OK, I see what's happening. In your script you're reading the ages from a file with a fixed shape and then passing that fixed shape array back to yt whenever yt calls the _stellar_age field function. That doesn't work because yt field functions operate on chunks of the dataset, not the full dataset, so in order for your field function to work, you need a way to map from particle IDs in the original ramses output file to the particle indexes in the data file you're reading. The error you're getting is telling you that the size of the chunk (1170 particles) does not agree with the size of the stellar_age field returned by your field function (31990).

I'm not sure how you're generating your original fortran file so I don't know if this will necessarily work for you, but I was able to get your output_00080 test script to work by modifying your `_stellar_age` function to look like this:

    def _stellar_age(field, data):
        data_ids = data['stars', 'particle_identity']
        _, mask, _ = np.intersect1d(ids, data_ids, return_indices=True)
        return YTArray(ages[mask], "Myr")
    ds.add_field(("stars", "star_age"), function=_stellar_age,
               units="Myr", particle_type=True, force_override=True)

See the documentation for intersect1d to see what I'm doing here to get the indices of the overlaps:

https://docs.scipy.org/doc/numpy-1.15.0/reference/generated/numpy.intersect1d.html

On Wed, Feb 6, 2019 at 3:40 AM <lhw28@cam.ac.uk> wrote:

Hi again Nathan,

I have modified my script to run on the output_00080 cosmological RAMSES run from http://yt-project.org/data/.
The script is uploaded with link: http://use.yt/upload/9d91ea29.

When I run this example I get a similar traceback:

Traceback (most recent call last):
File "/home/lhw28/.local/lib/python3.6/site-packages/yt/data_objects/data_containers.py", line 308, in _generate_fluid_field
finfo.check_available(gen_obj)
File "/home/lhw28/.local/lib/python3.6/site-packages/yt/fields/derived_field.py", line 204, in check_available
validator(data)
File "/home/lhw28/.local/lib/python3.6/site-packages/yt/fields/derived_field.py", line 470, in __call__
raise NeedsGridType(self.ghost_zones,self.fields)
yt.fields.field_exceptions.NeedsGridType: (0, None)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "yt_issue.py", line 58, in <module>
center=centre, data_source=box)
File "/home/lhw28/.local/lib/python3.6/site-packages/yt/data_objects/construction_data_containers.py", line 270, in __init__
self.get_data(field)
File "/home/lhw28/.local/lib/python3.6/site-packages/yt/data_objects/construction_data_containers.py", line 344, in get_data
self._handle_chunk(chunk, fields, tree)
File "/home/lhw28/.local/lib/python3.6/site-packages/yt/data_objects/construction_data_containers.py", line 450, in _handle_chunk
d = chunk[field] * dl
File "/home/lhw28/.local/lib/python3.6/site-packages/yt/data_objects/data_containers.py", line 255, in __getitem__
self.get_data(f)
File "/home/lhw28/.local/lib/python3.6/site-packages/yt/data_objects/data_containers.py", line 1382, in get_data
self._generate_fields(fields_to_generate)
File "/home/lhw28/.local/lib/python3.6/site-packages/yt/data_objects/data_containers.py", line 1402, in _generate_fields
fd = self._generate_field(field)
File "/home/lhw28/.local/lib/python3.6/site-packages/yt/data_objects/data_containers.py", line 292, in _generate_field
tr = self._generate_fluid_field(field)
File "/home/lhw28/.local/lib/python3.6/site-packages/yt/data_objects/data_containers.py", line 310, in _generate_fluid_field
rv = self._generate_spatial_fluid(field, ngt_exception.ghost_zones)
File "/home/lhw28/.local/lib/python3.6/site-packages/yt/data_objects/data_containers.py", line 330, in _generate_spatial_fluid
ind += o.select(self.selector, self[field], rv, ind)
File "/home/lhw28/.local/lib/python3.6/site-packages/yt/data_objects/data_containers.py", line 255, in __getitem__
self.get_data(f)
File "/home/lhw28/.local/lib/python3.6/site-packages/yt/data_objects/data_containers.py", line 1382, in get_data
self._generate_fields(fields_to_generate)
File "/home/lhw28/.local/lib/python3.6/site-packages/yt/data_objects/data_containers.py", line 1402, in _generate_fields
fd = self._generate_field(field)
File "/home/lhw28/.local/lib/python3.6/site-packages/yt/data_objects/data_containers.py", line 292, in _generate_field
tr = self._generate_fluid_field(field)
File "/home/lhw28/.local/lib/python3.6/site-packages/yt/data_objects/data_containers.py", line 312, in _generate_fluid_field
rv = finfo(gen_obj)
File "/home/lhw28/.local/lib/python3.6/site-packages/yt/fields/derived_field.py", line 256, in __call__
dd = self._function(self, data)
File "/home/lhw28/.local/lib/python3.6/site-packages/yt/fields/particle_fields.py", line 133, in particle_density
pos = data[ptype, coord_name].convert_to_units("code_length")
File "/home/lhw28/.local/lib/python3.6/site-packages/yt/data_objects/octree_subset.py", line 73, in __getitem__
tr = super(OctreeSubset, self).__getitem__(key)
File "/home/lhw28/.local/lib/python3.6/site-packages/yt/data_objects/data_containers.py", line 255, in __getitem__
self.get_data(f)
File "/home/lhw28/.local/lib/python3.6/site-packages/yt/data_objects/data_containers.py", line 1325, in get_data
self.get_data(apply_fields[filter_type])
File "/opt/ioa/software/anaconda/anaconda36/envs/20181213_2_py36/lib/python3.6/contextlib.py", line 88, in __exit__
next(self.gen)
File "/home/lhw28/.local/lib/python3.6/site-packages/yt/data_objects/particle_filters.py", line 53, in apply
raise YTIllDefinedFilter(self, tr.shape, filter.shape)
yt.utilities.exceptions.YTIllDefinedFilter: Filter '<yt.data_objects.particle_filters.ParticleFilter object at 0x7f25c23609e8>' ill-defined. Applied to shape (1175, 3) but is shape (31990,).

I realised I never mentioned what version of YT I am using. In case it's important, it's 3.5.0. (And I'm using Python 3.6.3).

Thanks for your help,
Lewis
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