From f239d7f2d34727331557c49c62ef577ea9d8d236 Mon Sep 17 00:00:00 2001
From: chrishavlin <chris.havlin@gmail.com>
Date: Fri, 7 Jul 2023 12:43:08 -0500
Subject: [PATCH] updating docs

---
 README.md               |  4 ++--
 docs/quickstart.rst     | 37 ++++++++++++++++----------------
 src/yt_napari/viewer.py | 47 ++++++++++++++++++++++++++++++++++++++++-
 3 files changed, 66 insertions(+), 22 deletions(-)

diff --git a/README.md b/README.md
index e4daa23..e68b184 100644
--- a/README.md
+++ b/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"
          }]
 }
diff --git a/docs/quickstart.rst b/docs/quickstart.rst
index 8f75273..db7e0a3 100644
--- a/docs/quickstart.rst
+++ b/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"
+                              }]}
              }]
     }
 
diff --git a/src/yt_napari/viewer.py b/src/yt_napari/viewer.py
index 49c14b7..e4b614e 100644
--- a/src/yt_napari/viewer.py
+++ b/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