605 lines
23 KiB
Python
605 lines
23 KiB
Python
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import plotly.graph_objs as go
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from _plotly_utils.basevalidators import ColorscaleValidator
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from ._core import apply_default_cascade, init_figure, configure_animation_controls
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from .imshow_utils import rescale_intensity, _integer_ranges, _integer_types
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import pandas as pd
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import numpy as np
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import itertools
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from plotly.utils import image_array_to_data_uri
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try:
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import xarray
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xarray_imported = True
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except ImportError:
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xarray_imported = False
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_float_types = []
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def _vectorize_zvalue(z, mode="max"):
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alpha = 255 if mode == "max" else 0
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if z is None:
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return z
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elif np.isscalar(z):
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return [z] * 3 + [alpha]
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elif len(z) == 1:
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return list(z) * 3 + [alpha]
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elif len(z) == 3:
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return list(z) + [alpha]
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elif len(z) == 4:
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return z
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else:
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raise ValueError(
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"zmax can be a scalar, or an iterable of length 1, 3 or 4. "
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"A value of %s was passed for zmax." % str(z)
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)
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def _infer_zmax_from_type(img):
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dt = img.dtype.type
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rtol = 1.05
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if dt in _integer_types:
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return _integer_ranges[dt][1]
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else:
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im_max = img[np.isfinite(img)].max()
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if im_max <= 1 * rtol:
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return 1
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elif im_max <= 255 * rtol:
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return 255
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elif im_max <= 65535 * rtol:
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return 65535
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else:
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return 2**32
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def imshow(
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img,
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zmin=None,
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zmax=None,
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origin=None,
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labels={},
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x=None,
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y=None,
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animation_frame=None,
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facet_col=None,
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facet_col_wrap=None,
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facet_col_spacing=None,
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facet_row_spacing=None,
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color_continuous_scale=None,
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color_continuous_midpoint=None,
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range_color=None,
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title=None,
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template=None,
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width=None,
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height=None,
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aspect=None,
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contrast_rescaling=None,
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binary_string=None,
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binary_backend="auto",
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binary_compression_level=4,
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binary_format="png",
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text_auto=False,
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) -> go.Figure:
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"""
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Display an image, i.e. data on a 2D regular raster.
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Parameters
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----------
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img: array-like image, or xarray
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The image data. Supported array shapes are
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- (M, N): an image with scalar data. The data is visualized
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using a colormap.
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- (M, N, 3): an image with RGB values.
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- (M, N, 4): an image with RGBA values, i.e. including transparency.
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zmin, zmax : scalar or iterable, optional
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zmin and zmax define the scalar range that the colormap covers. By default,
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zmin and zmax correspond to the min and max values of the datatype for integer
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datatypes (ie [0-255] for uint8 images, [0, 65535] for uint16 images, etc.). For
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a multichannel image of floats, the max of the image is computed and zmax is the
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smallest power of 256 (1, 255, 65535) greater than this max value,
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with a 5% tolerance. For a single-channel image, the max of the image is used.
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Overridden by range_color.
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origin : str, 'upper' or 'lower' (default 'upper')
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position of the [0, 0] pixel of the image array, in the upper left or lower left
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corner. The convention 'upper' is typically used for matrices and images.
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labels : dict with str keys and str values (default `{}`)
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Sets names used in the figure for axis titles (keys ``x`` and ``y``),
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colorbar title and hoverlabel (key ``color``). The values should correspond
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to the desired label to be displayed. If ``img`` is an xarray, dimension
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names are used for axis titles, and long name for the colorbar title
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(unless overridden in ``labels``). Possible keys are: x, y, and color.
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x, y: list-like, optional
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x and y are used to label the axes of single-channel heatmap visualizations and
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their lengths must match the lengths of the second and first dimensions of the
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img argument. They are auto-populated if the input is an xarray.
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animation_frame: int or str, optional (default None)
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axis number along which the image array is sliced to create an animation plot.
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If `img` is an xarray, `animation_frame` can be the name of one the dimensions.
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facet_col: int or str, optional (default None)
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axis number along which the image array is sliced to create a facetted plot.
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If `img` is an xarray, `facet_col` can be the name of one the dimensions.
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facet_col_wrap: int
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Maximum number of facet columns. Wraps the column variable at this width,
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so that the column facets span multiple rows.
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Ignored if `facet_col` is None.
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facet_col_spacing: float between 0 and 1
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Spacing between facet columns, in paper units. Default is 0.02.
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facet_row_spacing: float between 0 and 1
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Spacing between facet rows created when ``facet_col_wrap`` is used, in
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paper units. Default is 0.0.7.
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color_continuous_scale : str or list of str
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colormap used to map scalar data to colors (for a 2D image). This parameter is
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not used for RGB or RGBA images. If a string is provided, it should be the name
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of a known color scale, and if a list is provided, it should be a list of CSS-
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compatible colors.
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color_continuous_midpoint : number
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If set, computes the bounds of the continuous color scale to have the desired
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midpoint. Overridden by range_color or zmin and zmax.
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range_color : list of two numbers
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If provided, overrides auto-scaling on the continuous color scale, including
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overriding `color_continuous_midpoint`. Also overrides zmin and zmax. Used only
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for single-channel images.
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title : str
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The figure title.
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template : str or dict or plotly.graph_objects.layout.Template instance
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The figure template name or definition.
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width : number
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The figure width in pixels.
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height: number
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The figure height in pixels.
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aspect: 'equal', 'auto', or None
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- 'equal': Ensures an aspect ratio of 1 or pixels (square pixels)
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- 'auto': The axes is kept fixed and the aspect ratio of pixels is
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adjusted so that the data fit in the axes. In general, this will
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result in non-square pixels.
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- if None, 'equal' is used for numpy arrays and 'auto' for xarrays
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(which have typically heterogeneous coordinates)
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contrast_rescaling: 'minmax', 'infer', or None
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how to determine data values corresponding to the bounds of the color
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range, when zmin or zmax are not passed. If `minmax`, the min and max
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values of the image are used. If `infer`, a heuristic based on the image
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data type is used.
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binary_string: bool, default None
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if True, the image data are first rescaled and encoded as uint8 and
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then passed to plotly.js as a b64 PNG string. If False, data are passed
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unchanged as a numerical array. Setting to True may lead to performance
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gains, at the cost of a loss of precision depending on the original data
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type. If None, use_binary_string is set to True for multichannel (eg) RGB
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arrays, and to False for single-channel (2D) arrays. 2D arrays are
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represented as grayscale and with no colorbar if use_binary_string is
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True.
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binary_backend: str, 'auto' (default), 'pil' or 'pypng'
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Third-party package for the transformation of numpy arrays to
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png b64 strings. If 'auto', Pillow is used if installed, otherwise
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pypng.
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binary_compression_level: int, between 0 and 9 (default 4)
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png compression level to be passed to the backend when transforming an
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array to a png b64 string. Increasing `binary_compression` decreases the
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size of the png string, but the compression step takes more time. For most
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images it is not worth using levels greater than 5, but it's possible to
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test `len(fig.data[0].source)` and to time the execution of `imshow` to
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tune the level of compression. 0 means no compression (not recommended).
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binary_format: str, 'png' (default) or 'jpg'
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compression format used to generate b64 string. 'png' is recommended
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since it uses lossless compression, but 'jpg' (lossy) compression can
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result if smaller binary strings for natural images.
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text_auto: bool or str (default `False`)
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If `True` or a string, single-channel `img` values will be displayed as text.
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A string like `'.2f'` will be interpreted as a `texttemplate` numeric formatting directive.
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Returns
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-------
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fig : graph_objects.Figure containing the displayed image
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See also
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--------
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plotly.graph_objects.Image : image trace
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plotly.graph_objects.Heatmap : heatmap trace
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Notes
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-----
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In order to update and customize the returned figure, use
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`go.Figure.update_traces` or `go.Figure.update_layout`.
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If an xarray is passed, dimensions names and coordinates are used for
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axes labels and ticks.
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"""
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args = locals()
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apply_default_cascade(args)
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labels = labels.copy()
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nslices_facet = 1
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if facet_col is not None:
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if isinstance(facet_col, str):
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facet_col = img.dims.index(facet_col)
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nslices_facet = img.shape[facet_col]
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facet_slices = range(nslices_facet)
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ncols = int(facet_col_wrap) if facet_col_wrap is not None else nslices_facet
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nrows = (
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nslices_facet // ncols + 1
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if nslices_facet % ncols
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else nslices_facet // ncols
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)
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else:
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nrows = 1
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ncols = 1
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if animation_frame is not None:
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if isinstance(animation_frame, str):
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animation_frame = img.dims.index(animation_frame)
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nslices_animation = img.shape[animation_frame]
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animation_slices = range(nslices_animation)
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slice_dimensions = (facet_col is not None) + (
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animation_frame is not None
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) # 0, 1, or 2
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facet_label = None
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animation_label = None
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img_is_xarray = False
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# ----- Define x and y, set labels if img is an xarray -------------------
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if xarray_imported and isinstance(img, xarray.DataArray):
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dims = list(img.dims)
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img_is_xarray = True
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pop_indexes = []
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if facet_col is not None:
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facet_slices = img.coords[img.dims[facet_col]].values
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pop_indexes.append(facet_col)
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facet_label = img.dims[facet_col]
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if animation_frame is not None:
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animation_slices = img.coords[img.dims[animation_frame]].values
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pop_indexes.append(animation_frame)
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animation_label = img.dims[animation_frame]
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# Remove indices in sorted order.
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for index in sorted(pop_indexes, reverse=True):
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_ = dims.pop(index)
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y_label, x_label = dims[0], dims[1]
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# np.datetime64 is not handled correctly by go.Heatmap
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for ax in [x_label, y_label]:
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if np.issubdtype(img.coords[ax].dtype, np.datetime64):
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img.coords[ax] = img.coords[ax].astype(str)
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if x is None:
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x = img.coords[x_label].values
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if y is None:
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y = img.coords[y_label].values
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if aspect is None:
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aspect = "auto"
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if labels.get("x", None) is None:
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labels["x"] = x_label
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if labels.get("y", None) is None:
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labels["y"] = y_label
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if labels.get("animation_frame", None) is None:
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labels["animation_frame"] = animation_label
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if labels.get("facet_col", None) is None:
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labels["facet_col"] = facet_label
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if labels.get("color", None) is None:
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labels["color"] = xarray.plot.utils.label_from_attrs(img)
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labels["color"] = labels["color"].replace("\n", "<br>")
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else:
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if hasattr(img, "columns") and hasattr(img.columns, "__len__"):
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if x is None:
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x = img.columns
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if labels.get("x", None) is None and hasattr(img.columns, "name"):
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labels["x"] = img.columns.name or ""
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if hasattr(img, "index") and hasattr(img.index, "__len__"):
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if y is None:
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y = img.index
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if labels.get("y", None) is None and hasattr(img.index, "name"):
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labels["y"] = img.index.name or ""
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if labels.get("x", None) is None:
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labels["x"] = ""
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if labels.get("y", None) is None:
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labels["y"] = ""
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if labels.get("color", None) is None:
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labels["color"] = ""
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if aspect is None:
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aspect = "equal"
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# --- Set the value of binary_string (forbidden for pandas)
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if isinstance(img, pd.DataFrame):
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if binary_string:
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raise ValueError("Binary strings cannot be used with pandas arrays")
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is_dataframe = True
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else:
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is_dataframe = False
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# --------------- Starting from here img is always a numpy array --------
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img = np.asanyarray(img)
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# Reshape array so that animation dimension comes first, then facets, then images
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if facet_col is not None:
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img = np.moveaxis(img, facet_col, 0)
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if animation_frame is not None and animation_frame < facet_col:
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animation_frame += 1
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facet_col = True
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if animation_frame is not None:
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img = np.moveaxis(img, animation_frame, 0)
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animation_frame = True
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args["animation_frame"] = (
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"animation_frame"
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if labels.get("animation_frame") is None
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else labels["animation_frame"]
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)
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iterables = ()
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if animation_frame is not None:
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iterables += (range(nslices_animation),)
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if facet_col is not None:
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iterables += (range(nslices_facet),)
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# Default behaviour of binary_string: True for RGB images, False for 2D
|
||
|
|
if binary_string is None:
|
||
|
|
binary_string = img.ndim >= (3 + slice_dimensions) and not is_dataframe
|
||
|
|
|
||
|
|
# Cast bools to uint8 (also one byte)
|
||
|
|
if img.dtype == bool:
|
||
|
|
img = 255 * img.astype(np.uint8)
|
||
|
|
|
||
|
|
if range_color is not None:
|
||
|
|
zmin = range_color[0]
|
||
|
|
zmax = range_color[1]
|
||
|
|
|
||
|
|
# -------- Contrast rescaling: either minmax or infer ------------------
|
||
|
|
if contrast_rescaling is None:
|
||
|
|
contrast_rescaling = "minmax" if img.ndim == (2 + slice_dimensions) else "infer"
|
||
|
|
|
||
|
|
# We try to set zmin and zmax only if necessary, because traces have good defaults
|
||
|
|
if contrast_rescaling == "minmax":
|
||
|
|
# When using binary_string and minmax we need to set zmin and zmax to rescale the image
|
||
|
|
if (zmin is not None or binary_string) and zmax is None:
|
||
|
|
zmax = img.max()
|
||
|
|
if (zmax is not None or binary_string) and zmin is None:
|
||
|
|
zmin = img.min()
|
||
|
|
else:
|
||
|
|
# For uint8 data and infer we let zmin and zmax to be None if passed as None
|
||
|
|
if zmax is None and img.dtype != np.uint8:
|
||
|
|
zmax = _infer_zmax_from_type(img)
|
||
|
|
if zmin is None and zmax is not None:
|
||
|
|
zmin = 0
|
||
|
|
|
||
|
|
# For 2d data, use Heatmap trace, unless binary_string is True
|
||
|
|
if img.ndim == 2 + slice_dimensions and not binary_string:
|
||
|
|
y_index = slice_dimensions
|
||
|
|
if y is not None and img.shape[y_index] != len(y):
|
||
|
|
raise ValueError(
|
||
|
|
"The length of the y vector must match the length of the first "
|
||
|
|
+ "dimension of the img matrix."
|
||
|
|
)
|
||
|
|
x_index = slice_dimensions + 1
|
||
|
|
if x is not None and img.shape[x_index] != len(x):
|
||
|
|
raise ValueError(
|
||
|
|
"The length of the x vector must match the length of the second "
|
||
|
|
+ "dimension of the img matrix."
|
||
|
|
)
|
||
|
|
|
||
|
|
texttemplate = None
|
||
|
|
if text_auto is True:
|
||
|
|
texttemplate = "%{z}"
|
||
|
|
elif text_auto is not False:
|
||
|
|
texttemplate = "%{z:" + text_auto + "}"
|
||
|
|
|
||
|
|
traces = [
|
||
|
|
go.Heatmap(
|
||
|
|
x=x,
|
||
|
|
y=y,
|
||
|
|
z=img[index_tup],
|
||
|
|
coloraxis="coloraxis1",
|
||
|
|
name=str(i),
|
||
|
|
texttemplate=texttemplate,
|
||
|
|
)
|
||
|
|
for i, index_tup in enumerate(itertools.product(*iterables))
|
||
|
|
]
|
||
|
|
autorange = True if origin == "lower" else "reversed"
|
||
|
|
layout = dict(yaxis=dict(autorange=autorange))
|
||
|
|
if aspect == "equal":
|
||
|
|
layout["xaxis"] = dict(scaleanchor="y", constrain="domain")
|
||
|
|
layout["yaxis"]["constrain"] = "domain"
|
||
|
|
colorscale_validator = ColorscaleValidator("colorscale", "imshow")
|
||
|
|
layout["coloraxis1"] = dict(
|
||
|
|
colorscale=colorscale_validator.validate_coerce(
|
||
|
|
args["color_continuous_scale"]
|
||
|
|
),
|
||
|
|
cmid=color_continuous_midpoint,
|
||
|
|
cmin=zmin,
|
||
|
|
cmax=zmax,
|
||
|
|
)
|
||
|
|
if labels["color"]:
|
||
|
|
layout["coloraxis1"]["colorbar"] = dict(title_text=labels["color"])
|
||
|
|
|
||
|
|
# For 2D+RGB data, use Image trace
|
||
|
|
elif (
|
||
|
|
img.ndim >= 3
|
||
|
|
and (img.shape[-1] in [3, 4] or slice_dimensions and binary_string)
|
||
|
|
) or (img.ndim == 2 and binary_string):
|
||
|
|
rescale_image = True # to check whether image has been modified
|
||
|
|
if zmin is not None and zmax is not None:
|
||
|
|
zmin, zmax = (
|
||
|
|
_vectorize_zvalue(zmin, mode="min"),
|
||
|
|
_vectorize_zvalue(zmax, mode="max"),
|
||
|
|
)
|
||
|
|
x0, y0, dx, dy = (None,) * 4
|
||
|
|
error_msg_xarray = (
|
||
|
|
"Non-numerical coordinates were passed with xarray `img`, but "
|
||
|
|
"the Image trace cannot handle it. Please use `binary_string=False` "
|
||
|
|
"for 2D data or pass instead the numpy array `img.values` to `px.imshow`."
|
||
|
|
)
|
||
|
|
if x is not None:
|
||
|
|
x = np.asanyarray(x)
|
||
|
|
if np.issubdtype(x.dtype, np.number):
|
||
|
|
x0 = x[0]
|
||
|
|
dx = x[1] - x[0]
|
||
|
|
else:
|
||
|
|
error_msg = (
|
||
|
|
error_msg_xarray
|
||
|
|
if img_is_xarray
|
||
|
|
else (
|
||
|
|
"Only numerical values are accepted for the `x` parameter "
|
||
|
|
"when an Image trace is used."
|
||
|
|
)
|
||
|
|
)
|
||
|
|
raise ValueError(error_msg)
|
||
|
|
if y is not None:
|
||
|
|
y = np.asanyarray(y)
|
||
|
|
if np.issubdtype(y.dtype, np.number):
|
||
|
|
y0 = y[0]
|
||
|
|
dy = y[1] - y[0]
|
||
|
|
else:
|
||
|
|
error_msg = (
|
||
|
|
error_msg_xarray
|
||
|
|
if img_is_xarray
|
||
|
|
else (
|
||
|
|
"Only numerical values are accepted for the `y` parameter "
|
||
|
|
"when an Image trace is used."
|
||
|
|
)
|
||
|
|
)
|
||
|
|
raise ValueError(error_msg)
|
||
|
|
if binary_string:
|
||
|
|
if zmin is None and zmax is None: # no rescaling, faster
|
||
|
|
img_rescaled = img
|
||
|
|
rescale_image = False
|
||
|
|
elif img.ndim == 2 + slice_dimensions: # single-channel image
|
||
|
|
img_rescaled = rescale_intensity(
|
||
|
|
img, in_range=(zmin[0], zmax[0]), out_range=np.uint8
|
||
|
|
)
|
||
|
|
else:
|
||
|
|
img_rescaled = np.stack(
|
||
|
|
[
|
||
|
|
rescale_intensity(
|
||
|
|
img[..., ch],
|
||
|
|
in_range=(zmin[ch], zmax[ch]),
|
||
|
|
out_range=np.uint8,
|
||
|
|
)
|
||
|
|
for ch in range(img.shape[-1])
|
||
|
|
],
|
||
|
|
axis=-1,
|
||
|
|
)
|
||
|
|
img_str = [
|
||
|
|
image_array_to_data_uri(
|
||
|
|
img_rescaled[index_tup],
|
||
|
|
backend=binary_backend,
|
||
|
|
compression=binary_compression_level,
|
||
|
|
ext=binary_format,
|
||
|
|
)
|
||
|
|
for index_tup in itertools.product(*iterables)
|
||
|
|
]
|
||
|
|
|
||
|
|
traces = [
|
||
|
|
go.Image(source=img_str_slice, name=str(i), x0=x0, y0=y0, dx=dx, dy=dy)
|
||
|
|
for i, img_str_slice in enumerate(img_str)
|
||
|
|
]
|
||
|
|
else:
|
||
|
|
colormodel = "rgb" if img.shape[-1] == 3 else "rgba256"
|
||
|
|
traces = [
|
||
|
|
go.Image(
|
||
|
|
z=img[index_tup],
|
||
|
|
zmin=zmin,
|
||
|
|
zmax=zmax,
|
||
|
|
colormodel=colormodel,
|
||
|
|
x0=x0,
|
||
|
|
y0=y0,
|
||
|
|
dx=dx,
|
||
|
|
dy=dy,
|
||
|
|
)
|
||
|
|
for index_tup in itertools.product(*iterables)
|
||
|
|
]
|
||
|
|
layout = {}
|
||
|
|
if origin == "lower" or (dy is not None and dy < 0):
|
||
|
|
layout["yaxis"] = dict(autorange=True)
|
||
|
|
if dx is not None and dx < 0:
|
||
|
|
layout["xaxis"] = dict(autorange="reversed")
|
||
|
|
else:
|
||
|
|
raise ValueError(
|
||
|
|
"px.imshow only accepts 2D single-channel, RGB or RGBA images. "
|
||
|
|
"An image of shape %s was provided. "
|
||
|
|
"Alternatively, 3- or 4-D single or multichannel datasets can be "
|
||
|
|
"visualized using the `facet_col` or/and `animation_frame` arguments."
|
||
|
|
% str(img.shape)
|
||
|
|
)
|
||
|
|
|
||
|
|
# Now build figure
|
||
|
|
col_labels = []
|
||
|
|
if facet_col is not None:
|
||
|
|
slice_label = (
|
||
|
|
"facet_col" if labels.get("facet_col") is None else labels["facet_col"]
|
||
|
|
)
|
||
|
|
col_labels = [f"{slice_label}={i}" for i in facet_slices]
|
||
|
|
fig = init_figure(args, "xy", [], nrows, ncols, col_labels, [])
|
||
|
|
for attr_name in ["height", "width"]:
|
||
|
|
if args[attr_name]:
|
||
|
|
layout[attr_name] = args[attr_name]
|
||
|
|
if args["title"]:
|
||
|
|
layout["title_text"] = args["title"]
|
||
|
|
elif args["template"].layout.margin.t is None:
|
||
|
|
layout["margin"] = {"t": 60}
|
||
|
|
|
||
|
|
frame_list = []
|
||
|
|
for index, trace in enumerate(traces):
|
||
|
|
if (facet_col and index < nrows * ncols) or index == 0:
|
||
|
|
fig.add_trace(trace, row=nrows - index // ncols, col=index % ncols + 1)
|
||
|
|
if animation_frame is not None:
|
||
|
|
for i, index in zip(range(nslices_animation), animation_slices):
|
||
|
|
frame_list.append(
|
||
|
|
dict(
|
||
|
|
data=traces[nslices_facet * i : nslices_facet * (i + 1)],
|
||
|
|
layout=layout,
|
||
|
|
name=str(index),
|
||
|
|
)
|
||
|
|
)
|
||
|
|
if animation_frame:
|
||
|
|
fig.frames = frame_list
|
||
|
|
fig.update_layout(layout)
|
||
|
|
# Hover name, z or color
|
||
|
|
if binary_string and rescale_image and not np.all(img == img_rescaled):
|
||
|
|
# we rescaled the image, hence z is not displayed in hover since it does
|
||
|
|
# not correspond to img values
|
||
|
|
hovertemplate = "%s: %%{x}<br>%s: %%{y}<extra></extra>" % (
|
||
|
|
labels["x"] or "x",
|
||
|
|
labels["y"] or "y",
|
||
|
|
)
|
||
|
|
else:
|
||
|
|
if trace["type"] == "heatmap":
|
||
|
|
hover_name = "%{z}"
|
||
|
|
elif img.ndim == 2:
|
||
|
|
hover_name = "%{z[0]}"
|
||
|
|
elif img.ndim == 3 and img.shape[-1] == 3:
|
||
|
|
hover_name = "[%{z[0]}, %{z[1]}, %{z[2]}]"
|
||
|
|
else:
|
||
|
|
hover_name = "%{z}"
|
||
|
|
hovertemplate = "%s: %%{x}<br>%s: %%{y}<br>%s: %s<extra></extra>" % (
|
||
|
|
labels["x"] or "x",
|
||
|
|
labels["y"] or "y",
|
||
|
|
labels["color"] or "color",
|
||
|
|
hover_name,
|
||
|
|
)
|
||
|
|
fig.update_traces(hovertemplate=hovertemplate)
|
||
|
|
if labels["x"]:
|
||
|
|
fig.update_xaxes(title_text=labels["x"], row=1)
|
||
|
|
if labels["y"]:
|
||
|
|
fig.update_yaxes(title_text=labels["y"], col=1)
|
||
|
|
configure_animation_controls(args, go.Image, fig)
|
||
|
|
fig.update_layout(template=args["template"], overwrite=True)
|
||
|
|
return fig
|