pyTEMlib 0.2025.4.1__py3-none-any.whl → 0.2025.9.1__py3-none-any.whl

pyTEMlib/file_tools_qt.py

@@ -1,193 +0,0 @@
-import os
-import numpy as np
-import h5py
-
-Qt_available = True
-try:
-    from PyQt5 import QtCore, QtWidgets, QtGui
-except:
-    print('Qt dialogs are not available')
-    Qt_available = False
-
-from PIL import Image, ImageQt
-import matplotlib.pyplot as plt
-import warnings
-warnings.filterwarnings('ignore')
-
-
-if Qt_available:
-    import pyTEMlib.file_tools as ft
-
-
-    class FileIconDialog(QtWidgets.QDialog):
-        """Qt5 Dialog to select directories or files from a list of Thumbnails
-
-        The dialog converts the name of the nion file to the one in Nion's swift software,
-        The dialog converts the name of the nion file to the one in Nion's swift software,
-        because it is otherwise incomprehensible. Any Icon in a hf5 file will be displayed.
-
-        Attributes
-        ----------
-        dir_name: str
-            name of starting directory
-        extension: list of str
-            extensions of files to be listed  in widget
-
-        Methods
-        -------
-        set_icon
-        set_all_icons
-        select
-        get_directory
-        update
-
-        Example
-        -------
-        >>file_view = pyTEMlib.file_tools_qt.FileIconDialog('.')
-        >>dataset = pyTEMlib.file_tools.open_file(file_view.file_name)
-        >>view=dataset.plot()
-
-        """
-
-        def __init__(self, dir_name=None, extension=None):
-            super().__init__(None, QtCore.Qt.WindowStaysOnTopHint)
-            self.setModal(True)
-
-            self.save_path = False
-            self.dir_dictionary = {}
-            self.dir_list = ['.', '..']
-            self.display_list = ['.', '..']
-            self.icon_size = 100
-            self.file_name = None
-
-            self.dir_name = '.'
-            if dir_name is None:
-                self.dir_name = ft.get_last_path()
-                self.save_path = True
-            elif os.path.isdir(dir_name):
-                self.dir_name = dir_name
-
-            self.get_directory()
-
-            # setting geometry
-            self.setGeometry(100, 100, 500, 400)
-
-            # creating a QListWidget
-            self.list_widget = QtWidgets.QListWidget(self)
-            self.list_widget.setIconSize(QtCore.QSize(self.icon_size, self.icon_size))
-            self.layout = QtWidgets.QVBoxLayout()
-            self.layout.addWidget(self.list_widget)
-
-            self.update()
-
-            button_layout = QtWidgets.QHBoxLayout()
-
-            button_select = QtWidgets.QPushButton('Select')
-            button_layout.addWidget(button_select)
-            button_get_icon = QtWidgets.QPushButton('Get Icon')
-            button_layout.addWidget(button_get_icon)
-            button_get_all_icons = QtWidgets.QPushButton('Get All Icons')
-            button_layout.addWidget(button_get_all_icons)
-
-            self.layout.addLayout(button_layout)
-            self.setLayout(self.layout)
-
-            self.list_widget.itemDoubleClicked.connect(self.select)
-            button_select.clicked.connect(self.select)
-            button_get_icon.clicked.connect(self.set_icon)
-            button_get_all_icons.clicked.connect(self.set_all_icons)
-
-            # showing all the widgets
-            self.exec_()
-
-        def set_icon(self):
-            plt.ioff()
-            figure = plt.figure(figsize=(1, 1))
-            item = self.list_widget.currentItem().text()
-            index = self.display_list.index(item)
-            file_name = os.path.abspath(os.path.join(self.dir_name, self.dir_list[index]))
-            dataset = ft.open_file(file_name)
-            dataset.set_thumbnail(figure=figure)
-            plt.close()
-            plt.ion()
-            self.update()
-
-        def set_all_icons(self):
-
-            plt.ioff()
-            figure = plt.figure(figsize=(1, 1))
-            for item in self.dir_list:
-                file_name = os.path.join(self.dir_name, item)
-                if os.path.isfile(file_name):
-                    base_name, extension = os.path.splitext(file_name)
-                    if extension in ['.hf5', '.dm3', '.dm4', '.ndata', '.hf5']:
-                        try:
-                            dataset = ft.open_file(file_name)
-                            dataset.set_thumbnail(figure=figure)
-                            dataset.h5_dataset.file.close()
-                        except:
-                            pass
-            plt.close()
-            plt.ion()
-            self.update()
-
-        def select(self):
-            item = self.list_widget.currentItem().text()
-            index = self.display_list.index(item)
-            item = os.path.abspath(os.path.join(self.dir_name, self.dir_list[index]))
-            self.setWindowTitle(" Chooser " + os.path.abspath(self.dir_name))
-            if os.path.isdir(item):
-                self.dir_name = item
-                self.update()
-
-            elif os.path.isfile(os.path.join(self.dir_name, item)):
-                self.setWindowTitle(f" Selected File: {item}")
-                self.file_name = item
-                self.close()
-
-        def get_directory(self):
-
-            dir_list = os.listdir(self.dir_name)
-            file_dict = ft.update_directory_list(self.dir_name)
-
-            sort = np.argsort(file_dict['directory_list'])
-            self.dir_list = ['.', '..']
-            self.display_list = ['.', '..']
-            for j in sort:
-                self.display_list.append(f"{file_dict['directory_list'][j]}")
-                self.dir_list.append(file_dict['directory_list'][j])
-
-            sort = np.argsort(file_dict['display_file_list'])
-
-            for i, j in enumerate(sort):
-                if '--' in dir_list[j]:
-                    self.display_list.append(f"{file_dict['display_file_list'][j]}")
-                else:
-                    self.display_list.append(f"{file_dict['display_file_list'][j]}")
-                self.dir_list.append(file_dict['file_list'][j])
-
-        def update(self):
-            self.get_directory()
-            self.setWindowTitle("File Chooser " + os.path.abspath(self.dir_name))
-            # creating a QListWidget
-            default_icons = QtWidgets.QFileIconProvider()
-            self.list_widget.clear()
-
-            item_list = []
-            for index, item_text in enumerate(self.dir_list):
-                if os.path.isdir(os.path.join(self.dir_name, item_text)):
-                    icon = default_icons.icon(QtWidgets.QFileIconProvider.Folder)
-                elif item_text[-4:] == '.hf5':
-                    try:
-                        f = h5py.File(os.path.join(self.dir_name, item_text), 'r')
-                        if 'Thumbnail' in f:
-                            picture = ImageQt.ImageQt(Image.fromarray(f['Thumbnail/Thumbnail'][()]))
-                            icon = QtGui.QIcon(QtGui.QPixmap.fromImage(picture))
-                        else:
-                            icon = default_icons.icon(QtWidgets.QFileIconProvider.File)
-                    except:
-                        icon = default_icons.icon(QtWidgets.QFileIconProvider.File)
-                else:
-                    icon = default_icons.icon(QtWidgets.QFileIconProvider.File)
-                item_list.append(QtWidgets.QListWidgetItem(icon, self.display_list[index]))
-                self.list_widget.addItem(item_list[-1])

pyTEMlib/image_dialog.py

@@ -1,158 +0,0 @@
-"""
-Input Dialog for Image Analysis
-
-Author: Gerd Duscher
-
-"""
-# -*- coding: utf-8 -*-
-
-import numpy as np
-import sidpy
-
-Qt_available = True
-try:
-    from PyQt5 import QtCore,  QtWidgets
-except:
-    Qt_available = False
-    # print('Qt dialogs are not available')
-
-from matplotlib.widgets import SpanSelector
-from skimage import exposure
-
-from pyTEMlib.image_dlg import *
-from pyTEMlib.microscope import microscope
-
-_version = 000
-
-if Qt_available:
-    class ImageDialog(QtWidgets.QDialog):
-        """
-            Input Dialog for Image Analysis
-
-            Opens a PyQt5 GUi Dialog that allows to set the experimental parameter necessary for a Quantification.
-
-
-            The dialog operates on a sidpy dataset
-            """
-
-        def __init__(self, dataset, parent=None):
-            super(ImageDialog, self).__init__(parent)
-            if not isinstance(dataset, sidpy.Dataset):
-                raise TypeError("we need a sidpy.Dataset")
-            self.parent = parent
-            self.debug = 0
-            self.dataset = dataset
-            self.image = np.array(self.dataset)
-            self.v_min = np.array(dataset).min()
-            self.v_max = np.array(dataset).max()
-
-            self.ui = UiDialog(self)
-            self.setWindowTitle('Image Info')
-
-            self.dataset.plot()
-            self.histogram()
-            self.cid = self.ui.histogram.axes.figure.canvas.mpl_connect('button_press_event', self.onclick)
-
-            self.span = SpanSelector(self.ui.histogram.axes, self.on_select, 'horizontal', useblit=False,
-                                     button=1, minspan=5,
-                                     rectprops=dict(alpha=0.3, facecolor='blue'))
-            minimum_info = {'size': self.dataset.shape,
-                            'exposure_time': 0.0,
-                            'convergence_angle': 0.0,
-                            'acceleration_voltage': 100.0,
-                            'binning': 1, 'conversion': 1.0,
-                            'flux': 1.0, 'current': 1.0}
-
-            if 'experiment' not in self.dataset.metadata:
-                self.dataset.metadata['experiment'] = {}
-            for key, value in minimum_info.items():
-                if key not in self.dataset.metadata['experiment']:
-                    self.dataset.metadata['experiment'][key] = value
-            self.experiment = self.dataset.metadata['experiment']
-            self.set_action()
-            self.update()
-
-        def histogram(self, bins=256):
-            ax_hist = self.ui.histogram.axes
-            ax_hist.clear()
-
-            hist, bin_edges = np.histogram(np.array(self.image), range=[self.v_min, self.v_max], bins=bins, density=True)
-            ax_hist.plot(np.array(bin_edges)[:-1], np.array(hist))
-
-            image = self.image * 1.0
-            image[image < self.v_min] = self.v_min
-            image[image > self.v_max] = self.v_max
-
-            img_cdf, bins = exposure.cumulative_distribution(np.array(image), bins)
-            ax_hist.plot(bins, img_cdf * hist.max(), 'r')
-            ax_hist.figure.canvas.draw()
-            self.span = SpanSelector(self.ui.histogram.axes, self.on_select, 'horizontal', useblit=False,
-                                     button=1, minspan=5,
-                                     rectprops=dict(alpha=0.3, facecolor='blue'))
-            self.plot()
-
-        def onclick(self, event):
-            if event.dblclick:
-                self.v_min = np.array(self.dataset).min()
-                self.v_max = np.array(self.dataset).max()
-                self.histogram()
-
-        def on_select(self, v_min, v_max):
-            self.v_min = v_min
-            self.v_max = v_max
-            self.histogram()
-
-        def plot(self):
-            ax = self.dataset.view.axis
-            img = self.dataset.view.img
-            img.set_data(self.image)
-            img.set_clim(vmin=self.v_min, vmax=self.v_max)
-            ax.figure.canvas.draw()
-
-        def on_enter(self):
-            sender = self.sender()
-            if 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.E0Edit:
-                value = float(str(sender.displayText()).strip())
-                self.experiment['acceleration_voltage'] = value * 1000.0
-                sender.setText(f"{value:.2f}")
-
-        def on_list_enter(self):
-            sender = self.sender()
-            if sender == self.ui.TEMList:
-                microscope.set_microscope(self.ui.TEMList.currentText())
-                self.setWindowTitle(microscope.name)
-
-                self.experiment['microscope'] = microscope.name
-                self.experiment['convergence_angle'] = microscope.alpha
-                self.experiment['acceleration_voltage'] = microscope.E0
-                self.update()
-
-        def update(self):
-            self.ui.convEdit.setText(f"{self.experiment['convergence_angle']:.2f}")
-            self.ui.E0Edit.setText(f"{self.experiment['acceleration_voltage']/1000.:.2f}")
-
-            self.ui.timeEdit.setText(f"{self.experiment['exposure_time']:.6f}")
-            size_text = f'{self.dataset.shape[0]}'
-            for size in self.dataset.shape[1:]:
-                size_text = size_text + f' x {size}'
-            self.ui.sizeEdit.setText(size_text)
-
-            # 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 set_action(self):
-            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.E0Edit.editingFinished.connect(self.on_enter)

pyTEMlib/image_dlg.py

@@ -1,146 +0,0 @@
-"""
-Gui for image_dialog
-
-Author: Gerd Duscher
-
-"""
-# -*- coding: utf-8 -*-
-Qt_available = True
-try:
-    from PyQt5 import QtCore, QtGui, QtWidgets
-except:
-    Qt_available = False
-    # print('Qt dialogs are not available')
-
-from matplotlib.figure import Figure
-
-from pyTEMlib.microscope import microscope
-
-if Qt_available:
-    from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as Canvas
-
-    class MySICanvas(Canvas):
-        def __init__(self, parent, width=10, height=10, dpi=100):
-            self.figure = Figure(figsize=(width, height), dpi=dpi)
-            self.figure.subplots_adjust(bottom=.2)
-            Canvas.__init__(self, self.figure)
-            self.setParent(parent)
-
-            Canvas.setSizePolicy(self, QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Expanding)
-
-            Canvas.updateGeometry(self)
-
-
-    class UiDialog(object):
-        def __init__(self, dialog, parent=None):
-            dialog.setObjectName('Image Info')
-            dialog.resize(371, 184)
-
-            valid_float = QtGui.QDoubleValidator()
-            # valid_int = QtGui.QIntValidator()
-            self.histogram = MySICanvas(parent, width=10, height=10, dpi=70)
-
-            # Defining a plot instance (axes) and assigning a variable to it
-            self.histogram.axes = self.histogram.figure.add_subplot(1, 1, 1)
-
-            self.TEM = []
-            self.TEM = microscope.get_available_microscope_names()
-
-            plot_layout = QtWidgets.QGridLayout()
-
-            # Adding histogram
-            plot_layout.addWidget(self.histogram, 0, 0)
-
-            # making a single widget out of histogram
-            histogram_plot = QtWidgets.QWidget()
-            histogram_plot.setLayout(plot_layout)
-
-            layout = self.layout = QtWidgets.QGridLayout()
-            self.layout.setVerticalSpacing(2)
-
-            self.separator1 = QtWidgets.QLabel()
-            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("Microscope")
-            layout.addWidget(self.separator1, 0, 0, 1, 3)
-            row = 0
-            layout.addWidget(self.separator1, 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.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.separator2 = QtWidgets.QLabel()
-            self.separator2.setAutoFillBackground(True)
-            self.separator2.setAlignment(QtCore.Qt.AlignCenter)
-            self.separator2.setMaximumHeight(50)
-            self.separator2.setPalette(palette)
-
-            row += 1
-            ######################################################################
-            self.separator2.setText("Image")
-            layout.addWidget(self.separator2, row, 0, 1, 4)
-            ######################################################################
-            row += 1
-            self.sizeLabel = QtWidgets.QLabel("Size")
-            self.sizeEdit = QtWidgets.QLineEdit(" 1 x 1")
-            self.sizeEdit.setValidator(valid_float)
-            self.sizeUnit = QtWidgets.QLabel("px")
-
-            self.layout.addWidget(self.sizeLabel, row, 0)
-            self.layout.addWidget(self.sizeEdit, row, 1)
-            self.layout.addWidget(self.sizeUnit, row, 2)
-
-            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.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("Histogram")
-            self.layout.addWidget(self.separator3, row, 0, 1, 4)
-            ######################################################################
-
-            row += 1
-            layout.addWidget(histogram_plot, row, 0, 1, 3)
-            dialog.setLayout(layout)