microeye 2.3.2__py3-none-any.whl

microEye/hardware/widgets/scan_acquisition.py

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+import os
+from enum import Enum
+
+import numpy as np
+import pyqtgraph as pg
+import qdarkstyle
+import tifffile as tf
+from pyqtgraph.parametertree import Parameter
+
+from microEye.qt import (
+    QApplication,
+    Qt,
+    QtWidgets,
+    Signal,
+    getExistingDirectory,
+    getSaveFileName,
+)
+from microEye.utils import Tree
+from microEye.utils.uImage import uImage
+
+
+class TileImage:
+    def __init__(self, uImage: uImage, index, position) -> None:
+        self.uImage = uImage
+        self.index = index
+        self.position = position
+
+
+class TiledImageSelector(QtWidgets.QWidget):
+    positionSelected = Signal(float, float)
+
+    def __init__(self, images: list[TileImage]) -> None:
+        super().__init__()
+
+        self.images = images
+
+        central_layout = QtWidgets.QHBoxLayout()
+        self.setLayout(central_layout)
+
+        imageWidget = pg.GraphicsLayoutWidget()
+        imageWidget.ci.setContentsMargins(0, 0, 0, 0)
+        imageWidget.ci.setSpacing(0)
+        imageWidget.sceneObj.sigMouseClicked.connect(self.clicked)
+
+        for _idx, tImg in enumerate(images):
+            vb: pg.ViewBox = imageWidget.addViewBox(*tImg.index)
+            vb.setMouseEnabled(False, False)
+            vb.setDefaultPadding(0.004)
+            vb.setAspectLocked(True)
+            vb.invertY()
+            # menu: QMenu = vb.getMenu(None)
+            # vb.action = QAction("Save Raw Data (.tif)")
+            # menu.addAction(vb.action)
+            # vb.action.triggered.connect(
+            #     lambda: self.save_raw_data(tImg))
+            img = pg.ImageItem(tImg.uImage._view)
+            vb.addItem(img)
+            vb.item = tImg
+
+        self.imgView = pg.ImageView()
+        self.setWindowTitle('Tiled Image Selector')
+
+        central_layout.addWidget(imageWidget, 3)
+        central_layout.addWidget(self.imgView, 4)
+
+    def clicked(self, event):
+        if event.modifiers() == Qt.ShiftModifier and event.button() == Qt.LeftButton:
+            self.save_raw_data(event.currentItem.item)
+        elif (
+            event.modifiers() == Qt.ControlModifier and event.button() == Qt.LeftButton
+        ):
+            self.save_raw_data_all()
+        else:
+            if event.double():
+                self.positionSelected.emit(*event.currentItem.item.position)
+            else:
+                self.setWindowTitle(
+                    'Tiled Image Selector ({}, {}) ({}, {})'.format(
+                        *event.currentItem.item.index, *event.currentItem.item.position
+                    )
+                )
+                self.imgView.setImage(event.currentItem.addedItems[0].image)
+
+    def save_raw_data(self, img: TileImage):
+        filename = None
+        if filename is None:
+            filename, _ = getSaveFileName(
+                self, 'Save Raw Data', filter='Tiff Files (*.tif)'
+            )
+
+        if len(filename) > 0:
+            tf.imwrite(filename, img.uImage.image, photometric='minisblack')
+
+    def save_raw_data_all(self):
+        directory = None
+        if directory is None:
+            directory = str(getExistingDirectory(self, 'Select Directory'))
+
+        if len(directory) > 0:
+            for idx, tImg in enumerate(self.images):
+                tf.imwrite(
+                    directory
+                    + f'/{idx:03d}_image_y{tImg.index[0]:02d}_x{tImg.index[1]:02d}.tif',
+                    tImg.uImage.image,
+                    photometric='minisblack',
+                )
+
+
+class ScanParams(Enum):
+    '''
+    Enum class defining Scanning Acquisition parameters.
+    '''
+
+    DELAY = 'Delay [ms]'
+    XY_SCAN = 'XY SCAN'
+    Z_SCAN = 'Z SCAN'
+    X_STEP = 'XY SCAN.X Steps'
+    Y_STEP = 'XY SCAN.Y Steps'
+    Z_STEP = 'Z SCAN.Z Steps'
+    X_STEP_SIZE = 'XY SCAN.X Step Size [um]'
+    Y_STEP_SIZE = 'XY SCAN.Y Step Size [um]'
+    Z_STEP_SIZE = 'Z SCAN.Z Step Size [nm]'
+    AVG_FRAMES = 'XY SCAN.Average [Frames]'
+
+    XY_START = 'XY SCAN.Start XY-Scan'
+    XY_LAST = 'XY SCAN.Last XY-Scan'
+    XY_STOP = 'XY SCAN.Stop XY-Scan'
+
+    N_FRAMES = 'Z SCAN.Frames per Z-Slice'
+    Z_REVERSED = 'Z SCAN.Reversed'
+    Z_DIRECTORY = 'Z SCAN.Save Directory'
+    Z_START = 'Z SCAN.Start Z-Scan'
+    Z_STOP = 'Z SCAN.Stop Z-Scan'
+    Z_CAL = 'Z SCAN.Start Z-Calibration'
+
+    def __str__(self):
+        '''
+        Return the last part of the enum value (Param name).
+        '''
+        return self.value.split('.')[-1]
+
+    def get_path(self):
+        '''
+        Return the full parameter path.
+        '''
+        return self.value.split('.')
+
+
+class ScanAcquisitionWidget(Tree):
+    PARAMS = ScanParams
+    startAcquisitionXY = Signal(tuple)
+    stopAcquisitionXY = Signal()
+    openLastTileXY = Signal()
+    startAcquisitionZ = Signal(tuple)
+    startCalibrationZ = Signal(tuple)
+    stopAcquisitionZ = Signal()
+
+    moveZ = Signal(bool, int)
+
+    directoryChanged = Signal(str)
+
+    def __init__(self) -> None:
+        super().__init__()
+
+        self._directory = os.path.join(os.path.expanduser('~'), 'Desktop')
+
+    def create_parameters(self):
+        '''
+        Create the parameter tree structure.
+
+        This method creates and sets up the parameter tree structure for the
+        `PzFocView` class.
+        '''
+        params = [
+            {
+                'name': str(ScanParams.DELAY),
+                'type': 'int',
+                'value': 200,
+                'limits': [1, 1e4],
+                'step': 50,
+            },
+            {
+                'name': str(ScanParams.XY_SCAN),
+                'type': 'group',
+                'children': [
+                    {
+                        'name': str(ScanParams.X_STEP),
+                        'type': 'int',
+                        'value': 4,
+                        'limits': [1, 100],
+                        'step': 1,
+                    },
+                    {
+                        'name': str(ScanParams.Y_STEP),
+                        'type': 'int',
+                        'value': 4,
+                        'limits': [1, 100],
+                        'step': 1,
+                    },
+                    {
+                        'name': str(ScanParams.X_STEP_SIZE),
+                        'type': 'float',
+                        'value': 50.0,
+                        'limits': [0.1, 500],
+                        'step': 1,
+                        'dec': False,
+                        'decimals': 3,
+                    },
+                    {
+                        'name': str(ScanParams.Y_STEP_SIZE),
+                        'type': 'float',
+                        'value': 50.0,
+                        'limits': [0.1, 500],
+                        'step': 1,
+                        'dec': False,
+                        'decimals': 3,
+                    },
+                    {
+                        'name': str(ScanParams.AVG_FRAMES),
+                        'type': 'int',
+                        'value': 1,
+                        'limits': [1, 128],
+                        'step': 1,
+                    },
+                    {'name': str(ScanParams.XY_START), 'type': 'action'},
+                    {'name': str(ScanParams.XY_STOP), 'type': 'action'},
+                    {'name': str(ScanParams.XY_LAST), 'type': 'action'},
+                ],
+            },
+            {
+                'name': str(ScanParams.Z_SCAN),
+                'type': 'group',
+                'children': [
+                    {
+                        'name': str(ScanParams.Z_STEP),
+                        'type': 'int',
+                        'value': 5,
+                        'limits': [2, 1e4],
+                        'step': 1,
+                    },
+                    {
+                        'name': str(ScanParams.Z_STEP_SIZE),
+                        'type': 'int',
+                        'value': 25,
+                        'limits': [1, 2e4],
+                        'step': 1,
+                    },
+                    {
+                        'name': str(ScanParams.N_FRAMES),
+                        'type': 'int',
+                        'value': 10,
+                        'limits': [1, 1e9],
+                        'step': 1,
+                    },
+                    {
+                        'name': str(ScanParams.Z_REVERSED),
+                        'type': 'bool',
+                        'value': False,
+                    },
+                    {
+                        'name': str(ScanParams.Z_DIRECTORY),
+                        'type': 'file',
+                        'directory': os.path.join(os.path.expanduser('~'), 'Desktop'),
+                        'value': os.path.join(os.path.expanduser('~'), 'Desktop'),
+                        'fileMode': 'Directory',
+                    },
+                    {'name': str(ScanParams.Z_START), 'type': 'action'},
+                    {'name': str(ScanParams.Z_STOP), 'type': 'action'},
+                    {'name': str(ScanParams.Z_CAL), 'type': 'action'},
+                ],
+            },
+        ]
+
+        self.param_tree = Parameter.create(name='', type='group', children=params)
+        self.param_tree.sigTreeStateChanged.connect(self.change)
+        self.header().setSectionResizeMode(
+            QtWidgets.QHeaderView.ResizeMode.ResizeToContents
+        )
+
+        self.get_param(ScanParams.XY_START).sigActivated.connect(
+            lambda: self.startScanning(True)
+        )
+        self.get_param(ScanParams.XY_STOP).sigActivated.connect(
+            lambda: self.stopAcquisitionXY.emit()
+        )
+        self.get_param(ScanParams.XY_LAST).sigActivated.connect(
+            lambda: self.openLastTileXY.emit()
+        )
+
+        self.get_param(ScanParams.Z_START).sigActivated.connect(
+            lambda: self.startScanning(False)
+        )
+        self.get_param(ScanParams.Z_STOP).sigActivated.connect(
+            lambda: self.stopAcquisitionZ.emit()
+        )
+        self.get_param(ScanParams.Z_CAL).sigActivated.connect(
+            lambda: self.startScanning(None)
+        )
+
+        self.get_param(ScanParams.Z_DIRECTORY).sigValueChanged.connect(
+            self.directory_changed
+        )
+
+    def startScanning(self, XY: bool):
+        '''
+        Starts the scanning process based on the provided XY parameter.
+
+        Parameters
+        ----------
+        XY : bool, optional
+            If True, starts XY scanning with the parameters set in the
+            GUI. If False, starts Z scanning with the parameters set in
+            the GUI. If None, starts calibration for Z scanning with
+            the parameters set in the GUI.
+
+        '''
+        if XY is None:
+            self.startCalibrationZ.emit(self.get_params(False))
+            return
+
+        if XY:
+            self.startAcquisitionXY.emit(self.get_params(XY))
+        else:
+            self.startAcquisitionZ.emit(self.get_params(XY))
+
+    def directory_changed(self, param, value):
+        '''Slot for browse clicked event'''
+        self._directory = value
+        self.directoryChanged.emit(self._directory)
+
+    def get_params(self, XY: bool):
+        '''
+        Returns the scanning parameters for XY or Z scan.
+
+        Parameters
+        ----------
+        XY : bool
+            If True, returns parameters for XY scan. If False, returns
+            parameters for Z scan.
+
+        Returns
+        -------
+        tuple
+            A tuple of scanning parameters depending on the value of XY.
+
+            If XY is True, returns:
+                - Number of X steps
+                - Number of Y steps
+                - X Step size (um)
+                - Y Step size (um)
+                - Delay (ms)
+                - Average (frames)
+
+            If XY is False, returns:
+                - Number of Z steps
+                - Z Step size (nm)
+                - Delay (ms)
+                - Number of Frames
+                - Reversed (bool)
+        '''
+        if XY:
+            return (
+                self.get_param_value(ScanParams.X_STEP),
+                self.get_param_value(ScanParams.Y_STEP),
+                self.get_param_value(ScanParams.X_STEP_SIZE),
+                self.get_param_value(ScanParams.Y_STEP_SIZE),
+                self.get_param_value(ScanParams.DELAY),
+                self.get_param_value(ScanParams.AVG_FRAMES),
+            )
+        else:
+            return (
+                self.get_param_value(ScanParams.Z_STEP),
+                self.get_param_value(ScanParams.Z_STEP_SIZE),
+                self.get_param_value(ScanParams.DELAY),
+                self.get_param_value(ScanParams.N_FRAMES),
+                self.get_param_value(ScanParams.Z_REVERSED),
+            )
+
+    def setActionsStatus(self, status: bool):
+        '''
+        Enables or disables the scanning actions based on the provided status parameter.
+
+        Parameters
+        ----------
+        status : bool
+            The status to set for the scanning actions.
+            If True, the actions are enabled.
+            If False, the actions are disabled.
+
+        '''
+        self.get_param(ScanParams.XY_START).setOpts(enabled=status)
+        # self.get_param(ScanParams.XY_STOP).setOpts(enabled=status)
+        self.get_param(ScanParams.XY_LAST).setOpts(enabled=status)
+        self.get_param(ScanParams.Z_START).setOpts(enabled=status)
+        # self.get_param(ScanParams.Z_STOP).setOpts(enabled=status)
+        self.get_param(ScanParams.Z_CAL).setOpts(enabled=status)
+        self.get_param(ScanParams.Z_DIRECTORY).setOpts(enabled=status)
+
+    def __str__(self):
+        return 'Scan Acquistion'
+
+if __name__ == '__main__':
+    x = np.linspace(255, 0, 256)
+    y = np.linspace(0, 255, 256)
+    z = np.concatenate([x, y])
+    image = np.tile(z, (512, 1)).T
+
+    data = []
+
+    for i in range(10):
+        for j in range(10):
+            uImg = uImage(image)
+            uImg.equalizeLUT()
+            tImg = TileImage(uImg, [i, j], [17, 17])
+            data.append(tImg)
+
+    app = QApplication([])
+    app.setStyleSheet(qdarkstyle.load_stylesheet(qt_api='pyqt5'))
+
+    win = TiledImageSelector(data)
+    win.positionSelected.connect(lambda x, y: print(x, y))
+    win.show()
+
+    app.exec()

microEye/icons/close.svg

@@ -0,0 +1,88 @@
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+   height="9.9724722mm"
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+   sodipodi:docname="close.svg"
+   xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
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+   xmlns:svg="http://www.w3.org/2000/svg"
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+   xmlns:cc="http://creativecommons.org/ns#"
+   xmlns:dc="http://purl.org/dc/elements/1.1/">
+  <defs
+     id="defs2" />
+  <sodipodi:namedview
+     id="base"
+     pagecolor="#313131"
+     bordercolor="#898989"
+     borderopacity="1"
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+     inkscape:snap-intersection-paths="true"
+     inkscape:object-paths="true"
+     inkscape:snap-midpoints="true"
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+     id="metadata5">
+    <rdf:RDF>
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+        <dc:type
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+    </g>
+  </g>
+</svg>

microEye/icons/min.svg

@@ -0,0 +1,83 @@
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+   width="9.9724712mm"
+   height="9.9724722mm"
+   viewBox="0 0 9.9724711 9.9724718"
+   version="1.1"
+   id="svg8"
+   inkscape:version="1.1.2 (b8e25be833, 2022-02-05)"
+   sodipodi:docname="min.svg"
+   xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
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+   xmlns="http://www.w3.org/2000/svg"
+   xmlns:svg="http://www.w3.org/2000/svg"
+   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+   xmlns:cc="http://creativecommons.org/ns#"
+   xmlns:dc="http://purl.org/dc/elements/1.1/">
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+     id="defs2" />
+  <sodipodi:namedview
+     id="base"
+     pagecolor="#313131"
+     bordercolor="#898989"
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+     inkscape:snap-intersection-paths="true"
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+     inkscape:snap-midpoints="true"
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microEye/launcher.py

@@ -0,0 +1,42 @@
+import argparse
+import os
+
+from microEye import ARGS
+
+
+def main():
+    # access the parsed arguments
+    module_name = ARGS.module
+
+    if module_name == 'mieye':
+        from microEye.hardware import miEye_module
+
+        try:
+            import vimba as vb
+        except Exception:
+            vb = None
+
+        if vb:
+            with vb.Vimba.get_instance() as vimba:
+                app, window = miEye_module.StartGUI()
+                app.exec()
+        else:
+            app, window = miEye_module.StartGUI()
+            app.exec()
+    elif module_name == 'viewer':
+        from microEye.analysis.multi_viewer import multi_viewer
+
+        app, window = multi_viewer.StartGUI('')
+
+        app.exec()
+    else:
+        print('For help: \n>>> microEye -h')
+        from microEye.utils.micro_launcher import microLauncher
+
+        app, window = microLauncher.StartGUI()
+
+        app.exec()
+
+
+if __name__ == '__main__':
+    main()