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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,115 @@ | ||
| From f1a39b863281de51d350e7b1eebbe7d404d40abc Mon Sep 17 00:00:00 2001 | ||
| From: Grzegorz Bokota <bokota+github@gmail.com> | ||
| Date: Wed, 24 Jan 2024 16:35:15 +0100 | ||
| Subject: [PATCH] Fix `Labels.data_setitem` setting of view by taking dims | ||
| order into account (#6616) | ||
|
|
||
| closes #6615 | ||
|
|
||
| In #6607, we started painting into both the data and the slice view. | ||
| (And this was already happening and broken when painting into lazy | ||
| arrays such as zarr and dask, #6112.) However, when setting the view we | ||
| need to take into account the axis ordering used when slicing (some axes | ||
| may be transposed). This manifested as an index error in #6615. | ||
|
|
||
| In this PR, we add an `indices_order` argument to `index_in_slice` | ||
| function and the function returns indices in the requested order, which | ||
| we can then use to set the view. | ||
| --- | ||
| napari/layers/labels/_tests/test_labels.py | 10 +++++++++- | ||
| napari/layers/labels/labels.py | 4 +++- | ||
| napari/utils/_indexing.py | 14 +++++++++----- | ||
| 3 files changed, 21 insertions(+), 7 deletions(-) | ||
|
|
||
| diff --git a/napari/layers/labels/_tests/test_labels.py b/napari/layers/labels/_tests/test_labels.py | ||
| index 9d5a5339..f93de038 100644 | ||
| --- a/napari/layers/labels/_tests/test_labels.py | ||
| +++ b/napari/layers/labels/_tests/test_labels.py | ||
| @@ -697,6 +697,14 @@ def test_data_setitem_multi_dim(): | ||
| ) | ||
|
|
||
|
|
||
| +def test_data_setitiem_transposed_axes(): | ||
| + data = np.zeros((10, 100), dtype=np.uint32) | ||
| + labels = Labels(data) | ||
| + labels.data_setitem((np.array([9]), np.array([99])), 1) | ||
| + labels._slice_dims([0, 0], 2, [1, 0]) | ||
| + labels.data_setitem((np.array([9]), np.array([99])), 2) | ||
| + | ||
| + | ||
| def test_selecting_label(): | ||
| """Test selecting label.""" | ||
| np.random.seed(0) | ||
| @@ -823,7 +831,7 @@ def test_paint_2d(): | ||
|
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|
|
||
| def test_paint_2d_xarray(): | ||
| - """Test the memory usage of painting an xarray indirectly via timeout.""" | ||
| + """Test the memory usage of painting a xarray indirectly via timeout.""" | ||
| now = time.monotonic() | ||
| data = xr.DataArray(np.zeros((3, 3, 1024, 1024), dtype=np.uint32)) | ||
|
|
||
| diff --git a/napari/layers/labels/labels.py b/napari/layers/labels/labels.py | ||
| index 63c792ed..6efe3f0c 100644 | ||
| --- a/napari/layers/labels/labels.py | ||
| +++ b/napari/layers/labels/labels.py | ||
| @@ -1492,7 +1492,9 @@ class Labels(_ImageBase): | ||
| self.data[indices] = value | ||
|
|
||
| pt_not_disp = self._get_pt_not_disp() | ||
| - displayed_indices = index_in_slice(indices, pt_not_disp) | ||
| + displayed_indices = index_in_slice( | ||
| + indices, pt_not_disp, self._slice_input.order | ||
| + ) | ||
| if isinstance(value, np.ndarray): | ||
| visible_values = value[elements_in_slice(indices, pt_not_disp)] | ||
| else: | ||
| diff --git a/napari/utils/_indexing.py b/napari/utils/_indexing.py | ||
| index 5b6fe9ef..03c1099e 100644 | ||
| --- a/napari/utils/_indexing.py | ||
| +++ b/napari/utils/_indexing.py | ||
| @@ -35,7 +35,9 @@ def elements_in_slice( | ||
|
|
||
|
|
||
| def index_in_slice( | ||
| - index: Tuple[npt.NDArray[np.int_], ...], position_in_axes: Dict[int, int] | ||
| + index: Tuple[npt.NDArray[np.int_], ...], | ||
| + position_in_axes: Dict[int, int], | ||
| + indices_order: Tuple[int, ...], | ||
| ) -> Tuple[npt.NDArray[np.int_], ...]: | ||
| """Convert a NumPy fancy indexing expression from data to sliced space. | ||
|
|
||
| @@ -45,6 +47,8 @@ def index_in_slice( | ||
| A NumPy fancy indexing expression [1]_. | ||
| position_in_axes : dict[int, int] | ||
| A dictionary mapping sliced (non-displayed) axes to a slice position. | ||
| + indices_order : tuple of int | ||
| + The order of the indices in data view. | ||
|
|
||
| Returns | ||
| ------- | ||
| @@ -55,9 +59,9 @@ def index_in_slice( | ||
| Examples | ||
| -------- | ||
| >>> index = (np.arange(5), np.full(5, 1), np.arange(4, 9)) | ||
| - >>> index_in_slice(index, {0: 3}) | ||
| + >>> index_in_slice(index, {0: 3}, (0, 1, 2)) | ||
| (array([1]), array([7])) | ||
| - >>> index_in_slice(index, {1: 1, 2: 8}) | ||
| + >>> index_in_slice(index, {1: 1, 2: 8}, (0, 1, 2)) | ||
| (array([4]),) | ||
|
|
||
| References | ||
| @@ -66,7 +70,7 @@ def index_in_slice( | ||
| """ | ||
| index_in_slice = elements_in_slice(index, position_in_axes) | ||
| return tuple( | ||
| - ix[index_in_slice] | ||
| - for i, ix in enumerate(index) | ||
| + index[i][index_in_slice] | ||
| + for i in indices_order | ||
| if i not in position_in_axes | ||
| ) | ||
| -- | ||
| 2.34.1 | ||
|
|
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| From ddadd98ad16124d121042d3f09622ed01c5747b2 Mon Sep 17 00:00:00 2001 | ||
| From: Grzegorz Bokota <bokota+github@gmail.com> | ||
| Date: Tue, 30 Jan 2024 00:39:09 +0100 | ||
| Subject: [PATCH] Move Nick and Loic to emeritus, sort emeritus core devs | ||
| (#339) | ||
|
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||
| # Description | ||
|
|
||
| Move Nicholas Sofroniew and Loic Royer to emeritus core developers and | ||
| sort this list alphabetically. | ||
| --- | ||
| docs/community/team.md | 10 +++++----- | ||
| 1 file changed, 5 insertions(+), 5 deletions(-) | ||
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| diff --git a/docs/community/team.md b/docs/community/team.md | ||
| index 0b7d316d..726dfcaa 100644 | ||
| --- a/docs/community/team.md | ||
| +++ b/docs/community/team.md | ||
| @@ -12,21 +12,21 @@ napari is a consensus-based community project. Anyone with an interest in the pr | ||
| - [Kevin Yamauchi](https://github.com/napari/napari/commits?author=kevinyamauchi) - [@kevinyamauchi](https://github.com/kevinyamauchi)* | ||
| - [Kira Evans](https://github.com/napari/napari/commits?author=kne42) - [@kne42](https://github.com/kne42) | ||
| - [Kyle Harrington](https://github.com/napari/napari/commits?author=kephale) - [@kephale](https://github.com/kephale)* | ||
| -- [Loic Royer](https://github.com/napari/napari/commits?author=royerloic) - [@royerloic](https://github.com/royerloic)^ | ||
| - [Lorenzo Gaifas](https://github.com/napari/napari/commits?author=brisvag) - [@brisvag](https://github.com/brisvag) | ||
| - [Wouter-Michiel Vierdag](https://github.com/napari/napari/commits?author=melonora) - [@melonora](https://github.com/melonora) | ||
| -- [Nicholas Sofroniew](https://github.com/napari/napari/commits?author=sofroniewn) - [@sofroniewn](https://github.com/sofroniewn)^ | ||
| - [Peter Sobolewski](https://github.com/napari/napari/commits?author=psobolewskiPhD) - [@psobolewskiPhD](https://github.com/psobolewskiPhD) | ||
|
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| ## Emeritus Core Developers | ||
|
|
||
| +- [Ahmet Can Solak](https://github.com/napari/napari/commits?author=AhmetCanSolak) - [@AhmetCanSolak](https://github.com/AhmetCanSolak) | ||
| +- [Alister Burt](https://github.com/napari/napari/commits?author=alisterburt) - [@alisterburt](https://github.com/alisterburt) | ||
| +- [Justine Larsen](https://github.com/napari/napari/commits?author=justinelarsen) - [@justinelarsen](https://github.com/justinelarsen) | ||
| +- [Loic Royer](https://github.com/napari/napari/commits?author=royerloic) - [@royerloic](https://github.com/royerloic)^ | ||
| +- [Nicholas Sofroniew](https://github.com/napari/napari/commits?author=sofroniewn) - [@sofroniewn](https://github.com/sofroniewn)^ | ||
| - [Shannon Axelrod](https://github.com/napari/napari/commits?author=shanaxel42) - [@shanaxel42](https://github.com/shanaxel42) | ||
| - [Talley Lambert](https://github.com/napari/napari/commits?author=tlambert03) - [@tlambert03](https://github.com/tlambert03)^ | ||
| -- [Justine Larsen](https://github.com/napari/napari/commits?author=justinelarsen) - [@justinelarsen](https://github.com/justinelarsen) | ||
| - [Ziyang Liu](https://github.com/napari/napari/commits?author=potating-potato) - [@potating-potato](https://github.com/potating-potato) | ||
| -- [Ahmet Can Solak](https://github.com/napari/napari/commits?author=AhmetCanSolak) - [@AhmetCanSolak](https://github.com/AhmetCanSolak) | ||
| -- [Alister Burt](https://github.com/napari/napari/commits?author=alisterburt) - [@alisterburt](https://github.com/alisterburt) | ||
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| <sub>* on the napari [steering council](https://napari.org/community/governance.html#steering-council).</sub> |