Mikko Heikkinen mikkohei13
mikkohei13
/ process-named-places.py
Created
October 13, 2023 11:10
Convert FinBIF named places file (line transects) into geojson
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| import json | |
| def process_geojson_with_properties(input_filename, output_filename): | |
| # Load the JSON file | |
| with open(input_filename, "r") as file: | |
| data = json.load(file) | |
| # Extract all items under "results" | |
| results = data.get("results", []) |
mikkohei13
/ forecast_species.py
Created
August 25, 2023 09:24
Estimate future observation counts based on laji.fi data
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| import json | |
| from statsmodels.tsa.holtwinters import Holt | |
| # Load the JSON data | |
| with open("pyjamalude-years.json", "r") as file: | |
| data = json.load(file) | |
| ''' | |
| Estimate future observation counts based on laji.fi data |
mikkohei13
/ ai-model-comparison-set3.csv
Created
July 7, 2023 18:35
Comparison of Naturalis and iNaturalist species recognition models.
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| File unique identifier;Prediction by Naturalis;Probability by Naturalis;True or false by Naturalis;Prediction by iNat;Probability by iNat;True or false by iNat | |
| _test_set_3/(Acanthosomatidae) Elasmucha grisea Parent Bug_8.jpg;Elasmucha grisea;0.894348;1;Elasmucha grisea;0.314679;1 | |
| _test_set_3/(Aphrophoridae) Aphrophora alni_3.jpg;Aphrophora alni;1;1;Aphrophora alni;0.410643;1 | |
| _test_set_3/(Cercopidae) Cercopis vulnerata_2.jpg;Cercopis vulnerata;1;1;Cercopis vulnerata;0.460223;1 | |
| _test_set_3/(Cicadellidae) Adarrus ocellaris_3.jpg;Errastunus ocellaris;0.973848;0;Speudotettix subfusculus;0.303513;0 | |
| _test_set_3/(Cicadellidae) Aguriahana stellulata_4.jpg;Aguriahana stellulata;0.999827;1;Aguriahana;0.433531;1 | |
| _test_set_3/(Cicadellidae) Arthaldeus pascuellus_4.jpg;Arthaldeus pascuellus;1;1;Graminella nigrifrons;0.347305;0 | |
| _test_set_3/(Cicadellidae) Athysanus argentarius_5.jpg;Athysanus argentarius;0.999749;1;Athysanus argentarius;0.491078;1 | |
| _test_set_3/(Cicadellidae) Batracomorphus irroratus_5.jpg;Iassus lanio;0.699501 |
mikkohei13
/ weekly_species_heatmaps.py
Created
June 1, 2023 08:39
Script reads laji.fi data file, and a heatmap of weekly species distribution.
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| import pandas as pd | |
| import seaborn as sns | |
| import matplotlib.pyplot as plt | |
| from sklearn.preprocessing import MinMaxScaler | |
| rarity_threshold = 100 | |
| # Read datafile that has number of observations for each species | |
| df = pd.read_csv('species_rarity.csv', sep='\t') |
mikkohei13
/ weekly_species_charts.py
Created
June 1, 2023 08:34
Script reads laji.fi citatable data file, and creates Excel file and a line chart of weekly species distribution.
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| import pandas as pd | |
| import matplotlib.pyplot as plt | |
| # Load the csv file | |
| df = pd.read_csv('rows_HBF.75704.tsv', sep='\t') | |
| # Remove those without a day of year | |
| df = df.dropna(subset=['Gathering.Conversions.DayOfYearBegin']) |
mikkohei13
/ birdatlas-treevolume.csv
Created
February 13, 2023 16:45
Data from Finnish bird atlas: observations with 100 m accuracy compared to tree volume data (gaussian filtered) from Luke. Data CC-BY 4.0.
We can make this file beautiful and searchable if this error is corrected: It looks like row 2 should actually have 1 column, instead of 13 in line 1.
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| fid;common_name_finnish;count;unique;min;max;range;sum;mean;median;stddev;minority;majority;q1;q3;iqr | |
| 187;tulipäähippiäinen;1;1;255,7875214;255,79;0,00;255,79;255,79;255,79;0,00;255,79;255,7875214;255,79;255,79;0,00 | |
| 201;puukiipijät;1;1;235,3859253;235,39;0,00;235,39;235,39;235,39;0,00;235,39;235,3859253;235,39;235,39;0,00 | |
| 222;hömötiainen × lapintiainen;1;1;210,9716034;210,97;0,00;210,97;210,97;210,97;0,00;210,97;210,9716034;210,97;210,97;0,00 | |
| 175;pikkusieppo;29;29;79,25;303,37;224,11;5629,43;194,12;185,46;64,38;79,25;79,25;148,34;245,10;96,77 | |
| 180;kanahaukka (alalaji gentilis);1;1;165,2255707;165,23;0,00;165,23;165,23;165,23;0,00;165,23;165,2255707;165,23;165,23;0,00 | |
| 195;idänuunilintu;13;13;9,39;293,14;283,74;2079,52;159,96;175,33;79,21;9,39;9,39;104,69;209,42;104,73 | |
| 8;hippiäinen;376;359;0,00;354,92;354,92;54432,47;144,77;142,78;77,85;0,67;0,00;94,62;193,35;98,73 | |
| 82;peukaloinen;353;347;0,00;357,88;357,88;50821,14;143,97;144,19;76,40;0,02;0,00;90,73;198,19;107,46 | |
| 69;sirittäjä;190;188;0,00;318,41;318,41;27312,49 |
mikkohei13
/ finland_simple_outline.geojson
Created
February 11, 2023 22:10
GeoJSON file of the outline of Finland, simplified for very small maps.
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mikkohei13
/ minimaps.py
Last active
February 12, 2023 09:09
Generates small PNG maps of Finland with a dot at given coordinates.
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| # Generates small maps of Finland with a dot at given coordinates. | |
| import geopandas as gpd | |
| import matplotlib.pyplot as plt | |
| from pyproj import Proj, transform | |
| # Load a GeoJSON file with outline of Finland into a GeoDataFrame | |
| geojson = gpd.read_file('fin.geojson') |
mikkohei13
/ inat-sound.py
Created
February 6, 2023 14:11
Python script to fetch sound files from iNaturalist API
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| ''' | |
| Script to download sound files from iNaturalist. | |
| Mikko Heikkinen / Luomus, 2023-02-06 | |
| Requires "requests" library. | |
| input: iNat API URL with parameters | |
| output: files divided into folders by taxon |
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| import os | |
| from os import listdir | |
| from PIL import Image | |
| # get the path/directory | |
| source_dir = "images/Carpocoris_fuscispinus" | |
| target_dir = "images/carp_fusc_crop" | |
| limit = 300 |