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# -*- coding: utf-8 -*-
"""
Module :mod:`runner` defines the entry point of xrt - :func:`run_ray_tracing`,
containers for job properties and functions for running the processes or
threads and accumulating the resulting histograms.
"""
__author__ = "Konstantin Klementiev, Roman Chernikov"
__date__ = "26 Mar 2016"
import os
import sys
import time
import inspect
import pickle
import numpy as np
import matplotlib as mpl
import matplotlib.pyplot as plt
import multiprocessing
import errno
import threading
if sys.version_info < (3, 1):
import Queue
else:
import queue
Queue = queue
import uuid # is needed on some platforms with pyopencl # analysis:ignore
from . import multipro
from .backends import raycing
# _DEBUG = True
__fdir__ = os.path.abspath(os.path.dirname(__file__))
runCardVals = None
runCardProcs = None
_plots = []
def retry_on_eintr(function, *args, **kw):
"""
Suggested in:
http://mail.python.org/pipermail/python-list/2011-February/1266462.html
as a solution for `IOError: [Errno 4] Interrupted system call` in Linux.
"""
while True:
try:
return function(*args, **kw)
except IOError as e:
if e.errno == errno.EINTR:
continue
else:
raise
class RunCardVals(object):
"""
Serves as a global container for a sub-set of run properties passed by the
user to :func:`run_ray_tracing`. The sub-set is limited to pickleable
objects for passing it to job processes or threads.
"""
def __init__(self, threads, processes, repeats, updateEvery, pickleEvery,
backend, globalNorm, runfile):
if threads >= processes:
self.Event = threading.Event
self.Queue = Queue.Queue
else:
self.Event = multiprocessing.Event
self.Queue = multiprocessing.Queue
self.stop_event = self.Event()
self.finished_event = self.Event()
self.stop_event.clear()
self.finished_event.clear()
self.threads = threads
self.processes = processes
self.repeats = repeats
self.updateEvery = updateEvery
self.pickleEvery = pickleEvery
self.backend = backend
self.globalNorm = globalNorm
self.runfile = runfile
self.passNo = 0
self.savedResults = []
self.iteration = 0
self.lastRunsPickleName = os.path.join(__fdir__, 'lastRuns.pickle')
self.lastRuns = []
try:
with open(self.lastRunsPickleName, 'rb') as f:
self.lastRuns = pickle.load(f)
except: # analysis:ignore
pass
if self.lastRuns:
raycing.colorPrint("The last {0} run{1}".format(
len(self.lastRuns), 's' if len(self.lastRuns) > 1 else ''),
fcolor='GREEN')
for lastRun in self.lastRuns:
if len(lastRun) > 3:
print("{0}::".format(lastRun[3]))
st0 = time.strftime("%a, %d %b %Y %H:%M:%S", lastRun[0])
if (time.strftime("%a, %d %b %Y", lastRun[0]) ==
time.strftime("%a, %d %b %Y", lastRun[1])):
st1 = time.strftime("%H:%M:%S", lastRun[1])
else:
st1 = time.strftime("%a, %d %b %Y %H:%M:%S", lastRun[1])
print("start: {0}; stop: {1}; duration: {2:.1f} s".format(
st0, st1, lastRun[2]))
class RunCardProcs(object):
"""
Serves as a global container for a sub-set of run properties passed by the
user to :func:`run_ray_tracing` limited to functions. These cannot be
passed to job processes or threads (because are not pickleable) and have to
be executed by the job server (this module).
"""
def __init__(self, afterScript, afterScriptArgs, afterScriptKWargs):
self.afterScript = afterScript
self.afterScriptArgs = afterScriptArgs
self.afterScriptKWargs = afterScriptKWargs
self.generatorNorm = None
self.generatorPlot = None
def set_repeats(repeats=0):
if runCardVals is not None:
runCardVals.repeats = repeats
def _simple_generator():
"""
The simplest generator for running only one ray-tracing study. Search
examples for generators that run complex ray-tracing studies.
"""
yield
def start_jobs():
"""
Restores the plots if requested and if the persistent files exist and
starts the qt timer of the 1st plot.
"""
for plot in _plots:
if plot.persistentName:
plot.restore_plots()
try:
plot.fig.canvas.manager.set_window_title(plot.title)
except AttributeError:
pass
runCardVals.iteration = np.int64(0)
noTimer = len(_plots) == 0 or\
(plt.get_backend().lower() in (x.lower() for x in
mpl.rcsetup.non_interactive_bk))
if noTimer:
print("The job is running... ")
while True:
sys.stdout.flush()
res = dispatch_jobs()
tFromStart = time.time() - runCardVals.tstart
msg = '{0} of {1} in {2:.1f} s'.format(
runCardVals.iteration, runCardVals.repeats, tFromStart)
if os.name == 'posix':
sys.stdout.write("\r\x1b[K " + msg)
else:
sys.stdout.write("\r ")
print(msg+' ')
if res:
return
else:
plot = _plots[0]
plot.areProcessAlreadyRunning = False
plot.timer = plot.fig.canvas.new_timer()
plot.timer.add_callback(plot.timer_callback)
plot.timer.start()
def dispatch_jobs():
"""Runs the jobs in separate processes or threads and collects the resulted
histograms from the output queues. One cannot run this function in a loop
because the redrawing will not work. Instead, it is started from a timer
event handler of a qt-graph."""
if (runCardVals.iteration >= runCardVals.repeats) or \
runCardVals.stop_event.is_set():
on_finish()
return True
one_iteration()
if (runCardVals.iteration >= runCardVals.repeats) or \
runCardVals.stop_event.is_set():
on_finish()
return True
if runCardVals.iteration % runCardVals.updateEvery == 0:
for plot in _plots:
plot.plot_plots()
if runCardVals.pickleEvery:
if runCardVals.iteration % runCardVals.pickleEvery == 0:
for plot in _plots:
plot.store_plots()
if len(_plots) > 0:
_plots[0].areProcessAlreadyRunning = False
def one_iteration():
"""The body of :func:`dispatch_jobs`."""
plots2Pickle = [plot.card_copy() for plot in _plots]
outPlotQueues = [runCardVals.Queue() for plot in _plots]
alarmQueue = runCardVals.Queue()
# in the 1st iteration the plots may require some of x, y, e limits to be
# calculated and thus this case is special:
cpus = max(runCardVals.threads, runCardVals.processes)
if runCardVals.iteration == 0:
runCardVals.uniqueFirstRun = False
if hasattr(runCardVals, 'beamLine'):
bl = runCardVals.beamLine
bl.forceAlign = False
for oe in bl.oes + bl.slits + bl.screens:
if raycing.is_auto_align_required(oe):
bl.forceAlign = True
runCardVals.uniqueFirstRun = True
break
if not runCardVals.uniqueFirstRun:
for plot in _plots:
xLimitsDefined = (plot.xaxis.limits is not None) and\
(not isinstance(plot.xaxis.limits, str))
yLimitsDefined = (plot.yaxis.limits is not None) and\
(not isinstance(plot.yaxis.limits, str))
cLimitsDefined = (plot.caxis.limits is not None) and\
(not isinstance(plot.caxis.limits, str)) or plot.ePos == 0
if not (xLimitsDefined and yLimitsDefined and cLimitsDefined):
runCardVals.uniqueFirstRun = True
break
if runCardVals.uniqueFirstRun:
cpus = 1
elif runCardVals.iteration == 1:
if runCardVals.uniqueFirstRun: # balances the 1st iteration
cpus -= 1
if cpus < 1:
cpus = 1
if runCardVals.backend.startswith('raycing'):
runCardVals.beamLine.alarms = []
if runCardVals.threads >= runCardVals.processes or cpus == 1:
BackendOrProcess = multipro.BackendThread
else:
BackendOrProcess = multipro.BackendProcess
processes = [BackendOrProcess(runCardVals, plots2Pickle, outPlotQueues,
alarmQueue, icpu) for icpu in range(cpus)]
# print('top process:', os.getpid())
for pid, p in enumerate(processes):
p.ppid = pid + runCardVals.iteration
p.start()
for p in processes:
if runCardVals.backend.startswith('raycing'):
runCardVals.beamLine.alarms = retry_on_eintr(alarmQueue.get)
for alarm in runCardVals.beamLine.alarms:
raycing.colorPrint(alarm, 'RED')
outList = [0, ]
for plot, aqueue in zip(_plots, outPlotQueues):
outList = retry_on_eintr(aqueue.get)
if len(outList) == 0:
continue
if (runCardVals.iteration >= runCardVals.repeats) or \
runCardVals.stop_event.is_set():
continue
plot.nRaysAll += outList[13]
if runCardVals.backend.startswith('shadow'):
plot.nRaysNeeded += outList[14]
elif runCardVals.backend.startswith('raycing'):
nRaysVarious = outList[14]
plot.nRaysAlive += nRaysVarious[0]
plot.nRaysGood += nRaysVarious[1]
plot.nRaysOut += nRaysVarious[2]
plot.nRaysOver += nRaysVarious[3]
plot.nRaysDead += nRaysVarious[4]
plot.nRaysAccepted += nRaysVarious[5]
plot.nRaysAcceptedE += nRaysVarious[6]
plot.nRaysSeeded += nRaysVarious[7]
plot.nRaysSeededI += nRaysVarious[8]
plot.displayAsAbsorbedPower = outList[15]
for iaxis, axis in enumerate(
[plot.xaxis, plot.yaxis, plot.caxis]):
if (iaxis == 2) and (not plot.ePos):
continue
axis.total1D += outList[0+iaxis*3]
axis.total1D_RGB += outList[1+iaxis*3]
if runCardVals.iteration == 0:
axis.binEdges = outList[2+iaxis*3]
plot.total2D += outList[9]
plot.total2D_RGB += outList[10]
if plot.fluxKind.lower().endswith('4d'):
plot.total4D += outList[11]
elif plot.fluxKind.lower().endswith('pca'):
plot.total4D.append(outList[11])
plot.intensity += outList[12]
if runCardVals.iteration == 0: # needed for multiprocessing
plot.set_axes_limits(*outList.pop())
tFromStart = time.time() - runCardVals.tstart
plot.textStatus.set_text(
"{0} of {1} in {2:.1f} s (right click to stop)".format(
runCardVals.iteration+1, runCardVals.repeats, tFromStart))
# aqueue.task_done()
if len(outList) > 0:
runCardVals.iteration += 1
for p in processes:
p.join(60.)
if hasattr(runCardVals, 'beamLine'):
bl = runCardVals.beamLine
bl.forceAlign = False
if bl.flowSource == 'legacy':
bl.flowSource = 'done_once'
def on_finish():
"""Executed on exit from the ray-tracing iteration loop."""
if len(_plots) > 0:
plot = _plots[0]
if plt.get_backend().lower() not in (
x.lower() for x in mpl.rcsetup.non_interactive_bk):
plot.timer.stop()
plot.timer.remove_callback(plot.timer_callback)
plot.areProcessAlreadyRunning = False
for plot in _plots:
if plot.fluxKind.startswith('E') and \
plot.fluxKind.lower().endswith('pca'):
xbin, zbin = plot.xaxis.bins, plot.yaxis.bins
plot.total4D = np.concatenate(plot.total4D).reshape(-1, xbin, zbin)
plot.field3D = plot.total4D
plot.textStatus.set_text('')
plot.fig.canvas.mpl_disconnect(plot.cidp)
plot.plot_plots()
plot.save()
runCardVals.tstop = time.time()
runCardVals.tstopLong = time.localtime()
raycing.colorPrint('The ray tracing with {0} iteration{1} took {2:0.1f} s'
.format(runCardVals.iteration,
's' if runCardVals.iteration > 1 else '',
runCardVals.tstop-runCardVals.tstart),
fcolor="GREEN")
runCardVals.finished_event.set()
for plot in _plots:
if runCardVals.globalNorm or plot.persistentName:
plot.store_plots()
if runCardVals.stop_event.is_set():
raycing.colorPrint('Interrupted by user after iteration {0}'.format(
runCardVals.iteration), fcolor='YELLOW')
return
try:
if runCardProcs.generatorPlot is not None:
if sys.version_info < (3, 1):
runCardProcs.generatorPlot.next()
else:
next(runCardProcs.generatorPlot)
except StopIteration:
pass
else:
for plot in _plots:
plot.clean_plots()
start_jobs()
return
if runCardVals.globalNorm:
aSavedResult = -1
print('normalizing ...')
for aRenormalization in runCardProcs.generatorNorm:
for plot in _plots:
aSavedResult += 1
saved = runCardVals.savedResults[aSavedResult]
plot.clean_plots()
saved.restore(plot)
try:
plot.fig.canvas.manager.set_window_title(plot.title)
except AttributeError:
pass
for runCardVals.passNo in [1, 2]:
plot.plot_plots()
plot.save('_norm' + str(runCardVals.passNo))
print('finished')
runCardVals.lastRuns.append([runCardVals.tstartLong, runCardVals.tstopLong,
runCardVals.tstop-runCardVals.tstart,
runCardVals.runfile])
try:
with open(runCardVals.lastRunsPickleName, 'wb') as f:
pickle.dump(runCardVals.lastRuns[-10:], f, protocol=2)
except OSError: # Read-only file system
pass # no history tracking of last 10 runs
# plt.close('all')
if runCardProcs.afterScript:
runCardProcs.afterScript(
*runCardProcs.afterScriptArgs, **runCardProcs.afterScriptKWargs)
def normalize_sibling_plots(plots):
print('normalization started')
max1Dx = 0
max1Dy = 0
max1Dc = 0
max1Dx_RGB = 0
max1Dy_RGB = 0
max1Dc_RGB = 0
max2D_RGB = 0
for plot in plots:
if max1Dx < plot.xaxis.max1D:
max1Dx = plot.xaxis.max1D
if max1Dy < plot.yaxis.max1D:
max1Dy = plot.yaxis.max1D
if max1Dc < plot.caxis.max1D:
max1Dc = plot.caxis.max1D
if max1Dx_RGB < plot.xaxis.max1D_RGB:
max1Dx_RGB = plot.xaxis.max1D_RGB
if max1Dy_RGB < plot.yaxis.max1D_RGB:
max1Dy_RGB = plot.yaxis.max1D_RGB
if max1Dc_RGB < plot.caxis.max1D_RGB:
max1Dc_RGB = plot.caxis.max1D_RGB
if max2D_RGB < plot.max2D_RGB:
max2D_RGB = plot.max2D_RGB
for plot in plots:
plot.xaxis.globalMax1D = max1Dx
plot.yaxis.globalMax1D = max1Dy
plot.caxis.globalMax1D = max1Dc
plot.xaxis.globalMax1D_RGB = max1Dx_RGB
plot.yaxis.globalMax1D_RGB = max1Dy_RGB
plot.caxis.globalMax1D_RGB = max1Dc_RGB
plot.globalMax2D_RGB = max2D_RGB
for runCardVals.passNo in [1, 2]:
for plot in plots:
plot.plot_plots()
plot.save('_norm' + str(runCardVals.passNo))
print('normalization finished')
def run_ray_tracing(
plots=[], repeats=1, updateEvery=1, pickleEvery=None, energyRange=None,
backend='raycing', beamLine=None, threads=1, processes=1,
generator=None, generatorArgs=[], generatorKWargs='auto', globalNorm=0,
afterScript=None, afterScriptArgs=[], afterScriptKWargs={}):
u"""
This function is the entry point of xrt.
Parameters are all optional except the 1st one. Please use them as keyword
arguments because the list of parameters may change in future versions.
*plots*: instance of :class:`~xrt.plotter.XYCPlot` or a sequence of
instances or an empty sequence if no graphical output is wanted.
*repeats*: int
The number of ray tracing runs. It should be stressed that
accumulated are not rays, which would be limited by the physical
memory, but rather the histograms from each run are summed up. In
this way the number of rays is unlimited.
*updateEvery*: int
Redrawing rate. Redrawing happens when the current iteration index
is divisible by *updateEvery*.
*pickleEvery*: int
Saving rate. Applicable to plots with a defined *persistentName*.
If None, the pickling will happen once at the end.
*energyRange*: [*eMin*: float, *eMax*: float]
Only in `shadow` backend: If not None, sets the energy range of
shadow source. Alternatively, this can be done directly inside
the *generator*.
*backend*: str
so far supported: {'shadow' | 'raycing' | 'dummy'}
*beamLine*: instance of :class:`~xrt.backends.raycing.BeamLine`, used
with `raycing` backend.
*threads*, *processes*: int or str
The number of parallel threads or processes, should not be greater
than the number of cores in your computer, otherwise it gives no
gain. The bigger of the two will be used as a signal for using
either :mod:`threading` or :mod:`multiprocessing`. If they are
equal, :mod:`threading` is used. See also
:ref:`performance tests<tests>`. If 'all' is given then the number
returned by multiprocessing.cpu_count() will be used.
.. warning::
You cannot use multiprocessing in combination with OpenCL
because the resources (CPU or GPU) are already shared by
OpenCL. You will get an error if *processes* > 1. You can still
use *threads* > 1 but with a little gain.
.. note::
For the :mod:`shadow` backend you must create ``tmp0``,
``tmp1`` etc. directories (counted by *threads* or *processes*)
in your working directory. Even if the execution is not
parallelized, there must be ``tmp0`` with the shadow files
prepared in it.
*generator*: generator object
A generator for running complex ray-tracing studies. It must modify
the optics, specify the graph limits, define the output file names
etc. in a loop and return to xrt by ``yield``.
See the supplied examples.
*generatorArgs*, *generatorKWargs*: list and (dictionary or 'auto')
If *generatorKWargs* is 'auto', the following keyword dictionary
will be used for the generator: kwargs = {} if *generator* is
defined within the caller of :func:`run_ray_tracing` or if
*generatorArgs* is not empty, otherwise
kwargs = {'plots'=pots, 'beamLine'=beamLine}.
.. _globalNorm:
*globalNorm*: bool
If True, the intensity of the histograms will be normalized to the
global maximum throughout the series of graphs. There are two
flavors of normalization:
1) only the heights of 1D histograms are globally normalized while
the brightness is kept with the normalization to the local
maximum (i.e. the maximum in the given graph).
2) both the heights of 1D histograms and the brightness of 1D and
2D histograms are globally normalized.
The second way is physically more correct but sometimes is less
visual: some of the normalized pictures may become too dark, e.g.
when you compare focused and strongly unfocused images. Both
normalizations are saved with suffixes ``_norm1`` and ``_norm2``
for you to select the better one.
Here is a normalization example where the intensity maximum was
found throughout a series of images for filters of different
thickness. The brightest image was for the case of no filter (not
shown here) and the normalization shown below was done relative to
that image:
+------------------+-----------------------------------------+
| normalized | |
| to local maximum | |image_nonorm| |
+------------------+-----------------------------------------+
| global | |
| normalization, | |
| type 1 | |image_norm1| |
+------------------+-----------------------------------------+
| global | |
| normalization, | |
| type 2 | |image_norm2| |
+------------------+-----------------------------------------+
.. |image_nonorm| imagezoom:: _images/filterFootprint2_I400mum.png
:scale: 50 %
.. |image_norm1| imagezoom:: _images/filterFootprint2_I400mum_norm1.png
:scale: 50 %
.. |image_norm2| imagezoom:: _images/filterFootprint2_I400mum_norm2.png
:scale: 50 %
*afterScript*: function object
This function is executed at the end of the current script. For
example, it may run the next ray-tracing script.
*afterScriptArgs*, *afterScriptKWargs*: list and dictionary
args and kwargs for *afterScript*.
"""
global runCardVals, runCardProcs, _plots
frm = inspect.stack()[1]
mod = inspect.getmodule(frm[0])
runfile = mod.__file__
# patch for starting a script with processes>1 from Spyder console
if not hasattr(mod, "__spec__"):
mod.__spec__ = None
if isinstance(plots, (list, tuple)):
_plots = plots
else:
_plots = [plots, ]
for plot in _plots:
if backend == 'raycing':
if plot.caxis.useCategory:
plot.caxis.limits = [raycing.hueMin, raycing.hueMax]
if isinstance(plot.rayFlag, int):
plot.rayFlag = plot.rayFlag,
if updateEvery < 1:
updateEvery = 1
if (repeats > 1) and (updateEvery > repeats):
updateEvery = repeats
cpuCount = multiprocessing.cpu_count()
if isinstance(processes, str):
if processes.startswith('a'): # all
processes = cpuCount
else:
processes = max(cpuCount // 2, 1)
if isinstance(threads, str):
if threads.startswith('a'): # all
threads = cpuCount
else:
threads = max(cpuCount // 2, 1)
runCardVals = RunCardVals(threads, processes, repeats, updateEvery,
pickleEvery, backend, globalNorm, runfile)
runCardProcs = RunCardProcs(
afterScript, afterScriptArgs, afterScriptKWargs)
runCardVals.cwd = os.getcwd()
if backend.startswith('shadow'):
from .backends import shadow
cpuCount = max(processes, threads)
shadow.check_shadow_dirs(cpuCount, runCardVals.cwd)
runCardVals.fWiggler, runCardVals.fPolar, runCardVals.blockNRays = \
shadow.init_shadow(cpuCount, runCardVals.cwd, energyRange)
elif backend == 'raycing':
runCardVals.beamLine = beamLine
if generator is None:
runCardProcs.generatorPlot = _simple_generator()
else:
if generatorKWargs == 'auto':
if (generator.__name__ in sys._getframe(1).f_locals) or\
len(generatorArgs) > 0:
# generator is defined within the caller function
kwargs = {}
else:
# outside the caller
kwargs = {'plots': plots, 'beamLine': beamLine}
else:
kwargs = generatorKWargs
runCardProcs.generatorPlot = generator(*generatorArgs, **kwargs)
if globalNorm:
runCardProcs.generatorNorm = generator(*generatorArgs, **kwargs)
if runCardProcs.generatorPlot is not None:
if sys.version_info < (3, 1):
runCardProcs.generatorPlot.next()
else:
next(runCardProcs.generatorPlot)
runCardVals.tstart = time.time()
runCardVals.tstartLong = time.localtime()
start_jobs()
plt.show()
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