Merge pull request #378 from w-k-jones/3d_area_calculation

Implement area calculation for footprint of 3D objects

Author: w-k-jones

.github/workflows/check_formatting.yml

@@ -19,4 +19,5 @@ jobs:
         shell: bash -l {0}
         run:
           mamba install --quiet --yes --file requirements.txt black &&
-          black tobac --check --diff
+          black --version &&
+          black tobac --check --diff 

doc/tobac.rst

@@ -7,7 +7,26 @@ Submodules
 tobac.analysis module
 ---------------------
 
-.. automodule:: tobac.analysis
+tobac.analysis.cell_analysis module
+---------------------
+
+.. automodule:: tobac.analysis.cell_analysis
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tobac.analysis.feature_analysis module
+---------------------
+
+.. automodule:: tobac.analysis.feature_analysis
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tobac.analysis.spatial module
+---------------------
+
+.. automodule:: tobac.analysis.spatial
    :members:
    :undoc-members:
    :show-inheritance:
@@ -71,18 +90,26 @@ tobac.tracking module
 tobac.utils modules
 ------------------
 
-tobac.utils.general module
+tobac.utils.bulk_statistics module
 ------------------
 
-.. automodule:: tobac.utils.general
+.. automodule:: tobac.utils.bulk_statistics
    :members:
    :undoc-members:
    :show-inheritance:
 
-tobac.utils.bulk_statistics module
+tobac.utils.decorators module
 ------------------
 
-.. automodule:: tobac.utils.bulk_statistics
+.. automodule:: tobac.utils.decorators
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tobac.utils.general module
+------------------
+
+.. automodule:: tobac.utils.general
    :members:
    :undoc-members:
    :show-inheritance:
@@ -95,6 +122,14 @@ tobac.utils.mask module
    :undoc-members:
    :show-inheritance:
 
+tobac.utils.periodic_boundaries module
+------------------
+
+.. automodule:: tobac.utils.periodic_boundaries
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 
 tobac.wrapper module
 --------------------

examples/Basics/Idealized-Case-1_Tracking-of-a-Test-Blob-in-2D.ipynb

@@ -1,10 +1,10 @@
-from setuptools import setup
-
 """
 This code is from the python documentation and is
 designed to read in the version number.
 See: https://packaging.python.org/en/latest/guides/single-sourcing-package-version/
 """
+
+from setuptools import setup
 from pathlib import Path
 
 
@@ -37,6 +37,14 @@ def get_requirements(requirements_filename):
     return requirements
 
 
+def get_packages(package_name):
+    package = Path(package_name)
+    packages = [
+        str(path.parent).replace("/", ".") for path in package.rglob("__init__.py")
+    ]
+    return packages
+
+
 PACKAGE_NAME = "tobac"
 
 # See classifiers list at: https://pypi.org/classifiers/
@@ -86,7 +94,7 @@ def get_requirements(requirements_filename):
         "peter.marinescu@colostate.edu",
     ],
     license="BSD-3-Clause License",
-    packages=[PACKAGE_NAME, PACKAGE_NAME + ".utils", PACKAGE_NAME + ".utils.internal"],
+    packages=get_packages(PACKAGE_NAME),
     install_requires=get_requirements("requirements.txt"),
     test_requires=["pytest"],
     zip_safe=False,

setup.py

@@ -29,47 +29,53 @@
     plot_mask_cell_track_follow,
     plot_mask_cell_track_static,
     plot_mask_cell_track_static_timeseries,
-)
-from .plotting import (
     plot_lifetime_histogram,
     plot_lifetime_histogram_bar,
     plot_histogram_cellwise,
     plot_histogram_featurewise,
-)
-from .plotting import plot_mask_cell_track_3Dstatic, plot_mask_cell_track_2D3Dstatic
-from .plotting import (
+    plot_mask_cell_track_3Dstatic,
+    plot_mask_cell_track_2D3Dstatic,
     plot_mask_cell_individual_static,
     plot_mask_cell_individual_3Dstatic,
+    animation_mask_field,
+    make_map,
+    map_tracks,
 )
-from .plotting import animation_mask_field
-from .plotting import make_map, map_tracks
-from .analysis import (
+from tobac.analysis.cell_analysis import (
     cell_statistics,
     cog_cell,
     lifetime_histogram,
-    histogram_featurewise,
     histogram_cellwise,
-)
-from .analysis import calculate_velocity, calculate_distance, calculate_area
-from .analysis import calculate_nearestneighbordistance
-from .analysis import (
     velocity_histogram,
+    calculate_overlap,
+)
+from tobac.analysis.feature_analysis import (
+    histogram_featurewise,
+    calculate_nearestneighbordistance,
     nearestneighbordistance_histogram,
     area_histogram,
 )
-from .analysis import calculate_overlap
-from .utils import (
+from tobac.analysis.spatial import (
+    calculate_velocity,
+    calculate_distance,
+    calculate_area,
+)
+from .utils.mask import (
     mask_cell,
     mask_cell_surface,
     mask_cube_cell,
     mask_cube_untracked,
     mask_cube,
     column_mask_from2D,
+    mask_features,
+    mask_features_surface,
+    mask_cube_features,
+)
+from .utils.general import (
     get_bounding_box,
+    add_coordinates,
+    get_spacings,
 )
-from .utils import mask_features, mask_features_surface, mask_cube_features
-
-from .utils import add_coordinates, get_spacings
 from .feature_detection import feature_detection_multithreshold
 from .tracking import linking_trackpy
 from .wrapper import maketrack