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

melage/{widgets/brain_extraction.py → plugins/bet/main/BET.py}

@@ -6,26 +6,18 @@ __AUTHOR__ = 'Bahram Jafrasteh'
 import os
 import warnings
 import numpy as np
-import nibabel as nib
 import trimesh
 from numba import jit, prange
-from PyQt5 import QtCore, QtGui, QtWidgets
-
 from numba.typed import List
-from melage.utils.brain_extraction_helper import sphere, closest_integer_point, bresenham3d, l2norm, l2normarray, diagonal_dot
+from .utils import sphere, closest_integer_point, bresenham3d, l2norm, l2normarray, diagonal_dot
+
 
-from PyQt5.QtCore import pyqtSignal
-import sys
-from PyQt5.QtWidgets import QDialog, QApplication, QPushButton, QVBoxLayout
-from PyQt5.QtCore import Qt
 
 def to_str(val):
     return '{:.2f}'.format(val)
 
-class BET(QDialog):
-    closeSig = pyqtSignal()
-    betcomp = pyqtSignal()
-    datachange = pyqtSignal()
+class BET:
+
 
     """
     https://github.com/vanandrew/brainextractor
@@ -35,17 +27,23 @@ Smith SM. Fast robust automated brain extraction. Hum Brain Mapp.
     This class takes in a Nifti1Image class and generates
     the brain surface and mask.
     """
-    def __init__(self, parent=None
-                 ):
-        super(BET, self).__init__(parent)
-
-
+    def __init__(self, img=None,
+                 res=None):
         """
         Initialization of Brain Extractor
 
-        Computes image range/thresholds and
-        estimates the brain radius
         """
+        self.res = res
+        # store the image
+        self.img = img
+
+        # store conveinent references
+        self.data = img  # 3D data
+        self.rdata = img.ravel()  # flattened data
+        self.shape = img.shape  # 3D shape
+        self.rshape = np.multiply.reduce(img.shape)  # flattened shape
+        self._progress = 5
+
     def set_pars(self, t02t: float = 0.02,
                  t98t: float = 0.98,
                  bt: float = 0.5,
@@ -67,40 +65,11 @@ Smith SM. Fast robust automated brain extraction. Hum Brain Mapp.
         self.n_iter = n_iter
         # get image resolution
         # store brain extraction parameters
-        self.setupUi()
-    def setData(self, img, res):
-        self.res = res
-        # store the image
-        self.img = img
 
-        # store conveinent references
-        self.data = img # 3D data
-        self.rdata = img.ravel()  # flattened data
-        self.shape = img.shape  # 3D shape
-        self.rshape = np.multiply.reduce(img.shape)  # flattened shape
 
-    def get_params(self):
-        state = self.checkbox_thresholding.isChecked()
-        if state:
-            from melage.utils.utils import Threshold_MultiOtsu
-            numc = int(self.histogram_threshold_min.value())
-            thresholds = Threshold_MultiOtsu(self.img, numc)
-            t02t = thresholds[0]
-            t98t = thresholds[-1]
-        else:
-            t02t = self.histogram_threshold_min.value()/100
-            t98t = self.histogram_threshold_max.value()/100
-
-
-        bt = self.fractional_threshold.value()/100
-        d1 = self.search_distance_max.value()
-        d2 = self.search_distance_min.value()
-        rmin = self.radcurv_min.value()
-        rmax = self.radcurv_max.value()
-        n_iter = self.iteration.value()
-        return [t02t, t98t, bt, d1, d2, rmin, rmax,n_iter]
-    def update_params(self):
-        [t02t, t98t, bt, d1, d2, rmin, rmax,n_iter] = self.get_params()
+
+    def update_params(self, info, state):
+        [t02t, t98t, bt, d1, d2, rmin, rmax,n_iter] = info
         # store brain extraction parameters
         #print("Parameters: bt=%f, d1=%f, d2=%f, rmin=%f, rmax=%f" % (bt, d1, d2, rmin, rmax))
         self.bt = bt
@@ -118,7 +87,7 @@ Smith SM. Fast robust automated brain extraction. Hum Brain Mapp.
         # get thresholds from histogram
         sorted_data = np.sort(self.rdata)
         self.tmin = np.min(sorted_data)
-        state = self.checkbox_thresholding.isChecked()
+
         if state:
             self.t2 = t02t
             self.t98 = t98t
@@ -129,230 +98,12 @@ Smith SM. Fast robust automated brain extraction. Hum Brain Mapp.
         self.t = (self.t98 - self.t2) * 0.1 + self.t2 #brain/background threshold
         #print("tmin: %f, t2: %f, t: %f, t98: %f, tmax: %f" % (self.tmin, self.t2, self.t, self.t98, self.tmax))
 
-    def activate_advanced(self, value):
-        self.widget.setEnabled(value)
-
-    def setupUi(self):
-        Dialog = self.window()
-        Dialog.setObjectName("N4")
-        Dialog.resize(310, 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")
-        self.comboBox_image.addItem("")
-        self.comboBox_image.addItem("")
-        self.comboBox_image.currentIndexChanged.connect(self.datachange)
-        self.hbox.addWidget(self.comboBox_image, 1)
-        self.pushButton = QtWidgets.QPushButton()
-
-        self.pushButton.setObjectName("pushButton")
-        self.pushButton.pressed.connect(self.accepted_emit)
-
-        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.hbox2.addWidget(self.pushButton, 0)
-
-
-        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.label_2 = QtWidgets.QLabel(self.splitter_3)
-        self.label_2.setAlignment(QtCore.Qt.AlignCenter)
-        self.label_2.setObjectName("label_2")
-        self.iteration = QtWidgets.QSpinBox(self.splitter_3)
-        self.iteration.setObjectName("iteration")
-
-        self.iteration.setMaximum(10000)
-        self.iteration.setMinimum(1)
-        self.iteration.setValue(self.n_iter)
-        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_thresholding = QtWidgets.QCheckBox(self.splitter)
-        #self.checkbox_thresholding.setAlignment(QtCore.Qt.AlignCenter)
-        self.checkbox_thresholding.setObjectName("checkbox_thresholding")
-        self.checkbox_thresholding.setChecked(True)
-        self.checkbox_thresholding.stateChanged.connect(self.change_hist_threshold)
-
-        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.fractional_threshold = QtWidgets.QDoubleSpinBox(self.splitter_2)
-        self.fractional_threshold.setObjectName("fractional_threshold")
-        self.fractional_threshold.setValue((self.ft) * 100)
-        self.fractional_threshold.setMaximum(100)
-        self.fractional_threshold.setMinimum(0)
-        self.gridLayout.addWidget(self.splitter_2, 2, 0, 1, 1)
-        self.splitter_4 = QtWidgets.QSplitter(self.widget)
-        self.splitter_4.setOrientation(QtCore.Qt.Horizontal)
-        self.splitter_4.setObjectName("splitter_4")
-        self.label_4 = QtWidgets.QLabel(self.splitter_4)
-        self.label_4.setAlignment(QtCore.Qt.AlignCenter)
-        self.label_4.setObjectName("label_4")
-        self.search_distance_min = QtWidgets.QDoubleSpinBox(self.splitter_4)
-        self.search_distance_min.setObjectName("search_distance_min")
-        self.search_distance_min.setValue(self.sd_min)
-        self.search_distance_min.setMaximum(10000)
-        self.search_distance_min.setMinimum(0)
-        self.search_distance_max = QtWidgets.QDoubleSpinBox(self.splitter_4)
-        self.search_distance_max.setObjectName("search_distance_max")
-        self.search_distance_max.setValue(self.sd_max)
-        self.search_distance_max.setMaximum(10000)
-        self.search_distance_max.setMinimum(0)
-        self.gridLayout.addWidget(self.splitter_4, 3, 0, 1, 1)
-        self.splitter_5 = QtWidgets.QSplitter(self.widget)
-        self.splitter_5.setOrientation(QtCore.Qt.Horizontal)
-        self.splitter_5.setObjectName("splitter_5")
-        self.label_5 = QtWidgets.QLabel(self.splitter_5)
-        self.label_5.setAlignment(QtCore.Qt.AlignCenter)
-        self.label_5.setObjectName("label_5")
-        self.radcurv_min = QtWidgets.QDoubleSpinBox(self.splitter_5)
-        self.radcurv_min.setObjectName("radcurv_min")
-        self.radcurv_min.setValue(self.r_min)
-        self.radcurv_min.setMaximum(10000)
-        self.radcurv_min.setMinimum(0)
-        self.radcurv_max = QtWidgets.QDoubleSpinBox(self.splitter_5)
-        self.radcurv_max.setObjectName("radcurv_max")
-        self.radcurv_max.setValue(self.r_max)
-        self.radcurv_max.setMaximum(10000)
-        self.radcurv_max.setMinimum(0)
-        self.widget.setEnabled(False)
-        self.gridLayout.addWidget(self.splitter_5, 4, 0, 1, 1)
-
-        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 change_hist_threshold(self, val):
-        value = not val
-        if not val:
-            self.histogram_threshold_max.setEnabled(value)
-            self.histogram_threshold_min.setMaximum(100)
-            self.histogram_threshold_min.setMinimum(0)
-            self.histogram_threshold_min.setValue(2)
-        else:
-            self.histogram_threshold_max.setEnabled(value)
-            vl = self.histogram_threshold_min.value()
-            if vl>10:
-                self.histogram_threshold_min.setValue(10)
-            elif vl<4:
-                self.histogram_threshold_min.setValue(6)
-            self.histogram_threshold_min.setMaximum(10)
-            self.histogram_threshold_min.setMinimum(4)
-
-
-    def clear(self):
-        self.res = None
-        # store the image
-        self.img = None
 
-        # store conveinent references
-        self.data = None # 3D data
-        self.rdata = None  # flattened data
-        self.shape = None  # 3D shape
-        self.rshape = None  # flattened shape
-        self.mask = None
-
-    def retranslateUi(self, Dialog):
-        _translate = QtCore.QCoreApplication.translate
-        Dialog.setWindowTitle(_translate("Dialog", "BET"))
-        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.pushButton.setText(_translate("Dialog", "Apply"))
-        self.label_2.setText(_translate("Dialog", "Iterations"))
-        self.checkbox_thresholding.setText(_translate("Dialog", "Adaptive Thresholding"))
-        self.label.setText(_translate("Dialog", "Fractional Threshold"))
-        self.label_4.setText(_translate("Dialog", "Search Distance (mm)"))
-        self.label_5.setText(_translate("Dialog", "Radius of curvature"))
-
-    def closeEvent(self, a0: QtGui.QCloseEvent) -> None:
-        self.closeSig.emit()
-        super(BET, self).closeEvent(a0)
-
-    def accepted_emit(self):
-        try:
-            self.label_pr.setVisible(True)
-            self.label_pr.setText('Initialization...')
-            self.progressBar.setValue(0)
-            self.update_params()
-            self.progressBar.setValue(5)
-            self._progress = 5
-            self.initialization()
-            self.label_pr.setText('preparation...')
-            self.run()
-            self.progressBar.setValue(98)
-            self.label_pr.setText('Computing mask...')
-            self.mask = self.compute_mask()
-            self.label_pr.setVisible(False)
-            self._progress = 100
-            self.progressBar.setValue(self._progress)
-            self._progress =0
-            self.betcomp.emit()
-        except Exception as e:
-            print(e)
-
-    def initialization(self):
+
+
+    def initialization(self, progressBar, lbl_status):
         pv = self._progress
-        self.progressBar.setValue(pv+1)
+        progressBar.setValue(pv+1)
         # find the center of mass of image
         ic, jc, kc = np.meshgrid(
             np.arange(self.shape[0]), np.arange(self.shape[1]), np.arange(self.shape[2]), indexing="ij", copy=False
@@ -375,7 +126,7 @@ Smith SM. Fast robust automated brain extraction. Hum Brain Mapp.
 
         # generate initial surface
         #print("Initializing surface...")
-        self.label_pr.setText('Initializing surface...')
+        lbl_status.setText('Initializing surface...')
         self.surface = trimesh.creation.icosphere(subdivisions=4, radius=self.r)
         self.surface = self.surface.apply_transform([[1, 0, 0, ci], [0, 1, 0, cj], [0, 0, 1, ck], [0, 0, 0, 1]])
 
@@ -387,7 +138,7 @@ Smith SM. Fast robust automated brain extraction. Hum Brain Mapp.
         self.vertex_neighbors_idx = List([np.array(i) for i in self.surface.vertex_neighbors])
         # compute location of vertices in face array
         self.face_vertex_idxs = np.zeros((self.num_vertices, 6, 2), dtype=np.int32)
-        self.progressBar.setValue(pv+4)
+        progressBar.setValue(pv+4)
         for v in range(self.num_vertices):
             f, i = np.asarray(self.faces == v).nonzero()
             self.face_vertex_idxs[v, : i.shape[0], 0] = f
@@ -395,13 +146,13 @@ Smith SM. Fast robust automated brain extraction. Hum Brain Mapp.
             if i.shape[0] == 5:
                 self.face_vertex_idxs[v, 5, 0] = -1
                 self.face_vertex_idxs[v, 5, 1] = -1
-        self.progressBar.setValue(pv + 7)
+        progressBar.setValue(pv + 7)
         self._progress += 12
-        self.update_surface_attributes()
-        #print("Brain extractor initialization complete!")
+        self.update_surface_attributes(progressBar)
+        print("Brain extractor initialization complete!")
 
     @staticmethod
-    @jit(nopython=True, cache=True)
+    #@jit(nopython=True, cache=True)
     def compute_face_normals(num_faces, faces, vertices):
         """
         Compute face normals
@@ -473,11 +224,11 @@ Smith SM. Fast robust automated brain extraction. Hum Brain Mapp.
             vertex_normals[vertex_idx] /= l2norm(vertex_normals[vertex_idx])
         return vertex_normals
 
-    def rebuild_surface(self):
+    def rebuild_surface(self, progressBar):
         """
         Rebuilds the surface mesh for given updated vertices
         """
-        self.update_surface_attributes()
+        self.update_surface_attributes(progressBar)
         self.surface = trimesh.Trimesh(vertices=self.vertices, faces=self.faces)
 
     @staticmethod
@@ -504,27 +255,27 @@ Smith SM. Fast robust automated brain extraction. Hum Brain Mapp.
         # return optimized surface attributes
         return neighbors, neighbors_size, centroids
 
-    def update_surface_attributes(self):
+    def update_surface_attributes(self, progressBar):
         """
         Updates attributes related to the surface
         """
         init = self._progress
-        self.progressBar.setValue(init+1)
+        progressBar.setValue(init+1)
         self.triangles = self.vertices[self.faces]
         self.face_normals = self.compute_face_normals(self.num_faces, self.faces, self.vertices)
-        self.progressBar.setValue(init+1)
+        progressBar.setValue(init+1)
         self.face_angles = self.compute_face_angles(self.triangles)
-        self.progressBar.setValue(init+1)
+        progressBar.setValue(init+1)
         self.vertex_normals = self.compute_vertex_normals(
             self.num_vertices, self.faces, self.face_normals, self.face_angles, self.face_vertex_idxs
         )
-        self.progressBar.setValue(init+1)
+        progressBar.setValue(init+1)
         self.vertex_neighbors, self.vertex_neighbors_size, self.vertex_neighbors_centroids = self.update_surf_attr(
             self.vertices, self.vertex_neighbors_idx
         )
-        self.progressBar.setValue(init+1)
+        progressBar.setValue(init+1)
         self.l = self.get_mean_intervertex_distance(self.vertices, self.vertex_neighbors, self.vertex_neighbors_size)
-        self.progressBar.setValue(init+1)
+        progressBar.setValue(init+1)
         self._progress += 6
     @staticmethod
     @jit(nopython=True, cache=True)
@@ -541,7 +292,7 @@ Smith SM. Fast robust automated brain extraction. Hum Brain Mapp.
             mivd[v] = np.mean(vd)
         return np.mean(mivd)
 
-    def run(self):
+    def run(self, progressBar, lbl_status):
         """
         Runs the extraction step.
 
@@ -567,14 +318,14 @@ Smith SM. Fast robust automated brain extraction. Hum Brain Mapp.
         u3 = np.zeros(self.vertices.shape)
         u = np.zeros(self.vertices.shape)
         pv = self._progress
-        self.progressBar.setValue(pv+1)
+        progressBar.setValue(pv+1)
         self._progress += 20
 
         # surface deformation loop
         for i in range(iterations):
             #print("Iteration: %d" % i, end="\r")
-            self.label_pr.setText('{}/{}'.format(i+1, iterations))
-            self.progressBar.setValue(self._progress)
+            lbl_status.setText('{}/{}'.format(i+1, iterations))
+            progressBar.setValue(self._progress)
 
             self._progress += 1
             if self._progress>100:
@@ -608,13 +359,13 @@ Smith SM. Fast robust automated brain extraction. Hum Brain Mapp.
             self.vertices += u
 
             # just update the surface attributes
-            self.update_surface_attributes()
+            self.update_surface_attributes(progressBar)
 
         self._progress = 90
-        self.progressBar.setValue(self._progress)
+        progressBar.setValue(self._progress)
         # update the surface
-        self.rebuild_surface()
-        self.label_pr.setText('Post Processing...')
+        self.rebuild_surface(progressBar)
+        lbl_status.setText('Post Processing...')
 
         #print("")
         #print("Complete.")
@@ -833,23 +584,7 @@ Smith SM. Fast robust automated brain extraction. Hum Brain Mapp.
         u3 = f3.reshape(-1,1) * normals
         # get displacement vector
         u[:, :] = u1 + u2 + u3
-def run():
-    import sys
-    app = QtWidgets.QApplication(sys.argv)
-    file = '/home/binibica/Paper_seg/results/prep/2_X_20180202_X_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 standardize
-    #nibf = standardize(nibf)
-    window = BET()
-    window.setData(nibf, res)
-    window.set_pars()
-    window.show()
-    sys.exit(app.exec_())
-
-if __name__ == '__main__':
-
-    run()
+
+
+