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ImageDialog.py
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#####################################################################
#
# Part of pycrosGUI
# of pycroscopy ecosystem
#
# ImageDialog: SImage processing dialog.
#
#
####################################################################
from PyQt5 import QtCore
from PyQt5 import QtGui
from PyQt5 import QtWidgets
import pyqtgraph as pg
import numpy as np
import sidpy
import scipy
from pyTEMlib import image_tools
import pyTEMlib.probe_tools
import pyTEMlib.atom_tools
class ImageDialog(QtWidgets.QWidget):
def __init__(self, parent=None):
super(ImageDialog, self).__init__(parent)
self.parent = parent
self.set_energy = True
layout = self.get_sidbar()
self.setLayout(layout)
self.setWindowTitle("Image")
def get_sidbar(self):
validfloat = QtGui.QDoubleValidator()
validint = QtGui.QIntValidator()
layout = QtWidgets.QGridLayout()
row = 0
self.mainList = QtWidgets.QComboBox(self)
self.mainList.addItem("None")
layout.addWidget(self.mainList, row,0, 1, 3)
layout.setColumnStretch(0, 3)
self.mainList.activated[str].connect(self.update_image_dataset)
row += 1
self.regButton = QtWidgets.QPushButton()
self.regButton.setStyleSheet('QPushButton {background-color: blue; color: white;}')
self.regButton.setText("Registration")
layout.addWidget(self.regButton, row,0, 1, 3)
layout.setColumnStretch(0, 3)
#self.scaleButton.clicked.connect(self.rigi_registration)
row += 1
self.rigid_regButton = QtWidgets.QPushButton()
self.rigid_regButton.setText("Rigid Reg.")
self.rigid_regButton.setCheckable(True)
layout.addWidget(self.rigid_regButton, row, 0)
self.rigid_regButton.clicked.connect(self.rigid_registration)
self.demon_regButton = QtWidgets.QPushButton()
self.demon_regButton.setText("Demon Reg.")
self.demon_regButton.setCheckable(True)
layout.addWidget(self.demon_regButton, row, 1)
self.demon_regButton.clicked.connect(self.demon_registration)
self.all_regButton = QtWidgets.QPushButton()
self.all_regButton.setText("Both Reg.")
self.all_regButton.setCheckable(True)
layout.addWidget(self.all_regButton, row, 2)
#self.all_regButton.clicked.connect(self.all_registration)
row += 1
self.sumButton = QtWidgets.QPushButton()
self.sumButton.setText("Sum")
self.sumButton.setCheckable(True)
layout.addWidget(self.sumButton, row, 0)
self.sumButton.clicked.connect(self.sum_stack)
self.averageButton = QtWidgets.QPushButton()
self.averageButton.setText("Average")
self.averageButton.setCheckable(True)
layout.addWidget(self.averageButton, row, 1)
self.averageButton.clicked.connect(self.average_stack)
self.driftButton = QtWidgets.QPushButton()
self.driftButton.setText("Get Drift")
self.driftButton.setCheckable(True)
layout.addWidget(self.driftButton, row, 2)
#self.driftButton.clicked.connect(self.get_drift)
row += 1
self.processButton = QtWidgets.QPushButton()
self.processButton.setStyleSheet('QPushButton {background-color: blue; color: white;}')
self.processButton.setText("Process")
layout.addWidget(self.processButton, row,0, 1, 3)
layout.setColumnStretch(0, 3)
# self.scaleButton.clicked.connect(self.cursor2energy_scale)
row += 1
self.atom_sizeLabel = QtWidgets.QLabel("atom_size")
self.atom_sizeEdit = QtWidgets.QLineEdit(" 100.0")
self.atom_sizeEdit.setValidator(validfloat)
#self.atom_sizeEdit.editingFinished.connect(self.set_energy_scale)
self.atom_sizeUnit = QtWidgets.QLabel("A")
layout.addWidget(self.atom_sizeLabel,row,0)
layout.addWidget(self.atom_sizeEdit,row,1)
layout.addWidget(self.atom_sizeUnit,row,2)
row += 1
self.deconButton = QtWidgets.QPushButton()
self.deconButton.setText("LR Decon")
self.deconButton.setCheckable(True)
layout.addWidget(self.deconButton, row, 0)
self.deconButton.clicked.connect(self.decon_lr)
self.atomsButton = QtWidgets.QPushButton()
self.atomsButton.setText("Find Atoms")
self.atomsButton.setCheckable(True)
layout.addWidget(self.atomsButton, row, 1)
self.atomsButton.clicked.connect(self.find_atoms)
self.refineButton = QtWidgets.QPushButton()
self.refineButton.setText("Refine Atoms")
self.refineButton.setCheckable(True)
layout.addWidget(self.refineButton, row, 2)
return layout
def update_sidebar(self):
if '_relationship' not in self.parent.datasets:
return
image_list = ['None']
image_index = 0
if 'image' in self.parent.datasets['_relationship']:
self.key = self.parent.datasets['_relationship']['image']
else:
self.key = 'None'
for index, key in enumerate(self.parent.datasets.keys()):
if isinstance(self.parent.datasets[key], sidpy.Dataset):
if 'IMAG' in self.parent.datasets[key].data_type.name:
image_list.append(f'{key}: {self.parent.datasets[key].title}')
if key == self.key:
image_index = index + 1
if image_index >len(image_list) - 1:
image_index = len(image_list) - 1
self.mainList.clear()
for item in image_list:
self.mainList.addItem(item)
self.mainList.setCurrentIndex(image_index)
self.update_image_dataset()
if 'IMAG' in self.parent.dataset.data_type.name:
dims = self.parent.dataset.get_dimensions_by_type(sidpy.DimensionType.SPATIAL, return_axis=True)
if len(dims) <1:
dims = self.parent.dataset.get_dimensions_by_type(sidpy.DimensionType.RECIPROCAL, return_axis=True)
x = dims[0]
pixel_size_x = x[1] - x[0]
self.atom_sizeEdit.setText(f'{pixel_size_x*4:.2f}')
self.atom_sizeUnit.setText(x.units)
self.atom_sizeLabel.setText('Atom size')
def update_image_dataset(self, value=0):
self.key = self.mainList.currentText().split(':')[0]
if self.key not in self.parent.datasets.keys():
return
if 'None' in self.key:
return
self.parent.main = self.key
self.parent.set_dataset()
self.dataset = self.parent.dataset
self.parent.plotUpdate()
def sum_stack(self, value=0):
if self.dataset.data_type.name == 'IMAGE_STACK':
dims = self.parent.dataset.get_dimensions_by_type(sidpy.DimensionType.TEMPORAL, return_axis=False)
key =f'Sum-{self.parent.main}'
name = f'Sum-{self.dataset.title}'
dataset = self.parent.dataset.sum(axis=dims[0])
dataset.metadata = self.parent.dataset.metadata.copy()
self.add_image_dataset(key, name, dataset, data_type='IMAGE')
def average_stack(self, value=0):
if self.parent.dataset.data_type.name == 'IMAGE_STACK':
dims = self.parent.dataset.get_dimensions_by_type(sidpy.DimensionType.TEMPORAL, return_axis=False)
key =f'Sum-{self.parent.main}'
name = f'Sum-{self.dataset.title}'
dataset = self.parent.dataset.mean(axis=dims[0])
dataset.metadata = self.parent.dataset.metadata.copy()
self.add_image_dataset(key, name, dataset, data_type='IMAGE')
def rigid_registration(self, checked):
if self.parent.dataset.data_type.name == 'IMAGE_STACK':
key =f'RigidReg-{self.parent.main}'
name = f'RigidReg-{self.dataset.title}'
dataset = image_tools.rigid_registration(self.parent.dataset)
dataset.metadata = self.parent.dataset.metadata.copy()
self.add_image_dataset(key, name, dataset, data_type='IMAGE_STACK')
self.rigid_regButton.setChecked(False)
def demon_registration(self, value=0):
if self.parent.dataset.data_type.name == 'IMAGE_STACK':
key =f'DemonReg-{self.parent.main}'
name = f'DemonReg-{self.dataset.title}'
dataset = image_tools.demon_registration(self.parent.dataset)
dataset.metadata = self.parent.dataset.metadata.copy()
self.add_image_dataset(key, name, dataset, data_type='IMAGE_STACK')
self.demon_regButton.setChecked(False)
def add_image_dataset(self, key, name, dataset, data_type='IMAGE'):
self.parent.datasets[key] = dataset
self.parent.datasets['_relationship'][key] = key
self.parent.datasets[key].data_type = data_type
self.parent.datasets[key].title = name
self.parent.datasets['_relationship']['image'] = key
self.update_sidebar()
def decon_lr(self):
if self.parent.dataset.data_type.name != 'IMAGE':
return
if 'probe' not in self.parent.dataset.metadata.keys():
print('decon 1')
atom_size = float(self.atom_sizeEdit.displayText())
if hasattr(self.dataset, 'x'):
scale = self.parent.dataset.x[1]-self.parent.dataset.x[0]
else:
scale = 1.
gauss_diameter = atom_size/scale
probe = pyTEMlib.probe_tools.make_gauss(self.parent.dataset.shape[0], self.parent.dataset.shape[1], gauss_diameter)
else:
probe = self.parent.dataset.metadata['probe']['probe']
print('Deconvolution of ', self.parent.dataset.title)
LR_dataset = image_tools.decon_lr(self.dataset, probe, verbose=False)
key =f'LRdeconvol-{self.parent.main}'
name = f'LRdeconvol-{self.dataset.title}'
self.add_image_dataset(key, name, LR_dataset, data_type='IMAGE')
self.deconButton.setChecked(False)
def find_atoms(self, value=0):
atom_size = float(self.atom_sizeEdit.displayText())
if hasattr(self.dataset, 'x'):
scale = self.parent.dataset.x[1]-self.parent.dataset.x[0]
else:
scale = 1.
atoms = pyTEMlib.atom_tools.find_atoms(self.parent.dataset, atom_size=atom_size/scale, threshold=0.)
if 'atoms' not in self.parent.dataset.metadata.keys():
self.parent.dataset.metadata['atoms'] = {}
self.parent.dataset.metadata['atoms']['positions'] = atoms
self.parent.dataset.metadata['atoms']['size'] = atom_size
self.parent.dataset.metadata['plot']['additional_features'] = 'Image'
self.parent.plotUpdate()
self.atomsButton.setChecked(False)
def get_additional_features(self):
if 'plot' not in self.parent.dataset.metadata.keys():
self.parent.dataset.metadata['plot'] = {}
if 'additional_features' not in self.parent.dataset.metadata['plot'].keys():
self.parent.dataset.metadata['plot']['additional_features'] = []
plot_features = {}
if 'atoms' in self.parent.dataset.metadata:
atoms = np.array(self.parent.dataset.metadata['atoms']['positions'])[:, :2]
size = self.parent.dataset.metadata['atoms']['size']
# pg.mkPen('r', width=size)
plot_features["atoms"] = pg.ScatterPlotItem(pos=np.array(atoms)[:,:2], pen=None , symbol='o', size=10, brush=pg.mkBrush(200,0,0,50), name='atoms')
plot_features["atoms"].setZValue(100)
#plot_features["atoms2"] = pg.ScatterPlotItem(pos=np.array(atoms)[:,:2]+[0,3], pen=pg.mkPen('b', width=size) , symbol='o', size=size, name='atoms')
plot_features["atoms3"] = pg.ScatterPlotItem(pos=np.array(atoms)[:,:2]+[2,4], pen=pg.mkPen('orange', width=1) , symbol='o', size=10, name='atoms')
return plot_features