From 644bec91129b9dc02c0f42c997c7f8b6746809ad Mon Sep 17 00:00:00 2001 From: "Edgar P. Burkhart" Date: Fri, 11 Mar 2022 13:40:51 +0100 Subject: [PATCH 1/9] LFS --- swash/data/Hstru.dat | 4 +++- swash/data/Poro.dat | 4 +++- swash/data/Psize.dat | 4 +++- swash/data/bathyhires.dat | 4 +++- swash/data/buoyarthabathy.dat | 4 +++- 5 files changed, 15 insertions(+), 5 deletions(-) diff --git a/swash/data/Hstru.dat b/swash/data/Hstru.dat index 4168f19..7572dc3 100755 --- a/swash/data/Hstru.dat +++ b/swash/data/Hstru.dat @@ -1 +1,3 @@ -0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 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3.680653 3.9711192 4.0166274 4.0342569 4.0601056 4.0301073 3.9983119 4.3613894 5.751144 8.5008125 9.4027008 9.3922735 9.3858863 9.3987603 9.3911168 9.3818578 9.3475402 \ No newline at end of file +version https://git-lfs.github.com/spec/v1 +oid sha256:d76300be9349c43d90b0db444f00667a34617d0c2c53164a1e5504d1fe1f9bf7 +size 21996 From 1323a6b5fe40e212a2712e46684a8a8205a9661d Mon Sep 17 00:00:00 2001 From: "Edgar P. Burkhart" Date: Fri, 11 Mar 2022 14:10:56 +0100 Subject: [PATCH 2/9] Add swash data to data --- data/data/Hstru.dat | 3 +++ data/data/Poro.dat | 3 +++ data/data/Psize.dat | 3 +++ data/data/bathyhires.dat | 3 +++ data/data/buoyarthabathy.dat | 3 +++ 5 files changed, 15 insertions(+) create mode 100755 data/data/Hstru.dat create mode 100755 data/data/Poro.dat create mode 100755 data/data/Psize.dat create mode 100755 data/data/bathyhires.dat create mode 100755 data/data/buoyarthabathy.dat diff --git a/data/data/Hstru.dat b/data/data/Hstru.dat new file mode 100755 index 0000000..7572dc3 --- /dev/null +++ b/data/data/Hstru.dat @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:752dec83ecb9ee7fb94f4b1d2f46ce0e4ebbf504002714b798e704fd705e64e8 +size 2639 diff --git a/data/data/Poro.dat b/data/data/Poro.dat new file mode 100755 index 0000000..ead67c1 --- /dev/null +++ b/data/data/Poro.dat @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:0b1ea84701b4c5daa9e37293b3a8c84aff9357a425969c5d1720f13ab4ec7606 +size 1308 diff --git a/data/data/Psize.dat b/data/data/Psize.dat new file mode 100755 index 0000000..6adc185 --- /dev/null +++ b/data/data/Psize.dat @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:eaa82206c1a952bdfd10ba322149514d2a3aaf7db7a08d0f89d96fa282bfdc43 +size 900 diff --git a/data/data/bathyhires.dat b/data/data/bathyhires.dat new file mode 100755 index 0000000..2a86fb2 --- /dev/null +++ b/data/data/bathyhires.dat @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:cd7a7e42abc9ec28c5cfe91964e8cb6d7807a947463cd708edf835386b6f5c2c +size 4809 diff --git a/data/data/buoyarthabathy.dat b/data/data/buoyarthabathy.dat new file mode 100755 index 0000000..98b7dfc --- /dev/null +++ b/data/data/buoyarthabathy.dat @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:d76300be9349c43d90b0db444f00667a34617d0c2c53164a1e5504d1fe1f9bf7 +size 21996 From 8ff521ee0b2072d4e88321c91707e85f73250d47 Mon Sep 17 00:00:00 2001 From: "Edgar P. Burkhart" Date: Fri, 11 Mar 2022 14:11:48 +0100 Subject: [PATCH 3/9] Updates in data --- data/.gitignore | 1 + data/config.ini | 7 ++++--- data/processing/projection.py | 37 +++++++++-------------------------- 3 files changed, 14 insertions(+), 31 deletions(-) create mode 100644 data/.gitignore diff --git a/data/.gitignore b/data/.gitignore new file mode 100644 index 0000000..e2e7327 --- /dev/null +++ b/data/.gitignore @@ -0,0 +1 @@ +/out diff --git a/data/config.ini b/data/config.ini index e0e702f..9d968b8 100644 --- a/data/config.ini +++ b/data/config.ini @@ -1,7 +1,8 @@ [bathy] -inp=Database_20220224.xyz -sub=bathy_sub.npy -out=bathy.npy +inp=data/Database_20220224.xyz +sub=out/bathy_sub.npy +out=out/bathy.npy +step=1 [artha] lat=43.398450 diff --git a/data/processing/projection.py b/data/processing/projection.py index 4f63591..6a7b2dd 100644 --- a/data/processing/projection.py +++ b/data/processing/projection.py @@ -32,7 +32,7 @@ bathy = np.stack( *projection.cartesian(bathy_curvi[:, 0], bathy_curvi[:, 1]), bathy_curvi[:, 2], ), - axis=1 + axis=1, ) log.debug(f"Cartesian bathy: {bathy}") @@ -46,37 +46,18 @@ buoy_curvi = np.array( artha = np.asarray(projection.cartesian(*artha_curvi)) buoy = np.asarray(projection.cartesian(*buoy_curvi)) - -def display(): - x = np.linspace(bathy[:, 0].min(), bathy[:, 0].max()) - y = np.linspace(bathy[:, 1].min(), bathy[:, 1].max()) - - X, Y = np.meshgrid(x, y) - - Z = interpolate.griddata( - bathy[:, :2], bathy[:, 2], (X, Y), method="nearest" - ) - - fix, ax = plt.subplots() - ax.pcolormesh(X, Y, Z) - ax.scatter(*artha, c="k") - ax.scatter(*buoy, c="k") - - ax.axis("equal") - return ax - - D = np.diff(np.stack((artha, buoy)), axis=0) -x = np.arange(-150, np.sqrt((D**2).sum()) + 150) +x = np.arange( + -150, + np.sqrt((D**2).sum()) + 150, + config.getfloat("bathy", "step", fallback=1), +) theta = np.angle(D.dot((1, 1j))) coords = artha + (x * np.stack((np.cos(theta), np.sin(theta)))).T -z = interpolate.griddata(bathy[:,:2], bathy[:,2], coords) +log.info("Interpolating bathymetry in 1D") +z = interpolate.griddata(bathy[:, :2], bathy[:, 2], coords) +log.debug(z) -ax = display() -ax.scatter(*coords.T, c="k", marker=".") -fig_1d, ax_1d = plt.subplots() -ax_1d.plot(x, z) -plt.show(block=True) From cb5966c9ce0e9cde1510684329a0b0d3ad29b00c Mon Sep 17 00:00:00 2001 From: "Edgar P. Burkhart" Date: Fri, 11 Mar 2022 14:42:42 +0100 Subject: [PATCH 4/9] Use high res smoothed bathymetry for breakwater --- data/config.ini | 2 ++ data/data/Hstru.dat | 0 data/data/Poro.dat | 0 data/data/Psize.dat | 0 data/data/bathyhires.dat | 0 data/data/buoyarthabathy.dat | 0 data/processing/projection.py | 37 ++++++++++++++++++++++++++++++++++- 7 files changed, 38 insertions(+), 1 deletion(-) mode change 100755 => 100644 data/data/Hstru.dat mode change 100755 => 100644 data/data/Poro.dat mode change 100755 => 100644 data/data/Psize.dat mode change 100755 => 100644 data/data/bathyhires.dat mode change 100755 => 100644 data/data/buoyarthabathy.dat diff --git a/data/config.ini b/data/config.ini index 9d968b8..d8da6b7 100644 --- a/data/config.ini +++ b/data/config.ini @@ -1,5 +1,7 @@ [bathy] inp=data/Database_20220224.xyz +hires=data/bathyhires.dat +hires_step=0.5 sub=out/bathy_sub.npy out=out/bathy.npy step=1 diff --git a/data/data/Hstru.dat b/data/data/Hstru.dat old mode 100755 new mode 100644 diff --git a/data/data/Poro.dat b/data/data/Poro.dat old mode 100755 new mode 100644 diff --git a/data/data/Psize.dat b/data/data/Psize.dat old mode 100755 new mode 100644 diff --git a/data/data/bathyhires.dat b/data/data/bathyhires.dat old mode 100755 new mode 100644 diff --git a/data/data/buoyarthabathy.dat b/data/data/buoyarthabathy.dat old mode 100755 new mode 100644 diff --git a/data/processing/projection.py b/data/processing/projection.py index 6a7b2dd..ae62196 100644 --- a/data/processing/projection.py +++ b/data/processing/projection.py @@ -21,6 +21,7 @@ config = configparser.ConfigParser() config.read("config.ini") bathy_inp = pathlib.Path(config.get("bathy", "sub")) +hires_inp = pathlib.Path(config.get("bathy", "hires")) bathy_out = pathlib.Path(config.get("bathy", "out")) log.info(f"Loading bathymetry from {bathy_inp}") @@ -58,6 +59,40 @@ coords = artha + (x * np.stack((np.cos(theta), np.sin(theta)))).T log.info("Interpolating bathymetry in 1D") z = interpolate.griddata(bathy[:, :2], bathy[:, 2], coords) -log.debug(z) +log.debug(f"z: {z}") +_hires = np.genfromtxt(hires_inp)[::-1] +bathy_hires = np.stack( + ( + np.linspace( + 0, + (_hires.size - 1) * config.getfloat("bathy", "hires_step"), + _hires.size, + ), + _hires, + ), + axis=1, +) +del _hires +log.debug(f"Bathy hires: {bathy_hires}") +z_cr = 5 +hires_crossing = np.diff(np.signbit(bathy_hires[:, 1] - z_cr)).nonzero()[0][-1] +log.debug(f"Hires crossing: {hires_crossing}") +z_crossing = np.diff(np.signbit(z - z_cr)).nonzero()[0][-1] +log.debug(f"Z crossing: {z_crossing}") + +x_min_hires = x[z_crossing] + ( + bathy_hires[:, 0].min() - bathy_hires[hires_crossing, 0] +) +x_max_hires = x[z_crossing] + ( + bathy_hires[:, 0].max() - bathy_hires[hires_crossing, 0] +) +log.debug(f"Replacing range: [{x_min_hires},{x_max_hires}]") + +flt_x = (x > x_min_hires) & (x < x_max_hires) +z[flt_x] = interpolate.griddata( + (bathy_hires[:, 0],), + bathy_hires[:, 1], + (x[flt_x] - x[z_crossing] + bathy_hires[hires_crossing, 0]), +) From 187e8f0ce74d68c916c08f81377c25dc446c04da Mon Sep 17 00:00:00 2001 From: "Edgar P. Burkhart" Date: Fri, 11 Mar 2022 14:55:16 +0100 Subject: [PATCH 5/9] Change config --- data/config.ini | 14 +++++++++----- data/processing/projection.py | 14 +++++++++----- data/processing/subdomain.py | 6 ++++-- 3 files changed, 22 insertions(+), 12 deletions(-) diff --git a/data/config.ini b/data/config.ini index d8da6b7..4a6214a 100644 --- a/data/config.ini +++ b/data/config.ini @@ -1,9 +1,13 @@ -[bathy] -inp=data/Database_20220224.xyz -hires=data/bathyhires.dat +[inp] +root=data +base=Database_20220224.xyz +hires=bathyhires.dat hires_step=0.5 -sub=out/bathy_sub.npy -out=out/bathy.npy + +[out] +root=out +sub=bathy_sub.npy +out=bathy.npy step=1 [artha] diff --git a/data/processing/projection.py b/data/processing/projection.py index ae62196..c0de89e 100644 --- a/data/processing/projection.py +++ b/data/processing/projection.py @@ -20,9 +20,11 @@ log.info("Starting bathymetry pre-processing") config = configparser.ConfigParser() config.read("config.ini") -bathy_inp = pathlib.Path(config.get("bathy", "sub")) -hires_inp = pathlib.Path(config.get("bathy", "hires")) -bathy_out = pathlib.Path(config.get("bathy", "out")) +inp_root = pathlib.Path(config.get("inp", "root")) +out_root = pathlib.Path(config.get("out", "root")) +bathy_inp = out_root.joinpath(config.get("out", "sub")) +hires_inp = inp_root.joinpath(config.get("inp", "hires")) +bathy_out = inp_root.joinpath(config.get("out", "out")) log.info(f"Loading bathymetry from {bathy_inp}") bathy_curvi = np.load(bathy_inp) @@ -51,7 +53,7 @@ D = np.diff(np.stack((artha, buoy)), axis=0) x = np.arange( -150, np.sqrt((D**2).sum()) + 150, - config.getfloat("bathy", "step", fallback=1), + config.getfloat("out", "step", fallback=1), ) theta = np.angle(D.dot((1, 1j))) @@ -66,7 +68,7 @@ bathy_hires = np.stack( ( np.linspace( 0, - (_hires.size - 1) * config.getfloat("bathy", "hires_step"), + (_hires.size - 1) * config.getfloat("inp", "hires_step"), _hires.size, ), _hires, @@ -96,3 +98,5 @@ z[flt_x] = interpolate.griddata( bathy_hires[:, 1], (x[flt_x] - x[z_crossing] + bathy_hires[hires_crossing, 0]), ) + + diff --git a/data/processing/subdomain.py b/data/processing/subdomain.py index 88c3d96..73f62bd 100644 --- a/data/processing/subdomain.py +++ b/data/processing/subdomain.py @@ -33,8 +33,10 @@ domain[0] -= 0.002 domain[1] += 0.002 log.debug(f"domain: {domain}") -bathy_inp = pathlib.Path(config.get("bathy", "inp")) -bathy_out = pathlib.Path(config.get("bathy", "sub")) +inp_root = pathlib.Path(config.get("inp", "root")) +out_root = pathlib.Path(config.get("out", "root")) +bathy_inp = inp_root.joinpath(config.get("inp", "base")) +bathy_out = out_root.joinpath(config.get("out", "sub")) log.info(f"Reading bathymetry from '{bathy_inp}'") raw_bathy = np.genfromtxt(bathy_inp) log.debug(f"Initial size: {raw_bathy.shape}") From 3707db4080a353a46a7d05be536a1dc8aef0b54b Mon Sep 17 00:00:00 2001 From: "Edgar P. Burkhart" Date: Fri, 11 Mar 2022 15:20:29 +0100 Subject: [PATCH 6/9] Add zero filled poro --- data/processing/projection.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/data/processing/projection.py b/data/processing/projection.py index c0de89e..dbf8adf 100644 --- a/data/processing/projection.py +++ b/data/processing/projection.py @@ -99,4 +99,7 @@ z[flt_x] = interpolate.griddata( (x[flt_x] - x[z_crossing] + bathy_hires[hires_crossing, 0]), ) - +np.savetxt(out_root.joinpath("bathy.dat"), z, newline=" ") +np.savetxt(out_root.joinpath("hstru.dat"), np.zeros(z.shape), newline=" ") +np.savetxt(out_root.joinpath("poro.dat"), np.zeros(z.shape), newline=" ") +np.savetxt(out_root.joinpath("psize.dat"), np.zeros(z.shape), newline=" ") From 232ece2c28824e55cf9ea3b6a46b95e9e9ce3d93 Mon Sep 17 00:00:00 2001 From: "Edgar P. Burkhart" Date: Fri, 11 Mar 2022 16:02:36 +0100 Subject: [PATCH 7/9] Switched genfromtxt to loadtxt --- data/processing/projection.py | 2 +- data/processing/subdomain.py | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/data/processing/projection.py b/data/processing/projection.py index dbf8adf..dc3fa20 100644 --- a/data/processing/projection.py +++ b/data/processing/projection.py @@ -63,7 +63,7 @@ log.info("Interpolating bathymetry in 1D") z = interpolate.griddata(bathy[:, :2], bathy[:, 2], coords) log.debug(f"z: {z}") -_hires = np.genfromtxt(hires_inp)[::-1] +_hires = np.loadtxt(hires_inp)[::-1] bathy_hires = np.stack( ( np.linspace( diff --git a/data/processing/subdomain.py b/data/processing/subdomain.py index 73f62bd..a2d6e13 100644 --- a/data/processing/subdomain.py +++ b/data/processing/subdomain.py @@ -38,7 +38,7 @@ out_root = pathlib.Path(config.get("out", "root")) bathy_inp = inp_root.joinpath(config.get("inp", "base")) bathy_out = out_root.joinpath(config.get("out", "sub")) log.info(f"Reading bathymetry from '{bathy_inp}'") -raw_bathy = np.genfromtxt(bathy_inp) +raw_bathy = np.loadtxt(bathy_inp) log.debug(f"Initial size: {raw_bathy.shape}") bathy = raw_bathy[ @@ -46,6 +46,7 @@ bathy = raw_bathy[ axis=1 ) ] +del raw_bathy log.debug(f"Final size: {bathy.shape}") log.info(f"Saving subdomain to 'bathy'") From dcd7b1df7dfb395ea0f2c3ef8419b2def3009381 Mon Sep 17 00:00:00 2001 From: "Edgar P. Burkhart" Date: Mon, 14 Mar 2022 13:34:21 +0100 Subject: [PATCH 8/9] Modified limits of bathy export --- data/config.ini | 2 ++ data/processing/projection.py | 5 ++--- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/data/config.ini b/data/config.ini index 4a6214a..bec1798 100644 --- a/data/config.ini +++ b/data/config.ini @@ -9,6 +9,8 @@ root=out sub=bathy_sub.npy out=bathy.npy step=1 +left=0 +right=150 [artha] lat=43.398450 diff --git a/data/processing/projection.py b/data/processing/projection.py index dc3fa20..a172385 100644 --- a/data/processing/projection.py +++ b/data/processing/projection.py @@ -3,7 +3,6 @@ import configparser import logging import pathlib -import matplotlib.pyplot as plt import numpy as np from scipy import interpolate @@ -51,8 +50,8 @@ buoy = np.asarray(projection.cartesian(*buoy_curvi)) D = np.diff(np.stack((artha, buoy)), axis=0) x = np.arange( - -150, - np.sqrt((D**2).sum()) + 150, + config.getfloat("out", "left", fallback=0), + np.sqrt((D**2).sum()) + config.getfloat("out", "right", fallback=0), config.getfloat("out", "step", fallback=1), ) theta = np.angle(D.dot((1, 1j))) From aac1d54f6e292f61a375b8f2dfe777c19f39cf48 Mon Sep 17 00:00:00 2001 From: "Edgar P. Burkhart" Date: Mon, 14 Mar 2022 14:16:25 +0100 Subject: [PATCH 9/9] Switched side --- data/processing/projection.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/data/processing/projection.py b/data/processing/projection.py index a172385..746862f 100644 --- a/data/processing/projection.py +++ b/data/processing/projection.py @@ -98,7 +98,7 @@ z[flt_x] = interpolate.griddata( (x[flt_x] - x[z_crossing] + bathy_hires[hires_crossing, 0]), ) -np.savetxt(out_root.joinpath("bathy.dat"), z, newline=" ") +np.savetxt(out_root.joinpath("bathy.dat"), z[::-1], newline=" ") np.savetxt(out_root.joinpath("hstru.dat"), np.zeros(z.shape), newline=" ") np.savetxt(out_root.joinpath("poro.dat"), np.zeros(z.shape), newline=" ") np.savetxt(out_root.joinpath("psize.dat"), np.zeros(z.shape), newline=" ")