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Create test implementations of new commondata format #1436

Closed
Zaharid opened this issue Oct 15, 2021 · 9 comments
Closed

Create test implementations of new commondata format #1436

Zaharid opened this issue Oct 15, 2021 · 9 comments
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@cschwan @alecandido @enocera @scarlehoff
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data toolchain

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@Zaharid
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Zaharid commented Oct 15, 2021

To make things in #1416 more concrete we agreed to try and produce test implementations of the (still fuzzy) current version of the idea for a couple of datasets.

The datasets should be one DIS and one hadronic and one of them should involve multiple (COMPOUND) fktables.

These should have:

  • A metadata file with the informations in the "runcards" folder, PLOTTING file, COMPOUND file and others.
  • A kinematics file with bin edges and central value in some format.
  • A data file with experimental central value and uncertainties (probably in a separate file).

The uncertainties should support a way of specifying correlated systematics across datasets. Probably also some way to deal with additive vs multiplicative.

Regarding formats, I would think for this a text format of some sort is more adequate (easier to read and exchange around) and also one that trivially round trips with pandas (ie better than csv), so maybe something like json.
@enocera
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enocera commented Nov 10, 2021 •
edited
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Let me see whether I can make any of the above a little more concrete. For the time being, let's focus on the dataset currently called NMCPD. It corresponds to the F2d/F2p ratio measured by NMC. This is the only COMPOUND DIS dataset.
I understand that we want the following files.

  1. * A metadata file with the informations in the "runcards" folder, PLOTTING file, COMPOUND file and others.

My understanding is that this is the first file that a developer would write when implementing a new dataset (or migrating an old dataset to the new format). I think that it should be as simple (minimal) as possible. Let's call it METADATA_NMCPD.json. A possible incarnation may look like as follows.

{
    "setname":  "NMPCPD",
    "arXiv":    "hep-ex/9611022",
    "hepdata":  "https://www.hepdata.net/record/ins426595",
    "ndata":    260,
    "nsys_exp": 5, 
    "proctype": "DIS_F2R",
    "compound": "RATIO",
    "experiment": "NMC",
    "nnpdf31_process": "DIS NC"
}

Here I already have some questions:

  • how are COMPOUND datasets treated by the new tool chain that produces FK tables?
  • which kind of information is actually required from the PLOTTING file?
  • which information should we import from the metadata.txt in the "runcard" folder?
  1. * A kinematics file with bin edges and central value in some format.

  2. * A data file with experimental central value and uncertainties (probably in a separate file).

I understand that these files should be the output of a small python script (for each dataset) that would eventually replace the current filter files in buildmaster. The file METADATA_<nameexp>.json is used as input to such a python script. Let's call the outputs KINEMATICS_NMCPD.json, DATA_NMCPD.json and EXP_UNCS_NMCPD.json. Possible incarnations of these outputs may look like as follows.

KINEMATICS_NMCPD.json 
```
{
    "kinematics_avg": [
	{ "x": [0.0015,
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    ]
    "kinematics_min": [
	{ "x": null },
	{ "Q2": null },
	{ "y": null }
    ]
    "kinematics_max": [
	{ "x": null },
	{ "Q2": null },
	{ "y": null }
    ]
}
```
DATA_NMCPD.json 
```
{
    "data" : [0.9815,
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}
```
EXP_UNCS_NMCPD.json 
```
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    ]    
}
```

Some remarks.

  • Incidentally, I realised that, in this specific experiment, the inelasticity y wasn't defined in the original buildmaster implementation, a fact that leads to a column of zeroes. This is inconsequential, however this is incorrect. That's an example of why, in my opinion, we shouldn't just "filter" the current COMMONDATA to convert old data into the new format. A fresh implementation may fix all these small bugs. With a fresh implementation we can also make sure that the data is retrieved from Hepdata as much as possible (NMC is on Hepdata, but the current rawdata file was taken from somewhere else - it's impossible to tell from where).
  • For some datasets, bin edges are not specified (as in the above case).
  • It's not yet clear to me how to accommodate dataset variants.
  • I think that the format is sufficiently flexible to accommodate multi-differential distributions (shouldn't it be just a matter of adding more entries to the KINEMATICS file?). I also think that we can specify "extrinsic" uncertainties in the METADATA and then have additional files, in a format similar to the EXP_UNC file, for these.

@alecandido
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alecandido commented Nov 10, 2021 •
edited
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May I suggest to use a details tag?

Like the following:

<details><summary>ciao come va?</summary>
<pre>
bene grazie
</pre>
</details>

Very long output makes the end of answer (and the rest of the conversation) a bit harder to access...

@alecandido
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I reply to things I'm aware of, but @cschwan's answer would be better than mine.

  • the flow of information between this and runcards should be the other way round: you define things in commondata, then if they are needed even in runcards we import them (though might be useful to take something during implementation since @cschwan already carefully worked out some stuffs)
  • at the moment plotting and metadata in runcards are together in a single file: I would say that we don't have to be consistent, but it would be nicer to be; so if we want them split we should rework even runcards ones (that takes nothing, it's just a matter of choices)
  • this is a bit trivial and maybe opinionated: I would not rely on filenames to group things, better to put in a single folder 
    <DATASET>/
|-- metadata.json
|-- plotting.json
|-- kinematics.json
|-- data.json
|-- exp_uncs.json
  • I'm not sure .json is the best format for these kind of data (standard is good, but maybe a suitable format might even be binary, if it's a standard one), but since it's not readable in any case, I would suggest to minimize blanks, and make it on a single line (i.e. like in standard library compact example, see next), or otherwise to compress them 
    import json
json.dumps([1, 2, 3, {'4': 5, '6': 7}], separators=(',', ':'))

@Zaharid
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Zaharid commented Nov 17, 2021

Let me see whether I can make any of the above a little more concrete. For the time being, let's focus on the dataset currently called NMCPD. It corresponds to the F2d/F2p ratio measured by NMC. This is the only COMPOUND DIS dataset. I understand that we want the following files.

1. > ```
   > * A metadata file with the informations in the "runcards" folder, PLOTTING file, COMPOUND file and others.
   > ```

My understanding is that this is the first file that a developer would write when implementing a new dataset (or migrating an old dataset to the new format). I think that it should be as simple (minimal) as possible. Let's call it METADATA_NMCPD.json. A possible incarnation may look like as follows.

{
    "setname":  "NMPCPD",
    "arXiv":    "hep-ex/9611022",
    "hepdata":  "https://www.hepdata.net/record/ins426595",
    "ndata":    260,
    "nsys_exp": 5, 
    "proctype": "DIS_F2R",
    "compound": "RATIO",
    "experiment": "NMC",
    "nnpdf31_process": "DIS NC"
}

As discussed, I think the YAML format may be more adequate for this.

Here I already have some questions:

* how are `COMPOUND` datasets treated by the new tool chain that produces FK tables?

I would think that very similarly to now from the point of view of the input information required (?)

* which kind of information is actually required from the `PLOTTING` file?

At this stage, I would say "all of it" and in the same format.

* which information should we import from the `metadata.txt` in the "runcard" folder?

All?

1. > ```
   > * A kinematics file with bin edges and central value in some format.
   > ```

2. > ```
   > * A data file with experimental central value and uncertainties (probably in a separate file).
   > ```

I understand that these files should be the output of a small python script (for each dataset) that would eventually replace the current filter files in buildmaster. The file METADATA_<nameexp>.json is used as input to such a python script. Let's call the outputs KINEMATICS_NMCPD.json, DATA_NMCPD.json and EXP_UNCS_NMCPD.json. Possible incarnations of these outputs may look like as follows.

As @alecandido was saying, having these in a folder might be a good idea.

KINEMATICS_NMCPD.json
DATA_NMCPD.json
EXP_UNCS_NMCPD.json

Some remarks.

* Incidentally, I realised that, in this specific experiment, the inelasticity `y` wasn't defined in the original buildmaster implementation, a fact that leads to a column of zeroes. This is inconsequential, however this is incorrect. That's an example of why, in my opinion, we shouldn't just "filter" the current `COMMONDATA` to convert old data into the new format. A fresh implementation may fix all these small bugs. With a fresh implementation we can also make sure that the data is retrieved from Hepdata as much as possible (NMC is on Hepdata, but the current rawdata file was taken from somewhere else - it's impossible to tell from where).

* For some datasets, bin edges are not specified (as in the above case).

I think inventing them (on a case by case basis) might be better than complicating the format with undefined support.

* It's not yet clear to me how to accommodate dataset variants.

Would need to be thought, but once everything is in a folder, it would be a matter of adding the files plus various kinds of information in the runcard, such as what are the variants and what is the default variant. For example (haven't really thought this too much):

variants:
   atlas_correlation_choice:
        exp_uncertainties_data:  EXP_UNC_ATLAS.json

default_variant: None # Ignore the above by default.
* I think that the format is sufficiently flexible to accommodate multi-differential distributions (shouldn't it be just a matter of adding more entries to the `KINEMATICS` file?). I also think that we can specify "extrinsic" uncertainties in the `METADATA` and then have additional files, in a format similar to the `EXP_UNC` file, for these.

Yes, we should just have n kinematics. The external uncertainties would be a file with the same format and added to the runcard.

That begs the question if we should have yet another piece of configuration for what the defaults are (as discussed elsewhere).

@enocera
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enocera commented Nov 17, 2021

@Zaharid Thanks for the detailed replies, that I'm going to use to work further on the prototype.

@scarlehoff
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@enocera I'm available for both helping with the prototype and acting as a pressure element, just let me know.

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enocera commented Jan 13, 2022

@scarlehoff Thanks - this is appreciated. I'll open a PR soon-ish and we will start from there.

@enocera
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enocera commented Jan 13, 2022

@scarlehoff You've got my blessing to piss me off.

@enocera enocera mentioned this issue Jan 19, 2022
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@scarlehoff
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Superseded by #1709

@scarlehoff scarlehoff mentioned this issue Dec 6, 2024
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