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Refactor VectorField() function #620

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merged 8 commits into from
Feb 26, 2024
Merged

Refactor VectorField() function #620

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8aec705
reorganize VectorField
Sichao25 Nov 27, 2023
d721457
refactor vecfld training
Sichao25 Nov 28, 2023
ba2e174
create more helper functions
Sichao25 Nov 28, 2023
2b1457f
update docstr
Sichao25 Nov 28, 2023
38ba1c2
rename VectorField2D3D to Topography2D3D
Sichao25 Nov 28, 2023
97b23a9
debug dynode import
Sichao25 Nov 28, 2023
5d704e6
add missing import
Sichao25 Nov 28, 2023
dbb833c
Merge branch 'master' into cluster
Sichao25 Feb 21, 2024
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2 changes: 1 addition & 1 deletion dynamo/plot/scVectorField.py
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Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,7 @@
velocity_on_grid,
)
from ..tools.utils import update_dict
from ..vectorfield.topography import VectorField
from ..vectorfield.VectorField import VectorField
from ..vectorfield.utils import vecfld_from_adata
from .scatters import docstrings, scatters, scatters_interactive
from .utils import (
Expand Down
20 changes: 10 additions & 10 deletions dynamo/plot/topography.py
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Original file line number Diff line number Diff line change
Expand Up @@ -20,11 +20,11 @@
from ..tools.utils import nearest_neighbors, update_dict
from ..vectorfield.scVectorField import BaseVectorField
from ..vectorfield.topography import ( # , compute_separatrices
VectorField,
VectorField2D,
Topography2D,
)
from ..vectorfield.topography import topography as _topology # , compute_separatrices
from ..vectorfield.utils import vecfld_from_adata
from ..vectorfield.VectorField import VectorField
from ..vectorfield.vector_calculus import curl, divergence
from .scatters import docstrings, scatters, scatters_interactive
from .utils import (
Expand All @@ -42,7 +42,7 @@


def plot_flow_field(
vecfld: VectorField2D,
vecfld: Topography2D,
x_range: npt.ArrayLike,
y_range: npt.ArrayLike,
n_grid: int = 100,
Expand Down Expand Up @@ -182,7 +182,7 @@ def plot_flow_field(


def plot_nullclines(
vecfld: VectorField2D,
vecfld: Topography2D,
vecfld_dict: Dict[str, Any] = None,
lw: float = 3,
background: Optional[float] = None,
Expand Down Expand Up @@ -240,7 +240,7 @@ def plot_nullclines(
max_[1] + (max_[1] - min_[1]) * 0.1,
]

vecfld2d = VectorField2D(vecfld, X_data=vecfld_dict["X"])
vecfld2d = Topography2D(vecfld, X_data=vecfld_dict["X"])
vecfld2d.find_fixed_points_by_sampling(25, xlim, ylim)

if vecfld2d.get_num_fixed_points() > 0:
Expand All @@ -266,7 +266,7 @@ def plot_nullclines(


def plot_fixed_points_2d(
vecfld: VectorField2D,
vecfld: Topography2D,
marker: str = "o",
markersize: float = 200,
cmap: Optional[str] = None,
Expand Down Expand Up @@ -358,7 +358,7 @@ def plot_fixed_points_2d(


def plot_fixed_points(
vecfld: VectorField2D,
vecfld: Topography2D,
vecfld_dict: Dict[str, Any] = None,
marker: str = "o",
markersize: int = 200,
Expand Down Expand Up @@ -431,7 +431,7 @@ def plot_fixed_points(
max_[1] + (max_[1] - min_[1]) * 0.1,
]

vecfld = VectorField2D(vecfld, X_data=vecfld_dict["X"])
vecfld = Topography2D(vecfld, X_data=vecfld_dict["X"])
vecfld.find_fixed_points_by_sampling(25, xlim, ylim)
if vecfld.get_num_fixed_points() > 0:
vecfld.compute_nullclines(xlim, ylim, find_new_fixed_points=True)
Expand Down Expand Up @@ -642,7 +642,7 @@ def plot_traj(


def plot_separatrix(
vecfld: VectorField2D,
vecfld: Topography2D,
x_range: npt.ArrayLike,
y_range: npt.ArrayLike,
t: npt.ArrayLike,
Expand Down Expand Up @@ -706,7 +706,7 @@ def plot_separatrix(
max_[1] + (max_[1] - min_[1]) * 0.1,
]

vecfld2d = VectorField2D(vecfld, X_data=vecfld_dict["X"])
vecfld2d = Topography2D(vecfld, X_data=vecfld_dict["X"])
vecfld2d.find_fixed_points_by_sampling(25, xlim, ylim)

fps, ftypes = vecfld2d.get_fixed_points(get_types=True)
Expand Down
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