cellsystem.logging package¶
Subpackages¶
Submodules¶
cellsystem.logging.full module¶
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class
cellsystem.logging.full.
FullLog
(*args, **kwargs)[source]¶ Bases:
cellsystem.logging.core.multi.MultiLog
A log that records geometric information, mutations, ancestry and prints the actions to the screen.
Each part can be accesed with:
log[{{logname}}]
where {{logname}} can be one of: ‘geometry’, ‘mutations’, ‘ancestry’ or ‘printer’.
also, each log can be (de)activated with:
# Deactivate log log[{{logname}}].silence() # Rectivate log log[{{logname}}].activate()
cellsystem.logging.geometric module¶
Geometric Logging¶
This module defines functionality for following the geometric evolution of the cell blob through time.
The classes GeometricLog and WorldLines are defined here.
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class
cellsystem.logging.geometric.
GeometricLog
(*args, **kwargs)[source]¶ Bases:
cellsystem.logging.core.weak.WeakLog
Registers the geometric positions of the cells.
cellsystem.logging.simple module¶
cellsystem.logging.treelogs module¶
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class
cellsystem.logging.treelogs.
AncestryLog
(*args, **kwargs)[source]¶ Bases:
cellsystem.logging.treelogs.TreeLog
A tree log that maintains a “family tree”.
Each leaf represents a cell. When that cell divides, the leaf branches into leaves representing the daughters.
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class
cellsystem.logging.treelogs.
MutationsLog
(*args, **kwargs)[source]¶ Bases:
cellsystem.logging.treelogs.TreeLog
A tree log that maintains a record of genome branching events.
Each leaf represents a genome that may be present in one or more cells. When one of those cells mutates, the new genome is added as a child of that leaf.
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class
cellsystem.logging.treelogs.
TreeLog
(*args, **kwargs)[source]¶ Bases:
cellsystem.logging.core.weak.WeakLog
Base class for logs that grow trees.
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alive_nodes
¶
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Module contents¶
Logging classes.
Classes related to the recording of the simulation progress, analysis and history.
-
class
cellsystem.logging.
FullLog
(*args, **kwargs)[source]¶ Bases:
cellsystem.logging.core.multi.MultiLog
A log that records geometric information, mutations, ancestry and prints the actions to the screen.
Each part can be accesed with:
log[{{logname}}]
where {{logname}} can be one of: ‘geometry’, ‘mutations’, ‘ancestry’ or ‘printer’.
also, each log can be (de)activated with:
# Deactivate log log[{{logname}}].silence() # Rectivate log log[{{logname}}].activate()
-
class
cellsystem.logging.
PrinterLog
(*args, **kwargs)[source]¶ Bases:
cellsystem.logging.core.log.Log
Simple logger that limits to print the action.
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class
cellsystem.logging.
MutationsLog
(*args, **kwargs)[source]¶ Bases:
cellsystem.logging.treelogs.TreeLog
A tree log that maintains a record of genome branching events.
Each leaf represents a genome that may be present in one or more cells. When one of those cells mutates, the new genome is added as a child of that leaf.
-
class
cellsystem.logging.
AncestryLog
(*args, **kwargs)[source]¶ Bases:
cellsystem.logging.treelogs.TreeLog
A tree log that maintains a “family tree”.
Each leaf represents a cell. When that cell divides, the leaf branches into leaves representing the daughters.
-
class
cellsystem.logging.
GeometricLog
(*args, **kwargs)[source]¶ Bases:
cellsystem.logging.core.weak.WeakLog
Registers the geometric positions of the cells.