[WIP][CR] Adding vitamins and toxin levels monitor functions to Blood Analyser CBM #37582

eilaattwood · 2020-01-31T09:01:25Z

Summary

SUMMARY: Features "Add vitamins and toxin levels monitor functions to Blood Analyser CBM"

Purpose of change

#37508 - Vitamins level monitor implementation

Describe the solution

Adding vitamins and toxin levels monitor functions to Blood Analyser CBM

Describe alternatives you've considered

Not really. However, it's just the part of the work, i think, we could also add an item that can perform quick test without CBM

Testing

WIP
Created a character with Blood Analyser CBM and tryed to run it. Nothing awful happened.

Additional context

Comment required about how information should be presented to the player. And maybe what else should be added.

Added initial implementation of analysing blood for vitamin and toxin levels

src/bionics.cpp

tenmillimaster · 2020-01-31T13:57:36Z

The "toxins" are byproducts of unchecked mutation by the Blob, exposing you to cellular structures and other cellular building blocks never seen before on the prime plane (the place where the game plays out). As such, there wouldn't be a way to predict what the contaminant is, and thus no way to determine what level it's at in blood. (Short of physically separating all components out of the blood somehow, which is infeasible for an implant.)

anothersimulacrum · 2020-01-31T14:21:35Z

src/bionics.cpp

+        static const std::set<vitamin_id> trackable_vits = {vitamin_id( "iron" ), vitamin_id( "calcium" ), vitamin_id( "vitA" ), vitamin_id( "vitB" ), vitamin_id( "vitC" ), vitamin_id( "mutant_toxin" )};
+        for( const auto &v : vit_all ) {
+            if( trackable_vits.count( v.first ) ) {
+                vit.push_back( v.second.name() + _( " level is " ) + to_string( vitamin_get( v.first ) ) );


Just printing the raw integer value here isn't helpful, because nobody knows what that means.
I'd suggest adding a vitamin::get_string_level() or something of the sort that gives you a string based on how much of the vitamin you have, and how close you are to each stage of either excess/deficiency.

Yeap, that's why I asked for a comment how it should be finally represented. And what those numbers are really mean in reality.

eilaattwood · 2020-02-02T10:48:16Z

The "toxins" are byproducts of unchecked mutation by the Blob, exposing you to cellular structures and other cellular building blocks never seen before on the prime plane (the place where the game plays out). As such, there wouldn't be a way to predict what the contaminant is, and thus no way to determine what level it's at in blood. (Short of physically separating all components out of the blood somehow, which is infeasible for an implant.)

But the game UI directly shows us the toxin percentage in the mutant meat...

scorpion451 · 2020-02-02T19:55:53Z

When there's no specific toxin to test for (say, Bob works in a batch chemical plant and has a laundry list of things that could be making him sick), what you look for are the easily detected effects of toxicity. Metabolic panels have been giving a general idea of overall organ health via automated testing machines since the 1950's. It can't tell you what the toxin is, but it can tell you that something is damaging the kidneys and liver or throwing electrolyte levels out of whack, and how bad it's gotten.

There are also additional simple tests that the CMB could easily look for as a compliment to the general metabolic analysis, such as inflammatory chemicals like histamines and cytokines, and high levels of cellular debris in the blood (meaning cells are dying off at an unusually high rate somewhere).

You could get super-detailed here if you wanted, but it makes sense to distill it down to a general "toxin buildup" rating for simplicity and clarity rather than trying to simulate all the individual values and require a course in hematology to read the results.

eilaattwood · 2020-02-03T08:52:09Z

May anyone point me where that vitamin levels came from and what exactly do they mean? They are just magic abstract numbers or they have some meaning behind them?

tenmillimaster · 2020-02-04T10:56:35Z

When there's no specific toxin to test for (say, Bob works in a batch chemical plant and has a laundry list of things that could be making him sick), what you look for are the easily detected effects of toxicity. Metabolic panels have been giving a general idea of overall organ health via automated testing machines since the 1950's. It can't tell you what the toxin is, but it can tell you that something is damaging the kidneys and liver or throwing electrolyte levels out of whack, and how bad it's gotten.

Ok, to do a comprehensive metabolic panel we're probably gonna need some reagents which probably can't be re-used and will need to be sourced.

We can use ion selective electrodes for some of the simple Ions. Sourcing some protons to do a bicarb titration probably won't be terribly difficult.

The rest present challenges, necessitating compounds not found in the human body, or questions as to how to harvest them from the body.

Test	Reagent needed
Albumin	supply of bromocresol purple
Blood Urea Nitrogen (BUN)	supply of urease
Creatinine	supply of creatinase or picrate salts
Total Bilirubin	supply of sulfanilic acid
Total Protein	supply of copper sulfate
Alanine Aminotransferase (ALT)	l-alanine harvesting method
Alkaline Phosphatase (ALP)	p-nitrophenyl-phosphate or other suitable bio phosphate harvesting method
Aspartate Aminotransferase (AST)	Aspartic acid harvesting method

How do you propose to do that, and justify an expensive implant with likely lower precision than a traditional test panel? And how would the implant know to report "toxins" just based on this panel? It would report the panel, not toxins.

esotericist · 2020-02-04T11:10:18Z

May anyone point me where that vitamin levels came from and what exactly do they mean? They are just magic abstract numbers or they have some meaning behind them?

for the normal vitamins: they are literally the percentage of RDA (as per FDA) for the food item in question.

for the mutant meat: same basic concept, except we have a much lower threshold for mutant meat toxicity than we would vitaminosis.

nothing really magic here, just having an idea of how much of each you should (or can) have a day.

eilaattwood · 2020-02-05T06:21:07Z

May anyone point me where that vitamin levels came from and what exactly do they mean? They are just magic abstract numbers or they have some meaning behind them?

for the normal vitamins: they are literally the percentage of RDA (as per FDA) for the food item in question.

for the mutant meat: same basic concept, except we have a much lower threshold for mutant meat toxicity than we would vitaminosis.

nothing really magic here, just having an idea of how much of each you should (or can) have a day.

Okay, that's about vitamin levels in the food. But what about vitamin levels in the character? Are they just a sum of food that was consumed? How can I align in-game levels with the IRL normal levels? That is what I can't understand.

src/bionics.cpp

anothersimulacrum · 2020-02-07T14:00:22Z

src/bionics.cpp

+        const int effect_spacing = ( good.empty() && bad.empty() ) ? 1 : good.size() + bad.size();
+        const size_t win_h = std::min( static_cast<size_t>( TERMY ),
+                                       effect_spacing + vit.size() + tox.size() + drug.size() + cnt.size() + 2 );
+        //const int win_w = 46;


Please remove any commented out code, it's no longer useful.

Suggested change

//const int win_w = 46;

Will do when figure out how exactly I should optimize Analyzer window width.

anothersimulacrum · 2020-02-07T14:00:26Z

src/vitamin.cpp

+        } else if( id_ == "iron" ) {
+            norm_level = 1.23f;
+        } else if( id_ == "calcium" ) {
+            norm_level = 1.1f;


This data (norm_level), should probably be in JSON, not hardcoded.

Or dynamically determined.

anothersimulacrum · 2020-02-07T14:01:29Z

src/bionics.cpp

-        const int win_w = 46;
+        const std::map<vitamin_id, vitamin> &vit_all = vitamin::all();
+        for( const auto &v : vit_all ) {
+            if( !v.second.has_flag( "NO_DISPLAY" ) && !v.second.has_flag( "NOT_IN_BLOOD" ) ) {


Please document the new flag and the additional behavior of the old one.

Maybe we shouldn't check NO_DISPLAY here at all. If vitamin is not showing in comestibles UI doesn't necessary mean it shouldn't be displayed by Blood Analyzer.

I think there's definitely use for a flag that means that the vitamin is never displayed - perhaps the food one should have a separate flag?

I wanted to use NOT_IN_BLOOD flag to tell Blood Analyzer to ignore that vitamin... Maybe should change it to BLOOD_ANALYZER to do the opposite - only show vitamins with this flag.

anothersimulacrum · 2020-02-07T14:05:17Z

src/vitamin.cpp

+        } else if( id_ == "calcium" ) {
+            norm_level = 1.1f;
+        }
+        const float v_level = norm_level * qty / disease_[0].first;


Some vitamins don't have anything in disease_, this will be attempting to access a non-existing member of a vector.
Additionally, this means that vitamins that use disease_excess_ will always get the default message.
Also, this element is supposed to be loaded as 0 if it is not specified. I'm not sure if that would happen in practice, but there could be potential for a divide by zero here.

Fair point, thanks.

anothersimulacrum · 2020-02-07T14:10:11Z

src/vitamin.cpp

+            }
+        }
+    }
+    return string_format( "%s level is %d.", name(), qty );


This appears to just give you the exact vitamin level if the vitamin is either a disease_excess vitamin (addressed earlier), or quantity is 0.
I don't think the vitamin quantity should ever be directly displayed, because it's not information that makes much sense to the player, and they have no need to know it - I'd suggest changing this message to %s level is normal, or something similar.

Just changed it to output empty string. Unknown vitamins shouldn't be shown by Analyzer at all.

Co-Authored-By: anothersimulacrum <anothersimulacrum@gmail.com>

scorpion451 · 2020-02-09T22:01:52Z

In response to the reagents thing on the metabolic panel: they aren't necessary. The reagents are just for color reactions- they react with the targeted molecules to form distinctive colors, which makes it easy to automatically analyze even with simple machinery.

Best compact advanced option would be a spectrography-based scanner- lets you detect the component molecules of a sample based on how it fluoresces or absorbs various frequencies of light. Literally have handheld ones these days that you can point at a leaf and get a read on chlorophyll concentrations. The really cool ones can monitor chemical reactions in a living cell by analyzing how the spectrography signature changes over time.

stale · 2020-03-11T05:34:49Z

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions. Please do not 'bump' or comment on this issue unless you are actively working on it. Stale issues, and stale issues that are closed are still considered.

ZhilkinSerg · 2020-03-16T20:30:21Z

Closing to clean up PR queue. Feel free to ping me to reopen after 0.E is out.

Update bionics.cpp

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Added initial implementation of analysing blood for vitamin and toxin levels

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ifreund added <Enhancement / Feature> New features, or enhancements on existing Bionics CBM (Compact Bionic Modules) Items: Food / Vitamins Comestibles and drinks [C++] Changes (can be) made in C++. Previously named `Code` labels Feb 1, 2020

weekly-digest bot mentioned this pull request Feb 2, 2020

Weekly Digest (26 January, 2020 - 2 February, 2020) #37641

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eilaattwood added 2 commits February 3, 2020 10:02

Rework display feature to check for flags instead of list

0b674d2

astyle

5968490

eilaattwood added 2 commits February 3, 2020 10:58

Added placeholder for vitamin::get_string_level function

7c8c3bc

Added print functions for all vitamin types

47346bd

eilaattwood added 3 commits February 7, 2020 14:57

Initial implementation of vitamin::get_string_level

f8430a5

Update vitamin.cpp

d2979b8

Update vitamin.cpp

4f349e2

anothersimulacrum reviewed Feb 7, 2020

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eilaattwood and others added 5 commits February 7, 2020 16:17

Update src/bionics.cpp

eb04686

Co-Authored-By: anothersimulacrum <anothersimulacrum@gmail.com>

Update src/bionics.cpp

ddce6be

Co-Authored-By: anothersimulacrum <anothersimulacrum@gmail.com>

Update src/bionics.cpp

469b274

Co-Authored-By: anothersimulacrum <anothersimulacrum@gmail.com>

Added check for zero value.

0e78ebc

Update src/bionics.cpp

1fe66e6

Co-Authored-By: anothersimulacrum <anothersimulacrum@gmail.com>

Fixed typo

5dfeab4

This was referenced Feb 9, 2020

Weekly Digest (2 February, 2020 - 9 February, 2020) #37848

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Weekly Digest (2 February, 2020 - 9 February, 2020) #37851

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This was referenced Feb 16, 2020

Weekly Digest (9 February, 2020 - 16 February, 2020) #38055

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Weekly Digest (9 February, 2020 - 16 February, 2020) #38058

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stale bot added the stale Closed for lack of activity, but still valid. label Mar 11, 2020

ZhilkinSerg closed this Mar 16, 2020

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[WIP][CR] Adding vitamins and toxin levels monitor functions to Blood Analyser CBM #37582

[WIP][CR] Adding vitamins and toxin levels monitor functions to Blood Analyser CBM #37582

eilaattwood commented Jan 31, 2020

tenmillimaster commented Jan 31, 2020

anothersimulacrum Jan 31, 2020

eilaattwood Jan 31, 2020

eilaattwood commented Feb 2, 2020

scorpion451 commented Feb 2, 2020 •

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eilaattwood commented Feb 3, 2020

tenmillimaster commented Feb 4, 2020 •

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esotericist commented Feb 4, 2020

eilaattwood commented Feb 5, 2020

anothersimulacrum Feb 7, 2020

eilaattwood Feb 7, 2020

anothersimulacrum Feb 7, 2020

anothersimulacrum Feb 10, 2020

anothersimulacrum Feb 7, 2020

eilaattwood Feb 7, 2020

anothersimulacrum Feb 7, 2020

eilaattwood Feb 7, 2020

anothersimulacrum Feb 7, 2020

eilaattwood Feb 7, 2020

anothersimulacrum Feb 7, 2020

eilaattwood Feb 7, 2020

scorpion451 commented Feb 9, 2020

stale bot commented Mar 11, 2020

ZhilkinSerg commented Mar 16, 2020

[WIP][CR] Adding vitamins and toxin levels monitor functions to Blood Analyser CBM #37582

[WIP][CR] Adding vitamins and toxin levels monitor functions to Blood Analyser CBM #37582

Conversation

eilaattwood commented Jan 31, 2020

Summary

Purpose of change

Describe the solution

Describe alternatives you've considered

Testing

Additional context

tenmillimaster commented Jan 31, 2020

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eilaattwood commented Feb 2, 2020

scorpion451 commented Feb 2, 2020 • edited Loading

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tenmillimaster commented Feb 4, 2020 • edited Loading

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eilaattwood commented Feb 5, 2020

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scorpion451 commented Feb 9, 2020

stale bot commented Mar 11, 2020

ZhilkinSerg commented Mar 16, 2020

scorpion451 commented Feb 2, 2020 •

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tenmillimaster commented Feb 4, 2020 •

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