mzDataManager

Presentation

Main class used for converting mzData files into matlab files.

Definition

class mzDataManager(BaseModel):
    mzDataPath : str = None
    exportPath : str = None
    useDirectory : bool = True

How to use

With path

manager = mzDataManager(
    mzDataPath = "Some/Path",
    exportPath = "Some/Export/Path",
)

The path you specify in those arguments will be stored in the class, so when you use the integrated functions, you only need to specify the relative path to the file.

Without path

manager = mzDataManager(useDirectory=False)

Setting up the class this way will require to specify each time you call a function to give the full path and the export directory.

Functions

mzDataXMLread

Presentation

This function reads a .mzData.xml file and returns a mzData structure which can be modified before saving it’s data to a .mat file (See mzData class for further details).

Definition

def mzDataXMLread(self@mzDataManager, fileName : str, customDirectory : bool = False)

How to use

# Considering that mzDataManager class has been intialized before and stored as manager variable

content = manager.mzDataXMLread(
    fileName=Path2File
)

Parameters

• If directories were provided in the init process :

  • fileName : Relative path of the mzData.xml file to read

  • customDirectory : Set this parameter to True if you provide a full path which is different than the one specified in the init process.

• Otherwise :

  • fileName : Full path to the mzData.xml file to read

  • customDirectory : Does nothing

Outputs

• Outputs a mzData class containing the content of the file parsed.

saveMatfile

Presentation

Saves a mzData class into a .mat file with all metadata included.

Definition

def saveMatfile(self@mzDataManager, mzData : mzData, remove : bool = False, dir2Save : str = None, force : bool = False)

How to use

# Considering that mzDataManager class has been intialized before and stored as manager variable

# Considering also the variable content which is the result of the function mzDataXMLread presented above

manager.saveMatFile(
    mzData=content
)

Parameters

• mzData : The mzData structure to save as a .mat file. (See here for the .mat file structure)

• remove : Should the original file (so the original .mzData.xml file) be removed when save is complete ?

• force : If a .mat file already exists with the same name in the export folder, should it be replaced ? If this parameter is set to False, save will be aborted if a file is found.

• If directories were not provided during init process:

  • dir2save : Full directory specifying where to save the converted file. If this parameter is set while a directory was specified in the init process, this value is prioritized.

Outputs
If function ran correctly, no output, otherwise raises the error.

convertFile

Presentation

All in one function. Reads mzData.xml file and automatically saves it into the export folder. No transition to the mzData class.

Definition

def convertFile(self@mzDataManager, fileName : str, customDirectory : bool = False, dir2Save : str = None, force : bool = False, remove : bool = False)

How to use

# Considering that mzDataManager class has been intialized before and stored as manager variable

manager.convertFile(
    fileName=FileName
)

Parameters

• fileName :
  

  • Should be the full path to the file and it’s extension (.mzdata.xml) to convert if no value was given to mzDataPath when initializing the class.

  • Otherwise, the file’s relative path with it’s extension (.mzdata.xml)

• customDirectory : Set this parameter to True if the fileName is in a different path than the one given in configuration.

• dir2Save : Save directory to save the .mat file. If path was given in configuration, it is not needed. This parameter will be prioritised over the path given in configuration (if any).

• force : If a file has the same name in the converted folder, should it be replaced ? (File will not be saved if sibling found in convert folder and this parameter set to False.)

• remove : Should the original file be removed when it is saved as .mat file ?

Outputs
No outputs