Backend heatmap #566

kitzbergerg · 2023-07-03T17:36:48Z

Implementation of the backends heatmap.
Resolves #457, resolves #635, resolves #494.

Basics

I added a line to /doc/CHANGELOG.md
The PR is rebased with current master.
Details of what you changed are in commit messages.
References to issues, e.g. close #X, are in the commit messages.
The buildserver is happy.

Checklist

Review

I've tested the code
I've read through the whole code
Examples are well chosen and understandable

backend/src/controller/map.rs

markus2330 · 2023-07-03T18:00:37Z

Great to see this! 🚀

…d, scale f32 values to be 0-1

kitzbergerg · 2023-07-06T16:59:36Z

@Bushuo There is an error in storybook. It seems to also scan the generated definitions file which contains an example of the geometry in json. Would you mind fixing that? Probably the best solution would be to exclude the definitions.ts from storybook somehow, if that is not possible I don't really know how to handle that.

Bushuo · 2023-07-07T20:57:53Z

@Bushuo There is an error in storybook. It seems to also scan the generated definitions file which contains an example of the geometry in json. Would you mind fixing that? Probably the best solution would be to exclude the definitions.ts from storybook somehow, if that is not possible I don't really know how to handle that.

@kitzbergerg Hi, I looked at it.
I don't want to fix it, as it is quite complicated.
It can be avoided though, by putting the json code inside of backticks like {"rings":[[{"x":0.0,"y":0.0},{"x":5.0,"y":0.0},{"x":5.0,"y":5.0},{"x":0.0,"y":5.0},{"x":0.0,"y":0.0}]],"srid":4326}
This will tell mdx to treat it as a code block and thus ignore any reserved characters.

kitzbergerg · 2023-07-08T19:06:16Z

@markus2330 This is now finished I would say. It is a bit difficult to test as many things are not yet in place, but I will provide some scripts that can be used.

@markus2330 @Bushuo Here are a few issues/implementation details that appeared related to this:

I believe the (x,y) coordinates of plantings are set wrong in the frontend. Coordinates in PostGIS are (0,0) at the bottom left, so this needs to be fixed. (Done by changing the coordinate system in the backend to be (0,0) at top left.)
Add plant relations to scraper #606 Plant relations cannot yet be inserted into the database with the scraper (unless I missed something).
The polygon for the map still has to be created in the frontend. Currently it is just a hardcoded dummy implementation.
Implement Heat-Map on the Frontend #592 The generated map needs to be moved and scaled in the frontend.

Steps

Here are the steps I used to test the heatmap:

Create the database.
Insert the plants using the scraper (cd scraper && npm run insert)
Start the backend.
Create a map (can be done in the frontend as well).

curl --location 'http://localhost:8080/api/maps' \
--header 'Authorization: Bearer <token>' \
--header 'Content-Type: application/json' \
--data '{
    "name": "Test1",
    "creation_date": "2023-07-06",
    "is_inactive": false,
    "zoom_factor": 100,
    "honors": 0,
    "visits": 0,
    "harvested": 0,
    "privacy": "public",
    "description": "",
    "geometry": {
        "rings": [
            [
                {
                    "x": 0.0,
                    "y": 0.0
                },
                {
                    "x": 100.0,
                    "y": 0.0
                },
                {
                    "x": 100.0,
                    "y": 100.0
                },
                {
                    "x": 50.0,
                    "y": 100.0
                },
                {
                    "x": 50.0,
                    "y": 50.0
                },
                {
                    "x": 0.0,
                    "y": 50.0
                },
                {
                    "x": 0.0,
                    "y": 0.0
                }
            ]
        ],
        "srid": 4326
    }
}'

Insert some dummy relations and plantings

INSERT INTO relations
VALUES (1, 2, 'companion'),
       (1, 3, 'neutral'),
       (1, 4, 'antagonist');

INSERT INTO plantings
VALUES ('00000000-0000-0000-0000-000000000000', 2, 1, 10, 10, 0, 0, 0, 0, 0),
       ('00000000-0000-0000-0000-000000000001', 2, 2, 11, 10, 0, 0, 0, 0, 0),
       ('00000000-0000-0000-0000-000000000002', 2, 2, 23, 10, 0, 0, 0, 0, 0),
       ('00000000-0000-0000-0000-000000000003', 2, 2, 40, 10, 0, 0, 0, 0, 0),
       ('00000000-0000-0000-0000-000000000004', 2, 2, 10, 20, 0, 0, 0, 0, 0),
       ('00000000-0000-0000-0000-000000000005', 2, 3, 10, 20, 0, 0, 0, 0, 0);

Execute the request (Probably better to use swagger or Postman otherwise you can't see the image).

curl --location 'http://localhost:8080/api/maps/1/layers/plants/heatmap?plant_id=1&layer_id=2' \
--header 'Authorization: Bearer <token>'

Bushuo · 2023-07-08T20:57:13Z

@kitzbergerg

I believe the (x,y) coordinates of plantings are set wrong in the frontend. Coordinates in PostGIS are (0,0) at the bottom left, so this needs to be fixed.

Yes, placement is indeed currently wrong. We changed the plant from a square to a circle which broke it.
It was intended though, that (x,y) is the plantings center point.

Should this be the bottom left of the planting?
I don't understand, please explain.

markus2330

This is certainly a big step forwards, great to have the endpoint. I would prefer integer used more. Documentation etc. is a bit weak. Thanks for adding the test protocol, it now worked for me but I couldn't reproduce it with self-planted plantings. Probably a bigger map is needed for that (it should be 1ha per default anyways).

About the (not previously discussed) implementation in plpgsql (we actually said it should be in Rust or directly in a SQL query using PostGIS) I am not sure. The main concern is the performance: please check it as part of your thesis.

doc/tests/protocols/MTP_2023-07-8_Heatmap_V1.md

backend/src/test/plant_layer_heatmap.rs

markus2330 · 2023-07-14T06:22:57Z

doc/tests/protocols/MTP_2023-07-8_Heatmap_V1.md

@@ -0,0 +1,104 @@
+# Test Protocol Heatmap


Link test protocol from use case.

I don't know what this is supposed to mean. There is no test protocol for the use case in plant layer.
Should I link to the usecase? Something like ../usecases/current/plants_layer?

In the use case (plants layer), there should be a link to this test protocol doc/tests/protocols/MTP_2023-07-8_Heatmap_V1.md.

markus2330 · 2023-07-14T06:24:15Z

frontend/src/features/maps/routes/MapCreateForm.tsx

@@ -127,6 +127,20 @@ export default function MapCreateForm() {
      privacy: mapInput.privacy,
      description: mapInput.description,
      location: !Number.isNaN(mapInput.location.latitude) ? mapInput.location : undefined,
+      // TODO: implement selector


Please describe better what you mean here. Do you mean #494, then please link to the issue.

I think this refers to #349 (#494 is a duplciate of that?).
Simply said when a map is created the user needs to specify the boundaries of the map. This boundary is then used by the heatmap (and maybe other layers like the base layer?).

I made a distinction between these two issues (one for backend, other for frontend).

Simply said when a map is created the user needs to specify the boundaries of the map. This boundary is then used by the heatmap (and maybe other layers like the base layer?).

Please read the use cases, the map needs to be created without the boundaries. So it must be possible to set a boundary afterwards.

Should the map boundary be part of the base layer or part of the map? As far as I understand the following means it is part of map: these boarders are stored in the map and not subjective to "alternatives" (for the base_layer use case).
If so that would mean I simply need to set the field to nullable and add an option to update the boundary?

Yes, the map boundary must be part of the map.

backend/src/model/entity/plant_layer.rs

markus2330 · 2023-07-14T07:36:43Z

Usually the left-over issues should be created by the implementer of a PR.
I created them for this PR:

I believe the (x,y) coordinates of plantings are set wrong in the frontend. Coordinates in PostGIS are (0,0) at the bottom left, so this needs to be fixed. (Done by changing the coordinate system in the backend to be (0,0) at top left.)

#635

Plant relations cannot yet be inserted into the database with the scraper (unless I missed something).

#636

The polygon for the map still has to be created in the frontend. Currently it is just a hardcoded dummy implementation.

#349

The generated map needs to be moved and scaled in the frontend.

#637

… backend_heatmap

markus2330 · 2023-07-15T14:32:10Z

jenkins build please

badnames

Very well done.

@markus2330 Just one question:
How often is this heatmap supposed to be updated?
As it is now, it seems to be quite resource intensive to generate.

badnames · 2023-07-15T20:56:14Z

backend/src/service/plant_layer.rs

        entity::plant_layer,
    },
 };

+/// Generates a heatmap signaling ideal locations for planting the plant.
+/// The return values are raw bytes of an PNG image.


Suggested change

/// The return values are raw bytes of an PNG image.

/// The return values are raw bytes of a PNG image.

markus2330 · 2023-07-16T07:57:46Z

How often is this heatmap supposed to be updated?

It always gets generated freshly, as it is different for every plant and after basically every change in the map.

As it is now, it seems to be quite resource intensive to generate.

Is this just your general feeling or do have specific concerns?

kitzbergerg added 3 commits July 3, 2023 19:18

simply heatmap returning matrix of 0.5

863fec3

only calculate score for intersection with map_polygon, add TODOs

0db085b

update utoipa API doc

f3e4200

markus2330 reviewed Jul 3, 2023

View reviewed changes

backend/src/controller/map.rs Outdated Show resolved Hide resolved

kitzbergerg added 10 commits July 3, 2023 22:10

move heatmap to plant_layer

ba0839a

add rustdoc

fde4b78

return image from heatmap endpoint, throw error on non existant map i…

0eaff84

…d, scale f32 values to be 0-1

fix clippy errors

81ecd3a

set geometry of map in frontend

c146127

rename map_geom field to geometry

5a75959

fix tests by adding geometry to maps

bc75d9c

add test for heatmap

7a0fe79

Merge branch 'master' into backend_heatmap

32064ed

fix error in frontend

878e39e

kitzbergerg added 7 commits July 8, 2023 13:50

use bounding box and granularity to calculate heatmap

fbe0f5f

add colors to heatmap, fix index out of bounds

b0f9ce4

add more detailed heatmap tests

1098e1f

fix clippy errors

9530eba

add score based on plants relation on layer

3a86842

refactor SQL queries and add better doc

c839a35

fix tests and add negative test

c8204ef

kitzbergerg marked this pull request as ready for review July 8, 2023 18:50

kitzbergerg requested review from markus2330 and Bushuo July 8, 2023 19:06

add heatmap to changelog

0b5c826

markus2330 suggested changes Jul 14, 2023

View reviewed changes

This was referenced Jul 14, 2023

document coordinate system #635

Closed

frontend: use&scale heatmap while planting #637

Closed

kitzbergerg added 11 commits July 14, 2023 22:35

update test protocol according to suggestions

b555522

update frontend according to suggestions

fb6c459

update heatmap sql according to suggestions

aaa1919

add more detailed heatmap endpoint description

c012c33

use integers instead of floats for bounding box and granularity

f302321

improve rustdoc error message on heatmap

0df1e8e

Merge branch 'master' of github.com:ElektraInitiative/PermaplanT into…

fae9e89

… backend_heatmap

improve rustdoc error message on heatmap in service

7f7357a

add doc about how to update the schema.patch file

21235f9

fix mdbook error

cd9e36a

add doc about the coordinate system

35078f2

kitzbergerg requested a review from markus2330 July 15, 2023 09:28

kitzbergerg added 6 commits July 15, 2023 17:30

move coordinate system doc to solution

bd2d722

allow for updating the maps geometry

439ba82

change values in SQL to floats

1646929

change from brown to grey for low scores in heatmap

a6ee00f

fix clippy errors

934edc6

Merge branch 'master' into backend_heatmap

aa97b0d

kitzbergerg added the please merge label Jul 15, 2023

set geometry of UpdateMap as Option in typeshare

652904e

badnames approved these changes Jul 15, 2023

View reviewed changes

markus2330 mentioned this pull request Jul 16, 2023

heatmap: document algorithm how to move/scale heatmap #649

Closed

1 task

markus2330 merged commit 7fa730d into master Jul 16, 2023

markus2330 deleted the backend_heatmap branch July 16, 2023 16:54

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Backend heatmap #566

Backend heatmap #566

kitzbergerg commented Jul 3, 2023 •

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	/// The return values are raw bytes of an PNG image.
	/// The return values are raw bytes of a PNG image.

Backend heatmap #566

Backend heatmap #566

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kitzbergerg commented Jul 3, 2023 • edited Loading

Basics

Checklist

Review

markus2330 commented Jul 3, 2023

kitzbergerg commented Jul 6, 2023

Bushuo commented Jul 7, 2023

kitzbergerg commented Jul 8, 2023 • edited Loading

Steps

Bushuo commented Jul 8, 2023

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