From 71ab0183abbcdb6dcbb8cd9488e445830cb31325 Mon Sep 17 00:00:00 2001
From: Eric Teunis de Boone <ericteunis@deboone.nl>
Date: Thu, 2 Feb 2023 08:57:03 +0100
Subject: [PATCH 01/11] ZH: change figsize to (12,8)

---
 .../airshower_beacon_simulation/ac_show_signal_to_noise.py      | 2 +-
 .../airshower_beacon_simulation/ba_measure_beacon_phase.py      | 2 +-
 .../airshower_beacon_simulation/bb_measure_clock_phase.py       | 2 +-
 .../airshower_beacon_simulation/bc_baseline_phase_deltas.py     | 2 +-
 .../airshower_beacon_simulation/bd_antenna_phase_deltas.py      | 2 +-
 .../airshower_beacon_simulation/ca_period_from_shower.py        | 2 +-
 .../cb_report_measured_antenna_time_offsets.py                  | 2 +-
 simulations/airshower_beacon_simulation/da_reconstruction.py    | 2 +-
 .../airshower_beacon_simulation/dc_grid_power_time_fixes.py     | 2 +-
 .../airshower_beacon_simulation/view_beaconed_antenna.py        | 2 +-
 10 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/simulations/airshower_beacon_simulation/ac_show_signal_to_noise.py b/simulations/airshower_beacon_simulation/ac_show_signal_to_noise.py
index cda7241..adb1d86 100755
--- a/simulations/airshower_beacon_simulation/ac_show_signal_to_noise.py
+++ b/simulations/airshower_beacon_simulation/ac_show_signal_to_noise.py
@@ -34,7 +34,7 @@ if __name__ == "__main__":
     args = parser.parse_args()
 
     fname = "ZH_airshower/mysim.sry"
-    figsize = (9,6)
+    figsize = (12,8)
 
     fig_dir = args.fig_dir
     show_plots = args.show_plots
diff --git a/simulations/airshower_beacon_simulation/ba_measure_beacon_phase.py b/simulations/airshower_beacon_simulation/ba_measure_beacon_phase.py
index 613acda..20e07a8 100755
--- a/simulations/airshower_beacon_simulation/ba_measure_beacon_phase.py
+++ b/simulations/airshower_beacon_simulation/ba_measure_beacon_phase.py
@@ -36,7 +36,7 @@ if __name__ == "__main__":
     show_plots = args.show_plots
 
     fname = "ZH_airshower/mysim.sry"
-    figsize = (9,6)
+    figsize = (12,8)
 
     print("use_AxB_trace:", use_AxB_trace, "use_beacon_trace:",use_beacon_trace)
 
diff --git a/simulations/airshower_beacon_simulation/bb_measure_clock_phase.py b/simulations/airshower_beacon_simulation/bb_measure_clock_phase.py
index a16fa76..eb324a5 100755
--- a/simulations/airshower_beacon_simulation/bb_measure_clock_phase.py
+++ b/simulations/airshower_beacon_simulation/bb_measure_clock_phase.py
@@ -23,7 +23,7 @@ if __name__ == "__main__":
     args = parser.parse_args()
 
     fname = "ZH_airshower/mysim.sry"
-    figsize = (9,6)
+    figsize = (12,8)
     c_light = lib.c_light
     show_plots = args.show_plots
 
diff --git a/simulations/airshower_beacon_simulation/bc_baseline_phase_deltas.py b/simulations/airshower_beacon_simulation/bc_baseline_phase_deltas.py
index 887cd0e..a19358d 100755
--- a/simulations/airshower_beacon_simulation/bc_baseline_phase_deltas.py
+++ b/simulations/airshower_beacon_simulation/bc_baseline_phase_deltas.py
@@ -24,7 +24,7 @@ if __name__ == "__main__":
     args = parser.parse_args()
 
     fname = "ZH_airshower/mysim.sry"
-    figsize = (9,6)
+    figsize = (12,8)
     c_light = 3e8*1e-9
     show_plots = args.show_plots
     ref_ant_id = None if True else [50] # leave None for all baselines
diff --git a/simulations/airshower_beacon_simulation/bd_antenna_phase_deltas.py b/simulations/airshower_beacon_simulation/bd_antenna_phase_deltas.py
index 746ca9b..48b7685 100755
--- a/simulations/airshower_beacon_simulation/bd_antenna_phase_deltas.py
+++ b/simulations/airshower_beacon_simulation/bd_antenna_phase_deltas.py
@@ -26,7 +26,7 @@ if __name__ == "__main__":
     args = parser.parse_args()
 
     fname = "ZH_airshower/mysim.sry"
-    figsize = (9,6)
+    figsize = (12,8)
 
     show_plots = args.show_plots
     ref_ant_id = None # leave None for all baselines
diff --git a/simulations/airshower_beacon_simulation/ca_period_from_shower.py b/simulations/airshower_beacon_simulation/ca_period_from_shower.py
index 6f9e85f..1ffe608 100755
--- a/simulations/airshower_beacon_simulation/ca_period_from_shower.py
+++ b/simulations/airshower_beacon_simulation/ca_period_from_shower.py
@@ -155,7 +155,7 @@ if __name__ == "__main__":
     args = parser.parse_args()
 
     fname = "ZH_airshower/mysim.sry"
-    figsize = (9,6)
+    figsize = (12,8)
 
     fig_dir = args.fig_dir
     fig_subdir = path.join(fig_dir, 'shifts/')
diff --git a/simulations/airshower_beacon_simulation/cb_report_measured_antenna_time_offsets.py b/simulations/airshower_beacon_simulation/cb_report_measured_antenna_time_offsets.py
index 6a00681..46ac28c 100755
--- a/simulations/airshower_beacon_simulation/cb_report_measured_antenna_time_offsets.py
+++ b/simulations/airshower_beacon_simulation/cb_report_measured_antenna_time_offsets.py
@@ -23,7 +23,7 @@ if __name__ == "__main__":
     args = parser.parse_args()
 
     fname = "ZH_airshower/mysim.sry"
-    figsize = (9,6)
+    figsize = (12,8)
 
     fig_dir = args.fig_dir # set None to disable saving
     show_plots = args.show_plots
diff --git a/simulations/airshower_beacon_simulation/da_reconstruction.py b/simulations/airshower_beacon_simulation/da_reconstruction.py
index 6bc4291..1395913 100755
--- a/simulations/airshower_beacon_simulation/da_reconstruction.py
+++ b/simulations/airshower_beacon_simulation/da_reconstruction.py
@@ -34,7 +34,7 @@ if __name__ == "__main__":
     args = parser.parse_args()
 
     fname = "ZH_airshower/mysim.sry"
-    figsize = (9,6)
+    figsize = (12,8)
 
     fig_dir = args.fig_dir
     fig_subdir = path.join(fig_dir, 'reconstruction')
diff --git a/simulations/airshower_beacon_simulation/dc_grid_power_time_fixes.py b/simulations/airshower_beacon_simulation/dc_grid_power_time_fixes.py
index 585f080..fbade2c 100755
--- a/simulations/airshower_beacon_simulation/dc_grid_power_time_fixes.py
+++ b/simulations/airshower_beacon_simulation/dc_grid_power_time_fixes.py
@@ -45,7 +45,7 @@ if __name__ == "__main__":
         wanted_cases = valid_cases
 
     fname = "ZH_airshower/mysim.sry"
-    figsize = (9,6)
+    figsize = (12,8)
 
     fig_dir = args.fig_dir
     show_plots = args.show_plots
diff --git a/simulations/airshower_beacon_simulation/view_beaconed_antenna.py b/simulations/airshower_beacon_simulation/view_beaconed_antenna.py
index 5af931e..4ea412c 100755
--- a/simulations/airshower_beacon_simulation/view_beaconed_antenna.py
+++ b/simulations/airshower_beacon_simulation/view_beaconed_antenna.py
@@ -28,7 +28,7 @@ if __name__ == "__main__":
     args = parser.parse_args()
 
     fname = "ZH_airshower/mysim.sry"
-    figsize = (9,6)
+    figsize = (12,8)
 
     plot_ft_amplitude = args.ft
     plot_geometry = args.geom

From 040f27bd7891467a75f48575ae74af493844d515 Mon Sep 17 00:00:00 2001
From: Eric Teunis de Boone <ericteunis@deboone.nl>
Date: Thu, 2 Feb 2023 14:27:25 +0100
Subject: [PATCH 02/11] ZH: Makefile with config.mk to control properties of
 the beacon

---
 .../airshower_beacon_simulation/.gitignore    |  1 +
 .../airshower_beacon_simulation/Makefile      | 32 +++++++++++++++----
 2 files changed, 26 insertions(+), 7 deletions(-)
 create mode 100644 simulations/airshower_beacon_simulation/.gitignore

diff --git a/simulations/airshower_beacon_simulation/.gitignore b/simulations/airshower_beacon_simulation/.gitignore
new file mode 100644
index 0000000..aee2e4c
--- /dev/null
+++ b/simulations/airshower_beacon_simulation/.gitignore
@@ -0,0 +1 @@
+config.mk
diff --git a/simulations/airshower_beacon_simulation/Makefile b/simulations/airshower_beacon_simulation/Makefile
index d7e3fb1..fa18822 100644
--- a/simulations/airshower_beacon_simulation/Makefile
+++ b/simulations/airshower_beacon_simulation/Makefile
@@ -3,17 +3,32 @@
 
 FIG_DIR := ./figures
 
-all: beacon clocks phases findks reconstruct
+-include config.mk
 
+MAX_K ?= 3
+CLK_DEV ?= 20
+TRACE_N ?= 4096
+TRACE_PRE ?= 500
+NOISE_SIGMA ?= 1e4
+
+BEAC_AMP ?= 1e3 0 0
+BEAC_F ?= 51.53e-3
+BEAC_DECAY ?= 0
+
+PB_LOW ?= 0.03
+PB_HIGH ?= 0.08
+
+
+all: beacon clocks phases findks vary-fixes reconstruct
 
 beacon:
-	./aa_generate_beacon.py | tee figures/aa.log
-	./ab_modify_clocks.py 0 | tee figures/ab.log
+	./aa_generate_beacon.py -N ${TRACE_N} -P ${TRACE_PRE} -n ${NOISE_SIGMA} -a ${BEAC_AMP} -f ${BEAC_F} -l ${PB_LOW} -u ${PB_HIGH} -d ${BEAC_DECAY} | tee ${FIG_DIR}/aa.log
+	./ab_modify_clocks.py 0 | tee ${FIG_DIR}/ab.log
 	./ac_show_signal_to_noise.py --no-show-plots --fig-dir=${FIG_DIR}
-	./view_beaconed_antenna.py 72 -p x -p y -p z --no-show-plots --fig-dir=${FIG_DIR}
+	./view_beaconed_antenna.py 72 -p x -p y -p z -p n -p b --ft --no-show-plots --fig-dir=${FIG_DIR}
 
 clocks:
-	./ab_modify_clocks.py 15 --gaussian
+	./ab_modify_clocks.py ${CLK_DEV} --gaussian
 
 phases:
 	./ba_measure_beacon_phase.py --no-show-plots --fig-dir=${FIG_DIR}
@@ -22,13 +37,16 @@ phases:
 	./bd_antenna_phase_deltas.py --no-show-plots --fig-dir=${FIG_DIR}
 
 findks:
-	./ca_period_from_shower.py --no-show-plots --fig-dir=${FIG_DIR}
+	./ca_period_from_shower.py --max-k ${MAX_K} --no-show-plots --fig-dir=${FIG_DIR}
 	./cb_report_measured_antenna_time_offsets.py --no-show-plots --fig-dir=${FIG_DIR}
 
+vary-fixes:
+	./dc_grid_power_time_fixes.py --no-show-plots --fig-dir=${FIG_DIR}
+
 reconstruct:
 	./da_reconstruction.py --no-show-plots --fig-dir=${FIG_DIR}
 	./db_longitudinal_figure.py --no-show-plots --fig-dir=${FIG_DIR}
-	./dc_grid_power_time_fixes.py --no-show-plots --fig-dir=${FIG_DIR}
+
 dist-clean:
 	rm -f ZH_airshower/antennas.hdf5
 	rm -f ZH_airshower/clocks.csv

From ad7a62604b49984b39073cf80cf08797ec0bd0ef Mon Sep 17 00:00:00 2001
From: Eric Teunis de Boone <ericteunis@deboone.nl>
Date: Thu, 2 Feb 2023 14:57:55 +0100
Subject: [PATCH 03/11] ZH: CLI args for baseline phase determination

---
 simulations/airshower_beacon_simulation/Makefile   |  4 ++--
 .../bc_baseline_phase_deltas.py                    | 14 ++++++++++----
 2 files changed, 12 insertions(+), 6 deletions(-)

diff --git a/simulations/airshower_beacon_simulation/Makefile b/simulations/airshower_beacon_simulation/Makefile
index fa18822..1a5067d 100644
--- a/simulations/airshower_beacon_simulation/Makefile
+++ b/simulations/airshower_beacon_simulation/Makefile
@@ -1,6 +1,5 @@
 .PHONY: all
 
-
 FIG_DIR := ./figures
 
 -include config.mk
@@ -18,6 +17,7 @@ BEAC_DECAY ?= 0
 PB_LOW ?= 0.03
 PB_HIGH ?= 0.08
 
+REF_ANTS ?=
 
 all: beacon clocks phases findks vary-fixes reconstruct
 
@@ -33,7 +33,7 @@ clocks:
 phases:
 	./ba_measure_beacon_phase.py --no-show-plots --fig-dir=${FIG_DIR}
 	./bb_measure_clock_phase.py --no-show-plots --fig-dir=${FIG_DIR}
-	./bc_baseline_phase_deltas.py --no-show-plots --fig-dir=${FIG_DIR}
+	./bc_baseline_phase_deltas.py ${REF_ANTS} --no-show-plots --fig-dir=${FIG_DIR}
 	./bd_antenna_phase_deltas.py --no-show-plots --fig-dir=${FIG_DIR}
 
 findks:
diff --git a/simulations/airshower_beacon_simulation/bc_baseline_phase_deltas.py b/simulations/airshower_beacon_simulation/bc_baseline_phase_deltas.py
index a19358d..84f167a 100755
--- a/simulations/airshower_beacon_simulation/bc_baseline_phase_deltas.py
+++ b/simulations/airshower_beacon_simulation/bc_baseline_phase_deltas.py
@@ -21,13 +21,14 @@ if __name__ == "__main__":
 
     from scriptlib import MyArgumentParser
     parser = MyArgumentParser()
+    parser.add_argument('ref_ant_idx', default=None, nargs='*', type=int, help='Reference Antenna Indices for Baselines(ref_ant_idx, *). Leave empty to use all available antennas. (Default: %(default)s) ')
     args = parser.parse_args()
 
     fname = "ZH_airshower/mysim.sry"
     figsize = (12,8)
     c_light = 3e8*1e-9
     show_plots = args.show_plots
-    ref_ant_id = None if True else [50] # leave None for all baselines
+    ref_ant_id = args.ref_ant_idx # leave None for all baselines
 
     ####
     fname_dir = path.dirname(fname)
@@ -44,14 +45,15 @@ if __name__ == "__main__":
     f_beacon, tx, antennas = beacon.read_beacon_hdf5(antennas_fname)
 
     # run over all baselines
-    if ref_ant_id is None:
+    if not ref_ant_id:
         print("Doing all baselines")
-        baselines = list(combinations(antennas,2))
+        baselines = combinations(antennas,2)
+
     # use ref_ant
     else:
         ref_ants = [antennas[i] for i in ref_ant_id]
         print("Doing all baselines with {}".format([int(a.name) for a in ref_ants]))
-        baselines = list(product(ref_ants, antennas))
+        baselines = product(ref_ants, antennas)
 
     # For now, only one beacon_frequency is supported
     freq_names = antennas[0].beacon_info.keys()
@@ -60,7 +62,11 @@ if __name__ == "__main__":
 
     freq_name = next(iter(freq_names))
 
+    # Collect baselines from optional generators
+    baselines = list(baselines)
+
     # Get phase difference per baseline
+
     phase_diffs = np.empty( (len(baselines), 2) )
     for i, base in enumerate(baselines):
         if i%1000==0:

From a66782064e950d417b9e5bd18c2d402e7cff67a1 Mon Sep 17 00:00:00 2001
From: Eric Teunis de Boone <ericteunis@deboone.nl>
Date: Thu, 2 Feb 2023 16:42:16 +0100
Subject: [PATCH 04/11] ZH: scriptlib nicer myargumentparser

---
 .../airshower_beacon_simulation/scriptlib.py     | 16 ++++++++++------
 1 file changed, 10 insertions(+), 6 deletions(-)

diff --git a/simulations/airshower_beacon_simulation/scriptlib.py b/simulations/airshower_beacon_simulation/scriptlib.py
index 165f32f..0edc5d6 100644
--- a/simulations/airshower_beacon_simulation/scriptlib.py
+++ b/simulations/airshower_beacon_simulation/scriptlib.py
@@ -4,9 +4,13 @@ Some preconfigured ArgumentParser
 
 from argparse import ArgumentParser
 
-def MyArgumentParser(default_fig_dir='./figures', default_show_plots=False, **kwargs):
+def MyArgumentParser(
+        default_fig_dir='./figures',
+        default_show_plots=False,
+        **kwargs):
     """
-    A somewhat preconfigured ArgumentParser
+    A somewhat preconfigured ArgumentParser to be shared across
+    multiple scripts.
 
     Set show_plots=True to by default enable showing plots.
     Likewise, set fig_dir=None to by default disable saving figures.
@@ -14,11 +18,11 @@ def MyArgumentParser(default_fig_dir='./figures', default_show_plots=False, **kw
     parser = ArgumentParser(**kwargs)
 
     # Whether to show plots
-    parser.add_argument('--show-plots', action='store_true')
-    parser.add_argument('--no-show-plots', dest='show-plots', action='store_false')
-    parser.set_defaults(show_plots=default_show_plots)
+    group1 = parser.add_mutually_exclusive_group(required=False)
+    group1.add_argument('--show-plots', action='store_true', default=default_show_plots, help='Default: %(default)s')
+    group1.add_argument('--no-show-plots', dest='show-plots', action='store_false')
 
     # Figures directory
-    parser.add_argument('--fig-dir', type=str, default=default_fig_dir)
+    parser.add_argument('--fig-dir', type=str, default=default_fig_dir, help='Set None to disable saving figures. (Default: %(default)s)')
 
     return parser

From 47916e2e88efac6f0c4461f63022213abd9e70e5 Mon Sep 17 00:00:00 2001
From: Eric Teunis de Boone <ericteunis@deboone.nl>
Date: Thu, 2 Feb 2023 17:55:37 +0100
Subject: [PATCH 05/11] ZH: separate data-dir and input-dir on cli

---
 .../airshower_beacon_simulation/Makefile      | 39 +++++++++++--------
 .../aa_generate_beacon.py                     | 16 ++++++--
 .../ab_modify_clocks.py                       |  6 +--
 .../ac_show_signal_to_noise.py                |  3 +-
 .../ba_measure_beacon_phase.py                |  3 +-
 .../bb_measure_clock_phase.py                 |  3 +-
 .../bc_baseline_phase_deltas.py               |  3 +-
 .../bd_antenna_phase_deltas.py                |  3 +-
 .../ca_period_from_shower.py                  | 12 ++++--
 ...cb_report_measured_antenna_time_offsets.py |  3 +-
 .../da_reconstruction.py                      | 12 ++++--
 .../db_longitudinal_figure.py                 |  4 +-
 .../dc_grid_power_time_fixes.py               | 12 ++++--
 .../airshower_beacon_simulation/scriptlib.py  |  4 ++
 .../view_beaconed_antenna.py                  |  3 +-
 15 files changed, 76 insertions(+), 50 deletions(-)

diff --git a/simulations/airshower_beacon_simulation/Makefile b/simulations/airshower_beacon_simulation/Makefile
index 1a5067d..b90d0c9 100644
--- a/simulations/airshower_beacon_simulation/Makefile
+++ b/simulations/airshower_beacon_simulation/Makefile
@@ -19,35 +19,40 @@ PB_HIGH ?= 0.08
 
 REF_ANTS ?=
 
+DATA_DIR ?= ./data
+INPUT_DIR ?= ./ZH_airshower/
+
 all: beacon clocks phases findks vary-fixes reconstruct
 
 beacon:
-	./aa_generate_beacon.py -N ${TRACE_N} -P ${TRACE_PRE} -n ${NOISE_SIGMA} -a ${BEAC_AMP} -f ${BEAC_F} -l ${PB_LOW} -u ${PB_HIGH} -d ${BEAC_DECAY} | tee ${FIG_DIR}/aa.log
-	./ab_modify_clocks.py 0 | tee ${FIG_DIR}/ab.log
-	./ac_show_signal_to_noise.py --no-show-plots --fig-dir=${FIG_DIR}
-	./view_beaconed_antenna.py 72 -p x -p y -p z -p n -p b --ft --no-show-plots --fig-dir=${FIG_DIR}
+	./aa_generate_beacon.py -N ${TRACE_N} -P ${TRACE_PRE} -n ${NOISE_SIGMA} -a ${BEAC_AMP} -f ${BEAC_F} -l ${PB_LOW} -u ${PB_HIGH} -d ${BEAC_DECAY} --data-dir ${DATA_DIR} --input-fname ${INPUT_DIR} | tee ${FIG_DIR}/aa.log
+	./ab_modify_clocks.py 0 --data-dir ${DATA_DIR} | tee ${FIG_DIR}/ab.log
+	./ac_show_signal_to_noise.py --no-show-plots --fig-dir=${FIG_DIR} --data-dir ${DATA_DIR}
+	./view_beaconed_antenna.py 72 -p x -p y -p z -p n -p b --ft --no-show-plots --fig-dir=${FIG_DIR} --data-dir ${DATA_DIR}
 
 clocks:
-	./ab_modify_clocks.py ${CLK_DEV} --gaussian
+	./ab_modify_clocks.py ${CLK_DEV} --gaussian --data-dir ${DATA_DIR}
 
 phases:
-	./ba_measure_beacon_phase.py --no-show-plots --fig-dir=${FIG_DIR}
-	./bb_measure_clock_phase.py --no-show-plots --fig-dir=${FIG_DIR}
-	./bc_baseline_phase_deltas.py ${REF_ANTS} --no-show-plots --fig-dir=${FIG_DIR}
-	./bd_antenna_phase_deltas.py --no-show-plots --fig-dir=${FIG_DIR}
+	./ba_measure_beacon_phase.py --no-show-plots --fig-dir=${FIG_DIR} --data-dir ${DATA_DIR}
+	./bb_measure_clock_phase.py --no-show-plots --fig-dir=${FIG_DIR} --data-dir ${DATA_DIR}
+	./bc_baseline_phase_deltas.py ${REF_ANTS} --no-show-plots --fig-dir=${FIG_DIR} --data-dir ${DATA_DIR}
+	./bd_antenna_phase_deltas.py --no-show-plots --fig-dir=${FIG_DIR} --data-dir ${DATA_DIR}
 
 findks:
-	./ca_period_from_shower.py --max-k ${MAX_K} --no-show-plots --fig-dir=${FIG_DIR}
-	./cb_report_measured_antenna_time_offsets.py --no-show-plots --fig-dir=${FIG_DIR}
+	./ca_period_from_shower.py --input-fname ${INPUT_DIR} --max-k ${MAX_K} --no-show-plots --fig-dir=${FIG_DIR} --data-dir ${DATA_DIR}
+	./cb_report_measured_antenna_time_offsets.py --no-show-plots --fig-dir=${FIG_DIR} --data-dir ${DATA_DIR}
 
 vary-fixes:
-	./dc_grid_power_time_fixes.py --no-show-plots --fig-dir=${FIG_DIR}
+	./dc_grid_power_time_fixes.py --no-show-plots --fig-dir=${FIG_DIR} --data-dir ${DATA_DIR} --input-fname ${INPUT_DIR}
 
 reconstruct:
-	./da_reconstruction.py --no-show-plots --fig-dir=${FIG_DIR}
-	./db_longitudinal_figure.py --no-show-plots --fig-dir=${FIG_DIR}
+	./da_reconstruction.py --no-show-plots --fig-dir=${FIG_DIR} --data-dir ${DATA_DIR} --input-fname ${INPUT_DIR}
+	./db_longitudinal_figure.py --no-show-plots --fig-dir=${FIG_DIR} --data-dir ${DATA_DIR}
 
 dist-clean:
-	rm -f ZH_airshower/antennas.hdf5
-	rm -f ZH_airshower/clocks.csv
-	rm -f ZH_airshower/tx.json
+	rm -vf ${DATA_DIR}/antennas.hdf5
+	rm -vf ${DATA_DIR}/ca_breaked_run
+	rm -vf ${DATA_DIR}/res.pkl
+	rm -vf ${DATA_DIR}/clocks.csv
+	rm -vf ${DATA_DIR}/tx.json
diff --git a/simulations/airshower_beacon_simulation/aa_generate_beacon.py b/simulations/airshower_beacon_simulation/aa_generate_beacon.py
index 0f77fd2..2ac92a9 100755
--- a/simulations/airshower_beacon_simulation/aa_generate_beacon.py
+++ b/simulations/airshower_beacon_simulation/aa_generate_beacon.py
@@ -289,16 +289,24 @@ if __name__ == "__main__":
     parser.add_argument('-N', '--new-trace-length', type=float, help='resize airshower trace (Default: %(default)d)', default=1e4)
     parser.add_argument('-P', '--pre-trace-length', type=float, help='amount of trace to prepend the airshower when resizing (Default: %(default)d)', default=2e3)
 
+    # Input directory
+    parser.add_argument('--input-fname', type=str, default=None, help='Path to mysim.sry, either directory or path. If empty it takes DATA_DIR and appends mysim.sry. (Default: %(default)s)')
+    parser.add_argument('--data-dir', type=str, default="./ZH_airshower", help='Path to Data Directory. (Default: %(default)s)')
+
     args = parser.parse_args()
 
+    if not args.input_fname:
+        args.input_fname = args.data_dir
+
+    if path.isdir(args.input_fname):
+        args.input_fname = path.join(args.input_fname, "mysim.sry")
+
     ##
     ## End of ArgumentParsing
     ##
 
     rng = np.random.default_rng()
 
-    fname = "ZH_airshower/mysim.sry"
-
     # Noise properties
     noise_sigma = args.noise_sigma # mu V/m set to None to ignore
 
@@ -337,7 +345,7 @@ if __name__ == "__main__":
         block_filter = lambda x, dt, low, high: x
 
     ####
-    fname_dir = path.dirname(fname)
+    fname_dir = args.data_dir
     tx_fname = path.join(fname_dir, tx_fname)
     antennas_fname = path.join(fname_dir, antennas_fname)
 
@@ -354,7 +362,7 @@ if __name__ == "__main__":
     print("Noise sigma [muV/m]:", noise_sigma)
 
     # read in antennas
-    ev = REvent(fname)
+    ev = REvent(args.input_fname)
     N_antennas = len(ev.antennas)
 
     # initialize hdf5 file
diff --git a/simulations/airshower_beacon_simulation/ab_modify_clocks.py b/simulations/airshower_beacon_simulation/ab_modify_clocks.py
index 0c33300..f9e8654 100755
--- a/simulations/airshower_beacon_simulation/ab_modify_clocks.py
+++ b/simulations/airshower_beacon_simulation/ab_modify_clocks.py
@@ -27,6 +27,8 @@ if __name__ == "__main__":
     parser.add_argument('--gaussian',   action='store_const', const='gauss', dest='dist_type')
     parser.set_defaults(dist_type='gauss')
 
+    parser.add_argument('--data-dir', type=str, default="./data", help='Path to Data Directory. (Default: %(default)s)')
+
     args = parser.parse_args()
 
     max_clock_offset = args.max_clock_offset # ns
@@ -35,10 +37,8 @@ if __name__ == "__main__":
     seed = 12345
     rng = np.random.default_rng(seed)
 
-    fname = "ZH_airshower/mysim.sry"
-
     ####
-    fname_dir = path.dirname(fname)
+    fname_dir = args.data_dir
     clocks_fname = path.join(fname_dir, clocks_fname)
     antennas_fname = path.join(fname_dir, beacon.antennas_fname)
 
diff --git a/simulations/airshower_beacon_simulation/ac_show_signal_to_noise.py b/simulations/airshower_beacon_simulation/ac_show_signal_to_noise.py
index adb1d86..1c8fad9 100755
--- a/simulations/airshower_beacon_simulation/ac_show_signal_to_noise.py
+++ b/simulations/airshower_beacon_simulation/ac_show_signal_to_noise.py
@@ -33,14 +33,13 @@ if __name__ == "__main__":
 
     args = parser.parse_args()
 
-    fname = "ZH_airshower/mysim.sry"
     figsize = (12,8)
 
     fig_dir = args.fig_dir
     show_plots = args.show_plots
 
     ####
-    fname_dir = path.dirname(fname)
+    fname_dir = args.data_dir
     antennas_fname = path.join(fname_dir, beacon.antennas_fname)
     tx_fname = path.join(fname_dir, beacon.tx_fname)
 
diff --git a/simulations/airshower_beacon_simulation/ba_measure_beacon_phase.py b/simulations/airshower_beacon_simulation/ba_measure_beacon_phase.py
index 20e07a8..8b097d4 100755
--- a/simulations/airshower_beacon_simulation/ba_measure_beacon_phase.py
+++ b/simulations/airshower_beacon_simulation/ba_measure_beacon_phase.py
@@ -35,13 +35,12 @@ if __name__ == "__main__":
 
     show_plots = args.show_plots
 
-    fname = "ZH_airshower/mysim.sry"
     figsize = (12,8)
 
     print("use_AxB_trace:", use_AxB_trace, "use_beacon_trace:",use_beacon_trace)
 
     ####
-    fname_dir = path.dirname(fname)
+    fname_dir = args.data_dir
     antennas_fname = path.join(fname_dir, beacon.antennas_fname)
 
     fig_dir = args.fig_dir # set None to disable saving
diff --git a/simulations/airshower_beacon_simulation/bb_measure_clock_phase.py b/simulations/airshower_beacon_simulation/bb_measure_clock_phase.py
index eb324a5..a83f717 100755
--- a/simulations/airshower_beacon_simulation/bb_measure_clock_phase.py
+++ b/simulations/airshower_beacon_simulation/bb_measure_clock_phase.py
@@ -22,7 +22,6 @@ if __name__ == "__main__":
     parser = MyArgumentParser()
     args = parser.parse_args()
 
-    fname = "ZH_airshower/mysim.sry"
     figsize = (12,8)
     c_light = lib.c_light
     show_plots = args.show_plots
@@ -31,7 +30,7 @@ if __name__ == "__main__":
     remove_absolute_phase_offset_minimum = True
 
     ####
-    fname_dir = path.dirname(fname)
+    fname_dir = args.data_dir
     antennas_fname = path.join(fname_dir, beacon.antennas_fname)
 
     fig_dir = args.fig_dir # set None to disable saving
diff --git a/simulations/airshower_beacon_simulation/bc_baseline_phase_deltas.py b/simulations/airshower_beacon_simulation/bc_baseline_phase_deltas.py
index 84f167a..d3028c1 100755
--- a/simulations/airshower_beacon_simulation/bc_baseline_phase_deltas.py
+++ b/simulations/airshower_beacon_simulation/bc_baseline_phase_deltas.py
@@ -24,14 +24,13 @@ if __name__ == "__main__":
     parser.add_argument('ref_ant_idx', default=None, nargs='*', type=int, help='Reference Antenna Indices for Baselines(ref_ant_idx, *). Leave empty to use all available antennas. (Default: %(default)s) ')
     args = parser.parse_args()
 
-    fname = "ZH_airshower/mysim.sry"
     figsize = (12,8)
     c_light = 3e8*1e-9
     show_plots = args.show_plots
     ref_ant_id = args.ref_ant_idx # leave None for all baselines
 
     ####
-    fname_dir = path.dirname(fname)
+    fname_dir = args.data_dir
     antennas_fname = path.join(fname_dir, beacon.antennas_fname)
     time_diffs_fname = 'time_diffs.hdf5' if False else antennas_fname
 
diff --git a/simulations/airshower_beacon_simulation/bd_antenna_phase_deltas.py b/simulations/airshower_beacon_simulation/bd_antenna_phase_deltas.py
index 48b7685..6abd475 100755
--- a/simulations/airshower_beacon_simulation/bd_antenna_phase_deltas.py
+++ b/simulations/airshower_beacon_simulation/bd_antenna_phase_deltas.py
@@ -25,14 +25,13 @@ if __name__ == "__main__":
     parser = MyArgumentParser()
     args = parser.parse_args()
 
-    fname = "ZH_airshower/mysim.sry"
     figsize = (12,8)
 
     show_plots = args.show_plots
     ref_ant_id = None # leave None for all baselines
 
     ####
-    fname_dir = path.dirname(fname)
+    fname_dir = args.data_dir
     antennas_fname = path.join(fname_dir, beacon.antennas_fname)
     time_diffs_fname = 'time_diffs.hdf5' if False else antennas_fname
     fig_dir = args.fig_dir # set None to disable saving
diff --git a/simulations/airshower_beacon_simulation/ca_period_from_shower.py b/simulations/airshower_beacon_simulation/ca_period_from_shower.py
index 1ffe608..bd9ac33 100755
--- a/simulations/airshower_beacon_simulation/ca_period_from_shower.py
+++ b/simulations/airshower_beacon_simulation/ca_period_from_shower.py
@@ -152,9 +152,15 @@ if __name__ == "__main__":
     from scriptlib import MyArgumentParser
     parser = MyArgumentParser(default_fig_dir="./figures/periods_from_shower_figures/")
     parser.add_argument('--max-k', type=float, default=2, help='Maximum abs(k) allowed to be shifted. (Default: %(default)d)')
+    parser.add_argument('--input-fname', type=str, default=None, help='Path to mysim.sry, either directory or path. If empty it takes DATA_DIR and appends mysim.sry. (Default: %(default)s)')
     args = parser.parse_args()
 
-    fname = "ZH_airshower/mysim.sry"
+    if not args.input_fname:
+        args.input_fname = args.data_dir
+
+    if path.isdir(args.input_fname):
+        args.input_fname = path.join(args.input_fname, "mysim.sry")
+
     figsize = (12,8)
 
     fig_dir = args.fig_dir
@@ -170,7 +176,7 @@ if __name__ == "__main__":
     apply_signal_window_from_max = True
 
     ####
-    fname_dir = path.dirname(fname)
+    fname_dir = args.data_dir
     antennas_fname = path.join(fname_dir, beacon.antennas_fname)
     time_diffs_fname = 'time_diffs.hdf5' if not True else antennas_fname
 
@@ -188,7 +194,7 @@ if __name__ == "__main__":
     # Read in antennas from file
     _, tx, antennas = beacon.read_beacon_hdf5(antennas_fname)
     # Read original REvent
-    ev = REvent(fname)
+    ev = REvent(args.input_fname)
     # .. patch in our antennas
     ev.antennas = antennas
 
diff --git a/simulations/airshower_beacon_simulation/cb_report_measured_antenna_time_offsets.py b/simulations/airshower_beacon_simulation/cb_report_measured_antenna_time_offsets.py
index 46ac28c..547216f 100755
--- a/simulations/airshower_beacon_simulation/cb_report_measured_antenna_time_offsets.py
+++ b/simulations/airshower_beacon_simulation/cb_report_measured_antenna_time_offsets.py
@@ -22,14 +22,13 @@ if __name__ == "__main__":
     parser = MyArgumentParser()
     args = parser.parse_args()
 
-    fname = "ZH_airshower/mysim.sry"
     figsize = (12,8)
 
     fig_dir = args.fig_dir # set None to disable saving
     show_plots = args.show_plots
 
     ####
-    fname_dir = path.dirname(fname)
+    fname_dir = args.data_dir
     antennas_fname = path.join(fname_dir, beacon.antennas_fname)
     time_diffs_fname = 'time_diffs.hdf5' if not True else antennas_fname
 
diff --git a/simulations/airshower_beacon_simulation/da_reconstruction.py b/simulations/airshower_beacon_simulation/da_reconstruction.py
index 1395913..d85d764 100755
--- a/simulations/airshower_beacon_simulation/da_reconstruction.py
+++ b/simulations/airshower_beacon_simulation/da_reconstruction.py
@@ -31,9 +31,15 @@ if __name__ == "__main__":
 
     from scriptlib import MyArgumentParser
     parser = MyArgumentParser()
+    parser.add_argument('--input-fname', type=str, default=None, help='Path to mysim.sry, either directory or path. If empty it takes DATA_DIR and appends mysim.sry. (Default: %(default)s)')
     args = parser.parse_args()
 
-    fname = "ZH_airshower/mysim.sry"
+    if not args.input_fname:
+        args.input_fname = args.data_dir
+
+    if path.isdir(args.input_fname):
+        args.input_fname = path.join(args.input_fname, "mysim.sry")
+
     figsize = (12,8)
 
     fig_dir = args.fig_dir
@@ -43,7 +49,7 @@ if __name__ == "__main__":
     remove_beacon_from_traces = True
 
     ####
-    fname_dir = path.dirname(fname)
+    fname_dir = args.data_dir
     antennas_fname = path.join(fname_dir, beacon.antennas_fname)
     pickle_fname = path.join(fname_dir, 'res.pkl')
     tx_fname = path.join(fname_dir, beacon.tx_fname)
@@ -58,7 +64,7 @@ if __name__ == "__main__":
     _, tx, antennas = beacon.read_beacon_hdf5(antennas_fname)
     _, __, txdata = beacon.read_tx_file(tx_fname)
     # Read original REvent
-    ev = REvent(fname)
+    ev = REvent(args.input_fname)
     # .. patch in our antennas
     ev.antennas = antennas
 
diff --git a/simulations/airshower_beacon_simulation/db_longitudinal_figure.py b/simulations/airshower_beacon_simulation/db_longitudinal_figure.py
index 63f1da2..c5da800 100755
--- a/simulations/airshower_beacon_simulation/db_longitudinal_figure.py
+++ b/simulations/airshower_beacon_simulation/db_longitudinal_figure.py
@@ -28,13 +28,11 @@ if __name__ == "__main__":
     parser = MyArgumentParser()
     args = parser.parse_args()
 
-    fname = "ZH_airshower/mysim.sry"
-
     fig_dir = args.fig_dir
     show_plots = args.show_plots
 
     ####
-    fname_dir = path.dirname(fname)
+    fname_dir = args.data_dir
     antennas_fname = path.join(fname_dir, beacon.antennas_fname)
     pickle_fname = path.join(fname_dir, 'res.pkl')
 
diff --git a/simulations/airshower_beacon_simulation/dc_grid_power_time_fixes.py b/simulations/airshower_beacon_simulation/dc_grid_power_time_fixes.py
index fbade2c..210e158 100755
--- a/simulations/airshower_beacon_simulation/dc_grid_power_time_fixes.py
+++ b/simulations/airshower_beacon_simulation/dc_grid_power_time_fixes.py
@@ -32,6 +32,7 @@ if __name__ == "__main__":
 
     from scriptlib import MyArgumentParser
     parser = MyArgumentParser()
+    parser.add_argument('--input-fname', type=str, default=None, help='Path to mysim.sry, either directory or path. If empty it takes DATA_DIR and appends mysim.sry. (Default: %(default)s)')
 
     group = parser.add_argument_group('figures')
     for case in valid_cases:
@@ -39,12 +40,17 @@ if __name__ == "__main__":
 
     args = parser.parse_args()
 
+    if not args.input_fname:
+        args.input_fname = args.data_dir
+
+    if path.isdir(args.input_fname):
+        args.input_fname = path.join(args.input_fname, "mysim.sry")
+
     wanted_cases = args.figures
 
     if not wanted_cases or 'all' in wanted_cases:
         wanted_cases = valid_cases
 
-    fname = "ZH_airshower/mysim.sry"
     figsize = (12,8)
 
     fig_dir = args.fig_dir
@@ -54,7 +60,7 @@ if __name__ == "__main__":
     apply_signal_window_from_max = True
 
     ####
-    fname_dir = path.dirname(fname)
+    fname_dir = args.data_dir
     antennas_fname = path.join(fname_dir, beacon.antennas_fname)
     pickle_fname = path.join(fname_dir, 'res.pkl')
     tx_fname = path.join(fname_dir, beacon.tx_fname)
@@ -67,7 +73,7 @@ if __name__ == "__main__":
     _, tx, antennas = beacon.read_beacon_hdf5(antennas_fname)
     _, __, txdata = beacon.read_tx_file(tx_fname)
     # Read original REvent
-    ev = REvent(fname)
+    ev = REvent(args.input_fname)
     bak_ants = ev.antennas
     # .. patch in our antennas
     ev.antennas = antennas
diff --git a/simulations/airshower_beacon_simulation/scriptlib.py b/simulations/airshower_beacon_simulation/scriptlib.py
index 0edc5d6..90f0046 100644
--- a/simulations/airshower_beacon_simulation/scriptlib.py
+++ b/simulations/airshower_beacon_simulation/scriptlib.py
@@ -7,6 +7,7 @@ from argparse import ArgumentParser
 def MyArgumentParser(
         default_fig_dir='./figures',
         default_show_plots=False,
+        default_data_dir='./ZH_airshower',
         **kwargs):
     """
     A somewhat preconfigured ArgumentParser to be shared across
@@ -22,6 +23,9 @@ def MyArgumentParser(
     group1.add_argument('--show-plots', action='store_true', default=default_show_plots, help='Default: %(default)s')
     group1.add_argument('--no-show-plots', dest='show-plots', action='store_false')
 
+    # Data directory
+    parser.add_argument('--data-dir', type=str, default=default_data_dir, help='Path to Data Directory. (Default: %(default)s)')
+
     # Figures directory
     parser.add_argument('--fig-dir', type=str, default=default_fig_dir, help='Set None to disable saving figures. (Default: %(default)s)')
 
diff --git a/simulations/airshower_beacon_simulation/view_beaconed_antenna.py b/simulations/airshower_beacon_simulation/view_beaconed_antenna.py
index 4ea412c..22ec5e5 100755
--- a/simulations/airshower_beacon_simulation/view_beaconed_antenna.py
+++ b/simulations/airshower_beacon_simulation/view_beaconed_antenna.py
@@ -27,7 +27,6 @@ if __name__ == "__main__":
 
     args = parser.parse_args()
 
-    fname = "ZH_airshower/mysim.sry"
     figsize = (12,8)
 
     plot_ft_amplitude = args.ft
@@ -40,7 +39,7 @@ if __name__ == "__main__":
         args.polarisations = ['x','y', 'z']
 
     ####
-    fname_dir = path.dirname(fname)
+    fname_dir = args.data_dir
     antennas_fname = path.join(fname_dir, beacon.antennas_fname)
     tx_fname = path.join(fname_dir, beacon.tx_fname)
 

From 6d3a983cad56bc39dab8e6dc1d048137cce29550 Mon Sep 17 00:00:00 2001
From: Eric Teunis de Boone <ericteunis@deboone.nl>
Date: Thu, 2 Feb 2023 18:09:10 +0100
Subject: [PATCH 06/11] ZH: cli optional clock seed

---
 simulations/airshower_beacon_simulation/Makefile            | 3 ++-
 simulations/airshower_beacon_simulation/ab_modify_clocks.py | 3 ++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/simulations/airshower_beacon_simulation/Makefile b/simulations/airshower_beacon_simulation/Makefile
index b90d0c9..923582c 100644
--- a/simulations/airshower_beacon_simulation/Makefile
+++ b/simulations/airshower_beacon_simulation/Makefile
@@ -21,6 +21,7 @@ REF_ANTS ?=
 
 DATA_DIR ?= ./data
 INPUT_DIR ?= ./ZH_airshower/
+SEED ?= 12345
 
 all: beacon clocks phases findks vary-fixes reconstruct
 
@@ -31,7 +32,7 @@ beacon:
 	./view_beaconed_antenna.py 72 -p x -p y -p z -p n -p b --ft --no-show-plots --fig-dir=${FIG_DIR} --data-dir ${DATA_DIR}
 
 clocks:
-	./ab_modify_clocks.py ${CLK_DEV} --gaussian --data-dir ${DATA_DIR}
+	./ab_modify_clocks.py ${CLK_DEV} --seed ${SEED} --gaussian --data-dir ${DATA_DIR}
 
 phases:
 	./ba_measure_beacon_phase.py --no-show-plots --fig-dir=${FIG_DIR} --data-dir ${DATA_DIR}
diff --git a/simulations/airshower_beacon_simulation/ab_modify_clocks.py b/simulations/airshower_beacon_simulation/ab_modify_clocks.py
index f9e8654..1532cdd 100755
--- a/simulations/airshower_beacon_simulation/ab_modify_clocks.py
+++ b/simulations/airshower_beacon_simulation/ab_modify_clocks.py
@@ -23,6 +23,7 @@ if __name__ == "__main__":
 
     parser = ArgumentParser()
     parser.add_argument('max_clock_offset', nargs='?', type=float, default=25, help='(Default: %(default)d)')
+    parser.add_argument('-s', '--seed', type=int, nargs='?', default=None, help='Fix seed if supplied.')
     parser.add_argument('--uniform', action='store_const', const='uniform', dest='dist_type')
     parser.add_argument('--gaussian',   action='store_const', const='gauss', dest='dist_type')
     parser.set_defaults(dist_type='gauss')
@@ -34,7 +35,7 @@ if __name__ == "__main__":
     max_clock_offset = args.max_clock_offset # ns
     remake_clock_offsets = True
 
-    seed = 12345
+    seed = args.seed
     rng = np.random.default_rng(seed)
 
     ####

From d6ae5d3334f074d684de4cec8f4caede43097ae9 Mon Sep 17 00:00:00 2001
From: Eric Teunis de Boone <ericteunis@deboone.nl>
Date: Thu, 2 Feb 2023 18:09:46 +0100
Subject: [PATCH 07/11] ZH: fixup ref_ant_idx * ad7a626 - (3 hours ago) ZH: CLI
 args for baseline phase determination

---
 .../airshower_beacon_simulation/bc_baseline_phase_deltas.py   | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/simulations/airshower_beacon_simulation/bc_baseline_phase_deltas.py b/simulations/airshower_beacon_simulation/bc_baseline_phase_deltas.py
index d3028c1..a3c067f 100755
--- a/simulations/airshower_beacon_simulation/bc_baseline_phase_deltas.py
+++ b/simulations/airshower_beacon_simulation/bc_baseline_phase_deltas.py
@@ -121,10 +121,10 @@ if __name__ == "__main__":
             if plot_residuals:
                 phase_residuals = lib.phase_mod(phase_diffs[:,1] - my_phase_diffs)
 
-                fig.suptitle("Difference between Measured and Actual phase difference\n for Baselines (i,j" + (')' if ref_ant_id is None else '='+str([ int(a.name) for a in ref_ants])+')'))
+                fig.suptitle("Difference between Measured and Actual phase difference\n for Baselines (i,j" + (')' if not ref_ant_id else '='+str([ int(a.name) for a in ref_ants])+')'))
                 axs[-1].set_xlabel("Baseline Phase Residual $\\Delta\\varphi_{ij_{meas}} - \\Delta\\varphi_{ij_{true}}$ [rad]")
             else:
-                fig.suptitle("Comparison Measured and Actual phase difference\n for Baselines (i,j"  + (')' if ref_ant_id is None else '='+str([ int(a.name) for a in ref_ants])+')'))
+                fig.suptitle("Comparison Measured and Actual phase difference\n for Baselines (i,j"  + (')' if not ref_ant_id else '='+str([ int(a.name) for a in ref_ants])+')'))
                 axs[-1].set_xlabel("Baseline Phase $\\Delta\\varphi_{ij}$ [rad]")
 
 

From ac97c96a4168541e77649f4f94c5e8954aadbbd0 Mon Sep 17 00:00:00 2001
From: Eric Teunis de Boone <ericteunis@deboone.nl>
Date: Thu, 2 Feb 2023 19:27:01 +0100
Subject: [PATCH 08/11] ZH: more cli arguments to k-finding

---
 .../airshower_beacon_simulation/Makefile      |  2 +-
 .../aa_generate_beacon.py                     |  4 ++--
 .../ca_period_from_shower.py                  | 21 +++++++++++++------
 3 files changed, 18 insertions(+), 9 deletions(-)

diff --git a/simulations/airshower_beacon_simulation/Makefile b/simulations/airshower_beacon_simulation/Makefile
index 923582c..379779c 100644
--- a/simulations/airshower_beacon_simulation/Makefile
+++ b/simulations/airshower_beacon_simulation/Makefile
@@ -41,7 +41,7 @@ phases:
 	./bd_antenna_phase_deltas.py --no-show-plots --fig-dir=${FIG_DIR} --data-dir ${DATA_DIR}
 
 findks:
-	./ca_period_from_shower.py --input-fname ${INPUT_DIR} --max-k ${MAX_K} --no-show-plots --fig-dir=${FIG_DIR} --data-dir ${DATA_DIR}
+	./ca_period_from_shower.py --input-fname ${INPUT_DIR} --max-k ${MAX_K} --no-show-plots --fig-dir=${FIG_DIR} --data-dir ${DATA_DIR} -l ${PB_LOW} -u ${PB_HIGH}
 	./cb_report_measured_antenna_time_offsets.py --no-show-plots --fig-dir=${FIG_DIR} --data-dir ${DATA_DIR}
 
 vary-fixes:
diff --git a/simulations/airshower_beacon_simulation/aa_generate_beacon.py b/simulations/airshower_beacon_simulation/aa_generate_beacon.py
index 2ac92a9..8fb41a6 100755
--- a/simulations/airshower_beacon_simulation/aa_generate_beacon.py
+++ b/simulations/airshower_beacon_simulation/aa_generate_beacon.py
@@ -282,8 +282,8 @@ if __name__ == "__main__":
 
     # Bandpass
     parser.add_argument('-p', '--use-passband', type=bool, default=True, help='(Default: %(default)d)')
-    parser.add_argument('-l', '--passband-low',  type=float, default=30e-3, help='Lower frequency [GHz] of the passband filter. (set -1 for np.inf) (Default: %(default)d)')
-    parser.add_argument('-u', '--passband-high', type=float, default=80e-3, help='Upper frequency [GHz] of the passband filter. (set -1 for np.inf) (Default: %(default)d)')
+    parser.add_argument('-l', '--passband-low',  type=float, default=30e-3, help='Lower frequency [GHz] of the passband filter. (set -1 for np.inf) (Default: %(default)g)')
+    parser.add_argument('-u', '--passband-high', type=float, default=80e-3, help='Upper frequency [GHz] of the passband filter. (set -1 for np.inf) (Default: %(default)g)')
 
     # Trace length modification
     parser.add_argument('-N', '--new-trace-length', type=float, help='resize airshower trace (Default: %(default)d)', default=1e4)
diff --git a/simulations/airshower_beacon_simulation/ca_period_from_shower.py b/simulations/airshower_beacon_simulation/ca_period_from_shower.py
index bd9ac33..30435c5 100755
--- a/simulations/airshower_beacon_simulation/ca_period_from_shower.py
+++ b/simulations/airshower_beacon_simulation/ca_period_from_shower.py
@@ -151,7 +151,14 @@ if __name__ == "__main__":
 
     from scriptlib import MyArgumentParser
     parser = MyArgumentParser(default_fig_dir="./figures/periods_from_shower_figures/")
+    parser.add_argument('--quick_run', action='store_true', help='Use a very coarse grid (6x6)')
+
     parser.add_argument('--max-k', type=float, default=2, help='Maximum abs(k) allowed to be shifted. (Default: %(default)d)')
+    parser.add_argument('-N', '--N_runs', type=int, default=5, help='Maximum amount of iterations to grid search. (Default: %(default)d)')
+
+    parser.add_argument('-l', '--passband-low',  type=float, default=30e-3, help='Lower frequency [GHz] of the passband filter. (set -1 for np.inf) (Default: %(default)g)')
+    parser.add_argument('-u', '--passband-high', type=float, default=80e-3, help='Upper frequency [GHz] of the passband filter. (set -1 for np.inf) (Default: %(default)g)')
+
     parser.add_argument('--input-fname', type=str, default=None, help='Path to mysim.sry, either directory or path. If empty it takes DATA_DIR and appends mysim.sry. (Default: %(default)s)')
     args = parser.parse_args()
 
@@ -171,10 +178,13 @@ if __name__ == "__main__":
     allowed_ks = np.arange(-max_k, max_k+1, dtype=int)
     Xref = 400
 
-    N_runs = 3
+    N_runs = args.N_runs
     remove_beacon_from_trace = True
     apply_signal_window_from_max = True
 
+    low_bp  = args.passband_low  if args.passband_low  >= 0 else np.inf # GHz
+    high_bp = args.passband_high if args.passband_high >= 0 else np.inf # GHz
+
     ####
     fname_dir = args.data_dir
     antennas_fname = path.join(fname_dir, beacon.antennas_fname)
@@ -207,7 +217,7 @@ if __name__ == "__main__":
     f_beacon = ev.antennas[0].beacon_info[freq_name]['freq']
 
     # Prepare polarisation and passbands
-    rit.set_pol_and_bp(ev, low=0.03, high=0.08)
+    rit.set_pol_and_bp(ev, low=low_bp, high=high_bp)
 
     ##
     ## Manipulate time and traces of each antenna
@@ -303,14 +313,13 @@ if __name__ == "__main__":
     scale2d = dXref*np.tan(np.deg2rad(2.))
     scale4d = dXref*np.tan(np.deg2rad(4.))
 
-    if False: #quicky
-        x_coarse = np.linspace(-scale2d, scale2d, 4)
-        y_coarse = np.linspace(-scale2d, scale2d, 4)
+    if args.quick_run: #quicky
+        x_coarse = np.linspace(-scale2d, scale2d, 6)
+        y_coarse = np.linspace(-scale2d, scale2d, 6)
 
         x_fine = x_coarse/4
         y_fine = y_coarse/4
     else: # long
-        N_runs = 5
         x_coarse = np.linspace(-scale4d, scale4d, 40)
         y_coarse = np.linspace(-scale4d, scale4d, 40)
 

From 8eb2431ec6a1a1f66c45749443c8777879f90204 Mon Sep 17 00:00:00 2001
From: Eric Teunis de Boone <ericteunis@deboone.nl>
Date: Thu, 2 Feb 2023 19:33:02 +0100
Subject: [PATCH 09/11] ZH: setup .gitignore in local root

---
 simulations/airshower_beacon_simulation/.gitignore              | 2 ++
 simulations/airshower_beacon_simulation/figures/.gitignore      | 2 --
 .../figures/periods_from_shower_figures/shifts/.gitignore       | 2 --
 3 files changed, 2 insertions(+), 4 deletions(-)
 delete mode 100644 simulations/airshower_beacon_simulation/figures/.gitignore
 delete mode 100644 simulations/airshower_beacon_simulation/figures/periods_from_shower_figures/shifts/.gitignore

diff --git a/simulations/airshower_beacon_simulation/.gitignore b/simulations/airshower_beacon_simulation/.gitignore
index aee2e4c..5791952 100644
--- a/simulations/airshower_beacon_simulation/.gitignore
+++ b/simulations/airshower_beacon_simulation/.gitignore
@@ -1 +1,3 @@
 config.mk
+figures
+data
diff --git a/simulations/airshower_beacon_simulation/figures/.gitignore b/simulations/airshower_beacon_simulation/figures/.gitignore
deleted file mode 100644
index d6b7ef3..0000000
--- a/simulations/airshower_beacon_simulation/figures/.gitignore
+++ /dev/null
@@ -1,2 +0,0 @@
-*
-!.gitignore
diff --git a/simulations/airshower_beacon_simulation/figures/periods_from_shower_figures/shifts/.gitignore b/simulations/airshower_beacon_simulation/figures/periods_from_shower_figures/shifts/.gitignore
deleted file mode 100644
index d6b7ef3..0000000
--- a/simulations/airshower_beacon_simulation/figures/periods_from_shower_figures/shifts/.gitignore
+++ /dev/null
@@ -1,2 +0,0 @@
-*
-!.gitignore

From 583577b807b76fb040e8ee9af0cdd327aa21dca6 Mon Sep 17 00:00:00 2001
From: Eric Teunis de Boone <ericteunis@deboone.nl>
Date: Fri, 3 Feb 2023 11:56:11 +0100
Subject: [PATCH 10/11] ZH: ba measure phase: mask strong peak for every trace

---
 .../ba_measure_beacon_phase.py                | 98 +++++++++++--------
 1 file changed, 55 insertions(+), 43 deletions(-)

diff --git a/simulations/airshower_beacon_simulation/ba_measure_beacon_phase.py b/simulations/airshower_beacon_simulation/ba_measure_beacon_phase.py
index 8b097d4..6cc51f7 100755
--- a/simulations/airshower_beacon_simulation/ba_measure_beacon_phase.py
+++ b/simulations/airshower_beacon_simulation/ba_measure_beacon_phase.py
@@ -23,21 +23,28 @@ if __name__ == "__main__":
 
     from scriptlib import MyArgumentParser
     parser = MyArgumentParser()
-    parser.add_argument('--no-use-AxB', dest='use_AxB_trace', action='store_false')
+
+    group1 = parser.add_mutually_exclusive_group()
+    group1.add_argument('--AxB', dest='use_AxB_trace', action='store_true', help='Only use AxB trace, if both AxB and beacon are not used, we use the antenna polarisations.')
+    group1.add_argument('--beacon', dest='use_beacon_trace', action='store_true', help='Only use the beacon trace')
+
+    parser.add_argument('--N-mask', type=float, default=500, help='Mask N_MASK samples around the absolute maximum of the trace. (Default: %(default)d)')
+
     args = parser.parse_args()
 
     f_beacon_band = (49e-3,55e-3) #GHz
     allow_frequency_fitting = False
     read_frequency_from_file = True
+    N_mask = int(args.N_mask)
 
-    use_AxB_trace = args.use_AxB_trace
-    use_beacon_trace = True # only applicable if AxB = False
+    use_only_AxB_trace = args.use_AxB_trace
+    use_only_beacon_trace = args.use_beacon_trace # only applicable if AxB = False
 
     show_plots = args.show_plots
 
     figsize = (12,8)
 
-    print("use_AxB_trace:", use_AxB_trace, "use_beacon_trace:",use_beacon_trace)
+    print("use_only_AxB_trace:", use_only_AxB_trace, "use_only_beacon_trace:", use_only_beacon_trace)
 
     ####
     fname_dir = args.data_dir
@@ -83,59 +90,64 @@ if __name__ == "__main__":
             h5ant = group[name]
 
             # use E_AxB only instead of polarisations
-            if use_AxB_trace:
-                if 'E_AxB' not in h5ant.keys():
-                    print(f"Antenna does not have 'E_AxB' in {name}")
+            if use_only_AxB_trace:
+                traces_key = 'E_AxB'
+                if traces_key not in h5ant.keys():
+                    print(f"Antenna does not have '{traces_key}' in {name}")
                     sys.exit(1)
 
-                traces = h5ant['E_AxB']
-
+                traces = h5ant[traces_key]
                 t_trace = traces[0]
                 test_traces = [ traces[1] ]
                 orients = ['E_AxB']
 
-                # TODO: refine masking
-                # use beacon but remove where E_AxB-Beacon != 0
-                if True:
-                    N_pre, N_post = 250, 250 # TODO: make this configurable
+            # Only beacon
+            elif use_only_beacon_trace:
+                traces_key = 'filtered_traces'
+                if traces_key not in h5ant.keys():
+                    print(f"Antenna file corrupted? no '{traces_key}' in {name}")
+                    sys.exit(1)
 
-                    max_idx = np.argmax(test_traces[0])
-
-                    low_idx = max(0, max_idx-N_pre)
-                    high_idx = min(len(t_trace), max_idx+N_post)
-
-                    t_mask = np.ones(len(t_trace), dtype=bool)
-                    t_mask[low_idx:high_idx] = False
-
-                    t_trace = t_trace[t_mask]
-                    for j, t in enumerate(test_traces):
-                        test_traces[j] = t[t_mask]
-                        orients[j] = orients[j] + ' masked'
+                traces = h5ant[traces_key]
+                t_trace = traces[0]
+                test_traces = [traces[4]]
+                orients = ['B']
 
             # use separate polarisations
             else:
-                if 'traces' not in h5ant.keys():
-                    print(f"Antenna file corrupted? no 'traces' in {name}")
+                traces_key = 'filtered_traces'
+                if traces_key not in h5ant.keys():
+                    print(f"Antenna file corrupted? no '{traces_key}' in {name}")
                     sys.exit(1)
 
-                traces = h5ant['traces']
+                traces = h5ant[traces_key]
                 t_trace = traces[0]
+                test_traces = [traces[i] for i in range(1,4)]
+                orients = ['Ex', 'Ey', 'Ez']
 
-                if use_beacon_trace:
-                    # only take the Beacon trace
-                    test_traces = [traces[4]]
-                    orients = ['B']
-                else:
-                    test_traces = traces[1:]
-                    orients = ['Ex', 'Ey', 'Ez', 'B']
-
-            # modify the length of the traces
+            # Really only select the first component
             if False:
-                t_trace = t_trace[:len(t_trace)//2]
-                half_traces = []
-                for trace in test_traces:
-                    half_traces.append( trace[:len(trace)//2])
-                test_traces = half_traces
+                test_traces = [test_traces[0]]
+                orients = [orients[0]]
+
+            # TODO: refine masking
+            # use beacon but remove where E_AxB-Beacon != 0
+            # Uses the first traces as reference
+            if N_mask and orients[0] != 'B':
+                N_pre, N_post = N_mask//2, N_mask//2
+
+                max_idx = np.argmax(test_traces[0])
+
+                low_idx = max(0, max_idx-N_pre)
+                high_idx = min(len(t_trace), max_idx+N_post)
+
+                t_mask = np.ones(len(t_trace), dtype=bool)
+                t_mask[low_idx:high_idx] = False
+
+                t_trace = t_trace[t_mask]
+                for j, t in enumerate(test_traces):
+                    test_traces[j] = t[t_mask]
+                    orients[j] = orients[j] + ' masked'
 
             # Do Fourier Transforms
             # to find phases and amplitudes
@@ -155,7 +167,7 @@ if __name__ == "__main__":
                 amps = [ 3e-7 ]
 
             # choose highest amp
-            idx = 0
+            idx = np.argmax(amps)
             if False and len(beacon_phases) > 1:
                 #idx = np.argmax(amplitudes, axis=-1)
                 raise NotImplementedError

From 5137f87bd98182ff1a1606e729f8e6e949d81f27 Mon Sep 17 00:00:00 2001
From: Eric Teunis de Boone <ericteunis@deboone.nl>
Date: Fri, 3 Feb 2023 12:00:32 +0100
Subject: [PATCH 11/11] ZH: ba* do not plot antennas[70]

---
 .../airshower_beacon_simulation/ba_measure_beacon_phase.py      | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/simulations/airshower_beacon_simulation/ba_measure_beacon_phase.py b/simulations/airshower_beacon_simulation/ba_measure_beacon_phase.py
index 6cc51f7..36348e4 100755
--- a/simulations/airshower_beacon_simulation/ba_measure_beacon_phase.py
+++ b/simulations/airshower_beacon_simulation/ba_measure_beacon_phase.py
@@ -187,7 +187,7 @@ if __name__ == "__main__":
             # for reporting using plots
             found_data[i] = frequency, beacon_phase, amplitude
 
-            if (show_plots or fig_dir) and (i == 0 or i == 72 or i == 70):
+            if (show_plots or fig_dir) and (i == 0 or i == 72):
                 p2t = lambda phase: phase/(2*np.pi*f_beacon)
 
                 fig, ax = plt.subplots(figsize=figsize)