compiled-knowledge 4.0.0a5__cp313-cp313-macosx_10_13_universal2.whl

ck/in_out/parse_net.py

@@ -0,0 +1,480 @@
+from __future__ import annotations
+
+import string
+from typing import Protocol, Optional, List
+
+from ck.in_out.parser_utils import ParseError, ParserInput
+from ck.pgm import PGM, Factor, State
+from ck.utils.iter_extras import combos_ranges
+
+
+def read_network(input_stream, *, name: Optional[str] = None, network_builder: Optional[NetworkBuilder] = None) -> PGM:
+    """
+    Parser for Hugin "net" file format.
+
+    Read a network and return it as a PGM.
+    The input can be a string or a stream.
+    If the input is empty, then its is treated as an error.
+
+    This input is expected to conform to the following format.
+
+    <network> ::= <net_block> <node_block>* <potential_block>*
+
+    <net_block> ::= 'net' <block>
+
+    <node_block> ::= 'node' <NAME> <block>
+
+    <potential_block> ::= 'potential' <link> <block>
+
+    <block> ::= '{' <sentence>* '}'
+    <sentence> ::= <NAME> '=' <value> ';'
+
+    <link> ::= '(' <NAME> ')'
+             | '(' <NAME> '|' <NAME>+ ')'
+
+    <value> ::= <STRING> | <NUMBER> | <list>
+    <list> ::='(' <value>* ')'
+
+    The sentences of a <net_block> are ignored.
+
+    The sentences of a <node_block>
+        <name> of 'states' mandatory, with value that is a list of <STRING>
+        other sentences are ignored.
+
+    The sentences of a <potential_block>
+        <name> of 'data' mandatory, with value that is a list of (list of)* <NUMBER> (shape matching the link)
+        other sentences are ignored.
+
+    Here is a simple example input:
+        net{}
+        node a
+        {
+          states = ( "a0" "a1" );
+        }
+        node b
+        {
+          states = ( "b0" "b1" "b2" );
+        }
+
+        potential ( a )
+        {
+          data = ( 0.5 0.5 );
+        }
+        potential ( b | a )
+        {
+          data = ((0.4 0.4 0.2)(0.4 0.4 0.2)) ;
+        }
+    """
+    # Decorate the input stream
+    input_stream = ParserInput(input_stream)
+
+    if network_builder is None:
+        network_builder = PGM_NetworkBuilder(PGM_NetworkBuilder.add_function_dense)
+
+    bn = network_builder.start(name)
+
+    try:
+        _read_net(network_builder, bn, input_stream)
+        c = _read_past_space(input_stream)
+        if len(c) != 0:
+            input_stream.raise_error('unexpected extra characters at end of input')
+    except ParseError as e:
+        raise e
+    except Exception as e:
+        input_stream.raise_error(e)
+
+    return network_builder.done(bn)
+
+
+class NetworkBuilder(Protocol):
+    """
+    This is a protocol used by read_network to build the network
+    """
+
+    def start(self, name) -> object:
+        ...
+
+    def add_node(self, network, name, states):
+        ...
+
+    def add_factor(self, network, child_name, parent_names, data):
+        ...
+
+    def done(self, network) -> PGM:
+        ...
+
+
+class PGM_NetworkBuilder(NetworkBuilder):
+    """
+    This implementation of NetworkBuilder build a PGM object.
+    At construction time, pass one of the add_function_[...] methods
+    to the constructor, which selects the type of potential function
+    that is used to hold parameters.
+    """
+
+    @staticmethod
+    def add_function_dense(factor: Factor, data):
+        function = factor.set_dense()
+        shape = function.shape
+
+        def my_iter():
+            for key in combos_ranges(shape, flip=True):
+                parent = key[1:]
+                child = key[0]
+                d = data
+                for i in parent:
+                    d = d[i]
+                yield d[child]
+
+        function.set_iter(my_iter())
+
+    @staticmethod
+    def add_function_cpt(factor: Factor, data):
+        function = factor.set_cpt()
+        shape = function.shape
+        parent_shape = shape[1:]
+        for parent in combos_ranges(parent_shape):
+            cpd = data
+            for i in parent:
+                cpd = cpd[i]
+            function.set_cpd(parent, cpd)
+
+    @staticmethod
+    def add_function_sparse(factor: Factor, data):
+        function = factor.set_sparse()
+        shape = function.shape
+        for key in combos_ranges(shape):
+            parent = key[1:]
+            child = key[0]
+            d = data
+            for i in parent:
+                d = d[i]
+            function[key] = d[child]
+
+    @staticmethod
+    def add_function_compact(factor: Factor, data):
+        function = factor.set_compact()
+        shape = function.shape
+        for key in combos_ranges(shape):
+            parent = key[1:]
+            child = key[0]
+            d = data
+            for i in parent:
+                d = d[i]
+            function[key] = d[child]
+
+    def __init__(self, potential_function_type):
+        """
+        Args:
+            potential_function_type: should be one of:
+                PGM_NetworkBuilder.add_function_dense,
+                PGM_NetworkBuilder.add_function_cpt,
+                PGM_NetworkBuilder.add_function_sparse,
+                PGM_NetworkBuilder.add_function_compact.
+        """
+        self.add_pot_function = potential_function_type
+
+    def start(self, name):
+        return [PGM(name), {}]
+
+    def add_node(self, pgm_pair, name, states):
+        pgm, rv_map = pgm_pair
+        rv = pgm.new_rv(name, states)
+        rv_map[name] = rv
+
+    def add_factor(self, pgm_pair, child_name, parent_names, data):
+        pgm, rv_map = pgm_pair
+        rvs = [rv_map[rv_name] for rv_name in [child_name] + parent_names]
+        factor = pgm.new_factor(*rvs)
+        self.add_pot_function(factor, data)
+
+    def done(self, pgm_pair) -> PGM:
+        pgm, rv_map = pgm_pair
+        return pgm
+
+
+def _read_net(network_builder: NetworkBuilder, bn, input_stream) -> None:
+    _read_net_block(input_stream)
+    _read_blocks(network_builder, bn, input_stream)
+
+
+def _pass_callback(*_) -> None:
+    pass
+
+
+def _read_past_space(input_stream) -> str:
+    """
+    Returns:
+        either empty string, '', if end of input, otherwise a single character string that is not whitespace.
+    """
+    return input_stream.read_past_space(single_line=False, comment_char='%')
+
+
+def _read_name(input_stream) -> str:
+    """
+    Returns:
+        the read name
+    """
+    c = _read_past_space(input_stream)
+    name = ""
+    while len(c) == 1:
+        if (
+                c in string.ascii_letters
+                or c in string.digits
+                or c in "_-."
+        ):
+            name += c
+        else:
+            input_stream.pushback(c)
+            break
+        c = input_stream.read_one()
+
+    if len(name) == 0:
+        input_stream.raise_error('expected a name but none read')
+
+    return name
+
+
+def _read_keyword(input_stream) -> str:
+    """
+    Returns:
+        the read keyword
+    """
+    c = _read_past_space(input_stream)
+    keyword = ""
+    while len(c) == 1:
+        if c in string.ascii_letters:
+            keyword += c
+        else:
+            input_stream.pushback(c)
+            break
+        c = input_stream.read_one()
+    if len(keyword) == 0:
+        input_stream.raise_error('expected a keyword but none read')
+    return keyword.lower()
+
+
+def _read_net_block(input_stream) -> None:
+    keyword = _read_keyword(input_stream)
+    if keyword != 'net':
+        input_stream.raise_error(f'expected keyword "net" but got: {keyword!r}')
+    _read_block(_pass_callback, input_stream)
+
+
+def _read_blocks(network_builder, bn, input_stream) -> None:
+    lookahead = _read_past_space(input_stream)
+    while lookahead != '':
+        input_stream.pushback(lookahead)
+        keyword = _read_keyword(input_stream)
+        if keyword == 'node':
+            _read_node_block(network_builder, bn, input_stream)
+        elif keyword == 'potential':
+            _read_potential_block(network_builder, bn, input_stream)
+        else:
+            input_stream.raise_error(f'expected keyword "node" or "potential" but got: {keyword!r}')
+        lookahead = _read_past_space(input_stream)
+
+
+def _read_node_block(network_builder, bn, input_stream) -> None:
+    """
+    Assumes already read the 'node' keyword from the input.
+    """
+    name = _read_name(input_stream)
+
+    names = [name, None]
+    states = [None]
+
+    def callback(_name: str, _value):
+        if _name == 'label':
+            if names[1] is not None:
+                input_stream.raise_error(f'duplicate "label" sentence in node: {_name}')
+            names[0] = names[1] = _value
+        elif _name == 'states':
+            if states[0] is not None:
+                input_stream.raise_error(f'duplicate "states" sentence in node: {_name}')
+            assert _value is not None
+            states[0] = _value
+
+    _read_block(callback, input_stream)
+
+    states: Optional[List[State]] = states[0]
+    name: str = names[0]
+
+    if states is None:
+        input_stream.raise_error(f'no "states" found in node: {name}')
+    elif len(states) < 2:
+        input_stream.raise_error(f'must be at least 2 states in a node: {name}')
+    network_builder.add_node(bn, name, states)
+
+
+def _read_potential_block(network_builder, bn, input_stream):
+    """
+    Assumes already read the 'potential' keyword from the input.
+    """
+    link = _read_link(input_stream)
+    data = [None]
+
+    def callback(name, value):
+        if name == 'data':
+            if data[0] is not None:
+                input_stream.raise_error(f'duplicate "data" sentence in potential: {link}')
+            assert value is not None
+            data[0] = value
+
+    _read_block(callback, input_stream)
+    network_builder.add_factor(bn, link[0], link[1:], data[0])
+
+
+def _read_link(input_stream) -> List[str]:
+    """
+    Returns:
+        the read link
+    """
+    c = _read_past_space(input_stream)
+    if c != '(':
+        input_stream.raise_error('reading a link, expected "("')
+
+    name = _read_name(input_stream)
+    link = [name]
+
+    c = _read_past_space(input_stream)
+    if c == ')':
+        return link
+    if c != '|':
+        input_stream.raise_error('reading a link, expected ")" or "|"')
+
+    c = _read_past_space(input_stream)
+    while c != ')':
+        if c == '':
+            input_stream.raise_error('unexpected end of input while reading a link for a potential')
+        input_stream.pushback(c)
+        name = _read_name(input_stream)
+        link.append(name)
+        c = _read_past_space(input_stream)
+    return link
+
+
+def _read_block(sentence_callback, input_stream):
+    c = _read_past_space(input_stream)
+    if c != '{':
+        input_stream.raise_error('parse error - expected "{"')
+    c = _read_past_space(input_stream)
+    while c != '}':
+        if c == '':
+            input_stream.raise_error('parse error - unexpected end of input while reading a block')
+        input_stream.pushback(c)
+        _read_sentence(sentence_callback, input_stream)
+        c = _read_past_space(input_stream)
+
+
+def _read_sentence(sentence_callback, input_stream):
+    name = _read_name(input_stream)
+    c = _read_past_space(input_stream)
+    if c != '=':
+        input_stream.raise_error('parse error - expected "="')
+    value = _read_value(input_stream)
+    c = _read_past_space(input_stream)
+    if c != ';':
+        input_stream.raise_error('parse error - expected ";"')
+    sentence_callback(name, value)
+
+
+def _read_value(input_stream) -> List | str | float:
+    """
+    Returns:
+        (value, lookahead)
+    """
+    lookahead = _read_past_space(input_stream)
+    if lookahead == '':
+        input_stream.raise_error('parse error - expected value - unexpected end of input')
+
+    input_stream.pushback(lookahead)
+    if lookahead == '(':
+        # reading a list
+        value = _read_list(input_stream)
+    elif lookahead == '"':
+        # reading a string
+        value = _read_string(input_stream)
+    else:
+        # reading a number
+        value = _read_number(input_stream)
+    return value
+
+
+def _read_list(input_stream) -> List:
+    """
+    Returns:
+        the read list of values
+    """
+    c = _read_past_space(input_stream)
+    if c != '(':
+        input_stream.raise_error('parse error - expected "("')
+    result = []
+    c = _read_past_space(input_stream)
+    while c != ')':
+        if c == '':
+            input_stream.raise_error('parse error - unexpected end of input while reading list')
+        input_stream.pushback(c)
+        value = _read_value(input_stream)
+        result.append(value)
+        c = _read_past_space(input_stream)
+    return result
+
+
+def _read_string(input_stream) -> str:
+    """
+    Returns:
+        the read string value
+    """
+    c = _read_past_space(input_stream)
+    if c != '"':
+        input_stream.raise_error('parse error - expected open quote (")')
+    result = ""
+    while True:
+        c = input_stream.read_one()
+        if c == '':
+            input_stream.raise_error('parse error - unexpected end of input while reading string')
+        if c == '"':
+            break
+        if c == '\\':
+            c = input_stream.read_one()
+            if c in '\\\'\"':
+                pass
+            elif c == 'n':
+                c = '\n'
+            elif c == 'r':
+                c = '\r'
+            elif c == 'v':
+                c = '\v'
+            elif c == 'f':
+                c = '\f'
+            elif c == 'a':
+                c = '\a'
+            elif c == 'b':
+                c = '\b'
+            elif c == 't':
+                c = '\t'
+            else:
+                input_stream.raise_error(f'parse error - unexpected escape code while reading string: \\{c}')
+        result += c
+    return result
+
+
+def _read_number(input_stream) -> float:
+    """
+    Return:
+        the read numeric value
+    """
+    value = ''
+    c = _read_past_space(input_stream)
+    while len(c) == 1:
+        if not (c in string.digits or c in ".eE+-"):
+            input_stream.pushback(c)
+            break
+        value += c
+        c = input_stream.read_one()
+    try:
+        value = float(value)
+    except ValueError:
+        input_stream.raise_error('parse error - could not parse number')
+    return value

ck/in_out/parser_utils.py

@@ -0,0 +1,185 @@
+"""
+Support for parsers.
+
+Defines:
+    ParserInput
+    ParseError.
+"""
+import re as _re
+import string as _string
+from io import StringIO as _StringIO
+
+
+class ParseError(Exception):
+    """
+    Raised when a parse error occurs.
+    Keeps track of the location of the error (line number and character position in the line).
+    """
+
+    def __init__(self, line_num: int, char_pos: int, message: str):
+        full_msg = f'line {line_num}, pos {char_pos}: {message}'
+        super(ParseError, self).__init__(full_msg)
+        self.line_num: int = line_num
+        self.char_pos: int = char_pos
+
+
+class ParserInput:
+    """
+    A wrapper for an input stream of characters with
+    integrated exception raising and infinite pushback.
+    """
+
+    def __init__(self, input_stream):
+        self._input = _check_input(input_stream)
+        self._prev_line_len = 0
+        self._cur_line = 1
+        self._cur_char = 1
+        self._lookahead = []
+
+    def read_one(self) -> str:
+        """
+        Read one character from the input stream.
+
+        Returns:
+            a character from the input stream,  or '' if EOF.
+        """
+        if len(self._lookahead) > 0:
+            c = self._lookahead.pop()
+        else:
+            c = self._input.read(1)
+        if c == '\n':
+            self._prev_line_len = self._cur_char
+            self._cur_line += 1
+            self._cur_char = 1
+        else:
+            self._cur_char += 1
+        return c
+
+    def readline(self) -> str:
+        """
+        Returns:
+             the next line (including the trailing '\n') or '' if EOF.
+        """
+        line = ''
+        while True:
+            c = self.read_one()
+            line += c
+            if c == '' or c == '\n':
+                return line
+
+    def read_past_space(self, single_line: bool, comment_char=None) -> str:
+        """
+        Returns:
+            either empty string, '', if end of input, otherwise a single character string that is not whitespace.
+            If single_line is True, then '\n' is treated as eof.
+        """
+        c = self.read_one()
+        while True:
+            if not single_line:
+                while len(c) == 1 and c in _string.whitespace:
+                    c = self.read_one()
+            else:
+                while len(c) == 1 and c in _string.whitespace and c != '\n':
+                    c = self.read_one()
+
+            if comment_char is None or c != comment_char:
+                break
+
+            # in a comment
+            c = self.read_one()
+            while len(c) == 1 and c != '\n':
+                c = self.read_one()
+
+        if single_line and c == '\n':
+            self.pushback('\n')
+            c = ''
+
+        return c
+
+    def pushback(self, c: str) -> None:
+        """
+        Push a character back to the input stream.
+
+        Args:
+            c: a character to push back to the input stream.
+        """
+        assert (len(c) == 1)
+        self._lookahead.append(c)
+        # Do our best to keep the input position counters sensible
+        if c == '\n':
+            self._cur_line -= 1
+            self._cur_char = self._prev_line_len
+            self._prev_line_len = 0
+        else:
+            self._cur_char -= 1
+
+    def raise_error(self, message: str) -> None:
+        """
+        Raise a ParseError with the given message and the current line number and character position.
+
+        Args:
+            message: the error message.
+        """
+        if isinstance(message, Exception):
+            message = f'Exception: {message.__class__.__name__} {message}'
+        raise ParseError(self._cur_line, self._cur_char, message)
+
+
+def _check_input(input_stream):
+    """
+    If the given argument is a string, then wrap it in a StringIO.
+    """
+    if isinstance(input_stream, str):
+        return _StringIO(input_stream)
+    else:
+        return input_stream
+
+
+def escape_string(s: str, *, double_quotes: bool = False, single_quotes: bool = False) -> str:
+    """
+    Return the given string with backslash escaping for special characters.
+    Args:
+        s: The string to process.
+        double_quotes: should double quotes be escaped?
+        single_quotes: should single quotes be escaped?
+
+    Returns:
+
+    """
+    s = s.replace('\\', '\\\\')  # must come first
+    s = s.replace('\n', '\\n')
+    s = s.replace('\r', '\\r')
+    s = s.replace('\v', '\\v')
+    s = s.replace('\f', '\\f')
+    s = s.replace('\f', '\\f')
+    s = s.replace('\a', '\\a')
+    s = s.replace('\b', '\\b')
+    s = s.replace('\t', '\\t')
+    if double_quotes:
+        s = s.replace('"', '\\"')
+    if single_quotes:
+        s = s.replace("'", "\\'")
+    return s
+
+
+def clean_string(s: str, valid_chars: str = '[a-zA-Z0-9_]', replace_char: str = '_') -> str:
+    """
+    Remove any invalid char from the given string and replace with
+    the given 'replace_char'
+
+    Args:
+        s: The string to process.
+        valid_chars: the set of valid characters (as a regular expression).
+        replace_char: the character to replace invalid characters with.
+
+    Returns:
+        the cleaned string.
+    """
+    re = _re.compile(valid_chars)
+    result = ''
+    for c in s:
+        if re.match(c):
+            result += c
+        else:
+            result += replace_char
+    return result

ck/in_out/pgm_pickle.py

@@ -0,0 +1,42 @@
+import pickle
+from pathlib import Path
+
+from ck.pgm import PGM
+
+
+def write_pickle(pgm: PGM, file) -> None:
+    """
+    Write the PGM as a pickle file.
+
+    Args:
+        pgm: The PGM to write.
+        file: Either a file name, file Path, or an object with a write method.
+    """
+    if isinstance(file, (str, Path)):
+        with open(file, 'wb') as f:
+            pickle.dump(pgm, f)
+    else:
+        pickle.dump(pgm, file)
+
+
+def read_pickle(file) -> PGM:
+    """
+    Read a PGM as a pickle file.
+
+    Args:
+        file: Either a file name, file Path, or an object with a read method.
+    
+    Returns:
+        A PGM object.
+        
+    Raises:
+        RuntimeError: if the unpickled object is not a PGM.
+    """
+    if isinstance(file, (str, Path)):
+        with open(file, 'rb') as f:
+            pgm = pickle.load(f)
+    else:
+        pgm = pickle.load(file)
+    if not isinstance(pgm, PGM):
+        raise RuntimeError('not a PGM object')
+    return pgm