Utility¶
Classes, functions, and exceptions that serve as the backbone of handling NMR data
DataFrame¶
- class nmrPype.utils.DataFrame.DataFrame(file: str = '', header: dict = {}, array: ndarray | None = None, verb: int = 0, inc: int = 16)¶
Object containing the nmr data vectors as well as the header. Contains methods for accessing and modifying the data based on the header included with the data.
- Parameters:
file (str) – Input file or stream for initializing frame
header (dict) – Header to initialize, by default obtained from file or set
array (Array [numpy.ndarray or None]) – Array to initialize, by default obtained from file or set
- getArray() ndarray | None¶
Dataframe array variable getter
- Returns:
self.array – Object’s current ndarray
- Return type:
Array
- getCurrDim() int¶
Obtain current dim for Dataframe based on dim order
- Returns:
Current direct dimension
- Return type:
int
- getDimOrder(dim: int) int¶
Convert order number into correct dimension index
- Parameters:
dim (int) –
Dimension Index
1 = Direct
2 = First Indirect
3 = Second Indirect
4 = Third Indirect
and so on..
- Returns:
Integer corresponding to the inputted dimension specifically for this dataset
- Return type:
int
- getHeader() dict¶
Dataframe header variable getter
- Returns:
self.header – Object’s current header
- Return type:
dict
- getInc() int¶
Obtain verbose increment vlue
- Returns:
Integer corresponding to verbose output loop increment
- Return type:
int
- getParam(param: str, dim: int = 0) float¶
Obtain header parameter from dictionary given key and dimension
- Parameters:
param (str) – Header parameter to obtain value from
dim (int) – Dimension of parameter
- Returns:
Float value of header parameter
- Return type:
float
- getVerb() int¶
Obtain verbosity value
- Returns:
Integer corresponding to verbosity value
- Return type:
int
- runFunc(targetFunction: str, arguments: dict = {}) int¶
runFunc completes the following:
Checks for valid function call
Passes function arguments to function call
Uses function call to process array based on function implementation
Update the data’s header accordingly
Can be called outside of command-line mode if arguments are passed with proper keys
- Parameters:
targetFunction (str) – Function Code (e.g. FT, SP, ZF)
arguments (dict) – Dictionary of arguments to pass to function initialization (May become a kwargs in the future for user simplicity)
- Returns:
Integer exit code obtained by the function itself (e.g. 0 success 1 fail)
- Return type:
int
- setArray(array: ndarray | None) int¶
Dataframe array variable setter
- Parameters:
array (Array) – New array to assign to data frame
- Returns:
Integer exit code (e.g. 0 success 1 fail)
- Return type:
int
- setHeader(dic: dict) int¶
Dataframe header variable setter
- Parameters:
dic (dict) – New header to assign to data frame
- Returns:
Integer exit code (e.g. 0 success 1 fail)
- Return type:
int
- setInc(level: int)¶
Set verbosity increment
- Parameters:
level (int) – Integer for verbose output loop increment
- setParam(param: str, value: float, dim: int = 0) int¶
Set given header parameter’s value to inputted value
- Parameters:
param (str) – Header parameter to set value to
value (float) – Value to replace header value with
dim (int) – Dimension of parameter
- Returns:
Integer exit code (e.g. 0 success 1 fail)
- Return type:
int
- setVerb(level: int)¶
Set verbosity value
- Parameters:
level (int) – Integer for new verbosity value
- updateParamSyntax(param, dim: int) str¶
Converts header keywords from ND to proper parameter syntax if necessary
- Parameters:
dim (int) – Target parameter dimension
- Returns:
param – Parameter string with updated syntax
- Return type:
str
- updatePipeCount(reset: bool = False) int¶
Increment the FDPIPECOUNT parameter or reset to zero Modify FDPIPEFLAG, FDCUBEFLAG, and FDFILECOUNT if needed
- Parameters:
reset (bool) – Whether or not to reset pipe count or increment pipe count
- Returns:
Integer exit code (e.g. 0 success 1 fail)
- Return type:
int
Error Handling¶
Exception classes and Exception handler for NMR data
Exceptions¶
- exception nmrPype.utils.FileIOError¶
Exception called when there is an error in reading/writing the data
- exception nmrPype.utils.FunctionError¶
Exception called when attempting to run a function fails
- exception nmrPype.utils.PipeBurst¶
Exception called when the main script reaches an exception, a.k.a. something broke. Just done for the nice name opportunity honestly
- exception nmrPype.utils.UnknownHeaderParam¶
Exception called when there is an attempt to call a nonexistent header param
Error Handling Function¶
This function is an error-handling helper function for nmrPype. It can output to the stderr and continue, or terminate running.
- param e:
Exception that called this error handler
- type e:
Exception
- param new_e:
New exception to pass onto the chain
- type new_e:
Exception
- param msg:
Error message to output to the screen
- type msg:
str
- param ePrint:
Whether to print to standard error stream or raise and error
- type ePrint:
bool