Add new termite example #251
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Thanks for this PR, I'm terribly sorry we didn't get back to you sooner. In general, if no one gets back to you within 3 days, please ping us! @Sahil-Chhoker @sanika-n since most of us are reviewing 100+ proposals, could (one of) you maybe review this example? |
I can take a look at this tomorrow. |
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Important Review skippedAuto reviews are disabled on this repository. Please check the settings in the CodeRabbit UI or the You can disable this status message by setting the WalkthroughThe changes introduce a termite simulation using the Mesa framework. A new README provides an overview, installation instructions, and simulation details. An interactive visualization is added via a new Changes
Sequence Diagram(s)sequenceDiagram
participant User
participant Viz as SolaraViz
participant Model as TermiteModel
participant Agent as Termite Agent
participant Renderer as Visualization Component
User->>Viz: Start simulation
Viz->>Model: Initialize termite model with parameters
Model->>Agent: Create termite agents on grid
loop Simulation Steps
Agent->>Model: Execute step (move, pick up/drop wood chip)
Model->>Renderer: Update visualization
end
Renderer-->>User: Display updated simulation view
Poem
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Actionable comments posted: 3
🧹 Nitpick comments (17)
examples/termites/termites/model.py (4)
13-24: Improve docstring completeness for__init__The method docstring has two minor issues:
- It's missing documentation for the
seedparameter- There's a grammatical error in "Grid heights" (should be "Grid height")
- """Initialize the model. - - Args: - num_termites: Number of Termite Agents, - width: Grid width. - height: Grid heights. - wood_chip_density: Density of wood chips in the grid. - """ + """Initialize the model. + + Args: + num_termites: Number of Termite Agents. + width: Grid width. + height: Grid height. + wood_chip_density: Density of wood chips in the grid. + seed: Random seed for reproducibility. + """
24-26: Store width and height as instance variablesYou're using width and height to set up the grid and property layer, but you're not storing these values as instance variables. This might be useful for future reference or for other methods in the class.
super().__init__(seed=seed) self.num_termites = num_termites self.wood_chip_density = wood_chip_density + self.width = width + self.height = height
41-42: Fix comment syntaxThe comment has an extra triple quote which should be removed.
- # Adding PropertyLayer to the grid""" + # Adding PropertyLayer to the grid
51-52: Consider adding data collection capabilitiesThe current model implementation focuses on simulation without data collection. Consider adding a mechanism for collecting metrics over time, such as the number and size of wood chip piles, to help analyze the emergent behavior.
You could add a
DataCollectorto track metrics like wood chip pile sizes, average pile distance, or termite movement patterns, which would allow for quantitative analysis of the simulation outcomes.examples/termites/README.md (5)
18-18: Fix abbreviation formatThe abbreviation "i.e" should include the second period.
-Make sure that you have installed the `latest` version of mesa i.e `3.2.0.dev0` +Make sure that you have installed the `latest` version of mesa i.e. `3.2.0.dev0`🧰 Tools
🪛 LanguageTool
[uncategorized] ~18-~18: The abbreviation “i.e.” (= that is) requires two periods.
Context: ... installed thelatestversion of mesa i.e3.2.0.dev0## Usage To run the simu...(I_E)
37-37: Fix subject-verb agreementThe verb "interacts" doesn't agree with the plural subject "termites".
-- **Grid:** A two-dimensional toroidal grid where termites interacts with the wood chips. The toroidal nature means agents exiting one edge re-enter from the opposite edge, +- **Grid:** A two-dimensional toroidal grid where termites interact with the wood chips. The toroidal nature means agents exiting one edge re-enter from the opposite edge,🧰 Tools
🪛 LanguageTool
[uncategorized] ~37-~37: This verb does not appear to agree with the subject. Consider using a different form.
Context: ...imensional toroidal grid where termites interacts with the wood chips. The toroidal natur...(AI_EN_LECTOR_REPLACEMENT_VERB_AGREEMENT)
37-37: Remove trailing commaThere's an unnecessary trailing comma at the end of this sentence.
-- **Grid:** A two-dimensional toroidal grid where termites interacts with the wood chips. The toroidal nature means agents exiting one edge re-enter from the opposite edge, +- **Grid:** A two-dimensional toroidal grid where termites interact with the wood chips. The toroidal nature means agents exiting one edge re-enter from the opposite edge.🧰 Tools
🪛 LanguageTool
[uncategorized] ~37-~37: This verb does not appear to agree with the subject. Consider using a different form.
Context: ...imensional toroidal grid where termites interacts with the wood chips. The toroidal natur...(AI_EN_LECTOR_REPLACEMENT_VERB_AGREEMENT)
39-39: Fix extra spacingThere are two consecutive spaces between "storing" and "the".
-- **PropertyLayer:** A data structure overlaying the grid, storing the presence of wood chips at each cell. +- **PropertyLayer:** A data structure overlaying the grid, storing the presence of wood chips at each cell.
18-26: Enhance installation instructionsThe current installation instructions could be more specific about how to install the required version of Mesa.
-Make sure that you have installed the `latest` version of mesa i.e `3.2.0.dev0` +Make sure that you have installed the `latest` version of mesa i.e. `3.2.0.dev0` + +```bash +pip install mesa==3.2.0.dev0 +``` + ## Usage🧰 Tools
🪛 LanguageTool
[uncategorized] ~18-~18: The abbreviation “i.e.” (= that is) requires two periods.
Context: ... installed thelatestversion of mesa i.e3.2.0.dev0## Usage To run the simu...(I_E)
examples/termites/termites/agents.py (4)
16-16: Fix typo in docstringThere's a typo in "startin cell" which should be "starting cell".
- cell: The startin cell (position) of the agent. + cell: The starting cell (position) of the agent.
9-9: Fix attribute documentation styleThe attribute documentation uses parentheses which is not the conventional Python style. Remove the parentheses for better readability.
- hasWoodChip(bool): True if the agent is carrying a wood chip. + hasWoodChip: bool. True if the agent is carrying a wood chip.
32-32: Fix typo in commentThere's a typo in "Termite agnet" which should be "Termite agent".
- # Termite agnet is not carrying any woodchip + # Termite agent is not carrying any woodchip
41-41: Fix grammatical errors in commentThere are two grammatical errors in this comment:
- "a empty space" should be "an empty space"
- "it's neighbourhood" should be "its neighbourhood" (possessive form)
- then search for a empty space (no agent and no woodcell) in it's neighbourhood and drop the wood chip + then search for an empty space (no agent and no woodcell) in its neighbourhood and drop the wood chipexamples/termites/app.py (4)
37-39: Add slider configuration for width and height parametersCurrently,
widthandheightparameters don't have slider configurations likenum_termitesandwood_chip_density. Consider adding sliders for these parameters to provide users with more control over the simulation environment."wood_chip_density": { "type": "SliderFloat", "value": 0.1, "label": "Wood Chip Density", "min": 0.01, "max": 1, "step": 0.1, }, - "width": 60, - "height": 60, + "width": { + "type": "SliderInt", + "value": 60, + "label": "Grid Width", + "min": 20, + "max": 150, + "step": 10, + }, + "height": { + "type": "SliderInt", + "value": 60, + "label": "Grid Height", + "min": 20, + "max": 150, + "step": 10, + }, }
3-3: Consider using relative import for project structure consistencyYou're using an absolute import
from termites.model import TermiteModelwhich might cause issues depending on how the project is installed or structured. Consider using a relative import for better maintainability.-from termites.model import TermiteModel +from .termites.model import TermiteModelNote: The exact relative import pattern might vary depending on your project structure.
16-17: Add docstring to agent_portrayal functionAdding a docstring would improve code documentation and make the function's purpose clearer to other developers.
def agent_portrayal(agent): + """ + Define the visual representation of termite agents. + + Args: + agent: The termite agent to portray. + + Returns: + dict: A dictionary with marker style, color based on whether the agent + is carrying a wood chip, and size. + """ return {"marker": ">", "color": "red" if agent.hasWoodChip else "black", "size": 10}
44-48: Add docstring to post_process functionAdding a docstring would improve code documentation and make the function's purpose clearer to other developers.
def post_process(ax): + """ + Adjust the visual aspects of the plot. + + Args: + ax: The matplotlib axes object to modify. + """ ax.set_aspect("equal") ax.set_xticks([]) ax.set_yticks([])
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examples/termites/termites/model.py (1)
examples/termites/termites/agents.py (2)
Termite(4-61)step(26-61)
examples/termites/termites/agents.py (1)
examples/termites/termites/model.py (1)
step(51-52)
examples/termites/app.py (1)
examples/termites/termites/model.py (1)
TermiteModel(8-52)
🪛 LanguageTool
examples/termites/README.md
[style] ~10-~10: This phrase is redundant. Consider writing “space”.
Context: ...her, place the carried chip in a nearby empty space. 3. If not carrying a chip and encounte...
(EMPTY_HOLE)
[uncategorized] ~18-~18: The abbreviation “i.e.” (= that is) requires two periods.
Context: ... installed the latest version of mesa i.e 3.2.0.dev0 ## Usage To run the simu...
(I_E)
[uncategorized] ~37-~37: This verb does not appear to agree with the subject. Consider using a different form.
Context: ...imensional toroidal grid where termites interacts with the wood chips. The toroidal natur...
(AI_EN_LECTOR_REPLACEMENT_VERB_AGREEMENT)
examples/termites/termites/agents.py
Outdated
| else: | ||
| # Termite agent has a wood chip | ||
| if self.hasWoodChip: | ||
| # search for neighbors | ||
| wood_chip_neighbors = [x for x in self.cell.neighborhood if x.woodcell] | ||
| if wood_chip_neighbors: | ||
| # drop the Wood chip | ||
| self.hasWoodChip = False | ||
| self.cell.woodcell = True |
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🛠️ Refactor suggestion
Optimize wood chip dropping behavior
The current implementation of the behavior when a termite is carrying a wood chip but there's no wood chip at its current location could potentially be improved. Based on the PR objectives, the simulation is intended to form piles of wood chips, but the current logic only checks if there are neighboring cells with wood chips without considering larger pile formation.
Consider enhancing the logic to prefer dropping wood chips near larger existing piles by counting the number of wood chips in the neighborhood:
else:
# Termite agent has a wood chip
if self.hasWoodChip:
# search for neighbors
wood_chip_neighbors = [x for x in self.cell.neighborhood if x.woodcell]
if wood_chip_neighbors:
- # drop the Wood chip
- self.hasWoodChip = False
- self.cell.woodcell = True
+ # Count wood chips in each neighbor's neighborhood to find denser clusters
+ neighbor_scores = {}
+ for neighbor in self.cell.neighborhood:
+ if not neighbor.woodcell and neighbor.is_empty:
+ # Count wood chips in this neighbor's neighborhood
+ count = sum(1 for n in neighbor.neighborhood if n.woodcell)
+ if count > 0: # Only consider cells with at least one wood chip nearby
+ neighbor_scores[neighbor] = count
+
+ if neighbor_scores:
+ # Choose the cell with the highest wood chip density in its neighborhood
+ best_cell = max(neighbor_scores.items(), key=lambda x: x[1])[0]
+ self.cell = best_cell
+ self.hasWoodChip = False
+ self.cell.woodcell = True
+ else:
+ # If no good location found, use the original method
+ self.hasWoodChip = False
+ self.cell.woodcell = TrueThis enhancement would encourage termites to drop wood chips where there are already concentrations of wood chips, leading to larger pile formation as mentioned in the PR objectives.
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| else: | |
| # Termite agent has a wood chip | |
| if self.hasWoodChip: | |
| # search for neighbors | |
| wood_chip_neighbors = [x for x in self.cell.neighborhood if x.woodcell] | |
| if wood_chip_neighbors: | |
| # drop the Wood chip | |
| self.hasWoodChip = False | |
| self.cell.woodcell = True | |
| else: | |
| # Termite agent has a wood chip | |
| if self.hasWoodChip: | |
| # search for neighbors | |
| wood_chip_neighbors = [x for x in self.cell.neighborhood if x.woodcell] | |
| if wood_chip_neighbors: | |
| # Count wood chips in each neighbor's neighborhood to find denser clusters | |
| neighbor_scores = {} | |
| for neighbor in self.cell.neighborhood: | |
| if not neighbor.woodcell and neighbor.is_empty: | |
| # Count wood chips in this neighbor's neighborhood | |
| count = sum(1 for n in neighbor.neighborhood if n.woodcell) | |
| if count > 0: # Only consider cells with at least one wood chip nearby | |
| neighbor_scores[neighbor] = count | |
| if neighbor_scores: | |
| # Choose the cell with the highest wood chip density in its neighborhood | |
| best_cell = max(neighbor_scores.items(), key=lambda x: x[1])[0] | |
| self.cell = best_cell | |
| self.hasWoodChip = False | |
| self.cell.woodcell = True | |
| else: | |
| # If no good location found, use the original method | |
| self.hasWoodChip = False | |
| self.cell.woodcell = True |
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Yes, with the introduction of neighbor_score and logic around it, the termite agents can form larger piles. But they are currently struggling with combining these small/medium-sized piles to form a single larger pile.
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@Spartan-71 I understand the challenge - forming larger piles locally is now possible, but merging these separate piles into a single large pile remains difficult. Here's an approach that could help with this global pile merging behavior:
def step(self):
# First decide if we should move randomly or toward a large pile
if self.hasWoodChip:
# When carrying a chip, occasionally search for larger piles within extended radius
if self.random.random()
< 0.3: # 30% chance to look for larger piles
self.move_toward_largest_pile(search_radius=5) # Search in wider radius
else:
self.move() # Random movement
else:
self.move() # Random movement when not carrying a chip
# Check if wood chip is present on the current cell
if self.cell.woodcell:
# Determine whether to pick up a chip based on local pile density
local_density = sum(1 for n in self.cell.neighborhood if n.woodcell)
# More likely to pick up from smaller piles (lower density)
pickup_probability = 0.9 - (local_density / 10) # Scales from 0.9 to ~0.0
if not self.hasWoodChip and self.random.random() < pickup_probability:
# Pick up the wood chip (more likely if it's isolated or in a small pile)
self.hasWoodChip = True
self.cell.woodcell = False
elif self.hasWoodChip:
# Find a good place to drop near a dense pile
empty_neighbors = [x for x in self.cell.neighborhood if x.is_empty and not x.woodcell]
if empty_neighbors:
# Move to empty cell and drop
self.cell = self.random.choice(empty_neighbors)
self.hasWoodChip = False
self.cell.woodcell = True
else:
# Current cell has no wood chip
if self.hasWoodChip:
# Check if we're near other wood chips
wood_chip_neighbors = [x for x in self.cell.neighborhood if x.woodcell]
if wood_chip_neighbors:
# Try to find the best location with highest density in an extended area
best_spot = self.find_best_drop_location(radius=3)
if best_spot:
self.cell = best_spot
# Drop the wood chip at current location
self.hasWoodChip = False
self.cell.woodcell = True
def move_toward_largest_pile(self, search_radius=5):
"""Move toward the largest pile within the given search radius."""
# Find cells with wood chips in an extended radius
pile_locations = []
visited = set()
queue = [(self.cell, 0)] # (cell, distance)
while queue:
current, distance = queue.pop(0)
if current in visited or distance > search_radius:
continue
visited.add(current)
if current.woodcell:
pile_locations.append(current)
if distance < search_radius:
for neighbor in current.neighborhood:
if neighbor not in visited:
queue.append((neighbor, distance + 1))
if not pile_locations:
self.move() # No piles found, move randomly
return
# Calculate pile sizes by checking density around each pile location
pile_sizes = {}
for loc in pile_locations:
size = 1 # Start with 1 for the cell itself
for n in loc.neighborhood:
if n.woodcell:
size += 1
pile_sizes[loc] = size
# Move toward a larger pile with some probability (weighted by size)
weights = [size for size in pile_sizes.values()]
target = self.random.choices(list(pile_sizes.keys()), weights=weights, k=1)[0]
# Move one step toward the target pile
path = self.find_path_to(target)
if path and len(path) > 1:
self.cell = path[1] # Move to the next cell in the path
def find_best_drop_location(self, radius=3):
"""Find the best location to drop a wood chip within the given radius."""
# Similar to move_toward_largest_pile but returns the best cell to drop
# Implementation would find cells near high-density areas but with an empty spot
# [Code would be similar to move_toward_largest_pile but with different selection criteria]
pass
def find_path_to(self, target):
"""Find a path to the target cell using breadth-first search."""
# Simple BFS implementation to find path
# [BFS implementation code here]
passThis enhanced algorithm introduces several key improvements:
- Probability-based wood chip pickup: Termites are more likely to pick up chips from smaller piles and less likely from larger ones
- Extended sensing radius: Termites can detect larger piles beyond their immediate neighborhood
- Directed movement: Termites carrying wood chips occasionally move toward larger detected piles
- Weighted selection: Larger piles have a higher chance of attracting termites with wood chips
You'd need to implement the helper methods like find_path_to() and complete find_best_drop_location(), but this approach should help termites gradually consolidate smaller piles into larger ones over time.
Would you like me to elaborate on any specific part of this solution?
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Actionable comments posted: 0
♻️ Duplicate comments (3)
examples/termites/termites/model.py (1)
44-49: 🛠️ Refactor suggestionValidate number of termites to prevent errors.
The code doesn't validate that
num_termitesdoesn't exceed the number of available cells in the grid, which could cause an error withrandom.sample.+ # Ensure num_termites doesn't exceed available cells + total_cells = width * height + if self.num_termites > total_cells: + self.num_termites = total_cells + print(f"Warning: Number of termites limited to total cells: {total_cells}") + # Creating and adding termite agents to the grid Termite.create_agents( self, self.num_termites, self.random.sample(self.grid.all_cells.cells, k=self.num_termites), )examples/termites/termites/agents.py (1)
53-61: Optimize wood chip dropping behavior.The current implementation could be improved to better form wood chip piles as mentioned in the PR objectives.
else: # Termite agent has a wood chip if self.hasWoodChip: # search for neighbors wood_chip_neighbors = [x for x in self.cell.neighborhood if x.woodcell] if wood_chip_neighbors: - # drop the Wood chip - self.hasWoodChip = False - self.cell.woodcell = True + # Count wood chips in each neighbor's neighborhood to find denser clusters + neighbor_scores = {} + for neighbor in self.cell.neighborhood: + if not neighbor.woodcell and neighbor.is_empty: + # Count wood chips in this neighbor's neighborhood + count = sum(1 for n in neighbor.neighborhood if n.woodcell) + if count > 0: # Only consider cells with at least one wood chip nearby + neighbor_scores[neighbor] = count + + if neighbor_scores: + # Choose the cell with the highest wood chip density in its neighborhood + best_cell = max(neighbor_scores.items(), key=lambda x: x[1])[0] + self.cell = best_cell + self.hasWoodChip = False + self.cell.woodcell = True + else: + # If no good location found, use the original method + self.hasWoodChip = False + self.cell.woodcell = Trueexamples/termites/app.py (1)
41-41:⚠️ Potential issueModel initialization parameters mismatch with model_params.
There's an inconsistency between the default values in
model_params(50 termites, 60x60 grid) and the actual model instance (400 termites, 100x100 grid). This could confuse users since changing the sliders won't match the initial state.-model = TermiteModel(num_termites=400, width=100, height=100, wood_chip_density=0.1) +model = TermiteModel( + num_termites=model_params["num_termites"]["value"], + width=model_params["width"], + height=model_params["height"], + wood_chip_density=model_params["wood_chip_density"]["value"] +)
🧹 Nitpick comments (7)
examples/termites/termites/model.py (2)
8-24: The class definition looks good, but the docstring could be more detailed.The TermiteModel class has appropriate parameters and a good basic docstring. Consider enhancing the docstring with more details about the model's purpose, mechanics, and expected emergent behavior.
41-42: Fix the comment formatting.There's an extra set of quotes at the end of this comment.
- # Adding PropertyLayer to the grid""" + # Adding PropertyLayer to the gridexamples/termites/README.md (2)
18-18: Fix the abbreviation format.The abbreviation "i.e." (that is) requires two periods.
-Make sure that you have installed the `latest` version of mesa i.e `3.2.0.dev0` +Make sure that you have installed the `latest` version of mesa i.e. `3.2.0.dev0`🧰 Tools
🪛 LanguageTool
[uncategorized] ~18-~18: The abbreviation “i.e.” (= that is) requires two periods.
Context: ... installed thelatestversion of mesa i.e3.2.0.dev0## Usage To run the simu...(I_E)
37-37: Fix subject-verb agreement.The verb should agree with the plural subject "termites".
-A two-dimensional toroidal grid where termites interacts with the wood chips. The toroidal nature means agents exiting one edge re-enter from the opposite edge, +A two-dimensional toroidal grid where termites interact with the wood chips. The toroidal nature means agents exiting one edge re-enter from the opposite edge,🧰 Tools
🪛 LanguageTool
[uncategorized] ~37-~37: This verb does not appear to agree with the subject. Consider using a different form.
Context: ...imensional toroidal grid where termites interacts with the wood chips. The toroidal natur...(AI_EN_LECTOR_REPLACEMENT_VERB_AGREEMENT)
examples/termites/termites/agents.py (3)
12-21: Fix typo in docstring.There's a typo in the initialization method's docstring.
- cell: The startin cell (position) of the agent. + cell: The starting cell (position) of the agent.
31-38: Fix typo in comment.There's a misspelling in the comment.
- # Termite agnet is not carrying any woodchip + # Termite agent is not carrying any woodchip
39-52: Fix apostrophe in comment and consider clearer variable naming.There's an incorrect apostrophe usage in the comment.
- then search for a empty space (no agent and no woodcell) in it's neighbourhood and drop the wood chip + then search for a empty space (no agent and no woodcell) in its neighbourhood and drop the wood chip
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examples/termites/README.md(1 hunks)examples/termites/app.py(1 hunks)examples/termites/termites/agents.py(1 hunks)examples/termites/termites/model.py(1 hunks)
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examples/termites/termites/model.py (1)
examples/termites/termites/agents.py (2)
Termite(4-61)step(26-61)
examples/termites/termites/agents.py (1)
examples/termites/termites/model.py (1)
step(51-52)
examples/termites/app.py (1)
examples/termites/termites/model.py (1)
TermiteModel(8-52)
🪛 LanguageTool
examples/termites/README.md
[style] ~10-~10: This phrase is redundant. Consider writing “space”.
Context: ...her, place the carried chip in a nearby empty space. 3. If not carrying a chip and encounte...
(EMPTY_HOLE)
[uncategorized] ~18-~18: The abbreviation “i.e.” (= that is) requires two periods.
Context: ... installed the latest version of mesa i.e 3.2.0.dev0 ## Usage To run the simu...
(I_E)
[uncategorized] ~37-~37: This verb does not appear to agree with the subject. Consider using a different form.
Context: ...imensional toroidal grid where termites interacts with the wood chips. The toroidal natur...
(AI_EN_LECTOR_REPLACEMENT_VERB_AGREEMENT)
🔇 Additional comments (14)
examples/termites/termites/model.py (3)
1-5: LGTM! Imports are appropriate for the model.The imports correctly bring in the necessary modules for the termite model, including numpy for array operations, Mesa's Model class, grid components, and the local Termite agent class.
28-39: LGTM! Grid and wood chip distribution setup is well-implemented.The implementation correctly sets up an OrthogonalMooreGrid with 8 neighbors per cell and creates a PropertyLayer for the wood chips, with random distribution based on the specified density.
51-52: LGTM! Step method is appropriately simple.The step method correctly shuffles and calls the step method of each agent, which handles the core simulation logic.
examples/termites/README.md (2)
1-14: The introduction and summary effectively explain the model's purpose.The README provides a good overview of the termite simulation, its inspiration from NetLogo, and the emergent behavior of the decentralized organization system.
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[style] ~10-~10: This phrase is redundant. Consider writing “space”.
Context: ...her, place the carried chip in a nearby empty space. 3. If not carrying a chip and encounte...(EMPTY_HOLE)
42-44: LGTM! References section properly credits the original model.The references section appropriately cites the NetLogo Termites model that inspired this implementation.
examples/termites/termites/agents.py (2)
4-10: LGTM! The class definition and docstring clearly explain the agent behavior.The Termite class is well-defined with a clear docstring explaining the agent's behavior and attributes.
22-25: LGTM! Move method is simple and effective.The move method correctly implements random movement by selecting a random neighboring cell.
examples/termites/app.py (7)
1-4: LGTM! Imports are appropriate for the visualization.The imports correctly bring in the necessary components from Mesa for visualization.
5-13: LGTM! The wood chip portrayal settings are well-defined.The portrayal for wood chips has appropriate color, transparency, and other visual settings.
16-17: LGTM! Agent portrayal function is clear and effective.The function properly differentiates between termites carrying wood chips (red) and those without (black).
20-39: LGTM! Model parameters are well-configured with appropriate ranges.The sliders for adjusting termite count and wood chip density have reasonable default values and ranges.
44-48: LGTM! Post-processing function creates a clean visualization.The function correctly sets equal aspect ratio and removes ticks for a cleaner presentation.
50-55: LGTM! Space component setup is well-configured.The visualization component correctly incorporates agent and property layer portrayals with appropriate settings.
57-64: LGTM! SolaraViz setup is complete with appropriate parameters.The visualization is properly configured with the model, components, parameters, and render intervals.
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Thanks Sahil! @Spartan-71 please let us know if/what you find useful of the coderabbit review! We’re still testing if this is useful for Mesa (and if so, what parts, fine tuning, etc.) (CC @adamamer20) |
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@Spartan-71, this was just an AI review, I will do a proper review tomorrow, in the mean time you can look at the comments. |
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The code itself is good, I have some questions regarding the model itself,
- Did you find the wood chip dropping behavior suggested by coderabbit useful or it makes more sense to have simple calculations?
- Is there no interaction between the termites?
- Does it affect the simulation in any way that many termites can be on the same cell? Or would it make sense if only one termite per cell?
- Another thing I noticed that I am unable to replicate the results, are you sure you are not missing anything?
Yeah, it is slightly more optimized since the size of the woodchip piles that are getting formed are larger as compared to the previous one. Though I need to figure out a way to optimize this part a bit more so that it replicates the behaviour found in NetLogo's Model.
Yes, there is no interaction.
As per my understanding of this example, many termites on one cell don't improve the simulation in any way.
As mentioned under the Review section of this PR:
Currently, the simulation is not as optimized as the one present on the NetLogo website. Termites can form medium-sized piles but are unable to combine them to ultimately form a single big pile of wood chips, the step function still needs more optimization |
I found this useful not only to point out minor typos/grammatical errors and logical errors, but it also did a pretty good job in optimizing the model's behaviour. I believe this will save a lot of maintainers' time. |
What's your game plan for this? If you want to discuss anything, you can ask (though I may not be the best person for this). First step could be comparing the model to the one present on NetLogo directly and figuring out the differences between the logic. |
Yeah, I'm looking into the Netlogos logic for the termites step function. Will give an update soon. |
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Love the discussion here! By the way, it's perfectly fine to merge this PR with "simple" behavior, and then modify the behavior in follow-up PRs. That way no PR gets too big to review. You can apply the principle of Atomic Commits also on PRs! |
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Hey @Sahil-Chhoker, I have changed the logic for the termites step function, which now mimics the Netlogos logic.
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I like the new logic, but it feels too computation-heavy. If you look at the image below:
You can clearly see the main performance bottlenecks: Another concern I have is that this model is supposed to be simple—where basic calculations lead to interesting emergent behavior. But right now, we’re calculating everything, which defeats that purpose. |
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Can't the logic be more simplified? One way to reduce the commutations needed by This kills the computations for both |
Agreed. I have experimented with different radii, but with radius < 3, the model was heading towards local optimal solution i.e forming small piles, which then aren't getting combined to create a bigger one. So 3 seemed to be an optimal value.
Initially, I tried the basic logic only, but the model struggled forming even medium-sized piles with the new optimization suggested by coderabbit; medium-sized piles were getting formed, but then again, it struggled with combining those piles. So I feel this is the way to achieve the expected behaviour. |
This is good, but then it doesn't simulate the real termites' behaviour, i.e looking around themselves in search of chips rather than randomly travelling to a location in the colony. If simulating the real behaviour is not as important as computation, then we can consider moving to a random position in the grid to reduce the computation and think of more optimizations. |
I think it does simulate real behavior, because the termites search around randomly for wood chips and return once found. It makes perfect sense to me to just search randomly than to do complicated calculations to keep the termite near the nest. |
examples/termites/termites/agents.py
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| def wiggle(self): | ||
| # Move the agent to a random neighboring cell. | ||
| self.cell = self.cell.get_neighborhood(radius=3).select_random_cell() |
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Simplify it to cell = self.model.random.choice(self.model.grid.all_cells.cells)
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If I mag ask, why? Isn’t it more logical they choose a cell nearby? Is it performance?
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I initially tried the same (radius=1), but the model struggled to form even medium-sized piles, and there was no chance of combining these piles even after 10k+ steps. Also, performance was the bottleneck.
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If I mag ask, why? Isn’t it more logical they choose a cell nearby? Is it performance?
I also should add to it, termites are meant to search for woodchips, and its not mentioned anywhere that they should search their vicinity, therefore this approach just makes that search faster.
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Sounds valid. @Spartan-71 could you add this in one or two lines of documentation/comment?
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Also just reduce the docstrings and comments a little, they feel too access at some places. |
for more information, see https://pre-commit.ci
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While performance is definitely relevant, I think valid behavior is more important in a showcase model. Of course, if you can further optimize it, that’s always useful. |
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There is something wrong with the pytests. I'm already using
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I can say that the newly recommended behavior is very valid, it may be a little different from that of the netlogo's implementation, but in no way wrong, and also performant, so it's a win-win. |
| self.wood_chips_layer = PropertyLayer( | ||
| "woodcell", (width, height), default_value=False, dtype=bool | ||
| ) | ||
| self.wood_chips_layer.data = np.random.choice( |
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This is a smart way to initialize the PropertyLayer! That’s one of the advantages of using a standard data structure underneath, it can directly be accessed and modified. @Spartan-71, was this intuitive, or should we document this possibility better?
CC @quaquel basically a two-liner to initialize the PorpertyLayers, really cool.
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I think we should document this.
| self.hasWoodChip = True | ||
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| for _ in range(10): | ||
| new_cell = self.cell.neighborhood.select_random_cell() |
Add New Termite Simulation Example
Summary
This PR introduces a new termite simulation example inspired by the classic termite wood chip gathering behavior. The simulation models termites moving randomly on a grid containing scattered wood chips, following simple rules to form piles over time.
Features
Implementation Details
Visualization
Remark
stepfunction needs refinement. Would love to discuss the logic for the step function with the community.Notes
Summary by CodeRabbit
New Features
Documentation