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Slice operator #53

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merged 23 commits into from
Jul 7, 2023
Merged

Slice operator #53

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5083d62
in progress (will fail tests)
chrishavlin Jun 26, 2023
e096d1f
in progress, can kind of load from json
chrishavlin Jun 27, 2023
9bfdd97
passing tests locally but not very functional yet...
chrishavlin Jun 29, 2023
f97932f
(in progress) widget rebuild: multi selections.
chrishavlin Jun 30, 2023
9df74ef
loading runs, some things to fix
chrishavlin Jul 3, 2023
36e8d32
fix the log business
chrishavlin Jul 3, 2023
285a0b8
widg_id always goes up
chrishavlin Jul 3, 2023
9ba45dc
use the _model_ingestor layer sanitization
chrishavlin Jul 5, 2023
f5a1f59
check for existing ref layer in napari layers
chrishavlin Jul 5, 2023
235800e
account for initial aspect ratio
chrishavlin Jul 5, 2023
0854d0c
slices working!
chrishavlin Jul 6, 2023
8351a1b
tests passing locally, need to increase coverage
chrishavlin Jul 6, 2023
e115005
filename can now refer to a _ytnapari_ callable
chrishavlin Jul 6, 2023
89216bc
slicing in viewer.Scene, tests pass locally
chrishavlin Jul 6, 2023
d992d3b
deprecate rather than remove add_to_scene
chrishavlin Jul 7, 2023
c5e5c7f
warning stack level
chrishavlin Jul 7, 2023
fe85281
improve teset coverage
chrishavlin Jul 7, 2023
e59d8c0
more coverage improvements
chrishavlin Jul 7, 2023
7b0ea09
more coverage
chrishavlin Jul 7, 2023
a0ba7c5
update notebooks
chrishavlin Jul 7, 2023
f239d7f
updating docs
chrishavlin Jul 7, 2023
04c5252
slice notebook
chrishavlin Jul 7, 2023
9e87f50
update readme
chrishavlin Jul 7, 2023
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34 changes: 17 additions & 17 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -74,30 +74,30 @@ left_edge = ds.domain_center - ds.arr([40, 40, 40], 'kpc')
right_edge = ds.domain_center + ds.arr([40, 40, 40], 'kpc')
res = (600, 600, 600)

yt_scene.add_to_viewer(viewer,
ds,
("enzo", "Temperature"),
left_edge = left_edge,
right_edge = right_edge,
resolution = res)

yt_scene.add_to_viewer(viewer,
ds,
("enzo", "Density"),
left_edge = left_edge,
right_edge = right_edge,
resolution = res)
yt_scene.add_region(viewer,
ds,
("enzo", "Temperature"),
left_edge=left_edge,
right_edge=right_edge,
resolution=res)

yt_scene.add_region(viewer,
ds,
("enzo", "Density"),
left_edge=left_edge,
right_edge=right_edge,
resolution=res)

nbscreenshot(viewer)
```

![Loading a subset of a yt dataset in napari from a Jupyter notebook](./assets/images/readme_ex_001.png)

`yt_scene.add_to_viewer` accepts any of the keyword arguments allowed by `viewer.add_image`. See the full documentation (https://yt-napari.readthedocs.io/) for more examples, including additional helper methods for linking layer appearance.
`yt_scene.add_to_viewer` accepts any of the keyword arguments allowed by `viewer.add_image`. See the full documentation (https://yt-napari.readthedocs.io/en/stable/) for more examples, including additional helper methods for linking layer appearance.

### loading a selection from a yt dataset interactively

`yt-napari` provides a two ways to sample a yt dataset and load in an image layer into a Napari viewer: the yt Reader plugin and json file specification.
`yt-napari` provides two ways to sample a yt dataset and load in an image layer into a Napari viewer: the yt Reader plugin and json file specification.

#### using the yt Reader plugin

Expand All @@ -115,13 +115,13 @@ To load a different field or section, adjust the values and click "Load" again.
```json
{"$schema": "https://raw.githubusercontent.com/data-exp-lab/yt-napari/main/src/yt_napari/schemas/yt-napari_0.0.1.json",
"data": [{"filename": "IsolatedGalaxy/galaxy0030/galaxy0030",
"selections": [{
"selections": {"regions": [{
"fields": [{"field_name": "Temperature", "field_type": "enzo", "take_log": true},
{"field_name": "Density", "field_type": "enzo", "take_log": true}],
"left_edge": [460.0, 460.0, 460.0],
"right_edge": [560.0, 560.0, 560.0],
"resolution": [600, 600, 600]
}],
}]},
"edge_units": "kpc"
}]
}
Expand Down
96 changes: 48 additions & 48 deletions docs/examples/ytnapari_scene_01_intro.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -41,11 +41,11 @@
"name": "stderr",
"output_type": "stream",
"text": [
"yt : [INFO ] 2022-03-08 19:25:04,825 Parameters: current_time = 0.0060000200028298\n",
"yt : [INFO ] 2022-03-08 19:25:04,826 Parameters: domain_dimensions = [32 32 32]\n",
"yt : [INFO ] 2022-03-08 19:25:04,828 Parameters: domain_left_edge = [0. 0. 0.]\n",
"yt : [INFO ] 2022-03-08 19:25:04,829 Parameters: domain_right_edge = [1. 1. 1.]\n",
"yt : [INFO ] 2022-03-08 19:25:04,830 Parameters: cosmological_simulation = 0\n"
"yt : [INFO ] 2023-07-07 12:10:53,595 Parameters: current_time = 0.0060000200028298\n",
"yt : [INFO ] 2023-07-07 12:10:53,596 Parameters: domain_dimensions = [32 32 32]\n",
"yt : [INFO ] 2023-07-07 12:10:53,597 Parameters: domain_left_edge = [0. 0. 0.]\n",
"yt : [INFO ] 2023-07-07 12:10:53,604 Parameters: domain_right_edge = [1. 1. 1.]\n",
"yt : [INFO ] 2023-07-07 12:10:53,605 Parameters: cosmological_simulation = 0\n"
]
}
],
Expand Down Expand Up @@ -77,7 +77,7 @@
"id": "7759684f-8854-4fad-adfb-8004ebf3d01b",
"metadata": {},
"source": [
"The new `yt_scene` object will have a method, `add_to_viewer` that will uniformly sample the dataset and add the new sample to the viewer:"
"The new `yt_scene` object will have a method, `add_region` that will uniformly sample the dataset within a rectalinear region and add the new sample to the viewer:"
]
},
{
Expand All @@ -90,8 +90,8 @@
"name": "stderr",
"output_type": "stream",
"text": [
"Parsing Hierarchy : 100%|███████████████████| 173/173 [00:00<00:00, 4132.70it/s]\n",
"yt : [INFO ] 2022-03-08 19:25:04,966 Gathering a field list (this may take a moment.)\n"
"Parsing Hierarchy : 100%|██████████████████████████████████████████████████| 173/173 [00:00<00:00, 9528.50it/s]\n",
"yt : [INFO ] 2023-07-07 12:11:31,861 Gathering a field list (this may take a moment.)\n"
]
}
],
Expand All @@ -100,19 +100,19 @@
"right_edge = ds.domain_center + ds.arr([40, 40, 40], 'kpc')\n",
"res = (600, 600, 600)\n",
"\n",
"yt_scene.add_to_viewer(viewer,\n",
" ds,\n",
" (\"enzo\", \"Temperature\"),\n",
" left_edge = left_edge,\n",
" right_edge = right_edge,\n",
" resolution= res)\n",
"yt_scene.add_region(viewer,\n",
" ds,\n",
" (\"enzo\", \"Temperature\"),\n",
" left_edge = left_edge,\n",
" right_edge = right_edge,\n",
" resolution= res)\n",
"\n",
"yt_scene.add_to_viewer(viewer,\n",
" ds,\n",
" (\"enzo\", \"Density\"),\n",
" left_edge = left_edge,\n",
" right_edge = right_edge,\n",
" resolution = res)"
"yt_scene.add_region(viewer,\n",
" ds,\n",
" (\"enzo\", \"Density\"),\n",
" left_edge = left_edge,\n",
" right_edge = right_edge,\n",
" resolution = res)"
]
},
{
Expand Down Expand Up @@ -151,19 +151,19 @@
},
{
"cell_type": "code",
"execution_count": 7,
"execution_count": 6,
"id": "83009ffe-7675-4431-bf8e-5c13c4fc7d29",
"metadata": {},
"outputs": [],
"source": [
"left_edge = ds.domain_center - ds.arr([20, 20, 20], 'kpc')\n",
"right_edge = ds.domain_center + ds.arr([10, 10, 10], 'kpc')\n",
"yt_scene.add_to_viewer(viewer,\n",
" ds,\n",
" (\"enzo\", \"TotalEnergy\"),\n",
" left_edge = left_edge,\n",
" right_edge = right_edge,\n",
" resolution=(200, 200, 200))"
"yt_scene.add_region(viewer,\n",
" ds,\n",
" (\"enzo\", \"TotalEnergy\"),\n",
" left_edge = left_edge,\n",
" right_edge = right_edge,\n",
" resolution=(200, 200, 200))"
]
},
{
Expand Down Expand Up @@ -202,7 +202,7 @@
},
{
"cell_type": "code",
"execution_count": 10,
"execution_count": 7,
"id": "c3302d60-eec4-484c-a1fc-9d534351720b",
"metadata": {},
"outputs": [],
Expand All @@ -212,36 +212,36 @@
},
{
"cell_type": "code",
"execution_count": 12,
"execution_count": 8,
"id": "c584f4ab-c6c8-4d8d-93b5-8799cd14f8a8",
"metadata": {},
"outputs": [],
"source": [
"left_edge = ds.domain_center - ds.arr([10, 10, 10], 'kpc')\n",
"right_edge = ds.domain_center + ds.arr([10, 10, 10], 'kpc')\n",
"yt_scene.add_to_viewer(viewer,\n",
" ds,\n",
" (\"enzo\", \"Density\"),\n",
" left_edge = left_edge,\n",
" right_edge = right_edge, \n",
" resolution=(600, 600, 600),\n",
" colormap=\"magma\",\n",
" contrast_limits=(3.4, 6.4))\n",
"yt_scene.add_region(viewer,\n",
" ds,\n",
" (\"enzo\", \"Density\"),\n",
" left_edge = left_edge,\n",
" right_edge = right_edge, \n",
" resolution=(600, 600, 600),\n",
" colormap=\"magma\",\n",
" contrast_limits=(3.4, 6.4))\n",
"\n",
"yt_scene.add_to_viewer(viewer,\n",
" ds,\n",
" (\"enzo\", \"Temperature\"),\n",
" left_edge = left_edge,\n",
" right_edge = right_edge, \n",
" resolution=(300, 300, 300),\n",
" colormap=\"yellow\",\n",
" contrast_limits=(4., 6.),\n",
" opacity=0.6)"
"yt_scene.add_region(viewer,\n",
" ds,\n",
" (\"enzo\", \"Temperature\"),\n",
" left_edge = left_edge,\n",
" right_edge = right_edge, \n",
" resolution=(300, 300, 300),\n",
" colormap=\"yellow\",\n",
" contrast_limits=(4., 6.),\n",
" opacity=0.6)"
]
},
{
"cell_type": "code",
"execution_count": 13,
"execution_count": 9,
"id": "b2f04137-fcfa-4504-a0f5-345ed3b6ec14",
"metadata": {},
"outputs": [],
Expand Down Expand Up @@ -292,7 +292,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.0"
"version": "3.9.16"
}
},
"nbformat": 4,
Expand Down
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