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Add CrownProfile class #311

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merged 13 commits into from
Sep 30, 2024
Merged

Add CrownProfile class #311

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ece4d03
Merge pull request #310 from ImperialCollegeLondon/develop
davidorme Sep 30, 2024
9d725f6
CrownProfile and calculate_canopy_radius
davidorme Sep 27, 2024
8e10767
Canopy -> crown in functions and docstrings
davidorme Sep 27, 2024
8dfdfd5
More canopy -> crown
davidorme Sep 27, 2024
de41267
Move crown trait functions for crown_qm and crown_z_max into flora mo…
davidorme Sep 27, 2024
e3800db
Move crown_r0 and crown_zmax allometry functions into t_model_functions
davidorme Sep 27, 2024
9073bec
Fixing tests
davidorme Sep 27, 2024
e8afa77
Typo in crown radius attribute
davidorme Sep 30, 2024
d28afee
Moar typos
davidorme Sep 30, 2024
b2a5edd
Yet moar typos
davidorme Sep 30, 2024
deae519
Added a simple validation that CanopyProfile gets the same answers as…
davidorme Sep 30, 2024
062d820
Renaming canopy_functions to crown
davidorme Sep 30, 2024
502968d
Docstring fixes from @j-emberton
davidorme Sep 30, 2024
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10 changes: 5 additions & 5 deletions pyrealm/demography/canopy.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
from scipy.optimize import root_scalar # type: ignore [import-untyped]

from pyrealm.demography.canopy_functions import (
calculate_relative_canopy_radius_at_z,
calculate_relative_crown_radius_at_z,
calculate_stem_projected_crown_area_at_z,
calculate_stem_projected_leaf_area_at_z,
solve_community_projected_canopy_area,
Expand Down Expand Up @@ -114,7 +114,7 @@ def _calculate_canopy(self, community: Community) -> None:
community.stem_traits.m,
community.stem_traits.n,
community.stem_traits.q_m,
community.stem_allometry.canopy_z_max,
community.stem_allometry.crown_z_max,
community.cohort_data["n_individuals"],
target_area,
False, # validate
Expand All @@ -134,7 +134,7 @@ def _calculate_canopy(self, community: Community) -> None:
# NOTE - here and in the calls below, validate=False is enforced because the
# Community class structures and code should guarantee valid inputs and so
# turning off the validation internally should simply speed up the code.
self.stem_relative_radius = calculate_relative_canopy_radius_at_z(
self.stem_relative_radius = calculate_relative_crown_radius_at_z(
z=self.layer_heights,
stem_height=community.stem_allometry.stem_height,
m=community.stem_traits.m,
Expand All @@ -149,7 +149,7 @@ def _calculate_canopy(self, community: Community) -> None:
crown_area=community.stem_allometry.crown_area,
stem_height=community.stem_allometry.stem_height,
q_m=community.stem_traits.q_m,
z_max=community.stem_allometry.canopy_z_max,
z_max=community.stem_allometry.crown_z_max,
validate=False,
)

Expand All @@ -161,6 +161,6 @@ def _calculate_canopy(self, community: Community) -> None:
stem_height=community.stem_allometry.stem_height,
f_g=community.stem_traits.f_g,
q_m=community.stem_traits.q_m,
z_max=community.stem_allometry.canopy_z_max,
z_max=community.stem_allometry.crown_z_max,
validate=False,
)
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