BrainAtlasNaming Class Reference

Central naming rules for brain atlas files. More...

#include <BrainAtlasNaming.h>

Classes
struct	Parts
	Components extracted from an atlas filename. More...

Static Public Member Functions
static string	rmhaName (string stem)
	Builds the canonical ROI atlas filename.
static string	anatName (string stem, string modality)
	Builds the canonical anatomical header filename.
static string	rawName (string stem, string modality)
	Builds the canonical anatomical raw image filename.
static string	keyName (string stem, string keyType)
	Builds the canonical atlas key filename.
static string	stemOf (string prefix, string animal)
	Constructs an atlas stem.
static string	stripAtlasSuffix (string s)
	Removes a trailing "Atlas" suffix.
static bool	isEncryptedPrefix (string stemOrName)
	Determines whether an atlas should be treated as encrypted.
static string	prefixPattern ()
	Regular expression fragment matching a valid atlas prefix.
static string	atlasSuffixPattern ()
	Regular expression fragment matching the mandatory "Atlas" suffix used by .rmha and key file names.

Detailed Description

Central naming rules for brain atlas files.

This class encapsulates all filename generation and parsing rules used by both built-in and custom atlases.

Canonical file layout

Given a stem consisting of:

<stem> = <prefix><animal>

Example stems:

invicroMouse
MyCustomRat
Mouse

the following filenames are generated:

<stem>Atlas.rmha
<stem>CT.mhd
<stem>CT.raw
<stem>Atlas-Key-AllRegions.csv

Scope

The active matching functions (used by SegmentationServiceNMCT to populate the atlas/animal combo boxes) only recognize names in the exact canonical form above – i.e. what CustomBrainAtlasWizard actually produces. Older files that omit the "Atlas" suffix or append a version tag after it (e.g. legacy invicroRatAtlas54.rmha) are not recognized; duplicate such files under a compliant name instead of relying on this class to parse them.

All filename creation functions produce the canonical naming format.

Member Function Documentation

anatName()

static string anatName ( string  stem, string  modality  )

static

Builds the canonical anatomical header filename.

Parameters

stem	Atlas stem.
modality	Imaging modality (CT, MR, PET, etc.).

Returns

Filename of the form:

<stem><modality>.mhd

atlasSuffixPattern()

static string atlasSuffixPattern ( )

static

Regular expression fragment matching the mandatory "Atlas" suffix used by .rmha and key file names.

This is required, not optional: CustomBrainAtlasWizard always appends "Atlas" (see createNewAtlasCompleteInputs()), so this class only recognizes names that include it. It intentionally does not match older names that omitted "Atlas" or appended a version tag after it (e.g. legacy invicroRatAtlas54.rmha) – such files should be duplicated under a compliant name rather than accepted here.

Only use this for .rmha/key filenames. Anatomical (.mhd) file names never contain "Atlas" at all (see anatName()) and must not use this pattern.

Returns

Regular expression fragment.

isEncryptedPrefix()

static bool isEncryptedPrefix ( string  stemOrName )

static

Determines whether an atlas should be treated as encrypted.

Atlas names beginning with either "invicro" or "encrypted" are considered encrypted.

Comparison is case-insensitive.

Parameters

stemOrName

Atlas stem or filename.

Returns

True if the atlas is recognized as encrypted.

keyName()

static string keyName ( string  stem, string  keyType  )

static

Builds the canonical atlas key filename.

Parameters

stem	Atlas stem.
keyType	Key type such as AllRegions or AllRegionsLeft.

Returns

Filename of the form:

<stem>Atlas-Key-<keyType>.csv

prefixPattern()

static string prefixPattern ( )

static

Regular expression fragment matching a valid atlas prefix.

The pattern accepts letters, digits, underscores, periods, and hyphens.

This pattern is shared by all atlas discovery and parsing logic.

Returns

Regular expression fragment.

rawName()

static string rawName ( string  stem, string  modality  )

static

Builds the canonical anatomical raw image filename.

Parameters

stem	Atlas stem.
modality	Imaging modality.

Returns

Filename of the form:

<stem><modality>.raw

rmhaName()

static string rmhaName ( string  stem )

static

Builds the canonical ROI atlas filename.

Parameters

stem	Atlas stem (<prefix><animal>).

Returns

Filename of the form:

<stem>Atlas.rmha

stemOf()

static string stemOf ( string  prefix, string  animal  )

static

Constructs an atlas stem.

The stem is simply the concatenation of the prefix and animal name and does not include the "Atlas" suffix or modality.

Example:

stemOf("MyCustom", "Mouse")
    -> "MyCustomMouse"

Parameters

prefix	Optional atlas prefix.
animal	Animal name.

Returns

Concatenated atlas stem.

stripAtlasSuffix()

static string stripAtlasSuffix ( string  s )

static

Removes a trailing "Atlas" suffix.

If the supplied string ends with "Atlas", that suffix is removed. Otherwise the input is returned unchanged.

Parameters

s	Input string.

Returns

String without a trailing "Atlas".