Getting started

Installing qpformat

qpformat is written in pure Python and supports Python version 3.5 and higher. qpformat depends on several other scientific Python packages, including:

To install qpformat, use one of the following methods (package dependencies will be installed automatically):

  • from PyPI:
    pip install qpformat
  • from sources:
    pip install -e . or python install

User API

Qpformat supports several file formats that are categorized into qpformat.file_formats.SingleData (the experimental data file format contains only one phase image) and qpformat.file_formats.SeriesData (the experimental data file format supports multiple phase images). From these base classes, all data file formats are derived. The idea is that experimental data is not loaded into memory until the get_qpimage method is called which returns a qpimage.QPImage object.

Basic Usage

To extract the (unwrapped) phase from a DHM image, use the qpformat.load_data() method. The file format type is determined automatically by qpformat.

import qpformat
# The data are not loaded into memory, only the meta data is read
dataset = qpformat.load_data("/path/to/hologram_image.tif")
# Get the quantitative phase data (a qpimage.QPImage is returned)
qpi = dataset.get_qpimage()
# Get the 2D phase image data as a numpy array
phase = qpi.pha

The object qpi is an instance of qpimage.QPImage which comes with an elaborate set of background correction methods. Note that qpformat.load_data() accepts keyword arguments that allow to define the setup metadata as well as the hologram reconstruction parameters.

Command-line program “qpinfo”

This command-line program allows checking whether a file (or directory) contains quantitative phase data with a file format supported by qpformat.

usage: qpinfo [-h] path

The command yields the type of the format, the corresponding class name in qpformat, as well as the meta data associated with the dataset (e.g. wavelength, pixel size).