Topology Module¶
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class
topology.Tree_Grid(x_max, y_max, patch_area, I0, k, delta_h, phi_act, lday, ndim=5, dim_names=['GroundLight', 'LianaCoverage', 'Temperature', 'WindSpeed', 'Humidity'])[source]¶ Represent space as a grid.
- Args:
- x_maxint
Number of horizontal cells
- y_maxint
Number of vertical cells
- patch_areafloat
Area of each patch (cell) in squared meters
- I0float
Incoming irradiance on top of canopy [umol photon / m^2s]
- kfloat
Light extinction coefficient.
- delta_h :float
Height of each vertical layer.
- phi_actfloat
Photosynthetic active period.
- ldayint
Mean day length during the vegetation period phi_act.
- ndimint
Number of dimensions. One per environmental variable.
- dim_nameslist
A list of ‘ndim’ strings representing the names of dimensions.
- Attributes:
- LAIsdict
Dictionary with patches as keys and a list of averaged Leaf Area Indices (one for each vertical layer) as values.
- CCAsdict
Dictionary with patches as keys a a list of Cummulative Crown Areas (one for each vertical layer) as values.
- trees_per_patchlist
Dictionary with patches (‘(x,y)’) as keys and a list of tree ids as values
- total_area :float
Area of all simulated patches in ha
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calculate_liana_biomass()[source]¶ Calculate the biomass of lianas in one patch based on the coverage.
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calculate_liana_coverage()[source]¶ Calculate the coverage (%) os lianas in on patch based on the previous coverage, temperature, humidity and wind speed
- Returns:
None
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check_CCA(h0, h1, patch)[source]¶ Check if the there is enough space forthe new plants to be established
Note: Cummulative Crown Area is homogeneized at the patch level
- Args:
- h0float
Allometric paramenter used to calculate initial height
- h1float
Allometric paramenter used to calculate initial height
- patchtuple
(x,y), patch that will have the light conditions assessed.
- Returns: bool.
True if there is enough space.
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check_light(min_light, patch)[source]¶ Check if the light intensity at ground level meets the needs for seed germination.
Note: Ligth intensity is homogeneized at the patch level.
- Args:
- min_lightfloat
Minimum light intensity at ground for seeds to germinate.
- patchtuple
(x,y), patch that will have the light conditions assessed.
- Returns: bool.
True if light level is above minimum.
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cohorts(patches)[source]¶ Assemble cohorts based on tree type and age.
Uses the trees_per_type() and trees_by_age_groups() methods to organize a dictionary of dictionaries containing the indices of trees in each age group within each type
- Args:
- Patches :list
A list of tuples representing patch coordinatas
[(x1,y1),(x2,y2)…]
- Returns: dict
- cohorsts: a dictionary with trees organized by type and age:
{FunctionalType1:{AgeGroup1:[tree1,tree2,tree3…]}}
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exeeding_CCA()[source]¶ Finds which patches have the cummulative crown area bigger than the patch area in at least one layer.
- Returns: list
Alist of patchs ([(x,y),(x,y),…,(x,y)])
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ground_level_light()[source]¶ Calculate the amount of light that reaches the ground.
The value per patch is stored in the “GroundLight” dimension. Values are homogeneized at the patch level.
- Returns:
None.
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patch_based_CCA(trees_per_patch)[source]¶ Calculate the Leaf Area Index for each patch in the grid.
- Args:
trees_per_patch : dict Dictionary in which keys are patches (‘(x,y)’)’ and values are lists of the trees ids in that patch.
- Returns: dict
L_per_layer: dictionary in which the keys are the same as the ones in trees_per_patch and values are a list of the CCA per vertical layer
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patch_based_LAI(trees_per_patch)[source]¶ Calculate the Leaf Area Index for each patch in the grid.
- Args:
- trees_per_patch :dict
Dictionary in which keys are patch coordinates (x,y) and values are a list of the tree ids in that patch.
- Returns: dict
L_per_layer: dictionary in which the keys are patch coordinates(‘(x,y)’)-the same as the ones in trees_per_patch- and values are a list of the LAI per vertical layer
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seed_establishment(seedbank)[source]¶ Check if the seeds in the seedbank have the light and space conditions to germinate.
Note: All seeds in the given seedbank are assumed to have the same conditions. Multiple calls to this method passing different seedbanks allow the representation of different requirements.
All established individuals are initiated with a predefined DBH (the same for all individuals), but initial height is calculated based on functional relationships and only if there is enough space in that layer a new individual will be stablished.
Args:
- seedbankdict
Dictionary with Functional Type (FT) and list of seed positions as values.
- lminfloat
Minimum light intensity at ground level for seed to germinate.
- h0float
Allometric paramenter used to calculate initial height.
- h1float
Allometric paramenter used to calculate initial height.
- Returns: dict
est_seeds: a dictionary with patches as keys (‘(x,y)’) and number of established seeds as values.
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trees_in_patches(patches)[source]¶ Make a list of tree ids and their respective positions.
- Args:
- patchlist
A list of tuples representing the patch coordinates ‘(x,y)’.
- Returns: list
id_pos: a list tuples with tree ids and positions ‘(id,(x_pos,y_pos))’
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trees_per_age_groups(list_of_trees)[source]¶ Return a dictionary in which keys are a age group and values are lists containing the id of the respective trees.
- Args:
- list_of_trees: list
A list with the id of trees.
- Returns: dict
A dictionary age as keys and a list of tree ids as values.