Aerial Intelligence for Responders

This repository provides information to build geo-spatial datasets and train models to automatically map regions of interest. The goal of this project is to assist automated mapping efforts for use in providing humanitarian relief after natural disasters, for example.

So far, our project has a structured pipeline to extract satellite imagery using IBM's PAIRS API, and labelled bounding boxes using overpy; an OpenStreetMap Python API. We then provide pipelines to fruther transform the raw data into specific formats required by a couple of object detection and semantic segmentation deep learning models. After passing the data through these trasnforms, we provide scripts to train and evaluate the model performance on the extracted datasets. Currently, training must be done on personal resources. (In the coming weeks, we will provide checkpoint files for pre-trained models that have worked well on our data.)

The overall strcuture of the project can be divided into the following components:

A pipleine to extract raw labelled data.
A pipeline to transform the raw data into specific formats required by the following single-stage models:
- YOLO (deprecated)
- PIXOR (bounding box detection)
- RefineNet (semantic segmentation)
Scripts to train and evaluate each of the abovementioned models.

Dependencies and Setup

Install IBM Pairs Geoscope by following these instructions. Complete all optional steps. Used for retrieving satellite imagery.
Create IBM PAIRS account at https://ibmpairs.mybluemix.net
git clone https://github.com/Dieblitzen/AIR-Project.git
Once in the repository's directory, run conda env create -f environment.yml
Create AIR-Project/ibmpairspass.txt and add pairs.res.ibm.com:<email@email.com>:<password> to file

DataPipeline

The file DataPipeline.py is the script to be run to extract raw, labelled data. This script creates a new (local) directory to store the labelled satellite data for a particular area.

Note, that to run this script, one also needs another file named ibmpairspass.txt that must contain the following line of text:
pairs.res.ibm.com:[PAIRS user email][PAIRS user password]

To run DataPipeline.py, use the following:

python DataPipeline.py --data_path [directory name] --query_path [path/to/query.json] --classes [path/to/classes.json] --tile_size [Integer n] --overlap [Integer n]

Each aspect of the above script is explained below:

--data_path: This is simply the name of your directory that will store the the extracted data. It is advised to name your directory data_path_regionName (eg: data_path_dallas).
--query_path: This is the path to a .json file that specifies a PAIRS query for a certain region, including the layers that should be returned (for now, must be only RGB layers). For example queries, please check PAIRS_Queries/...
--classes: This is the path to the .json file that contains exactly the classes (or keys) that we want labelled info for. Each "key" or "tag" must correspond to one that is used by the Overpass API. For references on how to look for tags, please check this link. The structure of this file is simply a dictionary of "super classes" (more generic keys like "building") and an associated list of "sub classes" (eg: "hospital", "parking" etc. The "other" tag is used for any label/box of a particular superclass that doesn't fit into any subclass tag). For reference, please check classes.json.
--tile_size: This is simply an integer that specifies the size of the square tile (in pixels) that the entire area will be "cut up" into. For example, a tile size of 224 corresponds to 224 x 224 square tiles that will partition the entire area. Leftover tiles at the edges smaller than 224x224 will not be included. We only support square tiles for now.
--overlap: This is the number of pixels that adjacent tiles will share with each other (default 0). (Eg: if your tile size is 224 and your overlap is 24, then the first tile will be im_arr[0:224, 0:224, :] and the second will be im_arr[0:224, 200:424, :] and so on...)

Running the above command will generate three directories: data_path/images, data_path/annotations and data_path/raw_data. The raw_data simply contains a .jpg image of the entire queried area, along with a annotations.pkl file that contains all the raw bounding boxes (in pixels) for the entire image. More concretely, the annotations are stored as a dictionary in the following format:

{
  'super_class_1': 
  {
    'sub_class_1': 
    [
      [list of (pixel_x, pixel_y) nodes for label 1], [list of (pixel_x, pixel_y) nodes for label 2], ...
    ],
    'sub_class_2':
    [
      [list of (pixel_x, pixel_y) nodes for label 1], ...
    ],
    ...
  },
  'super_class_2':
  {
    'sub_class_1': ...
  },
  ...
}

The data_path/annotations directory contains .json files for annotations for each tile, in the same format as above. Note that each annotation_i.json file will contain pixel node coordinates with respect to the tile's frame, and not the global 'full area' frame.

Finally, data_path/images directory simply contains .jpg files for each tiled image from the entire area. Thus, image_i.jpg in this folder is simply the i'th tile.

Image Segementation Dataset

The file ImSeg/ImSeg_Dataset.py is the script to transform the raw dataset into the format that could be used in our semantic segementation model (RefineNet). This script creates a new (local) directory named im_seg to store the train, test, validation dataset and the model predictions with images and labels in the image segmentation format.

Note, to run this scipt, one needs to run DataPipeline.py first to create the raw dataset with images and labels.

To run ImSeg_Dataset.py, use the following:

python ImSeg/ImSeg_Dataset.py --data_path [directory name] --classes_path [path/to/classes.json] --split 0.8 0.1 0.1 --tile [True or False]

Each aspect of the above script is explained below:

--data_path: This is simply the name of your directory that stored the the raw dataset generated by running DataPipeline.py.
--classes_path: This is the path to the .json file that contains exactly the classes (or keys) that we want labelled info for (the same as the --classes argument in the DataPipeline.py).
--split: Exactly 3 percentages separated by spaces that add to 1.0, specifying the amount of data to be added to each of the train/val/test directories respectively.
--tile: This is to choose whether to visualize a random sequence of 20 tiles in the train dataset for image segmentation. It is set to be False by default.

Running the above command will generate the data_path/im_seg/ directory which will contain 4 additional directories: train, val, test and out. These four directories simply correspond to the train, test, validation datasets for model training/inference. They contain the images and labels in the image segmentation format. Each directory will contain two folders, images and annotations, to store the processed images in .jpg format and corresponding image segmentation labels in .json format respectively. Notice that out is empty when initializing the dataset and will be used to store model prediction results.

The images and annotations in data_path/images and data_path/annotations are first randomly shuffled (together, so as to preserve the correct image -> annotation mapping). Then, based on the --split, the corresponding proportion of the shuffled images and annotations are copied over to the data_path/im_seg/train/..., data_path/im_seg/val/... and data_path/im_seg/test/... directories (eg: inside the data_path/im_seg/train/images/ and data_path/im_seg/train/annotations/ directories). The names of the images/annotations inside the train/val/test directories are simply i.jpg and i.json (respectively). The mapping containing data_path/im_seg/train/images/i.jpg to its original image in data_path/images/img_j.jpg is stored in the json file path_map.json (for each image and annotation in the train, val and test directories).

Each image segementation annotation contains a list of c 1-d arrays corresponding to each of the c classes. Each of these arrays is a bit-mask for the pixels in the image tile. Eg: if the 2nd array has a 1 in the 384th position and a 0 in the 385th position, that means that the 384th pixel in the image tile belongs to the 2nd class, while the 385th pixel does not. Note that the classes are sorted in alphabetical order according to the string [super_class]:[sub_class]. Each label will be in the format of a dictionary that contains two keys, "annotation" and "img", and will be stored as i.json for the i'th image. More concretely, i.json will be in the following format:

{
  "annotation": [arrays of the one-hot encoding for each class],
  "img": "i.jpg"
}

Combining Datasets

You can combine already created datasets in two ways:

Using
```
python Dataset.py --data_path [/path/to/data_path_new] --classes_path [path/to/classes.json] --combine [path/to/data_path_1] [path/to/data_path_2] ...
```
- --data_path: The name of the new directory that will contain the combined dataset (if doesn't already exist, it will be created).
- --classes_path: This is the path to the .json file that contains exactly the classes (or keys) for which we want labelled info.
- --combine: Separate the paths to the datasets you want to combine using spaces.
This will assume that each of data_path_1, data_path_2 etc. are datasets created using DataPipeline.py and have their images/ and annotations/ directories set up. Then, combining these datasets will create a new dataset under the name [data_path_new] with its data_path_new/images/ directory a concatenation of the images in data_path_1/images, data_path_2/images etc. (similarly for annotations).
Note that using this script will not copy over any of the images or annotations you might have in the data_path_[i]/im_seg/train/... directories (for any of train, val or test.) Therefore, you can create a new data_path_new/im_seg/... directory by using ImSeg_Dataset.py (explained above).
Using
```
python ImSeg/ImSeg_Dataset.py --data_path [/path/to/data_path_new] --classes_path [path/to/classes.json] --combine [path/to/data_path_1] [path/to/data_path_2] ... 
```
- --data_path: The name of the new directory that will contain the combined dataset (if doesn't already exist, it will be created)
- --classes_path: This is the path to the .json file that contains exactly the classes (or keys) for which we want labelled info.
- --combine: Separate the paths to the datasets you want to combine using spaces.
This will assume that directories for data_path_1/im_seg/..., data_path_2/im_seg/... etc. already exist (i.e. each of the data_path_[i] are image segmentation datasets). This script also copies over the images (and annotations) in the data_path_[i]/images directories into the data_path_new/images directory (same for annotations) just like the previous method. However, it also preserves the train/val/test splits in each of the data_path_[i]/im_seg/... directories by copying over the images and annotations in data_path_[i]/im_seg/train/... into the data_path_new/im_seg/train/... directory (same for the val and test directories). This makes it possible to compare models trained on individual datasets with those trained on combined datasets (since the training/validation images don't get mixed up).

PIXOR Dataset Generation (deprecated)

The file PIXOR_Data.py is a script that takes in tile images and annotations from ./data_path, and generate input data and output labels in the format specified by the PIXOR model. To generate the dataset, a PIXOR_Dataset object must be created. Then, the build_dataset() function can be called on the object to generate the dataset. This process is exemplified in the test_pixor.py file. Inserting the directory name of the dataset question into the appropriate location will create the PIXOR_Dataset object for that dataset.

To run test_pixor.py, simply run: python test_pixor.py

After the script is finished running, there will be a new pixor folder in the dataset directory. This folder is structured as follows:

pixor
|--test 
|  |--box_annotations
|     |--0.npy
|     |--1.npy
|     ...
|  |--class_annotations
|     |--0.npy
|     |--1.npy
|     ...
|  |--images
|     |--0.jpg
|     |--1.jpg
|     ...
|--train
   ...
|--val
   …

The test, train, and val folder each hold the data that will be used during training, testing, and validation. The default spit for train, test, validation datasets is .8, .1, .1 respectively. This can be changed in the PIXOR_Dataset.py file.

Within each stratification of the dataset, there are box_annotations, class_annotations, and images folders. The naming convention for the files within the folders is that it is the id of the tile image followed by the file format. Files with the same id number describe features of the same input. The box_annotations folder contains the bounding box representation [dx, dy, sin(heading), cos(heading), width, length] as specified by the PIXOR model for each pixel in the corresponding image. The class_annotations folder contains the building class label represented as an integer for each of the pixels in the image. The images folder contains the jpeg images.

samar-khanna/AIR-Project