melage 0.0.65__py3-none-any.whl

melage/widgets/Segmentation/__init__.py

@@ -0,0 +1,588 @@
+__AUTHOR__ = 'Bahram Jafrasteh'
+
+"""
+    Main BrainExtractor class
+"""
+import os
+import numpy as np
+import nibabel as nib
+from PyQt5 import QtCore, QtGui, QtWidgets
+from functools import partial
+
+from PyQt5.QtCore import pyqtSignal
+import sys
+from PyQt5.QtWidgets import QDialog, QApplication, QPushButton, QVBoxLayout
+from PyQt5.QtCore import Qt
+from melage.utils.utils import convert_to_ras, LargestCC
+
+
+def to_str(val):
+    return '{:.2f}'.format(val)
+
+
+def remove_zero(f_data, value=0):
+    """
+    Remove non segmented areas from image
+    :param f_data:
+    :param value:
+    :return:
+    """
+
+    xs, ys, zs = np.where(f_data > value)  # find zero values
+    tol = 4
+
+    min_max = []
+    for x in [xs, ys, zs]:
+        minx = min(x) - tol if min(x) - tol > 1 else min(x)
+        maxx = max(x) + tol if max(x) + tol < f_data.shape[0] - 1 else max(x)
+        min_max.append([minx, maxx])
+    f_data = f_data[min_max[0][0]:min_max[0][1] + 1, min_max[1][0]:min_max[1][1] + 1, min_max[2][0]:min_max[2][1] + 1]
+
+    return f_data, min_max
+
+
+def centralize_image(img, maxas=128, border=None):
+    """
+    Put image in the center
+    :param img:
+    :param maxas:
+    :param border:
+    :return:
+    """
+
+    n = img.shape
+    if type(maxas) != list:
+        maxas = [maxas, maxas, maxas]
+    pads = np.array([maxas[i] - a for i, a in enumerate(n)])
+    pads_r = pads // 2
+    pads_l = pads - pads_r
+    npads_l = pads_l * -1
+    npads_r = pads_r * -1
+    if border is None:
+        border = img[0, 0, 0]
+    new_img = np.ones((maxas[0], maxas[1], maxas[2])) * border
+
+    pads_r[pads_r < 0] = 0
+    pads_l[pads_l < 0] = 0
+    npads_l[npads_l < 0] = 0
+    npads_r[npads_r < 0] = 0
+    # print(pads_l, pads_r)
+    new_img[pads_r[0]:maxas[0] - pads_l[0], pads_r[1]:maxas[1] - pads_l[1], pads_r[2]:maxas[2] - pads_l[2]] = img[
+                                                                                                              npads_r[
+                                                                                                                  0]:n[
+                                                                                                                         0] -
+                                                                                                                     npads_l[
+                                                                                                                         0],
+                                                                                                              npads_r[
+                                                                                                                  1]:n[
+                                                                                                                         1] -
+                                                                                                                     npads_l[
+                                                                                                                         1],
+                                                                                                              npads_r[
+                                                                                                                  2]:n[
+                                                                                                                         2] -
+                                                                                                                     npads_l[
+                                                                                                                         2]]
+    return new_img, [pads, pads_l, pads_r, npads_l, npads_r, n]
+
+
+class Tissue_Seg(QDialog):
+    """
+    This class has been implemented to use deep learning algorithms for brain extraction
+    """
+    closeSig = pyqtSignal()
+    betcomp = pyqtSignal(int)
+    datachange = pyqtSignal()
+    back_orig = pyqtSignal(int)
+
+    backbutton = pyqtSignal()
+    """
+
+    """
+
+    def __init__(self, parent=None
+                 ):
+        super(Tissue_Seg, self).__init__(parent)
+        # self.load_filepath = 'widgets/Hybrid_latest.pth'
+        self._curent_weight_dir = os.path.dirname(os.path.join(os.getcwd()))
+        """
+        Initialization of Brain Extractor
+
+        Computes image range/thresholds and
+        estimates the brain radius
+        """
+
+    def set_pars(self, threshold=50, remove_extra_bone=True):
+        # print("Initializing...")
+
+        # get image resolution
+
+        self.threshold = threshold
+        self.borderp = 0.0
+
+        # store brain extraction parameters
+        self.setupUi()
+
+    def setData(self, img, res):
+        # store the image
+        self.img = img
+        self.initial_mask = None
+        self.shape = img.shape  # 3D shape
+
+    def activate_advanced(self, value):
+        self.widget.setEnabled(value)
+
+    def setupUi(self):
+        Dialog = self.window()
+        Dialog.setObjectName("N4")
+        Dialog.resize(500, 220)
+        self.grid_main = QtWidgets.QGridLayout(self)
+        self.grid_main.setContentsMargins(0, 0, 0, 0)
+        self.grid_main.setObjectName("gridLayout")
+
+        self.hbox = QtWidgets.QHBoxLayout()
+        self.hbox.setContentsMargins(0, 0, 0, 0)
+        self.hbox.setObjectName("gridLayout")
+        self.grid_main.addLayout(self.hbox, 0, 0)
+
+        self.checkBox = QtWidgets.QCheckBox()
+        self.hbox.addWidget(self.checkBox, 0)
+        self.checkBox.setObjectName("checkBox")
+        self.checkBox.stateChanged.connect(self.activate_advanced)
+        self.comboBox_image = QtWidgets.QComboBox()
+        self.comboBox_image.setGeometry(QtCore.QRect(20, 10, 321, 25))
+        self.comboBox_image.setObjectName("comboBox")
+        for i in range(2):
+            self.comboBox_image.addItem("")
+        self.comboBox_image.currentIndexChanged.connect(self.datachange)
+
+        self.comboBox_models = QtWidgets.QComboBox()
+        self.comboBox_models.setGeometry(QtCore.QRect(20, 10, 321, 25))
+        self.comboBox_models.setObjectName("comboBox")
+        for i in range(3):
+            self.comboBox_models.addItem("")
+        self.comboBox_models.currentIndexChanged.connect(partial(self.parChanged, True))
+
+        self.hbox.addWidget(self.comboBox_image, 1)
+        self.hbox.addWidget(self.comboBox_models, 2)
+
+        self.progressBar = QtWidgets.QProgressBar()
+        self.progressBar.setEnabled(False)
+        self.progressBar.setProperty("value", 0)
+        self.progressBar.setAlignment(QtCore.Qt.AlignCenter)
+        self.progressBar.setObjectName("progressBar")
+        self.progressBar.setMaximum(100)
+
+        self.hbox2 = QtWidgets.QHBoxLayout()
+        self.hbox2.setContentsMargins(0, 0, 0, 0)
+        self.hbox2.setObjectName("gridLayout")
+        self.hbox2.addWidget(self.progressBar, 1)
+
+        self.widget = QtWidgets.QWidget()
+        self.widget.setObjectName("widget")
+        self.gridLayout = QtWidgets.QGridLayout(self.widget)
+        self.gridLayout.setContentsMargins(0, 0, 0, 0)
+        self.gridLayout.setObjectName("gridLayout")
+        self.splitter_3 = QtWidgets.QSplitter(self.widget)
+        self.splitter_3.setOrientation(QtCore.Qt.Horizontal)
+        self.splitter_3.setObjectName("splitter_3")
+
+        self.gridLayout.addWidget(self.splitter_3, 0, 0, 1, 1)
+        self.splitter = QtWidgets.QSplitter(self.widget)
+        self.splitter.setOrientation(QtCore.Qt.Horizontal)
+        self.splitter.setObjectName("splitter")
+
+
+        self.checkbox_post = QtWidgets.QCheckBox(self.splitter)
+        # self.checkbox_post.setAlignment(QtCore.Qt.AlignCenter)
+
+
+        # self.checkbox_bone = QtWidgets.QCheckBox(self.splitter)
+        # self.checkbox_bone.setObjectName("histogram_bone")
+        # self.checkbox_bone.setChecked(False)
+        self.label_type = QtWidgets.QLabel(self.splitter)
+        self.label_type.setAlignment(QtCore.Qt.AlignCenter)
+        self.label_type.setObjectName("label")
+        self.spinbox_num_tissue = QtWidgets.QSpinBox(self.splitter)
+
+        self.spinbox_num_tissue.setMaximum(50)
+        self.spinbox_num_tissue.setMinimum(2)
+        self.spinbox_num_tissue.setSingleStep(1)
+        self.spinbox_num_tissue.setValue(3)
+
+        #self.spinbox_num_tissue.setGeometry(QtCore.QRect(20, 10, 321, 25))
+        #self.spinbox_num_tissue.setObjectName("comboBox")
+        #self.spinbox_num_tissue.setCurrentIndex(0)
+        #self.spinbox_num_tissue.currentIndexChanged.connect(partial(self.parChanged, False))
+        #for i in range(2):
+        #    self.spinbox_num_tissue.addItem("")
+
+        # self.histogram_threshold_min = QtWidgets.QDoubleSpinBox(self.splitter)
+        # self.histogram_threshold_min.setObjectName("histogram_threshold_min")
+        # self.histogram_threshold_min.setValue(6)#(self.ht_min)*100)
+        # self.histogram_threshold_min.setMaximum(10)
+        # self.histogram_threshold_min.setMinimum(0)
+
+        # self.histogram_threshold_max = QtWidgets.QDoubleSpinBox(self.splitter)
+        # self.histogram_threshold_max.setObjectName("histogram_threshold_max")
+        # self.histogram_threshold_max.setValue((self.ht_max) * 100)
+        # self.histogram_threshold_max.setMaximum(100)
+        # self.histogram_threshold_max.setMinimum(0)
+
+        # self.histogram_threshold_min.setEnabled(True)
+        # self.histogram_threshold_max.setEnabled(False)
+
+        self.gridLayout.addWidget(self.splitter, 1, 0, 1, 1)
+
+        self.splitter_2 = QtWidgets.QSplitter(self.widget)
+        self.splitter_2.setOrientation(QtCore.Qt.Horizontal)
+        self.splitter_2.setObjectName("splitter_2")
+
+        self.label = QtWidgets.QLabel(self.splitter_2)
+        self.label.setAlignment(QtCore.Qt.AlignCenter)
+        self.label.setObjectName("label")
+        self.max_iter = QtWidgets.QSpinBox(self.splitter_2)
+        self.max_iter.setObjectName("fractional_threshold")
+
+        self.max_iter.setMaximum(1000)
+        self.max_iter.setMinimum(2)
+        self.max_iter.setSingleStep(1)
+        self.max_iter.setValue(50)
+
+
+
+        # self.label_pma = QtWidgets.QLabel(self.splitter_2)
+        # self.label_pma.setAlignment(QtCore.Qt.AlignCenter)
+        # self.label_pma.setObjectName("label")
+        # self.border_pix = QtWidgets.QDoubleSpinBox(self.splitter_2)
+        # self.border_pix.setObjectName("PMA")
+        # self.border_pix.setValue((self.borderp))
+        # self.border_pix.setMaximum(150)
+        # self.border_pix.setMinimum(0)
+        # self.border_pix.setSingleStep(5)
+        # self.border_pix.valueChanged.connect(partial(self.parChanged, False))
+        self.gridLayout.addWidget(self.splitter_2, 2, 0, 1, 1)
+
+        self.splitter_3 = QtWidgets.QSplitter(self.widget)
+        self.splitter_3.setOrientation(QtCore.Qt.Horizontal)
+        self.splitter_3.setObjectName("splitter_3")
+
+
+        self.pushButton = QtWidgets.QPushButton()
+
+        self.pushButton.setObjectName("pushButton")
+        self.pushButton.pressed.connect(self.accepted_emit)
+        self.hbox2.addWidget(self.pushButton, 0)
+        self.pushButton.setDefault(True)
+        self.gridLayout.addWidget(self.splitter_3, 3, 0, 1, 1)
+
+        self.widget.setEnabled(False)
+
+        self.grid_main.addWidget(self.widget)
+        self.grid_main.addLayout(self.hbox2, 20, 0)
+
+        self.label_pr = QtWidgets.QLabel()
+        self.label_pr.setAlignment(QtCore.Qt.AlignCenter)
+        self.label_pr.setObjectName("label_2")
+        self.label_pr.setText('fdfdf')
+        self.label_pr.setVisible(False)
+
+        self.grid_main.addWidget(self.label_pr)
+        self.retranslateUi(Dialog)
+        QtCore.QMetaObject.connectSlotsByName(Dialog)
+
+    def resetParams(self, state):
+
+        self.init_im_rec = None
+        self.initial_mask = None
+
+
+
+    def parChanged(self, model_changed=True):
+        """
+        if model parameter changed the user needs to run the algorithm again
+        :param model_changed:
+        :return:
+        """
+        self.initial_mask = None
+        if model_changed:
+            ci = self.comboBox_models.currentIndex()
+            if ci == 0:
+                self.max_iter.setValue(50)
+
+            elif ci == 1:
+                self.max_iter.setValue(50)
+            elif ci == 2:
+                self.max_iter.setValue(1)
+            else:
+                return
+
+
+
+    def clear(self):
+        # store the image
+        self.img = None
+        self.shape = None  # 3D shape
+        self.mask = None
+        self.im_rec = None
+        self.initial_mask = None
+        self.init_im_rec = None
+
+    def retranslateUi(self, Dialog):
+        _translate = QtCore.QCoreApplication.translate
+        Dialog.setWindowTitle(_translate("Dialog", "Tissue Segmetnation"))
+        self.checkBox.setText(_translate("Dialog", "Advanced"))
+        self.comboBox_image.setItemText(0, _translate("Dialog", "View 1"))
+        self.comboBox_image.setItemText(1, _translate("Dialog", "View 2"))
+        #self.spinbox_num_tissue.setItemText(0, _translate("Dialog", "Ultrasound"))
+        #self.spinbox_num_tissue.setItemText(1, _translate("Dialog", "MRI"))
+        self.comboBox_models.setItemText(0, _translate("Dialog", "esFCM"))
+        self.comboBox_models.setItemText(1, _translate("Dialog", "FCM"))
+        self.comboBox_models.setItemText(2, _translate("Dialog", "GMM"))
+
+
+        self.pushButton.setText(_translate("Dialog", "Apply"))
+
+        self.checkbox_post.setText(_translate("Dialog", "PostCorr."))
+        # self.checkbox_bone.setText(_translate("Dialog", "Remove extra bone"))
+
+        self.label.setText(_translate("Dialog", "No. Iteration"))
+        self.label_type.setText(_translate("Dialog", "Image type"))
+
+        # self.label_pma.setText(_translate("Dialog", "Border Pixels"))
+
+
+    def closeEvent(self, a0: QtGui.QCloseEvent) -> None:
+        self.closeSig.emit()
+        super(Tissue_Seg, self).closeEvent(a0)
+
+    def accepted_emit(self):
+        if not hasattr(self, 'initial_mask'):
+            return
+        try:
+            self.label_pr.setVisible(True)
+            self.label_pr.setText('Initialization...')
+
+
+            self.progressBar.setValue(5)
+            self._progress = 5
+
+            if self.initial_mask is None:
+                self.mask = self.initialization()
+
+
+
+
+            """
+            a = self.initial_mask.get_fdata().copy()
+            a *= self.mask
+            from melage.utils.utils import standardize
+            a = standardize(-a, 20)
+            a[self.mask==0] = -1
+            a = nib.Nifti1Image(a, self.initial_mask.affine, self.initial_mask.header)
+            a.to_filename('/home/binibica/eco/172_X_20210325_seg0.nii.gz')
+            """
+
+            self.im_seg = nib.Nifti1Image(self.mask, self.img.affine, self.img.header)
+            self.progressBar.setValue(98)
+            self.label_pr.setVisible(False)
+            self._progress = 100
+            self.progressBar.setValue(self._progress)
+            self._progress = 0
+            self.betcomp.emit(True)
+
+        except Exception as e:
+            print(e)
+            self.screen_error_msgbox(e.args[0])
+
+    def screen_error_msgbox(self, text=None):
+        if text is None:
+            text = 'There is an error. Screen is not captured. Please check the content.'
+        MessageBox = QtWidgets.QMessageBox(self)
+        MessageBox.setText(str(text))
+        MessageBox.setWindowTitle('Warning')
+        MessageBox.show()
+        self.progressBar.setValue(0)
+
+    def initialization(self):
+        ci = self.comboBox_models.currentIndex()
+        use_ssim = True
+        equalize = False
+        padding = 0
+        image_range = 1000
+        tissue_labels = None
+        num_tissues = self.spinbox_num_tissue.value()
+        fuzziness = 3
+        post_correction = self.checkbox_post.isChecked()
+        constraint = False
+        InitMethod = 'otsu'
+        if num_tissues>3 and not constraint:
+            post_correction = False
+            InitMethod = "kmeans"
+
+        epsilon = 5e-3
+        max_iter = self.max_iter.value()
+        image_used, pad_zero = remove_zero(self.img.get_fdata(), 0)
+        if ci == 0:
+            from melage.widgets.Segmentation.FCM import esFCM
+
+
+            model = esFCM(image_used, self.img.affine,
+                          image_range, num_tissues, fuzziness,
+                          epsilon=epsilon, max_iter=max_iter,
+                          padding=padding,
+                          tissuelabels=tissue_labels,
+                          mask=image_used>0, use_ssim=use_ssim)
+            try:
+                model.initialize_fcm(initialization_method=InitMethod)
+            except:
+                model.initialize_fcm(initialization_method='kmeans')
+
+            model.fit(self.progressBar)
+            seg1 = model.predict(use_softmax=True).astype('int')
+            seg_init2 = np.zeros(self.img.shape)
+            seg_init2[pad_zero[0][0]:pad_zero[0][1] + 1, pad_zero[1][0]:pad_zero[1][1] + 1,
+            pad_zero[2][0]:pad_zero[2][1] + 1] = seg1
+            return seg_init2
+
+        elif ci == 1:
+            from melage.widgets.Segmentation.FCM import FCM_pure as FCM
+            model = FCM(image_used, self.img.affine, None,
+                          image_range, num_tissues, fuzziness,
+                          epsilon=epsilon, max_iter=max_iter,
+                          padding=padding, constraint=False, post_correction=True, mask =image_used>0)
+            try:
+                model.initialize_fcm(initialization_method=InitMethod)
+            except:
+                model.initialize_fcm(initialization_method='kmeans')
+            model.fit(self.progressBar)
+            seg1 = model.predict(use_softmax=True).astype('int')
+            seg_init2 = np.zeros(self.img.shape)
+            seg_init2[pad_zero[0][0]:pad_zero[0][1] + 1, pad_zero[1][0]:pad_zero[1][1] + 1,
+            pad_zero[2][0]:pad_zero[2][1] + 1] = seg1
+            return seg_init2
+        elif ci == 2:
+            self.max_iter.setValue(1)
+        else:
+            return
+
+    def compute_mask(self, mask):
+        """
+        Convert surface mesh to volume
+        """
+        threshold = self.max_iter.value()
+        try:
+            import surfa as sf
+            if type(mask) == sf.image.framed.Volume:
+                label = mask.copy()
+                label = (label < threshold).connected_component_mask(k=1, fill=True)
+                return label.data.astype('int')
+        except:
+            pass
+
+        # from nibabel.processing import resample_from_to
+        from skimage.measure import label as label_connector
+        from scipy.ndimage import binary_fill_holes
+
+        im_mask = mask.get_fdata().copy()
+        # from utils.utils import Threshold_MultiOtsu
+
+        ind = im_mask >= threshold
+        im_mask[ind] = 0
+        im_mask[~ind] = 1
+        """
+
+        if self.checkbox_bone.isChecked():
+            A = self.img.get_fdata() * im_mask
+            thresholds = Threshold_MultiOtsu(A, 5)
+            im_mask[A > thresholds[-1]] = 0
+        """
+        # label correction
+        label_correction = False
+
+        labels = im_mask
+        labels = binary_fill_holes(labels)
+        labels, labels_freq = LargestCC(labels, connectivity=1)
+        argmax = np.argmax(
+            [self.img.get_fdata()[labels == el].sum() for el in range(len(labels_freq)) if el != 0]) + 1
+        # connectivity = 1
+        # labels = label_connector(labels, connectivity=connectivity)
+        # labels[labels>1]=1
+        # frequency = np.bincount(labels.flat)
+        # argmax = [el for el in np.argsort(-frequency) if el != 0][0]
+        # argmax = np.argmax([self.img.get_fdata()[labels == el].sum() for el in range(len(frequency)) if el != 0]) + 1
+        ind = labels != argmax
+        labels[ind] = 0
+        labels[~ind] = 1
+
+        if label_correction:
+            connectivity = 1
+            labels = label_connector(im_mask, connectivity=connectivity)
+            # labels[labels>1]=1
+            frequency = np.bincount(labels.flat)
+            # argmax = [el for el in np.argsort(-frequency) if el != 0][0]
+            argmax = np.argmax(
+                [self.img.get_fdata()[labels == el].sum() for el in range(len(frequency)) if el != 0]) + 1
+            ind = labels != argmax
+            labels[ind] = 0
+            # labels[~ind]=0
+            labels = binary_fill_holes(labels)
+            for slc in range(labels.shape[0]):
+                im = labels[slc, :, :]
+                if im.max() == 0:
+                    continue
+                labels[slc, :, :] = binary_fill_holes(im)
+            for slc in range(labels.shape[1]):
+                im = labels[:, slc, :]
+                if im.max() == 0:
+                    continue
+                labels[:, slc, :] = binary_fill_holes(im)
+
+            for slc in range(labels.shape[2]):
+                im = labels[:, :, slc]
+                if im.max() == 0:
+                    continue
+
+                lbl = label_connector(im, connectivity=connectivity)
+                frequency = np.bincount(lbl.flat)
+                argmax = [el for el in np.argsort(-frequency) if el != 0][0]
+                ind_remove = frequency < 0.1 * frequency[argmax]
+                if ind_remove.any():
+                    index_remove = np.argwhere(ind_remove)
+                    for el in index_remove:
+                        ind = lbl == el
+                        lbl[ind] = 0
+                    lbl[lbl > 0] = 1
+                else:
+                    continue
+                labels[:, :, slc] = lbl.copy()
+
+            for slc in range(labels.shape[2]):
+                im = labels[:, :, slc]
+                if im.max() == 0:
+                    continue
+                labels[:, :, slc] = binary_fill_holes(im)
+
+        return labels.astype('int')
+
+
+def run():
+    import sys
+    app = QtWidgets.QApplication(sys.argv)
+    file = 't1_withoutmask.nii.gz'
+    import nibabel as nib
+    # m = nib.load(file)
+    # res = m.header["pixdim"][1]
+    # nibf = m.get_fdata()
+    from melage.utils.utils import normalize_mri
+    # nibf = standardize(nibf)
+    window = Tissue_Seg()
+    # window.setData(m, res)
+    window.set_pars()
+    window.show()
+    sys.exit(app.exec_())
+
+
+if __name__ == '__main__':
+    run()
+