add filesystem modes instructions

Signed-off-by: Florian Agbuya <fa@m-labs.ph>

README.md

@@ -8,14 +8,14 @@
 ## Building
 ### Reproducible build with Nix
 1. Run `nix build .#packages.armv7l-linux.fast-servo-sd-image` to build the sd card image.
-2. Run `nix build .#packages.armv7l-linux.fast-servo-gui` to build the GUI
+2. Run `nix build .#packages.armv7l-linux.fast-servo-gui` to build the GUI.
 3. Run `nix develop` to build a dev shell having access the GUI.
 
 ### Flashing
-1. Plug in your SD card to your computer and run `lsblk` to locate SD card
+1. Plug in your SD card to your computer and run `lsblk` to locate SD card.
 2. If there are any partitions on the SD card, run `umount <mount point>` all the related mount points.
-3. Run `sudo dd if=<path to the SD Card Image> of=/dev/<SD Card Device Name in lsblk> bs=4M status=progress oflag=sync`
-4. Eject the SD Card before removal
+3. Run `sudo dd if=<path to the SD Card Image> of=/dev/<SD Card Device Name in lsblk> bs=4M status=progress oflag=sync`.
+4. Eject the SD Card before removal.
 
 ## Configuration
 You can modify the followings by altering the files directly on the SD card. You can do that by inserting the SD card to a computer in Linux Operating system.
@@ -30,23 +30,33 @@ You can modify the followings by altering the files directly on the SD card. You
 
 You should append the ssh public key of your PC here with hostname removed.
 - Instructions:
-    1. Run `ssh-keygen`
+    1. Run `ssh-keygen`.
     2. Type a filename for key to be saved. Let's say `foo`.
     3. Type `Return(Enter)` twice when it asks for your passphrase. Fast-servo's ssh authentication is passwordless.
     4. Open the generated public key file `foo.pub`.
-    5. Append the public key to the file `/etc/ssh/authorized_keys.d/root` with `@hostname` removed. 
-        Sample ssh public key: `ssh-ed25519 xxx...xxx username@hostname`
+    5. Append the public key to the file `/etc/ssh/authorized_keys.d/root` with `@hostname` removed(if any). For example, if sample ssh public key is `ssh-ed25519 xxx...xxx username@hostname`, you should append `ssh-ed25519 xxx...xxx username` to that file.
 
 ## Usage
-1. Make sure the onboard DIP Switch is in the following condition.
+1. Make sure the onboard DIP Switch is in the following positions.
     - EN: OFF
     - MODE: ON
 2. Install the SD Card, power up the board via the power jack or PoE and plug in the RJ45 Ethernet cable.
-3. Wait for all the front panel LEDs except the termination status LEDs to turn off. It can take a minutes or two for first boot. If it does not boot up, try to flash the SD Card again.
-4. By default, linien-server starts up automatically. In case linien-server crashes, it will restart itself. Logs are stored in `/root/linien-server-log`. 
+3. It can take a minutes or two for first boot. If it does not boot up, try to flash the SD Card again. The following table describes PL initialization status with the status of the front panel LEDs L0, L1, L2, L3.
+
+| L0  | L1 | L2   | L3  | Meaning |
+|-----|----|------|-----|------------------------|
+| On  | On  | On  | On  | Si5340 Clock Generator fails to initialize |
+| On  | On  | X   | X   | LTC2195 Adc fails to initialize |
+| X   | X   | On  | On  | AD9117-2 Dac fails to initialize |
+| Off | Off | Off | Off | Fast-Servo PL initialization is successful |
+
+Note: X = Don't Care
+
+For debugging, you can hook up a USB-to-UART adapter and power cycle to the board to check the boot log. Or if able, ssh into the board and run `python -m pyfastservo.initialize` to check its log.
+4. By default, linien-server starts up automatically if PL Init is successful. In case linien-server crashes, it will restart itself. Logs are stored in `/root/linien-server-log`. 
 ssh access is not required for linien client if linien-server is started. If not, then linien client will ssh into the fast-servo device to start the linien-server service.
 
-    Here are some commands to interact with the linien-server service once you `ssh <fast servo ip address> -p 3030` into fast-servo. 
+Here are some commands for interacting with the linien-server service once you `ssh <fast servo ip address> -p 3030` into fast-servo. 
 
 | Description                                          | Command                                 |
 |------------------------------------------------------|-----------------------------------------|
@@ -56,5 +66,15 @@ ssh access is not required for linien client if linien-server is started. If not
 | Set the linien-server service to start at bootup     | `linien-server enable`                  |
 | Set the linien-server service not to start at bootup | `linien-server disable`                 |
 
-4. In the dev shell, run `linien` to launch the GUI. Add new device. Username is `root`.
+4. In the dev shell, run `linien` to launch the GUI. Add new device. Fill in the hostname/ip address of the device and leave the other fields with default value unchanged.
 5. Select the newly added device and click connect in the GUI to connect and start the GUI.
+6. To save the parameters to be loaded at start up, you would need to shutdown the linien-server service by clicking the corresponding button on the GUI, will ssh into the fast-servo and stop the linien-server service. Removing the power input on Fast-Servo will not save any parameter. Alternatively, you can save and load settings to/from a file on your PC via the GUI. 
+
+## Filesystem Modes
+By default, the SD card is mounted in read-only mode with RAM overlay to prevent data corruption when power is unexpectedly removed.
+
+To change the filesystem mode:
+1. Set read-only mode: `fs-mode ro`
+2. Set read-write mode: `fs-mode rw`
+
+The system will automatically reboot after changing modes.

fast-servo/linien-common-fast-servo-hardware-specific.patch

@@ -1,15 +1,17 @@
 diff --git a/linien-common/linien_common/common.py b/linien-common/linien_common/common.py
-index 854d776..a310dbe 100644
+index 854d776..98de41f 100644
 --- a/linien-common/linien_common/common.py
 +++ b/linien-common/linien_common/common.py
-@@ -25,8 +25,8 @@ from typing import Dict, Iterable, List, Tuple, Union
+@@ -25,8 +25,10 @@ from typing import Dict, Iterable, List, Tuple, Union
  import numpy as np
  from scipy.signal import correlate, resample
  
 -MHz = 0x10000000 / 8
 -Vpp = ((1 << 14) - 1) / 4
-+MHz = 0x10000000 / 8
-+Vpp = (1 << 14 - 1) / 0.355 * 0.85
++CORDIC_GAIN = 1.6467602570986222
++
++MHz = (2 ** 32) / 125.0
++Vpp = (2 ** 14 - 1) / CORDIC_GAIN
  # conversion of bits to V
  ANALOG_OUT_V = 1.8 / ((2**15) - 1)
  

fast-servo/linien-gateware/cores/dac.py

@@ -30,9 +30,9 @@ class DAC(Module, AutoCSR):
 
         phase_shift_en, phase_shift_dir = phase_shift_ctrl
 
-        self.dac_ctrl = CSRStorage(5)
-        self.output_value_ch0 = CSRStorage(14)
-        self.output_value_ch1 = CSRStorage(14)
+        self.dac_ctrl = CSRStorage(5, reset=0b00111)
+        self.output_value_ch0 = CSRStorage(14, reset=0x1FFF)
+        self.output_value_ch1 = CSRStorage(14, reset=0x1FFF)
 
         manual_override = Signal()
         ch0_pd = Signal()

fast-servo/linien-gateware/fast_servo_soc.py

@@ -89,7 +89,7 @@ class CRG(Module):
                 p_CLKOUT1_DIVIDE=8,
                 p_CLKOUT1_PHASE=0.0,
                 p_CLKOUT1_DUTY_CYCLE=0.5,
-                o_CLKOUT1=clk_sys,  # 1000MHz / 8 -> 120MHz
+                o_CLKOUT1=clk_sys,  # 1000MHz / 8 -> 125MHz
                 
                 p_CLKOUT2_DIVIDE=4,
                 p_CLKOUT2_PHASE=0.0,
@@ -290,7 +290,7 @@ class BaseSoC(PS7, AutoCSR):
 class LED(Module, AutoCSR):
     def __init__(self, led):
         
-        self.led_out = CSRStorage(1)
+        self.led_out = CSRStorage(1, reset=1)
 
         self.comb += led.eq(self.led_out.storage)
 

fast-servo/linien-gui-add-afe_gain-combo-boxes.patch

@@ -1,3 +1,25 @@
+diff --git a/linien-common/linien_common/common.py b/linien-common/linien_common/common.py
+index 8f671c2..8b8bb30 100644
+--- a/linien-common/linien_common/common.py
++++ b/linien-common/linien_common/common.py
+@@ -285,6 +285,8 @@ def combine_error_signal(
+     channel_mixing: int,
+     combined_offset: int,
+     chain_factor_width: int = 8,
++    gain_a: int = 1,
++    gain_b: int = 1,
+ ) -> np.ndarray:
+     if not dual_channel:
+         signal = error_signals[0]
+@@ -292,7 +294,7 @@ def combine_error_signal(
+         a_factor, b_factor = convert_channel_mixing_value(channel_mixing)
+ 
+         signal = [
+-            (a_factor * a + b_factor * b) >> chain_factor_width
++            int(((a_factor * a) / gain_a + (b_factor * b) / gain_b) / 2 ** chain_factor_width)
+             for a, b in zip(*error_signals)
+         ]
+ 
 diff --git a/linien-gui/linien_gui/ui/general_panel.py b/linien-gui/linien_gui/ui/general_panel.py
 index cad2d91..499146d 100644
 --- a/linien-gui/linien_gui/ui/general_panel.py
@@ -130,3 +152,112 @@ index 6c2bd45..79f4580 100644
           <item>
            <widget class="QGroupBox" name="dualChannelMixingGroupBox">
             <property name="title">
+diff --git a/linien-gui/linien_gui/ui/plot_widget.py b/linien-gui/linien_gui/ui/plot_widget.py
+index ef03de1..7412549 100644
+--- a/linien-gui/linien_gui/ui/plot_widget.py
++++ b/linien-gui/linien_gui/ui/plot_widget.py
+@@ -112,6 +112,8 @@ class PlotWidget(pg.PlotWidget):
+         )
+         self.app = get_linien_app_instance()
+         self.app.connection_established.connect(self.on_connection_established)
++        self.adc1_afe_gain = 1
++        self.adc2_afe_gain = 1
+ 
+         self.getAxis("bottom").enableAutoSIPrefix(False)
+         self.showGrid(x=True, y=True)
+@@ -226,6 +228,12 @@ class PlotWidget(pg.PlotWidget):
+         self.cached_plot_data = []
+         self._should_reposition_reset_view_button = False
+ 
++    def on_adc_afe_gain_1_changed(self, value):
++        self.adc1_afe_gain = 10 if value else 1
++
++    def on_adc_afe_gain_2_changed(self, value):
++        self.adc2_afe_gain = 10 if value else 1
++
+     def on_connection_established(self):
+         self.parameters = self.app.parameters
+         self.control = self.app.control
+@@ -249,6 +257,8 @@ class PlotWidget(pg.PlotWidget):
+         )
+         self.parameters.automatic_mode.add_callback(self.on_automatic_mode_changed)
+         self.parameters.lock.add_callback(self.on_lock_changed)
++        self.parameters.adc_afe_10x_gain_1.add_callback(self.on_adc_afe_gain_1_changed)
++        self.parameters.adc_afe_10x_gain_2.add_callback(self.on_adc_afe_gain_2_changed)
+ 
+     def _to_data_coords(self, event):
+         pos = self.plotItem.vb.mapSceneToView(event.pos())
+@@ -504,7 +514,7 @@ class PlotWidget(pg.PlotWidget):
+                         scale_history_times(
+                             self.monitor_signal_history_data["times"], timescale
+                         ),
+-                        np.array(self.monitor_signal_history_data["values"]) / V,
++                        np.array(self.monitor_signal_history_data["values"]) / V / self.adc2_afe_gain,
+                     )
+                 self.plot_autolock_target_line(None)
+             else:
+@@ -521,6 +531,8 @@ class PlotWidget(pg.PlotWidget):
+                     dual_channel,
+                     self.parameters.channel_mixing.value,
+                     self.parameters.combined_offset.value if dual_channel else 0,
++                    gain_a = self.adc1_afe_gain,
++                    gain_b = self.adc2_afe_gain,
+                 )
+ 
+                 if self.plot_paused:
+@@ -539,26 +551,31 @@ class PlotWidget(pg.PlotWidget):
+                 self.monitorSignalHistory.setVisible(False)
+ 
+                 self.combinedErrorSignal.setVisible(True)
+-                self.combinedErrorSignal.setData(
+-                    list(range(len(error_signal_1))), error_signal_1 / V
+-                )
++                if dual_channel:
++                    self.combinedErrorSignal.setData(
++                        list(range(len(combined_error_signal))), combined_error_signal / V
++                    )
++                else:
++                    self.combinedErrorSignal.setData(
++                        list(range(len(error_signal_1))), error_signal_1 / V / self.adc1_afe_gain
++                    )
+ 
+                 self.errorSignal1.setVisible(dual_channel)
+                 if error_signal_1 is not None:
+                     self.errorSignal1.setData(
+-                        list(range(len(error_signal_1))), error_signal_1 / V
++                        list(range(len(error_signal_1))), error_signal_1 / V / self.adc1_afe_gain
+                     )
+ 
+                 self.errorSignal2.setVisible(dual_channel)
+                 if error_signal_2 is not None:
+                     self.errorSignal2.setData(
+-                        list(range(len(error_signal_2))), error_signal_2 / V
++                        list(range(len(error_signal_2))), error_signal_2 / V / self.adc2_afe_gain
+                     )
+ 
+                 self.monitorSignal.setVisible(not dual_channel)
+                 if monitor_signal is not None:
+                     self.monitorSignal.setData(
+-                        list(range(len(monitor_signal))), monitor_signal / V
++                        list(range(len(monitor_signal))), monitor_signal / V / self.adc2_afe_gain
+                     )
+ 
+                 self.plot_autolock_target_line(combined_error_signal)
+@@ -593,7 +610,7 @@ class PlotWidget(pg.PlotWidget):
+                                 self.parameters.offset_a.value,
+                                 getattr(self.app.settings, f"plot_color_{color}").value,
+                             )
+-                            / V
++                            / V / self.adc1_afe_gain
+                         )
+ 
+                         self.signal_power1.emit(
+@@ -616,7 +633,7 @@ class PlotWidget(pg.PlotWidget):
+                                     f"plot_color_{Color.ERROR2.value}",
+                                 ).value,
+                             )
+-                            / V
++                            / V / self.adc2_afe_gain
+                         )
+ 
+                         self.signal_power2.emit(

fast-servo/linien-gui-do-not-draw-signal-strength.patch

@@ -0,0 +1,17 @@
+diff --git a/linien-gui/linien_gui/ui/plot_widget.py b/linien-gui/linien_gui/ui/plot_widget.py
+index fe20e66..f5d03c3 100644
+--- a/linien-gui/linien_gui/ui/plot_widget.py
++++ b/linien-gui/linien_gui/ui/plot_widget.py
+@@ -680,8 +680,10 @@ class PlotWidget(pg.PlotWidget):
+         fill.setBrush(brush)
+ 
+         invisible_pen = pg.mkPen("k", width=0.00001)
+-        signal.setData(x, upper, pen=invisible_pen)
+-        neg_signal.setData(x, lower, pen=invisible_pen)
++        # Painter path exceeds +/-32767 pixels. Error when OpenGL is enabled
++        # signal.setData(x, upper, pen=invisible_pen)
++        # neg_signal.setData(x, lower, pen=invisible_pen)
++
+         return np.max([np.max(upper), -1 * np.min(lower)]) * V
+ 
+     def plot_autolock_target_line(self, combined_error_signal):

fast-servo/linien-gui-do-not-use-opengl.patch

@@ -1,13 +0,0 @@
-diff --git a/linien-gui/linien_gui/ui/plot_widget.py b/linien-gui/linien_gui/ui/plot_widget.py
-index f3b81ce..7d865a3 100644
---- a/linien-gui/linien_gui/ui/plot_widget.py
-+++ b/linien-gui/linien_gui/ui/plot_widget.py
-@@ -40,7 +40,7 @@ from pyqtgraph.Qt import QtCore
- # NOTE: this is required for using a pen_width > 1. There is a bug though that causes
- # the plot to be way too small. Therefore, we call PlotWidget.resize() after a while
- pg.setConfigOptions(
--    useOpenGL=True,
-+    useOpenGL=False,
-     # by default, pyqtgraph tries to clean some things up using atexit. This causes
-     # problems with rpyc objects as their connection is already closed. Therefore, we
-     # disable this cleanup.

fast-servo/linien-gui-fast-servo-hardware-specific.patch

@@ -65,11 +65,11 @@ index 3d8b8bf..72f6159 100644
                </property>
                <property name="minimum">
 -               <double>-1.000000000000000</double>
-+               <double>-0.250000000000000</double>
++               <double>-0.50000000000000</double>
                </property>
                <property name="maximum">
 -               <double>1.000000000000000</double>
-+               <double>0.250000000000000</double>
++               <double>0.50000000000000</double>
                </property>
                <property name="singleStep">
                 <double>0.100000000000000</double>
@@ -78,7 +78,7 @@ index 3d8b8bf..72f6159 100644
                </property>
                <property name="maximum">
 -               <double>1.000000000000000</double>
-+               <double>0.250000000000000</double>
++               <double>0.50000000000000</double>
                </property>
                <property name="singleStep">
                 <double>0.100000000000000</double>
@@ -122,10 +122,88 @@ index 6d8af14..29c8a63 100644
            </property>
            <property name="maximum">
 -           <double>2.000000000000000</double>
-+           <double>0.500000000000000</double>
++           <double>1.000000000000000</double>
            </property>
            <property name="singleStep">
             <double>0.100000000000000</double>
+diff --git a/linien-gui/linien_gui/ui/optimization_panel.ui b/linien-gui/linien_gui/ui/optimization_panel.ui
+index 3bf165f..6694112 100644
+--- a/linien-gui/linien_gui/ui/optimization_panel.ui
++++ b/linien-gui/linien_gui/ui/optimization_panel.ui
+@@ -61,7 +61,11 @@
+                <number>30</number>
+               </property>
+               <item>
+-               <widget class="CustomDoubleSpinBoxNoSign" name="optimization_mod_freq_min"/>
++               <widget class="CustomDoubleSpinBoxNoSign" name="optimization_mod_freq_min">
++                <property name="decimals">
++                 <number>4</number>
++                </property>
++               </widget>
+               </item>
+               <item>
+                <widget class="QLabel" name="label_24">
+@@ -84,6 +88,9 @@
+                   <verstretch>0</verstretch>
+                  </sizepolicy>
+                 </property>
++                <property name="decimals">
++                 <number>4</number>
++                </property>
+                 <property name="value">
+                  <double>10.000000000000000</double>
+                 </property>
+@@ -115,7 +122,10 @@
+               <item>
+                <widget class="CustomDoubleSpinBoxNoSign" name="optimization_mod_amp_min">
+                 <property name="maximum">
+-                 <double>2.000000000000000</double>
++                 <double>1.000000000000000</double>
++                </property>
++                <property name="singleStep">
++                 <double>0.100000000000000</double>
+                 </property>
+                </widget>
+               </item>
+@@ -135,10 +145,13 @@
+               <item>
+                <widget class="CustomDoubleSpinBoxNoSign" name="optimization_mod_amp_max">
+                 <property name="maximum">
+-                 <double>2.000000000000000</double>
++                 <double>1.000000000000000</double>
++                </property>
++                <property name="singleStep">
++                 <double>0.100000000000000</double>
+                 </property>
+                 <property name="value">
+-                 <double>2.000000000000000</double>
++                 <double>1.000000000000000</double>
+                 </property>
+                </widget>
+               </item>
+diff --git a/linien-gui/linien_gui/ui/new_device_dialog.ui b/linien-gui/linien_gui/ui/new_device_dialog.ui
+index 38c3513..e543744 100644
+--- a/linien-gui/linien_gui/ui/new_device_dialog.ui
++++ b/linien-gui/linien_gui/ui/new_device_dialog.ui
+@@ -52,7 +52,7 @@
+            <item>
+             <widget class="QLineEdit" name="host">
+              <property name="text">
+-              <string>rp-xxxxxx.local</string>
++              <string>192.168.1.129</string>
+              </property>
+             </widget>
+            </item>
+@@ -67,6 +67,9 @@
+              <property name="wordWrap">
+               <bool>true</bool>
+              </property>
++             <property name="visible">
++              <bool>false</bool>
++             </property>
+             </widget>
+            </item>
+           </layout>
 diff --git a/linien-gui/linien_gui/ui/sweep_control.py b/linien-gui/linien_gui/ui/sweep_control.py
 index 7d2bb2d..e98c169 100644
 --- a/linien-gui/linien_gui/ui/sweep_control.py
@@ -136,6 +214,32 @@ index 7d2bb2d..e98c169 100644
          # set control boundaries
 -        self.setMinimum(-1.0)
 -        self.setMaximum(1.0)
-+        self.setMinimum(-0.25)
-+        self.setMaximum(0.25)
++        self.setMinimum(-0.5)
++        self.setMaximum(0.5)
          self.setSingleStep(0.001)
+diff --git a/linien-client/linien_client/device.py b/linien-client/linien_client/device.py
+index 727fbba..2f0f704 100644
+--- a/linien-client/linien_client/device.py
++++ b/linien-client/linien_client/device.py
+@@ -48,7 +48,7 @@ class Device:
+ 
+     def __post_init__(self):
+         if self.host == "":
+-            self.host = "rp-xxxxxx.local"
++            self.host = "192.168.1.129"
+         if self.username == "":
+             self.username = "root"
+         if self.password == "":
+diff --git a/linien-gui/linien_gui/ui/device_manager.py b/linien-gui/linien_gui/ui/device_manager.py
+index 16994ad..85abcf2 100644
+--- a/linien-gui/linien_gui/ui/device_manager.py
++++ b/linien-gui/linien_gui/ui/device_manager.py
+@@ -151,7 +151,7 @@ class DeviceManager(QtWidgets.QMainWindow):
+             ]
+         ) -> None:
+             question = (
+-                "Linien on RedPitaya is running with different parameters than the "
++                "Linien on Fast-Servo is running with different parameters than the "
+                 "ones saved locally on this machine. Do you want to upload the local "
+                 "parameters or keep the remote ones? Note that remote parameters are "
+                 "only saved if Linien server was shut down properly, not when "

fast-servo/linien-server-fast-servo-hardware-specific.patch

@@ -29,7 +29,7 @@ index fe482d7..04a3c24 100644
          # ------------------- SWEEP PARAMETERS -----------------------------------------
  
 -        self.sweep_amplitude = Parameter(min_=0.001, max_=1, start=1, loggable=True)
-+        self.sweep_amplitude = Parameter(min_=0.001, max_=0.25, start=0.25, loggable=True)
++        self.sweep_amplitude = Parameter(min_=0.001, max_=0.5, start=0.5, loggable=True)
          """
          Amplitude of the sweep in units of 0.5 * Vpp of the output (2 V for fast outputs
          (range +/- 1 V) and 0.9 V for slow outputs (range 0 V to 1.8 V)). That means an
@@ -37,7 +37,7 @@ index fe482d7..04a3c24 100644
          """
  
 -        self.sweep_center = Parameter(min_=-1, max_=1, start=0, loggable=True)
-+        self.sweep_center = Parameter(min_=-0.25, max_=0.25, start=0, loggable=True)
++        self.sweep_center = Parameter(min_=-0.5, max_=0.5, start=0, loggable=True)
          """
          The center position of the sweep. If a fast output is used for the sweep this is
          the sweep center position in volts. If the slow output is used the interval
@@ -50,14 +50,14 @@ index 2b8f697..65e9732 100644
              logic_sweep_step=int(
                  DEFAULT_SWEEP_SPEED
 -                * self.parameters.sweep_amplitude.value
-+                * self.parameters.sweep_amplitude.value * 4
++                * self.parameters.sweep_amplitude.value
                  / (2**self.parameters.sweep_speed.value)
              ),
              # NOTE: Sweep center is set by `logic_out_offset`.
 -            logic_sweep_min=-1 * max_(self.parameters.sweep_amplitude.value * 8191),
 -            logic_sweep_max=max_(self.parameters.sweep_amplitude.value * 8191),
-+            logic_sweep_min=-1 * max_(self.parameters.sweep_amplitude.value * 32767),
-+            logic_sweep_max=max_(self.parameters.sweep_amplitude.value * 32767),
++            logic_sweep_min=-1 * max_(self.parameters.sweep_amplitude.value * 16384),
++            logic_sweep_max=max_(self.parameters.sweep_amplitude.value * 16384),
              logic_mod_freq=(
                  self.parameters.modulation_frequency.value
                  if not self.parameters.pid_only_mode.value
@@ -66,7 +66,20 @@ index 2b8f697..65e9732 100644
                  int(self.parameters.offset_b.value), 14
              ),
 -            logic_out_offset=int(self.parameters.sweep_center.value * 8191),
-+            logic_out_offset=int(self.parameters.sweep_center.value * 32767),
++            logic_out_offset=int(self.parameters.sweep_center.value * 16384),
              logic_combined_offset=twos_complement(
                  self.parameters.combined_offset.value, 14
              ),
+diff --git a/linien-common/linien_common/config.py b/linien-common/linien_common/config.py
+index 6ba92e6..8d8c554 100644
+--- a/linien-common/linien_common/config.py
++++ b/linien-common/linien_common/config.py
+@@ -24,7 +24,7 @@ logger.setLevel(logging.DEBUG)
+ 
+ ACQUISITION_PORT = 19321
+ SERVER_PORT = 18862
+-DEFAULT_SWEEP_SPEED = (125 * 2048) << 6
++DEFAULT_SWEEP_SPEED = 2 ** 40 / (125 * 10 ** 6 ) * 3800
+ 
+ USER_DATA_PATH = Path(AppDirs("linien").user_data_dir)
+ USER_DATA_PATH.mkdir(parents=True, exist_ok=True)

fast-servo/pyfastservo/adc.py

@@ -146,6 +146,7 @@ def print_adc_channel(ch):
         print(f"Final ADC_CH1: 0x{adc_ch1:04x}")
 
 def configure_ltc2195():
+    # Calling this fn stops the PL input clock momentarily, triggers PL reset.
     print()
     print("### Initializing LTC2195 Adc")
     spi = spidev.SpiDev()

fast-servo/pyfastservo/dac.py

@@ -110,12 +110,17 @@ def dac_self_calibration(spi):
     return True
 
 def set_dac_input_override(enable=True):
+    # It is enabled by default after PL reset.
+    #   Disable it during PL init to routes the DAC output from linien-server
+
     reg_contents = read_from_memory(CTRL_ADDR, 1)[0]
     to_write = reg_contents | 0b1 if enable else reg_contents & 0b110
     write_to_memory(CTRL_ADDR, to_write)
     print(f"Enable DAC Input Override: {enable}")
 
 def power_down_afe(channel, power_down=True):
+    # It is enabled by default after PL reset.
+    #   Disable it during PL init
     assert channel in (0, 1)
 
     bitmask = 1 << (channel + 1) & 0b111

fast-servo/pyfastservo/fp_leds.py

@@ -20,6 +20,7 @@
 import mmap
 import os
 import time
+import argparse
 
 from pyfastservo.common import (
     LED0_BASE_ADDR,
@@ -34,7 +35,29 @@ ON = 1
 OFF = 0
 
 
-def main():
+def turn_on_led(led, on):
+    f = os.open("/dev/mem", os.O_SYNC | os.O_RDWR)
+    addrs = [LED0_BASE_ADDR, LED1_BASE_ADDR, LED2_BASE_ADDR, LED3_BASE_ADDR]
+    addr = addrs[led]
+
+    with mmap.mmap(
+        f,
+        PAGESIZE,
+        mmap.MAP_SHARED,
+        mmap.PROT_READ | mmap.PROT_WRITE,
+        offset=addr & ~MAP_MASK,
+    ) as mem:
+        start_addr = addr & MAP_MASK
+        stop_addr = start_addr + 4
+        if on:
+            mem[start_addr:stop_addr] = ON.to_bytes(4, "little")
+        else:
+            mem[start_addr:stop_addr] = OFF.to_bytes(4, "little")
+        contents = mem[start_addr:stop_addr]
+    os.close(f)
+
+
+def turn_off_all_leds():
     addrs = [LED0_BASE_ADDR, LED1_BASE_ADDR, LED2_BASE_ADDR, LED3_BASE_ADDR]
 
     f = os.open("/dev/mem", os.O_SYNC | os.O_RDWR)
@@ -46,21 +69,18 @@ def main():
             mmap.PROT_READ | mmap.PROT_WRITE,
             offset=addr & ~MAP_MASK,
         ) as mem:
-            for i in range(6):
-                start_addr = addr & MAP_MASK
-                stop_addr = start_addr + 4
-                print(
-                    f"addr: 0x{addr:x}\tstart_addr: 0x{start_addr}\tstop_addr: 0x{stop_addr}"
-                )
-                mem[start_addr:stop_addr] = ON.to_bytes(4, "little")
-                contents = mem[start_addr:stop_addr]
-                time.sleep(0.5)
-                mem[start_addr:stop_addr] = OFF.to_bytes(4, "little")
-                contents = mem[start_addr:stop_addr]
-                time.sleep(0.5)
-
+            start_addr = addr & MAP_MASK
+            stop_addr = start_addr + 4
+            mem[start_addr:stop_addr] = OFF.to_bytes(4, "little")
     os.close(f)
 
 
+def main():
+    parser = argparse.ArgumentParser()
+    parser.add_argument("led", type=int)
+    parser.add_argument("state", type=int)
+    args = parser.parse_args()
+    turn_on_led(args.led, bool(args.state))
+
 if __name__ == "__main__":
     main()

fast-servo/pyfastservo/initialize.py

@@ -17,21 +17,32 @@
 # You should have received a copy of the GNU General Public License
 # along with this program. If not, see <https://www.gnu.org/licenses/>.
 
-from pyfastservo import adc, si5340, dac
+from pyfastservo import adc, si5340, dac, fp_leds
+from time import sleep
 
 def main():
     print()
     print("### PL Initialization")
     print()
 
-    # Set output voltage to be 0V after AD9117-2 soft reset
-    # DAC starts up in unsigned Data Format. Set DAC to output 0V before Clock is provided to it
-    dac.set_dac_input_override_value(0x1FFF)
-    dac.set_dac_input_override(True)
+    si5340_ok, adc_ok, dac_ok  = False, False, False
 
     si5340_ok = si5340.configure_si5340()
-    adc_ok = adc.configure_ltc2195()
-    dac_ok = dac.configure_ad9117()
+    sleep(0.1)
+    # Do not touch any CSR Register(s) if PL Clock cannot be init-ed.
+    #   Otherwise, the OS will hang up.
+    if si5340_ok:
+        # Configuring the LTC2195 would stop PL input clock momentarily and trigger PL reset.
+        adc_ok = adc.configure_ltc2195()
+        sleep(0.1)
+        if adc_ok:
+            fp_leds.turn_on_led(0, False)
+            fp_leds.turn_on_led(1, False)
+        dac_ok = dac.configure_ad9117()
+        sleep(0.1)
+        if dac_ok:
+            fp_leds.turn_on_led(2, False)
+            fp_leds.turn_on_led(3, False)
 
     if si5340_ok and adc_ok and dac_ok:
         print()
@@ -44,6 +55,7 @@ def main():
         print(f"LTC2195 Adc Init Status: {"Success" if adc_ok else "Failed"}")
         print(f"Ad9117 Dac Init Status: {"Success" if dac_ok else "Failed"}")
         print()
+        exit(1)
 
 if __name__ == "__main__":
     main()

fast-servo/pyfastservo/si5340.py

@@ -93,6 +93,9 @@ def check_los_status(bus):
     return not xaxb_los
 
 def configure_si5340():
+    # After PL Reset, this fn needs to be called before accessing any CSR registers.
+    #   Otherwise, the system may hang up.
+
     print()
     print("### Initializing Si5340 Clock Generator")
     with SMBus(BUS_NO) as bus:

flake.lock

@@ -18,11 +18,11 @@
     },
     "nixpkgs": {
       "locked": {
-        "lastModified": 1736867362,
-        "narHash": "sha256-i/UJ5I7HoqmFMwZEH6vAvBxOrjjOJNU739lnZnhUln8=",
+        "lastModified": 1743367904,
+        "narHash": "sha256-sOos1jZGKmT6xxPvxGQyPTApOunXvScV4lNjBCXd/CI=",
         "owner": "NixOS",
         "repo": "nixpkgs",
-        "rev": "9c6b49aeac36e2ed73a8c472f1546f6d9cf1addc",
+        "rev": "7ffe0edc685f14b8c635e3d6591b0bbb97365e6c",
         "type": "github"
       },
       "original": {
@@ -64,11 +64,11 @@
     "src-migen": {
       "flake": false,
       "locked": {
-        "lastModified": 1735131698,
-        "narHash": "sha256-P4vaF+9iVekRAC2/mc9G7IwI6baBpPAxiDQ8uye4sAs=",
+        "lastModified": 1738906518,
+        "narHash": "sha256-GproDJowtcgbccsT+I0mObzFhE483shcS8MSszKXwlc=",
         "owner": "m-labs",
         "repo": "migen",
-        "rev": "4c2ae8dfeea37f235b52acb8166f12acaaae4f7c",
+        "rev": "2828df54594673653a641ab551caf6c6b1bfeee5",
         "type": "github"
       },
       "original": {
@@ -80,11 +80,11 @@
     "src-misoc": {
       "flake": false,
       "locked": {
-        "lastModified": 1736416570,
-        "narHash": "sha256-tbcN/fzejZIaYbTbwk8Ir1glYevESqMinMeDB3z8oxg=",
+        "lastModified": 1741935500,
+        "narHash": "sha256-rbh4++/M1FQw57fUKow1MNXpmFfguUH5LlxfklDvUjs=",
         "ref": "refs/heads/master",
-        "rev": "1f5318e9edc1085ac77e9b85b8f5e03371dba54c",
-        "revCount": 2464,
+        "rev": "ebeff99217e6e23eb410d7c208d1f17443a57322",
+        "revCount": 2496,
         "submodules": true,
         "type": "git",
         "url": "https://github.com/m-labs/misoc.git"

flake.nix

@@ -32,7 +32,7 @@
             ./fast-servo/linien-server-fast-servo-hardware-specific.patch
             ./fast-servo/linien-gui-fast-servo-hardware-specific.patch
             ./fast-servo/linien-gui-add-afe_gain-combo-boxes.patch
-            ./fast-servo/linien-gui-do-not-use-opengl.patch
+            ./fast-servo/linien-gui-do-not-draw-signal-strength.patch
             ./fast-servo/linien-gui-hide-password-box.patch
             ./fast-servo/linien-gui-do-not-check-for-update.patch
             ./fast-servo/linien-client-ssh-port-change.patch
@@ -64,6 +64,7 @@
           ./not-os-patches/pr-34.patch
           ./not-os-patches/iproute2.patch
           ./not-os-patches/user_defined_ip_settings.patch
+          ./not-os-patches/init_script_service.patch
         ];
       };
 
@@ -411,6 +412,25 @@
         hardeningDisable = [ "fortify" ];
       };
 
+      fs-mode = pkgs-armv7l.writeScriptBin "fs-mode" ''
+        if [ "$1" = "ro" ]; then
+          mount -o remount,rw /boot
+          rm -f /boot/fs_mode_rw
+          echo "System will boot in read-only mode after reboot."
+          sync
+          reboot
+        elif [ "$1" = "rw" ]; then
+          mount -o remount,rw /boot
+          touch /boot/fs_mode_rw
+          echo "System will boot in read-write mode after reboot."
+          sync
+          reboot
+        else
+          echo "Usage: fs-mode [ro|rw]"
+          exit 1
+        fi
+      '';
+
       board-package-set = { board }: let
         not-os-configured = (import patched-not-os {
           inherit nixpkgs;
@@ -420,6 +440,7 @@
             ({ config, pkgs, lib, ... }: {
               environment.systemPackages = [
                 (pkgs.python3.withPackages(ps: with ps; [ pyfastservo linien-server]))
+                fs-mode
               ];
               boot.postBootCommands = lib.mkAfter ''
 
@@ -431,8 +452,6 @@
                 cp ${fast-servo-gateware}/gateware.bin /lib/firmware/
                 echo gateware.bin > /sys/class/fpga_manager/fpga0/firmware
 
-                # Initialize All PL Peripherals
-                python3 -m pyfastservo.initialize
               '';
             })];
           system = "x86_64-linux";

not-os-patches/init_script_service.patch

@@ -0,0 +1,55 @@
+diff --git a/runit.nix b/runit.nix
+index 982823d..906fa24 100644
+--- a/runit.nix
++++ b/runit.nix
+@@ -28,6 +28,23 @@ in
+   environment.systemPackages = [ compat ];
+   environment.etc = lib.mkMerge [
+     {
++      "pl_init".source = pkgs.writeScript "pl_init" ''
++        #!/bin/sh
++        exec 2>&1
++
++        python -m pyfastservo.initialize
++        EXIT_CODE=$?
++
++        if [ $EXIT_CODE -eq 0 ]; then
++            # Add Symlink linien service to /etc/service
++            ln -sf /etc/linien-server /etc/service/linien-server
++        else
++            echo "PL Initialization failed. Linien Server Service is not Started."
++        fi
++
++        exit 0
++      '';
++
+       "runit/1".source = pkgs.writeScript "1" ''
+         #!${pkgs.runtimeShell}
+         ${lib.optionalString config.not-os.simpleStaticIp ''
+@@ -53,6 +70,8 @@ in
+         touch /etc/runit/stopit
+         chmod 0 /etc/runit/stopit
+         ${if true then "" else "${pkgs.dhcpcd}/sbin/dhcpcd"}
++
++        /etc/pl_init
+       '';
+       "runit/2".source = pkgs.writeScript "2" ''
+         #!${pkgs.runtimeShell}
+diff --git a/zynq_image.nix b/zynq_image.nix
+index 0dad456..fce8797 100644
+--- a/zynq_image.nix
++++ b/zynq_image.nix
+@@ -51,11 +51,11 @@ in {
+         hostname ${config.networking.hostName}
+         exec setsid agetty ttyPS0 115200
+       '';
+-      "service/linien-server/run".source = pkgs.writeShellScript "linien-server" ''
++      "linien-server/run".source = pkgs.writeShellScript "linien-server" ''
+         exec 2>&1
+         exec setsid linien-server run
+       '';
+-      "service/linien-server/log/run".source = pkgs.writeShellScript "linien-server-logger" ''
++      "linien-server/log/run".source = pkgs.writeShellScript "linien-server-logger" ''
+         exec 2>&1
+         mkdir -p /root/linien-server-log
+         exec svlogd -tt /root/linien-server-log

not-os-patches/pr-28.patch

@@ -59,7 +59,7 @@ index d7b0bf3..70353a1 100644
        '';
      }
 diff --git a/stage-1.nix b/stage-1.nix
-index 331fecd..aa5148e 100644
+index 331fecd..f1f73cb 100644
 --- a/stage-1.nix
 +++ b/stage-1.nix
 @@ -117,11 +117,6 @@ let
@@ -74,18 +74,63 @@ index 331fecd..aa5148e 100644
      root=/dev/vda
      realroot=tmpfs
      for o in $(cat /proc/cmdline); do
-@@ -164,7 +159,9 @@ let
+@@ -163,20 +158,41 @@ let
+     chmod 755 /mnt/
      mkdir -p /mnt/nix/store/
  
- 
+-
 -    ${if config.not-os.nix then ''
+-    # make the store writeable
+-    mkdir -p /mnt/nix/.ro-store /mnt/nix/.overlay-store /mnt/nix/store
+-    mount $root /mnt/nix/.ro-store -t squashfs
+-    if [ $realroot = $1 ]; then
+-      mount tmpfs -t tmpfs /mnt/nix/.overlay-store -o size=1G
+-    fi
+-    mkdir -pv /mnt/nix/.overlay-store/work /mnt/nix/.overlay-store/rw
+-    modprobe overlay
+-    mount -t overlay overlay -o lowerdir=/mnt/nix/.ro-store,upperdir=/mnt/nix/.overlay-store/rw,workdir=/mnt/nix/.overlay-store/work /mnt/nix/store
+-    '' else ''
+-    # readonly store
+-    mount $root /mnt/nix/store/ -t squashfs
 +    ${if config.not-os.sd && config.not-os.nix then ''
-+    mount $root /mnt
-+    '' else if config.not-os.nix then ''
-     # make the store writeable
-     mkdir -p /mnt/nix/.ro-store /mnt/nix/.overlay-store /mnt/nix/store
-     mount $root /mnt/nix/.ro-store -t squashfs
-@@ -190,6 +187,11 @@ let
++      mkdir -p /boot
++      mount -t vfat -o ro /dev/mmcblk0p1 /boot
++      USE_READONLY=1
++      if [ -e /boot/rw_mode ]; then
++        echo "Found rw_mode flag, enabling read-write mode"
++        USE_READONLY=0
++      fi
++      if [ "$USE_READONLY" = "1" ]; then
++        mkdir -p /mnt.ro /mnt.overlay
++        mount -o ro $root /mnt.ro
++        mount -t tmpfs -o size=1G tmpfs /mnt.overlay
++        mkdir -p /mnt.overlay/upper /mnt.overlay/work
++        mount -t overlay overlay -o lowerdir=/mnt.ro,upperdir=/mnt.overlay/upper,workdir=/mnt.overlay/work /mnt
++        mkdir -p /mnt/boot
++      else
++        mount $root /mnt
++        mkdir -p /mnt/boot
++      fi
++      mount --move /boot /mnt/boot
++    ''
++    else if config.not-os.nix then ''
++      # make the store writeable
++      mkdir -p /mnt/nix/.ro-store /mnt/nix/.overlay-store /mnt/nix/store
++      mount $root /mnt/nix/.ro-store -t squashfs
++      if [ $realroot = $1 ]; then
++        mount tmpfs -t tmpfs /mnt/nix/.overlay-store -o size=1G
++      fi
++      mkdir -pv /mnt/nix/.overlay-store/work /mnt/nix/.overlay-store/rw
++      modprobe overlay
++      mount -t overlay overlay -o lowerdir=/mnt/nix/.ro-store,upperdir=/mnt/nix/.overlay-store/rw,workdir=/mnt/nix/.overlay-store/work /mnt/nix/store
++    ''
++    else ''
++      # readonly store
++      mount $root /mnt/nix/store/ -t squashfs
+     ''}
+ 
+     ${lib.optionalString enablePlymouth ''
+@@ -190,6 +206,11 @@ let
    initialRamdisk = pkgs.makeInitrd {
      contents = [ { object = bootStage1; symlink = "/init"; } ];
    };
@@ -97,7 +142,7 @@ index 331fecd..aa5148e 100644
  in
  {
    options = {
-@@ -205,6 +207,7 @@ in
+@@ -205,6 +226,7 @@ in
    config = {
      system.build.bootStage1 = bootStage1;
      system.build.initialRamdisk = initialRamdisk;
@@ -152,10 +197,10 @@ index c61f9d6..fbdf0fd 100644
    };
  }
 diff --git a/zynq_image.nix b/zynq_image.nix
-index 3fa23ab..069fe89 100644
+index 3fa23ab..1790801 100644
 --- a/zynq_image.nix
 +++ b/zynq_image.nix
-@@ -1,66 +1,89 @@
+@@ -1,66 +1,91 @@
 -{ config, pkgs, ... }:
 +{ lib, config, pkgs, ... }:
  
@@ -167,6 +212,8 @@ index 3fa23ab..069fe89 100644
 +  customKernel = (pkgs.linux_6_6.override {
      extraConfig = ''
        OVERLAY_FS y
++      NLS_CODEPAGE_437 y
++      NLS_ISO8859_1 y
 +      MEDIA_SUPPORT n
 +      FB n
 +      DRM n