xmipp3.viewers.viewer_structure_map module

class xmipp3.viewers.viewer_structure_map.Annotation3D(s, xyz, *args, **kwargs)[source]

Bases: Annotation

Annotate the point xyz with text s

Annotate the point xy with text text.

In the simplest form, the text is placed at xy.

Optionally, the text can be displayed in another position xytext. An arrow pointing from the text to the annotated point xy can then be added by defining arrowprops.

  • text (str) – The text of the annotation.

  • xy ((float, float)) – The point (x, y) to annotate. The coordinate system is determined by xycoords.

  • xytext ((float, float), default: *xy*) – The position (x, y) to place the text at. The coordinate system is determined by textcoords.

  • xycoords (str or .Artist or .Transform or callable or (float, float), default: ‘data’) – The coordinate system that xy is given in. The following types of values are supported:

    • One of the following strings:



      ‘figure points’

      Points from the lower left of the figure

      ‘figure pixels’

      Pixels from the lower left of the figure

      ‘figure fraction’

      Fraction of figure from lower left

      ‘subfigure points’

      Points from the lower left of the subfigure

      ‘subfigure pixels’

      Pixels from the lower left of the subfigure

      ‘subfigure fraction’

      Fraction of subfigure from lower left

      ‘axes points’

      Points from lower left corner of axes

      ‘axes pixels’

      Pixels from lower left corner of axes

      ‘axes fraction’

      Fraction of axes from lower left


      Use the coordinate system of the object being annotated (default)


      (theta, r) if not native ‘data’ coordinates

      Note that ‘subfigure pixels’ and ‘figure pixels’ are the same for the parent figure, so users who want code that is usable in a subfigure can use ‘subfigure pixels’.

    • An .Artist: xy is interpreted as a fraction of the artist’s ~matplotlib.transforms.Bbox. E.g. (0, 0) would be the lower left corner of the bounding box and (0.5, 1) would be the center top of the bounding box.

    • A .Transform to transform xy to screen coordinates.

    • A function with one of the following signatures:

      def transform(renderer) -> Bbox
      def transform(renderer) -> Transform

      where renderer is a .RendererBase subclass.

      The result of the function is interpreted like the .Artist and .Transform cases above.

    • A tuple (xcoords, ycoords) specifying separate coordinate systems for x and y. xcoords and ycoords must each be of one of the above described types.

    See plotting-guide-annotation for more details.

  • textcoords (str or .Artist or .Transform or callable or (float, float), default: value of xycoords) – The coordinate system that xytext is given in.

    All xycoords values are valid as well as the following strings:



    ‘offset points’

    Offset (in points) from the xy value

    ‘offset pixels’

    Offset (in pixels) from the xy value

  • arrowprops (dict, optional) – The properties used to draw a .FancyArrowPatch arrow between the positions xy and xytext. Defaults to None, i.e. no arrow is drawn.

    For historical reasons there are two different ways to specify arrows, “simple” and “fancy”:

    Simple arrow:

    If arrowprops does not contain the key ‘arrowstyle’ the allowed keys are:




    The width of the arrow in points


    The width of the base of the arrow head in points


    The length of the arrow head in points


    Fraction of total length to shrink from both ends


    Any key to matplotlib.patches.FancyArrowPatch

    The arrow is attached to the edge of the text box, the exact position (corners or centers) depending on where it’s pointing to.

    Fancy arrow:

    This is used if ‘arrowstyle’ is provided in the arrowprops.

    Valid keys are the following ~matplotlib.patches.FancyArrowPatch parameters:




    the arrow style


    the connection style


    see below; default is (0.5, 0.5)


    default is bounding box of the text


    default is None


    default is 2 points


    default is 2 points


    default is text size (in points)


    default is 1.


    any key for matplotlib.patches.PathPatch

    The exact starting point position of the arrow is defined by relpos. It’s a tuple of relative coordinates of the text box, where (0, 0) is the lower left corner and (1, 1) is the upper right corner. Values <0 and >1 are supported and specify points outside the text box. By default (0.5, 0.5) the starting point is centered in the text box.

  • annotation_clip (bool or None, default: None) – Whether to draw the annotation when the annotation point xy is outside the axes area.

    • If True, the annotation will only be drawn when xy is within the axes.

    • If False, the annotation will always be drawn.

    • If None, the annotation will only be drawn when xy is within the axes and xycoords is ‘data’.

  • **kwargs – Additional kwargs are passed to ~matplotlib.text.Text.

Return type


See also



Draw the Artist (and its children) using the given renderer.

This has no effect if the artist is not visible (.Artist.get_visible returns False).


renderer (.RendererBase subclass.)


This method is overridden in the Artist subclasses.

set(*, agg_filter=<UNSET>, alpha=<UNSET>, animated=<UNSET>, anncoords=<UNSET>, annotation_clip=<UNSET>, backgroundcolor=<UNSET>, bbox=<UNSET>, clip_box=<UNSET>, clip_on=<UNSET>, clip_path=<UNSET>, color=<UNSET>, fontfamily=<UNSET>, fontproperties=<UNSET>, fontsize=<UNSET>, fontstretch=<UNSET>, fontstyle=<UNSET>, fontvariant=<UNSET>, fontweight=<UNSET>, gid=<UNSET>, horizontalalignment=<UNSET>, in_layout=<UNSET>, label=<UNSET>, linespacing=<UNSET>, math_fontfamily=<UNSET>, multialignment=<UNSET>, parse_math=<UNSET>, path_effects=<UNSET>, picker=<UNSET>, position=<UNSET>, rasterized=<UNSET>, rotation=<UNSET>, rotation_mode=<UNSET>, sketch_params=<UNSET>, snap=<UNSET>, text=<UNSET>, transform=<UNSET>, transform_rotates_text=<UNSET>, url=<UNSET>, usetex=<UNSET>, verticalalignment=<UNSET>, visible=<UNSET>, wrap=<UNSET>, x=<UNSET>, y=<UNSET>, zorder=<UNSET>)

Set multiple properties at once.

Supported properties are


agg_filter: a filter function, which takes a (m, n, 3) float array and a dpi value, and returns a (m, n, 3) array alpha: scalar or None animated: bool anncoords: unknown annotation_clip: bool or None backgroundcolor: color bbox: dict with properties for .patches.FancyBboxPatch clip_box: .Bbox clip_on: bool clip_path: Patch or (Path, Transform) or None color or c: color figure: .Figure fontfamily or family: {FONTNAME, ‘serif’, ‘sans-serif’, ‘cursive’, ‘fantasy’, ‘monospace’} fontproperties or font or font_properties: .font_manager.FontProperties or str or pathlib.Path fontsize or size: float or {‘xx-small’, ‘x-small’, ‘small’, ‘medium’, ‘large’, ‘x-large’, ‘xx-large’} fontstretch or stretch: {a numeric value in range 0-1000, ‘ultra-condensed’, ‘extra-condensed’, ‘condensed’, ‘semi-condensed’, ‘normal’, ‘semi-expanded’, ‘expanded’, ‘extra-expanded’, ‘ultra-expanded’} fontstyle or style: {‘normal’, ‘italic’, ‘oblique’} fontvariant or variant: {‘normal’, ‘small-caps’} fontweight or weight: {a numeric value in range 0-1000, ‘ultralight’, ‘light’, ‘normal’, ‘regular’, ‘book’, ‘medium’, ‘roman’, ‘semibold’, ‘demibold’, ‘demi’, ‘bold’, ‘heavy’, ‘extra bold’, ‘black’} gid: str horizontalalignment or ha: {‘center’, ‘right’, ‘left’} in_layout: bool label: object linespacing: float (multiple of font size) math_fontfamily: str multialignment or ma: {‘left’, ‘right’, ‘center’} parse_math: bool path_effects: .AbstractPathEffect picker: None or bool or float or callable position: (float, float) rasterized: bool rotation: float or {‘vertical’, ‘horizontal’} rotation_mode: {None, ‘default’, ‘anchor’} sketch_params: (scale: float, length: float, randomness: float) snap: bool or None text: object transform: .Transform transform_rotates_text: bool url: str usetex: bool or None verticalalignment or va: {‘center’, ‘top’, ‘bottom’, ‘baseline’, ‘center_baseline’} visible: bool wrap: bool x: float y: float zorder: float

class xmipp3.viewers.viewer_structure_map.XmippProtStructureMapViewer(**kwargs)[source]

Bases: ProtocolViewer

Wrapper to visualize different type of data objects with the Xmipp program xmipp_showj

xmipp3.viewers.viewer_structure_map.annotate3D(ax, s, *args, **kwargs)[source]

add anotation text s to to Axes3d ax

class xmipp3.viewers.viewer_structure_map.projectionPlot(coords, labels, weights)[source]

Bases: object

KruskalMST(triples, N)[source]
find(parent, i)[source]
plotContour(x, y)[source]
plotConvolution(x, y)[source]
plotScatter(x, y)[source]
projectMatrix(M, coords)[source]
union(parent, rank, x, y)[source]