The two-volume open access book set LNCS 14576 + 14577 constitutes the proceedings of the 33rd European Symposium on Programming, ESOP 2024, which was held during April 6-11, 2024, in Luxemburg, as ...part of the European Joint Conferences on Theory and Practice of Software, ETAPS 2024. The 25 full papers and 1 fresh perspective paper presented in these proceedings were carefully reviewed and selected from 72 submissions. The papers were organized in topical sections as follows: Part I: Effects and modal types; bidirectional typing and session types; dependent types; Part II: Quantum programming and domain-specific languages; verification; program analysis; abstract interpretation.
Engineering a Compiler, Third Edition covers the latest developments in compiler technology, with new chapters focusing on semantic elaboration (the problems that arise in generating code from the ...ad-hoc syntax-directed translation schemes in a generated parser), on runtime support for naming and addressability, and on code shape for expressions, assignments and control-structures. Leading educators and researchers, Keith Cooper and Linda Torczon, have revised this popular text with a fresh approach to learning important techniques for constructing a modern compiler, combining basic principles with pragmatic insights from their own experience building state-of-the-art compilers.
Recognition and interpretation of paleoclimate signals in sedimentary proxy datasets are time consuming and subjective. Acycle is a comprehensive and easy-to-use software package for time series ...analysis in paleoclimate research and education. It is designed to speed paleoclimate time series analysis, especially cyclostratigraphy, and to provide objective methods for estimating astrochronology. Acycle provides for detrending with multiple options to track and remove secular trends. A selection of power spectral analysis methodologies is offered for the detection of periodic signals. Many of the functions are specific to cyclostratigraphy and astrochronology that are not found in standard statistical packages. A specialized function is provided to assess the astronomical (Milankovitch) forcing of paleoclimate series and search for the most likely sedimentation rate by evaluating the correlation coefficient between power spectra of an astronomical solution and sedimentary proxy data. Sedimentary noise modeling (for past sea-level changes) is also provided in Acycle. As an example, Acycle is applied to a sedimentary proxy series from the cyclostratigraphy of the Paleocene-Eocene thermal maximum (PETM) in Core BH9/05 from the Paleogene Central Basin, Svalbard. Acycle detects significant astronomical forcing in the proxy series and relatively stable sedimentation rates during and after the PETM. Acycle runs in the MATLAB environment or as stand-alone software on Windows and Macintosh OS X, and is open-source software.
•Acycle is signal processing software for paleoclimate research and education.•Many of the functions are specific to cyclostratigraphy and astrochronology.•Acycle includes models for sedimentary noise and sedimentation rate.•A fully implemented graphical user interface facilitates operator use.
Condor
, an open-source simulation tool to predict X-ray scattering amplitudes for flash X-ray imaging experiments, is introduced.
Flash X-ray imaging has the potential to determine structures down ...to molecular resolution without the need for crystallization. The ability to accurately predict the diffraction signal and to identify the optimal experimental configuration within the limits of the instrument is important for successful data collection. This article introduces
Condor
, an open-source simulation tool to predict X-ray far-field scattering amplitudes of isolated particles for customized experimental designs and samples, which the user defines by an atomic or a refractive index model. The software enables researchers to test whether their envisaged imaging experiment is feasible, and to optimize critical parameters for reaching the best possible result. It also aims to support researchers who intend to create or advance reconstruction algorithms by simulating realistic test data.
Condor
is designed to be easy to use and can be either installed as a Python package or used from its web interface (
http://lmb.icm.uu.se/condor
). X-ray free-electron lasers have high running costs and beam time at these facilities is precious. Data quality can be substantially improved by using simulations to guide the experimental design and simplify data analysis.
The
WavePropaGator
(
WPG
) package is a new interactive cross-platform open-source software framework for modeling of coherent and partially coherent X-ray wavefront propagation. The
WPG
addresses ...the needs of beamline scientists and user groups to facilitate the design, optimization and improvement of X-ray optics to meet their experimental requirements. The paper presents a general description of the package and gives some recent application examples.
This article describes the
WavePropaGator
(
WPG
) package, a new interactive software framework for coherent and partially coherent X-ray wavefront propagation simulations. The package has been developed at European XFEL for users at the existing and emerging free-electron laser (FEL) facilities, as well as at the third-generation synchrotron sources and future diffraction-limited storage rings. The
WPG
addresses the needs of beamline scientists and user groups to facilitate the design, optimization and improvement of X-ray optics to meet their experimental requirements. The package uses the
Synchrotron Radiation Workshop
(
SRW
) C/C++ library and its Python binding for numerical wavefront propagation simulations. The framework runs reliably under Linux, Microsoft Windows 7 and Apple Mac OS X and is distributed under an open-source license. The available tools allow for varying source parameters and optics layouts and visualizing the results interactively. The wavefront history structure can be used for tracking changes in every particular wavefront during propagation. The batch propagation mode enables processing of multiple wavefronts in workflow mode. The paper presents a general description of the package and gives some recent application examples, including modeling of full X-ray FEL beamlines and start-to-end simulation of experiments.
An overview of how the well established
CFEL–ASG Software Suite
(
CASS
) can be used for serial femtosecond crystallography data is given.
CASS
Foucar
et al.
(2012).
Comput. Phys. Commun.
183
, ...2207–2213 is a well established software suite for experiments performed at any sort of light source. It is based on a modular design and can easily be adapted for use at free-electron laser (FEL) experiments that have a biological focus. This article will list all the additional functionality and enhancements of
CASS
for use with FEL experiments that have been introduced since the first publication. The article will also highlight some advanced experiments with biological aspects that have been performed.
A description is given of a single-particle X-ray imaging reconstruction and simulation package using the expand–maximize–compress algorithm, named
Dragonfly
.
Single-particle imaging (SPI) with ...X-ray free-electron lasers has the potential to change fundamentally how biomacromolecules are imaged. The structure would be derived from millions of diffraction patterns, each from a different copy of the macromolecule before it is torn apart by radiation damage. The challenges posed by the resultant data stream are staggering: millions of incomplete, noisy and un-oriented patterns have to be computationally assembled into a three-dimensional intensity map and then phase reconstructed. In this paper, the
Dragonfly
software package is described, based on a parallel implementation of the expand–maximize–compress reconstruction algorithm that is well suited for this task. Auxiliary modules to simulate SPI data streams are also included to assess the feasibility of proposed SPI experiments at the Linac Coherent Light Source, Stanford, California, USA.
This article describes the software package
OnDA
: online data analysis and feedback for serial X-ray imaging.
This article describes a free and open-source data analysis utility designed for fast ...online feedback during serial X-ray diffraction and scattering experiments:
OnDA
(online data analysis). Three complete real-time monitors for common types of serial X-ray imaging experiments are presented. These monitors are capable of providing the essential information required for quick decision making in the face of extreme rates of data collection. In addition, a set of modules, functions and algorithms that allow developers to modify the provided monitors or develop new ones are provided. The emphasis here is on simple, modular and scalable code that is based on open-source libraries and protocols.
OnDA
monitors have already proven to be invaluable tools in several experiments, especially for scoring and monitoring of diffraction data during serial crystallography experiments at both free-electron laser and synchrotron facilities. It is felt that in the future the kind of fast feedback that
OnDA
monitors provide will help researchers to deal with the expected very high throughput data flow at next-generation facilities such as the European X-ray free-electron laser.
An integration optimization, triage and analysis tool (
IOTA
) is presented, which uses a grid-search approach to maximize the success of indexing and integrating serial X-ray free-electron laser ...diffraction images.
IOTA
also includes several useful tools for on-site diffraction data processing.
Serial femtosecond crystallography (SFX) uses an X-ray free-electron laser to extract diffraction data from crystals not amenable to conventional X-ray light sources owing to their small size or radiation sensitivity. However, a limitation of SFX is the high variability of the diffraction images that are obtained. As a result, it is often difficult to determine optimal indexing and integration parameters for the individual diffraction images. Presented here is a software package, called
IOTA
, which uses a grid-search technique to determine optimal spot-finding parameters that can in turn affect the success of indexing and the quality of integration on an image-by-image basis. Integration results can be filtered using
a priori
information about the Bravais lattice and unit-cell dimensions and analyzed for unit-cell isomorphism, facilitating an improvement in subsequent data-processing steps.
Here
cppxfel
, a software package for integration and post-refinement of serial femtosecond crystallography data, is released.
As serial femtosecond crystallography expands towards a variety of ...delivery methods, including chip-based methods, and smaller collected data sets, the requirement to optimize the data analysis to produce maximum structure quality is becoming increasingly pressing. Here
cppxfel
, a software package primarily written in C++, which showcases several data analysis techniques, is released. This software package presently indexes images using DIALS (diffraction integration for advanced light sources) and performs an initial orientation matrix refinement, followed by post-refinement of individual images against a reference data set.
Cppxfel
is released with the hope that the unique and useful elements of this package can be repurposed for existing software packages. However, as released, it produces high-quality crystal structures and is therefore likely to be also useful to experienced users of X-ray free-electron laser (XFEL) software who wish to maximize the information extracted from a limited number of XFEL images.
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