mzData

Presentation

This is the Base class which holds all the data collected from a given mzdata.xml file. This is the data class used when the mzDataManager creates a .mat file.
You can create your own instances of this class if your data is not collected from the mzData files.

Definition

class mzData(BaseModel):
    fileName : str = None
    filePath : str = None
    metadata : dict = None
    mz : list[list[float]] = [[]]
    intensities : list[list[float]] = [[]]
    time : list[float] = []
    oneStruct : bool = True

How to use

There are two ways of creating this class, the first one is the following :

# Class creation
data = mzData()

# The script below could be called anywhere you want, just be sure to fill all necessary data before calling the saveMatfile function from the mzdataManager class.
data.fileName = "sample.mzdata.xml"
data.filePath = "some/path/"
data.metadata = {
    'software' : 'someSoftware',
    'analyser' : 'John Doe',
    'detector' : 'someDetector'
}
data.mz = mzList
data.intensities = intensitiesList
data.time = timeList
data.oneStruct = True

If you have all informations at the same time, you could use the second way of defining the class :

data = mzData(
    fileName = "sample.mzdata.xml",
    filePath = "some/path/",
    metadata = {
    'software' : 'someSoftware',
    'analyser' : 'John Doe',
    'detector' : 'someDetector'
    },
    mz = mzList,
    intensities = intensitiesList,
    time = timeList
)

Functions

fromDict

Presentation

Use fromDict function to populate the current mzData class based on a given dict.

Definition

def fromDict(self@mzData, toParse : Any, mat : matStruct = matStruct())

How to use

To use this function, you need to specify how the dictionnary is built with the parameter mat which is of type matStruct class (The dictionnary could contain more elements, but only elements listed in the parameter will be parsed). The second parameter is the data to parse toParse.

Warning

This data must always be a dictionnary. Meaning that the toParse parameter must be either of type dict or it’s equivalent in str. Anything other than this will raise an error.

Call this function like this:

data.fromDict(mat=someMatStructure, toParse=dictionnaryRepresentationOfData)

If the structure is the default one, you can omit the mat parameter.

toDict

Presentation

Use this function to convert mzData structure into a dictionnary representation of the data. This function is automatically called inside the saveMatfile function in the mzDataManager class.

Definition

def toDict(self@mzData, mat : matStruct, partialSave : bool = False) -> dict

How to use

This function takes two input parameters. The first one, mat is a matStruct class which specifies how the dictionnary should be generated. See matStruct class for further details.
The second input parameter is a boolean partialSave. Set this parameter to True if you want to save a partial structure (i.e an incomplete mzData structure where, for example, time values are not specified. This parameter is by default set to False). If an incomplete structure is found and partialSave is not True, an error of class mzDataError will be raised.

With an already created mzData object, call the function like follows :

convertedDict = data.toDict(mat=someMatStruct, partialSave=False)

The dictionnary generated will be containing the content inside the data variable.

setAttribute

Presentation

This function gives the possibility to the user to define new properties or modify existing one inside the extra field of the class.

Definition

def setAttribute(self@mzData, attributeName : str, attributeValue : Any)

How to use

The setAttribue function expects two input variables. The first one attributeName is a str and will be the new property’s name. The second one called attributeValue corresponds to it’s given value. This value could be a string, an integer or a dictionnary.

Info

Sets are not allowed at this time.

For example, let’s say you want to create a new attribute called uniqueIdentifier which will be equal to an integer. To define such attribute, use the following code :

# Considering that the data variable is an instance of the mzData class initialized with the default values.

data.setAttribute(attributeName="uniqueIdentifier", attributeValue=2846)

It is not possible yet to define an empty attribute with no value associated with it. This is a feature which will be added in a future release.

Warning

Whenever you create a new attribute, you need to give it a value even if it is a blank string.

getAttribute

Presentation

This one is pretty straight forward, returns the current value associated with the given attribute name.

Definition

def getAttribute(self@mzData, attributeName : str)

How to use

This function takes one parameter attributeName as a str. Here is how to get the associated value of the attribute uniqueIdentifier defined above :

ID = data.getAttribute(attributeName="uniqueIdentifier")
# ID should be equal to 2846

If the attribute doesn’t exists, an error will be thrown by this function with the type mzDataError.

getAttributeNames

Presentation

This function returns all defined attributes names as a list of string values.

Definition

def getAttributesNames(self@mzData)

How to use

The usage of getAttributeNames function is pretty straight forward. From an already created mzData object call the function as shown below :

# Considering data a variable of `mzData` class

attributes = data.getAttributesNames()

# With previously defined attributes in this page, this function should results :
# attributes = ["uniqueIdentifier"]

deleteAttribute

Presentation

deleteAttribute function removes the given attribute name as a str from the list of custom attributes. Throws an error if the attribute name is not found.

Definition

def deleteAttribute(self@mzData, attributeName : str)

How to use

From an already initialized mzData class, use the following code to call this function :

data.deleteAttribute(attributeName="uniqueIdentifier")

This function is a void, so it doesn’t returns any value. If an error occurs, it will be thrown.

clearAttributes

Presentation

This function removes all custom user defined attributes. Use this function carefully because it removes everything. Use removeAttribute to have a better control over the available attributes.

Definition

def clearAttributes(self@mzData)

How to use

data.clearAttributes()

There is no return to this function.