        current folder is used by default.', u'', u'    **factor_prefix** : string', u'', u'        The prefix that any exported filenames for', u'        factors/components', u'        begin with', u'', u'    **factor_format** : string', u'', u'        The extension of the format that you wish to save to.', u'', u'    **loading_prefix** : string', u'', u'        The prefix that any exported filenames for', u'        factors/components', u'        begin with', u'', u'    **loading_format** : string', u'', u'        The extension of the format that you wish to save to.', u'        Determines', u'        the kind of output.', u'            - For image formats (tif, png, jpg, etc.), plots are', u'            created', u'              using the plotting flags as below, and saved at', u'              600 dpi.', u'              One plot per loading is saved.', u'            - For multidimensional formats (rpl, hdf5), arrays are', u'            saved', u'              in single files.  All loadings are contained in the', u'              one', u'              file.', u'            - For spectral formats (msa), each loading is saved to a', u'              separate file.', u'', u'    **multiple_files** : Bool', u'', u'        If True, on exporting a file per factor and per loading will', u'         be', u'        created. Otherwise only two files will be created, one for', u'        the', u'        factors and another for the loadings. The default value can', u'        be', u'        chosen in the preferences.', u'', u'    **save_figures** : Bool', u'', u'        If True the same figures that are obtained when using the', u'        plot', u'        methods will be saved with 600 dpi resolution', u'', u'    **Plotting options (for save_figures = True ONLY)** : ', u'', u'    **----------------------------------------------** : ', u'', u'    **calibrate** : bool', u'', u'        if True, calibrates plots where calibration is available', u'        from', u'        the axes_manager.  If False, plots are in pixels/channels.', u'', u'    **same_window** : bool', u'', u'        if True, plots each factor to the same window.', u'', u'    **comp_label** : string, the label that is either the plot title', u'', u'        (if plotting in separate windows) or the label in the legend', u'        (if plotting in the same window)', u'', u'    **cmap** : The colormap used for the factor image, or for peak', u'', u'        characteristics, the colormap used for the scatter plot of', u'        some peak characteristic.', u'', u'    **per_row** : int, the number of plots in each row, when the', u'', u'    **same_window** : ', u'', u'        parameter is True.', u'', u'    **save_figures_format** : str', u'', u'        The image format extension.', u'', u'.. seealso::', u'', u'    :obj:`get_decomposition_factors`, :obj:`get_decomposition_loadings.`']:43: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy/hyperspy/signal.py:docstring of hyperspy.signal.MVATools.export_decomposition_results:28: WARNING: Bullet list ends without a blank line; unexpected unindent.
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/home/fjd29/Python/hyperspy/hyperspy/signal.py:docstring of hyperspy.signal.MVATools.export_decomposition_results:44: WARNING: Definition list ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy/hyperspy/signal.py:docstring of hyperspy.signal.MVATools.export_decomposition_results:100: WARNING: Title underline too short.

See Also
-------
[u'MVATools.get_bss_factors()', u':module: hyperspy.signal', u'', u'Return the blind source separtion factors as a Signal.', u'', u'See Also', u'-------', u'get_bss_loadings, export_bss_results.']:6: SEVERE: Unexpected section title.

See Also
-------
/home/fjd29/Python/hyperspy/hyperspy/signal.py:docstring of hyperspy.signal.MVATools.export_decomposition_results:109: WARNING: Title underline too short.

See Also
-------
[u'MVATools.get_bss_loadings()', u':module: hyperspy.signal', u'', u'Return the blind source separtion loadings as a Signal.', u'', u'See Also', u'-------', u'get_bss_factors, export_bss_results.']:6: SEVERE: Unexpected section title.

See Also
-------
<autodoc>:0: WARNING: Title underline too short.

See Also
-------
[u'MVATools.get_decomposition_factors()', u':module: hyperspy.signal', u'', u'Return the decomposition factors as a Signal.', u'', u'See Also', u'-------', u'get_decomposition_loadings, export_decomposition_results.']:6: SEVERE: Unexpected section title.

See Also
-------
/home/fjd29/Python/hyperspy/hyperspy/signal.py:docstring of hyperspy.signal.MVATools.get_bss_factors:5: WARNING: Title underline too short.

See Also
-------
[u'MVATools.get_decomposition_loadings()', u':module: hyperspy.signal', u'', u'Return the decomposition loadings as a Signal.', u'', u'See Also', u'-------', u'get_decomposition_factors, export_decomposition_results.']:6: SEVERE: Unexpected section title.

See Also
-------
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[u"Signal.split(axis='auto', number_of_parts='auto', step_sizes='auto')", u':module: hyperspy.signal', u'', u'Splits the data into several signals.', u'', u'The split can be defined by giving the number_of_parts, a homogeneous', u"step size or a list of customized step sizes. By default ('auto'),", u'the function is the reverse of utils.stack().', u'', u':Parameters:', u'', u"    **axis** : {'auto' | int | string}", u'', u'        Specify the data axis in which to perform the splitting', u'        operation.  The axis can be specified using the index of the', u'        axis in `axes_manager` or the axis name.', u"        - If 'auto' and if the object has been created with utils.stack,", u'        split will return the former list of signals', u"        (options stored in 'metadata._HyperSpy.Stacking_history'", u'         else the last navigation axis will be used.', u'', u"    **number_of_parts** : {'auto' | int}", u'', u'        Number of parts in which the SI will be splitted. The', u'        splitting is homegenous. When the axis size is not divisible', u'        by the number_of_parts the reminder data is lost without', u"        warning. If number_of_parts and step_sizes is 'auto',", u'        number_of_parts equals the length of the axis,', u'        step_sizes equals one  and the axis is supress from each sub_spectra.', u'', u"    **step_sizes** : {'auto' | list of ints | int}", u'', u"        Size of the splitted parts. If 'auto', the step_sizes equals one.", u'        If int, the splitting is homogenous.', u'', u':Returns:', u'', u'    **list of the splitted signals** : ', u'', u'.. rubric:: Examples', u'', u'>>> s=signals.Spectrum(random.random([4,3,2]))', u'>>> s', u'    <Spectrum, title: , dimensions: (3, 4|2)>', u'>>> s.split()', u'    [<Spectrum, title: , dimensions: (3 |2)>,', u'    <Spectrum, title: , dimensions: (3 |2)>,', u'    <Spectrum, title: , dimensions: (3 |2)>,', u'    <Spectrum, title: , dimensions: (3 |2)>]', u'>>> s.split(step_sizes=2)', u'    [<Spectrum, title: , dimensions: (3, 2|2)>,', u'    <Spectrum, title: , dimensions: (3, 2|2)>]', u'>>> s.split(step_sizes=[1,2])', u'    [<Spectrum, title: , dimensions: (3, 1|2)>,', u'    <Spectrum, title: , dimensions: (3, 2|2)>]']:19: ERROR: Unexpected indentation.
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[u'Signal1DTools.calibrate(*args, **kwargs)', u':module: hyperspy.signal', u'', u'Calibrate the spectral dimension using a gui.', u'', u'It displays a window where the new calibration can be set by:', u'* Setting the offset, units and scale directly', u'* Selection a range by dragging the mouse on the spectrum figure', u' and', u'setting the new values for the given range limits', u'', u':Raises:', u'', u'    **SignalDimensionError if the signal dimension is not 1.** : ', u'', u'.. rubric:: Notes', u'', u'For this method to work the output_dimension must be 1. Set the', u'view', u'accordingly']:8: ERROR: Unexpected indentation.
<autodoc>:0: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy/hyperspy/signal.py:docstring of hyperspy.signal.Signal1DTools.estimate_shift1D:61: WARNING: Title underline too short.

Parameters
---------
[u'Signal1DTools.find_peaks1D_ohaver(xdim=None, slope_thresh=0, amp_thresh=None, subchannel=True, medfilt_radius=5, maxpeakn=30000, peakgroup=10)', u':module: hyperspy.signal', u'', u'Find peaks along a 1D line (peaks in spectrum/spectra).', u'', u'Function to locate the positive peaks in a noisy x-y data set.', u'', u'Detects peaks by looking for downward zero-crossings in the', u'first', u"derivative that exceed 'slope_thresh'.", u'', u'Returns an array containing position, height, and width of each', u'peak.', u'', u"'slope_thresh' and 'amp_thresh', control sensitivity: higher", u'values will', u'neglect smaller features.', u'', u'peakgroup is the number of points around the top peak to search', u'around', u'', u'Parameters', u'---------', u'', u'slope_thresh : float (optional)', u'               1st derivative threshold to count the peak', u'               default is set to 0.5', u'               higher values will neglect smaller features.', u'', u'amp_thresh : float (optional)', u'             intensity threshold above which', u'             default is set to 10% of max(y)', u'             higher values will neglect smaller features.', u'', u'medfilt_radius : int (optional)', u'             median filter window to apply to smooth the data', u'             (see scipy.signal.medfilt)', u'             if 0, no filter will be applied.', u'             default is set to 5', u'', u'peakgroup : int (optional)', u'            number of points around the "top part" of the peak', u'            default is set to 10', u'', u'maxpeakn : int (optional)', u'           number of maximum detectable peaks', u'           default is set to 5000', u'', u'subpix : bool (optional)', u'         default is set to True', u'', u':Returns:', u'', u'    **peaks** : structured array of shape _navigation_shape_in_array in which', u'', u'    **each cell contains an array that contains as many structured arrays as** : ', u'', u'    **peaks where found at that location and which fields: position, width,** : ', u'', u'    **height contains position, height, and width of each peak.** : ', u'', u':Raises:', u'', u'    **SignalDimensionError if the signal dimension is not 1.** : ']:22: SEVERE: Unexpected section title.

Parameters
---------
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[u'EELSCLEdge(element_subshell, GOS=None)', u':module: hyperspy._components.eels_cl_edge', u'', u'Bases: :class:`hyperspy.component.Component`', u'', u'', u'', u'EELS core loss ionisation edge from hydrogenic or tabulated', u'Hartree-Slater GOS with splines for fine structure fitting.', u'', u'Hydrogenic GOS are limited to K and L shells.', u'', u"Currently it only supports Peter Rez's Hartree Slater cross sections", u'parametrised as distributed by Gatan in their', u'Digital Micrograph (DM) software. If Digital Micrograph is installed', u'in the system HyperSpy in the standard location HyperSpy should', u'find the path to the HS GOS folder. Otherwise, the location of the', u'folder can be defined in HyperSpy preferences, which can be done through', u'    preferences.gui() or the preferences.EELS.eels_gos_files_path variable.', u'', u'Calling this class with a numpy.array', u'', u':Parameters:', u'', u'    **element_subshell** : str', u'', u"        For example, 'Ti_L3' for the GOS of the titanium L3 subshell", u'        ', u'', u"    **GOS** : {'hydrogenic', 'Hartree-Slater', None}", u'', u'        The GOS to use. If None it will use the Hartree-Slater GOS if', u'        they are available, otherwise it will use the hydrogenic GOS.', u'', u'.. rubric:: Attributes', u'', u'.. autosummary::', u'   :toctree:', u'', u'   fine_structure_smoothing', u'   fine_structure_active', u'====================  =========  ==========', u'        onset_energy  Parameter  ', u'                                 The edge onset position', u'           intensity  Parameter  ', u'                                 The factor by which the cross section is multiplied, what in', u'                                 favourable cases is proportional to the number of atoms of', u'                                 the element. It is a component.Parameter instance.', u'                                 It is fixed by default.', u'fine_structure_coeff  Parameter  ', u'                                 The coefficients of the spline that fits the fine structure.', u'                                 Fix this parameter to fix the fine structure. It is a', u'                                 component.Parameter instance.', u'     effective_angle  Parameter  ', u'                                 The effective collection angle. It is automatically', u'                                 calculated by set_microscope_parameters. It is a', u'                                 component.Parameter instance. It is fixed by default.', u'====================  =========  ==========', u'', u'.. rubric:: Methods', u'', u'.. autosummary::', u'   :toctree:', u'', u'   connect', u'   disconnect', u'   export', u'   fetch_stored_values', u'   fetch_values_from_array', u'   fine_structure_coeff_to_txt', u'   function', u'   get_fine_structure_as_spectrum', u'   grad_intensity', u'   init_parameters', u'   plot', u'   set_microscope_parameters', u'   set_parameters_free', u'   set_parameters_not_free', u'   store_current_parameters_in_map', u'   summary', u'   txt_to_fine_structure_coeff', u'   update_number_parameters', u'', u'', u'.. py:attribute:: EELSCLEdge.E0', u'   :module: hyperspy._components.eels_cl_edge', u'', u'   ', u'   ', u'   ', u'   ', u'', u'.. py:attribute:: EELSCLEdge.collection_angle', u'   :module: hyperspy._components.eels_cl_edge', u'', u'   ', u'   ', u'   ', u'   ', u'', u'.. py:attribute:: EELSCLEdge.convergence_angle', u'   :module: hyperspy._components.eels_cl_edge', u'', u'   ', u'   ', u'   ', u'   ', u'', u'.. py:attribute:: EELSCLEdge.fine_structure_active', u'   :module: hyperspy._components.eels_cl_edge', u'', u'   ', u'   ', u'   ', u'   ', u'', u'.. py:method:: EELSCLEdge.fine_structure_coeff_to_txt(filename)', u'   :module: hyperspy._components.eels_cl_edge', u'', u'   ', u'   ', u'   ', u'   ', u'', u'.. py:attribute:: EELSCLEdge.fine_structure_smoothing', u'   :module: hyperspy._components.eels_cl_edge', u'', u'   ', u'   ', u'   Controls the level of the smoothing of the fine structure.', u'   ', u'   It must a real number between 0 and 1. The higher close to 0', u'   the higher the smoothing.', u'   ', u'', u'.. py:attribute:: EELSCLEdge.fine_structure_width', u'   :module: hyperspy._components.eels_cl_edge', u'', u'   ', u'   ', u'   ', u'   ', u'', u'.. py:method:: EELSCLEdge.function(E)', u'   :module: hyperspy._components.eels_cl_edge', u'', u'   ', u'   ', u'   Returns the number of counts in barns', u'   ', u'   ', u'', u'.. py:method:: EELSCLEdge.get_fine_structure_as_spectrum()', u'   :module: hyperspy._components.eels_cl_edge', u'', u'   ', u'   ', u'   Returns a spectrum containing the fine structure.', u'   ', u'   ', u'   .. rubric:: Notes', u'   ', u'   ', u'   The fine structure is corrected from multiple scattering if', u'   the model was convolved with a low-loss spectrum', u'   ', u'', u'.. py:method:: EELSCLEdge.grad_intensity(E)', u'   :module: hyperspy._components.eels_cl_edge', u'', u'   ', u'   ', u'   ', u'   ', u'', u'.. py:method:: EELSCLEdge.set_microscope_parameters(E0, alpha, beta, energy_scale)', u'   :module: hyperspy._components.eels_cl_edge', u'', u'   ', u'   ', u'   ', u'   ', u'   ', u'   :Parameters:', u'   ', u'       **E0** : float', u'   ', u'           Electron beam energy in keV.', u'   ', u'       **alpha: float** : ', u'   ', u'           Convergence angle in mrad.', u'   ', u'       **beta: float** : ', u'   ', u'           Collection angle in mrad.', u'   ', u'       **energy_scale** : float', u'   ', u'           The energy step in eV.', u'   ', u'', u'.. py:method:: EELSCLEdge.txt_to_fine_structure_coeff(filename)', u'   :module: hyperspy._components.eels_cl_edge']:16: ERROR: Unexpected indentation.
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/home/fjd29/Python/hyperspy/hyperspy/_components/eels_cl_edge.py:docstring of hyperspy._components.eels_cl_edge.EELSCLEdge:40: ERROR: Malformed table.
Column span alignment problem in table line 5.

====================  =========  ==========
        onset_energy  Parameter  
                                 The edge onset position
           intensity  Parameter  
                                 The factor by which the cross section is multiplied, what in
                                 favourable cases is proportional to the number of atoms of
                                 the element. It is a component.Parameter instance.
                                 It is fixed by default.
fine_structure_coeff  Parameter  
                                 The coefficients of the spline that fits the fine structure.
                                 Fix this parameter to fix the fine structure. It is a
                                 component.Parameter instance.
     effective_angle  Parameter  
                                 The effective collection angle. It is automatically
                                 calculated by set_microscope_parameters. It is a
                                 component.Parameter instance. It is fixed by default.
====================  =========  ==========
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/home/fjd29/Python/hyperspy/hyperspy/_components/volume_plasmon_drude.py:docstring of hyperspy._components.volume_plasmon_drude.VolumePlasmonDrude:11: ERROR: Malformed table.

+------------+-----------------+
| Parameter  |    Attribute    |
+------------+-----------------+
|    E_p     |  plasmon_energy |
+------------+-----------------+
| delta_E_p  |fwhm|
+------------+-----------------+
| intensity  |   intensity     |
+------------+-----------------+
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/home/fjd29/Python/hyperspy/hyperspy/_signals/dielectric_function.py:docstring of hyperspy._signals.dielectric_function.DielectricFunction.get_number_of_effective_electrons:1: WARNING: Definition list ends without a blank line; unexpected unindent.
[u'DielectricFunction.get_number_of_effective_electrons(nat, cumulative=False)', u':module: hyperspy._signals.dielectric_function', u'', u'Compute the number of effective electrons using the Bethe f-sum', u'        rule.', u'', u'        The Bethe f-sum rule gives rise to two definitions of the effective', u'        number (see [Egerton2011]_):', u'        $n_{\\mathrm{eff}}\\left(-\\Im\\left(\\epsilon^{-1}', u'ight)', u'ight)$ that', u"        we'll call neff1 and", u'        $n_{\\mathrm{eff}}\\left(\\epsilon_{2}', u"ight)$ that we'll call neff2. This", u'        method computes both.', u'', u':Parameters:', u'', u'    **nat: float** : ', u'', u'            Number of atoms (or molecules) per unit volume of the', u'            sample.', u'        cumulative : bool', u'            If False calculate the number of effective electrons up to the', u'            higher energy-loss of the spectrum. If True, calculate the', u'            number of effective electrons as a function of the energy-loss up', u'            to the higher energy-loss of the spectrum. *True is only supported', u'            by SciPy newer than 0.13.2*.', u'', u':Returns:', u'', u'    **neff1, neff2: Signal** : ', u'', u'        Signal instances containing neff1 and neff2. The signal and', u'        navigation dimensions are the same as the current signal if', u'        `cumulative` is True, otherwise the signal dimension is 0', u'        and the navigation dimension is the same as the current', u'        signal.', u'', u'.. rubric:: Notes', u'', u'.. [Egerton2011] Ray Egerton, "Electron Energy-Loss', u'Spectroscopy in the Electron Microscope", Springer-Verlag, 2011.']:11: ERROR: Unexpected indentation.
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[u'EDSSpectrum.get_take_off_angle()', u':module: hyperspy._signals.eds', u'', u'Calculate the take-off-angle (TOA).', u'', u'TOA is the angle with which the X-rays leave the surface towards', u"the detector. Parameters are read in 'SEM.tilt_stage',", u"'Acquisition_instrument.SEM.Detector.EDS.azimuth_angle' and 'SEM.Detector.EDS.elevation_angle'", u" in 'metadata'.", u'', u':Returns:', u'', u'    **take_off_angle: float (Degree)** : ', u'', u'.. seealso::', u'', u'    :obj:`utils.eds.take_off_angle`', u'', u'.. rubric:: Notes', u'', u'Defined by M. Schaffer et al., Ultramicroscopy 107(8), pp 587-597 (2007)']:8: ERROR: Unexpected indentation.
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/home/fjd29/Python/hyperspy/hyperspy/_signals/eels.py:docstring of hyperspy._signals.eels.EELSSpectrum.fourier_log_deconvolution:4: WARNING: Definition list ends without a blank line; unexpected unindent.
[u'EELSSpectrum.fourier_ratio_deconvolution(ll, fwhm=None, threshold=None, extrapolate_lowloss=True, extrapolate_coreloss=True)', u':module: hyperspy._signals.eels', u'', u'Performs Fourier-ratio deconvolution.', u'', u'The core-loss should have the background removed. To reduce', u' the noise amplication the result is convolved with a', u'Gaussian function.', u'', u':Parameters:', u'', u'    **ll: EELSSpectrum** : ', u'', u'        The corresponding low-loss (ll) EELSSpectrum.', u'', u'    **fwhm** : float or None', u'', u'        Full-width half-maximum of the Gaussian function by which', u'        the result of the deconvolution is convolved. It can be', u'        used to select the final SNR and spectral resolution. If', u'        None, the FWHM of the zero-loss peak of the low-loss is', u'        estimated and used.', u'', u'    **threshold** : {None, float}', u'', u'        Truncation energy to estimate the intensity of the', u'        elastic scattering. If None the threshold is taken as the', u'         first minimum after the ZLP centre.', u'', u'    **extrapolate_lowloss, extrapolate_coreloss** : bool', u'', u'        If True the signals are extrapolated using a power law,', u'', u'.. rubric:: Notes', u'', u'For details see: Egerton, R. Electron Energy-Loss', u'Spectroscopy in the Electron Microscope. Springer-Verlag, 2011.']:27: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy/hyperspy/_signals/eels.py:docstring of hyperspy._signals.eels.EELSSpectrum.kramers_kronig_analysis:24: WARNING: Definition list ends without a blank line; unexpected unindent.
[u'EELSSpectrum.kramers_kronig_analysis(zlp=None, iterations=1, n=None, t=None, delta=0.5, full_output=False)', u':module: hyperspy._signals.eels', u'', u'Calculate the complex', u'dielectric function from a single scattering distribution (SSD) using', u'the Kramers-Kronig relations.', u'', u'It uses the FFT method as in [Egerton2011]_.  The SSD is an', u'EELSSpectrum instance containing SSD low-loss EELS with no zero-loss', u'peak. The internal loop is devised to approximately subtract the', u'surface plasmon contribution supposing an unoxidized planar surface and', u'neglecting coupling between the surfaces. This method does not account', u'for retardation effects, instrumental broading and surface plasmon', u'excitation in particles.', u'', u'Note that either refractive index or thickness are required.', u'If both are None or if both are provided an exception is raised.', u'', u':Parameters:', u'', u'    **zlp: {None, number, Signal}** : ', u'', u'        ZLP intensity. It is optional (can be None) if `t` is None and `n`', u'        is not None and the thickness estimation is not required. If `t`', u'        is not None, the ZLP is required to perform the normalization and', u'        if `t` is not None, the ZLP is required to calculate the thickness.', u'        If the ZLP is the same for all spectra, the integral of the ZLP', u'        can be provided as a number. Otherwise, if the ZLP intensity is not', u'        the same for all spectra, it can be provided as i) a Signal', u'        of the same dimensions as the current signal containing the ZLP', u'        spectra for each location ii) a Signal of signal dimension 0', u'        and navigation_dimension equal to the current signal containing the', u'        integrated ZLP intensity.', u'', u'    **iterations: int** : ', u'', u'        Number of the iterations for the internal loop to remove the', u'        surface plasmon contribution. If 1 the surface plasmon contribution', u'        is not estimated and subtracted (the default is 1).', u'', u'    **n: {None, float}** : ', u'', u'        The medium refractive index. Used for normalization of the', u'        SSD to obtain the energy loss function. If given the thickness', u'        is estimated and returned. It is only required when `t` is None.', u'', u'    **t: {None, number, Signal}** : ', u'', u'        The sample thickness in nm. Used for normalization of the', u'        SSD to obtain the energy loss function. It is only required when', u'        `n` is None. If the thickness is the same for all spectra it can be', u'        given by a number. Otherwise, it can be provided as a Signal with', u'        signal dimension 0 and navigation_dimension equal to the current', u'        signal.', u'', u'    **delta** : float', u'', u'        A small number (0.1-0.5 eV) added to the energy axis in', u'        specific steps of the calculation the surface loss correction to', u'        improve stability.', u'', u'    **full_output** : bool', u'', u'        If True, return a dictionary that contains the estimated', u'        thickness if `t` is None and the estimated surface plasmon', u'        excitation and the spectrum corrected from surface plasmon', u'        excitations if `iterations` > 1.', u'', u':Returns:', u'', u'    **eps: DielectricFunction instance** : ', u'', u'        The complex dielectric function results,', u'            $\\epsilon = \\epsilon_1 + i*\\epsilon_2$,', u'        contained in an DielectricFunction instance.', u'', u'    **output: Dictionary (optional)** : ', u'', u'        A dictionary of optional outputs with the following keys:', u'', u'        ``thickness``', u'            The estimated  thickness in nm calculated by normalization of', u'            the SSD (only when `t` is None)', u'', u'        ``surface plasmon estimation``', u'           The estimated surface plasmon excitation (only if', u'           `iterations` > 1.)', u'', u':Raises:', u'', u'    **ValuerError** : ', u'', u'        If both `n` and `t` are undefined (None).', u'', u'    **AttribureError** : ', u'', u'        If the beam_energy or the collection angle are not defined in', u'        metadata.', u'', u'.. rubric:: Notes', u'', u"This method is based in Egerton's Matlab code [Egerton2011]_ with some", u'minor differences:', u'', u'* The integrals are performed using the simpsom rule instead of using', u'  a summation.', u'* The wrap-around problem when computing the ffts is workarounded by', u'  padding the signal instead of substracting the reflected tail.', u'', u'.. [Egerton2011] Ray Egerton, "Electron Energy-Loss', u'   Spectroscopy in the Electron Microscope", Springer-Verlag, 2011.']:109: WARNING: Duplicate explicit target name: "egerton2011".
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[u'EELSSpectrum.kramers_kronig_analysis(zlp=None, iterations=1, n=None, t=None, delta=0.5, full_output=False)', u':module: hyperspy._signals.eels', u'', u'Calculate the complex', u'dielectric function from a single scattering distribution (SSD) using', u'the Kramers-Kronig relations.', u'', u'It uses the FFT method as in [Egerton2011]_.  The SSD is an', u'EELSSpectrum instance containing SSD low-loss EELS with no zero-loss', u'peak. The internal loop is devised to approximately subtract the', u'surface plasmon contribution supposing an unoxidized planar surface and', u'neglecting coupling between the surfaces. This method does not account', u'for retardation effects, instrumental broading and surface plasmon', u'excitation in particles.', u'', u'Note that either refractive index or thickness are required.', u'If both are None or if both are provided an exception is raised.', u'', u':Parameters:', u'', u'    **zlp: {None, number, Signal}** : ', u'', u'        ZLP intensity. It is optional (can be None) if `t` is None and `n`', u'        is not None and the thickness estimation is not required. If `t`', u'        is not None, the ZLP is required to perform the normalization and', u'        if `t` is not None, the ZLP is required to calculate the thickness.', u'        If the ZLP is the same for all spectra, the integral of the ZLP', u'        can be provided as a number. Otherwise, if the ZLP intensity is not', u'        the same for all spectra, it can be provided as i) a Signal', u'        of the same dimensions as the current signal containing the ZLP', u'        spectra for each location ii) a Signal of signal dimension 0', u'        and navigation_dimension equal to the current signal containing the', u'        integrated ZLP intensity.', u'', u'    **iterations: int** : ', u'', u'        Number of the iterations for the internal loop to remove the', u'        surface plasmon contribution. If 1 the surface plasmon contribution', u'        is not estimated and subtracted (the default is 1).', u'', u'    **n: {None, float}** : ', u'', u'        The medium refractive index. Used for normalization of the', u'        SSD to obtain the energy loss function. If given the thickness', u'        is estimated and returned. It is only required when `t` is None.', u'', u'    **t: {None, number, Signal}** : ', u'', u'        The sample thickness in nm. Used for normalization of the', u'        SSD to obtain the energy loss function. It is only required when', u'        `n` is None. If the thickness is the same for all spectra it can be', u'        given by a number. Otherwise, it can be provided as a Signal with', u'        signal dimension 0 and navigation_dimension equal to the current', u'        signal.', u'', u'    **delta** : float', u'', u'        A small number (0.1-0.5 eV) added to the energy axis in', u'        specific steps of the calculation the surface loss correction to', u'        improve stability.', u'', u'    **full_output** : bool', u'', u'        If True, return a dictionary that contains the estimated', u'        thickness if `t` is None and the estimated surface plasmon', u'        excitation and the spectrum corrected from surface plasmon', u'        excitations if `iterations` > 1.', u'', u':Returns:', u'', u'    **eps: DielectricFunction instance** : ', u'', u'        The complex dielectric function results,', u'            $\\epsilon = \\epsilon_1 + i*\\epsilon_2$,', u'        contained in an DielectricFunction instance.', u'', u'    **output: Dictionary (optional)** : ', u'', u'        A dictionary of optional outputs with the following keys:', u'', u'        ``thickness``', u'            The estimated  thickness in nm calculated by normalization of', u'            the SSD (only when `t` is None)', u'', u'        ``surface plasmon estimation``', u'           The estimated surface plasmon excitation (only if', u'           `iterations` > 1.)', u'', u':Raises:', u'', u'    **ValuerError** : ', u'', u'        If both `n` and `t` are undefined (None).', u'', u'    **AttribureError** : ', u'', u'        If the beam_energy or the collection angle are not defined in', u'        metadata.', u'', u'.. rubric:: Notes', u'', u"This method is based in Egerton's Matlab code [Egerton2011]_ with some", u'minor differences:', u'', u'* The integrals are performed using the simpsom rule instead of using', u'  a summation.', u'* The wrap-around problem when computing the ffts is workarounded by', u'  padding the signal instead of substracting the reflected tail.', u'', u'.. [Egerton2011] Ray Egerton, "Electron Energy-Loss', u'   Spectroscopy in the Electron Microscope", Springer-Verlag, 2011.']:109: WARNING: duplicate citation Egerton2011, other instance in /home/fjd29/Python/hyperspy/doc/api/hyperspy._signals.rst
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/home/fjd29/Python/hyperspy/hyperspy/io_plugins/digital_micrograph.py:docstring of hyperspy.io_plugins.digital_micrograph.DigitalMicrographReader.parse_struct_definition:3: WARNING: Definition list ends without a blank line; unexpected unindent.
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<autodoc>:0: WARNING: Definition list ends without a blank line; unexpected unindent.
[u'LearningResults.load(filename)', u':module: hyperspy.learn.mva', u'', u'Load the results of a previous decomposition and', u' demixing analysis from a file.', u'Parameters', u'----------', u'filename : string']:6: SEVERE: Unexpected section title.

Parameters
----------
[u'LearningResults.save(filename, overwrite=None)', u':module: hyperspy.learn.mva', u'', u'Save the result of the decomposition and demixing analysis', u'Parameters', u'----------', u'filename : string', u'overwrite : {True, False, None}', u"    If True(False) overwrite(don't overwrite) the file if it exists.", u'    If None (default) ask what to do if file exists.']:8: ERROR: Unexpected indentation.
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/home/fjd29/Python/hyperspy/hyperspy/misc/spectrum_tools.py:docstring of hyperspy.misc.spectrum_tools.find_peaks_ohaver:18: WARNING: Title underline too short.

Parameters
---------
[u'find_peaks_ohaver(y, x=None, slope_thresh=0.0, amp_thresh=None, medfilt_radius=5, maxpeakn=30000, peakgroup=10, subchannel=True)', u':module: hyperspy.misc.spectrum_tools', u'', u'', u'', u'Find peaks along a 1D line.', u'', u'Function to locate the positive peaks in a noisy x-y data set.', u'', u'Detects peaks by looking for downward zero-crossings in the first', u"derivative that exceed 'slope_thresh'.", u'', u'Returns an array containing position, height, and width of each peak.', u'', u"'slope_thresh' and 'amp_thresh', control sensitivity: higher values will", u'neglect smaller features.', u'', u'Parameters', u'---------', u'y : array', u'    1D input array, e.g. a spectrum', u'', u'x : array (optional)', u'    1D array describing the calibration of y (must have same shape as y)', u'', u'slope_thresh : float (optional)', u'               1st derivative threshold to count the peak', u'               default is set to 0.5', u'               higher values will neglect smaller features.', u'', u'amp_thresh : float (optional)', u'             intensity threshold above which', u'             default is set to 10% of max(y)', u'             higher values will neglect smaller features.', u'', u'medfilt_radius : int (optional)', u'                 median filter window to apply to smooth the data', u'                 (see scipy.signal.medfilt)', u'                 if 0, no filter will be applied.', u'                 default is set to 5', u'', u'peakgroup : int (optional)', u'            number of points around the "top part" of the peak', u'            default is set to 10', u'', u'maxpeakn : int (optional)', u'          number of maximum detectable peaks', u'          default is set to 30000', u'', u'subchannel : bool (optional)', u'         default is set to True', u'', u':Returns:', u'', u'    **P** : structured array of shape (npeaks) and fields: position, width, height', u'', u'        contains position, height, and width of each peak', u'', u'.. rubric:: Notes', u'', u'', u"Original code from T. C. O'Haver, 1995.", u'Version 2  Last revised Oct 27, 2006 Converted to Python by', u'Michael Sarahan, Feb 2011.', u'Revised to handle edges better.  MCS, Mar 2011', u'', u'.. rubric:: Examples', u'', u'', u'>>> x = arange(0,50,0.01)', u'>>> y = cos(x)', u'>>> one_dim_findpeaks(y, x,0,0)', u'array([[  1.68144859e-05,   9.99999943e-01,   3.57487961e+00],', u'       [  6.28318614e+00,   1.00000003e+00,   3.57589018e+00],', u'       [  1.25663708e+01,   1.00000002e+00,   3.57600673e+00],', u'       [  1.88495565e+01,   1.00000002e+00,   3.57597295e+00],', u'       [  2.51327421e+01,   1.00000003e+00,   3.57590284e+00],', u'       [  3.14159267e+01,   1.00000002e+00,   3.57600856e+00],', u'       [  3.76991124e+01,   1.00000002e+00,   3.57597984e+00],', u'       [  4.39822980e+01,   1.00000002e+00,   3.57591479e+00]])']:16: SEVERE: Unexpected section title.

Parameters
---------
/home/fjd29/Python/hyperspy/doc/api/hyperspy.misc.rst:59: WARNING: toctree references unknown document u'api/hyperspy.misc.utils.DictionaryTreeBrowser.export'
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/home/fjd29/Python/hyperspy/doc/api/hyperspy.misc.rst:59: WARNING: toctree references unknown document u'api/hyperspy.misc.utils.DictionaryTreeBrowser.add_node'
[u'swapelem(obj, i, j)', u':module: hyperspy.misc.utils', u'', u'', u'', u'Swaps element having index i with', u'element having index j in object obj IN PLACE.', u'', u'E.g.', u">>> L = ['a', 'b', 'c']", u'>>> spwapelem(L, 1, 2)', u'>>> print L', u"    ['a', 'c', 'b']"]:10: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy/doc/api/hyperspy.misc.borrowed.astroML.rst:39: WARNING: toctree references unknown document u'api/hyperspy.misc.borrowed.astroML.bayesian_blocks.Events.fitness'
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/home/fjd29/Python/hyperspy/doc/api/hyperspy.misc.borrowed.astroML.rst:39: WARNING: toctree references unknown document u'api/hyperspy.misc.borrowed.astroML.bayesian_blocks.Events.prior'
/home/fjd29/Python/hyperspy/doc/api/hyperspy.misc.borrowed.astroML.rst:39: WARNING: toctree references unknown document u'api/hyperspy.misc.borrowed.astroML.bayesian_blocks.Events.validate_input'
[u'FitnessFunc(p0=0.05, gamma=None)', u':module: hyperspy.misc.borrowed.astroML.bayesian_blocks', u'', u'Bases: :class:`object`', u'', u'', u'', u'Base class for fitness functions', u'', u'Each fitness function class has the following:', u'- fitness(...) : compute fitness function.', u'   Arguments accepted by fitness must be among [T_k, N_k, a_k, b_k, c_k]', u'- prior(N, Ntot) : compute prior on N given a total number of points Ntot', u'', u'.. rubric:: Methods', u'', u'.. autosummary::', u'   :toctree:', u'', u'   fitness', u'   gamma_prior', u'   p0_prior', u'   prior', u'   validate_input', u'', u'', u'.. py:attribute:: FitnessFunc.args', u'   :module: hyperspy.misc.borrowed.astroML.bayesian_blocks', u'', u'   ', u'   ', u'   ', u'   ', u'', u'.. py:method:: FitnessFunc.fitness(**kwargs)', u'   :module: hyperspy.misc.borrowed.astroML.bayesian_blocks', u'', u'   ', u'   ', u'   ', u'   ', u'', u'.. py:method:: FitnessFunc.gamma_prior(N, Ntot)', u'   :module: hyperspy.misc.borrowed.astroML.bayesian_blocks', u'', u'   ', u'   ', u'   Basic prior, parametrized by gamma (eq. 3 in Scargle 2012)', u'   ', u'   ', u'', u'.. py:method:: FitnessFunc.p0_prior(N, Ntot)', u'   :module: hyperspy.misc.borrowed.astroML.bayesian_blocks', u'', u'   ', u'   ', u'   ', u'   ', u'', u'.. py:method:: FitnessFunc.prior(N, Ntot)', u'   :module: hyperspy.misc.borrowed.astroML.bayesian_blocks', u'', u'   ', u'   ', u'   ', u'   ', u'', u'.. py:method:: FitnessFunc.validate_input(t, x, sigma)', u'   :module: hyperspy.misc.borrowed.astroML.bayesian_blocks', u'', u'   ', u'   ', u'   Check that input is valid']:9: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy/hyperspy/misc/borrowed/astroML/bayesian_blocks.py:docstring of hyperspy.misc.borrowed.astroML.bayesian_blocks.FitnessFunc:8: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy/doc/api/hyperspy.misc.borrowed.astroML.rst:82: WARNING: toctree references unknown document u'api/hyperspy.misc.borrowed.astroML.bayesian_blocks.FitnessFunc.fitness'
/home/fjd29/Python/hyperspy/doc/api/hyperspy.misc.borrowed.astroML.rst:82: WARNING: toctree references unknown document u'api/hyperspy.misc.borrowed.astroML.bayesian_blocks.FitnessFunc.gamma_prior'
/home/fjd29/Python/hyperspy/doc/api/hyperspy.misc.borrowed.astroML.rst:82: WARNING: toctree references unknown document u'api/hyperspy.misc.borrowed.astroML.bayesian_blocks.FitnessFunc.p0_prior'
/home/fjd29/Python/hyperspy/doc/api/hyperspy.misc.borrowed.astroML.rst:82: WARNING: toctree references unknown document u'api/hyperspy.misc.borrowed.astroML.bayesian_blocks.FitnessFunc.prior'
/home/fjd29/Python/hyperspy/doc/api/hyperspy.misc.borrowed.astroML.rst:82: WARNING: toctree references unknown document u'api/hyperspy.misc.borrowed.astroML.bayesian_blocks.FitnessFunc.validate_input'
/home/fjd29/Python/hyperspy/doc/api/hyperspy.misc.borrowed.astroML.rst:161: WARNING: toctree references unknown document u'api/hyperspy.misc.borrowed.astroML.bayesian_blocks.PointMeasures.fitness'
/home/fjd29/Python/hyperspy/doc/api/hyperspy.misc.borrowed.astroML.rst:161: WARNING: toctree references unknown document u'api/hyperspy.misc.borrowed.astroML.bayesian_blocks.PointMeasures.gamma_prior'
/home/fjd29/Python/hyperspy/doc/api/hyperspy.misc.borrowed.astroML.rst:161: WARNING: toctree references unknown document u'api/hyperspy.misc.borrowed.astroML.bayesian_blocks.PointMeasures.p0_prior'
/home/fjd29/Python/hyperspy/doc/api/hyperspy.misc.borrowed.astroML.rst:161: WARNING: toctree references unknown document u'api/hyperspy.misc.borrowed.astroML.bayesian_blocks.PointMeasures.prior'
/home/fjd29/Python/hyperspy/doc/api/hyperspy.misc.borrowed.astroML.rst:161: WARNING: toctree references unknown document u'api/hyperspy.misc.borrowed.astroML.bayesian_blocks.PointMeasures.validate_input'
/home/fjd29/Python/hyperspy/doc/api/hyperspy.misc.borrowed.astroML.rst:213: WARNING: toctree references unknown document u'api/hyperspy.misc.borrowed.astroML.bayesian_blocks.RegularEvents.fitness'
/home/fjd29/Python/hyperspy/doc/api/hyperspy.misc.borrowed.astroML.rst:213: WARNING: toctree references unknown document u'api/hyperspy.misc.borrowed.astroML.bayesian_blocks.RegularEvents.gamma_prior'
/home/fjd29/Python/hyperspy/doc/api/hyperspy.misc.borrowed.astroML.rst:213: WARNING: toctree references unknown document u'api/hyperspy.misc.borrowed.astroML.bayesian_blocks.RegularEvents.p0_prior'
/home/fjd29/Python/hyperspy/doc/api/hyperspy.misc.borrowed.astroML.rst:213: WARNING: toctree references unknown document u'api/hyperspy.misc.borrowed.astroML.bayesian_blocks.RegularEvents.prior'
/home/fjd29/Python/hyperspy/doc/api/hyperspy.misc.borrowed.astroML.rst:213: WARNING: toctree references unknown document u'api/hyperspy.misc.borrowed.astroML.bayesian_blocks.RegularEvents.validate_input'
/home/fjd29/Python/hyperspy/doc/api/hyperspy.misc.borrowed.astroML.rst:41: WARNING: toctree references unknown document u'api/hyperspy.misc.borrowed.astroML.histtools.KnuthF.bins'
/home/fjd29/Python/hyperspy/doc/api/hyperspy.misc.borrowed.astroML.rst:41: WARNING: toctree references unknown document u'api/hyperspy.misc.borrowed.astroML.histtools.KnuthF.eval'
/home/fjd29/Python/hyperspy/doc/api/hyperspy.misc.eels.rst:15: WARNING: toctree references unknown document u'api/hyperspy.misc.eels.base_gos.GOSBase.get_parametrized_energy_axis'
/home/fjd29/Python/hyperspy/doc/api/hyperspy.misc.eels.rst:15: WARNING: toctree references unknown document u'api/hyperspy.misc.eels.base_gos.GOSBase.get_parametrized_qaxis'
/home/fjd29/Python/hyperspy/doc/api/hyperspy.misc.eels.rst:15: WARNING: toctree references unknown document u'api/hyperspy.misc.eels.base_gos.GOSBase.get_qaxis_and_gos'
/home/fjd29/Python/hyperspy/doc/api/hyperspy.misc.eels.rst:15: WARNING: toctree references unknown document u'api/hyperspy.misc.eels.base_gos.GOSBase.read_elements'
/home/fjd29/Python/hyperspy/hyperspy/misc/eels/hartree_slater_gos.py:docstring of hyperspy.misc.eels.hartree_slater_gos.HartreeSlaterGOS:28: ERROR: Malformed table.
Column span alignment problem in table line 3.

======================================    ==========
                         readgosfile()    
                                          Read the GOS files of the element subshell from the location
                                          defined in Preferences.
get_qaxis_and_gos(ienergy, qmin, qmax)    
                                          given the energy axis index and qmin and qmax values returns
                                          the qaxis and gos between qmin and qmax using linear
                                          interpolation to include qmin and qmax in the range.
======================================    ==========
/home/fjd29/Python/hyperspy/hyperspy/misc/eels/hydrogenic_gos.py:docstring of hyperspy.misc.eels.hydrogenic_gos.HydrogenicGOS:35: ERROR: Malformed table.
Column span alignment problem in table line 5.

======================================    ==========
                     parametrize_GOS()    
                                          Parametrize the GOS to speed up the calculation.
get_qaxis_and_gos(ienergy, qmin, qmax)    
                                          Given the energy axis index and qmin and qmax values returns
                                          the qaxis and gos between qmin and qmax using linear
                                          interpolation to include qmin and qmax in the range.
======================================    ==========
/home/fjd29/Python/hyperspy/hyperspy/misc/eels/tools.py:docstring of hyperspy.misc.eels.tools.eels_constant:11: WARNING: Definition list ends without a blank line; unexpected unindent.
[u'eels_constant(s, zlp, t)', u':module: hyperspy.misc.eels.tools', u'', u'', u'', u'Calculate the constant of proportionality (k) in the relationship', u'    between the EELS signal and the dielectric function.', u'    dielectric function from a single scattering distribution (SSD) using', u'    the Kramers-Kronig relations.', u'', u'    $S(E)=', u'rac{I_{0}t}{\\pi a_{0}m_{0}v^{2}}\\ln\\left[1+\\left(', u'rac{\x08eta}', u'    {   heta_{E}}', u'ight)^{2}', u'ight]\\Im(', u'rac{-1}{\\epsilon(E)})=', u'    k\\Im(', u'rac{-1}{\\epsilon(E)})$', u'', u':Parameters:', u'', u'    **zlp: {number, Signal}** : ', u'', u'            If the ZLP is the same for all spectra, the intengral of the ZLP', u'            can be provided as a number. Otherwise, if the ZLP intensity is not', u'            the same for all spectra, it can be provided as i) a Signal', u'            of the same dimensions as the current signal containing the ZLP', u'            spectra for each location ii) a Signal of signal dimension 0', u'            and navigation_dimension equal to the current signal containing the', u'            integrated ZLP intensity.', u'        t: {None, number, Signal}', u'            The sample thickness in nm. If the thickness is the same for all', u'            spectra it can be given by a number. Otherwise, it can be provided', u'            as a Signal with signal dimension 0 and navigation_dimension equal', u'            to the current signal.', u'', u':Returns:', u'', u'    **k: Signal instance** : ']:11: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy/hyperspy/misc/eels/tools.py:docstring of hyperspy.misc.eels.tools.eels_constant:14: WARNING: Block quote ends without a blank line; unexpected unindent.
[u'eels_constant(s, zlp, t)', u':module: hyperspy.misc.eels.tools', u'', u'', u'', u'Calculate the constant of proportionality (k) in the relationship', u'    between the EELS signal and the dielectric function.', u'    dielectric function from a single scattering distribution (SSD) using', u'    the Kramers-Kronig relations.', u'', u'    $S(E)=', u'rac{I_{0}t}{\\pi a_{0}m_{0}v^{2}}\\ln\\left[1+\\left(', u'rac{\x08eta}', u'    {   heta_{E}}', u'ight)^{2}', u'ight]\\Im(', u'rac{-1}{\\epsilon(E)})=', u'    k\\Im(', u'rac{-1}{\\epsilon(E)})$', u'', u':Parameters:', u'', u'    **zlp: {number, Signal}** : ', u'', u'            If the ZLP is the same for all spectra, the intengral of the ZLP', u'            can be provided as a number. Otherwise, if the ZLP intensity is not', u'            the same for all spectra, it can be provided as i) a Signal', u'            of the same dimensions as the current signal containing the ZLP', u'            spectra for each location ii) a Signal of signal dimension 0', u'            and navigation_dimension equal to the current signal containing the', u'            integrated ZLP intensity.', u'        t: {None, number, Signal}', u'            The sample thickness in nm. If the thickness is the same for all', u'            spectra it can be given by a number. Otherwise, it can be provided', u'            as a Signal with signal dimension 0 and navigation_dimension equal', u'            to the current signal.', u'', u':Returns:', u'', u'    **k: Signal instance** : ']:15: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy/hyperspy/misc/eels/tools.py:docstring of hyperspy.misc.eels.tools.eels_constant:18: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy/hyperspy/misc/eels/tools.py:docstring of hyperspy.misc.eels.tools.eels_constant:31: WARNING: Block quote ends without a blank line; unexpected unindent.
[u"imsave(filename, data, photometric=None, planarconfig=None, resolution=None, description=None, software='tifffile.py', byteorder=None, bigtiff=False, compress=0, extratags=())", u':module: hyperspy.misc.io.tifffile', u'', u'', u'', u'Write image data to TIFF file.', u'', u'Image data are written in one stripe per plane.', u'Dimensions larger than 2 or 3 (depending on photometric mode and', u'planar configuration) are flattened and saved as separate pages.', u"The 'sample_format' and 'bits_per_sample' TIFF tags are derived from", u'the data type.', u'', u':Parameters:', u'', u'    **filename** : str', u'', u'        Name of file to write.', u'', u'    **data** : array_like', u'', u'        Input image. The last dimensions are assumed to be image height,', u'        width, and samples.', u'', u"    **photometric** : {'minisblack', 'miniswhite', 'rgb'}", u'', u'        The color space of the image data.', u'        By default this setting is inferred from the data shape.', u'', u"    **planarconfig** : {'contig', 'planar'}", u'', u'        Specifies if samples are stored contiguous or in separate planes.', u'        By default this setting is inferred from the data shape.', u"        'contig': last dimension contains samples.", u"        'planar': third last dimension contains samples.", u'', u'    **resolution** : (float, float) or ((int, int), (int, int))', u'', u'        X and Y resolution in dots per inch as float or rational numbers.', u'', u'    **description** : str', u'', u'        The subject of the image. Saved with the first page only.', u'', u'    **software** : str', u'', u'        Name of the software used to create the image.', u'        Saved with the first page only.', u'', u"    **byteorder** : {'<', '>'}", u'', u'        The endianness of the data in the file.', u"        By default this is the system's native byte order.", u'', u'    **bigtiff** : bool', u'', u'        If True, the BigTIFF format is used.', u'        By default the standard TIFF format is used for data less than 2000 MB.', u'', u'    **compress** : int', u'', u'        Values from 0 to 9 controlling the level of zlib compression.', u'        If 0, data are written uncompressed (default).', u'', u'    **extratags: sequence of tuples** : ', u'', u'        Additional tags as [(code, dtype, count, value, writeonce)].', u'        code : int', u'            The TIFF tag Id.', u'        dtype : str', u'            Data type of items in `value` in Python struct format.', u'            One of B, s, H, I, 2I, b, h, i, f, d, Q, or q.', u'        count : int', u'            Number of data values. Not used for string values.', u'        value : sequence', u'            `Count` values compatible with `dtype`.', u'        writeonce : bool', u'            If True, the tag is written to the first page only.', u'', u'.. rubric:: Examples', u'', u'', u">>> data = numpy.ones((2, 5, 3, 301, 219), 'float32') * 0.5", u">>> imsave('temp.tif', data, compress=6)", u'', u">>> data = numpy.ones((5, 301, 219, 3), 'uint8') + 127", u'>>> value = u\'{"shape": %s}\' % str(list(data.shape))', u">>> imsave('temp.tif', data, extratags=[(270, 's', 0, value, True)])"]:66: ERROR: Unexpected indentation.
docstring of hyperspy.misc.io.tifffile.imsave:69: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy/doc/api/hyperspy.misc.io.rst:503: WARNING: toctree references unknown document u'api/hyperspy.misc.io.tifffile.TiffSequence.asarray'
/home/fjd29/Python/hyperspy/doc/api/hyperspy.misc.io.rst:503: WARNING: toctree references unknown document u'api/hyperspy.misc.io.tifffile.TiffSequence.close'
/home/fjd29/Python/hyperspy/hyperspy/misc/mpfit/mpfit.py:docstring of hyperspy.misc.mpfit.mpfit:4: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy/hyperspy/misc/mpfit/mpfit.py:docstring of hyperspy.misc.mpfit.mpfit:9: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy/hyperspy/misc/mpfit/mpfit.py:docstring of hyperspy.misc.mpfit.mpfit:12: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy/hyperspy/misc/mpfit/mpfit.py:docstring of hyperspy.misc.mpfit.mpfit:132: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy/hyperspy/misc/mpfit/mpfit.py:docstring of hyperspy.misc.mpfit.mpfit:142: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy/hyperspy/misc/mpfit/mpfit.py:docstring of hyperspy.misc.mpfit.mpfit:144: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy/hyperspy/misc/mpfit/mpfit.py:docstring of hyperspy.misc.mpfit.mpfit:145: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy/hyperspy/misc/mpfit/mpfit.py:docstring of hyperspy.misc.mpfit.mpfit:147: WARNING: Definition list ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy/hyperspy/misc/mpfit/mpfit.py:docstring of hyperspy.misc.mpfit.mpfit:222: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy/hyperspy/misc/mpfit/mpfit.py:docstring of hyperspy.misc.mpfit.mpfit:264: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy/hyperspy/misc/mpfit/mpfit.py:docstring of hyperspy.misc.mpfit.mpfit:265: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy/hyperspy/misc/mpfit/mpfit.py:docstring of hyperspy.misc.mpfit.mpfit:284: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy/hyperspy/misc/mpfit/mpfit.py:docstring of hyperspy.misc.mpfit.mpfit:285: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy/hyperspy/misc/mpfit/mpfit.py:docstring of hyperspy.misc.mpfit.mpfit:305: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy/hyperspy/misc/mpfit/mpfit.py:docstring of hyperspy.misc.mpfit.mpfit:390: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy/hyperspy/misc/mpfit/mpfit.py:docstring of hyperspy.misc.mpfit.mpfit:391: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy/hyperspy/misc/mpfit/mpfit.py:docstring of hyperspy.misc.mpfit.mpfit:399: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy/doc/api/hyperspy.misc.mpfit.rst:435: WARNING: toctree references unknown document u'api/hyperspy.misc.mpfit.mpfit.mpfit.blas_enorm32'
/home/fjd29/Python/hyperspy/doc/api/hyperspy.misc.mpfit.rst:435: WARNING: toctree references unknown document u'api/hyperspy.misc.mpfit.mpfit.mpfit.blas_enorm64'
/home/fjd29/Python/hyperspy/doc/api/hyperspy.misc.mpfit.rst:435: WARNING: toctree references unknown document u'api/hyperspy.misc.mpfit.mpfit.mpfit.calc_covar'
/home/fjd29/Python/hyperspy/doc/api/hyperspy.misc.mpfit.rst:435: WARNING: toctree references unknown document u'api/hyperspy.misc.mpfit.mpfit.mpfit.call'
/home/fjd29/Python/hyperspy/doc/api/hyperspy.misc.mpfit.rst:435: WARNING: toctree references unknown document u'api/hyperspy.misc.mpfit.mpfit.mpfit.defiter'
/home/fjd29/Python/hyperspy/doc/api/hyperspy.misc.mpfit.rst:435: WARNING: toctree references unknown document u'api/hyperspy.misc.mpfit.mpfit.mpfit.enorm'
/home/fjd29/Python/hyperspy/doc/api/hyperspy.misc.mpfit.rst:435: WARNING: toctree references unknown document u'api/hyperspy.misc.mpfit.mpfit.mpfit.fdjac2'
/home/fjd29/Python/hyperspy/doc/api/hyperspy.misc.mpfit.rst:435: WARNING: toctree references unknown document u'api/hyperspy.misc.mpfit.mpfit.mpfit.lmpar'
/home/fjd29/Python/hyperspy/doc/api/hyperspy.misc.mpfit.rst:435: WARNING: toctree references unknown document u'api/hyperspy.misc.mpfit.mpfit.mpfit.parinfo'
/home/fjd29/Python/hyperspy/doc/api/hyperspy.misc.mpfit.rst:435: WARNING: toctree references unknown document u'api/hyperspy.misc.mpfit.mpfit.mpfit.qrfac'
/home/fjd29/Python/hyperspy/doc/api/hyperspy.misc.mpfit.rst:435: WARNING: toctree references unknown document u'api/hyperspy.misc.mpfit.mpfit.mpfit.qrsolv'
/home/fjd29/Python/hyperspy/doc/api/hyperspy.misc.mpfit.rst:435: WARNING: toctree references unknown document u'api/hyperspy.misc.mpfit.mpfit.mpfit.tie'
<autodoc>:0: ERROR: Error in "py:module" directive:
no content permitted.

.. py:module:: hyperspy.misc.mpfit.mpfitexpr

    Copyright (C) 2009 Sergey Koposov
/home/fjd29/Python/hyperspy/doc/api/hyperspy.models.rst:48: WARNING: toctree references unknown document u'api/hyperspy.models.eelsmodel.EELSModel.add_signal_range'
/home/fjd29/Python/hyperspy/doc/api/hyperspy.models.rst:48: WARNING: toctree references unknown document u'api/hyperspy.models.eelsmodel.EELSModel.append'
/home/fjd29/Python/hyperspy/doc/api/hyperspy.models.rst:48: WARNING: toctree references unknown document u'api/hyperspy.models.eelsmodel.EELSModel.as_signal'
/home/fjd29/Python/hyperspy/doc/api/hyperspy.models.rst:48: WARNING: toctree references unknown document u'api/hyperspy.models.eelsmodel.EELSModel.assign_current_values_to_all'
/home/fjd29/Python/hyperspy/doc/api/hyperspy.models.rst:48: WARNING: toctree references unknown document u'api/hyperspy.models.eelsmodel.EELSModel.count'
/home/fjd29/Python/hyperspy/doc/api/hyperspy.models.rst:48: WARNING: toctree references unknown document u'api/hyperspy.models.eelsmodel.EELSModel.disable_adjust_position'
/home/fjd29/Python/hyperspy/doc/api/hyperspy.models.rst:48: WARNING: toctree references unknown document u'api/hyperspy.models.eelsmodel.EELSModel.disable_background'
/home/fjd29/Python/hyperspy/doc/api/hyperspy.models.rst:48: WARNING: toctree references unknown document u'api/hyperspy.models.eelsmodel.EELSModel.disable_edges'
/home/fjd29/Python/hyperspy/doc/api/hyperspy.models.rst:48: WARNING: toctree references unknown document u'api/hyperspy.models.eelsmodel.EELSModel.disable_fine_structure'
/home/fjd29/Python/hyperspy/doc/api/hyperspy.models.rst:48: WARNING: toctree references unknown document u'api/hyperspy.models.eelsmodel.EELSModel.disable_free_onset_energy'
/home/fjd29/Python/hyperspy/doc/api/hyperspy.models.rst:48: WARNING: toctree references unknown document u'api/hyperspy.models.eelsmodel.EELSModel.disable_plot_components'
/home/fjd29/Python/hyperspy/doc/api/hyperspy.models.rst:48: WARNING: toctree references unknown document u'api/hyperspy.models.eelsmodel.EELSModel.enable_adjust_position'
/home/fjd29/Python/hyperspy/doc/api/hyperspy.models.rst:48: WARNING: toctree references unknown document u'api/hyperspy.models.eelsmodel.EELSModel.enable_background'
/home/fjd29/Python/hyperspy/doc/api/hyperspy.models.rst:48: WARNING: toctree references unknown document u'api/hyperspy.models.eelsmodel.EELSModel.enable_edges'
/home/fjd29/Python/hyperspy/doc/api/hyperspy.models.rst:48: WARNING: toctree references unknown document u'api/hyperspy.models.eelsmodel.EELSModel.enable_fine_structure'
/home/fjd29/Python/hyperspy/doc/api/hyperspy.models.rst:48: WARNING: toctree references unknown document u'api/hyperspy.models.eelsmodel.EELSModel.enable_free_onset_energy'
/home/fjd29/Python/hyperspy/doc/api/hyperspy.models.rst:48: WARNING: toctree references unknown document u'api/hyperspy.models.eelsmodel.EELSModel.enable_plot_components'
/home/fjd29/Python/hyperspy/doc/api/hyperspy.models.rst:48: WARNING: toctree references unknown document u'api/hyperspy.models.eelsmodel.EELSModel.export_results'
/home/fjd29/Python/hyperspy/doc/api/hyperspy.models.rst:48: WARNING: toctree references unknown document u'api/hyperspy.models.eelsmodel.EELSModel.extend'
/home/fjd29/Python/hyperspy/doc/api/hyperspy.models.rst:48: WARNING: toctree references unknown document u'api/hyperspy.models.eelsmodel.EELSModel.fetch_stored_values'
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/home/fjd29/Python/hyperspy/doc/index.rst:7: WARNING: Title underline too short.

Welcome to HyperSpy's documentation!
===================================
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Energy-Dispersive X-Rays Spectrometry (EDS)
******************************************
/home/fjd29/Python/hyperspy/doc/user_guide/eels.rst:208: ERROR: Figure caption must be a paragraph or empty comment.

.. figure::  images/curve_fitting_BN.png
   :align:   center
   :width:   500

   Curve fitting quantification of a boron nitride EELS core-loss spectrum from
   `The EELS Data Base
   <http://pc-web.cemes.fr/eelsdb/index.php?page=home.php>`_
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maximum 1 argument(s) allowed, 5 supplied.

.. code-block:: bash
   $ hyperspy qtconsole --pylab_inline
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"Loading" zadata from a numpy array
---------------------------------
/home/fjd29/Python/hyperspy/doc/user_guide/getting_started.rst:265: WARNING: Title underline too short.

"Loading" zadata from a numpy array
---------------------------------
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