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Allow loading of patterns from arbitrary scan group names in h5ebsd files #188

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merged 3 commits into from
May 23, 2020

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@hakonanes hakonanes commented May 23, 2020

Description

Any HDF5 top group name for scan groups is allowed, not just "Scan 1", "Scan 2", etc., which is the case for v0.2.1. Addresses #184 (and fixes #185).

Checklist

Minimal example of the bug fix or new feature

If e.g. an EDAX TSL HDF5 file has the standard h5ebsd top groups "Manufacturer" and "Version" and three scans with group names "Scan 1", "Hello, C3PO!" and "Just the best patterns", all or some of the scans can be read into separate EBSD objects:

>>> import kikuchipy as kp
# Read multiple scans at once
>>> s1, s2, s3 = kp.load("my_file.h5", scan_group_names=["Scan 1", "Hello, C3PO!", "Just the best patterns")
# Read a single scan which is not the first scan in the file
>>> s_not_first = kp.load("my_file.h5", scan_group_names="Hello, C3PO!")
# Read the first scan in the file
>>> s = kp.load("my_file.h5")

For reviewers

  • Check that the PR title is short, concise, and will make sense 1 year
    later.
  • Check that new functions are imported in corresponding __init__.py.
  • Check that new features, API changes, and deprecations are mentioned in
    the unreleased section in doc/changelog.rst.

Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
@hakonanes hakonanes added bug Something isn't working documentation This relates to the documentation backport labels May 23, 2020
@hakonanes hakonanes added this to the v0.2.2 milestone May 23, 2020
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Coverage Status

Coverage remained the same at 100.0% when pulling eee788b on hakonanes:fix-h5ehsd-reader-top-group into d82a939 on kikuchipy:master.

@hakonanes hakonanes merged commit a863304 into pyxem:master May 23, 2020
@hakonanes hakonanes deleted the fix-h5ehsd-reader-top-group branch May 23, 2020 18:30
hakonanes added a commit to hakonanes/kikuchipy that referenced this pull request May 23, 2020
…iles (pyxem#188)

* Improve h5ebsd reader to allow any top group names with scans

Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>

* Improve h5ebsd reader, allow arbitrary top group name for scans

Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>

* Update changelog with h5ebsd reader fix

Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
@hakonanes hakonanes mentioned this pull request May 23, 2020
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hakonanes added a commit that referenced this pull request May 23, 2020
* Use numpy.fft instead of scipy.fft

Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>

* Use required dask[array] selector

Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>

* Allow loading of patterns from arbitrary scan group names in h5ebsd files (#188)

* Improve h5ebsd reader to allow any top group names with scans

Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>

* Improve h5ebsd reader, allow arbitrary top group name for scans

Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>

* Update changelog with h5ebsd reader fix

Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
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Fix IQ documentation wrongly calling non-existant kikuchipy.util.pattern module
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