bgc_data_processing.core.variables.vars
¶
Variables.
BaseVar(name, unit, var_type, default=np.nan, name_format='%-15s', value_format='%15s')
¶
Bases: ABC
Class to store Meta data on a variable of interest.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
name |
str
|
'Official' name for the variable : name to use when displaying the variable. |
required |
unit |
str
|
Variable unit (written using the following format: [deg_C] for Celsius degree of [kg] for kilograms). |
required |
var_type |
str
|
Variable type (str, int, datetime...). It will be used to convert the data using df[variable].astype(type) |
required |
default |
Any
|
Default value to set instead of nan., by default np.nan |
nan
|
name_format |
str
|
Format to use to save the data name and unit in a csv of txt file. , by default "%-15s" |
'%-15s'
|
value_format |
str
|
Format to use to save the data value in a csv of txt file., by default "%15s" |
'%15s'
|
Examples:
>>> var_lat = BaseVar("LATITUDE", "[deg_N]", float, 7, 6, "%-12s", "%12.6f")
Class to store Meta data on a variable of interest.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
name |
str
|
'Official' name for the variable : name to use when displaying the variable. |
required |
unit |
str
|
Variable unit (written using the following format: [deg_C] for Celsius degree of [kg] for kilograms). |
required |
var_type |
str
|
Variable type (str, int, datetime...). It will be used to convert the data using df[variable].astype(type) |
required |
default |
Any
|
Default value to set instead of nan., by default np.nan |
nan
|
name_format |
str
|
Format to use to save the data name and unit in a csv of txt file. , by default "%-15s" |
'%-15s'
|
value_format |
str
|
Format to use to save the data value in a csv/txt file., by default "%15s" |
'%15s'
|
Examples:
>>> var_lat = BaseVar("LATITUDE", "[deg_N]", float, 7, 6, "%-12s", "%12.6f")
Source code in src/bgc_data_processing/core/variables/vars.py
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|
is_feature = False
class-attribute
instance-attribute
¶
exist_in_dset: bool = None
class-attribute
instance-attribute
¶
name = name
instance-attribute
¶
unit = unit
instance-attribute
¶
type = var_type
instance-attribute
¶
default = default
instance-attribute
¶
name_format = name_format
instance-attribute
¶
value_format = value_format
instance-attribute
¶
label: str
property
¶
Returns the label to use to find the variable data in a dataframe.
Returns:
Type | Description |
---|---|
str
|
label. |
__hash__()
¶
Hashing method.
Returns:
Type | Description |
---|---|
int
|
Hashed object. |
Source code in src/bgc_data_processing/core/variables/vars.py
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|
__str__()
¶
Convert the variable to a string.
Returns:
Type | Description |
---|---|
str
|
name - unit (type) |
Source code in src/bgc_data_processing/core/variables/vars.py
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|
__repr__()
¶
Represent the variable as string.
Returns:
Type | Description |
---|---|
str
|
name_unit_type |
Source code in src/bgc_data_processing/core/variables/vars.py
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|
__eq__(__o)
¶
Test variable equality.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
__o |
object
|
Object to test equality with. |
required |
Returns:
Type | Description |
---|---|
bool
|
True if both are instance of basevar with same representation. |
Source code in src/bgc_data_processing/core/variables/vars.py
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|
TemplateVar
¶
Bases: BaseVar
Class to define default variable as a template to ease variable instantiation.
building_informations()
¶
Self's informations to instanciate object with same informations as self.
Returns:
Type | Description |
---|---|
dict
|
arguments to use when initiating an instance of BaseVar. |
Source code in src/bgc_data_processing/core/variables/vars.py
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|
in_file_as(*args)
¶
Return an ExistingVar.
New object has same attributes as self and the property 'aliases' correctly set up using ExistingVar._set_aliases method.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
args |
str | tuple[str, str, list]
|
Name(s) of the variable in the dataset and the corresponding flags. Aliases are ranked: first will be the only one used if present in dataset. If not second will be checked, and so on.. Aliases are supposed to be formatted as : (alias, flag_alias, flag_values), where alias (str) is the name of the column storing the variable in the dataset, flag_alias (str) is the name of the column storing the variable's flag in the dataset and flag_values (list) is the list of correct values for the flag. If there is no flag columns, flag_alias and flag_values can be set to None, or the argument can be reduced to the variable column name only. |
()
|
Returns:
Type | Description |
---|---|
ExistingVar
|
Variable with correct loading informations. |
Examples:
To instantiate a variable specifying a flag column to use:
>>> default_var = TemplateVar("PSAL", "[psu]", float, 10, 9, "%-10s", "%10.3f")
>>> instanciated_var = default_var.in_file_as(("CTDSAL", "CTDSAL_FLAG_W", [2]))
To instantiate a variable without flag columns to use:
>>> default_var = TemplateVar("PSAL", "[psu]", float, 10, 9, "%-10s", "%10.3f")
>>> instanciated_var = default_var.in_file_as(("CTDSAL",None,None))
# or equivalently:
>>> default_var = TemplateVar("PSAL", "[psu]", float, 10, 9, "%-10s", "%10.3f")
>>> instanciated_var = default_var.in_file_as("CTDSAL")
To instantiate a variable with multiple possible aliases and flags:
>>> default_var = TemplateVar("PSAL", "[psu]", float, 10, 9, "%-10s", "%10.3f")
>>> instanciated_var = default_var.in_file_as(
>>> ("CTDSAL1", "CTDSAL1_FLAG_W", [2]),
>>> ("CTDSAL2", "CTDSAL2_FLAG_W", [2]),
>>> )
To instantiate a variable with multiple possible aliases and some flags:
>>> default_var = TemplateVar("PSAL", "[psu]", float, 10, 9, "%-10s", "%10.3f")
>>> instanciated_var = default_var.in_file_as(
>>> ("CTDSAL1", "CTDSAL1_FLAG_W", [2]),
>>> ("CTDSAL2", None, None),
>>> )
# or equivalently:
To instantiate a variable with multiple possible aliases and some flags:
>>> default_var = TemplateVar("PSAL", "[psu]", float, 10, 9, "%-10s", "%10.3f")
>>> instanciated_var = default_var.in_file_as(
>>> ("CTDSAL1", "CTDSAL1_FLAG_W", [2]),
>>> "CTDSAL2",
>>> )
Source code in src/bgc_data_processing/core/variables/vars.py
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|
not_in_file()
¶
Return a NotExistingVar object with same attributes as self.
Returns:
Type | Description |
---|---|
NotExistingVar
|
Instanciated variable. |
Source code in src/bgc_data_processing/core/variables/vars.py
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|
NotExistingVar(name, unit, var_type, default=np.nan, name_format='%-15s', value_format='%15s')
¶
Bases: BaseVar
Class to represent variables which don't exist in the dataset.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
name |
str
|
'Official' name for the variable : name to use when displaying the variable. |
required |
unit |
str
|
Variable unit (written using the following format: [deg_C] for Celsius degree of [kg] for kilograms). |
required |
var_type |
str
|
Variable type (str, int, datetime...). It will be used to convert the data using df[variable].astype(type) |
required |
default |
Any
|
Default value to set instead of nan., by default np.nan |
nan
|
name_format |
str
|
Format to use to save the data name and unit in a csv of txt file. , by default "%-15s" |
'%-15s'
|
value_format |
str
|
Format to use to save the data value in a csv of txt file., by default "%15s" |
'%15s'
|
Class to represent variables which don't exist in the dataset.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
name |
str
|
'Official' name for the variable : name to use when displaying the variable. |
required |
unit |
str
|
Variable unit (written using the following format: [deg_C] for Celsius degree of [kg] for kilograms). |
required |
var_type |
str
|
Variable type (str, int, datetime...). It will be used to convert the data using df[variable].astype(type) |
required |
default |
Any
|
Default value to set instead of nan., by default np.nan |
nan
|
name_format |
str
|
Format to use to save the data name and unit in a csv of txt file. , by default "%-15s" |
'%-15s'
|
value_format |
str
|
Format to use to save the data value in a csv/txt file., by default "%15s" |
'%15s'
|
Source code in src/bgc_data_processing/core/variables/vars.py
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|
__default_exist_in_dset: bool = False
class-attribute
instance-attribute
¶
__default_remove_if_nan: bool = False
class-attribute
instance-attribute
¶
__default_remove_if_all_nan: bool = False
class-attribute
instance-attribute
¶
exist_in_dset = self.__default_exist_in_dset
instance-attribute
¶
remove_if_nan: bool
property
¶
True if the variable must be removed if NaN.
Returns:
Type | Description |
---|---|
bool
|
True if the variable must be removed if NaN. |
remove_if_all_nan: bool
property
¶
Whether the variable must be removed if all same are NaN.
If True, then the variable must be removed when this variable and other 'remove if all nan' variables are NaN.
Returns:
Type | Description |
---|---|
bool
|
True if the variable must be removed when this variable and other 'remove if all nan' variables are NaN. |
from_template(template)
classmethod
¶
Instantiate a NotExistingVar from a TemplateVar.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
template |
TemplateVar
|
Template variable to build from. |
required |
Returns:
Type | Description |
---|---|
NotExistingVar
|
NotExistingVar from template. |
Source code in src/bgc_data_processing/core/variables/vars.py
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|
set_default(default)
¶
Set the default value for the variable column.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
default |
Any
|
Value to use as default |
required |
Returns:
Type | Description |
---|---|
NotExistingVar
|
Self. |
Source code in src/bgc_data_processing/core/variables/vars.py
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|
remove_when_all_nan()
¶
Set self._remove_if_all_nan to True.
Returns:
Type | Description |
---|---|
NotExistingVar
|
self |
Source code in src/bgc_data_processing/core/variables/vars.py
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|
remove_when_nan()
¶
Set self._remove_if_nan to True.
Returns:
Type | Description |
---|---|
NotExistingVar
|
self |
Source code in src/bgc_data_processing/core/variables/vars.py
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|
ExistingVar(name, unit, var_type, default=np.nan, name_format='%-15s', value_format='%15s')
¶
Bases: NotExistingVar
Class to represent variables existing in the dataset.
This class allows to specify flag columns, correction functions...
Parameters:
Name | Type | Description | Default |
---|---|---|---|
name |
str
|
'Official' name for the variable : name to use when displaying the variable. |
required |
unit |
str
|
Variable unit (written using the following format: [deg_C] for Celsius degree of [kg] for kilograms). |
required |
var_type |
str
|
Variable type (str, int, datetime...). It will be used to convert the data using df[variable].astype(type) |
required |
default |
Any
|
Default value to set instead of nan., by default np.nan |
nan
|
name_format |
str
|
Format to use to save the data name and unit in a csv of txt file. , by default "%-15s" |
'%-15s'
|
value_format |
str
|
Format to use to save the data value in a csv of txt file., by default "%15s" |
'%15s'
|
Class to represent variables existing in the dataset.
This class allows to specify flag columns, correction functions...
Parameters:
Name | Type | Description | Default |
---|---|---|---|
name |
str
|
'Official' name for the variable : name to use when displaying the variable. |
required |
unit |
str
|
Variable unit (written using the following format: [deg_C] for Celsius degree of [kg] for kilograms). |
required |
var_type |
str
|
Variable type (str, int, datetime...). It will be used to convert the data using df[variable].astype(type) |
required |
default |
Any
|
Default value to set instead of nan., by default np.nan |
nan
|
name_format |
str
|
Format to use to save the data name and unit in a csv of txt file. , by default "%-15s" |
'%-15s'
|
value_format |
str
|
Format to use to save the data value in a csv/txt file., by default "%15s" |
'%15s'
|
Source code in src/bgc_data_processing/core/variables/vars.py
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|
__default_exist_in_dset: bool = True
class-attribute
instance-attribute
¶
__default_correction: callable = None
class-attribute
instance-attribute
¶
__default_aliases: list[tuple[str, str, list]] = []
class-attribute
¶
exist_in_dset = self.__default_exist_in_dset
instance-attribute
¶
correction = self.__default_correction
instance-attribute
¶
aliases: list[tuple[str, str, list]]
property
¶
Getter for aliases.
Returns:
Type | Description |
---|---|
list[tuple[str, str, list]]
|
alias, flag column alias (None if not), values to keep from flag column (None if not) |
remove_if_all_nan: bool
property
¶
Whether or not to suppress the row when this an other variables are NaN.
Returns:
Type | Description |
---|---|
bool
|
True if this variable must be included when removing where some variables are all nan. |
remove_if_nan: bool
property
¶
Whether or not to suppress the row when the variable is np.nan.
Returns:
Type | Description |
---|---|
bool
|
True if rows must be removed when this variable is nan. |
from_template(template)
classmethod
¶
Instantiate a ExistingVar from a TemplateVar.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
template |
TemplateVar
|
Template variable to build from. |
required |
Returns:
Type | Description |
---|---|
ExistingVar
|
ExistingVar from template. |
Source code in src/bgc_data_processing/core/variables/vars.py
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|
set_aliases(*args)
¶
Set aliases for the variable.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
args |
str | tuple[str, str, list]
|
Name(s) of the variable in the dataset and the corresponding flags. Aliases are ranked: first alias will be the only one considered if present in dataset. If not second will be checked, and so on.. Aliases are supposed to be formatted as : (alias, flag_alias, flag_values), where alias (str) is the name of the column storing the variable in the dataset, flag_alias (str) is the name of the column storing the variable's flag in the dataset and flag_values (list) is the list of correct values for the flag. If there is no flag columns, flag_alias and flag_values can be set to None, or the argument can be reduced to the variable column name only. |
()
|
Returns:
Type | Description |
---|---|
ExistingVar
|
Updated version of self |
Raises:
Type | Description |
---|---|
VariableInstantiationError
|
If one of the arguments length is different than 1 and 3. |
ValueError
|
If one of the arguments is not an instance of string or Iterable. |
Source code in src/bgc_data_processing/core/variables/vars.py
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|
correct_with(function)
¶
Correction function definition.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
function |
Callable
|
Function to apply to the dataframe row storing this variable's values. |
required |
Returns:
Type | Description |
---|---|
ExistingVar
|
self. |
Raises:
Type | Description |
---|---|
VariableInstantiationError
|
If the given object is not callable. |
Source code in src/bgc_data_processing/core/variables/vars.py
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|
ParsedVar
¶
Bases: BaseVar
Variables parsed from a csv file.
__repr__()
¶
Represent the parsed variable as a string.
Returns:
Type | Description |
---|---|
str
|
name_unit |
Source code in src/bgc_data_processing/core/variables/vars.py
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|
FeatureVar(feature)
¶
Bases: BaseVar
Variable resulting of an operation between variables.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
feature |
BaseFeature
|
Feature the variable comes from. |
required |
Source code in src/bgc_data_processing/core/variables/vars.py
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|
is_feature = True
class-attribute
instance-attribute
¶
exist_in_dset: bool = False
class-attribute
instance-attribute
¶
required_vars = feature.required_variables
instance-attribute
¶
feature: BaseFeature
property
¶
Feature for the variable.
is_loadable(loaded_list)
¶
Find if the variable can be made using given some loaded variables.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
loaded_list |
list[ExistingVar | NotExistingVar]
|
List of available variables. |
required |
Returns:
Type | Description |
---|---|
bool
|
True if the variable is loadable. |
Source code in src/bgc_data_processing/core/variables/vars.py
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|