WARNING: sphinx.ext.pngmath has been deprecated. Please use sphinx.ext.imgmath instead.
WARNING: unsupported build info format in '/home/fjd29/Python/hyperspy3/doc/_build/html/.buildinfo', building all
/home/fjd29/Python/hyperspy3/hyperspy/component.py:docstring of hyperspy.component.Component.as_dictionary:5: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/hyperspy/component.py:docstring of hyperspy.component.Component.as_dictionary:6: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/component.py:docstring of hyperspy.component.Component.as_dictionary:10: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/hyperspy/component.py:docstring of hyperspy.component.Component.as_dictionary:11: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/component.py:docstring of hyperspy.component.Component.as_dictionary:15: WARNING: Definition list ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/component.py:docstring of hyperspy.component.Component.export:12: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/hyperspy/component.py:docstring of hyperspy.component.Component.export:19: WARNING: Definition list ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/component.py:docstring of hyperspy.component.Component.notebook_interaction:5: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/hyperspy/component.py:docstring of hyperspy.component.Component.notebook_interaction:6: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/component.py:docstring of hyperspy.component.Parameter.as_dictionary:20: WARNING: Definition list ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/component.py:docstring of hyperspy.component.Parameter.notebook_interaction:5: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/hyperspy/component.py:docstring of hyperspy.component.Parameter.notebook_interaction:6: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/events.py:docstring of hyperspy.events.Event.connect:5: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/hyperspy/events.py:docstring of hyperspy.events.Event.connect:6: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/events.py:docstring of hyperspy.events.Event.disconnect:11: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/hyperspy/events.py:docstring of hyperspy.events.Event.disconnect:12: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/events.py:docstring of hyperspy.events.Event.suppress:6: SEVERE: Unexpected section title.

Example usage
-------------
/home/fjd29/Python/hyperspy3/hyperspy/events.py:docstring of hyperspy.events.Event.suppress_callback:7: SEVERE: Unexpected section title.

Example usage
-------------
/home/fjd29/Python/hyperspy3/hyperspy/events.py:docstring of hyperspy.events.EventSuppressor:5: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/hyperspy/events.py:docstring of hyperspy.events.EventSuppressor:13: SEVERE: Unexpected section title.

Example usage
-------------
/home/fjd29/Python/hyperspy3/hyperspy/events.py:docstring of hyperspy.events.Events.suppress:6: SEVERE: Unexpected section title.

Example usage
-------------
/home/fjd29/Python/hyperspy3/hyperspy/interactive.py:docstring of hyperspy.interactive.interactive:26: WARNING: Inline emphasis start-string without end-string.
/home/fjd29/Python/hyperspy3/hyperspy/interactive.py:docstring of hyperspy.interactive.interactive:26: WARNING: Inline strong start-string without end-string.
/home/fjd29/Python/hyperspy3/hyperspy/io.py:docstring of hyperspy.io.load:10: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/hyperspy/io.py:docstring of hyperspy.io.load:18: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/logger.py:docstring of hyperspy.logger.set_log_level:7: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/hyperspy/logger.py:docstring of hyperspy.logger.set_log_level:16: SEVERE: Unexpected section title.

Example use
-----------
/home/fjd29/Python/hyperspy3/hyperspy/model.py:docstring of hyperspy.model.BaseModel.as_dictionary:17: WARNING: Definition list ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/model.py:docstring of hyperspy.model.BaseModel.fit:13: WARNING: Definition list ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/roi.py:docstring of hyperspy.roi.BaseInteractiveROI.add_widget:6: SEVERE: Unexpected section title.

Arguments:
----------
/home/fjd29/Python/hyperspy3/hyperspy/roi.py:docstring of hyperspy.roi.BaseInteractiveROI.add_widget:14: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/hyperspy/roi.py:docstring of hyperspy.roi.BaseInteractiveROI.interactive:5: SEVERE: Unexpected section title.

Arguments:
----------
/home/fjd29/Python/hyperspy3/hyperspy/roi.py:docstring of hyperspy.roi.BaseInteractiveROI.interactive:21: WARNING: Inline strong start-string without end-string.
/home/fjd29/Python/hyperspy3/hyperspy/roi.py:docstring of hyperspy.roi.Line2DROI.profile_line:3: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/hyperspy/roi.py:docstring of hyperspy.roi.Line2DROI.profile_line:5: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/samfire.py:docstring of hyperspy.samfire.Samfire.change_strategy:4: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/hyperspy/signal.py:docstring of hyperspy.signal.BaseSignal.indexmax:19: SEVERE: Unexpected section title.

Usage
-----
/home/fjd29/Python/hyperspy3/hyperspy/signal.py:docstring of hyperspy.signal.BaseSignal.split:13: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/hyperspy/signal.py:docstring of hyperspy.signal.BaseSignal.valuemax:19: SEVERE: Unexpected section title.

Usage
-----
/home/fjd29/Python/hyperspy3/hyperspy/signal.py:docstring of hyperspy.signal.MVATools.export_bss_results:5: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/hyperspy/signal.py:docstring of hyperspy.signal.MVATools.export_bss_results:6: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/signal.py:docstring of hyperspy.signal.MVATools.export_bss_results:20: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/hyperspy/signal.py:docstring of hyperspy.signal.MVATools.export_bss_results:21: WARNING: Bullet list ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/signal.py:docstring of hyperspy.signal.MVATools.export_bss_results:25: WARNING: Definition list ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/signal.py:docstring of hyperspy.signal.MVATools.export_bss_results:26: WARNING: Bullet list ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/signal.py:docstring of hyperspy.signal.MVATools.export_bss_results:29: WARNING: Definition list ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/signal.py:docstring of hyperspy.signal.MVATools.export_decomposition_results:27: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/hyperspy/signal.py:docstring of hyperspy.signal.MVATools.export_decomposition_results:28: WARNING: Bullet list ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/signal.py:docstring of hyperspy.signal.MVATools.export_decomposition_results:32: WARNING: Definition list ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/signal.py:docstring of hyperspy.signal.MVATools.export_decomposition_results:33: WARNING: Bullet list ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/signal.py:docstring of hyperspy.signal.MVATools.export_decomposition_results:37: WARNING: Definition list ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/signal.py:docstring of hyperspy.signal.MVATools.export_decomposition_results:43: WARNING: Definition list ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/samfire.py:docstring of hyperspy.samfire.Samfire.backup:3: ERROR: Unknown target name: "backup".
/home/fjd29/Python/hyperspy3/hyperspy/_components/eels_cl_edge.py:docstring of hyperspy._components.eels_cl_edge.EELSCLEdge.notebook_interaction:5: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/hyperspy/_components/eels_cl_edge.py:docstring of hyperspy._components.eels_cl_edge.EELSCLEdge.notebook_interaction:6: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/_components/gaussian2d.py:docstring of hyperspy._components.gaussian2d.Gaussian2D:6: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/_components/scalable_fixed_pattern.py:docstring of hyperspy._components.scalable_fixed_pattern.ScalableFixedPattern.notebook_interaction:5: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/hyperspy/_components/scalable_fixed_pattern.py:docstring of hyperspy._components.scalable_fixed_pattern.ScalableFixedPattern.notebook_interaction:6: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/_components/volume_plasmon_drude.py:docstring of hyperspy._components.volume_plasmon_drude.VolumePlasmonDrude:9: ERROR: Malformed table.

+------------+-----------------+
| Parameter  |    Attribute    |
+------------+-----------------+
|    E_p     |  plasmon_energy |
+------------+-----------------+
| delta_E_p  |fwhm|
+------------+-----------------+
| intensity  |   intensity     |
+------------+-----------------+
/home/fjd29/Python/hyperspy3/hyperspy/_signals/complex_signal.py:docstring of hyperspy._signals.complex_signal.ComplexSignal.plot:53: WARNING: Inline strong start-string without end-string.
/home/fjd29/Python/hyperspy3/hyperspy/_signals/complex_signal2d.py:docstring of hyperspy._signals.complex_signal2d.ComplexSignal2D.plot:76: WARNING: Inline strong start-string without end-string.
/home/fjd29/Python/hyperspy3/hyperspy/_signals/dielectric_function.py:docstring of hyperspy._signals.dielectric_function.DielectricFunction.get_number_of_effective_electrons:7: WARNING: Definition list ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/_signals/dielectric_function.py:docstring of hyperspy._signals.dielectric_function.DielectricFunction.get_number_of_effective_electrons:9: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/hyperspy/_signals/dielectric_function.py:docstring of hyperspy._signals.dielectric_function.DielectricFunction.get_number_of_effective_electrons:11: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/_signals/dielectric_function.py:docstring of hyperspy._signals.dielectric_function.DielectricFunction.get_number_of_effective_electrons:15: SEVERE: Unexpected section title.

Parameters
----------
/home/fjd29/Python/hyperspy3/hyperspy/_signals/dielectric_function.py:docstring of hyperspy._signals.dielectric_function.DielectricFunction.get_number_of_effective_electrons:27: SEVERE: Unexpected section title.

Returns
-------
/home/fjd29/Python/hyperspy3/hyperspy/_signals/dielectric_function.py:docstring of hyperspy._signals.dielectric_function.DielectricFunction.get_number_of_effective_electrons:36: SEVERE: Unexpected section title.

Notes
-----
/home/fjd29/Python/hyperspy3/hyperspy/_signals/dielectric_function.py:docstring of hyperspy._signals.dielectric_function.DielectricFunction.get_number_of_effective_electrons:38: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/_signals/eds.py:docstring of hyperspy._signals.eds.EDSSpectrum.plot:5: WARNING: Bullet list ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/_signals/eels.py:docstring of hyperspy._signals.eels.EELSSpectrum.fourier_ratio_deconvolution:5: WARNING: Definition list ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/_signals/eels.py:docstring of hyperspy._signals.eels.EELSSpectrum.fourier_ratio_deconvolution:17: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/hyperspy/_signals/eels.py:docstring of hyperspy._signals.eels.EELSSpectrum.kramers_kronig_analysis:57: WARNING: Definition list ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/_signals/eels.py:docstring of hyperspy._signals.eels.EELSSpectrum.kramers_kronig_analysis:82: WARNING: Duplicate explicit target name: "egerton2011".
/home/fjd29/Python/hyperspy3/hyperspy/_signals/hologram_image.py:docstring of hyperspy._signals.hologram_image.HologramImage.estimate_sideband_size:4: WARNING: Inline interpreted text or phrase reference start-string without end-string.
/home/fjd29/Python/hyperspy3/hyperspy/_signals/hologram_image.py:docstring of hyperspy._signals.hologram_image.HologramImage.reconstruct_phase:3: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/hyperspy/_signals/hologram_image.py:docstring of hyperspy._signals.hologram_image.HologramImage.reconstruct_phase:11: WARNING: Inline interpreted text or phrase reference start-string without end-string.
/home/fjd29/Python/hyperspy3/hyperspy/_signals/hologram_image.py:docstring of hyperspy._signals.hologram_image.HologramImage.reconstruct_phase:15: WARNING: Inline interpreted text or phrase reference start-string without end-string.
/home/fjd29/Python/hyperspy3/hyperspy/_signals/hologram_image.py:docstring of hyperspy._signals.hologram_image.HologramImage.reconstruct_phase:17: WARNING: Inline interpreted text or phrase reference start-string without end-string.
/home/fjd29/Python/hyperspy3/hyperspy/_signals/hologram_image.py:docstring of hyperspy._signals.hologram_image.HologramImage.reconstruct_phase:27: WARNING: Inline interpreted text or phrase reference start-string without end-string.
/home/fjd29/Python/hyperspy3/hyperspy/_signals/hologram_image.py:docstring of hyperspy._signals.hologram_image.HologramImage.reconstruct_phase:39: WARNING: Inline interpreted text or phrase reference start-string without end-string.
/home/fjd29/Python/hyperspy3/hyperspy/_signals/signal1d.py:docstring of hyperspy._signals.signal1d.Signal1D.align1D:11: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/hyperspy/_signals/signal1d.py:docstring of hyperspy._signals.signal1d.Signal1D.align1D:12: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/_signals/signal1d.py:docstring of hyperspy._signals.signal1d.Signal1D.calibrate:5: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/hyperspy/_signals/signal1d.py:docstring of hyperspy._signals.signal1d.Signal1D.calibrate:6: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/_signals/signal1d.py:docstring of hyperspy._signals.signal1d.Signal1D.estimate_shift1D:3: WARNING: Definition list ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/_signals/signal1d.py:docstring of hyperspy._signals.signal1d.Signal1D.estimate_shift1D:11: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/hyperspy/_signals/signal1d.py:docstring of hyperspy._signals.signal1d.Signal1D.estimate_shift1D:12: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/_signals/signal1d.py:docstring of hyperspy._signals.signal1d.Signal1D.integrate_in_range:6: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/hyperspy/_signals/signal1d.py:docstring of hyperspy._signals.signal1d.Signal1D.integrate_in_range:11: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/_signals/signal1d.py:docstring of hyperspy._signals.signal1d.Signal1D.interpolate_in_between:4: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/hyperspy/_signals/signal1d.py:docstring of hyperspy._signals.signal1d.Signal1D.interpolate_in_between:5: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/_signals/signal1d.py:docstring of hyperspy._signals.signal1d.Signal1D.remove_background:4: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/hyperspy/_signals/signal1d.py:docstring of hyperspy._signals.signal1d.Signal1D.remove_background:6: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/_signals/signal1d.py:docstring of hyperspy._signals.signal1d.Signal1D.shift1D:4: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/hyperspy/_signals/signal1d.py:docstring of hyperspy._signals.signal1d.Signal1D.shift1D:5: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/_signals/signal1d.py:docstring of hyperspy._signals.signal1d.Signal1D.smooth_lowess:5: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/hyperspy/_signals/signal1d.py:docstring of hyperspy._signals.signal1d.Signal1D.smooth_lowess:6: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/_signals/signal1d.py:docstring of hyperspy._signals.signal1d.Signal1D.smooth_savitzky_golay:5: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/hyperspy/_signals/signal1d.py:docstring of hyperspy._signals.signal1d.Signal1D.smooth_savitzky_golay:6: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/_signals/signal1d.py:docstring of hyperspy._signals.signal1d.Signal1D.smooth_tv:3: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/hyperspy/_signals/signal1d.py:docstring of hyperspy._signals.signal1d.Signal1D.smooth_tv:4: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/_signals/signal1d.py:docstring of hyperspy._signals.signal1d.find_peaks_ohaver:14: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/hyperspy/_signals/signal1d.py:docstring of hyperspy._signals.signal1d.find_peaks_ohaver:16: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/_signals/signal2d.py:docstring of hyperspy._signals.signal2d.Signal2D.align2D:7: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/hyperspy/_signals/signal2d.py:docstring of hyperspy._signals.signal2d.Signal2D.align2D:8: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/_signals/signal2d.py:docstring of hyperspy._signals.signal2d.Signal2D.align2D:27: WARNING: Inline interpreted text or phrase reference start-string without end-string.
/home/fjd29/Python/hyperspy3/hyperspy/_signals/signal2d.py:docstring of hyperspy._signals.signal2d.Signal2D.align2D:34: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/_signals/signal2d.py:docstring of hyperspy._signals.signal2d.Signal2D.create_model:3: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/hyperspy/_signals/signal2d.py:docstring of hyperspy._signals.signal2d.Signal2D.create_model:4: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/_signals/signal2d.py:docstring of hyperspy._signals.signal2d.Signal2D.crop_image:9: SEVERE: Unexpected section title.

See also:
---------
/home/fjd29/Python/hyperspy3/hyperspy/_signals/signal2d.py:docstring of hyperspy._signals.signal2d.Signal2D.estimate_shift2D:8: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/hyperspy/_signals/signal2d.py:docstring of hyperspy._signals.signal2d.Signal2D.estimate_shift2D:13: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/_signals/signal2d.py:docstring of hyperspy._signals.signal2d.Signal2D.estimate_shift2D:21: WARNING: Inline interpreted text or phrase reference start-string without end-string.
/home/fjd29/Python/hyperspy3/hyperspy/_signals/signal2d.py:docstring of hyperspy._signals.signal2d.Signal2D.estimate_shift2D:50: WARNING: Inline interpreted text or phrase reference start-string without end-string.
/home/fjd29/Python/hyperspy3/hyperspy/_signals/signal2d.py:docstring of hyperspy._signals.signal2d.Signal2D.estimate_shift2D:56: WARNING: Duplicate explicit target name: "1".
/home/fjd29/Python/hyperspy3/hyperspy/_signals/signal2d.py:docstring of hyperspy._signals.signal2d.Signal2D.estimate_shift2D:57: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/_signals/signal2d.py:docstring of hyperspy._signals.signal2d.Signal2D.align2D:27: ERROR: Duplicate target name, cannot be used as a unique reference: "1".
/home/fjd29/Python/hyperspy3/hyperspy/_signals/signal2d.py:docstring of hyperspy._signals.signal2d.Signal2D.estimate_shift2D:50: ERROR: Duplicate target name, cannot be used as a unique reference: "1".
/home/fjd29/Python/hyperspy3/hyperspy/_signals/eels.py:docstring of hyperspy._signals.eels.EELSSpectrum.kramers_kronig_analysis:82: WARNING: duplicate citation Egerton2011, other instance in /home/fjd29/Python/hyperspy3/doc/api/hyperspy._signals.rst
/home/fjd29/Python/hyperspy3/hyperspy/drawing/utils.py:docstring of hyperspy.drawing.utils.plot_images:71: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/hyperspy/drawing/utils.py:docstring of hyperspy.drawing.utils.plot_images:95: WARNING: Inline strong start-string without end-string.
/home/fjd29/Python/hyperspy3/hyperspy/drawing/widget.py:docstring of hyperspy.drawing.widget.ResizersMixin:8: SEVERE: Unexpected section title.

Attributes:
-----------
/home/fjd29/Python/hyperspy3/hyperspy/drawing/_widgets/line2d.py:docstring of hyperspy.drawing._widgets.line2d.Line2DWidget:25: WARNING: Definition list ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/drawing/_widgets/line2d.py:docstring of hyperspy.drawing._widgets.line2d.angle_between:4: ERROR: Inconsistent literal block quoting.
/home/fjd29/Python/hyperspy3/hyperspy/drawing/_widgets/range.py:docstring of hyperspy.drawing._widgets.range.RangeWidget.set_bounds:3: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/hyperspy/drawing/_widgets/range.py:docstring of hyperspy.drawing._widgets.range.RangeWidget.set_bounds:4: WARNING: Bullet list ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/drawing/_widgets/range.py:docstring of hyperspy.drawing._widgets.range.RangeWidget.set_bounds:7: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/drawing/_widgets/range.py:docstring of hyperspy.drawing._widgets.range.RangeWidget.set_ibounds:3: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/hyperspy/drawing/_widgets/range.py:docstring of hyperspy.drawing._widgets.range.RangeWidget.set_ibounds:4: WARNING: Bullet list ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/drawing/_widgets/range.py:docstring of hyperspy.drawing._widgets.range.RangeWidget.set_ibounds:7: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/drawing/_widgets/rectangles.py:docstring of hyperspy.drawing._widgets.rectangles.RectangleWidget.set_bounds:3: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/hyperspy/drawing/_widgets/rectangles.py:docstring of hyperspy.drawing._widgets.rectangles.RectangleWidget.set_bounds:4: WARNING: Bullet list ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/drawing/_widgets/rectangles.py:docstring of hyperspy.drawing._widgets.rectangles.RectangleWidget.set_bounds:9: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/drawing/_widgets/rectangles.py:docstring of hyperspy.drawing._widgets.rectangles.RectangleWidget.set_ibounds:3: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/hyperspy/drawing/_widgets/rectangles.py:docstring of hyperspy.drawing._widgets.rectangles.RectangleWidget.set_ibounds:4: WARNING: Bullet list ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/drawing/_widgets/rectangles.py:docstring of hyperspy.drawing._widgets.rectangles.RectangleWidget.set_ibounds:9: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/external/progressbar.py:docstring of hyperspy.external.progressbar.progressbar:11: SEVERE: Unexpected section title.

Parameters
----------
/home/fjd29/Python/hyperspy3/hyperspy/external/progressbar.py:docstring of hyperspy.external.progressbar.progressbar:93: SEVERE: Unexpected section title.

Returns
-------
/home/fjd29/Python/hyperspy3/hyperspy/external/astroML/bayesian_blocks.py:docstring of hyperspy.external.astroML.bayesian_blocks.FitnessFunc:5: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/hyperspy/external/astroML/bayesian_blocks.py:docstring of hyperspy.external.astroML.bayesian_blocks.FitnessFunc:6: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/external/astroML/bayesian_blocks.py:docstring of hyperspy.external.astroML.bayesian_blocks.bayesian_blocks:66: WARNING: Duplicate explicit target name: "1".
/home/fjd29/Python/hyperspy3/hyperspy/external/astroML/histtools.py:docstring of hyperspy.external.astroML.histtools.knuth_bin_width:26: WARNING: Duplicate explicit target name: "1".
/home/fjd29/Python/hyperspy3/hyperspy/external/astroML/bayesian_blocks.py:docstring of hyperspy.external.astroML.bayesian_blocks:6: ERROR: Duplicate target name, cannot be used as a unique reference: "1".
/home/fjd29/Python/hyperspy3/hyperspy/external/astroML/bayesian_blocks.py:docstring of hyperspy.external.astroML.bayesian_blocks.bayesian_blocks:3: ERROR: Duplicate target name, cannot be used as a unique reference: "1".
/home/fjd29/Python/hyperspy3/hyperspy/external/astroML/histtools.py:docstring of hyperspy.external.astroML.histtools.knuth_bin_width:1: ERROR: Duplicate target name, cannot be used as a unique reference: "1".
/home/fjd29/Python/hyperspy3/hyperspy/external/mpfit/mpfit.py:docstring of hyperspy.external.mpfit.mpfit:4: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/external/mpfit/mpfit.py:docstring of hyperspy.external.mpfit.mpfit:9: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/hyperspy/external/mpfit/mpfit.py:docstring of hyperspy.external.mpfit.mpfit:12: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/hyperspy/external/mpfit/mpfit.py:docstring of hyperspy.external.mpfit.mpfit:132: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/hyperspy/external/mpfit/mpfit.py:docstring of hyperspy.external.mpfit.mpfit:142: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/hyperspy/external/mpfit/mpfit.py:docstring of hyperspy.external.mpfit.mpfit:144: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/hyperspy/external/mpfit/mpfit.py:docstring of hyperspy.external.mpfit.mpfit:145: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/external/mpfit/mpfit.py:docstring of hyperspy.external.mpfit.mpfit:147: WARNING: Definition list ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/external/mpfit/mpfit.py:docstring of hyperspy.external.mpfit.mpfit:222: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/external/mpfit/mpfit.py:docstring of hyperspy.external.mpfit.mpfit:264: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/hyperspy/external/mpfit/mpfit.py:docstring of hyperspy.external.mpfit.mpfit:265: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/external/mpfit/mpfit.py:docstring of hyperspy.external.mpfit.mpfit:284: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/hyperspy/external/mpfit/mpfit.py:docstring of hyperspy.external.mpfit.mpfit:285: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/external/mpfit/mpfit.py:docstring of hyperspy.external.mpfit.mpfit:305: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/external/mpfit/mpfit.py:docstring of hyperspy.external.mpfit.mpfit:390: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/hyperspy/external/mpfit/mpfit.py:docstring of hyperspy.external.mpfit.mpfit:391: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/external/mpfit/mpfit.py:docstring of hyperspy.external.mpfit.mpfit:399: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/external/mpfit/mpfitexpr.py:docstring of hyperspy.external.mpfit.mpfitexpr:0: ERROR: Error in "py:module" directive:
no content permitted.

.. py:module:: hyperspy.external.mpfit.mpfitexpr

    Copyright (C) 2009 Sergey Koposov
/home/fjd29/Python/hyperspy3/hyperspy/gui/tools.py:docstring of hyperspy.gui.tools.LineInSignal1D:5: SEVERE: Unexpected section title.

Attributes:
-----------
/home/fjd29/Python/hyperspy3/hyperspy/io_plugins/bcf.py:docstring of hyperspy.io_plugins.bcf.BCF_reader.parse_hypermap:10: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/hyperspy/io_plugins/bcf.py:docstring of hyperspy.io_plugins.bcf.BCF_reader.parse_hypermap:11: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/io_plugins/bcf.py:docstring of hyperspy.io_plugins.bcf.BCF_reader.py_parse_hypermap:15: WARNING: Title underline too short.

Arguments:
---------
/home/fjd29/Python/hyperspy3/hyperspy/io_plugins/bcf.py:docstring of hyperspy.io_plugins.bcf.BCF_reader.py_parse_hypermap:15: SEVERE: Unexpected section title.

Arguments:
---------
/home/fjd29/Python/hyperspy3/hyperspy/io_plugins/bcf.py:docstring of hyperspy.io_plugins.bcf.BCF_reader.py_parse_hypermap:26: SEVERE: Unexpected section title.

Returns:
---------
/home/fjd29/Python/hyperspy3/hyperspy/io_plugins/bcf.py:docstring of hyperspy.io_plugins.bcf.HyperHeader.estimate_map_depth:9: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/hyperspy/io_plugins/bcf.py:docstring of hyperspy.io_plugins.bcf.SFS_reader.get_file:6: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/hyperspy/io_plugins/bcf.py:docstring of hyperspy.io_plugins.bcf.file_reader:7: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/hyperspy/io_plugins/bcf.py:docstring of hyperspy.io_plugins.bcf.file_reader:9: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/io_plugins/bcf.py:docstring of hyperspy.io_plugins.bcf.file_reader:11: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/hyperspy/io_plugins/bcf.py:docstring of hyperspy.io_plugins.bcf.file_reader:13: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/io_plugins/bcf.py:docstring of hyperspy.io_plugins.bcf.file_reader:15: WARNING: Definition list ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/io_plugins/digital_micrograph.py:docstring of hyperspy.io_plugins.digital_micrograph.DigitalMicrographReader.read_string:3: WARNING: Definition list ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/io_plugins/edax.py:docstring of hyperspy.io_plugins.edax.get_ipr_dtype_list:34: WARNING: Inline emphasis start-string without end-string.
/home/fjd29/Python/hyperspy3/hyperspy/io_plugins/emd.py:docstring of hyperspy.io_plugins.emd.EMD.load_from_emd:3: WARNING: Inline emphasis start-string without end-string.
/home/fjd29/Python/hyperspy3/hyperspy/io_plugins/ripple.py:docstring of hyperspy.io_plugins.ripple.file_reader:30: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/io_plugins/ripple.py:docstring of hyperspy.io_plugins.ripple.file_reader:31: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/io_plugins/ripple.py:docstring of hyperspy.io_plugins.ripple.write_raw:4: SEVERE: Unexpected section title.

Parameters:
-----------
/home/fjd29/Python/hyperspy3/doc/api/hyperspy.io_plugins.rst:138: WARNING: autodoc: failed to import module 'hyperspy.io_plugins.unbcf_fast'; the following exception was raised:
Traceback (most recent call last):
  File "/home/fjd29/Anaconda/anaconda3/lib/python3.5/site-packages/Sphinx-1.4.1-py3.5.egg/sphinx/ext/autodoc.py", line 507, in import_object
    __import__(self.modname)
ImportError: /home/fjd29/Python/hyperspy3/hyperspy/io_plugins/unbcf_fast.cpython-35m-x86_64-linux-gnu.so: undefined symbol: PyFPE_jbuf
/home/fjd29/Python/hyperspy3/hyperspy/learn/mva.py:docstring of hyperspy.learn.mva.LearningResults.load:3: WARNING: Definition list ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/learn/mva.py:docstring of hyperspy.learn.mva.LearningResults.save:5: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/hyperspy/learn/mva.py:docstring of hyperspy.learn.mva.LearningResults.save:6: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/learn/mva.py:docstring of hyperspy.learn.mva.MVA.blind_source_separation:38: WARNING: Inline strong start-string without end-string.
/home/fjd29/Python/hyperspy3/hyperspy/learn/rpca.py:docstring of hyperspy.learn.rpca.orpca:45: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/hyperspy/learn/rpca.py:docstring of hyperspy.learn.rpca.orpca:55: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/doc/api/hyperspy.misc.rst:7: WARNING: toctree contains reference to nonexisting document 'api/hyperspy.misc.holography'
/home/fjd29/Python/hyperspy3/hyperspy/misc/example_signals_loading.py:docstring of hyperspy.misc.example_signals_loading.load_object_hologram:6: WARNING: Bullet list ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/misc/example_signals_loading.py:docstring of hyperspy.misc.example_signals_loading.load_reference_hologram:6: WARNING: Bullet list ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/misc/export_dictionary.py:docstring of hyperspy.misc.export_dictionary.export_to_dictionary:9: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/hyperspy/misc/export_dictionary.py:docstring of hyperspy.misc.export_dictionary.export_to_dictionary:10: WARNING: Bullet list ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/misc/export_dictionary.py:docstring of hyperspy.misc.export_dictionary.export_to_dictionary:13: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/misc/export_dictionary.py:docstring of hyperspy.misc.export_dictionary.export_to_dictionary:15: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/hyperspy/misc/export_dictionary.py:docstring of hyperspy.misc.export_dictionary.export_to_dictionary:17: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/misc/export_dictionary.py:docstring of hyperspy.misc.export_dictionary.load_from_dictionary:10: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/hyperspy/misc/export_dictionary.py:docstring of hyperspy.misc.export_dictionary.load_from_dictionary:12: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/misc/test_utils.py:docstring of hyperspy.misc.test_utils.assert_warns:16: WARNING: Inline substitution_reference start-string without end-string.
/home/fjd29/Python/hyperspy3/hyperspy/misc/utils.py:docstring of hyperspy.misc.utils.swapelem:8: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/hyperspy/misc/eds/utils.py:docstring of hyperspy.misc.eds.utils.quantification_cross_section:5: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/hyperspy/misc/eds/utils.py:docstring of hyperspy.misc.eds.utils.quantification_cross_section:6: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/misc/eels/tools.py:docstring of hyperspy.misc.eels.tools.eels_constant:7: WARNING: Definition list ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/misc/eels/tools.py:docstring of hyperspy.misc.eels.tools.eels_constant:9: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/hyperspy/misc/eels/tools.py:docstring of hyperspy.misc.eels.tools.eels_constant:10: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/misc/eels/tools.py:docstring of hyperspy.misc.eels.tools.eels_constant:13: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/hyperspy/misc/eels/tools.py:docstring of hyperspy.misc.eels.tools.eels_constant:14: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/misc/eels/tools.py:docstring of hyperspy.misc.eels.tools.eels_constant:18: SEVERE: Unexpected section title.

Parameters
----------
/home/fjd29/Python/hyperspy3/hyperspy/misc/eels/tools.py:docstring of hyperspy.misc.eels.tools.eels_constant:34: SEVERE: Unexpected section title.

Returns
-------
/home/fjd29/Python/hyperspy3/hyperspy/samfire_utils/samfire_pool.py:docstring of hyperspy.samfire_utils.samfire_pool.SamfirePool:7: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/hyperspy/samfire_utils/samfire_pool.py:docstring of hyperspy.samfire_utils.samfire_pool.SamfirePool:8: WARNING: Bullet list ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/hyperspy/samfire_utils/samfire_pool.py:docstring of hyperspy.samfire_utils.samfire_pool.SamfirePool.parse:7: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/doc/citing.rst:43: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/fjd29/Python/hyperspy3/doc/citing.rst:None: WARNING: nonlocal image URI found: https://zenodo.org/badge/doi/10.5281/zenodo.240660.svg
/home/fjd29/Python/hyperspy3/doc/dev_guide.rst:5: WARNING: Duplicate explicit target name: "github".
/home/fjd29/Python/hyperspy3/doc/index.rst:7: WARNING: Title underline too short.

Welcome to HyperSpy's documentation!
===================================
/home/fjd29/Python/hyperspy3/doc/user_guide/.ipynb_checkpoints/model-checkpoint.rst:212: WARNING: Duplicate explicit target name: "model_components-label".
/home/fjd29/Python/hyperspy3/doc/user_guide/.ipynb_checkpoints/model-checkpoint.rst:None: WARNING: image file not readable: user_guide/.ipynb_checkpoints/images/notebook_widgets.png
/home/fjd29/Python/hyperspy3/doc/user_guide/.ipynb_checkpoints/model-checkpoint.rst:None: WARNING: image file not readable: user_guide/.ipynb_checkpoints/images/model_adjust_position.png
/home/fjd29/Python/hyperspy3/doc/user_guide/bibliography.rst:16: WARNING: duplicate citation Egerton2011, other instance in /home/fjd29/Python/hyperspy3/doc/api/hyperspy._signals.rst
/home/fjd29/Python/hyperspy3/doc/user_guide/eds.rst:338: WARNING: Title underline too short.

Finding elements from energy
^^^^^^^^^^^^^^^^
/home/fjd29/Python/hyperspy3/doc/user_guide/eds.rst:338: WARNING: Title underline too short.

Finding elements from energy
^^^^^^^^^^^^^^^^
/home/fjd29/Python/hyperspy3/doc/user_guide/eds.rst:356: WARNING: malformed hyperlink target.
/home/fjd29/Python/hyperspy3/doc/user_guide/eds.rst:375: WARNING: Duplicate explicit target name: "eds_plot-label".
/home/fjd29/Python/hyperspy3/doc/user_guide/eds.rst:440: WARNING: Title underline too short.

Geting the intensity of an X-ray line
-------------------
/home/fjd29/Python/hyperspy3/doc/user_guide/eds.rst:440: WARNING: Title underline too short.

Geting the intensity of an X-ray line
-------------------
/home/fjd29/Python/hyperspy3/doc/user_guide/eels.rst:163: ERROR: Error in "code-block" directive:
maximum 1 argument(s) allowed, 11 supplied.

.. code-block:: python
    >>> m.components.N_K
    <N_K (EELSCLEdge component)>
    >>> m.components.B_K
    <B_K (EELSCLEdge component)>
/home/fjd29/Python/hyperspy3/doc/user_guide/eels.rst:211: 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>`_
/home/fjd29/Python/hyperspy3/doc/user_guide/electron_holography.rst:79: WARNING: image file not readable: user_guide/images/holography_unwrapped_phase.png:align:center
/home/fjd29/Python/hyperspy3/doc/user_guide/examples/index.rst:7: ERROR: Unknown directive type "htmlonly".

.. htmlonly::

    :Release: |version|
    :Date: |today|
/home/fjd29/Python/hyperspy3/doc/user_guide/index.rst:10: WARNING: toctree contains reference to nonexisting document 'user_guide/samfire'
/home/fjd29/Python/hyperspy3/doc/user_guide/index.rst:10: WARNING: toctree contains reference to nonexisting document 'user_guide/credits'
/home/fjd29/Python/hyperspy3/doc/user_guide/install.rst:123: ERROR: Unexpected indentation.
/home/fjd29/Python/hyperspy3/doc/user_guide/install.rst:5: WARNING: Duplicate explicit target name: "anaconda".
/home/fjd29/Python/hyperspy3/doc/user_guide/install.rst:5: WARNING: Duplicate explicit target name: "pip".
/home/fjd29/Python/hyperspy3/doc/user_guide/io.rst:5: WARNING: Duplicate explicit target name: "open standard format".
/home/fjd29/Python/hyperspy3/doc/user_guide/io.rst:532: WARNING: Title underline too short.

Bruker composite file
----------------
/home/fjd29/Python/hyperspy3/doc/user_guide/io.rst:532: WARNING: Title underline too short.

Bruker composite file
----------------
/home/fjd29/Python/hyperspy3/doc/user_guide/model.rst:199: WARNING: Duplicate explicit target name: "model_components-label".
/home/fjd29/Python/hyperspy3/doc/user_guide/model.rst:570: WARNING: duplicate label model.fitting, other instance in /home/fjd29/Python/hyperspy3/doc/user_guide/.ipynb_checkpoints/model-checkpoint.rst
/home/fjd29/Python/hyperspy3/doc/user_guide/model.rst:999: WARNING: duplicate label samfire-label, other instance in /home/fjd29/Python/hyperspy3/doc/user_guide/.ipynb_checkpoints/model-checkpoint.rst
/home/fjd29/Python/hyperspy3/doc/user_guide/model.rst:871: WARNING: duplicate label storing_models-label, other instance in /home/fjd29/Python/hyperspy3/doc/user_guide/.ipynb_checkpoints/model-checkpoint.rst
/home/fjd29/Python/hyperspy3/doc/user_guide/model.rst:773: WARNING: duplicate label model.starting, other instance in /home/fjd29/Python/hyperspy3/doc/user_guide/.ipynb_checkpoints/model-checkpoint.rst
/home/fjd29/Python/hyperspy3/doc/user_guide/model.rst:354: WARNING: duplicate label model_indexing-label, other instance in /home/fjd29/Python/hyperspy3/doc/user_guide/.ipynb_checkpoints/model-checkpoint.rst
/home/fjd29/Python/hyperspy3/doc/user_guide/model.rst:741: WARNING: duplicate label model.visualization, other instance in /home/fjd29/Python/hyperspy3/doc/user_guide/.ipynb_checkpoints/model-checkpoint.rst
/home/fjd29/Python/hyperspy3/doc/user_guide/mva.rst:183: ERROR: Error in "code-block" directive:
maximum 1 argument(s) allowed, 6 supplied.

.. code-block:: python
     The long way:
     >>> s.decomposition(normalize_poissonian_noise=True)

     Because it is the first argument we could have simply written:
     >>> s.decomposition(True)
/home/fjd29/Python/hyperspy3/doc/user_guide/mva.rst:271: WARNING: Title underline too short.

Non-negative matrix factorization
----------------------------
/home/fjd29/Python/hyperspy3/doc/user_guide/mva.rst:271: WARNING: Title underline too short.

Non-negative matrix factorization
----------------------------
/home/fjd29/Python/hyperspy3/doc/user_guide/mva.rst:320: ERROR: Unknown target name: "plot".
../CHANGES.txt:9: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../CHANGES.txt:19: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../CHANGES.txt:2: WARNING: Duplicate explicit target name: "bugs fixed".
../CHANGES.txt:2: WARNING: Duplicate explicit target name: "bugs fixed".
../CHANGES.txt:2: WARNING: Duplicate explicit target name: "bugs fixed".
../CHANGES.txt:2: WARNING: Duplicate explicit target name: "bugs fixed".
../CHANGES.txt:2: WARNING: Duplicate explicit target name: "bugs fixed".
../CHANGES.txt:2: WARNING: Duplicate explicit target name: "enhancements".
../CHANGES.txt:2: WARNING: Duplicate explicit target name: "bugs fixed".
../CHANGES.txt:2: WARNING: Duplicate explicit target name: "feature".
../CHANGES.txt:2: WARNING: Duplicate explicit target name: "documentation".
../CHANGES.txt:364: WARNING: Duplicate explicit target name: "changes_0.7.1".
/home/fjd29/Python/hyperspy3/doc/user_guide/.ipynb_checkpoints/model-checkpoint.rst:: WARNING: document isn't included in any toctree
/home/fjd29/Python/hyperspy3/doc/user_guide/examples/index.rst:: WARNING: document isn't included in any toctree
/home/fjd29/Python/hyperspy3/doc/user_guide/utils.rst:: WARNING: document isn't included in any toctree
WARNING: inline latex 'f(x,y) = \\frac{A}{2\\pi s_x s_y}}}e^{-\\frac{\\left(x-x0\\right)\n^{2}}{2s_{x}^{2}}\\frac{\\left(y-y0\\right)^{2}}{2s_{y}^{2}}}\n\n': latex exited with error
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l.14 ...^{2}}{2s_{y}^{2}}}\end{split}\end{aligned}
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<recently read> \endgroup 
                          
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                                                  {\vskip #1\relax }
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                     {\ifdim #1>\displaywidth \dimen@ \prevdepth \nointerlin...
l.14 ...^{2}}}\end{split}\end{aligned}\end{align*}
                                                  
! Too many }'s.
\endalign ->\math@cr \black@ \totwidth@ \egroup 
                                                \ifingather@ \restorealignst...
l.14 ...^{2}}}\end{split}\end{aligned}\end{align*}
                                                  

! LaTeX Error: \begin{document} ended by \end{align*}.

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l.14 ...^{2}}}\end{split}\end{aligned}\end{align*}
                                                  
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l.14 ...^{2}}}\end{split}\end{aligned}\end{align*}
                                                  
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<recently read> \endgroup 
                          
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[1] (./math.aux) )
(see the transcript file for additional information)
Output written on math.dvi (1 page, 580 bytes).
Transcript written on math.log.

WARNING: inline latex 'f(x) =\n\\begin{cases}\n  0     $ \\quad \\text{if } x < n \\\\\n  A/2     $ \\quad \\text{if } x = n \\\\\n  A     $ \\quad \\text{if } x > n \\\\\n\\end{cases}': latex exited with error
[stdout]
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[1] (./math.aux) )
(see the transcript file for additional information)
Output written on math.dvi (1 page, 484 bytes).
Transcript written on math.log.

/home/fjd29/Python/hyperspy3/doc/api/hyperspy._components.rst:20: WARNING: Pygments lexer name 'ipython' is not known
/home/fjd29/Python/hyperspy3/doc/citing.rst:9: WARNING: Pygments lexer name 'bibtex' is not known
/home/fjd29/Python/hyperspy3/doc/user_guide/getting_started.rst:84: WARNING: Could not lex literal_block as "python". Highlighting skipped.
/home/fjd29/Python/hyperspy3/hyperspy/signal.py:docstring of hyperspy.signal.BaseSignal.map:None: WARNING: more than one target found for cross-reference 'function': hyperspy._components.eels_double_power_law.DoublePowerLaw.function, hyperspy._components.eels_vignetting.Vignetting.function, hyperspy._components.bleasdale.Bleasdale.function, hyperspy._components.voigt.Voigt.function, hyperspy._components.arctan.Arctan.function, hyperspy._components.power_law.PowerLaw.function, hyperspy._components.gaussian2d.Gaussian2D.function, hyperspy.tests.samfire.test_strategy.someweight.function, hyperspy._components.expression.Expression.function, hyperspy._components.exponential.Exponential.function, hyperspy.samfire_utils.weights.red_chisq.ReducedChiSquaredWeight.function, hyperspy._components.volume_plasmon_drude.VolumePlasmonDrude.function, hyperspy._components.polynomial.Polynomial.function, hyperspy._components.offset.Offset.function, hyperspy._components.pes_core_line_shape.PESCoreLineShape.function, hyperspy._components.gaussian.Gaussian.function, hyperspy._components.lorentzian.Lorentzian.function, hyperspy._components.pes_see.SEE.function, hyperspy._components.logistic.Logistic.function, hyperspy._components.error_function.Erf.function, hyperspy._components.rc.RC.function, hyperspy._components.heaviside.HeavisideStep.function, hyperspy._components.eels_cl_edge.EELSCLEdge.function, hyperspy._components.scalable_fixed_pattern.ScalableFixedPattern.function
/home/fjd29/Python/hyperspy3/hyperspy/signal.py:docstring of hyperspy.signal.ModelManager.store:None: WARNING: more than one target found for cross-reference 'model': hyperspy.samfire.Samfire.model, hyperspy.model, hyperspy.tests.model, hyperspy.utils.model
/home/fjd29/Python/hyperspy3/hyperspy/_signals/eds_sem.py:docstring of hyperspy._signals.eds_sem.EDSSEMSpectrum.get_calibration_from:None: WARNING: more than one target found for cross-reference 'signal': hyperspy.models.model1d.Model1D.signal, hyperspy.tests.signal, hyperspy.drawing.signal, hyperspy.model.BaseModel.signal, hyperspy.docstrings.signal, hyperspy.models.model2d.Model2D.signal, hyperspy.signal
/home/fjd29/Python/hyperspy3/hyperspy/_signals/eds_tem.py:docstring of hyperspy._signals.eds_tem.EDSTEMSpectrum.get_calibration_from:None: WARNING: more than one target found for cross-reference 'signal': hyperspy.models.model1d.Model1D.signal, hyperspy.tests.signal, hyperspy.drawing.signal, hyperspy.model.BaseModel.signal, hyperspy.docstrings.signal, hyperspy.models.model2d.Model2D.signal, hyperspy.signal
/home/fjd29/Python/hyperspy3/hyperspy/_signals/eds_tem.py:docstring of hyperspy._signals.eds_tem.EDSTEMSpectrum.vacuum_mask:None: WARNING: more than one target found for cross-reference 'signal': hyperspy.models.model1d.Model1D.signal, hyperspy.tests.signal, hyperspy.drawing.signal, hyperspy.model.BaseModel.signal, hyperspy.docstrings.signal, hyperspy.models.model2d.Model2D.signal, hyperspy.signal
/home/fjd29/Python/hyperspy3/hyperspy/drawing/utils.py:docstring of hyperspy.drawing.utils.create_figure:None: WARNING: more than one target found for cross-reference 'function': hyperspy._components.eels_double_power_law.DoublePowerLaw.function, hyperspy._components.eels_vignetting.Vignetting.function, hyperspy._components.bleasdale.Bleasdale.function, hyperspy._components.voigt.Voigt.function, hyperspy._components.arctan.Arctan.function, hyperspy._components.power_law.PowerLaw.function, hyperspy._components.gaussian2d.Gaussian2D.function, hyperspy.tests.samfire.test_strategy.someweight.function, hyperspy._components.expression.Expression.function, hyperspy._components.exponential.Exponential.function, hyperspy.samfire_utils.weights.red_chisq.ReducedChiSquaredWeight.function, hyperspy._components.volume_plasmon_drude.VolumePlasmonDrude.function, hyperspy._components.polynomial.Polynomial.function, hyperspy._components.offset.Offset.function, hyperspy._components.pes_core_line_shape.PESCoreLineShape.function, hyperspy._components.gaussian.Gaussian.function, hyperspy._components.lorentzian.Lorentzian.function, hyperspy._components.pes_see.SEE.function, hyperspy._components.logistic.Logistic.function, hyperspy._components.error_function.Erf.function, hyperspy._components.rc.RC.function, hyperspy._components.heaviside.HeavisideStep.function, hyperspy._components.eels_cl_edge.EELSCLEdge.function, hyperspy._components.scalable_fixed_pattern.ScalableFixedPattern.function
/home/fjd29/Python/hyperspy3/hyperspy/drawing/utils.py:docstring of hyperspy.drawing.utils.on_figure_window_close:None: WARNING: more than one target found for cross-reference 'function': hyperspy._components.eels_double_power_law.DoublePowerLaw.function, hyperspy._components.eels_vignetting.Vignetting.function, hyperspy._components.bleasdale.Bleasdale.function, hyperspy._components.voigt.Voigt.function, hyperspy._components.arctan.Arctan.function, hyperspy._components.power_law.PowerLaw.function, hyperspy._components.gaussian2d.Gaussian2D.function, hyperspy.tests.samfire.test_strategy.someweight.function, hyperspy._components.expression.Expression.function, hyperspy._components.exponential.Exponential.function, hyperspy.samfire_utils.weights.red_chisq.ReducedChiSquaredWeight.function, hyperspy._components.volume_plasmon_drude.VolumePlasmonDrude.function, hyperspy._components.polynomial.Polynomial.function, hyperspy._components.offset.Offset.function, hyperspy._components.pes_core_line_shape.PESCoreLineShape.function, hyperspy._components.gaussian.Gaussian.function, hyperspy._components.lorentzian.Lorentzian.function, hyperspy._components.pes_see.SEE.function, hyperspy._components.logistic.Logistic.function, hyperspy._components.error_function.Erf.function, hyperspy._components.rc.RC.function, hyperspy._components.heaviside.HeavisideStep.function, hyperspy._components.eels_cl_edge.EELSCLEdge.function, hyperspy._components.scalable_fixed_pattern.ScalableFixedPattern.function
/home/fjd29/Python/hyperspy3/hyperspy/io_plugins/ripple.py:docstring of hyperspy.io_plugins.ripple.read_raw:None: WARNING: more than one target found for cross-reference 'A': hyperspy._components.pes_see.SEE.A, hyperspy._components.gaussianhf.GaussianHF.A, hyperspy._components.error_function.Erf.A
/home/fjd29/Python/hyperspy3/hyperspy/samfire_utils/samfire_pool.py:docstring of hyperspy.samfire_utils.samfire_pool.SamfirePool.prepare_workers:None: WARNING: more than one target found for cross-reference 'samfire': hyperspy.tests.samfire, hyperspy.utils.samfire, hyperspy.samfire
/home/fjd29/Python/hyperspy3/doc/user_guide/.ipynb_checkpoints/model-checkpoint.rst:208: WARNING: undefined label: http://groups.google.com/group/hyperspy-users (if the link has no caption the label must precede a section header)
/home/fjd29/Python/hyperspy3/doc/user_guide/.ipynb_checkpoints/model-checkpoint.rst:948: WARNING: undefined label: storing_models (if the link has no caption the label must precede a section header)
/home/fjd29/Python/hyperspy3/doc/user_guide/eds.rst:361: WARNING: citation not found: Chantler2005
/home/fjd29/Python/hyperspy3/doc/user_guide/eds.rst:394: WARNING: undefined label: visualization_multi_dim (if the link has no caption the label must precede a section header)
/home/fjd29/Python/hyperspy3/doc/user_guide/eds.rst:615: WARNING: undefined label: setting axis properties (if the link has no caption the label must precede a section header)
/home/fjd29/Python/hyperspy3/doc/user_guide/io.rst:213: WARNING: more than one target found for cross-reference 'metadata': hyperspy.samfire.Samfire.metadata, hyperspy.io_plugins.semper_unf.SemperFormat.metadata
/home/fjd29/Python/hyperspy3/doc/user_guide/io.rst:263: WARNING: undefined label: hdf5 (if the link has no caption the label must precede a section header)
/home/fjd29/Python/hyperspy3/doc/user_guide/model.rst:195: WARNING: undefined label: http://groups.google.com/group/hyperspy-users (if the link has no caption the label must precede a section header)
/home/fjd29/Python/hyperspy3/doc/user_guide/model.rst:935: WARNING: undefined label: storing_models (if the link has no caption the label must precede a section header)
/home/fjd29/Python/hyperspy3/doc/user_guide/tools.rst:883: WARNING: undefined label: signal2d.crop (if the link has no caption the label must precede a section header)
/home/fjd29/Python/hyperspy3/doc/user_guide/visualisation.rst:780: WARNING: undefined label: navigator_options (if the link has no caption the label must precede a section header)
../CHANGES.txt:105: WARNING: undefined label: eds_absorption_db-label (if the link has no caption the label must precede a section header)
../CHANGES.txt:137: WARNING: undefined label: model_components-label (if the link has no caption the label must precede a section header)
../CHANGES.txt:240: WARNING: undefined label: magic-label (if the link has no caption the label must precede a section header)
../CHANGES.txt:245: WARNING: undefined label: model_components-label (if the link has no caption the label must precede a section header)
../CHANGES.txt:395: WARNING: undefined label: headless-label (if the link has no caption the label must precede a section header)
../CHANGES.txt:430: WARNING: undefined label: inline_plotting (if the link has no caption the label must precede a section header)
../CHANGES.txt:488: WARNING: undefined label: eds_plot-label (if the link has no caption the label must precede a section header)
WARNING: favicon file 'hyperspy_logo.ico' does not exist
