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Non uniform axes #2399

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merged 312 commits into from Jul 5, 2021
Merged

Non uniform axes #2399

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65df081
Updated docstring.
jlaehne Jan 3, 2020
6c94469
Fixed test.
jlaehne Jan 3, 2020
c5c95be
Fixed test.
jlaehne Jan 3, 2020
b65b384
Warning for sum/nansum, docstrings.
jlaehne Jan 3, 2020
e293e1f
Redefined FunctionalDataAxis with offset/scale.
jlaehne Jan 3, 2020
8f4eae6
Corrected typos in docstrings
jlaehne Jan 3, 2020
2f5dd51
Set offset to 0 in FunctionalDataAxis for consistency
francisco-dlp Jan 6, 2020
44c7ad7
Implement scale and offset by amending expression
francisco-dlp Jan 6, 2020
10ec1dd
Make all parameters traits
francisco-dlp Jan 6, 2020
8f07bf8
Make expression keyword mandatory
francisco-dlp Jan 6, 2020
8120a3f
Fix bugs and check that the input is right
francisco-dlp Jan 7, 2020
df0bd7f
Move import to imports block
francisco-dlp Jan 7, 2020
bbd5efd
Fix LinearDataAxis
francisco-dlp Jan 7, 2020
f39c179
Make function private
francisco-dlp Jan 7, 2020
58af525
Update tests
francisco-dlp Jan 7, 2020
b5cbbff
Add x kwarg to FDA and fix crop and slice_me bugs
francisco-dlp Jan 8, 2020
a5cf5de
Restore LA crop, slice_me and as_quantity
francisco-dlp Jan 8, 2020
b40cb16
Fix bug and tests
francisco-dlp Jan 8, 2020
fa46709
Merge remote-tracking branch 'upstream/RELEASE_next_patch' into non-l…
francisco-dlp Jan 8, 2020
8116833
Fix DataAxis.crop
francisco-dlp Jan 8, 2020
81f8086
Raise error when changing the size attribute of a FDA
francisco-dlp Jan 8, 2020
88eec29
Add method to convert to FDA
francisco-dlp Jan 8, 2020
d95f011
Merge remote-tracking branch 'upstream/RELEASE_next_minor' into non_u…
francisco-dlp Jan 8, 2020
37e3a4a
Fix wrong merge
francisco-dlp Jan 8, 2020
dbe0e9c
Merge branch 'non_uniform_axes' into non-linear-axis_FunctionalDA
francisco-dlp Jan 8, 2020
c007002
Add kwargs to method for par init
francisco-dlp Jan 15, 2020
49a6bd8
FDA.x is now a hspy axis + fix _get_axis_dict
francisco-dlp Jan 16, 2020
9eb9086
Set size when slicing linear axis
francisco-dlp Jan 16, 2020
1ee3db5
Move slice_me to DataAxis
francisco-dlp Jan 16, 2020
3bb1d18
Fix FDA slice_me
francisco-dlp Jan 16, 2020
ed52820
Remove _get_axis_dictionary
francisco-dlp Jan 16, 2020
a8cc9ac
Make x a trait for validation
francisco-dlp Jan 16, 2020
d208b83
Remove unnecessary if
francisco-dlp Jan 16, 2020
2c46c68
Revert "Redefined FunctionalDataAxis with offset/scale."
jlaehne Jan 16, 2020
9869201
Merge pull request #2302 from jlaehne/typo
ericpre Jan 16, 2020
e492f69
wqMerge remote-tracking branch 'upstream/RELEASE_next_minor' into non…
francisco-dlp Jan 17, 2020
a49f846
Merge branch 'non_uniform_axes' of https://github.com/hyperspy/hypers…
francisco-dlp Jan 17, 2020
c048c4e
Merge branch 'non_uniform_axes' into non-linear-axis_FunctionalDA
francisco-dlp Jan 17, 2020
d5b2736
Merge pull request #2303 from jlaehne/non-linear-axis_sum-diff
francisco-dlp Jan 17, 2020
cecee6b
Merge remote-tracking branch 'upstream/RELEASE_next_minor' into non_u…
francisco-dlp Jan 29, 2020
3d95d65
Merge branch 'non_uniform_axes' into non-linear-axis_FunctionalDA
francisco-dlp Jan 29, 2020
1610253
Merge remote-tracking branch 'upstream/RELEASE_next_minor' into non-l…
francisco-dlp May 15, 2020
bd3abbb
Fix test tolerance
francisco-dlp May 15, 2020
2534f72
Avoid test failure due to ipywidgets
francisco-dlp May 15, 2020
d9ebfe0
Fix BSS test
francisco-dlp May 15, 2020
a94722f
Fix axis size bug, thanks @jlahene
francisco-dlp May 17, 2020
c9f0f11
Fix DataAxis.size not updated
francisco-dlp May 17, 2020
698a3fd
Use non-uniform instead of non-linear axes
francisco-dlp May 17, 2020
61e1722
linear -> uniform
francisco-dlp May 17, 2020
fb3363d
Make create_axis private
francisco-dlp May 17, 2020
a597d3c
Replace NonUniformAxisError with NotImplementedError
francisco-dlp May 17, 2020
2801d2b
more changes to 'uniform' + docs
jlaehne May 17, 2020
d093750
Raise NotImplementedError for most EELS and holography methods
francisco-dlp May 18, 2020
83e144a
Merge pull request #45 from jlaehne/pr2299-doc-corrections
francisco-dlp May 18, 2020
f1d12e1
Merge branch 'non-linear-axis_FunctionalDA' of https://github.com/fra…
francisco-dlp May 18, 2020
9aa2c0c
Adapt update_axes_attributes_from
francisco-dlp May 18, 2020
43198f2
Merge remote-tracking branch 'upstream/RELEASE_next_minor' into non-l…
francisco-dlp May 18, 2020
554d257
CircleROI not implemented
francisco-dlp May 18, 2020
98ffd08
updated FDA in user guide + add. corrections
jlaehne May 18, 2020
694ac89
Some more NotImplementedErrors
francisco-dlp May 19, 2020
eebdd5b
consistently non-uniform (w/ dash)
jlaehne May 19, 2020
952858b
Merge pull request #2299 from francisco-dlp/non-linear-axis_FunctionalDA
francisco-dlp May 19, 2020
645dcd6
Solve merge conflicts
jlaehne May 19, 2020
847d74e
Merge pull request #2400 from jlaehne/pr2299-doc-corrections2
francisco-dlp May 20, 2020
a70b2b6
Solve merge conflicts
jlaehne May 31, 2020
8052dbb
Fix FDA dictionary
jlaehne May 31, 2020
0418a24
non_linear to non_uniform
jlaehne May 31, 2020
b60c167
fix/append IO test
jlaehne May 31, 2020
289d427
fix IO test
jlaehne May 31, 2020
1d678e4
Fix FDA hdf5-IO, test
jlaehne May 31, 2020
fe08ea6
remove comment
jlaehne May 31, 2020
32591e3
Fix test
jlaehne May 31, 2020
0fb8582
Fix test
jlaehne May 31, 2020
d836223
Pass axes or dict to Signal initialization.
jlaehne May 31, 2020
70b90d4
Add _type to axis dict/attributes
jlaehne May 31, 2020
bb5e93d
_type to **kwargs
jlaehne Jun 2, 2020
4325c2d
fixed tests, added legacy saving
jlaehne Jun 3, 2020
42c4fc8
_type only in dict, not attribute
jlaehne Jun 24, 2020
2015ecc
docstrings/user guide
jlaehne Jun 24, 2020
7e8d3a4
Merge remote-tracking branch 'upstream/RELEASE_next_minor' into non_u…
ericpre Aug 24, 2020
5ee400e
fix merge conflicts
jlaehne Aug 25, 2020
a6e1cf5
Added new formats
jlaehne Aug 25, 2020
450afcb
Merge branch 'RELEASE_next_minor' into non_uniform_axes
actions-user Aug 26, 2020
d0a81a6
Merge branch 'RELEASE_next_minor' into non_uniform_axes
actions-user Aug 27, 2020
7558403
Merge branch 'RELEASE_next_minor' into non_uniform_axes
actions-user Aug 31, 2020
c1de7a2
Merge branch 'non_uniform_axes' into non-linear-axis_roi
jlaehne Aug 31, 2020
5138736
Fix for #2452
jlaehne Aug 31, 2020
b56219e
Merge branch 'RELEASE_next_minor' into non_uniform_axes
actions-user Sep 1, 2020
ed835d6
Merge branch 'RELEASE_next_minor' into non_uniform_axes
actions-user Sep 2, 2020
2cfc49d
Merge branch 'RELEASE_next_minor' into non_uniform_axes
actions-user Sep 3, 2020
20bdcfa
Merge branch 'RELEASE_next_minor' into non_uniform_axes
actions-user Sep 4, 2020
b8fcce0
Merge branch 'RELEASE_next_minor' into non_uniform_axes
actions-user Sep 8, 2020
26ca8d7
Merge branch 'non_uniform_axes' into non-linear-axis_roi
jlaehne Sep 8, 2020
c320089
remove legacy
jlaehne Sep 8, 2020
2ddf4bd
made hyperspy.axes.create_axis public
jlaehne Sep 8, 2020
6ac8756
Update user guide
jlaehne Sep 8, 2020
02057af
Added tests
jlaehne Sep 8, 2020
34b08ff
user guide
jlaehne Sep 8, 2020
d820f00
Merge branch 'RELEASE_next_minor' into non_uniform_axes
actions-user Sep 9, 2020
aa8b2e7
Merge branch 'RELEASE_next_minor' into non_uniform_axes
actions-user Sep 10, 2020
b8c6087
Merge branch 'RELEASE_next_minor' into non_uniform_axes
actions-user Sep 11, 2020
9787bc2
Merge pull request #2512 from jlaehne/non-uniform-axis-index-out-of-b…
ericpre Sep 11, 2020
137ddcb
Merge branch 'RELEASE_next_minor' into non_uniform_axes
actions-user Sep 12, 2020
01e5619
fix merge conflict/test
jlaehne Sep 13, 2020
58d4857
Fixed warning
jlaehne Sep 13, 2020
b0a195d
Merge branch 'RELEASE_next_minor' into non_uniform_axes
actions-user Sep 24, 2020
51060e6
Merge remote-tracking branch 'upstream/RELEASE_next_minor' into non_u…
ericpre Oct 1, 2020
6fdd88e
Merge branch 'RELEASE_next_minor' into non_uniform_axes
actions-user Oct 15, 2020
7d47de6
Merge branch 'RELEASE_next_minor' into non_uniform_axes
actions-user Oct 27, 2020
0febbae
Merge branch 'RELEASE_next_minor' into non_uniform_axes
actions-user Nov 1, 2020
0286823
Merge pull request #2304 from jlaehne/non-linear-axis_roi
ericpre Nov 2, 2020
9a416ab
Merge remote-tracking branch 'upstream/RELEASE_next_minor' into non_u…
ericpre Dec 26, 2020
472a424
Fix tests which were depending on the calculation of the derivative.
ericpre Dec 26, 2020
7fa9d27
Skip test using derivative of lazy signal and numpy < 1.17.0.
ericpre Dec 26, 2020
f587d04
Merge remote-tracking branch 'upstream/RELEASE_next_minor' into non_u…
ericpre Dec 27, 2020
e79878b
Merge branch 'RELEASE_next_minor' into non_uniform_axes
actions-user Dec 28, 2020
1ec6b57
Merge branch 'RELEASE_next_minor' into non_uniform_axes
actions-user Dec 31, 2020
96b1deb
generalised the iterpath property
thomasaarholt Aug 2, 2020
4f81747
fix test
thomasaarholt Aug 3, 2020
2087ced
fix failing test
thomasaarholt Aug 3, 2020
106719c
revert a change, custom iterpath must follow numpy indexing, not hype…
thomasaarholt Aug 3, 2020
192029c
fix reversed custom iterpath issue
thomasaarholt Aug 4, 2020
3214c99
much simpler ndindex implementation
thomasaarholt Aug 4, 2020
5ae5ff6
now takes shape in hyperspy order
thomasaarholt Aug 4, 2020
7c66a7f
full coverage on tests now
thomasaarholt Aug 5, 2020
97a3de1
one more coverage bit
thomasaarholt Aug 5, 2020
1dc919f
@ericpre comments
thomasaarholt Oct 4, 2020
a5ef0b4
add docstring
thomasaarholt Oct 4, 2020
847673f
fix ericpre comments and add and fix tests
thomasaarholt Oct 19, 2020
42f4b46
Move and change _iterpath -> iterpath
thomasaarholt Oct 19, 2020
bd63a56
fix typo
thomasaarholt Oct 19, 2020
ee5f14e
check if progressbar length is known
thomasaarholt Oct 30, 2020
dbd0e15
Add GeneratorLen, more improvements
thomasaarholt Nov 11, 2020
5dfff68
add documentation
thomasaarholt Nov 11, 2020
1c8f3bf
warning -> logging
thomasaarholt Jan 13, 2021
d0d76fc
Merge pull request #2459 from thomasaarholt/general_iterpath
ericpre Jan 14, 2021
5d79ace
Merge branch 'RELEASE_next_minor' into non_uniform_axes
actions-user Jan 16, 2021
3d1a09d
Merge remote-tracking branch 'upstream/RELEASE_next_minor' into non_u…
ericpre Feb 12, 2021
13ad33b
try to fix attributes in axis conversion
jlaehne Feb 14, 2021
bb8a152
add missing tests
jlaehne Feb 14, 2021
26c3239
Fix removing traits when changing DataAxis type.
ericpre Feb 16, 2021
d0c822f
Merge branch 'RELEASE_next_minor' into non_uniform_axes
actions-user Feb 17, 2021
178fe00
Merge pull request #4 from ericpre/nua_fix-conversion
jlaehne Feb 17, 2021
0577c06
clean up
jlaehne Feb 17, 2021
928829a
Merge pull request #2649 from jlaehne/nua_fix-conversion
ericpre Feb 17, 2021
7c0b6dc
Merge remote-tracking branch 'upstream/RELEASE_next_minor' into non_u…
ericpre Mar 9, 2021
4cc16a1
Merge branch 'RELEASE_next_minor' into non_uniform_axes
actions-user Mar 13, 2021
e450c81
Merge branch 'RELEASE_next_minor' into non_uniform_axes
actions-user Mar 14, 2021
b481ed8
Merge remote-tracking branch 'upstream/RELEASE_next_minor' into non_u…
ericpre Mar 22, 2021
9b84524
Merge remote-tracking branch 'upstream/RELEASE_next_minor' into non_u…
ericpre Mar 28, 2021
60493a5
Merge branch 'RELEASE_next_minor' into non_uniform_axes
actions-user Mar 29, 2021
59839a6
update check axis calibration
jlaehne Apr 1, 2021
deecdc9
axes class docstrings
jlaehne Apr 1, 2021
71897b1
improve coverage
jlaehne Apr 1, 2021
b79cc62
Merge branch 'RELEASE_next_minor' into non_uniform_axes
actions-user Apr 2, 2021
76c8f2e
Merge remote-tracking branch 'upstream/RELEASE_next_minor' into non_u…
ericpre Apr 21, 2021
02b292e
Merge branch 'RELEASE_next_patch' into RELEASE_next_minor
actions-user Apr 24, 2021
0c82333
Merge branch 'RELEASE_next_minor' into non_uniform_axes
actions-user Apr 24, 2021
0d21d6c
Merge branch 'non_uniform_axes' into nua_is_binned
jlaehne Apr 27, 2021
747f746
Merge remote-tracking branch 'upstream/RELEASE_next_minor' into RELEA…
jlaehne Apr 27, 2021
63ab587
merge RELEASE_next_minor
jlaehne Apr 27, 2021
d047bdb
Merge branch 'non_uniform_axes' into nua_is_binned
jlaehne Apr 27, 2021
3ce16ce
fix value2index
jlaehne Apr 27, 2021
bd67d36
simplify check_axes_calibration
jlaehne May 2, 2021
a4e9ceb
Update getting_started.rst
jlaehne May 2, 2021
58ed06a
fix index_in_array issue in convert_to_non_uniform_axis
jlaehne May 2, 2021
07d1e64
fix fitting for binned non-uniform
jlaehne May 3, 2021
3b1a310
fix model estimators and other binned scale occurences
jlaehne May 3, 2021
7f133bc
add tests and fixes
jlaehne May 3, 2021
f465672
fix tests and add checks for nua
jlaehne May 3, 2021
8a61ae5
fix tests and correct depcrecated collections loading
jlaehne May 3, 2021
42da27d
fix deprecated collections loading
jlaehne May 3, 2021
cfdc0da
pint for unit comparison
jlaehne May 3, 2021
095eba6
fix unit comparison
jlaehne May 3, 2021
3ebb886
Merge pull request #2693 from jlaehne/nua_is_binned
ericpre May 4, 2021
cc2f59d
Merge branch 'non_uniform_axes' into nua_binned_fixes
jlaehne May 4, 2021
2e805b9
stack along non-uniform axes
jlaehne May 5, 2021
691fbe1
add tests for NotImplemented errors
jlaehne May 5, 2021
db820d1
increase coverage of axes.py
jlaehne May 5, 2021
9e6a058
fix IO
jlaehne May 5, 2021
6d73c87
add tests for nua calibrate
jlaehne May 5, 2021
d7a95dc
further tests not implemented
jlaehne May 5, 2021
7b599ee
Revert "fix IO"
jlaehne May 5, 2021
f79a610
revert duplicate check on rebin
jlaehne May 5, 2021
820f180
first comments resolved
jlaehne May 6, 2021
48ad87e
Remove duplicated method in BaseDataAxis.
ericpre May 6, 2021
d3ba5b8
more comments resolved
jlaehne May 6, 2021
94cf419
add raises sections to docstrings
jlaehne May 9, 2021
967fe74
last review comments, stack for FDA
jlaehne May 9, 2021
a3b7b87
Merge pull request #2728 from jlaehne/nua_binned_fixes
thomasaarholt May 10, 2021
ce1abe6
clarifications sum/integrate1D
jlaehne May 11, 2021
31421c2
user guide
jlaehne May 11, 2021
ae1c085
Merge pull request #2733 from ericpre/remove_duplicated_method
jlaehne May 11, 2021
d1bcd1c
Merge pull request #2737 from jlaehne/nua_integrate
ericpre May 11, 2021
0ccac36
Re-implementation of artificial luminescence data (with tests)
LMSC-NTappy May 12, 2021
f8a2681
Fixed typo
LMSC-NTappy May 16, 2021
09413dd
fixes value2index, _get_scaling_factor and implement tests
ericpre May 10, 2021
7e0d46b
changed scalar test (caused tests to fail with some python versions)
LMSC-NTappy May 16, 2021
cf75cb1
cleanup
LMSC-NTappy May 16, 2021
b28db3e
cleanup
LMSC-NTappy May 16, 2021
06d8335
Import scipy submodule explicitely
ericpre May 16, 2021
a737190
Merge pull request #2742 from LMSC-NTappy/artificialdata_nonlinearaxis_2
ericpre May 17, 2021
2262a2a
Incorporating fixes from @eprestat
LMSC-NTappy May 18, 2021
914bebd
Implemented rounding function
LMSC-NTappy May 18, 2021
a84c955
Fix circular import
ericpre May 18, 2021
dc6ea98
Fix _parse_value_from_string with relative string for non uniform axis
ericpre May 17, 2021
022abc0
Raise ValueError when using unit conversion with non-uniform axis
ericpre May 18, 2021
4d0849a
Fix typo and remove connection to handler for is_binned attribute.
ericpre May 20, 2021
922d54f
Move gui decorator to BaseDataAxis so that all type of axis get the gui.
ericpre May 20, 2021
a6af988
Merge branch 'RELEASE_next_minor' into non_uniform_axes
ericpre May 20, 2021
e7eecb9
Merge pull request #2752 from ericpre/fix_is_binned_gui
francisco-dlp May 21, 2021
d61c4ec
Comment explaining in which subclass BaseDataAxis methods are tested
LMSC-NTappy May 25, 2021
674f3e7
Update remaining python2-syntax super()
LMSC-NTappy May 25, 2021
a31e792
Implement uniformaxis value2index tests as single function
LMSC-NTappy May 25, 2021
0c6da6e
Merge pull request #2747 from ericpre/fix_parse_value_string_nua
jlaehne May 25, 2021
2e757e9
Remove unnecessary warning.
ericpre May 26, 2021
f24dd8a
Unify value2index docstrings
LMSC-NTappy May 27, 2021
b87213a
implement numba functions for finding closest index
LMSC-NTappy May 27, 2021
9574ada
Merge branch 'fixes_binned_nua_2_rebase' of https://github.com/LMSC-N…
LMSC-NTappy May 27, 2021
516b193
Merge pull request #2743 from LMSC-NTappy/fixes_binned_nua_2_rebase
jlaehne May 27, 2021
3ae22f2
non-uniform updates
jlaehne Jun 2, 2021
df155a6
test correction
jlaehne Jun 2, 2021
985f5da
fix error in io.py
jlaehne Jun 2, 2021
4b00e68
add io test
jlaehne Jun 2, 2021
3fa6a08
fix test
jlaehne Jun 3, 2021
2be5ddc
fix test
jlaehne Jun 3, 2021
c246645
fix test
jlaehne Jun 3, 2021
0703570
fixes based on review
jlaehne Jun 3, 2021
f6fc3ca
change to IOError to TypeError
jlaehne Jun 3, 2021
6d4de2a
fix test
jlaehne Jun 3, 2021
edd9937
Merge pull request #2761 from jlaehne/nua_lastcatches
ericpre Jun 3, 2021
3f91fe8
convert index to int
jlaehne Jun 7, 2021
72df017
Add tests for rounding
jlaehne Jun 8, 2021
dac2ced
fix rounding floor
jlaehne Jun 8, 2021
a67980b
fix rounding
jlaehne Jun 8, 2021
5ebe28e
simplify round, fix value_changed test
jlaehne Jun 10, 2021
9b6a944
use bias to round up
jlaehne Jun 10, 2021
a50e108
fix rounding
jlaehne Jun 11, 2021
74d2afb
rounding docstring
jlaehne Jun 14, 2021
c977edd
round half-to-even
jlaehne Jun 22, 2021
ef35be2
Revert "round half-to-even"
jlaehne Jun 24, 2021
aa43a08
Use round half towards zero as rounding method for non uniform axis
ericpre Jun 24, 2021
3644d22
Use round half towards zero as rounding method for uniform axis
ericpre Jun 24, 2021
7a55b07
Run black on array_tools.py
ericpre Jun 24, 2021
3561a67
Merge pull request #7 from ericpre/nua_value2index_fix
jlaehne Jun 28, 2021
0659013
Fix inconsistency in value2index for uniform and non-uniform axis.
ericpre Jun 30, 2021
595be28
Skip a test on aarch64
ericpre Jun 30, 2021
2bfef10
Merge pull request #2765 from jlaehne/nua_value2index_fix
ericpre Jul 1, 2021
0f0fbe5
Merge remote-tracking branch 'upstream/RELEASE_next_minor' into non_u…
ericpre Jul 1, 2021
102909d
Add entry to changelog.
ericpre Jul 5, 2021
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1 change: 1 addition & 0 deletions doc/index.rst
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Expand Up @@ -17,6 +17,7 @@ Welcome to HyperSpy's documentation!
user_guide/install.rst
user_guide/getting_started.rst
user_guide/signal.rst
user_guide/axes.rst
user_guide/interactive_operations_ROIs.rst
user_guide/signal1d.rst
user_guide/signal2d.rst
Expand Down