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] 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)