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When is transpose not lazy? #2576

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djhoese opened this issue Nov 26, 2018 · 1 comment · Fixed by #2746
Closed

When is transpose not lazy? #2576

djhoese opened this issue Nov 26, 2018 · 1 comment · Fixed by #2746

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@djhoese
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djhoese commented Nov 26, 2018

Code Sample, a copy-pastable example if possible

import xarray as xr
import dask.array as da 
from dask.diagnostics import ProgressBar
a = xr.DataArray(da.zeros((3, 5, 5), chunks=(1, 2, 2)), dims=('bands', 'y', 'x'))

with ProgressBar():
    b = a.transpose('y', 'x', 'bands')
# dask does not show a progress bar due to no computation

with ProgressBar():
    b = a.transpose('y', 'x', 'bands')
    b.compute()
# dask computes the array (since we told it to) and we see a progress bar

Question

The documentation for transpose says that it is not lazy. Is this only in certain situations? By not lazy does it mean that when the data is computed that the transpose task will require all data to be loaded at once (one large chunk) or does it mean that the transpose operation will immediately compute the transposed array? My test above does not seem to compute the data when transpose is called.

Or is the documentation just outdated?

@shoyer
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shoyer commented Nov 26, 2018

Transpose on arrays stored with dask is definitely always lazy. The docs are out of sync here -- I think this language predates the use of dask into xarray!

The language is referring to cases where you're loading data from disk with open_dataset() without using dask. Indexing is lazy in those cases, but not transpose.

@dcherian dcherian mentioned this issue Mar 7, 2019
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dcherian pushed a commit to dcherian/xarray that referenced this issue Mar 7, 2019
dcherian pushed a commit to dcherian/xarray that referenced this issue Mar 7, 2019
dcherian added a commit that referenced this issue Mar 12, 2019
* Friendlier io title.

* Fix lists.

* Fix *args, **kwargs

"inline emphasis..."

* misc

* Reference xarray_extras for csv writing. Closes #2289

* Add metpy accessor. Closes #461

* fix transpose docstring. Closes #2576

* Revert "Fix lists."

This reverts commit 39983a5.

* Revert "Fix *args, **kwargs"

This reverts commit 1b9da35.

* Add MetPy to related projects.

* Add Weather and Climate specific page.

* Add hvplot.

* Note open_dataset, mfdataset open files as read-only (closes #2345).

* Update metpy 1

Co-Authored-By: dcherian <dcherian@users.noreply.github.com>

* Update doc/weather-climate.rst

Co-Authored-By: dcherian <dcherian@users.noreply.github.com>
pletchm pushed a commit to pletchm/xarray that referenced this issue Mar 21, 2019
* Friendlier io title.

* Fix lists.

* Fix *args, **kwargs

"inline emphasis..."

* misc

* Reference xarray_extras for csv writing. Closes pydata#2289

* Add metpy accessor. Closes pydata#461

* fix transpose docstring. Closes pydata#2576

* Revert "Fix lists."

This reverts commit 39983a5.

* Revert "Fix *args, **kwargs"

This reverts commit 1b9da35.

* Add MetPy to related projects.

* Add Weather and Climate specific page.

* Add hvplot.

* Note open_dataset, mfdataset open files as read-only (closes pydata#2345).

* Update metpy 1

Co-Authored-By: dcherian <dcherian@users.noreply.github.com>

* Update doc/weather-climate.rst

Co-Authored-By: dcherian <dcherian@users.noreply.github.com>
pletchm pushed a commit to pletchm/xarray that referenced this issue Mar 21, 2019
* Friendlier io title.

* Fix lists.

* Fix *args, **kwargs

"inline emphasis..."

* misc

* Reference xarray_extras for csv writing. Closes pydata#2289

* Add metpy accessor. Closes pydata#461

* fix transpose docstring. Closes pydata#2576

* Revert "Fix lists."

This reverts commit 39983a5.

* Revert "Fix *args, **kwargs"

This reverts commit 1b9da35.

* Add MetPy to related projects.

* Add Weather and Climate specific page.

* Add hvplot.

* Note open_dataset, mfdataset open files as read-only (closes pydata#2345).

* Update metpy 1

Co-Authored-By: dcherian <dcherian@users.noreply.github.com>

* Update doc/weather-climate.rst

Co-Authored-By: dcherian <dcherian@users.noreply.github.com>
shoyer pushed a commit that referenced this issue Mar 26, 2019
…ns with size>1 (#2757)

* Quarter offset implemented (base is now latest pydata-master). (#2721)

* Quarter offset implemented (base is now latest pydata-master).

* Fixed issues raised in review (#2721 (review))

* Updated whats-new.rst with info on quarter offset support.

* Updated whats-new.rst with info on quarter offset support.

* Update doc/whats-new.rst

Co-Authored-By: jwenfai <jwenfai@gmail.com>

* Added support for quarter frequencies when resampling CFTimeIndex. Less redundancy in CFTimeIndex resampling tests.

* Removed normalization code (unnecessary for cftime_range) in cftime_offsets.py. Removed redundant lines in whats-new.rst.

* Removed invalid option from _get_day_of_month docstring. Added tests back in that raises ValueError when resampling (base=24 when resampling to daily freq, e.g., '8D').

* Minor edits to docstrings/comments

* lint

* Add `Dataset.drop_dims` (#2767)

* ENH: Add Dataset.drop_dims()

* Drops full dimensions and any corresponding variables in a
  Dataset
* Fixes GH1949

* DOC: Add Dataset.drop_dims() documentation

* Improve name concat (#2792)

* Added tests of desired name inferring behaviour

* Infers names

* updated what's new

* Don't use deprecated np.asscalar() (#2800)

It got deprecated in numpy 1.16 and throws a ton of warnings due to
that.
All the function does is returning .item() anyway, which is why it got
deprecated.

* Add support for cftime.datetime coordinates with coarsen (#2778)

* some docs updates (#2746)

* Friendlier io title.

* Fix lists.

* Fix *args, **kwargs

"inline emphasis..."

* misc

* Reference xarray_extras for csv writing. Closes #2289

* Add metpy accessor. Closes #461

* fix transpose docstring. Closes #2576

* Revert "Fix lists."

This reverts commit 39983a5.

* Revert "Fix *args, **kwargs"

This reverts commit 1b9da35.

* Add MetPy to related projects.

* Add Weather and Climate specific page.

* Add hvplot.

* Note open_dataset, mfdataset open files as read-only (closes #2345).

* Update metpy 1

Co-Authored-By: dcherian <dcherian@users.noreply.github.com>

* Update doc/weather-climate.rst

Co-Authored-By: dcherian <dcherian@users.noreply.github.com>

* Drop failing tests writing multi-dimensional arrays as attributes (#2810)

These aren't valid for netCDF files.

Fixes GH2803

* Push back finalizing deprecations for 0.12 (#2809)

0.12 will already have a big change in dropping Python 2.7 support. I'd rather
wait a bit longer to finalize these deprecations to minimize the impact on
users.

* enable loading remote hdf5 files (#2782)

* attempt at loading remote hdf5

* added a couple tests

* rewind bytes after reading header

* addressed comments for tests and error message

* fixed pep8 formatting

* created _get_engine_from_magic_number function, new tests

* added description in whats-new

* fixed test failure on windows

* same error on windows and nix

* Release 0.12.0

* Add whats-new for 0.12.1

* Rework whats-new for 0.12

* DOC: Update donation links

* DOC: remove outdated warning (#2818)

* Allow expand_dims() method to support inserting/broadcasting dimensions with size>1 (#2757)

 * Make using dim_kwargs for python 3.5 illegal -- a ValueError is thrown

 * dataset.expand_dims() method take dict like object where values represent length of dimensions or coordinates of dimesnsions

 * dataarray.expand_dims() method take dict like object where values represent length of dimensions or coordinates of dimesnsions

 * Add alternative option to passing a dict to the dim argument, which is now an optional kwarg, passing in each new dimension as its own kwarg

 * Add expand_dims enhancement from issue 2710 to whats-new.rst

 * Fix test_dataarray.TestDataArray.test_expand_dims_with_greater_dim_size tests to pass in python 3.5 using ordered dicts instead of regular dicts. This was needed because python 3.5 and earlier did not maintain insertion order for dicts

 * Restrict core logic to use 'dim' as a dict--it will be converted into a dict on entry if it is a str or a sequence of str

 * Don't cast dim values (coords) as a list since IndexVariable/Variable will internally convert it into a numpy.ndarray. So just use IndexVariable((k,), v)

 * TypeErrors should be raised for invalid input types, rather than ValueErrors.

 * Force 'dim' to be OrderedDict for python 3.5

* Allow expand_dims() method to support inserting/broadcasting dimensions with size>1 (#2757)

 * use .size attribute to determine the size of a dimension, rather than converting to a list, which can be slow for large iterables

 * Make using dim_kwargs for python 3.5 illegal -- a ValueError is thrown

 * dataset.expand_dims() method take dict like object where values represent length of dimensions or coordinates of dimesnsions

 * dataarray.expand_dims() method take dict like object where values represent length of dimensions or coordinates of dimesnsions

 * Add alternative option to passing a dict to the dim argument, which is now an optional kwarg, passing in each new dimension as its own kwarg

 * Add expand_dims enhancement from issue 2710 to whats-new.rst

 * Fix test_dataarray.TestDataArray.test_expand_dims_with_greater_dim_size tests to pass in python 3.5 using ordered dicts instead of regular dicts. This was needed because python 3.5 and earlier did not maintain insertion order for dicts

 * Restrict core logic to use 'dim' as a dict--it will be converted into a dict on entry if it is a str or a sequence of str

 * Don't cast dim values (coords) as a list since IndexVariable/Variable will internally convert it into a numpy.ndarray. So just use IndexVariable((k,), v)

 * TypeErrors should be raised for invalid input types, rather than ValueErrors.

 * Force 'dim' to be OrderedDict for python 3.5

* Allow expand_dims() method to support inserting/broadcasting dimensions with size>1 (#2757)

 * Move enhancement description up to 0.12.1

 * use .size attribute to determine the size of a dimension, rather than converting to a list, which can be slow for large iterables

 * Make using dim_kwargs for python 3.5 illegal -- a ValueError is thrown

 * dataset.expand_dims() method take dict like object where values represent length of dimensions or coordinates of dimesnsions

 * dataarray.expand_dims() method take dict like object where values represent length of dimensions or coordinates of dimesnsions

 * Add alternative option to passing a dict to the dim argument, which is now an optional kwarg, passing in each new dimension as its own kwarg

 * Add expand_dims enhancement from issue 2710 to whats-new.rst

 * Fix test_dataarray.TestDataArray.test_expand_dims_with_greater_dim_size tests to pass in python 3.5 using ordered dicts instead of regular dicts. This was needed because python 3.5 and earlier did not maintain insertion order for dicts

 * Restrict core logic to use 'dim' as a dict--it will be converted into a dict on entry if it is a str or a sequence of str

 * Don't cast dim values (coords) as a list since IndexVariable/Variable will internally convert it into a numpy.ndarray. So just use IndexVariable((k,), v)

 * TypeErrors should be raised for invalid input types, rather than ValueErrors.

 * Force 'dim' to be OrderedDict for python 3.5
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