Merge branch 'RC_v1.5.x' into dev_developer_guide

doc/conf.py

@@ -19,15 +19,14 @@
     "sphinx_rtd_theme",
     "sphinx.ext.napoleon",
     "nbsphinx",
-   "sphinx_gallery.load_style",
+    "sphinx_gallery.load_style",
 ]
 
 
 html_theme = "sphinx_rtd_theme"
 
 html_static_path = ["_static"]
-
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 
 
 project = "tobac"
@@ -81,3 +80,18 @@ def setup(app):
 napoleon_preprocess_types = False
 napoleon_type_aliases = None
 napoleon_attr_annotations = True
+
+nbsphinx_thumbnails = {
+    "examples/Basics/Idealized-Case-1_Tracking-of-a-Test-Blob-in-2D": "_static/thumbnails/Basics_Idealized-Case-1_Tracking-of-a-Test-Blob-in-2D_Thumbnail.png",
+    "examples/Basics/Idealized-Case-2_Two_crossing_Blobs": "_static/thumbnails/Basics_Idealized-Case-2_Two_crossing_Blobs_Thumbnail.png",
+    "examples/Basics/Methods-and-Parameters-for-Feature-Detection_Part_1": "_static/thumbnails/Basics_Methods-and-Parameters-for-Feature-Detection_Part_1_Thumbnail.png",
+    "examples/Basics/Methods-and-Parameters-for-Feature-Detection_Part_2": "_static/thumbnails/Basics_Methods-and-Parameters-for-Feature-Detection_Part_2_Thumbnail.png",
+    "examples/Basics/Methods-and-Parameters-for-Linking": "_static/thumbnails/Basics_Methods-and-Parameters-for-Linking_Thumbnail.png",
+    "examples/Basics/Methods-and-Parameters-for-Segmentation": "_static/thumbnails/Basics_Methods-and-Parameters-for-Segmentation_Thumbnail.png",
+    "examples/Example_OLR_Tracking_model/Example_OLR_Tracking_model": "_static/thumbnails/Example_OLR_Tracking_model_Thumbnail.png",
+    "examples/Example_OLR_Tracking_satellite/Example_OLR_Tracking_satellite": "_static/thumbnails/Example_OLR_Tracking_satellite_Thumbnail.png",
+    "examples/Example_Precip_Tracking/Example_Precip_Tracking": "_static/thumbnails/Example_Precip_Tracking_Thumbnail.png",
+    "examples/Example_Track_on_Radar_Segment_on_Satellite/Example_Track_on_Radar_Segment_on_Satellite": "_static/thumbnails/Example_Track_on_Radar_Segment_on_Satellite_Thumbnail.png",
+    "examples/Example_Updraft_Tracking/Example_Updraft_Tracking": "_static/thumbnails/Example_Updraft_Tracking_Thumbnail.png",
+    "examples/Example_vorticity_tracking_model/Example_vorticity_tracking_model": "_static/thumbnails/Example_vorticity_tracking_model_Thumbnail.png",
+}

doc/examples.rst

@@ -6,30 +6,30 @@ tobac is provided with a set of Jupyter notebooks that show examples of the appl
 .. nbgallery::
    :caption: Fundamentals of Detection and Tracking
 
-   Test Blob in 2D <examples4doc/Basics/Idealized-Case-1_Tracking-of-a-Test-Blob-in-2D>
-   Two crossing Blobs <examples4doc/Basics/Idealized-Case-2_Two_crossing_Blobs.ipynb>
-   
-   On Feature Detection: Part 1 <examples4doc/Basics/Methods-and-Parameters-for-Feature-Detection_Part_1.ipynb> 
-   On Feature Detection: Part 2 <examples4doc/Basics/Methods-and-Parameters-for-Feature-Detection_Part_2.ipynb>
-   On Segmentation <examples4doc/Basics/Methods-and-Parameters-for-Segmentation.ipynb>
-   On Linking <examples4doc/Basics/Methods-and-Parameters-for-Linking.ipynb>  
+   Test Blob in 2D <examples/Basics/Idealized-Case-1_Tracking-of-a-Test-Blob-in-2D>
+   Two crossing Blobs <examples/Basics/Idealized-Case-2_Two_crossing_Blobs.ipynb>
+
+   On Feature Detection: Part 1 <examples/Basics/Methods-and-Parameters-for-Feature-Detection_Part_1.ipynb>
+   On Feature Detection: Part 2 <examples/Basics/Methods-and-Parameters-for-Feature-Detection_Part_2.ipynb>
+   On Segmentation <examples/Basics/Methods-and-Parameters-for-Segmentation.ipynb>
+   On Linking <examples/Basics/Methods-and-Parameters-for-Linking.ipynb>
 
 
 
 
 .. nbgallery::
    :caption: Examples of Using *tobac* with Observations
-   
-   OLR from GOES-13 Satellite <examples4doc/Example_OLR_Tracking_satellite/Example_OLR_Tracking_satellite>
-   Combine Radar & Satellite <examples4doc/Example_Track_on_Radar_Segment_on_Satellite/Example_Track_on_Radar_Segment_on_Satellite>
+
+   OLR from GOES-13 Satellite <examples/Example_OLR_Tracking_satellite/Example_OLR_Tracking_satellite>
+   Combine Radar & Satellite <examples/Example_Track_on_Radar_Segment_on_Satellite/Example_Track_on_Radar_Segment_on_Satellite>
 
 
 .. nbgallery::
    :caption: Examples of Using *tobac* with Model Data
 
-   WRF OLR <examples4doc/Example_OLR_Tracking_model/Example_OLR_Tracking_model>
-   WRF Precip <examples4doc/Example_Precip_Tracking/Example_Precip_Tracking>
-   WRF Updrafts <examples4doc/Example_Updraft_Tracking/Example_Updraft_Tracking>
-   WRF Mesoscale Vorticity <examples4doc/Example_vorticity_tracking_model/Example_vorticity_tracking_model> 
+   WRF OLR <examples/Example_OLR_Tracking_model/Example_OLR_Tracking_model>
+   WRF Precip <examples/Example_Precip_Tracking/Example_Precip_Tracking>
+   WRF Updrafts <examples/Example_Updraft_Tracking/Example_Updraft_Tracking>
+   WRF Mesoscale Vorticity <examples/Example_vorticity_tracking_model/Example_vorticity_tracking_model>
 
-The notebooks can be found in the **examples** folder as part of the python package. The necessary input data for these examples is avaliable on zenodo and can be downloaded automatically by the Jupyter notebooks.
+The notebooks can be found in the **examples** folder as part of the python package. The necessary input data for these examples is avaliable on zenodo and can be downloaded automatically by the Jupyter notebooks.

tobac/feature_detection.py

@@ -31,7 +31,6 @@
 import iris
 import xarray as xr
 
-from tobac.tracking import build_distance_function
 from tobac.utils import internal as internal_utils
 from tobac.utils import decorators
 
@@ -1545,8 +1544,8 @@ def filter_min_distance(
     # Check if we have PBCs.
     if PBC_flag in ["hdim_1", "hdim_2", "both"]:
         # Note that we multiply by dxy to get the distances in spatial coordinates
-        dist_func = build_distance_function(
-            min_h1 * dxy, max_h1 * dxy, min_h2 * dxy, max_h2 * dxy, PBC_flag
+        dist_func = pbc_utils.build_distance_function(
+            min_h1 * dxy, max_h1 * dxy, min_h2 * dxy, max_h2 * dxy, PBC_flag, is_3D
         )
         features_tree = BallTree(feature_locations, metric="pyfunc", func=dist_func)
         neighbours = features_tree.query_radius(feature_locations, r=min_distance)

tobac/segmentation.py

@@ -181,6 +181,10 @@ def add_markers(
                 h2_end_coord=hdim_2_max,
                 PBC_flag=PBC_flag,
             )
+            # Build distance function ahead of time, 3D always true as we then reduce
+            dist_func = pbc_utils.build_distance_function(
+                0, h1_len, 0, h2_len, PBC_flag, True
+            )
             for seed_box in all_seed_boxes:
                 # Need to see if there are any other points seeded
                 # in this seed box first.
@@ -205,6 +209,7 @@ def add_markers(
                                 local_index[1] + seed_box[0],
                                 local_index[2] + seed_box[2],
                             )
+
                             # If it's a background marker, we can just set it
                             # with the feature we're working on.
                             if curr_box_pt == bg_marker:
@@ -213,18 +218,14 @@ def add_markers(
                             # it has another feature in it. Calculate the distance
                             # from its current set feature and the new feature.
                             if is_3D:
-                                curr_coord = (row["vdim"], row["hdim_1"], row["hdim_2"])
+                                curr_coord = np.array(
+                                    (row["vdim"], row["hdim_1"], row["hdim_2"])
+                                )
                             else:
-                                curr_coord = (0, row["hdim_1"], row["hdim_2"])
-
-                            dist_from_curr_pt = pbc_utils.calc_distance_coords_pbc(
-                                np.array(global_index),
-                                np.array(curr_coord),
-                                min_h1=0,
-                                max_h1=h1_len,
-                                min_h2=0,
-                                max_h2=h2_len,
-                                PBC_flag=PBC_flag,
+                                curr_coord = np.array((0, row["hdim_1"], row["hdim_2"]))
+
+                            dist_from_curr_pt = dist_func(
+                                np.array(global_index), curr_coord
                             )
 
                             # This is technically an O(N^2) operation, but
@@ -234,21 +235,19 @@ def add_markers(
                                 features["feature"] == curr_box_pt
                             ].iloc[0]
                             if is_3D:
-                                orig_coord = (
-                                    orig_row["vdim"],
-                                    orig_row["hdim_1"],
-                                    orig_row["hdim_2"],
+                                orig_coord = np.array(
+                                    (
+                                        orig_row["vdim"],
+                                        orig_row["hdim_1"],
+                                        orig_row["hdim_2"],
+                                    )
                                 )
                             else:
-                                orig_coord = (0, orig_row["hdim_1"], orig_row["hdim_2"])
-                            dist_from_orig_pt = pbc_utils.calc_distance_coords_pbc(
-                                np.array(global_index),
-                                np.array(orig_coord),
-                                min_h1=0,
-                                max_h1=h1_len,
-                                min_h2=0,
-                                max_h2=h2_len,
-                                PBC_flag=PBC_flag,
+                                orig_coord = np.array(
+                                    (0, orig_row["hdim_1"], orig_row["hdim_2"])
+                                )
+                            dist_from_orig_pt = dist_func(
+                                np.array(global_index), orig_coord
                             )
                             # The current point center is further away
                             # than the original point center, so do nothing