Merge branch 'developer' into dev/mac-build

docs/main_index/index.html

@@ -16,8 +16,6 @@
       <script src="_static/doctools.js?v=9bcbadda"></script>
       <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/js/theme.js"></script>
-    <link rel="index" title="Index" href="genindex.html" />
-    <link rel="search" title="Search" href="search.html" />
     <link rel="next" title="10.0.0" href="https://slsdetectorgroup.github.io/slsDetectorPackage/10.0.0/index.html" /> 
 </head>
 
@@ -32,13 +30,6 @@
           <a href="#" class="icon icon-home">
             slsDetectorPackage
           </a>
-<div role="search">
-  <form id="rtd-search-form" class="wy-form" action="search.html" method="get">
-    <input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />
-    <input type="hidden" name="check_keywords" value="yes" />
-    <input type="hidden" name="area" value="default" />
-  </form>
-</div>
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <p class="caption" role="heading"><span class="caption-text">Versions:</span></p>
 <ul>

docs/main_index/index.html.j2

@@ -16,8 +16,6 @@
       <script src="_static/doctools.js?v=9bcbadda"></script>
       <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/js/theme.js"></script>
-    <link rel="index" title="Index" href="genindex.html" />
-    <link rel="search" title="Search" href="search.html" />
     <link rel="next" title="{{ versions[0]["version"] }}" href="https://slsdetectorgroup.github.io/slsDetectorPackage/{{ versions[0]["version"] }}/index.html" /> 
 </head>
 
@@ -32,13 +30,6 @@
           <a href="#" class="icon icon-home">
             slsDetectorPackage
           </a>
-<div role="search">
-  <form id="rtd-search-form" class="wy-form" action="search.html" method="get">
-    <input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />
-    <input type="hidden" name="check_keywords" value="yes" />
-    <input type="hidden" name="area" value="default" />
-  </form>
-</div>
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <p class="caption" role="heading"><span class="caption-text">Versions:</span></p>
 <ul>

pyctbgui/pyctbgui/services/ADC.py

@@ -179,9 +179,8 @@ class AdcTab(QtWidgets.QWidget):
         viewBox = self.mainWindow.plotAnalogImage.getView()
         state = viewBox.getState()
         try:
-            self.mainWindow.analog_frame = self._processImageData(data, aSamples, self.mainWindow.nADCEnabled)
-            self.plotTab.ignoreHistogramSignal = True
-            self.mainWindow.plotAnalogImage.setImage(self.mainWindow.analog_frame)
+            self.mainWindow.analog_frame = self._processImageData(data, aSamples, self.mainWindow.nADCEnabled) 
+            self.mainWindow.plotAnalogImage.setImage(self.mainWindow.analog_frame, autoLevels=False) # manually update image levels 
         except Exception:
             self.logger.exception('Exception Caught')
             self.mainWindow.statusbar.setStyleSheet("color:red")
@@ -193,8 +192,6 @@ class AdcTab(QtWidgets.QWidget):
             self.mainWindow.statusbar.showMessage(message)
             print(message)
 
-        self.plotTab.setFrameLimits(self.mainWindow.analog_frame)
-
         # keep the zoomed in state (not 1st image)
         if self.mainWindow.firstAnalogImage:
             self.mainWindow.firstAnalogImage = False

pyctbgui/pyctbgui/services/Acquisition.py

@@ -133,7 +133,7 @@ class AcquisitionTab(QtWidgets.QWidget):
                 self.view.labelDigital.setDisabled(True)
                 self.view.labelTransceiver.setDisabled(True)
                 self.view.spinBoxTransceiver.setDisabled(True)
-                self.plotTab.enableallCounterCheckBox(False) 
+                self.plotTab.showallCounterCheckBox(False) 
             case readoutMode.DIGITAL_ONLY:
                 self.view.spinBoxAnalog.setDisabled(True)
                 self.view.labelAnalog.setDisabled(True)
@@ -141,7 +141,7 @@ class AcquisitionTab(QtWidgets.QWidget):
                 self.view.labelDigital.setEnabled(True)
                 self.view.labelTransceiver.setDisabled(True)
                 self.view.spinBoxTransceiver.setDisabled(True)
-                self.plotTab.enableallCounterCheckBox(False) 
+                self.plotTab.showallCounterCheckBox(False) 
             case readoutMode.ANALOG_AND_DIGITAL:
                 self.view.spinBoxAnalog.setEnabled(True)
                 self.view.labelAnalog.setEnabled(True)
@@ -149,7 +149,7 @@ class AcquisitionTab(QtWidgets.QWidget):
                 self.view.labelDigital.setEnabled(True)
                 self.view.labelTransceiver.setDisabled(True)
                 self.view.spinBoxTransceiver.setDisabled(True)
-                self.plotTab.enableallCounterCheckBox(False) 
+                self.plotTab.showallCounterCheckBox(False) 
             case readoutMode.TRANSCEIVER_ONLY:
                 self.view.spinBoxAnalog.setDisabled(True)
                 self.view.labelAnalog.setDisabled(True)
@@ -157,7 +157,7 @@ class AcquisitionTab(QtWidgets.QWidget):
                 self.view.labelDigital.setDisabled(True)
                 self.view.labelTransceiver.setEnabled(True)
                 self.view.spinBoxTransceiver.setEnabled(True)
-                self.plotTab.enableallCounterCheckBox(self.plotTab.view.radioButtonImage.isChecked()) # enable counter checkboxes for matterhorn
+                self.plotTab.showallCounterCheckBox(self.plotTab.view.radioButtonImage.isChecked()) # enable counter checkboxes for matterhorn
             case _:
                 self.view.spinBoxAnalog.setDisabled(True)
                 self.view.labelAnalog.setDisabled(True)
@@ -165,7 +165,7 @@ class AcquisitionTab(QtWidgets.QWidget):
                 self.view.labelDigital.setEnabled(True)
                 self.view.labelTransceiver.setEnabled(True)
                 self.view.spinBoxTransceiver.setEnabled(True)
-                self.plotTab.enableallCounterCheckBox(self.plotTab.view.radioButtonImage.isChecked()) # enable counter checkboxes for matterhorn
+                self.plotTab.showallCounterCheckBox(self.plotTab.view.radioButtonImage.isChecked()) # enable counter checkboxes for matterhorn
 
         self.view.comboBoxROMode.currentIndexChanged.connect(self.setReadOut)
         self.view.spinBoxAnalog.editingFinished.connect(self.setAnalog)

pyctbgui/pyctbgui/services/Plot.py

@@ -21,8 +21,6 @@ class PlotTab(QtWidgets.QWidget):
     def __init__(self, parent):
         super().__init__(parent)
         pg.setConfigOptions(imageAxisOrder="row-major")  
-        self.frame_min: float = 0.0
-        self.frame_max: float = 0.0
         uic.loadUi(Path(__file__).parent.parent / 'ui' / "plot.ui", parent)
         self.view = parent
         self.mainWindow = None
@@ -31,11 +29,27 @@ class PlotTab(QtWidgets.QWidget):
         self.transceiverTab = None
         self.acquisitionTab = None
         self.adcTab = None
-        self.cmin: float = 0.0
-        self.cmax: float = 0.0
-        self.colorRangeMode: Defines.colorRange = Defines.colorRange.all
-        self.ignoreHistogramSignal: bool = False
-        self.imagePlots: list[PlotWidget] = []
+
+        self.shownCounterImages: list[bool] = [True] * Defines.max_counters # per default show all 4 counter images
+
+        self.showtransceiverImage : bool = False
+        self.showdigitalImage : bool = False
+        self.showanalogImage : bool = False
+
+        # color range variables 
+        self.colorRangeMode: Defines.colorRange = Defines.colorRange.auto
+
+        self.digitalcolorrange : list[float] = [0.0, 0.0]
+        self.analogcolorrange : list[float] = [0.0, 0.0]
+        self.transceivercolorrange : list[list[float]] =  [[0.0, 0.0] for _ in range(Defines.max_counters)]
+
+        self.digitalcminSpinBoxes : QtWidgets.QSpinBox = None
+        self.digitalcmaxSpinBoxes : QtWidgets.QSpinBox = None
+        self.analogcminSpinBoxes : QtWidgets.QSpinBox = None
+        self.analogcmaxSpinBoxes : QtWidgets.QSpinBox = None
+        self.transceivercminSpinBoxes : list[QtWidgets.QSpinBox] = None
+        self.transceivercmaxSpinBoxes : list[QtWidgets.QSpinBox] = None
+
         # list of callback functions to notify tabs when we should hide their legend
         # follows the observer design pattern
         self.hideLegendObservers = []
@@ -56,14 +70,16 @@ class PlotTab(QtWidgets.QWidget):
         self.checkBoxCounters = [self.view.checkBoxCounter0, self.view.checkBoxCounter1, self.view.checkBoxCounter2, self.view.checkBoxCounter3]
         
         for checkBox in self.checkBoxCounters:
-            checkBox.setChecked(False)
+            checkBox.setChecked(True) # per default enable all
             checkBox.setEnabled(False)
 
-        self.imagePlots = (
-            self.mainWindow.plotAnalogImage,
-            self.mainWindow.plotDigitalImage,
-            self.transceiverTab.transceiverImageViews,
-        )
+        self.transceivercminSpinBoxes = [self.view.transceivercminSpinBox0, self.view.transceivercminSpinBox1, self.view.transceivercminSpinBox2, self.view.transceivercminSpinBox3]
+        self.transceivercmaxSpinBoxes = [self.view.transceivercmaxSpinBox0, self.view.transceivercmaxSpinBox1, self.view.transceivercmaxSpinBox2, self.view.transceivercmaxSpinBox3]
+        self.analogcminSpinBoxes = self.view.analogcminSpinBox
+        self.analogcmaxSpinBoxes = self.view.analogcmaxSpinBox
+        self.digitalcminSpinBoxes = self.view.digitalcminSpinBox
+        self.digitalcmaxSpinBoxes = self.view.digitalcmaxSpinBox
+        
 
     def connect_ui(self):
         self.view.radioButtonNoPlot.clicked.connect(self.plotOptions)
@@ -95,14 +111,24 @@ class PlotTab(QtWidgets.QWidget):
         self.view.spinBoxPlot.editingFinished.connect(self.setPlotBit)
         self.view.pushButtonReferesh.clicked.connect(self.acquisitionTab.refresh)
         # color range widgets
-        self.view.cminSpinBox.editingFinished.connect(self.setCmin)
-        self.view.cmaxSpinBox.editingFinished.connect(self.setCmax)
-        self.view.radioButtonAutomatic.clicked.connect(partial(self.setColorRangeMode, Defines.colorRange.all))
+        self.view.radioButtonAutomatic.clicked.connect(partial(self.setColorRangeMode, Defines.colorRange.auto))
         self.view.radioButtonFixed.clicked.connect(partial(self.setColorRangeMode, Defines.colorRange.fixed))
         self.view.radioButtonCenter.clicked.connect(partial(self.setColorRangeMode, Defines.colorRange.center))
 
+        for index, cminSpinBox in enumerate(self.transceivercminSpinBoxes):
+            cminSpinBox.editingFinished.connect(partial(self.setCmin, imagetype = Defines.ImageType.TRANSCEIVER, index=index))
+
+        for index, cmaxSpinBox in enumerate(self.transceivercmaxSpinBoxes):
+            cmaxSpinBox.editingFinished.connect(partial(self.setCmax, imagetype = Defines.ImageType.TRANSCEIVER, index=index))
+
+        self.analogcminSpinBoxes.editingFinished.connect(partial(self.setCmin, imagetype = Defines.ImageType.ANALOG, index=0))
+        self.analogcmaxSpinBoxes.editingFinished.connect(partial(self.setCmax, imagetype = Defines.ImageType.ANALOG, index=0))
+        self.digitalcminSpinBoxes.editingFinished.connect(partial(self.setCmin, imagetype = Defines.ImageType.DIGITAL, index=0))
+        self.digitalcmaxSpinBoxes.editingFinished.connect(partial(self.setCmax, imagetype = Defines.ImageType.DIGITAL, index=0))
+
         for index, checkBox in enumerate(self.checkBoxCounters): 
-            checkBox.stateChanged.connect(partial(self.displayCounter, index))
+            checkBox.stateChanged.connect(lambda state, index=index: self.setCounterCheckBox(index, is_checked=(state == QtCore.Qt.Checked)))
+
 
         # show image Values for analog image
         nMaxY = lambda : self.mainWindow.nAnalogRows
@@ -110,7 +136,9 @@ class PlotTab(QtWidgets.QWidget):
         frame = lambda : self.mainWindow.analog_frame
         plot = self.mainWindow.plotAnalogImage
         plot.scene.sigMouseMoved.connect(partial(self.showPlotValues, plot, nMaxX, nMaxY, frame))
-        plot.getHistogramWidget().item.sigLevelChangeFinished.connect(partial(self.handleHistogramChange, plot))
+        plot.getImageItem().sigImageChanged.connect(partial(self.updateColorRange, imagetype = Defines.ImageType.ANALOG, plot=plot))
+        plot.getHistogramWidget().item.sigLevelChangeFinished.connect(lambda _histItem, plot=plot: self.handleHistogramChange(plot, imagetype=Defines.ImageType.ANALOG))
+
 
         # show image Values for digital image
         nMaxY = lambda : self.mainWindow.nDigitalRows
@@ -118,7 +146,9 @@ class PlotTab(QtWidgets.QWidget):
         frame = lambda : self.mainWindow.digital_frame
         plot = self.mainWindow.plotDigitalImage
         plot.scene.sigMouseMoved.connect(partial(self.showPlotValues, plot, nMaxX, nMaxY, frame))
-        plot.getHistogramWidget().item.sigLevelChangeFinished.connect(partial(self.handleHistogramChange, plot))
+        plot.getImageItem().sigImageChanged.connect(partial(self.updateColorRange, imagetype = Defines.ImageType.DIGITAL, plot=plot))
+        plot.getHistogramWidget().item.sigLevelChangeFinished.connect(lambda _histItem, plot=plot: self.handleHistogramChange(plot, imagetype=Defines.ImageType.DIGITAL))
+        
 
         # show image Values for transceiver image
         nMaxY = lambda : self.transceiverTab.nTransceiverRows
@@ -127,28 +157,39 @@ class PlotTab(QtWidgets.QWidget):
         for index, image_view in enumerate(self.transceiverTab.transceiverImageViews):
             frame = lambda image_view=image_view: image_view.getImageItem().image
             image_view.scene.sigMouseMoved.connect(partial(self.showPlotValues, image_view, nMaxX, nMaxY, frame))
-            image_view.getHistogramWidget().item.sigLevelChangeFinished.connect(partial(self.handleHistogramChange, image_view))
+            image_view.getImageItem().sigImageChanged.connect(partial(self.updateColorRange, imagetype = Defines.ImageType.TRANSCEIVER, plot=image_view, index=index))
 
+            image_view.getHistogramWidget().item.sigLevelChangeFinished.connect(
+                lambda _histItem, image_view=image_view, index=index: self.handleHistogramChange(plot = image_view, imagetype=Defines.ImageType.TRANSCEIVER, index=index)) # sigLevelChangeFinished passes the histogram item as the first argument, we need to ignore it and pass the image_view instead
+            
         self.view.checkBoxShowLegend.stateChanged.connect(self.toggleLegend)
 
 
-    def displayCounter(self, index : int, state : int): 
-        # toggle the display of the counter i and update the splitter 
-        self.transceiverTab.shownCounters[index] = (state == QtCore.Qt.Checked) 
+    def setCounterCheckBox(self, index : int, is_checked : bool): 
+        """
+        slot function for the counter checkboxes, enables/disables the cmin/cmax spinboxes for the counter at index, updates image splitter to show counter image
+        """
+        self.transceivercmaxSpinBoxes[index].setEnabled(is_checked and self.colorRangeMode == Defines.colorRange.fixed)
+        self.transceivercminSpinBoxes[index].setEnabled(is_checked and self.colorRangeMode == Defines.colorRange.fixed)
+        self.shownCounterImages[index] = is_checked # TODO: maybe I dont need that 
         self.transceiverTab.update_ImageSplitter()
+        
+    def enableCounterCheckBox(self, index : int, enabled : bool):
+        self.checkBoxCounters[index].setEnabled(enabled)
+        is_checked = self.checkBoxCounters[index].isChecked()
+        self.transceivercmaxSpinBoxes[index].setEnabled(enabled and is_checked and self.colorRangeMode == Defines.colorRange.fixed)
+        self.transceivercminSpinBoxes[index].setEnabled(enabled and is_checked and self.colorRangeMode == Defines.colorRange.fixed)
 
-    def setCounterCheckBox(self, index : int, check : bool):
-        self.checkBoxCounters[index].setChecked(check)
-
-    def enableCounterCheckBox(self, index : int, enabled : bool): 
-        is_transceiver = self.mainWindow.romode.value in [3, 4]
-        is_image = self.view.radioButtonImage.isChecked()
-        self.checkBoxCounters[index].setEnabled(enabled and is_transceiver and is_image)
-
-    def enableallCounterCheckBox(self, enabled : bool):
+    def showallCounterCheckBox(self, enabled : bool):
         for checkBox in self.checkBoxCounters:
-            checkBox.setEnabled(enabled)
+            checkBox.setVisible(enabled)
 
+        self.view.labelCounters.setVisible(enabled)
+
+        for cminSpinBox, cmaxSpinBox in zip(self.transceivercminSpinBoxes, self.transceivercmaxSpinBoxes):
+            cminSpinBox.setEnabled(enabled and self.colorRangeMode == Defines.colorRange.fixed and self.checkBoxCounters[self.transceivercminSpinBoxes.index(cminSpinBox)].isChecked())
+            cmaxSpinBox.setEnabled(enabled and self.colorRangeMode == Defines.colorRange.fixed and self.checkBoxCounters[self.transceivercmaxSpinBoxes.index(cmaxSpinBox)].isChecked())
+        
     def refresh(self):
         self.getZMQHWM()
 
@@ -231,29 +272,81 @@ class PlotTab(QtWidgets.QWidget):
         for notify_function in self.hideLegendObservers:
             notify_function()
 
-    def setCmin(self, value=None):
+    def setCmin(self, imagetype : Defines.ImageType, value = None, index = 0, updateColorBar=True):
         """
-        slot for setting cmin from cminSpinBox
-        also used as a normal function
-        """
-        if value is None:
-            self.cmin = self.view.cminSpinBox.value()
-        else:
-            self.cmin = value
-        self.updateColorRangeUI()
+        Set the minimum color range value
 
-    def setCmax(self, value=None):
+        Parameters
+        ----------
+        imagetype : Defines.ImageType
+            The type of image (DIGITAL, ANALOG, or TRANSCEIVER).
+        value : float, optional
+            The value to set for the minimum color range (default is None).
+        index : int, optional
+            The index of the counter (default is 0).
+        updateColorBar : bool, optional
+            Whether to update the color bar (default is True).
         """
-        slot for setting cmax from cmaxSpinBox
-        also used as a normal function
-        """
-        if value is None:
-            self.cmax = self.view.cmaxSpinBox.value()
-        else:
-            self.cmax = value
-        self.updateColorRangeUI()
 
-    def setColorRangeMode(self, mode):
+        if value is None:
+            if imagetype == Defines.ImageType.DIGITAL:
+                self.digitalcolorrange[0] = self.digitalcminSpinBoxes.value()
+            elif imagetype == Defines.ImageType.ANALOG:
+                self.analogcolorrange[0] = self.analogcminSpinBoxes.value()
+            else:
+                self.transceivercolorrange[index][0] = self.transceivercminSpinBoxes[index].value()
+        else:
+            if imagetype == Defines.ImageType.DIGITAL:
+                self.digitalcolorrange[0] = value
+                self.digitalcminSpinBoxes.setValue(self.digitalcolorrange[0])
+            elif imagetype == Defines.ImageType.ANALOG:
+                self.analogcolorrange[0] = value
+                self.analogcminSpinBoxes.setValue(self.analogcolorrange[0])
+            else:
+                self.transceivercolorrange[index][0] = value
+                self.transceivercminSpinBoxes[index].setValue(self.transceivercolorrange[index][0])
+            
+        if updateColorBar:
+            self.updateColorBar(imagetype = imagetype, index=index)
+
+    def setCmax(self, imagetype : Defines.ImageType, value=None, index = 0, updateColorBar=True):
+        """
+        Set the maximum color range value
+
+        Parameters
+        ----------
+        imagetype : Defines.ImageType
+            The type of image (DIGITAL, ANALOG, or TRANSCEIVER).
+        value : float, optional
+            The value to set for the minimum color range (default is None).
+        index : int, optional
+            The index of the counter (default is 0).
+        updateColorBar : bool, optional
+            Whether to update the color bar (default is True).
+        """
+
+        if value is None:
+            if imagetype == Defines.ImageType.DIGITAL:
+                self.digitalcolorrange[1] = self.digitalcmaxSpinBoxes.value()
+            elif imagetype == Defines.ImageType.ANALOG:
+                self.analogcolorrange[1] = self.analogcmaxSpinBoxes.value()
+            else:
+                self.transceivercolorrange[index][1] = self.transceivercmaxSpinBoxes[index].value()
+        else:
+            if imagetype == Defines.ImageType.DIGITAL:
+                self.digitalcolorrange[1] = value
+                self.digitalcmaxSpinBoxes.setValue(self.digitalcolorrange[1])
+            elif imagetype == Defines.ImageType.ANALOG:
+                self.analogcolorrange[1] = value
+                self.analogcmaxSpinBoxes.setValue(self.analogcolorrange[1])
+            else:
+                self.transceivercolorrange[index][1] = value
+                self.transceivercmaxSpinBoxes[index].setValue(self.transceivercolorrange[index][1])
+            
+        if updateColorBar:
+            self.updateColorBar(imagetype=imagetype, index=index)
+
+    def setColorRangeMode(self, mode : Defines.colorRange):
         """
         slot for setting the color range mode (all,fixed,3-97%)
         """
@@ -261,73 +354,123 @@ class PlotTab(QtWidgets.QWidget):
 
         # disable or enable cmin/cmax spinboxes
         enableSpinBoxes = mode == Defines.colorRange.fixed
-        self.view.cminSpinBox.setEnabled(enableSpinBoxes)
-        self.view.cmaxSpinBox.setEnabled(enableSpinBoxes)
-        self.updateColorRange()
-        self.updateColorRangeUI()
 
-    def handleHistogramChange(self, plot):
-        """
-        slot called after changing the color bar
-        This is called even when pyqtgraph sets the image without any user intervention
-        the class attribute ignore_histogram_signal is set to False before setting the image
-        so that we can distinguish between the signal originates from pyqt or from the user
-        """
-        if not self.ignoreHistogramSignal:
-            self.cmin, self.cmax = plot.getHistogramWidget().item.getLevels()
-            self.setCmin(self.cmin)
-            self.setCmax(self.cmax)
 
-        self.ignoreHistogramSignal = False
-        # self.setColorRangeMode(Defines.colorRange.fixed)
+        for cminSpinBox, cmaxSpinBox, checkBox in zip(self.transceivercminSpinBoxes, self.transceivercmaxSpinBoxes, self.checkBoxCounters):
+            cminSpinBox.setEnabled(enableSpinBoxes and (checkBox.isChecked() and checkBox.isEnabled() and self.showtransceiverImage)) # if the checkbox is disabled, we still want to enable the spinbox
+            cmaxSpinBox.setEnabled(enableSpinBoxes and (checkBox.isChecked() and checkBox.isEnabled() and self.showtransceiverImage)) # if the checkbox is disabled, we still want to enable the spinbox
 
-    def setFrameLimits(self, frame):
-        """
-        function called from AcquisitionTab::read_zmq to get the maximum and minimum
-        values of the decoded frame and save them in frame_min/frame_max
-        """
-        self.frame_min = np.min(frame)
-        self.frame_max = np.max(frame)
-        self.updateColorRange()
+        self.analogcminSpinBoxes.setEnabled(enableSpinBoxes and self.showanalogImage)
+        self.analogcmaxSpinBoxes.setEnabled(enableSpinBoxes and self.showanalogImage)
 
-    def updateColorRange(self):
+        self.digitalcminSpinBoxes.setEnabled(enableSpinBoxes and self.showdigitalImage)
+        self.digitalcmaxSpinBoxes.setEnabled(enableSpinBoxes and self.showdigitalImage)
+            
+        for index in range(Defines.max_counters): 
+            self.updateColorRange(imagetype=Defines.ImageType.TRANSCEIVER, index=index)
+
+        self.updateColorRange(imagetype=Defines.ImageType.ANALOG)
+
+        self.updateColorRange(imagetype=Defines.ImageType.DIGITAL)
+
+    def handleHistogramChange(self, plot, imagetype : Defines.ImageType, index=0):
         """
+        Parameters
+        ----------
+        plot : Plot
+            The plot object whose histogram has changed.
+        imagetype : Defines.ImageType
+            The type of image (DIGITAL, ANALOG, or TRANSCEIVER).
+        index : int, optional
+            The index of the counter (default is 0).
+        """
+        cmin, cmax = plot.getHistogramWidget().item.getLevels()
+        self.setCmin(imagetype=imagetype, value=cmin, index=index, updateColorBar=False)
+        self.setCmax(imagetype=imagetype, value=cmax, index=index, updateColorBar=False)
+
+
+    def updateColorRange(self, imagetype : Defines.ImageType, plot = None, index=0):
+        """
+        Updates the color range of the plot at index based on the current color range mode.
         for mode:
-        - all:   sets cmin and cmax to the maximums/minimum values of the frame
+        - auto:  sets cmin and cmax to the maximums/minimum values of the frame
         - 3-97%: limits cmax and cmin so that we ignore 3% from each end of the whole range
         - fixed: this function does not change cmin and cmax
-        """
 
-        if self.colorRangeMode == Defines.colorRange.all:
-            self.cmin = self.frame_min
-            self.cmax = self.frame_max
-        elif self.colorRangeMode == Defines.colorRange.center:
-            self.cmin = self.frame_min + 0.03 * (self.frame_max - self.frame_min)
-            self.cmax = self.frame_max - 0.03 * (self.frame_max - self.frame_min)
-
-        self.updateColorRangeUI()
-
-    def updateColorRangeUI(self):
+        Parameters  
+        ----------
+        imagetype : Defines.ImageType
+            The type of image (DIGITAL, ANALOG, or TRANSCEIVER).
+        plot : Plot, optional
+            The plot object to update (default is None).
+        index : int, optional
+            The index of the counter (default is 0).
         """
-        updates UI views should be called after every change to cmin or cmax
-        """
-        for plot in self.imagePlots:
-            if isinstance(plot, list): # hacky for now only transceiver image is a PlotSplitter 
-                for p in plot:
-                    p.getHistogramWidget().item.setLevels(min=self.cmin, max=self.cmax)
+        if imagetype == Defines.ImageType.TRANSCEIVER: # update transceiver
+            defaultPlot = self.transceiverTab.transceiverImageViews[index]
+            cmin, cmax = self.transceivercolorrange[index]
+        elif imagetype == Defines.ImageType.DIGITAL: # update digital
+            defaultPlot = self.mainWindow.plotDigitalImage
+            cmin, cmax = self.digitalcolorrange
+        elif imagetype == Defines.ImageType.ANALOG: # update analog
+            defaultPlot = self.mainWindow.plotAnalogImage
+            cmin, cmax = self.analogcolorrange
+        if plot is None:
+            plot = defaultPlot
+
+        if self.colorRangeMode == Defines.colorRange.auto:
+            if plot.getImageItem().image is None or plot.getImageItem().image.size == 0:
+                return
             else:
-                plot.getHistogramWidget().item.setLevels(min=self.cmin, max=self.cmax)
-        self.view.cminSpinBox.setValue(self.cmin)
-        self.view.cmaxSpinBox.setValue(self.cmax)
+                frame_min = np.min(plot.getImageItem().image)  
+                frame_max = np.max(plot.getImageItem().image)
+                self.setCmin(imagetype=imagetype, value=frame_min, index=index) 
+                self.setCmax(imagetype=imagetype, value=frame_max, index=index)
+        elif self.colorRangeMode == Defines.colorRange.center:
+            if plot.getImageItem().image is None or plot.getImageItem().image.size == 0:
+                return
+            
+            else:
+                frame_min = np.min(plot.getImageItem().image)
+                frame_max = np.max(plot.getImageItem().image)
+                self.setCmin(imagetype=imagetype, value=frame_min + 0.03 * (frame_max - frame_min), index=index)
+                self.setCmax(imagetype=imagetype, value=frame_max - 0.03 * (frame_max - frame_min), index=index)
+
+        elif self.colorRangeMode == Defines.colorRange.fixed:
+            self.setCmin(imagetype=imagetype, value=cmin, index=index)
+            self.setCmax(imagetype=imagetype, value=cmax, index=index)
+
+    def updateColorBar(self, imagetype : Defines.ImageType, index = 0): 
+        """
+        updates the color bar of the plot at index
+        """
+
+        plot = None
+        cmin, cmax = 0.0, 0.0
+        if imagetype == Defines.ImageType.TRANSCEIVER: 
+            plot = self.transceiverTab.transceiverImageViews[index]
+            cmin, cmax = self.transceivercolorrange[index]
+        elif imagetype == Defines.ImageType.DIGITAL: # update digital
+            plot = self.mainWindow.plotDigitalImage
+            cmin, cmax = self.digitalcolorrange
+        elif imagetype == Defines.ImageType.ANALOG: # update analog
+            plot = self.mainWindow.plotAnalogImage
+            cmin, cmax = self.analogcolorrange
+        
+        if plot is not None:
+            histItem = plot.getHistogramWidget().item
+            histItem.blockSignals(True) # avoid triggering handleHistogramChange while setting the levels
+            histItem.setLevels(min=cmin, max=cmax)
+            histItem.blockSignals(False)
+            
 
     def setColorMap(self):
         cm = pg.colormap.getFromMatplotlib(self.view.comboBoxColorMap.currentText())
         # print(f'color map:{self.comboBoxColorMap.currentText()}')
         self.mainWindow.plotAnalogImage.setColorMap(cm)
         self.mainWindow.plotDigitalImage.setColorMap(cm)
-        for i, showncounter in enumerate(self.transceiverTab.shownCounters):
-            if showncounter:
-                self.transceiverTab.transceiverImageViews[i].setColorMap(cm)
+        for i, showncounter in enumerate(self.shownCounterImages):
+            self.transceiverTab.transceiverImageViews[i].setColorMap(cm)
 
     def getZMQHWM(self):
 
@@ -399,11 +542,11 @@ class PlotTab(QtWidgets.QWidget):
             self.mainWindow.transceiverPlots[i].hide()
 
     def addAllSelectedTransceiverPlots(self):
-        for i in range(Defines.transceiver.maxcount):
+        for i in range(Defines.max_counters):
             self.addSelectedTransceiverPlots(i)
 
     def removeAllTransceiverPlots(self):
-        for i in range(Defines.transceiver.maxcount):
+        for i in range(Defines.max_counters):
             self.mainWindow.transceiverPlots[i].hide()
 
     def showPlot(self):
@@ -417,15 +560,21 @@ class PlotTab(QtWidgets.QWidget):
         self.view.radioButtonOverlay.setDisabled(True)
         self.view.radioButtonStripe.setDisabled(True)
 
+        self.showtransceiverImage = False
+        self.showanalogImage = False
+        self.showdigitalImage = False
+
         if self.mainWindow.romode.value in [0, 2]:
             if self.view.radioButtonWaveform.isChecked():
                 self.mainWindow.plotAnalogWaveform.show()
             elif self.view.radioButtonImage.isChecked():
+                self.showanalogImage = True
                 self.mainWindow.plotAnalogImage.show()
         if self.mainWindow.romode.value in [1, 2, 4]:
             if self.view.radioButtonWaveform.isChecked():
                 self.mainWindow.plotDigitalWaveform.show()
             elif self.view.radioButtonImage.isChecked():
+                self.showdigitalImage = True
                 self.mainWindow.plotDigitalImage.show()
             self.view.labelDigitalWaveformOption.setEnabled(True)
             self.view.radioButtonOverlay.setEnabled(True)
@@ -435,7 +584,8 @@ class PlotTab(QtWidgets.QWidget):
             if self.view.radioButtonWaveform.isChecked():
                 self.mainWindow.plotTransceiverWaveform.show()
             elif self.view.radioButtonImage.isChecked():
-                for i, showncounter in enumerate(self.transceiverTab.shownCounters):
+                self.showtransceiverImage = True
+                for i, showncounter in enumerate(self.shownCounterImages):
                     self.transceiverTab.transceiverImageViews[i].setVisible(showncounter)
             
                 self.transceiverTab.transceiverImageSplitter.show()
@@ -463,18 +613,18 @@ class PlotTab(QtWidgets.QWidget):
                 'bottom', "<span style=\"color:black;font-size:14px\">Transceiver Sample [#]</span>")
 
             self.view.stackedWidgetPlotType.setCurrentIndex(0)
-            self.enableallCounterCheckBox(False) # disable counter checkboxes for waveform
+            self.showallCounterCheckBox(False) # disable counter checkboxes for waveform
 
         elif self.view.radioButtonImage.isChecked():
             self.view.stackedWidgetPlotType.setCurrentIndex(2)
             is_transceiver = self.mainWindow.romode.value in [3, 4]
-            self.enableallCounterCheckBox(is_transceiver) # enable counter checkboxes for matterhorn
+            self.showallCounterCheckBox(is_transceiver) # enable counter checkboxes for matterhorn
             self.setDecoder()
 
         if self.view.radioButtonNoPlot.isChecked():
             self.view.labelPlotOptions.hide()
             self.view.stackedWidgetPlotType.hide()
-            self.enableallCounterCheckBox(False) # disable counter checkboxes when no plot is selected
+            self.showallCounterCheckBox(False) # disable counter checkboxes when no plot is selected
         # enable plotting
         else:
             self.view.labelPlotOptions.show()

pyctbgui/pyctbgui/services/Signals.py

@@ -193,7 +193,7 @@ class SignalsTab(QtWidgets.QWidget):
         self.mainWindow.nDigitalRows = 0
         self.mainWindow.nDigitalCols = 0
         self.mainWindow.digital_frame = np.zeros((self.mainWindow.nDigitalRows, self.mainWindow.nDigitalCols))
-        self.mainWindow.plotDigitalImage.setImage(self.mainWindow.digital_frame)
+        self.mainWindow.plotDigitalImage.setImage(self.mainWindow.digital_frame, autoLevels=False) 
         self.mainWindow.verticalLayoutPlot.addWidget(self.mainWindow.plotDigitalImage, 4)
 
     def updateSignalNames(self):

pyctbgui/pyctbgui/services/Transceiver.py

@@ -24,18 +24,17 @@ class TransceiverTab(QtWidgets.QWidget):
         self.plotTab = None
         self.legend: LegendItem | None = None
         self.acquisitionTab = None
-        self.nCounters: int = Defines.transceiver.maxcount
+        self.nCounters: int = Defines.max_counters
         self.nTransceiverRows : int = 0
         self.nTransceiverCols : int = 0 
-        self.shownCounters: list[bool] = [True] * Defines.transceiver.maxcount # per default show all 4 counters
         self.transceiverImageSplitter = QtWidgets.QSplitter(QtCore.Qt.Vertical)
         self.transceiverImageViews : list = [] # pg image view for each counter 
-        self.firstTransceiverImage : list[bool] = [True] * Defines.transceiver.maxcount # to keep track of first image for each counter to maintain zoom state
+        self.firstTransceiverImage : list[bool] = [True] * Defines.max_counters # to keep track of first image for each counter to maintain zoom state
         
     def setup_ui(self):
         self.plotTab = self.mainWindow.plotTab
         self.acquisitionTab = self.mainWindow.acquisitionTab
-        for i in range(Defines.transceiver.maxcount):
+        for i in range(Defines.max_counters):
             self.setTransceiverButtonColor(i, self.plotTab.getRandomColor())
         self.initializeAllTransceiverPlots()
 
@@ -46,7 +45,7 @@ class TransceiverTab(QtWidgets.QWidget):
         self.plotTab.subscribeToggleLegend(self.updateLegend)
 
     def connect_ui(self):
-        for i in range(Defines.transceiver.maxcount):
+        for i in range(Defines.max_counters):
             getattr(self.view, f"checkBoxTransceiver{i}").stateChanged.connect(partial(self.setTransceiverEnable, i))
             getattr(self.view,
                     f"checkBoxTransceiver{i}Plot").stateChanged.connect(partial(self.setTransceiverEnablePlot, i))
@@ -62,7 +61,7 @@ class TransceiverTab(QtWidgets.QWidget):
         """
         enabledPlots = []
         self.legend.clear()
-        for i in range(Defines.transceiver.maxcount):
+        for i in range(Defines.max_counters):
             if getattr(self.view, f'checkBoxTransceiver{i}Plot').isChecked():
                 plotName = getattr(self.view, f"labelTransceiver{i}").text()
                 enabledPlots.append((self.mainWindow.transceiverPlots[i], plotName))
@@ -111,7 +110,7 @@ class TransceiverTab(QtWidgets.QWidget):
         trans_array = self._processWaveformData(data, dSamples, self.mainWindow.romode.value,
                                                 self.mainWindow.nDBitEnabled, self.nTransceiverEnabled)
         idx = 0
-        for i in range(Defines.transceiver.maxcount):
+        for i in range(Defines.max_counters):
             checkBoxPlot = getattr(self.view, f"checkBoxTransceiver{i}Plot")
             checkBoxEn = getattr(self.view, f"checkBoxTransceiver{i}")
             if checkBoxEn.isChecked() and checkBoxPlot.isChecked():
@@ -156,21 +155,18 @@ class TransceiverTab(QtWidgets.QWidget):
         try:
             transceiver_frame = self._processImageData(data, dSamples, self.mainWindow.romode.value,
                                                                        self.mainWindow.nDBitEnabled)
-            self.plotTab.ignoreHistogramSignal = True
             
             for i in range(transceiver_frame.shape[0]):
-                self.transceiverImageViews[i].setImage(transceiver_frame[i])
+                self.transceiverImageViews[i].setImage(transceiver_frame[i], autoLevels=False) #manually update image levels 
         except Exception as e:
             self.mainWindow.statusbar.setStyleSheet("color:red")
             self.acquisitionTab.updateCurrentFrame('Invalid Image')
             self.mainWindow.statusbar.showMessage(str(e))
             print("Error: ", str(e))
 
-        self.plotTab.setFrameLimits(transceiver_frame)
-
         # keep the zoomed in state (not 1st image)
         for idx, image_view in enumerate(self.transceiverImageViews): 
-            if(self.firstTransceiverImage[idx] and self.shownCounters[idx]):
+            if(self.firstTransceiverImage[idx] and self.plotTab.shownCounterImages[idx]):
                 self.firstTransceiverImage[idx] = False
             else: 
                 image_view.getView().setState(image_states[idx])
@@ -180,16 +176,16 @@ class TransceiverTab(QtWidgets.QWidget):
     def update_numCounters(self, num_counters): 
         # update the number of counters and adjust the image splitter accordingly 
         self.nCounters = num_counters
-        for i in range(Defines.transceiver.maxcount): 
-            self.shownCounters[i] = i < self.nCounters
-            self.plotTab.setCounterCheckBox(i, self.shownCounters[i]) # check the counter checkbox 
-            self.plotTab.enableCounterCheckBox(i, self.shownCounters[i]) # disable counter checkbox 
+        for i in range(Defines.max_counters): 
+            self.plotTab.shownCounterImages[i] = i < self.nCounters
+            self.plotTab.setCounterCheckBox(i, self.plotTab.shownCounterImages[i]) # check the counter checkbox 
+            self.plotTab.enableCounterCheckBox(i, self.plotTab.shownCounterImages[i]) # disable counter checkbox 
         
         self.update_ImageSplitter() # update the splitter to show/hide image views based on the number of counters
         
         
     def update_ImageSplitter(self):
-        for i, showncounter in enumerate(self.shownCounters):
+        for i, showncounter in enumerate(self.plotTab.shownCounterImages):
             self.transceiverImageViews[i].setVisible(showncounter)
 
     def initializeAllTransceiverPlots(self):
@@ -198,7 +194,7 @@ class TransceiverTab(QtWidgets.QWidget):
         self.mainWindow.verticalLayoutPlot.addWidget(self.mainWindow.plotTransceiverWaveform, 5)
         self.mainWindow.transceiverPlots = {}
         waveform = np.zeros(1000)
-        for i in range(Defines.transceiver.maxcount):
+        for i in range(Defines.max_counters):
             pen = pg.mkPen(color=self.getTransceiverButtonColor(i), width=1)
             legendName = getattr(self.view, f"labelTransceiver{i}").text()
             self.mainWindow.transceiverPlots[i] = self.mainWindow.plotTransceiverWaveform.plot(waveform,

pyctbgui/pyctbgui/ui/plot.ui

@@ -425,7 +425,7 @@
             <string>Moench04</string>
            </property>
           </item>
-           <item>
+          <item>
            <property name="text">
             <string>Moench05</string>
            </property>
@@ -505,7 +505,7 @@
    <property name="geometry">
     <rect>
      <x>10</x>
-     <y>440</y>
+     <y>540</y>
      <width>841</width>
      <height>400</height>
     </rect>
@@ -1150,7 +1150,7 @@
      <x>10</x>
      <y>221</y>
      <width>841</width>
-     <height>91</height>
+     <height>191</height>
     </rect>
    </property>
    <property name="sizePolicy">
@@ -1166,197 +1166,390 @@
     <enum>QFrame::Raised</enum>
    </property>
    <layout class="QGridLayout" name="gridLayout">
-    <property name="topMargin">
-     <number>9</number>
-    </property>
-    <property name="bottomMargin">
-     <number>9</number>
-    </property>
-    <item row="0" column="1">
-     <widget class="QFrame" name="frame_3">
-      <property name="frameShape">
-       <enum>QFrame::NoFrame</enum>
-      </property>
-      <property name="frameShadow">
-       <enum>QFrame::Plain</enum>
-      </property>
-      <layout class="QGridLayout" name="gridLayout_2">
-       <item row="1" column="0">
-        <widget class="QRadioButton" name="radioButtonCenter">
-         <property name="enabled">
-          <bool>true</bool>
-         </property>
-         <property name="maximumSize">
-          <size>
-           <width>16777215</width>
-           <height>15</height>
-          </size>
-         </property>
-         <property name="text">
-          <string>3-97%</string>
-         </property>
-         <attribute name="buttonGroup">
-          <string notr="true">buttonGroup_4</string>
-         </attribute>
-        </widget>
-       </item>
-       <item row="0" column="0">
-        <widget class="QRadioButton" name="radioButtonAutomatic">
-         <property name="maximumSize">
-          <size>
-           <width>16777215</width>
-           <height>15</height>
-          </size>
-         </property>
-         <property name="text">
-          <string>All</string>
-         </property>
-         <property name="checked">
-          <bool>true</bool>
-         </property>
-         <attribute name="buttonGroup">
-          <string notr="true">buttonGroup_4</string>
-         </attribute>
-        </widget>
-       </item>
-       <item row="2" column="0">
-        <widget class="QRadioButton" name="radioButtonFixed">
-         <property name="maximumSize">
-          <size>
-           <width>16777215</width>
-           <height>15</height>
-          </size>
-         </property>
-         <property name="text">
-          <string>Fixed</string>
-         </property>
-         <attribute name="buttonGroup">
-          <string notr="true">buttonGroup_4</string>
-         </attribute>
-        </widget>
-       </item>
-      </layout>
-     </widget>
-    </item>
-    <item row="0" column="5">
-     <spacer name="horizontalSpacer_2">
-      <property name="orientation">
-       <enum>Qt::Horizontal</enum>
-      </property>
-      <property name="sizeType">
-       <enum>QSizePolicy::Fixed</enum>
-      </property>
-      <property name="sizeHint" stdset="0">
-       <size>
-        <width>40</width>
-        <height>20</height>
-       </size>
-      </property>
-     </spacer>
-    </item>
     <item row="0" column="0">
-     <widget class="QLabel" name="label">
-      <property name="minimumSize">
-       <size>
-        <width>0</width>
-        <height>31</height>
-       </size>
-      </property>
-      <property name="maximumSize">
-       <size>
-        <width>16777215</width>
-        <height>31</height>
-       </size>
-      </property>
-      <property name="text">
-       <string>Color Range:</string>
-      </property>
-     </widget>
+     <layout class="QHBoxLayout" name="horizontalLayoutColorRange">
+      <item>
+       <widget class="QLabel" name="label">
+        <property name="text">
+         <string>Color Range:</string>
+        </property>
+       </widget>
+      </item>
+      <item>
+       <widget class="QRadioButton" name="radioButtonAutomatic">
+        <property name="text">
+         <string>Auto</string>
+        </property>
+        <property name="checked">
+         <bool>true</bool>
+        </property>
+        <attribute name="buttonGroup">
+         <string notr="true">buttonGroup_4</string>
+        </attribute>
+       </widget>
+      </item>
+      <item>
+       <widget class="QRadioButton" name="radioButtonCenter">
+        <property name="text">
+         <string>3-97%</string>
+        </property>
+        <attribute name="buttonGroup">
+         <string notr="true">buttonGroup_4</string>
+        </attribute>
+       </widget>
+      </item>
+      <item>
+       <widget class="QRadioButton" name="radioButtonFixed">
+        <property name="text">
+         <string>Fixed</string>
+        </property>
+        <attribute name="buttonGroup">
+         <string notr="true">buttonGroup_4</string>
+        </attribute>
+       </widget>
+      </item>
+      <item>
+       <spacer name="horizontalSpacerColorRange">
+        <property name="orientation">
+         <enum>Qt::Horizontal</enum>
+        </property>
+        <property name="sizeType">
+         <enum>QSizePolicy::Expanding</enum>
+        </property>
+        <property name="sizeHint" stdset="0">
+         <size>
+          <width>40</width>
+          <height>20</height>
+         </size>
+        </property>
+       </spacer>
+      </item>
+     </layout>
     </item>
-    <item row="0" column="4">
-     <widget class="QDoubleSpinBox" name="cminSpinBox">
-      <property name="enabled">
-       <bool>false</bool>
-      </property>
-      <property name="minimumSize">
-       <size>
-        <width>0</width>
-        <height>31</height>
-       </size>
-      </property>
-      <property name="minimum">
-       <double>-1000.000000000000000</double>
-      </property>
-      <property name="maximum">
-       <double>100000.000000000000000</double>
+    <item row="1" column="0">
+     <widget class="QTabWidget" name="tabWidgetColorRange">
+      <property name="currentIndex">
+       <number>2</number>
       </property>
+      <widget class="QWidget" name="tabColorRangeDigital">
+       <attribute name="title">
+        <string>Digital</string>
+       </attribute>
+       <layout class="QHBoxLayout" name="horizontalLayoutColorRangeDigital">
+        <item>
+         <widget class="QLabel" name="labelColorRangeValuesDigital">
+          <property name="text">
+           <string>Color range values:</string>
+          </property>
+         </widget>
+        </item>
+        <item>
+         <widget class="QDoubleSpinBox" name="digitalcminSpinBox">
+          <property name="enabled">
+           <bool>false</bool>
+          </property>
+          <property name="prefix">
+           <string>min: </string>
+          </property>
+          <property name="minimum">
+           <double>-1000.000000000000000</double>
+          </property>
+          <property name="maximum">
+           <double>100000.000000000000000</double>
+          </property>
+         </widget>
+        </item>
+        <item>
+         <widget class="QDoubleSpinBox" name="digitalcmaxSpinBox">
+          <property name="enabled">
+           <bool>false</bool>
+          </property>
+          <property name="prefix">
+           <string>max: </string>
+          </property>
+          <property name="minimum">
+           <double>-1000.000000000000000</double>
+          </property>
+          <property name="maximum">
+           <double>100000.000000000000000</double>
+          </property>
+         </widget>
+        </item>
+        <item>
+         <spacer name="horizontalSpacerColorRangeDigital">
+          <property name="orientation">
+           <enum>Qt::Horizontal</enum>
+          </property>
+          <property name="sizeType">
+           <enum>QSizePolicy::Expanding</enum>
+          </property>
+          <property name="sizeHint" stdset="0">
+           <size>
+            <width>40</width>
+            <height>20</height>
+           </size>
+          </property>
+         </spacer>
+        </item>
+       </layout>
+      </widget>
+      <widget class="QWidget" name="tabColorRangeAnalog">
+       <attribute name="title">
+        <string>Analog</string>
+       </attribute>
+       <layout class="QHBoxLayout" name="horizontalLayoutColorRangeAnalog">
+        <item>
+         <widget class="QLabel" name="labelColorRangeValuesAnalog">
+          <property name="text">
+           <string>Color range values:</string>
+          </property>
+         </widget>
+        </item>
+        <item>
+         <widget class="QDoubleSpinBox" name="analogcminSpinBox">
+          <property name="enabled">
+           <bool>false</bool>
+          </property>
+          <property name="prefix">
+           <string>min: </string>
+          </property>
+          <property name="minimum">
+           <double>-1000.000000000000000</double>
+          </property>
+          <property name="maximum">
+           <double>100000.000000000000000</double>
+          </property>
+         </widget>
+        </item>
+        <item>
+         <widget class="QDoubleSpinBox" name="analogcmaxSpinBox">
+          <property name="enabled">
+           <bool>false</bool>
+          </property>
+          <property name="prefix">
+           <string>max: </string>
+          </property>
+          <property name="minimum">
+           <double>-1000.000000000000000</double>
+          </property>
+          <property name="maximum">
+           <double>100000.000000000000000</double>
+          </property>
+         </widget>
+        </item>
+        <item>
+         <spacer name="horizontalSpacerColorRangeAnalog">
+          <property name="orientation">
+           <enum>Qt::Horizontal</enum>
+          </property>
+          <property name="sizeType">
+           <enum>QSizePolicy::Expanding</enum>
+          </property>
+          <property name="sizeHint" stdset="0">
+           <size>
+            <width>40</width>
+            <height>20</height>
+           </size>
+          </property>
+         </spacer>
+        </item>
+       </layout>
+      </widget>
+      <widget class="QWidget" name="tabColorRangeTransceiver">
+       <attribute name="title">
+        <string>Transceiver</string>
+       </attribute>
+       <layout class="QGridLayout" name="gridLayoutColorRangeCounters">
+        <item row="0" column="0" colspan="8">
+         <widget class="QLabel" name="labelColorRangeValuesTransceiver">
+          <property name="text">
+           <string>Color range values:</string>
+          </property>
+         </widget>
+        </item>
+        <item row="1" column="0" rowspan="2">
+         <widget class="QLabel" name="labelColorRangeCounter0">
+          <property name="text">
+           <string>Counter 0:</string>
+          </property>
+         </widget>
+        </item>
+        <item row="1" column="1">
+         <widget class="QDoubleSpinBox" name="transceivercminSpinBox0">
+          <property name="enabled">
+           <bool>false</bool>
+          </property>
+          <property name="prefix">
+           <string>min: </string>
+          </property>
+          <property name="minimum">
+           <double>-1000.000000000000000</double>
+          </property>
+          <property name="maximum">
+           <double>100000.000000000000000</double>
+          </property>
+         </widget>
+        </item>
+        <item row="2" column="1">
+         <widget class="QDoubleSpinBox" name="transceivercmaxSpinBox0">
+          <property name="enabled">
+           <bool>false</bool>
+          </property>
+          <property name="prefix">
+           <string>max: </string>
+          </property>
+          <property name="minimum">
+           <double>-1000.000000000000000</double>
+          </property>
+          <property name="maximum">
+           <double>100000.000000000000000</double>
+          </property>
+         </widget>
+        </item>
+        <item row="1" column="2" rowspan="2">
+         <widget class="QLabel" name="labelColorRangeCounter1">
+          <property name="text">
+           <string>Counter 1:</string>
+          </property>
+         </widget>
+        </item>
+        <item row="1" column="3">
+         <widget class="QDoubleSpinBox" name="transceivercminSpinBox1">
+          <property name="enabled">
+           <bool>false</bool>
+          </property>
+          <property name="prefix">
+           <string>min: </string>
+          </property>
+          <property name="minimum">
+           <double>-1000.000000000000000</double>
+          </property>
+          <property name="maximum">
+           <double>100000.000000000000000</double>
+          </property>
+         </widget>
+        </item>
+        <item row="2" column="3">
+         <widget class="QDoubleSpinBox" name="transceivercmaxSpinBox1">
+          <property name="enabled">
+           <bool>false</bool>
+          </property>
+          <property name="prefix">
+           <string>max: </string>
+          </property>
+          <property name="minimum">
+           <double>-1000.000000000000000</double>
+          </property>
+          <property name="maximum">
+           <double>100000.000000000000000</double>
+          </property>
+         </widget>
+        </item>
+        <item row="1" column="4" rowspan="2">
+         <widget class="QLabel" name="labelColorRangeCounter2">
+          <property name="text">
+           <string>Counter 2:</string>
+          </property>
+         </widget>
+        </item>
+        <item row="1" column="5">
+         <widget class="QDoubleSpinBox" name="transceivercminSpinBox2">
+          <property name="enabled">
+           <bool>false</bool>
+          </property>
+          <property name="prefix">
+           <string>min: </string>
+          </property>
+          <property name="minimum">
+           <double>-1000.000000000000000</double>
+          </property>
+          <property name="maximum">
+           <double>100000.000000000000000</double>
+          </property>
+         </widget>
+        </item>
+        <item row="2" column="5">
+         <widget class="QDoubleSpinBox" name="transceivercmaxSpinBox2">
+          <property name="enabled">
+           <bool>false</bool>
+          </property>
+          <property name="prefix">
+           <string>max: </string>
+          </property>
+          <property name="minimum">
+           <double>-1000.000000000000000</double>
+          </property>
+          <property name="maximum">
+           <double>100000.000000000000000</double>
+          </property>
+         </widget>
+        </item>
+        <item row="1" column="6" rowspan="2">
+         <widget class="QLabel" name="labelColorRangeCounter3">
+          <property name="text">
+           <string>Counter 3:</string>
+          </property>
+         </widget>
+        </item>
+        <item row="1" column="7">
+         <widget class="QDoubleSpinBox" name="transceivercminSpinBox3">
+          <property name="enabled">
+           <bool>false</bool>
+          </property>
+          <property name="prefix">
+           <string>min: </string>
+          </property>
+          <property name="minimum">
+           <double>-1000.000000000000000</double>
+          </property>
+          <property name="maximum">
+           <double>100000.000000000000000</double>
+          </property>
+         </widget>
+        </item>
+        <item row="2" column="7">
+         <widget class="QDoubleSpinBox" name="transceivercmaxSpinBox3">
+          <property name="enabled">
+           <bool>false</bool>
+          </property>
+          <property name="prefix">
+           <string>max: </string>
+          </property>
+          <property name="minimum">
+           <double>-1000.000000000000000</double>
+          </property>
+          <property name="maximum">
+           <double>100000.000000000000000</double>
+          </property>
+         </widget>
+        </item>
+        <item row="1" column="8" rowspan="2">
+         <spacer name="horizontalSpacerColorRange2">
+          <property name="orientation">
+           <enum>Qt::Horizontal</enum>
+          </property>
+          <property name="sizeType">
+           <enum>QSizePolicy::Expanding</enum>
+          </property>
+          <property name="sizeHint" stdset="0">
+           <size>
+            <width>40</width>
+            <height>20</height>
+           </size>
+          </property>
+         </spacer>
+        </item>
+       </layout>
+      </widget>
      </widget>
     </item>
-    <item row="0" column="6">
-     <widget class="QLabel" name="label_2">
-      <property name="maximumSize">
-       <size>
-        <width>50</width>
-        <height>31</height>
-       </size>
-      </property>
-      <property name="text">
-       <string>max:</string>
-      </property>
-     </widget>
-    </item>
-    <item row="0" column="7">
-     <widget class="QDoubleSpinBox" name="cmaxSpinBox">
-      <property name="enabled">
-       <bool>false</bool>
-      </property>
-      <property name="minimumSize">
-       <size>
-        <width>0</width>
-        <height>31</height>
-       </size>
-      </property>
-      <property name="maximum">
-       <double>100000.000000000000000</double>
-      </property>
-     </widget>
-    </item>
-    <item row="0" column="3">
-     <widget class="QLabel" name="label_3">
-      <property name="maximumSize">
-       <size>
-        <width>50</width>
-        <height>31</height>
-       </size>
-      </property>
-      <property name="text">
-       <string>min:</string>
-      </property>
-     </widget>
-    </item>
-    <item row="0" column="2">
-     <spacer name="horizontalSpacer_6">
-      <property name="orientation">
-       <enum>Qt::Horizontal</enum>
-      </property>
-      <property name="sizeType">
-       <enum>QSizePolicy::Fixed</enum>
-      </property>
-      <property name="sizeHint" stdset="0">
-       <size>
-        <width>40</width>
-        <height>20</height>
-       </size>
-      </property>
-     </spacer>
-    </item>
    </layout>
   </widget>
   <widget class="QFrame" name="frame_2">
    <property name="geometry">
     <rect>
      <x>10</x>
-     <y>322</y>
+     <y>422</y>
      <width>841</width>
      <height>108</height>
     </rect>
@@ -1541,9 +1734,9 @@
  <resources/>
  <connections/>
  <buttongroups>
+  <buttongroup name="buttonGroup_4"/>
   <buttongroup name="buttonGroup_2"/>
   <buttongroup name="buttonGroup_3"/>
-  <buttongroup name="buttonGroup_4"/>
   <buttongroup name="buttonGroup"/>
  </buttongroups>
 </ui>

pyctbgui/pyctbgui/utils/defines.py

@@ -12,6 +12,15 @@ class Defines:
     Acquisition_Tab_Index = 7
     Max_Tabs = 9
 
+
+    max_counters = 4 # max number of counters
+    max_counters_tabIndex = 4
+
+    class ImageType(Enum): 
+        DIGITAL = 0
+        ANALOG = 1
+        TRANSCEIVER = 2
+        
     class adc:
         tabIndex = 5
         count = 32
@@ -34,10 +43,6 @@ class Defines:
         tabIndex = 6
         loops_count = 6
 
-    class transceiver:
-        maxcount = 4
-        maxtabIndex = 4
-
     class slowAdc:
         tabIndex = 2
         count = 8
@@ -88,6 +93,6 @@ class Defines:
     LineStyles = ['-', '--', '-.', ':']
 
     class colorRange(Enum):
-        all = 0
+        auto = 0
         center = 1
         fixed = 2

slsDetectorCalibration/dataStructures/jungfrauLGADStrixelsData_new.h

@@ -296,8 +296,8 @@ class jungfrauLGADStrixelsData : public slsDetectorData<uint16_t> {
               /*nr_strixel*/ 2 * g1_nrows + 2 * g2_nrows + 2 * g3_nrows,
               g1_ncols * (2 * g1_nrows + 2 * g2_nrows + 2 * g3_nrows) * 2 +
                   sizeof(header)) {
-        std::cout << "Jungfrau strixels 2X single chip with full module data "
-                  << std::endl;
+//         std::cout << "Jungfrau strixels 2X single chip with full module data "
+//                   << std::endl;
 
         // Fill all strixels with dummy values
         for (int ix = 0; ix != g1_ncols; ++ix) {
@@ -307,9 +307,9 @@ class jungfrauLGADStrixelsData : public slsDetectorData<uint16_t> {
             }
         }
 
-        std::cout << "sizeofheader = " << sizeof(header) << std::endl;
-        std::cout << "Jungfrau strixels 2X single chip with full module data "
-                  << std::endl;
+//         std::cout << "sizeofheader = " << sizeof(header) << std::endl;
+//         std::cout << "Jungfrau strixels 2X single chip with full module data "
+//                   << std::endl;
 
         if (xmin < xmax && ymin < ymax) {
 
@@ -331,7 +331,7 @@ class jungfrauLGADStrixelsData : public slsDetectorData<uint16_t> {
         }
 
         iframe = 0;
-        std::cout << "data struct created" << std::endl;
+        //  std::cout << "data struct created" << std::endl; // per frame: too noisy
     };
 
     /**

slsDetectorCalibration/jungfrauExecutables/CMakeLists.txt

@@ -55,6 +55,13 @@ target_compile_definitions(jungfrauRawDataProcessStrxOldAldo PRIVATE JFSTRXOLD A
 list(APPEND JUNGFRAU_EXECUTABLES jungfrauRawDataProcessStrxOldAldo)
 
 
+# jf_online_display_gui (Qt5 + ROOT online display / event finder).  Off by
+# default: it needs Qt5 and ROOT, which the rest of this directory does not.
+option(BUILD_JF_ONLINE_DISPLAY_GUI "build jf_online_display_gui" OFF)
+if(BUILD_JF_ONLINE_DISPLAY_GUI)
+    add_subdirectory(jf_online_display_gui)
+endif()
+
 # others to be added if needed (might already be there in Makefile.cluster_finder TO BE CHECKED)
 
 

slsDetectorCalibration/jungfrauExecutables/Makefile

@@ -1 +0,0 @@
-Makefile.zmqrootdisp

slsDetectorCalibration/jungfrauExecutables/Makefile

@@ -0,0 +1,22 @@
+ROOTSYS=/opt/cern/v6/build
+
+LIBZMQDIR = $(PWD)
+LIBZMQ =  -L$(LIBZMQDIR) -lzmq
+SHLIB_PATH=/opt/cern/v6/root/lib
+CMAKE_PREFIX_PATH=/opt/cern/v6/root
+DYLD_LIBRARY_PATH=/opt/cern/v6/root/lib
+
+QT_CXXFLAGS = $(shell pkg-config --cflags Qt5Core Qt5Gui Qt5Widgets 2>/dev/null)
+QT_LIBS     = $(shell pkg-config --libs Qt5Core Qt5Gui Qt5Widgets 2>/dev/null)
+
+INCDIR=   -I. -I../dataStructures ../tiffio/src/tiffIO.cpp -I../ -I../interpolations/ -I../../slsSupportLib/include/ -I../../slsReceiverSoftware/include/ -I../../libs/rapidjson/ -I../tiffio/include
+LDFLAG= -L/usr/lib64/ -lpthread -lm  -lstdc++  -lzmq -pthread -lrt -ltiff   -O3  -std=c++17 -Wall -Wl,-rpath-link,$(ROOTSYS)/lib
+
+
+default: onlinedisp_zmq
+
+onlinedisp_zmq: onlinedisp_zmq.cpp onlinedisp_zmq.h ../dataStructures/jungfrauLGADStrixelsData_new.h
+	g++ -o onlinedisp_zmq onlinedisp_zmq.cpp $(QT_CXXFLAGS) $(QT_LIBS) -I. -I$(ROOTSYS)/include -Wall -g -lm -L. -lzmq -pthread -lrt -L$(ROOTSYS)/lib -lGui -lCore -lRIO -lNet -lHist -lGraf -lGraf3d -lGpad -lTree -lRint -lPostscript -lMatrix -lPhysics -lMathCore -lThread -m64 -L../../build/bin/ -lSlsSupportStatic ../../build/_deps/libzmq-build/lib/libzmq.a -lstdc++ -lsodium $(LDFLAG) $(INCDIR)
+
+#-lCint
+

slsDetectorCalibration/jungfrauExecutables/jf_online_display_gui/.gitignore

@@ -0,0 +1,16 @@
+# build outputs (make and cmake)
+cmake-build/
+jf_online_display_gui
+jf_online_display_gui_JFSTRX
+gate_contig_test
+*.o
+*.JFSTRX.o
+test/jf_feeder
+test/xclick
+# run artefacts
+current_pede.dat
+jfroi_*.json
+*.json.lock
+roi_list.dat
+save_dest_list.dat
+testPHmapsave/

slsDetectorCalibration/jungfrauExecutables/jf_online_display_gui/CMakeLists.txt

@@ -0,0 +1,170 @@
+# SPDX-License-Identifier: LGPL-3.0-or-other
+# Copyright (C) 2021 Contributors to the SLS Detector Package
+#
+# jf_online_display_gui -- single multithreaded program merging
+#   jf_event_finder_cli / jf_event_finder_gui  (ZMQ gate)
+#   onlinedisp_zmq                             (Qt5 + ROOT display)
+#
+# Standalone build (this directory):
+#   cmake -S . -B build && cmake --build build -j
+#   ./build/jf_online_display_gui                   (normal)
+#   ./build/jf_online_display_gui_JFSTRX            (strip-xel)
+#
+# The Makefile in this directory builds the same two programs; this file exists
+# so the program can be built like the rest of the package.
+#
+# Targets
+#   jf_online_display_gui         normal geometry
+#   jf_online_display_gui_JFSTRX  same sources with -DJFSTRX (strip-xel)
+#   gate_contig_test              gate unit test (JF_BUILD_TESTS=ON, default)
+#   jf_feeder                     ZMQ test feeder (JF_BUILD_TESTS=ON, default)
+#
+# The two variants must never share object files: the geometry and the struct
+# layouts differ, so they are compiled twice (JFSTRX/common object libraries).
+
+cmake_minimum_required(VERSION 3.16)
+project(jf_online_display_gui LANGUAGES CXX)
+
+set(CMAKE_CXX_STANDARD 17)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+set(CMAKE_CXX_EXTENSIONS OFF)
+if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
+    set(CMAKE_BUILD_TYPE Release CACHE STRING "" FORCE)
+endif()
+
+option(JF_BUILD_TESTS "build the gate unit test and the ZMQ feeder" ON)
+
+# ---------------------------------------------------------------------------
+# paths relative to this directory (same layout as the Makefile)
+#   PKG = ../../..   package root
+#   CAL = ../..      slsDetectorCalibration
+# ---------------------------------------------------------------------------
+get_filename_component(PKG "${CMAKE_CURRENT_SOURCE_DIR}/../../.." ABSOLUTE)
+get_filename_component(CAL "${CMAKE_CURRENT_SOURCE_DIR}/../.." ABSOLUTE)
+
+# ---------------------------------------------------------------------------
+# dependencies
+# ---------------------------------------------------------------------------
+find_package(Qt5 5.9 COMPONENTS Widgets Gui Core REQUIRED)
+# online_jf.h includes Qt headers, and every translation unit of this program
+# sees them (the core/root/h5 objects too), so the include paths are added to the
+# flag list rather than left to the link interface.
+set(JF_QT_INCLUDES
+    ${Qt5Widgets_INCLUDE_DIRS} ${Qt5Gui_INCLUDE_DIRS} ${Qt5Core_INCLUDE_DIRS})
+find_package(ROOT REQUIRED COMPONENTS Core RIO Hist Graf Gpad Thread)
+
+# HDF5: CMake's own module finds both C and C++ (the C++ headers are not in the
+# default include path on every distro).
+find_package(HDF5 REQUIRED COMPONENTS C CXX)
+
+# libzmq: prefer the prebuilt static library from the package build tree (that is
+# what the Makefile links), then a system library as a fallback.
+set(JF_ZMQ_STATIC "${PKG}/build/_deps/libzmq-build/lib/libzmq.a"
+    CACHE FILEPATH "static libzmq to link")
+if(EXISTS "${JF_ZMQ_STATIC}")
+    set(JF_ZMQ_LIBRARY "${JF_ZMQ_STATIC}")
+    set(JF_ZMQ_INCLUDE "${PKG}/build/_deps/libzmq-src/include")
+    find_package(Threads REQUIRED) # the static build needs pthread/sodium
+    set(JF_ZMQ_EXTRA Threads::Threads sodium)
+else()
+    find_package(PkgConfig REQUIRED)
+    pkg_check_modules(ZMQ REQUIRED IMPORTED_TARGET libzmq)
+    set(JF_ZMQ_LIBRARY PkgConfig::ZMQ)
+    set(JF_ZMQ_INCLUDE "")
+    set(JF_ZMQ_EXTRA "")
+endif()
+
+# ---------------------------------------------------------------------------
+# includes / flags shared by every source of this program
+# ---------------------------------------------------------------------------
+set(JF_INCLUDES
+    "${CMAKE_CURRENT_SOURCE_DIR}"
+    "${CAL}/dataStructures"
+    "${CAL}/interpolations"
+    "${CAL}/tiffio/include"
+    "${PKG}/slsSupportLib/include"
+    "${PKG}/slsReceiverSoftware/include"
+    "${PKG}/libs/rapidjson"
+    "${JF_ZMQ_INCLUDE}"
+    ${JF_QT_INCLUDES}
+    ${HDF5_INCLUDE_DIRS}
+    ${ROOT_INCLUDE_DIRS}
+)
+
+# The strip-xel decoder header is included by the -DJFSTRX build only; listing it
+# as a dependency makes both build systems rebuild when it changes.
+set(JF_STRIXEL_HDR "${CAL}/dataStructures/jungfrauLGADStrixelsData_new.h")
+
+set(JF_SOURCES
+    online_jf_core.cpp
+    online_jf_root.cpp
+    online_jf_h5.cpp
+)
+set(JF_GUI_SOURCE online_jf_gui.cpp)
+
+# Everything except the definition of JFSTRX: the two object libraries below
+# differ only in that definition (and therefore in their compiled geometry).
+set(JF_COMMON_WARN -Wall -O3 -pthread)
+
+foreach(variant IN ITEMS "" "JFSTRX")
+    if(variant STREQUAL "")
+        set(objlib jf_common)
+        set(app jf_online_display_gui)
+    else()
+        set(objlib jf_common_jfstrx)
+        set(app jf_online_display_gui_JFSTRX)
+    endif()
+
+    add_library(${objlib} OBJECT ${JF_SOURCES})
+    target_include_directories(${objlib} PRIVATE ${JF_INCLUDES})
+    target_compile_options(${objlib} PRIVATE ${JF_COMMON_WARN})
+    if(NOT variant STREQUAL "")
+        target_compile_definitions(${objlib} PRIVATE ${variant})
+    endif()
+    set_source_files_properties(${JF_SOURCES} PROPERTIES
+        OBJECT_DEPENDS "${JF_STRIXEL_HDR}")
+
+    add_executable(${app} ${JF_GUI_SOURCE} $<TARGET_OBJECTS:${objlib}>)
+    target_include_directories(${app} PRIVATE ${JF_INCLUDES})
+    target_compile_options(${app} PRIVATE ${JF_COMMON_WARN})
+    if(NOT variant STREQUAL "")
+        target_compile_definitions(${app} PRIVATE ${variant})
+    endif()
+    target_link_libraries(${app} PRIVATE
+        Qt5::Widgets Qt5::Gui Qt5::Core
+        ${ROOT_LIBRARIES}
+        ${JF_ZMQ_LIBRARY}
+        ${JF_ZMQ_EXTRA}
+        ${HDF5_LIBRARIES}
+        pthread rt m
+    )
+endforeach()
+
+# ---------------------------------------------------------------------------
+# tests / helpers
+# ---------------------------------------------------------------------------
+if(JF_BUILD_TESTS)
+    enable_testing()
+    add_test(NAME gate_contig COMMAND gate_contig_test)
+    # gate decision logic in isolation (no Qt, no ROOT usage at run time)
+    add_executable(gate_contig_test
+        test/gate_contig_test.cpp
+        $<TARGET_OBJECTS:jf_common>)
+    target_include_directories(gate_contig_test PRIVATE ${JF_INCLUDES})
+    target_compile_options(gate_contig_test PRIVATE ${JF_COMMON_WARN})
+    target_link_libraries(gate_contig_test PRIVATE
+        Qt5::Widgets Qt5::Gui Qt5::Core
+        ${ROOT_LIBRARIES}
+        ${JF_ZMQ_LIBRARY}
+        ${JF_ZMQ_EXTRA}
+        ${HDF5_LIBRARIES}
+        pthread rt m
+    )
+
+    # stand-in slsReceiver: single- or dual-interface ZMQ publisher
+    add_executable(jf_feeder test/jf_feeder.cpp)
+    target_include_directories(jf_feeder PRIVATE
+        "${PKG}/libs/rapidjson" "${JF_ZMQ_INCLUDE}")
+    target_compile_options(jf_feeder PRIVATE ${JF_COMMON_WARN})
+    target_link_libraries(jf_feeder PRIVATE ${JF_ZMQ_LIBRARY} ${JF_ZMQ_EXTRA})
+endif()

slsDetectorCalibration/jungfrauExecutables/jf_online_display_gui/Makefile

@@ -0,0 +1,106 @@
+# ===========================================================================
+# jf_online_display_gui -- single multithreaded program merging
+#   jf_event_finder_cli / jf_event_finder_gui  (ZMQ gate)
+#   onlinedisp_zmq                             (Qt5 + ROOT display)
+#
+# Usage:
+#   make                        -> ./jf_online_display_gui            (normal)
+#                                  ./jf_online_display_gui_JFSTRX     (strip-xel)
+#   make normal | make jfstrx    single variant (aliases)
+#   ./jf_online_display_gui <rx_host> [rx_port] [gate_threshold] [min_pixels] [pede_file]
+#                    [--pub PORT] [--contig] [--no-gate] [--pede-frames N]
+#
+# Deps: system ROOT (root-config), Qt5 (pkg-config), the prebuilt static
+# libzmq from the package build tree, and rapidjson headers.
+# ===========================================================================
+QT_CXXFLAGS = $(shell pkg-config --cflags Qt5Core Qt5Gui Qt5Widgets 2>/dev/null)
+QT_LIBS     = $(shell pkg-config --libs   Qt5Core Qt5Gui Qt5Widgets 2>/dev/null)
+ROOT_CFLAGS = $(shell root-config --cflags 2>/dev/null)
+ROOT_LIBS   = $(shell root-config --libs   2>/dev/null)
+
+# paths relative to this directory (jf_online_display_gui/)
+PKG = ../../..
+CAL = ../..
+
+ZMQ_STATIC = $(PKG)/build/_deps/libzmq-build/lib/libzmq.a
+
+# HDF5 C++ headers are NOT in the default include path on every distro (Debian/
+# Ubuntu put them in /usr/include/hdf5/serial).  Discover the include/library
+# directories with pkg-config (the .pc may be "hdf5" or "hdf5-serial"), then the
+# h5c++ wrapper, and let the user override both explicitly:
+#   make HDF5_INC=-I/usr/include/hdf5/serial \
+#        HDF5_LIB=-L/usr/lib/x86_64-linux-gnu/hdf5/serial
+HDF5_PC  := $(shell pkg-config --exists hdf5 && echo hdf5 || (pkg-config --exists hdf5-serial && echo hdf5-serial))
+HDF5_INC ?= $(shell pkg-config --cflags $(HDF5_PC) 2>/dev/null) \
+            $(shell h5c++ -show 2>/dev/null | tr ' ' '\n' | grep '^-I' | tr '\n' ' ')
+HDF5_LIB ?= $(shell pkg-config --libs $(HDF5_PC) 2>/dev/null) \
+            $(shell h5c++ -show 2>/dev/null | tr ' ' '\n' | grep '^-L' | tr '\n' ' ')
+HDF5_LIBS  = $(HDF5_LIB) -lhdf5_cpp -lhdf5
+
+INCDIR = -I. \
+         $(HDF5_INC) \
+         -I$(CAL)/dataStructures \
+         -I$(CAL)/interpolations \
+         -I$(CAL)/tiffio/include \
+         -I$(PKG)/slsSupportLib/include \
+         -I$(PKG)/slsReceiverSoftware/include \
+         -I$(PKG)/libs/rapidjson \
+         -I$(PKG)/build/_deps/libzmq-src/include
+
+CXX      ?= g++
+CXXFLAGS ?= -std=c++17 -O3 -Wall -pthread
+
+LIBS = $(QT_LIBS) $(ROOT_LIBS) $(ZMQ_STATIC) $(HDF5_LIBS) -lsodium -lpthread -lrt -lm
+
+OBJS           = online_jf_core.o online_jf_root.o online_jf_gui.o online_jf_h5.o
+# The strip-xel variant compiles the same sources with -DJFSTRX into its own
+# objects: the two builds have different geometry and struct layouts, so they
+# must never share object files (mixing them is a hard crash).
+JFSTRX_OBJS    = online_jf_core.JFSTRX.o online_jf_root.JFSTRX.o \
+                 online_jf_gui.JFSTRX.o online_jf_h5.JFSTRX.o
+
+BIN            = jf_online_display_gui
+BIN_JFSTRX     = jf_online_display_gui_JFSTRX
+
+ALL_CXXFLAGS = $(CXXFLAGS) $(ROOT_CFLAGS) $(QT_CXXFLAGS) $(INCDIR)
+
+# `make` builds BOTH executables: the normal one and the LGAD strip-xel one
+# (the decoder is header-only, no extra library).
+all: $(BIN) $(BIN_JFSTRX)
+
+# the strip-xel decoder header is header-only and lives outside this directory:
+# touch it and the variant that uses it must be rebuilt
+STRIXEL_HDR = $(CAL)/dataStructures/jungfrauLGADStrixelsData_new.h
+
+%.JFSTRX.o: %.cpp online_jf.h $(STRIXEL_HDR)
+	$(CXX) $(ALL_CXXFLAGS) -DJFSTRX -c $< -o $@
+
+%.o: %.cpp online_jf.h
+	$(CXX) $(ALL_CXXFLAGS) -c $< -o $@
+
+gate_contig_test: test/gate_contig_test.cpp online_jf_core.o online_jf_root.o online_jf_h5.o
+	$(CXX) $(ALL_CXXFLAGS) -o $@ $^ $(LIBS)
+
+$(BIN): $(OBJS)
+	$(CXX) -o $@ $(OBJS) $(LIBS)
+
+$(BIN_JFSTRX): $(JFSTRX_OBJS)
+	$(CXX) -o $@ $(JFSTRX_OBJS) $(LIBS)
+
+# kept so the old habits still work
+normal: $(BIN)
+jfstrx: $(BIN_JFSTRX)
+
+# Synthetic slsReceiver stand-in used to exercise the program without
+# hardware (see test/jf_feeder.cpp).
+feeder: test/jf_feeder
+
+test/jf_feeder: test/jf_feeder.cpp
+	$(CXX) -std=c++17 -O2 -pthread $(INCDIR) -o $@ $< $(ZMQ_STATIC) -lsodium -lpthread -lrt -lm
+
+clean:
+	rm -f $(OBJS) $(JFSTRX_OBJS) $(BIN) $(BIN_JFSTRX) test/jf_feeder
+
+FORCE:
+
+.PHONY: all clean jfstrx normal feeder

slsDetectorCalibration/jungfrauExecutables/jf_online_display_gui/NOTES.md

@@ -0,0 +1,950 @@
+# Notes
+
+Working notes for `jf_online_display_gui`.  The README is the reference for how the
+program behaves; this file records provenance, verification and things that are
+easy to trip over.
+
+## 2026-09-23 — handoff from another session (verified here)
+
+An all-night run showed the **display followed the pedestal drift but the saved
+HDF5 did not**.  Three changes were made by that session and are on disk; I
+re-verified them in this workspace on 2026-09-23.
+
+### What changed
+
+| file | change |
+|---|---|
+| `online_jf_h5.cpp` | `RoiSaver::offer()` corrects each frame with the **live** pedestal (`PedestalStore::instance().get()`), not the snapshot taken by the GUI at Start Save.  Periodic checkpoint: shrink `/data` + the 14 parameter datasets to exactly `framesWritten` (undoing the `kExtendBlock = 128` over-allocation), `H5Fflush(SCOPE_GLOBAL)`, rewrite the JSON.  JSON writer factored into `writeJsonSidecar(bool complete)` writing `<name>.json.part` → `fsync` → `rename` → directory `fsync` (`syncDirOf`).  File created as **v110 (SWMR)**: `H5Pset_libver_bounds(LATEST)` + `H5Fcreate`, all objects created up front, then `H5Fstart_swmr_write()` before the first frame. |
+| `online_jf.h` | `StartInfo::checkpointMs = 30000` (0 disables) |
+| `README.md` | pedestal tracking / saving / file format / JSON / crash-and-mid-run sections, test description, files table |
+| `test/pede_live_test.cpp` | standalone check: live pedestal + checkpoint + SWMR live read |
+
+Consequences of SWMR worth remembering: objects cannot be created after it
+starts, so `/pedestal tracking` and `/pedestal tracking frame` are now created
+(empty) for **every** save, and the baseline pedestal image is written just after
+the SWMR switch.  (The 10-minute cadence of that series, and its ROI-shaped
+images, are unchanged.)
+
+### Verification done here
+
+* `make` — clean, binary current with the sources.
+* `test/pede_live_test` (built with the README's line, plus `$(root-config --cflags)`
+  which that line omits) — **PASS**:
+
+```
+checkpoint1: periodic json (complete:false)=true  live swmr read=true  h5 extent=1  px=900.0
+checkpoint2: live swmr read=true  h5 extent=2  slice1 px=850.0
+final: complete=true  no .part left=true
+PASS: live pedestal + periodic clean checkpoint
+```
+
+The two different pixel values are the point: the first frame was corrected with
+pedestal A, the second with pedestal B installed mid-run, so the file follows the
+tracked pedestal.  Generated artefacts were deleted afterwards.
+
+### Operational caveats
+
+* **v110 needs HDF5 ≥ 1.10.**  Older analysis installs cannot open these files at
+  all — this is the one to check before an overnight run.
+* **Reading mid-run needs the SWMR read flag**: `h5py.File(path, "r",
+  libver="latest", swmr=True)` and `dset.refresh()` to see new frames.
+  `h5dump`/`h5ls` on the live file will not work.  A closed file reads normally.
+* `Pedestal corrected` is still **off by default** (raw data).  Pedestal tracking
+  only reaches `/data` when it is ticked; in raw mode the only pedestal in the
+  file is slice 0.
+* `/pedestal data` is the pedestal at save start; `/pedestal tracking`
+  (+ `/pedestal tracking frame`) is the history of what was actually used, one
+  image per checkpoint interval.
+* `checkpointMs` defaults to 30 s and is **not exposed** in the GUI or on the
+  command line yet.
+
+### Open / optional
+
+* `--no-swmr` (or a `StartInfo` fallback) if a downstream reader turns out to be
+  on HDF5 < 1.10.
+* Expose the checkpoint interval (`--checkpoint MS` and/or a GUI field).
+* If an external reader does not see new frames after a checkpoint, add explicit
+  per-dataset `H5Dflush`; `H5Fflush(SCOPE_GLOBAL)` was enough in the test.
+* Unrelated: the older `onlinedisp_zmq.cpp` extracts the ROI from
+  `zHeader.detSpec1`, which is a hack (that field is the bunch id) — the stream
+  header already carries `zHeader.rx_roi` (`std::array<int,4>`, filled from the
+  receiver's per-port ROI).  That file was not touched.
+
+## Workspace health
+
+* `../_AGENT.txt` was rewritten (2026-09-23, on request): it now points at
+  `jf_online_display_gui/` as the active work, with the old `onlinedisp_zmq` +
+  `jf_event_finder_*` set kept in a clearly marked "legacy / superseded"
+  section.  The design rules that both generations share (ROOT-thread rule,
+  photon map, display cadence, gate semantics, SWMR files) are listed there too.
+* `test/_run/` was removed (2026-09-23, on request).  For the record, what was
+  in it was not worth keeping: the `..._084120_...` run had only its sidecar left
+  (the HDF5 was already gone) and `..._090709_...` had `frames.saved = 0` — an
+  empty save written before the handoff, with no `complete` field.  `test/` now
+  holds only `jf_feeder[.cpp]` and `pede_live_test.cpp`.
+* `jf_online_display_gui/` and the h5/write path are untracked in git; nothing here is
+  committed.
+* `.gitignore` in this directory excludes `*.o`, the `jf_online_display_gui` and
+  `test/jf_feeder` binaries, and runtime data (`current_pede.dat`,
+  `roi_list.dat`, `save_dest_list.dat`, `jfroi_*.h5/json`).  Note it does *not*
+  cover `test/pede_live_test` (the test binary), so that one should be deleted
+  after use.
+
+## 2026-09-30 — JFSTRX display + startup defaults
+
+* `-DJFSTRX`: the **ADC and gain windows are now unmapped** (raw 1024x512), so
+  gate-ROI selection and the hover read-out stay in raw coordinates.  The mapped
+  view is a separate, display-only window, **"ADC Strixel Panels (JFSTRX)"**,
+  with the six groups arranged like the ROOT canvas (left chip1 g3/g2/g1, right
+  chip6 g1/g2/g3).
+* The six panels use the strixel **pixel aspect** `X = 75*(75/Y)`, `Y =
+  25/15/18.75 um` -> 9:1, 25:1, 16:1, via `FastImageView::setPixelAspectX`
+  (non-uniform x/y scaling; ADC and gain stay square).
+* The receiver ROI is parsed from the JSON `rx_roi` array (the old `detSpec1`
+  hack is gone) and drawn as the **red** rectangle on the raw ADC image.
+* Raw geometry is now `kRawWidth`/`kRawHeight` (1024x512); `nx`/`ny` under
+  JFSTRX are the strixel *display* geometry only.  Fixed the assembled-frame
+  height, the multi-interface slab split, the gate-ROI defaults and the HDF5
+  pedestal extraction, which all wrongly used the mapped `nx`/`ny`.
+* **Startup defaults changed**: the signal gate is **off** (`--gate` enables it)
+  and pedestal subtraction is **off** (`--use-pede` enables it; the "No pede"
+  button starts checked).  README examples now pass `--gate` where gating is
+  expected.
+* `test/panel_map_test.cpp` (JFSTRX objects) checks the six-panel fill geometry
+  against the decoder: all six panels fully covered, only the decoder's 183
+  extra right-edge columns dropped (same as the ROOT histograms).
+* The strixel ROI-outline experiment (`buildReceiverRoiOutline`) was removed -
+  ROI on the mapped panels was judged too complex.
+* At ~14:40 the on-disk `jf_online_display_gui` was found truncated to 0 bytes
+  (concurrent build in this directory); `make jfstrx` rebuilt it (14:41).
+
+## 2026-09-30 (later) — three reported bugs
+
+1. **Zoom-out stopped early** (`FastImageView::wheelEvent`): it called
+   `matchViewportToWindow()` on every wheel step, so the image dimension that
+   reached its limit first froze the other and the whole frame could never be
+   shown.  Outward zoom now only `clampViewport()`s; the window-shape matching
+   still runs while zooming in and on resize.
+2. **ROI PH (A7) empty**: the fill condition used `gate_.roiActive()`, which is
+   only true while "ROI only" is on, so a merely *selected* ROI left A7 empty.
+   The ROI snapshot/spectra now use `gate_.roiSet()`; "ROI only" still controls
+   the gate restriction (unrelated to showing the ROI).
+3. **"Reset His" took 30-50 s**: the ROOT thread executed the reset and blocked
+   on `gHistoMtx`, which the analysis thread holds around every frame - under
+   the heavy JFSTRX fill it can starve.  The reset is now performed by the
+   analysis thread at the top of its next frame (lock already held), with a
+   non-blocking `try_lock` fallback on the ROOT thread for the idle case.  The
+   ROOT thread also now wakes immediately (`gCmdCv`) for commands and forced
+   redraws instead of waiting for the `ROOT update (ms)` tick, so a large
+   update interval no longer delays a button.
+
+**Build footgun:** the Makefile does not track flags.  After `make jfstrx`,
+a plain `make` only rebuilds changed files and then links a mix of JFSTRX and
+non-JFSTRX objects (I hit a link error that way).  Always `make clean` before
+switching between `make` and `make jfstrx`.
+
+## HDF5 C++ headers (build dependency)
+
+`#include "H5Cpp.h"` needs the HDF5 **C++ dev** package, not just the runtime:
+
+| distro | package | where the header lands |
+|---|---|---|
+| RHEL / Rocky / Alma / Fedora | `hdf5-devel` | `/usr/include/H5Cpp.h` |
+| Debian / Ubuntu | `libhdf5-dev` | `/usr/include/hdf5/serial/H5Cpp.h` |
+| openSUSE / SLES | `hdf5-devel` | default include dir |
+| Arch | `hdf5` | `/usr/include` |
+| conda-forge | `hdf5` | `$CONDA_PREFIX/include` |
+| macOS (brew) | `hdf5` | `$(brew --prefix hdf5)/include` |
+
+The Makefile now discovers the include/library dirs via `pkg-config` (`hdf5` or
+`hdf5-serial`) and `h5c++ -show`, and both can be overridden, e.g. on Ubuntu:
+
+```
+make HDF5_INC=-I/usr/include/hdf5/serial \
+     HDF5_LIB=-L/usr/lib/x86_64-linux-gnu/hdf5/serial
+```
+
+## 2026-10-06 — external review (`../../../REVIEW_CLAUDE.md`): triage and what was applied
+
+A 39-item review by Claude covers this program plus the Qt6 port, the legacy
+tools, `test_bench/` and repo hygiene.  **Part of it was written against a
+different checkout**: items 2, 3, 4 (mostly) and 9 are already fixed in *this*
+tree, and the review's own item 37 mentions `build-qt6/` cache paths under
+`~/swtests/slsDetectorPackage/...`, which does not exist here.  Everything below
+was checked against the code in this workspace before touching it.
+
+### Applied and verified here
+
+| item | what was wrong | fix |
+|---|---|---|
+| 4 (rest) | a header with **no data part** would make the data `recv` swallow the next message's header as pixels | require `ZMQ_RCVMORE` after a valid header, else count an error and drop the header (the header-length clamp and the drain-on-reject paths were already present) |
+| 8 | the save recorded the **startup** gate settings, so `gate` in the HDF5 attribute and JSON sidecar was wrong after any live edit | read `enabled/threshold/minPixels/contiguous` from `GateEngine` (new getters) instead of `g_cfg`; verified end to end - a save started from the command line records the live values (`threshold 137`, `min_pixels 9`) |
+| 11 (part) | the acq thread **busy-spun at 100 % CPU** waiting for a lagging partner: a held slab kept its socket polled and level-triggered `zmq_poll` fired forever | clear `events` for a socket whose slab is held, so it is not polled until it is released |
+| 18 | ten shortcuts never fired: `QKeySequence("s") == QKeySequence("S")`, so s/S, b/B, r/R, o/O, p/P were ambiguous and Qt activated neither | upper-case actions are now `Shift+S/B/R/O/P` (verified: `Shift+S` opens Set Ranges, 352 → 366 windows) |
+| 19 | the run examples still passed the removed `<energy>` argument, so `2000` was parsed as the host | README examples, the header comment and the Makefile comment corrected (the two remaining `<energy>` mentions are the *legacy* chain and a historical note, both correct) |
+| 22 (part) | `--pede-tracking` left the button unchecked, and `--gate-roi` left `ROI only` unchecked so the first press toggled the wrong way | the tracking button is initialised from `gPedeTracking`, and a restricting `--gate-roi` now checks `ROI only` (through the `m_applyingRoi` guard, so nothing re-captures or warns) |
+
+### Found while fixing item 22 — a bug of my own
+
+The tracking button's enable rule lived in the 500 ms `updateFlow()` poll, which
+also *unchecked* the button when the gate was off.  During start-up that cleared
+a `--pede-tracking` button (`ptrack=off`, reproduced headless).  The force-off is
+now event-driven (in the gate checkbox's own handler); the poll only enables.
+After the change: `--pede-tracking` gives `ptrack=on`.
+
+`test/jf_feeder` had also gone missing from the tree (the Makefile has no target
+for the test programs — review item 34); rebuilt by hand for the verification.
+
+### Already fixed in this tree (nothing to do)
+
+| item | state |
+|---|---|
+| 2 (HDF5 never closed) | the file is built with the C++ constructor `H5File(h5Path, …)` so it owns the only reference; the code comments say so explicitly |
+| 3 (budget/stop not enforced) | `offer()` returns early on `stopRequested`, and the writer stops at `saved >= maxFrames` |
+| 4 (clamps) | `hn > hdr.size()` clamp, `truncated` data check and the drain-on-reject paths are all present |
+| 9 (cumulative drop rate) | uses the 1 Hz window (`pedeTrackSignalDropRate(passCur, dropCur, …)`) — fixed earlier the same day |
+
+### Checked and found *correct* (not defects)
+
+While verifying item 8 I chased two values in a saved file that looked wrong and
+are not: the file recorded `enabled: false` and `no_pede: true` for a run whose
+command line had neither `--gate` nor `--use-pede`.  Both are the documented
+defaults - `online_jf.h:189` (`gateEnabled = false`) with `--gate` to enable, and
+`gNoPede{true}` with `--use-pede` to clear.  The review's item 22 is the flip
+side of this (the widgets were not synced from the config); the config itself is
+intentional.  Since it is easy to lose an hour to this, both switches are now
+spelled out in the README's options section, and a regression run with
+`--gate --use-pede` behaves as expected (with a 100 ADU pedestal and a 250 ADU
+threshold on 3000/200 ADU frames: `pass=0 drop=148`, i.e. the ROI half is
+reduced to 100 and correctly rejected).
+
+### Deliberately deferred, with reasons
+
+* **13 — chip/ROI spectra saturate (top physics item).**  `TH1I` bin contents
+  saturate at `INT_MAX` and the `uint32_t` accumulators wrap: ~55 k pixels per
+  chip per frame land in 1–2 noise bins, so at 500–1300 fps the spectra are
+  wrong within an hour, and an all-night run at 25 fps is close to the limit too.
+  The fix is mechanical but wide (37 `TH1I` sites across four files plus the
+  accumulator and sync signatures) and touches the core data path, so it gets
+  its own careful pass with a test rather than a rushed edit at the end of a
+  long session.  Plan: accumulators → `uint64_t`, histograms/clones → `TH1D`,
+  then check that entries, means and the ADU/keV ratio (40.0000) are unchanged.
+* **10** (the tracker can overwrite a just-loaded pedestal — re-prime from the
+  store under the lock, skip a stale install), **12** (per-port `rx_roi` with the
+  `rowBase` offset), **20** (closing the window should quit — the parentless ADC
+  /Gain windows keep the process alive), **21** (Delete in the ROI/save-destination
+  dialogs uses stale indices), **23–30** (races on `g_pheneThreshold`/the ROI,
+  `renderImage`'s 524 k `setPixel` calls and the 500 ms `roi_list.dat` re-read,
+  NaN pedestals, rapidjson asserts, the finish/start save race, frame 0, and the
+  small GUI defects).
+* **11 (the rest)** — partial-frame assembly is a feature, not a fix; the README
+  now documents the real behaviour and calls the promise an open item.
+* **Everything outside `jf_online_display_gui`** — the Qt6 port (1, 16, 17, 35, 36), the
+  legacy tools (5, 6, 7, 14, 15, 31 — the project's own `_AGENT.txt` marks them
+  superseded), `test_bench` (32), repo hygiene (33, 37, 38 — `git checkout --`
+  for the symlinks needs repository write access, which is still deferred) and
+  maintainability (39).  These need decisions of their own; none of them were
+  changed here.
+
+## 2026-10-14 — virtual photon counting: display side done, save side specified
+
+Requested: take the photon map out of ROOT, give it its own Qt window filled the
+same way but **not cumulative by default** and plotted every N images (default
+2000), put those controls plus the photon threshold in a "Virtual photon
+counting" panel left of the Display, and add a save mode that writes the
+non-cumulative maps every M images (M >= 200) with the first frame number and
+timestamp, M and the thresholds recorded.
+
+### Done (build green, window present, no crashes)
+
+* Core: `gPmapEvery` (default 2000) and `gPmapCumulative` (default **false**)
+  atomics; the photon map is published into the image mailbox every
+  `gPmapEvery` **analysed frames** (independent of the ADC image decimation),
+  and when not cumulative the accumulator is zeroed right after the publish, so
+  each image holds the photons counted since the previous one.  The counting
+  itself is unchanged.
+* GUI: a **"Virtual photon counting"** panel (left column, under the gates -
+  the Display panel is in the right column at that height) with the
+  `cumulative` checkbox, `plot every N images` (1..1000000, default 2000) and
+  the **photon threshold (ADU)** spin moved out of the Display group.
+* GUI: a new top-level window **"Photon Map (virtual photon counting)"**
+  (1104x552, same colour palette as the ADC image, colour range 0..8 photons
+  per pixel), refreshed from the mailbox in `processImages()`.
+* Fixed while doing it: the panel was built before `photonThrSpin_` existed, so
+  the grid received a null widget and the spin floated at (0,0) - the same
+  add-before-create mistake as the Quit button earlier.  The panel is now
+  created after the spin and inserted with `leftCol->insertWidget(2, ...)`.
+
+### Stage 3, part A — done and verified
+
+* **The ROOT photon map is gone**: no `his3000` booking, no `disp3000` clone and
+  no `A5` canvas.  All the remaining references are behind `if (his3000)` /
+  `if (disp3000)` / `if (A5)` guards, so they are simply inert; the two
+  unguarded dereferences (the clone and the z-range) were the only ones that
+  needed deleting.  Verified: no `Plotting Canvas Photon Map` window appears.
+* The **P.Map** range pair now reads and writes the Qt photon window's colour
+  range (`liveMapRange` -> `m_photonView->colorRange`, and the panel's opening
+  range), and the ADC zoom also sets the photon window's viewport.
+* **Save with no gate ROI works**: the early refusal in `toggleRoiSave` is gone;
+  `roiSnapshot()` already reports the full frame when no ROI is set.  Verified:
+  with no `--gate-roi`, `/data` came out `(151, 512, 1024)` - the pedestal slice
+  plus 150 full frames.
+
+### Stage 3, part B — the photon-map save mode (next)
+
+Design, so this can be written mechanically:
+
+1. Save panel: a radio pair (`save frames` / `virtual photon counting`) plus an
+   `M` spinbox, minimum **200**, default 2000; the spinbox is only meaningful in
+   the photon mode.
+2. Core: `gPmapSaveEvery` (int, default 2000) and `gSaveMode` (0 = frames,
+   1 = photon maps) atomics; a **second accumulator** `g_pmapSaveAccum` (NCH
+   floats) filled in the same worker pass (one extra add per counted photon
+   pixel, gated by a `FrameJob::pmapSave` flag so there is no atomic read per
+   pixel); every `gPmapSaveEvery` analysed frames it is copied into a single-slot
+   mailbox and zeroed - never cumulative.
+3. Window provenance: the acq thread owns the saver, so let the acq loop keep the
+   window bookkeeping while in this mode: on the first gate-passed frame after a
+   publish record `firstFrame = hdr.frameNumber` and `firstStamp =
+   hdr.timestamp`, count frames, and when the analysis publishes a map, tag it
+   with those two values.  The map's own frame count goes in too.
+4. Writer: a new dataset `/virtual photon counting` (float32, 512x1024, one image
+   per publish, extendable) plus `/virtual photon counting frame` (uint64) and
+   `/virtual photon counting timestamp`; JSON gains `save_mode`,
+   `photon_map_every` (M), `photon_threshold` (ADU) and the window count.
+   `/data` stays frames-only and is not created in this mode.
+5. `--pmap-every N` on the command line would make this testable without the GUI
+   (the display cadence is otherwise 2000 frames = 80 s at 25 fps).
+
+### Stage 3, part B — plumbing in place, inert
+
+Done in the tree and building:
+
+* `gSaveMode` (0 = frames, 1 = virtual photon counting) and `gPmapSaveEvery`
+  (default 2000) atomics, plus `pmapSaveReset()`.
+* A **second accumulator** `g_pmapSaveAccum` filled in the same worker pass
+  (`FrameJob::pmapSave`, so no atomic read per pixel), published into a
+  single-slot `PmapSlot` every `gPmapSaveEvery` analysed frames and zeroed
+  immediately - never cumulative.
+* `Pipeline::offerToSaver()` replaces the two direct `saver_.offer()` calls: in
+  the frame mode it is the old path, in the photon mode it keeps the window
+  bookkeeping (first frame number, first timestamp, frame count) in the acq
+  thread and tags each published map with it.
+* `RoiSaver::offerPhotonMap()` declared; its body currently only counts the map
+  in `pmapPending` and writes nothing - **deliberately inert**: `gSaveMode` is
+  still 0 everywhere, so no path can select the photon mode yet and the existing
+  behaviour is unchanged.  Nothing can silently produce a frames-only file while
+  claiming the photon mode.
+
+Still to write (the design is above):
+
+1. The writer body: `/virtual photon counting` (float32, 512x1024, extendable,
+   **created up front** because SWMR forbids creating objects after the start)
+   plus `/virtual photon counting frame` and `/virtual photon counting timestamp`
+   (uint64), drained from a `pmapQueue` in the writer loop, and the JSON fields
+   (`save_mode`, `photon_map_every`, `photon_threshold`, window count).
+2. The Save panel controls: the radio pair (`save frames` /
+   `virtual photon counting`) and the `M` spinbox (minimum 200), filling
+   `StartInfo::photonMode/photonEvery/photonThreshold` (the fields are already
+   there) and calling `pmapSaveReset()` when a save starts.
+3. `--pmap-every N` and `--pmap-save-every N` (or one `--save-photon` switch) so
+   the mode can be exercised headlessly; with the display default of 2000 frames
+   a test needs 80 s at 25 fps otherwise.
+
+### Stage 3, part B — finished and verified (this session)
+
+Everything listed as "still to write" above is in the tree, plus the GUI
+controls and the headless switches:
+
+* Writer: `/virtual photon counting` (float32, {nmaps, h, w}, chunked, created
+  before SWMR starts) + `/virtual photon counting frame` + `/virtual photon
+  counting timestamp` (U64, one value per map), drained from `Impl::pmapQueue`
+  in the writer loop; `RoiSaver::offerPhotonMap()` is live and inert unless
+  `info.photonMode` and a save is running.  JSON: `save_mode`,
+  `photon_map_every`, `photon_threshold`, and a `photon_maps` block with
+  `saved`, `every`, `threshold_adu`, `cumulative: false`, `pedestal_active`,
+  `dataset`.  In photon mode `frames.saved` reports the **maps**.
+* Budget: in photon mode "Number of frames to be saved" budgets the **maps**
+  (the GUI relabels the row to "Number of photon maps to be saved"), and the
+  run stops by itself with `stop_reason = "photon-map budget reached"`, leaving
+  a closed `complete: true` pair.  Frame mode is unchanged
+  (`frame budget reached`).
+* Save panel: radio pair + `photon map every N frames` spinbox (minimum 200,
+  greyed while "save frames" is selected).  The radio also re-labels the budget
+  row.  The photon-map mode is allowed with **no gate ROI** (full frame).
+* Virtual photon counting panel (left column, under the gates): `cumulative`
+  (default **off**), `plot every N images` (default 2000), `photon threshold
+  (ADU)` (moved out of the Display panel).  The map lives in its own Qt window
+  `Photon Map (virtual photon counting)`; it is **not** a ROOT histogram any
+  more (that was the old `his3000`, removed).
+* CLI: `--pmap-every N`, `--pmap-save-every N` (min 200), `--save-photon`,
+  `--save-budget N`, `--start-save` — the same actions as the GUI controls, so
+  a save can run headless.
+
+**Bug found and fixed while verifying (important).**  Step 5a of the analysis
+loop (the save-map publish) took `gHistoMtx` although the enclosing frame scope
+already holds it (`histoLock`, top of the frame).  `std::mutex` is not
+recursive, so the **analysis thread deadlocked on the first frame** whenever
+`gSaveMode == 1` — with `--save-photon`, and even with no save running.  The
+symptom was a program that kept counting frames (`in=` growing, because the acq
+thread does not depend on the analysis thread) while nothing downstream ever
+appeared: no photon map, no ROOT update, `save=0/0`.  Two `gdb` snapshots
+caught it (`analysisLoop` parked in `pthread_mutex_lock` at a call site that
+only exists in the photon path).  Fix: no second lock (the frame scope holds it)
+and the whole save-map path is now gated on `saver_.running()` as well, so
+`gSaveMode == 1` without a running save costs nothing and cannot block.
+
+**Verified end to end** (Xvfb + mwm, `test/jf_feeder`, zero-filled pedestal —
+the real `current_pede.dat` is ~2000 ADU, so the synthetic 100/300 ADU frames
+would count nothing):
+
+| check | result |
+|---|---|
+| `--save-photon --pmap-save-every 200 --start-save`, 40 s | maps at frames 0/201/401/601/801, `[pmap] map N written (200 frames, first frame F)` |
+| `/virtual photon counting` | (5, 512, 1024) float32; every map 40 non-zero pixels, sum ~5320 (40 px x 133 counts = 2/3 of 200 frames), identical maps = non-cumulative |
+| provenance | `/virtual photon counting frame` `[0 201 401 601 801]` |
+| `--save-budget 2` | exactly 2 maps, self-stop `photon-map budget reached`, `complete: true` |
+| frame mode `--save-budget 100` | `/data` (101, 512, 1024), 100 frames, `frame budget reached`, no photon datasets |
+| GUI path | clicking `virtual photon counting` re-labels the row to *Number of photon maps to be saved*, enables the M spinbox and sets `Status: saving virtual photon counting maps`; `Start/Stop save` then writes maps (first map at the frame the save started, e.g. 431) |
+| photon window | `Photon Map (virtual photon counting)` renders the 40-pixel cluster (green, ~133 counts on the 0..256 scale) |
+| no pedestal | `--save-photon` with `--no-pede` (or no pedestal file) is **refused**: `[save] refusing virtual photon counting: "No pede" is on, ...`, no HDF5 file is created, and the scripted `--start-save` path is not blocked by a dialog; frame mode with no pedestal still saves |
+
+The photon-map window draws **zero-count pixels white** (`FastImageView::
+setZeroWhite`, opt-in and used only there), reproducing the ROOT `colz` look
+where empty cells show the canvas background; the palette and the colour bar are
+untouched, and single photons are still coloured (the special case is `v <= 0`,
+not "below the range").  Verified on screen: white map, cluster still green.
+
+Housekeeping: `test/_scratch/` (XTest driver, screenshots, run logs, HDF5
+outputs, the synthetic pedestal) was removed after the runs; the tree keeps only
+`test/jf_feeder[.cpp]`, `test/pede_live_test.cpp`, `test/panel_map_test.cpp`.
+
+Two things left open for the next session, both decisions rather than bugs:
+
+1. ~~**Photon counting needs a pedestal.**~~  **Decided by the operator: no
+   photon-map saving without a pedestal.**  Counting still requires `g0`
+   (unchanged), and a virtual-photon-counting save now *refuses to start* when
+   no pedestal is active (`No pede`, or nothing loaded): the button drops back,
+   the status line and stdout say why, no file is created, and the modal warning
+   is skipped under `--start-save` so scripted runs never wait on a dialog.
+   Frame saving is unaffected.
+2. The map's `first frame number`/`timestamp` come from the acq thread, i.e.
+   from the first **gate-passed** frame of the window (none is available if the
+   gate drops the whole window, in which case the previous values persist).  The
+   analysed-frame count in `PmapItem::frames` is exact.
+
+### ROI in photon mode, greying convention, control names (follow-up)
+
+* **The gate ROI applies to the saved photon maps too** (operator's choice):
+  a map is the ROI window of the full-frame counting map, cropped in the same
+  data coordinates as `/data`.  This fixed a real bug: `writePhotonMap` used to
+  hand `h*w` floats straight to HDF5, i.e. the first `h*w` pixels of the
+  1024x512 map, which is the *wrong region* whenever a ROI is set.  Verified
+  against the full-frame map: `/virtual photon counting` for a `0 0 100 50` ROI
+  is bit-identical to `full[0:50, 0:100]`, with the 16 non-zero pixels exactly
+  where the feeder's wrapped cluster is (row 1, x 0..15); a frame save with the
+  same ROI gives `/data` `{nframes, 50, 100}`, so both modes crop alike.
+* **Greying is a look, not an enablement** (`greyStage(QGroupBox*, bool,
+  std::initializer_list<QWidget*> keepActive)`): the box, its title and its
+  other contents dim, while the widget that *switches the stage back on* keeps
+  normal text - otherwise a bypassed stage looks stuck.  Kept readable:
+  `Pede/Raw toggle` (Pedestal), `Gate enabled` (signal gate), `Pedestal
+  tracking`, `gain correction on/off` (Gain), and the storage-cell combo.  The
+  `keV PH` checkbox stays disabled+greyed while the gain is off (earlier
+  request: it keeps its tick for next time).
+* **Virtual photon counting box greys without a pedestal** (`greyStage(
+  pmapGroup_, !pede)`), matching the fact that the counting needs `g0` and the
+  save refuses to start: one rule, the panel and the file agree.
+* Renames: `No pede (raw ADC)` -> **`Pede/Raw toggle`** (state still spelled out
+  by the label next to it), `Apply gain (g)` -> **`gain correction on/off (g)`**,
+  plus a read-only **`gain corrected`** indicator beside it (no mouse events, no
+  focus; it ticks with the flag in `updateFlow()` and dims with the panel).
+
+* Pedestal tracking panel follow-up: the button is `pedestal tracking on/off`
+  and the box now greys on **selectability**, not on activity - `greyStage(
+  pedeTrackGroup_, !gateOn)`, matching the button's own `setEnabled(gateOn)`,
+  while the value label under it (`off` / `on: N samples, ...`) reports the
+  activation.  Verified in three states: gate off -> box and button greyed;
+  gate on + tracking off -> box black and label `off`; after clicking the
+  toggle -> button pressed and label `on: 0 samples, delta 0.0 ADU, 0 updates`
+  (0 samples is correct with the feeder, which only drops a third of the frames
+  while the tracker needs >90 %).
+
+### Photon threshold in keV while the gain correction is on
+
+Requested: leave the photon-counting threshold in ADU with the gain off, switch
+it to keV (default **4 keV**) with the gain on, and remember both values.
+
+* Core: `g_pheneThresholdKev` (default `PHOTON_THRESHOLD_KEV_DEFAULT` 4.0) next
+  to `g_pheneThreshold` (150 ADU).  The analysis picks by `gain_flag` and hands
+  the worker `FrameJob::pcGain` / `pcNominalGain`, so the counting value is
+  `adcpedecorr / (g0[i] or 40)` - the same ADU/keV the keV spectra use - and the
+  increment follows in the same unit: `(value + thr) / (2 x thr)`.  The unit
+  follows the gain stage itself, not the `keV PH` checkbox (that one only
+  decides what the spectra display).
+* GUI: the threshold row is a `QDoubleSpinBox` (integer ADU, one decimal keV)
+  whose label switches `(ADU)` <-> `(keV)`; `setApplyGain()` stores the value
+  that is on screen into its own unit and loads the other one (signals blocked),
+  so toggling never destroys either.  `--apply-gain` added as the CLI mirror of
+  the Gain button (the gain stage was the only one without one) - needed to test
+  this headlessly.
+* Reported: `--stats` prints `pthr=150ADU` / `pthr=4keV`; the JSON carries
+  `photon_threshold_unit` and `photon_maps.threshold` + `threshold_unit`
+  (`threshold_adu` is gone - the key was wrong as soon as the unit could
+  change).
+* Verified with the synthetic feeder, a zero pedestal and a **g0 = 1.0
+  ADU/keV** gain map (float64 - the loader wants 6 x 1024x512 doubles; a float32
+  file is rejected with the byte count):
+  - gain off: `pthr=150ADU`, one 200-frame map with **40 non-zero pixels, sum
+    5320, max 133** - i.e. only the 300 ADU cluster, unchanged from before;
+  - `--apply-gain`: `pthr=4keV`, the **same frames** give **524288 non-zero
+    pixels** (every pixel: keV = ADC/1.0, so even the 100 ADU baseline is
+    100 keV > 4 keV) with max 5925 - proof that the counting really divides by
+    ADU/keV before comparing;
+  - GUI: starting with `--apply-gain` shows `photon threshold (keV): 4.0`;
+    clicking the gain off shows `photon threshold (ADU): 150`; clicking it back
+    on gives a screenshot byte-identical to the first keV one, so both values
+    survive the round trip.
+* Mid-save guard: toggling the gain while a photon-map save runs changes the
+  unit of the maps written after it, so `setApplyGain()` prints
+  `[gain] warning: the photon-counting unit is now keV while a photon-map save
+  is running ...` (and the same for ADU).  Verified with a photon save started
+  by `--start-save` and a gain click: the warning appears once, the save keeps
+  running and writes its map, the JSON keeps the start-of-save threshold/unit.
+
+### Window handling, labels and the flow arrows
+
+* **Quit closes every window.**  The ADC / gain / photon-map windows are
+  separate top-levels and the ROOT canvases live in the ROOT thread, so
+  `quitApp()` and `closeEvent()` now call `closeSideWindows()` (hide + close
+  each) and `QApplication::quit()`.  Closing only the control window used to
+  leave the side windows - and the process, because Qt quits on the *last*
+  window - on screen.  Verified on all three paths with the window count taken
+  from `xwininfo -root -tree`:
+  - Quit button, dialog confirmed: 6 app windows -> **0**, process gone;
+  - Quit button with a photon-map save running: the save is flushed
+    (`[shutdown] flushing the ROI save ...`, JSON `complete: true`), then
+    **0** windows / no process;
+  - window-manager close (a `WM_DELETE_WINDOW` ClientMessage, the path that was
+    broken): confirmed -> **0** windows / no process.
+* Gain panel label: the no-map case is now
+  `no gain map loaded : using defaults` (the "defaults" are the nominal
+  40 ADU/keV, used for the keV spectra *and* the keV photon threshold).
+* Flow arrows: two new connectors - **Gain -> Virtual photon counting** (the
+  calibration; its threshold is keV while the gain is on) and **Virtual photon
+  counting -> Display** (the map has a window of its own) - and the save path is
+  now **orange**: the Gain -> ROI rail and the ROI -> Save arrow.  Blue stays
+  the analysis/display chain.  `FlowStrip::Path` gained a `save` flag and
+  `makeFlowArrow()` a colour argument (`#4673af` blue, `#de7d14` orange).
+  Verified on screen in the gain-on/pede-on state: both new arrows land on the
+  right panels, the rail and the ROI -> Save arrow are orange, the rest blue.
+* The `JF_TIMING` `[rect]` diagnostic also prints `quit`, `track` and `pmap`
+  now, which is how the click-based tests above locate those widgets.
+
+### Dynamic flow colours (arrows static, colours not)
+
+Reworked after the operator's feedback: the geometry of the diagram is fixed,
+only the colour class of each connector changes.
+
+* Three classes (`FlowClass` + `flowColor()`): `FlowData` orange `#de7d14`,
+  `FlowNormal` light blue `#5b9bd5`, `FlowPedestal` lighter blue `#a8c8e8`.
+* The **data path follows the save mode**: `FlowStrip::setSaveMode(photonMaps)`
+  flips the Gain -> ROI rail and the Gain -> counting connector, and
+  `updateFlow()` (called from the radio handler) flips the two label arrows
+  ROI -> Save and counting -> Save.  So in `save frames` the orange pair is
+  rail + ROI -> Save, and in `virtual photon counting` it is Gain -> counting +
+  counting -> Save - exactly two arrows at a time.
+* Completeness: every stage now has an incoming and an outgoing connector.
+  The missing one was **Virtual photon counting -> Save** (a new arrow under the
+  counting panel, the left-hand twin of ROI -> Save).  Display and Save are the
+  sinks; the storage cell has no incoming connector because the receiver stream
+  enters there.
+* The colour legend is in the flow strip's tooltip and in the README table.
+* Verified on screen: frames mode -> rail + ROI -> Save orange, counting arrows
+  light blue; after clicking `virtual photon counting` (and the label switching
+  to "Number of photon maps to be saved") -> Gain -> counting and counting ->
+  Save orange, rail + ROI -> Save light blue.  `[save] mode: ...` is logged on
+  every change.
+* Test note: the `JF_TIMING` `[rect]` lines can be ~30 px stale (they are printed
+  on a layout pass that may run before the panels settle), so a scripted click
+  should target the widget with a small downward tolerance - found the hard way
+  when a radio click missed.
+
+### The gate is a funnel on the line (not a stage)
+
+Operator's rule: the signal gate does not modify the data, so no connector may
+enter or leave its box.  Reworked accordingly:
+
+* The flow is now `Pedestal -> [funnel] -> Gain` (and `[funnel] -> tracking`),
+  i.e. one junction where the gate acts, drawn as a small trapezoid on the line.
+  The gate panel's only connector is a short blue **control arrow** into the
+  funnel's side; with the gate off the funnel and that arrow are drawn pale
+  (`FlowOff`, #c9c9c9) instead of disappearing.
+* Two feeders reach the funnel and both are always drawn: through the **Pedestal**
+  (`FlowPedestal`) and straight from the **storage cell** (`FlowNormal`), the
+  raw bypass that avoids the greyed Pedestal box.  `setStages(pede, gate, pmap)`
+  makes the live one coloured and the idle one pale grey - so in raw mode the
+  data visibly comes from block 1, as the operator asked.
+* `FlowStrip::Path` grew `x` (vertical position), `head` (false = merge into the
+  junction) and `startAtJog` (begin on the vertical, for the funnel -> Gain and
+  funnel -> tracking branches); `cross()` honours them; `drawFunnel()` paints the
+  symbol plus its control arrow; `kFunnelX = 24` is where the flow passes the
+  gate.
+* `updateFlow()` calls `setStages(pede, gateOn, gSaveMode == 1)`, so the four
+  states (pede/raw x gate on/off) are all live: verified with screenshots in all
+  four combinations - pedestal feeder live + funnel blue (pede+gate), funnel and
+  control arrow pale (pede+no gate), bypass live and pedestal feeder pale
+  (raw+gate), and the bypass stays live with the funnel pale (raw+no gate).
+
+### Flow diagram, final pass (operator's corrections)
+
+* **Lighter blue is now only the pedestal tracking pair** - the gate block ->
+  tracking input and the tracking -> Pedestal feedback.  The storage cell ->
+  Pedestal and Pedestal -> funnel connectors are part of the data flow, so they
+  are orange like the rest of the route.
+* **Orange is the whole save route**, entry point to Save panel, and it follows
+  the mode: frames = storage cell -> Pedestal -> funnel -> Gain -> ROI -> Save,
+  maps = ... -> Gain -> VPC -> Save.  Display-only branches stay light blue, and
+  in photon mode the Gain -> ROI rail is light blue as well.
+* **A route that carries no data is not drawn** (the operator found the pale
+  grey confusing): the raw bypass exists only in raw mode, the Pedestal path
+  only while the pedestal is in use, and only the selected mode's Save arrow
+  (ROI -> Save or VPC -> Save) is shown.  The one thing that still greys is the
+  gate funnel when the gate is off.
+* The **tracking input** now leaves the top-right corner of the gate block
+  (`yIn(sigGroup_, 6)`), not the funnel.
+* Verified with screenshots in four states: pede+gate frames (orange: SC ->
+  Pedestal -> funnel -> Gain -> rail -> ROI -> Save; bypass absent; tracking
+  pair lighter blue), the same in photon mode (orange through Gain -> counting
+  and the counting -> Save arrow, rail light blue, ROI -> Save absent),
+  raw+gate frames (orange storage cell -> funnel -> Gain -> ROI -> Save; the
+  Pedestal box carries no in/out at all, only the tracking feedback),
+  and pede+no-gate (funnel and its control arrow pale, everything else
+  unchanged).
+
+### The display path and the save path can differ (last refinement)
+
+The operator pointed out that the orange route must follow the *save* logic, not
+the `Pede/Raw` toggle: `flowStageStates()` now computes
+
+* `displayPede = PedestalStore::loaded() && !gNoPede`  (unchanged: the display,
+  gate, spectra and the map accumulation),
+* `savePede = (gSaveMode == 1) || (saveCorrected_ && !gNoPede)`  (the maps always
+  need `g0`; the frames are corrected only with the checkbox),
+* and `FlowStrip::setStages(displayPede, savePede, gateOn, photonMaps)` draws:
+
+| situation | what the diagram shows |
+|---|---|
+| display pede, `save frames`, `Pedestal corrected` **off** (the default!) | Pedestal feeder **light blue** (display only) + bypass **orange** (the file) - both live, the divergence visible |
+| `Pedestal corrected` **on** (or photon maps) | Pedestal feeder **orange**, bypass not drawn |
+| `Pede/Raw` = raw (both raw) | Pedestal path not drawn at all, bypass orange |
+| photon mode | pedestal route orange through Gain -> counting -> Save; the Gain -> ROI rail is light blue and the ROI -> Save arrow is absent |
+
+`saveCorrected_` also got a `toggled -> updateFlow()` connection (it had none) so
+the diagram follows the checkbox, and a `saveCorrected` entry in the `[rect]`
+geometry diagnostics for the click tests.
+
+Verified with screenshots: `--use-pede --gate` in frames mode showed the blue
+storage cell -> Pedestal -> funnel next to the orange storage cell -> funnel ->
+Gain -> ROI -> Save (both feeders into one funnel), and clicking `Pedestal
+corrected` turned the pedestal route orange and removed the bypass.
+
+### ROI input arrow + "Unset ROI" button
+
+* The ROI's incoming connector is now mode-dependent and always orange:
+  `Gain -> ROI` (the rail) while frames are written, `counting -> ROI` (a new
+  connector) while the maps are - they are cropped to the ROI on the way out, so
+  the ROI is only ever on the save path.  Only one of the two is drawn at a
+  time; `setStages()` flips them with `p4_.on = !photonMaps` / `p9_.on =
+  photonMaps`.
+* New **Unset ROI** button in the ROI panel (`unsetRoi()`): releases the "ROI
+  only" restriction if it is on, then `GateEngine::clearRoi()` (so `roiSet_` and
+  `roiOn_` are false and the rectangle is the full frame), clears the yellow
+  overlay, resets the counters and updates the read-outs.  The ROI list file is
+  not touched.
+* Verified: with `--gate-roi 100 50 200 100 --gate --stats` the live line showed
+  `roi=200x100@100,50`; clicking **Unset ROI** logged `[roi] ROI unset: full
+  frame` and the same line then showed `roi=off`, the panel reading
+  "no ROI selected | gate: full frame".  In `--save-photon` (photon mode) the
+  screenshot shows the orange connector from the counting panel into the ROI and
+  no rail from the Gain.
+
+### Save-time locking, truthful JSON, ROI->Save, and small labels
+
+Operator requests, all in and verified with a running `--save-photon` run:
+
+* **The arrow into the Save panel always leaves the ROI** (never the counting
+  panel): `arrPmapDown_` is gone, `arrRoiDown_` is always drawn and always
+  orange.  The maps reach the file through the ROI, which is also why the ROI's
+  own input flips between the Gain (frames) and the counting (maps).
+* `cumulative` -> **`cumulative (toggle to reset)`**, and the toggle now really
+  resets (`resetHis()`), so the label is true.
+* **`Pedestal corrected` moved under the `save frames` radio** (it is a property
+  of the saved frames; the maps are always pedestal-subtracted) and is greyed
+  while the photon-map mode is selected.
+* **The save counters no longer read 0 in photon mode**: `RoiSaver::Status`
+  gained `pmaps` + `photonMode` (Impl::pmapsInFile, fed by the writer loop), so
+  the GUI status line says "N maps written, M dropped" and `--stats` says
+  `save=1map/0` instead of `0/0`.
+* **Settings are locked while a save runs** (`applySaveLock()`): the whole save
+  panel except `Start/Stop save` and the status label, the storage-cell filter,
+  the manual pedestal work, the gain correction (keV PH stays live) and the
+  ROI select/load/unset buttons.  Live on purpose: everything display-only, the
+  pedestal tracker, the gate **threshold** and **min pixels**.  Those two open
+  `Changing settings during a run, are you sure?`; No puts the old value back
+  (`pipeline_.gate().threshold()/minPixels()`), Yes applies it and sets
+  `gGateChangedDuringSave`, which makes `writeJsonSidecar()` add
+  `gate_settings_modified_during_run: true` and a `gate_settings_note` (the
+  `gate` block stays the criterion from save start).  The lock is applied on
+  start, released on stop - including the automatic stop (budget/error), which
+  `updateStatus()` detects through `m_saveWasRunning`.
+* Verified on screen during a running photon-map save: save panel greyed except
+  Start/Stop, SC/pede/gain greyed, Threshold 150.0 and Min pixels 5 live, the
+  Virtual photon counting panel's two display controls live with the new label,
+  the photon threshold greyed, `Pedestal corrected` greyed under the frames
+  radio, and the Save status reading "1 map written, 0 dropped".
+
+### Layout bug (mine), destination list, "queue full"
+
+* **The `virtual photon counting` radio was rendered outside the Save box.**  When
+  I moved `Pedestal corrected` under the `save frames` radio I dropped the
+  `saveForm->addRow(saveModePhoton_);` line, so the radio had no layout slot and
+  Qt gave it a default geometry (measured: x=9, y=915, 100x30 - i.e. floating at
+  the left edge above the Save box, which is exactly what showed up as a stray
+  "Virtual phot..." fragment).  Re-added; the `[rect]` diagnostic now reads
+  `saveFramesRadio 21,996 | saveCorrected 21,1025 | savePhotonRadio 21,1054`,
+  all 788 px wide inside the box.  (`layoutFlow()` also repaints the central
+  widget after solving now, which is cheap insurance against leftovers in the
+  pads' wake.)
+* **The previous-destinations list is no longer polluted by the default**: the
+  start-up `--h5-dir`/`--h5-base` pair is captured once (`saveDefaultDir_`,
+  `saveDefaultBase_`) and a save that uses exactly that pair logs
+  `[save] <dir>/<base> is the default destination, not added to the
+  previous-destinations list` instead of recording it.  Verified: the list stayed
+  at 22 lines over a `--start-save` run with the default destination.  My own
+  test entries (`*_scratch*`, 23 of them) were pruned from
+  `save_dest_list.dat`; the real `/mnt/sls_det_storage/...` destinations and the
+  `test/_run`/`testPHmapsave` entries were left alone.
+* The dropped counter now reads `(writer behind: queue full)` and the README
+  explains it: the writer buffers at most 4096 items / 256 MB, so a slower disk
+  than the stream means the excess is dropped (and still counted by the gate
+  counters).
+
+* The drop note was attached unconditionally, so a healthy run read
+  "0 dropped (queue full)" - a problem that was not there.  It now says
+  `0 dropped (nothing lost)` while nothing is lost and only switches to
+  `(writer behind: queue full)` when the counter is non-zero.  Verified on a
+  running photon-map save: "1 map written, 0 dropped (nothing lost)".
+
+* The "Changing settings during a run, are you sure?" popup is now raised only
+  when **`Gate enabled` is ticked** (`confirmGateChangeDuringRun` returns early
+  on `!pipeline_.gate().enabled()`): with the gate off (passthrough) the
+  threshold and min-pixels change nothing about the saved frames, so they go
+  through silently and no `gate_settings_*` note is written.  Verified with a
+  running save: gate on + clicking a gate spinbox -> dialog shown and declining
+  logged `[save] gate change refused during the run (Min pixels above threshold
+  -> 6)`; the same click with `--no-gate` -> no dialog, no log line.
+
+### Image windows redrawn as plots (frame, axes, pixel grid, scale panel)
+
+Operator request: replace the side colour bar with a panel and make the images
+read as plots.
+
+* `FastImageView::imageRect()` now reserves axis margins (52 left / 26 bottom /
+  6 top-right) instead of the old bar strip; `paintEvent()` draws the frame,
+  tick labels outside the plot (Y = data rows, row 0 at the bottom), a dotted
+  grid inside it, and keeps the gate-ROI / receiver-ROI overlays as before.
+* `m_sx` (screen pixels per image pixel, from the last paint) drives the pixel
+  detail: thin outlines from 16 px, in-pixel values from 50 px
+  (`setIntegerValues(true)` for the photon map -> whole numbers, one decimal for
+  the real-valued images).  The label colour is chosen from the luminance of the
+  pixel that was actually painted; the loops are capped (<=256 px visible for
+  the grid, <=64 for the labels) so a deep zoom can never stall the painter.
+* The colour bar is off (`m_showBar = false`; `scaleRect()` returns an empty
+  rect so the old drag code is inert) and each image window now carries a
+  `ScalePanel` under it: `ScaleHisto` (the image's own 256-bin distribution with
+  the mapped range highlighted, refreshed at most every 300 ms from
+  `renderImage()`), a palette chooser wired to `paletteLut()` (kept in sync with
+  the `b`/`Shift+B`/`c` shortcuts), a lin/log switch, and min/max spin boxes
+  (also synced from `Set Ranges...`).
+* log mode maps `log10(max(v, 1e-2))` against `log10(max(range, 1e-2))`, so
+  values <= 0 land at 1e-2 = -2 instead of -inf, and the "zero is white" rule
+  for the photon map still applies first.
+* Verified on screen: the framed plot with the X labels (475..505) and Y labels
+  (97..90, high at the top) outside the frame, the dotted grid, the per-pixel
+  outlines at ~33 screen px/pixel, and the panel below with the histogram,
+  `palette: Col (jet)`, `lin`, `min -200.0`, `max 1000.0` (the ADC defaults).
+  Not yet seen on screen: the in-pixel numbers (they need >50 px/pixel, my
+  scripted wheel zoom stopped at ~33) and the histogram with a varied image
+  (a uniform test frame gives a single bin).  The old bar's drag-to-stretch on
+  the scale is gone by design: the range is set with the spin boxes (dragging on
+  the histogram is a possible follow-up).
+
+* Scale histogram refined to the operator's spec: fixed 38 px strip (the image
+  keeps the window stretch, the panel has a fixed height - about a tenth of the
+  window), one **solid** bar per bin whose width is the bin spacing on screen,
+  and the two range markers pinned at **1/4 and 3/4** of the width with the value
+  axis rescaling under them (the drawn window is the selected range widened by
+  half a range on each side, so dragging a marker moves that end of the range
+  and the marker snaps back to its fixed spot).  The bars are draggable
+  (`onRangeChanged` -> the panel pushes the new range into the view and the spin
+  boxes) and the ends are printed next to the markers.  A **second lin/log
+  switch** was added: `image` for the intensity mapping, `histo` for the bar
+  heights (log10(count+1)); the histogram's value axis always follows the image
+  switch.  Verified on screen: the thin strip with the two orange markers at
+  1/4 and 3/4 labelled `702.7` and `1000`, and a drag of the left marker moving
+  `min` from -200 to 702.7 (the bars were off-window by then, which is the
+  fixed-marker behaviour).
+
+### Palette list widened to the matplotlib family
+
+The scale panel's palette chooser now offers 18 maps instead of 3 (the original
+`Col (jet)`, the two ROOT-like greys, then the new ones).  The `Palette` enum
+keeps `Color/BW1/BW2` first so the `b` / `Shift+B` / `c` shortcuts and
+`setPaletteChoice()` keep working, and `paletteName()` (new, in
+`online_jf_root.cpp`, deliberately outside the anonymous namespace) feeds the
+combo so the names live in one place.
+
+* New: Turbo, Viridis, Plasma, Inferno, Magma, Cividis, Hot, Grey (linear),
+  Grey reversed, Coolwarm, BWR, Seismic, RdBu, YlGnBu, Sunset.
+* Anchors: the perceptually uniform ones are matplotlib's published anchors and
+  Turbo is Google's; the diverging/sequential set uses matplotlib's definitions
+  and the ColorBrewer / Paul Tol anchors (YlGnBu, Sunset) as republished in
+  `bokeh/palettes.py`, which is where I looked them up - bokeh's licence header
+  attributes Viridis/Magma/Plasma/Inferno to Nathaniel Smith et al. (CC0),
+  Turbo to Google (Apache-2.0), the Brewer maps to Cynthia Brewer (Apache-2.0)
+  and Tol's to Paul Tol (BSD-3).  Everything is interpolated by the existing
+  piecewise-linear `PaletteDef`, whose stop/colour arrays were grown from 5 to
+  24 entries to hold the 15-anchor turbo ramp; the LUTs are now one
+  `g_luts[kNumPalettes][256]` table built by the same `buildLut()` loop, so a new
+  palette is only an enum entry plus its anchors.
+* Verified: the entry list builds and the app runs; selecting `Seismic
+  (diverging)` in the ADC window turned the image seismic-blue (raw ~100 ADU on
+  the -200..1000 range lands just below the white midpoint, as expected) with
+  the panel and histogram following.
+
+* The **gain window** lost its scale panel entirely (no histogram, no palette /
+  lin-log / range controls): its image holds four valid numbers - the gain bits
+  0..3 - so there is neither a distribution to show nor a scale to choose.  It
+  now uses a fixed `Palette::Gain4` map (0 muted blue, 1 muted green, 2 muted
+  yellow, 3 muted red, all desaturated on purpose so a large flat map does not
+  glare) with the range pinned to 0..3, and whole-number in-pixel labels.  The
+  palette is in the enum but deliberately **not** in the chooser loop
+  (`i <= int(Palette::Sunset)`), so the three image windows keep their own
+  choices.
+
+* In-pixel numbers: the font now also has to fit the *width* of the label, not
+  just the pixel height - five characters for the photon counts, six for the
+  real-valued images ("XXXXX.y"), at ~0.62 em per digit, still capped at 0.30 em
+  of the pixel so the "small tidy number" look is kept (range now 7..20 px).
+  At 50 px/pixel that is 12 px instead of 15, which is what makes five digits
+  fit; the widest label stays under the pixel edge for every zoom level above
+  the 50 px threshold.
+
+### Zoom coordination switch (Display panel)
+
+Operator request: zooming used to be ADC-master only (the ADC view propagated to
+the gain/photon windows and the ROOT plots, never the other way round).  Now
+`zoomTo(FastImageView *src, ...)` takes the view that asked, and every image view
+reports its zoom through the same wiring (`wireZoom()` for ADC, gain and photon),
+so **any** window zooms all of them.  A new `zoom coordination` checkbox in the
+Display panel (default **on**) gates the propagation: when it is off, `zoomTo()`
+returns immediately, so each window keeps its own zoom and nothing is pushed to
+the others - including the ROOT canvases, which as a consequence no longer follow
+the ADC while the box is off (say the word if they should keep following it
+regardless).  Both transitions are logged (`[zoom] coordination on/off`) and
+every coordinated zoom logs its source (`[zoom] coordinated from ADC/gain/photon`).
+
+Verified: with the default on, five wheel steps over the ADC window produced 10
+`coordinated from ADC` events (two per step: wheel plus the drag path); the
+checkbox is present at a sane place in the Display panel
+(`[rect] zoomCoord 476,730 333x23`, ticked).  The OFF case is a single
+`if (!zoomCoord_) return;` on that same path.
+
+### Makefile: both variants from one `make`
+
+`make jfstrx` used to rebuild the *same* binary with `-DJFSTRX` (the old
+`.buildflags` stamp existed only to force a full rebuild when switching), so the
+two variants overwrote each other.  Now the objects and the executables are
+separate:
+
+* `online_jf_*.o` + `jf_online_display_gui` (normal),
+* `online_jf_*.JFSTRX.o` + `jf_online_display_gui_JFSTRX` (compiled with
+  `-DJFSTRX`),
+
+and `all` builds both, so the two can never be mixed by accident (they have
+different geometry and struct layouts).  `make normal` and `make jfstrx` remain
+as aliases, the flag stamp is gone, `clean` removes both sets, and `.gitignore`
+covers the second binary and the `.JFSTRX.o` files.
+
+* Zoomed images were painted over the axes: the scaled image is much larger than
+  the plot area (only the viewport window is meant to be visible), and the ROI
+  overlays were drawn in widget coordinates without a clip, so a ROI partly
+  outside the visible window ran across the tick labels and up to the window
+  edge.  `paintEvent()` now sets `setClipRect(ir)` around the image and around
+  the two overlays (restoring before the axes so the frame, grid and labels are
+  drawn on top of a clean widget).  Verified by sampling a deep-zoom screenshot:
+  the margin left of the frame is the widget's black background, not image
+  colour, while the plot interior still carries the image.
+
+* The strip-xel decoder (../../dataStructures/jungfrauLGADStrixelsData_new.h)
+  dumped its header on every construction - "Jungfrau strixels 2X single chip
+  with full module data" / "sizeofheader = 112" - once per displayed frame in
+  the JFSTRX build.  Those three `std::cout` statements are commented out (the
+  header is shared, outside this project, so the edit needed the wider sandbox
+  permission; it is a comment-only change and easy to revert).
+* Deepest zoom is now build-dependent (`kMinViewport`): 8 image pixels across in
+  the plain build as before, **2** in the JFSTRX build, so single strixel pixels
+  can be inspected (the mapped panels are ~1000 x 1900).  The same constant
+  guards `setViewport()` and `zoomTo()`, so a coordinated zoom propagates down
+  to the new limit.
+
+### Dual-interface alignment: drain fast, pair index-aligned, shed on backlog
+
+Operator report: after the machine had been busy for a while the two interfaces
+stopped being aligned and never recovered, with the deltas fluctuating. There
+were two causes, one on each side.
+
+* **Holding a slab is back-pressure.** The old pairing stopped polling an
+  interface whose slab was waiting for its partner (`events = 0`) and accepted
+  only *equal* frame numbers. That fills slsReceiver's ZMQ ring, and the
+  receiver then skips frames **on its own side** - per interface, not per
+  frame - so the two frame numbers drift apart and, with exact matching, never
+  meet again. Waiting "until the partner catches up" made it worse.
+
+What the code does now (`Pipeline::tryAssemble()` in `online_jf_core.cpp`):
+
+* **Always drain.** Every socket is polled on every turn and drained down to
+  its newest message (bounded to 32 messages per socket and wake-up, so no
+  interface is starved). Nothing is ever held, so the receiver's buffer stays
+  empty - the whole point at 2 kHz.
+* **Pair index-aligned or not at all.** When the newest slabs carry different
+  frame numbers (one interface skipped), the pair is **dropped** (`resync`) and
+  the next one is tried, so every frame that is displayed or saved is stitched
+  from a single detector frame. No chasing, no unbounded wait, no half frames.
+* **Latch for a permanent offset.** If nothing pairs for 500 ms the offset is
+  structural (an interface that keeps skipping), so the newest slabs are paired
+  anyway (`skewedPairs_`, logged) to keep the stream alive; strict pairing
+  comes back by itself as soon as a pair matches again.
+* **Decimation is manual by default**, `--decimate 2|4|8` (1 frame in N, dropped
+  by detector frame number so both interfaces drop the same ones).  The automatic
+  ladder (1 -> 2 -> 4 -> 8, stepping back up after 5 s clean) only runs with
+  `--auto-decimate`: frames are queued in the *gate*, so the backlog is
+  `framesIn - framesPass - framesDrop - framesScDrop` - counting gate rejects as
+  backlog used to pin the ladder at 1/8 whenever the gate rejected anything.
+* **A silent interface is reported, not waited for**, so a dead stream cannot
+  freeze the pipeline.
+* Audit: `--stats` prints `resync` / `behind` / `incomplete` and the
+  per-second `[align] keep=1/<N> shed=<n>` line; ladder steps and "dropping the
+  pair" messages are rate-limited.
+
+Verified against the live receiver `10.1.1.106 30026+30027` at ~2000 frames/s:
+20 s runs alone and with eight CPU hogs (`yes`) both keep `drop=0`,
+`in == pass`, `keep=1/1`, `shed=0`, with no unpaired-interface message. The
+synthetic feeder with equal keys gives `resync=0`; with a permanent one-frame
+offset (`dual ... 1`) the latch keeps ~16 frames/s at 20 fps instead of
+stalling. At 2 kHz the interfaces are a frame apart often enough that roughly
+one pair in four is dropped by the strict rule - the intended trade (aligned
+frames only). A one-frame lookahead per interface (swap two buffers, no copy)
+would recover them; it is the obvious follow-up if the saved-frame rate ever
+matters.

slsDetectorCalibration/jungfrauExecutables/jf_online_display_gui/test/gate_contig_test.cpp

@@ -0,0 +1,184 @@
+// Unit test for the gate's contiguity proxy ("Contiguous (N px within circle,
+// r = N/2+1)").
+//
+// The rule must be: pass when SOME circle of radius r contains at least N
+// above-threshold pixels.  It used to require every above-threshold pixel to be
+// within r of the centroid, which rejected perfectly valid events (two
+// separated clusters) - the bug this test pins down.
+//
+// Build: make gate_contig_test   Run: ./test/gate_contig_test
+#include "online_jf.h"
+
+#include <algorithm>
+#include <cstdio>
+#include <utility>
+#include <vector>
+
+namespace {
+
+int gFail = 0;
+
+void expect(const char *what, bool got, bool want) {
+    const bool ok = (got == want);
+    if (!ok)
+        gFail++;
+    std::printf("%-58s %s (got %s, want %s)\n", what, ok ? "ok  " : "FAIL",
+                got ? "pass" : "drop", want ? "pass" : "drop");
+}
+
+struct Frame {
+    std::vector<short> px = std::vector<short>(NCH, 0);
+
+    void hit(int x, int y, short v = 2000) {
+        px[static_cast<size_t>(y) * kRawWidth + x] = v;
+    }
+    void clear() { std::fill(px.begin(), px.end(), 0); }
+};
+
+// Runs the real GateEngine over the frame, raw ADC values, no pedestals.
+bool passes(GateEngine &g, Frame &f) {
+    uint64_t above = 0;
+    bool scDropped = false;
+    return g.evaluate(f.px.data(), NCH, 0, nullptr, 0, 0, above, &scDropped);
+}
+
+} // namespace
+
+int main() {
+    GateEngine g;
+    g.setEnabled(true);
+    g.setThreshold(1000.0f); // the frame's hits are 2000 -> above threshold
+    g.setMinPixels(5);
+    g.setContiguous(true);
+
+    Frame f;
+
+    // 1. one tight cluster of exactly N hits: must pass
+    f.clear();
+    for (int i = 0; i < 5; i++)
+        f.hit(100 + i, 100);
+    expect("5 hits in a row (spread 4 px <= 2r)", passes(g, f), true);
+
+    // 2. a compact blob: must pass
+    f.clear();
+    f.hit(300, 200);
+    f.hit(301, 200);
+    f.hit(302, 200);
+    f.hit(301, 201);
+    f.hit(301, 199);
+    expect("5 hits in a compact cross", passes(g, f), true);
+
+    // 3. N hits far apart, no cluster: must be rejected
+    f.clear();
+    for (int i = 0; i < 5; i++)
+        f.hit(100 + 100 * i, 300);
+    expect("5 isolated hits 100 px apart", passes(g, f), false);
+
+    // 4. fewer than N hits, however tight: must be rejected
+    f.clear();
+    for (int i = 0; i < 4; i++)
+        f.hit(500 + i, 400);
+    expect("4 hits (below min pixels)", passes(g, f), false);
+
+    // 5. THE REPORTED BUG: two separated clusters, each with N hits.
+    //    The centroid falls between them, which used to reject the frame.
+    f.clear();
+    for (int i = 0; i < 5; i++)
+        f.hit(100 + i, 50); // cluster A
+    for (int i = 0; i < 5; i++)
+        f.hit(700 + i, 450); // cluster B
+    expect("two clusters of 5, 700 px apart (must pass)", passes(g, f), true);
+
+    // 6. two groups of 4: no circle holds 5 -> reject
+    f.clear();
+    for (int i = 0; i < 4; i++)
+        f.hit(100 + i, 60);
+    for (int i = 0; i < 4; i++)
+        f.hit(600 + i, 440);
+    expect("two clusters of 4 (no circle holds 5)", passes(g, f), false);
+
+    // 7. a spread-out event with one dense core: pass
+    f.clear();
+    for (int i = 0; i < 5; i++)
+        f.hit(400 + i, 300);
+    f.hit(800, 100);
+    f.hit(900, 200);
+    expect("dense core plus 2 stragglers", passes(g, f), true);
+
+    // 8. N follows min_pixels: 3 hits pass when min_pixels is 3
+    g.setMinPixels(3);
+    f.clear();
+    for (int i = 0; i < 3; i++)
+        f.hit(200 + i, 200);
+    expect("3 hits with min_pixels = 3", passes(g, f), true);
+    f.clear();
+    for (int i = 0; i < 2; i++)
+        f.hit(200 + i, 200);
+    expect("2 hits with min_pixels = 3", passes(g, f), false);
+
+    // 9. contiguity off: the plain count decides (2 hits < 3 -> reject)
+    g.setContiguous(false);
+    f.clear();
+    f.hit(10, 10);
+    f.hit(900, 400);
+    expect("contiguity off, 2 hits with min_pixels = 3", passes(g, f), false);
+    f.clear();
+    for (int i = 0; i < 3; i++)
+        f.hit(10 + i, 10);
+    expect("contiguity off, 3 hits with min_pixels = 3", passes(g, f), true);
+
+    // ---- hot pixel mask taken from a photon map ---------------------------
+    {
+        GateEngine h;
+        h.setEnabled(true);
+        h.setThreshold(1000.0f);
+        h.setMinPixels(5);
+        h.setContiguous(false);
+        h.setHotSuppress(true);
+
+        // The map has two very bright pixels: those are the hot ones.
+        std::vector<float> map(NCH, 0.0f);
+        map[10 * kRawWidth + 10] = 400.0f;
+        map[10 * kRawWidth + 11] = 900.0f;
+        hotSetMaskFromMap(map.data(), map.size(), 100.0);
+        std::printf("mask from map > 100: %llu px (want 2)\n",
+                    static_cast<unsigned long long>(hotPixelCount()));
+        if (hotPixelCount() != 2)
+            gFail++;
+
+        Frame f3;
+        // 5 hits, two of them on the masked pixels -> only 3 count -> drop
+        f3.clear();
+        for (int i = 0; i < 5; i++)
+            f3.hit(10 + i, 10);
+        expect("5 hits, 2 on hot pixels (min 5)", passes(h, f3), false);
+
+        // a real cluster away from the mask still passes
+        f3.clear();
+        for (int i = 0; i < 5; i++)
+            f3.hit(300 + i, 300);
+        expect("real cluster of 5 with the mask active", passes(h, f3), true);
+
+        // cleared mask: the hot pixels count again
+        hotClearMask();
+        expect("after hotClearMask, 5 hits count", passes(h, f3), true);
+        f3.clear();
+        for (int i = 0; i < 5; i++)
+            f3.hit(10 + i, 10);
+        expect("after hotClearMask, the 5 hits pass", passes(h, f3), true);
+
+        // suppression off: the mask is ignored by the gate
+        hotSetMaskFromMap(map.data(), map.size(), 100.0);
+        h.setHotSuppress(false);
+        f3.clear();
+        for (int i = 0; i < 5; i++)
+            f3.hit(10 + i, 10);
+        expect("suppression off, masked pixels count again", passes(h, f3),
+               true);
+        hotClearMask();
+    }
+
+    std::printf("\n%s (%d failure(s))\n", gFail ? "FAILED" : "all tests passed",
+                gFail);
+    return gFail ? 1 : 0;
+}

slsDetectorCalibration/jungfrauExecutables/jf_online_display_gui/test/jf_feeder.cpp

@@ -0,0 +1,233 @@
+// SPDX-License-Identifier: LGPL-3.0-or-other
+// ===========================================================================
+// test/jf_feeder.cpp -- synthetic slsReceiver stand-in.
+//
+// Publishes the same <json header><binary frame> ZMQ message pair that
+// slsReceiver sends, so jf_online_display_gui can be exercised without hardware.
+//
+// Every 3rd frame carries NO signal; the other frames carry a 40-pixel
+// cluster at ADC 300 on a baseline of 100.  With
+//     ./jf_online_display_gui 400 127.0.0.1 30777 --stats --pede /nonexistent
+// the gate threshold is 200, so exactly 2/3 of the frames must pass.
+//
+//   make feeder
+//   ./test/jf_feeder tcp://*:30777 200 20 &
+//   ./jf_online_display_gui 400 127.0.0.1 30777 --stats --pede /nonexistent
+//
+// Subscriber mode (counts the frames republished by --pub):
+//   ./test/jf_feeder sub tcp://127.0.0.1:30778 8
+//
+// 4th positional arg = initial silent period in seconds (idle-receiver test).
+// ===========================================================================
+#include <zmq.h>
+
+#include <chrono>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
+#include <string>
+#include <thread>
+#include <vector>
+
+namespace {
+
+int runSubscriber(const char *addr, int seconds) {
+    void *ctx = zmq_ctx_new();
+    void *sub = zmq_socket(ctx, ZMQ_SUB);
+    int rcvtimeo = 200;
+    zmq_setsockopt(sub, ZMQ_RCVTIMEO, &rcvtimeo, sizeof(rcvtimeo));
+    zmq_setsockopt(sub, ZMQ_SUBSCRIBE, "", 0);
+    if (zmq_connect(sub, addr) != 0) {
+        fprintf(stderr, "connect %s failed: %s\n", addr,
+                zmq_strerror(zmq_errno()));
+        return 1;
+    }
+    printf("subscriber: connected to %s for %d s\n", addr, seconds);
+    fflush(stdout);
+
+    std::vector<char> data(2 * 1024 * 1024);
+    char hdr[16384];
+    int frames = 0, endMarkers = 0;
+    int dumped = 0;
+    const auto deadline =
+        std::chrono::steady_clock::now() + std::chrono::seconds(seconds);
+    while (std::chrono::steady_clock::now() < deadline) {
+        const int hn = zmq_recv(sub, hdr, sizeof(hdr) - 1, 0);
+        if (hn < 0)
+            continue;
+        hdr[hn] = '\0';
+        const bool isData = (strstr(hdr, "\"data\":1") != nullptr);
+        if (isData)
+            frames++;
+        else if (strstr(hdr, "\"data\":0") != nullptr)
+            endMarkers++;
+        int more = 0;
+        size_t moreSize = sizeof(more);
+        zmq_getsockopt(sub, ZMQ_RCVMORE, &more, &moreSize);
+        int dn = -1;
+        if (more)
+            dn = zmq_recv(sub, data.data(), data.size(), 0);
+        if (dumped < 3) {
+            dumped++;
+            char head[400];
+            snprintf(head, sizeof(head), "%.399s", hdr);
+            printf("subscriber: hdr_len=%d data_len=%d more=%d head=%s\n", hn,
+                   dn, more, head);
+            fflush(stdout);
+        }
+    }
+    printf("subscriber: received %d data frames, %d end markers\n", frames,
+           endMarkers);
+    fflush(stdout);
+    zmq_close(sub);
+    zmq_ctx_term(ctx);
+    return frames > 0 ? 0 : 1;
+}
+
+// Dual-interface stand-in: two PUB sockets on base and base+1, each sending
+// one 1024x256 Y-slab of the same frame (the slsReceiver multi-UDP-interface
+// layout).  The bottom slab is filled with botVal, the top slab with topVal,
+// so the assembled image can be verified from the gate counters.
+//   ./test/jf_feeder dual <basePort> <nframes> <fps> [delaySec] [botVal]
+//                       [topVal] [topLagFrames]
+int runDual(const char *baseStr, int nframes, int fps, int delayMs, int botVal,
+            int topVal, int topLag) {
+    const int base = atoi(baseStr);
+    const int W = 1024, H = 256;
+    const int bytes = W * H * 2;
+
+    void *ctx = zmq_ctx_new();
+    void *bot = zmq_socket(ctx, ZMQ_PUB);
+    void *top = zmq_socket(ctx, ZMQ_PUB);
+    int hwm = 1000;
+    zmq_setsockopt(bot, ZMQ_SNDHWM, &hwm, sizeof(hwm));
+    zmq_setsockopt(top, ZMQ_SNDHWM, &hwm, sizeof(hwm));
+    const std::string a0 = "tcp://*:" + std::to_string(base);
+    const std::string a1 = "tcp://*:" + std::to_string(base + 1);
+    if (zmq_bind(bot, a0.c_str()) != 0 || zmq_bind(top, a1.c_str()) != 0) {
+        fprintf(stderr, "dual bind failed: %s\n", zmq_strerror(zmq_errno()));
+        return 1;
+    }
+    printf("feeder: dual mode on %s and %s, %d frames at %d fps "
+           "(bot=%d top=%d topLag=%d)\n",
+           a0.c_str(), a1.c_str(), nframes, fps, botVal, topVal, topLag);
+    fflush(stdout);
+
+    std::vector<short> slab(W * H);
+    std::this_thread::sleep_for(std::chrono::milliseconds(delayMs));
+
+    auto sendSlab = [&](void *sock, int value, int frameNo) {
+        for (size_t i = 0; i < slab.size(); i++)
+            slab[i] = static_cast<short>(value);
+        char hdr[512];
+        // detSpec3 bits 8-11 carry the storage cell; cycle 0..15 so the SC
+        // filter can be exercised end to end
+        const unsigned detSpec3 = ((unsigned)(frameNo % 16) & 0xF) << 8;
+        const int hn = snprintf(
+            hdr, sizeof(hdr),
+            "{\"jsonversion\":5,\"data\":1,\"size\":%d,"
+            "\"shape\":[%d,%d],\"frameNumber\":%d,\"frameIndex\":%d,"
+            "\"detSpec1\":0,\"detSpec3\":%u}",
+            bytes, W, H, frameNo, frameNo, detSpec3);
+        zmq_send(sock, hdr, hn, ZMQ_SNDMORE);
+        zmq_send(sock, slab.data(), bytes, 0);
+    };
+
+    for (int f = 0; f < nframes; f++) {
+        sendSlab(bot, botVal, f);
+        const int topFrame = (f - topLag >= 0) ? f - topLag : f;
+        sendSlab(top, topVal, topFrame);
+        std::this_thread::sleep_for(
+            std::chrono::milliseconds(1000 / (fps > 0 ? fps : 1)));
+    }
+    const char *endhdr = "{\"jsonversion\":5,\"data\":0}";
+    zmq_send(bot, endhdr, strlen(endhdr), 0);
+    zmq_send(top, endhdr, strlen(endhdr), 0);
+    printf("feeder: dual done\n");
+    fflush(stdout);
+    zmq_close(bot);
+    zmq_close(top);
+    zmq_ctx_term(ctx);
+    return 0;
+}
+
+} // namespace
+
+int main(int argc, char **argv) {
+    if (argc > 1 && std::string(argv[1]) == "sub") {
+        const char *addr = (argc > 2) ? argv[2] : "tcp://127.0.0.1:30778";
+        const int seconds = (argc > 3) ? atoi(argv[3]) : 8;
+        return runSubscriber(addr, seconds);
+    }
+    if (argc > 1 && std::string(argv[1]) == "dual") {
+        return runDual(argc > 2 ? argv[2] : "30777", argc > 3 ? atoi(argv[3]) : 60,
+                       argc > 4 ? atoi(argv[4]) : 25,
+                       argc > 5 ? atoi(argv[5]) * 1000 : 800,
+                       argc > 6 ? atoi(argv[6]) : 100,
+                       argc > 7 ? atoi(argv[7]) : 150,
+                       argc > 8 ? atoi(argv[8]) : 0);
+    }
+
+    const char *addr = (argc > 1) ? argv[1] : "tcp://*:30777";
+    const int nframes = (argc > 2) ? atoi(argv[2]) : 200;
+    const int fps = (argc > 3) ? atoi(argv[3]) : 20;
+    // optional 4th arg: stay bound and connected but SILENT for N seconds
+    // first (checks that an idle-but-alive receiver is not called "stopped")
+    const int delayMs = (argc > 4) ? atoi(argv[4]) * 1000 : 800;
+    const int NCH = 524288;
+
+    void *ctx = zmq_ctx_new();
+    void *pub = zmq_socket(ctx, ZMQ_PUB);
+    int hwm = 1000;
+    zmq_setsockopt(pub, ZMQ_SNDHWM, &hwm, sizeof(hwm));
+    if (zmq_bind(pub, addr) != 0) {
+        fprintf(stderr, "bind %s failed: %s\n", addr,
+                zmq_strerror(zmq_errno()));
+        return 1;
+    }
+    printf("feeder: bound %s, sending %d frames at %d fps\n", addr, nframes,
+           fps);
+    fflush(stdout);
+
+    std::vector<short> frame(NCH);
+    std::this_thread::sleep_for(std::chrono::milliseconds(delayMs));
+
+    // detSpec1 packs the receiver ROI as 4 x uint16: xmin|xmax|ymin|ymax
+    const unsigned long long detSpec1 = ((unsigned long long)10u << 48) |
+                                        ((unsigned long long)400u << 32) |
+                                        ((unsigned long long)20u << 16) | 300u;
+
+    for (int f = 0; f < nframes; f++) {
+        const bool signal = (f % 3) != 0;
+        for (int i = 0; i < NCH; i++)
+            frame[i] = 100; // baseline, gain 0
+        if (signal)
+            for (int k = 0; k < 40; k++)
+                frame[1000 + k] = 300; // 40 px above the 200 threshold
+
+        char hdr[512];
+        const int hn = snprintf(
+            hdr, sizeof(hdr),
+            "{\"jsonversion\":5,\"data\":1,\"size\":%d,\"detSpec1\":%llu,"
+            "\"frameIndex\":%d,\"bitmode\":1,\"fileIndex\":0,"
+            "\"detshape\":[1,1],\"shape\":[1024,512],\"acqIndex\":%d,"
+            "\"frameNumber\":%d,\"expLength\":0,\"packetNumber\":0,"
+            "\"timestamp\":0,\"modId\":0,\"row\":0,\"column\":0,\"detSpec2\":0,"
+            "\"detSpec3\":%u,\"detSpec4\":0,\"detType\":0,\"version\":0,"
+            "\"flipRows\":0,\"quad\":0,\"completeImage\":1}",
+            NCH * 2, detSpec1, f, f, f,
+            ((unsigned)(f % 16) & 0xF) << 8);
+        zmq_send(pub, hdr, hn, ZMQ_SNDMORE);
+        zmq_send(pub, frame.data(), NCH * 2, 0);
+        std::this_thread::sleep_for(
+            std::chrono::milliseconds(1000 / (fps > 0 ? fps : 1)));
+    }
+
+    const char *endhdr = "{\"jsonversion\":5,\"data\":0}";
+    zmq_send(pub, endhdr, strlen(endhdr), 0);
+    printf("feeder: done\n");
+    fflush(stdout);
+    zmq_close(pub);
+    zmq_ctx_term(ctx);
+    return 0;
+}

slsDetectorCalibration/jungfrauExecutables/jf_online_display_gui/test/panel_map_test.cpp

@@ -0,0 +1,65 @@
+// Standalone JFSTRX check that the six-panel fill geometry is consistent with
+// the strixel decoder: every real (non-dummy) mapped pixel must land inside a
+// valid panel at an in-range local coordinate, and each panel must be fully
+// covered by the decoder map (so no panel stays empty / has holes).
+#include "online_jf.h"
+
+#include "jungfrauLGADStrixelsData_new.h"
+#include "sls/sls_detector_defs.h"
+#include "slsDetectorData.h"
+
+#include <cstdio>
+
+using header = sls::defs::sls_receiver_header;
+
+int main() {
+    initGeometry();
+    jungfrauLGADStrixelsData *dec = new jungfrauLGADStrixelsData();
+    const int g1_nrows = 165, g2_nrows = 320, g3_nrows = 476;
+    const int mc6g3_start = g1_nrows + g2_nrows + g3_nrows;
+    static const int panelStartY[kNumAdcPanels] = {0,   165, 485,
+                                                   1757, 1437, 961};
+    long perPanel[kNumAdcPanels] = {0};
+    long real = 0;
+    long dropped = 0; // real pixels outside the booked panel rectangles
+    bool ok = true;
+    for (int ipx = 0; ipx < nx; ++ipx) {
+        for (int ipy = 0; ipy < ny; ++ipy) {
+            if (dec->dataMap[ipy][ipx] == int(sizeof(header)))
+                continue; // dummy strixel
+            ++real;
+            const int group = dec->groupmap[ipy][ipx];
+            if (group < 0 || group > 2) {
+                ok = false;
+                continue;
+            }
+            const int base = (ipy >= mc6g3_start) ? 3 : 0;
+            const int p = base + group;
+            const int lx = ipx;
+            const int ly = ipy - panelStartY[p];
+            if (lx < 0 || lx >= kAdcPanelW[p] || ly < 0 || ly >= kAdcPanelH[p]) {
+                // the decoder maps a couple of extra right-edge columns for
+                // chip1 g2/g3 that the ROOT histograms (and these panels) do
+                // not book; dropping them matches the original display
+                ++dropped;
+                continue;
+            }
+            ++perPanel[p];
+        }
+    }
+    delete dec;
+
+    std::printf("mapped %d x %d, real pixels %ld, dropped edge pixels %ld\n",
+                nx, ny, real, dropped);
+    for (int p = 0; p < kNumAdcPanels; ++p) {
+        const long need = long(kAdcPanelW[p]) * kAdcPanelH[p];
+        std::printf("panel %d: %dx%d  filled %ld/%ld%s\n", p, kAdcPanelW[p],
+                    kAdcPanelH[p], perPanel[p], need,
+                    perPanel[p] == need ? "" : "  <-- NOT FULL");
+        if (perPanel[p] != need)
+            ok = false;
+    }
+    std::printf("%s\n", ok ? "PASS: six-panel geometry"
+                           : "FAIL: six-panel geometry");
+    return ok ? 0 : 1;
+}

slsDetectorCalibration/jungfrauExecutables/jf_online_display_gui/test/pede_live_test.cpp

@@ -0,0 +1,171 @@
+// Standalone check for the ROI writer (no hardware, no GUI):
+//
+//   1. a Pedestal corrected save follows the LIVE pedestal, not the snapshot
+//      taken at Start Save (one frame before, one after a mid-run swap);
+//   2. the periodic checkpoint leaves a CLEAN pair on disk while the save is
+//      still running: the JSON sidecar is published atomically (.part ->
+//      rename) and the HDF5 is shrunk to exactly the frames written, so a
+//      copy taken at a checkpoint boundary is self-consistent.
+//
+// Not part of the build; compile by hand, see README "Testing without
+// hardware".
+#include "online_jf.h"
+
+#include "H5Cpp.h"
+
+#include <algorithm>
+#include <chrono>
+#include <cstdio>
+#include <fstream>
+#include <memory>
+#include <sstream>
+#include <string>
+#include <thread>
+#include <vector>
+
+using namespace H5;
+
+static bool fileExists(const std::string &p) {
+    std::ifstream f(p);
+    return f.good();
+}
+
+static std::string readFile(const std::string &p) {
+    std::ifstream f(p, std::ios::binary);
+    std::ostringstream ss;
+    ss << f.rdbuf();
+    return ss.str();
+}
+
+// Read the /data frame count and the first pixel of one slice from the LIVE
+// file with the SWMR read flag - exactly what an external checker does while
+// the save runs.
+static bool readSlice(const std::string &path, hsize_t slice, hsize_t &frames,
+                      float &px) {
+    hid_t f = H5Fopen(path.c_str(), H5F_ACC_RDONLY | H5F_ACC_SWMR_READ,
+                      H5P_DEFAULT);
+    if (f < 0)
+        return false;
+    hid_t d = H5Dopen2(f, "/data", H5P_DEFAULT);
+    if (d < 0) {
+        H5Fclose(f);
+        return false;
+    }
+    hid_t s = H5Dget_space(d);
+    hsize_t dims[3] = {0, 0, 0};
+    H5Sget_simple_extent_dims(s, dims, nullptr);
+    frames = dims[0];
+    bool ok = false;
+    if (dims[0] > slice) {
+        hsize_t off[3] = {slice, 0, 0};
+        hsize_t cnt[3] = {1, 1, 1};
+        H5Sselect_hyperslab(s, H5S_SELECT_SET, off, nullptr, cnt, nullptr);
+        hid_t m = H5Screate_simple(3, cnt, nullptr);
+        ok = H5Dread(d, H5T_NATIVE_FLOAT, m, s, H5P_DEFAULT, &px) >= 0;
+        H5Sclose(m);
+    }
+    H5Sclose(s);
+    H5Dclose(d);
+    H5Fclose(f);
+    return ok;
+}
+
+// wait until the periodic JSON says at least `saved` frames are committed
+static std::string waitJson(const std::string &jsonPath, uint64_t saved) {
+    const std::string needle = "\"saved\": " + std::to_string(saved);
+    for (int i = 0; i < 100; i++) {
+        if (fileExists(jsonPath)) {
+            const std::string t = readFile(jsonPath);
+            if (t.find(needle) != std::string::npos)
+                return t;
+        }
+        std::this_thread::sleep_for(std::chrono::milliseconds(50));
+    }
+    return {};
+}
+
+int main() {
+    const int W = 1024, H = 4;
+    const hsize_t h = 4, w = 8;
+
+    RoiSaver saver;
+    RoiSaver::StartInfo info;
+    info.x = 0;
+    info.y = 0;
+    info.w = static_cast<int>(w);
+    info.h = static_cast<int>(h);
+    info.dir = ".";
+    info.baseName = "pede_live_test";
+    info.corrected = true;
+    info.checkpointMs = 300; // fast checkpoints for the test
+
+    auto setA = std::make_shared<PedeSet>();
+    std::fill(setA->g0.begin(), setA->g0.end(), 100.0f);
+    PedestalStore::instance().install(setA);
+    info.peds = setA; // the snapshot the GUI would have taken at Start Save
+
+    std::string err;
+    if (!saver.start(info, err)) {
+        std::printf("FAIL start: %s\n", err.c_str());
+        return 1;
+    }
+    const std::string h5 = saver.status().h5Path;
+    const std::string js = saver.status().jsonPath;
+
+    std::vector<short> frame(static_cast<size_t>(W) * H, 1000);
+    SavedFrameHeader h1;
+    h1.frameNumber = 1;
+    saver.offer(frame.data(), W, H, h1);
+
+    // --- checkpoint 1: exactly one frame, corrected with pedestal A -------
+    const std::string j1 = waitJson(js, 1);
+    if (j1.empty()) {
+        std::printf("FAIL: no periodic JSON with 1 frame\n");
+        return 2;
+    }
+    const bool liveMid = j1.find("\"complete\": false") != std::string::npos;
+    hsize_t n1 = 0;
+    float p1 = -1.0f;
+    const bool live1 = readSlice(h5, 0, n1, p1); // live file, SWMR read
+    std::printf("checkpoint1: periodic json (complete:false)=%s  live swmr "
+                "read=%s  h5 extent=%llu  px=%.1f (expect true, true, 1, 900)\n",
+                liveMid ? "true" : "false", live1 ? "true" : "false",
+                (unsigned long long)n1, p1);
+
+    // --- the tracker swaps the pedestal mid-run ---------------------------
+    auto setB = std::make_shared<PedeSet>();
+    std::fill(setB->g0.begin(), setB->g0.end(), 150.0f);
+    PedestalStore::instance().install(setB);
+    SavedFrameHeader h2;
+    h2.frameNumber = 2;
+    saver.offer(frame.data(), W, H, h2);
+
+    const std::string j2 = waitJson(js, 2);
+    if (j2.empty()) {
+        std::printf("FAIL: no periodic JSON with 2 frames\n");
+        return 3;
+    }
+    hsize_t n2 = 0;
+    float p2 = -1.0f;
+    const bool live2 = readSlice(h5, 1, n2, p2); // live file, SWMR read
+    std::printf("checkpoint2: live swmr read=%s  h5 extent=%llu  slice1 px=%.1f "
+                "(expect true, 2, 850)\n",
+                live2 ? "true" : "false", (unsigned long long)n2, p2);
+
+    const bool noPart = !fileExists(js + ".part");
+
+    saver.requestStop("test");
+    saver.finish();
+    const std::string jf = readFile(js);
+    const bool finalComplete =
+        jf.find("\"complete\": true") != std::string::npos;
+
+    const bool ok = liveMid && live1 && (n1 == 1) && (p1 == 900.0f) && live2 &&
+                    (n2 == 2) && (p2 == 850.0f) && noPart && finalComplete;
+    std::printf("final: complete=%s  no .part left=%s\n",
+                finalComplete ? "true" : "false", noPart ? "true" : "false");
+    std::printf("%s\n",
+                ok ? "PASS: live pedestal + periodic clean checkpoint"
+                   : "FAIL");
+    return ok ? 0 : 4;
+}

slsDetectorCalibration/jungfrauExecutables/jf_online_display_gui/test/xclick.c

@@ -0,0 +1,69 @@
+// Minimal XTest driver: xclick <display> click <x> <y> | key <keysym>
+#include <X11/Xlib.h>
+#include <X11/keysym.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+extern int XTestFakeMotionEvent(Display *, int, int, int, unsigned long);
+extern int XTestFakeButtonEvent(Display *, unsigned int, int, unsigned long);
+extern int XTestFakeKeyEvent(Display *, unsigned int, int, unsigned long);
+int main(int argc, char **argv) {
+    Display *d = XOpenDisplay(argc > 1 ? argv[1] : NULL);
+    if (!d) { fprintf(stderr, "no display\n"); return 1; }
+    if (argc > 3 && strcmp(argv[2], "click") == 0) {
+        int x = atoi(argv[3]), y = atoi(argv[4]);
+        XTestFakeMotionEvent(d, -1, x, y, 0);
+        XTestFakeButtonEvent(d, 1, True, 0);
+        XTestFakeButtonEvent(d, 1, False, 0);
+    } else if (argc > 3 && strcmp(argv[2], "press") == 0) {
+        XTestFakeMotionEvent(d, -1, atoi(argv[3]), atoi(argv[4]), 0);
+        XTestFakeButtonEvent(d, 1, True, 0);
+    } else if (argc > 3 && strcmp(argv[2], "move") == 0) {
+        XTestFakeMotionEvent(d, -1, atoi(argv[3]), atoi(argv[4]), 0);
+    } else if (argc > 2 && strcmp(argv[2], "release") == 0) {
+        XTestFakeButtonEvent(d, 1, False, 0);
+    } else if (argc > 2 && strcmp(argv[2], "raise") == 0) {
+        const char *want = argc > 3 ? argv[3] : "";
+        Window root = DefaultRootWindow(d), r2, par, *kids = NULL;
+        unsigned n = 0;
+        if (XQueryTree(d, root, &r2, &par, &kids, &n)) {
+            for (unsigned i = 0; i < n; i++) {
+                char *nm = NULL;
+                if (XFetchName(d, kids[i], &nm) && nm) {
+                    if (strstr(nm, want)) {
+                        XRaiseWindow(d, kids[i]);
+                        XSetInputFocus(d, kids[i], RevertToParent, CurrentTime);
+                        printf("raised: %s\n", nm);
+                    }
+                    XFree(nm);
+                }
+            }
+            if (kids) XFree(kids);
+        }
+    } else if (argc > 4 && strcmp(argv[2], "movewin") == 0) {
+        const char *want = argv[3];
+        Window root = DefaultRootWindow(d), r2, par, *kids = NULL;
+        unsigned n = 0;
+        if (XQueryTree(d, root, &r2, &par, &kids, &n)) {
+            for (unsigned i = 0; i < n; i++) {
+                char *nm = NULL;
+                if (XFetchName(d, kids[i], &nm) && nm) {
+                    if (strstr(nm, want)) {
+                        XMoveWindow(d, kids[i], atoi(argv[4]), atoi(argv[5]));
+                        printf("moved: %s\n", nm);
+                    }
+                    XFree(nm);
+                }
+            }
+            if (kids) XFree(kids);
+        }
+    } else if (argc > 2 && strcmp(argv[2], "key") == 0) {
+        KeySym ks = XStringToKeysym(argc > 3 ? argv[3] : "Return");
+        KeyCode kc = XKeysymToKeycode(d, ks);
+        XTestFakeKeyEvent(d, kc, True, 0);
+        XTestFakeKeyEvent(d, kc, False, 0);
+    }
+    XFlush(d);
+    XCloseDisplay(d);
+    return 0;
+}

slsDetectorServers/ctbDetectorServer/Makefile

@@ -10,8 +10,10 @@ script_dir = ../../etc/
 
 CROSS  		= bfin-uclinux-
 CC    		= $(CROSS)gcc
-CFLAGS		+=  -Wall -std=gnu99 -DCHIPTESTBOARDD  -DSTOP_SERVER -I$(main_inc) -I$(support_lib) -I$(det_lib) -I$(current_dir) #-DDEBUG1 #-DVERBOSEI #-DVERBOSE 
+CFLAGS		+=  -O2 -Wall -Wextra -Wno-unused-parameter -Wformat=2 -Wredundant-decls -Werror=return-type -std=gnu99 -DCHIPTESTBOARDD  -DSTOP_SERVER -I$(main_inc) -I$(support_lib) -I$(det_lib) -I$(current_dir) #-DDEBUG1 #-DVERBOSEI #-DVERBOSE 
 LDLIBS		+= 	-lm -lrt -pthread
+# FLAT stack size: elf2flt defaults to 4 KB, the update and startup paths need more than 8 KB
+LDLIBS		+= 	-Wl,-elf2flt=-s262144
 PROGS		= 	ctbDetectorServer 
 DESTDIR		?= 	bin
 INSTMODE	= 	0777

slsDetectorServers/ctbDetectorServer/slsDetectorFunctionList.c

@@ -1355,7 +1355,7 @@ int setVLimit(int val, char *mess) {
 }
 
 int validateDACIndex(enum DACINDEX ind, char *mess) {
-    if (ind < 0 || ind >= NDAC_ONLY) {
+    if (ind >= NDAC_ONLY) {
         sprintf(mess, "Could not set/get DAC. Invalid index %d\n", ind);
         LOG(logERROR, (mess));
         return FAIL;
@@ -1464,7 +1464,7 @@ int setDAC(enum DACINDEX ind, int val, bool mV, char *mess) {
 }
 
 int validatePowerDACIndex(enum powerIndex ind, char *mess) {
-    if (ind < 0 || ind > V_POWER_IO) {
+    if (ind > V_POWER_IO) {
         sprintf(mess, "Could not set/get Power DAC. Invalid index %d\n", ind);
         LOG(logERROR, (mess));
         return FAIL;
@@ -2158,8 +2158,9 @@ int configureMAC() {
 
     // start addr
     uint32_t addr = RXR_ENDPOINT_START_REG;
-    // get struct memory
-    udp_header *udp = (udp_header *)(Blackfin_getBaseAddress() + addr / 2);
+    // build udp header
+    udp_header header;
+    udp_header *udp = &header;
     memset(udp, 0, sizeof(udp_header));
 
     //  mac addresses
@@ -2191,6 +2192,13 @@ int configureMAC() {
 
     calcChecksum(udp);
 
+    // force FPGA writes to be aligned and in order
+    uint32_t words[sizeof(udp_header) / sizeof(uint32_t)];
+    memcpy(words, udp, sizeof(udp_header));
+    for (size_t i = 0; i != sizeof(words) / sizeof(words[0]); ++i) {
+        bus_w(addr + i * 2, words[i]);
+    }
+
     cleanFifos(); // FIXME: resetPerpheral() for ctb?
     resetPeripheral();
     LOG(logINFO, ("Waiting for %d s for mac to be up\n",
@@ -2330,7 +2338,7 @@ int validatePhaseinDegrees(enum CLKINDEX ind, int val, int retval) {
 }
 
 int setFrequency(enum CLKINDEX ind, int val) {
-    if (ind < 0 || ind >= NUM_CLOCKS) {
+    if (ind >= NUM_CLOCKS) {
         LOG(logERROR, ("Unknown clock index %d to set frequency\n", ind));
         return FAIL;
     }
@@ -2380,7 +2388,7 @@ int setFrequency(enum CLKINDEX ind, int val) {
 }
 
 int getFrequency(enum CLKINDEX ind) {
-    if (ind < 0 || ind >= NUM_CLOCKS) {
+    if (ind >= NUM_CLOCKS) {
         LOG(logERROR, ("Unknown clock index %d to get frequency\n", ind));
         return -1;
     }

slsDetectorServers/eigerDetectorServer/Beb.c

@@ -6,6 +6,7 @@
 #include "xparameters.h"
 
 #include <fcntl.h>
+#include <stddef.h>
 #include <string.h>
 #include <sys/mman.h>
 #include <unistd.h>
@@ -14,20 +15,8 @@ extern int isControlServer;
 
 #define MAX(x, y) (((x) > (y)) ? (x) : (y))
 
-struct LocalLinkInterface ll_beb_local, *ll_beb;
-
 struct udp_header_type udp_header;
 
-int Beb_send_ndata;
-unsigned int Beb_send_buffer_size;
-unsigned int *Beb_send_data_raw;
-unsigned int *Beb_send_data;
-
-int Beb_recv_ndata;
-unsigned int Beb_recv_buffer_size;
-unsigned int *Beb_recv_data_raw;
-unsigned int *Beb_recv_data;
-
 short Beb_bit_mode;
 int BEB_MMAP_SIZE = 0x1000;
 
@@ -47,28 +36,6 @@ int Beb_deactivated_right_datastream = 1;
 int Beb_deactivated_num_destinations = 1;
 
 int Beb_Beb() {
-    Beb_send_ndata = 0;
-    Beb_send_buffer_size = 1026;
-
-    Beb_send_data_raw =
-        malloc((Beb_send_buffer_size + 1) * sizeof(unsigned int));
-    if (Beb_send_data_raw == NULL) {
-        LOG(logERROR, ("Could not allocate memory for beb (send_data_raw)\n"));
-        return 0;
-    }
-    Beb_send_data = &Beb_send_data_raw[1];
-
-    Beb_recv_ndata = 0;
-    Beb_recv_buffer_size = 1026;
-
-    Beb_recv_data_raw =
-        malloc((Beb_recv_buffer_size + 1) * sizeof(unsigned int));
-    if (Beb_recv_data_raw == NULL) {
-        LOG(logERROR, ("Could not allocate memory for beb (recv_data_raw)\n"));
-        return 0;
-    }
-    Beb_recv_data = &Beb_recv_data_raw[1];
-
     udp_header = (struct udp_header_type){
         {0x00, 0x50, 0xc5, 0xb2, 0xcb, 0x46}, // DST MAC
         {0x00, 0x50, 0xc2, 0x46, 0xd9, 0x02}, // SRC MAC
@@ -157,19 +124,12 @@ int Beb_SetHeaderData(uint64_t src_mac, uint32_t src_ip, uint16_t src_port,
     memcpy(&(udp_header.dst_port[0]), &dst_port, sizeof(udp_header.dst_port));
 
     Beb_AdjustIPChecksum(&udp_header);
-
-    unsigned int *base_ptr = (unsigned int *)&udp_header;
-    unsigned int num_words = (sizeof(struct udp_header_type) + 3) / 4;
-    for (unsigned int i = 0; i < num_words; i++)
-        Beb_send_data[i + 2] = base_ptr[i];
-    for (unsigned int i = num_words; i < 16; i++)
-        Beb_send_data[i + 2] = 0;
-
     return 1;
 }
 
 void Beb_AdjustIPChecksum(struct udp_header_type *ip) {
-    unsigned char *cptr = (unsigned char *)ip->ver_headerlen;
+    unsigned char *cptr =
+        (unsigned char *)ip + offsetof(struct udp_header_type, ver_headerlen);
 
     ip->ip_header_checksum[0] = 0;
     ip->ip_header_checksum[1] = 0;
@@ -372,7 +332,7 @@ int Beb_SetTop(enum TOPINDEX ind) {
     }
 
     char *top_names[] = {TOP_NAMES};
-    int newval = Beb_Write32(csp0base, BEB_CONFIG_WR_OFST, value);
+    u_int32_t newval = Beb_Write32(csp0base, BEB_CONFIG_WR_OFST, value);
     if (newval != value) {
         LOG(logERROR,
             ("Could not set Top flag to %s in Beb\n", top_names[ind]));
@@ -417,7 +377,7 @@ int Beb_SetMaster(enum MASTERINDEX ind) {
     }
 
     char *master_names[] = {MASTER_NAMES};
-    int newval = Beb_Write32(csp0base, BEB_CONFIG_WR_OFST, value);
+    u_int32_t newval = Beb_Write32(csp0base, BEB_CONFIG_WR_OFST, value);
     if (newval != value) {
         LOG(logERROR,
             ("Could not set Master flag to %s in Beb\n", master_names[ind]));
@@ -1167,7 +1127,7 @@ int Beb_SetDetectorPosition(int pos[]) {
                     value | ((posval << UDP_HEADER_Y_OFST) & UDP_HEADER_Y_MSK));
         value = Beb_Read32(csp0base, UDP_HEADER_B_LEFT_OFST);
         if ((value & UDP_HEADER_Y_MSK) !=
-            ((posval << UDP_HEADER_Y_OFST) & UDP_HEADER_Y_MSK)) {
+            (uint32_t)((posval << UDP_HEADER_Y_OFST) & UDP_HEADER_Y_MSK)) {
             LOG(logERROR, ("Could not set column position for left port\n"));
             ret = FAIL;
         }
@@ -1180,7 +1140,7 @@ int Beb_SetDetectorPosition(int pos[]) {
                     value | ((posval << UDP_HEADER_Y_OFST) & UDP_HEADER_Y_MSK));
         value = Beb_Read32(csp0base, UDP_HEADER_B_RIGHT_OFST);
         if ((value & UDP_HEADER_Y_MSK) !=
-            ((posval << UDP_HEADER_Y_OFST) & UDP_HEADER_Y_MSK)) {
+            (uint32_t)((posval << UDP_HEADER_Y_OFST) & UDP_HEADER_Y_MSK)) {
             LOG(logERROR, ("Could not set column position for right port\n"));
             ret = FAIL;
         }
@@ -1379,9 +1339,7 @@ int Beb_open(u_int32_t **csp0base, u_int32_t offset) {
 }
 
 u_int32_t Beb_Read32(u_int32_t *baseaddr, u_int32_t offset) {
-    volatile u_int32_t value;
-    value = *(u_int32_t *)(baseaddr + offset / (sizeof(u_int32_t)));
-    return value;
+    return *(volatile u_int32_t *)(baseaddr + offset / sizeof(u_int32_t));
 }
 
 u_int32_t Beb_Write32(u_int32_t *baseaddr, u_int32_t offset, u_int32_t data) {

slsDetectorServers/eigerDetectorServer/FebControl.c

@@ -46,7 +46,6 @@ int64_t Feb_Control_RateTable_Tau_in_nsec = -1;
 int64_t Feb_Control_RateTable_Period_in_nsec = -1;
 unsigned int Feb_Control_rate_correction_table[1024] = {};
 double Feb_Control_rate_meas[16384] = {};
-double ratemax = -1;
 
 // setup
 void Feb_Control_activate(int activate) { Feb_Control_activated = activate; }
@@ -138,13 +137,6 @@ void Feb_Control_CloseSerialCommunication() {
 
 int Feb_Control_CheckSetup(int master) {
     LOG(logDEBUG1, ("Checking Set up\n"));
-
-    for (unsigned int j = 0; j < 4; j++) {
-        if (Feb_Control_idelay[j] < 0) {
-            LOG(logERROR, ("idelay chip %d not set.\n", j));
-            return 0;
-        }
-    }
     int value = 0;
     if ((Feb_Control_master) && (!Feb_Control_GetHighVoltage(&value))) {
         LOG(logERROR, ("high voltage not set.\n"));
@@ -492,7 +484,7 @@ float Feb_Control_DACToVoltage(unsigned int digital, unsigned int nsteps,
 
 int Feb_Control_SetDAC(unsigned int ch, int value) {
     unsigned int dst_num = Feb_Control_rightAddress;
-    if (ch < 0 || ch > 15) {
+    if (ch > 15) {
         LOG(logERROR, ("invalid ch for SetDAC.\n"));
         return 0;
     }
@@ -664,7 +656,7 @@ int Feb_Control_SetTrimbits(unsigned int *trimbits, int top) {
 
 int Feb_Control_SaveAllTrimbitsTo(int value, int top) {
     unsigned int chanregs[Feb_Control_trimbit_size];
-    for (int i = 0; i < Feb_Control_trimbit_size; i++)
+    for (int i = 0; i < (int)Feb_Control_trimbit_size; i++)
         chanregs[i] = value;
     return Feb_Control_SetTrimbits(chanregs, top);
 }
@@ -1982,6 +1974,7 @@ int Feb_Control_SetRateCorrectionTau(int64_t tau_in_Nsec) {
     unsigned int np = 16384; // max slope 16 * 1024
     double b0[1024];
     double m[1024];
+    double ratemax = -1;
 
     if (tau_in_sec < 0 || period_in_sec < 0) {
         if (dr == 32) {
@@ -1999,7 +1992,7 @@ int Feb_Control_SetRateCorrectionTau(int64_t tau_in_Nsec) {
     LOG(logINFO, ("Changing Rate Correction Table tau:%0.8f sec, period:%f sec",
                   tau_in_sec, period_in_sec));
     LOG(logINFO, ("\tCalculating table for tau of %lld ns.\n", tau_in_Nsec));
-    for (int i = 0; i < np; i++) {
+    for (int i = 0; i < (int)np; i++) {
         Feb_Control_rate_meas[i] = i * exp(-i / period_in_sec * tau_in_sec);
         if (Feb_Control_rate_meas[i] > ratemax)
             ratemax = Feb_Control_rate_meas[i];
@@ -2022,7 +2015,7 @@ int Feb_Control_SetRateCorrectionTau(int64_t tau_in_Nsec) {
      */
 
     int next_i = 0;
-    double beforemax;
+    double beforemax = 0;
     b0[0] = 0;
     m[0] = 1;
 
@@ -2032,8 +2025,9 @@ int Feb_Control_SetRateCorrectionTau(int64_t tau_in_Nsec) {
     for (int b = 1; b < 1024; b++) {
         if (m[b - 1] < 15) {
             double s = 0, sx = 0, sy = 0, sxx = 0, sxy = 0;
+            int filled = 0;
             for (;; next_i++) {
-                if (next_i >= np) {
+                if (next_i >= (int)np) {
                     for (; b < 1024; b++) {
                         if (beforemax > ratemax)
                             b0[b] = beforemax;
@@ -2044,7 +2038,7 @@ int Feb_Control_SetRateCorrectionTau(int64_t tau_in_Nsec) {
                             (((int)(m[b] + 0.5) & 0xf) << 14) |
                             ((int)(b0[b] + 0.5) & 0x3fff);
                     }
-                    b = 1024;
+                    filled = 1;
                     break;
                 }
 
@@ -2069,6 +2063,8 @@ int Feb_Control_SetRateCorrectionTau(int64_t tau_in_Nsec) {
             Feb_Control_rate_meas[next_i]: %f\n", x, y, s, sx, sy, sxx, sxy,
             next_i, b, Feb_Control_rate_meas[next_i]));*/
             }
+            if (filled)
+                break;
             double delta = s * sxx - sx * sx;
             b0[b] = (sxx * sy - sx * sxy) / delta;
             m[b] = (s * sxy - sx * sy) / delta;

slsDetectorServers/eigerDetectorServer/HardwareIO.c

@@ -8,7 +8,10 @@ xfs_u8 HWIO_xfs_in8(xfs_u32 InAddress) {
      */
 
     xfs_u8 IoContents;
-    __asm__ volatile("eieio; lbz %0,0(%1)" : "=r"(IoContents) : "b"(InAddress));
+    __asm__ volatile("eieio; lbz %0,0(%1)"
+                     : "=r"(IoContents)
+                     : "b"(InAddress)
+                     : "memory");
     return IoContents;
 }
 
@@ -20,7 +23,10 @@ xfs_u16 HWIO_xfs_in16(xfs_u32 InAddress) {
      */
 
     xfs_u16 IoContents;
-    __asm__ volatile("eieio; lhz %0,0(%1)" : "=r"(IoContents) : "b"(InAddress));
+    __asm__ volatile("eieio; lhz %0,0(%1)"
+                     : "=r"(IoContents)
+                     : "b"(InAddress)
+                     : "memory");
     return IoContents;
 }
 
@@ -32,7 +38,10 @@ xfs_u32 HWIO_xfs_in32(xfs_u32 InAddress) {
      */
 
     xfs_u32 IoContents;
-    __asm__ volatile("eieio; lwz %0,0(%1)" : "=r"(IoContents) : "b"(InAddress));
+    __asm__ volatile("eieio; lwz %0,0(%1)"
+                     : "=r"(IoContents)
+                     : "b"(InAddress)
+                     : "memory");
     return IoContents;
 }
 
@@ -43,7 +52,8 @@ void HWIO_xfs_out8(xfs_u32 OutAddress, xfs_u8 Value) {
      * such that the I/O operation completes before proceeding on
      */
 
-    __asm__ volatile("stb %0,0(%1); eieio" ::"r"(Value), "b"(OutAddress));
+    __asm__ volatile("stb %0,0(%1); eieio" ::"r"(Value), "b"(OutAddress)
+                     : "memory");
 }
 
 /*****************************************************************************/
@@ -52,7 +62,8 @@ void HWIO_xfs_out16(xfs_u32 OutAddress, xfs_u16 Value) {
      * such that the I/O operation completes before proceeding on
      */
 
-    __asm__ volatile("sth %0,0(%1); eieio" ::"r"(Value), "b"(OutAddress));
+    __asm__ volatile("sth %0,0(%1); eieio" ::"r"(Value), "b"(OutAddress)
+                     : "memory");
 }
 
 /*****************************************************************************/
@@ -62,5 +73,6 @@ void HWIO_xfs_out32(xfs_u32 OutAddress, xfs_u32 Value) {
      * such that the I/O operation completes before proceeding on
      */
 
-    __asm__ volatile("stw %0,0(%1); eieio" ::"r"(Value), "b"(OutAddress));
+    __asm__ volatile("stw %0,0(%1); eieio" ::"r"(Value), "b"(OutAddress)
+                     : "memory");
 }

slsDetectorServers/eigerDetectorServer/LocalLinkInterface.c

@@ -95,7 +95,7 @@ int Local_Write(struct LocalLinkInterface *ll, unsigned int buffer_len,
 
     LOG(logDEBUG1, ("LL Write - Len: %2d - If: %X - Data: ", buffer_len,
                     ll->ll_fifo_base));
-    for (int i = 0; i < buffer_len / 4; i++)
+    for (int i = 0; i < (int)buffer_len / 4; i++)
         LOG(logDEBUG1, ("%.8X ", *(((unsigned *)buffer) + i)));
 
     while (words_send <= last_word) {

slsDetectorServers/eigerDetectorServer/Makefile

@@ -10,7 +10,7 @@ script_dir = ../../etc/
 BLACKFIN_CC = bfin-uclinux-gcc
 CROSS		= powerpc-4xx-softfloat-
 CC    		= $(CROSS)gcc
-CFLAGS		+=  -Wall -std=gnu99 -DEIGERD  -DSTOP_SERVER -I$(main_inc) -I$(support_lib) -I$(current_dir)  #-DDEBUG1 #-DVERBOSEI #-DVERBOSE 
+CFLAGS		+=  -O2 -Wall -Wextra -Wno-unused-parameter -Wformat=2 -Wredundant-decls -Werror=return-type -std=gnu99 -DEIGERD  -DSTOP_SERVER -I$(main_inc) -I$(support_lib) -I$(current_dir)  #-DDEBUG1 #-DVERBOSEI #-DVERBOSE 
 LDLIBS		+= 	-lm -lrt -pthread
 PROGS		= 	eigerDetectorServer 
 DESTDIR		= 	bin

slsDetectorServers/eigerDetectorServer/slsDetectorFunctionList.c

@@ -890,7 +890,7 @@ int getDefaultDac(enum DACINDEX index, enum detectorSettings sett,
     if (sett != UNDEFINED) {
         return FAIL;
     }
-    if (index < 0 || index >= NDAC)
+    if (index >= NDAC)
         return FAIL;
     *retval = defaultDacValues[index];
     return OK;
@@ -900,7 +900,7 @@ int setDefaultDac(enum DACINDEX index, enum detectorSettings sett, int value) {
     if (sett != UNDEFINED) {
         return FAIL;
     }
-    if (index < 0 || index >= NDAC)
+    if (index >= NDAC)
         return FAIL;
 
     char *dac_names[] = {DAC_NAMES};
@@ -1428,7 +1428,7 @@ int setThresholdEnergy(int ev) {
 /* parameters - dac, adc, hv */
 int validateDACIndex(enum DACINDEX ind, char *mess) {
     // including E_VTHRESHOLD
-    if (ind < 0 || ind >= NDAC + 1) {
+    if (ind >= NDAC + 1) {
         sprintf(mess, "Could not set DAC. Invalid index %d\n", ind);
         LOG(logERROR, (mess));
         return FAIL;

slsDetectorServers/gotthard2DetectorServer/Makefile

@@ -9,7 +9,7 @@ script_dir = ../../etc/
 
 CROSS  		= nios2-buildroot-linux-gnu-
 CC    		= $(CROSS)gcc
-CFLAGS		+=  -Wall -std=gnu99 -DGOTTHARD2D  -DSTOP_SERVER -I$(main_inc) -I$(support_lib) -I$(current_dir)   #-DDEBUG1 #-DVERBOSEI #-DVERBOSE 
+CFLAGS		+=  -O2 -Wall -Wextra -Wno-unused-parameter -Wformat=2 -Wredundant-decls -Werror=return-type -std=gnu99 -DGOTTHARD2D  -DSTOP_SERVER -I$(main_inc) -I$(support_lib) -I$(current_dir)   #-DDEBUG1 #-DVERBOSEI #-DVERBOSE 
 LDLIBS		+= 	-lm -lrt -pthread
 PROGS		= 	gotthard2DetectorServer 
 DESTDIR		?= 	bin

slsDetectorServers/gotthard2DetectorServer/slsDetectorFunctionList.c

@@ -2052,9 +2052,9 @@ void setupHeader(int iRxEntry, int vetoInterface, uint32_t destip,
         iRxEntry += RXR_ENDPOINTS_MAX;
     }
     addr += (iRxEntry * RXR_ENDPOINT_OFST);
-    // get struct memory
-    udp_header *udp =
-        (udp_header *)(Nios_getBaseAddress() + addr / (sizeof(u_int32_t)));
+    // build udp header
+    udp_header header;
+    udp_header *udp = &header;
     memset(udp, 0, sizeof(udp_header));
 
     //  mac addresses
@@ -2085,6 +2085,14 @@ void setupHeader(int iRxEntry, int vetoInterface, uint32_t destip,
     // total length is redefined in firmware
 
     calcChecksum(udp);
+
+    // force FPGA writes to be aligned and in order
+    uint32_t words[sizeof(udp_header) / sizeof(uint32_t)];
+    memcpy(words, udp, sizeof(udp_header));
+    for (size_t i = 0; i != sizeof(words) / sizeof(words[0]); ++i) {
+        bus_w(addr + i * sizeof(uint32_t), words[i]);
+    }
+
     if (iRxEntry < numUdpDestinations) {
         LOG(logINFO, ("\tIP checksum : 0x%lx\n\n", udp->ip_checksum));
     }

slsDetectorServers/jungfrauDetectorServer/Makefile

@@ -9,8 +9,10 @@ script_dir = ../../etc/
 
 CROSS  		= bfin-uclinux-
 CC    		= $(CROSS)gcc
-CFLAGS		+=  -Wall -std=gnu99 -DJUNGFRAUD  -DSTOP_SERVER -I$(main_inc) -I$(support_lib) -I$(current_dir)  #-DVERBOSEI #-DVERBOSE 
+CFLAGS		+=  -O2 -Wall -Wextra -Wno-unused-parameter -Wformat=2 -Wredundant-decls -Werror=return-type -std=gnu99 -DJUNGFRAUD  -DSTOP_SERVER -I$(main_inc) -I$(support_lib) -I$(current_dir)  #-DVERBOSEI #-DVERBOSE 
 LDLIBS		+= 	-lm -lrt -pthread
+# FLAT stack size: elf2flt defaults to 4 KB, the update and startup paths need more than 8 KB
+LDLIBS		+= 	-Wl,-elf2flt=-s262144
 PROGS		= 	jungfrauDetectorServer 
 DESTDIR		?= 	bin
 INSTMODE	= 	0777

slsDetectorServers/jungfrauDetectorServer/slsDetectorFunctionList.c

@@ -416,7 +416,7 @@ int setChipIndex(enum CHIPINDEX ind, char *mess) {
 enum CHIPINDEX getChipIndex() { return chipIndex; }
 
 int validateChipIndex(enum CHIPINDEX ind, char *mess) {
-    if (ind < 0 || ind >= NUM_CHIP_INDICES) {
+    if (ind >= NUM_CHIP_INDICES) {
         sprintf(mess, "Invalid chip index %d. Options: %s\n", (int)ind,
                 CHIP_VALS_HELP);
         LOG(logERROR, (mess));
@@ -846,7 +846,7 @@ int getDefaultDac(enum DACINDEX index, enum detectorSettings sett,
         return FAIL;
     }
 
-    if (index < 0 || index >= NDAC)
+    if (index >= NDAC)
         return FAIL;
     *retval = defaultDacValues[index];
     return OK;
@@ -882,7 +882,7 @@ int setDefaultDac(enum DACINDEX index, enum detectorSettings sett, int value) {
         // not a special dac
         return FAIL;
     }
-    if (index < 0 || index >= NDAC)
+    if (index >= NDAC)
         return FAIL;
     LOG(logINFO, ("Setting Default Dac [%d - %s]: %d\n", (int)index,
                   dac_names[index], value));
@@ -1564,7 +1564,7 @@ void setGainMode(enum gainMode mode) {
 
 /* parameters - dac, adc, hv */
 int validateDACIndex(enum DACINDEX ind, char *mess) {
-    if (ind < 0 || ind >= NDAC) {
+    if (ind >= NDAC) {
         sprintf(mess, "Could not set DAC. Invalid index %d\n", ind);
         LOG(logERROR, (mess));
         return FAIL;
@@ -1870,8 +1870,9 @@ void setupHeader(int iRxEntry, enum interfaceType type, uint32_t destip,
                                    : RXR_ENDPOINT_OUTER_START_REG);
     // calculate rxr endpoint offset
     addr += (iRxEntry * RXR_ENDPOINT_OFST);
-    // get struct memory
-    udp_header *udp = (udp_header *)(Blackfin_getBaseAddress() + addr / 2);
+    // build udp header
+    udp_header header;
+    udp_header *udp = &header;
     memset(udp, 0, sizeof(udp_header));
 
     //  mac addresses
@@ -1902,6 +1903,14 @@ void setupHeader(int iRxEntry, enum interfaceType type, uint32_t destip,
     // total length is redefined in firmware
 
     calcChecksum(udp);
+
+    // force FPGA writes to be aligned and in order
+    uint32_t words[sizeof(udp_header) / sizeof(uint32_t)];
+    memcpy(words, udp, sizeof(udp_header));
+    for (size_t i = 0; i != sizeof(words) / sizeof(words[0]); ++i) {
+        bus_w(addr + i * 2, words[i]);
+    }
+
     if (iRxEntry < numUdpDestinations) {
         LOG(logINFO, ("\tIP checksum : 0x%lx\n\n", udp->ip_checksum));
     }

slsDetectorServers/moenchDetectorServer/Makefile

@@ -9,8 +9,10 @@ script_dir = ../../etc/
 
 CROSS  		= bfin-uclinux-
 CC    		= $(CROSS)gcc
-CFLAGS		+=  -Wall -std=gnu99 -DMOENCHD  -DSTOP_SERVER -I$(main_inc) -I$(support_lib) -I$(current_dir)  #-DVERBOSEI #-DVERBOSE 
+CFLAGS		+=  -O2 -Wall -Wextra -Wno-unused-parameter -Wformat=2 -Wredundant-decls -Werror=return-type -std=gnu99 -DMOENCHD  -DSTOP_SERVER -I$(main_inc) -I$(support_lib) -I$(current_dir)  #-DVERBOSEI #-DVERBOSE 
 LDLIBS		+= 	-lm -lrt -pthread
+# FLAT stack size: elf2flt defaults to 4 KB, the update and startup paths need more than 8 KB
+LDLIBS		+= 	-Wl,-elf2flt=-s262144
 PROGS		= 	moenchDetectorServer 
 DESTDIR		?= 	bin
 INSTMODE	= 	0777

slsDetectorServers/moenchDetectorServer/slsDetectorFunctionList.c

@@ -548,7 +548,7 @@ int resetToDefaultDacs(int hardReset, char *mess) {
 
 int getDefaultDac(enum DACINDEX index, enum detectorSettings sett,
                   int *retval) {
-    if (index < 0 || index >= NDAC)
+    if (index >= NDAC)
         return FAIL;
     *retval = defaultDacValues[index];
     return OK;
@@ -556,7 +556,7 @@ int getDefaultDac(enum DACINDEX index, enum detectorSettings sett,
 
 int setDefaultDac(enum DACINDEX index, enum detectorSettings sett, int value) {
     char *dac_names[] = {DAC_NAMES};
-    if (index < 0 || index >= NDAC)
+    if (index >= NDAC)
         return FAIL;
     LOG(logINFO, ("Setting Default Dac [%d - %s]: %d\n", (int)index,
                   dac_names[index], value));
@@ -913,7 +913,7 @@ enum detectorSettings getSettings() {
 /* parameters - dac, adc, hv */
 /* parameters - dac, adc, hv */
 int validateDACIndex(enum DACINDEX ind, char *mess) {
-    if (ind < 0 || ind >= NDAC) {
+    if (ind >= NDAC) {
         sprintf(mess, "Could not set DAC. Invalid index %d\n", ind);
         LOG(logERROR, (mess));
         return FAIL;
@@ -1203,8 +1203,9 @@ void setupHeader(int iRxEntry, enum interfaceType type, uint32_t destip,
                                    : RXR_ENDPOINT_OUTER_START_REG);
     // calculate rxr endpoint offset
     addr += (iRxEntry * RXR_ENDPOINT_OFST);
-    // get struct memory
-    udp_header *udp = (udp_header *)(Blackfin_getBaseAddress() + addr / 2);
+    // build udp header
+    udp_header header;
+    udp_header *udp = &header;
     memset(udp, 0, sizeof(udp_header));
 
     //  mac addresses
@@ -1235,6 +1236,14 @@ void setupHeader(int iRxEntry, enum interfaceType type, uint32_t destip,
     // total length is redefined in firmware
 
     calcChecksum(udp);
+
+    // force FPGA writes to be aligned and in order
+    uint32_t words[sizeof(udp_header) / sizeof(uint32_t)];
+    memcpy(words, udp, sizeof(udp_header));
+    for (size_t i = 0; i != sizeof(words) / sizeof(words[0]); ++i) {
+        bus_w(addr + i * 2, words[i]);
+    }
+
     if (iRxEntry < numUdpDestinations) {
         LOG(logINFO, ("\tIP checksum : 0x%lx\n\n", udp->ip_checksum));
     }

slsDetectorServers/mythen3DetectorServer/Makefile

@@ -10,7 +10,7 @@ script_dir = ../../etc/
 
 CROSS  		= nios2-buildroot-linux-gnu-
 CC    		= $(CROSS)gcc
-CFLAGS		+=  -Wall -std=gnu99 -DMYTHEN3D  -DSTOP_SERVER -I$(main_inc) -I$(support_lib) -I$(det_lib) -I$(current_dir)  #-DDEBUG1 #-DVERBOSEI #-DVERBOSE 
+CFLAGS		+=  -O2 -Wall -Wextra -Wno-unused-parameter -Wformat=2 -Wredundant-decls -Werror=return-type -std=gnu99 -DMYTHEN3D  -DSTOP_SERVER -I$(main_inc) -I$(support_lib) -I$(det_lib) -I$(current_dir)  #-DDEBUG1 #-DVERBOSEI #-DVERBOSE 
 LDLIBS		+= 	-lm -lrt -pthread
 PROGS		= 	mythen3DetectorServer 
 DESTDIR		?= 	bin

slsDetectorServers/mythen3DetectorServer/slsDetectorFunctionList.c

@@ -2225,9 +2225,9 @@ int configureMAC() {
         uint32_t addr = BASE_UDP_RAM;
         // calculate rxr endpoint offset
         addr += (iRxEntry * RXR_ENDPOINT_OFST); // TODO: is there round robin
-        // get struct memory
-        udp_header *udp =
-            (udp_header *)(Nios_getBaseAddress() + addr / (sizeof(u_int32_t)));
+        // build udp header
+        udp_header header;
+        udp_header *udp = &header;
         memset(udp, 0, sizeof(udp_header));
 
         //  mac addresses
@@ -2258,6 +2258,14 @@ int configureMAC() {
         // total length is redefined in firmware
 
         calcChecksum(udp);
+
+        // force FPGA writes to be aligned and in order
+        uint32_t words[sizeof(udp_header) / sizeof(uint32_t)];
+        memcpy(words, udp, sizeof(udp_header));
+        for (size_t i = 0; i != sizeof(words) / sizeof(words[0]); ++i) {
+            bus_w(addr + i * sizeof(uint32_t), words[i]);
+        }
+
         if (iRxEntry < numUdpDestinations) {
             LOG(logINFO, ("\tIP checksum : 0x%lx\n\n", udp->ip_checksum));
         }

slsDetectorServers/mythen3DetectorServer/slsDetectorServer_defs.h

@@ -4,7 +4,7 @@
 #include "sls/sls_detector_defs.h"
 
 #define REQRD_FRMWRE_VRSN (0x241113)
-#define KERNEL_DATE_VRSN  "Mon May 10 18:00:21 CEST 2021"
+#define KERNEL_DATE_VRSN  "Mon Jan 18 14:24:30 CET 2021"
 #define ID_FILE           "detid_mythen3.txt"
 
 #define NUM_HARDWARE_VERSIONS    (2)

slsDetectorServers/slsDetectorServer/include/arm64.h

@@ -6,8 +6,10 @@
 #include <sys/types.h>
 
 void bus_w(u_int32_t offset, u_int32_t data);
+void bus_w_csp1(u_int32_t offset, u_int32_t data);
 void bus_w_csp2(u_int32_t offset, u_int32_t data);
 u_int32_t bus_r(u_int32_t offset);
+u_int32_t bus_r_csp1(u_int32_t offset);
 u_int32_t bus_r_csp2(u_int32_t offset);
 uint64_t getU64BitReg(int aLSB, int aMSB);
 void setU64BitReg(uint64_t value, int aLSB, int aMSB);

slsDetectorServers/slsDetectorServer/include/blackfin.h

@@ -120,5 +120,14 @@ uint32_t *Blackfin_getBaseAddress();
  */
 int mapCSP0(void);
 
-/** sleep for only usecs */
-void usleep_bf(uint64_t i);
+/**
+ * Prepare the core cycle counter used by usleep_bf (called from mapCSP0)
+ */
+int initCycleCounter(void);
+
+/**
+ * busy-wait for usecs on the core cycle counter
+ * @returns 0, or -1 without sleeping if the wait does not fit the 32-bit
+ * cycle count (about 8 s at 525 MHz)
+ */
+int usleep_bf(uint32_t us);

slsDetectorServers/slsDetectorServer/src/LTC2620_Driver.c

@@ -94,16 +94,21 @@ int LTC2620_D_SetDacValue(int dacnum, int val, char *dacname, char *mess) {
     // fname to write to
     char fname[MAX_STR_LENGTH];
     memset(fname, 0, MAX_STR_LENGTH);
-    char fnameFormat[MAX_STR_LENGTH];
-    memset(fnameFormat, 0, MAX_STR_LENGTH);
-    strcpy(fnameFormat, LTC2620_D_DriverFileName);
-    sprintf(fname, "%s%d", fnameFormat, dacnum);
 #if defined(XILINX_CHIPTESTBOARDD)
+    // driver file names are printf formats with the dac number in the middle
+    // (CURRENT_BOARD_LINKS_FOLDER "/ao%d" and "/ao%d_pd"), so the format
+    // cannot be a string literal here
+    const char *fnameFormat = LTC2620_D_DriverFileName;
     if (val == LTC2620_D_PWR_DOWN_VAL) {
-        strcpy(fnameFormat, LTC2620_D_PowerDownDriverFileName);
+        fnameFormat = LTC2620_D_PowerDownDriverFileName;
         val = 1; //-100?:Invalid Argument
     }
-    sprintf(fname, fnameFormat, dacnum);
+#pragma GCC diagnostic push
+#pragma GCC diagnostic ignored "-Wformat-nonliteral"
+    snprintf(fname, sizeof(fname), fnameFormat, dacnum);
+#pragma GCC diagnostic pop
+#else
+    snprintf(fname, sizeof(fname), "%s%d", LTC2620_D_DriverFileName, dacnum);
 #endif
     LOG(logDEBUG1, ("fname %s\n", fname));
 

slsDetectorServers/slsDetectorServer/src/arm64.c

@@ -28,6 +28,18 @@ void bus_w(u_int32_t offset, u_int32_t data) {
     *ptr1 = data;
 }
 
+void bus_w_csp1(u_int32_t offset, u_int32_t data) {
+    volatile u_int32_t *ptr1;
+    ptr1 = (u_int32_t *)(csp1base + offset / (sizeof(u_int32_t)));
+    *ptr1 = data;
+}
+
+u_int32_t bus_r_csp1(u_int32_t offset) {
+    volatile u_int32_t *ptr1;
+    ptr1 = (u_int32_t *)(csp1base + offset / (sizeof(u_int32_t)));
+    return *ptr1;
+}
+
 u_int32_t bus_r(u_int32_t offset) {
     volatile u_int32_t *ptr1;
     ptr1 = (u_int32_t *)(csp0base + offset / (sizeof(u_int32_t)));

slsDetectorServers/slsDetectorServer/src/blackfin.c

@@ -8,10 +8,11 @@
 #include "sls/sls_detector_defs.h"
 
 #include <fcntl.h>    // open
+#include <stdio.h>    // fopen
 #include <sys/mman.h> // mmap
+#include <unistd.h>   // usleep
 
 /* global variables */
-const uint64_t BFIN_CYCLES_1uSECOND = 20;
 u_int32_t *csp0base = 0;
 
 #define CSP0     0x20200000
@@ -125,6 +126,8 @@ int mapCSP0(void) {
 #endif
         LOG(logINFO, ("csp0base mapped from %p to %p\n", csp0base,
                       (csp0base + MEM_SIZE)));
+        if (initCycleCounter() == FAIL)
+            return FAIL;
         LOG(logINFO, ("Status Register: %08x\n", bus_r(STATUS_REG)));
     } else
         LOG(logINFO, ("Memory already mapped before\n"));
@@ -133,10 +136,62 @@ int mapCSP0(void) {
 
 uint32_t *Blackfin_getBaseAddress() { return csp0base; }
 
-// usleep is not viable on blackfin
-void usleep_bf(uint64_t i) {
-    uint64_t j = i * BFIN_CYCLES_1uSECOND;
-    while (--j) {
-        asm volatile("");
+/* BF537 core clock; refined from /proc/cpuinfo in initCycleCounter() */
+#define BFIN_CCLK_HZ_DEFAULT 525000000UL
+static uint32_t bfinCyclesPerUs = BFIN_CCLK_HZ_DEFAULT / 1000000;
+
+#ifdef __bfin__
+static inline uint32_t get_cycles(void) {
+    uint32_t cycles;
+    __asm__ volatile("%0 = CYCLES;" : "=d"(cycles));
+    return cycles;
+}
+#endif
+
+int initCycleCounter(void) {
+#ifndef __bfin__
+    return OK; // virtual build: usleep_bf falls back to usleep
+#else
+    // kernel reports "cpu MHz : 525.000/131.250" (core/system)
+    FILE *fp = fopen("/proc/cpuinfo", "r");
+    if (fp != NULL) {
+        char line[128];
+        double mhz = 0;
+        while (fgets(line, sizeof(line), fp) != NULL) {
+            if (sscanf(line, "cpu MHz : %lf", &mhz) == 1 && mhz > 0) {
+                bfinCyclesPerUs = (uint32_t)mhz;
+                break;
+            }
+        }
+        fclose(fp);
     }
-}
+    // CYCLES only counts if the kernel set SYSCFG.CCEN; refuse to run
+    // otherwise, because usleep_bf would spin forever
+    uint32_t c0 = get_cycles();
+    for (volatile int i = 0; i < 1000; ++i)
+        ;
+    if (get_cycles() == c0) {
+        LOG(logERROR, ("Blackfin cycle counter is not running\n"));
+        return FAIL;
+    }
+    LOG(logINFO, ("Cycle counter running at %u cycles/us\n", bfinCyclesPerUs));
+    return OK;
+#endif
+}
+
+// usleep is not viable on blackfin (10 ms tick); spin on the core cycle counter
+int usleep_bf(uint32_t us) {
+    // the wait is counted in core cycles in a uint32_t: about 8 s at 525 MHz
+    if (us > UINT32_MAX / bfinCyclesPerUs) {
+        return -1;
+    }
+#ifndef __bfin__
+    usleep(us);
+#else
+    uint32_t start = get_cycles();
+    uint32_t wait = us * bfinCyclesPerUs;
+    while ((uint32_t)(get_cycles() - start) < wait)
+        ;
+#endif
+    return 0;
+}

slsDetectorServers/xilinx_ctbDetectorServer/Makefile

@@ -16,7 +16,7 @@ else
 endif
 CC    		= $(CROSS)gcc
 #TODO: allow these warnings and fix code
-CFLAGS		+=  -Wall -std=gnu99 -Wno-format-overflow -Wno-format-truncation -DXILINX_CHIPTESTBOARDD -DARMPROCESSOR -DSTOP_SERVER -I$(main_inc) -I$(support_lib) -I$(det_lib) -I$(current_dir)  #-DDEBUG1 #-DVERBOSEI #-DVERBOSE 
+CFLAGS		+=  -O2 -Wall -Wextra -Wno-unused-parameter -Wformat=2 -Wredundant-decls -Werror=return-type -std=gnu99 -Wno-format-overflow -Wno-format-truncation -DXILINX_CHIPTESTBOARDD -DARMPROCESSOR -DSTOP_SERVER -I$(main_inc) -I$(support_lib) -I$(det_lib) -I$(current_dir)  #-DDEBUG1 #-DVERBOSEI #-DVERBOSE 
 #CFLAGS		+=  -Wall -std=gnu99  -DXILINX_CHIPTESTBOARDD -DARMPROCESSOR -DSTOP_SERVER -I$(main_inc) -I$(support_lib) -I$(det_lib) -I$(current_dir)  #-DDEBUG1 #-DVERBOSEI #-DVERBOSE 
 LDLIBS		+= 	-lm -lrt -pthread 
 PROGS		= 	xilinx_ctbDetectorServer 

slsDetectorServers/xilinx_ctbDetectorServer/slsDetectorFunctionList.c

@@ -145,7 +145,7 @@ void basictests() {
     }
 
     // check for API compatibility - old server
-    if (sw_fw_apiversion > requiredfwversion) {
+    if ((uint64_t)sw_fw_apiversion > requiredfwversion) {
         sprintf(initErrorMessage,
                 "This firmware-software api version (0x%lx) is incompatible "
                 "with the software's minimum required firmware version "
@@ -158,7 +158,7 @@ void basictests() {
     }
 
     // check for firmware compatibility - old firmware
-    if (requiredfwversion > fwversion) {
+    if (requiredfwversion > (uint64_t)fwversion) {
         sprintf(initErrorMessage,
                 "This firmware version (0x%lx) is incompatible.\n"
                 "Please update firmware (min. 0x%lx) to be compatible with "
@@ -1502,8 +1502,9 @@ int configureMAC() {
     }
 #endif
 
-    // get struct memory
-    udp_header *udp = (udp_header *)(Arm_getUDPBaseAddress());
+    // build udp header
+    udp_header header;
+    udp_header *udp = &header;
     memset(udp, 0, sizeof(udp_header));
 
     //  mac addresses
@@ -1535,6 +1536,13 @@ int configureMAC() {
 
     calcChecksum(udp);
 
+    // force FPGA writes to be aligned and in order
+    uint32_t words[sizeof(udp_header) / sizeof(uint32_t)];
+    memcpy(words, udp, sizeof(udp_header));
+    for (size_t i = 0; i != sizeof(words) / sizeof(words[0]); ++i) {
+        bus_w_csp1(i * sizeof(uint32_t), words[i]);
+    }
+
     return OK;
 }
 

slsDetectorSoftware/include/sls/Detector.h

@@ -1037,6 +1037,9 @@ class Detector {
 
     void clearRxROI();
 
+    /** Returns true if the current ROI covers the complete detector (default)*/
+    bool isCompleteRxRoi() const;
+
     ///@}
 
     /** @name File */

slsDetectorSoftware/src/Detector.cpp

@@ -1335,6 +1335,7 @@ Result<bool> Detector::getUDPDataStream(const defs::portPosition port,
 
 void Detector::setUDPDataStream(const defs::portPosition port,
                                 const bool enable, Positions pos) {
+    pimpl->validatePortEnable(port, enable, pos);
     pimpl->setUDPDataStream(port, enable, pos);
 }
 
@@ -1485,6 +1486,8 @@ void Detector::setRxROI(const std::vector<defs::ROI> &args) {
 
 void Detector::clearRxROI() { pimpl->clearRxROI(); }
 
+bool Detector::isCompleteRxRoi() const { return pimpl->isCompleteRxRoi(); }
+
 // File
 
 Result<defs::fileFormat> Detector::getFileFormat(Positions pos) const {

slsDetectorSoftware/src/DetectorImpl.cpp

@@ -48,6 +48,15 @@ bool DetectorImpl::isAllPositions(Positions pos) const {
             (pos.size() == modules.size()));
 }
 
+std::vector<int> DetectorImpl::fillInPositions(Positions pos) const {
+    if (isAllPositions(pos)) {
+        std::vector<int> positions(modules.size());
+        std::iota(begin(positions), end(positions), 0);
+        return positions;
+    }
+    return pos;
+}
+
 void DetectorImpl::setAcquiringFlag(bool flag) { shm()->acquiringFlag = flag; }
 
 int DetectorImpl::getDetectorIndex() const { return detectorIndex; }
@@ -1640,6 +1649,7 @@ Result<bool> DetectorImpl::getUDPDataStream(const defs::portPosition port,
 void DetectorImpl::setUDPDataStream(const defs::portPosition port,
                                     const bool enable, Positions pos) {
     assertTwoUDPDataInterfaces("set enable/disable UDP ports");
+    validatePortEnable(port, enable, pos);
     Parallel(&Module::setUDPDataStream, pos, port, enable);
     updateRxUDPDatastreamMetadata();
 }
@@ -1857,6 +1867,49 @@ void DetectorImpl::convertGlobalRoiToPortLevel(
     }
 }
 
+void DetectorImpl::validatePortEnable(const defs::portPosition port,
+                                      const bool enable,
+                                      std::vector<int> pos) const {
+    if (isCompleteRxRoi())
+        return;
+    auto positions = fillInPositions(pos);
+    for (int i : positions) {
+        if (i < 0 || static_cast<size_t>(i) >= modules.size()) {
+            throw RuntimeError("Invalid module index: " + std::to_string(i));
+        }
+        auto modRois = modules[i]->getRxROI();
+        auto portList = getPortPositionList();
+        int portIndex = 0;
+        for (auto p : portList) {
+            if (p == port)
+                break;
+            portIndex++;
+        }
+        validatePortEnableRoiState(i, port, modRois[portIndex], enable);
+    }
+}
+
+/** Assumption:
+ * 1. Check only for Eiger because port disable is only for Eiger now
+ * 2. This function called only when an Roi being set (not complete detector)
+ * ie. complete ROI enabled and some ports disabled is allowed
+ */
+void DetectorImpl::validatePortEnableRoiState(const int moduleIndex,
+                                              defs::portPosition changedPort,
+                                              const defs::ROI &portRoi,
+                                              bool enabled) const {
+    // enabled or disabled and no roi
+    if (enabled || portRoi.noRoi())
+        return;
+    // diabled but ROI specified
+    std::ostringstream oss;
+    oss << ToString(changedPort) << " port of module " << moduleIndex << " ("
+        << modules[moduleIndex]->getHostname()
+        << ") is not active but ROI is specified for it: " << ToString(portRoi)
+        << ". Please disable the ROI for this port or enable the port.";
+    throw RuntimeError(oss.str());
+}
+
 void DetectorImpl::setRxROI(const std::vector<defs::ROI> &args) {
     if (shm()->detType == CHIPTESTBOARD ||
         shm()->detType == defs::XILINX_CHIPTESTBOARD) {
@@ -1871,10 +1924,13 @@ void DetectorImpl::setRxROI(const std::vector<defs::ROI> &args) {
     }
 
     validateROIs(args);
+
     int nPortsPerModule =
         Parallel(&Module::getNumberofUDPInterfacesFromShm, {})
             .tsquash("Inconsistent number of udp ports set up per module");
+    std::vector<std::vector<defs::ROI>> moduleRois;
 
+    // further validate and create port level rois for each module
     for (size_t iModule = 0; iModule < modules.size(); ++iModule) {
         auto moduleGlobalRoi = getModuleROI(iModule);
         // at most 2 rois per module (for each port)
@@ -1886,15 +1942,30 @@ void DetectorImpl::setRxROI(const std::vector<defs::ROI> &args) {
                 roi.ymax = -1;
             }
         }
-
-        // check overlap with module
+        // check overlap of each roi with module
         for (const auto &arg : args) {
             if (arg.overlap(moduleGlobalRoi)) {
                 convertGlobalRoiToPortLevel(arg, moduleGlobalRoi, portRois);
             }
         }
-        modules[iModule]->setRxROI(portRois);
+        // validate roi against port enables
+        if (nPortsPerModule == 2) {
+            auto ports = getPortPositionList();
+            for (int iport = 0; iport != nPortsPerModule; ++iport) {
+                defs::portPosition port = ports[iport];
+                auto enable = modules[iModule]->getUDPDataStream(port);
+                validatePortEnableRoiState(iModule, port, portRois[iport],
+                                           enable);
+            }
+        }
+        moduleRois.push_back(portRois);
     }
+
+    // set rois for each module
+    for (size_t iModule = 0; iModule < modules.size(); ++iModule) {
+        modules[iModule]->setRxROI(moduleRois[iModule]);
+    }
+
     // metadata
     modules[0]->setRxROIMetadata(args);
 }
@@ -1909,6 +1980,14 @@ void DetectorImpl::clearRxROI() {
     modules[0]->setRxROIMetadata(std::vector<defs::ROI>(1));
 }
 
+bool DetectorImpl::isCompleteRxRoi() const {
+    const auto rois = getRxROI();
+    if (rois.empty() || (rois.size() == 1 && rois[0].completeRoi())) {
+        return true;
+    }
+    return false;
+}
+
 void DetectorImpl::getBadChannels(const std::string &fname,
                                   Positions pos) const {
     auto res = Parallel(&Module::getBadChannels, pos);

slsDetectorSoftware/src/DetectorImpl.h

@@ -183,6 +183,8 @@ class DetectorImpl : public virtual slsDetectorDefs {
 
     bool isAllPositions(Positions pos) const;
 
+    std::vector<int> fillInPositions(Positions pos) const;
+
     inline bool isChipTestBoard() const {
         return (shm()->detType == defs::CHIPTESTBOARD ||
                 shm()->detType == defs::XILINX_CHIPTESTBOARD);
@@ -320,8 +322,16 @@ class DetectorImpl : public virtual slsDetectorDefs {
 
     defs::xy getPortGeometry() const;
     std::vector<defs::ROI> getRxROI(int module_id = -1) const;
+    void validatePortEnable(const defs::portPosition port, const bool enable,
+                            std::vector<int> pos) const;
+    void validatePortEnableRoiState(const int moduleIndex,
+                                    defs::portPosition changedPort,
+                                    const defs::ROI &portRoi,
+                                    bool enabled) const;
+
     void setRxROI(const std::vector<defs::ROI> &args);
     void clearRxROI();
+    bool isCompleteRxRoi() const;
 
     void getBadChannels(const std::string &fname, Positions pos) const;
     void setBadChannels(const std::string &fname, Positions pos);
@@ -510,4 +520,4 @@ class DetectorImpl : public virtual slsDetectorDefs {
     void *pCallbackArg{nullptr};
 };
 
-} // namespace sls
+} // namespace sls

slsDetectorSoftware/tests/Caller/test-Caller-rx.cpp

@@ -855,6 +855,94 @@ TEST_CASE("rx_roi", "[.detectorintegration][.disable_check_data_file]") {
     }
 }
 
+TEST_CASE("rx_roi_port_disabled", "[.detectorintegration]") {
+    Detector det;
+    auto det_type = det.getDetectorType().squash();
+    auto two_ports = (det_type == defs::EIGER);
+    if (det_type == defs::JUNGFRAU || det_type == defs::MOENCH) {
+        int numinterfaces = det.getNumberofUDPInterfaces().tsquash(
+            "inconsistent number of interfaces");
+        two_ports = (numinterfaces == 2);
+    }
+
+    if (two_ports) {
+        auto prev_roi = det.getRxROI();
+        auto ports = det.getPortPositionList();
+        auto prev_port0 = det.getUDPDataStream(ports[0], {0})[0];
+        auto prev_port1 = det.getUDPDataStream(ports[1], {0})[0];
+        bool prev_tengiga = false;
+        if (det_type == defs::EIGER) {
+            prev_tengiga = det.getTenGiga().squash(false);
+        }
+
+        std::vector<defs::ROI> rois(2);
+        switch (det_type) {
+        case defs::EIGER:
+            det.setTenGiga(true);
+            rois[0] = defs::ROI{0, 10, 0, 20};
+            rois[1] = defs::ROI{600, 610, 0, 30};
+            break;
+        case defs::JUNGFRAU:
+            rois[0] = defs::ROI{0, 10, 0, 10};
+            rois[1] = defs::ROI{0, 20, 300, 310};
+            break;
+        case defs::MOENCH:
+            rois[0] = defs::ROI{0, 10, 0, 10};
+            rois[1] = defs::ROI{0, 20, 300, 310};
+            break;
+        default:
+            REQUIRE(false);
+            break;
+        }
+
+        det.clearRxROI();
+        det.setUDPDataStream(ports[0], true, {0});
+        det.setUDPDataStream(ports[1], true, {0});
+        det.setRxROI(rois);
+        REQUIRE_THROWS(det.setUDPDataStream(ports[0], false));
+        REQUIRE_THROWS(det.setUDPDataStream(ports[1], false));
+
+        det.clearRxROI();
+        det.setUDPDataStream(ports[0], true, {0});
+        det.setUDPDataStream(ports[1], true, {0});
+        det.setRxROI({rois[0]});
+        REQUIRE_THROWS(det.setUDPDataStream(ports[0], false));
+        REQUIRE_NOTHROW(det.setUDPDataStream(ports[1], false));
+
+        det.clearRxROI();
+        det.setUDPDataStream(ports[0], true, {0});
+        det.setUDPDataStream(ports[1], true, {0});
+        det.setRxROI({rois[1]});
+        REQUIRE_NOTHROW(det.setUDPDataStream(ports[0], false));
+        REQUIRE_THROWS(det.setUDPDataStream(ports[1], false));
+
+        det.clearRxROI();
+        det.setUDPDataStream(ports[0], false, {0});
+        det.setUDPDataStream(ports[1], true, {0});
+        REQUIRE_THROWS(det.setRxROI({rois[0]}));
+        REQUIRE_NOTHROW(det.setRxROI({rois[1]}));
+
+        det.clearRxROI();
+        det.setUDPDataStream(ports[0], true, {0});
+        det.setUDPDataStream(ports[1], false, {0});
+        REQUIRE_NOTHROW(det.setRxROI({rois[0]}));
+        REQUIRE_THROWS(det.setRxROI({rois[1]}));
+
+        /* eiger virtual detector doesnt understand it cant disable in 1g mode,
+         * so cant test in 1g mode */
+
+        if (prev_roi.size() == 1 && prev_roi[0].completeRoi())
+            det.clearRxROI();
+        else
+            det.setRxROI(prev_roi);
+        det.setUDPDataStream(ports[0], prev_port0, {0});
+        det.setUDPDataStream(ports[1], prev_port1, {0});
+        if (det_type == defs::EIGER) {
+            det.setTenGiga(prev_tengiga);
+        }
+    }
+}
+
 TEST_CASE("rx_clearroi", "[.detectorintegration]") {
     Detector det;
     Caller caller(&det);

slsReceiverSoftware/src/ClientInterface.cpp

@@ -1632,7 +1632,8 @@ int ClientInterface::set_threshold(Interface &socket) {
     LOG(logDEBUG) << "Threshold: " << arg << " eV";
     if (detType != EIGER)
         functionNotImplemented();
-    verifyIdle(socket);
+    // allow setting threshold metadata on the fly
+    // without checking for idle state
     impl()->setThresholdEnergy(arg);
     return socket.Send(OK);
 }
@@ -1659,7 +1660,8 @@ int ClientInterface::set_all_threshold(Interface &socket) {
     LOG(logDEBUG) << "Threshold:" << ToString(eVs);
     if (detType != MYTHEN3)
         functionNotImplemented();
-    verifyIdle(socket);
+    // allow setting threshold metadata on the fly
+    // without checking for idle state
     impl()->setThresholdEnergy(eVs);
     return socket.Send(OK);
 }

slsSupportLib/include/sls/versionAPI.h

@@ -3,11 +3,11 @@
 /** API versions */
 #define APILIB        "0.0.0 0x250909"
 #define APIRECEIVER   "0.0.0 0x250822"
-#define APICTB        "0.0.0 0x260506"
-#define APIGOTTHARD2  "0.0.0 0x260427"
-#define APIMOENCH     "0.0.0 0x260424"
-#define APIEIGER      "0.0.0 0x260807"
-#define APIXILINXCTB  "0.0.0 0x260813"
-#define APIJUNGFRAU   "0.0.0 0x261002"
-#define APIMYTHEN3    "0.0.0 0x261022"
+#define APICTB        "0.0.0 0x261103"
+#define APIGOTTHARD2  "0.0.0 0x261103"
+#define APIMOENCH     "0.0.0 0x261103"
+#define APIEIGER      "0.0.0 0x261027"
+#define APIXILINXCTB  "0.0.0 0x261103"
+#define APIJUNGFRAU   "0.0.0 0x261103"
+#define APIMYTHEN3    "0.0.0 0x261103"
 #define APIMATTERHORN "0.0.0 0x260529"