pydotthz 1.0.0

This Python Package allows interfacing with dotThz files.

Interface with dotTHz files using Python

This crate provides an easy way to interface with dotTHz files in Python.

Install it

pip install pydotthz

or

pip3 install pydotthz

and then use like specified in the following example:

from pathlib import Path
import numpy as np
from pydotthz import DotthzFile, DotthzMeasurement, DotthzMetaData

if __name__ == "__main__":
    # Sample data
    time = np.linspace(0, 1, 100)  # your time array
    data = np.random.rand(100)  # example 3D data array

    # save the file
    path1 = Path("test1.thz")
    with DotthzFile(path1, "w") as file:
        file["Measurement 1"] = DotthzMeasurement()

        # create meta-data
        meta_data = DotthzMetaData()
        meta_data.user = "John Doe"
        meta_data.version = "1.00"
        meta_data.instrument = "Toptica TeraFlash Pro"
        meta_data.mode = "THz-TDS/Transmission"

        file["Measurement 1"].meta_data = meta_data

        # for thzVer 1.00, we need to transpose the array!
        # important: do not manipulate keys on the `dataset` field, otherwise it won't be written to the file.
        file["Measurement 1"]["Sample"] = np.array([time, data]).T

    del file  # optional, not required as the file is already closed

    # create and save a second file
    path2 = Path("test2.thz")
    with DotthzFile(path2, "w") as file:
        file["Measurement 2"] = DotthzMeasurement()
    del file  # optional, not required as the file is already closed

    # open the first file again in append mode and the second in read mode
    with DotthzFile(path1, "a") as file1, DotthzFile(path2) as file2:
        measurements = file2.measurements
        for name, measurement in measurements.items():
            file1[name] = measurement
    del file1  # optional, not required as the file is already closed

    with DotthzFile(path1, "r") as file1:
        # read the first measurement
        key = list(file1.measurements.keys())[0]
        print(file1.measurements.get(key).meta_data)
        print(file1.measurements.get(key).datasets)

    # read out an image file:
    path3 = Path("tests/test_files/test_image.thz")
    with DotthzFile(path3, "r") as image_file:
        # read the first group/measurement
        key = list(image_file.measurements.keys())[0]
        print(image_file.measurements.get(key).meta_data)
        datasets = image_file.measurements.get(key).datasets
        print(datasets.keys())

        # from the first dataset, extract the image:
        time_trace = datasets["time"]
        image = datasets["dataset"]

        # print image dimensions
        print(image.shape)

    # save an image file:
    path4 = Path("tests/test_files/test_image_2.thz")
    with DotthzFile(path4, "w") as file:

        file.measurements["Image"] = DotthzMeasurement()

        # set meta_data
        meta_data = DotthzMetaData()
        meta_data.user = "John Doe"
        meta_data.email = "[e-mail]"
        meta_data.institution = "University of Bern"
        meta_data.orcid = "ORCID"
        meta_data.description = "some comment"
        meta_data.date = "date"
        meta_data.time = "time"
        meta_data.version = "1.10"
        meta_data.instrument = "Toptica TeraFlash Pro"
        meta_data.mode = "THz-TDS/Transmission"

        # add more keys from your "info" dictionary ...
        # for (key, value) in info.items():
        #    meta_data.add_field(key, value)

        file.measurements["Image"].meta_data = meta_data

        # important: do not manipulate keys on the `dataset` field, otherwise it won't be written to the file.
        file.measurements["Image"]["time"] = time_trace
        file.measurements["Image"]["dataset"] = image

Requires hdf5 to be installed.