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Commit f8a16eb1 authored by Wuttke, Joachim's avatar Wuttke, Joachim
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rm old directory devtools/ad-hoc/JWu

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devtools/ad-hoc/JWu/bornplot2.py deleted 100644 → 0
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− 167
View file @ e1fc8f17
"""
Utilities to plot form factors of particles in Born approximation
"""
import numpy
import matplotlib as mpl
import matplotlib.pyplot as plt
import bornagain as ba
from bornagain import nanometer, degree, angstrom, deg2rad
class BinRange:
def __init__(self, vmin, vmax, n):
self.vmin = vmin
self.vmax = vmax
self.n = n
def origin_index(self):
return int((0.-self.vmin)/(self.vmax-self.vmin)*self.n)
def range(self):
return self.vmax - self.vmin
class DetPars:
def __init__(self, bins_per_dimension, y_min, y_max, z_min, z_max):
self.y = BinRange(y_min, y_max, bins_per_dimension)
self.z = BinRange(z_min, z_max, bins_per_dimension)
def rectangle(self):
return self.y.vmin, self.y.vmax, self.z.vmin, self.z.vmax
class Result:
def __init__(self, idx, data, title=""):
self.idx = idx
self.data = data
self.title = title
def make_plot(results, detPars, name, nrow=1):
"""Make a plot consisting of one detector image for each Result in results,
plus one common color scale.
:param results: List of simulation results
:param detPars: Detector limits
:param name: Filename for plot during save
:param nrow: Number of rows for different plots
"""
mpl.rcParams['image.interpolation'] = 'none'
n = len(results)
ncol = 1+(n-1)//nrow
# Parameters as fraction of subfig size.
yskip = 0.2 # +ncol*0.02
bottomskip = yskip
topskip = yskip/2
xskip = 0.21
leftskip = xskip
rightskip = 0.28+ncol*0.03
xtot = ncol*1.0 + (ncol-1)*xskip + leftskip + rightskip
ytot = nrow*1.0 + (nrow-1)*yskip + bottomskip + topskip
# We need parameters as fraction of total fig size.
xskip /= xtot
leftskip /= xtot
rightskip /= xtot
yskip /= ytot
bottomskip /= ytot
topskip /= ytot
# Set total figure dimensions.
ftot = 5
fontsize = 18+36.0/(ncol+2)
# Create the figure 'fig' and its subplots axes ('tmp'->'axes').
fig, tmp = plt.subplots(nrow, ncol, figsize=(ftot*xtot, ftot*ytot))
if n > 1:
axes = tmp.flat
else:
axes = [tmp]
# Always the same color scale, to facilitate comparisons between figures.
norm = mpl.colors.LogNorm(1e-10, 1)
# Plot the subfigures.
for res in results:
ax = axes[res.idx]
im = ax.imshow(res.data,
norm=norm,
extent=detPars.rectangle(),
aspect=1)
ax.set_xlabel(r'$k_y/k_x$', fontsize=fontsize)
if res.idx % ncol == 0:
ax.set_ylabel(r'$k_z/k_x$', fontsize=fontsize)
if res.title != "":
ax.set_title(res.title, fontsize=fontsize)
ax.tick_params(axis='both', which='major', labelsize=fontsize*21/24)
# Adjust whitespace around and between subfigures.
plt.subplots_adjust(wspace=xskip, hspace=yskip,
left=leftskip, right=1-rightskip,
bottom=bottomskip, top=1-topskip)
# Plot the color scale.
cbar_ax = fig.add_axes([1-rightskip+0.4*xskip, bottomskip,
0.25*xskip, 1-bottomskip-topskip])
cb = fig.colorbar(im, cax=cbar_ax)
cb.set_label(r'$\left|F(q)\right|^2/V^{\,2}$', fontsize=fontsize)
# Output to file or display.
plt.savefig(name+".pdf", format="pdf", bbox_inches='tight')
plt.show()
def get_sample(ff, trafo):
"""Build and return a sample consisting of uncorrelated particles with given
form factor and transformation operator
:param ff: Form factor
:param trafo: Optional rotation
"""
# defining materials
m_ambience = ba.HomogeneousMaterial("Air", 0.0, 0.0)
m_particle = ba.HomogeneousMaterial("Particle", 1e-5, 0)
# collection of particles
particle = ba.Particle(m_particle, ff)
particle_layout = ba.ParticleLayout()
if trafo is not None:
particle.setRotation(trafo)
particle_layout.addParticle(particle)
else:
particle_layout.addParticle(particle)
air_layer = ba.Layer(m_ambience)
air_layer.addLayout(particle_layout)
multi_layer = ba.MultiLayer()
multi_layer.addLayer(air_layer)
return multi_layer
def get_simulation(detPars, ff, trafo=None):
"""Create and return GISAXS simulation
:param detPars: Detector limits
:param sample
"""
simulation = ba.GISASSimulation()
detector = ba.RectangularDetector(detPars.y.n, detPars.y.range(), detPars.z.n, detPars.z.range())
detector.setPerpendicularToSampleX(1., -detPars.y.vmin, -detPars.z.vmin)
simulation.setDetector(detector)
simulation.setBeamParameters(1.0*nanometer, 0, 0)
sample = get_sample(ff, trafo)
simulation.setSample(sample)
return simulation
def run_sim(simulation, detPars):
"""Run simulation and return plottable results
"""
simulation.runSimulation()
data = simulation.result().array()
nor = data[detPars.z.n - detPars.z.origin_index() - 1, detPars.y.origin_index()]
data /= nor
return data + 1e-80 # for log scale
def run_simulation(detPars, ff, trafo=None):
"""Create simulation, run it, and return plottable results
:param detPars: Detector limits
:param ff: Form factor
:param trafo: Optional rotation
"""
return run_sim( get_simulation(detPars, tt, trafo), detPars )
devtools/ad-hoc/JWu/par_changed.py deleted 100644 → 0
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View file @ e1fc8f17
"""
Plot form factors.
"""
import bornagain as ba
from bornagain import nanometer, degree
import bornplot2 as bp
import math
import inspect
det = bp.DetPars( 400, -.25, .25, -.25, .25 )
n = 3
results = []
edge = 30
title = 'E=30'
trafo = ba.RotationY(26.5651*degree)
ff = ba.FormFactorTruncatedCube(edge*nanometer,2*nanometer)
sim = bp.get_simulation(det,ff,trafo)
data = bp.run_sim( sim, det )
results.append( bp.Result(0, data, title) )
pool = ff.getParameterPool()
print( pool.getParameterNames() )
print( ff.getLength() )
print( ff.volume() )
pool.setParameterValue('Length', 10 )
print( ff.getLength() )
print( ff.volume() )
title = 'E=10'
data = bp.run_sim( sim, det )
results.append( bp.Result(1, data, title) )
bp.make_plot( results, det, "tmp" )
devtools/ad-hoc/JWu/partial_history.txt deleted 100644 → 0
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− 44
View file @ e1fc8f17
# Release 1.2.0
| date | hostname | sysinfo | tr | total | MultiLayer | CylindersInD | RotatedPyram | CoreShell | SquareLattic | RadialParaCr | HexParaCryst | SSCA | Mesocrystal | PolMagCyl |
| 2015-06-30 15:16:12 | jcnsopc126 | linuxx8664gcc | 0 | 20.120 | 1.686 | 1.156 | 1.947 | 0.974 | 2.814 | 1.177 | 2.055 | 3.835 | 1.831 | 2.644 |
| 2015-06-30 15:16:37 | jcnsopc126 | linuxx8664gcc | 0 | 20.044 | 1.678 | 1.176 | 2.018 | 0.979 | 2.829 | 1.202 | 2.069 | 3.835 | 1.823 | 2.436 |
| 2015-06-30 15:17:36 | jcnsopc126 | linuxx8664gcc | 0 | 20.347 | 1.699 | 1.319 | 2.010 | 1.003 | 2.822 | 1.197 | 2.031 | 3.861 | 1.890 | 2.515 |
| 2015-06-30 15:19:12 | jcnsopc126 | linuxx8664gcc | 0 | 19.853 | 1.684 | 1.156 | 1.951 | 0.979 | 2.815 | 1.187 | 2.026 | 3.798 | 1.832 | 2.426 |
# Release 1.3.0
| date | hostname | sysinfo | tr | total | MultiLayer | CylindersInD | RotatedPyram | CoreShell | SquareLattic | RadialParaCr | HexParaCryst | SSCA | Mesocrystal | PolMagCyl |
| 2015-07-31 14:38:50 | jcnsopc63 | linuxx8664gcc | 0 | 15.590 | 1.537 | 0.977 | 1.673 | 0.855 | 2.524 | 0.996 | 1.874 | 1.505 | 1.581 | 2.068 |
# after some development, why it is slower now not clear (there was minor OutputData refactoring
| date | hostname | sysinfo | tr | total | MultiLayer | CylindersInD | RotatedPyram | CoreShell | SquareLattic | RadialParaCr | HexParaCryst | SSCA | Mesocrystal | PolMagCyl |
| 2015-09-23 14:54:52 | jcnsopc126 | linuxx8664gcc | 0 | 17.658 | 1.692 | 1.148 | 1.602 | 0.983 | 2.793 | 1.174 | 2.163 | 1.742 | 1.868 | 2.495 |
# after masking
| date | hostname | sysinfo | tr | total | MultiLayer | CylindersInD | RotatedPyram | CoreShell | SquareLattic | RadialParaCr | HexParaCryst | SSCA | Mesocrystal | PolMagCyl |
| 2015-09-28 17:19:17 | jcnsopc126 | linuxx8664gcc | 0 | 21.595 | 2.108 | 1.412 | 1.888 | 1.275 | 3.615 | 1.496 | 2.478 | 2.139 | 2.340 | 2.845 |
# working on mask performance
| date | hostname | sysinfo | tr | total | MultiLayer | CylindersInD | RotatedPyram | CoreShell | SquareLattic | RadialParaCr | HexParaCryst | SSCA | Mesocrystal | PolMagCyl |
| 2015-09-29 11:41:26 | jcnsopc126 | linuxx8664gcc | 0 | 18.188 | 1.793 | 1.172 | 1.647 | 1.012 | 2.945 | 1.290 | 2.197 | 1.798 | 1.849 | 2.486 |
| 2015-09-29 11:46:58 | jcnsopc126 | linuxx8664gcc | 0 | 17.975 | 1.852 | 1.165 | 1.586 | 0.977 | 2.834 | 1.183 | 2.136 | 1.860 | 1.879 | 2.502 |
# after RectangularDetector refactoring
| date | hostname | sysinfo | tr | total | MultiLayer | CylindersInD | RotatedPyram | CoreShell | SquareLattic | RadialParaCr | HexParaCryst | SSCA | Mesocrystal | PolMagCyl |
| 2015-10-21 10:42:06 | jcnsopc126 | linuxx8664gcc | 0 | 19.284 | 1.781 | 1.333 | 1.785 | 1.133 | 3.145 | 1.404 | 2.156 | 1.847 | 1.884 | 2.818 |
| 2015-10-21 10:42:30 | jcnsopc126 | linuxx8664gcc | 0 | 19.756 | 1.737 | 1.336 | 1.842 | 1.200 | 3.262 | 1.397 | 2.116 | 1.912 | 2.013 | 2.942|
# PreRelease state. Seems that much worser. Simulation normalize?
| date | hostname | sysinfo | tr | total | MultiLayer | CylindersInD | RotatedPyram | CoreShell | SquareLattic | RadialParaCr | HexParaCryst | SSCA | Mesocrystal | PolMagCyl |
| 2015-10-28 17:04:26 | jcnsopc126 | linuxx8664gcc | 0 | 25.693 | 2.573 | 1.693 | 2.410 | 1.472 | 4.134 | 1.748 | 2.856 | 2.376 | 2.715 | 3.716|
# PreRelease. Moved checkPolarizationPresent() out of the loop.
| date | hostname | sysinfo | tr | total | MultiLayer | CylindersInD | RotatedPyram | CoreShell | SquareLattic | RadialParaCr | HexParaCryst | SSCA | Mesocrystal | PolMagCyl |
| 2015-10-29 09:17:30 | jcnsopc126 | linuxx8664gcc | 0 | 20.586 | 2.386 | 1.166 | 1.773 | 0.890 | 3.449 | 1.195 | 2.570 | 1.687 | 2.452 | 3.020 |
# PreRelease. If I try to backup mP_specular_info->getInCoefficients(alpha_i, 0.0, wavelength)); in InterferenceFunctionStrategy
| date | hostname | sysinfo | tr | total | MultiLayer | CylindersInD | RotatedPyram | CoreShell | SquareLattic | RadialParaCr | HexParaCryst | SSCA | Mesocrystal | PolMagCyl |
| 2015-10-29 09:41:25 | jcnsopc126 | linuxx8664gcc | 0 | 19.921 | 2.416 | 0.984 | 1.654 | 0.778 | 3.333 | 1.027 | 2.923 | 1.505 | 2.359 | 2.942 |
# PreRelease-1.5.0
| date | hostname | sysinfo | tr | total | MultiLayer | CylindersInD | RotatedPyram | CoreShell | SquareLattic | RadialParaCr | HexParaCryst | SSCA | Mesocrystal | PolMagCyl |
| 2016-02-11 14:10:57 | jcnsopc126 | linuxx8664gcc | 0 | 18.247 | 1.981 | 0.920 | 1.418 | 0.696 | 2.578 | 0.950 | 3.899 | 1.381 | 2.008 | 2.417 |
devtools/ad-hoc/JWu/perf-log-old2yaml.py deleted 100755 → 0
+ 0
− 127
View file @ e1fc8f17
#!/usr/bin/env python3
'''
To be used only once: convert performance log from legacy format to YAML
'''
import datetime, re, sys, pytz, yaml
from collections import OrderedDict
from pytz import timezone
################################################################################
# Improved YAML dumper, to write dicts and lists in nice form
################################################################################
class FlowSeq( list ): pass
# The improved YAML dumper
def improved_dump(data, stream=None, Dumper=yaml.Dumper, **kwds):
class ImprovedDumper(Dumper):
pass
def odict_representer(dumper, data):
return dumper.represent_mapping(
yaml.resolver.BaseResolver.DEFAULT_MAPPING_TAG,
data.items())
def flowseq_representer(dumper, data):
return dumper.represent_sequence(
yaml.resolver.BaseResolver.DEFAULT_SEQUENCE_TAG,
data,
flow_style=True )
ImprovedDumper.add_representer(OrderedDict, odict_representer)
ImprovedDumper.add_representer(FlowSeq, flowseq_representer)
return yaml.dump(data, stream, ImprovedDumper,
allow_unicode=True, encoding='utf-8',
default_flow_style=False, indent=4, width=70, **kwds)
# Just for documentation, not used here: the corresponding loader.
def improved_load(stream, Loader=yaml.Loader, object_pairs_hook=OrderedDict):
class ImprovedLoader(Loader):
pass
def construct_mapping(loader, node):
loader.flatten_mapping(node)
return object_pairs_hook(loader.construct_pairs(node))
ImprovedLoader.add_constructor(
yaml.resolver.BaseResolver.DEFAULT_MAPPING_TAG,
construct_mapping)
return yaml.load(stream, ImprovedLoader)
################################################################################
# Time conversion
################################################################################
garching = timezone('Europe/Berlin')
def nice_datetime( dt ):
rounded = dt - datetime.timedelta(microseconds=dt.microsecond)
return garching.localize(rounded).isoformat()
################################################################################
# Standarized blocks
################################################################################
def coder(value, offset_coder, offset, precision):
ret = OrderedDict()
ret['value'] = value
ret['offset_coder'] = offset_coder
ret['offset'] = offset
ret['precision'] = precision
return ret
def scan(j):
ret = OrderedDict()
ret['scan_parameters'] = OrderedDict()
ret['scan_parameters']['omgs'] = 0.1*j
ret['time'] = 2.02
ret['monitor'] = random.randint(10000, 40000)
ret['image'] = "img%04i" % j
return ret
################################################################################
# Main
################################################################################
o = []
fni = 'partial_history.txt'
fno = 'performance_log2.yaml'
fd = open( fni, 'r' )
ti = fd.read()
fd.close()
aa = re.split( r'\n\s*?\n', ti )
for a in aa: # block
bb = re.split( r'\n', a.rstrip() )
m = re.match( r'#\s*(.*)', bb[0] )
if not m:
raise "block header not found"
comment = m.group(1)
# print("### "+comment[0:20]+" --> %i" %( len(bb)-2 ) )
header = re.split( r'\s*\|\s*', bb[1] )[1:-1]
if header[0]!="date":
raise "unexpected block header"
nentry = len(header)
outcome = []
for b in bb[2:]:
c = re.split( r'\s*\|\s*', b )[1:-1]
# print("'"+b+"'")
if len(c)!=len(header):
raise "wrong number of records"
result = OrderedDict()
for i in range(len(header)):
out = c[i]
if header[i]=="tr":
out = int(out)
elif i>3:
out = float(out)
result[header[i]] = out
outcome.append( result )
entry = OrderedDict()
entry['version'] = comment
entry['outcome'] = outcome
o.append( entry )
yaml_str = improved_dump( o )
fd = open( fno, 'wb' )
fd.write( yaml_str )
fd.close()
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