Uploading everything in a folder to iNaturalist with python

Since pyinaturalist recently came out I thought it would be a good time to try and write a script to automatically upload files to iNaturalist. Few if any example scripts are out there and this should make it easier for other people to write one which matches their workflow.

This script assumes a large number of photos of the same species. This might happen for example if you were trying to map every tree on a property. The workflow would consist of taking a single geotagged photo of each individual then separating out the photos so each one is in a folder which starts with its taxon ID. For example aphids would go in a folder named '52381' or '52381 Aphids' or '52381-Aphididae'

If you don't have python, I suggest installing Anaconda then pyinaturalist. You will then need to get an app ID.

Open this script, add your user name, password, app id, secret, and the time zone of the photos. Then run the script. It should upload everything jpg file in the folder as the file you select.

# Input your user name here:
user = ''

# Input your password here:
passw = ''

# Input your app ID and secret here:
app = ''
secret = ''


# Input the time zone for the photos here, options can be found at the
# website below
# https://gist.github.com/mjrulesamrat/0c1f7de951d3c508fb3a20b4b0b33a98
time_zone = 'America/Los_Angeles'



# tkinter used to choose a file
from tkinter import filedialog
from tkinter import Tk

# os used to get a folder name
import os

# pillow used to get exif data from the photos
import PIL
from PIL import ExifTags

# This is used to upload the photos.
import pyinaturalist

from pyinaturalist.rest_api import create_observations
from pyinaturalist.rest_api import get_access_token

print("Running")

# This code lets you choose a photo, can delete and replace with folder_name=''
root = Tk()
filename =  filedialog.askopenfilename(initialdir = "/",
                                    title = "Select one of the .jpg files in "
                                    "the folder to be uploaded. All files in "
                                    "the folder will be uploaded. The folder "
                                    "name should start with the taxon number",
                                    filetypes = (("jpeg files","*.jpg"),
                                    ("all files","*.*")))
root.withdraw()

#
folder_name = os.path.dirname(filename) +'/'
print('Uploading all photos in ' + folder_name + ' as a unique observation')

# Makes a list of all files in the folder inside element 2 of a tuple
for file in os.walk(folder_name):
    if file[0] == folder_name:
        files = file

# Creates list of all the file paths for every file in the folder.
file_paths = []
for file in files[2]:   # All files are in files[2]
    file_path = files[0] + file  # files[0] has the path to the folder
    file_paths.append(file_path) # Makes a big list of paths


# This function returns the latitude and longitude of a .jpg image
def get_lat_long(image):
    # Gets all the exif data from the photo
    exif = {
        PIL.ExifTags.TAGS[k]: v
        for k, v in image._getexif().items()
        if k in PIL.ExifTags.TAGS
    }

    # From all the exif data, pulls the GPS data
    gps_info = exif.get('GPSInfo')
    # The GPS data is in a odd format, so have to dig for it a bit. This was
    # only tested on files lightroom tagged.
    latitude_direction = str(gps_info.get(1)[0])
    latitude_degrees = float(gps_info.get(2)[0][0])
    minutes = float(gps_info.get(2)[1][0])
    multiplier = float(gps_info.get(2)[1][1])
    latitude_minutes = minutes/multiplier
    seconds = float(gps_info.get(2)[2][0])
    multiplier = float(gps_info.get(2)[2][1])
    latitude_seconds = seconds/multiplier
   
   
    # The sign is changed depending on if this is N or S
    if latitude_direction == 'N' or latitude_direction == 'n':
        latitude = latitude_degrees+latitude_minutes/60 + latitude_seconds/3600
    elif latitude_direction == 'S' or latitude_direction == 's':
        latitude = -(latitude_degrees+latitude_minutes/60 + latitude_seconds/3600)
       
    longitude_direction = gps_info.get(3)[0]
    longitude_degrees = gps_info.get(4)[0][0]
    minutes = float(gps_info.get(4)[1][0])
    multiplier = float(gps_info.get(4)[1][1])
    longitude_minutes = minutes/multiplier
    seconds = float(gps_info.get(4)[2][0])
    multiplier = float(gps_info.get(4)[2][1])
    longitude_seconds = seconds/multiplier
    # The sign is changed depending on if this is E or W
    if longitude_direction == 'E' or longitude_direction == 'e':
        longitude = longitude_degrees+longitude_minutes/60 +longitude_seconds/3600
    elif longitude_direction == 'W' or longitude_direction == 'w':
        longitude = -(longitude_degrees+longitude_minutes/60 +longitude_seconds/3600)
   
    latitude_longitude = [latitude, longitude]
   
    # Returns a list with both latitude and longiude in decimal format.
    return latitude_longitude
   
# Pulls the date information from
def get_date(image):
    # Gets all the exif data from the photo
    exif = {
        PIL.ExifTags.TAGS[k]: v
        for k, v in img._getexif().items()
        if k in PIL.ExifTags.TAGS
    }
    # Pulls the date and time from the exif format
    date = exif.get('DateTime').split()[0]
    time = exif.get('DateTime').split()[1]
    # Reformats the date to use - instead of :
    for character in date:
        if character == ':':
            date = date.replace(character, '-')
    # Combines the date and time to match the format pyinaturalist wants,
    date_time = str(date) + 'T' + str(time)
    # returns a date and time formatted to submit to iNaturalist with
    # pyinaturalist
    return date_time


# This presumes the name of the folder starts with the taxon number.It finds
# the taxon number by looking at the folder name and taking all the digits it
# sees. This allows you to name the folder "##### species name" to quickly
# tell where photos go. For example anything in '52381-Aphididae' is uploaded
# as an aphid.
def get_taxon(folder):
    taxon = ''
    folder =os.path.split(os.path.dirname(folder_name))[-1]
    for character in folder:
        if character.isdigit():
            taxon = taxon + character
    return taxon


# This is getting a token to allow photos to be uploaded.
token = get_access_token(username=user, password=passw,
                         app_id=app,
                         app_secret=secret)

# This goes to every file, checks if it is a jpg, gets the gps coordinates,
# get the time, and uploads it to iNaturalist.
for file in file_paths:
   if file[-3:] == 'jpg' or file[-3:] == 'JPG' or file[-3:] == 'Jpg':
       print('Uploading ' + file)
       try:
           img = PIL.Image.open(file)
           coordinates = get_lat_long(img)
       except:
           coordinates = 'No Coordinates'
       try:
           img = PIL.Image.open(file)
           date_time = get_date(img)
       except:
           date_time = 'No Date or Time' 
          
       # This requires the folder name to start with the taxon number.
       taxon = get_taxon(folder_name)   

       params = {'observation':
                    {'taxon_id': taxon,  # Vespa Crabro
                     'observed_on_string': date_time,
                     'time_zone': time_zone,
                     'description': '',
                     'tag_list': '',
                     'latitude': coordinates[0],
                     'longitude': coordinates[1],
                     'positional_accuracy': 50, # meters,
       

                     'observation_field_values_attributes':
                        [{'observation_field_id': '','value': ''}],
                     },}
       r = create_observations(params=params, access_token=token)
       
       new_observation_id = r[0]['id']

      
       from pyinaturalist.rest_api import add_photo_to_observation

       r = add_photo_to_observation(observation_id=new_observation_id,
                        file_object=open(file, 'rb'),
                        access_token=token)

print("Program complete")