"""
.. _image_representations_example:

Image Data Representations
~~~~~~~~~~~~~~~~~~~~~~~~~~
This example demonstrates how to use :meth:`~pyvista.ImageDataFilters.points_to_cells`
and :meth:`~pyvista.ImageDataFilters.cells_to_points` to re-mesh
:class:`~pyvista.ImageData`.

These filters can be used to ensure that image data has an appropriate representation
when generating plots and/or when using either point- or cell-based filters such as
:meth:`ImageDataFilters.image_threshold <pyvista.ImageDataFilters.image_threshold>`
(point-based) and
:meth:`DataSetFilters.threshold <pyvista.DataSetFilters.threshold>` (cell-based).

"""

# %%#
# Representations of 3D Volumes
# -----------------------------
# Create image data of a 3D volume with eight points and a discrete scalar data
# array.
import numpy as np
import pyvista as pv

# sphinx_gallery_thumbnail_number = 3


data_array = [8, 7, 6, 5, 4, 3, 2, 1]
points_volume = pv.ImageData(dimensions=(2, 2, 2))
points_volume.point_data['Data'] = data_array

# %%#
# If we plot the volume, it is represented as a single cell with eight points,
# and the point data is interpolated to color the cell.

points_volume.plot(show_edges=True)

# %%#
# However, in many applications (e.g. 3D medical imaging), the scalar data arrays
# represent discretized samples at the centers of voxels. As such, it may
# be more appropriate to represent the data as eight voxel cells instead of
# eight points. We can use :meth:`~pyvista.ImageDataFilters.points_to_cells` to
# generate a cell-based representation.

cells_volume = points_volume.points_to_cells()

# %%#
# Now, when we plot the volume, we have a more appropriate representation with
# eight voxel cells and the scalar data is no longer interpolated.

cells_volume.plot(show_edges=True)

# %%#
# Let's plot the two representations together for comparison.
#
# For visualization, we color the points volume (inner mesh) and only show the edges
# of the cells volume (outer mesh). We also plot the cell centers in red. Note
# how the centers of the image of the cells correspond to the points of the points image.

cell_centers = cells_volume.cell_centers()
cell_edges = cells_volume.extract_all_edges()

pl = pv.Plotter()
pl.add_mesh(points_volume, color=True, show_edges=True, opacity=0.7)
pl.add_mesh(cell_edges, color='black', line_width=2)
pl.add_points(
    cell_centers,
    render_points_as_spheres=True,
    color='red',
    point_size=20,
)
pl.camera.azimuth = -25
pl.camera.elevation = 25
pl.show()

# %%#
# As long as only one kind of scalar data is used (i.e. either point or cell
# data, but not both), it is possible to move between representations without
# loss of data.

array_before = points_volume.active_scalars
array_after = points_volume.points_to_cells().cells_to_points().active_scalars
np.array_equal(array_before, array_after)

# %%#
# Point Filters with Image Data
# -----------------------------
# Use a point representation of the image when working with point-based
# filters such as :meth:`~pyvista.ImageDataFilters.image_threshold`. If the
# image only has cell data, use :meth:`~pyvista.ImageDataFilters.cells_to_points`
# re-mesh the input first. Here, we reuse the point-based image defined earlier.
#
# For context, we first show the input data array.

points_volume.point_data['Data']

# %%#
# Now apply the filter and print the result.

points_ithresh = points_volume.image_threshold(2)
points_ithresh.point_data['Data']

# %%#
# The filter returns binary point data as expected. Values equal to or greater
# or than the threshold of ``2`` are ones and less than the threshold are zeros.
#
# However, in plotting it, the point values are linearly interpolated. For
# visualizing binary data, this interpolation is not desirable.

points_ithresh.plot(show_edges=True)

# %%#
# To better visualize the result, convert the image of the point returned by the
# filter to a cell representation with :meth:`~pyvista.ImageDataFilters.points_to_cells`
# before plotting.

points_ithresh_as_cells = points_ithresh.points_to_cells()
points_ithresh_as_cells.plot(show_edges=True)

# %%#
# The binary data is now correctly visualized as binary data.

# %%#
# Cell Filters with Image Data
# ----------------------------
# Use a cell representation of the image when working with cell-based filters
# such as :meth:`~pyvista.DataSetFilters.threshold`. If the image only has point
# data, use :meth:`~pyvista.ImageDataFilters.points_to_cells` to re-mesh the
# input first. Here, we reuse the cell-based image created earlier.
#
# For context, we first show the input data array.

cells_volume.cell_data['Data']

# %%#
# Now apply the filter and print the result.

cells_thresh = cells_volume.threshold(2)
cells_thresh.cell_data['Data']

# %%#
# When the input is cell data, this filter returns seven discrete values greater
# than or equal to the threshold value of ``2`` as expected.
#
# If we plot the result, the cells also produce the correct visualization.

cells_thresh.plot(show_edges=True)

# %%#
# However, if we apply the same filter to a point-based representation of the
# image, the filter does not produce the desired result.

points_thresh = points_volume.threshold(2)
points_thresh.point_data['Data']

# %%#
# In this case, since the image of the point only has a single cell, the filter has no
# effect on the data array's values. The thresholded values are the same as the
# input values.
#
# Plotting the result confirms this. The plot is identical to the initial plot
# of the point-based image shown at the beginning of this example.

points_thresh.plot(show_edges=True)

# %%#
# Representations of 2D Images
# ----------------------------
# The filters :meth:`~pyvista.ImageDataFilters.points_to_cells` and
# :meth:`~pyvista.ImageDataFilters.cells_to_points` can similarly be used
# with 2D images.
#
# For this example, we create a 4x4 2D grayscale image with 16 points to represent
# 16 pixels.

data_array = np.linspace(0, 255, 16, dtype=np.uint8)[::-1]
points_image = pv.ImageData(dimensions=(4, 4, 1))
points_image.point_data['Data'] = data_array

# %%#
# Plot the image. As before, the plot does not appear correct since the point
# data is interpolated, and nine cells are shown rather than the desired 16
# (one for each pixel).

plot_kwargs = dict(
    cpos='xy',
    zoom='tight',
    show_axes=False,
    cmap='gray',
    clim=[0, 255],
    show_edges=True,
)
points_image.plot(**plot_kwargs)

# %%#
# To visualize the image correctly, we first use
# :meth:`~pyvista.ImageDataFilters.points_to_cells` to get a cell-based representation of
# the image and plot the result. The plot now correctly shows 16-pixel cells with discrete
# values.

cells_image = points_image.points_to_cells()
cells_image.plot(**plot_kwargs)

# %%#
# Let's plot the two representations together for comparison.
#
# For visualization, we color the points image (inner mesh) and show the cells
# image (outer mesh) as a wireframe. We also plot the cell centers in red. Note
# how the centers of the image of the cells correspond to the points of the points image.

cell_centers = cells_image.cell_centers()

pl = pv.Plotter()
pl.add_mesh(points_image, color=True, opacity=0.7)
pl.add_mesh(cells_image, style='wireframe', color='black', line_width=2)
pl.add_points(
    cell_centers,
    render_points_as_spheres=True,
    color='red',
    point_size=20,
)
pl.view_xy()
pl.show()
# %%
# .. tags:: filter
