region_str: TypeError: 'numpy.bool' object cannot be interpreted as an integer

[Firestar-Reimu]

import astropy.units as u
from spectral_cube import SpectralCube as sc

file = "HI4PI_RA60_80_DEC-13_2.fits"
cube = sc.read(file)

region_str = "fk5; circle(70, -5, 0.1)"
sub_cube = cube.subcube_from_ds9region(region_str)

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
Cell In[14], [line 2](vscode-notebook-cell:?execution_count=14&line=2)
      1 region_str = "fk5; circle(70, -5, 0.1)"
----> [2](vscode-notebook-cell:?execution_count=14&line=2) sub_cube = cube.subcube_from_ds9region(region_str)

File ~/.miniconda/lib/python3.13/site-packages/spectral_cube/spectral_cube.py:2058, in BaseSpectralCube.subcube_from_ds9region(self, ds9_region, allow_empty)
   2055 else:
   2056     raise TypeError("{0} should be a DS9 string".format(ds9_region))
-> [2058](https://untitled+.vscode-resource.vscode-cdn.net/~/.miniconda/lib/python3.13/site-packages/spectral_cube/spectral_cube.py:2058) return self.subcube_from_regions(region_list, allow_empty)

File ~/.miniconda/lib/python3.13/site-packages/spectral_cube/spectral_cube.py:2166, in BaseSpectralCube.subcube_from_regions(self, region_list, allow_empty, minimize)
   2163 # by using ceil / floor above, we potentially introduced a NaN buffer
   2164 # that we can now crop out
   2165 if minimize:
-> [2166](https://untitled+.vscode-resource.vscode-cdn.net/~/.miniconda/lib/python3.13/site-packages/spectral_cube/spectral_cube.py:2166)     return masked_subcube.minimal_subcube(spatial_only=True)
   2167 else:
   2168     return masked_subcube

File ~/.miniconda/lib/python3.13/site-packages/spectral_cube/spectral_cube.py:1890, in BaseSpectralCube.minimal_subcube(self, spatial_only)
   1881 """
   1882 Return the minimum enclosing subcube where the mask is valid
   1883 
   (...)   1887     Only compute the minimal subcube in the spatial dimensions
   1888 """
   1889 if self._mask is not None:
-> [1890](https://untitled+.vscode-resource.vscode-cdn.net/~/.miniconda/lib/python3.13/site-packages/spectral_cube/spectral_cube.py:1890)     return self[self.subcube_slices_from_mask(self._mask,
   1891                                               spatial_only=spatial_only)]
   1892 else:
   1893     return self[:]

File ~/.miniconda/lib/python3.13/site-packages/spectral_cube/spectral_cube.py:1936, in BaseSpectralCube.subcube_slices_from_mask(self, region_mask, spatial_only)
   1933 if not include.any():
   1934     return (slice(0),)*3
-> [1936](https://untitled+.vscode-resource.vscode-cdn.net/~/.miniconda/lib/python3.13/site-packages/spectral_cube/spectral_cube.py:1936) slices = ndimage.find_objects(np.broadcast_arrays(include,
   1937                                                   self._data)[0])[0]
   1939 if spatial_only:
   1940     slices = (slice(None), slices[1], slices[2])

File ~/.miniconda/lib/python3.13/site-packages/scipy/ndimage/_measurements.py:308, in find_objects(input, max_label)
    305 if max_label < 1:
    306     max_label = input.max()
--> [308](https://untitled+.vscode-resource.vscode-cdn.net/~/.miniconda/lib/python3.13/site-packages/scipy/ndimage/_measurements.py:308) return _nd_image.find_objects(input, max_label)

TypeError: 'numpy.bool' object cannot be interpreted as an integer

[Firestar-Reimu]

I don't know why this code turns error, this code ran well 2 weeks ago

I don't know what is wrong with this region_str

[Firestar-Reimu]

I test this on my old computer and I confirmed that one of the packages update cause this issue

after I downgraded scipy astropy and numpy I find

It is numpy

numpy 2.2.4 --> numpy 2.3.0

[Firestar-Reimu]

/home/firestar/.miniforge/lib/python3.13/site-packages/scipy/ndimage/_measurements.py:308:
DeprecationWarning: In future, it will be an error for 'np.bool' scalars to be interpreted as an index
  return _nd_image.find_objects(input, max_label)

scipy/scipy#23455

[Firestar-Reimu]

Solved, you have edited your code in f95ba1c#diff-4c5d229004bd151b9b974549d135ab1ef9959aa6126188c21624b5448b283d7c but you have not released to pip/conda-forge

and I am still using the 0.6.6 version in January

[Firestar-Reimu]

When will the next version be released?

[e-koch]

Hi @Firestar-Reimu -- thanks for following up! I suggest sticking to the current main branch for now. We'll have a release in the coming month.

[fastradiobeth]

Checking in on this thread - I also came across the same problem a few weeks ago. Has this been resolved in 0.6.7?

[Firestar-Reimu]

I think it is resolved, checked with numpy 2.3.5 and spectral-cube 0.6.7