"""
.. _opacity_example:

Plot with Opacity
~~~~~~~~~~~~~~~~~

Plot a mesh's scalar array with an :class:`~pyvista.opacity_transfer_function`
or opacity mapping based on a scalar array.
"""

# sphinx_gallery_thumbnail_number = 2
import pyvista as pv
from pyvista import examples

# Load St Helens DEM and warp the topography
image = examples.download_st_helens()
mesh = image.warp_by_scalar()


# %%
# Global Value
# ++++++++++++
#
# You can also apply a global opacity value to the mesh by passing a single
# float between 0 and 1 which would enable you to see objects behind the mesh:

pl = pv.Plotter()
pl.add_mesh(
    image.contour(),
    line_width=5,
)
pl.add_mesh(mesh, opacity=0.85, color=True)
pl.show()

# %%
# Note that you can specify ``use_transparency=True`` to convert opacities to
# transparencies in any of the following examples.


# %%
# Transfer Functions
# ++++++++++++++++++
#
# It's possible to apply an opacity mapping to any scalar array plotted. You
# can specify either a single static value to make the mesh transparent on all
# cells, or use a transfer function where the scalar array plotted is mapped
# to the opacity. We have several predefined transfer functions.
#
# Opacity transfer functions are:
#
# - ``'linear'``: linearly vary (increase) opacity across the plotted scalar
#   range from low to high
# - ``'linear_r'``: linearly vary (increase) opacity across the plotted scalar
#   range from high to low
# - ``'geom'``: on a log scale, vary (increase) opacity across the plotted scalar
#   range from low to high
# - ``'geom_r'``: on a log scale, vary (increase) opacity across the plotted scalar
#   range from high to low
# - ``'sigmoid'``: vary (increase) opacity on a sigmoidal s-curve across the plotted
#   scalar range from low to high
# - ``'sigmoid_r'``: vary (increase) opacity on a sigmoidal s-curve across the plotted
#   scalar range from high to low

# Show the linear opacity transfer function
mesh.plot(opacity='linear')

# %%

# Show the sigmoid opacity transfer function
mesh.plot(opacity='sigmoid')

# %%
# It's also possible to use your own transfer function that will be linearly
# mapped to the scalar array plotted. For example, we can create an opacity
# mapping as:
opacity = [0, 0.2, 0.9, 0.6, 0.3]

# %%
# When given a minimized opacity mapping like that above, PyVista interpolates
# it across a range of how many colors are shown when mapping the scalars.
# Linear interpolation is used by default, but other kinds of interpolation
# can be used if ``scipy`` is available.
# Curious what that opacity transfer function looks like? You can fetch it:

# Have PyVista interpolate the transfer function
tf = pv.opacity_transfer_function(opacity, 256).astype(float) / 255.0

import matplotlib.pyplot as plt

plt.plot(tf)
plt.title('My Interpolated Opacity Transfer Function')
plt.ylabel('Opacity')
plt.xlabel('Index along scalar mapping')
plt.show()

# %%
# That opacity mapping will have an opacity of 0.0 at the minimum scalar range,
# a value or 0.9 at the middle of the scalar range, and a value of 0.3 at the
# maximum of the scalar range:

mesh.plot(opacity=opacity)

# %%
# Opacity mapping is often useful when plotting DICOM images. For example,
# download the sample knee DICOM image:
knee = examples.download_knee()

# %%
# And here we inspect the DICOM image with a few different opacity mappings:
pl = pv.Plotter(shape=(2, 2), border=False)

pl.add_mesh(knee, cmap='bone', scalar_bar_args={'title': 'No Opacity'})
pl.view_xy()

pl.subplot(0, 1)
pl.add_mesh(
    knee, cmap='bone', opacity='linear', scalar_bar_args={'title': 'Linear Opacity'}
)
pl.view_xy()

pl.subplot(1, 0)
pl.add_mesh(
    knee, cmap='bone', opacity='sigmoid', scalar_bar_args={'title': 'Sigmoidal Opacity'}
)
pl.view_xy()

pl.subplot(1, 1)
pl.add_mesh(
    knee, cmap='bone', opacity='geom_r', scalar_bar_args={'title': 'Log Scale Opacity'}
)
pl.view_xy()


pl.show()

# %%
# Opacity by Array
# ++++++++++++++++
#
# You can also use a scalar array associated with the mesh to give each cell
# its own opacity/transparency value derived from a scalar field. For example,
# an uncertainty array from a modelling result could be used to hide regions of
# a mesh that are uncertain and highlight regions that are well resolved.
#
# The following is a demonstration of plotting a mesh with colored values and
# using a second array to control the transparency of the mesh

model = examples.download_model_with_variance()
contours = model.contour(10, scalars='Temperature')
contours.array_names

# %%
# Make sure to flag ``use_transparency=True`` since we want areas of high
# variance to have high transparency.
#
# Also, since the opacity array must be between 0 and 1, we normalize
# the temperature variance array by the maximum value.  That way high
# variance will be completely transparent.

contours['Temperature_var'] /= contours['Temperature_var'].max()

pl = pv.Plotter(shape=(1, 2))

pl.subplot(0, 0)
pl.add_text('Opacity by Array')
pl.add_mesh(
    contours.copy(),
    scalars='Temperature',
    opacity='Temperature_var',
    use_transparency=True,
    cmap='bwr',
)

pl.subplot(0, 1)
pl.add_text('No Opacity')
pl.add_mesh(contours, scalars='Temperature', cmap='bwr')
pl.show()
# %%
# .. tags:: plot
