pyTEMlib 0.2020.11.1__py3-none-any.whl → 0.2024.8.4__py3-none-any.whl

pyTEMlib/info_dialog.py

@@ -1,237 +0,0 @@
-"""
-InfoDialog for interactive_eels
-"""
-
-from PyQt5 import QtCore,  QtWidgets
-
-import numpy as np
-import sidpy
-from pyTEMlib import info_dlg
-import pyTEMlib.eels_tools as eels
-import pyTEMlib.interactive_eels as ieels
-from pyTEMlib.microscope import microscope
-
-from pyTEMlib import file_tools as ft
-_version = 000
-
-
-class InfoDialog(QtWidgets.QDialog):
-    """
-    EELS Input Dialog for Chemical Analysis
-
-    Opens a PyQt5 GUi Dialog that allows to set the experimental parameter necessary for a Quantification.
-
-
-    The dialog operates on a sidpy dataset which
-    -reads and sets the spectral dimension with ``offset`` and ``dispersion``.
-    -reads and writes an 'experiment' dictionary in the metadata of the sidpy Dataset.
-
-    access dimension with dataset.energy_scale
-    access experimental parameters with ``dataset.metadata['experiment']``
-
-    experimental parameters are:
-    -acquisition time
-    -convergence angle
-    -collection angle
-    -acceleration voltage
-
-    -flux of electrons
-    """
-
-    def __init__(self, dataset=None):
-        super().__init__(None, QtCore.Qt.WindowStaysOnTopHint)
-        # Create an instance of the GUI
-        self.ui = info_dlg.UiDialog(self)
-        self.set_action()
-
-        self.dataset = dataset
-        self.spec_dim = []
-        self.energy_scale = np.array([])
-        self.experiment = {}
-        self.energy_dlg = None
-        self.axis = None
-        self.show()
-
-        if dataset is None:
-            # make a dummy dataset for testing
-            dataset = ft.make_dummy_dataset(sidpy.DataTypes.SPECTRUM)
-        if not isinstance(dataset, sidpy.Dataset):
-            raise TypeError('dataset has to be a sidpy dataset')
-
-        self.set_dataset(dataset)
-
-        self.dataset.plot()
-        if hasattr(self.dataset.view, 'axes'):
-            self.axis = self.dataset.view.axes[-1]
-        elif hasattr(self.dataset.view, 'axis'):
-            self.axis = self.dataset.view.axis
-        self.figure = self.axis.figure
-        self.plot()
-        self.update()
-
-    def set_dataset(self, dataset):
-        self.dataset = dataset
-        if not hasattr(self.dataset, '_axes'):
-            self.dataset._axes = self.dataset.axes
-        if not hasattr(self.dataset, 'meta_data'):
-            self.dataset.meta_data = {}
-
-        self.spec_dim = ft.get_dimensions_by_type(sidpy.DimensionTypes.SPECTRAL, dataset)
-        if len(self.spec_dim) != 1:
-            raise TypeError('We need exactly one SPECTRAL dimension')
-        self.spec_dim = self.spec_dim[0]
-        self.energy_scale = self.spec_dim[1].values.copy()
-
-        minimum_info = {'offset': self.energy_scale[0],
-                        'dispersion': self.energy_scale[1] - self.energy_scale[0],
-                        'exposure_time': 0.0,
-                        'convergence_angle': 0.0, 'collection_angle': 0.0,
-                        'acceleration_voltage': 100.0, 'binning': 1, 'conversion': 1.0,
-                        'flux': 1.0, 'current': 1.0}
-
-        if 'DM' in self.dataset.original_metadata:
-            if 'experiment' not in self.dataset.metadata:
-                self.dataset.metadata['experiment'] = {}
-
-            self.dataset.metadata['experiment'].update(eels.read_dm3_eels_info(self.dataset.original_metadata))
-
-        self.experiment = self.dataset.metadata['experiment']
-
-        for key, item in minimum_info.items():
-            if key not in self.experiment:
-                self.experiment[key] = item
-
-    def set_dimension(self):
-        self.spec_dim = ft.get_dimensions_by_type(sidpy.DimensionTypes.SPECTRAL, self.dataset)
-        self.spec_dim = self.spec_dim[0]
-        old_energy_scale = self.spec_dim[1]
-        self.dataset.set_dimension(self.spec_dim[0], sidpy.Dimension(np.array(self.energy_scale),
-                                                                     name=old_energy_scale.name,
-                                                                     dimension_type=sidpy.DimensionTypes.SPECTRAL,
-                                                                     units='eV',
-                                                                     quantity='energy loss'))
-
-    def update(self):
-
-        self.ui.offsetEdit.setText(f"{self.experiment['offset']:.3f}")
-        self.ui.dispersionEdit.setText(f"{self.experiment['dispersion']:.3f}")
-        self.ui.timeEdit.setText(f"{self.experiment['exposure_time']:.6f}")
-
-        self.ui.convEdit.setText(f"{self.experiment['convergence_angle']:.2f}")
-        self.ui.collEdit.setText(f"{self.experiment['collection_angle']:.2f}")
-        self.ui.E0Edit.setText(f"{self.experiment['acceleration_voltage']/1000.:.2f}")
-
-        self.ui.binningEdit.setText(f"{self.experiment['binning']}")
-        self.ui.conversionEdit.setText(f"{self.experiment['conversion']:.2f}")
-        self.ui.fluxEdit.setText(f"{self.experiment['flux']:.2f}")
-        self.ui.VOAEdit.setText(f"{self.experiment['current']:.2f}")
-
-    def on_enter(self):
-        sender = self.sender()
-
-        if sender == self.ui.offsetEdit:
-            value = float(str(sender.displayText()).strip())
-            self.experiment['offset'] = value
-            sender.setText(f"{value:.2f}")
-            self.energy_scale = self.energy_scale - self.energy_scale[0] + value
-            self.set_dimension()
-            self.plot()
-        elif sender == self.ui.dispersionEdit:
-            value = float(str(sender.displayText()).strip())
-            self.experiment['dispersion'] = value
-            self.energy_scale = np.arange(len(self.energy_scale)) * value + self.energy_scale[0]
-            self.set_dimension()
-            self.plot()
-            sender.setText(f"{value:.3f}")
-        elif sender == self.ui.timeEdit:
-            value = float(str(sender.displayText()).strip())
-            self.experiment['exposure_time'] = value
-            sender.setText(f"{value:.2f}")
-        elif sender == self.ui.convEdit:
-            value = float(str(sender.displayText()).strip())
-            self.experiment['convergence_angle'] = value
-            sender.setText(f"{value:.2f}")
-        elif sender == self.ui.collEdit:
-            value = float(str(sender.displayText()).strip())
-            self.experiment['collection_angle'] = value
-            sender.setText(f"{value:.2f}")
-        elif sender == self.ui.E0Edit:
-            value = float(str(sender.displayText()).strip())
-            self.experiment['acceleration_voltage'] = value*1000.0
-            sender.setText(f"{value:.2f}")
-        elif sender == self.ui.E0Edit:
-            value = float(str(sender.displayText()).strip())
-            self.experiment['acceleration_voltage'] = value
-            sender.setText(f"{value:.2f}")
-        elif sender == self.ui.binXEdit or sender == self.ui.binYEdit:
-            if self.dataset.data_type == sidpy.DataTypes.SPECTRAL_IMAGE:
-                bin_x = int(self.ui.binXEdit.displayText())
-                bin_y = int(self.ui.binYEdit.displayText())
-                self.dataset.view.set_bin([bin_x, bin_y])
-                self.ui.binXEdit.setText(str(self.dataset.view.bin_x))
-                self.ui.binYEdit.setText(str(self.dataset.view.bin_y))
-        else:
-            print('not supported yet')
-
-    def plot(self):
-        if self.dataset.data_type == sidpy.DataTypes.SPECTRAL_IMAGE:
-            spectrum = self.dataset.view.get_spectrum()
-            self.axis = self.dataset.view.axes[1]
-        else:
-            spectrum = np.array(self.dataset)
-            self.axis = self.dataset.view.axis
-
-        x_limit = self.axis.get_xlim()
-        y_limit = self.axis.get_ylim()
-        self.axis.clear()
-
-        self.axis.plot(self.energy_scale, spectrum, label='spectrum')
-        self.axis.set_xlim(x_limit)
-        self.axis.set_ylim(y_limit)
-        self.figure.canvas.draw_idle()
-
-    def on_list_enter(self):
-        sender = self.sender()
-        if sender == self.ui.TEMList:
-            microscope.set_microscope(self.ui.TEMList.currentText())
-            self.experiment['microscope'] = microscope.name
-            self.experiment['convergence_angle'] = microscope.alpha
-            self.experiment['collection_angle'] = microscope.beta
-            self.experiment['acceleration_voltage'] = microscope.E0
-            self.update()
-
-    def set_energy_scale(self):
-        self.energy_dlg = ieels.EnergySelector(self.dataset)
-
-        self.energy_dlg.signal_selected[bool].connect(self.set_energy)
-        self.energy_dlg.show()
-
-    def set_energy(self, k):
-        self.spec_dim = ft.get_dimensions_by_type(sidpy.DimensionTypes.SPECTRAL, self.dataset)
-        self.spec_dim = self.spec_dim[0]
-
-        self.energy_scale = self.spec_dim[1]
-        self.experiment['offset'] = self.energy_scale[0]
-        self.experiment['dispersion'] = self.energy_scale[1] - self.energy_scale[0]
-        self.update()
-
-    def on_check(self):
-        pass
-
-    def set_action(self):
-        self.ui.offsetEdit.editingFinished.connect(self.on_enter)
-        self.ui.dispersionEdit.editingFinished.connect(self.on_enter)
-        self.ui.timeEdit.editingFinished.connect(self.on_enter)
-
-        self.ui.TEMList.activated[str].connect(self.on_list_enter)
-
-        self.ui.convEdit.editingFinished.connect(self.on_enter)
-        self.ui.collEdit.editingFinished.connect(self.on_enter)
-        self.ui.E0Edit.editingFinished.connect(self.on_enter)
-        self.ui.binningEdit.editingFinished.connect(self.on_enter)
-        self.ui.conversionEdit.editingFinished.connect(self.on_enter)
-        self.ui.fluxEdit.editingFinished.connect(self.on_enter)
-        self.ui.VOAEdit.editingFinished.connect(self.on_enter)
-        self.ui.energy_button.clicked.connect(self.set_energy_scale)
-        self.ui.binXEdit.editingFinished.connect(self.on_enter)
-        self.ui.binYEdit.editingFinished.connect(self.on_enter)

pyTEMlib/info_dlg.py

@@ -1,202 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-InfoDialog user interface definitions
-"""
-
-from PyQt5 import QtCore, QtGui, QtWidgets
-from pyTEMlib.microscope import microscope
-
-
-class UiDialog(object):
-    def __init__(self, dialog):
-        dialog.setObjectName('Spectrum Info')
-        dialog.resize(371, 184)
-
-        valid_float = QtGui.QDoubleValidator()
-        valid_int = QtGui.QIntValidator()
-
-        self.TEM = []
-        self.TEM = microscope.get_available_microscope_names()
-
-        self.layout = QtWidgets.QGridLayout()
-        self.layout.setVerticalSpacing(2)
-
-        self.separator1 = QtWidgets.QLabel(dialog)
-        self.separator1.setAutoFillBackground(True)
-        palette = self.separator1.palette()
-        palette.setColor(self.separator1.backgroundRole(), QtCore.Qt.blue)
-        palette.setColor(self.separator1.foregroundRole(), QtCore.Qt.white)
-        self.separator1.setAlignment(QtCore.Qt.AlignCenter)
-        self.separator1.setMaximumHeight(50)
-
-        self.separator1.setPalette(palette)
-        ######################################################################
-        self.separator1.setText("Energy Scale")
-
-        row = 0
-        self.layout.addWidget(self.separator1, row, 0, 1, 4)
-        ######################################################################
-
-        row += 1
-        self.offsetLabel = QtWidgets.QLabel("Offset")
-        self.offsetEdit = QtWidgets.QLineEdit(" 1.00")
-        self.offsetEdit.setValidator(valid_float)
-        self.offsetUnit = QtWidgets.QLabel("eV")
-
-        self.layout.addWidget(self.offsetLabel, row, 0)
-        self.layout.addWidget(self.offsetEdit, row, 1)
-        self.layout.addWidget(self.offsetUnit, row, 2)
-
-        row += 1
-        self.dispersionLabel = QtWidgets.QLabel("Dispersion")
-        self.dispersionEdit = QtWidgets.QLineEdit(" 1.00")
-        self.dispersionEdit.setValidator(valid_float)
-        self.dispersionUnit = QtWidgets.QLabel("eV/channel")
-
-        self.layout.addWidget(self.dispersionLabel, row, 0)
-        self.layout.addWidget(self.dispersionEdit, row, 1)
-        self.layout.addWidget(self.dispersionUnit, row, 2)
-
-        row += 1
-        self.energy_button = QtWidgets.QPushButton('Set Energy Scale', dialog)
-        self.energy_button.setCheckable(True)
-
-        self.layout.addWidget(self.energy_button, row, 1)
-
-        row += 1
-        self.timeLabel = QtWidgets.QLabel("Exp. Time")
-        self.timeEdit = QtWidgets.QLineEdit(" 100.0")
-        self.timeEdit.setValidator(valid_float)
-        self.timeUnit = QtWidgets.QLabel("s")
-
-        self.layout.addWidget(self.timeLabel, row, 0)
-        self.layout.addWidget(self.timeEdit, row, 1)
-        self.layout.addWidget(self.timeUnit, row, 2)
-
-        self.separator2 = QtWidgets.QLabel(dialog)
-        self.separator2.setAutoFillBackground(True)
-        self.separator2.setAlignment(QtCore.Qt.AlignCenter)
-        self.separator2.setMaximumHeight(50)
-        self.separator2.setPalette(palette)
-
-        row += 1
-        ######################################################################
-        self.separator2.setText("Microscope")
-        self.layout.addWidget(self.separator2, row, 0, 1, 4)
-        ######################################################################
-
-        row += 1
-        self.TEMList = QtWidgets.QComboBox()
-        self.TEMList.setEditable(False)
-        self.TEMList.addItems(self.TEM)
-
-        self.layout.addWidget(self.TEMList, row, 1)
-
-        row += 1
-        self.convLabel = QtWidgets.QLabel("Conv. Angle")
-        self.convEdit = QtWidgets.QLineEdit(" 100.0")
-        self.convEdit.setValidator(valid_float)
-        self.convUnit = QtWidgets.QLabel("mrad")
-        self.layout.addWidget(self.convLabel, row, 0)
-        self.layout.addWidget(self.convEdit, row, 1)
-        self.layout.addWidget(self.convUnit, row, 2)
-
-        row += 1
-        self.collLabel = QtWidgets.QLabel("Coll. Angle")
-        self.collEdit = QtWidgets.QLineEdit(" 10.0")
-        self.collEdit.setValidator(valid_float)
-        self.collUnit = QtWidgets.QLabel("mrad")
-        self.layout.addWidget(self.collLabel, row, 0)
-        self.layout.addWidget(self.collEdit, row, 1)
-        self.layout.addWidget(self.collUnit, row, 2)
-
-        row += 1
-        self.E0Label = QtWidgets.QLabel("Acc. Voltage")
-        self.E0Edit = QtWidgets.QLineEdit(" 100.0")
-        self.E0Edit.setValidator(valid_float)
-        self.E0Unit = QtWidgets.QLabel("kV")
-        self.layout.addWidget(self.E0Label, row, 0)
-        self.layout.addWidget(self.E0Edit, row, 1)
-        self.layout.addWidget(self.E0Unit, row, 2)
-
-        self.separator3 = QtWidgets.QLabel(dialog)
-        self.separator3.setAutoFillBackground(True)
-        self.separator3.setAlignment(QtCore.Qt.AlignCenter)
-        self.separator3.setMaximumHeight(50)
-        self.separator3.setPalette(palette)
-
-        row += 1
-        ######################################################################
-        self.separator3.setText("Quantification")
-        self.layout.addWidget(self.separator3, row, 0, 1, 4)
-        ######################################################################
-
-        row += 1
-        self.binningLabel = QtWidgets.QLabel("Binning")
-        self.binningEdit = QtWidgets.QLineEdit(" 1")
-        self.binningEdit.setValidator(valid_int)
-        self.layout.addWidget(self.binningLabel, row, 0)
-        self.layout.addWidget(self.binningEdit, row, 1)
-
-        row += 1
-        self.conversionLabel = QtWidgets.QLabel("Conversion")
-        self.conversionEdit = QtWidgets.QLineEdit(" 25.0")
-        self.conversionEdit.setValidator(valid_float)
-        self.conversionUnit = QtWidgets.QLabel("e<sup>-</sup>/counts")
-        self.layout.addWidget(self.conversionLabel, row, 0)
-        self.layout.addWidget(self.conversionEdit, row, 1)
-        self.layout.addWidget(self.conversionUnit, row, 2)
-        row += 1
-        self.fluxLabel = QtWidgets.QLabel("Flux")
-        self.fluxEdit = QtWidgets.QLineEdit(" 100.0")
-        self.fluxEdit.setValidator(valid_float)
-        self.fluxUnit = QtWidgets.QLabel("e<sup>-</sup>/s")
-        self.layout.addWidget(self.fluxLabel, row, 0)
-        self.layout.addWidget(self.fluxEdit, row, 1)
-        self.layout.addWidget(self.fluxUnit, row, 2)
-        row += 1
-        self.VOALabel = QtWidgets.QLabel("Measurement")
-        self.VOAEdit = QtWidgets.QLineEdit(" 10.0")
-        self.VOAEdit.setValidator(valid_float)
-        self.VOAUnit = QtWidgets.QLabel("pA")
-        self.layout.addWidget(self.VOALabel, row, 0)
-        self.layout.addWidget(self.VOAEdit, row, 1)
-        self.layout.addWidget(self.VOAUnit, row, 2)
-
-        self.separator4 = QtWidgets.QLabel(dialog)
-        self.separator4.setAutoFillBackground(True)
-        self.separator4.setAlignment(QtCore.Qt.AlignCenter)
-        self.separator4.setMaximumHeight(50)
-        self.separator4.setPalette(palette)
-        ######################################################################
-        self.separator4.setText("Spectrum Image")
-
-        row += 1
-        self.layout.addWidget(self.separator4, row, 0, 1, 4)
-        ######################################################################
-
-        self.binXLabel = QtWidgets.QLabel('Bin X:')
-        self.binXEdit = QtWidgets.QLineEdit('1')
-        self.binXEdit.setValidator(valid_int)
-        self.binXUnit = QtWidgets.QLabel('pixel')
-
-        row += 1
-        self.layout.addWidget(self.binXLabel, row, 0)
-        self.layout.addWidget(self.binXEdit, row, 1)
-        self.layout.addWidget(self.binXUnit, row, 2)
-
-        self.binYLabel = QtWidgets.QLabel('Bin Y:')
-        self.binYEdit = QtWidgets.QLineEdit('1')
-        self.binYEdit.setValidator(valid_int)
-        self.binYUnit = QtWidgets.QLabel('pixel')
-
-        row += 1
-        self.layout.addWidget(self.binYLabel, row, 0)
-        self.layout.addWidget(self.binYEdit, row, 1)
-        self.layout.addWidget(self.binYUnit, row, 2)
-
-        dialog.setLayout(self.layout)
-
-        dialog.setWindowTitle("Spectrum Info")
-
-        QtCore.QMetaObject.connectSlotsByName(dialog)