pyiron_base.utils.parser module

General purpose output parser

class pyiron_base.utils.parser.LogTag(tag_dict, h5_dict=None, key_dict=None)

Bases: object

LogTag object to parse for a specific pattern in the output file

Parameters:

• tag_dict (dict) – Dictionary with tags/patterns as key and an additional dictionary to describe the data structure. The data structure dictionary can contain the following keys: - “arg”: position of the argument - or dimension (“:”, “:,:”) - “type”: Python data type - “h5”: HDF5 key to store the information - “rows”: number of rows from the line where the tag was found - “splitTag”: split the tag - [True/False] - “splitArg”: split the argument - [True/False] - “lineSkip”: skip a line - “func”: function to convert the data

• h5_dict (dict) – Translation dictionary of output tags as keys to the tags used on the HDF5 file as values.

• key_dict (dict) – Translation dictionary of python internal tags as keys to the output tags as values.

apply_func(val)

Apply the function on a given value

Parameters:

val (dict, list, float, int) – value to apply the function on

Returns:

result of applying the function

Return type:

dict, list, float, int

arg()

Get tag argument

Returns:

tag arguments

Return type:

str

property current

Get the current tag

Returns:

current tag

Return type:

dict

property dyn_tags

Get dynamic tags

Returns:

dynamic tags

Return type:

dict

get_item(item, default)

If item is part of the current dictionary keys the corresponding value is returned otherwise the default is returned.

Parameters:

• item (str) – dictionary key

• default (list, dict, int, float) – Default value

Returns:

The values connected to the key item in the current dictionary and if item is not a

key in the current dictionary return the default value.

Return type:

list, dict, int, float

h5()

Translate current tag to HDF5 tag using the tag dictionary

Returns:

hdf5 key name

Return type:

str

property h5_dict

Get translation dictionary of output tags as keys to the tags used on the HDF5 file as values.

Returns:

h5 dictionary

Return type:

dict

is_func()

Check if a function is defined to convert the data - if “func” is included in the tag_dict dictionary

Returns:

[True/ False]

Return type:

bool

is_item(item_line, start=0)

Check if the current line - item_line - matches one of the provided tags, if that is the case set the tag to be the current tag and update the val_list with the corresponding values.

Parameters:

• item_line (str) – Line of the output file

• start (int) – Character to start with when parsing the item_line - default=0

Returns:

[True/False]

Return type:

bool

property key_dict

Get translation dictionary of python internal tags as keys to the output tags as values.

Returns:

key dictionary

Return type:

dict

line_skip()

Check how many lines should be skipped.

Returns:

[True/ False]

Return type:

bool

resolve_dynamic_variable(val)

Resolve dynamic variable using the key_dict dictionary

Parameters:

val – values to resolve

rows()

Number of rows to parse

Returns:

number of rows

Return type:

int, str

set_item(tag_vals, log_file)

Set LogTag item

Parameters:

• tag_vals (dict) – tag value dictionary

• log_file (Logstatus) – Logstatus object

Returns:

tag name, tag values, rows, line skip [True/False]

Return type:

list

property tag_dict

Get tag dictionary with tags/patterns as key and an additional dictionary to describe the data structure. The data structure dictionary can contain the following keys: - “arg”: position of the argument - or dimension (“:”, “:,:”) - “type”: Python data type - “h5”: HDF5 key to store the information - “rows”: number of rows from the line where the tag was found - “splitTag”: split the tag - [True/False] - “splitArg”: split the argument - [True/False] - “lineSkip”: skip a line - “func”: function to convert the data

Returns:

tag dictionary

Return type:

dict

property tag_first_word

Get first word of the tag

Returns:

first word

Return type:

str

property tag_name

Get tag name

Returns:

tag name

Return type:

str

test_split()

Check if the argument or the tag should be split - if “splitArg” or “splitTag” is included in the tag_dict dictionary.

Returns:

[True/ False]

Return type:

bool

translate(item)

Translate current tag to HDF5 tag using the h5_dict dictionary

Parameters:

item (str) – Python tag

Returns:

HDF5 tag

Return type:

str

class pyiron_base.utils.parser.Logstatus(h5=None, iter_levels=1)

Bases: object

Generic Parser for parsing output files by searching for a specific pattern structure and extracting the data that follows the pattern into the status_dict dictionary.

Parameters:

iter_levels (int) – Levels of iteration - default = 1

append(title, data_to_append, vec=False)

Append data to the LogStatus object status_dict dictionary

Parameters:

• title (str) – Title of the data to append

• data_to_append (list,dict) – the data can be of various types

• vec (bool) – [True/False] if the data is a single vector instead of a matrix or a tensor

combine_mat(x_key, xy_key, xz_key, y_key, yz_key, z_key, combined_key)

Combine three lists representing the x,y,z coordinates, by accessing them from the status_dict dictionary, combining them, store them under the combined_key and remove the other three keys.

Parameters:

• x_key (str) – key of the x coordinates

• y_key (str) – key of the y coordinates

• z_key (str) – key of the z coordinates

• combined_key (str) – name of the combined coordinates

combine_xyz(x_key, y_key, z_key, combined_key, as_vector=False)

Combine three lists representing the x,y,z coordinates, by accessing them from the status_dict dictionary, combining them, store them under the combined_key and remove the other three keys.

Parameters:

• x_key (str) – key of the x coordinates

• y_key (str) – key of the y coordinates

• z_key (str) – key of the z coordinates

• combined_key (str) – name of the combined coordinates

convert_unit(key, factor)

extract_file(file_name, tag_dict, h5_dict=None, key_dict=None)

Main function of the LogStatus class to extract data from an output file by searching for the tag dictionary

Parameters:

• file_name (str) – absolute path to the output file

• tag_dict (dict) – Dictionary with tags/patterns as key and an additional dictionary to describe the data structure. The data structure dictionary can contain the following keys: - “arg”: position of the argument - or dimension (“:”, “:,:”) - “type”: Python data type - “h5”: HDF5 key to store the information - “rows”: number of rows from the line where the tag was found - “splitTag”: split the tag - [True/False] - “splitArg”: split the argument - [True/False] - “lineSkip”: skip a line - “func”: function to convert the data

• h5_dict (dict) – Translation dictionary of output tags as keys to the tags used on the HDF5 file as values.

• key_dict (dict) – Translation dictionary of python internal tags as keys to the output tags as values.

extract_from_list(list_of_lines, tag_dict, h5_dict=None, key_dict=None)

Main function of the LogStatus class to extract data from an output file by searching for the tag dictionary

Parameters:

• file_name (str) – absolute path to the output file

• tag_dict (dict) – Dictionary with tags/patterns as key and an additional dictionary to describe the data structure. The data structure dictionary can contain the following keys: - “arg”: position of the argument - or dimension (“:”, “:,:”) - “type”: Python data type - “h5”: HDF5 key to store the information - “rows”: number of rows from the line where the tag was found - “splitTag”: split the tag - [True/False] - “splitArg”: split the argument - [True/False] - “lineSkip”: skip a line - “func”: function to convert the data

• h5_dict (dict) – Translation dictionary of output tags as keys to the tags used on the HDF5 file as values.

• key_dict (dict) – Translation dictionary of python internal tags as keys to the output tags as values.

static extract_item(l_item)

Method to extract information from a single line - currently very specific for the Lammps output

Parameters:

l_item (str) – line to extract information from

Returns:

the tag_string as string and the arguments as list

Return type:

str, list

raise_iter(dim=0)

Increase the iteration level

Parameters:

dim (int) – position - default = 0

reset_iter(dim=0)

Reset iteration level

Parameters:

dim (int) – reset value - default = 0

to_hdf(hdf)

Store the LogStatus object status_dict dictionary in an HDF5 file

Parameters:

hdf (ProjectHDFio) – HDF5 object to store the dictionary in.

pyiron_base.utils.parser.extract_data_from_file(file_name, tag, num_args=1)

General purpose routine to extract any static from a log (text) file

Parameters:

• file_name (str) – file name or path to the file, can either be absolute or relative

• tag (str) – string at the beginning of the line

• num_args (int) – number of arguments separated by ‘ ‘ or ‘,’ to extract after the tag

Returns:

List of arguments extracted as strings

Return type:

list

pyiron_base.utils.parser.extract_data_from_str_lst(str_lst, tag, num_args=1)

General purpose routine to extract any static from a log (text) file

Parameters:

• file_name (str) – file name or path to the file, can either be absolute or relative

• tag (str) – string at the beginning of the line

• num_args (int) – number of arguments separated by ‘ ‘ or ‘,’ to extract after the tag

Returns:

List of arguments extracted as strings

Return type:

list