Deepcell

🐛 Bug Fixes

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<summary>Fix bug in `is_valid_lineage`; daughters can be \< parent. willgraf (88)</summary>

No need to check if the daughters are in `all_cells`, as we check that for each lineage. Just check that the daughter is in the lineage.

Don't return False as a shortcut, just warn and continue to the next label. This will enable all warnings to be shown.
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🐛 Bug Fixes

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<summary>Remove `pathlib` from `setup.py`; fix build issues zverozabr (86)</summary>

Fixes 85

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🧰 Maintenance

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<summary>Bump version to 0.5.3. willgraf (87)</summary>


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🐛 Bug Fixes

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<summary>Speed up `trks_stats` by a factor of 5 willgraf (84)</summary>

`trks_stats` is used to calculate various statistics on a trks file. The old implementation ended up calling `np.unique` inside a double for loop, which caused the runtime to spike. These changes update the internal logic to greatly improve the runtime (namely, by separating the logic into two different for loops, updating the time complexity from O(batch * frames * cells) to O(batch*(frames+cells)).

Some example times on the current registry tracking data (all times include time to run `load_trks`):

- `test.trks` from 227s to 47s
- `val.trks` from 549s to 110s
- `train.trks` from 1968s to 386s
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🐛 Bug Fixes

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<summary>Use `np.any` instead of `np.sum` when finding all frames that contain a given object. willgraf (82)</summary>

`np.sum` counts all the frames the object is in, but we really only care that it exists in the given frame, not the number. `np.any` is about 3x faster (in my examples lineage), and should help speed up the slowest code in both `is_valid_lineage` and `relabel_sequential_lineage`.

Additionally, `is_valid_lineage` has some improved warning messages, and saves a single loop across the cells by iteratively removing the cells with the lineage from a set of all cells.
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🧰 Maintenance

<details>
<summary>Bump the version to 0.5.1. willgraf (83)</summary>


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This release supports TensorFlow 1.14.x and 1.15.x as well as python 2.7 and 3.6+.

Features

* Updated `match_nodes` to return IoU directly instead of indices. (267)

* Added `get_anchor_parameters` to automatically determine feature pyramid parameters (269)

* Added new custom layer, `ConvGRU2D` (278)

* Updated `layer_test` testing routine (279)

* Travis will now tag and push a `latest-gpu` image with every release. (281)

* Speed up the pixel-wise transform (286, 295)

* Add temporal information options to the featurenets. (282)

* Improve docstrings for sphinx compatibility. (310)

* Improved data quality for cytoplasm and phase data. (318)

* Added new `model_zoo.PanopticNet` and `SemanticDataGenerator` to generalize a model for learning multiple tasks simultaneously, both regression and classification. (319)

* Added `Application` objects to easily use models with a simple API. (341)

* Simplified transform names (376).


Bugfixes

* `deepcell-tracking` has been updated to 0.2.4, which resolves some ISBI function bugs. (267)

* Updated `tf.image.resize_images` to `tf.image.resize` as the former is deprecated. (268)

* Correct upper limit for clipping boxes (277)

* Fixed broken data links and README links (292, 300, 307)

* Migrate general utility functions into a new package `deepcell-toolbox` (319).

* Fixed RetinaNet interpolation bug (357)

Breaking Changes

* Support for TensorFlow 1.10.x - 1.13.x has been dropped.

* The default `TF_VERSION` in the Dockerfile has been updated to `1.14.0-gpu`, as many users were expecting this. (281, 311)

* `MaskRCNN` has been refactored to `RetinaMask` (360).

* `/scripts` has been migrated to `/notebooks` (374).

* `deepcell.notebooks` has been removed (390).

🐛 Bug Fixes

<details>
<summary>Fix bad warning message in `is_valid_lineage` willgraf (77)</summary>

There is a bad label in one of the parent checks. This PR updates the message for accuracy.
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<details>
<summary>Validate parent lineage field as well as daughters. willgraf (76)</summary>

73 updated `is_valid_lineage` to do better of all cells. However, there is no extra validation of the `parent` field, which is used in the `isbi_utils` functions.

This PR adds some basic validation of the `parent` lineage field to improve the validation of the lineage objects.
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