Code

Refactor gtda/diagrams#454

Code

Merged

ulupo merged 54 commits intogiotto-ai:mastergiotto-ai/giotto-tda:masterfrom ulupo:fix_amplitudeulupo/giotto-tda:fix_amplitudeCopy head branch name to clipboardAug 14, 2020

+934-639

Commits

Commits on Aug 10, 2020

• First attempt at Amplitude fix

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  f157d65

• First attempt at Amplitude fix

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  08c37f9

• Merge remote-tracking branch 'origin/fix_amplitude' into fix_amplitude

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  ba30225

Commits on Aug 11, 2020

• Use output kwarg of scipy's gaussian_filter, be explicit about dtypes

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  0e33e30

• Fix y-axis in PersistenceImage plots

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  5472034

• Style improvements

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  c53a629

• Duplicate hovertext on persistence pairs with multiplicity in plot_diagram

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  81445c4

• Minor improvements with slicing, naming and integer conversions in gtda.diagrams._metrics

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  ad9444f

• Change reflect mode of gaussian_filter to "constant"

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  d7b311f

• Fix PersistenceLandscape plot method

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  a959fde

• Improve tests for plot methods in gtda.diagrams.representations

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  9a550a2

• Minor docstring linting

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  f284ef5

• Miscellaneous docstring improvements in gtda/diagrams

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  03c4fcd

• Fix validation dictionary for metric_params in the case of PersistenceImage

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  861a0e6

• Change default value of order in Amplitude, from 2. to None (vector features)

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  0852b02

• Change meaning of default None for weight_function in PersistenceImage

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  011bac7

• Improve code style and clarity in plot methods in gtda.diagrams.representations

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  ce6fef0

Commits on Aug 12, 2020

• Refactor gtda/diagrams/_metrics.py to fix several bugs

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  433ec6c

• Fix trace name when homology dimension is np.inf in BettiCurve and Silhouette

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  d1975f1

• Improve tests of plot methods in representations

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  8b1d7ff

• Improve test coverage of Amplitude and PairwiseDistance

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  ddb11ab

• Improve variable name after @wreise's suggestion

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  5540b26

• Add test of zero weight_function for PersistenceImage

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  0817d7d

• Make behaviour of Scaler.fit when the metric is persistence image the same as Amplitude

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  16a9ae2

• Delete never-used _matrix_wrapper and _arrays_wrapper functions

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  f8248ee

• Remove _pad from gtda.diagrams._utils as it is never used

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  bf84a09

• Make copy=True in calls to check_diagrams in Scaler.transform and Scaler.inverse_transform

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  a532cc8

• Make homology_dimensions_ attributes tuples instead of lists, with integers when possible

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  17b906e

• Remove forgotten commented lines

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  436b58f

• Avoid applying smoothing twice in persistence_images following @wreise's review

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  12673a7

• Implement suggestion by @wreise to avoid excessive hovertext in plot_diagrams

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  6e223eb

• Fix small bug introduced in Filtering in 17b906e, add new tests for Filtering

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  9ec759c

• Improve code style

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  3ee195a

• Hard-code zero array outputs by heats and persistence_images when step sizes are zero

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  aad9cf7

• Add homology_dimensions kwarg to _bin

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  a1d26aa

• Adapt choices of min_values, max_values and sigmas in hypothesis-based tests

  Show description for 629b55d
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  629b55d

• Fix linting

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  7eda16f

• Minor style improvements

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  63225e9

• Add useful inline comments

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  fd45b12

• Make tests of HeatKernel and PersistenceImage less flaky

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  4bcfba7

• Typo fix

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  ee5b8f9

• Make all homology dimensions equal in test_hk_big_sigma

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  5afcb77

• Cover use of plotly_params kwarg in diagram preprocessing classes plot methods

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  2ee1a4c

• Simplify plot code following 17b906e

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  5986492

• Extract some common logic from plot methods in gtda.diagrams.representations

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  42210c2

• Fix typo

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  cb05605

• Fix linting

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  9bf36d0

• Silence expected warnings from image transformers in test_common

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  85412f4

Commits on Aug 13, 2020

• Implement @wreise's suggestion to abstract away sorting and integer conversion of fit hom dims

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  c2367aa

• Linting

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  2cd5f60

• Reintroduced accidentally deleted line in Silhouette

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  27dcf93

• Fix use of non-default weight functions in Amplitude, PairwiseDistance and Filtering with persistence-image metric

  Show description for 4001abf
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  4001abf

• Refactor _subdiagrams to be able to throw informative errors on expected input properties

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  a6ee6d1

• Fix variable name

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  0af413f