xrt-1.1.0

xrt-1.1.0

LICENSE.txt

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+The MIT License
+---------------
+
+Copyright (c) 2014 Konstantin Klementiev, Roman Chernikov
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

PKG-INFO

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+Metadata-Version: 1.1
+Name: xrt
+Version: 1.1.0
+Summary: Ray tracing and wave propagation in x-ray regime, primarily meant for modeling synchrotron beamlines and beamline elements
+Home-page: http://pythonhosted.org/xrt
+Author: ('Konstantin Klementiev', 'Roman Chernikov')
+Author-email: first DOT last AT gmail DOT com
+License: MIT License
+Description: 
+        Package xrt (XRayTracer) is a python software library for ray tracing and wave
+        propagation in x-ray regime. It is primarily meant for modeling synchrotron
+        sources, beamlines and beamline elements. Includes a GUI tool for creating
+        scripts.
+
+        Features of xrt
+        ---------------
+        * *Rays and waves*. Classical ray tracing and wave propagation via Kirchhoff
+          integrals, also freely intermixed. No further approximations, such as thin
+          lens or paraxial. The optical surfaces may have figure errors, analytical or
+          measured. In wave propagation, partially coherent radiation is treated by
+          incoherent addition of coherently diffracted fields generated per electron.
+
+        * *Publication quality graphics*. 1D and 2D position histograms are
+          *simultaneously* coded by hue and brightness. Typically, colors represent
+          energy and brightness represents beam intensity. The user may select other
+          quantities to be encoded by colors: angular and positional distributions,
+          various polarization properties, beam categories, number of reflections,
+          incidence angle etc. Brightness can also encode partial flux for a selected
+          polarization and incident or absorbed power. Publication quality plots are
+          provided by matplotlib with image formats PNG, PostScript, PDF and SVG.
+
+        * *Unlimited number of rays*. The colored histograms are *cumulative*. The
+          accumulation can be stopped and resumed.
+
+        * *Parallel execution*. xrt can be run in parallel in several threads or
+          processes (can be opted), which accelerates the execution on multi-core
+          computers. Alternatively, xrt can use the power of GPUs via OpenCL for
+          running special tasks such as the calculation of an undulator source or
+          performing wave propagation.
+
+        * *Scripting in Python*. xrt can be run within Python scripts to generate a
+          series of images under changing geometrical or physical parameters. The image
+          brightness and 1D histograms can be normalized to the global maximum
+          throughout the series.
+
+        * *Synchrotron sources*. Bending magnet, wiggler, undulator and elliptic
+          undulator are calculated internally within xrt. There is also a legacy
+          approach to sampling synchrotron sources using the codes `ws` and `urgent`
+          which are parts of XOP package. Please look the section `Comparison of
+          synchrotron source codes` for the comparison between the implementations. If
+          the photon source is one of the synchrotron sources, the total flux in the
+          beam is reported not just in number of rays but in physical units of ph/s.
+          The total power or absorbed power can be opted instead of flux and is
+          reported in W. The power density can be visualized by isolines. The magnetic
+          gap of undulators can be tapered. Undulators can be calculated in near field.
+          Undulators can be calculated on GPU, with a high gain in computation speed,
+          which is important for tapering and near field calculations.
+
+        * *Shapes*. There are several predefined shapes of optical elements implemented
+          as python classes. The inheritance mechanism simplifies creation of other
+          shapes. The user specifies methods for the surface height and the surface
+          normal. For asymmetric crystals, the normal to the atomic planes can be
+          additionally given. The surface and the normals are defined either in local
+          (x, y) coordinates or in user-defined parametric coordinates. Parametric
+          representation enables closed shapes such as capillaries or wave guides. It
+          also enables exact solutions for complex shapes (e.g. a logarithmic spiral)
+          without any expansion. The methods of finding the intersections of rays with
+          the surface are very robust and can cope with pathological cases as sharp
+          surface kinks. Notice that the search for intersection points does not
+          involve any approximation and has only numerical inaccuracy which is set by
+          default as 1 fm. Any surface can be combined with a (differently and variably
+          oriented) crystal structure and/or (variable) grating vector. Surfaces can be
+          faceted.
+
+        * *Energy dispersive elements*. Implemented are crystals in dynamical
+          diffraction, gratings (also with efficiency calculations), Fresnel zone
+          plates, Bragg-Fresnel optics and multilayers in dynamical diffraction.
+          Crystals can work in Bragg or Laue cases, in reflection or in transmission.
+          The two-field polarization phenomena are fully preserved, also within the
+          Darwin diffraction plateau, thus enabling the ray tracing of crystal-based
+          phase retarders.
+
+        * *Materials*. The material properties are incorporated using three different
+          tabulations of the scattering factors, with differently wide and differently
+          dense energy meshes. Refractive index and absorption coefficient are
+          calculated from the scattering factors. Two-surface bodies, such as plates or
+          refractive lenses, are treated with both refraction and absorption.
+
+        * *Multiple reflections*. xrt can trace multiple reflections in a single
+          optical element. This is useful, for example in 'whispering gallery' optics
+          or in Montel or Wolter mirrors.
+
+        * *Non-sequential optics*. xrt can trace non-sequential optics where different
+          parts of the incoming beam meet different surfaces. Examples of such optics
+          are poly-capillaries and Wolter mirrors.
+
+        * *Global coordinate system*. The optical elements are positioned in a global
+          coordinate system. This is convenient for modeling a real synchrotron
+          beamline. The coordinates in this system can be directly taken from a CAD
+          library. The optical surfaces are defined in their local systems for the
+          user's convenience.
+
+        * *Beam categories*. xrt discriminates rays by several categories: `good`,
+          `out`, `over` and `dead`. This distinction simplifies the adjustment of
+          entrance and exit slits. An alarm is triggered if the fraction of dead rays
+          exceeds a specified level.
+
+        * *Portability*. xrt runs on Windows and Unix-like platforms, wherever you can
+          run python.
+
+        * *Examples*. xrt comes with many examples, see the galleries.
+
+        xrtQook -- a GUI for creating scripts
+        -------------------------------------
+        The main interface to xrt is through a python script. Many examples of such
+        scripts can be found in the supplied folder 'examples'. The script imports the
+        modules of xrt, instantiates beamline parts, such as synchrotron or geometric
+        sources, various optical elements, apertures and screens, specifies required
+        materials for reflection, refraction or diffraction, defines plots and sets job
+        parameters.
+
+        The Qt tool xrtQook takes these ingredients and prepares a ready to use script
+        that can be run within the tool itself or in an external Python context.
+        xrtQook features a parallelly updated help panel that, unlike the main
+        documentation, provides a complete list of parameters for the used classes,
+        also including those from the parental classes. xrtQook writes/reads the
+        recipes of beamlines into/from xml files.
+
+        Dependencies
+        ------------
+        numpy, scipy and matplotlib are required. If you use OpenCL for calculations on
+        GPU or CPU, you need AMD/NVIDIA drivers, ``Intel CPU only OpenCL runtime``
+        (these are search key words), pytools and pyopencl. Spiderlib is highly
+        recommended for nicer view of xrtQook.
+
+        Python 2 and 3
+        --------------
+        The code can run in both Python branches without any modification.
+
+Platform: OS Independent
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Science/Research
+Classifier: Natural Language :: English
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 2
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Topic :: Scientific/Engineering :: Physics
+Classifier: Topic :: Scientific/Engineering :: Visualization

README.txt

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+Installation
+------------
+
+Unzip the .zip file into a suitable directory and use
+sys.path.append(path-to-xrt)
+in your script. You can also install xrt to the standard location by running 
+python setup.py install from the directory where you have unzipped the archive,
+which is less convenient if you try different versions of xrt and/or different
+versions of python.
+
+To run xrtQook, simply start xrtQook.pyw from xrt/xrtQook or, if you have
+installed xrt by running setup.py, type �xrtQook.pyw� from any location.
+
+Note that python-64-bit is by ~20% faster than the 32-bit version (tested with
+WinPython).

doc/Makefile

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+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+PAPER         =
+BUILDDIR      = _build
+
+# Internal variables.
+PAPEROPT_a4     = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+# the i18n builder cannot share the environment and doctrees with the others
+I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+
+.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext
+
+help:
+	@echo "Please use \`make <target>' where <target> is one of"
+	@echo "  html       to make standalone HTML files"
+	@echo "  dirhtml    to make HTML files named index.html in directories"
+	@echo "  singlehtml to make a single large HTML file"
+	@echo "  pickle     to make pickle files"
+	@echo "  json       to make JSON files"
+	@echo "  htmlhelp   to make HTML files and a HTML help project"
+	@echo "  qthelp     to make HTML files and a qthelp project"
+	@echo "  devhelp    to make HTML files and a Devhelp project"
+	@echo "  epub       to make an epub"
+	@echo "  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
+	@echo "  latexpdf   to make LaTeX files and run them through pdflatex"
+	@echo "  text       to make text files"
+	@echo "  man        to make manual pages"
+	@echo "  texinfo    to make Texinfo files"
+	@echo "  info       to make Texinfo files and run them through makeinfo"
+	@echo "  gettext    to make PO message catalogs"
+	@echo "  changes    to make an overview of all changed/added/deprecated items"
+	@echo "  linkcheck  to check all external links for integrity"
+	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
+
+clean:
+	-rm -rf $(BUILDDIR)/*
+
+html:
+	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+dirhtml:
+	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
+
+singlehtml:
+	$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
+	@echo
+	@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
+
+pickle:
+	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
+	@echo
+	@echo "Build finished; now you can process the pickle files."
+
+json:
+	$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
+	@echo
+	@echo "Build finished; now you can process the JSON files."
+
+htmlhelp:
+	$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
+	@echo
+	@echo "Build finished; now you can run HTML Help Workshop with the" \
+	      ".hhp project file in $(BUILDDIR)/htmlhelp."
+
+qthelp:
+	$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
+	@echo
+	@echo "Build finished; now you can run "qcollectiongenerator" with the" \
+	      ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
+	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/xrt.qhcp"
+	@echo "To view the help file:"
+	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/xrt.qhc"
+
+devhelp:
+	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
+	@echo
+	@echo "Build finished."
+	@echo "To view the help file:"
+	@echo "# mkdir -p $$HOME/.local/share/devhelp/xrt"
+	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/xrt"
+	@echo "# devhelp"
+
+epub:
+	$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
+	@echo
+	@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
+
+latex:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo
+	@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
+	@echo "Run \`make' in that directory to run these through (pdf)latex" \
+	      "(use \`make latexpdf' here to do that automatically)."
+
+latexpdf:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo "Running LaTeX files through pdflatex..."
+	$(MAKE) -C $(BUILDDIR)/latex all-pdf
+	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+text:
+	$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
+	@echo
+	@echo "Build finished. The text files are in $(BUILDDIR)/text."
+
+man:
+	$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
+	@echo
+	@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
+
+texinfo:
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo
+	@echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
+	@echo "Run \`make' in that directory to run these through makeinfo" \
+	      "(use \`make info' here to do that automatically)."
+
+info:
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo "Running Texinfo files through makeinfo..."
+	make -C $(BUILDDIR)/texinfo info
+	@echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
+
+gettext:
+	$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
+	@echo
+	@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
+
+changes:
+	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
+	@echo
+	@echo "The overview file is in $(BUILDDIR)/changes."
+
+linkcheck:
+	$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
+	@echo
+	@echo "Link check complete; look for any errors in the above output " \
+	      "or in $(BUILDDIR)/linkcheck/output.txt."
+
+doctest:
+	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
+	@echo "Testing of doctests in the sources finished, look at the " \
+	      "results in $(BUILDDIR)/doctest/output.txt."