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How to use _add_markers method in pytest-play

Best Python code snippet using pytest-play_python

figures.py

Source:figures.py

...67        """68        path = join(dirpath, name+'.{}'.format(fmt))69        kw = dict(dpi=dpi, transparent=transparent, rasterized=rasterized)70        fig.savefig(path, format=fmt, **kwargs)71    def _add_markers(self, x, y, c, **kwargs):72        """73        Add markers to axis.74        Args:75            x, y (array like) - marker x and y positions76            c (array like) - marker colors77            kwargs: keyword arguments for matplotlib.pyplot.scatter78        """79        if len(self.fig.axes) == 0:80            ax = self.fig.subplots()81        ax = self.fig.axes[0]82        # add markers to plot83        ax.scatter(x, y, c=c, **kwargs)84    def format(self, **kwargs):85        """ Format all figure axes. """86        for ax in self.fig.axes:87            self.format_axis(ax, **kwargs)88    def format_axis(self, ax):89        """ Format individual axis. """90        pass91class CellSelection(Figure):92    """93    Visualize cell selection by overlaying cell position markers on top of an image of a single RGB layer.94    Inherited attributes:95        name (str) - figure name ('selection')96        directory (str) - default path for saving figure97        fig (matplotlib.figure.Figure)98        axes (matplotlib.axes.AxesSubplots)99    """100    def __init__(self, layer, data, channel='r', **kwargs):101        """102        Instantiate cell selection figure.103        Args:104            layer (Layer) - RGB image layer105            data (pd.DataFrame) - selected cell measurement data106            channel (str) - color channel to be added107            kwargs: keyword arguments for render108        """109        Figure.__init__(self, name='selection')110        self.render(layer, data, **kwargs)111    def render(self, layer, data, channel='r', figsize=(3, 3)):112        """113        Render figure.114        Args:115            layer (Layer) - RGB image layer116            data (pd.DataFrame) - selected cell measurement data117            channel (str) - color channel to be added118            figsize (tuple) - figure dimensions119        """120        # create figure121        self.fig = self.create_figure(figsize)122        self.add_axes()123        # add image124        self.add_image(layer, channel=channel)125        # add cell position markers126        self.add_markers(data)127    def add_image(self, layer, channel='r'):128        """129        Add scalar image to figure.130        Args:131            layer (Layer) - RGB image layer132            channel (str) - color channel to be added133        """134        _ = layer.get_channel(channel).show(ax=ax, segments=False, cmap=None)135        _ = ax.axis('off')136    def add_markers(self, data, color_by='genotype', xykey=None, **kwargs):137        """138        Add cell position markers to axis.139        Args:140            data (pd.DataFrame) - selected cell measurement data141            color_by (str) - cell measurement attribute used to color markers142            xykey (list) - attribute keys for cell x/y positions143            kwargs: keyword arguments for markers144        """145        if xykey is None:146            xykey = ['centroid_x', 'centroid_y']147        # get cell coordinates and color vector148        x, y = data[xykey].values.T149        # get color vector and colormap150        c = data[color_by]151        cmap = ListedColormap(['y', 'c', 'm'], 'indexed', 3)152        # add markers to plot153        self._add_markers(x, y, c, cmap=cmap, vmin=0, vmax=2, **kwargs)154class Scatterplot(Figure):155    """156    Scatter points in XY plane.157    Attributes:158        xvar, yvar (str) - cell measurement features to be scattered159    Inherited attributes:160        name (str) - figure name161        directory (str) - default path for saving figure162        fig (matplotlib.figure.Figure)163        axes (matplotlib.axes.AxesSubplots)164    """165    def __init__(self, data, xvar, yvar, name, **kwargs):166        """167        Instantiate scatter plot.168        Args:169            data (pd.DataFrame) - selected cell measurement data170            xvar, yvar (str) - cell measurement features to be scattered171            name (str) - figure name172            kwargs: keyword arguments for173        """174        Figure.__init__(self, name=name)175        self.xvar, self.yvar = xvar, yvar176        self.render(data, **kwargs)177    def render(self, data, figsize=(2, 2)):178        """179        Render figure.180        Args:181            data (pd.DataFrame) - selected cell measurement data182            figsize (tuple) - figure dimensions183        """184        # create figure185        self.fig = self.create_figure(figsize)186        self.add_axes()187        # add data188        self._add_markers(data[self.xvar], data[self.yvar], c='k', s=1)189        # format axes190        self.format()191    def format_axis(self, ax):192        """193        Format axis.194        Args:195            ax (matplotlib.axes.AxesSubplot)196        """197        _ = ax.spines['top'].set_visible(False)198        _ = ax.spines['right'].set_visible(False)199        _ = ax.set_xlabel(self.x)200        _ = ax.set_ylabel(self.y)201class BackgroundCorrelation(Scatterplot):202    """...

tk_geo_mapper.py

Source:tk_geo_mapper.py

1# pylint: disable=C04132import sys3import os4import tkinter as tk5from PIL import Image, ImageTk6import numpy as np7sys.path.insert(0, os.getcwd())8from geo_mapping.geo_mapper import MapFitter, MapCoordinateTransformer9class TkGeoMapper:10    '''11    Given a latitude and longitude series describing a track.12    Fetches a map that fits the data. Adds the map to a canvas. Draws13    the track on the canvas overlaying the map.14    This was used for MapFitter images and other geo mapper classes.15    Look at GeoMapScrubber for a more useful widget that allows scrubbing16    forward and backward on a track in a map.17    '''18    def __init__(self,19                 latitude_series: np.ndarray,20                 longitude_series: np.ndarray,21                 marker_positions=None,22                 track_color='red'23                ):24        self._latitude_series = latitude_series25        self._longitude_series = longitude_series26        self._marker_positions = marker_positions27        self._track_color = track_color28        if self._marker_positions is None:29            self._add_markers = False30        else:31            self._add_markers = True32        assert self._latitude_series.size == self._longitude_series.size, \33               (f'latitude_series ({self._latitude_series.size}) '34                f'must be same size as longitude_series ({self._longitude_series.size})')35        self._map_fitter = MapFitter(self._latitude_series,36                                     self._longitude_series,37                                     add_markers=self._add_markers,38                                    )39        self._map_coordinate_transformer = \40            MapCoordinateTransformer(self._map_fitter.get_center_latitude(),41                                     self._map_fitter.get_center_longitude(),42                                     self._map_fitter.get_map_scaled_width(),43                                     self._map_fitter.get_map_scaled_height(),44                                     self._map_fitter.get_zoom(),45                                     self._map_fitter.get_scale(),46                                    )47        # laxy init48        self._root = None49        self._canvas = None50        self._map_on_canvas = None51        self._map_image = None52        self._x_y_series = None53        self._x_y_series_flattened = None54    def _setup_ui(self):55        self._root = tk.Tk()56        self._canvas = tk.Canvas(master=self._root,57                                 width=self._map_fitter.get_map_scaled_width(),58                                 height=self._map_fitter.get_map_scaled_height(),59                                )60        self._canvas.grid(row=0, column=0)61        self._map_on_canvas = self._canvas.create_image(0, 0, anchor='nw')62        self._canvas.itemconfig(self._map_on_canvas, image=self._get_map_image())63        self._canvas.create_line(*self._get_x_y_series_flattened(),64                                 fill=self._track_color,65                                )66        self._add_marker_dots()67    def _add_marker_dots(self):68        if self._marker_positions is not None:69            for position in self._marker_positions:70                y = self._map_coordinate_transformer.get_y_for_latitude(position[0])71                x = self._map_coordinate_transformer.get_x_for_longitude(position[1])72                self._canvas.create_oval(x-2, y-2, x+2, y+2, fill='blue')73    def _get_map_image(self):74        if self._map_image is None:75            self._map_image = ImageTk.PhotoImage(Image.open(self._map_fitter.get_map()))76        return self._map_image77    def _get_x_y_series(self):78        if self._x_y_series is None:79            r = []80            for idx in range(self._latitude_series.size):81                x = self._map_coordinate_transformer.get_x_for_longitude(self._longitude_series[idx]) # pylint: disable=C030182                y = self._map_coordinate_transformer.get_y_for_latitude(self._latitude_series[idx])83                r.append([x, y])84            self._x_y_series = r85        return self._x_y_series86    def _get_x_y_series_flattened(self):87        if self._x_y_series_flattened is None:88            self._x_y_series_flattened = [item for sublist in self._get_x_y_series() for item in sublist] # pylint: disable=C030189        return self._x_y_series_flattened90    def run(self):91        self._setup_ui()92        self._root.mainloop()...

create_map.py

Source:create_map.py

...21    22    m = folium.Map(location=[lat, lng], tiles='Stamen Terrain', zoom_start=4)23    m.choropleth(geo_data=open(filename).read())24    return m25def _add_markers(m, features):26    for feature in features:27        long, lat = feature['geometry']['coordinates']28        address = feature['properties']['Response']29        folium.CircleMarker(30            location=[lat, long],31            radius=8,32            popup=address,33            weight = 2,34            color='#3186cc',35            fill=True,36            fill_color='#ff9966',37            fill_opacity = .7538        ).add_to(m)39    40def folium_map(filename):41    with open(filename) as f:42        data = json.load(f)43    features = data['features']44    lat, long = get_center_map(data)45    m = folium.Map(location=[lat, long], zoom_start=4)46    _add_markers(m, features)47    ...

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