Config¶

Summary¶

Config is PyFLASH's package-wide settings object. It is a class with global attributes, not an instance that you create. Changing Config.SOME_SETTING affects later PyFLASH operations in the current Python process.

Use explicit function arguments when a function provides them. Use Config when you need to change a package-wide default such as colocalisation threshold, save behavior, colors, aliases, montage filename, or figure layout behavior.

How To Create It¶

Import it:

from PyFLASH import Config

print(Config.THRESHOLD)

Modify attributes directly:

from PyFLASH import Config

old = Config.SAVE_MODE
try:
    Config.SAVE_MODE = False
    # run plotting code here
finally:
    Config.SAVE_MODE = old

Use a try / finally block in scripts and tests so temporary global changes are restored.

Important Attributes¶

Attribute	Meaning
`THRESHOLD`	Default colocalisation threshold. Used when an experiment or object marker does not receive an explicit threshold.
`PIXEL_SIZE`	Microns per pixel used by coordinate conversions.
`SECTION_THICKNESS_UM`	Fallback section thickness in microns when ROI volume is unavailable.
`FALLBACK_USERS`	Optional usernames used by path resolution when moving data between machines.
`AB`, `CK`, `TOTAL_LABEL`, `COUNT_LABEL`, `CUBED`	Display-label constants used by naming and export helpers.
`COLORS`	Named PyFLASH palette. Condition builders resolve these keys before matplotlib color names.
`SAVE_MODE`	Global default for whether figure-saving helpers should save outputs.
`MONTAGE_FILENAME`	Filename stem for pipeline overview montages. The default starts with `!` so it sorts first in file browsers.
`SKIP_EXISTING`	When supported by saving code, skip saving outputs that already exist.
`EXPORT_HTML`	Save interactive HTML alongside supported plots when enabled.
`STATS_CACHE`	Cache statistical results within a session when enabled.
`HOUSE_STYLE`	Apply PyFLASH's default matplotlib style when plotting modules load.
`USE_PYFLASH_LAYOUT`	Use PyFLASH layout adjustments when saving figures.
`EFFECT_SIZES`	Compute effect sizes alongside p-values where supported.
`EFFECT_CI`	Compute bootstrap confidence intervals for supported effect sizes.
`EFFECT_CI_RESAMPLES`	Number of bootstrap resamples for effect-size confidence intervals.
`ALIASES`	Manual path/name alias overrides. `create_batch` combines these with auto-generated aliases.

Common Methods¶

Config itself does not define instance methods. Related module-level helpers live in PyFLASH.config:

Function	Use
`apply_matplotlib_fast_path()`	Lazily apply faster matplotlib rendering settings and keep SVG text editable.
`generate_palettes(colors=None)`	Generate blend palette strings from color pairs.
`check_directory(file_path)`	Resolve a path, including optional `Config.FALLBACK_USERS` substitutions.

Accepted By¶

Config is read by import, plotting, pipeline, export, path, and statistics code. Users usually do not pass it as an argument. They set class attributes before running the operation that needs the changed default.

Returned By¶

Config is imported from the package:

from PyFLASH import Config

It is not returned by a factory function.

Examples¶

Change the colocalisation threshold for a batch creation call:

from PyFLASH import Config, create_batch

old = Config.THRESHOLD
try:
    Config.THRESHOLD = 50
    batch = create_batch(
        "threshold-50",
        groups,
        "/path/to/output-folder",
        experiments="/path/to/experiment-parent-folder",
    )
finally:
    Config.THRESHOLD = old

Prefer an explicit argument when available:

batch = create_batch(
    "threshold-50",
    groups,
    "/path/to/output-folder",
    experiments="/path/to/experiment-parent-folder",
    threshold=50,
)

Customize condition color keys:

from PyFLASH import Config, GroupBuilder

Config.COLORS["control_grey"] = "#787a7c"

groups = (
    GroupBuilder("Diagnosis")
    .add("Control", "Control", color="control_grey")
    .add("AD", "AD", color="red")
    .build()
)

Restore the historical montage filename:

from PyFLASH import Config

Config.MONTAGE_FILENAME = "00 - Overview Montage"

Add manual aliases that should override auto-generated aliases:

from PyFLASH import Config

Config.ALIASES.update({
    "WeekEight": "W8",
    "Genotype": "GT",
})

Notes¶

Config changes are process-global. They affect later operations until you change them back.
import PyFLASH stays lightweight; plotting-related matplotlib settings are applied lazily when plotting or figure saving touches matplotlib.
SVG text is kept editable by the matplotlib fast-path helper.
Config.ALIASES is read during create_batch. Updating it after a batch is created does not automatically rewrite batch.aliases.