Sunday, April 7, 2019

Misadentures Near the Mule Mountains

I am always trying to get to places where the species have not been recorded on iNaturalist. As the number of users in Southern California have increased that has become progressively more difficult. There are still a few patches though. One such patch is the Mule Mountains, about thirty miles southwest of Blythe. While there are a couple observations near the edges of the mountains the site has yet to have extensive documentation. Even related sites such as Calflora do not show much about the site.

With this in mind, I headed to Coon Hollow Campground dragging along my 4 and 6 year old boys. Being ten or more miles down a dirt road and in an area with very few observations, this campground seemed a good starting point for some adventures. So I set up my tent, ate a bit then headed for the Mule Mountains.

Before heading on this trip I had scouted the site as well as I could on Google. There was a little road called Bradshaw Trail which looked like it was in good shape up until the edge of the Mule Mountains. It was pretty clear my Prius wasn't up for a crossing of the mountains, but the road looked good on Google up until the edge of the mountains.

When I reached this road, it was clear there was a problem with my plan. About fifty feet down the road there was a warning that it was only 4 wheel drive accessible. This should have stopped me cold, but the road was in such good condition! I reasoned that with how good the road looked at the four wheel drive sign I should be able to go slowly until I was obviously out of my league then turn back.

So I drove about a half mile. Then I hit the sand. I continued through the sand and was on solid road again. That knocked my senses into me. I decided to turn around. The road was pretty small though and I wasn't sure I could do a u-turn without getting stuck. Also, I was only one patch of sand away from good road. I elected to back through the sand and turn around when I got to the cross street. This probably would have worked. However I was of the opinion that I needed to go quickly or I would get stuck in the sand. So I went faster than I should have. I ended up getting too close to the edge of the road and got solidly stuck in the much deeper sand there.

After a half hour of trying to dig myself out with some friendly motorcyclists which stopped to help (people are so much nicer when you are with kids), I realized I remarkably had cell phone service. So I just paid the exorbitant fees tow truck companies charge to pull someone out of the situation like that.

So I spent the next two hours waiting for the tow truck photographing plants and insects as I was really quite in the middle of nowhere. The kids played in the sand.

Luckily once towed out, the car still worked. So I returned to camp vowing not to start the car up again until it was time to go home. The area around the campground was pretty much undocumented, and it seemed like I could easily walk to the Mule Mountains a mile or so east of the campground.

The next morning I woke up to a small mantis near my head in the tent! Great! I had seen one of those the night before at an improvised bug attracting light but my kids stepped on it before I could get a picture. So I took a few photos.

Then I smelled smoke! Smoke? I realized it was coming from either my flash or my camera. I am pretty sure one of the capacitors had previously failed on the flash so I figured it was finally dying for real.

After breakfast we started east toward the Mule Mountains. The kids seemed excited enough and in the morning cool it was the perfect time to walk a couple miles.

Perhaps half way to the edge of the mountains the older one starts complaining about his feet. He says his shoes are hurting his feet. I look at his feet. It seemed like something got through the holes in his crocks and made his feet itch. Ugh, why did I let him bring crocs? I gave up on the Mule Mountains and started to carry him back to camp. Luckily about half way back he stopped complaining and started walking, but at that point I wasn't going to be able to motivate him to turn back towards the mountains.

So we spent the rest of the day playing games and searching the dry stream bed. Luckily my flash was still working apparently normally. The camera had been starting to act a little funny though. At about 6 PM while I was taking a photo of a beetle the camera said "Camera Error Turn power off then on." Turning it off did nothing at all. So I pulled the battery. Same problem. Pulled off the lens to find that the shutter was stuck closed. The Sony a6300 camera had survived three years and 267,331 shutter actuations but it was finally good and dead. This is the last photo that camera is likely to take:

Luckily the camera had survived three quarters of the trip. However the last night and the drive back I was stuck with my cell phone. The camera seems like it could be repaired but to do so would not be cheap. I ended up purchasing a new A7III as a replacement.

Could have done without the towing bill and dead camera, but other than that was a pretty good trip. Managed to get 359 observations in a really obscure and lightly documented part of the desert. Kids seemed to hold up well to camping in primitive conditions so I may have to try a similar place next spring.

Sunday, February 10, 2019

Updated iNaturalist Upload Scripts

After a few rainy days I managed to come up with a python script using pyinaturalist which is at least as efficient as the existing upload method. For people uploading a large number of photos of the same species it is much more efficient.

The basic workflow is to put all the photos in a folder with the common name or scientific name and/or taxon number as the name of the folder.

You can put dozens of photos in any of these folders, so uploading fifty observations of the same species only requires running the script once. All the photos in every folder in the master folder will be uploaded as an individual observation.

What about uploading multiple photos to the same observation? This isn't much harder, add the photos to a sub-folder in the species folder. The script doesn't care what name, so I usually just leave these as "new folder." All the photos in this subfolder will be uploaded to an individual observation.

When you run the script, it gives you a few inputs to fill out:
The more annoying of these are "APP ID" and "APP Secret." You have to create an app for iNaturalist to upload through scripts. Fortunately this just takes a few seconds. The folder it wants is the main folder which contains all the species folders to be uploaded. Even if you are uploading just one species the folder with the photos will need to be in a master folder containing nothing but species folders to be uploaded.

Chances are you will want to go in the code and fill out default values for most of the entries so you will not have to fill them out every time you run the script. It is commented where to add them to the file.

Once the script is done, it moves all the files out of this folder, and puts them next to the main folder in a folder called "Uploaded." This should keep you from re-uploading everything if you lose connection mid-upload. Just run the script again, all the uploaded photos will now be gone. 

Since it got rather long, I uploaded it to Github as iNaturalist-Uploads. There are three files which all must be in the same folder. is the file which is run as a python script. The other two ( and have functions which I preferred to put in a different folder to keep it less messy. All three files need to be saved to the same folder to run.

This probably doesn't make sense for most users as it is way less intuitive than the site submission tool, but if you are experienced with python or have a ton of photos of a limited number of species to upload this starts to make sense.

Sunday, February 3, 2019

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
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


# 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","*.*")))

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,

# 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)
           img =
           coordinates = get_lat_long(img)
           coordinates = 'No Coordinates'
           img =
           date_time = get_date(img)
           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_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'),

print("Program complete")