melage 0.0.68__py3-none-any.whl → 1.0.0__py3-none-any.whl

melage/widgets/registrationWidget.py

@@ -1,342 +0,0 @@
-__AUTHOR__ = 'Bahram Jafrasteh'
-
-from melage.utils.utils import make_affine
-from PyQt5 import QtWidgets, QtCore, QtGui
-from PyQt5.QtCore import pyqtSignal
-from PyQt5.QtWidgets import QFileDialog
-from PyQt5.QtCore import Qt
-
-from melage.utils.source_folder import source_folder
-
-class RegistrationDialog(QtWidgets.QDialog):
-    """
-    Image to image registration dialogue
-    """
-    closeSig = pyqtSignal()
-    datachange = pyqtSignal()
-
-    def __init__(self, parent=None, source_dir = 'None'):
-        self.source_dir = source_dir
-        QtWidgets.QDialog.__init__(self, parent)
-        self.setWindowTitle("Child Window!")
-        self.setupUi()
-        self._sourceFolder = source_folder
-        #self.setFixedSize(800,120)
-        self.reg_weights_path = None
-
-    def closeEvent(self, a0: QtGui.QCloseEvent) -> None:
-        self.closeSig.emit()
-        super(RegistrationDialog, self).closeEvent(a0)
-
-    def setupUi(self):
-        self.filters = "NifTi (*.nii *.nii.gz)"
-        Form = self.window()
-        Form.setObjectName("Registration form")
-        #Form.resize(750, 120)
-        #self = QtWidgets.QWidget(Form)
-        #self.setGeometry(QtCore.QRect(11, 11, 731, 101))
-        self.setObjectName("widget")
-        self.setMinimumSize(750, 120)
-        sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Expanding)
-        sizePolicy.setHorizontalStretch(0)
-        sizePolicy.setVerticalStretch(0)
-        sizePolicy.setHeightForWidth(self.sizePolicy().hasHeightForWidth())
-        self.setSizePolicy(sizePolicy)
-
-        self.gridLayout = QtWidgets.QGridLayout(self)
-        self.gridLayout.setContentsMargins(10, 10, 10, 10)
-        self.gridLayout.setObjectName("gridLayout")
-        self.lineEdit_target = QtWidgets.QLineEdit(self)
-        self.lineEdit_target.setObjectName("lineEdit_target")
-        self.gridLayout.addWidget(self.lineEdit_target, 2, 1, 1, 4)
-        self.label_ref = QtWidgets.QLabel(self)
-        self.label_ref.setAlignment(QtCore.Qt.AlignCenter)
-        self.label_ref.setObjectName("label_ref")
-
-        self.checkBox_ref = QtWidgets.QCheckBox(self)
-        self.checkBox_ref.setObjectName("checkBox")
-
-
-        self.comboBox_image = QtWidgets.QComboBox(self)
-        #self.comboBox_image.setGeometry(QtCore.QRect(20, 10, 321, 25))
-        self.comboBox_image.setObjectName("comboBox")
-        self.comboBox_image.addItem("")
-        self.comboBox_image.addItem("")
-        #self.comboBox_image.currentIndexChanged.connect(self.datachange)
-
-        #
-        self.gridLayout.addWidget(self.checkBox_ref, 0, 0, 1, 2)
-
-        self._splitter0 = QtWidgets.QSplitter(self)
-        self._splitter0.setOrientation(QtCore.Qt.Horizontal)
-        self._splitter0.setObjectName("splitter")
-
-
-        self.label_criterion = QtWidgets.QLabel(self._splitter0)
-        self.label_criterion.setAlignment(QtCore.Qt.AlignCenter)
-        self.label_criterion.setObjectName("label_criterion")
-        #self.gridLayout.addWidget(self.label_criterion, 0, 2, 1, 1)
-
-        self.label_method = QtWidgets.QLabel(self)
-        self.label_method.setAlignment(QtCore.Qt.AlignCenter)
-        self.label_method.setObjectName("label_criterion")
-        self.gridLayout.addWidget(self.label_method, 0, 4, 1, 1)
-
-        self.combobox_criterion = QtWidgets.QComboBox(self._splitter0)
-        self.combobox_criterion.setObjectName("combobox_criterion")
-        self.gridLayout.addWidget(self._splitter0, 0, 2, 1, 1)
-        self._list_criterion = ['Mutual Information','Correlation', 'Joint Mutual Information', 'MSE']
-        for i, el in enumerate(self._list_criterion):
-            self.combobox_criterion.addItem("    {}    ".format(el))
-            self.combobox_criterion.setItemData(i, Qt.AlignCenter, Qt.TextAlignmentRole)
-        self.combobox_methods = QtWidgets.QComboBox(self)
-        self.combobox_methods.setObjectName("combobox_methods")
-        self._list_methods = [ 'Rigid', 'Spline','Free Form']
-        for i, el in enumerate(self._list_methods):
-            self.combobox_methods.addItem("    {}    ".format(el))
-            self.combobox_methods.setItemData(i, Qt.AlignCenter, Qt.TextAlignmentRole)
-        self.gridLayout.addWidget(self.combobox_methods, 0, 5, 1, 1)
-
-
-
-
-        self.gridLayout.addWidget(self.label_ref, 1, 0, 1, 1)
-
-        self.button_moving = QtWidgets.QPushButton(self)
-        self.button_moving.setObjectName("button_moving")
-        self.gridLayout.addWidget(self.button_moving, 2, 5, 1, 1)
-        self.lineEdit_fixed = QtWidgets.QLineEdit(self)
-        self.lineEdit_fixed.setObjectName("lineEdit")
-
-        self.button_fixed = QtWidgets.QPushButton(self)
-        self.button_fixed.setObjectName("button_fixed")
-        self.gridLayout.addWidget(self.button_fixed, 1, 5, 1, 1)
-
-
-        self.label_weights = QtWidgets.QLabel(self)
-        self.label_weights.setAlignment(QtCore.Qt.AlignCenter)
-        self.label_weights.setObjectName("label_ref")
-        self.gridLayout.addWidget(self.label_weights, 3, 0, 1, 1)
-        self.lineEdit_out = QtWidgets.QLineEdit(self)
-        self.lineEdit_out.setObjectName("lineEdit")
-        self.gridLayout.addWidget(self.lineEdit_out, 3, 1, 1, 4)
-        self.button_out = QtWidgets.QPushButton(self)
-        self.button_out.setObjectName("button_out")
-        self.gridLayout.addWidget(self.button_out, 3, 5, 1, 1)
-
-
-        self.label_moving = QtWidgets.QLabel(self)
-        self.label_moving.setAlignment(QtCore.Qt.AlignCenter)
-        self.label_moving.setObjectName("label_moving")
-        self.gridLayout.addWidget(self.label_moving, 2, 0, 1, 1)
-
-        self.lineEdit_fixed.setReadOnly(True)
-        self.lineEdit_target.setReadOnly(True)
-        self.lineEdit_out.setReadOnly(True)
-        self.gridLayout.addWidget(self.comboBox_image, 1, 1, 1, 4)
-        self.gridLayout.addWidget(self.lineEdit_fixed, 1, 1, 1, 4)
-        self.lineEdit_fixed.setVisible(False)
-
-        self.OK = QtWidgets.QPushButton(self)
-        self.OK.setObjectName("checkBox_5")
-        self.gridLayout.addWidget(self.OK, 4, 5, 2, 2)
-
-        self.checkBox_multir = QtWidgets.QCheckBox(self)
-        self.checkBox_multir.setObjectName("checkBox")
-        self.gridLayout.addWidget(self.checkBox_multir, 4, 0, 1, 1)
-
-
-        self.splitter = QtWidgets.QSplitter(self)
-        self.splitter.setOrientation(QtCore.Qt.Horizontal)
-        self.splitter.setObjectName("splitter")
-
-        self.label_nbins = QtWidgets.QLabel(self.splitter)
-        self.label_nbins.setAlignment(QtCore.Qt.AlignCenter)
-        self.label_nbins.setObjectName("label_ref")
-        #self.gridLayout.addWidget(self.label_nbins, 4, 1, 2, 2)
-        self.nobins = QtWidgets.QSpinBox(self.splitter)
-        self.nobins.setAlignment(QtCore.Qt.AlignCenter)
-        self.nobins.setObjectName("label_ref")
-        #self.nobins.setValidator(QtGui.QDoubleValidator())
-        #self.nobins.setMaxLength(2)
-        #self.nobins.setText('25')
-        self.nobins.setMaximum(200)
-        self.nobins.setMinimum(10)
-        self.nobins.setValue(25)
-
-
-        self.nobins.setSingleStep(10)
-
-        self.gridLayout.addWidget(self.splitter, 4, 1, 1, 1)
-
-        self.splitter2 = QtWidgets.QSplitter(self)
-        self.splitter2.setOrientation(QtCore.Qt.Horizontal)
-        self.splitter2.setObjectName("splitter")
-
-        self.label_sp = QtWidgets.QLabel(self.splitter2)
-        self.label_sp.setAlignment(QtCore.Qt.AlignCenter)
-        self.label_sp.setObjectName("label_ref")
-        #self.gridLayout.addWidget(self.label_sp, 4, 3, 1, 1)
-        self.sp = QtWidgets.QDoubleSpinBox(self.splitter2)
-        self.sp.setAlignment(QtCore.Qt.AlignCenter)
-        self.sp.setObjectName("label_ref")
-        self.gridLayout.addWidget(self.splitter2, 4, 2, 1, 1)
-        self.sp.setMaximum(1)
-        self.sp.setMinimum(0.01)
-        self.sp.setSingleStep(0.05)
-        #self.sp.setValidator(QtGui.QDoubleValidator())
-        #self.sp.setMaxLength(1)
-        #self.sp.setText()
-        self.checkBox_multir.setChecked(True)
-        self.checkBox_ref.setChecked(True)
-        self.button_fixed.setEnabled(False)
-        self.lineEdit_fixed.setEnabled(False)
-        self.comboBox_image.currentIndexChanged.connect(self.datachange)
-
-        self.button_fixed.clicked.connect(self.browse_ref)
-        self.button_moving.clicked.connect(self.browse_target)
-        self.button_out.clicked.connect(self.save_out)
-        self.OK.clicked.connect(self.runRegistration)
-        self.checkBox_ref.stateChanged.connect(self.activate_advanced)
-        self.retranslateUi(Form)
-        QtCore.QMetaObject.connectSlotsByName(Form)
-
-
-    def save_out(self, value):
-        from PyQt5.QtWidgets import QFileDialog
-        #from utils.utils import getCurrentCoordSystem
-
-        opts = QtWidgets.QFileDialog.DontUseNativeDialog
-        dialg = QFileDialog(self, "Open File", self.source_dir, filter='TFM (*.tfm)',options=opts)
-        dialg.setFileMode(QFileDialog.AnyFile)
-        dialg.setAcceptMode(QFileDialog.AcceptSave)
-        if dialg.exec_() == QFileDialog.Accepted:
-            self.reg_weights_path = dialg.selectedFiles()[0] + '.tfm'
-            self.lineEdit_out.setText(self.reg_weights_path)
-        return
-    def activate_advanced(self, value):
-        self.button_fixed.setEnabled(not value)
-        self.lineEdit_fixed.setEnabled(not value)
-        self.comboBox_image.setEnabled(value)
-        self.comboBox_image.setVisible(value)
-        self.lineEdit_fixed.setVisible(not value)
-
-    def setData(self, img):
-        self.file_fixed = img
-
-    def retranslateUi(self, Form):
-        _translate = QtCore.QCoreApplication.translate
-        Form.setWindowTitle(_translate("Form", "Registration"))
-
-        self.label_ref.setText(_translate("Form", "Fixed"))
-        self.label_nbins.setText(_translate("Form", "No Bins"))
-        self.label_sp.setText(_translate("Form", "Sampling"))
-        self.checkBox_ref.setText(_translate("Form", "Current image as reference"))
-        self.checkBox_multir.setText(_translate("Form", "MultiResolution"))
-        self.button_moving.setText(_translate("Form", "Moving"))
-        self.button_fixed.setText(_translate("Form", "Fixed"))
-        self.button_out.setText(_translate("Form", "Out"))
-        self.label_moving.setText(_translate("Form", "Moving"))
-        self.label_weights.setText(_translate("Form", "Weights"))
-        self.comboBox_image.setItemText(0, _translate("Dialog", "Top Image"))
-        self.comboBox_image.setItemText(1, _translate("Dialog", "Bottom Image"))
-        self.label_criterion.setText(_translate("Form", "Criterion"))
-        self.label_method.setText(_translate("Form", "Method"))
-        self.OK.setText(_translate("Form", "REGISTER"))
-
-
-    def accepted_emit(self):
-        self.lineEdit.text()
-        num = self.lineEdit.text()
-        if num=='' or float(num)==0:
-            self.message()
-            return False
-        txt = self.lineEdit2.text()
-        if txt=='':
-            self.message()
-            return False
-        self.ColorIndName.emit([num, txt])
-        self.accept()
-
-    def browse_ref(self):
-        fileObj = ['', '']
-        #if fileObj is None or type(fileObj) is bool:
-        opts = QtWidgets.QFileDialog.DontUseNativeDialog
-        dialg = QFileDialog( self, "Open File", self.source_dir, self.filters, options=opts)
-        dialg.setFileMode(QtWidgets.QFileDialog.ExistingFile)
-        if dialg.exec_() == QFileDialog.Accepted:
-            fileObj = dialg.selectedFiles()
-            if len(fileObj)>0:
-                self.file_fixed = fileObj[0]
-                self.lineEdit_fixed.setText(self.file_fixed)
-
-    def browse_target(self):
-        fileObj = ['', '']
-        #if fileObj is None or type(fileObj) is bool:
-        opts = QtWidgets.QFileDialog.DontUseNativeDialog
-        dialg = QFileDialog( self, "Open File", self.source_dir, self.filters, options=opts)
-        dialg.setFileMode(QtWidgets.QFileDialog.ExistingFile)
-        if dialg.exec_() == QFileDialog.Accepted:
-            fileObj = dialg.selectedFiles()
-            if len(fileObj)>0:
-                self.file_moving = fileObj[0]
-                self.lineEdit_target.setText(self.file_moving)
-    def runRegistration(self):
-        #self.file_moving = '/home/binibica/PycharmProjects/tmp/HPUM8_01.nii.gz'
-        #self.file_fixed ='/home/binibica/PycharmProjects/tmp/8149_X_20180111_X_t1_rescaled.nii.gz'
-
-        from melage.utils.registration import FFD_registration, RegistrationSpline, RegistrationRigid
-        from melage.utils.utils import read_nib_as_sitk
-
-        if not (hasattr(self, 'file_moving') and hasattr(self, 'file_fixed')):
-            return
-        if self.reg_weights_path is None:
-            return
-
-
-
-        method = self._list_methods[self.combobox_methods.currentIndex()].lower()
-        criterion = self._list_criterion[self.combobox_criterion.currentIndex()].lower()
-
-
-        normalized = True
-        params = dict()
-        params['fixed_mask'] = None
-        params['fixed_points'] = None
-        params['moving_points'] = None
-        params['MultiRes'] = self.checkBox_multir.isChecked()
-        params['nbins'] = int(self.nobins.value())
-        params['sp'] = self.sp.value()  # sampling percentage
-        import SimpleITK as sitk
-        if type(self.file_fixed)!= str:
-            fixed = read_nib_as_sitk(self.file_fixed)
-        else:
-            fixed = sitk.ReadImage(self.file_fixed, sitk.sitkFloat32)
-
-        moving = sitk.ReadImage(self.file_moving, sitk.sitkFloat32)
-
-        if normalized or criterion=='mse':
-            fixed = sitk.Normalize(fixed)
-            fixed = sitk.DiscreteGaussian(fixed, 2.0)
-            moving = sitk.Normalize(moving)
-            moving = sitk.DiscreteGaussian(moving, 2.0)
-        if method == 'Rigid':
-            out, outTx = RegistrationRigid(fixed, moving, criterion, *[params])
-        elif method=='Spline':
-            out, outTx = RegistrationSpline(fixed, moving, criterion, *[params])
-        elif method=='Free Form':
-            out, outTx = FFD_registration(fixed, moving, criterion, *[params])
-        else:
-            return
-        sitk.WriteTransform(outTx, self.reg_weights_path)
-
-
-def run():
-    import sys
-    app = QtWidgets.QApplication(sys.argv)
-    window = RegistrationDialog()
-    window.show()
-    sys.exit(app.exec_())
-
-if __name__ == '__main__':
-    run()

melage/widgets/settings_widget.py

@@ -1,77 +0,0 @@
-__AUTHOR__ = 'Bahram Jafrasteh'
-
-from PyQt5.QtWidgets import QWidget
-from PyQt5 import QtWidgets, QtCore
-from PyQt5.QtCore import pyqtSignal
-class settingsBN(QtWidgets.QMainWindow):
-    """
-    Setting MELAGE
-    """
-    newConfig = pyqtSignal(object)
-    def __init__(self, parent=None):
-        QWidget.__init__(self, parent)
-        self.setWindowTitle("Child Window!")
-        self.setupUi()
-
-
-    def setupUi(self):
-        Info = self.window()
-        Info.setObjectName("Info")
-        Info.resize(728, 569)
-        widget = QtWidgets.QWidget(Info)
-        widget.setGeometry(QtCore.QRect(10, 10, 676, 501))
-        widget.setObjectName("widget")
-        verticalLayout = QtWidgets.QVBoxLayout(widget)
-        verticalLayout.setContentsMargins(0, 0, 0, 0)
-        verticalLayout.setObjectName("verticalLayout")
-        spacerItem = QtWidgets.QSpacerItem(20, 88, QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Expanding)
-        verticalLayout.addItem(spacerItem)
-        horizontalLayout_2 = QtWidgets.QHBoxLayout()
-        horizontalLayout_2.setObjectName("horizontalLayout_2")
-        spacerItem1 = QtWidgets.QSpacerItem(158, 20, QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Minimum)
-        horizontalLayout_2.addItem(spacerItem1)
-        self.label_4 = QtWidgets.QLabel(widget)
-        self.label_4.setLayoutDirection(QtCore.Qt.LeftToRight)
-        self.label_4.setAutoFillBackground(False)
-        self.label_4.setAlignment(QtCore.Qt.AlignCenter)
-        self.label_4.setObjectName("label_4")
-        horizontalLayout_2.addWidget(self.label_4)
-        self.doubleSpinBox = QtWidgets.QDoubleSpinBox(widget)
-        self.doubleSpinBox.setObjectName("doubleSpinBox")
-        self.doubleSpinBox.setValue(10)
-        horizontalLayout_2.addWidget(self.doubleSpinBox)
-        self.label_5 = QtWidgets.QLabel(widget)
-        self.label_5.setAlignment(QtCore.Qt.AlignCenter)
-        self.label_5.setObjectName("label_5")
-        horizontalLayout_2.addWidget(self.label_5)
-        spacerItem2 = QtWidgets.QSpacerItem(198, 20, QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Minimum)
-        horizontalLayout_2.addItem(spacerItem2)
-        verticalLayout.addLayout(horizontalLayout_2)
-        spacerItem3 = QtWidgets.QSpacerItem(17, 338, QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Expanding)
-        verticalLayout.addItem(spacerItem3)
-        horizontalLayout = QtWidgets.QHBoxLayout()
-        horizontalLayout.setObjectName("horizontalLayout")
-        spacerItem4 = QtWidgets.QSpacerItem(290, 22, QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Minimum)
-        horizontalLayout.addItem(spacerItem4)
-        self.OK = QtWidgets.QPushButton(widget)
-        self.OK.setObjectName("OK")
-        horizontalLayout.addWidget(self.OK)
-        spacerItem5 = QtWidgets.QSpacerItem(290, 22, QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Minimum)
-        horizontalLayout.addItem(spacerItem5)
-        verticalLayout.addLayout(horizontalLayout)
-
-        self.retranslateUi(Info)
-        self.OK.clicked.connect(self.closeWindow)
-        QtCore.QMetaObject.connectSlotsByName(Info)
-
-    def closeWindow(self):
-        txt = self.doubleSpinBox.value()
-        self.newConfig.emit([float(txt)])
-        self.close()
-
-    def retranslateUi(self, Info):
-        _translate = QtCore.QCoreApplication.translate
-        Info.setWindowTitle(_translate("Info", "Settings"))
-        self.label_4.setText(_translate("Info", "Save every "))
-        self.label_5.setText(_translate("Info", "minutes"))
-        self.OK.setText(_translate("Info", "OK"))

melage/widgets/tranformationWidget.py

@@ -1,275 +0,0 @@
-__AUTHOR__ = 'Bahram Jafrasteh'
-
-from melage.utils.utils import make_affine
-from PyQt5 import QtWidgets, QtCore, QtGui
-from PyQt5.QtCore import pyqtSignal
-from PyQt5.QtWidgets import QFileDialog
-import numpy as np
-class TransformationDialog(QtWidgets.QDialog):
-    """
-    Image to image transformation widget
-    """
-    closeSig = pyqtSignal()
-
-
-    def __init__(self, parent=None, source_dir = 'None'):
-        self.source_dir = source_dir
-        QtWidgets.QDialog.__init__(self, parent)
-        self.setWindowTitle("Child Window!")
-        self.setupUi()
-        self.reg_weights_path = None
-    def closeEvent(self, a0: QtGui.QCloseEvent) -> None:
-        self.closeSig.emit()
-        super(TransformationDialog, self).closeEvent(a0)
-
-    def setupUi(self):
-        self.filters = "NifTi (*.nii *.nii.gz)"
-        Form = self.window()
-        Form.setObjectName("Registration form")
-        self.MessageBox = QtWidgets.QMessageBox(Form)
-        self.setObjectName("widget")
-        self.setMinimumSize(750, 120)
-        sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Expanding)
-        sizePolicy.setHorizontalStretch(0)
-        sizePolicy.setVerticalStretch(0)
-        sizePolicy.setHeightForWidth(self.sizePolicy().hasHeightForWidth())
-        self.setSizePolicy(sizePolicy)
-
-        self.gridLayout = QtWidgets.QGridLayout(self)
-        self.gridLayout.setContentsMargins(10, 10, 10, 10)
-        self.gridLayout.setObjectName("gridLayout")
-        self.lineEdit_target = QtWidgets.QLineEdit(self)
-        self.lineEdit_target.setObjectName("lineEdit_target")
-
-        self.label_moving = QtWidgets.QLabel(self)
-        self.label_moving.setAlignment(QtCore.Qt.AlignCenter)
-        self.label_moving.setObjectName("label_moving")
-
-        self.button_weights = QtWidgets.QPushButton(self)
-        self.button_weights.setObjectName("button_weights")
-
-        self.lineEdit_moving = QtWidgets.QLineEdit(self)
-        self.lineEdit_moving.setObjectName("lineEdit")
-
-        self.label_fixed = QtWidgets.QLabel(self)
-        self.label_fixed.setAlignment(QtCore.Qt.AlignCenter)
-        self.label_fixed.setObjectName("label_fixed")
-
-        self.button_fixed = QtWidgets.QPushButton(self)
-        self.button_fixed.setObjectName("button_fixed")
-
-        self.lineEdit_fixed = QtWidgets.QLineEdit(self)
-        self.lineEdit_fixed.setObjectName("lineEdit_fixed")
-        self.lineEdit_fixed.setReadOnly(True)
-        #self.gridLayout.addWidget(self.button_fixed, 2, 5, 1, 1)
-        #self.gridLayout.addWidget(self.label_fixed, 1, 0, 1, 1)
-        #self.gridLayout.addWidget(self.lineEdit_fixed, 1, 0, 1, 1)
-
-        self.button_moving = QtWidgets.QPushButton(self)
-        self.button_moving.setObjectName("button_moving")
-
-        self.label_out = QtWidgets.QLabel(self)
-        self.label_out.setAlignment(QtCore.Qt.AlignCenter)
-        self.label_out.setObjectName("label_out")
-
-        self.lineEdit_out = QtWidgets.QLineEdit(self)
-        self.lineEdit_out.setObjectName("lineEdit")
-
-        self.lineEdit_out.setReadOnly(True)
-        self.lineEdit_moving.setReadOnly(True)
-        self.lineEdit_target.setReadOnly(True)
-
-        self.button_out = QtWidgets.QPushButton(self)
-        self.button_out.setObjectName("button_out")
-
-        self.label_weights = QtWidgets.QLabel(self)
-        self.label_weights.setAlignment(QtCore.Qt.AlignCenter)
-        self.label_weights.setObjectName("label_weights")
-
-
-        self.splitter = QtWidgets.QSplitter(self)
-        self.splitter.setOrientation(QtCore.Qt.Horizontal)
-        self.splitter.setObjectName("splitter")
-        self.label_nch = QtWidgets.QLabel(self.splitter)
-        self.label_nch.setAlignment(QtCore.Qt.AlignCenter)
-        self.label_nch.setObjectName("label_ref")
-        #self.gridLayout.addWidget(self.label_nch, 4, 1, 2, 2)
-        self.noch = QtWidgets.QSpinBox(self.splitter)
-        self.noch.setAlignment(QtCore.Qt.AlignCenter)
-        self.noch.setObjectName("label_ref")
-        self.noch.setValue(3)
-        self.noch.setMaximum(99)
-        sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Expanding)
-        sizePolicy.setHorizontalStretch(0)
-        sizePolicy.setVerticalStretch(0)
-        sizePolicy.setHeightForWidth(self.sizePolicy().hasHeightForWidth())
-        self.splitter.setSizePolicy(sizePolicy)
-
-        self.OK = QtWidgets.QPushButton(self)
-        self.OK.setObjectName("checkBox_5")
-
-        self.gridLayout.addWidget(self.button_fixed, 1, 5, 1, 1)
-        self.gridLayout.addWidget(self.lineEdit_fixed, 1, 1, 1, 4)
-        self.gridLayout.addWidget(self.label_fixed, 1, 0, 1, 1)
-
-        self.gridLayout.addWidget(self.button_moving, 2, 5, 1, 1)
-        self.gridLayout.addWidget(self.lineEdit_moving, 2, 1, 1, 4)
-        self.gridLayout.addWidget(self.label_moving, 2, 0, 1, 1)
-        self.gridLayout.addWidget(self.splitter, 2,6,1,1)
-
-        self.gridLayout.addWidget(self.lineEdit_target, 3, 1, 1, 4)
-        self.gridLayout.addWidget(self.label_weights, 3, 0, 1, 1)
-        self.gridLayout.addWidget(self.button_weights, 3, 5, 1, 1)
-
-        self.gridLayout.addWidget(self.button_out, 4, 5, 1, 1)
-        self.gridLayout.addWidget(self.lineEdit_out, 4, 1, 1, 4)
-        self.gridLayout.addWidget(self.label_out, 4, 0, 1, 1)
-
-        self.gridLayout.addWidget(self.OK, 5, 5, 2, 2)
-
-        self.button_moving.clicked.connect(self.browse_ref)
-        self.button_weights.clicked.connect(self.browse_weights)
-        self.button_out.clicked.connect(self.save_out)
-        self.button_fixed.clicked.connect(self.browse_fixed)
-        self.OK.clicked.connect(self.ApplyTransform)
-        self.retranslateUi(Form)
-        QtCore.QMetaObject.connectSlotsByName(Form)
-
-
-    def save_out(self, value):
-        from PyQt5.QtWidgets import QFileDialog
-        #from utils.utils import getCurrentCoordSystem
-
-        opts = QtWidgets.QFileDialog.DontUseNativeDialog
-        dialg = QFileDialog(self, "Open File", self.source_dir, filter="NifTi (*.nii *.nii.gz)",options=opts)
-        dialg.setFileMode(QFileDialog.AnyFile)
-        dialg.setAcceptMode(QFileDialog.AcceptSave)
-        if dialg.exec_() == QFileDialog.Accepted:
-            self.file_out = dialg.selectedFiles()[0] + '.nii.gz'
-            self.lineEdit_out.setText(self.file_out)
-        return
-
-    def retranslateUi(self, Form):
-        _translate = QtCore.QCoreApplication.translate
-        Form.setWindowTitle(_translate("Form", "Transformation"))
-
-        self.label_moving.setText(_translate("Form", "Moving"))
-
-
-        self.button_weights.setText(_translate("Form", "Weights"))
-        self.button_moving.setText(_translate("Form", "Moving"))
-        self.button_out.setText(_translate("Form", "Out"))
-        self.label_weights.setText(_translate("Form", "Weights"))
-        self.label_out.setText(_translate("Form", "Out"))
-
-        self.label_fixed.setText(_translate("Form", "Fixed"))
-        self.button_fixed.setText(_translate("Form", "Fixed"))
-        self.label_nch.setText(_translate("Form", "NoCh"))
-
-        self.OK.setText(_translate("Form", "APPLY"))
-
-
-    def accepted_emit(self):
-        self.lineEdit.text()
-        num = self.lineEdit.text()
-        if num=='' or float(num)==0:
-            self.message()
-            return False
-        txt = self.lineEdit2.text()
-        if txt=='':
-            self.message()
-            return False
-        self.ColorIndName.emit([num, txt])
-        self.accept()
-
-    def browse_fixed(self):
-        opts = QtWidgets.QFileDialog.DontUseNativeDialog
-        dialg = QFileDialog( self, "Open File", self.source_dir, self.filters, options=opts)
-        dialg.setFileMode(QtWidgets.QFileDialog.ExistingFile)
-        if dialg.exec_() == QFileDialog.Accepted:
-            fileObj = dialg.selectedFiles()
-            if len(fileObj)>0:
-                self.file_fixed = fileObj[0]
-                self.lineEdit_fixed.setText(self.file_fixed)
-
-    def browse_ref(self):
-        fileObj = ['', '']
-        #if fileObj is None or type(fileObj) is bool:
-        opts = QtWidgets.QFileDialog.DontUseNativeDialog
-        dialg = QFileDialog( self, "Open File", self.source_dir, self.filters, options=opts)
-        dialg.setFileMode(QtWidgets.QFileDialog.ExistingFile)
-        if dialg.exec_() == QFileDialog.Accepted:
-            fileObj = dialg.selectedFiles()
-            if len(fileObj)>0:
-                self.file_moving = fileObj[0]
-                self.lineEdit_moving.setText(self.file_moving)
-
-    def browse_weights(self):
-        fileObj = ['', '']
-        #if fileObj is None or type(fileObj) is bool:
-        opts = QtWidgets.QFileDialog.DontUseNativeDialog
-        dialg = QFileDialog( self, "Open File", self.source_dir, "TFM (*.tfm)", options=opts)
-        dialg.setFileMode(QtWidgets.QFileDialog.ExistingFile)
-        if dialg.exec_() == QFileDialog.Accepted:
-            fileObj = dialg.selectedFiles()
-            if len(fileObj)>0:
-                self.file_weights = fileObj[0]
-                self.lineEdit_target.setText(self.file_weights)
-    def ApplyTransform(self):
-
-        from melage.utils.registration import apply_reg
-        if not (hasattr(self, 'file_weights') and hasattr(self, 'file_moving')):
-            return
-        if self.file_out is None:
-            return
-        import SimpleITK as sitk
-        from melage.utils.utils import read_file_with_cs, make_image
-
-        fixed = sitk.ReadImage(self.file_fixed)
-        outTx = sitk.ReadTransform(self.file_weights)
-        f_reader = sitk.ImageFileReader()
-        f_reader.SetFileName(self.file_moving)
-        f_reader.ReadImageInformation()
-        size = list(f_reader.GetSize())
-        if len(size) not in [3,4]:
-            self.MessageBox.setText('The number of dimensions should be 3 or 4 while it is {}'.format(len(size)))
-            self.MessageBox.setWindowTitle('Warning')
-            self.MessageBox.show()
-            return
-        total_labels = []
-        if len(size)==4:
-            if size[-1]!=self.noch.value():
-                self.MessageBox.setText('The number of channels is not as expected {}!={}'.format(size[-1], self.noch.value()))
-                self.MessageBox.setWindowTitle('Warning')
-                self.MessageBox.show()
-                return
-            size_total = size[-1]
-        else:
-            size_total = 1
-
-        for l in range(size_total):
-            f_reader.SetExtractIndex([0, 0, 0, l])
-            f_reader.SetExtractSize((size[0], size[1], size[2], 0))
-            moving = f_reader.Execute()
-            predicted = apply_reg(outTx, fixed, moving)
-            predicted = sitk.GetArrayFromImage(predicted).transpose()
-            total_labels.append(predicted)
-
-        fixed = read_file_with_cs(self.file_fixed)
-        total_labels = np.stack(total_labels, -1)
-        if len(total_labels)==1:
-            total_labels = total_labels[...,0]
-        total_labels = make_image(total_labels, fixed)
-        total_labels.to_filename(self.file_out)
-
-
-
-def run():
-    import sys
-    app = QtWidgets.QApplication(sys.argv)
-    window = TransformationDialog()
-    window.show()
-    sys.exit(app.exec_())
-
-if __name__ == '__main__':
-    run()