From 7d3fb94059f95430b0d893ef184483f527c1fe1b Mon Sep 17 00:00:00 2001
From: Farzaneh Labbaf <f.labbaf97@gmail.com>
Date: Thu, 23 Mar 2023 18:24:00 +0100
Subject: [PATCH] Change retrack button to retrack multiple frame with one
click
---
GUI_main.py | 51 +++++++++++++++++++++++++++++++++++++++++++-
init/InitButtons.py | 6 +++---
misc/BatchRetrack.py | 31 +++++++++++++++++++++++++++
3 files changed, 84 insertions(+), 4 deletions(-)
create mode 100644 misc/BatchRetrack.py
diff --git a/GUI_main.py b/GUI_main.py
index fc86fcf..2990a97 100644
--- a/GUI_main.py
+++ b/GUI_main.py
@@ -103,6 +103,9 @@ import ChangeOneCellValue as cocv
#a specific range of pictures.
import LaunchBatchPrediction as lbp
+#this file contains a dialog window where a time range can be selected to retrack
+import BatchRetrack as br
+
#this file initializes all the buttons present in the gui, sets the shortcuts
#to these buttons and also connect the buttons to the function that are
#triggered when the buttons are pressed.
@@ -968,7 +971,53 @@ class App(QMainWindow):
self.button_timeindex.clearFocus()
return
-
+ def BatchCellCorresp(self):
+ def reset():
+ self.ClearStatusBar()
+ self.Enable(self.button_cellcorrespondence)
+ self.button_cellcorrespondence.setChecked(False)
+
+ self.Disable(self.button_cellcorrespondence)
+ self.WriteStatusBar('retracking... ')
+
+ if(self.Tindex==self.reader.sizet-1):
+ QMessageBox.critical(self, "This is the last frame. Nothing to retrack after this")
+ reset()
+ return
+
+
+ # creates a dialog window from the BatchRetrack.py file
+ dlg = br.CustomDialog(self)
+
+ # this if tests if the user pressed 'ok' in the dialog window
+ if dlg.exec_() == QDialog.Accepted:
+ # it tests if the user has entered some values
+ if not (dlg.entry1.text()!= ''):
+ QMessageBox.critical(self, "Error", "No Time Specified")
+ reset()
+ return
+
+ # reads out the entry given by the user and converts the index
+ # to integers
+ time_value1 = int(dlg.entry1.text())
+
+ # it tests if the value is bigger than current frame
+ if (time_value1 < self.Tindex or time_value1 > self.reader.sizet-1):
+ QMessageBox.critical(self, "Error", 'Invalid Time Constraints')
+ reset()
+ return
+
+ for t in range(self.Tindex+1, time_value1+1):
+ log.debug('start correspondance for frame'.format(t))
+ #calls the cell correspondance for current time, t, and t+1
+ temp_mask = self.reader.CellCorrespondence(t, self.FOVindex)
+ self.reader.SaveMask(t, self.FOVindex, temp_mask)
+ log.debug('finish correspondance and savemask for frame'.format(t))
+
+ self.ReloadThreeMasks()
+ log.info('reload three frames')
+ reset()
+
def CellCorrespActivation(self):
self.Disable(self.button_cellcorrespondence)
self.WriteStatusBar('Doing the cell correspondence')
diff --git a/init/InitButtons.py b/init/InitButtons.py
index 60ab866..aed08a8 100644
--- a/init/InitButtons.py
+++ b/init/InitButtons.py
@@ -186,10 +186,10 @@ def Init(parent):
# MAKE THE CELL Correspondence
parent.button_cellcorrespondence.setEnabled(False)
parent.button_cellcorrespondence.setCheckable(True)
- parent.button_cellcorrespondence.clicked.connect(parent.CellCorrespActivation)
+ parent.button_cellcorrespondence.clicked.connect(parent.BatchCellCorresp)
parent.button_cellcorrespondence.setMaximumWidth(150)
- parent.button_cellcorrespondence.setStatusTip('Retrack cell ID numbers based on the previous frame.')
-
+ parent.button_cellcorrespondence.setStatusTip('Retrack cell ID numbers for next frame(s) or selected next frames based on this frame.')
+
# EXTRACT FLUORESCENCE IN DIFFERENT CHANNELS
parent.button_extractfluorescence.setEnabled(False)
parent.button_extractfluorescence.toggle()
diff --git a/misc/BatchRetrack.py b/misc/BatchRetrack.py
new file mode 100644
index 0000000..a52c810
--- /dev/null
+++ b/misc/BatchRetrack.py
@@ -0,0 +1,31 @@
+from PyQt5.QtWidgets import QApplication, QMainWindow, QMenu, QVBoxLayout, QSizePolicy, QMessageBox, QWidget, QPushButton, QShortcut, QComboBox, QDialog, QDialogButtonBox, QInputDialog, QLineEdit, QFormLayout, QLabel
+from PyQt5 import QtGui
+#from PyQt5.QtGui import QIcon, QKeySequence
+from PyQt5.QtCore import pyqtSignal, QObject, Qt
+#import PyQt package, allows for GUI interactions
+
+class CustomDialog(QDialog):
+
+ def __init__(self, *args, **kwargs):
+ super(CustomDialog, self).__init__(*args, **kwargs)
+ app, = args
+ self.setWindowTitle("Retrack")
+ self.setGeometry(100,100, 500,200)
+
+ self.entry1 = QLineEdit()
+ self.entry1.setValidator(QtGui.QIntValidator())
+ self.entry1.setMaxLength(4)
+ self.entry1.setAlignment(Qt.AlignRight)
+ self.labeltime = QLabel("Enter farme number between {} to {}".format(app.Tindex+1, app.reader.sizet-1))
+ flo = QFormLayout()
+ flo.addWidget(self.labeltime)
+ flo.addRow('retracking frames from {} (next frame) to '.format(app.Tindex+1), self.entry1)
+
+ QBtn = QDialogButtonBox.Ok | QDialogButtonBox.Cancel
+
+ self.buttonBox = QDialogButtonBox(QBtn)
+ self.buttonBox.accepted.connect(self.accept)
+ self.buttonBox.rejected.connect(self.reject)
+ flo.addWidget(self.buttonBox)
+ self.setLayout(flo)
+
\ No newline at end of file
--
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