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Small corrections to various pages #500

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32 changes: 16 additions & 16 deletions docs/source/Emitting_patterns_2Dprojection.ipynb
Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,7 @@
"id": "5726620d",
"metadata": {},
"source": [
"The function used below needs the file ``xpsi/utilities/ProjectionTool.py``. <b>You can use this file and correspondent functions also without having X-PSI installed. </b>"
"The function used below needs the file ``xpsi/utilities/ProjectionTool.py``. <b>You can also use this file and the corresponding functions without having X-PSI installed. </b>"
]
},
{
Expand Down Expand Up @@ -101,7 +101,7 @@
"metadata": {},
"source": [
"X-PSI models have one or two hot spots.\n",
"According to the X-PSI naming convention we refer to them as the primary ('p') and secondary ('s'), in case two hot spots are modeled."
"According to the X-PSI naming convention we refer to them as the primary ('p') and secondary ('s'), if two hot spots are modeled."
]
},
{
Expand Down Expand Up @@ -489,7 +489,7 @@
"id": "f0f7f8bb",
"metadata": {},
"source": [
"We can also change these contours to start from the center of the projection, instead of form the poles, by leaving the argument empty."
"We can also change these contours to start from the center of the projection, instead of from the poles, by leaving the argument empty."
]
},
{
Expand Down Expand Up @@ -719,7 +719,7 @@
"id": "ef79e90a",
"metadata": {},
"source": [
"Other names for hot spots with two emitting components are \"EDT\" ('E' for Eccentric) and \"CDT\" ('C' for concentric). In this case none of these could be our model, according to the configurations allowed by X-PSI, as the superseding component should have a smaller radius than the ceding one in those cases. This is also confirmed by the appearing warning, if we try to set the model to \"EDT\"."
"Other names for hot spots with two emitting components are \"EDT\" ('E' for Eccentric) and \"CDT\" ('C' for concentric). In this case none of these could be our model, according to the configurations allowed by X-PSI, as the superseding component should have a smaller radius than the ceding one in those cases. This is also confirmed by the warning that appears if we try to set the model to \"EDT\"."
]
},
{
Expand Down Expand Up @@ -1059,7 +1059,7 @@
"id": "b0d4d9d7",
"metadata": {},
"source": [
"The omitting is drawn in black. Note that these parameter values lead to the formation of an emitting arc, represented by the part of the blue circle not covered by the black one."
"The omitting region is drawn in black. Note that these parameter values lead to the formation of an emitting arc, represented by the part of the blue circle not covered by the black one."
]
},
{
Expand Down Expand Up @@ -1300,13 +1300,13 @@
"metadata": {},
"source": [
"In X-PSI we can also define models with 2 hot spots, a primary one and a secondary one.\n",
"According to the X-PSI naming convention, there are two way to build a two hot spot model: <br>\n",
"According to the X-PSI naming convention, there are two ways to build a two hot spot model: <br>\n",
"<ul>\n",
" <li>using two hot spot with different associated name, e.g. ST and PST, that becomes ST+PST model;</li>\n",
" <li>using two hot spots with different associated names, e.g. ST and PST, that becomes ST+PST model;</li>\n",
" <li>using the same geometry for both the hot spots, with the possible addition of restrictions on the parameter values of the secondary. We define them adding after the name of the hot spot:</li>\n",
" <ul>\n",
" <li><b>-S</b>: this means that all the properties of the secondary hot spot are derived from the properties of the primary hot spot; in particular we assume the secondary to have the same temperature and angular radius of the primary and to be antipodal respect to the primary.</li>\n",
" <li><b>-Ua</b>: models ending in this way (as in Salmi et al. 2022 __ADD__LINK) constraint the secondary location to be antipodal to the primary but leaves the angular radius and temperature free.</li>\n",
" <li><b>-Ua</b>: models ending in this way (as in `Salmi et al. 2022 <https://ui.adsabs.harvard.edu/abs/2022ApJ...941..150S/abstract>`_) constrain the secondary location to be antipodal to the primary but leave the angular radius and temperature free.</li>\n",
" <li><b>-U</b>: models ending in this way have no constraints on the properties of the secondary based on the ones of the primary.</li>\n",
" </ul>\n",
"</ul>\n",
Expand Down Expand Up @@ -1597,7 +1597,7 @@
"id": "ffca1026",
"metadata": {},
"source": [
"So here we see for example that the secondary hot spot has the shape of a ring (this is the topology associated to CST hot spots). The image also show that the antipodal image of the primary hot spot would overlap with the secondary."
"So here we see for example that the secondary hot spot has the shape of a ring (this is the topology associated with CST hot spots). The image also shows that the antipodal image of the primary hot spot would overlap with the secondary."
]
},
{
Expand Down Expand Up @@ -1692,7 +1692,7 @@
"id": "a8270727",
"metadata": {},
"source": [
"Let us transform the CST in PST."
"Let us transform the CST into PST."
]
},
{
Expand Down Expand Up @@ -1832,7 +1832,7 @@
"metadata": {},
"source": [
"<h3> TEST B.2.1) Testing 2 hot spot models composed of the same type of hot spot: symmetric case</h3>\n",
"Under this case, the string inputs recognised as points of view are only the ones relative to the primary hot spot."
"In this case, the string inputs recognised as points of view are only the ones relative to the primary hot spot."
]
},
{
Expand Down Expand Up @@ -1936,7 +1936,7 @@
"id": "1da4c7cf",
"metadata": {},
"source": [
"The point of view allowed follow the same logic as if the model was \"PST+PST\", so we have: \"I\" (from Earth), \"PE\" (primary emitting center), \"PO\" (primary omitting center), \"SE\" (secondary emitting center) and \"SO\" (secondary omitting center. When in doubt you can still type \"P\" or \"S\" and if those do not work, the option will appear in the error message."
"The point of view allowed follows the same logic as if the model was \"PST+PST\", so we have: \"I\" (from Earth), \"PE\" (primary emitting center), \"PO\" (primary omitting center), \"SE\" (secondary emitting center) and \"SO\" (secondary omitting center. When in doubt you can still type \"P\" or \"S\" and if those do not work, the option will appear in the error message."
]
},
{
Expand Down Expand Up @@ -2246,15 +2246,15 @@
"id": "516d3c99",
"metadata": {},
"source": [
"<h3> TEST B.2.3) Testing 2 hot spot models composed of the same type of hot spot: uncorrelated case<h3>"
"<h3> TEST B.2.3) Testing 2 hot spot models composed of the same type of hot spot: uncorrelated case</h3>"
]
},
{
"cell_type": "markdown",
"id": "e4e49e44",
"metadata": {},
"source": [
"In this case, the two hot spots of the model have the same name but their properties are completely uncorrelated. This is equivalent in writing twice the hot spot name divided by \"+\" (e.g. \"ST-U\" is equivalent to \"ST+ST\"). In case there are more different derived parameters between the two hot spots, the suggestion is to add the correspondent parameters in the dictionary and effectively convert your model to a \"-U\" model. In this case the points of view allowed through include centers of the primary as well of the secondary components."
"In this case, the two hot spots of the model have the same name but their properties are completely uncorrelated. This is equivalent to writing the hot spot name twice, joined by \"+\" (e.g. \"ST-U\" is equivalent to \"ST+ST\"). If there are more different derived parameters for the two hot spots, the suggestion is to add the corresponding parameters in the dictionary and effectively convert your model to a \"-U\" model. In this case the points of view allowed include centers of the primary as well of the secondary components."
]
},
{
Expand Down Expand Up @@ -2452,15 +2452,15 @@
"id": "960de114",
"metadata": {},
"source": [
"<h3>EXAMPLE: Circle of Hell (new prior on PST + another hot spot made by only emitting components) now allowed previously not allowed configurations</h3>"
"<h3>EXAMPLE: Circle of Hell (new prior on PST + another hot spot made by only emitting components), previously not allowed configurations that are now permitted</h3>"
]
},
{
"cell_type": "markdown",
"id": "01a9d271",
"metadata": {},
"source": [
"Below we show a couple of configurations that in Riley et al. 2019 were not allowed by the X-PSI prior for the ST+PST; but are now included in our priors. "
"Below we show a couple of configurations that in `Riley et al. 2019 <https://ui.adsabs.harvard.edu/abs/2019ApJ...887L..21R/abstract>`_ were not allowed by the X-PSI prior for ST+PST; but which are now included in our priors. "
]
},
{
Expand Down
4 changes: 2 additions & 2 deletions docs/source/Global_surface_emission.ipynb
Original file line number Diff line number Diff line change
Expand Up @@ -964,7 +964,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"Let's display a set of sky phase-averaged maps (which are indentical to the phase-resolved maps for this axisymmetric surface radiation field specification):"
"Let's display a set of sky phase-averaged maps (which are identical to the phase-resolved maps for this axisymmetric surface radiation field specification):"
]
},
{
Expand Down Expand Up @@ -1371,7 +1371,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"Note that although the star looks lensed, it is merely a projection (mimicking Scwarzschild light bending for an equatorial observer) that allows us to render all $4\\pi$ steradians of the surface. The real lensing is yet to come! First we need to force our exterior spacetime to be that of Schwarzschild:"
"Note that although the star looks lensed, it is merely a projection (mimicking Schwarzschild light bending for an equatorial observer) that allows us to render all $4\\pi$ steradians of the surface. The real lensing is yet to come! First we need to force our exterior spacetime to be that of Schwarzschild:"
]
},
{
Expand Down
8 changes: 4 additions & 4 deletions docs/source/Modeling.ipynb
Original file line number Diff line number Diff line change
Expand Up @@ -3620,7 +3620,7 @@
"\n",
"We interface with the sampler UltraNest is a similar manner as MultiNest: we define some runtime settings, and then pass those settings together with `likelihood` and `prior` objects to a wrapper from the [Sample](sample.rst) module. Note that the output below is generated with the temperature of the secondary hot region as a *free* parameter, similarly to the MultiNest example above. \n",
"\n",
"In this example, we will run the sampler with a maximum of a 10 iterations. For a real inference problem, we don't recommend this. See [UltraNest's FAQ](https://johannesbuchner.github.io/UltraNest/issues.html#how-should-i-choose-the-number-of-live-points) and references therin for more information about choosing sampler settings. \n",
"In this example, we will run the sampler with a maximum of a 10 iterations. For a real inference problem, we don't recommend this. See [UltraNest's FAQ](https://johannesbuchner.github.io/UltraNest/issues.html#how-should-i-choose-the-number-of-live-points) and references therein for more information about choosing sampler settings. \n",
"\n",
"To run UltraNest, we first define the parameters that are periodic or *wrapped* to inform UltraNest of boundary properties:"
]
Expand All @@ -3640,10 +3640,10 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"Next, we define the `sampler_params` which is a dictionary of the keyword arguments passed class `Sample.UltranestSampler` to initialise the sampler. UltraNest uses a reactive nested sampling algorithm, meaning it adapts the number of live points during the run. Therfore, we define a minimum (and maximum) number of live points instead of a fixed number. \n",
"Next, we define the `sampler_params` which is a dictionary of the keyword arguments passed class `Sample.UltranestSampler` to initialise the sampler. UltraNest uses a reactive nested sampling algorithm, meaning it adapts the number of live points during the run. Therefore, we define a minimum (and maximum) number of live points instead of a fixed number. \n",
"\n",
"Some useful keyword arguments that are not used in this example are: \n",
"- `log_dir` to specify the directory where the output files are stored. As a default, `log_dir='output'`, so the output will be stored in a foler called `output` in the current directory. Unless otherwise specified, UltraNest will automatically create fres sub-directiories called e.g. `run1` with incremeting numbers. \n",
"- `log_dir` to specify the directory where the output files are stored. As a default, `log_dir='output'`, so the output will be stored in a folder called `output` in the current directory. Unless otherwise specified, UltraNest will automatically create sub-directories called e.g. `run1` with incrementing numbers. \n",
"- `resume=True` for if you want to resume a run. As a default, `resume=subfolder` which creates a fresh sub-directory in `log_dir`\n"
]
},
Expand Down Expand Up @@ -4709,7 +4709,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"I'm actually unsure why a such small changes in the Poisson-distributed random variable expectations yields such large differences in the random variates for the same GSL RNG seed. For a substantial subset of elements, the random variates *are* equal, and that is not always where the difference in expectations is zero or relatively small. We consider this an open problem: please get in touch if you happen to read this and you have some insight you can share!"
"We're actually unsure why a such small changes in the Poisson-distributed random variable expectations yields such large differences in the random variates for the same GSL RNG seed. For a substantial subset of elements, the random variates *are* equal, and that is not always where the difference in expectations is zero or relatively small. We consider this an open problem: please get in touch if you happen to read this and you have some insight you can share!"
]
},
{
Expand Down
2 changes: 1 addition & 1 deletion docs/source/Modeling_without_statistics.ipynb
Original file line number Diff line number Diff line change
Expand Up @@ -118,7 +118,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"We can instanciate the `spacetime` by defining all parameters with a given value. In this case, all parameters will be fixed because the `bounds` are not specified (empty dictionary). **Note that all parameters must be defined at least once in `bounds` or `values`.** "
"We can instantiate the `spacetime` by defining all parameters with a given value. In this case, all parameters will be fixed because the `bounds` are not specified (empty dictionary). **Note that all parameters must be defined at least once in `bounds` or `values`.** "
]
},
{
Expand Down
6 changes: 3 additions & 3 deletions docs/source/Post-processing.ipynb
Original file line number Diff line number Diff line change
Expand Up @@ -397,7 +397,7 @@
"source": [
"## Background plot\n",
"\n",
"Plot the inferred background. Since the example is simple, we do not have all the samples needed in `post_equal_weight.dat` and the background distribution can not be plotted."
"Plot the inferred background. Since the example is simple, we do not have all the samples needed in `post_equal_weight.dat` and the background distribution cannot be plotted."
]
},
{
Expand Down Expand Up @@ -1159,7 +1159,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"Now let’s plot the standardised Poissonian residuals of the first run. Tou have different options of what to plot that are proposed here. You can choose to plot the bolometric pulse (data and model with the chi square), the clustering information and to blur the residuals. "
"Now let’s plot the standardised Poissonian residuals of the first run. You have different options of what to plot that are proposed here. You can choose to plot the bolometric pulse (data and model with the chi square), the clustering information and to blur the residuals. "
]
},
{
Expand Down Expand Up @@ -1265,7 +1265,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"For all the post processing can also choose a specific parameter vector `parameters_vector` to plot the associated plot instead of drawing random samples from the posterior. Here I take the truth and this can be done for ant of the following plot :"
"For all the post processing you can also choose a specific parameter vector `parameters_vector` to make the associated plot instead of drawing random samples from the posterior. Here we take the ground truth - this can be done for any of the following plots :"
]
},
{
Expand Down
7 changes: 3 additions & 4 deletions docs/source/acknowledgements.rst
Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,7 @@ Those involved in maintenance and development (technical and scientific).
* Lucien Mauviard-Haag (lucien.mauviard-haag[at]irap.omp.eu), IRAP
* Tuomo Salmi (tuomo.salmi[at]helsinki.fi), University of Helsinki
* Pierre Stammler (pstammler[at]irap.omp.eu), IRAP
* Serena Vinciguerra (s.vinciguerra[at]uva.nl), University of Amsterdam
* Serena Vinciguerra, University of Amsterdam
* Anna Watts (a.l.watts[at]uva.nl), University of Amsterdam

**Past members**
Expand Down Expand Up @@ -100,7 +100,6 @@ X-PSI see :ref:`applications`.
Funding
~~~~~~~

Development of X-PSI has been funded by two ERC Grants (PI Anna Watts),
ERC Starting Grant No. 639217 CSINEUTRONSTAR and ERC Consolidator
Grant No. 865768 AEONS. The IRAP team acknowledges the support of
Development of X-PSI has been funded by ERC Starting Grant No. 639217 CSINEUTRONSTAR, ERC Consolidator
Grant No. 865768 AEONS, and NWO ENW-XL grant OCENW.XL21.XL21.038 *Probing the phase diagram of Quantum Chromodynamics* (all PI Anna Watts). The IRAP team acknowledges the support of
the CNES in the development of X-PSI.
1 change: 1 addition & 0 deletions docs/source/applications.rst
Original file line number Diff line number Diff line change
Expand Up @@ -91,6 +91,7 @@ __ Zenodo_
PPM for other sources
*********************

**Das et al. 2024** `(ApJ submitted) <https://ui.adsabs.harvard.edu/abs/2024arXiv241116528D/abstract>`_ *Pulse Profiles of Accreting Neutron Stars from GRMHD Simulations*.

**Dorsman et al. 2024** `(MNRAS submitted) <https://ui.adsabs.harvard.edu/abs/2024arXiv240907908D/abstract>`_ *Parameter constraints for accreting millisecond pulsars with synthetic NICER data*.

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