pydata / pydata/xarray

[Question] Efficient shortcut for unstacking only parts of dimension?

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Description

Hi all, is there an efficient way to unstack only parts of a MultiIndex?

Consider for example the following array:

<xarray.Dataset>
Dimensions:                      (observations: 17525)
Coordinates:
  * observations                 (observations) MultiIndex
  - subtissue                    (observations) object 'Skin_Sun_Exposed_Lower_leg' ... 'Thyroid'
  - individual                   (observations) object 'GTEX-111FC' ... 'GTEX-ZZPU'
  - gene                         (observations) object 'ENSG00000140400' ... 'ENSG00000174233'
  - end                          (observations) object '5' '5' '5' ... '3' '3'
Data variables:
    fraser_min_pval              (observations) float64 dask.array<chunksize=(17525,), meta=np.ndarray>
    fraser_min_minus_log10_pval  (observations) float64 dask.array<chunksize=(17525,), meta=np.ndarray>

Here, I have a MultiIndex observations=["subtissue", "individual", "gene", "end"].
However, I would like to have end in its own dimension.
Currently, I have to do the following to solve this issue:

xrds.unstack("observations").stack(observations=["subtissue", "individual", "gene",])

However, this seems quite inefficient and introduces NaN's.

Output of xr.show_versions()

INSTALLED VERSIONS

commit: None
python: 3.7.6 | packaged by conda-forge | (default, Jan 7 2020, 22:33:48)
[GCC 7.3.0]
python-bits: 64
OS: Linux
OS-release: 3.10.0-1062.1.2.el7.x86_64
machine: x86_64
processor:
byteorder: little
LC_ALL: None
LANG: en_US.UTF-8
LOCALE: en_US.UTF-8
libhdf5: 1.10.5
libnetcdf: 4.7.3

xarray: 0.15.0
pandas: 1.0.0
numpy: 1.17.5
scipy: 1.4.1
netCDF4: 1.5.3
pydap: None
h5netcdf: 0.7.4
h5py: 2.10.0
Nio: None
zarr: 2.4.0
cftime: 1.0.4.2
nc_time_axis: None
PseudoNetCDF: None
rasterio: None
cfgrib: None
iris: None
bottleneck: None
dask: 2.10.1
distributed: 2.10.0
matplotlib: 3.1.3
cartopy: None
seaborn: 0.10.0
numbagg: None
setuptools: 45.1.0.post20200119
pip: 20.0.2
conda: None
pytest: 5.3.5
IPython: 7.12.0
sphinx: None

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by reading xarray's stack and unstack entry points and how they handle pandas MultiIndex dimensions. Investigate whether a partial unstack can preserve the remaining observations without introducing NaNs; done means an efficient supported operation that places end in its own dimension while retaining the other levels.

Written by the indexing model from the issue text.

Assessment

Tech stack
numpy, pandas, python
Domain
data
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
25/100

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