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Paleomagnetism.org 2

Source code for the paleomagnetism.org application version 2. This is an unreleased version under development and can be found at https://beta.paleomagnetism.org.

Licensing

The source code for Paleomagnetism.org 2.0.0 is licensed under MIT that can be found under the LICENSE file.

This repository includes third-party software stored inside the lib directory. The code in this folder may be constrained by additional licenses and should be treated as such. The distribution of third-party software through this repository is warranted because of scientific reproducibility that cannot be guaranteed through a dynamic CDN.

Disclaimer

Paleomagnetism.org and its data contributors take care to ensure that the software, data, and metadata are of the highest possible quality. Users of the application assume all responsibility and risk for use of the data and application. In no event shall Paleomagnetism.org or any data providers be liable for any damages caused by, but not limited to, erroneous data or results.

All data processed with Paleomagnetism.org are treated locally and not sent over a network. Resources required for the functionality of the application are fetched initially when the user visits the page. Data that have been submitted to the Data Library are free of use and cannot be reused in unaltered form for commercial use.

We kindly remind you to cite all sources.

Paleomagnetism.org © 2015-2019. All rights reserved.

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pmag2's Issues

Bedding - Core orientation - Interpretation portal

If you change the bedding or core orientation in the interpretation portal, the interpreted directions disappear. And you have to re-do it again.

This is especially a pain after finding a consistent mistake (i.e. forgot to apply declination correction or applied a wrong one) after analyzing all the collection.

Can this be changed to keep the interpretation?

Fix mobile client

Data importing pages broken

Interpretation table overflows

Graph backgrounds are transparent (problem on night mode)

Keyboard not available. Alternative?

rotation files

I have been trying the .rot files from Gplates and I am unsure how pmag 2.0 respond to this.

The rotation file has to be complete (until 0!) and it has to be written in intervals of 10 Million years, otherwise it does not plot. While I understand that paleomagnetism.org can't just make extrapolations as GPlates does, and therefore your file should contain steps to be reliable, it is a pain to get .rot files from the reconstruction Gplates exports and move all the plates you want until 0! Is there anyway to make that simpler?

Some Pmag 1.0 files do not open

It says it cannot recognize the type of PCA (I guess forced or not) into the statistics portal. And therefore it ignores it.

Also once you do that, you cannot upload again and you have to refresh.

Plat and Plong in statistics

Gday Mathijs,

I got a request from Eric Font that I have considered possible (I think I can try to program it since it is pretty simple, but for you it will be about a minute). They asked me why in the statistic portal the table does not print the pole lat and long in addition to the pole statistics. Obviously that is implemented in the Geography portal (where if two sites are combined you get an averaged geographic lat-long) but I agree with Eric that getting that directly in the table makes the process simpler (and cost nothing). Obviously if data has not geographic coordinates those fields will end up blank. I think it is decent idea, it is data we already calculate so why not printing it too?

He had another suggestion, that I am not sure if it is so interesting and at least harder to do. It is the possibility of plotting the VGP both centered in the pole and at its virtual geographic position in a stereonet with shortcut to cycle it (e.g. number 9). I told him that he can get the average and error from the geographic portal, but he is interested in specimen level distribution. I am not sure if this makes sense for anybody else, and if that is easy or not to add, but definitely I am sure I cannot do that.

BCN2G format not working for "broken" lines

In the binary 2G format sometimes there is a "broken" line that is then repeated. E.g. the 110mT step:

image

Start at the third row near the beginning and is followed by no measurements but only NULL bytes. Then in the middle of row 6 the 110mT step appears again but with correct measurements.

Example file:

160-1.txt

Magstrat suggestion

Maybe it is a good idea to add an inclination only statistics there (like inclination only "fold test") especially for people working in loong cores (IODP or ICDP) which turn when drilling so the only bedding information they have is the dip but not the strike.

This test maybe useful, as well and as a side effect, to compare sites with suspicions of vertical axis rotations (so a traditional fold-test may not work properly), if inclinations are much better after the correction, then you can suspect on local rotations (or in undetected structural problems, like plunging axes, shearing...)

Cheers!

Library temporary hidden files

Since AGU journals are asking by default having your data stored in FAIR repositories, I think our library should have a 'temporary option' like MAGIC. That would be only visible to the people with the link (reviewers and editors) while under review and would be open upon acceptance.

The privacy can avoid some misunderstandings (for example, the necessity of adding extra analyses and ending up with two persistent identifiers). I have had this with the preprint issue, in which sometimes people get a little confused with the versions and things like that.

Collection of details

1: In the beta version, statistic portal do not open (or not always) .dir (2.0) files. This does not happen in the Master version. Example:
H.dir.zip

2: When saving a .dir file in where I have fitted circles the interpretation opens the saved points in the statistics. However, if I open the .dir again in the interpretation, I can only see the fitted direction and not the interpreted circle (and I do not know how to recover the circle). I think the fit chosen (line or plane) is the one that has to be preserved in the .dir file by default -what the user interpret from the raw data. I like the idea of keeping the fitted points as well, but that has to be in addition, and not the only.

  1. This is a suggestion. I still think that the final great circle fit should be in the statistics section, where you can decide collections (in the end a great circle could be used for two components, with two fits, for example one original and an overprint). Also some times, It is a good idea combining several sites into localities with far more set points and then fit the circles more accurately. We can't do that now.

Geography portal import

Konnichiwa,

At the import in the Geography portal there is a "default" import but it is not explained how that file works. Apparently it works in specimens, but which is the order and kind of data can we add (like age, bedding or so on...)

Also, is it going to be possible to add literature data? I would like it but skipping the resampling (which adds 0 value in that particular portal where all the rest are already averages)

Cheers!

Grouping components

If I write groups for components in the interpretation portal (let's component VRM-ViscousRemanence, and componet MT- Medium temperature and HT- High...) Then I can export but without seeing anything in the stereonet. Is that correct? I would expect being able to see the different components (either all in the plot with colors or changing them with a shortcut) and the possibility to merge them or not or export them separately and fitting circles between them, for example.

Metadata statistic portal

Statistics portal creates automatically geographic metadata when you combine sites, how does it do it? Wouldn't it be a good policy to allow the user to be able to define group "metadata" that goes together with the core metadata? That would allow being able to set the coordinates of locality combining several sites without losing the core metadata, and at the same time allowing to choose where to show the parachutes in the map.
Perhaps with a pop-up when you combine sites suggesting group metadata? Maybe the group metadata may include a comment in which you explain briefly why you merged collections, example: "two flanks of the same fold separated by 2 km same component, grouped to obtain a better pole with 50 cores"

Importing data in the import window: empty stereonets

Hi Jollyfant,

I've been testing the importing windows both through .csv files and in the importing window and, although the software says it does it, the results do not show in the stereonets that appear empty (or do not show at all).

This is a thing that we would like to fix, if we want old farts to use the platform and share their older results combined with newer etc, we need that option. Because for most of them re-fitting the data in the interpretation portal won't be an option (although it would be the best one)

Grouping and exporting groups

Grouping is great and really helpful. However, when opening the .dir file in the statistics portal, both groups form part of the same collection, and there is not (at least an obvious)form to separate them. For example, I have this file (attached) with a clear present day overprint and one component that is to the South East. I have separated them in groups (3 groups, but one might be incorrect).

I think the possibility to separate those groups into different collections directly (and not saving two different files by deleting interpretations etc) will facilitate the workflow. In fact, if we can choose which groups to separate or not in the statistics portal into collections I do not think my previous concern about grouping is relevant. I think it is a good solution, that improves the workflow, and transparency, You share your .dir file with the groups you think you have, and then the statistics with the collections, that may merge some groups based on statistics.
z
?.dir.zip

Problems submission data to the library

I am trying to submit .pub files to the library. The files were originally .pmag, I re-exported them as .pub (I am planning also to do .col files with the .dir ones but wanted first this).

Files are the following:
Rezaeian_2020.zip

And for all of our readers (!!) this is the associated paper:
https://www.sciencedirect.com/science/article/pii/S0040195120301426#ec0005

And this is the associated DOI:
https://doi.org/10.1016/j.tecto.2020.228459

So if someone is reading this and want this files get them and cite us!

Problem deleting components

Hey,
If the user has set two or more components, when deleting a component in the interpretation portal, the code deletes the first fitted, regardless which one you are picking to trash.

Export .kml does not work

I have exported the kml file (attached) and it does not open in Google Earth.

Open of file "/Users/danielpastorgalan/Downloads/collections.kml" failed: Only a single root feature allowed within tag

I have checked for the error in internet. However, the answers I found are not coincident with the paleomagnetism produced files. After checking the file, I couldn't see any problem so I think the problem is the graphic repository where it points to get the symbols. I am not 100% sure.
collections.kml.zip

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