First version of paper for joss

.github/workflows/draft-pdf.yml

@@ -0,0 +1,27 @@
+on:
+  push:
+    paths:
+      - paper/**
+      - .github/workflows/draft-pdf.yml
+
+jobs:
+  paper:
+    runs-on: ubuntu-latest
+    name: Paper Draft
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Build draft PDF
+        uses: openjournals/openjournals-draft-action@master
+        with:
+          journal: joss
+          # This should be the path to the paper within your repo.
+          paper-path: paper/paper.md
+      - name: Upload
+        uses: actions/upload-artifact@v4
+        with:
+          name: paper
+          # This is the output path where Pandoc will write the compiled
+          # PDF. Note, this should be the same directory as the input
+          # paper.md
+          path: paper/paper.pdf

paper/paper.bib

@@ -0,0 +1,213 @@
+@article{losada_three-point_2024,
+    author = {Losada, J. M. and Helgeland, A. D. and Terry, J. L. and Garcia, O. E.},
+    title = "{A three-point velocity estimation method for two-dimensional coarse-grained imaging data}",
+    journal = {AIP Advances},
+    volume = {14},
+    number = {9},
+    pages = {095102},
+    year = {2024},
+    month = {09},
+    doi = {10.1063/5.0197251},
+}
+
+@article{dippolito_convective_2011,
+	title = {Convective transport by intermittent blob-filaments: {Comparison} of theory and experiment},
+	volume = {18},
+	number = {6},
+	journal = {Physics of Plasmas},
+	author = {D'Ippolito, D. A. and Myra, J. R. and Zweben, S. J.},
+	year = {2011},
+	doi = {10.1063/1.3594609},
+}
+
+@article{fiedler_coherent_1988,
+    title = {Coherent structures in turbulent flows},
+    journal = {Progress in Aerospace Sciences},
+    volume = {25},
+    number = {3},
+    pages = {231-269},
+    year = {1988},
+    issn = {0376-0421},
+    doi = {10.1016/0376-0421(88)90001-2},
+    author = {H.E. Fiedler},
+}
+
+@inproceedings{nosov_coherent_2009,
+    author = {V. V. Nosov and V. M. Grigoriev and P. G. Kovadlo and V. P. Lukin and E. V. Nosov and A. V. Torgaev},
+    title = {{Coherent structures in turbulent atmosphere}},
+    volume = {7296},
+    booktitle = {Fifteenth International Symposium on Atmospheric and Ocean Optics/Atmospheric Physics},
+    editor = {Gennadii G. Matvienko and Yurii N. Ponomarev},
+    organization = {International Society for Optics and Photonics},
+    publisher = {SPIE},
+    pages = {729609},
+    keywords = {turbulence, spectrum, coherent structure, Benard cell, stochastization scenario},
+    year = {2009},
+    doi = {10.1117/12.823804},
+}
+
+@article{zweben_invited_2017,
+	title = {Invited {Review} {Article}: {Gas} puff imaging diagnostics of edge plasma turbulence in magnetic fusion devices},
+	volume = {88},
+	issn = {10897623},
+	doi = {10.1063/1.4981873},
+	number = {4},
+	journal = {Review of Scientific Instruments},
+	author = {Zweben, S. J. and Terry, J. L. and Stotler, D. P. and Maqueda, R. J.},
+	year = {2017},
+	pmid = {28456269},
+    pages = {041101},
+}
+
+@article{offeddu_analysis_2023,
+    author = {Offeddu, N. and Wüthrich, C. and Han, W. and Theiler, C. and Golfinopoulos, T. and Terry, J. L. and Marmar, E. and Ravetta, A. and Van Parys, G.},
+    title = {Analysis techniques for blob properties from gas puff imaging data},
+    journal = {Review of Scientific Instruments},
+    volume = {94},
+    number = {3},
+    pages = {033512},
+    year = {2023},
+    month = {03},
+    issn = {0034-6748},
+    doi = {10.1063/5.0133506},
+}
+
+@article{garcia_stochastic_2016,
+    author = {Garcia, O. E. and Kube, R. and Theodorsen, A. and Pécseli, H. L.},
+    title = {Stochastic modelling of intermittent fluctuations in the scrape-off layer: Correlations, distributions, level crossings, and moment estimation},
+    journal = {Physics of Plasmas},
+    volume = {23},
+    number = {5},
+    pages = {052308},
+    year = {2016},
+    month = {05},
+    issn = {1070-664X},
+    doi = {10.1063/1.4951016},
+}
+
+@article{militello_two-dimensional_2018,
+    author = {Militello, F. and Farley, T. and Mukhi, K. and Walkden, N. and Omotani, J. T.},
+    title = {A two-dimensional statistical framework connecting thermodynamic profiles with filaments in the scrape off layer and application to experiments},
+    journal = {Physics of Plasmas},
+    volume = {25},
+    number = {5},
+    pages = {056112},
+    year = {2018},
+    month = {05},
+    issn = {1070-664X},
+    doi = {10.1063/1.5017919},
+}
+
+@article{losada_tde_2025,
+    author = {Losada, J. M. and Garcia, O. E.},
+    title = {Time delay velocity estimation from a superposition of localized and uncorrelated pulses},
+    journal = {Physics of Plasmas},
+    volume = {32},
+    number = {4},
+    pages = {042505},
+    year = {2025},
+    month = {04},
+    doi = {10.1063/5.0261066},
+}
+
+@article{militello_relation_2016,
+    doi = {10.1088/0741-3335/58/12/125004},
+    year = {2016},
+    month = {oct},
+    publisher = {IOP Publishing},
+    volume = {58},
+    number = {12},
+    pages = {125004},
+    author = {Militello, F and Omotani, J T},
+    title = {On the relation between non-exponential scrape off layer profiles and the dynamics of filaments},
+    journal = {Plasma Physics and Controlled Fusion},
+}
+
+@article{veltri_mhd_1999,
+    doi = {10.1088/0741-3335/41/3A/071},
+    url = {https://dx.doi.org/10.1088/0741-3335/41/3A/071},
+    year = {1999},
+    month = {mar},
+    publisher = {},
+    volume = {41},
+    number = {3A},
+    pages = {A787},
+    author = {Pierluigi Veltri},
+    title = {MHD turbulence in the solar wind: self-similarity, intermittency and coherent structures},
+    journal = {Plasma Physics and Controlled Fusion},
+}
+
+@article{lowen_power_1990,
+    author={Lowen, S.B. and Teich, M.C.},
+    journal={IEEE Transactions on Information Theory},
+    title={Power-law shot noise},
+    year={1990},
+    volume={36},
+    number={6},
+    pages={1302-1318},
+    doi={10.1109/18.59930}
+}
+
+@article{bak_self_1988,
+  title = {Self-organized criticality},
+  author = {Bak, Per and Tang, Chao and Wiesenfeld, Kurt},
+  journal = {Phys. Rev. A},
+  volume = {38},
+  issue = {1},
+  pages = {364--374},
+  numpages = {0},
+  year = {1988},
+  month = {Jul},
+  publisher = {American Physical Society},
+  doi = {10.1103/PhysRevA.38.364},
+  url = {https://link.aps.org/doi/10.1103/PhysRevA.38.364}
+}
+
+@article{kociscak_modeling_2023,
+	author = {{Kočiščák, S.} and {Kvammen, A.} and {Mann, I.} and {Sørbye, S. H.} and {Theodorsen, A.} and {Zaslavsky, A.}},
+	title = {Modeling Solar Orbiter dust detection rates in the inner heliosphere as a {Poisson} process},
+	DOI= "10.1051/0004-6361/202245165",
+	url= "https://doi.org/10.1051/0004-6361/202245165",
+	journal = {A&A},
+	year = 2023,
+	volume = 670,
+	pages = "A140",
+}
+
+@article{losada_stochastic_2023,
+    author = {Losada, J. M. and Theodorsen, A. and Garcia, O. E.},
+    title = {Stochastic modeling of blob-like plasma filaments in the scrape-off layer: Theoretical foundation},
+    journal = {Physics of Plasmas},
+    volume = {30},
+    number = {4},
+    pages = {042518},
+    year = {2023},
+    month = {04},
+    issn = {1070-664X},
+    doi = {10.1063/5.0144885},
+}
+
+@article{losada_stochastic_2024,
+    author = {Losada, J. M. and Paikina, O. and Garcia, O. E.},
+    title = {Stochastic modeling of blob-like plasma filaments in the scrape-off layer: Correlated amplitudes and velocities},
+    journal = {Physics of Plasmas},
+    volume = {31},
+    number = {4},
+    pages = {042514},
+    year = {2024},
+    month = {04},
+    issn = {1070-664X},
+    doi = {10.1063/5.0196938},
+}
+
+@article{hoyer_xarray_2017,
+  title     = {xarray: {N-D} labeled arrays and datasets in {Python}},
+  author    = {Hoyer, S. and J. Hamman},
+  journal   = {Journal of Open Research Software},
+  volume    = {5},
+  number    = {1},
+  year      = {2017},
+  publisher = {Ubiquity Press},
+  doi       = {10.5334/jors.148},
+  url       = {https://doi.org/10.5334/jors.148}
+}

paper/paper.md

@@ -0,0 +1,140 @@
+---
+title: 'Blobmodel: A Python package for generating superpositions of pulses in one and two dimensions'
+tags:
+  - Python
+  - pulses
+  - imaging data 
+  - tokamaks
+  - turbulence
+authors:
+  - name: Juan M. Losada
+    orcid: 0000-0003-2054-1384
+    equal-contrib: true
+    affiliation: 1
+  - name: Gregor Decristoforo
+    orcid: 0000-0002-7616-0946
+    equal-contrib: true # (This is how you can denote equal contributions between multiple authors)
+    affiliation: 1
+affiliations:
+ - name: UiT, The Arctic University of Norway
+   index: 1
+date: 11 February 2025
+bibliography: paper.bib
+
+---
+
+# Summary
+
+`blobmodel` is a Python library for generating synthetic data that mimics the behavior
+of moving pulses in a turbulent environment. It creates controlled datasets where the
+true motion of each pulse is known, allowing researchers to gain further understanding on
+the statistical outputs of such systems as well as to test and improve analysis 
+and tracking algorithms. While originally developed for studying
+turbulence in fusion experiments, `blobmodel` can be applied to any field where
+turbulence leads to the generation of structures propagating in one or two dimensions.
+The software is open source, easy to use, and designed to support reproducible research.
+
+# Statement of need
+
+Understanding and analyzing the motion of structures in turbulent systems is crucial
+in many areas of research, including plasma physics [@dippolito_convective_2011],
+fluid dynamics [@fiedler_coherent_1988], and atmospheric science [@nosov_coherent_2009]. 
+
+More widely, the study of the statistical characteristics resulting from the superposition
+of uncorrelated propagating pulses is of importance in fields such as astrophysical plasmas [@veltri_mhd_1999], 
+detection rates of interplanetary dust [@kociscak_modeling_2023], 
+$1/f$ noise in self-organized critical systems [@bak_self_1988], 
+and shot noise in electronics [@lowen_power_1990].
+
+In experimental studies, imaging diagnostics are often used to capture the 
+evolution of these structures [@zweben_invited_2017], but extracting reliable velocity information from such 
+data remains challenging [@offeddu_analysis_2023]. Many existing analysis methods rely on assumptions about 
+the underlying dynamics and must be tested against known reference data to ensure
+accuracy.
+
+Several stochastic models have been developed describing a point process resulting from the superposition of 
+uncorrelated structures with random arrival times [@garcia_stochastic_2016]; or propagating in one [@losada_stochastic_2023]
+or two [@militello_two-dimensional_2018] spatial dimensions. In the simplest cases, it is possible
+to derive analytical expressions for different statistical quantities such as probability density functions, 
+autocorrelation functions, power spectral densities and spatial dependence of the mean or other higher-order
+moments [@garcia_stochastic_2016; @militello_relation_2016; @losada_stochastic_2023]. More general scenarios 
+require numerical tools [@losada_stochastic_2024], and synthetic realizations of the model.
+
+`blobmodel` addresses this need by providing a framework for generating synthetic 
+datasets resulting from a superposition of uncorrelated pulses [@militello_two-dimensional_2018; @losada_tde_2025]:
+$$
+    \Phi(x,y,t) = \sum_{k=1}^{K} a_k \varphi\left( \frac{x-v_k(t-t_k)}{\ell_{x, k}}, \frac{(y-y_k)-w_k(t-t_k)}{\ell_{y, k}}\right) ,
+$$
+where:
+
+- $a_k$ represents the initial pulse amplitude.
+- $v_k$ and $w_k$ are the horizontal and vertical velocity components, respectively.
+- $t_k$ is the pulse arrival time at the position $x=0$, $y=y_k$.
+- $y_k$ is the pulse vertical position at time $t=t_k$.
+- $\ell_{x, k}$ and $\ell_{y, k}$ are the horizontal and vertical pulse sizes, respectively.
+- $\varphi$ is an unspecified pulse shape.
+
+All these parameters, except for the pulse shape $\varphi$ are assumed to be random variables. 
+Additionally, each pulse may be tilted on an angle given by an additional random variable $\theta_k$ with respect to its centre.
+
+The framework allows an explicit definition of all relevant process parameters, including:
+
+- All pulse parameters if defined as degenerate random variables.
+- All distribution functions of the pulse parameters otherwise.
+- Optionally, a drainage term $\tau_\shortparallel$ that models an exponential decay in the pulse amplitude through an
+additional factor $e^{-\frac{t-t_k}{\tau_\shortparallel}}$ in the pulse evolution.
+- Spatial and temporal resolution.
+- Degree of pulse overlap by setting different ratios of number of pulses to signal length and domain size.
+- Total duration of the process.
+
+This allows researchers to systematically test and benchmark
+tracking algorithms and velocity estimation techniques in a controlled setting. 
+Originally developed for studying turbulence-driven transport in fusion plasma
+experiments, blobmodel is applicable to any system where turbulence leads to the
+formation of moving structures in one or two-dimensional space. By offering an open-source
+and easily accessible tool, blobmodel supports the development and validation of 
+analysis methods used in experimental and computational research. 
+
+To the authors' knowledge, no other packages exist which provide a comprehensive, 
+open-source framework for generating synthetic datasets of uncorrelated, propagating
+pulses in one or two spatial dimensions, with fully customizable statistical distributions
+for pulse parameters and explicit control over spatial and temporal resolution, pulse overlap,
+and drainage effects, as implemented in `blobmodel`.
+
+For more details visit [blobmodel's documentation](https://blobmodel.readthedocs.io/en/latest/).
+
+The package has been used to generate synthetic data to study and compare the robustness of
+velocity estimation techniques on coarse-grained imaging data [@losada_three-point_2024].
+
+Additionally, theoretically predicted radial profiles from stochastic modelling
+[@garcia_stochastic_2016; @militello_relation_2016] agree with those obtained with `blobmodel`. 
+
+# Implementation details
+
+The evolution of the pulses is discretized by the `Blob` class in a three dimensional grid
+(two space and one time dimensions) according to the above formula. The discretization grid is provided
+by the `Geometry` and the superposition of all pulses is performed by the `Model` class, which also contains functions
+for the model initialization. The generation of pulses with pulse parameters following user-specified distribution
+functions is performed by the `BlobFactory`.
+
+Since the simulation domain has finite spatial extent, pulses may originate or extend beyond its boundaries.
+If a pulse has a non-bound shape, such as a Gaussian, its tails can still contribute to the
+superposition inside the domain. However, in long simulations, most pulses will exist outside the 
+domain for the majority of the time, making it computationally inefficient to account for all of them.
+To improve efficiency, a `speed_up` flag has been added to `Model.make_realization`. When enabled, the model
+ignores pulses whose contribution within the domain falls below a user-defined `error` threshold. 
+This allows for significant computational savings while maintaining accuracy in the simulation.
+
+Periodicity in the vertical direction is an optional feature. It is implemented by replicating each pulse 
+at vertical positions $y_b\pm L_y$, where $y_b$ is the pulse's original position and $L_y$ is the vertical
+size of the simulation domain. This ensures that blobs crossing the upper or lower boundaries are correctly 
+wrapped around, maintaining continuity in the periodic direction.
+
+This package is fully compatible with `xarray` [@hoyer_xarray_2017], with all outputs provided as `xarray` datasets
+for easy handling and analysis.
+
+# Acknowledgements
+
+This work was supported by the UiT Aurora Centre Program, UiT The Arctic University of Norway (2020).
+
+# References