melage 0.0.65__py3-none-any.whl → 1.0.0__py3-none-any.whl

melage/widgets/Segmentation/__init__.py

@@ -1,588 +0,0 @@
-__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()
-