From f8a16eb16396eab28e56cf4a121fb77b547acbf1 Mon Sep 17 00:00:00 2001
From: "Joachim Wuttke (o)" <j.wuttke@fz-juelich.de>
Date: Tue, 17 Nov 2020 09:04:08 +0100
Subject: [PATCH] rm old directory devtools/ad-hoc/JWu
---
devtools/ad-hoc/JWu/bornplot2.py | 167 -----------------------
devtools/ad-hoc/JWu/par_changed.py | 35 -----
devtools/ad-hoc/JWu/partial_history.txt | 44 ------
devtools/ad-hoc/JWu/perf-log-old2yaml.py | 127 -----------------
4 files changed, 373 deletions(-)
delete mode 100644 devtools/ad-hoc/JWu/bornplot2.py
delete mode 100644 devtools/ad-hoc/JWu/par_changed.py
delete mode 100644 devtools/ad-hoc/JWu/partial_history.txt
delete mode 100755 devtools/ad-hoc/JWu/perf-log-old2yaml.py
diff --git a/devtools/ad-hoc/JWu/bornplot2.py b/devtools/ad-hoc/JWu/bornplot2.py
deleted file mode 100644
index 25a2fa25e8a..00000000000
--- a/devtools/ad-hoc/JWu/bornplot2.py
+++ /dev/null
@@ -1,167 +0,0 @@
-"""
-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 )
diff --git a/devtools/ad-hoc/JWu/par_changed.py b/devtools/ad-hoc/JWu/par_changed.py
deleted file mode 100644
index 426fb1b2695..00000000000
--- a/devtools/ad-hoc/JWu/par_changed.py
+++ /dev/null
@@ -1,35 +0,0 @@
-"""
-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" )
diff --git a/devtools/ad-hoc/JWu/partial_history.txt b/devtools/ad-hoc/JWu/partial_history.txt
deleted file mode 100644
index 7db891cf5e3..00000000000
--- a/devtools/ad-hoc/JWu/partial_history.txt
+++ /dev/null
@@ -1,44 +0,0 @@
-# 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 |
diff --git a/devtools/ad-hoc/JWu/perf-log-old2yaml.py b/devtools/ad-hoc/JWu/perf-log-old2yaml.py
deleted file mode 100755
index 892ce94a391..00000000000
--- a/devtools/ad-hoc/JWu/perf-log-old2yaml.py
+++ /dev/null
@@ -1,127 +0,0 @@
-#!/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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