def initiate_plot(self, averagereward, transparency='on'):
self.exparr_x = self.explode(self.bm)
self.exparr = np.where(
self.exparr_x - averagereward < 0, 0,
self.exparr) #turns values below cutoff to 0 invisible waste
normarr = self.normalize(self.exparr)
self.facecolours = cm.plasma(normarr) # facecolours [x,y,z, (r,g,b,a)]
#ceilarr=np.ceil(normarr)
#normarr[normarr<=0.05]=0 #hide voxels less than 0.05
if transparency == 'on':
self.facecolours[:, :, :,
-1] = normarr #matches transperancy to normarr intensity
normarr_x = self.normalize(self.exparr_x)
self.facecolours_x = cm.plasma(
normarr_x) # facecolours [x,y,z, (r,g,b,a)]
#ceilarr=np.ceil(normarr)
#normarr[normarr<=0.05]=0 #hide voxels less than 0.05
self.facecolours_x[:, :, :,
-1] = normarr #matches transperancy to normarr intensity
else:
notransp = np.where(self.exparr_x - averagereward < 0, 0, 1)
self.facecolours[:, :, :, -1] = notransp
normarr_x = self.normalize(self.exparr_x)
self.facecolours_x = cm.plasma(
normarr_x) # facecolours [x,y,z, (r,g,b,a)]
#ceilarr=np.ceil(normarr)
#normarr[normarr<=0.05]=0 #hide voxels less than 0.05
self.facecolours_x[:, :, :,
-1] = notransp #matches transperancy to 1 for ore 0 for waste
def test_gumbel():
n_classes = 4
logits = tf.random.normal((1, n_classes))
temperatures = [0.1, 0.5, 1., 5., 10.]
M = 128 # number of samples used to approximate distribution mean
fig, axes = plt.subplots(nrows=2,
ncols=len(temperatures),
figsize=(14, 6),
subplot_kw={
'xticks': range(n_classes),
'yticks': [0., 0.5, 1.]
})
axes[0, 0].set_ylabel('Expectation')
axes[1, 0].set_ylabel('Gumbel Softmax Sample')
for n, t in enumerate(temperatures):
dist = RelaxedOneHotCategorical(logits, t)
mean = tf.zeros_like(logits)
for _ in range(M):
mean += dist.sample() / M
sample = dist.sample()
axes[0, n].set_title('T = {}'.format(t))
axes[0, n].set_ylim((0, 1.1))
axes[1, n].set_ylim((0, 1.1))
axes[0, n].bar(np.arange(n_classes),
mean.numpy().reshape(n_classes),
color=cm.plasma(0.75 * t / max(temperatures)))
axes[1, n].bar(np.arange(n_classes),
sample.numpy().reshape(n_classes),
color=cm.plasma(0.75 * t / max(temperatures)))
plt.show()
def updateHist(writer,model_id,outDictEpochs,targDictEpochs):
firstEpoch = list(outDictEpochs.keys())[0]
for i,vidName in enumerate(outDictEpochs[firstEpoch].keys()):
fig = plt.figure()
targBounds = np.array(utils.binaryToSceneBounds(targDictEpochs[firstEpoch][vidName][0]))
cmap = cm.plasma(np.linspace(0, 1, len(targBounds)))
width = 0.2*len(outDictEpochs.keys())
off = width/2
plt.bar(len(outDictEpochs.keys())+off,targBounds[:,1]+1-targBounds[:,0],width,bottom=targBounds[:,0],color=cmap,edgecolor='black')
for j,epoch in enumerate(outDictEpochs.keys()):
predBounds = np.array(utils.binaryToSceneBounds(outDictEpochs[epoch][vidName][0]))
cmap = cm.plasma(np.linspace(0, 1, len(predBounds)))
plt.bar(epoch-1,predBounds[:,1]+1-predBounds[:,0],1,bottom=predBounds[:,0],color=cmap,edgecolor='black')
writer.add_figure(model_id+"_val"+"_"+vidName,fig,firstEpoch)
def PlotModelsOverTime_DuskAndDawn(base_model,shifts,parameter_dict,null_model="None",reset=True):
# Setup of the base model
def base_newpars():
base_model.model['shift_hour'] = 0.0
base_model_out = update_and_sim_model(base_model,base_newpars)
base_dawn_time = base_model.model['dawn_time']
base_dusk_time = base_model.model['prev_dusk']
base_time_idxs_middle = GetTimeIdxs(base_model_out,base_model.model['dawn_time']+(9.5*(3/8)),base_model.model['dawn_time']+(9.5*(11/8)))
color_num = 1.0
index=0
for shift in shifts:
index = index + 1
#shift = 2.0 # TEMP
def shift_newpars():
base_model.model['shift_hour'] = shift
if reset == True:
update_model_woReset(base_model,parameter_dict)
shift_model_out = update_and_sim_model(base_model,shift_newpars)
# Find shifted dawn and dusk times
shift_dawn = base_dawn_time -9.5*(shift/24.0)
shift_dawn_time = shift_dawn*(24/9.5)-264
shift_dusk = base_dusk_time +9.5*(shift/24.0)
shift_dusk_time = shift_dusk*(24/9.5)-264
# Base
plt.plot(correct_time(shift_model_out['time'][base_time_idxs_middle],24/9.5,-264), shift_model_out['RPS6p'][base_time_idxs_middle], c=cm.plasma(color_num),linewidth=2.5)
plt.xticks([-12,-6,0,6,12])
if null_model == "Dusk":
plt.axvline(x=-12,ymin=0.0,ymax=0.075-shift*0.01,color=cm.plasma(color_num),alpha=0.1*index)
else:
plt.axvline(x=-12+shift,ymin=0.0,ymax=0.075-shift*0.01,color=cm.plasma(color_num),alpha=0.1*index)
if null_model == "Dawn":
plt.axvline(x=0,ymin=0.0,ymax=0.075-shift*0.01,color=cm.plasma(color_num),alpha=0.1*index)
else:
plt.axvline(x=0-shift,ymin=0.0,ymax=0.075-shift*0.01,color=cm.plasma(color_num),alpha=0.1*index)
plt.ylim(0.05,0.30)
# Shift Color
color_num = color_num - 1.0/len(shifts)
# Labels
plt.xlabel("Time")
plt.xlim([-15.0,9.0])
plt.ylabel("eS6-P")
def amp_xs_compute_true_u(cb,
nsamples,
amp_line,
pi_line,
kc=1,
plot=False,
write=False):
X = np.zeros((n_inputs))
y = np.zeros((1))
colors = iter(cm.plasma(np.arange(len(amp_line))))
for amp in amp_line:
for n in range(nsamples):
filename = "%.2f_init_kc%d_%d" % (amp, kc, n)
uu = cb.init_u(amp, phase=np.random.choice(pi_line))
_, abs_work = LW_solver(uu,
cb.itmax,
filename=filename,
write=write,
plot=plot)
for it in range(1, cb.itmax):
u_curr = np.load(
osp.join(abs_work, filename + "_it%d.npy" % (it)))
u_next = np.load(
osp.join(abs_work, filename + "_it%d.npy" % (it + 1)))
for j in range(1, len(uu) - 1):
X = np.block([[X], add_block(u_curr, cb.line_x, j)])
y = np.block([[y], [u_next[j]]])
X = np.delete(X, 0, axis=0)
y = np.delete(y, 0, axis=0)
return X, y
def animate(i):
plt.title( str(timedelta(seconds=i * 30) + start_date) )
lons = []
lats = []
vals = []
for station in stations:
for prn in ['G%02d' % x for x in range(1, 33)]:
if prn not in vtec[station] or i >= len(vtec[station][prn][0]):
continue
try:
ecef = vtec[station][prn][0][i]
except IndexError:
print(station, prn, i)
raise
if ecef is None:
continue
lat, lon, _ = coordinates.ecef2geodetic(ecef)
lon = lon if lon > 0 else lon + 360
lons.append(lon)
lats.append(lat)
vals.append(vtec[station][prn][1][i])
scatter.set_offsets(numpy.array(globe(lons, lats)).T)
max_tec = 60
scatter.set_color( cm.plasma(numpy.array(vals) / max_tec) )
def plot2d(
X: [torch.Tensor, np.ndarray],
targets: List[Any],
classes: List[str],
) -> List[wandb.Image]:
"""Returns a list of wandb.Image objects
:param X: 2D array to visualize
:type X: List[str]
:param targets: ground truth integers used to color each point
:type targets: List[Any]
:param classes: list of classes representing ground truth
:type classes: List[str]
"""
targets = np.array([classes[target] for target in targets])
unique_targets = np.unique(targets)
colors = cm.plasma(np.linspace(0, 1, len(unique_targets)))
f, ax = plt.subplots(1, figsize=(10, 10))
for (i, target), color in zip(enumerate(unique_targets), colors):
indices = np.where(targets == target)
num = len(indices[0])
ax.scatter(X[indices, 0],
X[indices, 1],
label='{} : {}'.format(target, num),
color=color)
ax.set_ylabel('Component 2')
ax.set_xlabel('Component 1')
ax.grid()
ax.legend(loc='best')
image = wandb.Image(plt)
plt.close()
return image
def plotModified(reference, histo, color=1):
# plot original histogram (reference) with ones resampled from it (histo),
# histo is either an array of histograms or a single histogram.
# reference is a dataframe element.
if color == 1:
colors = [cm.viridis(i) for i in np.linspace(0, 1, len(histo))]
elif color == 2:
colors = [cm.plasma(i) for i in np.linspace(0, 1, len(histo))]
else:
colors = [cm.inferno(i) for i in np.linspace(0, 1, len(histo))]
name = reference['hname']
vmin = reference['Xmin']
vmax = reference['Xmax']
# create an array with x values, from x_min to x_max and length as input histogram
x = vmin + (np.arange(len(histo[0]))) * float(
(vmax - vmin) / float(len(histo[0])))
x = x[1:-1]
for i in range(len(histo)):
plt.xlim(vmin, vmax)
histo_todraw = histo[i][1:-1]
#srun=df_plot.index.get_level_values('fromrun')[num]
#slumi=df_plot.index.get_level_values('fromlumi')[num]
plt.step(x,
histo_todraw,
where='mid',
label=(name + " LS " + str(reference['fromlumi']) + " Run " +
str(reference['fromrun'])),
color=colors[i])
def dist2A(Apos, data, percentile, plot=False, histtype="step"):
"""
Compute the of all points to each archetype
in: 1.Apos[j,k] = position of all j archetypes and k dimensions
2.data[i,k] = all i- sample points in k- dimensions
3.Do you want to plot: True
4. Which type of histogram: "bar", "stepfilled"
out: dists[j,i] = distance of the i´th data point to the j´th archetype
"""
#loop over all samples
samples = np.shape(data)[0]
n_a = np.shape(Apos)[0]
dists = np.zeros((n_a, samples))
archColors = cm.plasma(np.arange(n_a).astype(float) / (n_a))
for j in range(0, n_a):
for i in range(0, samples):
dists[j, i] = np.linalg.norm(np.abs(data[i, :] - Apos[j, :]))
dists[j, :] = dists[j, :] / max(dists[j, :])
if plot == True:
plt.figure()
plt.title("Amount of points vs distance to archetype", fontsize=18)
plt.xlabel("Normalized distance", fontsize=16)
plt.ylabel("Amount of sample points", fontsize=16)
for k in range(0, n_a):
plt.hist(dists[k, :],
int(percentile * np.shape(dists)[1]),
color=archColors[k, :],
histtype=histtype,
label="A" + str(k))
plt.legend()
plt.tight_layout()
plt.show()
return (dists)
def animate(i):
plt.title( str(timedelta(seconds=i * 30) + start_date) )
lons = []
lats = []
vals = []
for station in stations:
for prn in get_data.satellites:
if prn not in vtec[station] or i >= len(vtec[station][prn][0]):
continue
try:
ecef = vtec[station][prn][0][i]
except IndexError:
print(station, prn, i)
raise
if ecef is None:
continue
lat, lon, _ = coordinates.ecef2geodetic(ecef)
lon = lon if lon > 0 else lon + 360
lons.append(lon)
lats.append(lat)
vals.append(filtered[station][prn][i])
scatter.set_offsets(numpy.array((lons, lats)).T)
max_tec = 0.1
min_tec = -0.1
scatter.set_color( cm.plasma(numpy.maximum(numpy.array(vals) - min_tec, 0) / (max_tec - min_tec)) )
def generational_histogram(
rootdir: Path,
n_bins: int = 20,
min_gen: int = 0,
show: bool = True,
):
# OPTIMIZE: only scrape the ones with gen > min_gen
data: Dict[GeneRunID, float] = scrape_extracted_cache(rootdir)
# first make bins based on all data
bins, bin_centers = get_bins(data, n_bins)
# sort by generation
data_sorted: DefaultDict[int, List[float]] = sort_by_generation(data)
# plot each generation
gen_count: int = max(data_sorted.keys())
colors = cm.plasma(np.linspace(0, 1, gen_count - min_gen)) # type: ignore
for gen_k in range(min_gen, gen_count):
lst_v: List[float] = data_sorted[gen_k]
hist, _ = np.histogram(lst_v, bins)
plt.plot(
bin_centers,
hist,
'-',
label=f"gen_{gen_k}",
color=colors[gen_k - min_gen],
)
plt.legend()
if show:
plt.show()
def plotme(regression, ytypes, y, h=0.2):
if regression[0].canPlot():
new_x = regression[0].get_x()
x_min, x_max = new_x[:, 1].min() - .5, new_x[:, 1].max() + .5
y_min, y_max = new_x[:, 2].min() - .5, new_x[:, 2].max() + .5
xx, yy = np.meshgrid(np.arange(x_min, x_max, h),
np.arange(y_min, y_max, h))
fig1 = plt.figure("multi class")
Z = [
regression[i].predict(np.c_[xx.ravel(), yy.ravel()], scale=False)
for i in range(ytypes.size)
]
colors = cm.plasma(np.linspace(0, 1, ytypes.size))
for i in range(ytypes.size):
Z[i] = Z[i].reshape(xx.shape)
plt.contour(xx,
yy,
Z[i],
levels=[0.5],
colors=(tuple(colors[i]), 0))
plt.scatter(new_x[:, 1], new_x[:, 2], c=y, cmap=cm.plasma)
plt.xlim(xx.min(), xx.max())
plt.ylim(yy.min(), yy.max())
plt.xticks(())
plt.yticks(())
fig1.show()
def run_Model(self, reef, input_vector):
reef.convert_vector(self.communities, input_vector, self.sedsim,
self.flowsim) #model.py
self.initial_sed, self.initial_flow = reef.load_xml(
self.input, self.sedsim, self.flowsim)
if self.vis[0] == True:
reef.core.initialSetting(size=(8, 2.5),
size2=(8, 3.5)) # View initial parameters
reef.run_to_time(self.simtime, showtime=100.)
if self.vis[1] == True:
from matplotlib.cm import terrain, plasma
nbcolors = len(reef.core.coralH) + 10
colors = terrain(np.linspace(0, 1.8, nbcolors))
nbcolors = len(reef.core.layTime) + 3
colors2 = plasma(np.linspace(0, 1, nbcolors))
reef.plot.drawCore(lwidth=3,
colsed=colors,
coltime=colors2,
size=(9, 8),
font=8,
dpi=300)
output_core = reef.plot.core_timetodepth(
self.communities, self.core_depths) #modelPlot.py
# predicted_core = reef.convert_core(self.communities, output_core, self.core_depths) #model.py
# return predicted_core
print('output_core_shape', output_core.shape)
return output_core
def show_multi_output_mpl(df):
register_matplotlib_converters()
cols_list = []
for column in df.columns:
if 'raw' in column or 'treated' in column:
cols_list.append(column)
fig, axes = plt.subplots(figsize=(20, 10),
nrows=len(cols_list) + 1,
ncols=1)
plt.rc('lines', linewidth=0.5)
color = iter(cm.plasma(np.linspace(0.05, 0.8, len(cols_list) + 1)))
fig.subplots_adjust(hspace=0.5)
fig.suptitle('Output of multivariate filter')
axes_array = np.array(axes).flatten()
for ax, feature in zip(axes_array, cols_list):
ax.plot(df.index, df[feature], c=next(color))
ax.set(ylabel=feature.split(' ')[0].upper())
ax.tick_params(axis='x', which='both', bottom=False, labelbottom=False)
ax = axes_array[-1]
ax.plot(df.index, df['fault_count'], c='k')
ax.set(ylabel='fault count', xlabel='Date')
ax.set_xticklabels(df.index, rotation=45)
ax.xaxis.set_major_locator(mdates.MonthLocator())
ax.xaxis.set_major_formatter(mdates.DateFormatter('%b %y'))
plt.show()
def solve(self):
gui = ti.GUI('lbm solver', (self.nx, 2 * self.ny))
self.init()
for i in range(self.steps):
self.collide_and_stream()
self.update_macro_var()
self.apply_bc()
## code fragment displaying vorticity is contributed by woclass
vel = self.vel.to_numpy()
ugrad = np.gradient(vel[:, :, 0])
vgrad = np.gradient(vel[:, :, 1])
vor = ugrad[1] - vgrad[0]
vel_mag = (vel[:, :, 0]**2.0 + vel[:, :, 1]**2.0)**0.5
## color map
colors = [(1, 1, 0), (0.953, 0.490, 0.016), (0, 0, 0),
(0.176, 0.976, 0.529), (0, 1, 1)]
my_cmap = matplotlib.colors.LinearSegmentedColormap.from_list(
'my_cmap', colors)
vor_img = cm.ScalarMappable(norm=matplotlib.colors.Normalize(
vmin=-0.02, vmax=0.02),
cmap=my_cmap).to_rgba(vor)
vel_img = cm.plasma(vel_mag / 0.15)
img = np.concatenate((vor_img, vel_img), axis=1)
gui.set_image(img)
gui.show()
if (i % 1000 == 0):
print('Step: {:}'.format(i))
def show_pca_mpl(df, limits):
fig, ax = plt.subplots(figsize=(10, 10), nrows=1, ncols=1)
plt.rc('lines', linewidth=1)
color = iter(cm.plasma(np.linspace(0, 1, 4)))
start = limits['start_cal']
end = limits['end_cal']
ax.plot(df['pc_1'], df['pc_2'], 'o', markersize=0.5, c=next(color))
ax.plot(df['pc_1'].loc[start:end],
df['pc_2'].loc[start:end],
'o',
markersize=0.5,
c=next(color))
ax.set(ylabel='PC 2',
xlabel='PC 1',
title='Principal components of calibration and complete data sets')
# ### drawing the ellipse
ellipse_a = np.sqrt(limits['T2']) * limits['pc_std'][0]
ellipse_b = np.sqrt(limits['T2']) * limits['pc_std'][1]
t = np.linspace(0, 2 * np.pi, 100)
ax.plot(ellipse_a * np.cos(t), ellipse_b * np.sin(t), c=next(color))
ax.grid(which='major', axis='both')
ax.legend(['complete', 'calibration', 'limit {}'.format(limits['alpha'])])
plt.gca().set_aspect('equal')
plt.show()
def solve(self):
gui = ti.GUI('lbm solver', (self.nx, self.ny * 2))
self.init()
for i in range(self.steps):
self.collide_and_stream()
self.update_macro_var()
self.apply_bc()
self.get_display_var()
## vor
vel = self.vel.to_numpy()
ugrad = np.gradient(vel[:, :, 0])
vgrad = np.gradient(vel[:, :, 1])
du_dy = ugrad[1]
dv_dx = vgrad[0]
## vor = dv/dx - du/dy
vor = dv_dx - du_dy
## 颜色映射
colors = [(1, 1, 0), (0.953, 0.490, 0.016), (0, 0, 0),
(0.176, 0.976, 0.529), (0, 1, 1)]
my_cmap = matplotlib.colors.LinearSegmentedColormap.from_list(
'my_cmap', colors)
vor_img = cm.ScalarMappable(cmap=my_cmap).to_rgba(vor)
vel_img = cm.plasma(self.display_var.to_numpy() / 0.15)
# numpy 的 y 方向貌似和 taichi 相反
img = np.concatenate((vor_img, vel_img), axis=1)
gui.set_image(img)
# gui.show()
gui.show(f'frame/{i:04d}.png')
if (i % 1000 == 0):
print('Step: {:}'.format(i))
def blocked_feature_decay(decay, blocks, dists, gene_names, i_max, atype,
featuretype, plot):
"""
Block averaging of an input vector.
IN:
decay[2,n_samples] = array to block average (decay[0,:]=x-Axis, decay[1,:]=y-Axis)
blocks = Number of blocks to block average the input vector
For plotting:atype (0-noc) archetype to which the task decays
featuretype(0-m_tasks) decay of feature under consideration
OUT:
blockvec[blocks] = block averaged input vector y-Axis elements
blocktt[blocks] = x-Axis elements according to blockvec
error = statistical error in every block
sigmaB
bdata = number of elements compressed in every block
"""
blockvec, blocktt, error, sigmaB, bdata = blocking(decay[0, :],
decay[1, :],
blocks=blocks)
if (plot == True):
n_a = np.shape(dists)[0]
name = gene_names.iloc[i_max[atype, featuretype]]
archColors = cm.plasma(np.arange(n_a).astype(float) / (n_a))
plt.figure()
plt.plot(blocktt, blockvec, '-*', c=archColors[atype, :])
plt.suptitle(f"Blocked decay with respect to distance of A{atype}",
fontsize=14)
plt.title(f"{name}", fontsize=8)
plt.xlabel(f"Normalized distance of samples to A{atype}", fontsize=14)
plt.ylabel(f"Amount in samples", fontsize=14)
plt.show()
return blockvec, blocktt, error, sigmaB, bdata
def __init__(self,
board_size: int,
num_players: int,
window_size: Tuple[int, int] = (600, 600),
outside_border: int = 25,
grid_space_ratio: float = 6,
winner_player: int = None):
self.board_size = board_size
self.window_size = window_size
self.outside_border = outside_border
self.grid_space_ratio = grid_space_ratio
self.winner_player = winner_player
if winner_player is not None:
self.other_players = (np.arange(num_players - 1) + winner_player +
1) % num_players
self.colors = cm.plasma(np.linspace(0.1, 0.9, num_players))
self.colors = np.minimum(self.colors * 1.3, 1.0)
# Rendering Objects
self.viewer = None
self.grid = None
self.flat_grid = None
self.background = None
def add_multi_attention_plots(writer, tag, attention_weights, global_step):
attns = [attn[0].numpy() for attn in attention_weights]
for i, attn in enumerate(attns):
img = pack_attention_images(attn)
writer.add_image(f"{tag}/{i}",
cm.plasma(img),
global_step=global_step,
dataformats="HWC")
def animate(i):
plt.title(str("%0.2f" % (24 * i / 2880)))
lon = lons[i]
lat = lats[i]
val = values[i]
scatter.set_offsets(numpy.array(globe(lon, lat)).T)
scatter.set_color(cm.plasma(numpy.array(val) / 8))
def twoDimRepr(exp_id, model_id, start_epoch, paramPlot, plotRange):
''' Plot parameters trajectory across training epochs of a model.
The trajectories are ploted using t-sne and PCA representation
Args:
exp_id (str): the experience name
model_id (str): the model id
start_epoch (int): the epoch at which to start the plot
paramPlot (list): the parameters to plot (can be \'trueScores\', \'bias\', \'incons\' or \'diffs\'.)
plotRange (list): the axis limits to use. It should be a list of values like this (xMin,xMax,yMin,yMax).
'''
def getEpoch(path):
return findNumbers(
os.path.basename(path).replace("model{}".format(model_id), ""))
cleanNamesDict = {
"trueScores": "True Scores",
"bias": "Biases",
"diffs": "Ambiguities",
"incons": "Inconsistencies"
}
for key in paramPlot:
paramFiles = sorted(glob.glob(
"../results/{}/model{}_epoch*_{}.csv".format(
exp_id, model_id, key)),
key=findNumbers)
paramFiles = list(
filter(lambda x: getEpoch(x) > start_epoch, paramFiles))
colors = cm.plasma(np.linspace(0, 1, len(paramFiles)))
params = list(map(lambda x: np.genfromtxt(x)[:, 0], paramFiles))
repr_tsne = TSNE(n_components=2,
init='pca',
random_state=1,
learning_rate=20).fit_transform(params)
repr_pca = PCA(n_components=2).fit_transform(params)
plt.figure()
plt.title("model " + str(model_id) + " : " + cleanNamesDict[key])
plt.scatter(repr_tsne[:, 0], repr_tsne[:, 1], color=colors, zorder=2)
plt.savefig("../vis/{}/model{}_{}_tsne.png".format(
exp_id, model_id, key))
plt.figure()
plt.xlabel("First principal component")
plt.ylabel("Second principal component")
plt.title("model " + str(model_id) + " : " + cleanNamesDict[key])
plt.scatter(repr_pca[:, 0], repr_pca[:, 1], color=colors, zorder=2)
if plotRange:
plt.xlim(plotRange[0], plotRange[1])
plt.ylim(plotRange[2], plotRange[3])
plt.savefig("../vis/{}/model{}_{}_pca.png".format(
exp_id, model_id, key))
def plotArch(red_data, XC, noc):
"""
Visualize the position of archetypes and sample points in 3PC- projection
Note: For noc > 5 the verts_list(XC) function might has to be updated
in: 1. red_data[i,j]; i = samples, j = principle components (coordinates)
2. XC = output of PCHA Position of Archetypes
3. Number of components >= 6
"""
n_archetypes = np.shape(XC)[1]
dim = np.shape(XC)[0]
archColors = cm.plasma(
np.arange(n_archetypes).astype(float) / (n_archetypes))
if dim == 3:
verts = verts_list(XC)
srf = Poly3DCollection(verts, alpha=.25, facecolor='#800000')
fig = plt.figure()
#if np.shape(red_data)[1] == 3:
ax = fig.add_subplot(111, projection='3d')
ax.scatter(red_data[:, 0], red_data[:, 1], red_data[:, 2], c="k", s=5)
#ax.scatter(XC[0,:],XC[1,:],XC[2,:],c = "k",s=70)
for i in range(0, noc):
ax.scatter(XC[0, i],
XC[1, i],
XC[2, i],
s=70,
c=archColors[i, :],
label="A" + str(i))
ax.add_collection3d(srf)
ax.set_xlabel('1st pca component', fontsize=14)
ax.set_ylabel('2nd pca component', fontsize=14)
ax.set_zlabel('3rd pca component', fontsize=14)
ax.legend()
plt.tight_layout()
plt.show()
if dim == 2 and n_archetypes == 3:
verts = np.squeeze(np.asarray(verts_list(XC)))
verts = np.reshape(verts, (-1, 2))
verts = list(verts)
surf = plt.Polygon(XC.T, color='#800000', alpha=.25)
fig = plt.figure()
#if np.shape(red_data)[1] == 3:
ax = fig.add_subplot(111)
ax.scatter(red_data[:, 0], red_data[:, 1], c="k", s=5)
for i in range(0, noc):
ax.scatter(XC[0, i],
XC[1, i],
s=70,
c=archColors[i, :],
label="A" + str(i))
plt.gca().add_patch(surf)
ax.set_xlabel('1st pca component', fontsize=14)
ax.set_ylabel('2nd pca component', fontsize=14)
ax.legend()
plt.tight_layout()
plt.show()
def sradcmap():
# This function returns the colormap and bins for the PM spatial plots
# this is designed to have a vmin =0 and vmax = 140
# return cmap,bins
colors1 = cm.viridis(linspace(0, 1, 128))
colors2 = cm.plasma(linspace(.2, 1, 128))
colors = vstack((colors1, colors2))
return mcolors.LinearSegmentedColormap.from_list('sradcmap',
colors), arange(
0, 1410., 10)
def color_within_01(vals):
# vals is Nx1 in [-1, 1] (but could be larger)
vals = np.clip(vals, -1, 1)
# make [0, 1]
vals = (vals + 1) / 2.
# Append dummy end vals for consistent coloring
weights = np.hstack([vals, np.array([0, 1])])
# Drop the dummy colors
colors = cm.plasma(weights)[:-2, :3]
return colors
def load_mydelta_and_strat(fname, accel):
if np.isclose(accel, 5.):
Q_in = Q_options[0]
elif np.isclose(accel, 10.):
Q_in = Q_options[1]
elif np.isclose(accel, 20.):
Q_in = Q_options[2]
else:
raise NameError
if np.isclose(accel, 20.):
len_drift = 400.
else:
len_drift = 600.
drift_up = np.arange(len_drift, dtype=float) / len_drift * (
accel * Uinit - Q_in[-1]) + Q_in[-1]
Q_real = np.concatenate((Uinit * np.ones(400), Q_in, drift_up))
Q_real *= flux_scaling
# ^does this need adjusting for dt?
# add the subsidence curve. Same idea
SL_rate = np.concatenate(
(Uinit * np.ones(400), accel * Uinit * np.ones(1200)))
SL_trajectory = np.cumsum(SL_rate)
# DO NOT multiply by dt. Let's just scale everything to dt = 1 for now.
# add an initial water depth if necessary here:
SL_trajectory += 0.1
# load it up
f = open(fname, 'rb')
mydelta = pickle.load(f)
f.close()
# do the plot
color = [item / Q_real.max() for item in Q_real]
for i in xrange(num_pres_strata):
plot(mydelta.radial_distances,
mydelta.strata[i, :],
c=cm.plasma(color[i]))
# pick the rollovers & add them to the fig:
for i in xrange(num_pres_strata):
# fit a (SF-ST) angle line to each point. rollover is point with
# largest intersect
# remove unmodified floor:
notfloor = np.where(
np.logical_not(np.isclose(mydelta.strata[i, :], 0.)))[0]
c = ((SF - ST) * mydelta.radial_distances[notfloor] +
mydelta.strata[i, notfloor])
diff = np.diff(c)
rollover_subindexes = np.where(
np.diff((diff < 0.).astype(int)) == 1)[0]
rollover_index = notfloor[rollover_subindexes]
plot(mydelta.radial_distances[rollover_index],
mydelta.strata[i, rollover_index], 'k,')
def gene_expr_A(A_gene_space,
gene_names,
percentile,
plot=False,
rows=2,
cols=2):
"""
Finding the maxima in gene expressions, i.e. where in the gene space
do we find maxima, if we look at the Archetypes
in: 1. A_gene_space[i,k]; i = number of archetype; k = gene space
2. Names of all the gene expressions
3. Percentile <=1; which percentile of the maximum is considered
4. Do you want to plot the histogram?
5.Number of rows in the figure
6.Number of columns in the figure
out: A_i_maxd[i,k]: For archetype i, which genes k are over represented
This matrix has zeros, to match dimensions!
"""
g_dim = np.shape(A_gene_space)[1]
n_A = np.shape(A_gene_space)[0]
i_max = np.zeros((n_A, 30))
A_i_max = np.zeros((n_A, 30))
A_i_names = [
] #Output the names of the corresponding attributes with gne_names
#Minus because we want the biggest first and argsort(.) is in ascending order
sorted_expressions = np.argsort(-A_gene_space, axis=1)
archColors = cm.plasma(np.arange(n_A).astype(float) / (n_A))
#Evaluate maxima
for i in range(0, n_A):
i_max = np.where(
A_gene_space[i, :] >= percentile * max(A_gene_space[i, :]))[0]
#Put maxima in a list
for k in range(0, len(i_max)):
A_i_max[i, k] = i_max[k]
non0 = A_i_max[i, np.nonzero(A_i_max[i, :])][0]
non0 = non0.astype(int)
for j in range(0, len(non0)):
gene_index = non0[j]
A_i_names = np.append(A_i_names,
(gene_names.iloc[gene_index], "\t"))
A_i_names = np.append(A_i_names, "\n")
if plot == True:
g_space = np.arange(0, g_dim)
fig = plt.figure()
for i in range(0, n_A):
non0 = A_i_max[i, np.nonzero(A_i_max[i, :])][0]
non0 = non0.astype(int)
ax = fig.add_subplot(rows, cols, i + 1)
ax.scatter(g_space, A_gene_space[i, :], c="k")
ax.scatter(non0, A_gene_space[i, non0], c=archColors[i, :])
ax.set_xlabel("Expression Spectrum")
ax.set_ylabel("Amount")
ax.set_title(f"Archetype {i}")
fig.tight_layout()
return (A_i_max.astype(int), A_i_names, sorted_expressions)
def feature_decay(gene_data_m,
gene_names,
dists,
i_max,
atype,
featuretype,
plot=False):
"""
Decay of a specific feature in the samples, that is maximally represented in the position
of the Archetype, with respect to the normalized distance to the Archetype.
In: 1. gene_data_m[i,j] matrix of gene data. i = samples; j = characteristics
2. gene_names[j] list of the gene names
3. dists is output of dist2A(.)- function, i.e. for each sample point the distance to respective archetype
4. i_max is output of gene_expr_A(.), i.e array of indices of maximally expressed gene characteristics of archetypes
5. atype = n = integer. Which archetype to look at (0,1,2,...)
6. featuretype = which of the maximized features to look at. Which of the indices m from i_max[n,m]
7. Do you want to plot? True
Out: decay[2,i]: A list of sample points where decay[1,i] are the distances to archetype n and decay[2,i] is the decay of the feature under investigation
"""
n_a = np.shape(dists)[0]
archColors = cm.plasma(np.arange(n_a).astype(float) / (n_a))
a_sorted = np.zeros_like(dists)
for i in range(0, n_a):
a_sorted[i, :] = np.argsort(dists[i, :])
a_sorted = a_sorted.astype(int)
featuredecay = gene_data_m[a_sorted[atype, :], i_max[atype, featuretype]]
featuredist = dists[atype, a_sorted[atype, :]]
name = gene_names.iloc[i_max[atype, featuretype]]
decay = np.concatenate((featuredist, featuredecay), axis=0)
decay = np.reshape(decay, (2, len(featuredecay)))
#print(f"Decay of gene feature {name} with respect to normalized distance from archetype {atype} is under consideration.")
if plot == True:
archColors = cm.plasma(np.arange(n_a).astype(float) / (n_a))
plt.figure()
plt.plot(featuredist, featuredecay, "*-", c=archColors[atype, :])
plt.suptitle(f"Decay with respect to distance of A{atype}",
fontsize=14)
plt.title(f"{name}", fontsize=8)
plt.xlabel(f"Normalized distance of samples to A{atype}", fontsize=14)
plt.ylabel(f"Amount task/gene in samples", fontsize=14)
plt.show()
return (decay)
def index():
df = pd.read_csv('300_5000.csv')
lst1 = df['7'].abs()
df = pd.read_csv('300_5000.csv')
lst2 = df['8']
df = pd.read_csv('300_5000.csv')
lst3 = df['9']
fig = plt.figure
fig, ax = plt.subplots()
ax.set_xlim(lst2.min(), lst2.max() + 0.8)
ims = []
for i, n, g in zip(lst3, lst1, lst2):
x1 = 3
y1 = i
x2 = 1
y2 = n
x3 = 2
y3 = g
im3 = plt.barh(x3, y3, color=cm.plasma(g / lst1.max()))
im2 = plt.barh(x2, y2, color=cm.plasma(n / lst1.max()))
im = plt.barh(x1, y1, color=cm.plasma(i / lst1.max()))
ims.append(im3 + im2 + im)
plt.title("D")
anim = animation.ArtistAnimation(fig, ims)
FPS = 30
anim.save('static/img/anim' + str(FPS) + '.gif',
writer="imagemagick",
fps=FPS)
return render_template("index.html",
image='static/img/anim' + str(FPS) + '.gif')
def decode_confidence_map_sequence(confidence_maps):
conf_maps = []
confidence_maps = confidence_maps.transpose([0, 2, 3, 1])
for conf in confidence_maps:
conf = conf.reshape(conf.shape[0], conf.shape[1])
colored_image = cm.plasma(conf)
colored_image = Image.fromarray(
(colored_image[:, :, :3] * 255).astype(np.uint8))
conf_maps.append(np.array(colored_image))
conf_maps = torch.from_numpy(np.array(conf_maps).transpose([0, 3, 1, 2]))
return conf_maps
#!/usr/bin/env python2
# -*- coding: utf-8 -*-
"""
Created on Mon Feb 5 20:47:15 2018
@author: reini
"""
from __future__ import print_function
from matplotlib import cm
import numpy as np
def rgb_hex565(red, green, blue):
# take in the red, green and blue values (0-255) as 8 bit values and then combine
# and shift them to make them a 16 bit hex value in 565 format.
print ("0x%0.4X," % ((int(red * 31) << 11) | (int(green * 63) << 5) | (int(blue * 31))),end='')
rgb = cm.plasma(np.arange(256))
for i in np.arange(rgb.shape[0]):
rgb_hex565(rgb[i][0],rgb[i][1],rgb[i][2])
def main():
dirname = os.path.basename(os.getcwd())
config_file = parse_input()
config = loadconfig(config_file)
sdf_handles = []
sdf_files = config['sdf_files']
if type(sdf_files) is not type([]):
sdf_files = [sdf_files,]
for sdf_file in sdf_files:
try:
sdf_data = sdf.read(sdf_file)
except:
print("Warning: Failed to open '{}'".format(sdf_file))
else:
sdf_handles.append(sdf_data)
if len(sdf_handles) < 1:
print("Error: Unable to open any sdf files")
print("Exiting....")
return(-1)
#load sdf data (needs to be done before we can sanity check input)
sdf_e_px = getattr_from_any(sdf_handles, 'Particles_Px_electron').data
sdf_e_x = getattr_from_any(sdf_handles, 'Grid_Particles_electron').data[0]
sdf_e_y = getattr_from_any(sdf_handles, 'Grid_Particles_electron').data[1]
sdf_e_w = getattr_from_any(sdf_handles, 'Particles_Weight_electron').data
sdf_gridx = getattr_from_any(sdf_handles, 'Grid_Grid').data[0]
sdf_gridy = getattr_from_any(sdf_handles, 'Grid_Grid').data[1]
sdf_dens = getattr_from_any(sdf_handles, 'Derived_Number_Density_electron').data
try:
sdf_gridz = getattr_from_any(sdf_handles, 'Grid_Grid').data[2]
sdf_e_z = getattr_from_any(sdf_handles, 'Grid_Particles_electron').data[2]
is3d = True
except:
is3d = False
grids = {'xgrid':None
,'ygrid':None
,'zgrid':None
,'xbins':None
,'ybins':None
,'zbins':None}
for grid in grids:
try:
grids[grid] = float(config[grid])
except:
pass
if ((grids['xgrid'] is not None and grids['xbins'] is not None) or
(grids['ygrid'] is not None and grids['ybins'] is not None) or
(grids['zgrid'] is not None and grids['zbins'] is not None)):
print("Both gridsize and numbins are specified... "
"gridsize will take precedence")
if ((grids['xgrid'] is None and grids['xbins'] is None) or
(grids['ygrid'] is None and grids['ybins'] is None)):
print("Warning no gridsize or numbins specified, defaulting to "
"100 bins")
if grids['xbins'] is None:
grids['xbins'] = 100
if grids['ybins'] is None:
grids['ybins'] = 100
if is3d and (grids['zgrid'] is None and grids['zbins'] is None):
print("Warning no gridsize or numbins specified, defaulting to "
"100 bins")
grids['zbins'] = 100
try:
output_name = config['output_name']
except:
output_name = 'out'
try:
output_path = config['output_path']
except:
output_path = '.'
try:
pub_xmin = float(config['pub_xmin'])*1e6
except:
pub_xmin = None
try:
pub_xmax = float(config['pub_xmax'])*1e6
except:
pub_xmax = None
try:
pub_ymin = float(config['pub_ymin'])
except:
pub_ymin = None
try:
pub_ymax = float(config['pub_ymax'])
except:
pub_ymax = None
reset_origin = False
if 'reset_origin' in config:
if not 'false'.startswith(config['reset_origin'].lower()):
reset_origin = True
lineout_inset = False
if 'lineout_inset' in config:
if not 'false'.startswith(config['lineout_inset'].lower()):
lineout_inset = True
try:
lineout_xmin = float(config['lineout_xmin'])*1e6
except:
lineout_xmin = None
try:
lineout_xmax = float(config['lineout_xmax'])*1e6
except:
lineout_xmax = None
try:
lineout_ymin = float(config['lineout_ymin'])
except:
lineout_ymin = None
try:
lineout_ymax = float(config['lineout_ymax'])
except:
lineout_ymax = None
cutoff_px = float(config['cutoff_px']) * sc.m_e * sc.c
extents = {'xmin':sdf_e_x.min()
,'xmax':sdf_e_x.max()
,'ymin':sdf_e_y.min()
,'ymax':sdf_e_y.max()}
if is3d:
extents['zmin'] = sdf_e_z.min()
extents['zmax'] = sdf_e_z.max()
#parse in spatial limits and sanity check
limits = {}
for extent in extents:
try:
limits[extent] = float(config[extent])
except:
limits[extent] = extents[extent]
if limits['xmax'] < limits['xmin']:
limits['xmin'], limits['xmax'] = limits['xmax'], limits['xmin']
if limits['ymax'] < limits['ymin']:
limits['ymin'], limits['ymax'] = limits['ymax'], limits['ymin']
if is3d:
if limits['zmax'] < limits['zmin']:
limits['zmin'], limits['zmax'] = limits['zmax'], limits['zmin']
for extent in limits:
if extent.endswith('max'):
if limits[extent] > extents[extent]:
limits[extent] = extents[extent]
print("Warning {} out of range, ignoring".format(extent))
else:
if limits[extent] < extents[extent]:
limits[extent] = extents[extent]
print("Warning {} out of range, ignoring".format(extent))
#parse in ellipse parameters and sanity check
ellipse_sane = False
ell = {'centerx':None, 'radx':None,
'centery':0.0, 'rady':None}
if is3d:
ell['centerz'] = 0.0
ell['radz'] = None
for arg in ell:
try:
ell[arg] = float(config['ell_{}'.format(arg)])
except:
pass
if None not in ell.values():
ellipse_sane = True
if ((ell['centerx'] + ell['radx'] < limits['xmin'])
or (ell['centerx'] - ell['radx'] > limits['xmax'])
or (ell['centery'] + ell['rady'] < limits['ymin'])
or (ell['centery'] - ell['rady'] > limits['ymax'])):
print("Error, ellipse is entirely outside of view window")
return(-1)
if ((ell['centerx'] - ell['radx'] < limits['xmin'])
or (ell['centerx'] + ell['radx'] > limits['xmax'])
or (ell['centery'] - ell['rady'] < limits['ymin'])
or (ell['centery'] + ell['rady'] > limits['ymax'])):
print("Warning, ellipse is clipped by view window")
if is3d:
if ((ell['centerz'] + ell['radz'] < limits['zmin'])
or (ell['centerz'] - ell['radz'] > limits['zmax'])):
print("Error, ellipse is entirely outside of view window")
return(-1)
if ((ell['centerz'] - ell['radz'] < limits['zmin'])
or (ell['centerz'] + ell['radz'] > limits['zmax'])):
print("Warning, ellipse is clipped by view window")
#trim grid data to specfied limits
xargmin = np.argmin(np.abs(sdf_gridx - limits['xmin']))
xargmax = np.argmin(np.abs(sdf_gridx - limits['xmax']))
yargmin = np.argmin(np.abs(sdf_gridy - limits['ymin']))
yargmax = np.argmin(np.abs(sdf_gridy - limits['ymax']))
if is3d:
zargmin = np.argmin(np.abs(sdf_gridz - limits['zmin']))
zargmax = np.argmin(np.abs(sdf_gridz - limits['zmax']))
sdf_gridx = sdf_gridx[xargmin:xargmax]
sdf_gridy = sdf_gridy[yargmin:yargmax]
sdf_dens = sdf_dens[xargmin:xargmax,yargmin:yargmax]
if is3d:
sdf_gridz = sdf_gridz[zargmin:zargmax]
sdf_dens = sdf_dens[:,:,zargmin:zargmax]
#take on axis density slice for plotting
if is3d:
plot_dens_xy = sdf_dens[:,:,int(0.5*sdf_dens.shape[2])]
plot_dens_xz = sdf_dens[:,int(0.5*sdf_dens.shape[1]),:]
else:
plot_dens_xy = sdf_dens
### Electron selection magic happens here
energy_mask = sdf_e_px > cutoff_px
position_mask = np.full(sdf_e_px.shape, True, dtype=bool)
if ellipse_sane:
if is3d:
position_mask = (
((sdf_e_x - ell['centerx'])**2 / (ell['radx']**2)) +
((sdf_e_y - ell['centery'])**2 / (ell['rady']**2)) +
((sdf_e_z - ell['centerz'])**2 / (ell['radz']**2)) < 1 )
else:
position_mask = (
((sdf_e_x - ell['centerx'])**2 / (ell['radx']**2)) +
((sdf_e_y - ell['centery'])**2 / (ell['rady']**2)) < 1 )
bunch_electron_mask = np.where(np.logical_and(energy_mask,
position_mask))
bunch_electron_x = sdf_e_x[bunch_electron_mask].reshape(-1)
bunch_electron_y = sdf_e_y[bunch_electron_mask].reshape(-1)
bunch_electron_w = sdf_e_w[bunch_electron_mask].reshape(-1)
if is3d:
bunch_electron_z = sdf_e_z[bunch_electron_mask].reshape(-1)
print("Found {} particles meeting criteria".format(len(bunch_electron_w)))
### Histogram Grid creation ###
if grids['xgrid'] is not None:
xbins = np.arange(limits['xmin'],limits['xmax']+grids['xgrid'],grids['xgrid'])
else:
xbins = np.linspace(limits['xmin'],limits['xmax'],grids['xbins'])
if grids['ygrid'] is not None:
if limits['ymin'] * limits['ymax'] < 0:
ybins = np.sort(np.concatenate((
np.arange(0,limits['ymin']-grids['ygrid'],-grids['ygrid']),
np.arange(grids['ymin'],limits['ymax']+grids['ygrid'],grids['ygrid']))))
else:
ybins = np.arange(limits['ymin'],limits['ymax']+grids['ygrid'],grids['ygrid'])
else:
if limits['ymin'] * limits['ymax'] < 0:
ybins = np.sort(np.concatenate((
np.linspace(limits['ymin'],0,grids['ybins']//2),
np.linspace(0,limits['ymax'],grids['ybins']//2)[1:])))
else:
ybins = np.linspace(limits['ymin'],limits['ymax'],grids['ybins'])
if is3d:
if grids['zgrid'] is not None:
if limits['zmin'] * limits['zmax'] < 0:
zbins = np.sort(np.concatenate((
np.arange(0,limits['zmin']-grids['zgrid'],-grids['zgrid']),
np.arange(grids['zmin'],limits['zmax']+grids['zgrid'],grids['zgrid']))))
else:
zbins = np.arange(limits['zmin'],limits['zmax']+grids['zgrid'],grids['zgrid'])
else:
if limits['zmin'] * limits['zmax'] < 0:
zbins = np.sort(np.concatenate((
np.linspace(limits['zmin'],0,grids['zbins']//2),
np.linspace(0,limits['zmax'],grids['zbins']//2)[1:])))
else:
zbins = np.linspace(limits['zmin'],limits['zmax'],grids['ybins'])
display_limits = [ limits[l]*1e6 for l in ['xmin','xmax','ymin','ymax'] ]
### Histogram Creation ###
if is3d:
pos_data_3d = np.column_stack([bunch_electron_x
,bunch_electron_y
,bunch_electron_z])
counts3d, histedges = np.histogramdd(pos_data_3d
,bins=[xbins,ybins,zbins]
,weights=bunch_electron_w)
vols3d = np.einsum('i,j,k',*[np.diff(a) for a in histedges])
hist_dens3d = counts3d / vols3d
counts2d_xy = np.sum(counts3d, axis=2)
counts2d_xz = np.sum(counts3d, axis=1)
areas2d_xz = np.outer(np.diff(histedges[0]),np.diff(histedges[2]))
hist_dens2d_xz = counts2d_xz / areas2d_xz
counts1d_z = np.sum(counts3d, axis=(0,1))
print("max(hist_dens3d): {}".format(hist_dens3d.max()))
else:
pos_data_2d = np.column_stack([bunch_electron_x
,bunch_electron_y])
counts2d_xy, histedges = np.histogramdd(pos_data_2d
,bins=[xbins,ybins]
,weights=bunch_electron_w)
areas2d_xy = np.outer(np.diff(histedges[0]),np.diff(histedges[1]))
hist_dens2d_xy = counts2d_xy / areas2d_xy
counts1d_x = np.sum(counts2d_xy,axis=1)
counts1d_y = np.sum(counts2d_xy,axis=0)
print("max(hist_dens2d): {}".format(hist_dens2d_xy.max()))
print("max(sdf_dens): {}".format(sdf_dens.max()))
### Statistical Calculations
fwnm_lim = 100
bin_w_x = np.diff(histedges[0])
bin_ctr_x = histedges[0][:-1] + bin_w_x
bin_w_y = np.diff(histedges[1])
bin_ctr_y = histedges[1][:-1] + bin_w_y
if is3d:
bin_w_z = np.diff(histedges[2])
bin_ctr_z = histedges[2][:-1] + bin_w_z
nx_rms = bin_ctr_x[np.where(counts1d_x > counts1d_x.max()/np.e)]
nx_fwhm = bin_ctr_x[np.where(counts1d_x > counts1d_x.max()/2)]
nx_fwnm = bin_ctr_x[np.where(counts1d_x > counts1d_x.max()/fwnm_lim)]
rms_x = nx_rms.max() - nx_rms.min()
fwhm_x = nx_fwhm.max() - nx_fwhm.min()
fwnm_x = nx_fwnm.max() - nx_fwnm.min()
x_avg = np.average(bunch_electron_x, weights=bunch_electron_w)
x_vari = np.average((bunch_electron_x - x_avg)**2, weights=bunch_electron_w)
x_stdev = np.sqrt(x_vari)
print("X-avg: {}".format(x_avg))
print("Bunch RMS(x): {}".format(rms_x))
print("Bunch FWHM(x): {}".format(fwhm_x))
print("Bunch FW{}M(x): {}".format(fwnm_lim,fwnm_x))
print("Bunch pos stdev(x): {}".format(x_stdev))
print()
ny_rms = bin_ctr_y[np.where(counts1d_y > counts1d_y.max()/np.e)]
ny_fwhm = bin_ctr_y[np.where(counts1d_y > counts1d_y.max()/2)]
ny_fwnm = bin_ctr_y[np.where(counts1d_y > counts1d_y.max()/fwnm_lim)]
rms_y = ny_rms.max() - ny_rms.min()
fwhm_y = ny_fwhm.max() - ny_fwhm.min()
fwnm_y = ny_fwnm.max() - ny_fwnm.min()
y_avg = np.average(bunch_electron_y, weights=bunch_electron_w)
y_vari = np.average((bunch_electron_y - y_avg)**2, weights=bunch_electron_w)
y_stdev = np.sqrt(y_vari)
print("Bunch RMS(y): {}".format(rms_y))
print("Bunch FWHM(y): {}".format(fwhm_y))
print("Bunch FW{}M(y): {}".format(fwnm_lim,fwnm_y))
print("Bunch pos stdev(y): {}".format(y_stdev))
print()
if is3d:
nz_rms = bin_ctr_z[np.where(counts1d_z > counts1d_z.max()/np.e)]
nz_fwhm = bin_ctr_z[np.where(counts1d_z > counts1d_z.max()/2)]
nz_fwnm = bin_ctr_z[np.where(counts1d_z > counts1d_z.max()/fwnm_lim)]
rms_z = nz_rms.max() - nz_rms.min()
fwhm_z = nz_fwhm.max() - nz_fwhm.min()
fwnm_z = nz_fwnm.max() - nz_fwnm.min()
z_avg = np.average(bunch_electron_z, weights=bunch_electron_w)
z_vari = np.average((bunch_electron_z - z_avg)**2, weights=bunch_electron_w)
z_stdev = np.sqrt(z_vari)
print("Bunch RMS(z): {}".format(rms_z))
print("Bunch FWHM(z): {}".format(fwhm_z))
print("Bunch FW{}M(z): {}".format(fwnm_lim,fwnm_z))
print("Bunch pos stdev(z): {}".format(z_stdev))
print()
if not is3d:
unscaled_charge = np.sum(counts2d_xy)*sc.e
print("Unscaled charge: {}".format(unscaled_charge))
xm, ym, = np.meshgrid(bin_ctr_x, bin_ctr_y, indexing='ij')
bunch_charge_rad = np.sum(np.abs(ym)*counts2d_xy)*np.pi*sc.e
bunch_charge_dep = unscaled_charge*fwnm_y
print("Total charge(rad): {:03g}pc".format(bunch_charge_rad*1e12))
print("Total charge(depth): {:03g}pc".format(bunch_charge_dep*1e12))
else:
unscaled_charge = np.sum(counts3d)*sc.e
print("Total charge: {:03g}pc".format(unscaled_charge*1e12))
### Debug Plot ####
fig = mf.Figure(figsize=(12,12))
canvas = mplbea.FigureCanvasAgg(fig)
ax1 = fig.add_subplot(331)
ax1.imshow(plot_dens_xy.T
,aspect='auto'
,extent=display_limits
,origin='upper'
,norm=mc.LogNorm(1e23,1e26)
,cmap=mcm.plasma)
ax1.xaxis.set_major_locator(mt.LinearLocator(5))
if None not in ell.values():
ax1.add_patch(mpat.Ellipse((ell['centerx']*1e6,ell['centery']*1e6)
,2*ell['radx']*1e6
,2*ell['rady']*1e6
,fill=True
,fc='blue'
,alpha=0.2))
if is3d:
ax2 = fig.add_subplot(334)
ax2.imshow(plot_dens_xz.T
,aspect='auto'
,extent=display_limits
,origin='upper'
,norm=mc.LogNorm(1e23,1e26)
,cmap=mcm.plasma)
ax2.xaxis.set_major_locator(mt.LinearLocator(5))
if None not in ell.values():
ax2.add_patch(mpat.Ellipse((ell['centerx']*1e6,ell['centery']*1e6)
,2*ell['radx']*1e6
,2*ell['radz']*1e6
,fill=True
,fc='blue'
,alpha=0.2))
ax3 = fig.add_subplot(332)
ax3.imshow(hist_dens2d_xy.T
,aspect='auto'
,extent=display_limits
,origin='upper'
,norm=mc.LogNorm(np.ma.masked_equal(hist_dens2d_xy,0,copy=False).min()
,np.ma.masked_equal(hist_dens2d_xy,0,copy=False).max())
,cmap=mcm.plasma)
ax3.xaxis.set_major_locator(mt.LinearLocator(5))
if is3d:
ax4 = fig.add_subplot(335)
ax4.imshow(hist_dens2d_xz.T
,aspect='auto'
,extent=display_limits
,origin='upper'
,norm=mc.LogNorm(np.ma.masked_equal(hist_dens2d_xz,0,copy=False).min()
,np.ma.masked_equal(hist_dens2d_xz,0,copy=False).max())
,cmap=mcm.plasma)
ax4.xaxis.set_major_locator(mt.LinearLocator(5))
# Charge x-distribution
ax5 = fig.add_subplot(337)
bars = ax5.bar(bin_ctr_x*1e6
,counts1d_x
,width=bin_w_x*1e6
,linewidth=0
)
mask_count = np.ma.masked_equal(counts1d_x, 0, copy=False)
norm = mc.Normalize(mask_count.min(),mask_count.max())
for i,patch in enumerate(bars.patches):
if counts1d_x[i] > 0:
patch.set_facecolor(mcm.plasma(norm(counts1d_x[i])))
#Indicate extents of bunch measurements
ax5.axvline(nx_rms.min()*1e6,alpha=0.5, color='red')
ax5.axvline(nx_rms.max()*1e6,alpha=0.5, color='red')
ax5.axvline(nx_fwhm.min()*1e6,alpha=0.5, color='green')
ax5.axvline(nx_fwhm.max()*1e6,alpha=0.5, color='green')
ax5.axvline(nx_fwnm.min()*1e6,alpha=0.5, color='blue')
ax5.axvline(nx_fwnm.max()*1e6,alpha=0.5, color='blue')
#naive attempt to autoscale
delta = 0.1*(nx_fwnm.max() - nx_fwnm.min())
ax5.set_xlim((nx_fwnm.min()-delta)*1e6
,(nx_fwnm.max()+delta)*1e6)
ax5.set_xlabel(r'$z\ \mathrm{(\mu m)}$')
ax5.set_ylabel(r'$\mathrm{d}Q\ \mathrm{(C m^{-3})}$')
ax5.xaxis.set_major_locator(mt.MaxNLocator(5))
#Charge y_distribution
ax6 = fig.add_subplot(333)
bars = ax6.bar(bin_ctr_y*1e6
,counts1d_y
,width=bin_w_y*1e6
,linewidth=0
)
norm = mc.Normalize(counts1d_y.min(),counts1d_y.max())
for i,patch in enumerate(bars.patches):
if counts1d_y[i] > 0:
patch.set_facecolor(mcm.plasma(norm(counts1d_y[i])))
#Indicate extents of bunch measurements
ax6.axvline(ny_rms.min()*1e6,alpha=0.5, color='red')
ax6.axvline(ny_rms.max()*1e6,alpha=0.5, color='red')
ax6.axvline(ny_fwhm.min()*1e6,alpha=0.5, color='green')
ax6.axvline(ny_fwhm.max()*1e6,alpha=0.5, color='green')
ax6.axvline(ny_fwnm.min()*1e6,alpha=0.5, color='blue')
ax6.axvline(ny_fwnm.max()*1e6,alpha=0.5, color='blue')
#naive attempt to autoscale
delta = 0.1*(ny_fwnm.max() - ny_fwnm.min())
ax6.set_xlim((ny_fwnm.min()-delta)*1e6
,(ny_fwnm.max()+delta)*1e6)
ax6.set_xlabel(r'$z\ \mathrm{(\mu m)}$')
ax6.set_ylabel(r'$\mathrm{d}Q\ \mathrm{(C m^{-3})}$')
#z-density distribution
if is3d:
ax7 = fig.add_subplot(336)
bars = ax7.bar(bin_ctr_z*1e6
,counts1d_z
,width=bin_w_z*1e6
,linewidth=0
)
norm = mc.Normalize(counts1d_z.min(),counts1d_z.max())
for i,patch in enumerate(bars.patches):
if counts1d_z[i] > 0:
patch.set_facecolor(mcm.plasma(norm(counts1d_z[i])))
#Indicate extents of bunch measurements
ax7.axvline(nz_rms.min()*1e6,alpha=0.5, color='red')
ax7.axvline(nz_rms.max()*1e6,alpha=0.5, color='red')
ax7.axvline(nz_fwhm.min()*1e6,alpha=0.5, color='green')
ax7.axvline(nz_fwhm.max()*1e6,alpha=0.5, color='green')
ax7.axvline(nz_fwnm.min()*1e6,alpha=0.5, color='blue')
ax7.axvline(nz_fwnm.max()*1e6,alpha=0.5, color='blue')
#naive attempt to autoscale
delta = 0.1*(nz_fwnm.max() - nz_fwnm.min())
ax7.set_xlim((nz_fwnm.min()-delta)*1e6
,(nz_fwnm.max()+delta)*1e6)
ax7.set_xlabel(r'$z\ \mathrm{(\mu m)}$')
ax7.set_ylabel(r'$\mathrm{d}Q\ \mathrm{(C m^{-3})}$')
#Finally print all the numerical results
ax8 = fig.add_subplot(338)
ax8.axis('off')
# Bunch Charge
if is3d:
props_string = r'\noindent$Q = {:.3}\ \mathrm{{pC}}$\\ \\'.format(unscaled_charge*1e12)
else:
props_string = ''.join(
[r'\noindent$dQ = {:.3}\ \mathrm{{\mu C/m}}$\\'.format(unscaled_charge*1e6)
,r'$Q_w = {:.3}\ \mathrm{{pC}}$\\'.format(bunch_charge_dep*1e12)
,r'$Q_r = {:.3}\ \mathrm{{pC}}$\\ \\'.format(bunch_charge_rad*1e12)])
props_string += ''.join(
[r'$w_x(RMS) = {:.3}\ \mathrm{{\mu m}}$\\'.format(rms_x*1e6)
,r'$w_x(FWHM) = {:.3}\ \mathrm{{\mu m}}$\\'.format(fwhm_x*1e6)
,r'$w_x(FW{}M) = {:.3}\ \mathrm{{\mu m}}$\\'.format(fwnm_lim,fwnm_x*1e6)
,r'$\sigma_x = {:.3}\ \mathrm{{\mu m}}$\\ \\'.format(x_stdev*1e6)
,r'$w_y(RMS) = {:.3}\ \mathrm{{\mu m}}$\\'.format(rms_y*1e6)
,r'$w_y(FWHM) = {:.3}\ \mathrm{{\mu m}}$\\'.format(fwhm_y*1e6)
,r'$w_y(FW{}M) = {:.3}\ \mathrm{{\mu m}}$\\'.format(fwnm_lim,fwnm_y*1e6)
,r'$\sigma_y = {:.3}\ \mathrm{{\mu m}}$\\ \\'.format(y_stdev*1e6)])
if is3d:
props_string += ''.join(
[r'$w_z(RMS) = {:.3}\ \mathrm{{\mu m}}$\\'.format(rms_z*1e6)
,r'$w_z(FWHM) = {:.3}\ \mathrm{{\mu m}}$\\'.format(fwhm_z*1e6)
,r'$w_z(FW{}M) = {:.3}\ \mathrm{{\mu m}}$\\'.format(fwnm_lim,fwnm_z*1e6)
,r'$\sigma_z = {:.3}\ \mathrm{{\mu m}}$\\'.format(z_stdev*1e6)])
ax8.text(0,0.95
,props_string
,transform=ax8.transAxes
,verticalalignment='top'
)
fig.savefig('{}/{}_debug_fwhm.png'.format(output_path,output_name))
### Publication Plot
ax1loc=[0.09,0.15,0.37,0.625]
ax2loc=[0.59,0.15,0.37,0.625]
ax1cbloc=[0.09,0.8,0.37,0.05]
ax2cbloc=[0.59,0.8,0.37,0.05]
ax1norm=mc.LogNorm(1e23,1e26)
if reset_origin:
origin_offset = display_limits[0]
display_limits[0] = 0
display_limits[1] -= origin_offset
else:
origin_offset = 0
mpl.rcParams.update({'font.size': 8})
fig = mf.Figure(figsize=(3.2,2))
canvas = mplbea.FigureCanvasAgg(fig)
ax = fig.add_axes(ax1loc)
ax.imshow(plot_dens_xy.T
,aspect='auto'
,extent=display_limits
,origin='upper'
,norm=ax1norm
,cmap=mcm.plasma)
ax1cba = fig.add_axes(ax1cbloc)
ax1cb = mplcb.ColorbarBase(ax1cba
,cmap=mcm.plasma
,norm=ax1norm
,orientation='horizontal')
ax1cba.tick_params(top=True,labelbottom=False,labeltop=True,pad=-1)
ax1cb.set_ticks((ax1norm.vmin,ax1norm.vmax))
ax1cba.xaxis.set_label_position('top')
ax1cb.set_label(r"$n_e\ \mathrm{m^{-3}}$", labelpad=-4)
ax.xaxis.set_major_locator(mt.LinearLocator(3))
ax.yaxis.set_major_locator(mt.LinearLocator(3))
ax.set_xlabel(r'$z\ \mathrm{(\mu m)}$', labelpad=0)
ax.set_ylabel(r'$y \mathrm{(\mu m)}$', labelpad=-5)
ax2 = fig.add_axes(ax2loc)
counts, xbins, patches = ax2.hist(bunch_electron_x*1e6 - origin_offset
,bins=xbins*1e6 - origin_offset
,weights=bunch_electron_w*sc.e*1e12
,linewidth=0)
cnz = counts[np.nonzero(counts)]
pnz = np.asarray(patches)[np.nonzero(counts)]
try:
ax2nmax = float(config['pub_cmax'])
except:
ax2nmax = np.power(10,np.ceil(np.log10(cnz.max())))
try:
ax2nmin = float(config['pub_cmin'])
except:
ax2nmin = np.power(10,np.floor(np.log10(cnz.min())))
ax2norm = mc.LogNorm(ax2nmin, ax2nmax)
for count, patch in zip(cnz,pnz):
patch.set_facecolor(mcm.plasma(ax2norm(count)))
if lineout_inset:
insax = mil.inset_axes(ax2, width="50%", height="50%", loc=2)
iap = insax.get_position()
insax.set_position([iap.xmin + 0.05, iap.ymin, iap.width, iap.height])
for patch in patches:
patch_cpy = copy.copy(patch)
patch_cpy.axes = None
patch_cpy.figure = None
patch_cpy.set_transform(insax.transData)
insax.add_patch(patch_cpy)
insax.yaxis.set_ticks_position("right")
insax.autoscale()
insax.set_xlim(lineout_xmin, lineout_xmax)
insax.set_ylim(lineout_ymin, lineout_ymax)
insax.xaxis.set_major_locator(mt.LinearLocator(2))
insax.yaxis.set_major_locator(mt.LinearLocator(2))
insax.axes.tick_params(labelsize="small")
# [tick.label.set_fontsize(6) for tick in insax.xaxis.get_major_ticks()]
# [tick.label.set_fontsize(6) for tick in insax.yaxis.get_major_ticks()]
ax2cba = fig.add_axes(ax2cbloc)
ax2cb = mplcb.ColorbarBase(ax2cba
,cmap=mcm.plasma
,norm=ax2norm
,orientation='horizontal')
ax2cba.tick_params(top=True,labelbottom=False,labeltop=True,pad=-1)
ax2cb.set_ticks((ax2norm.vmin,ax2norm.vmax))
ax2cba.xaxis.set_label_position('top')
ax2cb.set_label(r"$\mathrm{d}Q/\mathrm{d}z\ \mathrm{nC/m}$", labelpad=-4)
ax2.set_xlim(pub_xmin, pub_xmax)
ax2.set_ylim(pub_ymin, pub_ymax)
ax2.xaxis.set_major_locator(mt.LinearLocator(3))
ax2.yaxis.set_major_locator(mt.LinearLocator(3))
ax2.set_xlabel(r'$z\ \mathrm{(\mu m)}$',labelpad=0)
ax2.set_ylabel(r'$\mathrm{d}Q/\mathrm{d}z\ \mathrm{(nC/m)}$',labelpad=0)
try:
fig.text(0.05,0.94,'{}'.format(config['title'])
,transform=fig.transFigure, fontsize=10)
except Exception as err:
print(err)
fig.savefig('{}/{}_pub_fwhm.png'.format(output_path,output_name) ,dpi=300)
import matplotlib.cm as cm
segment_size, ang = angles[2]
n_range = 301
start_p = 7000
delta_f = 30
for ii in range(start_p, start_p+n_range, delta_f):
plt.figure(figsize=(3*n_cols,3*n_rows))
for iseg, (segment_size, ang) in enumerate(angles):
plt.subplot(2, n_cols, iseg+1)
x = wormN.skeleton[ii,:,0]
y = wormN.skeleton[ii,:,1]
c = (ang[ii]+np.pi)/(2*np.pi)
c = np.pad(c, (segment_size,segment_size), 'edge')
c = cm.plasma(c)
plt.scatter(x, y, c=c)
plt.axis('equal')
plt.subplot(2,n_cols, iseg+1+n_cols)
dd = np.arange(ang[ii].size) + segment_size
plt.plot(dd, ang[ii], '.-')
plt.xlim(0, x.size)
#%%
# plt.figure(figsize = (15, 5))
def plot(data, min_size_px=512, extend_percentage=10, filename=False,
markers=True, gradient_lines=True, caption=False,
show_plot=True):
"""Plot data in a map.
Parameters
----------
data : array_like
The input data. Columns should be latitude, longitude, value.
If multiple value columns are given, one plot for each value
column is generated.
min_size_px : int, optional
Minimum size of generated plot in pixels. Defaults to 512.
extend_percentage : int, float, optional
Determines how much the shown map is extended around the
bounding box of the values. Given in percent of the bounding
box extents. Defaults to 10.
filename : str, list, optional
Filename of the generated png image. If `False`, the image is
not saved. If multiple value columns are given, this can also
be a list of filenames. Defaults to `False`.
markers : bool, optional
If `True`, markers for each value are plotted. Defaults to
`True`.
gradient_lines : bool, optional
If `True` gradient color lines are plotted between the values.
Defaults to `True`.
caption : str, list, optional
Caption printed on the plot if given. If multiple value
columns are given, this can also be a list of captions.
Defaults to `False`.
show_plot : bool, optional
If `True`, the generated plot is displayed. Defaults to
`True`.
"""
# Calculate bounding box and zoom.
lat_long_min, lat_long_max = calculate_bounding_coordinates(data, extend_percentage=extend_percentage)
zoom = calculate_optimal_zoom(lat_long_min, lat_long_max, min_size_px)
# Get map data from OpenStreetMaps.
dpi = 72
m = smopy.Map((*lat_long_min, *lat_long_max), z=zoom)
# Calculate resulting figure size.
size = m.to_pil().size
print(size)
figsize = (10/32 + size[0] / dpi, 10/32 + size[1] / dpi)
# Plot map and data for each value column.
for value_index in range(2, data.shape[1]):
# Convert map to matplotlib.
ax = m.show_mpl(figsize=figsize, dpi=dpi)
# Plot markers and gradient lines for each value.
for i, (lat, long, value) in enumerate(data[:,(0, 1, value_index)]):
loc_px = m.to_pixels(lat, long)
# Plot markers.
if markers:
ax.plot(*loc_px, 'o', color=cm.plasma(float(-value / 100)), markersize=10)
# Plot gradient lines.
## Skip first value and then plot line from last value to current value.
if i != 0 and gradient_lines:
# Calculate line length.
line_length = np.sqrt((last_loc_px[0] - loc_px[0]) ** 2 + (last_loc_px[1] - loc_px[1]) ** 2)
# Calculate x and y coordinates of line points.
x = np.linspace(last_loc_px[0], loc_px[0], line_length)
y = (loc_px[1] - last_loc_px[1]) * ((x - last_loc_px[0]) / (loc_px[0] - last_loc_px[0])) + last_loc_px[1]
# Generate a gradient color map.
colors = [cm.plasma(float(-((value - last_value) * i / len(x) + last_value) / 100)) for i in range(len(x))]
# Gradient lines are generated using scatter plots.
ax.scatter(x, y, c=colors, marker='o', s=1, edgecolor='face')
# Store last location and value for next gradient line.
last_loc_px = loc_px
last_value = value
# Get the extended bounding box in pixels.
x_min, y_min = m.to_pixels(lat_long_max[0], lat_long_min[1])
x_max, y_max = m.to_pixels(lat_long_min[0], lat_long_max[1])
# Set the axes limits to show only the extended bounding box.
ax.set_xlim(x_min, x_max)
ax.set_ylim(y_max, y_min)
# Add caption to the plot.
if caption is not False:
if isinstance(caption, str):
this_caption = caption
else:
this_caption = caption[value_index - 2]
ax.text(10 + x_min, y_max - 10, this_caption, fontsize=48, fontdict={'weight': 'bold'})
# Save plot if filename is given.
if filename is not False:
if isinstance(filename, str):
this_filename = filename
else:
this_filename = filename[value_index - 2]
plt.savefig(this_filename, pad_inches=0, bbox_inches='tight', dpi=dpi)
# Show plot if requested.
if show_plot:
plt.show()
# Close plot.
plt.close()
def plot_string(self):
"""self.strings内に格納されているStringを参照し，グラフ上に図示する
"""
# print self.string.pos, self.string.vec
i = 0 # to count how many line2D object
for s in self.strings:
start = 0
for j, pos1, pos2 in zip(range(len(s.pos) - 1), s.pos[:-1], s.pos[1:]):
dist_x = abs(self.lattice_X[pos1[0], pos1[1]] -
self.lattice_X[pos2[0], pos2[1]])
dist_y = abs(self.lattice_Y[pos1[0], pos1[1]] -
self.lattice_Y[pos2[0], pos2[1]])
# print j, pos1, pos2
# print dist_x, dist_y
# sqrt(2^{2} + (1/2)^{2}) ~ 2.06
if dist_x > 2.1 * self.lattice.dx or dist_y > 2.1 * self.lattice.dx:
x = s.pos_x[start:j + 1]
y = s.pos_y[start:j + 1]
X = [self.lattice_X[_x, _y] for _x, _y in zip(x, y)]
Y = [self.lattice_Y[_x, _y] for _x, _y in zip(x, y)]
self.lines[i].set_data(X, Y)
start = j + 1
i += 1
else:
x = s.pos_x[start:]
y = s.pos_y[start:]
X = [self.lattice_X[_x, _y] for _x, _y in zip(x, y)]
Y = [self.lattice_Y[_x, _y] for _x, _y in zip(x, y)]
self.lines[i].set_data(X, Y)
i += 1
num_plot_surface = 0
if self.plot_surface:
if self._num_surface == 1:
num_plot_surface = 1
neighbors = []
for bonding_pairs in self.bonding_pairs.values():
# print(bonding_pairs)
for pos in bonding_pairs.keys():
neighbors.append(pos)
neighbors = list(np.array(neighbors).T)
# print(neighbors)
X, Y = self.lattice_X[neighbors], self.lattice_Y[neighbors]
# print(X, Y)
self.lines[-1].set_data(X, Y)
# ===
else:
w = {}
for bonding_pairs in self.bonding_pairs.values():
# print(bonding_pairs)
for pos, bps in bonding_pairs.items():
for bp, _w in bps:
if w.has_key(_w):
w[_w].append(pos)
else:
w[_w] = [pos,]
num_plot_surface = len(w)
# W = sorted(w.keys(), reverse=True)
sum_w = np.sum([len(w[_w]) for _w in w.keys()])
W = [(_w, (_w * len(w[_w])) / sum_w) for _w in w.keys()]
ave_W = np.average(W, axis=0)[1]
min_W = np.exp(self.beta * (-2.5)) /sum_w
max_W = np.exp(self.beta * 2.5) /sum_w
for k, (wi, _w) in enumerate(W):
neighbors = list(np.array(w[wi]).T)
X, Y = self.lattice_X[neighbors], self.lattice_Y[neighbors]
self.lines[-(k + 1)].set_data(X, Y)
## color setting
dw = _w - ave_W
if min_W == ave_W:
_c = 0.5
elif dw < 0:
_c = (0.5 / (ave_W - min_W)) * (_w - min_W)
else:
_c = (0.5 / (max_W - ave_W)) * dw + 0.5
self.lines[-(k + 1)].set_color(cm.plasma(_c))
# 最終的に，iの数だけ線を引けばよくなる
# それ以上のオブジェクトはリセット
if self.plot_surface:
max_obj = len(self.lines) - num_plot_surface
else:
max_obj = len(self.lines)
for j in range(i, max_obj):
self.lines[j].set_data([], [])
return self.lines
def main():
config_file = parse_input()
config = loadconfig(config_file)
try:
sdf_data = sdf.read(config['sdf_file'])
except:
raise
dirname = os.path.basename(os.getcwd())
grids = {'xgrid':None
,'ygrid':None
,'xbins':None
,'ybins':None}
for grid in grids:
try:
grids[grid] = float(config[grid])
except:
pass
if ((grids['xgrid'] is not None and grids['xbins'] is not None) or
(grids['ygrid'] is not None and grids['ybins'] is not None)):
print("Both gridsize and numbins are specified... "
"gridsize will take precedence")
if ((grids['xgrid'] is None and grids['xbins'] is None) or
(grids['ygrid'] is None and grids['ybins'] is None)):
print("Warning no gridsize or numbins specified, defaulting to"
"100 bins")
if grids['xbins'] is None:
grids['xbins'] = 100
if grids['ybins'] is None:
grids['ybins'] = 100
try:
output_name = config['output_name']
except:
output_name = 'out'
try:
output_path = config['output_path']
except:
output_path = '.'
ell = {'center':None, 'width':None, 'height':None}
for arg in ell:
try:
ell[arg] = float(config['ell_{}'.format(arg)])
except:
pass
cutoff_px = float(config['cutoff_px']) * sc.m_e * sc.c
sdf_e_px = getattr(sdf_data, 'Particles_Px_electron').data
sdf_e_x = getattr(sdf_data, 'Grid_Particles_electron').data[0]
sdf_e_y = getattr(sdf_data, 'Grid_Particles_electron').data[1]
sdf_e_w = getattr(sdf_data, 'Particles_Weight_electron').data
sdf_gridx = getattr(sdf_data, 'Grid_Grid').data[0]
sdf_gridy = getattr(sdf_data, 'Grid_Grid').data[1]
sdf_dens = getattr(sdf_data, 'Derived_Number_Density_electron').data
try:
sdf_gridz = getattr(sdf_data, 'Grid_Grid').data[2]
sdf_e_z = getattr(sdf_data, 'Grid_Particles_electron').data[2]
is3d = True
except:
is3d = False
limits = {'xmin':sdf_e_x.min()
,'xmax':sdf_e_x.max()
,'ymin':sdf_e_y.min()
,'ymax':sdf_e_y.max()}
if is3d:
limits['zmin'] = sdf_e_z.min()
limits['zmax'] = sdf_e_z.max()
for limit in limits:
try:
limits[limit] = float(config[limit])
except:
pass
hist_limits = {}
for limit in limits:
try:
hist_limits[limit] = float(config['hist_'+limit])
except:
hist_limits[limit] = limits[limit]
xargmin = np.argmin(np.abs(sdf_gridx - limits['xmin']))
xargmax = np.argmin(np.abs(sdf_gridx - limits['xmax']))
yargmin = np.argmin(np.abs(sdf_gridy - limits['ymin']))
yargmax = np.argmin(np.abs(sdf_gridy - limits['ymax']))
if is3d:
zargmin = np.argmin(np.abs(sdf_gridz - limits['zmin']))
zargmax = np.argmin(np.abs(sdf_gridz - limits['zmax']))
sdf_gridx = sdf_gridx[xargmin:xargmax]
sdf_gridy = sdf_gridy[yargmin:yargmax]
sdf_dens = sdf_dens[xargmin:xargmax,yargmin:yargmax]
if is3d:
sdf_gridz = sdf_gridz[zargmin:zargmax]
### Electron selection magic happens here
energy_mask = sdf_e_px > cutoff_px
position_mask = np.full(sdf_e_px.shape, True, dtype=bool)
if None not in ell.values():
if is3d:
position_mask = (
((sdf_e_x - ell['center'])**2 / (0.25*ell['width']**2)) +
(sdf_e_y**2 / (0.25*ell['height']**2)) +
(sdf_e_z**2 / (0.25*ell['height']**2)) < 1 )
else:
position_mask = (
((sdf_e_x - ell['center'])**2 / (0.25*ell['width']**2)) +
(sdf_e_y**2 / (0.25*ell['height']**2)) < 1 )
bunch_electron_mask = np.where(np.logical_and(energy_mask,
position_mask))
bunch_electron_x = sdf_e_x[bunch_electron_mask].reshape(-1)
bunch_electron_y = sdf_e_y[bunch_electron_mask].reshape(-1)
bunch_electron_w = sdf_e_w[bunch_electron_mask].reshape(-1)
if is3d:
bunch_electron_z = sdf_e_z[bunch_electron_mask].reshape(-1)
if grids['xgrid'] is not None:
xbins = np.arange(hist_limits['xmin'],hist_limits['xmax']+grids['xgrid'],grids['xgrid'])
else:
xbins = np.linspace(hist_limits['xmin'],hist_limits['xmax'],grids['xbins'])
if grids['ygrid'] is not None:
if hist_limits['ymin'] * hist_limits['ymax'] < 0:
ybins = np.sort(np.concatenate((
np.arange(0,hist_limits['ymin']-grids['ygrid'],-grids['ygrid']),
np.arange(grids['ymin'],hist_limits['ymax']+grids['ygrid'],grids['ygrid']))))
else:
ybins = np.arange(hist_limits['ymin'],hist_limits['ymax']+grids['ygrid'],grids['ygrid'])
else:
if hist_limits['ymin'] * hist_limits['ymax'] < 0:
ybins = np.sort(np.concatenate((
np.linspace(hist_limits['ymin'],0,grids['ybins']//2),
np.linspace(0,hist_limits['ymax'],grids['ybins']//2)[1:])))
else:
ybins = np.linspace(hist_limits['ymin'],hist_limits['ymax'],grids['ybins'])
limlist = [ limits[l]*1e6 for l in ['xmin','xmax','ymin','ymax'] ]
hist_limlist = [ hist_limits[l]*1e6 for l in ['xmin','xmax','ymin','ymax'] ]
### Debug Plot ####
fig = mf.Figure(figsize=(8.3,11.7))
canvas = mplbea.FigureCanvasAgg(fig)
ax = fig.add_subplot(221)
ax.imshow(sdf_dens.T
,aspect='auto'
,extent=limlist
,origin='upper'
,norm=LogNorm(1e23,1e26)
,cmap=mcm.plasma)
if None not in ell.values():
ax.add_patch(mpat.Ellipse((ell['center']*1e6,0)
,ell['width']*1e6
,ell['height']*1e6
,fill=True
,fc='blue'
,alpha=0.2))
ax2 = fig.add_subplot(222)
counts, xedges, yedges = np.histogram2d(bunch_electron_x
,bunch_electron_y
,bins=[xbins,ybins]
,weights=bunch_electron_w)
areas = np.outer(np.diff(xedges),np.diff(yedges))
hist_dens = counts / areas
print("max(dens): {}".format(sdf_dens.max()))
print("max(hist): {}".format(hist_dens.max()))
ax2.imshow(hist_dens.T
,aspect='auto'
,extent=limlist
,origin='upper'
,norm=LogNorm(1e23,1e26)
,cmap=mcm.plasma)
ax3 = fig.add_subplot(223)
zcounts = ax3.hist(bunch_electron_x*1e6
,bins=xbins*1e6
,weights=bunch_electron_w*sc.e
# ,log=True
)[0]
ax3.set_xlim(limits['xmin']*1e6,limits['xmax']*1e6)
# ax3.set_ylim(1e11,5e12)
ax3.set_xlabel(r'$z\ \mathrm{(\mu m)}$')
ax3.set_ylabel(r'$\mathrm{d}Q\ \mathrm{(C m^{-3})}$')
ax.xaxis.set_major_locator(mt.MaxNLocator(5))
ax4 = fig.add_subplot(224)
ycounts = ax4.hist(bunch_electron_y*1e6
,bins=ybins*1e6
,weights=bunch_electron_w*sc.e
)[0]
ax4.set_xlim(limits['ymin']*1e6,limits['ymax']*1e6)
# ax3.set_ylim(1e11,5e12)
ax4.set_xlabel(r'$z\ \mathrm{(\mu m)}$')
ax4.set_ylabel(r'$\mathrm{d}Q\ \mathrm{(C m^{-3})}$')
xcentres = xedges[:-1] + np.diff(xedges)
ycentres = yedges[:-1] + np.diff(yedges)
xm, ym = np.meshgrid(xcentres, ycentres, indexing='ij')
nz = xcentres[np.where(zcounts > zcounts.max()/np.e)]
ax3.axvline(nz.min()*1e6,alpha=0.5)
ax3.axvline(nz.max()*1e6,alpha=0.5)
bunch_length = nz.max() - nz.min()
print("Bunch Length: {}".format(bunch_length))
nz = ycentres[np.where(ycounts > ycounts.max()/2)]
ax4.axvline(nz.min()*1e6,alpha=0.5)
ax4.axvline(nz.max()*1e6,alpha=0.5)
bunch_width = nz.max() - nz.min()
print("Bunch Width: {}".format(bunch_width))
x_avg = np.average(bunch_electron_x, weights=bunch_electron_w)
x_vari = np.average((bunch_electron_x - x_avg)**2, weights=bunch_electron_w)
x_stdev = np.sqrt(x_vari)
print("Bunch stdev: {}".format(x_stdev))
unscaled_charge = np.sum(counts*sc.e)
bunch_charge_rad = np.sum(np.pi*np.abs(ym)*counts*sc.e)
bunch_charge_dep = np.sum(bunch_width*counts*sc.e)
print("Total charge(rad): {}".format(bunch_charge_rad))
print("Total charge(depth): {}".format(bunch_charge_dep))
print("Unscaled charge: {}".format(unscaled_charge))
ax3.text(0.10,0.95,r'$Q_w = {:.3}\ \mathrm{{\mu C/m}}$'.format(unscaled_charge*1e6)
,transform=ax3.transAxes
)
ax3.text(0.10,0.90,r'$Q_w = {:.3}\ \mathrm{{pC}}$'.format(bunch_charge_dep*1e12)
,transform=ax3.transAxes
)
ax3.text(0.10,0.85,r'$Q_r = {:.3}\ \mathrm{{pC}}$'.format(bunch_charge_rad*1e12)
,transform=ax3.transAxes
)
ax4.text(0.55,0.90,r'$W_b = {:.3}\ \mathrm{{\mu m}}$'.format(bunch_width*1e6)
,transform=ax4.transAxes
)
ax4.text(0.55,0.85,r'$L_b = {:.3}\ \mathrm{{\mu m}}$'.format(bunch_length*1e6)
,transform=ax4.transAxes
)
ax4.text(0.55,0.80,r'$\sigma_x = {:.3}\ \mathrm{{\mu m}}$'.format(x_stdev*1e6)
,transform=ax4.transAxes
)
fig.savefig('{}/{}_debug_fwhm.png'.format(output_path,output_name))
### Publication Plot
ax1loc =[0.09,0.15,0.37,0.625]
ax2loc =[0.59,0.15,0.37,0.625]
ax1cbloc =[0.09,0.8,0.37,0.05]
ax2cbloc =[0.59,0.8,0.37,0.05]
ax1norm=LogNorm(1e23,1e26)
ax2norm = LogNorm(1,100)
if is3d:
plot_dens = sdf_dens[:,:,int(0.5*sdf_dens.shape[3])]
else:
plot_dens = sdf_dens
mpl.rcParams.update({'font.size': 8})
fig = mf.Figure(figsize=(3.2,2))
canvas = mplbea.FigureCanvasAgg(fig)
ax = fig.add_axes(ax1loc)
ax.imshow(plot_dens.T
,aspect='auto'
,extent=limlist
,origin='upper'
,norm=ax1norm
,cmap=mcm.plasma)
ax1cba = fig.add_axes(ax1cbloc)
ax1cb = mplcb.ColorbarBase(ax1cba
,cmap=mcm.plasma
,norm=ax1norm
,orientation='horizontal')
ax1cba.tick_params(top=True,labelbottom=False,labeltop=True,pad=-1)
ax1cb.set_ticks((ax1norm.vmin,ax1norm.vmax))
ax1cba.xaxis.set_label_position('top')
ax1cb.set_label(r"$n_e\ \mathrm{m^{-3}}$", labelpad=-4)
ax.xaxis.set_major_locator(mt.LinearLocator(3))
ax.yaxis.set_major_locator(mt.LinearLocator(3))
ax.set_xlabel(r'$z\ \mathrm{(\mu m)}$', labelpad=0)
ax.set_ylabel(r'$y \mathrm{(\mu m)}$', labelpad=-8)
ax2 = fig.add_axes(ax2loc)
counts, xbins, patches = ax2.hist(bunch_electron_x*1e6
,bins=xbins*1e6
,weights=bunch_electron_w*sc.e*1e9
,linewidth=0
)
for count, patch in zip(counts,patches):
patch.set_facecolor(mcm.plasma(ax2norm(count)))
ax2cba = fig.add_axes(ax2cbloc)
ax2cb = mplcb.ColorbarBase(ax2cba
,cmap=mcm.plasma
,norm=ax2norm
,orientation='horizontal')
ax2cba.tick_params(top=True,labelbottom=False,labeltop=True,pad=-1)
ax2cb.set_ticks((ax2norm.vmin,ax2norm.vmax))
ax2cba.xaxis.set_label_position('top')
ax2cb.set_label(r"$\mathrm{d}Q/\mathrm{d}z\ \mathrm{nC/m}$", labelpad=-4)
ax2.set_xlim(*hist_limlist[:2])
ax2.set_ylim(0,ax2norm.vmax)
ax2.xaxis.set_major_locator(mt.LinearLocator(3))
ax2.yaxis.set_major_locator(mt.LinearLocator(3))
ax2.set_xlabel(r'$z\ \mathrm{(\mu m)}$',labelpad=0)
ax2.set_ylabel(r'$\mathrm{d}Q/\mathrm{d}x\ \mathrm{(nC/m)}$',labelpad=-2)
ax2.text(0.05,0.85,'$dQ = {:.3}\mathrm{{\mu C/m}}$'.format(unscaled_charge*1e6)
,transform=ax2.transAxes
)
try:
fig.text(0.05,0.94,'{}'.format(config['title'])
,transform=fig.transFigure, fontsize=10)
except Exception as err:
print(err)
fig.savefig('{}/{}_pub_fwhm.png'.format(output_path,output_name) ,dpi=300)