phenotypic.abc_.MeasurementInfo#

class phenotypic.abc_.MeasurementInfo(value)[source]

Bases: str, Enum

Base class for creating standardized measurement information enumerations.

This class provides a structured way to define measurement types with consistent naming conventions, descriptive metadata, and automatic documentation generation. By inheriting from both str and Enum, MeasurementInfo enables measurement definitions to behave as enumeration members while maintaining string representation. The class automatically prefixes measurement labels with a category name, ensuring consistent naming across code and outputs.

Key Purposes:

Standardize measurement naming conventions (category_label format) to reduce errors
Centralize measurement definitions with labels and descriptions in one place
Automatically generate RST documentation tables from measurement definitions
Provide easy access to headers, labels, and category information for analysis workflows
Enable type-safe column names in measurement DataFrames

Usage with MeasureFeatures Subclasses:

MeasurementInfo enums are used internally by measurement operations ([MeasureSize](src/phenotypic/measure/_measure_size.py), [MeasureShape](src/phenotypic/measure/_measure_shape.py), [MeasureColor](src/phenotypic/measure/_measure_color.py), etc.) to define column names in output DataFrames. Each measurement class defines its own enum and uses the enum values as DataFrame column headers.

label

The short label for the measurement (without category prefix). Set automatically by __new__ from the first element of the enum value tuple.

Type:: str

desc

The description of what the measurement represents. Set automatically by __new__ from the second element of the enum value tuple. Defaults to empty string if not provided.

Type:: str

pair

A tuple of (label, description) for convenient access to both pieces of information together.

Type:: tuple[str, str]

CATEGORY

The category name returned by the category() classmethod. Provides instance-level access to the measurement category.

Type:: property

Examples

Define a custom measurement enumeration:

>>> from phenotypic.abc_ import MeasurementInfo
>>> class SHAPE(MeasurementInfo):
...     @classmethod
...     def category(cls):
...         return 'Shape'
...
...     AREA = ('Area', 'Total number of pixels in the detected object')
...     PERIMETER = ('Perimeter', 'Total length of object boundary in pixels')

Access measurement information and generate headers:

>>> SHAPE.AREA
<Shape_Area: 'Shape_Area'>
>>> str(SHAPE.AREA)
'Shape_Area'
>>> SHAPE.AREA.label
'Area'
>>> SHAPE.AREA.desc
'Total number of pixels in the detected object'
>>> SHAPE.AREA.CATEGORY
'Shape'
>>> SHAPE.get_labels()
['Area', 'Perimeter']
>>> SHAPE.get_headers()
['Shape_Area', 'Shape_Perimeter']

Use in DataFrame column naming (as MeasureFeatures do internally):

>>> import pandas as pd
>>> measurements = pd.DataFrame({
...     str(SHAPE.AREA): [1024, 956, 1101],
...     str(SHAPE.PERIMETER): [128, 120, 135]
... })
>>> measurements.columns.tolist()
['Shape_Area', 'Shape_Perimeter']
>>> measurements[str(SHAPE.AREA)]
0    1024
1     956
2    1101

Generate and append RST documentation:

>>> table = SHAPE.rst_table()
>>> class MeasureShape:
...     '''Measures object morphology.'''
...     pass
>>> MeasureShape.__doc__ = SHAPE.append_rst_to_doc(MeasureShape)

Methods

`encode`	Encode the string using the codec registered for encoding.
`replace`	Return a copy with all occurrences of substring old replaced by new.
`split`	Return a list of the substrings in the string, using sep as the separator string.
`rsplit`	Return a list of the substrings in the string, using sep as the separator string.
`join`	Concatenate any number of strings.
`capitalize`	Return a capitalized version of the string.
`casefold`	Return a version of the string suitable for caseless comparisons.
`title`	Return a version of the string where each word is titlecased.
`center`	Return a centered string of length width.
`count`	Return the number of non-overlapping occurrences of substring sub in string S[start:end].
`expandtabs`	Return a copy where all tab characters are expanded using spaces.
`find`	Return the lowest index in S where substring sub is found, such that sub is contained within S[start:end].
`partition`	Partition the string into three parts using the given separator.
`index`	Return the lowest index in S where substring sub is found, such that sub is contained within S[start:end].
`ljust`	Return a left-justified string of length width.
`lower`	Return a copy of the string converted to lowercase.
`lstrip`	Return a copy of the string with leading whitespace removed.
`rfind`	Return the highest index in S where substring sub is found, such that sub is contained within S[start:end].
`rindex`	Return the highest index in S where substring sub is found, such that sub is contained within S[start:end].
`rjust`	Return a right-justified string of length width.
`rstrip`	Return a copy of the string with trailing whitespace removed.
`rpartition`	Partition the string into three parts using the given separator.
`splitlines`	Return a list of the lines in the string, breaking at line boundaries.
`strip`	Return a copy of the string with leading and trailing whitespace removed.
`swapcase`	Convert uppercase characters to lowercase and lowercase characters to uppercase.
`translate`	Replace each character in the string using the given translation table.
`upper`	Return a copy of the string converted to uppercase.
`startswith`	Return True if S starts with the specified prefix, False otherwise.
`endswith`	Return True if S ends with the specified suffix, False otherwise.
`removeprefix`	Return a str with the given prefix string removed if present.
`removesuffix`	Return a str with the given suffix string removed if present.
`isascii`	Return True if all characters in the string are ASCII, False otherwise.
`islower`	Return True if the string is a lowercase string, False otherwise.
`isupper`	Return True if the string is an uppercase string, False otherwise.
`istitle`	Return True if the string is a title-cased string, False otherwise.
`isspace`	Return True if the string is a whitespace string, False otherwise.
`isdecimal`	Return True if the string is a decimal string, False otherwise.
`isdigit`	Return True if the string is a digit string, False otherwise.
`isnumeric`	Return True if the string is a numeric string, False otherwise.
`isalpha`	Return True if the string is an alphabetic string, False otherwise.
`isalnum`	Return True if the string is an alpha-numeric string, False otherwise.
`isidentifier`	Return True if the string is a valid Python identifier, False otherwise.
`isprintable`	Return True if the string is printable, False otherwise.
`zfill`	Pad a numeric string with zeros on the left, to fill a field of the given width.
`format`	Return a formatted version of S, using substitutions from args and kwargs.
`format_map`	Return a formatted version of S, using substitutions from mapping.
`maketrans`	Return a translation table usable for str.translate().
`category`	Return the category name for this measurement enumeration.
`get_labels`	Get all measurement labels without category prefix.
`get_headers`	Get all measurement headers with category prefix.
`rst_table`	Generate an RST (reStructuredText) table documenting the measurements.
`append_rst_to_doc`	Append the measurement documentation table to a module or class docstring.

Attributes

CATEGORY

Get the category name for this measurement instance.

classmethod category() → str[source]

Return the category name for this measurement enumeration.

Subclasses must implement this method to provide a category name that will be used to prefix all measurement labels. This ensures consistent naming conventions across the codebase.

Returns:

The category name (e.g., ‘Shape’, ‘Color’, ‘Texture’). This string is: prepended to each measurement label with an underscore separator to form the full header name (e.g., ‘Shape_Area’).

Return type:

str

Raises:

NotImplementedError – If not implemented by a subclass.

property CATEGORY: str

Get the category name for this measurement instance.

Provides instance-level access to the category name defined by the category() classmethod. This is useful when you have a measurement instance and need to know which category it belongs to without explicitly referencing the class.

Returns:: The category name from the enum class’s category() method.
Return type:: str

__str__() → str[source]

Return the string representation of this measurement as the prefixed name.

Returns the full enumeration value, which is the category-prefixed label (e.g., ‘Shape_Area’). This is used when the measurement is converted to a string or used in string formatting.

Returns:: The full prefixed name of the measurement (e.g., ‘{category}_{label}’).
Return type:: str

classmethod get_labels() → list[str][source]

Get all measurement labels without category prefix.

Returns a list of the short labels (without category prefix) for all measurements defined in this enumeration. These are the first element of each enum value tuple. Useful for creating human-readable lists or column names when the category context is already established.

Returns:

List of measurement labels in enumeration order (e.g.,: [‘Area’, ‘Perimeter’]). Does not include the category prefix; to get prefixed names, use get_headers().

Return type:

list[str]

classmethod get_headers() → list[str][source]

Get all measurement headers with category prefix.

Returns a list of the full enumeration values (with category prefix) for all measurements defined in this enumeration. These strings are suitable for use as DataFrame column names, dictionary keys, or in any context where the full categorized name is needed.

Returns:

List of prefixed measurement names in enumeration order: (e.g., [‘Shape_Area’, ‘Shape_Perimeter’]). Each header includes the category prefix separated by an underscore.

Return type:

list[str]

classmethod rst_table(*, title: str | None = None, header: tuple[str, str] = ('Name', 'Description')) → str[source]

Generate an RST (reStructuredText) table documenting the measurements.

Creates a formatted list-table in reStructuredText format that documents all measurements in this enumeration, including their labels and descriptions. This is useful for generating API documentation, parameter guides, or measurement reference tables that will be rendered in Sphinx documentation.

Parameters:

title (str, optional) – The title for the RST table. Defaults to the class name (e.g., ‘SHAPE’). The title is formatted as “Category: {title}” in the output.
header (tuple[str, str], optional) – A tuple of (left_column, right_column) header names. Defaults to (“Name”, “Description”). The left column typically contains measurement labels and the right column contains their descriptions.

Returns:

A formatted reStructuredText list-table string. The output includes:

RST list-table directive with the title
Column headers (Name and Description by default)
One row per measurement with label and description

The returned string is ready to be embedded in Sphinx documentation files or appended to docstrings.

Return type:

str

classmethod append_rst_to_doc(module: str | object) → str[source]

Append the measurement documentation table to a module or class docstring.

Generates the RST documentation table for this measurement enumeration and appends it to the provided module’s or class’s existing docstring. This is useful for automatically documenting which measurements a class produces or uses.

If the input is a string, it is treated as the docstring itself. If it is an object (class, function, module), its __doc__ attribute is used.

Parameters:

module (str | object) – Either a docstring string or an object (class, function, module) whose __doc__ attribute contains the docstring. The existing docstring is preserved, and the measurement table is appended with a blank line separator.

Returns:

The original docstring (or string) with the RST measurement table appended,: separated by two blank lines. The returned string is ready to be assigned back to the target’s __doc__ attribute.

Return type:

str

encode(encoding='utf-8', errors='strict')

Encode the string using the codec registered for encoding.

encoding: The encoding in which to encode the string.
errors: The error handling scheme to use for encoding errors. The default is ‘strict’ meaning that encoding errors raise a UnicodeEncodeError. Other possible values are ‘ignore’, ‘replace’ and ‘xmlcharrefreplace’ as well as any other name registered with codecs.register_error that can handle UnicodeEncodeErrors.

replace(old, new, count=-1, /)

Return a copy with all occurrences of substring old replaced by new.

count
Maximum number of occurrences to replace. -1 (the default value) means replace all occurrences.

If the optional argument count is given, only the first count occurrences are replaced.

split(sep=None, maxsplit=-1)

Return a list of the substrings in the string, using sep as the separator string.

sep
The separator used to split the string.

When set to None (the default value), will split on any whitespace character (including \n \r \t \f and spaces) and will discard empty strings from the result.

maxsplit
Maximum number of splits (starting from the left). -1 (the default value) means no limit.

Note, str.split() is mainly useful for data that has been intentionally delimited. With natural text that includes punctuation, consider using the regular expression module.

rsplit(sep=None, maxsplit=-1)

Return a list of the substrings in the string, using sep as the separator string.

sep
The separator used to split the string.

When set to None (the default value), will split on any whitespace character (including \n \r \t \f and spaces) and will discard empty strings from the result.

maxsplit
Maximum number of splits (starting from the left). -1 (the default value) means no limit.

Splitting starts at the end of the string and works to the front.

join(iterable, /)

Concatenate any number of strings.

The string whose method is called is inserted in between each given string. The result is returned as a new string.

Example: ‘.’.join([‘ab’, ‘pq’, ‘rs’]) -> ‘ab.pq.rs’

capitalize()

Return a capitalized version of the string.

More specifically, make the first character have upper case and the rest lower case.

casefold(): Return a version of the string suitable for caseless comparisons.

title()

Return a version of the string where each word is titlecased.

More specifically, words start with uppercased characters and all remaining cased characters have lower case.

center(width, fillchar=' ', /)

Return a centered string of length width.

Padding is done using the specified fill character (default is a space).

count(sub[, start[, end]]) → int: Return the number of non-overlapping occurrences of substring sub in string S[start:end]. Optional arguments start and end are interpreted as in slice notation.

expandtabs(tabsize=8)

Return a copy where all tab characters are expanded using spaces.

If tabsize is not given, a tab size of 8 characters is assumed.

find(sub[, start[, end]]) → int

Return the lowest index in S where substring sub is found, such that sub is contained within S[start:end]. Optional arguments start and end are interpreted as in slice notation.

Return -1 on failure.

partition(sep, /)

Partition the string into three parts using the given separator.

This will search for the separator in the string. If the separator is found, returns a 3-tuple containing the part before the separator, the separator itself, and the part after it.

If the separator is not found, returns a 3-tuple containing the original string and two empty strings.

index(sub[, start[, end]]) → int

Return the lowest index in S where substring sub is found, such that sub is contained within S[start:end]. Optional arguments start and end are interpreted as in slice notation.

Raises ValueError when the substring is not found.

ljust(width, fillchar=' ', /)

Return a left-justified string of length width.

Padding is done using the specified fill character (default is a space).

lower(): Return a copy of the string converted to lowercase.

lstrip(chars=None, /)

Return a copy of the string with leading whitespace removed.

If chars is given and not None, remove characters in chars instead.

rfind(sub[, start[, end]]) → int

Return the highest index in S where substring sub is found, such that sub is contained within S[start:end]. Optional arguments start and end are interpreted as in slice notation.

Return -1 on failure.

rindex(sub[, start[, end]]) → int

Return the highest index in S where substring sub is found, such that sub is contained within S[start:end]. Optional arguments start and end are interpreted as in slice notation.

Raises ValueError when the substring is not found.

rjust(width, fillchar=' ', /)

Return a right-justified string of length width.

Padding is done using the specified fill character (default is a space).

rstrip(chars=None, /)

Return a copy of the string with trailing whitespace removed.

If chars is given and not None, remove characters in chars instead.

rpartition(sep, /)

Partition the string into three parts using the given separator.

This will search for the separator in the string, starting at the end. If the separator is found, returns a 3-tuple containing the part before the separator, the separator itself, and the part after it.

If the separator is not found, returns a 3-tuple containing two empty strings and the original string.

splitlines(keepends=False)

Return a list of the lines in the string, breaking at line boundaries.

Line breaks are not included in the resulting list unless keepends is given and true.

strip(chars=None, /)

Return a copy of the string with leading and trailing whitespace removed.

If chars is given and not None, remove characters in chars instead.

swapcase(): Convert uppercase characters to lowercase and lowercase characters to uppercase.

translate(table, /)

Replace each character in the string using the given translation table.

table
Translation table, which must be a mapping of Unicode ordinals to Unicode ordinals, strings, or None.

The table must implement lookup/indexing via __getitem__, for instance a dictionary or list. If this operation raises LookupError, the character is left untouched. Characters mapped to None are deleted.

upper(): Return a copy of the string converted to uppercase.

startswith(prefix[, start[, end]]) → bool: Return True if S starts with the specified prefix, False otherwise. With optional start, test S beginning at that position. With optional end, stop comparing S at that position. prefix can also be a tuple of strings to try.

endswith(suffix[, start[, end]]) → bool: Return True if S ends with the specified suffix, False otherwise. With optional start, test S beginning at that position. With optional end, stop comparing S at that position. suffix can also be a tuple of strings to try.

removeprefix(prefix, /)

Return a str with the given prefix string removed if present.

If the string starts with the prefix string, return string[len(prefix):]. Otherwise, return a copy of the original string.

removesuffix(suffix, /)

Return a str with the given suffix string removed if present.

If the string ends with the suffix string and that suffix is not empty, return string[:-len(suffix)]. Otherwise, return a copy of the original string.

isascii()

Return True if all characters in the string are ASCII, False otherwise.

ASCII characters have code points in the range U+0000-U+007F. Empty string is ASCII too.

islower()

Return True if the string is a lowercase string, False otherwise.

A string is lowercase if all cased characters in the string are lowercase and there is at least one cased character in the string.

isupper()

Return True if the string is an uppercase string, False otherwise.

A string is uppercase if all cased characters in the string are uppercase and there is at least one cased character in the string.

istitle()

Return True if the string is a title-cased string, False otherwise.

In a title-cased string, upper- and title-case characters may only follow uncased characters and lowercase characters only cased ones.

isspace()

Return True if the string is a whitespace string, False otherwise.

A string is whitespace if all characters in the string are whitespace and there is at least one character in the string.

isdecimal()

Return True if the string is a decimal string, False otherwise.

A string is a decimal string if all characters in the string are decimal and there is at least one character in the string.

isdigit()

Return True if the string is a digit string, False otherwise.

A string is a digit string if all characters in the string are digits and there is at least one character in the string.

isnumeric()

Return True if the string is a numeric string, False otherwise.

A string is numeric if all characters in the string are numeric and there is at least one character in the string.

isalpha()

Return True if the string is an alphabetic string, False otherwise.

A string is alphabetic if all characters in the string are alphabetic and there is at least one character in the string.

isalnum()

Return True if the string is an alpha-numeric string, False otherwise.

A string is alpha-numeric if all characters in the string are alpha-numeric and there is at least one character in the string.

isidentifier()

Return True if the string is a valid Python identifier, False otherwise.

Call keyword.iskeyword(s) to test whether string s is a reserved identifier, such as “def” or “class”.

isprintable()

Return True if the string is printable, False otherwise.

A string is printable if all of its characters are considered printable in repr() or if it is empty.

zfill(width, /)

Pad a numeric string with zeros on the left, to fill a field of the given width.

The string is never truncated.

format(*args, **kwargs) → str: Return a formatted version of S, using substitutions from args and kwargs. The substitutions are identified by braces (‘{’ and ‘}’).

format_map(mapping) → str: Return a formatted version of S, using substitutions from mapping. The substitutions are identified by braces (‘{’ and ‘}’).

__format__(format_spec): Returns format using actual value type unless __str__ has been overridden.

static maketrans()

Return a translation table usable for str.translate().

If there is only one argument, it must be a dictionary mapping Unicode ordinals (integers) or characters to Unicode ordinals, strings or None. Character keys will be then converted to ordinals. If there are two arguments, they must be strings of equal length, and in the resulting dictionary, each character in x will be mapped to the character at the same position in y. If there is a third argument, it must be a string, whose characters will be mapped to None in the result.

__new_member__(label: str, desc: str | None = None)

Create a new measurement enumeration member with prefixed name.

Converts the input label and description into an enumeration member whose string value is automatically prefixed with the category name. The label and description are stored as instance attributes for convenient access.

This method is called automatically by Python’s Enum machinery when defining enum members. The enum member’s value becomes the full prefixed name (e.g., ‘Shape_Area’), while the label and description are stored separately as instance attributes.

Parameters:

label (str) – The short label for the measurement without category prefix (e.g., ‘Area’). This will be combined with the category name to create the full enumeration value.
desc (str, optional) – The description of what the measurement represents. If not provided, defaults to an empty string. This should briefly explain what the measurement measures.

Returns:

An enumeration member that behaves as a string with the value: ’{category}_{label}’ (e.g., ‘Shape_Area’). The instance also has label, desc, and pair attributes set.

Return type:

MeasurementInfo

phenotypic.abc_.MeasurementInfo#

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