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Merged
merged 3 commits into from
Apr 25, 2024
Merged

Limit field names to ten characters #181

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179b413
Rename fields to 10 chars max
henrykironde Apr 24, 2024
fccaf95
Update field rename changes to App files
henrykironde Apr 24, 2024
7d9ab38
Use Touch to create unused ouput files
henrykironde Apr 24, 2024
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4 changes: 2 additions & 2 deletions App/Zooniverse/functions.R
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Original file line number Diff line number Diff line change
Expand Up @@ -166,7 +166,7 @@ plot_nests<-function(df, bird_df, MAPBOX_ACCESS_TOKEN){

m<-leaflet(data=df) %>%
addProviderTiles("MapBox", layerId = "mapbox_id",options = providerTileOptions(id = mapbox_tileset, minZoom = 8, maxNativeZoom=24, maxZoom = 24, accessToken = MAPBOX_ACCESS_TOKEN)) %>%
addCircles(stroke = T,fillOpacity = 0.1,radius = 0.5,popup = ~htmlEscape(paste(round(sum_top1_s/num_obs_to,2),nest_id,sep=":"))) %>%
addCircles(stroke = T,fillOpacity = 0.1,radius = 0.5,popup = ~htmlEscape(paste(round(sum_top1/num_obs_to,2),nest_id,sep=":"))) %>%
addCircles(data = bird_df, stroke = T, fillOpacity = 0, radius = 0.2, color = ~species_colors(label),
popup = ~htmlEscape(paste(round(score,2), bird_id, sep=":")))
return(m)
Expand All @@ -193,7 +193,7 @@ update_nests<-function(mapbox_tileset, df, bird_df, show_nests, show_birds,
}
if (show_nests) {
map <- map %>%
addCircles(data=df,stroke = T,fillOpacity = 0.1,radius = 0.5,popup = ~htmlEscape(paste(round(sum_top1_s/num_obs_to,2),nest_id,sep=", ")))
addCircles(data=df,stroke = T,fillOpacity = 0.1,radius = 0.5,popup = ~htmlEscape(paste(round(sum_top1/num_obs_to,2),nest_id,sep=", ")))
}
if (show_birds) {
map <- map %>%
Expand Down
4 changes: 2 additions & 2 deletions Zooniverse/Snakefile
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Original file line number Diff line number Diff line change
Expand Up @@ -38,7 +38,7 @@ rule all:
zip, site=SITES, year=YEARS, flight=FLIGHTS),
expand(f"{working_dir}/processed_nests/{{year}}/{{site}}/{{site}}_{{year}}_processed_nests.shp",
zip, site=SITES, year=YEARS),
expand(f"{working_dir}/mapbox/{{year}}/{{site}}/{{flight}}.mbtiles",
expand(f"{working_dir}/mapbox/last_uploaded/{{year}}/{{site}}/{{flight}}.mbtiles",
zip, site=SITES, year=YEARS, flight=FLIGHTS)


Expand Down Expand Up @@ -131,7 +131,7 @@ rule upload_mapbox:
input:
f"{working_dir}/mapbox/{{year}}/{{site}}/{{flight}}.mbtiles"
output:
f"{working_dir}/mapbox/{{year}}/{{site}}/{{flight}}.mbtiles"
touch(f"{working_dir}/mapbox/last_uploaded/{{year}}/{{site}}/{{flight}}.mbtiles")
conda:
"EvergladesTools"
shell:
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4 changes: 2 additions & 2 deletions Zooniverse/combine_nests.py
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Expand Up @@ -31,8 +31,8 @@ def load_shapefile(x):
'last_obs': 'str',
'num_obs': 'int',
'species': 'str',
'sum_top1_s': 'float',
'num_obs_to': 'int',
'sum_top1': 'float',
'num_top1': 'int',
'bird_match': 'str'
})
shp["site"] = get_site(x)
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27 changes: 14 additions & 13 deletions Zooniverse/nest_detection.py
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Original file line number Diff line number Diff line change
Expand Up @@ -68,12 +68,12 @@ def compare_site(gdf):
# add target info to match
row = geopandas.GeoDataFrame(pd.DataFrame(row).transpose(), crs=matches.crs)
matches = geopandas.GeoDataFrame(pd.concat([matches, row], ignore_index=True))
matches["target_index"] = index
matches["target_ind"] = index
matches = matches.rename(columns={
"xmin": "matched_xmin",
"max": "matched_xmax",
"ymin": "matched_ymin",
"ymax": "matched_ymax"
"xmin": "match_xmin",
"xmax": "match_xmax",
"ymin": "match_ymin",
"ymax": "match_ymax"
})

results.append(matches)
Expand All @@ -82,8 +82,8 @@ def compare_site(gdf):
results = pd.concat(results)
else:
results = pd.DataFrame(columns=[
'matched_xmin', 'matched_ymin', 'xmax', 'matched_ymax', 'label', 'score', 'image_path', 'Date', 'bird_id',
'target_index', 'geometry'
'match_xmin', 'match_ymin', 'match_xmax', 'match_ymax', 'label', 'score', 'image_path', 'Site', 'Date',
'Year', 'event', 'file_posts', 'bird_id', 'target_ind'
])

return results
Expand All @@ -102,19 +102,20 @@ def detect_nests(bird_detection_file, year, site, savedir):
schema = {
"geometry": "Polygon",
"properties": {
'matched_xmin': 'float',
'matched_ymin': 'float',
'xmax': 'float',
'matched_ymax': 'float',
'match_xmin': 'float',
'match_ymin': 'float',
'match_xmax': 'float',
'match_ymax': 'float',
'label': 'str',
'score': 'float',
'image_path': 'str',
'Site': 'str',
'Date': 'str',
'Year': 'str',
'bird_id': 'int',
'event': 'str',
'target_index': 'int'
'file_posts': 'str',
'bird_id': 'int',
'target_ind': 'int'
}
}
if not results.empty:
Expand Down
18 changes: 9 additions & 9 deletions Zooniverse/process_nests.py
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Original file line number Diff line number Diff line change
Expand Up @@ -55,13 +55,13 @@ def process_nests(nest_file, year, site, savedir, min_score=0.3, min_detections=
top_score_data = summed_scores[summed_scores['sum'] == max(summed_scores['sum'])].reset_index()
nest_info = nest_data.groupby(['Site', 'Year', 'target_ind']).agg({
'Date': ['min', 'max', 'count'],
'matched_xm': ['mean'],
'matched_ym': ['mean'],
'xmax': ['mean'],
'matched__1': ['mean']
'match_xmin': ['mean'],
'match_ymin': ['mean'],
'match_xmax': ['mean'],
'match_ymax': ['mean']
}).reset_index()
xmean = (nest_info['matched_xm']['mean'][0] + nest_info['xmax']['mean']) / 2
ymean = (nest_info['matched_ym']['mean'][0] + nest_info['matched__1']['mean']) / 2
xmean = (nest_info['match_xmin']['mean'][0] + nest_info['match_xmax']['mean']) / 2
ymean = (nest_info['match_ymin']['mean'][0] + nest_info['match_ymax']['mean']) / 2
bird_match = ",".join([str(x) for x in nest_data["bird_id"]])
nests.append([
target_ind, nest_info['Site'][0], nest_info['Year'][0], xmean[0], ymean[0], nest_info['Date']['min'][0],
Expand All @@ -77,7 +77,7 @@ def process_nests(nest_file, year, site, savedir, min_score=0.3, min_detections=
nests = pd.DataFrame(nests,
columns=[
'nest_id', 'Site', 'Year', 'xmean', 'ymean', 'first_obs', 'last_obs', 'num_obs',
'species', 'sum_top1_score', 'num_obs_top1', 'bird_match'
'species', 'sum_top1', 'num_top1', 'bird_match'
])
nests_shp = geopandas.GeoDataFrame(nests, geometry=geopandas.points_from_xy(nests.xmean, nests.ymean))
nests_shp.crs = nests_data.crs
Expand All @@ -95,8 +95,8 @@ def process_nests(nest_file, year, site, savedir, min_score=0.3, min_detections=
'last_obs': 'str',
'num_obs': 'int',
'species': 'str',
'sum_top1_score': 'float',
'num_obs_top1': 'int',
'sum_top1': 'float',
'num_top1': 'int',
'bird_match': 'str'
}
}
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2 changes: 1 addition & 1 deletion Zooniverse/upload_mapbox.py
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Expand Up @@ -56,7 +56,7 @@ def retrieve_upload_status(self, upload_id):

def get_credentials():
"""Get credentials from mapbox.ini"""
with open("/blue/ewhite/everglades/mapbox/mapbox.ini", "rb") as f:
with open("/blue/ewhite/everglades/mapbox.ini", "rb") as f:
toml_dict = tomli.load(f)
access_token = toml_dict['mapbox']['access-token']
return access_token
Expand Down
2 changes: 1 addition & 1 deletion everglades_workflow.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
#SBATCH --mail-type=FAIL
#SBATCH --gpus=a100:4
#SBATCH --cpus-per-task=60
#SBATCH --mem=1200gb
#SBATCH --mem=600gb
#SBATCH --time=80:00:00
#SBATCH --partition=gpu
#SBATCH --output=/blue/ewhite/everglades/EvergladesTools/logs/everglades_workflow.out
Expand Down
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