pyTEMlib 0.2020.11.1__py3-none-any.whl → 0.2024.9.0__py3-none-any.whl

pyTEMlib/interactive_image.py

@@ -1,226 +1 @@
-"""
-Interactive EELS provides dialogs for input
-"""
-import numpy as np
-
-from PyQt5 import QtWidgets, QtCore, QtGui
-import sidpy
-import matplotlib.patches as patches
-from matplotlib.widgets import SpanSelector
-
-import matplotlib.pyplot as plt
-
-from IPython.display import display
-import ipywidgets as widgets
-from skimage import exposure
-
-from pyTEMlib import image_dlg
-import pyTEMlib.file_tools as ft
-import pyTEMlib.image_tools as it
-from pyTEMlib.microscope import microscope
-
-###
-
-from matplotlib.figure import Figure
-from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as Canvas
-
-
-class ImageDialog(QtWidgets.QWidget):
-    def __init__(self, dataset, parent=None):
-        super(ImageDialog, self).__init__(parent, QtCore.Qt.WindowStaysOnTopHint)
-
-        if dataset is None:
-            # make a dummy dataset for testing
-            dataset = ft.make_dummy_dataset(sidpy.DataTypes.IMAGE)
-        if not isinstance(dataset, sidpy.Dataset):
-            raise TypeError('dataset has to be a sidpy dataset')
-
-        self.image_dims = ft.get_dimensions_by_type([sidpy.DimensionTypes.RECIPROCAL, sidpy.DimensionTypes.SPATIAL],
-                                                    dataset)
-        if len(self.image_dims) != 2:
-            raise TypeError('We need exactly two SPATIAL or RECIPROCAL dimensions')
-        self.dim_x = self.image_dims[0][1]
-        self.dim_y = self.image_dims[1][1]
-        self.fov_x = 0.
-        self.fov_y = 0.
-        self.v_min = np.array(dataset).min()
-        self.v_max = np.array(dataset).max()
-
-        self.parent = parent
-
-        self.ui = image_dlg.UiDialog(self)
-
-        self.set_action()
-
-        self.dataset = dataset
-        self.image = np.array(self.dataset)
-
-        self.experiment = {}
-        self.set_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.histogram()
-
-        self.update()
-
-        self.spatial_dlg = None
-        self.histogram()
-        self.cid = self.ui.histogram.axes.figure.canvas.mpl_connect('button_press_event', self.onclick)
-
-        self.show()
-
-    def histogram(self, bins=256):
-        ax_hist = self.ui.histogram.axes
-        ax_hist.clear()
-
-        hist, bin_edges = np.histogram(self.image, bins=bins, range=[self.v_min, self.v_max], density=True)
-        ax_hist.plot(np.array(bin_edges)[:-1], np.array(hist))
-
-        ax_hist.set_yticks([])
-        self.span = SpanSelector(self.ui.histogram.axes, self.on_select, 'horizontal', useblit=False,
-                                 button=1,
-                                 rectprops=dict(alpha=0.5, facecolor='blue'))
-
-        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.plot()
-
-    def onclick(self, event):
-        if event.dblclick:
-            self.v_min = np.array(self.image).min()
-            self.v_max = np.array(self.image).max()
-            self.histogram()
-
-    def on_select(self, v_min, v_max):
-        self.v_min = v_min
-        self.v_max = v_max
-        # self.setWindowTitle(f'{v_min:.1f}, {v_max:.1f}')
-        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)
-        self.dataset.view.axis.figure.canvas.draw()
-
-    def update(self):
-        self.ui.fovXEdit.setText(f'{self.fov_x:.2f}')
-        self.ui.fovYEdit.setText(f'{self.fov_y:.2f}')
-        self.ui.timeEdit.setText(f"{self.experiment['exposure_time'] :.2f}")
-        self.ui.E0Edit.setText(f"{self.experiment['acceleration_voltage']/1000.:.2f}")
-        self.ui.collEdit.setText(f"{self.experiment['collection_angle']:.2f}")
-        self.ui.convEdit.setText(f"{self.experiment['convergence_angle']:.2f}")
-        self.ui.fluxEdit.setText(f"{self.experiment['flux']:.2f}")
-
-    def set_dataset(self):
-        extent = self.dataset.get_extent([self.image_dims[0][0], self.image_dims[1][0]])
-        self.fov_x = extent[1]-extent[0]
-        self.fov_y = extent[2]-extent[3]
-
-        self.ui.fovXUnit.setText(self.dim_x.units)
-        self.ui.fovYUnit.setText(self.dim_y.units)
-
-        minimum_info = {'FOV_x': self.fov_x,
-                        'FOV_y': self.fov_y,
-                        'exposure_time': 0.0,
-                        'convergence_angle': 0.0, 'collection_angle': 0.0,
-                        'acceleration_voltage': 0.0,
-                        'flux': 0.0}
-
-        if 'experiment' not in self.dataset.metadata:
-            self.dataset.metadata['experiment'] = {}
-        if 'DM' in self.dataset.original_metadata:
-            self.dataset.metadata['experiment'].update(it.read_dm3_image_info(self.dataset.original_metadata))
-
-        self.experiment = self.dataset.metadata['experiment']
-        for key, value in minimum_info.items():
-            if key not in self.experiment:
-                self.experiment[key] = value
-    def on_enter(self):
-        sender = self.sender()
-        if sender == self.ui.E0Edit:
-            self.experiment['acceleration_voltage'] = float(self.ui.E0Edit.displayText())
-        elif sender == self.ui.collEdit:
-            self.experiment['collection_angle'] = float(self.ui.collEdit.displayText())
-        elif sender == self.ui.convEdit:
-            self.experiment['convergence_angle'] = float(self.ui.convEdit.displayText())
-        elif sender == self.ui.timeEdit:
-            self.experiment['exposure_time'] = float(self.ui.timeEdit.displayText())
-        elif sender == self.ui.fovXEdit:
-            self.experiment['FOV_x'] = float(self.ui.fovXEdit.displayText())
-        elif sender == self.ui.fovYEdit:
-            self.experiment['FOV_y'] = float(self.ui.fovYEdit.displayText())
-        elif sender == self.ui.fluxEdit:
-            self.experiment['flux'] = float(self.ui.fluxEdit.displayText())
-        self.update()
-
-    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 on_check_enter(self):
-        sender = self.sender()
-        if sender == self.ui.logCheck:
-            if self.ui.logCheck.isChecked():
-                self.ui.gammaCheck.setChecked(False)
-                self.log_gamma = 1.0
-                self.ui.gammaEdit.setText(f'{self.log_gamma:.2f}')
-                self.image = np.log(1.0+np.array(self.dataset-self.dataset.min()+1e-12))
-                self.image = np.nan_to_num(self.image)
-                self.v_min = self.image.min()
-                self.v_max = self.image.max()
-            else:
-                self.image = np.array(self.dataset-self.dataset.min())
-                self.v_min = self.image.min()
-                self.v_max = self.image.max()
-            self.histogram()
-
-        elif sender == self.ui.gammaCheck:
-            if self.ui.gammaCheck.isChecked():
-                self.ui.logCheck.setChecked(False)
-                self.gamma = 0.8
-                self.ui.gammaEdit.setText(f'{self.gamma:.2f}')
-                self.image = np.array(self.dataset)**self.gamma
-                self.v_min = self.image.min()
-                self.v_max = self.image.max()
-            else:
-                self.image = np.array(self.dataset)
-                self.v_min = self.image.min()
-                self.v_max = self.image.max()
-            self.histogram()
-
-    def set_action(self):
-        self.ui.fovXEdit.editingFinished.connect(self.on_enter)
-        self.ui.fovYEdit.editingFinished.connect(self.on_enter)
-
-        self.ui.timeEdit.editingFinished.connect(self.on_enter)
-        self.ui.E0Edit.editingFinished.connect(self.on_enter)
-        self.ui.collEdit.editingFinished.connect(self.on_enter)
-        self.ui.convEdit.editingFinished.connect(self.on_enter)
-        self.ui.fluxEdit.editingFinished.connect(self.on_enter)
-
-        self.ui.TEMList.activated[str].connect(self.on_list_enter)
-
-        self.ui.logCheck.clicked.connect(self.on_check_enter)
-        self.ui.gammaCheck.clicked.connect(self.on_check_enter)
+from pyTEMlib import image_dialog