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Commit 3034e576 authored by Roman Belousov's avatar Roman Belousov
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Frozen and fixed beads

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dycpm/__init__.py
+ 9
− 4
View file @ 3034e576
......@@ -91,6 +91,8 @@ class State:
active_exponents (list[float]): Active exponents
surface_tension (list[float]): Surface tension between voxel types
modulation (list[float]): Modulation of spin interactions with distance
frozen (list[int]): Frozen voxel IDs (only MEDIUM and ECM types are accepted)
fixed (list[int]): Fixed voxel IDs (only MEDIUM and ECM types are accepted)
rng (dict|None): State of the random-number generator may be absent
"""
def __init__(self, **kwargs):
......@@ -115,8 +117,9 @@ class State:
active_exponents (list[float]): Active exponents
surface_tension (list[float]):
Required surface tension between voxel types
modulation (list[float]): Modulation of spin interactions with distance
(Optional)
modulation (list[float]): Modulation of spin interactions with distance (Optional)
frozen (list[int]): Frozen voxels (Optional)
fixed (list[int]): Fixed voxels (Optional)
rng (dict): Optional state of the random-number generator
"""
self.side = kwargs.pop('side')
......@@ -137,13 +140,15 @@ class State:
self.active_exponents = kwargs.pop('active_exponents', 8 * [0.0])
self.surface_tension = kwargs.pop('surface_tension')
self.modulation = kwargs.pop('modulation', [1.0, 1.0, 1.0])
self.frozen = kwargs.pop('frozen', [])
self.fixed = kwargs.pop('fixed', [])
if 'rng' in kwargs: self.rng = kwargs.pop('rng')
if len(kwargs) > 0:
raise TypeError(f'Unknown kwargs: {list(kwargs.keys())}')
def __getattr__(self, name):
if name == 'rng': return None
raise AttributeError()
raise AttributeError(f'State has no attribue `{name}`')
def to_json(self):
"""Return JSON-serializable data"""
......@@ -225,7 +230,7 @@ class State:
}
def ecm_coordinates(self):
"""Return center-of-mass coordinates of the ECM voxels"""
"""Return coordinates of the ECM voxels"""
return [self.voxel_coordinates(voxel) for voxel in self.ecm]
def volume(self, exclude_ecm = False):
......
src/data.rs
+ 17
− 1
View file @ 3034e576
......@@ -66,7 +66,7 @@ pub struct State {
/// Voxel ids of the ECM
#[serde(default)]
pub ecm: std::collections::HashSet<i64>,
pub ecm: std::collections::HashSet<VoxelId>,
/// The ecm production and degradation exponents
#[serde(default = "default_ecm_parameters")]
......@@ -119,6 +119,11 @@ pub struct State {
/// Spin interaction modulation
pub modulation: [f64; 3],
/// IDs of "frozen" voxels
pub frozen: std::collections::HashSet<VoxelId>,
/// IDs of "fixed" voxels
pub fixed: std::collections::HashSet<VoxelId>,
/// State of the random number generator
#[serde(default)]
pub rng: mt19937::MT19937
......@@ -205,6 +210,17 @@ impl State {
lattice[*voxel_id as usize] = ECM;
}
for frozen in self.frozen.iter() {
if lattice[*frozen as usize] > 0 {
panic!("Freezing a voxel (#{:?}) of a cell (#{:?}) not allowed", frozen, lattice[*frozen as usize])
}
}
for fixed in self.fixed.iter() {
if lattice[*fixed as usize] > 0 {
panic!("Freezing a voxel (#{:?}) of a cell (#{:?}) not allowed", fixed, lattice[*fixed as usize])
}
}
Ok(lattice)
}
......
src/simulation.rs
+ 9
− 3
View file @ 3034e576
......@@ -400,11 +400,15 @@ impl Kernel {
let mut target_values = Vec::<VoxelValue>::with_capacity(5);
target_values.push(voxel_value);
for triplet in &TARGET_NEIGHBORHOOD {
let neighbor_value = self.get_index_value(
let neighbor_index = [
voxel.index[0] + triplet[0],
voxel.index[1] + triplet[1],
voxel.index[2] + triplet[2]
);
];
let neighbor_id = self.index_to_id(neighbor_index[0], neighbor_index[1], neighbor_index[2]);
if self.state.frozen.contains(&neighbor_id) { continue }
let neighbor_value = self.get_index_value(neighbor_index[0], neighbor_index[1], neighbor_index[2]);
if neighbor_value != voxel_value && !target_values.contains(&neighbor_value) {
target_values.push(neighbor_value);
}
......@@ -746,6 +750,7 @@ impl Kernel {
/// Check if a voxel is active
fn is_active(&self, voxel: &Voxel) -> bool {
if self.state.frozen.contains(&voxel.id) || self.state.fixed.contains(&voxel.id) { return false }
let value = self.lattice[voxel.id as usize];
for triplet in &TARGET_NEIGHBORHOOD {
let neighbor_value = self.get_index_value(
......@@ -767,7 +772,8 @@ impl Kernel {
voxel.index[1] + triplet[1],
voxel.index[2] + triplet[2]
);
if 0 <= id && id < self.lattice.len() as i64 { self.front.insert(id); }
if !self.state.frozen.contains(&id) && !self.state.fixed.contains(&id)
&& 0 <= id && id < self.lattice.len() as i64 { self.front.insert(id); }
}
}
......
src/tests.rs
+ 9
− 9
View file @ 3034e576
......@@ -42,7 +42,7 @@ fn active_exponents() {
action_probabilities: [0.001, 0.999, 0.999], death_probability: 0f64,
growth_rate: [0.5, 0.5], division_distribution: vec![10f64],
volume_elasticity: [1.0, 1.5], active_exponents: [1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0],
surface_tension: [1.0, 2.0, 3.0, 4.0, 5.0], modulation: [1.0, 1.0, 1.0],
surface_tension: [1.0, 2.0, 3.0, 4.0, 5.0], modulation: [1.0, 1.0, 1.0], frozen: hashset![], fixed: hashset![],
rng: mt19937::MT19937::default()
};
......@@ -137,7 +137,7 @@ fn kernel_layout() {
action_probabilities: [0.001, 0.999, 0.999], death_probability: 0f64,
growth_rate: [0.5, 0.5], division_distribution: vec![10f64],
volume_elasticity: [1.0, 1.5], active_exponents: [0f64; 8],
surface_tension: [1.0, 2.0, 3.0, 4.0, 5.0], modulation: [1.0, 1.0, 1.0],
surface_tension: [1.0, 2.0, 3.0, 4.0, 5.0], modulation: [1.0, 1.0, 1.0], frozen: hashset![], fixed: hashset![],
rng: mt19937::MT19937::default()
};
assert_eq!(state.side, 3);
......@@ -306,7 +306,7 @@ fn cell_division() {
death_probability: 0f64,
growth_rate: [0.5, 0.5], division_distribution: vec![10f64],
volume_elasticity: [1.0, 1.5], active_exponents: [0f64; 8],
surface_tension: [1.0, 2.0, 3.0, 4.0, 5.0], modulation: [1.0, 1.0, 1.0],
surface_tension: [1.0, 2.0, 3.0, 4.0, 5.0], modulation: [1.0, 1.0, 1.0], frozen: hashset![], fixed: hashset![],
rng: mt19937::MT19937::default()
});
assert_eq!(kernel.state.cells.len(), 1);
......@@ -348,7 +348,7 @@ fn cell_division() {
death_probability: 0f64,
growth_rate: [0.5, 0.5], division_distribution: vec![10f64],
volume_elasticity: [1.0, 1.5], active_exponents: [0f64; 8],
surface_tension: [1.0, 2.0, 3.0, 4.0, 5.0], modulation: [1.0, 1.0, 1.0],
surface_tension: [1.0, 2.0, 3.0, 4.0, 5.0], modulation: [1.0, 1.0, 1.0], frozen: hashset![], fixed: hashset![],
rng: mt19937::MT19937::default()
});
assert_eq!(kernel.state.cells.len(), 1);
......@@ -371,7 +371,7 @@ fn cell_death() {
death_probability: 100f64,
growth_rate: [0.5, 0.5], division_distribution: vec![10f64],
volume_elasticity: [1.0, 1.5], active_exponents: [0f64; 8],
surface_tension: [1.0, 2.0, 3.0, 4.0, 5.0], modulation: [1.0, 1.0, 1.0],
surface_tension: [1.0, 2.0, 3.0, 4.0, 5.0], modulation: [1.0, 1.0, 1.0], frozen: hashset![], fixed: hashset![],
rng: mt19937::MT19937::default()
});
assert_eq!(kernel.state.cells.len(), 1);
......@@ -396,7 +396,7 @@ fn tensor_gyration() {
death_probability: 0f64,
growth_rate: [0.5, 0.5], division_distribution: vec![10f64],
volume_elasticity: [1.0, 1.5], active_exponents: [0f64; 8],
surface_tension: [1.0, 2.0, 3.0, 4.0, 5.0], modulation: [1.0, 1.0, 1.0],
surface_tension: [1.0, 2.0, 3.0, 4.0, 5.0], modulation: [1.0, 1.0, 1.0], frozen: hashset![], fixed: hashset![],
rng: mt19937::MT19937::default()
});
let cell = &kernel.state.cells[&2usize];
......@@ -456,7 +456,7 @@ fn connectivity_check() {
action_probabilities: [0.001, 0.999, 0.999],
death_probability: 0f64, growth_rate: [0.5, 0.5], division_distribution: vec![10f64],
volume_elasticity: [1.0, 1.5], active_exponents: [0f64; 8],
surface_tension: [1.0, 2.0, 3.0, 4.0, 5.0], modulation: [1.0, 1.0, 1.0],
surface_tension: [1.0, 2.0, 3.0, 4.0, 5.0], modulation: [1.0, 1.0, 1.0], frozen: hashset![], fixed: hashset![],
rng: mt19937::MT19937::default()
});
......@@ -478,7 +478,7 @@ fn planar_index() {
death_probability: 0f64,
growth_rate: [0.5, 0.5], division_distribution: vec![10f64],
volume_elasticity: [1.0, 1.5], active_exponents: [0f64; 8],
surface_tension: [1.0, 2.0, 3.0, 4.0, 5.0], modulation: [1.0, 1.0, 1.0],
surface_tension: [1.0, 2.0, 3.0, 4.0, 5.0], modulation: [1.0, 1.0, 1.0], frozen: hashset![], fixed: hashset![],
rng: mt19937::MT19937::default()
});
let voxel = kernel.get_voxel_by_id(13i64);
......@@ -574,7 +574,7 @@ fn kernel_getters() {
death_probability: 0f64,
growth_rate: [0.5, 0.5], division_distribution: vec![10f64],
volume_elasticity: [1.0, 1.5], active_exponents: [0f64; 8],
surface_tension: [1.0, 2.0, 3.0, 4.0, 5.0], modulation: [1.0, 1.0, 1.0],
surface_tension: [1.0, 2.0, 3.0, 4.0, 5.0], modulation: [1.0, 1.0, 1.0], frozen: hashset![], fixed: hashset![],
rng: mt19937::MT19937::default()
});
......
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