tramway.plot package¶
tramway.plot.mesh module¶
-
tramway.plot.mesh.
plot_points
(cells, min_count=None, style='.', size=8, color=None, axes=None, **kwargs)¶ Plot 2D points coloured by associated cell.
Parameters: - cells (Partition or FiniteElements) – full partition
- min_count (int) – discard cells with less than this number of associated points
- style (str) – point marker style
- size (int) – point marker size
- color (str or numpy.ndarray) – cell colours
Returns: handles of the various clouds of points
Return type: list
Extra keyword arguments are passed to matplotlib ‘s scatter or plot.
-
tramway.plot.mesh.
plot_voronoi
(cells, labels=None, color=None, style='-', centroid_style='g+', negative=None, linewidth=1, fallback_color='gray', verbose=True, axes=None)¶ Voronoi plot.
Parameters: - cells (Partition) – full partition
- labels (numpy.ndarray) – numerical labels for cell adjacency relationship
- color (str) – single-character colours in a string, e.g. ‘rrrbgy’
- style (str) – line style
- centroid_style (str) – marker style of the cell centers
- negative (any) – if
None
, do not plot edges corresponding to negative adjacency labels - linewidth (int) – line width
- fallback_color (str) – colour for missing edges
- verbose (bool) – print message about missing edges
- axes (matplotlib.axes.Axes) – figure axes
Returns: - list of handles of the plotted edges,
handle of the plotted centroids
Return type: tuple
-
tramway.plot.mesh.
plot_delaunay
(cells, labels=None, color=None, style='-', centroid_style='g+', negative=None, axes=None, linewidth=1, individual=False, fallback_color='gray')¶ Delaunay plot.
Parameters: - cells (Partition) – full partition
- labels (numpy.ndarray) – numerical labels for cell adjacency relationship
- color (str) – single-character colours in a string, e.g. ‘rrrbgy’
- style (str) – line style
- centroid_style (str) – marker style of the cell centers
- negative (any) – if
None
, do not plot edges corresponding to negative adjacency labels; if ‘voronoi’, plot the corresponding Voronoi edge instead, for edges with negative labels - axes (matplotlib.axes.Axes) – figure axes
- linewidth (int) – line width
- individual (bool) – plot each edge independently; this generates a lot of handles and takes time
- fallback_color (str) – colour for unexpected labels
Returns: - list of handles of the plotted edges,
handle of the plotted centroids
Return type: tuple
-
tramway.plot.mesh.
plot_distributed
(cells, vertex_color='g', vertex_style='x', edge_color='r', arrow_size=5, arrow_color='y')¶ Plot a
FiniteElements
object as a mesh.Parameters: - cells (tramway.inference.base.FiniteElements) – mesh prepared for the inference
- vertex_color (str) – colour for the cell centers
- vertex_style (str) – marker style for the cell centers
- edge_color (str) – colour of the edge between adjacent cells
- arrow_size (int) – size of the arrows along the edges
- arrow_color (str) – colour of the arrows along the edges
Returns: - list of handles of the edges,
handle of the cell centers (vertices), list of handles of the arrow segments
Return type: tuple
plot_distributed is similar to plot_delaunay but takes a
FiniteElements
object instead.
-
tramway.plot.mesh.
plot_indices
(*args, **kwargs)¶ Alias for
plot_cell_indices()
.plot_cell_indices was formerly named plot_indices.
-
tramway.plot.mesh.
plot_cell_indices
(cells, font_size=12, shift_indices=False, axes=None, **kwargs)¶ Plot cell indices at the cell centers.
Parameters: - cells (Partition or Tessellation or FiniteElements) – tessellation
- font_size (int) – alias for fontsize
- shift_indices (bool) – first cell is numbered 1 instead of 0
- axes (matplotlib.axes.Axes) – figure axes; new in 0.6
Returns: handles of the individual text elements
Return type: list
Trailing keyword arguments are passed to
text()
.
tramway.plot.map module¶
-
tramway.plot.map.
cell_to_polygon
(c, X, voronoi=None, bounding_box=None, region_point=None, return_voronoi=False)¶
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tramway.plot.map.
cell_to_polygon_
(i, vertices, cell_vertices, Av, xlim=None, ylim=None, try_fix_corners=True)¶
-
tramway.plot.map.
box_voronoi_2d
(tessellation, xlim, ylim)¶
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tramway.plot.map.
scalar_map_2d
(cells, values, aspect=None, clim=None, figure=None, axes=None, linewidth=1, delaunay=False, colorbar=True, alpha=None, colormap=None, unit=None, clabel=None, xlim=None, ylim=None, try_fix_corners=True, return_patches=False, **kwargs)¶ Plot a 2D scalar map as a colourful image.
Parameters: - cells (Partition or FiniteElements) – spatial description of the cells
- values (pandas.DataFrame or numpy.ndarray) – feature value at each cell, that will be represented as a colour
- aspect (str) – passed to
set_aspect()
- clim (2-element sequence) – passed to
set_clim()
- figure (matplotlib.figure.Figure) – figure handle
- axes (matplotlib.axes.Axes) – axes handle
- linewidth (int) – cell border line width
- delaunay (bool or dict) – overlay the Delaunay graph; if
dict
, options are passed toplot_delaunay()
- colorbar (bool or str or dict) – add a colour bar; if
dict
, options are passed tocolorbar()
; setting colorbar to ‘nice’ allows to produce a colorbar close to the figure of the same size as the figure - unit/clabel (str) – colorbar label, usually the unit of displayed feature
- alpha (float) – alpha value of the cells
- colormap (str) – colormap name; see also https://matplotlib.org/users/colormaps.html
- xlim (2-element sequence) – lower and upper x-axis bounds
- ylim (2-element sequence) – lower and upper y-axis bounds
- return_patches (bool) – returns PatchCollection patches and the corresponding bin indices.
Extra keyword arguments are passed to
PatchCollection()
.
-
tramway.plot.map.
field_map_2d
(cells, values, angular_width=30.0, overlay=False, aspect=None, figure=None, axes=None, cell_arrow_ratio=None, markercolor='y', markeredgecolor='k', markeralpha=0.8, markerlinewidth=None, transform=None, inferencemap=False, arrow_size=None, arrow_quantile_size=0.1, **kwargs)¶ Plot a 2D field (vector) map as arrows.
Parameters: - cells (Partition or FiniteElements) – spatial description of the cells
- values (pandas.DataFrame or numpy.ndarray) – value at each cell, represented as a colour
- angular_width (float) – angle of the tip of the arrows
- overlay (bool) – do not plot the amplitude as a scalar map
- aspect (str) – passed to
set_aspect()
- figure (matplotlib.figure.Figure) – figure handle
- axes (matplotlib.axes.Axes) – axes handle
- cell_arrow_ratio (float) – size of the largest arrow relative to the median
inter-cell distance; default is
0.4
if inferencemap isTrue
, else1
- markercolor (str) – colour of the arrows
- markeredgecolor (str) – colour of the border of the arrows
- markeralpha (float) – alpha value of the arrows
- markerlinewidth (float) – line width of the border of the arrows
- transform ('log', 'log10' or callable) – if overlay is
False
, transform applied to the amplitudes as a NumPy array; affects only the color-coded background map - inferencemap (bool) – if
True
, the arrow length only depends on the cell size - arrow_size (str) – new in 0.6; can be
'constant'
- arrow_quantile_size (float) – new in 0.6; applies if
arrow_size=='constant'
; the base arrow size is set equal to a quantile of the inter-cell distance
Extra keyword arguments are passed to
scalar_map_2d()
if called.If overlay is
True
, the marker-prefixed arguments can be renamed without the marker prefix. These arguments can only be keyworded.
-
tramway.plot.map.
scalar_map_3d
(cells, values, aspect=None, clim=None, figure=None, axes=None, colorbar=True, alpha=None, colormap=None, unit=None, clabel=None, xlim=None, ylim=None, zlim=None, triangulation_depth=2, **kwargs)¶ Plot a 2D scalar map as a colourful 3D surface.
Parameters: - cells (Tessellation or Partition) – spatial description of the cells
- values (pandas.DataFrame, numpy.ndarray or Maps) – feature value at each cell, that will be represented as a colour
- aspect (str) – passed to
set_aspect()
- clim (2-element sequence) – passed to
set_clim()
; note clim affects colour, not height. - figure (matplotlib.figure.Figure) – figure handle
- axes (matplotlib.axes.Axes) – axes handle
- colorbar (bool or str or dict) – add a colour bar; if
dict
, options are passed tocolorbar()
; setting colorbar to ‘nice’ allows to produce a colorbar close to the figure of the same size as the figure - unit/clabel (str) – colorbar label, usually the unit of displayed feature
- alpha (float) – alpha value of the cells
- colormap (str) – colormap name; see also https://matplotlib.org/users/colormaps.html
- xlim (2-element sequence) – lower and upper x-axis bounds
- ylim (2-element sequence) – lower and upper y-axis bounds
- zlim (2-element sequence) – lower and upper z-axis bounds; note zlim affects height, not colour.
Extra keyword arguments are passed to
PatchCollection()
.
tramway.plot.contour module¶
-
class
tramway.plot.contour.
ContourEditor
(figure, renderer=None)¶ Bases:
object
-
area
¶
-
axes
¶
-
cell
¶
-
cell_adjacency
¶
-
cell_centers
¶
-
cell_count
¶
-
cells
¶
-
curl
(F, dr, A)¶
-
delaunay
¶
-
dilation_adjacency
¶
-
draw
()¶
-
field
(cs)¶
-
find_cell
(pt)¶
-
integral
(contour, inner)¶
-
map
¶
-
refresh
()¶
-
step
¶
-
sum
(x, *args)¶
-
surface_area
(contour, inner)¶
-
tangent
(cs)¶
-
variable
¶
-
variables
¶
-
tramway.plot.tk.contour module¶
-
class
tramway.plot.tk.contour.
ContourEditingApp
(parent=None)¶ Bases:
tkinter.Frame
-
create_widgets
()¶
-
debug
¶
-
disable_widgets
()¶
-
enable_widgets
()¶
-
new_file
(*args, **kwargs)¶
-
set_maps
(maps)¶
-
-
class
tramway.plot.tk.contour.
FileChooser
(parent, filetypes={}, **kwargs)¶ Bases:
tkinter.Frame
-
open_input_file
()¶
-
-
class
tramway.plot.tk.contour.
TkContourEditor
(parent, **kwargs)¶ Bases:
matplotlib.backends.backend_tkagg.FigureCanvasTkAgg
-
cells
¶
-
debug
¶
-
map
¶
-
onclick
(event)¶
-
toggle_delaunay
(*args)¶
-
variables
¶
-
-
tramway.plot.tk.contour.
contour_utility
()¶
tramway.plot.bokeh subpackage¶
tramway.plot.bokeh.map module¶
-
tramway.plot.bokeh.map.
plot_points
(cells, style='circle', size=2, color=None, figure=None, **kwargs)¶ Plot molecule locations.
If no colour is explicitly defined, colouring is based on the cell index.
Parameters: - cells (Partition) – full partition
- style (str) – point marker style
- size (float) – point marker size (in screen units)
- color (str or numpy.ndarray) – cell colours
- figure (bokeh.plotting.figure.Figure) – figure handle
Returns: handles of the various clouds of points
Return type: list
-
tramway.plot.bokeh.map.
plot_trajectories
(trajs, color=None, loc_style='circle', figure=None, **kwargs)¶ Plot trajectories.
If no colour is explicitly defined, colouring is based on the trajectory index.
Parameters: - trajs (pandas.DataFrame) – full partition
- loc_style (str) – location marker style
- loc_size (float) – location marker size (in screen units)
- color (str or numpy.ndarray) – trajectory colours
- figure (bokeh.plotting.figure.Figure) – figure handle
Returns: handles of the glyphs
Return type: list
-
tramway.plot.bokeh.map.
plot_delaunay
(cells, labels=None, color=None, style='-', figure=None, linewidth=1, **kwargs)¶ Delaunay plot.
Parameters: - cells (Partition) – full partition
- labels (numpy.ndarray) – numerical labels for cell adjacency relationship
- color (str) – single-character colours in a string, e.g. ‘rrrbgy’
- style (str) – line style
- figure (bokeh.plotting.figure.Figure) – figure handle
- linewidth (int) – line width
Returns: - list of handles of the plotted edges,
handle of the plotted centroids
Return type: tuple
-
tramway.plot.bokeh.map.
scalar_map_2d
(cells, values, clim=None, figure=None, delaunay=False, colorbar=True, colormap=None, unit=None, clabel=None, colorbar_figure=None, xlim=None, ylim=None, try_fix_corners=True, **kwargs)¶ Plot an interactive 2D scalar map as a colourful image.
Parameters: - cells (Partition) – spatial description of the cells
- values (pandas.Series or pandas.DataFrame) – feature value at each cell/bin, encoded into a colour
- clim (2-element sequence) – passed to
set_clim()
- figure (bokeh.plotting.figure.Figure) – figure handle
- delaunay (bool or dict) – overlay the Delaunay graph; if
dict
, options are passed toplot_delaunay()
- colorbar (bool or str or dict) – add a colour bar; if
dict
, options are passed toColorBar()
- unit/clabel (str) – colorbar label, usually the unit of displayed feature
- colormap (str) – colormap name; see also https://matplotlib.org/users/colormaps.html
- xlim (2-element sequence) – lower and upper x-axis bounds
- ylim (2-element sequence) – lower and upper y-axis bounds
-
tramway.plot.bokeh.map.
field_map_2d
(cells, values, angular_width=30.0, figure=None, cell_arrow_ratio=None, markercolor='#bfbf00', markeredgecolor='#000000', markeralpha=0.8, markerlinewidth=None, inferencemap=False, **kwargs)¶ Plot a 2D field (vector) map as arrows.
Parameters: - cells (Partition or Distributed) – spatial description of the cells
- values (pandas.DataFrame or numpy.ndarray) – value at each cell, represented as a colour
- angular_width (float) – angle of the tip of the arrows
- figure (matplotlib.figure.Figure) – figure handle
- cell_arrow_ratio (float) – size of the largest arrow relative to the median
inter-cell distance; default is
0.4
if inferencemap isTrue
, else1
- markercolor (str) – colour of the arrows
- markeredgecolor (str) – colour of the border of the arrows
- markeralpha (float) – alpha value of the arrows
- markerlinewidth (float) – line width of the border of the arrows
- inferencemap (bool) – if
True
, the arrow length only depends on the cell size
-
tramway.plot.bokeh.map.
add_colorbar
(figure, colormap=None, low=0, high=1, unit=None, clabel=None, colorbar_figure=None)¶
tramway.plot.animation subpackage¶
This package is no longer maintained and is superseded by the mpl
functionalities of RWAnalyzer
.
See for example to_color_movie()
,
animate()
and
animate()
.
-
class
tramway.plot.animation.
VideoReader
(*args, **kwargs)¶ Bases:
object
-
class
tramway.plot.animation.
VideoWriter
(frame_rate, bit_rate=None, dots_per_inch=200, figure=None, axes=None, axis=True, verbose=True, **kwargs)¶ Bases:
object
-
grab_frame
(*args, **kwargs)¶
-
range
(N)¶
-
saving
(output_file)¶
-
-
class
tramway.plot.animation.
VideoWriterReader
(filepath, *args, **kwargs)¶ Bases:
object
-
axes
¶
-
figure
¶
-
fps
¶
-
grab_frame
(*args, **kwargs)¶
-
play
(fps=None, **kwargs)¶
-
range
(N)¶
-
saving
()¶
-
verbose
¶
-
-
exception
tramway.plot.animation.
Aborted
¶ Bases:
Exception
tramway.plot.animation.xyt module¶
-
tramway.plot.animation.xyt.
animate_trajectories_2d
(xyt, output_file=None, frame_rate=None, bit_rate=None, dots_per_inch=200, play=False, time_step=None, time_unit='s', color=None, line_width=1, marker_style='o', marker_size=4, figure=None, axes=None, bounding_box=None, axis=True, verbose=True, time_precision=2, **kwargs)¶ Animate 2D trajectories.
Parameters: - xyt (pandas.DataFrame) – nxyt data.
- output_file (str) – path to .mp4 file.
- frame_rate (float) – number of frames per second.
- bit_rate (int) – movie bitrate; see also
FFMpegWriter
. - dots_per_inch (int) – dpi argument passed to
saving()
. - play (bool) – play the movie once generated.
- time_step (float) – time step between successive frames.
- time_unit (str) – time unit for time display; if None, no title is displayed.
- color (list or numpy.ndarray or callable) – trajectory colour.
- line_width (float) – translocation line width.
- marker_style (str) – location marker style.
- marker_size (float) – location marker size.
- figure (matplotlib.figure.Figure) – figure handle.
- axes (matplotlib.axes.Axes) – axes handle.
- bounding_box (matplotlib.transforms.Bbox) – axis bounding box.
- axis (bool or str) – make the axes visible.
- verbose (bool) – ask for confirmation if the output file is to be overwritten
and draw a progress bar (module
tqdm
must be available). - time_precision (int) – number of decimals for time display.
Extra keyword arguments are passed to
FFMpegWriter
.
tramway.plot.animation.map module¶
-
tramway.plot.animation.map.
animate_map_2d
(_map, cells, output_file=None, frame_rate=1, bit_rate=None, dots_per_inch=200, play=False, time_step=None, time_unit='s', figure=None, axes=None, bounding_box=None, colormap=None, colorbar=True, axis=True, verbose=True, time_precision=2, **kwargs)¶ Animate 2D maps.
Parameters: - _map (pandas.DataFrame) – scalar or vector map.
- cells (tramway.tessellation.base.Partition) – spatial-temporal binning.
- output_file (str) – path to .mp4 file.
- frame_rate (float) – number of frames per second.
- bit_rate (int) – movie bitrate; see also
FFMpegWriter
. - dots_per_inch (int) – dpi argument passed to
saving()
. - play (bool) – play the movie once generated.
- time_step (float) – time step between successive frames.
- time_unit (str) – time unit for time display; if None, no title is displayed.
- figure (matplotlib.figure.Figure) – figure handle.
- axes (matplotlib.axes.Axes) – axes handle.
- bounding_box (matplotlib.transforms.Bbox) – axis bounding box.
- colormap (str) – colormap name; see also https://matplotlib.org/users/colormaps.html.
- colorbar (bool or str or dict) – see also
scalar_map_2d()
. - axis (bool or str) – make the axes visible.
- verbose (bool) – ask for confirmation if the output file is to be overwritten
and draw a progress bar (module
tqdm
must be available). - time_precision (int) – number of decimals for time display.
Extra keyword arguments are passed to
FFMpegWriter
.