def plot_surface(hdf5_file, case, time=[0], variable="Vx", plt_name="test.png", p=(0, 0)):
""" Plots the velocity values for the given component at the given time
Input:
hdf5_file: HDF5 file to read from
case: case name to read from
time: the time step to read from
variable: the variable to read (["Vx"],"Vy","Vz")
plt_name: the output name of the plot (default is test.png)
"""
import h5py
import numpy as np
import pandas as pd
from Functions import find_nearest
from matplotlib import pyplot as plt
from scipy.interpolate import griddata
tooth_length = 40.0
h5 = h5py.File(hdf5_file, "r")
# Read the available coordinates
df = pd.DataFrame(
{
"x": np.array(h5["{0}/y".format(case)].value) / tooth_length,
"y": -np.array(h5["{0}/x".format(case)].value) / tooth_length,
}
)
mask = h5["{0}/mask".format(case)].value / 40.0
mask = mask - mask[1]
# Rotate requested coordinate points
angle = -h5["{0}".format(case)].attrs["angle"]
# angle = -np.deg2rad(15)
# flow_angle = h5["{0}".format(case)].attrs['flow_angle']
flow_angle = angle
for mi in range(len(mask)):
mask[mi][0], mask[mi][1] = rotate(mask[mi][0], mask[mi][1], angle)
for ti in time:
df["vx"] = np.array(h5["{0}/{1}/{2}".format(case, ti, "Vy")].value)
df["vy"] = -np.array(h5["{0}/{1}/{2}".format(case, ti, "Vx")].value)
df["vz"] = np.array(h5["{0}/{1}/{2}".format(case, ti, "Vz")].value)
print " Rotating the flow to angle {0:.2f}".format(np.rad2deg(flow_angle))
df["vx_rot"], df["vy_rot"] = rotate(df.vx, df.vy, flow_angle)
df["x_rot"], df["y_rot"] = rotate(df.x, df.y, angle)
grid_x, grid_y = np.mgrid[
df["x_rot"].min() : df["x_rot"].max() : 75j, df["y_rot"].min() : df["y_rot"].max() : 150j
]
grid_vx = griddata(
(df["x_rot"].values, df["y_rot"].values), df["vx_rot"].values, (grid_x, grid_y), method="cubic"
)
grid_vy = griddata(
(df["x_rot"].values, df["y_rot"].values), df["vy_rot"].values, (grid_x, grid_y), method="cubic"
)
grid_vz = griddata((df["x_rot"].values, df["y_rot"].values), df["vz"].values, (grid_x, grid_y), method="cubic")
df_interpolated = pd.DataFrame(
{
"x": grid_x.ravel(),
"y": grid_y.ravel(),
"vx": grid_vx.ravel(),
"vy": grid_vy.ravel(),
"vz": grid_vz.ravel(),
}
)
# Re-center the array to the TE location at (0,0)
df_interpolated.y = df_interpolated.y - find_nearest(0, df_interpolated.y.values)[0]
df_interpolated.x = df_interpolated.x - find_nearest(0, df_interpolated.x.values)[0]
fig = plt.figure(figsize=(12, 8))
base_cmap = plt.get_cmap("RdYlBu_r")
plt.subplot(111, aspect=1)
cf = plt.contourf(
grid_x,
grid_y,
df_interpolated[variable].reshape(grid_x.shape),
# levels=[-200., -160., -120., -80., -40., 40., 80., 120.,
# 160., 200.],
cmap=base_cmap,
)
df_interpolated = df_interpolated.sort("y")
plt.quiver(
df_interpolated.x.values[::20],
df_interpolated.y.values[::20],
df_interpolated.vx.values[::20],
df_interpolated.vy.values[::20],
linewidths=(1,),
edgecolors=("k"),
scale=400,
)
clb = plt.colorbar(cf)
clb.set_label("$\\omega_z$")
plt.ylabel("$\\tilde x/2h$")
plt.xlabel("$\\tilde y/2h$")
# co = plt.contour(
# grid_x,
# grid_y,
# grid_z,
# c='k'
# )
plt.fill_between(mask[:, 1], min(-mask[:, 0]), -mask[:, 0], color="k")
# plt.scatter(0,0,s=300,color='r')
# plt.scatter(x_rot,y_rot,s=300)
if len(time) == 1:
plt.savefig(plt_name)
else:
plt.savefig("{0:05d}_{1}".format(ti, plt_name), bbox_inches="tight")
plt.cla()
h5.close()
return df["vx_rot"], df["vy_rot"], df["vz"]
def read_hdf5_time_series(hdf5_file, case, loc=(-0.1, 1)):
""" Reads an HDF5 file and returns the velocity components time series
Input:
hdf5_file: which HDF5 file to read
case: which case to extract the data from
(x,y): normalized coordinate location where to extract the data
from. (0,0) is the TE. This is in DaVis coordinates,
meaning that -x is the airfoil y coordinate
Output:
df: DataFrame
Returns zero if the coordinate is beyond the frame of view
"""
from progressbar import ProgressBar, Percentage, Bar, ETA, SimpleProgress
import h5py
import numpy as np
import pandas as pd
import re
from Functions import find_nearest
x = loc[0]
y = loc[1]
tooth_length = 40.0
h5 = h5py.File(hdf5_file, "r")
# Read all the available time steps
tn = sorted(map(int, re.findall("[0-9]+", " ".join([n for n in h5[case]]))))
# Prepare the velocity arrays
vx = np.zeros(len(tn))
vy = np.zeros(len(tn))
vz = np.zeros(len(tn))
time = np.zeros(len(tn))
# Read the available coordinates
h5_x = h5["{0}/x".format(case)].value / tooth_length
h5_y = h5["{0}/y".format(case)].value / tooth_length
# This is just 'angle' so that the flow is analized
# as going parallel to the serration surface, and not
# in the direction of the standard coordinate system
angle = -h5["{0}".format(case)].attrs["angle"]
x_rot, y_rot = rotate(x, y, angle)
xi, xn, xd = find_nearest(x_rot, np.unique(h5_x))
yi, yn, yd = find_nearest(y_rot, np.unique(h5_y))
if x_rot < min(h5_x) or x_rot > max(h5_x) or y_rot < min(h5_y) or y_rot > max(h5_y):
return None
ind = (xn == h5_x) * (yn == h5_y) # TODO: IS THIS RIGHT?!
print " Looking for coordinate points close to x = {0:.2f}" + " and y = {1:.2f}".format(x_rot, y_rot)
print " Found x = {0:.2f} and y = {1:.2f}".format(float(h5_x[ind]), float(h5_y[ind]))
progress = ProgressBar(
widgets=[Bar(), " ", Percentage(), " ", ETA(), " (timestep ", SimpleProgress(), ")"], maxval=len(tn)
).start()
for t, i in zip(tn, range(len(tn))):
vx[i] = h5["{0}/{1}/{2}".format(case, t, "Vx")][ind]
vy[i] = h5["{0}/{1}/{2}".format(case, t, "Vy")][ind]
vz[i] = h5["{0}/{1}/{2}".format(case, t, "Vz")][ind]
time[i] = h5["{0}/{1}".format(case, t)].attrs["time"]
progress.update(i)
progress.finish()
h5.close()
print " Rotating to angle {0:.2f}".format(np.rad2deg(angle))
vx_rot, vy_rot = rotate(vx, vy, angle)
return pd.DataFrame({"vx": vx_rot, "vy": vy_rot, "vz": vz, "t": time})
def get_time_resolved_wall_normal_line(
hdf5_file,
case,
x_locs=[0],
output_hdf="data.hdf5",
plot=False,
overwrite=False,
height_correction=0,
streamwise_correction=0,
rotation_correction=0,
):
""" Gets a wall normal line, interpolated data and creates a
time-resolved data frame with its information
Input:
hdf5_file: HDF5 file to read from
case: case name to read from
x: the 2h normalized location to read, where x=0 is the airfoil TE
output_hdf: how to name the pickle of the resulting data frame
"""
#######################################################
#######################################################
# IMPORTANT
#
# The coordinates coming from the HDF5 file are the
# vertical freestream coordinates of DaVis.
#
# The coordinates used for the local variables are
# already put to the left-to-right freestream
# coordinates
#
# Further, all coordinates are normalized to the
# tooth length, 2h
#
#######################################################
#######################################################
from progressbar import ProgressBar, Percentage, Bar, ETA, SimpleProgress
import h5py
import numpy as np
import pandas as pd
from scipy.interpolate import griddata
from copy import copy
from Functions import find_nearest
from os.path import isfile
if isfile(output_hdf) and not overwrite:
print " Pickle already exists; skipping, or specify " + "overwrite next time"
return 0
print " Extracting locations {0} \n".format(x_locs) + " for case {0} from its HDF5 database\n".format(
case
) + " into HDF {0}".format(output_hdf)
tooth_length = 40.0
aq_freq = 10000.0
h5 = h5py.File(hdf5_file, "r")
# Read the available coordinates
df = pd.DataFrame(
{
"x": np.array(h5["{0}/y".format(case)].value) / tooth_length,
"y": -np.array(h5["{0}/x".format(case)].value) / tooth_length,
}
)
# Rotate requested coordinate points
angle = -h5["{0}".format(case)].attrs["angle"]
flow_angle = angle
mask = h5["{0}/mask".format(case)].value / 40.0
mask = mask - mask[1]
mask_rot = copy(mask)
for mi in range(len(mask)):
mask_rot[mi][0], mask_rot[mi][1] = rotate(mask[mi][0], mask[mi][1], angle)
df["x_rot"], df["y_rot"] = rotate(df.x, df.y, angle)
available_times = sorted(
[int(f[0]) for f in h5["{0}".format(case)].iteritems() if not "mask" in f and not "x" in f and not "y" in f]
)
wall_normal_lines_DF = pd.DataFrame(columns=["x", "y", "vx", "vy", "vz"])
progress = ProgressBar(
widgets=[Bar(), " ", Percentage(), " ", ETA(), " (time step ", SimpleProgress(), ")"],
maxval=len(available_times),
).start()
t_x_cnt = 0
cnt = 50
df_columns = ["x", "y", "vx", "vy", "vz"]
hdf = pd.HDFStore(output_hdf)
df_xloc_wall_normal = pd.DataFrame(columns=df_columns)
for ti in available_times:
df["vx"] = np.array(h5["{0}/{1}/{2}".format(case, ti, "Vy")].value)
df["vy"] = -np.array(h5["{0}/{1}/{2}".format(case, ti, "Vx")].value)
df["vz"] = np.array(h5["{0}/{1}/{2}".format(case, ti, "Vz")].value)
df["vx_rot"], df["vy_rot"] = rotate(df.vx, df.vy, flow_angle)
df["x_rot"], df["y_rot"] = rotate(df.x, df.y, angle)
grid_x, grid_y = np.mgrid[
df["x_rot"].min() : df["x_rot"].max() : 150j, df["y_rot"].min() : df["y_rot"].max() : 75j
]
grid_vx = griddata(
(df["x_rot"].values, df["y_rot"].values), df["vx_rot"].values, (grid_x, grid_y), method="cubic"
)
grid_vy = griddata(
(df["x_rot"].values, df["y_rot"].values), df["vy_rot"].values, (grid_x, grid_y), method="cubic"
)
grid_vz = griddata((df["x_rot"].values, df["y_rot"].values), df["vz"].values, (grid_x, grid_y), method="cubic")
df_interpolated = pd.DataFrame(
{
"x": grid_x.ravel(),
"y": grid_y.ravel(),
"vx": grid_vx.ravel(),
"vy": grid_vy.ravel(),
"vz": grid_vz.ravel(),
}
)
# Re-center the array to the TE location at (0,0)
df_interpolated.y = df_interpolated.y - find_nearest(0, df_interpolated.y.values)[0]
df_interpolated.x = df_interpolated.x - find_nearest(0, df_interpolated.x.values)[0]
# Rotate x_locs
x_locs_rotated = []
for x_loc in x_locs:
x_loc_rotated, y0 = rotate(x_loc, 0, angle)
x_locs_rotated.append(x_loc_rotated)
if plot and ti == 0:
quick_plot_time_step(df=df_interpolated, mask=mask_rot, variable="vx", x_locs=x_locs_rotated)
for x_loc_rotated in x_locs_rotated:
nearest_available_x, tmp = find_nearest(x_loc_rotated, df_interpolated[df_interpolated.y == 0].x.values)
df_xloc_wall_normal_step = df_interpolated[
(df_interpolated.x == nearest_available_x)
& (df_interpolated.y > 0)
& (df_interpolated.y < 0.95 * df_interpolated.y.max())
]
df_xloc_wall_normal_step["ti"] = ti
df_xloc_wall_normal_step["t_real"] = ti / aq_freq
if df_xloc_wall_normal_step.empty:
print "Error, available rotated x coordinate not in mesh"
h5.close()
progress.finish()
print x_loc_rotated
break
if cnt == 50:
if t_x_cnt == cnt:
hdf.put(case, df_xloc_wall_normal.convert_objects(), format="table", data_columns=True)
else:
hdf.append(case, df_xloc_wall_normal.convert_objects(), format="table", data_columns=True)
df_xloc_wall_normal = pd.DataFrame(columns=df_columns)
cnt = 0
else:
df_xloc_wall_normal = df_xloc_wall_normal.append(df_xloc_wall_normal_step, ignore_index=True)
cnt += 1
t_x_cnt += 1
progress.update(t_x_cnt)
hdf.close()
h5.close()
progress.finish()
return wall_normal_lines_DF
vy = np.zeros(len(tn))
vz = np.zeros(len(tn))
time = np.zeros(len(tn))
# Read the available coordinates
h5_x = h5["{0}/x".format(case)].value / tooth_length
h5_y = h5["{0}/y".format(case)].value / tooth_length
# This is just 'angle' so that the flow is analized
# as going parallel to the serration surface, and not
# in the direction of the standard coordinate system
angle = -h5["{0}".format(case)].attrs['angle']
x_rot, y_rot = rotate(x, y, angle)
xi, xn, xd = find_nearest(x_rot, np.unique(h5_x))
yi, yn, yd = find_nearest(y_rot, np.unique(h5_y))
if x_rot<min(h5_x) or x_rot>max(h5_x)\
or y_rot<min(h5_y) or y_rot>max(h5_y):
return None
ind = (xn == h5_x) * (yn == h5_y) # TODO: IS THIS RIGHT?!
print " Looking for coordinate points close to x = {0:.2f}"\
+" and y = {1:.2f}".format(x_rot,y_rot)
print " Found x = {0:.2f} and y = {1:.2f}".format(
float(h5_x[ind]), float(h5_y[ind]))
progress = ProgressBar(widgets=[