class SimConfExportVisual(YamlABC):
'''
**Visual export subconfiguration** (i.e., YAML-backed wrapper exposing
settings globally applicable to all visual exports).
Attributes (Cell: Indices)
----------
is_show_cell_indices : bool
``True`` only if the 0-based indices of all cells are to be displayed
over all cell cluster visuals (e.g., as integers situated at cell
centres).
single_cell_index : int
0-based index of the cell to be visualized for all single cell visuals.
Defaults to 0, the index assigned to the first cell guaranteed to
exist. Note that cell indices are seed-specific and may be visualized
by enabling the :attr:`is_show_cell_indices` boolean.
'''
# ..................{ ALIASES ~ cell : index }..................
is_show_cell_indices = yaml_alias(
"['results options']['visuals']['cell indices']['show']", bool)
#FIXME, Consider generalizing this into a list.
single_cell_index = yaml_alias(
"['results options']['visuals']['cell indices']['single cell']", int)
class SimConfExportCSVs(YamlABC):
'''
YAML-backed subconfiguration for exporting *all* comma-separated value
(CSV) files enabled by the current YAML-formatted simulation configuration
file.
Attributes (After Solving)
----------
is_after_sim_save : bool
``True`` only if this configuration saves post-simulation CSV files.
anims_after_sim : YamlList
YAML-backed list of all post-simulation CSV files to be animated.
Ignored if :attr:`is_after_sim_save` is ``False``.
Attributes (Save)
----------
csv_filetype : str
Filetype of all CSV files saved by this configuration. Ignored if
:attr:`is_after_sim_save` is ``False``.
'''
# ..................{ ALIASES ~ after }..................
is_after_sim_save = yaml_alias(
"['results options']['after solving']['csvs']['save']", bool)
# ..................{ ALIASES ~ save }..................
filetype = yaml_alias("['results options']['save']['csvs']['filetype']",
str)
# ..................{ INITIALIZERS }..................
def __init__(self, *args, **kwargs) -> None:
# Initialize our superclass with all passed parameters.
super().__init__(*args, **kwargs)
# Encapsulate low-level lists of dictionaries with high-level wrappers.
self.csvs_after_sim = SimConfExportCSV.make_list()
# ..................{ LOADERS }..................
def load(self, *args, **kwargs) -> None:
# Load our superclass with all passed arguments.
super().load(*args, **kwargs)
# Load all subconfigurations of this configuration.
self.csvs_after_sim.load(conf=self._conf['results options']
['after solving']['csvs']['pipeline'])
def unload(self) -> None:
# Unload our superclass.
super().unload()
# Unload all subconfigurations of this configuration.
self.csvs_after_sim.unload()
class SimConfVisualCellsYAMLMixin(SimConfVisualCellsABC):
'''
Mixin of all **YAML-backed cell cluster visual subconfiguration** (i.e.,
configuration of a single visual export parsed from the current
YAML-formatted simulation configuration file) subclasses.
'''
# ..................{ ALIASES ~ colorbar }..................
is_color_autoscaled = yaml_alias("['colorbar']['autoscale']", bool)
color_min = yaml_alias("['colorbar']['minimum']", NumericSimpleTypes)
color_max = yaml_alias("['colorbar']['maximum']", NumericSimpleTypes)
class SimConfVisualCellsYAMLMixin(SimConfVisualCellsABC):
'''
Abstract mixin generalizing implementation common to all YAML-backed cell
cluster visual subconfiguration subclasses.
This mixin encapsulates configuration of a single visual (either in- or
post-simulation plot or animation) parsed from the current YAML-formatted
simulation configuration file. For generality, this mixin provides no
support for a YAML ``type`` key or corresponding :attr:`name` property.
'''
# ..................{ ALIASES ~ colorbar }..................
is_color_autoscaled = yaml_alias("['colorbar']['autoscale']", bool)
color_min = yaml_alias("['colorbar']['minimum']", NumericSimpleTypes)
color_max = yaml_alias("['colorbar']['maximum']", NumericSimpleTypes)
class SimConfCutListItem(YamlNamedMixin, YamlListItemABC):
'''
YAML-backed cut profile list item subconfiguration, encapsulating the
configuration of a single cut profile parsed from a list of these profiles
in the current YAML-formatted simulation configuration file.
Attributes
----------
picker_image_filename : str
Absolute or relative filename of the image mask whose pure-black pixels
define the region of the cell cluster whose cells are all to be removed
by this cut profile. See the
:attr:`SimConfTissueListItem.picker_image_filename` variable for
details.
'''
# ..................{ ALIASES }..................
picker_image_filename = yaml_alias("['image']", str)
# ..................{ SUPERCLASS }..................
@classmethod
@type_check
def make_default(cls, yaml_list: YamlList) -> YamlListItemABC:
# Duplicate the first tissue profile in our default configuration file.
return cls._make_loaded(
conf={
'name': yaml_list.get_item_name_uniquified('Cut ({})'),
'image': 'geo/circle/wedge.png',
})
class YamlBooledMixin(object):
'''
Mixin of all **YAML-backed booled configuration** (i.e., backed by a YAML
dictionary with top-level key ``enabled`` whose value is a boolean
specifying whether this configuration is enabled or disabled) subclasses.
This class is suitable for use as a multiple-inheritance mixin. To preserve
the expected method resolution order (MRO) semantics, this class should
typically be inherited *first* rather than *last* in subclasses.
Attributes
----------
is_enabled : bool
``True`` only if this list item is enabled.
'''
# ..................{ ALIASES }..................
is_enabled = yaml_alias("['enabled']", bool)
class SimConfPhase(YamlABC):
'''
YAML-backed simulation phase subconfiguration, encapsulating the
configuration of a single phase (e.g., seed, initialization, simulation)
parsed from the current YAML-formatted simulation configuration file.
Attributes (Path)
----------
. : .
.
Attributes (Time)
----------
. : .
.
'''
# ..................{ ALIASES ~ wut }..................
wut = yaml_alias("['wut']['wut']", int)
class SimConfTissueDefault(SimConfTissueABC, YamlABC):
'''
YAML-backed **default tissue profile** (i.e., profile applied to all cells
*not* already targeted by another tissue profile) subconfiguration,
encapsulating the configuration of a single tissue profile unconditionally
applicable to all cells parsed from a dictionary configuring at least this
profile in the current YAML-formatted simulation configuration file.
Attributes (Cell Picker)
----------
picker_image_filename : str
Absolute or relative filename of the image mask whose pure-black pixels
define the shape of the cell cluster to be populated with cells. See
the :attr:`SimConfTissueListItem.picker_image_filename` variable for
details.
'''
# ..................{ ALIASES ~ picker }..................
picker_image_filename = yaml_alias("['image']", str)
class YamlNamedMixin(object):
'''
Mixin of all **YAML-backed named configuration** (i.e., backed by a YAML
dictionary with top-level key ``name`` whose value is a human- and/or
machine-readable string identifying this configuration's presumably unique
name) subclasses.
This class is suitable for use as a multiple-inheritance mixin. To preserve
the expected method resolution order (MRO) semantics, this class should
typically be inherited *first* rather than *last* in subclasses.
Attributes
----------
name : str
Arbitrary string typically uniquely identifying this configuration
(e.g., ``spot``, naming a spatially isolated tissue profile).
'''
# ..................{ ALIASES }..................
name = yaml_alias("['name']", str)
class YamlTypedMixin(object):
'''
Mixin of all **YAML-backed typed configuration** (i.e., backed by a YAML
dictionary with top-level key ``type`` whose value is a machine-readable
string identifying this configuration's type) subclasses.
This class is suitable for use as a multiple-inheritance mixin. To preserve
the expected method resolution order (MRO) semantics, this class should
typically be inherited *first* rather than *last* in subclasses.
Attributes
----------
kind : str
Lowercase alphanumeric string uniquely identifying the type of this
configuration (e.g., ``voltage_membrane``, identifying a transmembrane
voltage). See each ``type`` key of the corresponding list in the
default simulation configuration file for real-world examples.
'''
# ..................{ ALIASES }..................
kind = yaml_alias("['type']", str)
class SimConfPlotAll(YamlABC):
'''
YAML-backed subconfiguration for exporting *all* plots (both in- and
post-simulation) enabled by the current YAML-formatted simulation
configuration file.
This subconfiguration saves (i.e., writes, serializes) in-memory plots to
on-disk cache, image, and/or video files configured by this configuration.
Attributes (After Solving)
----------
is_after_sim : bool
``True`` only if this configuration displays and/or saves
post-simulation plots.
is_after_sim_show : bool
``True`` only if this configuration displays post-simulation plots.
is_after_sim_save : bool
``True`` only if this configuration saves post-simulation plots.
Attributes (After Solving: Single-cell)
----------
plots_cell_after_sim : YamlList
YAML-backed list of all post-simulation single-cell plots to be
animated. Ignored if :attr:``is_after_sim`` is ``False``.
plots_cells_after_sim : YamlList
YAML-backed list of all post-simulation cell cluster plots to be
animated. Ignored if :attr:``is_after_sim`` is ``False``.
Attributes (Image)
----------
image_filetype : str
Filetype of all image files saved by this configuration. Ignored if
:attr:`is_after_sim_save` is ``False``.
image_dpi : int
Dots per inch (DPI) of all image files saved by this configuration.
Ignored if :attr:`is_after_sim_save` is ``False``.
'''
# ..................{ ALIASES ~ after }..................
is_after_sim_save = yaml_alias(
"['results options']['after solving']['plots']['save']", bool)
is_after_sim_show = yaml_alias(
"['results options']['after solving']['plots']['show']", bool)
# ..................{ ALIASES ~ save }..................
image_filetype = yaml_alias(
"['results options']['save']['plots']['filetype']", str)
image_dpi = yaml_alias_int_positive(
"['results options']['save']['plots']['dpi']")
# ..................{ INITIALIZERS }..................
def __init__(self, *args, **kwargs) -> None:
# Initialize our superclass with all passed parameters.
super().__init__(*args, **kwargs)
# Encapsulate low-level lists of dictionaries with high-level wrappers.
self.plots_cell_after_sim = SimConfVisualCellListItem.make_list()
self.plots_cells_after_sim = SimConfVisualCellsListItem.make_list()
# ..................{ LOADERS }..................
def load(self, *args, **kwargs) -> None:
# Load our superclass with all passed arguments.
super().load(*args, **kwargs)
# Load all subconfigurations of this configuration.
self.plots_cell_after_sim.load(conf=self._conf[
'results options']['after solving'][
'plots']['single cell pipeline'])
self.plots_cells_after_sim.load(conf=self._conf[
'results options']['after solving'][
'plots']['cell cluster pipeline'])
def unload(self) -> None:
# Unload our superclass.
super().unload()
# Unload all subconfigurations of this configuration.
self.plots_cell_after_sim.unload()
self.plots_cells_after_sim.unload()
# ..................{ PROPERTIES ~ after }..................
@property
def is_after_sim(self) -> bool:
return self.is_after_sim_save or self.is_after_sim_show
@is_after_sim.setter
@type_check
def is_after_sim(self, is_after_sim: bool) -> None:
self.is_after_sim_save = is_after_sim
self.is_after_sim_show = is_after_sim
class SimConfAnimAll(YamlABC):
'''
YAML-backed subconfiguration for exporting *all* animations (both
in- and post-simulation) enabled by the current YAML-formatted simulation
configuration file.
Attributes (General)
----------
is_overlay_current : bool
``True`` only if this configuration overlays streamlines (e.g., electric
current, concentration flux) onto appropriate animations.
Attributes (While Solving)
----------
is_while_sim : bool
``True`` only if this configuration displays and/or saves in-simulation
animations.
is_while_sim_save : bool
``True`` only if this configuration saves in-simulation animations.
is_while_sim_show : bool
``True`` only if this configuration displays in-simulation animations.
anim_while_sim : SimConfVisualCellsEmbedded
Generic configuration applicable to all in-simulation animations.
Ignored if :attr:``is_while_sim`` is ``False``.
Attributes (After Solving)
----------
is_after_sim : bool
``True`` only if this configuration displays and/or saves
post-simulation animations.
is_after_sim_save : bool
``True`` only if this configuration saves post-simulation animations.
is_after_sim_show : bool
``True`` only if this configuration displays post-simulation animations.
anims_after_sim : YamlList
YAML-backed list of all post-simulation animations to be animated.
Ignored if :attr:`is_after_sim` is ``False``.
Attributes (Images)
----------
is_images_save : bool
``True`` only if this configuration saves animation frames as images.
image_filetype : str
Filetype of all image files saved by this configuration. Ignored if
:attr:`is_images_save` is ``False``.
image_dpi : int
Dots per inch (DPI) of all image files saved by this configuration.
Ignored if :attr:`is_images_save` is ``False``.
Attributes (Video)
----------
is_video_save : bool
``True`` only if this configuration saves animation frames as video.
video_bitrate : int
Bitrate in bits per second of all video files saved by this
configuration. Ignored if :attr:`is_video_save` is `False`.
video_codec_names : SequenceTypes
List of the names of all encoder-specific codecs with which to encode
animations (in descending order of preference), automatically:
* Selecting the first codec supported by the selected writer.
* Replacing any codec named `auto` by the name of a recommended codec
specific to the selected writer and filetype. For details, see the
`betse.lib.matplotlib.writer.mplvideo.get_first_codec_name()`
function.
Ignored if :attr:`is_video_save` is `False`.
video_dpi : int
Dots per inch (DPI) of all frames of all video files saved by this
configuration. Ignored if :attr:`is_images_save` is `False`.
video_filetype : str
Filetype of all video files saved by this configuration. Supported
filetypes include:
* `mkv` (Matroska), an open-standard audio and video container
supporting all relevant codecs and hence the default.
* `avi`, Microsoft's obsolete proprietary audio and video container.
* `gif`, a proprietary image format supporting video animations.
* `ogv` (Theora), Xiph's open-standard audio and video container.
* `mov` (QuickTime), Apple's proprietary audio and video container.
* `mp4` (MPEG-4 Part 14), an open-standard audio and video container.
* `webm` (WebM), Google's proprietary audio and video container.
Ignored if :attr:`is_video_save` is `False`.
video_framerate : int
Framerate in frames per second of all video files saved by this
configuration. Ignored if :attr:`is_video_save` is `False`.
video_metadata : MappingType
Dictionary mapping from the alphabetic lowercase name of video metadata
supported by the active video encoder to that metadata's human-readable
string to be embedded in all video files saved by this configuration.
Supported names include: `title`, `artist`, `genre`, `subject`,
`copyright`, `srcform`, and `comment`. If this dictionary does *not*
contain a `copyright` key, such a key will be automatically synthesized
from the current year. Ignored if :attr:`is_video_save` is `False`.
video_writer_names : SequenceTypes
List of the names of all matplotlib animation writers with which to
encode animations (in order of descending preference), automatically
selecting the first writer installed on the current system. Supported
names include:
* ``ffmpeg``, an open-source cross-platform audio and video encoder.
* ``avconv``, an open-source cross-platform audio and video encoder
forked from (and largely interchangeable with) `ffmpeg`.
* ``mencoder``, an open-source cross-platform audio and video encoder
associated with MPlayer, a popular media player.
* ``imagemagick``, an open-source cross-platform image manipulation
suite supporting *only* creation of animated GIFs.
Ignored if :attr:`is_video_save` is ``False``.
'''
# ..................{ ALIASES }..................
is_overlay_current = yaml_alias(
"['results options']['overlay currents']", bool)
# ..................{ ALIASES ~ while }..................
is_while_sim_save = yaml_alias(
"['results options']['while solving']['animations']['save']", bool)
is_while_sim_show = yaml_alias(
"['results options']['while solving']['animations']['show']", bool)
# ..................{ ALIASES ~ after }..................
is_after_sim_save = yaml_alias(
"['results options']['after solving']['animations']['save']", bool)
is_after_sim_show = yaml_alias(
"['results options']['after solving']['animations']['show']", bool)
# ..................{ ALIASES ~ save : images }..................
is_images_save = yaml_alias(
"['results options']['save']['animations']['images']['enabled']", bool)
image_filetype = yaml_alias(
"['results options']['save']['animations']['images']['filetype']", str)
image_dpi = yaml_alias_int_positive(
"['results options']['save']['animations']['images']['dpi']")
# ..................{ ALIASES ~ save : video }..................
is_video_save = yaml_alias(
"['results options']['save']['animations']['video']['enabled']", bool)
video_bitrate = yaml_alias_int_positive(
"['results options']['save']['animations']['video']['bitrate']")
video_dpi = yaml_alias_int_positive(
"['results options']['save']['animations']['video']['dpi']")
video_filetype = yaml_alias(
"['results options']['save']['animations']['video']['filetype']", str)
video_framerate = yaml_alias_int_positive(
"['results options']['save']['animations']['video']['framerate']")
video_metadata = yaml_alias(
"['results options']['save']['animations']['video']['metadata']",
MappingType)
video_writer_names = yaml_alias(
"['results options']['save']['animations']['video']['writers']",
SequenceTypes)
video_codec_names = yaml_alias(
"['results options']['save']['animations']['video']['codecs']",
SequenceTypes)
# ..................{ INITIALIZERS }..................
def __init__(self, *args, **kwargs) -> None:
# Initialize our superclass with all passed parameters.
super().__init__(*args, **kwargs)
# Encapsulate low-level dictionaries with high-level wrappers.
self.anim_while_sim = SimConfVisualCellsEmbedded()
# Encapsulate low-level lists of dictionaries with high-level wrappers.
self.anims_after_sim = SimConfVisualCellsListItem.make_list()
# ..................{ LOADERS }..................
#FIXME: Default the "copyright" entry of video metadata to
#"@ {}".format(current_year)".
def load(self, *args, **kwargs) -> None:
# Load our superclass with all passed arguments.
super().load(*args, **kwargs)
# Load all subconfigurations of this configuration.
self.anim_while_sim.load(conf=self._conf[
'results options']['while solving']['animations'])
self.anims_after_sim.load(conf=self._conf[
'results options']['after solving']['animations']['pipeline'])
def unload(self) -> None:
# Unload our superclass.
super().unload()
# Unload all subconfigurations of this configuration.
self.anim_while_sim.unload()
self.anims_after_sim.unload()
# ..................{ PROPERTIES ~ while }..................
@property
def is_while_sim(self) -> bool:
return self.is_while_sim_save or self.is_while_sim_show
@is_while_sim.setter
@type_check
def is_while_sim(self, is_while_sim: bool) -> None:
self.is_while_sim_save = is_while_sim
self.is_while_sim_show = is_while_sim
# ..................{ PROPERTIES ~ after }..................
@property
def is_after_sim(self) -> bool:
return self.is_after_sim_save or self.is_after_sim_show
@is_after_sim.setter
@type_check
def is_after_sim(self, is_after_sim: bool) -> None:
self.is_after_sim_save = is_after_sim
self.is_after_sim_show = is_after_sim
class SimConfTissueListItem(SimConfTissueABC, YamlListItemABC):
'''
YAML-backed tissue profile list item subconfiguration, encapsulating the
configuration of a single tissue profile parsed from a list of these
profiles in the current YAML-formatted simulation configuration file.
Attributes
----------
is_gj_insular : bool
``True`` only if gap junctions originating at cells in this tissue are
**insular** (i.e., prevented from connecting to cells in other
tissues), implying these gap junctions to be strictly intra-tissue.
Attributes (Cell Picker)
----------
picker_type : CellsPickerType
Type of **tissue profile picker** (i.e., object assigning a subset of
all cells matching some criteria to this tissue profile).
picker_cells_color : str
**Hexadecimal-formatted color** (i.e., string of six hexadecimal digits
specifying this color's red, green, and blue components) of all circles
within the vector image (defined by the ``cells from svg`` setting in
the current simulation configuration) to be assigned to this tissue.
Ignored unless :attr:`picker_type` is :attr:`CellsPickerType.COLOR`.
picker_cells_index : SequenceTypes
Sequence of the indices of all cells to be assigned to this tissue.
Ignored unless :attr:`picker_type` is :attr:`CellsPickerType.INDICES`.
picker_cells_percent : float
**Percentage** (i.e., floating point number in the range ``[0.0,
100.0]``) of the total cell population to be randomly assigned to this
tissue. Ignored unless :attr:`picker_type` is
:attr:`CellsPickerType.PERCENT`.
picker_image_filename : str
Absolute or relative filename of the image mask whose pure-black pixels
(i.e., pixels whose red, green, and blue color components are all 0)
define the region of the cell cluster whose cells are all to be
assigned to this tissue. This image *must*:
* Be square (i.e., have equal width and height).
* Contain no alpha transparency layer.
Ignored unless :attr:`picker_type` is :attr:`CellsPickerType.IMAGE`.
'''
# ..................{ ALIASES }..................
is_gj_insular = yaml_alias("['insular']", bool)
# ..................{ ALIASES ~ picker }..................
picker_type = yaml_enum_alias("['cell targets']['type']", CellsPickerType)
#FIXME: Create a new yaml_alias_color() data descriptor validating this
#string to be a valid hexadecimal-formatted color.
#FIXME: In the YAML, if color specifications don't have quotations around
#them (e.g. '808080') the yaml sometimes thinks all numerical hex codes are
#strings (e.g. 008080), and sometimes integers (e.g. 800080), in which case
#the whole thing crashed with a type error! I'm not quite sure how to force
#it to read in a string... For now, I've put quotes around the hex code
#numeral...
picker_cells_color = yaml_alias("['cell targets']['color']", str)
picker_cells_index = yaml_alias("['cell targets']['indices']",
SequenceTypes)
picker_cells_percent = yaml_alias_float_percent(
"['cell targets']['percent']")
picker_image_filename = yaml_alias("['cell targets']['image']", str)
# ..................{ SUPERCLASS }..................
@classmethod
@type_check
def make_default(cls, yaml_list: YamlList) -> YamlListItemABC:
# Duplicate the first tissue profile in our default configuration file.
return cls._make_loaded(
conf={
'name': yaml_list.get_item_name_uniquified('Tissue ({})'),
'insular': True,
'diffusion constants': {
'Dm_Na': 1.0e-18,
'Dm_K': 15.0e-18,
'Dm_Cl': 2.0e-18,
'Dm_Ca': 1.0e-18,
'Dm_M': 1.0e-18,
'Dm_P': 0.0,
},
'cell targets': {
'type': 'all',
'color': 'ff0000',
'image': 'geo/circle/circle_base.png',
'indices': [3, 14, 15, 9, 265],
'percent': 50,
},
})
