melage 0.0.65__py3-none-any.whl

melage/widgets/tranformationWidget.py

@@ -0,0 +1,275 @@
+__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()