Comments (3)
This seems to be a known issue/decision with the handling of ExtensionDtypes
. Here's a related issue in the pandas repo: pandas-dev/pandas#22791.
This does not seem to be an issue in our specific implementation of the various MTZDtypes
because it also occurs for the pd.Int32Dtype
(which is also implemented as an ExtensionDtype
):
import reciprocalspaceship as rs
import numpy as np
import pandas as pd
ds = rs.DataSet({
"X" : np.arange(100),
"Y" : np.arange(100)
},
dtype=pd.Int32Dtype()
)
print(f"ds.dtypes:\n{ds.dtypes}\n")
print(f"ds[['X', 'Y']].to_numpy().dtype:\n {ds[['X', 'Y']].to_numpy().dtype}")
Output:
ds.dtypes:
X Int32
Y Int32
dtype: object
ds[['X', 'Y']].to_numpy().dtype:
object
from reciprocalspaceship.
Tracing the method calls, it seems that this eventually comes to here: https://github.com/pandas-dev/pandas/blob/122d50246bcffcf8c3f252146340ac02676a5bf6/pandas/core/dtypes/cast.py#L1501
It may be possible to implement our own logic for how various dtypes
get combined by implementing our own MTZDtype._get_common_dtype(types)
method.
My proposed logic for handling this would be the following:
if
all dtypes areisinstance(dtype, MTZInt32Dtype)
and have no NaNs, usenp.int32
elif
all dtypes areisinstance(dtype, MTZDtype)
, usenp.float32
else
use object
Since MTZ files are all backed by float32, it seems that we should be able to safely fall back to such a case when all dtypes are MTZDtypes
from reciprocalspaceship.
also related: pandas-dev/pandas#22224
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Related Issues (20)
- Cannot unstack_anomalous with other columns in index
- groupby apply drops cell and spacegroup HOT 2
- `stack_anomalous` inside `groupby` breaks `as_index=False` HOT 1
- Unstack anomalous taking into account Careless repeats HOT 10
- rs.utils.asu.in_asu() does not use the 'anomalous ASU' for stacked anomalous data. HOT 1
- function for cif file IO and possible support for multi-dataset files HOT 3
- `hkl_to_asu` does not annotate M/ISYM field correctly HOT 2
- support for read_precognition() for hkl without anomalous columns HOT 6
- unstack_anomalous makes data that phenix cannot interpret HOT 3
- API reference website display
- Return keys of dictionary in crystfel.py HOT 8
- add_rfree() does not consider Friedel mates HOT 2
- `rs.DataSet.reset_index()` call signature does not match pandas >1.5 HOT 1
- Used pandas.core.ops attribute does not appear to exist HOT 4
- A `rs.cifdump` utility? HOT 1
- No documentation of CrystFEL columns HOT 1
- mean_intensity_by_miller_index should use a grid HOT 1
- write_mtz SettingWithCopyWarning HOT 2
- Failure to correctly read Miller indices from cctbx-generated MTZ HOT 8
- RS requires set_index(["H","K","L"]) to create a multi_index using rs.DataSet HOT 5
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