crm_multilayer

../_images/multilayer-time-evolution.png

Time evolution of maximum, 95th percentile and mean y-coordinate of all cells in colony.

Usage of the crm_multilayer script
class Any(*args, **kwargs)

Bases: object

Special type indicating an unconstrained type.

  • Any is compatible with every type.

  • Any assumed to have all methods.

  • All values assumed to be instances of Any.

Note that all the above statements are true from the point of view of static type checkers. At runtime, Any should not be used with instance checks.

class GrowthRateSetter(kwds)

Bases: object

Defines how the growth rates of the daughter cells will be set

Explicit

alias of GrowthRateSetter_Explicit

NormalDistr

alias of GrowthRateSetter_NormalDistr

class MultilayerConfig(**kwds)

Bases: object

Contain s all parameters and configuration valuese of the crm_multilayer script

static load_from_toml_file(path)

Loads the MultilayerConfig from the file at the given path.

static load_from_toml_str(input)

Loads the MultilayerConfig from the given string.

approx_eq(other)
clone_with_args(**kwds)

Clones the current MultilayerConfig with new optional keyword arguments

Parameters:
to_toml_file(filename)

Saves the MultilayerConfig to the given file. This function will fail if the file already exists.

to_toml_string()

Converts the MultilayerConfig into a toml string.

agent_settings

Contains settings for the Agents of the simulation. See AgentSettings

config

Contains base configuration. See Configuration

dx

Padding of the domain for the position generation algorithm

n_vertices

Number of vertices to use per agent

randomize_positions

Controls how much positions are randomized in the beginning of the simulation

rng_seed

Random seed for position generation

class Path(*args, **kwargs)

Bases: PurePath

PurePath subclass that can make system calls.

Path represents a filesystem path but unlike PurePath, also offers methods to do system calls on path objects. Depending on your system, instantiating a Path will return either a PosixPath or a WindowsPath object. You can also instantiate a PosixPath or WindowsPath directly, but cannot instantiate a WindowsPath on a POSIX system or vice versa.

classmethod cwd()

Return a new path pointing to the current working directory.

classmethod home()

Return a new path pointing to the user’s home directory (as returned by os.path.expanduser(‘~’)).

absolute()

Return an absolute version of this path by prepending the current working directory. No normalization or symlink resolution is performed.

Use resolve() to get the canonical path to a file.

as_posix()

Return the string representation of the path with forward (/) slashes.

as_uri()

Return the path as a ‘file’ URI.

chmod(mode, *, follow_symlinks=True)

Change the permissions of the path, like os.chmod().

exists(*, follow_symlinks=True)

Whether this path exists.

This method normally follows symlinks; to check whether a symlink exists, add the argument follow_symlinks=False.

expanduser()

Return a new path with expanded ~ and ~user constructs (as returned by os.path.expanduser)

glob(pattern, *, case_sensitive=None)

Iterate over this subtree and yield all existing files (of any kind, including directories) matching the given relative pattern.

group()

Return the group name of the file gid.

Make this path a hard link pointing to the same file as target.

Note the order of arguments (self, target) is the reverse of os.link’s.

is_absolute()

True if the path is absolute (has both a root and, if applicable, a drive).

is_block_device()

Whether this path is a block device.

is_char_device()

Whether this path is a character device.

is_dir()

Whether this path is a directory.

is_fifo()

Whether this path is a FIFO.

is_file()

Whether this path is a regular file (also True for symlinks pointing to regular files).

is_junction()

Whether this path is a junction.

is_mount()

Check if this path is a mount point

is_relative_to(other, /, *_deprecated)

Return True if the path is relative to another path or False.

is_reserved()

Return True if the path contains one of the special names reserved by the system, if any.

is_socket()

Whether this path is a socket.

Whether this path is a symbolic link.

iterdir()

Yield path objects of the directory contents.

The children are yielded in arbitrary order, and the special entries ‘.’ and ‘..’ are not included.

joinpath(*pathsegments)

Combine this path with one or several arguments, and return a new path representing either a subpath (if all arguments are relative paths) or a totally different path (if one of the arguments is anchored).

lchmod(mode)

Like chmod(), except if the path points to a symlink, the symlink’s permissions are changed, rather than its target’s.

lstat()

Like stat(), except if the path points to a symlink, the symlink’s status information is returned, rather than its target’s.

match(path_pattern, *, case_sensitive=None)

Return True if this path matches the given pattern.

mkdir(mode=511, parents=False, exist_ok=False)

Create a new directory at this given path.

open(mode='r', buffering=-1, encoding=None, errors=None, newline=None)

Open the file pointed to by this path and return a file object, as the built-in open() function does.

owner()

Return the login name of the file owner.

read_bytes()

Open the file in bytes mode, read it, and close the file.

read_text(encoding=None, errors=None)

Open the file in text mode, read it, and close the file.

Return the path to which the symbolic link points.

relative_to(other, /, *_deprecated, walk_up=False)

Return the relative path to another path identified by the passed arguments. If the operation is not possible (because this is not related to the other path), raise ValueError.

The walk_up parameter controls whether .. may be used to resolve the path.

rename(target)

Rename this path to the target path.

The target path may be absolute or relative. Relative paths are interpreted relative to the current working directory, not the directory of the Path object.

Returns the new Path instance pointing to the target path.

replace(target)

Rename this path to the target path, overwriting if that path exists.

The target path may be absolute or relative. Relative paths are interpreted relative to the current working directory, not the directory of the Path object.

Returns the new Path instance pointing to the target path.

resolve(strict=False)

Make the path absolute, resolving all symlinks on the way and also normalizing it.

rglob(pattern, *, case_sensitive=None)

Recursively yield all existing files (of any kind, including directories) matching the given relative pattern, anywhere in this subtree.

rmdir()

Remove this directory. The directory must be empty.

samefile(other_path)

Return whether other_path is the same or not as this file (as returned by os.path.samefile()).

stat(*, follow_symlinks=True)

Return the result of the stat() system call on this path, like os.stat() does.

Make this path a symlink pointing to the target path. Note the order of arguments (link, target) is the reverse of os.symlink.

touch(mode=438, exist_ok=True)

Create this file with the given access mode, if it doesn’t exist.

Remove this file or link. If the path is a directory, use rmdir() instead.

walk(top_down=True, on_error=None, follow_symlinks=False)

Walk the directory tree from this directory, similar to os.walk().

with_name(name)

Return a new path with the file name changed.

with_segments(*pathsegments)

Construct a new path object from any number of path-like objects. Subclasses may override this method to customize how new path objects are created from methods like iterdir().

with_stem(stem)

Return a new path with the stem changed.

with_suffix(suffix)

Return a new path with the file suffix changed. If the path has no suffix, add given suffix. If the given suffix is an empty string, remove the suffix from the path.

write_bytes(data)

Open the file in bytes mode, write to it, and close the file.

write_text(data, encoding=None, errors=None, newline=None)

Open the file in text mode, write to it, and close the file.

property anchor

The concatenation of the drive and root, or ‘’.

property drive

The drive prefix (letter or UNC path), if any.

property name

The final path component, if any.

property parent

The logical parent of the path.

property parents

A sequence of this path’s logical parents.

property parts

An object providing sequence-like access to the components in the filesystem path.

property root

The root of the path, if any.

property stem

The final path component, minus its last suffix.

property suffix

The final component’s last suffix, if any.

This includes the leading period. For example: ‘.txt’

property suffixes

A list of the final component’s suffixes, if any.

These include the leading periods. For example: [‘.tar’, ‘.gz’]

class tqdm(*_, **__)

Bases: Comparable

Decorate an iterable object, returning an iterator which acts exactly like the original iterable, but prints a dynamically updating progressbar every time a value is requested.

Parameters:

  • iterable (iterable, optional) – Iterable to decorate with a progressbar. Leave blank to manually manage the updates.

  • desc (str, optional) – Prefix for the progressbar.

  • total (int or float, optional) – The number of expected iterations. If unspecified, len(iterable) is used if possible. If float(“inf”) or as a last resort, only basic progress statistics are displayed (no ETA, no progressbar). If gui is True and this parameter needs subsequent updating, specify an initial arbitrary large positive number, e.g. 9e9.

  • leave (bool, optional) – If [default: True], keeps all traces of the progressbar upon termination of iteration. If None, will leave only if position is 0.

  • file (io.TextIOWrapper or io.StringIO, optional) – Specifies where to output the progress messages (default: sys.stderr). Uses file.write(str) and file.flush() methods. For encoding, see write_bytes.

  • ncols (int, optional) – The width of the entire output message. If specified, dynamically resizes the progressbar to stay within this bound. If unspecified, attempts to use environment width. The fallback is a meter width of 10 and no limit for the counter and statistics. If 0, will not print any meter (only stats).

  • mininterval (float, optional) – Minimum progress display update interval [default: 0.1] seconds.

  • maxinterval (float, optional) – Maximum progress display update interval [default: 10] seconds. Automatically adjusts miniters to correspond to mininterval after long display update lag. Only works if dynamic_miniters or monitor thread is enabled.

  • miniters (int or float, optional) – Minimum progress display update interval, in iterations. If 0 and dynamic_miniters, will automatically adjust to equal mininterval (more CPU efficient, good for tight loops). If > 0, will skip display of specified number of iterations. Tweak this and mininterval to get very efficient loops. If your progress is erratic with both fast and slow iterations (network, skipping items, etc) you should set miniters=1.

  • ascii (bool or str, optional) – If unspecified or False, use unicode (smooth blocks) to fill the meter. The fallback is to use ASCII characters “ 123456789#”.

  • disable (bool, optional) – Whether to disable the entire progressbar wrapper [default: False]. If set to None, disable on non-TTY.

  • unit (str, optional) – String that will be used to define the unit of each iteration [default: it].

  • unit_scale (bool or int or float, optional) – If 1 or True, the number of iterations will be reduced/scaled automatically and a metric prefix following the International System of Units standard will be added (kilo, mega, etc.) [default: False]. If any other non-zero number, will scale total and n.

  • dynamic_ncols (bool, optional) – If set, constantly alters ncols and nrows to the environment (allowing for window resizes) [default: False].

  • smoothing (float, optional) – Exponential moving average smoothing factor for speed estimates (ignored in GUI mode). Ranges from 0 (average speed) to 1 (current/instantaneous speed) [default: 0.3].

  • bar_format (str, optional) –

    Specify a custom bar string formatting. May impact performance. [default: ‘{l_bar}{bar}{r_bar}’], where l_bar=’{desc}: {percentage:3.0f}%|’ and r_bar=’| {n_fmt}/{total_fmt} [{elapsed}<{remaining}, ‘

    ’{rate_fmt}{postfix}]’

    Possible vars: l_bar, bar, r_bar, n, n_fmt, total, total_fmt,

    percentage, elapsed, elapsed_s, ncols, nrows, desc, unit, rate, rate_fmt, rate_noinv, rate_noinv_fmt, rate_inv, rate_inv_fmt, postfix, unit_divisor, remaining, remaining_s, eta.

    Note that a trailing “: “ is automatically removed after {desc} if the latter is empty.

  • initial (int or float, optional) – The initial counter value. Useful when restarting a progress bar [default: 0]. If using float, consider specifying {n:.3f} or similar in bar_format, or specifying unit_scale.

  • position (int, optional) – Specify the line offset to print this bar (starting from 0) Automatic if unspecified. Useful to manage multiple bars at once (eg, from threads).

  • postfix (dict or *, optional) – Specify additional stats to display at the end of the bar. Calls set_postfix(**postfix) if possible (dict).

  • unit_divisor (float, optional) – [default: 1000], ignored unless unit_scale is True.

  • write_bytes (bool, optional) – Whether to write bytes. If (default: False) will write unicode.

  • lock_args (tuple, optional) – Passed to refresh for intermediate output (initialisation, iterating, and updating).

  • nrows (int, optional) – The screen height. If specified, hides nested bars outside this bound. If unspecified, attempts to use environment height. The fallback is 20.

  • colour (str, optional) – Bar colour (e.g. ‘green’, ‘#00ff00’).

  • delay (float, optional) – Don’t display until [default: 0] seconds have elapsed.

  • gui (bool, optional) – WARNING: internal parameter - do not use. Use tqdm.gui.tqdm(…) instead. If set, will attempt to use matplotlib animations for a graphical output [default: False].

Returns:

out

Return type:

decorated iterator.

classmethod external_write_mode(file=None, nolock=False)

Disable tqdm within context and refresh tqdm when exits. Useful when writing to standard output stream

classmethod get_lock()

Get the global lock. Construct it if it does not exist.

classmethod pandas(**tqdm_kwargs)
Registers the current tqdm class with

pandas.core. ( frame.DataFrame | series.Series | groupby.(generic.)DataFrameGroupBy | groupby.(generic.)SeriesGroupBy ).progress_apply

A new instance will be created every time progress_apply is called, and each instance will automatically close() upon completion.

Parameters:

tqdm_kwargs (arguments for the tqdm instance)

Examples

>>> import pandas as pd
>>> import numpy as np
>>> from tqdm import tqdm
>>> from tqdm.gui import tqdm as tqdm_gui
>>>
>>> df = pd.DataFrame(np.random.randint(0, 100, (100000, 6)))
>>> tqdm.pandas(ncols=50)  # can use tqdm_gui, optional kwargs, etc
>>> # Now you can use `progress_apply` instead of `apply`
>>> df.groupby(0).progress_apply(lambda x: x**2)

References

<https://stackoverflow.com/questions/18603270/ progress-indicator-during-pandas-operations-python>

classmethod set_lock(lock)

Set the global lock.

classmethod wrapattr(stream, method, total=None, bytes=True, **tqdm_kwargs)

stream : file-like object. method : str, “read” or “write”. The result of read() and

the first argument of write() should have a len().

>>> with tqdm.wrapattr(file_obj, "read", total=file_obj.size) as fobj:
...     while True:
...         chunk = fobj.read(chunk_size)
...         if not chunk:
...             break
classmethod write(s, file=None, end='\n', nolock=False)

Print a message via tqdm (without overlap with bars).

static format_interval(t)

Formats a number of seconds as a clock time, [H:]MM:SS

Parameters:

t (int) – Number of seconds.

Returns:

out – [H:]MM:SS

Return type:

str

static format_meter(n, total, elapsed, ncols=None, prefix='', ascii=False, unit='it', unit_scale=False, rate=None, bar_format=None, postfix=None, unit_divisor=1000, initial=0, colour=None, **extra_kwargs)

Return a string-based progress bar given some parameters

Parameters:

  • n (int or float) – Number of finished iterations.

  • total (int or float) – The expected total number of iterations. If meaningless (None), only basic progress statistics are displayed (no ETA).

  • elapsed (float) – Number of seconds passed since start.

  • ncols (int, optional) – The width of the entire output message. If specified, dynamically resizes {bar} to stay within this bound [default: None]. If 0, will not print any bar (only stats). The fallback is {bar:10}.

  • prefix (str, optional) – Prefix message (included in total width) [default: ‘’]. Use as {desc} in bar_format string.

  • ascii (bool, optional or str, optional) – If not set, use unicode (smooth blocks) to fill the meter [default: False]. The fallback is to use ASCII characters “ 123456789#”.

  • unit (str, optional) – The iteration unit [default: ‘it’].

  • unit_scale (bool or int or float, optional) – If 1 or True, the number of iterations will be printed with an appropriate SI metric prefix (k = 10^3, M = 10^6, etc.) [default: False]. If any other non-zero number, will scale total and n.

  • rate (float, optional) – Manual override for iteration rate. If [default: None], uses n/elapsed.

  • bar_format (str, optional) –

    Specify a custom bar string formatting. May impact performance. [default: ‘{l_bar}{bar}{r_bar}’], where l_bar=’{desc}: {percentage:3.0f}%|’ and r_bar=’| {n_fmt}/{total_fmt} [{elapsed}<{remaining}, ‘

    ’{rate_fmt}{postfix}]’

    Possible vars: l_bar, bar, r_bar, n, n_fmt, total, total_fmt,

    percentage, elapsed, elapsed_s, ncols, nrows, desc, unit, rate, rate_fmt, rate_noinv, rate_noinv_fmt, rate_inv, rate_inv_fmt, postfix, unit_divisor, remaining, remaining_s, eta.

    Note that a trailing “: “ is automatically removed after {desc} if the latter is empty.

  • postfix (*, optional) – Similar to prefix, but placed at the end (e.g. for additional stats). Note: postfix is usually a string (not a dict) for this method, and will if possible be set to postfix = ‘, ‘ + postfix. However other types are supported (#382).

  • unit_divisor (float, optional) – [default: 1000], ignored unless unit_scale is True.

  • initial (int or float, optional) – The initial counter value [default: 0].

  • colour (str, optional) – Bar colour (e.g. ‘green’, ‘#00ff00’).

Returns:

out

Return type:

Formatted meter and stats, ready to display.

static format_num(n)

Intelligent scientific notation (.3g).

Parameters:

n (int or float or Numeric) – A Number.

Returns:

out – Formatted number.

Return type:

str

static format_sizeof(num, suffix='', divisor=1000)

Formats a number (greater than unity) with SI Order of Magnitude prefixes.

Parameters:

  • num (float) – Number ( >= 1) to format.

  • suffix (str, optional) – Post-postfix [default: ‘’].

  • divisor (float, optional) – Divisor between prefixes [default: 1000].

Returns:

out – Number with Order of Magnitude SI unit postfix.

Return type:

str

static status_printer(file)

Manage the printing and in-place updating of a line of characters. Note that if the string is longer than a line, then in-place updating may not work (it will print a new line at each refresh).

clear(nolock=False)

Clear current bar display.

close()

Cleanup and (if leave=False) close the progressbar.

display(msg=None, pos=None)

Use self.sp to display msg in the specified pos.

Consider overloading this function when inheriting to use e.g.: self.some_frontend(**self.format_dict) instead of self.sp.

Parameters:

  • msg (str, optional. What to display (default: repr(self)).)

  • pos (int, optional. Position to moveto) – (default: abs(self.pos)).

moveto(n)
refresh(nolock=False, lock_args=None)

Force refresh the display of this bar.

Parameters:

  • nolock (bool, optional) – If True, does not lock. If [default: False]: calls acquire() on internal lock.

  • lock_args (tuple, optional) – Passed to internal lock’s acquire(). If specified, will only display() if acquire() returns True.

reset(total=None)

Resets to 0 iterations for repeated use.

Consider combining with leave=True.

Parameters:

total (int or float, optional. Total to use for the new bar.)

set_description(desc=None, refresh=True)

Set/modify description of the progress bar.

Parameters:

  • desc (str, optional)

  • refresh (bool, optional) – Forces refresh [default: True].

set_description_str(desc=None, refresh=True)

Set/modify description without ‘: ‘ appended.

set_postfix(ordered_dict=None, refresh=True, **kwargs)

Set/modify postfix (additional stats) with automatic formatting based on datatype.

Parameters:

  • ordered_dict (dict or OrderedDict, optional)

  • refresh (bool, optional) – Forces refresh [default: True].

  • kwargs (dict, optional)

set_postfix_str(s='', refresh=True)

Postfix without dictionary expansion, similar to prefix handling.

unpause()

Restart tqdm timer from last print time.

update(n=1)

Manually update the progress bar, useful for streams such as reading files. E.g.: >>> t = tqdm(total=filesize) # Initialise >>> for current_buffer in stream: … … … t.update(len(current_buffer)) >>> t.close() The last line is highly recommended, but possibly not necessary if t.update() will be called in such a way that filesize will be exactly reached and printed.

Parameters:

n (int or float, optional) – Increment to add to the internal counter of iterations [default: 1]. If using float, consider specifying {n:.3f} or similar in bar_format, or specifying unit_scale.

Returns:

out – True if a display() was triggered.

Return type:

bool or None

property format_dict

Public API for read-only member access.

monitor = None
monitor_interval = 10
crm_multilayer_main()
find_ml_config_path(ml_config: MultilayerConfig, out_path=PosixPath('out/crm_multilayer'))
glob(pathname, *, root_dir=None, dir_fd=None, recursive=False, include_hidden=False)

Return a list of paths matching a pathname pattern.

The pattern may contain simple shell-style wildcards a la fnmatch. Unlike fnmatch, filenames starting with a dot are special cases that are not matched by ‘*’ and ‘?’ patterns by default.

If include_hidden is true, the patterns ‘*’, ‘?’, ‘**’ will match hidden directories.

If recursive is true, the pattern ‘**’ will match any files and zero or more directories and subdirectories.

load_or_compute_container(ml_config: MultilayerConfig, out_path=PosixPath('out/crm_multilayer'), store_positions=True) → CellContainer
load_or_compute_ydata(ml_config: MultilayerConfig, out_path=PosixPath('out/crm_multilayer'), store_positions=True)
load_or_compute_ydata_samples(ml_configs, n_threads_total: int | None = None, out_path=PosixPath('out/crm_multilayer'), store_positions=True, show_progressbar=True)
plot_colony_height_over_time()
produce_ml_config(*args: tuple[str, Any]) → MultilayerConfig

Produces a MultilayerConfig with default parameters.

produce_ydata(container: CellContainer)
render_image(iteration: int, render_settings, cell_container_serialized: list[int], domain_size, out_path: Path)
render_image_helper(args)
run_sim(ml_config: MultilayerConfig, store_positions=True) → CellContainer
sample_parameters(*args: tuple[Any, float, float, float] | tuple[Any, float, float, int, str], ml_config_default: MultilayerConfig | None = None)