Loading various data

These are examples Python codes to load several types of data format. To try these examples, simply download the .py files and put it in module folder of your working directory. Then you can load corresponding files by load function as follows:

from lys import *
data = load("Replace this string with your filename to be loaded")

It is noted that the Python codes in this page is not fully tested. So there may be bugs. If you want to make your own file loader, see Loading your file

Gatan Digital Micrograph .dm3 files

Install dm3_lib(https://bitbucket.org/piraynal/pydm3reader/src/master/) and put examples/load_dm3.py into module folder.

import sys
import numpy as np
from lys import Wave, registerFileLoader

try:
    import dm3_lib as dm3

    def __loadDm3(name):
        data = dm3.DM3(name)
        w = Wave()
        w.data = data.imagedata
        if w.data.ndim == 2:  # image
            w.x = np.arange(0, data.pxsize[0] * w.data.shape[0], data.pxsize[0])
            w.y = np.arange(0, data.pxsize[0] * w.data.shape[1], data.pxsize[0])
        elif w.data.ndim == 3:  # spectrum imaging
            w.data = w.data.transpose(1, 2, 0)
            w.x = np.arange(0, data.pxsize[0] * w.data.shape[0], data.pxsize[0])
            w.y = np.arange(0, data.pxsize[0] * w.data.shape[1], data.pxsize[0])
            e0 = float(data.tags['root.ImageList.1.ImageData.Calibrations.Dimension.2.Origin'])
            de = float(data.tags['root.ImageList.1.ImageTags.EELS Spectrometer.Dispersion (eV/ch)'])
            w.z = np.linspace(-e0, -e0 + de * w.data.shape[2], w.data.shape[2])
        w.note = {}
        try:
            w.note['unit'] = data.pxsize[1]
            w.note['specimen'] = data.info['specimen'].decode()
            w.note['date'] = data.info['acq_date'].decode()
            w.note['mag'] = float(data.info['mag'].decode())
            w.note['time'] = data.info['acq_time'].decode()
            w.note['voltage'] = float(data.info['hv'].decode())
            w.note['mode'] = data.info['mode'].decode()
            w.note['exposure'] = data.tags['root.ImageList.1.ImageTags.DataBar.Exposure Time (s)']
            w.note['hbin'] = data.tags['root.ImageList.1.ImageTags.Acquisition.Parameters.Detector.hbin']
            w.note['vbin'] = data.tags['root.ImageList.1.ImageTags.Acquisition.Parameters.Detector.vbin']
            w.note['delay'] = data.tags['root.ImageList.1.ImageTags.Experiment.Laser.delay']
            w.note['power'] = data.tags['root.ImageList.1.ImageTags.Experiment.Laser.power']
            w.note['scanMode'] = data.tags['root.ImageList.1.ImageTags.Experiment.mode']
        except Exception:
            pass
        return w
except Exception:
    def __loadDm3(name):
        print("To use .dm3 files, install dm3_lib (https://bitbucket.org/piraynal/pydm3reader/src/master/)", file=sys.stderr)


registerFileLoader(".dm3", __loadDm3)

WaveMetrics Igor .pxt files

Install igor package(https://pypi.org/project/igor/) by excuting:

pip install igor

Then put examples/load_PXT.py into module folder.

import igor.packed
import igor.igorpy
import numpy as np

from lys import Wave, registerFileLoader


def __loadPxt(name):
    nam, ext = os.path.splitext(os.path.basename(name))
    (rec, data) = igor.packed.load(name)
    wav = igor.igorpy.Wave(data['root'][nam.encode('utf-8')])
    w = Wave()
    w.data = np.array(wav.data)
    w.data.flags.writeable = True
    note = [s.replace(" ", "").replace("\r", "").split("=") for s in wav.notes.decode().replace("\n\n", "\n").split("\n")]
    w.note = {}
    for n in note:
        if len(n) == 2:
            w.note[n[0].lower()] = n[1]
    if w.data.ndim == 1:
        w.x = wav.axis[0]
    if w.data.ndim >= 2:
        w.x = wav.axis[1]
        w.y = wav.axis[0]
    if w.data.ndim == 3:
        w.x = wav.axis[2]
        w.y = wav.axis[1]
        w.z = wav.axis[0]
    return w


registerFileLoader(".pxt", __loadPxt)

DICOM .dicom files

Install pydicom package(https://github.com/pydicom/pydicom) by executin:

pip install pydicom

Then put examples/load_DICOM.py into module folder.

import pydicom

from lys import Wave, registerFileLoader


def __loadDcm(name):
    data = pydicom.read_file(name)
    return Wave(data.pixel_array)


registerFileLoader(".pxt", __loadDcm)