diff --git a/get_and_plot_remote_sayma_data b/get_and_plot_remote_sayma_data
index bacc047..f9ab2e7 100755
--- a/get_and_plot_remote_sayma_data
+++ b/get_and_plot_remote_sayma_data
@@ -6,7 +6,7 @@
 # └── pi/
 #     └── mlabs-testsuite/
 #         ├── rp_get_sayma_data.py
-#         └── creotech-raw/
+#         └── raw/
 #             |   (possible existing data files, will be overwritten)
 #             ├── rp_..._y1_raw.bin.py
 #             ├── rp_..._y2_raw.bin.py
@@ -25,24 +25,27 @@
 export HOST=pi@rpi-2
 export HOSTPORT=6000
 
-if [[ $1 = "" ]] || [[ $2 = "" ]] || [[ $3 = "" ]] || [[ $4 = "" ]]
+if [[ $1 = "" ]] || [[ $2 = "" ]] || [[ $3 = "" ]] || [[ $4 = "" ]] || [[ $5 = "" ]]
 then
-    echo "Arguments: <RP#1 name> <RP#1 channel> <RP#2 name> <RP#2 channel>"
-    echo "(RP#1 and RP#2 can be the same)"
+    echo "Arguments: <RP#1 name> <RP#1 channel> <RP#2 name> <RP#1 channel> <RP#1 name>:<IN1 gain>,<IN2 gain> [<RP#2 name>:<IN1 gain>,<IN2 gain>]"
+    echo "(If RP#1 and RP#2 are the same, skip the bracketed arguments)"
+    echo "Examples: "
+    echo "(1) creotech-1 1 creotech-1 2 creotech-1:LV,HV"
+    echo "(2) creotech-1 1 creotech-2 1 creotech-1:LV,LV creotech-2:HV,HV"
     exit
 fi
 
 # Acquire data at the remote
 if [[ $1 = $3 ]]
 then
-	ssh -t -p $HOSTPORT $HOST "cd mlabs-testsuite && python3 rp_get_sayma_data.py creotech-raw $1"
+	ssh -t -p $HOSTPORT $HOST "cd mlabs-testsuite && python3 rp_get_sayma_data.py raw $5"
 else
-	ssh -t -p $HOSTPORT $HOST "cd mlabs-testsuite && python3 rp_get_sayma_data.py creotech-raw $1 $3"
+	ssh -t -p $HOSTPORT $HOST "cd mlabs-testsuite && python3 rp_get_sayma_data.py raw $5 $6"
 fi
 
 # Transfer data from remote to local
-scp -P $HOSTPORT $HOST:/home/pi/mlabs-testsuite/creotech-raw/rp_$1_y$2_raw.bin creotech-raw/
-scp -P $HOSTPORT $HOST:/home/pi/mlabs-testsuite/creotech-raw/rp_$3_y$4_raw.bin creotech-raw/
+scp -P $HOSTPORT $HOST:/home/pi/mlabs-testsuite/raw/rp_$1_y$2_raw.bin creotech-raw/
+scp -P $HOSTPORT $HOST:/home/pi/mlabs-testsuite/raw/rp_$3_y$4_raw.bin creotech-raw/
 
 # Plot data at local
 # (Note: requires numpy, matplotlib and scipy on local)
diff --git a/plot_sayma_data.py b/plot_sayma_data.py
index a90d90c..73e4434 100644
--- a/plot_sayma_data.py
+++ b/plot_sayma_data.py
@@ -46,15 +46,17 @@ def main():
     y1 = rp_raw_to_numpy(y1_raw)
     y2 = rp_raw_to_numpy(y2_raw)
 
-    # Note that RedPitaya's oscilloscope has a sampling rate @ 125MHz
+    # Define t as an array of timestamps (in seconds) for each sample
+    # (Note that RedPitaya's oscilloscope has a sampling rate @ 125MHz)
     t = np.arange(y1.shape[0])/125e6
     # Generate matrix Y by having arrays y1 and y2 as 2 rows
     y = np.c_[y1, y2].T
-    # Multiply an array of cos(2pi*9e6*t) with each row in Y;
-    # Then, downsample the array by 10 as Z.
+    # Element-wise multiply an array of cos(2pi*9e6*t) with each row in Y;
+    # Then, downsample the array by 10 as Z
     z = signal.decimate(y*np.exp(1j*2*np.pi*9e6*t), q=10, ftype="fir", zero_phase=True)[:, 10:]
     # Downsample Z by 10 again.
     z = signal.decimate(z, q=10, ftype="fir", zero_phase=True)[:, 10:]
+    # Element-wise multiply Z[0] with the conjugate of Z[1] to get the phase difference (i.e. angle(z0) - angle(z1)), and use the mean value.
     angle = np.angle(np.mean(z[0]*z[1].conj()))
 
     print(angle)
diff --git a/rp_get_sayma_data.py b/rp_get_sayma_data.py
index c48a1a9..a246555 100644
--- a/rp_get_sayma_data.py
+++ b/rp_get_sayma_data.py
@@ -6,9 +6,11 @@ import os
 
 
 class RPSCPI:
-    def __init__(self, rp_name, rp_host):
+    def __init__(self, rp_name, rp_host, ch1_gain, ch2_gain):
         self.name = rp_name
         self.host = rp_host
+        self.ch1_gain = ch1_gain
+        self.ch2_gain = ch2_gain
 
     def connect(self):
         self.sock = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
@@ -27,6 +29,8 @@ class RPSCPI:
 
     def trigger_prep(self):
         self.sendmsg("ACQ:RST")
+        self.sendmsg("ACQ:SOUR1:GAIN {}".format(self.ch1_gain.upper()))
+        self.sendmsg("ACQ:SOUR2:GAIN {}".format(self.ch2_gain.upper()))
         self.sendmsg("ACQ:START")
 
     async def trigger(self):
@@ -55,17 +59,30 @@ async def gather_trigger(rp_list):
 def main():
     parser = argparse.ArgumentParser(description="Data collection tool for Sayma DAC/TTL at RedPitaya")
     parser.add_argument("dir", help="output directory", type=str)
-    parser.add_argument("rps", help="name(s) of the target RedPitayas where data is collected "
-        "simultaneously; any of: " + " ".join(list(RP_IP_ADDRS.keys())),
+    parser.add_argument("rps_gains", metavar="RP_NAME:CH1_GAIN,CH2_GAIN",
+        help="choose LV (+-1V) gain or HV (+-20V) gain on each channel for RP named <RP_NAME>; "
+        "e.g. mlabs:LV,HV means LV for IN1 and HV for IN2 on RP mlabs;\n"
+        "<RP_NAME> must be one of: " + " ".join(list(RP_IP_ADDRS.keys())),
         type=str, nargs='+')
     parser.add_argument("--txt", help="save data as additional human-readable text files",
         action="store_true")
     args = parser.parse_args()
 
+    gains = dict()
+    try:
+        for gain in args.rps_gains:
+            rp_name, ch1ch2_gains = gain.split(':')
+            ch1_gain, ch2_gain = ch1ch2_gains.split(',')
+            gains[rp_name] = ch1_gain, ch2_gain
+            if rp_name == "" or ch1_gain == "" or ch2_gain == "":
+                raise SyntaxError("Must specify IN1 and IN2 gains for each target RP.")
+    except ValueError:
+        raise SyntaxError("Must specify input gains in the format of: <RP_NAME>:<CH1_GAIN>,<CH2_GAIN>")
+
     # Connect a socket to each RP
     rps = []
-    for rp_name in args.rps:
-        rp = RPSCPI(rp_name, RP_IP_ADDRS[rp_name])
+    for rp_name in gains:
+        rp = RPSCPI(rp_name, RP_IP_ADDRS[rp_name], *gains[rp_name])
         rp.connect()
         rps.append(rp)