File browser for napari

napari_browser.py

from qtpy.QtWidgets import (
    QPushButton,
    QComboBox,
    QTabWidget,
    QHBoxLayout,
    QFileDialog,
    QDialogButtonBox,
    QWidget,
    QSlider,
)
from qtpy.QtCore import Qt
import napari
import numpy as np
import skimage
from skimage import filters, io
from typing import (
    Dict,
    Any,
)
from aicsimageio import imread
from nptyping import NDArray
import os
import javabridge
import bioformats


def metadata(path: str) -> Dict[str, Any]:
    xml = bioformats.get_omexml_metadata(path)
    md = bioformats.omexml.OMEXML(xml)

    meta = {'AcquisitionDate': md.image().AcquisitionDate}
    meta['Name'] = md.image().Name
    meta['SizeC'] = md.image().Pixels.SizeC
    meta['SizeT'] = md.image().Pixels.SizeT
    meta['SizeX'] = md.image().Pixels.SizeX
    meta['SizeY'] = md.image().Pixels.SizeY
    meta['SizeZ'] = md.image().Pixels.SizeZ
    meta['PhysicalSizeX'] = md.image().Pixels.PhysicalSizeX
    meta['PhysicalSizeY'] = md.image().Pixels.PhysicalSizeY
    meta['PhysicalSizeZ'] = md.image().Pixels.PhysicalSizeZ
    meta['PositionX'] = md.image().Pixels.Plane().PositionX
    meta['PositionY'] = md.image().Pixels.Plane().PositionY
    meta['Timepoint'] = md.image().Pixels.Plane().DeltaT
    return(meta)


def load_bioformats(path: str) -> NDArray[int]:
    meta = metadata(path)

    image = np.empty((meta['SizeC'], meta['SizeT'], meta['SizeZ'],
                      meta['SizeX'], meta['SizeY']))
    with bioformats.ImageReader(path) as rdr:
        for c in range(0, meta['SizeC']):
            for t in range(0, meta['SizeT']):
                for z in range(0, meta['SizeZ']):
                    image[c, t, z, :, :] = rdr.read(c=c, z=z, t=t, series=None,
                                                    index=None, rescale=False, wants_max_intensity=False,
                                                    channel_names=None)

    return(np.squeeze(image))


class Processsing(QWidget):

    def __init__(self):
        super().__init__()
        self.layout = QHBoxLayout(self)

        # Initialize tab screen
        self.tabs = QTabWidget()
        self.tab1 = QWidget()
        self.tab2 = QWidget()
        self.tab3 = QWidget()

        # self.tabs.setTabPosition(QTabWidget.North)

        # Add tabs
        self.tabs.addTab(self.tab1, "Gaussian")
        self.tabs.addTab(self.tab2, "Median")
        self.tabs.addTab(self.tab3, "Sobel")

        # tab1
        self.tab1.layout = QHBoxLayout(self)
        self.sld1 = QSlider(Qt.Horizontal, self)
        self.btn1 = QPushButton("create result layer", self)
        # drop down menu
        self.cb = QComboBox()
        self.cb.addItems(["reflect", "constant", "nearest", "mirror", "wrap"])
        # set min and max slider
        self.sld1.setMinimum(0)
        self.sld1.setMaximum(10)
        # add widget to the tab
        self.tab1.layout.addWidget(self.sld1)
        self.tab1.layout.addWidget(self.btn1)
        self.tab1.layout.addWidget(self.cb)
        # set layout to the tab
        self.tab1.setLayout(self.tab1.layout)
        # connect different button/slider
        self.sld1.valueChanged[int].connect(self.updateValue)
        self.btn1.clicked.connect(self.buttonClicked)
        self.cb.currentIndexChanged.connect(self.modeChoice)

        # tab2
        self.tab2.layout = QHBoxLayout(self)
        self.sld2 = QSlider(Qt.Horizontal, self)
        self.btn2 = QPushButton("create result layer", self)
        self.cb2 = QComboBox()
        self.cb2.addItems(["diamond", "disk", "square"])
        self.sld2.setMinimum(0)
        self.sld2.setMaximum(10)
        self.tab2.layout.addWidget(self.sld2)
        self.tab2.layout.addWidget(self.btn2)
        self.tab2.layout.addWidget(self.cb2)
        self.tab2.setLayout(self.tab2.layout)
        self.sld2.valueChanged[int].connect(self.updateValue)
        self.btn2.clicked.connect(self.buttonClicked)
        self.cb2.currentIndexChanged.connect(self.morphoChoice)

        # tab3
        self.tab3.layout = QHBoxLayout(self)
        self.btn3 = QPushButton("create result layer", self)
        self.tab3.layout.addWidget(self.btn3)
        self.tab3.setLayout(self.tab3.layout)
        self.btn3.clicked.connect(self.buttonClicked)
        self.btn4 = QPushButton("sobel", self)
        self.tab3.layout.addWidget(self.btn4)
        self.tab3.setLayout(self.tab3.layout)
        self.btn4.clicked.connect(self.buttonClicked)

        # Add tabs to widget
        self.layout.addWidget(self.tabs)
        self.setLayout(self.layout)

    # return choices from drop down menu
    def morphoChoice(self):
        morpho = self.cb2.currentText()
        return(morpho)

    def modeChoice(self):
        mode = self.cb.currentText()
        return(mode)

    def updateValue(self, value):
        # findwhich slider is sending the value
        if self.sender() == self.sld1:
            result = filters.gaussian(viewer.layers['image_1'].data,
                                      sigma=value, mode=self.modeChoice(), preserve_range=True)
            # update napari layer 'result gauss'
            viewer.layers['result_gauss'].data = result
        elif self.sender() == self.sld2:
            selem = getattr(skimage.morphology.selem, self.morphoChoice())
            result = filters.median(viewer.layers['image_1'].data, selem=selem(value))
            viewer.layers['result_median'].data = result

    # Create a result layer to apply filter
    def buttonClicked(self):
        if self.sender() == self.btn1:
            viewer.add_image(viewer.layers['image_1'].data, name='result_gauss')
            self.sld1.setValue(0)
            self.sld2.setValue(0)
        elif self.sender() == self.btn2:
            viewer.add_image(viewer.layers['image_1'].data, name='result_median')
            self.sld1.setValue(0)
            self.sld2.setValue(0)
        elif self.sender() == self.btn3:
            viewer.add_image(viewer.layers['image_1'].data, name='result_sobel')
            self.sld1.setValue(0)
            self.sld2.setValue(0)
        elif self.sender() == self.btn4:
            result = filters.sobel(viewer.layers['image_1'].data)
            viewer.layers['result_sobel'].data = result
            # Need to adjust napari contrast to result of skimage "as_float"
            viewer.layers['result_sobel'].contrast_limits_range = viewer.layers['result_sobel']._calc_data_range()


class Open_files(QWidget):

    def __init__(self):
        super(QWidget, self).__init__()
        self.layout = QHBoxLayout(self)
        self.file_dialog = QFileDialog()
        self.file_dialog.setWindowFlags(Qt.Widget)
        self.file_dialog.setModal(False)
        self.file_dialog.setOption(QFileDialog.DontUseNativeDialog)
        # Remove open and cancel button from widget
        self.buttonBox = self.file_dialog.findChild(QDialogButtonBox, "buttonBox")
        self.buttonBox.clear()
        # Only open following file types
        self.file_dialog.setNameFilter("Images (*.czi *.nd2 *.tiff *.tif *.jpg *.png)")
        self.layout.addWidget(self.file_dialog)
        self.file_dialog.currentChanged.connect(self.open_path)

    def open_path(self, path):
        if os.path.isfile(path):
            viewer.layers.select_all()
            viewer.layers.remove_selected()
            if path.endswith((".tiff", ".tif", ".czi")):
                # Uses aicsimageio to open these files
                # (image.io but the channel in last dimension which doesn't)
                # work with napari
                image = imread(path)
            if path.endswith((".jpg", ".png")):
                image = io.imread(path)
            if path.endswith(".nd2"):
                # a little slow but dask_image imread doesn't work well
                javabridge.start_vm(class_path=bioformats.JARS)
                image = load_bioformats(path)
            viewer.add_image(image, name="image_1")


with napari.gui_qt():
    # create a viewer and add some images
    viewer = napari.Viewer()
    # add the gui to the viewer as a dock widget
    viewer.window.add_dock_widget(Open_files(), area="right")
    viewer.window.add_dock_widget(Processsing())