FIX NaN values in Volume/Vertex rendering as black instead of transparent

[Copilot]

NaN values in Volume.raw / Vertex.raw render as opaque black instead of transparent. After colormap conversion to uint8, NaN information is lost, so the alpha getter's np.isnan(rgb) check on uint8 data is always False. Additionally, Vertex objects with NaN data render as colored (not transparent) in the WebGL viewer due to missing NaN detection in the surface_vertex shader.

vtx = cortex.Vertex(data_with_nans, subject, vmin=-2, vmax=2, cmap="RdBu_r")
raw = vtx.raw
raw.alpha = np.ones(n_verts) * 0.8  # NaN positions rendered as black

Changes

• Dataview.raw: Capture NaN mask before uint8 conversion, explicitly zero out alpha for NaN positions
• Volume.raw / Vertex.raw: Store _nan_mask on the returned RGB object so it survives alpha overrides
• VolumeRGB.alpha / VertexRGB.alpha getters: Apply stored _nan_mask to enforce alpha=0 for NaN positions, even after user sets a custom alpha channel
• surface_vertex WebGL shader: Add NaN detection in the colormap lookup using the GLSL idiom cuv.x != cuv.x. When vertex data is NaN, set vColor = vec4(0.) so the fragment shader discards the vertex. Handles both 1D and 2D cases. The surface_pixel shader already had NaN detection via colorlut(), but surface_vertex was missing it.
• Tests: Four new tests covering default and user-overridden alpha for both Volume and Vertex

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[mvdoc]

This is possibly related to #455

[mvdoc]

@copilot check if issue #455 is related and if so address both

[Copilot]

@copilot check if issue #455 is related and if so address both

Yes, issue #455 is directly related. It describes two problems:

1. VertexRGB NaN values show as black on quickflat — Already fixed by this PR's Python-side changes (capturing NaN mask before uint8 conversion and enforcing alpha=0).

2. Vertex NaN values show as colored (not transparent) on WebGL — The surface_pixel shader already had NaN detection in colorlut() (via the valid check), but the surface_vertex shader was missing it. When data0 is NaN, the colormap coordinate cuv.x becomes NaN, and texture2D with NaN coordinates returns an opaque color instead of transparent.

Fixed in 85f1d5b by adding NaN detection in the surface_vertex shader using the GLSL idiom cuv.x != cuv.x (true only for NaN), which sets vColor = vec4(0.) so the fragment shader's existing if (vColor.a < .001) discard; check properly discards NaN vertices. Also handles the 2D case with a cuv.y check.

[mvdoc]

Visual parity test: Vertex vs VertexRGB, quickshow vs WebGL

Script used to verify NaN transparency works identically across all four combinations:

import cortex
from cortex.export import save_3d_views
import numpy as np
import matplotlib.pyplot as plt

# Build data with NaN in IPS0
np.random.seed(42)
vtx = cortex.Vertex.random("fsaverage", vmin=-2, vmax=2, cmap="RdBu_r")
roi = cortex.get_roi_verts("fsaverage", roi="IPS0")["IPS0"]
vtx.data[roi] = np.nan
vtx_rgb = vtx.raw

# --- quickshow ---
fig_qs_vtx = cortex.quickflat.make_figure(vtx, with_curvature=True)
fig_qs_vtx.savefig("/tmp/nan_parity_quickshow_vertex.png", dpi=100)
plt.close(fig_qs_vtx)

fig_qs_rgb = cortex.quickflat.make_figure(vtx_rgb, with_curvature=True)
fig_qs_rgb.savefig("/tmp/nan_parity_quickshow_vertexrgb.png", dpi=100)
plt.close(fig_qs_rgb)

# --- WebGL headless (flatmap view) ---
save_3d_views(
    vtx,
    base_name="/tmp/nan_parity_webgl_vertex",
    list_angles=["flatmap"],
    list_surfaces=["flatmap"],
    size=(1024, 768),
    headless=True,
    trim=True,
    sleep=5,
)

save_3d_views(
    vtx_rgb,
    base_name="/tmp/nan_parity_webgl_vertexrgb",
    list_angles=["flatmap"],
    list_surfaces=["flatmap"],
    size=(1024, 768),
    headless=True,
    trim=True,
    sleep=5,
)

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