Added a .json file to have centralised settings

if more than one script has to use them.

Author: wl-stepp

.gitignore

@@ -1,4 +1,4 @@
 __pycache__/
 *.pyc
-*.json
+settings.json
 *.pylintrc

ATS_settings.json

@@ -0,0 +1,18 @@
+{
+
+    "lebpc34": {
+        "imageFolder": "C:/Users/stepp/Documents/data_raw/SmartMito/",
+        "frameNumBinary": "C:/Users/stepp/Documents/data_raw/SmartMito/frameNum.dat",
+        "modelPath": "C:/Users/stepp/Documents/data_raw/SmartMito/model_Dora.h5",
+        "matlabPath": "C:/Users/stepp/Documents/data_raw/SmartMito/matlab_bin.dat"
+    },
+    "lebpc20": {
+        "imageFolder": "//lebnas1.epfl.ch/microsc125/Watchdog/",
+        "frameNumBinary": "E:/Watchdog/SmartMito/frameNum.dat",
+        "modelPath": "E:/Watchdog/SmartMito/model_Dora.h5",
+        "matlabPath": "//lebnas1.epfl.ch/microsc125/Watchdog/matlab_bin.dat"
+    },
+
+    "nnImageSize": 128
+
+}

NNGui.py

@@ -72,10 +72,10 @@ def __init__(self, app):
         self.loadBox = QGroupBox()
 
         # Connect the viewers
-        self.viewerOrig.vb.setXLink(self.viewerProc.vb)
-        self.viewerOrig.vb.setYLink(self.viewerProc.vb)
-        self.viewerNN.vb.setXLink(self.viewerProc.vb)
-        self.viewerNN.vb.setYLink(self.viewerProc.vb)
+        self.viewerOrig.viewBox.setXLink(self.viewerProc.viewBox)
+        self.viewerOrig.viewBox.setYLink(self.viewerProc.viewBox)
+        self.viewerNN.viewBox.setXLink(self.viewerProc.viewBox)
+        self.viewerNN.viewBox.setYLink(self.viewerProc.viewBox)
 
         # Slider and arrow buttons for frame traversal.
         self.sliderBox = QGroupBox()
@@ -97,7 +97,7 @@ def __init__(self, app):
 
         pen = pg.mkPen(color='#AAAAAA', style=Qt.DashLine)
         self.frameLine = pg.InfiniteLine(pos=0.5, angle=90, pen=pen)
-        self.outputPlot.pI.addItem(self.frameLine)
+        self.outputPlot.plotItem1.addItem(self.frameLine)
 
         # Connect functions to the interactive elements
         self.modelButton.clicked.connect(self.loadModel)
@@ -243,10 +243,10 @@ def loadData(self):
         # for x in range(N, len(outputData)):
         #     outputDataSmooth[x] = np.sum(outputData[x-N:x])/N
         self.app.processEvents()
+        self.outputPlot.deleteRects()
+        self.outputPlot.frames.setData([])
+        self.outputPlot.nnframeScatter.setData([])
         if self.mode == 'stack':
-            self.outputPlot.deleteRects()
-            self.outputPlot.frames.setData([])
-            self.outputPlot.nnframeScatter.setData([])
             self.outputPlot.nnline.setData(outputData)
             self.outputPlot.scatter.setData(range(0, len(outputData)), outputData)
         else:
@@ -262,7 +262,7 @@ def loadData(self):
         self.refreshGradients()
         self.onTimer()
         self.loadingStatusLabel.setText('Done')
-        self.viewerProc.vb.setRange(xRange=(0, postSize), yRange=(0, postSize))
+        self.viewerProc.viewBox.setRange(xRange=(0, postSize), yRange=(0, postSize))
 
     def loadModel(self):
         """ Load a .h5 model generated using Keras """

NNfeeder.py

@@ -7,9 +7,10 @@
 
 
 import numpy as np
-from imageTiles import getTilePositionsV2
 from skimage import exposure, filters, transform
 
+from ImageTiles import getTilePositionsV2
+
 
 def prepareNNImages(mitoFull, drpFull, nnImageSize=128):
     """Preprocess raw iSIM images before running them throught the neural network.

NetworkWatchdog.py

@@ -16,6 +16,7 @@
 """
 
 
+import json
 import os
 import re  # Regular expression module
 import sys
@@ -57,6 +58,10 @@ class NetworkWatchdog(QWidget):
 
     def __init__(self):
 
+        # Read settings from the json file depending on which computer we are on
+        with open('./ATS_settings.json') as file:
+            self.settings = json.load(file)[os.environ['COMPUTERNAME'].lower()]
+
         # Setting for the watchdogs
         patterns = ["*.tif"]
         ignorePatterns = ["*.txt", "*.tiff"]
@@ -67,11 +72,7 @@ def __init__(self):
 
         # Loading the NN model
         self.nnImageSize = 128
-        if os.environ['COMPUTERNAME'] == 'LEBPC20':
-            self.modelPath = 'E:/Watchdog/SmartMito/model_Dora.h5'
-        elif os.environ["COMPUTERNAME"] == 'LEBPC34':
-            self.modelPath = (
-                'C:/Users/stepp/Documents/data_raw/SmartMito/model_Dora.h5')
+        self.modelPath = self.settings['modelPath']
         self.model = keras.models.load_model(self.modelPath, compile=True)
         # Prep some structure to hold data
 
@@ -102,17 +103,18 @@ def __init__(self):
         self.linePen = pg.mkPen(color='#AAAAAA')
 
         # Assign the event handlers
-        myEventHandler.on_created = self.on_created
-        myEventHandler.on_deleted = self.on_deleted
-        myEventHandler.onModified = self.onModified
-        myEventHandler.onMoved = self.onMoved
+        myEventHandler.on_created = self.onCreated
+        myEventHandler.on_deleted = self.onDeleted
+        myEventHandler.on_modified = self.onModified
+        myEventHandler.on_moved = self.onMoved
         self.refreshGUI.connect(self.refreshViewBoxes)
         self.reinitGUI.connect(self.reinitializeViewBoxes)
-        self.viewerNN.vb.setXLink(self.viewerMerge.vb)
-        self.viewerNN.vb.setYLink(self.viewerMerge.vb)
+        self.viewerNN.viewBox.setXLink(self.viewerMerge.viewBox)
+        self.viewerNN.viewBox.setYLink(self.viewerMerge.viewBox)
 
         # More settings for the Watchdos
-        path = "//lebnas1.epfl.ch/microsc125/Watchdog/"
+        path = self.settings['imageFolder']
+        print('FOLDERFOLDERFOLDER', path)
         goRecursively = True
         self.myObserver = Observer()
         self.myObserver.schedule(
@@ -145,7 +147,7 @@ def __init__(self):
     def onCreated(self, event):
         """Do action when file is created in watchlocation"""
 
-    def ondeleted(self, event):
+    def onDeleted(self, event):
         """Do action when file is deleted in watchlocation"""
 
     def onModified(self, event):
@@ -169,8 +171,7 @@ def onModified(self, event):
             return
 
         # check framNumwrite.py output from the binary
-        file = open(os.path.join(
-            os.path.dirname(self.modelPath), 'binary_output.dat'), mode='rb')
+        file = open(os.path.join(self.settings['frameNumBinary']), mode='rb')
         content = file.read()
         file.close()
 
@@ -290,7 +291,7 @@ def onModified(self, event):
         self.outputX.append(timeX)  # (frameNum-1)/2)
 
         # Write output to binary for Matlab to read
-        writeBin(output, 0)
+        writeBin(output, printTime=0, path=self.settings['matlabPath'], filename='')
         # Write output to txt file for later
         file = open(txtFile, 'a')
         file.write('%d, %d\n' % (frameNum, output))
@@ -339,16 +340,17 @@ def reinitializeViewBoxes(self, inputSize):
         #     for line in viewer.lines:
         #         line.setPen(self.linePen)
         #         line.setZValue(100)
-        self.viewerMerge.vb.setRange(xRange=(0, inputSize), yRange=(0, inputSize))
+        self.viewerMerge.viewBox.setRange(xRange=(0, inputSize), yRange=(0, inputSize))
 
     def onMoved(self, event):
         """ start when a file was used in the watchlocation. Could be removed(?) """
 
-    def closeEvent(self):
+    def closeEvent(self, event):
         """ Terminate the watchdogs and clean up when the windows of the GUI is closed """
-        print('Watchdogs stopped')
+        print(event)
         self.myObserver.stop()
         self.myObserver.join()
+        print('Watchdogs stopped')
 
 
 def main():

SatsGUI.py

@@ -11,13 +11,12 @@
 from PyQt5.QtCore import Qt, pyqtSignal
 from PyQt5.QtWidgets import QApplication, QGridLayout, QWidget
 
-from nnIO import loadElapsedTime, loadiSIMmetadata, loadNNData
+from NNio import loadElapsedTime, loadiSIMmetadata, loadNNData
 
 # Adjust for different screen sizes
 QApplication.setAttribute(Qt.HighDpiScaleFactorRoundingPolicy.PassThrough)
 
 
-
 class RectItem(pg.GraphicsObject):
     """ Rectangle that can be added to a pg.ViewBox """
     def __init__(self, rect, color='#FFFFFF', parent=None):
@@ -234,5 +233,6 @@ def main():
 
     sys.exit(app.exec_())
 
+
 if __name__ == '__main__':
     main()

TestTifSaver.py

@@ -9,6 +9,7 @@
 """
 
 import glob
+import json
 import os
 import time
 
@@ -45,7 +46,6 @@ def main():
 
     inputData = dataPath + '180420_130.tif'
 
-
     mito = []
     drp = []
 
@@ -71,7 +71,11 @@ def main():
     print('Input : ', drp.shape)
     print('Input : ', np.shape(drp)[0])
 
-    nasPath = '//lebnas1.epfl.ch/microsc125/Watchdog/python_saver/'
+    with open('./ATS_settings.json') as file:
+        settings = json.load(file)[os.environ['COMPUTERNAME'].lower()]
+
+    nasPath = os.path.join(settings['imageFolder'], 'python_saver/')
+
     # Make new folder there as microManager would
     dirs = glob.glob(nasPath + '*/')
     if len(dirs) > 0:
@@ -93,10 +97,10 @@ def main():
 
         # First write mito then drp as watchdog waits for drp image
         io.imsave(mitoPath, mito[item, :, :].astype(np.uint16),
-                check_contrast=False)
+                  check_contrast=False)
         time.sleep(0.05)
         io.imsave(drpPath, drp[item, :, :].astype(np.uint16),
-                check_contrast=False)
+                  check_contrast=False)
         time2 = time.perf_counter()
         time.sleep(np.max([0, .3 - (time2 - time1)]))
         i = i + 1
@@ -112,10 +116,10 @@ def main():
         time.sleep(0.001)
     print('Done')
 
-
     del inputData
     del inputDataFilename1
     del inputDataFilename2
 
+
 if __name__ == '__main__':
     main()

binOutput.py

@@ -12,9 +12,6 @@
 import time
 from datetime import datetime
 
-if __name__ == "__main__":
-    main()
-
 
 def main():
     """ Use this to test a direct binary alternating value to the specified file. """
@@ -45,12 +42,15 @@ def main():
         print('done')
 
 
-def writeBin(output, printTime=0, path="//lebnas1.epfl.ch/microsc125/Watchdog/"):
+def writeBin(output, printTime=0, path="//lebnas1.epfl.ch/microsc125/Watchdog/",
+             filename='binary_output.dat'):
     """ Write a integer to a binary file that can be read by readBinNetwork.m from Matlab """
-    # Set the file location for the watched file here
-    # path = "//lebnas1.epfl.ch/microsc125/Watchdog/"
-    filename = 'binary_output.dat'
-    fullFileDir = ospath.join(path, filename)
+
+    if filename != '':
+        fullFileDir = ospath.join(path, filename)
+    else:
+        fullFileDir = path
+
     file = open(fullFileDir, 'wb')
     file.write(bytearray(output))
     file.close()
@@ -59,3 +59,7 @@ def writeBin(output, printTime=0, path="//lebnas1.epfl.ch/microsc125/Watchdog/")
         now = datetime.now()
         currentTime = now.strftime("%H:%M:%S.%f")
         print(f"{output} written at {currentTime}")
+
+
+if __name__ == "__main__":
+    main()

frameNumwrite.py

@@ -1,6 +1,7 @@
 """ Implements a class that is used to work together with NetworkWatchdog to skip files if it is
 to slow to process all the images. """
 
+import json
 import os
 import re
 import time
@@ -16,6 +17,9 @@ class FrameNumwrite():
     to enable NetworkWatchdog to skip the file if it is working on an older one. """
 
     def __init__(self):
+        with open('./ATS_settings.json') as file:
+            self.settings = json.load(file)[os.environ['COMPUTERNAME'].lower()]
+
         patterns = ["*.tif"]
         ignorePatterns = ["*.txt", "*.tiff"]
         ignoreDirectories = True
@@ -24,18 +28,14 @@ def __init__(self):
                                                      ignoreDirectories,
                                                      caseSensitive)
 
-        if os.environ['COMPUTERNAME'] == 'LEBPC20':
-            self.modelPath = 'E:/Watchdog/SmartMito/model_Dora.h5'
-        elif os.environ["COMPUTERNAME"] == 'LEBPC34':
-            self.modelPath = (
-                'C:/Users/stepp/Documents/data_raw/SmartMito/model_Dora.h5')
+        self.binaryPath = self.settings['frameNumBinary']
 
         self.frameNumOld = 100
 
         myEventHandler.on_deleted = self.onDeleted
         myEventHandler.on_created = self.onCreated
 
-        path = "//lebnas1.epfl.ch/microsc125/Watchdog/"
+        path = self.settings['imageFolder']
         goRecursively = True
         self.myObserver = Observer()
         self.myObserver.schedule(myEventHandler, path, recursive=goRecursively)
@@ -54,20 +54,16 @@ def onCreated(self, event):
             return
 
         if frameNum % 2 and frameNum:
-            writeBin(frameNum + 1, 0, os.path.dirname(self.modelPath))
+            writeBin(frameNum + 1, 0, path=self.settings['frameNumBinary'], filename='')
             print(int((frameNum-1)/2), ' written')
             self.frameNumOld = frameNum
 
-    def onDeleted(self):
+    def onDeleted(self, _):
         """ Signal if a file has been deleted, does not work very well. Used with TestTifSaver """
-        writeBin(0, 0, os.path.dirname(self.modelPath))
+        writeBin(0, 0, path=self.binaryPath, filename='')
         print(0, ' written')
 
 
-if __name__ == "__main__":
-    main()
-
-
 def main():
     """ Main instance of the Module """
 
@@ -81,3 +77,7 @@ def main():
     except KeyboardInterrupt:
         writer.myObserver.stop()
         writer.myObserver.join()
+
+
+if __name__ == "__main__":
+    main()