updating docs

README.md

@@ -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"
  }]
 }

docs/quickstart.rst

@@ -32,22 +32,22 @@ jupyter notebook interaction
  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_region(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", "Density"),
+ left_edge = left_edge,
+ right_edge = right_edge,
+ resolution = res)
 
 
-:code:`yt_scene.add_to_viewer` accepts any of the keyword arguments allowed by :code:`viewer.add_image`.
+:code:`yt_scene.add_region` accepts any of the keyword arguments allowed by :code:`viewer.add_image`.
 
 See :meth:`yt_napari.viewer.Scene` for all available methods and the :doc:`example notebooks <notebooks>` for further examples.
 
@@ -60,16 +60,15 @@ loading a json file from the napari gui
 
 .. code-block:: json
 
- {"$schema": "https://raw.githubusercontent.com/data-exp-lab/yt-napari/main/src/yt_napari/schemas/yt-napari_0.0.1.json",
+ {"$schema": "https://yt-napari.readthedocs.io/en/latest/_static/yt-napari_latest.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],
+ "left_edge": {"value": [460.0, 460.0, 460.0], "unit": "kpc"},
+ "right_edge": {"value": [560.0, 560.0, 560.0], "unit": "kpc"},
  "resolution": [600, 600, 600]
- }],
- "edge_units": "kpc"
+ }]}
  }]
  }
 

src/yt_napari/viewer.py

@@ -121,7 +121,7 @@ def add_region(
  **kwargs,
  ):
  """
- create a uniform sampling of ds and add it to the napari viewer
+ uniformly sample a region from a yt dataset and add it to a viewer
 
  Parameters
  ----------
@@ -242,6 +242,51 @@ def add_slice(
  link_to: Optional[Union[str, Layer]] = None,
  **kwargs,
  ):
+ """
+ sample an orthogonal slice from a yt dataset and add it to a viewer
+
+ Parameters
+ ----------
+ viewer: napari.Viewer
+ the active napari viewer
+ ds
+ the yt dataset to sample
+ normal: str, int
+ the normal axis of the slice, either an axis name or number
+ field: Tuple[str, str]
+ the field tuple to sample e.g., ('enzo', 'Density')
+ center: unyt_array
+ the center of the slice (3D)
+ width: unyt_quantity
+ the width of the slice
+ height: unyt_quantity
+ the height of the slice
+ resolution: Tuple[int, int]
+ the sampling resolution in each dimension, e.g., (400, 400)
+ take_log : Optional[bool]
+ if True, will take the log of the extracted data. Defaults to the
+ default behavior for the field set by ds.
+ periodic: Optional[bool]
+ use periodic bounds for the slice, default False
+ colormap : Optional[str]
+ the color map to use, default is "viridis"
+ link_to : Optional[Union[str, Layer]]
+ specify a layer to which the new layer should link
+ **kwargs :
+ any keyword argument accepted by Viewer.add_image()
+
+ Examples
+ --------
+
+ >>> import napari
+ >>> import yt
+ >>> from yt_napari.viewer import Scene
+ >>> viewer = napari.Viewer()
+ >>> ds = yt.load_sample("IsolatedGalaxy")
+ >>> yt_scene = Scene()
+ >>> yt_scene.add_slice(viewer, ds, "x", ("enzo", "Temperature"))
+
+ """
 
  if take_log is None:
  take_log = ds._get_field_info(field).take_log