diff --git a/GUI_main.py b/GUI_main.py
index 6732a302fd755097e2872cfaac2316f4bec662da..d93825e4dff3def1751c40a2725ce68bcdfaff52 100644
--- a/GUI_main.py
+++ b/GUI_main.py
@@ -150,7 +150,8 @@ class App(QMainWindow):
def __init__(self, nd2pathstr, hdfpathstr, newhdfstr):
super().__init__()
# initializes the window
-
+# set a title to the window
+ self.title = 'YeaZ 1.0'
# id is an integer that gives the id of the connection between the mouseclick method
# and the activation of the button.
@@ -166,7 +167,7 @@ class App(QMainWindow):
# it calls an object of the class Load Image from the InteractionDisk
-# file which is used to load images and masks from the nd2 file. To
+# file which is used to load images and masks from the nd2 file or tiff files. To
# initialize this object it needs the path of the nd2 file, of an
# existing hdf file and the name of a new hdf file. If the user has no
# hdf file yet the hdfpathstr will be empty and vice versa if the user
@@ -273,7 +274,7 @@ class App(QMainWindow):
self.button_segment = QCheckBox('Segment')
self.buttonlist.append(self.button_segment)
- self.button_cellcorespondance = QPushButton('Cell Correspondance')
+ self.button_cellcorespondance = QPushButton('Tracking')
self.buttonlist.append(self.button_cellcorespondance)
self.button_changecellvalue = QPushButton('Change cell value')
@@ -282,6 +283,9 @@ class App(QMainWindow):
self.button_extractfluorescence = QPushButton('Extract Fluorescence')
self.buttonlist.append(self.button_extractfluorescence)
+ self.button_hide_show = QPushButton('CNN')
+ self.buttonlist.append(self.button_hide_show)
+
self.initUI()
@@ -817,8 +821,43 @@ class App(QMainWindow):
# clear the message shown in the status bar
self.statusBar.clearMessage()
+
+ def ShowHideCNNbuttons(self):
+
+ """hide and show the buttons corresponding to the neural network.
+ this function is called by the button CNN which is hidden. But
+ if activated in the InitLayout.py then you can have a button
+ which hides the CNN buttons (which are now on the normal also
+ hidden...).
+ """
+
+
+ if self.button_hide_show.isChecked():
+
+
+ self.button_cnn.setVisible(True)
+ self.button_segment.setVisible(True)
+ self.button_savesegmask.setVisible(True)
+ self.button_threshold.setVisible(True)
+ self.button_SetThreshold.setVisible(True)
+ self.button_savethresholdmask.setVisible(True)
+ self.button_SetSegmentation.setVisible(True)
+
+
+ else:
+
+
+ self.button_cnn.setVisible(False)
+ self.button_segment.setVisible(False)
+ self.button_savesegmask.setVisible(False)
+ self.button_threshold.setVisible(False)
+ self.button_SetThreshold.setVisible(False)
+ self.button_savethresholdmask.setVisible(False)
+ self.button_SetSegmentation.setVisible(False)
+
+
def LaunchBatchPrediction(self):
"""This function is called whenever the button Launch CNN is pressed.
It allows to run the neural network over a time range and selected
@@ -882,10 +921,27 @@ class App(QMainWindow):
seg_val = 10
self.PredThreshSeg(t, dlg.listfov.row(item), thr_val, seg_val)
-
-
- #once it has iterated over all the fov, the message in
- #the status bar is cleared and the buttons are enabled.
+
+ # if tracker has been checked then apply it
+
+ if dlg.tracking_checkbox.isChecked():
+
+ if t != 0:
+
+ temp_mask,_ = self.reader.CellCorrespondance(t,dlg.listfov.row(item))
+ self.reader.SaveMask(t,dlg.listfov.row(item), temp_mask)
+
+ else:
+
+ temp_mask = self.reader.LoadSeg(t, dlg.listfov.row(item))
+ self.reader.SaveMask(t,dlg.listfov.row(item), temp_mask)
+
+
+
+ self.ReloadThreeMasks()
+
+ #once it has iterated over all the fov, the message in
+ #the status bar is cleared and the buttons are enabled.
self.statusBar.clearMessage()
self.EnableCNNButtons()
@@ -1159,10 +1215,86 @@ class App(QMainWindow):
# enables the neural network buttons if there is already an
# existing prediction for the current image.
self.EnableCNNButtons()
+
+
+
+ def ReloadThreeMasks(self):
+ """
+ A function which replots all the masks at the current time and fov
+ indices. Needed after the batch prediction is completed to display
+ the result of the NN.
+ """
+
+
+ if self.Tindex >= 0 and self.Tindex <= self.reader.sizet-1:
+
+
+ if self.Tindex == 0:
+ self.button_nextframe.setEnabled(True)
+
+ self.m.nextplotmask = self.reader.LoadMask(self.Tindex+1, self.FOVindex)
+
+ self.m.plotmask = self.reader.LoadMask(self.Tindex, self.FOVindex)
+
+
+ self.m.prevplotmask = np.zeros([self.reader.sizey, self.reader.sizex], dtype = np.uint16)
+
+
+ self.m.UpdateBckgrndPicture()
+ self.button_previousframe.setEnabled(False)
+
+
+ elif self.Tindex == self.reader.sizet-1:
+ self.button_previousframe.setEnabled(True)
+
+ self.m.prevplotmask = self.reader.LoadMask(self.Tindex-1, self.FOVindex)
+
+
+ self.m.plotmask = self.reader.LoadMask(self.Tindex, self.FOVindex)
+
+
+
+ self.m.nextplotmask = np.zeros([self.reader.sizey, self.reader.sizex], dtype = np.uint16)
+
+ self.m.UpdateBckgrndPicture()
+ self.button_nextframe.setEnabled(False)
+
+
+ else:
+
+ self.button_nextframe.setEnabled(True)
+ self.button_previousframe.setEnabled(True)
+
+ self.m.prevplotmask = self.reader.LoadMask(self.Tindex-1, self.FOVindex)
+
+
+ self.m.plotmask = self.reader.LoadMask(self.Tindex, self.FOVindex)
+
+
+ self.m.nextplotmask = self.reader.LoadMask(self.Tindex+1, self.FOVindex)
+
+ self.m.UpdateBckgrndPicture()
+
+ self.UpdateTitleSubplots()
+
+ if self.button_showval.isChecked():
+ self.m.ShowCellNumbersCurr()
+ self.m.ShowCellNumbersNext()
+ self.m.ShowCellNumbersPrev()
+
+ if self.button_hidemask.isChecked():
+ self.m.HideMask()
+ self.EnableCNNButtons()
+
+ else:
+
+ return
+
+
def ChangeTimeFrame(self):
- """This funcion is called whenever the user gives an new time index,
- to jump to the new given index, onces "enter" button is pressed.
+ """This funcion is called whenever the user gives a new time index,
+ to jump to the new given index, once "enter" button is pressed.
"""
# it reads out the text in the button and converts it to an int.
@@ -1221,6 +1353,7 @@ class App(QMainWindow):
self.UpdateTitleSubplots()
self.button_timeindex.clearFocus()
+ self.button_timeindex.setText(str(self.Tindex)+'/'+str(self.reader.sizet-1))
if self.button_showval.isChecked():
self.m.ShowCellNumbersCurr()
@@ -1235,16 +1368,7 @@ class App(QMainWindow):
self.button_timeindex.clearFocus()
return
-# def keyPressEvent(self, event):
-## print('keypressevengda211111')
-## print(event.key())
-# if not self.button_nextframe.isChecked() and event.key() == Qt.Key_Right:
-# self.button_nextframe.setChecked(True)
-# self.ForwardTime()
-# self.button_nextframe.setChecked(False)
-# else:
-# print('inside keypressevent')
-# event.ignore()
+
def CellCorrespActivation(self):
self.Disable(self.button_cellcorespondance)
@@ -1506,7 +1630,7 @@ class App(QMainWindow):
self.statusBar.clearMessage()
# if self.Tindex < self.reader.sizet - 1 :
# self.button_nextframe.setEnabled(True)
- self.button_timeindex.setText(str(self.Tindex))
+ self.button_timeindex.setText(str(self.Tindex)+'/'+str(self.reader.sizet-1))
def BackwardTime(self):
@@ -1588,7 +1712,7 @@ class App(QMainWindow):
# self.button_previousframe.setChecked(False)
self.statusBar.clearMessage()
- self.button_timeindex.setText(str(self.Tindex))
+ self.button_timeindex.setText(str(self.Tindex)+'/' + str(self.reader.sizet-1))
def MouseDraw(self):
@@ -1939,7 +2063,14 @@ class PlotCanvas(FigureCanvas):
# define three subplots corresponding to the previous, current and next
# time index.
fig, (self.ax2, self.ax, self.ax3) = plt.subplots(1,3, sharex = True, sharey = True)
-
+
+ # self.ax2.axis('tight')
+ # self.ax.axis('tight')
+ # self.ax3.axis('tight')
+
+ # plt.gca().xaxis.set_major_locator(plt.NullLocator())
+ # plt.gca().yaxis.set_major_locator(plt.NullLocator())
+ fig.subplots_adjust(bottom=0, top=1, left=0, right=1, wspace = 0.05, hspace = 0.05)
FigureCanvas.__init__(self, fig)
self.setParent(parent)