LoadLsm5D.py

"""This function loads .lsm files.

Given the filename of a .lsm files, this function gives as output the matrices
of the red and green channels maximum intensity projected plus the green channel
as it is. Inputs are the file-name and the channel number for nuclei and spots. 
"""


import numpy as np
import tifffile
from PyQt5 import QtWidgets



class LoadLsm5D:
    def __init__(self, fname, nucs_spts_ch):

        file_array                 =  tifffile.imread(fname)
        steps, z, c, x_len, y_len  =  file_array.shape

        pbar  =  ProgressBar(total1=steps)
        pbar.show()

        red_mtx    =  np.zeros((steps, x_len, y_len))
        green_mtx  =  np.zeros((steps, x_len, y_len))

        for t in range(steps):
            pbar.update_progressbar(t)
            for x in range(x_len):
                red_mtx[t, x, :]    =  file_array[t, :, nucs_spts_ch[0], x, :].max(0)
                green_mtx[t, x, :]  =  file_array[t, :, nucs_spts_ch[1], x, :].max(0)

        pbar.close()

        self.red_mtx    =  red_mtx
        self.green_mtx  =  green_mtx
        self.green4D    =  file_array[:, :, 0, :, :]


class ProgressBar(QtWidgets.QWidget):
    """Simple progressbar widget"""
    def __init__(self, parent=None, total1=20):
        super().__init__(parent)
        self.name_line1  =  QtWidgets.QLineEdit()

        self.progressbar1  =  QtWidgets.QProgressBar()
        self.progressbar1.setMinimum(1)
        self.progressbar1.setMaximum(total1)

        main_layout  =  QtWidgets.QGridLayout()
        main_layout.addWidget(self.progressbar1, 0, 0)

        self.setLayout(main_layout)
        self.setWindowTitle("Progress")
        self.setGeometry(500, 300, 300, 50)

    def update_progressbar(self, val1):
        """progress bar updater"""
        self.progressbar1.setValue(val1)
        QtWidgets.qApp.processEvents()