diff --git a/Dockerfile b/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..60ebab26ee6f9f599d7c523df5286dbae27c27f4 --- /dev/null +++ b/Dockerfile @@ -0,0 +1,63 @@ +FROM ubuntu:latest + +RUN apt-get update +RUN apt-get install python3 python3-pip -y +# FROM ubuntu:22.04 + +# RUN apt update +# RUN apt-get update +# RUN apt install python3.10 python3-pip -y + +# https://stackoverflow.com/questions/75608323/how-do-i-solve-error-externally-managed-environment-every-time-i-use-pip-3 +# https://veronneau.org/python-311-pip-and-breaking-system-packages.html +ENV PIP_BREAK_SYSTEM_PACKAGES 1 + + +################################################## +# Ubuntu setup +################################################## + +RUN apt-get update \ + && apt-get install -y wget \ + && rm -rf /var/lib/apt/lists/* + +RUN apt-get update && apt-get -y upgrade \ + && apt-get install -y --no-install-recommends \ + unzip \ + nano \ + git \ + g++ \ + gcc \ + htop \ + zip \ + ca-certificates \ + && rm -rf /var/lib/apt/lists/* + +################################################## +# ODTP setup +################################################## + +# Set up a new user named "user" with user ID 1000 +#RUN useradd -m -u 1000 user + +# Switch to the "user" user +USER 1000 + +# Set home to the user's home directory +ENV HOME=/home/user \ + PATH=/home/user/.local/bin:$PATH + +# Set the working directory to the user's home directory +WORKDIR $HOME/digiwild + +# Try and run pip command after setting the user with `USER user` to avoid permission issues with Python +RUN pip install --no-cache-dir --upgrade pip + +# Copy the current directory contents into the container at $HOME/app setting the owner to the user +COPY --chown=1000:1000 . $HOME/digiwild + +RUN pip3 install -r $HOME/digiwild/requirements.txt + +#RUN chown -R user:user /digiwild/data /digiwild/app/assets + +ENTRYPOINT ["python3", "/home/user/digiwild/app/main.py"] diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000000000000000000000000000000000000..0ad25db4bd1d86c452db3f9602ccdbe172438f52 --- /dev/null +++ b/LICENSE @@ -0,0 +1,661 @@ + GNU AFFERO GENERAL PUBLIC LICENSE + Version 3, 19 November 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU Affero General Public License is a free, copyleft license for +software and other kinds of works, specifically designed to ensure +cooperation with the community in the case of network server software. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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It is safest +to attach them to the start of each source file to most effectively +state the exclusion of warranty; and each file should have at least +the "copyright" line and a pointer to where the full notice is found. + + + Copyright (C) + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published + by the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If your software can interact with users remotely through a computer +network, you should also make sure that it provides a way for users to +get its source. For example, if your program is a web application, its +interface could display a "Source" link that leads users to an archive +of the code. There are many ways you could offer source, and different +solutions will be better for different programs; see section 13 for the +specific requirements. + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU AGPL, see +. diff --git a/app/.DS_Store b/app/.DS_Store new file mode 100644 index 0000000000000000000000000000000000000000..fbafeea98564ef9a71432e0e3ed8fdcbc07f2c36 Binary files /dev/null and b/app/.DS_Store differ diff --git a/app/.env.dist b/app/.env.dist new file mode 100644 index 0000000000000000000000000000000000000000..aab89b466c36b9c6fdd50b3821a6623f79841a16 --- /dev/null +++ b/app/.env.dist @@ -0,0 +1 @@ +PATH_ASSETS="YOUR_PATH_HERE" \ No newline at end of file diff --git a/app/__init__.py b/app/__init__.py new file mode 100644 index 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differ diff --git a/app/assets/config/config_checkbox_behavior.json b/app/assets/config/config_checkbox_behavior.json new file mode 100644 index 0000000000000000000000000000000000000000..73ebacfba6ea4871668d3fc191737a3d821ba179 --- /dev/null +++ b/app/assets/config/config_checkbox_behavior.json @@ -0,0 +1,42 @@ +{ + "Abnormal breathing": + { + "Description": "Problems breathing, breathing sounds" + }, + "Crash, Falling from the sky": + { + "Description": "Suddenly falling from the sky" + }, + "Diarrhea": + { + "Description": "Observed diarrhea" + }, + "Lameness": + { + "Description": "Apparent limping or not able to walk properly" + }, + "Neurological": + { + "Description": "Circling, incoordination, tremors, convulsions, fast eye movements" + }, + "Other abnormal behavior": + { + "Description": "Other than weakness, other than neurologic" + }, + "Unable to fly": + { + "Description": "Animal alert and tries to fly but can not take off" + }, + "Vomiting": + { + "Description": "Throwing up undigested food, regurgitating" + }, + "Weakness": + { + "Description": "Non responsive, does not fly away when approached, lethargy" + }, + "No changes": + { + "Description": "Animal is acting normally" + } +} \ No newline at end of file diff --git a/app/assets/config/config_checkbox_physical.json b/app/assets/config/config_checkbox_physical.json new file mode 100644 index 0000000000000000000000000000000000000000..5533d751f665af16c13b261d2c289c4483f74230 --- /dev/null +++ b/app/assets/config/config_checkbox_physical.json @@ -0,0 +1,68 @@ +{ + "Common": + { + "Blackened/burnt skin": { + "Description": "Burnt/ blackened/ charred skin or feathers"}, + "Blood": { + "Description": "Visible blood"}, + "Foreign body": { + "Description": "Objects in feathers"}, + "Fracture": { + "Description": "Obvious bone fracture"}, + "Injury": { + "Description": "Visible skin injury"}, + "Parasite": { + "Description": "Maggots, fleas, lice, louseflies"}, + "Swelling": { + "Description": "Marked swelling without injury"}, + "Warty or tumor-like growth, crusts": { + "Description": "Unusual growth, crusty tumor-like growth"} + }, + "Beak": + { + "Adhesion": { + "Description": "Material (food, saliva) around/ in the beak" + }, + "Deformation": { + "Description": "Unusual beak growth" + } + }, + "Body": + { + "Emaciation": { + "Description": "Breast muscles are not well developed"}, + "Fluffed up": { + "Description": "Plumage is fluffed up"}, + "Stained feathers": { + "Description": "Feces, dirt, dried blood"} + }, + "Feathers/Wings/Tail": + { + "Fluffed up": { + "Description": "Plumage is fluffed up"}, + "Feather abnormalities": { + "Description": "Discoloration, broken/ missing feathers"}, + "Stained feathers": { + "Description": "Feces, dirt, dried blood"}, + "Abnormal wing posture": { + "Description": "Wing is not used/ hangs on the side"}, + "Missing limb": { + "Description": "Missing limb"} + }, + "Head incl. eyes": + { + "Ear changes": { + "Description": "Swollen, crusts, plugged, discharge"}, + "Eye changes": { + "Description": "Red, swollen, discharge, crusts, eyes shut"}, + "Tilted head": { + "Description": "Wry neck, unusual neck posture, torticollis"} + }, + "Legs": + { + "Missing limb": { + "Description": "Missing limb"}, + "Deformation": { + "Description": "Abnormal form of limbs, toes, legs"} + } +} diff --git a/app/assets/config/config_dropdown_circumstances.json b/app/assets/config/config_dropdown_circumstances.json new file mode 100644 index 0000000000000000000000000000000000000000..8cdf696d322431d5c09d53c205b7245f60760043 --- /dev/null +++ b/app/assets/config/config_dropdown_circumstances.json @@ -0,0 +1,138 @@ +{ + "Collision with a means of transport": + { + "road vehicle": + { + "Options": { + "road_type" : ["highway", "main road", "secondary road", "local road/path/trail", "parking lot", "other road", "unknown road"] + }, + "Open": "Infrastructure_number" + }, + "train": + { + "Open": "Infrastructure_number" + }, + "aircraft": {}, + "boat": {}, + "other transport collision": {}, + "unknown": {} + }, + "Destruction / Deliberatly removed" : + { + "hunting": + { + "Options": { + "method" : ["shooting", "bow", "falconry", + "hounds hunting", "digging up", "other hunting", "unknow hunting"] + } + }, + "trap": + { + "Options": { + "method": ["killing trap", "pole trap", + "trap cage", "corvids nasse", "net", "cage trap", + "fall-trap", "glue trap", "insect trap", "other trap", "unknown trap"] + } + }, + "poisoning": {}, + "removal or direct capture": + { + "Options": {"method": ["gassing", "raptor captured at nest", + "brood destruction", "traffic/trade", "capture accident", + "scientific sample", "other removal", "unknown removal"] + } + }, + "fishing": + { + "Options": {"method" : ["drowned/tangled", "beached with capture indications", + "other fishing", "unknown fishing"] + } + }, + "other destruction": {}, + "unknown": {} + }, + "Indirect destruction": + { + "pylone and electric grid": + { + + "Options": { + "infrastructure" : ["electric line", "pole/pylon", "other structure", "unknown structure"] + }, + "Extra": + { + "Cause": ["collision", "electrocution"] + } + }, + "windfarm": {}, + "other collision": + { + "Options": { + "object": ["window", "building", "lighthouse", "cable", "wire fence/barbed wire", "other crash", "unknown crash"] + } + }, + "fall": + { + "Options": { + "location": ["chimney", "empty pole", "hole/well", "other fall", "unknown fall"] + } + }, + "development work": + { + "Options": { + "work_type" : ["transport infrastructure", "building", "other work", "unknown work"] + } + }, + "pollution / contamination": + { + "Options": { + "pollution_type" : ["oil pollution", "chemical pollution", "heavy metals", + "light", "noise", "plastic ingestion", "other pollution", "unknown pollution"] + }, + "agricultural net protection": {}, + "vegetal / forest work": + { + "Options": { + "work_type" : ["clearing/mowing/plowing", "tree felling/pruning", + "other forest work", "unknown forest work"] + } + } + }, + "other indirect destruction": {}, + "unknown": {} + }, + "Natural cause": + { + "predation": + { + "Options": { + "predator" : ["cat", "dog", "rooster/hen", "other domestic animal", "wild birds", + "wild mammal", "other predator", "unknown predator"] + } + }, + "weather": + { + "Options": { + "condition" : ["cold wave", "drought", "hail", "lightening", "storm", "other weather", "unknown weather"] + } + }, + "natural disaster": + { + "Options": { + "disaster" : ["fire", "avalanche", "rock fall", "mudslide", "volcanic eruption/ashes", "other natural disaster", "unknown natural disaster"] + } + }, + "nest fall": {}, + "stranding due to exhaustion": {}, + "disease/parasite": {}, + "accidental drowing": + { + "Options": { + "drowning_location" : ["drinking trough", "pool", "storm pool", "irrigation pool", "natural pool", "flood", "other location", "unknown location"] + } + }, + "other natural cause": {}, + "unknown": {} + }, + "Unknown": {} +} diff --git a/app/assets/config/config_followup.json b/app/assets/config/config_followup.json new file mode 100644 index 0000000000000000000000000000000000000000..b4de7d85069be7b2fdae89a347e0c4b2826a8527 --- /dev/null +++ b/app/assets/config/config_followup.json @@ -0,0 +1,23 @@ +{ + "Event follow-up": + { + "Animal collected": { + "Options": ["Yes", "No"] + }, + "Recipient": { + "Options": ["Veterinary", "Care center", "Local Museum", "National Museum", "Other"] + }, + "Radiography": { + "Options": ["Yes", "No", "Unknown"] + }, + "Given answer": { + "Options": ["Nothing", "Complaint against X", "Complaint", "Police call", "Discussion with the speaker", "Press release", "Unknown"] + }, + "Name of recipient / museum": { + "Open": {} + }, + "Collection reference": { + "Open": {} + } + } +} \ No newline at end of file diff --git a/app/assets/fonts/LiberationSans-Regular.ttf b/app/assets/fonts/LiberationSans-Regular.ttf new file mode 100644 index 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b/app/assets/tmp_json/.gitkeep new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/app/assets/tmp_json/tmp_wounded_dead.json b/app/assets/tmp_json/tmp_wounded_dead.json new file mode 100644 index 0000000000000000000000000000000000000000..9e26dfeeb6e641a33dae4961196235bdb965b21b --- /dev/null +++ b/app/assets/tmp_json/tmp_wounded_dead.json @@ -0,0 +1 @@ +{} \ No newline at end of file diff --git a/app/behavior/__init__.py b/app/behavior/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/app/behavior/__pycache__/__init__.cpython-312.pyc b/app/behavior/__pycache__/__init__.cpython-312.pyc new file mode 100644 index 0000000000000000000000000000000000000000..913df0ef6a819ee665ee3738d136ae3d8d66312e Binary files /dev/null and b/app/behavior/__pycache__/__init__.cpython-312.pyc differ diff --git a/app/behavior/__pycache__/behavior_checkbox.cpython-312.pyc b/app/behavior/__pycache__/behavior_checkbox.cpython-312.pyc new file mode 100644 index 0000000000000000000000000000000000000000..2e210f5d1f0a86117a1f9a2e0b444131d0ac184f Binary files /dev/null and b/app/behavior/__pycache__/behavior_checkbox.cpython-312.pyc differ diff --git a/app/behavior/__pycache__/class_behavior.cpython-312.pyc b/app/behavior/__pycache__/class_behavior.cpython-312.pyc new file mode 100644 index 0000000000000000000000000000000000000000..91743657d467f8e9728be5e98425dcc3da58aa19 Binary files /dev/null and b/app/behavior/__pycache__/class_behavior.cpython-312.pyc differ diff --git a/app/behavior/behavior_checkbox.py b/app/behavior/behavior_checkbox.py new file mode 100644 index 0000000000000000000000000000000000000000..70c4a445314b705f3eed0917803d26d74f60206e --- /dev/null +++ b/app/behavior/behavior_checkbox.py @@ -0,0 +1,30 @@ +import gradio as gr +from utils.utils_config import get_custom_config_dropdowns +from utils.utils_checkbox import create_checkbox +from utils.utils_visible import set_visible +from validation_submission.add_json import add_data_tmp + +def on_select_behavior(behavior_checkbox): + behavior_checkbox = [behavior.lower() for behavior in behavior_checkbox] + add_data_tmp("wounded_dead", "behaviors_type", behavior_checkbox) + +def retrieve_behavior_options_description(): + dropdown_config = get_custom_config_dropdowns("config_checkbox_behavior.json") + options = list(dropdown_config.keys()) + options = [option.title() for option in options] + descriptions =[] + for _,subdict in dropdown_config.items(): + descriptions.append(subdict["Description"]) + return options, descriptions + +def create_behavior_checkbox(section: str, visible): + options, descriptions = retrieve_behavior_options_description() + label_checkbox = "Behavior changes observed" + checkbox, text = create_checkbox("", section, label_checkbox, visible, options, descriptions) + return checkbox, text + +def show_behavior(choice, section: str): + visible = set_visible(choice) + checkbox, text = create_behavior_checkbox(section, visible) + add_data_tmp("wounded_dead", "behaviors_radio", choice) + return checkbox, text \ No newline at end of file diff --git a/app/behavior/class_behavior.py b/app/behavior/class_behavior.py new file mode 100644 index 0000000000000000000000000000000000000000..4d8d89dfec6764108bb4374e44f2a89a5d00b621 --- /dev/null +++ b/app/behavior/class_behavior.py @@ -0,0 +1,66 @@ +from pydantic import BaseModel, Field +from typing import Literal, List, Union, Optional + +class Behavior(BaseModel): + type: str + description: Optional[str] = None # Making the description field optional + +# --- Specific Behavior classes --- +class AbnormalBreathing(Behavior): + type: Literal['abnormal breathing'] + description: Optional[Literal["Problems breathing, breathing sounds"]] = None + +class CrashFalling(Behavior): + type: Literal['crash, falling from the sky'] + description: Optional[Literal["Suddenly falling from the sky"]] = None + +class Diarrhea(Behavior): + type: Literal['diarrhea'] + description: Optional[Literal["Observed diarrhea"]] = None + +class Lameness(Behavior): + type: Literal['lameness'] + description: Optional[Literal["Apparent limping or not able to walk properly"]] = None + +class Neurological(Behavior): + type: Literal['neurological'] + description: Optional[Literal["Circling, incoordination, tremors, convulsions, fast eye movements"]] = None + +class OtherAbnormalBehavior(Behavior): + type: Literal['other abnormal behavior'] + description: Optional[Literal["Other than weakness, other than neurologic"]] = None + +class UnableToFly(Behavior): + type: Literal['unable to fly'] + description: Optional[Literal["Animal alert and tries to fly but can not take off"]] = None + +class Vomiting(Behavior): + type: Literal['vomiting'] + description: Optional[Literal["Throwing up undigested food, regurgitating"]] = None + +class Weakness(Behavior): + type: Literal['weakness'] + description: Optional[Literal["Non responsive, does not fly away when approached, lethargy"]] = None + +class NoChanges(Behavior): + type: Literal['no changes'] + description: Optional[Literal["Animal is acting normally"]] = None + +# Union of all possible behaviors +BehaviorType = Union[ + AbnormalBreathing, + CrashFalling, + Diarrhea, + Lameness, + Neurological, + OtherAbnormalBehavior, + UnableToFly, + Vomiting, + Weakness, + NoChanges +] + +# Main class that logs multiple behaviors +class Behaviors(BaseModel): + behaviors_radio: str # e.g., "Yes" + behaviors_type: Optional[List[BehaviorType]] = None diff --git a/app/circumstances/__init__.py b/app/circumstances/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/app/circumstances/__pycache__/__init__.cpython-312.pyc b/app/circumstances/__pycache__/__init__.cpython-312.pyc new file mode 100644 index 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b/app/circumstances/__pycache__/class_circumstance.cpython-312.pyc new file mode 100644 index 0000000000000000000000000000000000000000..47af52d54738188667ee5275406c6a4d313a59d2 Binary files /dev/null and b/app/circumstances/__pycache__/class_circumstance.cpython-312.pyc differ diff --git a/app/circumstances/circumstances.py b/app/circumstances/circumstances.py new file mode 100644 index 0000000000000000000000000000000000000000..602268d031d2ecd279019adb194e8e438246e71b --- /dev/null +++ b/app/circumstances/circumstances.py @@ -0,0 +1,67 @@ +import gradio as gr +import os +from dotenv import load_dotenv + +from utils.utils_visible import set_visible +from validation_submission.add_json import add_data_tmp + +load_dotenv() +PATH = os.getcwd() + "/" +PATH_ASSETS = os.getenv('PATH_ASSETS') +LOGO_PATH = PATH + PATH_ASSETS + "logos" + +CAUSE_COL_WIDTH = "50px" + + +def show_circumstances(choice): + visible = set_visible(choice) + add_data_tmp("wounded_dead", + "circumstance_radio", + choice) + button_collision, button_deliberate_destruction, button_indirect_destruction, button_natural_cause, dropdown, dropdown_level2, openfield_level2, dropdown_extra_level2 = create_circumstances(visible) + return button_collision, button_deliberate_destruction, button_indirect_destruction, button_natural_cause, dropdown, dropdown_level2, openfield_level2, dropdown_extra_level2 + +def create_circumstances(visible): + button_collision, button_deliberate_destruction, button_indirect_destruction, button_natural_cause = create_circumstances_buttons(visible) + dropdown, dropdown_level2, openfield_level2, dropdown_extra_level2 = create_circumstances_dropdown(visible) + return button_collision, button_deliberate_destruction, button_indirect_destruction, button_natural_cause, dropdown, dropdown_level2, openfield_level2, dropdown_extra_level2 + +def create_circumstances_buttons(visible): + with gr.Row() as image_row: + with gr.Column(scale=1, min_width=CAUSE_COL_WIDTH): + button_collision = gr.Button("Collision with a means of transport", + visible=visible, + icon=LOGO_PATH + '/van.png', + elem_id="buttons-conditions") + + with gr.Column(scale=1, min_width=CAUSE_COL_WIDTH): + button_deliberate_destruction = gr.Button("Destruction / Deliberatly removed", + icon=LOGO_PATH + '/destruction.png', + visible=visible, + elem_id="buttons-conditions") + + with gr.Column(scale=1, min_width=CAUSE_COL_WIDTH): + button_indirect_destruction = gr.Button("Indirect destruction", + icon=LOGO_PATH + '/indirect.png', + visible=visible, + elem_id="buttons-conditions") + + with gr.Column(scale=1, min_width=CAUSE_COL_WIDTH): + button_natural_cause = gr.Button("Natural cause", + icon=LOGO_PATH + '/natural.png', + visible=visible, + elem_id="buttons-conditions") + return button_collision, button_deliberate_destruction, button_indirect_destruction, button_natural_cause + +def create_circumstances_dropdown(visible): + with gr.Row() as dropdown_row: + dropdown = gr.Dropdown(choices=[], + label="Choices will appear here...", + visible=visible, interactive=False, elem_id="dropdown-conditions") + openfield_level2 = gr.Textbox(visible=False, elem_id="dropdown-conditions") + dropdown_level2 = gr.Dropdown(choices=[], visible=False, elem_id="dropdown-conditions") + dropdown_extra_level2 = gr.Dropdown(choices=[], visible=False, elem_id="dropdown-conditions") + return dropdown, dropdown_level2, openfield_level2, dropdown_extra_level2 + + + \ No newline at end of file diff --git a/app/circumstances/circumstances_dropdowns.py b/app/circumstances/circumstances_dropdowns.py new file mode 100644 index 0000000000000000000000000000000000000000..a562620a61dae08a3b0392a3faa8cd27b1f6079a --- /dev/null +++ b/app/circumstances/circumstances_dropdowns.py @@ -0,0 +1,112 @@ +import gradio as gr +from utils.utils_config import get_custom_config_dropdowns +from validation_submission.add_json import add_data_tmp + +#--------------------------------------------------------- LEVEL 1 DROPDOWNS +def retrieve_config_options(label, dropdown_config): + options = list(dropdown_config[label].keys()) + options = [option.title() for option in options] + return options + +def reinitialise_level2(): + dropdown_level2 = gr.Dropdown(choices=[], visible=False) + openfield_level2 = gr.Textbox(visible=False) + dropdown_extra_level2 = gr.Dropdown(choices=[], visible=False) + return dropdown_level2, openfield_level2, dropdown_extra_level2 + +def create_dropdown_level1(label): + dropdown_config = get_custom_config_dropdowns("config_dropdown_circumstances.json") + options = retrieve_config_options(label, dropdown_config) + dropdown = gr.Dropdown(choices=options, label=label, interactive=True, visible=True) + dropdown_level2, openfield_level2, dropdown_extra_level2 = reinitialise_level2() + return dropdown, dropdown_level2, openfield_level2, dropdown_extra_level2 + +def dropdown_collision(): + label = "Collision with a means of transport" + add_data_tmp("wounded_dead", "circumstance", label.lower()) + return create_dropdown_level1(label) + +def dropdown_deliberate_destruction(): + label = "Destruction / Deliberatly removed" + add_data_tmp("wounded_dead", "circumstance", label.lower()) + return create_dropdown_level1(label) + +def dropdown_indirect_destruction(): + label = "Indirect destruction" + add_data_tmp("wounded_dead", "circumstance", label.lower()) + return create_dropdown_level1(label) + +def dropdown_natural_cause(): + label = "Natural cause" + add_data_tmp("wounded_dead", "circumstance", label.lower()) + return create_dropdown_level1(label) + + +#--------------------------------------------------------- LEVEL 2 DROPDOWNS +def get_options(value): + value = value.lower() + options_label = None + options_dropdown= None + open_field = None + extras = None + extras_label = None + dropdown_config = get_custom_config_dropdowns("config_dropdown_circumstances.json") + for _, sub_dict in dropdown_config.items(): + nested_dict = sub_dict.get(value) + if nested_dict is not None: + if "Options" in nested_dict.keys(): + options_dict = nested_dict["Options"] + options_label = list(options_dict.keys())[0] + options_dropdown = list(options_dict.values())[0] + options_dropdown = [option.title() for option in options_dropdown] + if "Open" in nested_dict.keys(): + open_field = nested_dict["Open"] + open_field = open_field.title() + if "Extra" in nested_dict.keys(): + for key, val in nested_dict["Extra"].items(): + extras_label = key + extras = val + extras = [extra.title() for extra in extras] + return options_label, options_dropdown, open_field, extras, extras_label + + +def on_select(evt: gr.SelectData): # SelectData is a subclass of EventData + options_label, options_dropdown, open_field, extras, extras_label = get_options(evt.value) + add_data_tmp("wounded_dead", + "circumstance_type", + {"type": (evt.value).lower(), + "option_dropdown_label" : options_label.lower() if options_label is not None else 'NA', + "open_field_label" : open_field.lower() if open_field is not None else 'NA', + "extra_label": extras_label.lower() if extras_label is not None else 'NA' + }) + if options_dropdown is not None: + dropdown_level2 = gr.Dropdown(choices=options_dropdown, label=evt.value, interactive=True, visible=True) + else: + dropdown_level2 = gr.Dropdown(choices=[], visible=False) + + if open_field is not None: + openfield_level2 = gr.Textbox(label=open_field, interactive=True, visible=True) + else: + openfield_level2 = gr.Textbox(visible=False) + + if extras is not None: + dropdown_extra_level2 = gr.Dropdown(choices=extras, label=extras_label, interactive=True, visible=True) + else: + dropdown_extra_level2 = gr.Dropdown(choices=[], visible=False) + return dropdown_level2, openfield_level2, dropdown_extra_level2 + +def on_select_dropdown_level2(evt: gr.SelectData): + add_data_tmp("wounded_dead", + "circumstance_option_dropdown", + evt.value.lower()) + +def on_select_dropdown_extra_level2(evt: gr.SelectData): + add_data_tmp("wounded_dead", + "circumstance_extra", + evt.value.lower()) + +def on_change_openfield_level2(openfield_level2_dead): + print("Saving open field") + add_data_tmp("wounded_dead", + "circumstance_open_field", + str(openfield_level2_dead).lower()) \ No newline at end of file diff --git a/app/circumstances/class_circumstance.py b/app/circumstances/class_circumstance.py new file mode 100644 index 0000000000000000000000000000000000000000..935f42a24ddf19c1e8c7047cdad72159e7c778e6 --- /dev/null +++ b/app/circumstances/class_circumstance.py @@ -0,0 +1,205 @@ +from pydantic import BaseModel, Field +from typing import Literal, List, Union, Optional + +# Base class for CircumstanceType with a discriminator field 'type' +class CircumstanceTypeBase(BaseModel): + type: str + +# Collision with means of transport +class RoadVehicleCollision(CircumstanceTypeBase): + type: Literal['road_vehicle'] + infrastructure_number: Optional[str] = None + road_type: Literal['highway', 'main road', + 'secondary road', 'local road/path/trail', + 'parking lot'] + +class TrainCollision(CircumstanceTypeBase): + type: Literal['train'] + infrastructure_number: str + +class AircraftCollision(CircumstanceTypeBase): + type: Literal['aircraft'] + +class BoatCollision(CircumstanceTypeBase): + type: Literal['boat'] + +class OtherTransportCollision(CircumstanceTypeBase): + type: Literal['other transport collision'] + +class UnknownTransportCollision(CircumstanceTypeBase): + type: Literal['unknown transport collision'] + +# Destruction / Deliberately removed +class HuntingDestruction(CircumstanceTypeBase): + type: Literal['hunting'] + method: Literal['shooting', 'bow', 'falconry', + 'hounds hunting', 'digging up', + "other hunting", "unknow hunting"] + +class TrapDestruction(CircumstanceTypeBase): + type: Literal['trap'] + method: Literal['killing trap', 'pole trap', 'trap cage', 'corvids nasse', + 'net', 'cage trap', 'fall-trap', 'glue trap', 'insect trap', + "other trap", "unknown trap"] + +class PoisoningDestruction(CircumstanceTypeBase): + type: Literal['poisoning'] + +class RemovalDestruction(CircumstanceTypeBase): + type: Literal['removal or direct capture'] + method: Literal['gassing', 'raptor captured at nest', 'brood destruction', + 'traffic/trade', 'capture accident', 'scientific sample', + "other removal", "unknown removal"] + +class FishingDestruction(CircumstanceTypeBase): + type: Literal['fishing'] + method: Literal['drowned/tangled', 'beached with capture indications', "other fishing", "unknown fishing"] + +class OtherDestruction(CircumstanceTypeBase): + type: Literal['other destruction'] + +class UnknownDestruction(CircumstanceTypeBase): + type: Literal['unknown destruction'] + +# Indirect destruction +class PylonElectricGridDestruction(CircumstanceTypeBase): + type: Literal['pylone and electric grid'] + infrastructure: Literal['electric line', 'pole/pylon', "other structure", "unknown structure"] + cause: Literal['collision', 'electrocution'] + +class WindfarmDestruction(CircumstanceTypeBase): + type: Literal['windfarm'] + +class OtherCollisionDestruction(CircumstanceTypeBase): + type: Literal['other collision'] + object: Literal['window', 'building', 'lighthouse', + 'cable', 'wire fence/barbed wire', 'other crash', 'unknown crash'] + +class FallDestruction(CircumstanceTypeBase): + type: Literal['fall'] + location: Literal['chimney', 'empty pole', 'hole/well', 'other fall', 'unknown fall'] + +class DevelopmentWorkDestruction(CircumstanceTypeBase): + type: Literal['development work'] + work_type: Literal['transport infrastructure', 'building', 'other work', 'unknown work'] + +class PollutionContaminationDestruction(CircumstanceTypeBase): + type: Literal['pollution / contamination'] + pollution_type: Literal['oil pollution', 'chemical pollution', 'heavy metals', + 'light', 'noise', + 'plastic ingestion', 'other pollution', 'unknown pollution'] + +class AgriculturalNetProtectionDestruction(CircumstanceTypeBase): + type: Literal['agricultural net protection'] + +class VegetalForestWorkDestruction(CircumstanceTypeBase): + type: Literal['vegetal / forest work'] + work_type: Literal['clearing/mowing/plowing', 'tree felling/pruning', + 'other forest work', 'unknown forest work'] + +class OtherIndirectDestruction(CircumstanceTypeBase): + type: Literal['other indirect desctruction'] + +class UnknownIndirectDestruction(CircumstanceTypeBase): + type: Literal['unknown indirect desctruction'] + +# Natural cause +class Predation(CircumstanceTypeBase): + type: Literal['predation'] + predator: Literal['cat', 'dog', 'rooster/hen', + 'other domestic animal', 'wild birds', + 'wild mammal', 'other predator', 'unknown predator'] + +class Weather(CircumstanceTypeBase): + type: Literal['weather'] + condition: Literal['cold wave', 'drought', 'hail', + 'lightening', 'storm', + 'other weather', 'unknown weather'] + +class NaturalDisaster(CircumstanceTypeBase): + type: Literal['natural disaster'] + disaster: Literal['fire', 'avalanche', 'rock fall', + 'mudslide', 'volcanic eruption/ashes', + 'other natural disaster', 'unknown natural disaster'] + +class NestFall(CircumstanceTypeBase): + type: Literal['nest fall'] + +class StrandingExhaustion(CircumstanceTypeBase): + type: Literal['stranding due to exhaustion'] + +class DiseaseParasite(CircumstanceTypeBase): + type: Literal['disease/parasite'] + +class AccidentalDrowning(CircumstanceTypeBase): + type: Literal['accidental drowning'] + drowning_location: Literal['drinking trough', 'pool', + 'storm pool', 'irrigation pool', + 'natural pool', 'flood', + 'other location', 'unknown location'] + +class OtherNaturalCause(CircumstanceTypeBase): + type: Literal['other natural cause'] + +class UnknownNaturalCause(CircumstanceTypeBase): + type: Literal['unknown natural cause'] + +# Unknown cause +class UnknownCircumstance(CircumstanceTypeBase): + type: Literal['unknown'] + +# Union of all possible CircumstanceTypes with 'type' as the discriminator +CircumstanceType = Union[ + RoadVehicleCollision, + TrainCollision, + AircraftCollision, + BoatCollision, + OtherTransportCollision, + UnknownTransportCollision, + HuntingDestruction, + TrapDestruction, + PoisoningDestruction, + RemovalDestruction, + FishingDestruction, + OtherDestruction, + UnknownDestruction, + PylonElectricGridDestruction, + WindfarmDestruction, + OtherCollisionDestruction, + FallDestruction, + DevelopmentWorkDestruction, + PollutionContaminationDestruction, + AgriculturalNetProtectionDestruction, + VegetalForestWorkDestruction, + OtherIndirectDestruction, + UnknownIndirectDestruction, + Predation, + Weather, + NaturalDisaster, + NestFall, + StrandingExhaustion, + DiseaseParasite, + AccidentalDrowning, + OtherNaturalCause, + UnknownNaturalCause, + UnknownCircumstance +] + +# Main Circumstance class +class Circumstances(BaseModel): + circumstance_radio: str # e.g., "Yes" + circumstance: Optional[str] = None # e.g., "COLLISION" + circumstance_type: Optional[CircumstanceType] = Field(None, discriminator='type') + + +# Example usage +# json_data = { +# "circumstance": "COLLISION", +# "circumstance_radio": "Yes", +# "circumstance_type": { +# "type": "Train", +# "infrastructure_number": "56" +# } +# } +# circumstance_instance = Circumstance(**json_data) +# circumstance_schema = Circumstance.schema_json(indent=2) \ No newline at end of file diff --git a/app/classes.py b/app/classes.py new file mode 100644 index 0000000000000000000000000000000000000000..d6a0679acaf1ba556c7efb70008c940ba57524e3 --- /dev/null +++ b/app/classes.py @@ -0,0 +1,46 @@ +from pydantic import BaseModel, Field +from typing import Optional +import numpy as np +from PIL import Image +import io +import base64 +import uuid + +from behavior.class_behavior import Behaviors +from circumstances.class_circumstance import Circumstances +from physical.class_physical import PhysicalAnomalies +from follow_up.class_follow_up import FollowUpEvents +from geolocalisation.class_geolocalisation import Geolocalisation + +class Wounded(BaseModel): + circumstances: Circumstances + behaviors: Behaviors + physical_anomalies: PhysicalAnomalies + follow_up_events: FollowUpEvents + +class Dead(BaseModel): + circumstances: Circumstances + physical_anomalies: PhysicalAnomalies + follow_up_events: FollowUpEvents + +class ImageBase64(BaseModel): + image: str + @classmethod + def to_base64(cls, pixel_data: list): + img_array = np.array(pixel_data, dtype=np.uint8) + img = Image.fromarray(img_array) + # Save the image to a bytes buffer + buffer = io.BytesIO() + img.save(buffer, format="PNG") + buffer.seek(0) + base64_str = base64.b64encode(buffer.read()).decode('utf-8') + return cls(image=base64_str) + +class Report(BaseModel): + identifier: str + image: ImageBase64 + geolocalisation: Geolocalisation + wounded_state: str + wounded: Optional[Wounded] = None + dead_state: str + dead: Optional[Dead] = None diff --git a/app/dead.py b/app/dead.py new file mode 100644 index 0000000000000000000000000000000000000000..20a87ef66536f33834b816eabe83b7a3a694cebc --- /dev/null +++ b/app/dead.py @@ -0,0 +1,40 @@ +import gradio as gr +from circumstances.circumstances import create_circumstances +from physical.physical_select_animal import create_bird_anatomy +from physical.physical_checkbox import process_body_parts +from follow_up.followup_events import create_followup_dropdowns, create_followup_open +from validation_submission.add_json import add_data_to_individual + +def show_section_dead(visible): + if visible==True: + add_data_to_individual("wounded_state", "No") + add_data_to_individual("dead_state", "Yes") + + with gr.Column(visible=visible, elem_id="dead") as section_dead: + gr.Markdown("# Dead Animal") + + gr.Markdown("## Do you know what conditions caused this?", label="description") + radio_cause = gr.Radio(["Yes", "No"], value=None, show_label=False, interactive=True) + button_collision, button_deliberate_destruction, button_indirect_destruction, button_natural_cause, dropdown, dropdown_level2, openfield_level2, dropdown_extra_level2 = create_circumstances(visible=False) + + gr.Markdown("## Are there physical changes on the bird?" , label="description") + radio_physical = gr.Radio(["Yes", "No"], value=None, show_label=False, interactive=True) + with gr.Row(): + physical_boxes = create_bird_anatomy(False, "dead") + with gr.Column(): + checkbox_beak, text_beak, checkbox_body, text_body, checkbox_feathers, text_feathers, checkbox_head, text_head, checkbox_legs, text_legs = process_body_parts("dead", "None") + + gr.Markdown("## Follow-Up Events", label="Title") + gr.Markdown("Please tell us what you did with the animal.", label="description") + with gr.Row(): + fe_collection_dropdown, fe_recepient_dropdown, fe_radio_dropdown, fe_answer_dropdown = create_followup_dropdowns(visible, "dead") + with gr.Row(): + fe_name_recipient, fe_collection_ref = create_followup_open(visible, "dead") + + + return section_dead, radio_cause, radio_physical,\ + button_collision, button_deliberate_destruction, button_indirect_destruction, button_natural_cause, \ + dropdown, dropdown_level2, openfield_level2, dropdown_extra_level2, \ + physical_boxes, \ + checkbox_beak, text_beak, checkbox_body, text_body, checkbox_feathers, text_feathers, checkbox_head, text_head, checkbox_legs, text_legs, \ + fe_collection_dropdown, fe_recepient_dropdown, fe_radio_dropdown, fe_answer_dropdown, fe_name_recipient, fe_collection_ref diff --git a/app/display.py b/app/display.py new file mode 100644 index 0000000000000000000000000000000000000000..9f1fdf92860e9fd06148504de3b54d892c82b61c --- /dev/null +++ b/app/display.py @@ -0,0 +1,120 @@ +import gradio as gr +import pandas as pd +from gradio_modal import Modal +from PIL import Image +from io import BytesIO +import base64 + +from validation_submission.submission import validate_save_individual +from validation_submission.get_json import get_json_all_individuals + +HEADERS = ["Identifier", "Location", "Wounded", "Dead"] + + +def save_display_individual(gallery, df, error_box): + individual, error_box = validate_save_individual(error_box) + if individual: + all_animals = get_json_all_individuals() + gallery_animals = process_animals_for_gallery(all_animals) + gallery = make_gallery(gallery_animals) + df_animals = process_animals_for_df(all_animals) + df = make_df(df_animals) + return gallery, df, error_box + +# ---------------------------------- +# GALLERY + +def convert_image(image_base64_str): + im = Image.open(BytesIO(base64.b64decode(image_base64_str))) + return im + +def set_gallery_size(len_animals): + if len_animals < 10: + num_cols=5 + num_rows=2 + else: + num_cols = len_animals/2 + num_rows = len_animals/(num_cols) + return num_cols, num_rows + +def process_animals_for_gallery(all_animals): + gallery_animals = [] + for _, animal in all_animals.items(): + image = convert_image(animal["image"]["image"]) + caption = animal["identifier"] + animal = (image, caption) + gallery_animals.append(animal) + return gallery_animals + +def make_gallery(gallery_animals): + num_cols, num_rows = set_gallery_size(len(gallery_animals)) + gallery = gr.Gallery( + label="Gallery of Records", elem_id="gallery", + columns=[num_cols], rows=[num_rows], + value=gallery_animals, + object_fit="contain", height="auto", interactive=False) + return gallery + +def keep_only_values(dict_to_filter): + info_text = "" + values_to_ignore = ["Yes", "No", "NA"] + if dict_to_filter: + for key, val in dict_to_filter.items(): + if type(val) is dict: + subset_text = keep_only_values(val) + info_text += f"{subset_text}" + elif type(val) is list: + for item in val: + if type(item) is dict: + subset_text = keep_only_values(item) + info_text += f"{subset_text}" + elif (val is not None) and (type(val) is not bool) and (val not in values_to_ignore): + info_text += f" {key} : {val} |" + else: + print("Ignoring value: ", val) + print("Associated key: ", key) + else: + info_text = "NaN" + return info_text + +# ---------------------------------- +# DATAFRAME + +def process_animals_for_df(all_animals): + df_animals = {} + identifiers =[] + geo =[] + wounded =[] + dead =[] + for _, animal in all_animals.items(): + identifier_value = animal["identifier"] + identifiers.append(identifier_value) + geo_dict = animal["geolocalisation"] + geo_values = keep_only_values(geo_dict) + geo.append(geo_values) + wounded_dict = animal["wounded"] + wounded_values = keep_only_values(wounded_dict) + wounded.append(wounded_values) + dead_dict = animal["dead"] + dead_values = keep_only_values(dead_dict) + dead.append(dead_values) + df_animals["Identifier"] = identifiers + df_animals["Location"] = geo + df_animals["Wounded"] = wounded + df_animals["Dead"] = dead + return df_animals + + +def make_df(df_animals): + df = pd.DataFrame.from_dict(df_animals) + styled_df = df.style.set_properties(**{ + 'min-width': '25px', + 'max-width': '50px', # Adjust width as needed + 'white-space': 'normal', # Allows text to wrap to the next line + 'word-wrap': 'break-word' # Breaks long words to fit within the width + }) + df_gradio = gr.DataFrame(visible=True, + value=styled_df, + headers=HEADERS, interactive=False) + return df_gradio + diff --git a/app/follow_up/__pycache__/class_follow_up.cpython-312.pyc b/app/follow_up/__pycache__/class_follow_up.cpython-312.pyc new file mode 100644 index 0000000000000000000000000000000000000000..393c9df40faf230d76c5fcb9d544efeffaf90373 Binary files /dev/null and b/app/follow_up/__pycache__/class_follow_up.cpython-312.pyc differ diff --git a/app/follow_up/__pycache__/followup_events.cpython-312.pyc b/app/follow_up/__pycache__/followup_events.cpython-312.pyc new file mode 100644 index 0000000000000000000000000000000000000000..539f07232de462cfca104f8b8fa8d1288f549950 Binary files /dev/null and b/app/follow_up/__pycache__/followup_events.cpython-312.pyc differ diff --git a/app/follow_up/class_follow_up.py b/app/follow_up/class_follow_up.py new file mode 100644 index 0000000000000000000000000000000000000000..4ff1cfe5769d5ec668b19cdca860450efa113111 --- /dev/null +++ b/app/follow_up/class_follow_up.py @@ -0,0 +1,50 @@ +from pydantic import BaseModel, Field +from typing import Literal, Union, Optional, List + +# --- Event follow-up classes --- + +class AnimalCollectedEvent(BaseModel): + type: Literal['animal collected'] + collected: Literal['yes', 'no'] + +class RecipientEvent(BaseModel): + type: Literal['recipient'] + recipient: Literal['veterinary', 'care center', + 'local museum', 'national museum', + 'other'] + +class RadiographyEvent(BaseModel): + type: Literal['radiography'] + radiography: Literal['yes', 'no', 'unknown'] + +class GivenAnswerEvent(BaseModel): + type: Literal['given answer'] + answer: Literal[ + 'nothing', + 'complaint against x', + 'complaint', + 'police call', + 'discussion with the speaker', + 'press release', + 'unknown' + ] + +class NameOfRecipientEvent(BaseModel): + type: Literal['recipient name'] + name: str + +class CollectionReferenceEvent(BaseModel): + type: Literal['collection reference'] + reference: str + +FollowUpEventType = Union[ + AnimalCollectedEvent, + RecipientEvent, + RadiographyEvent, + GivenAnswerEvent, + NameOfRecipientEvent, + CollectionReferenceEvent +] + +class FollowUpEvents(BaseModel): + follow_up_events: Optional[List[FollowUpEventType]] = None \ No newline at end of file diff --git a/app/follow_up/followup_events.py b/app/follow_up/followup_events.py new file mode 100644 index 0000000000000000000000000000000000000000..11bad2183a6ab8473c3293758a8afe6efa0d989d --- /dev/null +++ b/app/follow_up/followup_events.py @@ -0,0 +1,46 @@ +import gradio as gr +from utils.utils_config import get_custom_config_dropdowns +from validation_submission.add_json import add_data_tmp + +def create_followup_dropdowns(visible, elem_id): + followup_config = get_custom_config_dropdowns("config_followup.json") + followup_config = followup_config["Event follow-up"] + fe_collection_dropdown = create_fe_collection_dropdown(followup_config, visible, elem_id) + fe_recipient_dropdown = create_fe_recipient_dropdown(followup_config, visible, elem_id) + fe_radio_dropdown = create_fe_radio_dropdown(followup_config, visible, elem_id) + fe_answer_dropdown = create_fe_answer_dropdown(followup_config, visible, elem_id) + return fe_collection_dropdown, fe_recipient_dropdown, fe_radio_dropdown, fe_answer_dropdown + +def create_followup_open(visible, elem_id): + fe_name_recipient = gr.Textbox(label="Name of recipient / museum", visible=visible, + elem_id=elem_id, interactive=True) + fe_collection_ref = gr.Textbox(label="Collection reference", visible=visible, + elem_id=elem_id, interactive=True) + return fe_name_recipient, fe_collection_ref + + +def create_fe_collection_dropdown(followup_config, visible, elem_id): + fe_collection_dropdown = gr.Dropdown(choices=followup_config["Animal collected"]["Options"], label="Animal collected", + visible=visible, elem_id=elem_id, interactive=True) + return fe_collection_dropdown + +def create_fe_recipient_dropdown(followup_config, visible, elem_id): + fe_recipient_dropdown = gr.Dropdown(choices=followup_config["Recipient"]["Options"], label="Recipient", + visible=visible, elem_id=elem_id, interactive=True) + return fe_recipient_dropdown + +def create_fe_radio_dropdown(followup_config, visible, elem_id): + fe_radio_dropdown = gr.Dropdown(choices=followup_config["Radiography"]["Options"], label="Radiography", + visible=visible, elem_id=elem_id, interactive=True) + return fe_radio_dropdown + +def create_fe_answer_dropdown(followup_config, visible, elem_id): + fe_answer_dropdown = gr.Dropdown(choices=followup_config["Given answer"]["Options"], label="Given answer", + visible=visible, elem_id=elem_id, interactive=True) + return fe_answer_dropdown + +def save_fe(value, key): + add_data_tmp("wounded_dead", "followup " + key.lower(), value.lower()) + + + \ No newline at end of file diff --git a/app/geolocalisation/__init__.py 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mode 100644 index 0000000000000000000000000000000000000000..c67ea65b7204c4600fc3d53154cb2044e62d98c9 Binary files /dev/null and b/app/geolocalisation/__pycache__/js_geolocation.cpython-312.pyc differ diff --git a/app/geolocalisation/__pycache__/maps.cpython-312.pyc b/app/geolocalisation/__pycache__/maps.cpython-312.pyc new file mode 100644 index 0000000000000000000000000000000000000000..c35d1194bea626e876aeefefd8d0e27962b1f36d Binary files /dev/null and b/app/geolocalisation/__pycache__/maps.cpython-312.pyc differ diff --git a/app/geolocalisation/class_geolocalisation.py b/app/geolocalisation/class_geolocalisation.py new file mode 100644 index 0000000000000000000000000000000000000000..fa0f0a5316a51f5314abddcc8bd7970c010932ce --- /dev/null +++ b/app/geolocalisation/class_geolocalisation.py @@ -0,0 +1,16 @@ +from pydantic import BaseModel, Field +from typing import Literal, List, Union + +class Longitude(BaseModel): + type: Literal['longitude'] + value: float + +class Latitude(BaseModel): + type: Literal['latitude'] + value: float + +class Geolocalisation(BaseModel): + longitude: Longitude + latitude: Latitude + name: str + diff --git a/app/geolocalisation/js_geolocation.py b/app/geolocalisation/js_geolocation.py new file mode 100644 index 0000000000000000000000000000000000000000..055ee262a3bdd9b00fc483bc4d0b93381a99164f --- /dev/null +++ b/app/geolocalisation/js_geolocation.py @@ -0,0 +1,35 @@ +# JavaScript code to get location and update hidden_input +js_geocode = """ + function() { + var textbox = document.querySelector('#textbox_id textarea'); + console.log(textbox) + if (navigator.geolocation) { + navigator.geolocation.getCurrentPosition( + function(position) { + var data = { + 'latitude': position.coords.latitude, + 'longitude': position.coords.longitude, + 'accuracy': position.coords.accuracy + }; + console.log("Geolocation data:", data); + textbox.value = JSON.stringify(data); + textbox.dispatchEvent(new Event('input', { bubbles: true })); + }, + function(error) { + var data = {'error': error.message}; + console.log("Geolocation error:", data); + textbox.value = JSON.stringify(data); + textbox.dispatchEvent(new Event('input', { bubbles: true })); + } + ); + } else { + var data = {'error': 'Geolocation is not supported by this browser.'}; + console.log("Geolocation unsupported:", data); + textbox.value = JSON.stringify(data); + textbox.dispatchEvent(new Event('input', { bubbles: true })); + } + } +""" + +def display_location(location_json): + return location_json \ No newline at end of file diff --git a/app/geolocalisation/maps.py b/app/geolocalisation/maps.py new file mode 100644 index 0000000000000000000000000000000000000000..70af4eff68830a007b34bb979caa0158a46a6841 --- /dev/null +++ b/app/geolocalisation/maps.py @@ -0,0 +1,50 @@ +from geopy.geocoders import Nominatim +import gradio as gr +from validation_submission.add_json import add_data_to_individual +from geolocalisation.class_geolocalisation import Geolocalisation + + +def create_geolocalisation_object(lat, long, name): + try: + geolocalisation = Geolocalisation( + longitude={"type": "longitude", "value": long}, + latitude={"type": "latitude", "value": lat}, + name=name + ) + except: + print("Pydantic Error for Geolocalisation") + return geolocalisation + +def save_geolocalisation_to_json(geolocalisation): + geo_dict = geolocalisation.dict() + add_data_to_individual("geolocalisation", geo_dict) + +def get_location(address): + try: + # calling the Nominatim tool + loc = Nominatim(user_agent="GetLoc") + + # entering the location name + getLoc = loc.geocode(address) + + # latitude and longitude + lat = getLoc.latitude + lon = getLoc.longitude + + # Save values + geolocalisation = create_geolocalisation_object(lat, lon, address) + save_geolocalisation_to_json(geolocalisation) + + #display location processing + value = "Latitude = " + str(lat) + "\n" + "Longitude = " + str(lon) + identified_location= gr.Textbox(visible=True, interactive=False, + label="Identified GPS Location", + value=value) + return identified_location + + except: + error = "Please try another less precise location." + identified_location= gr.Textbox(visible=True, interactive=False, + label="Identified GPS Location", + value=error) + return identified_location \ No newline at end of file diff --git a/app/gradio_test/test_selectdata_event.py b/app/gradio_test/test_selectdata_event.py new file mode 100644 index 0000000000000000000000000000000000000000..3e6d0e5e935dc4b9cdf4397c65e1a1413126c5bc --- /dev/null +++ b/app/gradio_test/test_selectdata_event.py @@ -0,0 +1,16 @@ +import gradio as gr + +with gr.Blocks() as demo: + table = gr.Dataframe([[1, 2, 3], [4, 5, 6]]) + #gallery = gr.Gallery([("cat.jpg", "Cat"), ("dog.jpg", "Dog")]) + textbox = gr.Textbox("Hello World!") + statement = gr.Textbox() + + def on_select(evt: gr.SelectData): + return gr.Textbox(f"You selected {evt.value} at {evt.index} from {evt.target}") + + table.select(on_select, inputs=[table], outputs=[statement]) + #gallery.select(on_select, gallery, statement) + textbox.select(on_select, inputs=[textbox], outputs=[statement]) + +demo.launch(server_name="0.0.0.0", server_port=3131) \ No newline at end of file diff --git a/app/gradio_test/tests_delete_gallery.py b/app/gradio_test/tests_delete_gallery.py new file mode 100644 index 0000000000000000000000000000000000000000..d3cb1f8281e4ed8393e01dc4c60c621bb0749d9a --- /dev/null +++ b/app/gradio_test/tests_delete_gallery.py @@ -0,0 +1,25 @@ +import gradio as gr + +# Example initial image list +images = [ + "https://via.placeholder.com/150/0000FF", + "https://via.placeholder.com/150/FF0000", + "https://via.placeholder.com/150/00FF00" +] + +# Function to remove a selected image from the gallery +def delete_image(selected_image, image_list): + if selected_image in image_list: + image_list.remove(selected_image) # Remove the selected image + return image_list # Return the updated image list + +# Gradio app +with gr.Blocks() as demo: + gallery = gr.Gallery(value=images, label="Gallery") # Gallery of images + selected_image = gr.Dropdown(choices=images, label="Select Image to Delete") # Dropdown for selection + delete_button = gr.Button("Delete Selected Image") # Button to delete + + # When button is clicked, delete the selected image and update gallery + delete_button.click(fn=delete_image, inputs=[selected_image, gallery], outputs=gallery) + +demo.launch(server_name="0.0.0.0", server_port=3232) \ No newline at end of file diff --git a/app/main.py b/app/main.py new file mode 100644 index 0000000000000000000000000000000000000000..4be3fade10226fd378ce934fa6f40dd6a1dcc327 --- /dev/null +++ b/app/main.py @@ -0,0 +1,387 @@ +import gradio as gr +from gradio_modal import Modal + +from validation_submission.create_json import create_json_all_individuals, create_json_one_individual, create_tmp, reset_json +from validation_submission.add_json import add_data_to_individual +from validation_submission.validation import reset_error_box +from display import save_display_individual +from geolocalisation.maps import get_location +from functools import partial +from dead import show_section_dead +from wounded import show_section_wounded +from circumstances.circumstances import show_circumstances +from circumstances.circumstances_dropdowns import * +from physical.physical_select_animal import show_physical, find_bounding_box +from physical.physical_checkbox import on_select_body_part, hide_physical +from behavior.behavior_checkbox import show_behavior, on_select_behavior +from follow_up.followup_events import save_fe +from styling.style import * +from styling.theme import css + +from geolocalisation.js_geolocation import js_geocode, display_location + +# with gr.Blocks(theme=theme, css=css) as demo: +with gr.Blocks(theme='shivi/calm_seafoam') as demo: +#with gr.Blocks() as demo: + create_json_all_individuals() + # --------------------------------------------------------- + # Intro Text + with gr.Row(): + with gr.Column(scale=1): + title = gr.Markdown("# Welcome to Digiwild", label="Title") + description = gr.Markdown("Please record your wildlife observations here !", label="description") + with gr.Row(): + show_modal = gr.Button("Add an Animal", scale=3) + submit_button = gr.Button("Submit All Animals", scale=1) + df = gr.Dataframe(headers=["Identifier", "Location", "Wounded", "Dead"], visible=False, interactive=False) + gallery = gr.Gallery( + label="Gallery of Records", elem_id="gallery", + columns=[1], rows=[1], + object_fit="contain", height="auto", interactive=False) + + with Modal(visible=False) as modal: + # --------------------------------------------------------- + # Intro Text + with gr.Row(): + with gr.Column(scale=1): + title = gr.Markdown("# Animal Report", label="Title") + description = gr.Markdown("Please record your observation here.", label="description") + + # --------------------------------------------------------- + # Camera + with gr.Row(): + def save_image(camera): + add_data_to_individual("image", camera.tolist()) + + camera = gr.Image(elem_id="image") + camera.input(save_image, inputs=[camera]) + # --------------------------------------------------------- + # Location + #with gr.Row(): + with gr.Column(scale=1): + gr.Markdown("### Location") + gr.Markdown("#### Location (Using address)") + location = gr.Textbox(visible=True, interactive=True, label="Location of Sighting") + #display location processing + identified_location= gr.Textbox(visible=False, interactive=False, + label="Identified GPS Location") + with gr.Row(): + #to submit it + submit_location = gr.Button("Get Coordinates using address", + visible=True, interactive=True, scale=3) + submit_location.click(get_location, inputs=[location], outputs=[identified_location]) + #to clear it + clear_location = gr.ClearButton(components=[location, identified_location], + visible=True, interactive=True, scale=1 + ) + clear_location.click() + + # Geolocation + gr.Markdown("#### Location (Using GPS)") + location_data = gr.JSON(label="Identified GPS Location") + hidden_input = gr.Textbox(visible=False, elem_id="textbox_id") + btn_gpslocation = gr.Button("Get Coordinates using GPS (Permission required)") + btn_gpslocation.click(None, [], [], js=js_geocode) + hidden_input.change(display_location, inputs=hidden_input, outputs=location_data) + + + # Introducing text_box for Species + gr.Markdown("### General details") + with gr.Row(): + specie = gr.Textbox( + label="Species (if known)", + placeholder="e.g. European Robin, Common Blackbird", + info="Enter the species name if you can identify it. If unsure, provide your best guess or general description (e.g. 'small brown bird')", + visible=True, + interactive=True + ) + + # Number of individuals + with gr.Row(): + num_individuals = gr.Number( + label="Number of Individuals", + value=1, # Default value + minimum=1, + precision=0, # Only whole numbers + info="Enter the number of animals observed", + #placeholder="Enter number...", + visible=True, + interactive=True + ) + + # Introducing text_box for comments + with gr.Row(): + comments = gr.TextArea( + label="Additional Comments", + placeholder="Enter any additional observations or notes about the sighting...", + info="Optional: Add any relevant details about the animal(s) or circumstances", + lines=3, + max_lines=5, + visible=True, + interactive=True + ) + + + # --------------------------------------------------------- + # --------------------------------------------------------- + # Dead and Wounded Buttons + gr.Markdown("## The State of the Animal", label="Title") + gr.Markdown("Please tell us if the animal was wounded / sick or dead.", label="description") + with gr.Row() as block_form: + with gr.Column(scale=1): + butt_wounded = gr.Button("Wounded / Sick", elem_id="wounded") + with gr.Column(scale=1): + butt_dead = gr.Button("Dead", elem_id="dead") + + # --------------------------------------------------------- + # Initiate sections + section_dead, radio_circumstance_dead, radio_physical_dead,\ + button_collision_dead, button_deliberate_destruction_dead, button_indirect_destruction_dead, button_natural_cause_dead, \ + dropdown_dead, dropdown_level2_dead, openfield_level2_dead, dropdown_extra_level2_dead, \ + physical_boxes_dead, \ + checkbox_beak_dead, text_beak_dead, checkbox_body_dead, text_body_dead, checkbox_feathers_dead, text_feathers_dead, checkbox_head_dead, text_head_dead, checkbox_legs_dead, text_legs_dead, \ + fe_collection_dropdown_dead, fe_recepient_dropdown_dead, fe_radio_dropdown_dead, fe_answer_dropdown_dead, \ + fe_name_recipient_dead, fe_collection_ref_dead \ + = show_section_dead(False) + section_wounded, radio_circumstance_wounded, radio_behavior_wounded, radio_physical_wounded, \ + button_collision_wounded, button_deliberate_destruction_wounded, button_indirect_destruction_wounded, button_natural_cause_wounded, \ + dropdown_wounded, dropdown_level2_wounded, openfield_level2_wounded, dropdown_extra_level2_wounded, \ + behavior_checkbox, behavior_text, \ + physical_boxes_wounded, \ + checkbox_beak_wounded, text_beak_wounded, checkbox_body_wounded, text_body_wounded, checkbox_feathers_wounded, text_feathers_wounded, checkbox_head_wounded, text_head_wounded, checkbox_legs_wounded, text_legs_wounded, \ + fe_collection_dropdown_wounded, fe_recepient_dropdown_wounded, fe_radio_dropdown_wounded, fe_answer_dropdown_wounded, \ + fe_name_recipient_wounded, fe_collection_ref_wounded \ + = show_section_wounded(False) + + # --------------------------------------------------------- + # --------------------------------------------------------- + # --------------------------------------------------------- + # Dead Button Logic + partial_show_section_dead = partial(show_section_dead, True) + partial_hide_section_wounded = partial(show_section_wounded, False) + butt_dead.click(partial_show_section_dead, + inputs=None, + outputs=[section_dead, + radio_circumstance_dead, radio_physical_dead, + button_collision_dead, button_deliberate_destruction_dead, button_indirect_destruction_dead, button_natural_cause_dead, + dropdown_dead, dropdown_level2_dead, openfield_level2_dead, dropdown_extra_level2_dead, \ + physical_boxes_dead, \ + checkbox_beak_dead, text_beak_dead, checkbox_body_dead, text_body_dead, checkbox_feathers_dead, text_feathers_dead, checkbox_head_dead, text_head_dead, checkbox_legs_dead, text_legs_dead, \ + fe_collection_dropdown_dead, fe_recepient_dropdown_dead, fe_radio_dropdown_dead, fe_answer_dropdown_dead, \ + fe_name_recipient_dead, fe_collection_ref_dead \ + ]) + butt_dead.click(partial_hide_section_wounded, + inputs=None, + outputs=[section_wounded, + radio_circumstance_wounded, radio_behavior_wounded, radio_physical_wounded, + button_collision_wounded, button_deliberate_destruction_wounded, button_indirect_destruction_wounded, button_natural_cause_wounded, + dropdown_wounded, dropdown_level2_wounded, openfield_level2_wounded, dropdown_extra_level2_wounded, + behavior_checkbox, behavior_text, + physical_boxes_wounded, \ + checkbox_beak_wounded, text_beak_wounded, checkbox_body_wounded, text_body_wounded, checkbox_feathers_wounded, text_feathers_wounded, checkbox_head_wounded, text_head_wounded, checkbox_legs_wounded, text_legs_wounded, \ + fe_collection_dropdown_wounded, fe_recepient_dropdown_wounded, fe_radio_dropdown_wounded, fe_answer_dropdown_wounded, \ + fe_name_recipient_wounded, fe_collection_ref_wounded \ + ]) + + # --------------------------------------------------------- + # Wounded Button Logic + partial_show_section_wounded = partial(show_section_wounded, True) + partial_hide_section_dead = partial(show_section_dead, False) + + butt_wounded.click(partial_show_section_wounded, + inputs=None, + outputs=[section_wounded, + radio_circumstance_wounded, radio_behavior_wounded, radio_physical_wounded, + button_collision_wounded, button_deliberate_destruction_wounded, button_indirect_destruction_wounded, button_natural_cause_wounded, + dropdown_wounded, dropdown_level2_wounded, openfield_level2_wounded, dropdown_extra_level2_wounded, + behavior_checkbox, behavior_text, + physical_boxes_wounded, \ + checkbox_beak_wounded, text_beak_wounded, checkbox_body_wounded, text_body_wounded, checkbox_feathers_wounded, text_feathers_wounded, checkbox_head_wounded, text_head_wounded, checkbox_legs_wounded, text_legs_wounded, \ + fe_collection_dropdown_wounded, fe_recepient_dropdown_wounded, fe_radio_dropdown_wounded, fe_answer_dropdown_wounded, \ + fe_name_recipient_wounded, fe_collection_ref_wounded \ + ]) + butt_wounded.click(partial_hide_section_dead, inputs=None, outputs=[section_dead, + radio_circumstance_dead, radio_physical_dead, + button_collision_dead, button_deliberate_destruction_dead, button_indirect_destruction_dead, button_natural_cause_dead, + dropdown_dead, dropdown_level2_dead, openfield_level2_dead, dropdown_extra_level2_dead, \ + physical_boxes_dead, \ + checkbox_beak_dead, text_beak_dead, checkbox_body_dead, text_body_dead, checkbox_feathers_dead, text_feathers_dead, checkbox_head_dead, text_head_dead, checkbox_legs_dead, text_legs_dead, \ + fe_collection_dropdown_dead, fe_recepient_dropdown_dead, fe_radio_dropdown_dead, fe_answer_dropdown_dead, \ + fe_name_recipient_dead, fe_collection_ref_dead \ + ]) + # --------------------------------------------------------- + # --------------------------------------------------------- + # --------------------------------------------------------- + # --------------------------------------------------------- + # DEAD + # --------------------------------------------------------- + # Radio Circumstance Dead + radio_circumstance_dead.change(fn=show_circumstances, + inputs=[radio_circumstance_dead], + outputs=[button_collision_dead, button_deliberate_destruction_dead, button_indirect_destruction_dead, button_natural_cause_dead, + dropdown_dead, dropdown_level2_dead, openfield_level2_dead, dropdown_extra_level2_dead] + ) + + # Dropdowns Dead + button_collision_dead.click(dropdown_collision, + outputs=[dropdown_dead, dropdown_level2_dead, openfield_level2_dead, dropdown_extra_level2_dead]) + button_deliberate_destruction_dead.click(dropdown_deliberate_destruction, outputs=[dropdown_dead, dropdown_level2_dead, openfield_level2_dead, dropdown_extra_level2_dead]) + button_indirect_destruction_dead.click(dropdown_indirect_destruction, outputs=[dropdown_dead, dropdown_level2_dead, openfield_level2_dead, dropdown_extra_level2_dead]) + button_natural_cause_dead.click(dropdown_natural_cause, outputs=[dropdown_dead, dropdown_level2_dead, openfield_level2_dead, dropdown_extra_level2_dead]) + + dropdown_dead.select(on_select, None, [dropdown_level2_dead, openfield_level2_dead, dropdown_extra_level2_dead]) + dropdown_level2_dead.select(on_select_dropdown_level2) + openfield_level2_dead.change(on_change_openfield_level2, inputs=[openfield_level2_dead]) + dropdown_extra_level2_dead.select(on_select_dropdown_extra_level2) + # --------------------------------------------------------- + # Radio Physical Dead + radio_physical_dead.change(fn=show_physical, + inputs=[radio_physical_dead, gr.Text("dead", visible=False)], + outputs=[physical_boxes_dead]) + + # Checkbox Physical Dead + physical_boxes_dead.select(find_bounding_box, + inputs=[physical_boxes_dead, gr.Textbox(value="dead", visible=False)], + outputs=[checkbox_beak_dead, text_beak_dead, + checkbox_body_dead, text_body_dead, + checkbox_feathers_dead, text_feathers_dead, + checkbox_head_dead, text_head_dead, + checkbox_legs_dead, text_legs_dead + ]) + checkbox_beak_dead.select(on_select_body_part, inputs=[checkbox_beak_dead, gr.Text("beak", visible=False)]) + checkbox_body_dead.select(on_select_body_part, inputs=[checkbox_body_dead, gr.Text("body", visible=False)]) + checkbox_feathers_dead.select(on_select_body_part, inputs=[checkbox_feathers_dead, gr.Text("feathers", visible=False)]) + checkbox_head_dead.select(on_select_body_part, inputs=[checkbox_head_dead, gr.Text("head", visible=False)]) + checkbox_legs_dead.select(on_select_body_part, inputs=[checkbox_legs_dead, gr.Text("legs", visible=False)]) + # --------------------------------------------------------- + # --------------------------------------------------------- + # --------------------------------------------------------- + # --------------------------------------------------------- + # WOUNDED + # --------------------------------------------------------- + # Radio Circumstance Wounded + radio_circumstance_wounded.change(fn=show_circumstances, + inputs=[radio_circumstance_wounded], + outputs=[button_collision_wounded, button_deliberate_destruction_wounded, button_indirect_destruction_wounded, button_natural_cause_wounded, + dropdown_wounded, dropdown_level2_wounded, openfield_level2_wounded, dropdown_extra_level2_wounded] + ) + + # Dropdowns Circumstance Wounded + button_collision_wounded.click(dropdown_collision, + outputs=[dropdown_wounded, dropdown_level2_wounded, openfield_level2_wounded, dropdown_extra_level2_wounded]) + button_deliberate_destruction_wounded.click(dropdown_deliberate_destruction, outputs=[dropdown_wounded, dropdown_level2_wounded, openfield_level2_wounded, dropdown_extra_level2_wounded]) + button_indirect_destruction_wounded.click(dropdown_indirect_destruction, outputs=[dropdown_wounded, dropdown_level2_wounded, openfield_level2_wounded, dropdown_extra_level2_wounded]) + button_natural_cause_wounded.click(dropdown_natural_cause, outputs=[dropdown_wounded, dropdown_level2_wounded, openfield_level2_wounded, dropdown_extra_level2_wounded]) + + dropdown_wounded.select(on_select, None, [dropdown_level2_wounded, openfield_level2_wounded, dropdown_extra_level2_wounded]) + dropdown_level2_wounded.select(on_select_dropdown_level2) + openfield_level2_wounded.change(on_change_openfield_level2, inputs=[openfield_level2_wounded]) + dropdown_extra_level2_wounded.select(on_select_dropdown_extra_level2) + # --------------------------------------------------------- + # Radio Behavior Wounded + radio_behavior_wounded.change(fn=show_behavior, + inputs=[radio_behavior_wounded, gr.Text("wounded / sick", visible=False)], + outputs=[behavior_checkbox, behavior_text]) + behavior_checkbox.select(on_select_behavior, + inputs=[behavior_checkbox]) + # --------------------------------------------------------- + # Radio Physical Wounded + radio_physical_wounded.change(fn=show_physical, + inputs=[radio_physical_wounded, gr.Text("wounded / sick", visible=False)], + outputs=[physical_boxes_wounded]) + + # Checkbox Physical Wounded + physical_boxes_wounded.select(find_bounding_box, + inputs=[physical_boxes_wounded, gr.Textbox(value="wounded / sick", visible=False)], + outputs=[checkbox_beak_wounded, text_beak_wounded, + checkbox_body_wounded, text_body_wounded, + checkbox_feathers_wounded, text_feathers_wounded, + checkbox_head_wounded, text_head_wounded, + checkbox_legs_wounded, text_legs_wounded + ]) + checkbox_beak_wounded.select(on_select_body_part, inputs=[checkbox_beak_wounded, gr.Text("beak", visible=False)]) + checkbox_body_wounded.select(on_select_body_part, inputs=[checkbox_body_wounded, gr.Text("body", visible=False)]) + checkbox_feathers_wounded.select(on_select_body_part, inputs=[checkbox_feathers_wounded, gr.Text("feathers", visible=False)]) + checkbox_head_wounded.select(on_select_body_part, inputs=[checkbox_head_wounded, gr.Text("head", visible=False)]) + checkbox_legs_wounded.select(on_select_body_part, inputs=[checkbox_legs_wounded, gr.Text("legs", visible=False)]) + + # --------------------------------------------------------- + # Follow Up Events Wounded + fe_collection_dropdown_wounded.select(save_fe, inputs=[fe_collection_dropdown_wounded, gr.Textbox("animal collected", visible=False)]) + fe_recepient_dropdown_wounded.select(save_fe, inputs=[fe_recepient_dropdown_wounded, gr.Textbox("recipient", visible=False)]) + fe_radio_dropdown_wounded.select(save_fe, inputs=[fe_radio_dropdown_wounded, gr.Textbox("radiography", visible=False)]) + fe_answer_dropdown_wounded.select(save_fe, inputs=[fe_answer_dropdown_wounded, gr.Textbox("given answer", visible=False)]) + fe_name_recipient_wounded.input(save_fe, inputs=[fe_name_recipient_wounded, gr.Textbox("recipient name", visible=False)]) + fe_collection_ref_wounded.input(save_fe, inputs=[fe_collection_ref_wounded, gr.Textbox("collection reference", visible=False)]) + + # --------------------------------------------------------- + # Follow Up Events Dead + fe_collection_dropdown_dead.select(save_fe, inputs=[fe_collection_dropdown_dead, gr.Textbox("animal collected", visible=False)]) + fe_recepient_dropdown_dead.select(save_fe, inputs=[fe_recepient_dropdown_dead, gr.Textbox("recipient", visible=False)]) + fe_radio_dropdown_dead.select(save_fe, inputs=[fe_radio_dropdown_dead, gr.Textbox("radiography", visible=False)]) + fe_answer_dropdown_dead.select(save_fe, inputs=[fe_answer_dropdown_dead, gr.Textbox("given answer", visible=False)]) + fe_name_recipient_dead.input(save_fe, inputs=[fe_name_recipient_dead, gr.Textbox("recipient name", visible=False)]) + fe_collection_ref_dead.input(save_fe, inputs=[fe_collection_ref_dead, gr.Textbox("collection reference", visible=False)]) + + # --------------------------------------------------------- + # Error Box + error_box = gr.Text(value=None, visible=False) + + # --------------------------------------------------------- + # Add One Individual's Data to the Dataframe + # And Allow clearing of all previous output + with gr.Row(): + button_df = gr.Button("Submit Animal Report", scale = 3) + button_clear = gr.ClearButton(scale = 1, + components=[ + camera, + location, identified_location, + #dead reset + radio_circumstance_dead, radio_physical_dead, + button_collision_dead, button_deliberate_destruction_dead, button_indirect_destruction_dead, button_natural_cause_dead, + dropdown_dead, dropdown_level2_dead, openfield_level2_dead, dropdown_extra_level2_dead, + physical_boxes_dead, + checkbox_beak_dead, text_beak_dead, checkbox_body_dead, text_body_dead, checkbox_feathers_dead, text_feathers_dead, checkbox_head_dead, text_head_dead, checkbox_legs_dead, text_legs_dead, + fe_collection_dropdown_dead, fe_recepient_dropdown_dead, fe_radio_dropdown_dead, fe_answer_dropdown_dead, + fe_name_recipient_dead, fe_collection_ref_dead, + #wounded reset + radio_circumstance_wounded, radio_behavior_wounded, radio_physical_wounded, + button_collision_wounded, button_deliberate_destruction_wounded, button_indirect_destruction_wounded, button_natural_cause_wounded, + dropdown_wounded, dropdown_level2_wounded, openfield_level2_wounded, dropdown_extra_level2_wounded, + behavior_checkbox, behavior_text, + physical_boxes_wounded, + checkbox_beak_wounded, text_beak_wounded, checkbox_body_wounded, text_body_wounded, checkbox_feathers_wounded, text_feathers_wounded, checkbox_head_wounded, text_head_wounded, checkbox_legs_wounded, text_legs_wounded, + fe_collection_dropdown_wounded, fe_recepient_dropdown_wounded, fe_radio_dropdown_wounded, fe_answer_dropdown_wounded, + fe_name_recipient_wounded, fe_collection_ref_wounded, + error_box + ]) + button_close = gr.Button("Back to Display", scale = 1) + + + # --------------------------------------------------------- + # Button Click Logic + button_clear.click() + button_clear.click(hide_physical, + outputs=[checkbox_beak_wounded, text_beak_wounded, checkbox_body_wounded, text_body_wounded, checkbox_feathers_wounded, text_feathers_wounded, checkbox_head_wounded, text_head_wounded, checkbox_legs_wounded, text_legs_wounded]) + button_clear.click(hide_physical, + outputs=[checkbox_beak_dead, text_beak_dead, checkbox_body_dead, text_body_dead, checkbox_feathers_dead, text_feathers_dead, checkbox_head_dead, text_head_dead, checkbox_legs_dead, text_legs_dead]) + + button_clear.click(reset_error_box, inputs=[error_box], outputs=[error_box]) + button_clear.click(reset_json) + + button_df.click(save_display_individual, + inputs=[gallery, df, error_box], + outputs=[gallery, df, error_box] + ) + button_close.click(lambda: Modal(visible=False), None, modal) + + # --------------------------------------------------------- + # Event Functions of the landing page buttons + show_modal.click(lambda: Modal(visible=True), None, modal) + show_modal.click(create_json_one_individual) + show_modal.click(create_tmp) + #submit_button.click(save_and_rest_df, inputs=[df], outputs=[df]) + + +if __name__ == "__main__": + demo.launch(server_name="0.0.0.0", server_port=7860) \ No newline at 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0000000000000000000000000000000000000000..e8e5b45eae97b9d3d93a8563e7e8a8da6b401aa3 --- /dev/null +++ b/app/physical/class_physical.py @@ -0,0 +1,79 @@ +from pydantic import BaseModel, Field +from typing import Literal, List, Union, Optional + +# Define common anomalies as a Literal type +CommonAnomalies = Literal[ + 'blackened/burnt skin', + 'blood', + 'foreign body', + 'fracture', + 'injury', + 'parasite', + 'swelling', + 'warty or tumor-like growth, crusts' +] + +# --- Beak-related Anomalies --- +class BeakAnomaly(BaseModel): + type: Literal['beak'] + anomaly_type: List[Literal[ + 'adhesion', + 'deformation', + CommonAnomalies + ]] + +# --- Body-related Anomalies --- +class BodyAnomaly(BaseModel): + type: Literal['body'] + anomaly_type: List[Literal[ + 'emaciation', + 'fluffed up', + 'stained feathers', + CommonAnomalies + ]] + +# --- Legs-related Anomalies --- +class LegAnomaly(BaseModel): + type: Literal['legs'] + anomaly_type: List[Literal[ + 'missing limb', + 'deformation', + CommonAnomalies + ]] + +# --- Feathers/Wings/Tail-related Anomalies --- +class FeathersWingsTailAnomaly(BaseModel): + type: Literal['feathers/wings/tail'] + anomaly_type: List[Literal[ + 'fluffed up', + 'feather abnormalities', + 'stained feathers', + 'abnormal wing posture', + 'missing limb', + CommonAnomalies + ]] + +# --- Head-related Anomalies (including eyes) --- +class HeadAnomaly(BaseModel): + type: Literal['head incl. eyes'] + anomaly_type: List[Literal[ + 'ear changes', + 'eye changes', + 'tilted head', + CommonAnomalies + ]] + + +# Union of all possible anomaly types for specific body parts +AnomalyType = Union[ + BeakAnomaly, + BodyAnomaly, + LegAnomaly, + FeathersWingsTailAnomaly, + HeadAnomaly +] + +# Main PhysicalAnomaly class that logs anomalies across different body parts +class PhysicalAnomalies(BaseModel): + physical_radio: str + physical_anomalies_type: Optional[List[AnomalyType]] = None diff --git a/app/physical/physical_boxes_define.py b/app/physical/physical_boxes_define.py new file mode 100644 index 0000000000000000000000000000000000000000..5c3bedc6069a744366f6700a4dd5359bf7a7ab93 --- /dev/null +++ b/app/physical/physical_boxes_define.py @@ -0,0 +1,23 @@ +import geopandas as gpd +from shapely.geometry import box + +bounding_boxes = [ + # 'Head incl. eyes', + box(250, 375, 350, 485), + # 'Beak and mouth region', + box(200, 450, 250, 485), + # 'Feathers/Wings/Tail', + box(50, 100, 725, 355), + # 'Legs', + box(325, 585, 450, 675), + # 'Body' + box(275, 510, 500, 565) +] + +# Create a GeoDataFrame from these boxes +gdf = gpd.GeoDataFrame({'geometry': bounding_boxes, + 'name': ['Head incl. eyes', + 'Beak', + 'Feathers/Wings/Tail', + 'Legs', + 'Body']}) diff --git a/app/physical/physical_boxes_map.py b/app/physical/physical_boxes_map.py new file mode 100644 index 0000000000000000000000000000000000000000..cf6f62849fc785c05a803c5eada0063bd5804483 --- /dev/null +++ b/app/physical/physical_boxes_map.py @@ -0,0 +1,33 @@ +from PIL import Image, ImageDraw, ImageFont + +from physical_boxes_define import gdf + +from dotenv import load_dotenv +import os +load_dotenv() +PATH_ASSETS = os.getenv('PATH_ASSETS') + +# Function to draw the bounding boxes on the image +def draw_bounding_boxes(image_path, gdf): + image = Image.open(image_path+'bird.png').convert("RGB") + # Convert the image to an editable format + draw = ImageDraw.Draw(image) + + # Optional: Load a font (requires a TTF file) + # try: + font = ImageFont.truetype(PATH_ASSETS + "fonts/LiberationSans-Regular.ttf", + 20) + # except IOError: + # print("default") + # font = ImageFont.load_default() + + # Draw each bounding box on the image + for _, row in gdf.iterrows(): + xmin, ymin, xmax, ymax = row['geometry'].bounds + draw.rectangle([xmin, ymin, xmax, ymax], outline="purple", width=2) + draw.text((xmin, ymin-22), row['name'], fill="black", font=font) + + image.save(image_path+'bird_boxed.png', "PNG") + +if __name__ == "__main__": + draw_bounding_boxes(PATH_ASSETS + 'images/', gdf) \ No newline at end of file diff --git a/app/physical/physical_checkbox.py b/app/physical/physical_checkbox.py new file mode 100644 index 0000000000000000000000000000000000000000..b0a505350d0a7a28995050c6ee364f0b7fea89f0 --- /dev/null +++ b/app/physical/physical_checkbox.py @@ -0,0 +1,84 @@ +import gradio as gr +from utils.utils_config import get_custom_config_dropdowns +from utils.utils_checkbox import create_checkbox +from validation_submission.add_json import add_data_tmp +#--------------------------------------------------------- +def get_body_parts(): + dropdown_config = get_custom_config_dropdowns("config_checkbox_physical.json") + return list(dropdown_config.keys()) + +def retrieve_config_options(label, dropdown_config): + options = list(dropdown_config[label].keys()) + options = [option.title() for option in options] + return options + +def get_options_description(value): + dropdown_config = get_custom_config_dropdowns("config_checkbox_physical.json") + # get options + options_common = retrieve_config_options("Common", dropdown_config) + options_for_value = retrieve_config_options(value, dropdown_config) + options_common.extend(options_for_value) + options = options_common + # get descriptions + descriptions = [] + for key, sub_dict in dropdown_config.items(): + if key==value or key=="Common": + for _, option_dict in sub_dict.items(): + for description_tag, description in option_dict.items(): + if "Description"==description_tag: + descriptions.append(description) + return options, descriptions + +#--------------------------------------------------------- +def create_checkbox_beak(section, label_checkbox, visible): + body_part="Beak" + options, descriptions = get_options_description(body_part) + return create_checkbox(body_part, section, label_checkbox, visible, options, descriptions) + +def create_checkbox_body(section, label_checkbox, visible): + body_part="Body" + options, descriptions = get_options_description(body_part) + return create_checkbox(body_part, section, label_checkbox, visible, options, descriptions) + +def create_checkbox_feathers(section, label_checkbox, visible): + body_part="Feathers/Wings/Tail" + options, descriptions = get_options_description(body_part) + return create_checkbox(body_part, section, label_checkbox, visible, options, descriptions) + +def create_checkbox_head(section, label_checkbox, visible): + body_part="Head incl. eyes" + options, descriptions = get_options_description(body_part) + return create_checkbox(body_part, section, label_checkbox, visible, options, descriptions) + +def create_checkbox_legs(section, label_checkbox, visible): + body_part="Legs" + options, descriptions = get_options_description(body_part) + return create_checkbox(body_part, section, label_checkbox, visible, options, descriptions) + +#--------------------------------------------------------- +def process_body_parts(section, matched_box): + #take all except "Common" + body_parts = get_body_parts() + body_parts = body_parts[1:] + label_checkbox = "Physical changes to " + visibles = [True if matched_box==body_part else False for body_part in body_parts ] + checkbox_beak, text_beak = create_checkbox_beak(section, label_checkbox, visibles[0]) + checkbox_body, text_body = create_checkbox_body(section, label_checkbox, visibles[1]) + checkbox_feathers, text_feathers = create_checkbox_feathers(section, label_checkbox, visibles[2]) + checkbox_head, text_head = create_checkbox_head(section, label_checkbox, visibles[3]) + checkbox_legs, text_legs = create_checkbox_legs(section, label_checkbox, visibles[4]) + return checkbox_beak, text_beak, checkbox_body, text_body, checkbox_feathers, text_feathers, checkbox_head, text_head, checkbox_legs, text_legs + +#--------------------------------------------------------- + +def on_select_body_part(body_part_checkbox, body_part): + add_data_tmp("wounded_dead", "physical_type_"+body_part.lower(), body_part.lower()) + body_part_checkbox = [body_part_check.lower() for body_part_check in body_part_checkbox] + add_data_tmp("wounded_dead", "physical_anomaly_"+body_part.lower(), body_part_checkbox) + +#--------------------------------------------------------- + +def hide_physical(): + checkbox_beak, text_beak, checkbox_body, text_body, checkbox_feathers, text_feathers, checkbox_head, text_head, checkbox_legs, text_legs = process_body_parts("wounded", "None") + return checkbox_beak, text_beak, checkbox_body, text_body, checkbox_feathers, text_feathers, checkbox_head, text_head, checkbox_legs, text_legs + \ No newline at end of file diff --git a/app/physical/physical_select_animal.py b/app/physical/physical_select_animal.py new file mode 100644 index 0000000000000000000000000000000000000000..f78ccd7be3060beac58e91e29b3abeb391c42505 --- /dev/null +++ b/app/physical/physical_select_animal.py @@ -0,0 +1,50 @@ +import gradio as gr +from dotenv import load_dotenv +import os +from typing import List +from shapely.geometry import Point + +from physical.physical_checkbox import * +from physical.physical_boxes_define import gdf +from utils.utils_visible import set_visible + +load_dotenv() +PATH_ASSETS = os.getenv('PATH_ASSETS') + +# Function to find the matching bounding box for a given point and return the image with boxes +def find_bounding_box(evt: gr.SelectData, img, section: str): + x, y = evt.index[0], evt.index[1] + point = Point(x, y) + match = gdf[gdf.contains(point)] + if not match.empty: + matched_box = match.iloc[0]['name'] + checkbox_beak, text_beak, checkbox_body, text_body, checkbox_feathers, text_feathers, checkbox_head, text_head, checkbox_legs, text_legs = process_body_parts(section, matched_box) + else: + matched_box = None + checkbox_beak, text_beak, checkbox_body, text_body, checkbox_feathers, text_feathers, checkbox_head, text_head, checkbox_legs, text_legs = process_body_parts(section, matched_box) + return checkbox_beak, text_beak, checkbox_body, text_body, checkbox_feathers, text_feathers, checkbox_head, text_head, checkbox_legs, text_legs + + + +# Gradio app +def create_bird_anatomy(visible, section: str): + # Draw bounding boxes on the image + print + img_with_boxes = gr.Image(value=PATH_ASSETS+'images/bird_boxed.png', + show_label=False, + height="600px", + elem_id=section, + visible=visible) + return img_with_boxes + +def show_physical(choice, section: str): + visible = set_visible(choice) + physical_boxes = create_bird_anatomy(visible, section) + add_data_tmp("wounded_dead", "physical_radio", choice) + return physical_boxes + + + + + + diff --git a/app/styling/__init__.py b/app/styling/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/app/styling/__pycache__/__init__.cpython-312.pyc b/app/styling/__pycache__/__init__.cpython-312.pyc new file mode 100644 index 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gradio as gr + +gr.HTML(''' + + ''') + +# gr.HTML(''' +# +# ''') \ No newline at end of file diff --git a/app/styling/theme.py b/app/styling/theme.py new file mode 100644 index 0000000000000000000000000000000000000000..553e77112fd3c43e10877d69f87e8eafa194e008 --- /dev/null +++ b/app/styling/theme.py @@ -0,0 +1,105 @@ +import gradio as gr + +css= "" +css_old = """ +.gradio-container {background: url(https://openclipart.org/image/2000px/279687)} + +/* Main background */ +body { + background-color: #3B4C54; + color: #ffffff; /* Set default text color for contrast */ +} + +/* Secondary color for headers and panels */ +.gradio-container .card, +.gradio-container h1, +.gradio-container h2, +.gradio-container h3, +.gradio-container h4 { + background-color: #3F543B; + color: #ffffff; /* Ensuring text is readable */ +} + + + + +/* Background color for the wounded section */ +#wounded { + background-color: #503B54; + color: #ffffff; /* Ensures text is readable */ +} + +/* Olive green color for headers within the wounded section */ +#wounded h1, +#wounded h2, +#wounded h3, +#wounded h4, +#wounded h5, +#wounded h6 { + color: #ffffff; /* Olive green color for header text */ + background-color: #503B54; /* No background color for headers */ +} + +/* Styling dropdowns within the wounded section */ +#wounded select { + background-color: #3F543B; /* Olive green background */ + color: #ffffff; /* Ensures text is readable */ + border: 1px solid #3B4C54; /* Optional border for consistency */ +} + +/* Styling checkboxes within the wounded section */ +#wounded input[type="checkbox"] { + accent-color: #3F543B; /* Olive green color for the checkbox */ +} + +/* Additional checkbox label styling if needed */ +#wounded label { + color: #ffffff; /* Ensures labels are readable */ +} + + + + + +/* Background color for the dead section */ +#dead { + background-color: #54433B; + color: #ffffff; /* Ensures text is readable */ +} + +/* Brown color for headers within the dead section */ +#dead h1, +#dead h2, +#dead h3, +#dead h4, +#dead h5, +#dead h6 { + color: #ffffff; /* Olive green color for header text */ + background-color: #54433B; /* No background color for headers */ +} + + +#bird-boxes {background-color: #3B4C54} +#submit {background-color: #abb2bf} +#error {background-color: #e82323} +#valid {background-color: #07e63f} +""" + +# OLD THEME: + +# css = """ +# .gradio-container {background: url(https://openclipart.org/image/2000px/279687)} +# #image {background-color: #73b9ae} +# #dead {background-color: #333333} +# #wounded {background-color: #5e0724} +# #bird-boxes {background-color: #f2f3f3} +# #buttons-conditions {background-color: #b3b3b3} +# #dropdown-conditions {background-color: #b3b3b3} +# #followup {background-color: #38241c} +# #submit {background-color: #abb2bf} +# #error {background-color: #e82323} +# #valid {background-color: #07e63f} +# """ + +# theme = gr.themes.Soft(primary_hue="teal", secondary_hue="teal", neutral_hue="emerald", +# font=[gr.themes.GoogleFont("Inconsolata"), "Arial", "sans-serif"]) diff --git a/app/utils/__init__.py b/app/utils/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/app/utils/__pycache__/__init__.cpython-312.pyc b/app/utils/__pycache__/__init__.cpython-312.pyc new file mode 100644 index 0000000000000000000000000000000000000000..34ef111412a418a0a92b0de4f65dcc2b950580df Binary files /dev/null and b/app/utils/__pycache__/__init__.cpython-312.pyc differ diff --git a/app/utils/__pycache__/utils_checkbox.cpython-312.pyc b/app/utils/__pycache__/utils_checkbox.cpython-312.pyc new file mode 100644 index 0000000000000000000000000000000000000000..5f9a41540caf06e785248f6ee945b38b0b40bf6c Binary files /dev/null and b/app/utils/__pycache__/utils_checkbox.cpython-312.pyc differ diff --git a/app/utils/__pycache__/utils_config.cpython-312.pyc b/app/utils/__pycache__/utils_config.cpython-312.pyc new file mode 100644 index 0000000000000000000000000000000000000000..42432cb3f56d9cfd841db84588adbca91a05cec3 Binary files /dev/null and b/app/utils/__pycache__/utils_config.cpython-312.pyc differ diff --git a/app/utils/__pycache__/utils_visible.cpython-312.pyc b/app/utils/__pycache__/utils_visible.cpython-312.pyc new file mode 100644 index 0000000000000000000000000000000000000000..ed2009f9e1e0d50b09f84284b709b9c55196e681 Binary files /dev/null and b/app/utils/__pycache__/utils_visible.cpython-312.pyc differ diff --git a/app/utils/utils_checkbox.py b/app/utils/utils_checkbox.py new file mode 100644 index 0000000000000000000000000000000000000000..155cd6c79b9c948f524f517783b8155b6bcc7c8d --- /dev/null +++ b/app/utils/utils_checkbox.py @@ -0,0 +1,18 @@ +import gradio as gr + +#--------------------------------------------------------- +def create_checkbox(value, section, label_checkbox, visible, options, descriptions): + descriptions_info = "

".join([f"* **{option}**: {description}" for option, description in zip(options, descriptions)]) + checkbox = gr.CheckboxGroup(options, + label=label_checkbox + f" {value}:", + visible=visible, + interactive=True, + elem_id=section) + text = gr.Markdown(descriptions_info, + label = "Info", + visible=visible, + #interactive=False, + #lines=13, + #max_lines=15, + elem_id=section) + return checkbox, text \ No newline at end of file diff --git a/app/utils/utils_config.py b/app/utils/utils_config.py new file mode 100644 index 0000000000000000000000000000000000000000..c9231df8f6635a21d690dfe4bafb81a14dc6e04b --- /dev/null +++ b/app/utils/utils_config.py @@ -0,0 +1,20 @@ +import json +import os +from dotenv import load_dotenv +import os +load_dotenv() +PATH = os.getcwd() + "/" +PATH_ASSETS = os.getenv('PATH_ASSETS') +PATH_CONFIG = PATH + PATH_ASSETS + "config/" + +def load_config(file_path): + with open(file_path) as f: + config = json.load(f) + return config + +def get_custom_config_dropdowns(config_path): + dropdown_config_path = PATH_CONFIG + config_path + dropdown_config = load_config(dropdown_config_path) + return dropdown_config + + diff --git a/app/utils/utils_visible.py b/app/utils/utils_visible.py new file mode 100644 index 0000000000000000000000000000000000000000..7651bdea0c85315e2a45c4d154dcb9acd5611b97 --- /dev/null +++ b/app/utils/utils_visible.py @@ -0,0 +1,6 @@ +def set_visible(choice): + if choice=="Yes": + visible = True + else: + visible=False + return visible \ No newline at end of file diff --git a/app/validation_submission/__init__.py b/app/validation_submission/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/app/validation_submission/__pycache__/__init__.cpython-312.pyc b/app/validation_submission/__pycache__/__init__.cpython-312.pyc new file mode 100644 index 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a/app/validation_submission/__pycache__/submission.cpython-312.pyc b/app/validation_submission/__pycache__/submission.cpython-312.pyc new file mode 100644 index 0000000000000000000000000000000000000000..6260c629ab8eb1085841c4888bfcd16a3e763c3e Binary files /dev/null and b/app/validation_submission/__pycache__/submission.cpython-312.pyc differ diff --git a/app/validation_submission/__pycache__/validation.cpython-312.pyc b/app/validation_submission/__pycache__/validation.cpython-312.pyc new file mode 100644 index 0000000000000000000000000000000000000000..a32274cf97c6dd158654e2ed6a6ae26d5c6dd6c1 Binary files /dev/null and b/app/validation_submission/__pycache__/validation.cpython-312.pyc differ diff --git a/app/validation_submission/add_json.py b/app/validation_submission/add_json.py new file mode 100644 index 0000000000000000000000000000000000000000..c95f4172b7ebccff9b1a6b8c33e41ca7b462f2ba --- /dev/null +++ b/app/validation_submission/add_json.py @@ -0,0 +1,15 @@ +from validation_submission.create_json import create_json_one_individual, create_tmp +import json + +def add_data_to_individual(key, value): + with open("data/one_individual.json", 'r') as openfile: + one_individual = json.load(openfile) + one_individual[key] = value + create_json_one_individual(one_individual) + +def add_data_tmp(tmp_name, key, value): + with open(f"app/assets/tmp_json/tmp_{tmp_name}.json", 'r') as openfile: + tmp = json.load(openfile) + tmp[key] = value + create_tmp(tmp_name, tmp) + \ No newline at end of file diff --git a/app/validation_submission/create_json.py b/app/validation_submission/create_json.py new file mode 100644 index 0000000000000000000000000000000000000000..a538d6e7dba604f3d1cb7672f0a19629e74e1761 --- /dev/null +++ b/app/validation_submission/create_json.py @@ -0,0 +1,20 @@ +import json + +def create_json_one_individual(one_individual={}): + one_individual = json.dumps(one_individual) + with open("data/one_individual.json", "w") as outfile: + outfile.write(one_individual) + +def create_json_all_individuals(all_individuals={}): + all_individuals = json.dumps(all_individuals) + with open("data/all_individuals.json", "w") as outfile: + outfile.write(all_individuals) + +def create_tmp(tmp_name="wounded_dead", tmp={}): + tmp = json.dumps(tmp) + with open(f"app/assets/tmp_json/tmp_{tmp_name}.json", "w") as outfile: + outfile.write(tmp) + +def reset_json(): + create_json_one_individual() + create_tmp() \ No newline at end of file diff --git a/app/validation_submission/get_json.py b/app/validation_submission/get_json.py new file mode 100644 index 0000000000000000000000000000000000000000..03d77d8d4e8b69eaabdb3e21fafc4fb22a3d458e --- /dev/null +++ b/app/validation_submission/get_json.py @@ -0,0 +1,16 @@ +import json + +def get_json_one_individual(): + with open("data/one_individual.json", 'r') as openfile: + one_individual = json.load(openfile) + return one_individual + +def get_json_all_individuals(): + with open("data/all_individuals.json", "r") as openfile: + all_individuals = json.load(openfile) + return all_individuals + +def get_json_tmp(tmp_name): + with open(f"app/assets/tmp_json/tmp_{tmp_name}.json", "r") as openfile: + tmp_json = json.load(openfile) + return tmp_json \ No newline at end of file diff --git a/app/validation_submission/processing.py b/app/validation_submission/processing.py new file mode 100644 index 0000000000000000000000000000000000000000..a47051bbc6c84a3dafb6031d53553e530d121cf2 --- /dev/null +++ b/app/validation_submission/processing.py @@ -0,0 +1,55 @@ +#### PROCESS FUNCTIONS + +def process_circumstance(data): + fields_to_check = ["option_dropdown", "open_field", "extra"] + if data["circumstance_radio"] == "Yes": + for field in fields_to_check: + if data["circumstance_type"][field+"_label"] == "NA": + data["circumstance_type"].pop(field+"_label") + else : + val = data[f"circumstance_{field}"] + key = data["circumstance_type"][field+"_label"] + data["circumstance_type"][key] = val + data["circumstance_type"].pop(field+"_label") + return data + +def process_behaviors(data): + behaviors =[] + if data["behaviors_radio"] == "Yes": + for type in data["behaviors_type"]: + new_behavior = {} + new_behavior["type"] = type + behaviors.append(new_behavior) + data["behaviors_type"] = behaviors + return data + +def process_physical(data): + body_parts= ["beak", "body", "legs", "feathers/wings/tail", "head incl. eyes"] + anomalies=[] + reformatted = {} + reformatted["physical_radio"] = data["physical_radio"] + if data["physical_radio"] == "Yes": + for body_part in body_parts: + anomaly = {} + for key, val in data.items(): + if "type_"+ body_part in key: + anomaly["type"] = body_part + elif "anomaly_"+ body_part in key: + anomaly["anomaly_type"] = val + if anomaly: + anomalies.append(anomaly) + reformatted["physical_anomalies_type"] = anomalies + return reformatted + +def process_followup(data): + followup_events = [] + for key, val in data.items(): + followup_event={} + type = key.split("followup")[-1] + option = type.split(" ")[-1] + followup_event["type"] = type.strip() + followup_event[option.strip()] = val + followup_events.append(followup_event) + reformatted ={} + reformatted["follow_up_events"] = followup_events + return reformatted \ No newline at end of file diff --git a/app/validation_submission/submission.py b/app/validation_submission/submission.py new file mode 100644 index 0000000000000000000000000000000000000000..313df1e18d0b3bd261f187a6e922f1a333715d9e --- /dev/null +++ b/app/validation_submission/submission.py @@ -0,0 +1,17 @@ +import json +from validation_submission.get_json import get_json_all_individuals +from validation_submission.validation import validate_individual + +def validate_save_individual(error_box): + individual, error_box = validate_individual(error_box) + if individual: + save_to_all_individuals(individual.model_dump()) + return individual, error_box + +def save_to_all_individuals(one_individual): + all_individuals = get_json_all_individuals() + all_individuals[str(len(all_individuals))] = one_individual + all_individuals_for_json = json.dumps(all_individuals) + with open("data/all_individuals.json", "w") as outfile: + outfile.write(all_individuals_for_json) + return all_individuals \ No newline at end of file diff --git a/app/validation_submission/validation.py b/app/validation_submission/validation.py new file mode 100644 index 0000000000000000000000000000000000000000..9e170eabf09df25794f3b0965a62da3855457e6a --- /dev/null +++ b/app/validation_submission/validation.py @@ -0,0 +1,173 @@ +import uuid +from pydantic import ValidationError +import gradio as gr + +from validation_submission.get_json import get_json_tmp, get_json_one_individual +from circumstances.class_circumstance import Circumstances +from behavior.class_behavior import Behaviors +from physical.class_physical import PhysicalAnomalies +from follow_up.class_follow_up import FollowUpEvents +from classes import Report, Wounded, Dead, ImageBase64 +from validation_submission.processing import process_circumstance, process_behaviors, process_physical, process_followup + +def get_fields(data_dict, keyword): + extract = {} + for key, val in data_dict.items(): + if keyword in key: + extract[key] = val + return extract + +def validate_individual(error_box): + error_box = reset_error_box(error_box) + data = get_json_one_individual() + data["identifier"] = str(uuid.uuid4()) + if "image" in data.keys(): + img = ImageBase64.to_base64(data["image"]) + else: + img = None + if "geolocalisation" in data.keys(): + geolocalisation = data["geolocalisation"] + else: + geolocalisation = None + + error_behavior = None + error_circumstance = None + error_followup = None + error_physical = None + error_individual = None + if "wounded_state" not in data or "dead_state" not in data: + data["wounded_state"] = "No" + data["dead_state"] = "No" + if (data["wounded_state"] == "Yes") or (data["dead_state"] == "Yes"): + data_wounded_dead = get_json_tmp("wounded_dead") + circumstance, error_circumstance = validate_circumstance(data_wounded_dead) + physical, error_physical = validate_physical(data_wounded_dead) + followup, error_followup = validate_follow_up(data_wounded_dead) + + if data["wounded_state"]=="Yes": + print(physical) + behavior, error_behavior = validate_behavior(data_wounded_dead) + try : + individual = Report(identifier = data["identifier"], + image = img, + geolocalisation = geolocalisation, + wounded_state = data["wounded_state"], + wounded = Wounded(circumstances = circumstance, + behaviors = behavior, + physical_anomalies = physical, + follow_up_events = followup), + dead_state = data["dead_state"]) + except ValidationError as e: + print(e) + error_individual = e + + elif data["dead_state"]=="Yes": + try: + individual = Report(identifier = data["identifier"], + image = img, + geolocalisation = geolocalisation, + wounded_state = data["wounded_state"], + dead_state = data["dead_state"], + dead = Dead(circumstances = circumstance, + physical_anomalies = physical, + follow_up_events = followup) + ) + except ValidationError as e: + print(e) + error_individual = e + else: + try: + individual = Report(identifier = data["identifier"], + image = img, + geolocalisation = geolocalisation, + wounded_state = data["wounded_state"], + dead_state = data["dead_state"]) + except ValidationError as e: + print(e) + error_individual = e + if error_behavior or error_circumstance or error_followup or error_physical or error_individual: + error_box = show_error(error_box, error_behavior, error_circumstance, error_followup, error_physical, error_individual) + individual = None + else: + error_box= gr.Text(label="ALL VALID.", value="Record Registered. You can return to the Display.", visible=True, elem_id="valid") + return individual, error_box + +def show_error(error_box, error_behavior, error_circumstance, error_followup, error_physical, error_individual): + error_text = "" + if error_circumstance: + error_text += f"Error in circumstance: {error_circumstance}\n" + if error_behavior: + error_text += f"Error in behavior: {error_behavior}\n" + if error_physical: + error_text += f"Error in physical: {error_physical}\n" + if error_followup: + error_text += f"Error in follow-up: {error_followup}\n" + if error_individual: + error_text += f"Error in individual: {error_individual}\n" + error_text += "PLEASE CORRECT THESE ERRORS BEFORE SUBMITTING." + error_box= gr.Text(label="ERROR DETECTED !", value=error_text, visible=True, elem_id="error") + return error_box + +def reset_error_box(error_box): + error_box = gr.Text(value=None, visible=False) + return error_box + +#### VALIDATION FUNCTIONS +def validate_circumstance(data): + circumstance_raw = get_fields(data, "circumstance") + circumstance_formatted = process_circumstance(circumstance_raw) + try: + Circumstances.model_validate(circumstance_formatted) + circumstances = Circumstances(**circumstance_formatted) + error = None + except ValidationError as e: + error = e + print(e) + circumstances = None + return circumstances, error + + +def validate_behavior(data): + behaviors_raw = get_fields(data, "behaviors") + behaviors_formatted = process_behaviors(behaviors_raw) + try: + Behaviors.model_validate(behaviors_formatted) + behavior = Behaviors(**behaviors_formatted) + error = None + except ValidationError as e: + print(e) + print("Validation failed for the behaviors.") + behavior = None + error = e + return behavior, error + + +def validate_physical(data): + physical_raw = get_fields(data, "physical") + physical_formatted = process_physical(physical_raw) + try: + PhysicalAnomalies.model_validate(physical_formatted) + physical = PhysicalAnomalies(**physical_formatted) + error = None + except ValidationError as e: + print(e) + print("Validation failed for the physical anomalies.") + physical = None + error = e + return physical, error + +def validate_follow_up(data): + followup_raw = get_fields(data, "followup") + followup_formatted = process_followup(followup_raw) + try: + FollowUpEvents.model_validate(followup_formatted) + followup = FollowUpEvents(**followup_formatted) + error = None + except ValidationError as e: + print(e) + print("Validation failed for the follow-up events.") + followup = None + return followup, error + + + diff --git a/app/wounded.py b/app/wounded.py new file mode 100644 index 0000000000000000000000000000000000000000..30340ca8601363e12bcfe52c4125fcfabeb2a441 --- /dev/null +++ b/app/wounded.py @@ -0,0 +1,49 @@ +import gradio as gr +from circumstances.circumstances import create_circumstances +from physical.physical_select_animal import create_bird_anatomy +from physical.physical_checkbox import process_body_parts +from behavior.behavior_checkbox import create_behavior_checkbox +from follow_up.followup_events import create_followup_dropdowns, create_followup_open +from validation_submission.add_json import add_data_to_individual + +def show_section_wounded(visible): + if visible==True: + add_data_to_individual("wounded_state", "Yes") + add_data_to_individual("dead_state", "No") + + with gr.Column(visible=visible, elem_id="wounded") as wounded_section: + gr.Markdown("# Wounded / Sick Animal") + + gr.Markdown("## Do you know what conditions caused this?", label="description") + radio_cause = gr.Radio(["Yes", "No"], value=None, show_label=False, interactive=True) + button_collision, button_deliberate_destruction, button_indirect_destruction, button_natural_cause, dropdown, dropdown_level2, openfield_level2, dropdown_extra_level2 = create_circumstances(visible=False) + + gr.Markdown("## Is the bird displaying behavioural changes?" , label="description") + radio_behaviour = gr.Radio(["Yes", "No"], value=None, show_label=False, interactive=True) + with gr.Row(): + behavior_checkbox, behavior_text = create_behavior_checkbox("wounded", False) + + gr.Markdown("## Are there physical changes on the bird?" , label="description") + radio_physical = gr.Radio(["Yes", "No"], value=None, show_label=False, interactive=True) + with gr.Row(): + physical_boxes = create_bird_anatomy(False, "wounded") + with gr.Column(): + checkbox_beak, text_beak, checkbox_body, text_body, checkbox_feathers, text_feathers, checkbox_head, text_head, checkbox_legs, text_legs = process_body_parts("wounded", "None") + + + gr.Markdown("## Follow-Up Events", label="Title") + gr.Markdown("Please tell us what you did with the animal.", label="description") + with gr.Row(): + fe_collection_dropdown, fe_recepient_dropdown, fe_radio_dropdown, fe_answer_dropdown = create_followup_dropdowns(visible, "wounded") + with gr.Row(): + fe_name_recipient, fe_collection_ref = create_followup_open(visible, "wounded") + + + # Change variables and names + return wounded_section, radio_cause, radio_behaviour, radio_physical, \ + button_collision, button_deliberate_destruction, button_indirect_destruction, button_natural_cause, \ + dropdown, dropdown_level2, openfield_level2, dropdown_extra_level2, \ + behavior_checkbox, behavior_text, \ + physical_boxes, \ + checkbox_beak, text_beak, checkbox_body, text_body, checkbox_feathers, text_feathers, checkbox_head, text_head, checkbox_legs, text_legs, \ + fe_collection_dropdown, fe_recepient_dropdown, fe_radio_dropdown, fe_answer_dropdown, fe_name_recipient, fe_collection_ref diff --git a/data/.gitkeep b/data/.gitkeep new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/data/all_individuals.json b/data/all_individuals.json new file mode 100644 index 0000000000000000000000000000000000000000..9e26dfeeb6e641a33dae4961196235bdb965b21b --- /dev/null +++ b/data/all_individuals.json @@ -0,0 +1 @@ +{} \ No newline at end of file diff --git a/data/one_individual.json b/data/one_individual.json new file mode 100644 index 0000000000000000000000000000000000000000..9e26dfeeb6e641a33dae4961196235bdb965b21b --- /dev/null +++ b/data/one_individual.json @@ -0,0 +1 @@ +{} \ No newline at end of file diff --git a/requirements.txt b/requirements.txt new file mode 100644 index 0000000000000000000000000000000000000000..65e2914555f44c0328949b4b2bf626f23833737c --- /dev/null +++ b/requirements.txt @@ -0,0 +1,6 @@ +gradio +gradio_modal +geopy +geopandas +pillow +python-dotenv \ No newline at end of file diff --git a/test.py b/test.py new file mode 100644 index 0000000000000000000000000000000000000000..17728a5c334fc0d45d90b4d2683d3a915a14ad1d --- /dev/null +++ b/test.py @@ -0,0 +1,10 @@ +# app.py +import gradio as gr + +def greet(name): + return f"Hello, {name}!" + +demo = gr.Interface(fn=greet, inputs="text", outputs="text") + +if __name__ == "__main__": + demo.launch() \ No newline at end of file