ProTheRaMon : a GATE simulation framework for proton therapy range monitoring using PET imaging

Objective. This paper reports on the implementation and shows examples of the use of the ProTheRaMon framework for simulating the delivery of proton therapy treatment plans and range monitoring using positron emission tomography (PET). ProTheRaMon offers complete processing of proton therapy treatment plans, patient CT geometries, and intra-treatment PET imaging, taking into account therapy and imaging coordinate systems and activity decay during the PET imaging protocol specific to a given proton therapy facility. We present the ProTheRaMon framework and illustrate its potential use case and data processing steps for a patient treated at the Cyclotron Centre Bronowice (CCB) proton therapy center in Krakow, Poland. Approach. The ProTheRaMon framework is based on GATE Monte Carlo software, the CASToR reconstruction package and in-house developed Python and bash scripts. The framework consists of five separated simulation and data processing steps, that can be further optimized according to the user’s needs and specific settings of a given proton therapy facility and PET scanner design. Main results. ProTheRaMon is presented using example data from a patient treated at CCB and the J-PET scanner to demonstrate the application of the framework for proton therapy range monitoring. The output of each simulation and data processing stage is described and visualized. Significance. We demonstrate that the ProTheRaMon simulation platform is a high-performance tool, capable of running on a computational cluster and suitable for multi-parameter studies, with databases consisting of large number of patients, as well as different PET scanner geometries and settings for range monitoring in a clinical environment. Due to its modular structure, the ProTheRaMon framework can be adjusted for different proton therapy centers and/or different PET detector geometries. It is available to the community via github (Borys et al 2022)

A comparison of one- and two-dimensional approaches to modelling flood inundation over complex upland floodplains

A much understudied aspect of flood inundation is examined, i.e. upland environments with topographically complex floodplains. Although the presence of high-resolution topographic data (e.g. lidar) has improved the quality of river flood inundation predictions, the optimum dimensionality of hydraulic models for this purpose has yet to be fully evaluated for situations of both topographic and topological (i.e. the connectivity of floodplain features) complexity. In this paper, we present the comparison of three treatments of upland flood inundation using: (a) a one-dimensional (1D) model (HEC-RAS v. 3·1·2) with the domain defined as series of extended cross-sections; (b) the same 1D model, but with the floodplain defined by a series of storage cells, hydraulically connected to the main river channel and other storage cells on the floodplain according to floodplain topological characteristics; (c) a two-dimensional (2D) diffusion wave treatment, again with explicit representation of floodplain structural features. The necessary topographic and topological data were derived using lidar and Ordnance Survey Landline data. The three models were tested on a 6 km upland reach of the River Wharfe, UK. The models were assessed by comparison with measured inundation extent. The results showed that both the extended cross-section and the storage cell 1D modes were conceptually problematic. They also resulted in poorer model predictions, requiring incorrect parameterization of the main river to floodplain flux in order to approach anything like the level of agreement observed when the 2D diffusion wave treatment was assessed. We conclude that a coupled 1D-2D treatment is likely to provide the best modelling approach, with currently available technology, for complex floodplain configurations

Reconceptualising coarse sediment problems in rivers as catchment-scale and diffuse

This paper assesses river channel management activities in the context of the interaction between coarse sediment delivery, climate change, river channel response and flood risk. It uses two main sources of evidence: (1) an intensive instrumentation of an upland river catchment using both traditional hydrometric and novel sediment sensing methods; and (2) a sediment delivery model that combines a treatment of sediment generation from mass failure with a treatment of the connectivity of this failed material to the drainage network. The field instrumentation suggests that the precipitation events that deliver sediment from hillslopes to the drainage network are different to those that transfer sediment within the network itself. Extreme events, that could occur at any time in the year (i.e. they are not dependent on wet antecedent conditions), were crucial for sediment delivery. However, sustained high river flows were responsible for the majority of transfer within the river itself. Application of three downscaling methods to climate model predictions for the 2050s and 2080s suggested a significant increase in the number and potential volume of delivery events by the 2050s, regardless of the climate downscaling scenario used. First approximations suggested that this would translate into annual bed level aggradation rates of between 0.10 and 0.20 m per year in the downstream main channel reaches. Second, the importance of this delivery for flood risk studies was confirmed by simulating the effects of 16 months of measured in-channel simulation with river flows scaled for climate change to the 2050s and 2080s. Short-term sedimentation could result in similar magnitude increases in inundated area for 1 in 0.5 and 1 in 2 year floods to those predicted for the 2050s in relation to increases in flow magnitude. Finally, we were able to develop an alternative approach to river management in relation to coarse sediment delivery, based upon reducing the rates of coarse sediment delivery through highly localised woodland planting, under the assumption that reducing delivery rates should reduce the rate of channel migration and hence the magnitude of the bank erosion problem. Thus, the paper demonstrates the need to conceptualise local river management problems in upland river environments as point scale manifestations of a diffuse sediment delivery process, with a much more explicit focus on the catchment scale, if our river systems are to become more insulated from the impacts of future climate changes

Interactions between sediment delivery, channel change, climate change and flood risk in a temperate upland environment

This paper uses numerical simulation of flood inundation based on a coupled one-dimensional-two-dimensional treatment to explore the impacts upon flood extent of both long-term climate changes, predicted to the 2050s and 2080s, and short-term river channel changes in response to sediment delivery, for a temperate upland gravel-bed river. Results show that 16 months of measured in-channel sedimentation in an upland gravel-bed river cause about half of the increase in inundation extent that was simulated to arise from climate change. Consideration of the joint impacts of climate change and sedimentation emphasized the non-linear nature of system response, and the possibly severe and synergistic effects that come from combined direct effects of climate change and sediment delivery. Such effects are likely to be exacerbated further as a result of the impacts of climate change upon coarse sediment delivery. In generic terms, these processes are commonly overlooked in flood risk mapping exercises and are likely to be important in any river system where there are high rates of sediment delivery and long-term transfer of sediment to floodplain storage (i.e. alluviation involving active channel aggradation and migration). Similarly, attempts to reduce channel migration through river bank stabilization are likely to exacerbate this process as without bank erosion, channel capacity cannot be maintained. Finally, many flood risk mapping studies rely upon calibration based upon combining contemporary bed surveys with historical flood outlines, and this will lead to underestimation of the magnitude and frequency of floodplain inundation in an aggrading system for a flood of a given magnitude