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mfile

PROCESS MFILE.DAT IO library

process.core.io.mfile.

Notes: + 12/03/2014: Initial version + 12/03/2014: Added MFILE variable class + 12/03/2014: Added MFILE class for containing all info from file. + 12/03/2014: Added ability to read MFILE.DAT into class + 12/03/2014: Added ability write MFILE.DAT from class + 12/05/2014: Fixed mfile issue with strings in MFILE.DAT with no scans + 16/05/2014: Cleaned up MFileVariable + 19/05/2014: Cleaned up MFile and put some functions outside class. + 12/06/2014: Fixed error handling for "variable not in MFILE" errors + 16/06/2014: Fixed library path error; fix in get_scans + 24/11/2021: Global dictionary variables moved within the functions to avoid cyclic dependencies. This is because the dicts generation script imports, and inspects, process.

Compatible with PROCESS version 286

MFileVariable

Bases: dict

Class for containing a single mfile variable

Source code in process/core/io/mfile.py 
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class MFileVariable(dict):  # noqa: FURB189
    """Class for containing a single mfile variable"""

    def __init__(
        self, var_name, var_description, var_unit=None, var_flag=None, *args, **kwargs
    ):
        """
        An object class to contain information (and data values) for a single
        variable from the PROCESS machine readable output file (MFILE.DAT).
        Each class can contain all the scan values for the variable.

        Init defines the variable name and description from arguments:
          var_name --> variable name
          var_description --> variable description/long name

        The class contains the following:
            set_scan    --> function to set a scan number to a given value
            get_scan    --> function to retrieve a given scan
            get_scans   --> function to retrieve all scans.
        """
        self.var_name = var_name
        self.var_description = var_description
        self.var_unit = var_unit
        self.var_flag = var_flag
        self.latest_scan = 0
        super().__init__(*args, **kwargs)

    def __getattr__(self, name):
        result = self.get(name)
        if result:
            return result
        raise AttributeError(f"{self.__class__} object has no attribute {name}")

    def set_scan(self, scan_number, scan_value):
        """Sets the class attribute self.scan# where # is scan number

        Parameters
        ----------
        scan_number :
            scan number
        scan_value :
            value of parameter for scan
        """
        self[f"scan{scan_number:02}"] = scan_value
        if scan_number > self.latest_scan:
            self.latest_scan = scan_number

    def get_scan(self, scan_number):
        """Returns the value of a specific scan. For scan = -1 or None the last
        scan is given.

        Parameters
        ----------
        scan_number :
            scan number to return

        Returns
        -------
        type
            [single scan requested]
        """

        if scan_number is None or scan_number == -1:
            return self[f"scan{self.latest_scan:02}"]
        return self[f"scan{scan_number:02}"]

    def get_scans(self):
        """Returns a list of scan values in order of scan number

        Returns
        -------

            [List of all scans for variable]
        """
        return [v for k, v in sorted(filter(lambda x: "scan" in x[0], self.items()))]

    def get_number_of_scans(self):
        """Function to return the number of scans in the variable class"""
        return len([key for key in self.keys() if "scan" in key])

    @property
    def exists(self):
        return True

var_name = var_name instance-attribute

var_description = var_description instance-attribute

var_unit = var_unit instance-attribute

var_flag = var_flag instance-attribute

latest_scan = 0 instance-attribute

exists property

set_scan(scan_number, scan_value)

Sets the class attribute self.scan# where # is scan number

Parameters:

Name Type Description Default
scan_number

scan number

 required
scan_value

value of parameter for scan

 required
Source code in process/core/io/mfile.py 
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def set_scan(self, scan_number, scan_value):
    """Sets the class attribute self.scan# where # is scan number

    Parameters
    ----------
    scan_number :
        scan number
    scan_value :
        value of parameter for scan
    """
    self[f"scan{scan_number:02}"] = scan_value
    if scan_number > self.latest_scan:
        self.latest_scan = scan_number

get_scan(scan_number)

Returns the value of a specific scan. For scan = -1 or None the last scan is given.

Parameters:

Name Type Description Default
scan_number

scan number to return

 required

Returns:

Type Description
type

[single scan requested]
Source code in process/core/io/mfile.py 
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def get_scan(self, scan_number):
    """Returns the value of a specific scan. For scan = -1 or None the last
    scan is given.

    Parameters
    ----------
    scan_number :
        scan number to return

    Returns
    -------
    type
        [single scan requested]
    """

    if scan_number is None or scan_number == -1:
        return self[f"scan{self.latest_scan:02}"]
    return self[f"scan{scan_number:02}"]

get_scans()

Returns a list of scan values in order of scan number

Returns:

Type Description
[List of all scans for variable]
Source code in process/core/io/mfile.py 
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def get_scans(self):
    """Returns a list of scan values in order of scan number

    Returns
    -------

        [List of all scans for variable]
    """
    return [v for k, v in sorted(filter(lambda x: "scan" in x[0], self.items()))]

get_number_of_scans()

Function to return the number of scans in the variable class

Source code in process/core/io/mfile.py 
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def get_number_of_scans(self):
    """Function to return the number of scans in the variable class"""
    return len([key for key in self.keys() if "scan" in key])

MFileErrorClass

Error class for handling missing data from MFILE

Source code in process/core/io/mfile.py 
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class MFileErrorClass:
    """Error class for handling missing data from MFILE"""

    def __init__(self, item):
        self.item = item
        self.get_scan = self.get_error
        self.get_scans = self.get_error
        self.set_scan = self.get_error
        self.get_number_of_scans = self.get_error

    def get_error(self, *args, **kwargs):  # noqa: ARG002
        logger.error(f"Key '{self.item}' not in MFILE. KeyError! Check MFILE")

        if self.item == "error_status":
            # Missing error_status key means Process exited prematurely, usually
            # due to a "STOP 1"
            raise KeyError(
                "error_status not found in MFILE. Process probably exited prematurely"
            )
        return 0

    @property
    def exists(self):
        return False

item = item instance-attribute

get_scan = self.get_error instance-attribute

get_scans = self.get_error instance-attribute

set_scan = self.get_error instance-attribute

get_number_of_scans = self.get_error instance-attribute

exists property

get_error(*args, **kwargs)

Source code in process/core/io/mfile.py 
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def get_error(self, *args, **kwargs):  # noqa: ARG002
    logger.error(f"Key '{self.item}' not in MFILE. KeyError! Check MFILE")

    if self.item == "error_status":
        # Missing error_status key means Process exited prematurely, usually
        # due to a "STOP 1"
        raise KeyError(
            "error_status not found in MFILE. Process probably exited prematurely"
        )
    return 0

MFileDataDictionary

Bases: OrderedDict

Class object to act as a dictionary for the data.

Source code in process/core/io/mfile.py 
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class MFileDataDictionary(OrderedDict):
    """Class object to act as a dictionary for the data."""

    def __getattr__(self, name):
        result = self.get(name)
        if result:
            return result
        raise AttributeError(f"{self.__class__} object has no attribute {name}")

    def __getitem__(self, item):
        try:
            return dict.__getitem__(self, item)
        except KeyError:
            return MFileErrorClass(item)

DefaultOrderedDict

Bases: OrderedDict

Source code in process/core/io/mfile.py 
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class DefaultOrderedDict(OrderedDict):
    # Source: http://stackoverflow.com/a/6190500/562769
    def __init__(self, default_factory=None, *a, **kw):
        if default_factory is not None and not isinstance(default_factory):
            raise TypeError("first argument must be callable")
        OrderedDict.__init__(self, *a, **kw)
        self.default_factory = default_factory

    def __getitem__(self, key):
        try:
            return OrderedDict.__getitem__(self, key)
        except KeyError:
            return self.__missing__(key)

    def __missing__(self, key):
        if self.default_factory is None:
            return MFileErrorClass(key)
        self[key] = value = self.default_factory()
        return value

    def __reduce__(self):
        args = () if self.default_factory is None else (self.default_factory,)
        return type(self), args, None, None, self.items()

    def copy(self):
        return self.__copy__()

    def __copy__(self):
        return type(self)(self.default_factory, self)

    def __deepcopy__(self, memo):
        import copy

        return type(self)(self.default_factory, copy.deepcopy(self.items()))

    def __repr__(self):
        return (
            f"OrderedDefaultDict({self.default_factory}, {OrderedDict.__repr__(self)})"
        )

default_factory = default_factory instance-attribute

copy()

Source code in process/core/io/mfile.py 
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def copy(self):
    return self.__copy__()

MFile

Class object to store the MFile Objects

Source code in process/core/io/mfile.py 
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class MFile:
    """Class object to store the MFile Objects"""

    def __init__(self, filename="MFILE.DAT"):
        self.filename = filename
        self.data = DefaultOrderedDict()
        self.mfile_lines = []
        self.mfile_modules = {}
        self.des_name = []
        self.mfile_modules["Misc"] = []
        self.current_module = "Misc"
        if filename is not None:
            self.open_mfile()
            self.parse_mfile()

    def get_variables(self, *variables: str, scan: int = -1) -> list[Any]:
        """Get a number of variables from a single scan

        Parameters
        ----------
        *variables:

        scan:
             (Default value = -1)
        """
        return [self.get(v, scan=scan) for v in variables]

    def get(self, variable: str, *, scan: int = -1) -> Any:
        """Get variable data from a given scan

        Parameters
        ----------
        variable:

        scan:
             (Default value = -1)
        """
        return self.data[variable].get_scan(scan)

    def open_mfile(self):
        """Function to open MFILE.DAT"""
        with open(self.filename, encoding="utf-8") as mfile:
            self.mfile_lines = mfile.readlines()

        for i in range(len(self.mfile_lines)):
            if "*----" in self.mfile_lines[i] or "***" in self.mfile_lines[i]:
                self.mfile_lines = self.mfile_lines[:i]
                self.mfile_end = i
                return

    def parse_mfile(self):
        """Function to parse MFILE.DAT"""
        for line in (
            c for c in (clean_line(lines) for lines in self.mfile_lines) if c != [""]
        ):
            self.add_line(line)

    def add_line(self, line):
        """Function to read the line from MFILE and add to the appropriate
        class or create a new class if it is the first instance of it.

        Parameters
        ----------
        line :

        """
        if "#" in line[:2]:
            combined = " ".join(line[1:-1])
            exclusions = [
                "Feasible",
                "feasible",
                "Errors",
                "Waveforms",
                "Power Reactor Optimisation Code",
            ]
            if any(exclusion not in combined for exclusion in exclusions):
                self.current_module = combined
                self.mfile_modules[self.current_module] = []

        else:
            var_des = line[0]
            extracted_var_name = sort_brackets(line[1])

            if extracted_var_name == "":
                var_name = var_des
                self.des_name.append(var_name)
            else:
                var_name = extracted_var_name

            if "runtitle" in var_name:
                var_value = " ".join(line[2:])
            else:
                # Pass all value "words"
                var_value = sort_value(line[2:])
            var_unit = get_unit(var_des)
            var_flag = line[3] if len(line) >= 4 else None

            self.mfile_modules[self.current_module].append(var_name)
            self.add_to_mfile_variable(var_des, var_name, var_value, var_unit, var_flag)

    def add_to_mfile_variable(self, des, name, value, unit, flag, scan=None):
        """Function to add value to MFile class for that name/description

        Parameters
        ----------
        des :

        name :

        value :

        unit :

        flag :

        scan :
             (Default value = None)
        """
        var_key = des.lower().replace("_", " ") if name == "" else name.lower()

        if var_key in self.data:
            scan_num = scan or (self.data[var_key].get_number_of_scans() + 1)

            # Check for duplicate entries per scan point if there are scans and no scans
            a = len(self.data[var_key].get_scans())
            b = len(self.data["iscan"].get_scans()) if "iscan" in self.data else 1

            if var_key != "iscan":
                if a < b:
                    self.data[var_key].set_scan(scan_num, value)
            else:
                self.data[var_key].set_scan(scan_num, value)
        else:
            var = MFileVariable(
                name, des, unit, var_flag=flag, var_mod=self.current_module
            )
            self.data[var_key] = var
            self.data[var_key].set_scan(1, value)

    def write_to_json(self, keys_to_write=None, scan=-1, verbose=False):
        """Write MFILE object to JSON file

        Parameters
        ----------
        keys_to_write :
             (Default value = None)
        scan :
             (Default value = -1)
        verbose :
             (Default value = False)
        """

        if keys_to_write is None:
            keys_to_write = self.data.keys()

        filename = f"{self.filename}.json"

        dict_to_write = {}

        if scan == 0:
            for i in range(self.data["rmajor"].get_number_of_scans()):
                sub_dict = {}
                for item in keys_to_write:
                    dat_key = -1 if self.data[item].get_number_of_scans() == 1 else i + 1
                    data = self.data[item].get_scan(dat_key)
                    des = self.data[item].var_description.replace("_", " ")
                    entry = {"value": data, "description": des} if verbose else data
                    sub_dict[item] = entry
                dict_to_write[f"scan-{i + 1}"] = sub_dict
        else:
            for item in keys_to_write:
                # Initialize dat_key properly based on the number of scans
                if self.data[item].get_number_of_scans() == 1:
                    dat_key = -1
                else:
                    dat_key = (
                        scan if scan > 0 else 1
                    )  # Default to scan 1 if not specified
                data = self.data[item].get_scan(dat_key)
                des = self.data[item].var_description.replace("_", " ")
                entry = {"value": data, "description": des} if verbose else data
                dict_to_write[item] = entry

        with open(filename, "w") as fp:
            json.dump(dict_to_write, fp, indent=4)

filename = filename instance-attribute

data = DefaultOrderedDict() instance-attribute

mfile_lines = [] instance-attribute

mfile_modules = {} instance-attribute

des_name = [] instance-attribute

current_module = 'Misc' instance-attribute

get_variables(*variables, scan=-1)

Get a number of variables from a single scan

Parameters:

Name Type Description Default
*variables str
()
scan int

(Default value = -1)

 -1
Source code in process/core/io/mfile.py 
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def get_variables(self, *variables: str, scan: int = -1) -> list[Any]:
    """Get a number of variables from a single scan

    Parameters
    ----------
    *variables:

    scan:
         (Default value = -1)
    """
    return [self.get(v, scan=scan) for v in variables]

get(variable, *, scan=-1)

Get variable data from a given scan

Parameters:

Name Type Description Default
variable str
required
scan int

(Default value = -1)

 -1
Source code in process/core/io/mfile.py 
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def get(self, variable: str, *, scan: int = -1) -> Any:
    """Get variable data from a given scan

    Parameters
    ----------
    variable:

    scan:
         (Default value = -1)
    """
    return self.data[variable].get_scan(scan)

open_mfile()

Function to open MFILE.DAT

Source code in process/core/io/mfile.py 
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def open_mfile(self):
    """Function to open MFILE.DAT"""
    with open(self.filename, encoding="utf-8") as mfile:
        self.mfile_lines = mfile.readlines()

    for i in range(len(self.mfile_lines)):
        if "*----" in self.mfile_lines[i] or "***" in self.mfile_lines[i]:
            self.mfile_lines = self.mfile_lines[:i]
            self.mfile_end = i
            return

parse_mfile()

Function to parse MFILE.DAT

Source code in process/core/io/mfile.py 
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def parse_mfile(self):
    """Function to parse MFILE.DAT"""
    for line in (
        c for c in (clean_line(lines) for lines in self.mfile_lines) if c != [""]
    ):
        self.add_line(line)

add_line(line)

Function to read the line from MFILE and add to the appropriate class or create a new class if it is the first instance of it.

Parameters:

Name Type Description Default
line
required
Source code in process/core/io/mfile.py 
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def add_line(self, line):
    """Function to read the line from MFILE and add to the appropriate
    class or create a new class if it is the first instance of it.

    Parameters
    ----------
    line :

    """
    if "#" in line[:2]:
        combined = " ".join(line[1:-1])
        exclusions = [
            "Feasible",
            "feasible",
            "Errors",
            "Waveforms",
            "Power Reactor Optimisation Code",
        ]
        if any(exclusion not in combined for exclusion in exclusions):
            self.current_module = combined
            self.mfile_modules[self.current_module] = []

    else:
        var_des = line[0]
        extracted_var_name = sort_brackets(line[1])

        if extracted_var_name == "":
            var_name = var_des
            self.des_name.append(var_name)
        else:
            var_name = extracted_var_name

        if "runtitle" in var_name:
            var_value = " ".join(line[2:])
        else:
            # Pass all value "words"
            var_value = sort_value(line[2:])
        var_unit = get_unit(var_des)
        var_flag = line[3] if len(line) >= 4 else None

        self.mfile_modules[self.current_module].append(var_name)
        self.add_to_mfile_variable(var_des, var_name, var_value, var_unit, var_flag)

add_to_mfile_variable(des, name, value, unit, flag, scan=None)

Function to add value to MFile class for that name/description

Parameters:

Name Type Description Default
des
required
name
required
value
required
unit
required
flag
required
scan

(Default value = None)

 None
Source code in process/core/io/mfile.py 
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def add_to_mfile_variable(self, des, name, value, unit, flag, scan=None):
    """Function to add value to MFile class for that name/description

    Parameters
    ----------
    des :

    name :

    value :

    unit :

    flag :

    scan :
         (Default value = None)
    """
    var_key = des.lower().replace("_", " ") if name == "" else name.lower()

    if var_key in self.data:
        scan_num = scan or (self.data[var_key].get_number_of_scans() + 1)

        # Check for duplicate entries per scan point if there are scans and no scans
        a = len(self.data[var_key].get_scans())
        b = len(self.data["iscan"].get_scans()) if "iscan" in self.data else 1

        if var_key != "iscan":
            if a < b:
                self.data[var_key].set_scan(scan_num, value)
        else:
            self.data[var_key].set_scan(scan_num, value)
    else:
        var = MFileVariable(
            name, des, unit, var_flag=flag, var_mod=self.current_module
        )
        self.data[var_key] = var
        self.data[var_key].set_scan(1, value)

write_to_json(keys_to_write=None, scan=-1, verbose=False)

Write MFILE object to JSON file

Parameters:

Name Type Description Default
keys_to_write

(Default value = None)

 None
scan

(Default value = -1)

 -1
verbose

(Default value = False)

 False
Source code in process/core/io/mfile.py 
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def write_to_json(self, keys_to_write=None, scan=-1, verbose=False):
    """Write MFILE object to JSON file

    Parameters
    ----------
    keys_to_write :
         (Default value = None)
    scan :
         (Default value = -1)
    verbose :
         (Default value = False)
    """

    if keys_to_write is None:
        keys_to_write = self.data.keys()

    filename = f"{self.filename}.json"

    dict_to_write = {}

    if scan == 0:
        for i in range(self.data["rmajor"].get_number_of_scans()):
            sub_dict = {}
            for item in keys_to_write:
                dat_key = -1 if self.data[item].get_number_of_scans() == 1 else i + 1
                data = self.data[item].get_scan(dat_key)
                des = self.data[item].var_description.replace("_", " ")
                entry = {"value": data, "description": des} if verbose else data
                sub_dict[item] = entry
            dict_to_write[f"scan-{i + 1}"] = sub_dict
    else:
        for item in keys_to_write:
            # Initialize dat_key properly based on the number of scans
            if self.data[item].get_number_of_scans() == 1:
                dat_key = -1
            else:
                dat_key = (
                    scan if scan > 0 else 1
                )  # Default to scan 1 if not specified
            data = self.data[item].get_scan(dat_key)
            des = self.data[item].var_description.replace("_", " ")
            entry = {"value": data, "description": des} if verbose else data
            dict_to_write[item] = entry

    with open(filename, "w") as fp:
        json.dump(dict_to_write, fp, indent=4)

sort_value(value_words)

Parse value section of a line in MFILE.

value_words is a list of strings, which is then parsed.

Parameters:

Name Type Description Default
value_words List[str]

value of var in MFILE as list of strings

 required
value_words list[str]
required

Returns:

Type Description
Union[str, float]

string or float representation of value list
Source code in process/core/io/mfile.py 
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def sort_value(value_words: list[str]) -> str | float:
    """Parse value section of a line in MFILE.

    value_words is a list of strings, which is then parsed.

    Parameters
    ----------
    value_words : List[str]
        value of var in MFILE as list of strings
    value_words: list[str] :


    Returns
    -------
    Union[str, float]
        string or float representation of value list
    """
    if any(c in value_words[0] for c in ['"', "'"]):
        # First "word" begins with ": return words as single str
        return " ".join(value_words).strip().strip('"').strip()
    try:
        # Attempt float conversion of first word
        return float(value_words[0])
    except ValueError:
        # Log the exception with details
        logger.exception(f"Can't parse value in MFILE: {value_words}")
        # Return the original string as a fallback
        return " ".join(value_words).strip()

sort_brackets(var)

Function to sort bracket madness on variable name.

Parameters:

Name Type Description Default
var
required
Source code in process/core/io/mfile.py 
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def sort_brackets(var):
    """Function to sort bracket madness on variable name.

    Parameters
    ----------
    var :

    """
    if var != "":
        tmp_name = var.lstrip("(").split(")")
        if len(tmp_name) > 2:
            return tmp_name[0] + ")"
        return tmp_name[0]
    return ""

clean_line(line)

Cleans an MFILE line into the three parts we care about

Parameters:

Name Type Description Default
line
required
Source code in process/core/io/mfile.py 
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def clean_line(line):
    """Cleans an MFILE line into the three parts we care about

    Parameters
    ----------
    line :

    """
    return [item.strip("_ \n") for item in line.split(" ") if item != ""]

search_keys(dictionary, variable)

Searches the dictionary keys for matches to the variable name 'variable' in arguments.

Puts everything into lower case before searching.

Parameters:

Name Type Description Default
dictionary

dictionary to search in

 required
variable

variable name to search for

 required

Returns:

Type Description

List of matches to the searched for variable
Source code in process/core/io/mfile.py 
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def search_keys(dictionary, variable):
    """Searches the dictionary keys for matches to the variable name
    'variable' in arguments.

    Puts everything into lower case before searching.

    Parameters
    ----------
    dictionary :
        dictionary to search in
    variable :
        variable name to search for

    Returns
    -------
    :
        List of matches to the searched for variable
    """
    return [key for key in dictionary if variable.lower() in key.lower()]

search_des(dictionary, description)

Searches the dictionary descriptions for matches to the description 'description' from the arguments.

Puts everything into lower case before searching.

Parameters:

Name Type Description Default
dictionary

dictionary to search in

 required
variable

variable name to search for

 required

Returns:

Type Description

List of matches to the searched for description
Source code in process/core/io/mfile.py 
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def search_des(dictionary, description):
    """Searches the dictionary descriptions for matches to the description
    'description' from the arguments.

    Puts everything into lower case before searching.

    Parameters
    ----------
    dictionary :
        dictionary to search in
    variable :
        variable name to search for

    Returns
    -------
    :
        List of matches to the searched for description
    """
    descriptions = [dictionary[key].var_descript.lower() for key in dictionary.data]
    return [item for item in descriptions if description.lower() in item.lower()]

get_unit(variable_desc)

Returns the unit from a variable description if possible, else None.

Parameters:

Name Type Description Default
variable_desc
required
Source code in process/core/io/mfile.py 
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def get_unit(variable_desc):
    """Returns the unit from a variable description if possible, else None.

    Parameters
    ----------
    variable_desc :

    """
    candidate = variable_desc.rsplit("_", 1)[-1]
    if candidate.startswith("(") and candidate.endswith(")"):
        return candidate[1:-1]
    return None

is_number(val)

Check MFILE data entry

Parameters:

Name Type Description Default
val
required
Source code in process/core/io/mfile.py 
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def is_number(val):
    """Check MFILE data entry

    Parameters
    ----------
    val :

    """
    try:
        float(val)
        return True
    except ValueError:
        pass

    return False