Acquire Data from Shimadzu .daml Files#
The .daml files provided by Shimadzu come in an xml format where key data pieces (chromatogram, observed m/z ratios with their corresponding intensity and UV traces) are encoded in base64 format.
The following script extracts the data relevant to PyParse, and reformats it into a common structure.
- getShimadzuData.getData(input_dir)[source]#
Search the directory specified by the user to acquire any and all input LC-MS data that is present. Format this data into the preferred PyParse format.
- Parameters:
input_dir – A string specifying the directory to search for .daml files
- Returns:
A list comprising: a dictionary of all peaks in all wells (indexed by well); a dictionary of all chromatograms; a dictionary of all sample IDs; a dictionary total_area_abs of each well. Each of these dictionaries are indexed by well