crop(wcs=cube.extra_coords): dummy pixel components leak into points and errors

[nabobalis]

Describe the bug

When cropping with wcs=cube.extra_coords, sanitize_crop_inputs pads each point with None for the dummy PIXEL components ndcube adds for array axes without extra coords. That shows up in a few ways:

1. The count error counts the padding and (with Fix crop world-object order for WCSes with non-contiguous components #977) lists the dummy components. A 1-entry point on a 3-D cube with two extra coords on axis 0 reports "3 components ... 4 components", and passing the 4 listed entries reports "6 components".
2. The correctly sized point [time, None] fails with ValueError: Number of world inputs (1) does not match expected (2) when the extra coords share an array axis. This is the same on main and with Fix crop world-object order for WCSes with non-contiguous components #977.
3. With the class matching from Fix crop world-object order for WCSes with non-contiguous components #977, a wrongly typed Quantity given for a Time extra coord matches the dummy Quantity slot and is moved there. Main raised a clear TypeError; now it raises a UnitConversionError about pix, or, if the unit is pix, crops the dummy axis by pixel index.

One option for 1 and 3: in _get_crop_item, drop the trailing dummy components from the object list and the count, and re-append Nones after matching. That reads the private ExtraCoords._cube_array_axes_without_extra_coords, as sanitize_crop_inputs already does. 2 needs a separate fix in the default crop path.

To Reproduce

import numpy as np

import astropy.units as u
from astropy.time import Time
from astropy.wcs import WCS

from ndcube import NDCube

t = Time("2020-01-01") + np.arange(4) * u.s


def run(cube, label, *points):
    try:
        result = cube.crop(*points, wcs=cube.extra_coords).shape
    except Exception as e:
        result = f"{type(e).__name__}: {e}"
    print(f"{label:28} -> {result}")


# Two extra coords sharing array axis 0 of a 3-D cube.
cube = NDCube(np.zeros((4, 5, 6)), wcs=WCS(naxis=3))
cube.extra_coords.add("time", 0, t)
cube.extra_coords.add("exposure", 0, np.arange(4) * u.s)
run(cube, "[time]", [t[1]], [t[2]])
run(cube, "[time, None]", [t[1], None], [t[2], None])
run(cube, "[time, None, None, None]", [t[1], None, None, None], [t[2], None, None, None])
run(cube, "[time, exposure]", [t[1], 1 * u.s], [t[2], 2 * u.s])

# One time extra coord on array axis 0 of a 2-D cube; a Quantity is the wrong type.
cube = NDCube(np.zeros((4, 5)), wcs=WCS(naxis=2))
cube.extra_coords.add("time", 0, t)
run(cube, "[time]", [t[1]], [t[2]])
run(cube, "[1 pix] (wrong type)", [1 * u.pix], [2 * u.pix])
run(cube, "[1 m] (wrong type)", [1 * u.m], [2 * u.m])

On main (49b70c1):

[time]                       -> ValueError: 3 components in point 0 do not match WCS with 4 components.
[time, None]                 -> ValueError: Number of world inputs (1) does not match expected (2)
[time, None, None, None]     -> ValueError: 6 components in point 0 do not match WCS with 4 components.
[time, exposure]             -> (2, 5, 6)
[time]                       -> (2, 5)
[1 pix] (wrong type)         -> TypeError: <class 'astropy.units.quantity.Quantity'> of component 0 in point 0 is incompatible with WCS component temporal_0 <class 'astropy.time.core.Time'>.
[1 m] (wrong type)           -> TypeError: <class 'astropy.units.quantity.Quantity'> of component 0 in point 0 is incompatible with WCS component temporal_0 <class 'astropy.time.core.Time'>.

With #977:

[time]                       -> ValueError: 3 components in point 0 do not match WCS with 4 components. Each point must have one entry per world object (use None for a component that should not be cropped), in order: temporal_0 (Time), CUSTOM_0 (Quantity), pixel_1 (Quantity), pixel__1 (Quantity).
[time, None]                 -> ValueError: Number of world inputs (1) does not match expected (2)
[time, None, None, None]     -> ValueError: 6 components in point 0 do not match WCS with 4 components. Each point must have one entry per world object (use None for a component that should not be cropped), in order: temporal_0 (Time), CUSTOM_0 (Quantity), pixel_1 (Quantity), pixel__1 (Quantity).
[time, exposure]             -> (2, 5, 6)
[time]                       -> (2, 5)
[1 pix] (wrong type)         -> (4, 2)
[1 m] (wrong type)           -> UnitConversionError: 'm' (length) and 'pix' are not convertible

Screenshots

No response

System Details

• ndcube version: main (49b70c1) and Fix crop world-object order for WCSes with non-contiguous components #977
• astropy version: 7.2.0
• relevant package version(s): numpy 2.4.4, gwcs 1.0.3
• Python version: 3.14.4
• OS information: macOS

Installation method

git checkout