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Update example with more data #326

Merged
merged 23 commits into from
Jun 16, 2023
Merged

Update example with more data #326

merged 23 commits into from
Jun 16, 2023

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peterdesmet
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@peterdesmet peterdesmet commented Jun 9, 2023 •
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Fix #325

Make example data more complete

  • deployments.csv: no empty columns (added many properties, see Fill out more columns in example dataset #325)
  • media.csv: no empty columns (added exif, favourite, comment for 3 images that are used in manuscript figure)
  • observations.csv: no empty columns (added behavior, tags), except those related to individual
  • observations.csv: add bbox columns based on originalBoundingBox. I currently can't do this, because the original values don't seem to be absolute (too low) nor relative values
  • observations.csv: oddly enough bounding box info is missing (not stored) for the first image of the event (0e98b93e_1 and 7ab33b3a_1). This can be confusing as example data and I might need to fabricate a realistic bounding box

Update example pages layout

  • Now displays all deployment information
  • Draw bounding box on image
  • Add landing page for the example dataset (not just deployments) at https://tdwg.github.io/camtrap-dp/example/ and link to it
  • Add download button

Update schema

The EXIF data is expected to be JSON, so we indicated this as type=object. In a CSV file however, it is only possible to this as a string (where " need to be escaped to ""). If we however set type=string, it will fail data provided as JSON (where it is possible to express the EXIF data as an object). I therefore opted for type=any

peterdesmet and others added 13 commits June 5, 2023 11:31
@peterdesmet
Add homepage URL
09a114d
@peterdesmet @EmmaCartuyvels1
Add cameraID, cameraModel, cameraTilt, cameraHeading
fb1d7c5 
- cameraID: MICA uses camera numbers, but unknown which ones are used for these deployments specifically. Numbers were chosen that do correspond with the numbers used for the corresponding area
- cameraModel: Reconyx-HF2X
- cameraTilt: no data available, but all tilting down at about -15 degrees
- cameraHeading: derived from looking at Google maps (285 west, 350 north, 20 north, 55 northeast)

Co-Authored-By: EmmaCartuyvels1 <44839819+EmmaCartuyvels1@users.noreply.github.com>
@peterdesmet @EmmaCartuyvels1
Add detectionDistance, timestampIssues, baitUse, featureType
b13e429 
- detectionDistance: values as recorded in Agouti, converted to meters
- featureType we chose trailGame over waterSource, since the target species (Ondatra) uses the water ways as trails

Co-Authored-By: EmmaCartuyvels1 <44839819+EmmaCartuyvels1@users.noreply.github.com>
@peterdesmet @EmmaCartuyvels1
Add habitat
51aeac4 
Habitat is derived from the location descriptions in the MICA project report

Co-Authored-By: EmmaCartuyvels1 <44839819+EmmaCartuyvels1@users.noreply.github.com>
@peterdesmet @EmmaCartuyvels1
Add deploymentGroups, deploymentTags, update deploymentComments
ab12c5a 
- deploymentGroups: area codes + season (somewhat artificial, but shows use of |)
- deploymentTags: position of camera along river (also moved)
- deploymentComments: translate to English

Co-Authored-By: EmmaCartuyvels1 <44839819+EmmaCartuyvels1@users.noreply.github.com>
@peterdesmet @EmmaCartuyvels1
Update setupBy
062ecdf 
One anonymized cf. Agouti approach, one empty

Co-Authored-By: EmmaCartuyvels1 <44839819+EmmaCartuyvels1@users.noreply.github.com>
@peterdesmet
Add behavior=foraging for 3 events in first deployment
f4657bb 
For the second event it is not possible to annotate at media level, since it concerns a group
@peterdesmet
Add observationTags: "swimDirection: across"
0f6b7ce
@peterdesmet
Update example pages to show ALL deployment information as list
d3fc946
@peterdesmet
Revert 62c200a9 to machine classification
d3457e8 
- Ardea cinerea to Ardea
- Remove lifeStage
- add classificationTimestamp
- add classificationProbability
@peterdesmet
Add bounding box (and probability) as recorded in Agouti
e994e73
@peterdesmet
Add exifData, favourite and comments for 3 images used in paper
458d2e2
@peterdesmet
Change data type for exifDate to any
01632ac
@peterdesmet peterdesmet added documentation Improvements or additions to documentation term:update labels Jun 9, 2023
@peterdesmet peterdesmet added this to the 1.0 milestone Jun 9, 2023
@peterdesmet
Add bbox values
eaafce9 
Original bounding box is x1,y1,x2,y2 scaled to 640 width. The scaling factor is thus 0.3125

rel_x1 = x1/scale/2048 = bboxX
rel_y1 = y1/scale/1440 = bboxY
rel_x2 = x2/scale/2048
rel_y2 = y2/scale/1440
bboxWidth = rel_x2/rel_x1
bboxHeight = rel_y2/rel_y1

All are rounded to 5 decimals
@peterdesmet
Remove originalBoundingBox from tags, update classificationTimestamp
4df26f7 
The originalBoundingBox is in an format (see eaafce9) that is no longer used in Agouti. It would confuse users if we include it in the example dataset (it confused me)
@peterdesmet
Add missing bounding box
00a697e
@peterdesmet
Indicate bounding box on example as absolute div
8ee79c7
@peterdesmet peterdesmet marked this pull request as ready for review June 10, 2023 07:21
@peterdesmet
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@kbubnicki ready for review. Note the object to any date type change for exifData.

Thanks to @EmmaCartuyvels1 for providing all the deployment information.

The example page now looks like this (includes more deployment info + shows bounding box where available):

Example-dataset-Camtrap-DP

@peterdesmet peterdesmet merged commit 22f5309 into main Jun 16, 2023
@peterdesmet peterdesmet deleted the update_example branch June 16, 2023 09:32
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Fill out more columns in example dataset
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@peterdesmet @kbubnicki