diff --git a/.gitignore b/.gitignore index f9378eb..1195858 100644 --- a/.gitignore +++ b/.gitignore @@ -1,2 +1,7 @@ private .DS_Store +LICENSE +data +wdata +yolov5l.pt +env diff --git a/README.md b/README.md index 2f70203..2e94dc9 100644 --- a/README.md +++ b/README.md @@ -22,7 +22,7 @@ YOLTv5 is built to execute on a GPU-enabled machine. # update with geo packages conda install -c conda-forge gdal - conda install -c conda-forge osmnx=0.12 + conda install -c conda-forge osmnx==0.12 conda install -c conda-forge scikit-image conda install -c conda-forge statsmodels pip install torchsummary @@ -36,8 +36,7 @@ ___ Training preparation is accomplished via [prep_train.py](https://github.com/avanetten/yoltv5/blob/main/yoltv5/prep_train.py). To train a model, run: - cd /yoltv5 - python yolov5/train.py --img 640 --batch 16 --epochs 100 --data yoltv5_train_vehicles_8cat.yaml --weights yolov5l.pt + python yoltv5/yolov5/train.py --img 512 --batch 16 --epochs 100 --data configs/yoltv5_rareplanes_train_roles.yaml --weights yolov5l.pt ___ diff --git a/configs/yoltv5_rareplanes_train_roles.yaml b/configs/yoltv5_rareplanes_train_roles.yaml new file mode 100755 index 0000000..faf539e --- /dev/null +++ b/configs/yoltv5_rareplanes_train_roles.yaml @@ -0,0 +1,9 @@ +# Train/val/test sets as 1) dir: path/to/imgs, 2) file: path/to/imgs.txt, or 3) list: [path/to/imgs1, path/to/imgs2, ..] +path: /home/sait/yoltv5/wdata/ # dataset root dir +train: train/images/ # train images (relative to 'path') +val: valid/images/ # val images (relative to 'path') +test: # test images (optional) + +# Classes +nc: 7 # number of classes +names: ['Small Civil Transport/Utility', 'Medium Civil Transport/Utility', 'Large Civil Transport/Utility', 'Military Transport/Utility/AWAC', 'Military Bomber', 'Military Fighter/Interceptor/Attack', 'Military Trainer'] \ No newline at end of file diff --git a/configs/yoltv5_train_vehicles_8cat.yaml b/configs/yoltv5_train_vehicles_8cat.yaml index 167d4fe..1bb0255 100755 --- a/configs/yoltv5_train_vehicles_8cat.yaml +++ b/configs/yoltv5_train_vehicles_8cat.yaml @@ -1,5 +1,5 @@ # Train/val/test sets as 1) dir: path/to/imgs, 2) file: path/to/imgs.txt, or 3) list: [path/to/imgs1, path/to/imgs2, ..] -path: /data/ # dataset root dir +path: /wdata/ # dataset root dir train: train/images # train images (relative to 'path') val: val/images # val images (relative to 'path') test: # test images (optional) diff --git a/preprocessing.ipynb b/preprocessing.ipynb new file mode 100644 index 0000000..6836466 --- /dev/null +++ b/preprocessing.ipynb @@ -0,0 +1,93470 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [], + "source": [ + "import numpy as np\n", + "import geopandas as gpd\n", + "import geojson\n", + "import os\n", + "import sys\n", + "import pandas as pd\n", + "import glob\n", + "import shutil\n", + "import datetime\n", + "import rasterio\n", + "import fiona\n", + "import skimage\n", + "import shapely\n", + "import cv2\n", + "import multiprocessing\n", + "\n", + "\n", + "from osgeo import gdal\n", + "from osgeo import ogr\n", + "from osgeo import osr\n", + "\n", + "import argparse\n", + "from tqdm import tqdm\n", + "\n", + "from osgeo import ogr\n", + "from utils import convert_poly_coords, create_mask, convert, map_wrapper\n", + "from tile_utils import slice_im_plus_boxes" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [], + "source": [ + "def count_unique_index(df, by):\n", + " return df.groupby(by).size().reset_index().rename(columns={0: 'count'})" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [], + "source": [ + "dir_str = 'data/train/RarePlanes_train_geojson_aircraft_tiled/geojson_aircraft_tiled/'\n", + "directory = os.fsencode(dir_str)\n", + "\n", + "for file in os.listdir(directory):\n", + " filename = os.fsdecode(file)\n", + " file_base = filename.rsplit('.', -1)[0]\n", + " print(file_base)\n", + "\n", + " label_path = os.path.join(dir_str+file_base + '.geojson')\n", + " img_path = os.path.join(dir_str+file_base + '.')\n", + "\n", + " if filename.endswith(\".geojson\"):\n", + " geojson_path = dir_str+filename\n", + " with open(geojson_path) as f:\n", + " gjson = geojson.load(f)\n", + " else:\n", + " continue" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [], + "source": [ + "verbose = True\n", + "mask_burnValue = 255\n", + "sliceHeight, sliceWidth = 416, 416\n", + "cls_id = 0\n", + "valid_freq_iter = 6 # 6 corresponds to 1/6 of the data for validation\n", + "n_threads = 8\n", + "\n", + "# data directory \n", + "data_dir = 'data/'\n", + "data_dir_train = os.path.join(data_dir, 'train/RarePlanes_train_PS-RGB_tiled/PS-RGB_tiled/')\n", + "\n", + "# output dirs\n", + "out_dir_root = 'wdata'\n", + "#out_dir_root = os.path.join(data_dir, 'data_yolov5_2')\n", + "# make dirs\n", + "for d in [out_dir_root]:\n", + " os.makedirs(d, exist_ok=True)\n", + "\n", + "# iterate through data, create masks, pngs, and labels\n", + "subdirs = sorted(os.listdir(data_dir_train))\n", + "shape_list = []\n", + "input_args = []\n" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [], + "source": [ + "def prep_one(label_path, img_path, \n", + " subdir, suff, \n", + " out_dir_image, out_dir_label, out_dir_mask,\n", + " out_path_image, out_path_label, out_path_mask, \n", + " sliceHeight=416, sliceWidth=416, mask_burnValue=255, \n", + " cls_id=0,\n", + " verbose=True):\n", + " \n", + " # ##################\n", + " # # Image\n", + " # ##################\n", + "\n", + " im_tmp = skimage.io.imread(img_path)\n", + " h, w = im_tmp.shape[:2]\n", + " aspect_ratio = 1.0 * h / w\n", + " dx = np.abs(h - w)\n", + " max_dx = 3\n", + "\n", + " ##################\n", + " # Labels\n", + " ##################\n", + " \n", + " if label_path:\n", + " with fiona.open(label_path, \"r\") as annotation_collection:\n", + " annotations = [feature[\"geometry\"] for feature in annotation_collection] \n", + " # get pixel coords of bounding boxes\n", + " boxes, dhs = [], []\n", + " for a in annotations:\n", + " geom = shapely.geometry.Polygon(a['coordinates'][0])\n", + " pixel_geom = convert_poly_coords(geom, raster_src=img_path, \n", + " affine_obj=None, inverse=True,\n", + " precision=2)\n", + " # Get bounding box. object.bounds: Returns a (minx, miny, maxx, maxy) tuple.\n", + " minx, miny, maxx, maxy = pixel_geom.bounds\n", + " boxes.append([minx, miny, maxx, maxy])\n", + " dhs.append([maxy-miny])\n", + " \n", + " # set classes\n", + " classes = len(boxes) * [cls_id]\n", + " else:\n", + " classes, boxes = [], []\n", + " \n", + " ##################\n", + " # Process data\n", + " ##################\n", + "\n", + " # create masks\n", + " if out_path_mask and (not os.path.exists(out_path_mask)):\n", + " create_mask(img_path, label_path, out_path_mask,\n", + " burnValue=mask_burnValue)\n", + " \n", + " # tile data, if needed\n", + " if suff == '_tile':\n", + " # tile image, labels, and mask\n", + " out_name = subdir + '_PS-RGB'\n", + " # tile (also creates labels)\n", + " # for training, skip highly overlapped edge tiles\n", + " skip_highly_overlapped_tiles=True\n", + " slice_im_plus_boxes(\n", + " img_path, out_name, out_dir_image,\n", + " boxes=boxes, yolo_classes=classes, out_dir_labels=out_dir_label,\n", + " mask_path=out_path_mask, out_dir_masks=out_dir_mask,\n", + " sliceHeight=sliceHeight, sliceWidth=sliceWidth,\n", + " overlap=0.1, slice_sep='|',\n", + " skip_highly_overlapped_tiles=skip_highly_overlapped_tiles,\n", + " out_ext='.png', verbose=False)\n", + " \n", + " else:\n", + " # no tiling\n", + " # first let's process images, then later we'll make labels\n", + " \n", + " # simply copy to dest folder if object is yuge\n", + " if suff == '_yuge':\n", + " shutil.copyfile(img_path, out_path_image)\n", + " hfinal, wfinal = h, w\n", + " \n", + " # simply copy to dest folder if aspect ratio is reasonable\n", + " elif (0.9 < aspect_ratio < 1.1):\n", + " shutil.copyfile(img_path, out_path_image)\n", + " hfinal, wfinal = h, w\n", + " \n", + " # else let's add a border on right or bottom,\n", + " # (which doesn't affect pixel coords of labels).\n", + " else:\n", + " topBorderWidth, bottomBorderWidth, leftBorderWidth, rightBorderWidth = 0, 0, 0, 0\n", + " if h / w > 1.1:\n", + " rightBorderWidth = np.abs(h - w)\n", + " if h / w < 0.9:\n", + " bottomBorderWidth = np.abs(h - w)\n", + " # add border to image\n", + " # im_tmp = cv2.imread(out_path_image, 1) # make everything 3-channel?\n", + " outputImage = cv2.copyMakeBorder(\n", + " im_tmp,\n", + " topBorderWidth,\n", + " bottomBorderWidth,\n", + " leftBorderWidth,\n", + " rightBorderWidth,\n", + " cv2.BORDER_CONSTANT,\n", + " value=0)\n", + " skimage.io.imsave(out_path_image, outputImage)\n", + " # cv2.imwrite(out_path_image, outputImage)\n", + " hfinal, wfinal = outputImage.shape[:2]\n", + " \n", + " if out_path_mask:\n", + " # add border to mask\n", + " im_tmp2 = skimage.io.imread(out_path_mask)\n", + " #im2 = cv2.imread(out_path_mask, 0)\n", + " outputImage2 = cv2.copyMakeBorder(\n", + " im_tmp2,\n", + " topBorderWidth,\n", + " bottomBorderWidth,\n", + " leftBorderWidth,\n", + " rightBorderWidth,\n", + " cv2.BORDER_CONSTANT,\n", + " value=0)\n", + " skimage.io.imsave(out_path_mask, outputImage2)\n", + " # cv2.imwrite(out_path_mask, outputImage2)\n", + "\n", + " # make yolo labels\n", + " if out_path_label:\n", + " txt_outfile = open(out_path_label, \"w\")\n", + " # create yolo style labels\n", + " for class_tmp,box_tmp in zip(classes, boxes):\n", + " minx, miny, maxx, maxy = box_tmp\n", + " bb = convert((wfinal, hfinal), [minx, maxx, miny, maxy])\n", + " # (xb,yb,wb,hb) = bb\n", + " if (np.min(bb) < 0) or (np.max(bb) > 1):\n", + " print(\" yolo coords:\", bb)\n", + " raise ValueError(\" coords outside bounds, breaking!\")\n", + " outstring = str(class_tmp) + \" \" + \" \".join([str(a) for a in bb]) + '\\n'\n", + " if verbose: \n", + " print(\" outstring:\", outstring.strip())\n", + " txt_outfile.write(outstring)\n", + " txt_outfile.close()" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\n", + "\n", + "0 / 17445 100_1040010029990A00_tile_319.geojson\n", + "100_1040010029990A00_tile_319\n", + "geojson\n", + "data/train/RarePlanes_train_PS-RGB_tiled/PS-RGB_tiled/100_1040010029990A00_tile_319.geojson\n", + "data/train/RarePlanes_train_PS-RGB_tiled/PS-RGB_tiled/100_1040010029990A00_tile_319.png\n", + " h, w: 512 512\n", + " aspect_ratio: 1.0\n", + " n annotations: 2\n", 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9_10400100474E7400_tile_62.png.aux.xml\n", + "\n", + "\n", + "17427 / 17445 9_10400100474E7400_tile_69.geojson\n", + "9_10400100474E7400_tile_69\n", + "geojson\n", + "data/train/RarePlanes_train_PS-RGB_tiled/PS-RGB_tiled/9_10400100474E7400_tile_69.geojson\n", + "data/train/RarePlanes_train_PS-RGB_tiled/PS-RGB_tiled/9_10400100474E7400_tile_69.png\n", + " h, w: 512 512\n", + " aspect_ratio: 1.0\n", + " n annotations: 1\n", + "\n", + "\n", + "17428 / 17445 9_10400100474E7400_tile_69.png\n", + "\n", + "\n", + "17429 / 17445 9_10400100474E7400_tile_69.png.aux.xml\n", + "\n", + "\n", + "17430 / 17445 9_10400100474E7400_tile_70.geojson\n", + "9_10400100474E7400_tile_70\n", + "geojson\n", + "data/train/RarePlanes_train_PS-RGB_tiled/PS-RGB_tiled/9_10400100474E7400_tile_70.geojson\n", + "data/train/RarePlanes_train_PS-RGB_tiled/PS-RGB_tiled/9_10400100474E7400_tile_70.png\n", + " h, w: 512 512\n", + " aspect_ratio: 1.0\n", + " n annotations: 7\n", + "\n", + "\n", + "17431 / 17445 9_10400100474E7400_tile_70.png\n", + "\n", + "\n", + "17432 / 17445 9_10400100474E7400_tile_70.png.aux.xml\n", + "\n", + "\n", + "17433 / 17445 9_10400100474E7400_tile_71.geojson\n", + "9_10400100474E7400_tile_71\n", + "geojson\n", + "data/train/RarePlanes_train_PS-RGB_tiled/PS-RGB_tiled/9_10400100474E7400_tile_71.geojson\n", + "data/train/RarePlanes_train_PS-RGB_tiled/PS-RGB_tiled/9_10400100474E7400_tile_71.png\n", + " h, w: 512 512\n", + " aspect_ratio: 1.0\n", + " n annotations: 10\n", + "\n", + "\n", + "17434 / 17445 9_10400100474E7400_tile_71.png\n", + "\n", + "\n", + "17435 / 17445 9_10400100474E7400_tile_71.png.aux.xml\n", + "\n", + "\n", + "17436 / 17445 9_10400100474E7400_tile_79.geojson\n", + "9_10400100474E7400_tile_79\n", + "geojson\n", + "data/train/RarePlanes_train_PS-RGB_tiled/PS-RGB_tiled/9_10400100474E7400_tile_79.geojson\n", + "data/train/RarePlanes_train_PS-RGB_tiled/PS-RGB_tiled/9_10400100474E7400_tile_79.png\n", + " h, w: 512 512\n", + " aspect_ratio: 1.0\n", + " n annotations: 2\n", + "\n", + "\n", + "17437 / 17445 9_10400100474E7400_tile_79.png\n", + "\n", + "\n", + "17438 / 17445 9_10400100474E7400_tile_79.png.aux.xml\n", + "\n", + "\n", + "17439 / 17445 9_10400100474E7400_tile_97.geojson\n", + "9_10400100474E7400_tile_97\n", + "geojson\n", + "data/train/RarePlanes_train_PS-RGB_tiled/PS-RGB_tiled/9_10400100474E7400_tile_97.geojson\n", + "data/train/RarePlanes_train_PS-RGB_tiled/PS-RGB_tiled/9_10400100474E7400_tile_97.png\n", + " h, w: 512 512\n", + " aspect_ratio: 1.0\n", + " n annotations: 3\n", + "\n", + "\n", + "17440 / 17445 9_10400100474E7400_tile_97.png\n", + "\n", + "\n", + "17441 / 17445 9_10400100474E7400_tile_97.png.aux.xml\n", + "\n", + "\n", + "17442 / 17445 9_10400100474E7400_tile_98.geojson\n", + "9_10400100474E7400_tile_98\n", + "geojson\n", + "data/train/RarePlanes_train_PS-RGB_tiled/PS-RGB_tiled/9_10400100474E7400_tile_98.geojson\n", + "data/train/RarePlanes_train_PS-RGB_tiled/PS-RGB_tiled/9_10400100474E7400_tile_98.png\n", + " h, w: 512 512\n", + " aspect_ratio: 1.0\n", + " n annotations: 1\n", + "\n", + "\n", + "17443 / 17445 9_10400100474E7400_tile_98.png\n", + "\n", + "\n", + "17444 / 17445 9_10400100474E7400_tile_98.png.aux.xml\n" + ] + } + ], + "source": [ + "list_of_files = []\n", + "\n", + "for i, subdir in enumerate(subdirs):\n", + " # if i > 200:\n", + " # break\n", + " print(\"\\n\")\n", + " print(i, \"/\", len(subdirs), subdir)\n", + " suff = ''\n", + "\n", + " ##################\n", + " # Data Locs \n", + " ##################\n", + " file_base = subdir.rsplit('.', -1)[0]\n", + " file_ext = subdir.rsplit('.', -1)[1]\n", + " subdir = subdir.rsplit('.', -1)[0]\n", + " \n", + "\n", + " #Check for duplicates\n", + "\n", + " if file_base in list_of_files:\n", + " continue\n", + " else:\n", + " list_of_files.append(file_base)\n", + "\n", + " print(file_base)\n", + " print(file_ext)\n", + "\n", + " if file_ext == 'xml':\n", + " continue\n", + "\n", + " label_path = os.path.join(data_dir_train + file_base + '.geojson')\n", + " img_path = os.path.join(data_dir_train+file_base + '.png')\n", + "\n", + " print(label_path)\n", + " print(img_path)\n", + "\n", + " out_dir_tiff = os.path.join(out_dir_root, 'train')\n", + " os.makedirs(out_dir_tiff, exist_ok=True)\n", + " \n", + " ##################\n", + " # Image\n", + "\n", + "\n", + "\n", + "\n", + " ##################\n", + " \n", + " im_tmp = skimage.io.imread(img_path) # (assume pan is the same size as ps-rgb will be!)\n", + " # im_tmp = skimage.io.imread(ps_rgb_path)\n", + " h, w = im_tmp.shape[:2]\n", + " shape_list.append([subdir, h, w])\n", + " # im_tmp = skimage.io.imread(pan_path)\n", + " # h, w = im_tmp.shape\n", + " # shape_list.append([subdir + '_PAN', h, w])\n", + " aspect_ratio = 1.0 * h / w\n", + " dx = np.abs(h - w)\n", + " max_dx = 3\n", + "\n", + " ##################\n", + " # Labels\n", + " ##################\n", + " \n", + " with fiona.open(label_path, \"r\") as annotation_collection:\n", + " annotations = [feature[\"geometry\"] for feature in annotation_collection] \n", + " if verbose:\n", + " print(\" h, w:\", h, w)\n", + " print(\" aspect_ratio:\", aspect_ratio)\n", + " print(\" n annotations:\", len(annotations))\n", + " \n", + " ##################\n", + " # Set output paths\n", + " ##################\n", + " \n", + " # put every fifth item in valid\n", + " if (i % valid_freq_iter) == 0:\n", + " pop = 'valid'\n", + " else:\n", + " pop = 'train'\n", + " \n", + " # check if it's a huge square image (these all have a large circle centered in the middle,\n", + " # so we can skip for training)\n", + " if (((h >= 600) and (w >= 600) and (dx <= max_dx)) \\\n", + " or ((h >= 1000) and (w >= 1000) and (0.97 < aspect_ratio < 1.03))) \\\n", + " and (len(annotations) == 1): # skipped in original non-tiling version\n", + " # or (h * w > 800 * 800): # original version (no tiling)\n", + " suff = '_yuge'\n", + " \n", + " # # also can skip if the labels are huge\n", + " # elif np.max(dhs) > sliceHeight:\n", + " # suff = '_yuge'\n", + " \n", + " # look for large images with multiple annotatios\n", + " elif ((h >= 600) and (w >= 600)) and \\\n", + " (len(annotations) > 1): \n", + " suff = '_tile'\n", + " \n", + " else:\n", + " suff = ''\n", + "\n", + " # set output folders\n", + " # out_dir_tiff = os.path.join(out_dir_root, pop, 'PS-RGB' + suff)\n", + " out_dir_image = os.path.join(out_dir_root, pop, 'images' + suff)\n", + " out_dir_label = os.path.join(out_dir_root, pop, 'labels' + suff)\n", + " out_dir_mask = os.path.join(out_dir_root, pop, 'masks' + suff) \n", + " for d in [out_dir_image, out_dir_label, out_dir_mask]:\n", + " os.makedirs(d, exist_ok=True)\n", + " # output files\n", + " # ps_rgb_path = os.path.join(out_dir_tiff, subdir + '_PS-RGB.tif')\n", + " out_path_image = os.path.join(out_dir_image, subdir + '.png')\n", + " out_path_label = os.path.join(out_dir_label, subdir + '.txt')\n", + " out_path_mask = os.path.join(out_dir_mask, subdir + '.png') \n", + "\n", + " input_args.append([prep_one,\n", + " label_path, img_path, \n", + " subdir, suff, \n", + " out_dir_image, out_dir_label, out_dir_mask,\n", + " out_path_image, out_path_label, out_path_mask,\n", + " sliceHeight, sliceWidth, mask_burnValue, \n", + " cls_id,\n", + " verbose])" + ] + }, + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [ + { + "ename": "NameError", + "evalue": "name 'input_args' is not defined", + "output_type": "error", + "traceback": [ + "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[0;31mNameError\u001b[0m Traceback (most recent call last)", + "\u001b[1;32m/home/sait/rareplanes_analysis/preprocessing.ipynb Cell 7'\u001b[0m in \u001b[0;36m\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[39mprint\u001b[39m(\u001b[39m\"\u001b[39m\u001b[39mlen input_args\u001b[39m\u001b[39m\"\u001b[39m, \u001b[39mlen\u001b[39m(input_args))\n\u001b[1;32m 2\u001b[0m \u001b[39mprint\u001b[39m(\u001b[39m\"\u001b[39m\u001b[39mExecute...\u001b[39m\u001b[39m\\n\u001b[39;00m\u001b[39m\"\u001b[39m)\n\u001b[1;32m 3\u001b[0m \u001b[39mwith\u001b[39;00m multiprocessing\u001b[39m.\u001b[39mPool(n_threads) \u001b[39mas\u001b[39;00m pool:\n", + "\u001b[0;31mNameError\u001b[0m: name 'input_args' is not defined" + ] + } + ], + "source": [ + "print(\"len input_args\", len(input_args))\n", + "print(\"Execute...\\n\")\n", + "with multiprocessing.Pool(n_threads) as pool:\n", + " pool.map(map_wrapper, input_args)\n" + ] + } + ], + "metadata": { + "interpreter": { + "hash": "e55666fbbf217aa3df372b978577f47b6009e2f78e2ec76a584f49cd54a1e62c" + }, + "kernelspec": { + "display_name": "Python 2.7.18 64-bit", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.8.10" + }, + "orig_nbformat": 4 + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/yoltv5/__pycache__/core.cpython-38.pyc b/yoltv5/__pycache__/core.cpython-38.pyc new file mode 100644 index 0000000..70e5066 Binary files /dev/null and b/yoltv5/__pycache__/core.cpython-38.pyc differ diff --git a/yoltv5/__pycache__/geo.cpython-38.pyc b/yoltv5/__pycache__/geo.cpython-38.pyc new file mode 100644 index 0000000..666b7f1 Binary files /dev/null and b/yoltv5/__pycache__/geo.cpython-38.pyc differ diff --git a/yoltv5/__pycache__/prep_train.cpython-38.pyc b/yoltv5/__pycache__/prep_train.cpython-38.pyc new file mode 100644 index 0000000..0c1fdfb Binary files /dev/null and b/yoltv5/__pycache__/prep_train.cpython-38.pyc differ diff --git a/yoltv5/__pycache__/tile_ims_labels.cpython-38.pyc b/yoltv5/__pycache__/tile_ims_labels.cpython-38.pyc new file mode 100644 index 0000000..a89c005 Binary files /dev/null and b/yoltv5/__pycache__/tile_ims_labels.cpython-38.pyc differ diff --git a/yoltv5/__pycache__/tile_utils.cpython-38.pyc b/yoltv5/__pycache__/tile_utils.cpython-38.pyc new file mode 100644 index 0000000..6b2d1d1 Binary files /dev/null and b/yoltv5/__pycache__/tile_utils.cpython-38.pyc differ diff --git a/yoltv5/__pycache__/utils.cpython-38.pyc b/yoltv5/__pycache__/utils.cpython-38.pyc new file mode 100644 index 0000000..d14b7f1 Binary files /dev/null and b/yoltv5/__pycache__/utils.cpython-38.pyc differ diff --git a/yoltv5/__pycache__/utils_2.cpython-38.pyc b/yoltv5/__pycache__/utils_2.cpython-38.pyc new file mode 100644 index 0000000..f5c600a Binary files /dev/null and b/yoltv5/__pycache__/utils_2.cpython-38.pyc differ diff --git a/yoltv5/core.py b/yoltv5/core.py new file mode 100644 index 0000000..caacccd --- /dev/null +++ b/yoltv5/core.py @@ -0,0 +1,152 @@ +import os +import numpy as np +from shapely.wkt import loads +from shapely.geometry import Point +from shapely.geometry.base import BaseGeometry +import pandas as pd +import geopandas as gpd +import pyproj +import rasterio +from distutils.version import LooseVersion +import skimage +from fiona._err import CPLE_OpenFailedError +from fiona.errors import DriverError +from warnings import warn + + +def _check_rasterio_im_load(im): + """Check if `im` is already loaded in; if not, load it in.""" + if isinstance(im, str): + return rasterio.open(im) + elif isinstance(im, rasterio.DatasetReader): + return im + else: + raise ValueError( + "{} is not an accepted image format for rasterio.".format(im)) + + +def _check_skimage_im_load(im): + """Check if `im` is already loaded in; if not, load it in.""" + if isinstance(im, str): + return skimage.io.imread(im) + elif isinstance(im, np.ndarray): + return im + else: + raise ValueError( + "{} is not an accepted image format for scikit-image.".format(im)) + + +def _check_df_load(df): + """Check if `df` is already loaded in, if not, load from file.""" + if isinstance(df, str): + if df.lower().endswith('json'): + return _check_gdf_load(df) + else: + return pd.read_csv(df) + elif isinstance(df, pd.DataFrame): + return df + else: + raise ValueError(f"{df} is not an accepted DataFrame format.") + + +def _check_gdf_load(gdf): + """Check if `gdf` is already loaded in, if not, load from geojson.""" + if isinstance(gdf, str): + # as of geopandas 0.6.2, using the OGR CSV driver requires some add'nal + # kwargs to create a valid geodataframe with a geometry column. see + # https://github.com/geopandas/geopandas/issues/1234 + if gdf.lower().endswith('csv'): + return gpd.read_file(gdf, GEOM_POSSIBLE_NAMES="geometry", + KEEP_GEOM_COLUMNS="NO") + try: + return gpd.read_file(gdf) + except (DriverError, CPLE_OpenFailedError): + warn(f"GeoDataFrame couldn't be loaded: either {gdf} isn't a valid" + " path or it isn't a valid vector file. Returning an empty" + " GeoDataFrame.") + return gpd.GeoDataFrame() + elif isinstance(gdf, gpd.GeoDataFrame): + return gdf + else: + raise ValueError(f"{gdf} is not an accepted GeoDataFrame format.") + + +def _check_geom(geom): + """Check if a geometry is loaded in. + + Returns the geometry if it's a shapely geometry object. If it's a wkt + string or a list of coordinates, convert to a shapely geometry. + """ + if isinstance(geom, BaseGeometry): + return geom + elif isinstance(geom, str): # assume it's a wkt + return loads(geom) + elif isinstance(geom, list) and len(geom) == 2: # coordinates + return Point(geom) + + +def _check_crs(input_crs, return_rasterio=False): + """Convert CRS to the ``pyproj.CRS`` object passed by ``solaris``.""" + if not isinstance(input_crs, pyproj.CRS) and input_crs is not None: + out_crs = pyproj.CRS(input_crs) + else: + out_crs = input_crs + + if return_rasterio: + if LooseVersion(rasterio.__gdal_version__) >= LooseVersion("3.0.0"): + out_crs = rasterio.crs.CRS.from_wkt(out_crs.to_wkt()) + else: + out_crs = rasterio.crs.CRS.from_wkt(out_crs.to_wkt("WKT1_GDAL")) + + return out_crs + + +def get_data_paths(path, infer=False): + """Get a pandas dataframe of images and labels from a csv. + + This file is designed to parse image:label reference CSVs (or just image) + for inferencde) as defined in the documentation. Briefly, these should be + CSVs containing two columns: + + ``'image'``: the path to images. + ``'label'``: the path to the label file that corresponds to the image. + + Arguments + --------- + path : str + Path to a .CSV-formatted reference file defining the location of + training, validation, or inference data. See docs for details. + infer : bool, optional + If ``infer=True`` , the ``'label'`` column will not be returned (as it + is unnecessary for inference), even if it is present. + + Returns + ------- + df : :class:`pandas.DataFrame` + A :class:`pandas.DataFrame` containing the relevant `image` and `label` + information from the CSV at `path` (unless ``infer=True`` , in which + case only the `image` column is returned.) + + """ + df = pd.read_csv(path) + if infer: + return df[['image']] # no labels in those files + else: + return df[['image', 'label']] # remove anything extraneous + + +def get_files_recursively(path, traverse_subdirs=False, extension='.tif'): + """Get files from subdirs of `path`, joining them to the dir.""" + if traverse_subdirs: + walker = os.walk(path) + path_list = [] + for step in walker: + if not step[2]: # if there are no files in the current dir + continue + path_list += [os.path.join(step[0], fname) + for fname in step[2] if + fname.lower().endswith(extension)] + return path_list + else: + return [os.path.join(path, f) for f in os.listdir(path) + if f.endswith(extension)] \ No newline at end of file diff --git a/yoltv5/geo.py b/yoltv5/geo.py new file mode 100644 index 0000000..917f9a0 --- /dev/null +++ b/yoltv5/geo.py @@ -0,0 +1,841 @@ +import os +from core import _check_df_load, _check_gdf_load, _check_rasterio_im_load +from core import _check_geom, _check_crs +import numpy as np +import pandas as pd +import geopandas as gpd +from affine import Affine + +from osgeo import gdal +from osgeo import ogr +from osgeo import osr + +import rasterio +from rasterio.warp import calculate_default_transform, Resampling +from rasterio.warp import transform_bounds +from shapely.affinity import affine_transform +from shapely.wkt import loads +from shapely.geometry import Point, Polygon, LineString +from shapely.geometry import MultiLineString, MultiPolygon, mapping, box, shape +from shapely.geometry.collection import GeometryCollection +from shapely.ops import cascaded_union + +import json +from warnings import warn +import sys + + +def reproject(input_object, input_crs=None, + target_crs=None, target_object=None, dest_path=None, + resampling_method='cubic'): + """Reproject a dataset (df, gdf, or image) to a new coordinate system. + + This function takes a georegistered image or a dataset of vector geometries + and converts them to a new coordinate reference system. If no target CRS + is provided, the data will be converted to the appropriate UTM zone by + default. To convert a pixel-coordinate dataset to geographic coordinates or + vice versa, use :func:`solaris.vector.polygon.georegister_px_df` or + :func:`solaris.vector.polygon.geojson_to_px_gdf` instead. + + Arguments + --------- + input_object : `str` or :class:`rasterio.DatasetReader` or :class:`gdal.Dataset` or :class:`geopandas.GeoDataFrame` + An object to transform to a new CRS. If a string, it must be a path + to a georegistered image or vector dataset (e.g. a .GeoJSON). If the + object itself does not contain georeferencing information, the + coordinate reference system can be provided with `input_crs`. + input_crs : int, optional + The EPSG code integer for the input data's CRS. If provided and a CRS + is also associated with `input_object`, this argument's value has + precedence. + target_crs : int, optional + The EPSG code for the output projection. If values are not provided + for this argument or `target_object`, the input data will be + re-projected into the appropriate UTM zone. If both `target_crs` and + `target_object` are provided, `target_crs` takes precedence (and a + warning is raised). + target_object : str, optional + An object in the desired destination CRS. If neither this argument nor + `target_crs` is provided, the input will be projected into the + appropriate UTM zone. `target_crs` takes precedence if both it and + `target_object` are provided. + dest_path : str, optional + The path to save the output to (if desired). This argument is only + required if the input is a :class:`gdal.Dataset`; otherwise, it is + optional. + resampling_method : str, optional + The resampling method to use during reprojection of raster data. **Only + has an effect if the input is a :class:`rasterio.DatasetReader` !** + Possible values are + ``['cubic' (default), 'bilinear', 'nearest', 'average']``. + + Returns + ------- + output : :class:`rasterio.DatasetReader` or :class:`gdal.Dataset` or :class:`geopandas.GeoDataFrame` + An output in the same format as `input_object`, but reprojected + into the destination CRS. + """ + input_data, input_type = _parse_geo_data(input_object) + if input_crs is None: + input_crs = _check_crs(get_crs(input_data)) + else: + input_crs = _check_crs(input_crs) + if target_object is not None: + target_data, _ = _parse_geo_data(target_object) + else: + target_data = None + # get CRS from target_object if it's not provided + if target_crs is None and target_data is not None: + target_crs = get_crs(target_data) + + if target_crs is not None: + target_crs = _check_crs(target_crs) + output = _reproject(input_data, input_type, input_crs, target_crs, + dest_path, resampling_method) + else: + output = reproject_to_utm(input_data, input_type, input_crs, + dest_path, resampling_method) + return output + + +def _reproject(input_data, input_type, input_crs, target_crs, dest_path, + resampling_method='bicubic'): + + input_crs = _check_crs(input_crs) + target_crs = _check_crs(target_crs) + if input_type == 'vector': + output = input_data.to_crs(target_crs) + if dest_path is not None: + output.to_file(dest_path, driver='GeoJSON') + + elif input_type == 'raster': + + if isinstance(input_data, rasterio.DatasetReader): + transform, width, height = calculate_default_transform( + input_crs.to_wkt("WKT1_GDAL"), target_crs.to_wkt("WKT1_GDAL"), + input_data.width, input_data.height, *input_data.bounds + ) + kwargs = input_data.meta.copy() + kwargs.update({'crs': target_crs.to_wkt("WKT1_GDAL"), + 'transform': transform, + 'width': width, + 'height': height}) + + if dest_path is not None: + with rasterio.open(dest_path, 'w', **kwargs) as dst: + for band_idx in range(1, input_data.count + 1): + rasterio.warp.reproject( + source=rasterio.band(input_data, band_idx), + destination=rasterio.band(dst, band_idx), + src_transform=input_data.transform, + src_crs=input_data.crs, + dst_transform=transform, + dst_crs=target_crs.to_wkt("WKT1_GDAL"), + resampling=getattr(Resampling, resampling_method) + ) + output = rasterio.open(dest_path) + input_data.close() + + else: + output = np.zeros(shape=(height, width, input_data.count)) + for band_idx in range(1, input_data.count + 1): + rasterio.warp.reproject( + source=rasterio.band(input_data, band_idx), + destination=output[:, :, band_idx-1], + src_transform=input_data.transform, + src_crs=input_data.crs, + dst_transform=transform, + dst_crs=target_crs, + resampling=getattr(Resampling, resampling_method) + ) + + elif isinstance(input_data, gdal.Dataset): + if dest_path is not None: + gdal.Warp(dest_path, input_data, + dstSRS='EPSG:' + str(target_crs.to_epsg())) + output = gdal.Open(dest_path) + else: + raise ValueError('An output path must be provided for ' + 'reprojecting GDAL datasets.') + return output + + +def reproject_to_utm(input_data, input_type, input_crs=None, dest_path=None, + resampling_method='bicubic'): + """Convert an input to a UTM CRS (after determining the correct UTM zone). + + """ + if input_crs is None: + input_crs = get_crs(input_data) + if input_crs is None: + raise ValueError('An input CRS must be provided by input_data or' + ' input_crs.') + input_crs = _check_crs(input_crs) + + bounds = get_bounds(input_data, crs=_check_crs(4326)) # need in wkt84 for UTM zone + midpoint = [(bounds[1] + bounds[3])/2., (bounds[0] + bounds[2])/2.] + utm_epsg = latlon_to_utm_epsg(*midpoint) + + output = _reproject(input_data, input_type=input_type, input_crs=input_crs, + target_crs=utm_epsg, dest_path=dest_path, + resampling_method=resampling_method) + # cleanup + if os.path.isfile('tmp'): + os.remove('tmp') + + return output + + +def get_bounds(geo_obj, crs=None): + """Get the ``[left, bottom, right, top]`` bounds in any CRS. + + Arguments + --------- + geo_obj : a georeferenced raster or vector dataset. + crs : int, optional + The EPSG code (or other CRS format supported by rasterio.warp) + for the CRS the bounds should be returned in. If not provided, + the bounds will be returned in the same crs as `geo_obj`. + + Returns + ------- + bounds : list + ``[left, bottom, right, top]`` bounds in the input crs (if `crs` is + ``None``) or in `crs` if it was provided. + """ + input_data, input_type = _parse_geo_data(geo_obj) + if input_type == 'vector': + bounds = list(input_data.geometry.total_bounds) + elif input_type == 'raster': + if isinstance(input_data, rasterio.DatasetReader): + bounds = list(input_data.bounds) + elif isinstance(input_data, gdal.Dataset): + input_gt = input_data.GetGeoTransform() + min_x = input_gt[0] + max_x = min_x + input_gt[1]*input_data.RasterXSize + max_y = input_gt[3] + min_y = max_y + input_gt[5]*input_data.RasterYSize + + bounds = [min_x, min_y, max_x, max_y] + + if crs is not None: + crs = _check_crs(crs) + src_crs = get_crs(input_data) + # transform bounds to desired CRS + bounds = transform_bounds(src_crs.to_wkt("WKT1_GDAL"), + crs.to_wkt("WKT1_GDAL"), *bounds) + + return bounds + + +def get_crs(obj): + """Get a coordinate reference system from any georegistered object.""" + if isinstance(obj, gpd.GeoDataFrame): + return _check_crs(obj.crs) + elif isinstance(obj, rasterio.DatasetReader): + return _check_crs(obj.crs) + elif isinstance(obj, gdal.Dataset): + # rawr + return _check_crs(int(osr.SpatialReference(wkt=obj.GetProjection()).GetAttrValue( + 'AUTHORITY', 1))) + else: + raise TypeError("solaris doesn't know how to extract a crs from an " + "object of type {}".format(type(obj))) + + +def _parse_geo_data(input): + if isinstance(input, str): + if input.lower().endswith('json') or input.lower().endswith('csv'): + input_type = 'vector' + input_data = _check_df_load(input) + elif input.lower().endswith('tif') or input.lower().endswith('tiff'): + input_type = 'raster' + input_data = _check_rasterio_im_load(input) + else: + input_data = input + if isinstance(input_data, pd.DataFrame): + input_type = 'vector' + elif isinstance( + input_data, rasterio.DatasetReader + ) or isinstance( + input_data, gdal.Dataset + ): + input_type = 'raster' + else: + raise ValueError('The input format {} is not compatible with ' + 'solaris.'.format(type(input))) + return input_data, input_type + + +def reproject_geometry(input_geom, input_crs=None, target_crs=None, + affine_obj=None): + """Reproject a geometry or coordinate into a new CRS. + + Arguments + --------- + input_geom : `str`, `list`, or `Shapely `_ geometry + A geometry object to re-project. This can be a 2-member ``list``, in + which case `input_geom` is assumed to coorespond to ``[x, y]`` + coordinates in `input_crs`. It can also be a Shapely geometry object or + a wkt string. + input_crs : int, optional + The coordinate reference system for `input_geom`'s coordinates, as an + EPSG :class:`int`. Required unless `affine_transform` is provided. + target_crs : int, optional + The target coordinate reference system to re-project the geometry into. + If not provided, the appropriate UTM zone will be selected by default, + unless `affine_transform` is provided (and therefore CRSs are ignored.) + affine_transform : :class:`affine.Affine`, optional + An :class:`affine.Affine` object (or a ``[a, b, c, d, e, f]`` list to + convert to that format) to use for transformation. Has no effect unless + `input_crs` **and** `target_crs` are not provided. + + Returns + ------- + output_geom : Shapely geometry + A shapely geometry object: + - in `target_crs`, if one was provided; + - in the appropriate UTM zone, if `input_crs` was provided and + `target_crs` was not; + - with `affine_transform` applied to it if neither `input_crs` nor + `target_crs` were provided. + """ + input_geom = _check_geom(input_geom) + + if input_crs is not None: + input_crs = _check_crs(input_crs) + if target_crs is None: + geom = reproject_geometry(input_geom, input_crs, + target_crs=_check_crs(4326)) + target_crs = latlon_to_utm_epsg(geom.centroid.y, geom.centroid.x) + target_crs = _check_crs(target_crs) + gdf = gpd.GeoDataFrame(geometry=[input_geom], crs=input_crs.to_wkt()) + # create a new instance of the same geometry class as above with the + # new coordinates + output_geom = gdf.to_crs(target_crs.to_wkt()).iloc[0]['geometry'] + + else: + if affine_obj is None: + raise ValueError('If an input CRS is not provided, ' + 'affine_transform is required to complete the ' + 'transformation.') + elif isinstance(affine_obj, Affine): + affine_obj = affine_to_list(affine_obj) + + output_geom = affine_transform(input_geom, affine_obj) + + return output_geom + + +def gdf_get_projection_unit(vector_file): + """Get the projection unit for a vector_file or gdf. + + Arguments + --------- + vector_file : :py:class:`geopandas.GeoDataFrame` or geojson/shapefile + A vector file or gdf with georeferencing + + Notes + ----- + If vector file is already in UTM coords, the projection WKT is complex: + https://www.spatialreference.org/ref/epsg/wgs-84-utm-zone-11n/html/ + In this case, return the second instance of 'UNIT'. + + Returns + ------- + unit : String + The unit i.e. meter, metre, or degree, of the projection + """ + c = _check_gdf_load(vector_file).crs + return get_projection_unit(c) + + +def raster_get_projection_unit(image): + """Get the projection unit for an image. + + Arguments + --------- + image : raster image, GeoTIFF or other format + A raster file with georeferencing + + Notes + ----- + If raster is already in UTM coords, the projection WKT is complex: + https://www.spatialreference.org/ref/epsg/wgs-84-utm-zone-11n/html/ + In this case, return the second instance of 'UNIT'. + + Returns + ------- + unit : String + The unit i.e. meters or degrees, of the projection + """ + c = _check_rasterio_im_load(image).crs + return get_projection_unit(c) + + +def get_projection_unit(crs): + """Get the units of a specific SRS. + + Arguments + --------- + crs : :class:`pyproj.crs.CRS`, :class:`rasterio.crs.CRS`, `str`, or `int` + The coordinate reference system to retrieve a unit for. + + Returns + ------- + unit : str + The string-formatted unit. + """ + crs = _check_crs(crs) + unit = crs.axis_info[0].unit_name + + return unit + + + +def list_to_affine(xform_mat): + """Create an Affine from a list or array-formatted [a, b, d, e, xoff, yoff] + + Arguments + --------- + xform_mat : `list` or :class:`numpy.array` + A `list` of values to convert to an affine object. + + Returns + ------- + aff : :class:`affine.Affine` + An affine transformation object. + """ + # first make sure it's not in gdal order + if len(xform_mat) > 6: + xform_mat = xform_mat[0:6] + if rasterio.transform.tastes_like_gdal(xform_mat): + return Affine.from_gdal(*xform_mat) + else: + return Affine(*xform_mat) + + +def affine_to_list(affine_obj): + """Convert a :class:`affine.Affine` instance to a list for Shapely.""" + return [affine_obj.a, affine_obj.b, + affine_obj.d, affine_obj.e, + affine_obj.xoff, affine_obj.yoff] + + +def geometries_internal_intersection(polygons): + """Get the intersection geometries between all geometries in a set. + + Arguments + --------- + polygons : `list`-like + A `list`-like containing geometries. These will be placed in a + :class:`geopandas.GeoSeries` object to take advantage of `rtree` + spatial indexing. + + Returns + ------- + intersect_list + A `list` of geometric intersections between polygons in `polygons`, in + the same CRS as the input. + """ + # convert `polygons` to geoseries and get spatialindex + # TODO: Implement test to see if `polygon` items are actual polygons or + # WKT strings + if isinstance(polygons, gpd.GeoSeries): + gs = polygons + else: + gs = gpd.GeoSeries(polygons).reset_index(drop=True) + sindex = gs.sindex + gs_bboxes = gs.apply(lambda x: x.bounds) + + # find indices of polygons that overlap in gs + intersect_lists = gs_bboxes.apply(lambda x: list(sindex.intersection(x))) + intersect_lists = intersect_lists.dropna() + # drop all objects that only have self-intersects + # first, filter down to the ones that have _some_ intersection with others + intersect_lists = intersect_lists[ + intersect_lists.apply(lambda x: len(x) > 1)] + if len(intersect_lists) == 0: # if there are no real intersections + return GeometryCollection() # same result as failed union below + # the below is a royal pain to follow. what it does is create a dataframe + # with two columns: 'gs_idx' and 'intersectors'. 'gs_idx' corresponds to + # a polygon's original index in gs, and 'intersectors' gives a list of + # gs indices for polygons that intersect with its bbox. + intersect_lists.name = 'intersectors' + intersect_lists.index.name = 'gs_idx' + intersect_lists = intersect_lists.reset_index() + # first, we get rid of self-intersection indices in 'intersectors': + intersect_lists['intersectors'] = intersect_lists.apply( + lambda x: [i for i in x['intersectors'] if i != x['gs_idx']], + axis=1) + # for each row, we next create a union of the polygons in 'intersectors', + # and find the intersection of that with the polygon at gs[gs_idx]. this + # (Multi)Polygon output corresponds to all of the intersections for the + # polygon at gs[gs_idx]. we add that to a list of intersections stored in + # output_polys. + output_polys = [] + _ = intersect_lists.apply(lambda x: output_polys.append( + gs[x['gs_idx']].intersection(cascaded_union(gs[x['intersectors']])) + ), axis=1) + # we then generate the union of all of these intersections and return it. + return cascaded_union(output_polys) + + +def split_multi_geometries(gdf, obj_id_col=None, group_col=None, + geom_col='geometry'): + """Split apart MultiPolygon or MultiLineString geometries. + + Arguments + --------- + gdf : :class:`geopandas.GeoDataFrame` or `str` + A :class:`geopandas.GeoDataFrame` or path to a geojson containing + geometries. + obj_id_col : str, optional + If one exists, the name of the column that uniquely identifies each + geometry (e.g. the ``"BuildingId"`` column in many SpaceNet datasets). + This will be tracked so multiple objects don't get produced with + the same ID. Note that object ID column will be renumbered on output. + If passed, `group_col` must also be provided. + group_col : str, optional + A column to identify groups for sequential numbering (for example, + ``'ImageId'`` for sequential number of ``'BuildingId'``). Must be + provided if `obj_id_col` is passed. + geom_col : str, optional + The name of the column in `gdf` that corresponds to geometry. Defaults + to ``'geometry'``. + + Returns + ------- + :class:`geopandas.GeoDataFrame` + A `geopandas.GeoDataFrame` that's identical to the input, except with + the multipolygons split into separate rows, and the object ID column + renumbered (if one exists). + + """ + if obj_id_col and not group_col: + raise ValueError('group_col must be provided if obj_id_col is used.') + gdf2 = _check_gdf_load(gdf) + # drop duplicate columns (happens if loading a csv with geopandas) + gdf2 = gdf2.loc[:, ~gdf2.columns.duplicated()] + if len(gdf2) == 0: + return gdf2 + # check if the values in gdf2[geometry] are polygons; if strings, do loads + if isinstance(gdf2[geom_col].iloc[0], str): + gdf2[geom_col] = gdf2[geom_col].apply(loads) + split_geoms_gdf = pd.concat( + gdf2.apply(_split_multigeom_row, axis=1, geom_col=geom_col).tolist()) + gdf2 = gdf2.drop(index=split_geoms_gdf.index.unique()) # remove multipolygons + gdf2 = gpd.GeoDataFrame(pd.concat([gdf2, split_geoms_gdf], + ignore_index=True), crs=gdf2.crs) + + if obj_id_col: + gdf2[obj_id_col] = gdf2.groupby(group_col).cumcount()+1 + + return gdf2 + + +def get_subgraph(G, node_subset): + """ + Create a subgraph from G. Code almost directly copied from osmnx. + + Arguments + --------- + G : :class:`networkx.MultiDiGraph` + A graph to be subsetted + node_subset : `list`-like + The subset of nodes to induce a subgraph of `G` + + Returns + ------- + G2 : :class:`networkx`.MultiDiGraph + The subgraph of G that includes node_subset + """ + + node_subset = set(node_subset) + + # copy nodes into new graph + G2 = G.fresh_copy() + G2.add_nodes_from((n, G.nodes[n]) for n in node_subset) + + # copy edges to new graph, including parallel edges + if G2.is_multigraph: + G2.add_edges_from( + (n, nbr, key, d) + for n, nbrs in G.adj.items() if n in node_subset + for nbr, keydict in nbrs.items() if nbr in node_subset + for key, d in keydict.items()) + else: + G2.add_edges_from( + (n, nbr, d) + for n, nbrs in G.adj.items() if n in node_subset + for nbr, d in nbrs.items() if nbr in node_subset) + + # update graph attribute dict, and return graph + G2.graph.update(G.graph) + return G2 + + +def _split_multigeom_row(gdf_row, geom_col): + new_rows = [] + if isinstance(gdf_row[geom_col], MultiPolygon) \ + or isinstance(gdf_row[geom_col], MultiLineString): + new_polys = _split_multigeom(gdf_row[geom_col]) + for poly in new_polys: + row_w_poly = gdf_row.copy() + row_w_poly[geom_col] = poly + new_rows.append(row_w_poly) + return pd.DataFrame(new_rows) + + +def _split_multigeom(multigeom): + return list(multigeom) + + +def _reduce_geom_precision(geom, precision=2): + geojson = mapping(geom) + geojson['coordinates'] = np.round(np.array(geojson['coordinates']), + precision) + return shape(geojson) + + +def latlon_to_utm_epsg(latitude, longitude, return_proj4=False): + """Get the WGS84 UTM EPSG code based on a latitude and longitude value. + + Arguments + --------- + latitude : numeric + The latitude value for the coordinate. + longitude : numeric + The longitude value for the coordinate. + return_proj4 : bool, optional + Should the proj4 string be returned as well as the EPSG code? Defaults + to no (``False``)` + + Returns + ------- + epsg : int + The integer corresponding to the EPSG code for the relevant UTM zone + in WGS 84. + proj4 : str + The proj4 string for the CRS. Only returned if ``return_proj4=True``. + """ + zone_number, zone_letter = _latlon_to_utm_zone(latitude, longitude) + + if return_proj4: + if zone_letter == 'N': + direction_indicator = '+north' + elif zone_letter == 'S': + direction_indicator = '+south' + proj = "+proj=utm +zone={} {}".format(zone_number, + direction_indicator) + proj += " +ellps=WGS84 +datum=WGS84 +units=m +no_defs" + + if zone_letter == 'N': + epsg = 32600 + zone_number + elif zone_letter == 'S': + epsg = 32700 + zone_number + + return (epsg, proj) if return_proj4 else epsg + + +def _latlon_to_utm_zone(latitude, longitude, ns_only=True): + """Convert latitude and longitude to a UTM zone ID. + + This function modified from + `the python utm library `_. + + Arguments + --------- + latitude : numeric or :class:`numpy.ndarray` + The latitude value of a coordinate. + longitude : numeric or :class:`numpy.ndarray` + The longitude value of a coordinate. + ns_only : bool, optional + Should the full list of possible zone numbers be used or just the N/S + options? Defaults to N/S only (``True``). + + Returns + ------- + zone_number : int + The numeric portion of the UTM zone ID. + zone_letter : str + The string portion of the UTM zone ID. Note that by default this + function uses only the N/S designation rather than the full range of + possible letters. + """ + + # If the input is a numpy array, just use the first element + # User responsibility to make sure that all points are in one zone + if isinstance(latitude, np.ndarray): + latitude = latitude.flat[0] + if isinstance(longitude, np.ndarray): + longitude = longitude.flat[0] + + utm_val = None + + if 56 <= latitude < 64 and 3 <= longitude < 12: + utm_val = 32 + + elif 72 <= latitude <= 84 and longitude >= 0: + if longitude < 9: + utm_val = 31 + elif longitude < 21: + utm_val = 33 + elif longitude < 33: + utm_val = 35 + elif longitude < 42: + utm_val = 37 + + if latitude < 0: + zone_letter = "S" + else: + zone_letter = "N" + + if not -80 <= latitude <= 84: + warn('Warning: UTM projections not recommended for ' + 'latitude {}'.format(latitude)) + if utm_val is None: + utm_val = int((longitude + 180) / 6) + 1 + + return utm_val, zone_letter + + +def _get_coords(geom): + """Get coordinates from various shapely geometry types.""" + if isinstance(geom, Point) or isinstance(geom, LineString): + return geom.coords.xy + elif isinstance(geom, Polygon): + return geom.exterior.coords.xy + + +def bbox_corners_to_coco(bbox): + """Convert bbox from ``[minx, miny, maxx, maxy]`` to coco format. + + COCO formats bounding boxes as ``[minx, miny, width, height]``. + + Arguments + --------- + bbox : :class:`list`-like of numerics + A 4-element list of the form ``[minx, miny, maxx, maxy]``. + + Returns + ------- + coco_bbox : list + ``[minx, miny, width, height]`` shape. + """ + + return [bbox[0], bbox[1], bbox[2]-bbox[0], bbox[3]-bbox[1]] + + +def polygon_to_coco(polygon): + """Convert a geometry to COCO polygon format.""" + if isinstance(polygon, Polygon): + coords = polygon.exterior.coords.xy + elif isinstance(polygon, str): # assume it's WKT + coords = loads(polygon).exterior.coords.xy + elif isinstance(polygon, MultiPolygon): + raise ValueError("You have MultiPolygon types in your label df. Remove, explode, or fix these to be Polygon geometry types.") + else: + raise ValueError('polygon must be a shapely geometry or WKT.') + # zip together x,y pairs + coords = list(zip(coords[0], coords[1])) + coords = [item for coordinate in coords for item in coordinate] + + return coords + + +def split_geom(geometry, tile_size, resolution=None, + use_projection_units=False, src_img=None): + """Splits a vector into approximately equal sized tiles. + + Adapted from @lossyrob's Gist__ + + .. Gist: https://gist.github.com/lossyrob/7b620e6d2193cb55fbd0bffacf27f7f2 + + The more complex the geometry, the slower this will run, but geometrys with + around 10000 coordinates run in a few seconds time. You can simplify + geometries with shapely.geometry.Polygon.simplify if necessary. + + Arguments + --------- + geometry : str, optional + A shapely.geometry.Polygon, path to a single feature geojson, + or list-like bounding box shaped like [left, bottom, right, top]. + The geometry must be in the projection coordinates corresponding to + the resolution units. + tile_size : `tuple` of `int`s + The size of the input tiles in ``(y, x)`` coordinates. By default, + this is in pixel units; this can be changed to metric units using the + `use_metric_size` argument. + use_projection_units : bool, optional + Is `tile_size` in pixel units (default) or distance units? To set to distance units + use ``use_projection_units=True``. If False, resolution must be supplied. + resolution: `tuple` of `float`s, optional + (x resolution, y resolution). Used by default if use_metric_size is False. + Can be acquired from rasterio dataset object's metadata. + src_img: `str` or `raster`, optional + A rasterio raster object or path to a geotiff. The bounds of this raster and the geometry will be + intersected and the result of the intersection will be tiled. Useful in cases where the extent of + collected labels and source imagery partially overlap. The src_img must have the same projection units + as the geometry. + + Returns + ------- + tile_bounds : list (containing sublists like [left, bottom, right, top]) + + """ + if isinstance(geometry, str): + gj = json.loads(open(geometry).read()) + + features = gj['features'] + if not len(features) == 1: + print('Feature collection must only contain one feature') + sys.exit(1) + + geometry = shape(features[0]['geometry']) + + elif isinstance(geometry, list) or isinstance(geometry, np.ndarray): + assert len(geometry) == 4 + geometry = box(*geometry) + + if use_projection_units is False: + if resolution is None: + print("Resolution must be specified if use_projection_units is" + " False. Access it from src raster meta.") + return + # convert pixel units to CRS units to use during image tiling. + # NOTE: This will be imperfect for large AOIs where there isn't + # a constant relationship between the src CRS units and src pixel + # units. + if isinstance(resolution, (float, int)): + resolution = (resolution, resolution) + tmp_tile_size = [tile_size[0]*resolution[0], + tile_size[1]*resolution[1]] + else: + tmp_tile_size = tile_size + + if src_img is not None: + src_img = _check_rasterio_im_load(src_img) + geometry = geometry.intersection(box(*src_img.bounds)) + bounds = geometry.bounds + else: + bounds = geometry.bounds + + xmin = bounds[0] + xmax = bounds[2] + ymin = bounds[1] + ymax = bounds[3] + x_extent = xmax - xmin + y_extent = ymax - ymin + x_steps = np.ceil(x_extent/tmp_tile_size[1]) + y_steps = np.ceil(y_extent/tmp_tile_size[0]) + x_mins = np.arange(xmin, xmin + tmp_tile_size[1]*x_steps, + tmp_tile_size[1]) + y_mins = np.arange(ymin, ymin + tmp_tile_size[0]*y_steps, + tmp_tile_size[0]) + tile_bounds = [ + (i, j, i+tmp_tile_size[1], j+tmp_tile_size[0]) + for i in x_mins for j in y_mins if not geometry.intersection( + box(*(i, j, i+tmp_tile_size[1], j+tmp_tile_size[0]))).is_empty + ] + return tile_bounds diff --git a/yoltv5/post_process.py b/yoltv5/post_process.py index c678ee9..5530cbf 100755 --- a/yoltv5/post_process.py +++ b/yoltv5/post_process.py @@ -24,7 +24,7 @@ import os # import yoltv5 funcs -import utils +import utils_2 from prep_train import convert_poly_coords # from scorer import score_one @@ -1389,7 +1389,7 @@ def execute(pred_dir='/root/yoltv5/results/', prob = float(data_frac[5]) # get pixel coords of yolo coords yolt_box = data_frac[1:5] - pix_coords_float = utils.convert_reverse((im_w, im_h), yolt_box) + pix_coords_float = utils_2.convert_reverse((im_w, im_h), yolt_box) [x0, x1, y0, y1] = pix_coords_float # # convert to int? # [x0, x1, y0, y1] = [int(round(b, 2)) for b in pix_coords_float] diff --git a/yoltv5/prep_train.py b/yoltv5/prep_train.py index 86a0ca0..0aef71a 100755 --- a/yoltv5/prep_train.py +++ b/yoltv5/prep_train.py @@ -7,6 +7,7 @@ import os import sys + import math import shutil import rasterio @@ -41,9 +42,20 @@ import shutil from shapely.geometry import MultiLineString, MultiPolygon, mapping, box, shape +from osgeo import gdal +from osgeo import ogr +from osgeo import osr + +import argparse +from tqdm import tqdm + +from osgeo import ogr +from utils_2 import convert_poly_coords, create_mask, convert, map_wrapper +from tile_utils import slice_im_plus_boxes + # yolt funcs import tile_ims_labels -import utils +import utils_2 ############################################################################### ############################################################################### @@ -84,81 +96,6 @@ def get_geo_transform(raster_src): return affine_obj - -# https://github.com/CosmiQ/solaris/blob/master/solaris/vector/polygon.py -############################################################################### -def convert_poly_coords(geom, raster_src=None, affine_obj=None, inverse=False, - precision=None): - """Georegister geometry objects currently in pixel coords or vice versa. - Arguments - --------- - geom : :class:`shapely.geometry.shape` or str - A :class:`shapely.geometry.shape`, or WKT string-formatted geometry - object currently in pixel coordinates. - raster_src : str, optional - Path to a raster image with georeferencing data to apply to `geom`. - Alternatively, an opened :class:`rasterio.Band` object or - :class:`osgeo.gdal.Dataset` object can be provided. Required if not - using `affine_obj`. - affine_obj: list or :class:`affine.Affine` - An affine transformation to apply to `geom` in the form of an - ``[a, b, d, e, xoff, yoff]`` list or an :class:`affine.Affine` object. - Required if not using `raster_src`. - inverse : bool, optional - If true, will perform the inverse affine transformation, going from - geospatial coordinates to pixel coordinates. - precision : int, optional - Decimal precision for the polygon output. If not provided, rounding - is skipped. - Returns - ------- - out_geom - A geometry in the same format as the input with its coordinate system - transformed to match the destination object. - """ - - if not raster_src and not affine_obj: - raise ValueError("Either raster_src or affine_obj must be provided.") - - if raster_src is not None: - affine_xform = get_geo_transform(raster_src) - else: - if isinstance(affine_obj, Affine): - affine_xform = affine_obj - else: - # assume it's a list in either gdal or "standard" order - # (list_to_affine checks which it is) - if len(affine_obj) == 9: # if it's straight from rasterio - affine_obj = affine_obj[0:6] - affine_xform = list_to_affine(affine_obj) - - if inverse: # geo->px transform - affine_xform = ~affine_xform - - if isinstance(geom, str): - # get the polygon out of the wkt string - g = shapely.wkt.loads(geom) - elif isinstance(geom, shapely.geometry.base.BaseGeometry): - g = geom - else: - raise TypeError('The provided geometry is not an accepted format. ' - 'This function can only accept WKT strings and ' - 'shapely geometries.') - - xformed_g = shapely.affinity.affine_transform(g, [affine_xform.a, - affine_xform.b, - affine_xform.d, - affine_xform.e, - affine_xform.xoff, - affine_xform.yoff]) - if isinstance(geom, str): - # restore to wkt string format - xformed_g = shapely.wkt.dumps(xformed_g) - if precision is not None: - xformed_g = _reduce_geom_precision(xformed_g, precision=precision) - - return xformed_g - ############################################################################### #http://stackoverflow.com/questions/34372480/rotate-point-about-another-point-in-degrees-python @@ -196,39 +133,22 @@ def create_mask(im_path, label_path, out_path_mask, burnValue=255): ############################################################################### -def prep_one(pan_path, mul_path, label_path, ps_rgb_path, +def prep_one(label_path, img_path, subdir, suff, out_dir_image, out_dir_label, out_dir_mask, out_path_image, out_path_label, out_path_mask, sliceHeight=416, sliceWidth=416, mask_burnValue=255, cls_id=0, verbose=True): + + classes = [] - ################## - # Pan-sharpen - ################## - - # https://gdal.org/programs/gdal_pansharpen.html - # http://blog.cleverelephant.ca/2015/02/geotiff-compression-for-dummies.html - if 2 > 1: #not os.path.exists(ps_rgb_path): - if suff == 'yuge': - cmd = 'gdal_pansharpen.py ' + pan_path + ' ' \ - + mul_path + ' ' + ps_rgb_path + ' ' \ - + '-b 5 -b 3 -b 2 ' + '-spat_adjust none' \ - + ' -co COMPRESS=JPEG -co JPEG_QUALITY=40 -co PHOTOMETRIC=YCBCR -co TILED=YES' - else: - cmd = 'gdal_pansharpen.py ' + pan_path + ' ' \ - + mul_path + ' ' + ps_rgb_path + ' ' \ - + '-b 5 -b 3 -b 2 ' + '-spat_adjust none' \ - + ' -co COMPRESS=LZW' - print("Pan-sharpening cmd:", cmd) - os.system(cmd) # ################## # # Image # ################## - im_tmp = skimage.io.imread(ps_rgb_path) + im_tmp = skimage.io.imread(img_path) h, w = im_tmp.shape[:2] aspect_ratio = 1.0 * h / w dx = np.abs(h - w) @@ -240,21 +160,25 @@ def prep_one(pan_path, mul_path, label_path, ps_rgb_path, if label_path: with fiona.open(label_path, "r") as annotation_collection: - annotations = [feature["geometry"] for feature in annotation_collection] + polygons = [feature["geometry"] for feature in annotation_collection] + properties = [feature["properties"] for feature in annotation_collection] + + # get pixel coords of bounding boxes boxes, dhs = [], [] - for a in annotations: - geom = shapely.geometry.Polygon(a['coordinates'][0]) - pixel_geom = convert_poly_coords(geom, raster_src=ps_rgb_path, + for poly in polygons: + geom = shapely.geometry.Polygon(poly['coordinates'][0]) + pixel_geom = convert_poly_coords(geom, raster_src=img_path, affine_obj=None, inverse=True, precision=2) # Get bounding box. object.bounds: Returns a (minx, miny, maxx, maxy) tuple. minx, miny, maxx, maxy = pixel_geom.bounds boxes.append([minx, miny, maxx, maxy]) dhs.append([maxy-miny]) - - # set classes - classes = len(boxes) * [cls_id] + #get classes + for property in properties: + cls_id = int(property['role_id'])-1 + classes.append(cls_id) else: classes, boxes = [], [] @@ -264,7 +188,7 @@ def prep_one(pan_path, mul_path, label_path, ps_rgb_path, # create masks if out_path_mask and (not os.path.exists(out_path_mask)): - create_mask(ps_rgb_path, label_path, out_path_mask, + create_mask(img_path, label_path, out_path_mask, burnValue=mask_burnValue) # tile data, if needed @@ -275,7 +199,7 @@ def prep_one(pan_path, mul_path, label_path, ps_rgb_path, # for training, skip highly overlapped edge tiles skip_highly_overlapped_tiles=True tile_ims_labels.slice_im_plus_boxes( - ps_rgb_path, out_name, out_dir_image, + img_path, out_name, out_dir_image, boxes=boxes, yolo_classes=classes, out_dir_labels=out_dir_label, mask_path=out_path_mask, out_dir_masks=out_dir_mask, sliceHeight=sliceHeight, sliceWidth=sliceWidth, @@ -289,12 +213,12 @@ def prep_one(pan_path, mul_path, label_path, ps_rgb_path, # simply copy to dest folder if object is yuge if suff == '_yuge': - shutil.copyfile(ps_rgb_path, out_path_image) + shutil.copyfile(img_path, out_path_image) hfinal, wfinal = h, w # simply copy to dest folder if aspect ratio is reasonable elif (0.9 < aspect_ratio < 1.1): - shutil.copyfile(ps_rgb_path, out_path_image) + shutil.copyfile(img_path, out_path_image) hfinal, wfinal = h, w # else let's add a border on right or bottom, @@ -340,7 +264,7 @@ def prep_one(pan_path, mul_path, label_path, ps_rgb_path, # create yolo style labels for class_tmp,box_tmp in zip(classes, boxes): minx, miny, maxx, maxy = box_tmp - bb = utils.convert((wfinal, hfinal), [minx, maxx, miny, maxy]) + bb = utils_2.convert((wfinal, hfinal), [minx, maxx, miny, maxy]) # (xb,yb,wb,hb) = bb if (np.min(bb) < 0) or (np.max(bb) > 1): print(" yolo coords:", bb) @@ -682,7 +606,7 @@ def plot_training_bboxes(label_folder, image_folder, ignore_augment=True, cat_int = int(yolt_box[0]) color = colors[cat_int] yb = yolt_box[1:] - box0 = utils.convert_reverse(shape, yb) + box0 = utils_2.convert_reverse(shape, yb) # convert to int box1 = [int(round(b, 2)) for b in box0] [xmin, xmax, ymin, ymax] = box1 @@ -731,9 +655,9 @@ def plot_training_bboxes(label_folder, image_folder, ignore_augment=True, 0.75*ydiff)), (0, 0, 0), label_font_width) # title - # title = figname.split('/')[-1].split('_')[0] + ': Plot Threshold = ' + str(plot_thresh) # + ': thresh=' + str(plot_thresh) - #title_pos = (border[0], int(border[0]*0.66)) - # cv2.putText(img_mpl, title, title_pos, font, 1.7*font_size, (0,0,0), label_font_width, cv2.CV_AA)#, cv2.LINE_AA) + title = str(cat_int) + title_pos = (border[0], int(border[0]*0.66)) + cv2.putText(img_mpl, title, title_pos, font, 1.7*font_size, (0,0,0), label_font_width, cv2.CV_AA)#, cv2.LINE_AA) # cv2.putText(img_mpl, title, title_pos, font, 1.7*font_size, (0,0,0), label_font_width, cv2.CV_AA)#cv2.LINE_AA) if show_plot: @@ -1114,7 +1038,7 @@ def yolt_from_df(im_path, df_polys, yolt_coords = [] for row in obj_list: [index_nest, cat_nest, x0, y0, x1, y1] = row - yolt_row = [cat_nest] + list(utils.convert((w,h), [x0,x1,y0,y1])) + yolt_row = [cat_nest] + list(utils_2.convert((w,h), [x0,x1,y0,y1])) # cat_idx = cat_idx_dic[cat_nest] # yolt_row = [cat_idx, cat_nest] + list(convert.convert((w,h), [x0,x1,y0,y1])) yolt_coords.append(yolt_row) @@ -1212,7 +1136,7 @@ def yolt_from_df(im_path, df_polys, yolt_coords = [] for row in obj_list: [index_nest, cat_nest, x0, y0, x1, y1] = row - yolt_row = [cat_nest] + list(utils.convert((w,h), [x0,x1,y0,y1])) + yolt_row = [cat_nest] + list(utils_2.convert((w,h), [x0,x1,y0,y1])) # cat_idx = cat_idx_dic[cat_nest] # yolt_row = [cat_idx, cat_nest] + list(convert.convert((w,h), [x0,x1,y0,y1])) yolt_coords.append(yolt_row) @@ -1487,7 +1411,7 @@ def yolt_from_visdrone(im_path, label_path, yolt_coords = [] for row in obj_list: [index_nest, cat_nest, x0, y0, x1, y1] = row - yolt_row = [cat_nest] + list(utils.convert((w,h), [x0,x1,y0,y1])) + yolt_row = [cat_nest] + list(utils_2.convert((w,h), [x0,x1,y0,y1])) # cat_idx = cat_idx_dic[cat_nest] # yolt_row = [cat_idx, cat_nest] + list(convert.convert((w,h), [x0,x1,y0,y1])) yolt_coords.append(yolt_row) @@ -1666,7 +1590,7 @@ def yolt_from_df_v0(im_path, df_polys, yolt_coords = [] for row in obj_list: [index_nest, cat_nest, x0, y0, x1, y1] = row - yolt_row = [cat_nest] + list(utils.convert((w,h), [x0,x1,y0,y1])) + yolt_row = [cat_nest] + list(utils_2.convert((w,h), [x0,x1,y0,y1])) # cat_idx = cat_idx_dic[cat_nest] # yolt_row = [cat_idx, cat_nest] + list(convert.utils.convert((w,h), [x0,x1,y0,y1])) yolt_coords.append(yolt_row) @@ -1833,11 +1757,11 @@ def main(): n_threads = 8 # data directory - data_dir = '/data/' - data_dir_train = os.path.join(data_dir, 'train') + data_dir = 'data/' + data_dir_train = os.path.join(data_dir, 'train/RarePlanes_train_PS-RGB_tiled/PS-RGB_tiled/') # output dirs - out_dir_root = '/wdata' + out_dir_root = 'wdata/' # out_dir_root = os.path.join(data_dir, 'data_yolov5_2') # make dirs for d in [out_dir_root]: @@ -1847,6 +1771,8 @@ def main(): subdirs = sorted(os.listdir(data_dir_train)) shape_list = [] input_args = [] + list_of_files = [] + for i,subdir in enumerate(subdirs): # if i > 200: # break @@ -1857,22 +1783,38 @@ def main(): ################## # Data Locs ################## + file_base = subdir.rsplit('.', -1)[0] + file_ext = subdir.rsplit('.', -1)[1] + subdir = subdir.rsplit('.', -1)[0] - dir_tot = os.path.join(data_dir_train, subdir) - mul_path = os.path.join(dir_tot, subdir + '_MUL.tif') - pan_path = os.path.join(dir_tot, subdir + '_PAN.tif') - label_path = os.path.join(dir_tot, subdir + '_anno.geojson') - # set pan-sharpen folder - out_dir_tiff = os.path.join(out_dir_root, 'PS-RGB_train') + + #Check for duplicates + + if file_base in list_of_files: + continue + else: + list_of_files.append(file_base) + + print(file_base) + print(file_ext) + + if file_ext == 'xml': + continue + + label_path = os.path.join(data_dir_train + file_base + '.geojson') + img_path = os.path.join(data_dir_train+file_base + '.png') + + print(label_path) + print(img_path) + + out_dir_tiff = os.path.join(out_dir_root, 'train') os.makedirs(out_dir_tiff, exist_ok=True) - ps_rgb_path = os.path.join(out_dir_tiff, subdir + '_PS-RGB.tif') - - + ################## # Image ################## - im_tmp = skimage.io.imread(pan_path) # (assume pan is the same size as ps-rgb will be!) + im_tmp = skimage.io.imread(img_path) # (assume pan is the same size as ps-rgb will be!) # im_tmp = skimage.io.imread(ps_rgb_path) h, w = im_tmp.shape[:2] shape_list.append([subdir, h, w]) @@ -1912,15 +1854,6 @@ def main(): # or (h * w > 800 * 800): # original version (no tiling) suff = '_yuge' - # # also can skip if the labels are huge - # elif np.max(dhs) > sliceHeight: - # suff = '_yuge' - - # look for large images with multiple annotatios - elif ((h >= 500) and (w >= 500)) and \ - (len(annotations) > 1): - suff = '_tile' - else: suff = '' @@ -1933,12 +1866,12 @@ def main(): os.makedirs(d, exist_ok=True) # output files # ps_rgb_path = os.path.join(out_dir_tiff, subdir + '_PS-RGB.tif') - out_path_image = os.path.join(out_dir_image, subdir + '_PS-RGB.png') - out_path_label = os.path.join(out_dir_label, subdir + '_PS-RGB.txt') - out_path_mask = os.path.join(out_dir_mask, subdir + '_PS-RGB.png') + out_path_image = os.path.join(out_dir_image, subdir + '.png') + out_path_label = os.path.join(out_dir_label, subdir + '.txt') + out_path_mask = os.path.join(out_dir_mask, subdir + '.png') input_args.append([prep_one, - pan_path, mul_path, label_path, ps_rgb_path, + label_path, img_path, subdir, suff, out_dir_image, out_dir_label, out_dir_mask, out_path_image, out_path_label, out_path_mask, @@ -1953,7 +1886,7 @@ def main(): print("len input_args", len(input_args)) print("Execute...\n") with multiprocessing.Pool(n_threads) as pool: - pool.map(utils.map_wrapper, input_args) + pool.map(utils_2.map_wrapper, input_args) ################## @@ -1972,27 +1905,27 @@ def main(): im_list_train = [] for f in sorted([z for z in os.listdir(dtmp) if z.endswith('.png')]): im_list_train.append(os.path.join(dtmp, f)) - # tile train images - dtmp = os.path.join(out_dir_root, 'train', 'images' + '_tile') - im_list_train_tile = [] - for f in sorted([z for z in os.listdir(dtmp) if z.endswith('.png')]): - im_list_train_tile.append(os.path.join(dtmp, f)) + # # tile train images + # dtmp = os.path.join(out_dir_root, 'train', 'images' + '_til') + # im_list_train_tile = [] + # for f in sorted([z for z in os.listdir(dtmp) if z.endswith('.png')]): + # im_list_train_tile.append(os.path.join(dtmp, f)) # normal valid images dtmp = os.path.join(out_dir_root, 'valid', 'images' + '') im_list_valid = [] for f in sorted([z for z in os.listdir(dtmp) if z.endswith('.png')]): im_list_valid.append(os.path.join(dtmp, f)) - # tile valid images - dtmp = os.path.join(out_dir_root, 'valid', 'images' + '_tile') - im_list_valid_tile = [] - for f in sorted([z for z in os.listdir(dtmp) if z.endswith('.png')]): - im_list_valid_tile.append(os.path.join(dtmp, f)) - # yuge valid images - dtmp = os.path.join(out_dir_root, 'valid', 'images' + '_yuge') - im_list_valid_yuge = [] - for f in sorted([z for z in os.listdir(dtmp) if z.endswith('.png')]): - im_list_valid_yuge.append(os.path.join(dtmp, f)) + # # tile valid images + # dtmp = os.path.join(out_dir_root, 'valid', 'images' + '_tile') + # im_list_valid_tile = [] + # for f in sorted([z for z in os.listdir(dtmp) if z.endswith('.png')]): + # im_list_valid_tile.append(os.path.join(dtmp, f)) + # # yuge valid images + # dtmp = os.path.join(out_dir_root, 'valid', 'images' + '_yuge') + # im_list_valid_yuge = [] + # for f in sorted([z for z in os.listdir(dtmp) if z.endswith('.png')]): + # im_list_valid_yuge.append(os.path.join(dtmp, f)) # combine in different csvs # training @@ -2000,27 +1933,27 @@ def main(): list_tmp = im_list_train df_tmp = pd.DataFrame({'image': list_tmp}) df_tmp.to_csv(outpath_tmp, header=False, index=False) - # training + tile - outpath_tmp = os.path.join(out_dir_root, 'train+tile.txt') - list_tmp = im_list_train + im_list_train_tile - df_tmp = pd.DataFrame({'image': list_tmp}) - df_tmp.to_csv(outpath_tmp, header=False, index=False) + # # training + tile + # outpath_tmp = os.path.join(out_dir_root, 'train+tile.txt') + # list_tmp = im_list_train + im_list_train_tile + # df_tmp = pd.DataFrame({'image': list_tmp}) + # df_tmp.to_csv(outpath_tmp, header=False, index=False) # valid outpath_tmp = os.path.join(out_dir_root, 'valid.txt') list_tmp = im_list_valid df_tmp = pd.DataFrame({'image': list_tmp}) df_tmp.to_csv(outpath_tmp, header=False, index=False) - # valid + tile - outpath_tmp = os.path.join(out_dir_root, 'valid+tile.txt') - list_tmp = im_list_valid + im_list_valid_tile - df_tmp = pd.DataFrame({'image': list_tmp}) - df_tmp.to_csv(outpath_tmp, header=False, index=False) - # valid + tile + yuge - outpath_tmp = os.path.join(out_dir_root, 'valid+tile+yuge.txt') - list_tmp = im_list_valid + im_list_valid_tile + im_list_valid_yuge - df_tmp = pd.DataFrame({'image': list_tmp}) - df_tmp.to_csv(outpath_tmp, header=False, index=False) + # # valid + tile + # outpath_tmp = os.path.join(out_dir_root, 'valid+tile.txt') + # list_tmp = im_list_valid + im_list_valid_tile + # df_tmp = pd.DataFrame({'image': list_tmp}) + # df_tmp.to_csv(outpath_tmp, header=False, index=False) + # # valid + tile + yuge + # outpath_tmp = os.path.join(out_dir_root, 'valid+tile+yuge.txt') + # list_tmp = im_list_valid + im_list_valid_tile + im_list_valid_yuge + # df_tmp = pd.DataFrame({'image': list_tmp}) + # df_tmp.to_csv(outpath_tmp, header=False, index=False) # plot yolo data, to check labels, also copy .txt files to image folder print("Plot training bboxes") @@ -2028,10 +1961,10 @@ def main(): shuffle = False for im_dir_tmp in [ os.path.join(out_dir_root, 'train', 'images' + ''), - os.path.join(out_dir_root, 'train', 'images' + '_tile'), + # os.path.join(out_dir_root, 'train', 'images' + '_tile'), os.path.join(out_dir_root, 'valid', 'images' + ''), - os.path.join(out_dir_root, 'valid', 'images' + '_tile'), - os.path.join(out_dir_root, 'valid', 'images' + '_yuge') + # os.path.join(out_dir_root, 'valid', 'images' + '_tile'), + # os.path.join(out_dir_root, 'valid', 'images' + '_yuge') ]: label_dir_tmp = im_dir_tmp.replace('images', 'labels') suff = im_dir_tmp.split('images')[-1] diff --git a/yoltv5/tile_utils.py b/yoltv5/tile_utils.py new file mode 100644 index 0000000..8f5e637 --- /dev/null +++ b/yoltv5/tile_utils.py @@ -0,0 +1,180 @@ +import os +import time +import skimage +from utils_2 import convert +import os + +def slice_im_plus_boxes(image_path, out_name, out_dir_images, + boxes=[], yolo_classes=[], out_dir_labels=None, + mask_path=None, out_dir_masks=None, + sliceHeight=416, sliceWidth=416, + overlap=0.1, slice_sep='|', pad=0, + skip_highly_overlapped_tiles=False, + overwrite=False, + out_ext='.png', verbose=False): + + """ + Slice a large image into smaller windows, and also bin boxes + Adapted from: + https://github.com/avanetten/simrdwn/blob/master/simrdwn/core/slice_im.py + + Arguments + --------- + image_path : str + Location of image to slice + out_name : str + Root name of output files (coordinates will be appended to this) + out_dir_images : str + Output directory for images + boxes : arr + List of bounding boxes in image, in pixel coords + [ [xb0, yb0, xb1, yb1], ...] + Defaults to [] + yolo_classes : list + list of class of objects for each box [0, 1, 0, ...] + Defaults to [] + out_dir_labels : str + Output directory for labels + Defaults to None + sliceHeight : int + Height of each slice. Defaults to ``416``. + sliceWidth : int + Width of each slice. Defaults to ``416``. + overlap : float + Fractional overlap of each window (e.g. an overlap of 0.2 for a window + of size 256 yields an overlap of 51 pixels). + Default to ``0.1``. + slice_sep : str + Character used to separate outname from coordinates in the saved + windows. Defaults to ``|`` + out_ext : str + Extension of saved images. Defaults to ``.png``. + verbose : boolean + Switch to print relevant values to screen. Defaults to ``False`` + + Returns + ------- + None + """ + + if len(out_ext) == 0: + im_ext = '.' + image_path.split('.')[-1] + else: + im_ext = out_ext + + t0 = time.time() + image = skimage.io.imread(image_path) #, as_grey=False).astype(np.uint8) # [::-1] + print("image.shape:", image.shape) + if mask_path: + mask = skimage.io.imread(mask_path) + win_h, win_w = image.shape[:2] + win_size = sliceHeight*sliceWidth + dx = int((1. - overlap) * sliceWidth) + dy = int((1. - overlap) * sliceHeight) + + n_ims = 0 + for y0 in range(0, image.shape[0], dy): + for x0 in range(0, image.shape[1], dx): + out_boxes_yolo = [] + out_classes_yolo = [] + n_ims += 1 + + if (n_ims % 100) == 0: + print(n_ims) + + # make sure we don't have a tiny image on the edge + if y0+sliceHeight > image.shape[0]: + # skip if too much overlap (> 0.6) + if skip_highly_overlapped_tiles: + if (y0+sliceHeight - image.shape[0]) > (0.6*sliceHeight): + continue + else: + y = image.shape[0] - sliceHeight + else: + y = image.shape[0] - sliceHeight + else: + y = y0 + if x0+sliceWidth > image.shape[1]: + # skip if too much overlap (> 0.6) + if skip_highly_overlapped_tiles: + if (x0+sliceWidth - image.shape[1]) > (0.6*sliceWidth): + continue + else: + x = image.shape[1] - sliceWidth + else: + x = image.shape[1] - sliceWidth + else: + x = x0 + + xmin, xmax, ymin, ymax = x, x+sliceWidth, y, y+sliceHeight + + # find boxes that lie entirely within the window + if len(boxes) > 0: + out_path_label = os.path.join( + out_dir_labels, + out_name + slice_sep + str(y) + '_' + str(x) + '_' + + str(sliceHeight) + '_' + str(sliceWidth) + + '_' + str(pad) + '_' + str(win_w) + '_' + str(win_h) + + '.txt') + for j,b in enumerate(boxes): + yolo_class = yolo_classes[j] + xb0, yb0, xb1, yb1 = b + if (xb0 >= xmin) and (yb0 >= ymin) \ + and (xb1 <= xmax) and (yb1 <= ymax): + # get box coordinates within window + out_box_tmp = [xb0 - xmin, xb1 - xmin, + yb0 - ymin, yb1 - ymin] + print(" out_box_tmp:", out_box_tmp) + # out_boxes.append(out_box_tmp) + # convert to yolo coords (x,y,w,h) + yolo_coords = convert((sliceWidth, sliceHeight), + out_box_tmp) + print(" yolo_coords:", yolo_coords) + out_boxes_yolo.append(yolo_coords) + out_classes_yolo.append(yolo_class) + + # skip if no labels? + if len(out_boxes_yolo) == 0: + continue + + # save yolo labels + txt_outfile = open(out_path_label, "w") + for yolo_class, yolo_coord in zip(out_classes_yolo, out_boxes_yolo): + outstring = str(yolo_class) + " " + " ".join([str(a) for a in yolo_coord]) + '\n' + if verbose: + print(" outstring:", outstring.strip()) + txt_outfile.write(outstring) + txt_outfile.close() + + # save mask, if desired + if mask_path: + mask_c = mask[y:y + sliceHeight, x:x + sliceWidth] + outpath_mask = os.path.join( + out_dir_masks, + out_name + slice_sep + str(y) + '_' + str(x) + '_' + + str(sliceHeight) + '_' + str(sliceWidth) + + '_' + str(pad) + '_' + str(win_w) + '_' + str(win_h) + + im_ext) + skimage.io.imsave(outpath_mask, mask_c, check_contrast=False) + + # extract image + window_c = image[y:y + sliceHeight, x:x + sliceWidth] + outpath = os.path.join( + out_dir_images, + out_name + slice_sep + str(y) + '_' + str(x) + '_' + + str(sliceHeight) + '_' + str(sliceWidth) + + '_' + str(pad) + '_' + str(win_w) + '_' + str(win_h) + + im_ext) + if not os.path.exists(outpath): + skimage.io.imsave(outpath, window_c, check_contrast=False) + elif overwrite: + skimage.io.imsave(outpath, window_c, check_contrast=False) + else: + print("outpath {} exists, skipping".format(outpath)) + + print("Num slices:", n_ims, + "sliceHeight", sliceHeight, "sliceWidth", sliceWidth) + print("Time to slice", image_path, time.time()-t0, "seconds") + + return + diff --git a/yoltv5/utils_2.py b/yoltv5/utils_2.py new file mode 100644 index 0000000..7c2f7a6 --- /dev/null +++ b/yoltv5/utils_2.py @@ -0,0 +1,2116 @@ +import math +import multiprocessing +import os +import random +import time +import shutil +import sys +from subprocess import PIPE, STDOUT, Popen + + +from osgeo import gdal +from osgeo import ogr +from osgeo import osr + +import cv2 +import fiona +import geopandas as gpd +import matplotlib +import matplotlib.pyplot as plt +import numpy as np +import pandas as pd +import rasterio +import rasterio.mask +# import solaris.vector +import shapely +import skimage +import skimage.io +import skimage.transform +from affine import Affine +from matplotlib.collections import PolyCollection +from rasterio.crs import CRS +from rasterio.warp import transform_bounds +from rasterio.windows import Window +from rtree.core import RTreeError +# from ..utils.geo import list_to_affine, _reduce_geom_precision +# from ..utils.core import _check_gdf_load, _check_crs, _check_rasterio_im_load +#from ..raster.image import get_geo_transform +from shapely.geometry import (MultiLineString, MultiPolygon, Polygon, box, + mapping, shape) +from shapely.wkt import loads +from statsmodels.stats.weightstats import DescrStatsW + +from geo import affine_to_list, list_to_affine + +############################################################################### +############################################################################### + + +# https://github.com/CosmiQ/solaris/blob/master/solaris/utils/geo.py +############################################################################### +def _reduce_geom_precision(geom, precision=2): + geojson = mapping(geom) + geojson['coordinates'] = np.round(np.array(geojson['coordinates']), + precision) + return shape(geojson) + + +# https://github.com/CosmiQ/solaris/blob/master/solaris/raster/image.py +############################################################################### +def get_geo_transform(raster_src): + """Get the geotransform for a raster image source. + Arguments + --------- + raster_src : str, :class:`rasterio.DatasetReader`, or `osgeo.gdal.Dataset` + Path to a raster image with georeferencing data to apply to `geom`. + Alternatively, an opened :class:`rasterio.Band` object or + :class:`osgeo.gdal.Dataset` object can be provided. Required if not + using `affine_obj`. + Returns + ------- + transform : :class:`affine.Affine` + An affine transformation object to the image's location in its CRS. + """ + + if isinstance(raster_src, str): + affine_obj = rasterio.open(raster_src).transform + elif isinstance(raster_src, rasterio.DatasetReader): + affine_obj = raster_src.transform + elif isinstance(raster_src, gdal.Dataset): + affine_obj = Affine.from_gdal(*raster_src.GetGeoTransform()) + + return affine_obj + + +# https://github.com/CosmiQ/solaris/blob/master/solaris/vector/polygon.py +############################################################################### + +def convert_poly_coords(geom, raster_src=None, affine_obj=None, inverse=False, + precision=None): + """Georegister geometry objects currently in pixel coords or vice versa. + Arguments + --------- + geom : :class:`shapely.geometry.shape` or str + A :class:`shapely.geometry.shape`, or WKT string-formatted geometry + object currently in pixel coordinates. + raster_src : str, optional + Path to a raster image with georeferencing data to apply to `geom`. + Alternatively, an opened :class:`rasterio.Band` object or + :class:`osgeo.gdal.Dataset` object can be provided. Required if not + using `affine_obj`. + affine_obj: list or :class:`affine.Affine` + An affine transformation to apply to `geom` in the form of an + ``[a, b, d, e, xoff, yoff]`` list or an :class:`affine.Affine` object. + Required if not using `raster_src`. + inverse : bool, optional + If true, will perform the inverse affine transformation, going from + geospatial coordinates to pixel coordinates. + precision : int, optional + Decimal precision for the polygon output. If not provided, rounding + is skipped. + Returns + ------- + out_geom + A geometry in the same format as the input with its coordinate system + transformed to match the destination object. + """ + + if not raster_src and not affine_obj: + raise ValueError("Either raster_src or affine_obj must be provided.") + + if raster_src is not None: + affine_xform = get_geo_transform(raster_src) + else: + if isinstance(affine_obj, Affine): + affine_xform = affine_obj + else: + # assume it's a list in either gdal or "standard" order + # (list_to_affine checks which it is) + if len(affine_obj) == 9: # if it's straight from rasterio + affine_obj = affine_obj[0:6] + affine_xform = list_to_affine(affine_obj) + + if inverse: # geo->px transform + affine_xform = ~affine_xform + + if isinstance(geom, str): + # get the polygon out of the wkt string + g = shapely.wkt.loads(geom) + elif isinstance(geom, shapely.geometry.base.BaseGeometry): + g = geom + else: + raise TypeError('The provided geometry is not an accepted format. ' + 'This function can only accept WKT strings and ' + 'shapely geometries.') + + xformed_g = shapely.affinity.affine_transform(g, [affine_xform.a, + affine_xform.b, + affine_xform.d, + affine_xform.e, + affine_xform.xoff, + affine_xform.yoff]) + if isinstance(geom, str): + # restore to wkt string format + xformed_g = shapely.wkt.dumps(xformed_g) + if precision is not None: + xformed_g = _reduce_geom_precision(xformed_g, precision=precision) + + return xformed_g + +############################################################################### +#http://stackoverflow.com/questions/34372480/rotate-point-about-another-point-in-degrees-python +def rotate(origin, point, angle): + """ + Rotate a point counterclockwise by a given angle around a given origin. + + The angle should be given in radians. + """ + ox, oy = origin + px, py = point + + qx = ox + math.cos(angle) * (px - ox) - math.sin(angle) * (py - oy) + qy = oy + math.sin(angle) * (px - ox) + math.cos(angle) * (py - oy) + return qx, qy + + +############################################################################### +def create_mask(im_path, label_path, out_path_mask, burnValue=255): + with fiona.open(label_path, "r") as annotation_collection: + annotations = [feature["geometry"] for feature in annotation_collection] + with rasterio.open(im_path) as src: + out_image, out_transform = rasterio.mask.mask(src, annotations, + all_touched=False, invert=False, crop=False) + out_meta = src.meta + # clip + out_image = burnValue * np.clip(out_image, 0, 1) + htmp, wtmp = out_image.shape[1], out_image.shape[2] + out_meta.update({"driver": "GTiff", + "height": htmp, + "width": wtmp, + "transform": out_transform}) + with rasterio.open(out_path_mask, "w", **out_meta) as dest: + dest.write(out_image) + + +############################################################################### +def win_jitter(window_size, jitter_frac=0.1): + '''get x and y jitter''' + val = np.rint(jitter_frac * window_size) + dx = np.random.randint(-val, val) + dy = np.random.randint(-val, val) + + return dx, dy + + +############################################################################### +def get_window_geoms(df, window_size=416, jitter_frac=0.2, image_w=0, image_h=0, + geometry_col='geometry_poly_pixel', category_col='Category', + aug_count_dict=None, + verbose=False): + '''Iterate through dataframe and get square window cutouts centered on each + object, modulu some jitter, + set category_col to None if none exists + aug_count_dict is a dictionary detailing the number of augmentations to make, + set to None to not augment''' + + geom_windows, geom_windows_aug = [], [] + len_df = len(df) + i = 0 + for index, row in df.iterrows(): + cat = row[category_col] + if verbose and category_col: + print ("\n", i+1, "/", len_df, "category:", cat) + # print ("\n", index, row['Category']) + # get coords + geom_pix = row[geometry_col] + if type(geom_pix) == str: + geom_pix = loads(geom_pix) + # print(" geom_pix:", geom_pix) + #pix_coords = list(geom_pix.coords) + bounds = geom_pix.bounds + area = geom_pix.area + (minx, miny, maxx, maxy) = bounds + dx, dy = maxx-minx, maxy-miny + if verbose: + print (" bounds:", bounds ) + print (" dx, dy:", dx, dy ) + print (" area:", area ) + + # get centroid + centroid = geom_pix.centroid + #print "centroid:", centroid + cx_tmp, cy_tmp = list(centroid.coords)[0] + cx, cy = np.rint(cx_tmp), np.rint(cy_tmp) + + # get window coords, jitter, and shapely geometry for window + # do this multiple times if augmentations are desired + if aug_count_dict == None: + n_wins = 1 + else: + n_wins = 1 + aug_count_dict[cat] + if verbose and category_col: + print(" n_wins:", n_wins) + + for k in range(n_wins): + jx, jy = win_jitter(window_size, jitter_frac=jitter_frac) + x0 = cx - window_size/2 + jx + y0 = cy - window_size/2 + jy + # ensure window does not extend outside larger image + x0 = max(x0, 0) + x0 = int(min(x0, image_w - window_size)) + y0 = max(y0, 0) + y0 = int(min(y0, image_h - window_size)) + # set other side of square + x1 = x0 + window_size + y1 = y0 + window_size + win_p1 = shapely.geometry.Point(x0, y0) + win_p2 = shapely.geometry.Point(x1, y0) + win_p3 = shapely.geometry.Point(x1, y1) + win_p4 = shapely.geometry.Point(x0, y1) + pointList = [win_p1, win_p2, win_p3, win_p4, win_p1] + geom_window = shapely.geometry.Polygon([[p.x, p.y] for p in pointList]) + if verbose: + print (" geom_window.bounds", geom_window.bounds ) + # only append first to geom_window, others should be in windows_aug + if k == 0: + geom_windows.append(geom_window) + else: + geom_windows_aug.append(geom_window) + i += 1 + + return geom_windows, geom_windows_aug + + +############################################################################### +def tile_window_geoms(image_w, image_h, window_size=416, overlap_frac=0.2, + verbose=False): + '''Create tiled square window cutouts for given image size + Return a list of geometries for the windows + ''' + + sliceHeight = window_size + sliceWidth = window_size + dx = int((1. - overlap_frac) * sliceWidth) + dy = int((1. - overlap_frac) * sliceHeight) + + n_ims = 0 + geom_windows = [] + for y0 in range(0, image_h, dy):#sliceHeight): + for x0 in range(0, image_w, dx):#sliceWidth): + n_ims += 1 + # ensure window does not extend outside larger image + x0 = max(x0, 0) + x0 = max(0, int(min(x0, image_w - sliceWidth))) + y0 = max(y0, 0) + y0 = max(0, int(min(y0, image_h - sliceHeight))) + # set other side of square + x1 = x0 + sliceWidth + y1 = y0 + sliceHeight + win_p1 = shapely.geometry.Point(x0, y0) + win_p2 = shapely.geometry.Point(x1, y0) + win_p3 = shapely.geometry.Point(x1, y1) + win_p4 = shapely.geometry.Point(x0, y1) + pointList = [win_p1, win_p2, win_p3, win_p4, win_p1] + geom_window = shapely.geometry.Polygon([[p.x, p.y] for p in pointList]) + if verbose: + print (" geom_window.bounds", geom_window.bounds ) + # append + geom_windows.append(geom_window) + + return geom_windows + + +############################################################################### +def get_objs_in_window(df_, geom_window, min_obj_frac=0.7, + geometry_col='geometry_poly_pixel', category_col='Category', + use_box_geom=True, verbose=False): + '''Find all objects in the window + if use_box_geom, turn the shapefile object geom into a bounding box + return: [index_nest, cat_nest, x0_obj, y0_obj, x1_obj, y1_obj]''' + + (minx_win, miny_win, maxx_win, maxy_win) = geom_window.bounds + if verbose: + print ("geom_window.bounds:", geom_window.bounds) + + obj_list = [] + for index_nest, row_nest in df_.iterrows(): + cat_nest = row_nest[category_col] + geom_pix_nest_tmp = row_nest[geometry_col] + if type(geom_pix_nest_tmp) == str: + geom_pix_nest_tmp = loads(geom_pix_nest_tmp) + # if use_box_geom, turn the shapefile object geom into a bounding box + if use_box_geom: + (x0, y0, x1, y1) = geom_pix_nest_tmp.bounds + geom_pix_nest = shapely.geometry.box(x0, y0, x1, y1, ccw=True) + else: + geom_pix_nest = geom_pix_nest_tmp + + #pix_coords = list(geom_pix.coords) + #bounds_nest = geom_pix_nest.bounds + area_nest = geom_pix_nest.area + + # skip zero or negative areas + if area_nest <= 0: + continue + + # sometimes we get an invalid geometry, not sure why + try: + intersect_geom = geom_pix_nest.intersection(geom_window) + except: + # create a buffer around the exterior + geom_pix_nest = geom_pix_nest.buffer(0) + intersect_geom = geom_pix_nest.intersection(geom_window) + print ("Had to update geom_pix_nest:", geom_pix_nest.bounds ) + + intersect_bounds = intersect_geom.bounds + intersect_area = intersect_geom.area + intersect_frac = intersect_area / area_nest + + # skip if object not in window, else add to window + if intersect_frac < min_obj_frac: + continue + else: + # get window coords + (minx_nest, miny_nest, maxx_nest, maxy_nest) = intersect_bounds + dx_nest, dy_nest = maxx_nest - minx_nest, maxy_nest - miny_nest + x0_obj, y0_obj = minx_nest - minx_win, miny_nest - miny_win + x1_obj, y1_obj = x0_obj + dx_nest, y0_obj + dy_nest + + x0_obj, y0_obj, x1_obj, y1_obj = np.rint(x0_obj), np.rint(y0_obj),\ + np.rint(x1_obj), np.rint(y1_obj) + obj_list.append([index_nest, cat_nest, x0_obj, y0_obj, x1_obj, + y1_obj]) + if verbose: + print (" ", index_nest, "geom_obj.bounds:", geom_pix_nest.bounds ) + print (" intesect area:", intersect_area ) + print (" obj area:", area_nest ) + print (" intersect_frac:", intersect_frac ) + print (" intersect_bounds:", intersect_bounds ) + print (" category:", cat_nest ) + + return obj_list + + +############################################################################### +def get_image_window(im, window_geom): + '''Get sub-window in image''' + + bounds_int = [int(itmp) for itmp in window_geom.bounds] + (minx_win, miny_win, maxx_win, maxy_win) = bounds_int + window = im[miny_win:maxy_win, minx_win:maxx_win] + return window + + +############################################################################### +def plot_obj_list(window, obj_list, color_dic, thickness=2, + show_plot=False, outfile=''): + '''Plot the cutout, and the object bounds''' + + print ("window.shape:", window.shape ) + for row in obj_list: + [index_nest, cat_nest, x0_obj, y0_obj, x1_obj, y1_obj] = row + color = color_dic[cat_nest] + cv2.rectangle(window, (int(x0_obj), int(y0_obj)), + (int(x1_obj), int(y1_obj)), + (color), thickness) + if show_plot: + cv2.imshow(str(index_nest), window) + cv2.waitKey(0) + if outfile: + cv2.imwrite(outfile, window) + + +############################################################################### +def plot_training_bboxes(label_folder, image_folder, ignore_augment=True, + figsize=(10, 10), color=(0, 0, 255), thickness=2, + max_plots=100, sample_label_vis_dir=None, ext='.png', + show_plot=False, specific_labels=[], + label_dic=[], output_width=60000, shuffle=True, + verbose=False): + '''Plot bounding boxes for yolt + specific_labels allows user to pass in labels of interest''' + + out_suff = '' # '_vis' + + if sample_label_vis_dir and not os.path.exists(sample_label_vis_dir): + os.mkdir(sample_label_vis_dir) + + # boats, boats_harbor, airplanes, airports (blue, green, red, orange) + # remember opencv uses bgr, not rgb + colors = 40*[(255, 0, 0), (0, 255, 0), (0, 0, 255), (0, 140, 255), + (0, 255, 125), (125, 125, 125), (140, 200, 0), (50, 200, 255), + (0, 102, 0), (255, 0, 127), (51, 0, 105), (153, 0, 0), + (0, 128, 250), (255, 255, 100), (127, 0, 255), (153, 76, 0)] + #colorsmap = plt.cm.gist_rainbow + #colors = [colormap(i) for i in np.linspace(0, 0.9, len(archs))] + + if verbose: + print("colors:", colors) + + try: + cv2.destroyAllWindows() + except: + pass + + i = 0 + + if len(specific_labels) == 0: + label_list = os.listdir(label_folder) + # shuffle? + if shuffle: + random.shuffle(label_list) + + else: + label_list = specific_labels + + for label_file in label_list: + + if ignore_augment: + if (label_file == '.DS_Store') or (label_file.endswith(('_lr.txt', '_ud.txt', '_lrud.txt'))): + continue + # else: + # if (label_file == '.DS_Store'): + # continue + + if i >= max_plots: + # print "i, max_plots:", i, max_plots + return + else: + i += 1 + + if verbose: + print(i, "/", max_plots) + print(" label_file:", label_file) + + # get image + # root = label_file.split('.')[0] + root = label_file[:-4] + im_loc = os.path.join(image_folder, root + ext) + label_loc = os.path.join(label_folder, label_file) + if verbose: + print(" root:", root) + print(" label loc:", label_loc) + print(" image loc:", im_loc) + image0 = cv2.imread(im_loc, 1) + height, width = image0.shape[:2] + # resize output file + if output_width < width: + height_mult = 1.*height / width + output_height = int(height_mult * output_width) + outshape = (output_width, output_height) + image = cv2.resize(image0, outshape) + else: + image = image0 + + height, width = image.shape[:2] + shape = (width, height) + if verbose: + print("im.shape:", image.shape) + + # start plot (mpl) + #fig, ax = plt.subplots(figsize=figsize) + #img_mpl = cv2.cvtColor(image, cv2.COLOR_BGR2RGB) + # ax.imshow(img_mpl) + # just opencv + img_mpl = image + + # get and plot labels + # z = pd.read_csv(label_folder + label_file, sep = ' ', names=['cat', 'x', 'y', 'w', 'h']) + z = pd.read_csv(label_loc, sep=' ', names=['cat', 'x', 'y', 'w', 'h']) + # print "z", z.values + for yolt_box in z.values: + cat_int = int(yolt_box[0]) + color = colors[cat_int] + yb = yolt_box[1:] + box0 = convert_reverse(shape, yb) + # convert to int + box1 = [int(round(b, 2)) for b in box0] + [xmin, xmax, ymin, ymax] = box1 + # plot + cv2.rectangle(img_mpl, (xmin, ymin), + (xmax, ymax), (color), thickness) + + # add border + if label_dic: + + # https://codeyarns.files.wordpress.com/2015/03/20150311_opencv_fonts.png + font = cv2.FONT_HERSHEY_TRIPLEX # FONT_HERSHEY_SIMPLEX #_SIMPLEX _TRIPLEX + font_size = 0.25 + label_font_width = 1 + #text_offset = [3, 10] + if len(label_dic.items()) <= 10: + ydiff = 35 + else: + ydiff = 22 + + # add border + # http://docs.opencv.org/3.1.0/d3/df2/tutorial_py_basic_ops.html + # top, bottom, left, right - border width in number of pixels in corresponding directions + border = (0, 0, 0, 200) + border_color = (255, 255, 255) + label_font_width = 1 + img_mpl = cv2.copyMakeBorder(img_mpl, border[0], border[1], border[2], border[3], + cv2.BORDER_CONSTANT, value=border_color) + # add legend + xpos = img_mpl.shape[1] - border[3] + 15 + # for itmp, k in enumerate(sorted(label_dic.keys())): + # for itmp, (k, value) in enumerate(sorted(label_dic.items(), key=operator.itemgetter(1))): + for itmp, (k, value) in enumerate(sorted(label_dic.items(), key=lambda item: item[1])): + labelt = label_dic[k] + colort = colors[k] + #labelt, colort = label_dic[k] + text = '- ' + labelt # str(k) + ': ' + labelt + ypos = ydiff + (itmp) * ydiff + # cv2.putText(img_mpl, text, (int(xpos), int(ypos)), font, 1.5*font_size, colort, label_font_width, cv2.CV_AA)#, cv2.LINE_AA) + cv2.putText(img_mpl, text, (int(xpos), int(ypos)), font, 1.5 * + # font_size, colort, label_font_width, cv2.CV_AA) # cv2.LINE_AA) + font_size, colort, label_font_width, cv2.LINE_AA) + + # legend box + cv2.rectangle(img_mpl, (xpos-5, 2*border[0]), (img_mpl.shape[1]-10, ypos+int( + 0.75*ydiff)), (0, 0, 0), label_font_width) + + # title + # title = figname.split('/')[-1].split('_')[0] + ': Plot Threshold = ' + str(plot_thresh) # + ': thresh=' + str(plot_thresh) + #title_pos = (border[0], int(border[0]*0.66)) + # cv2.putText(img_mpl, title, title_pos, font, 1.7*font_size, (0,0,0), label_font_width, cv2.CV_AA)#, cv2.LINE_AA) + # cv2.putText(img_mpl, title, title_pos, font, 1.7*font_size, (0,0,0), label_font_width, cv2.CV_AA)#cv2.LINE_AA) + + if show_plot: + cv2.imshow(root, img_mpl) + cv2.waitKey(0) + + if sample_label_vis_dir: + fout = os.path.join(sample_label_vis_dir, root + out_suff + ext) + cv2.imwrite(fout, img_mpl) + + return + + +############################################################################### +def augment_training_data(label_folder, image_folder, + label_folder_out='', image_folder_out='', + hsv_range=[0.5, 1.5], + skip_hsv_transform=True, ext='.jpg'): + ''' + From yolt_data_prep_funcs.py + Rotate data to augment training sizeo + darknet c functions already to HSV transform, and left-right swap, so + skip those transforms + Image augmentation occurs in data.c load_data_detection()''' + + if len(label_folder_out) == 0: + label_folder_out = label_folder + if len(image_folder_out) == 0: + image_folder_out = image_folder + + hsv_diff = hsv_range[1] - hsv_range[0] + im_l_out = [] + for label_file in os.listdir(label_folder): + + # don't augment the already agumented data + if (label_file == '.DS_Store') or \ + (label_file.endswith(('_lr.txt', '_ud.txt', '_lrud.txt', '_rot90.txt', '_rot180.txt', '_rot270.txt'))): + continue + + # get image + print("image loc:", label_file) + root = label_file.split('.')[0] + im_loc = os.path.join(image_folder, root + ext) + + #image = skimage.io.imread(f, as_grey=True) + image = cv2.imread(im_loc, 1) + + # randoly scale in hsv space, create a list of images + if skip_hsv_transform: + img_hsv = image + else: + try: + img_hsv = cv2.cvtColor(image, cv2.COLOR_BGR2HSV) + except: + continue + + img_out_l = [] + np.random.seed(42) + + # three mirrorings + if skip_hsv_transform: + img_out_l = 6*[image] + + else: + for i in range(6): + im_tmp = img_hsv.copy() + # alter values for each of 2 bands (hue and saturation) + # for j in range(2): + # rand = hsv_range[0] + hsv_diff*np.random.random() # between 0,5 and 1.5 + # z0 = (im_tmp[:,:,j]*rand).astype(int) + # im_tmp[:,:,j] = z0 + # alter values for each of 3 bands (hue and saturation, value + for j in range(3): + # set 'value' range somewhat smaller + if j == 2: + rand = 0.7 + 0.6*np.random.random() + else: + rand = hsv_range[0] + hsv_diff * \ + np.random.random() # between 0,5 and 1.5 + z0 = (im_tmp[:, :, j]*rand).astype(int) + z0[z0 > 255] = 255 + im_tmp[:, :, j] = z0 + + # convert back to bgr and add to list of ims + img_out_l.append(cv2.cvtColor(im_tmp, cv2.COLOR_HSV2BGR)) + + # print "image.shape", image.shape + # reflect or flip image left to right (skip since yolo.c does this?) + image_lr = np.fliplr(img_out_l[0]) # (image) + image_ud = np.flipud(img_out_l[1]) # (image) + image_lrud = np.fliplr(np.flipud(img_out_l[2])) # (image_ud) + + #cv2.imshow("in", image) + #cv2.imshow("lr", image_lr) + #cv2.imshow("ud", image_ud) + #cv2.imshow("udlr", image_udlr) + + image_rot90 = np.rot90(img_out_l[3]) + image_rot180 = np.rot90(np.rot90(img_out_l[4])) + image_rot270 = np.rot90(np.rot90(np.rot90(img_out_l[5]))) + + # flip coords of bounding boxes too... + # boxes have format: (x,y,w,h) + z = pd.read_csv(os.path.join(label_folder, label_file), + sep=' ', names=['x', 'y', 'w', 'h']) + + # left right flip + lr_out = z.copy() + lr_out['x'] = 1. - z['x'] + + # left right flip + ud_out = z.copy() + ud_out['y'] = 1. - z['y'] + + # left right, up down, flip + lrud_out = z.copy() + lrud_out['x'] = 1. - z['x'] + lrud_out['y'] = 1. - z['y'] + + ################## + # rotate bounding boxes X degrees + origin = [0.5, 0.5] + point = [z['x'], z['y']] + + # 90 degrees + angle = -1*np.pi/2 + xn, yn = rotate(origin, point, angle) + rot_out90 = z.copy() + rot_out90['x'] = xn + rot_out90['y'] = yn + rot_out90['h'] = z['w'] + rot_out90['w'] = z['h'] + + # 180 degrees (same as lrud) + angle = -1*np.pi + xn, yn = rotate(origin, point, angle) + rot_out180 = z.copy() + rot_out180['x'] = xn + rot_out180['y'] = yn + + # 270 degrees + angle = -3*np.pi/2 + xn, yn = rotate(origin, point, angle) + rot_out270 = z.copy() + rot_out270['x'] = xn + rot_out270['y'] = yn + rot_out270['h'] = z['w'] + rot_out270['w'] = z['h'] + ################## + + # print to files, add to list + im_l_out.append(im_loc) + +# # reflect or flip image left to right (skip since yolo.c does this?) +# imout_lr = image_folder + root + '_lr.jpg' +# labout_lr = label_folder + root + '_lr.txt' +# cv2.imwrite(imout_lr, image_lr) +# lr_out.to_csv(labout_lr, sep=' ', header=False) +# #im_l_out.append(imout_lr) + + # flip vertically or rotate 180 randomly + if bool(random.getrandbits(1)): + # flip vertically + imout_ud = os.path.join(image_folder_out, root + '_ud' + ext) + labout_ud = os.path.join(label_folder_out, root + '_ud.txt') + cv2.imwrite(imout_ud, image_ud) + ud_out.to_csv(labout_ud, sep=' ', header=False) + im_l_out.append(imout_ud) + else: + im180_path = os.path.join(image_folder_out, root + '_rot180' + ext) + cv2.imwrite(os.path.join(im180_path), image_rot180) + rot_out180.to_csv(os.path.join(label_folder_out, + root + '_rot180.txt'), sep=' ', header=False) + im_l_out.append(im180_path) + + +# # lrud flip, same as rot180 +# # skip lrud flip because yolo does this sometimes +# imout_lrud = image_folder + root + '_lrud.jpg' +# labout_lrud = label_folder + root + '_lrud.txt' +# cv2.imwrite(imout_lrud, image_lrud) +# lrud_out.to_csv(labout_lrud, sep=' ', header=False) +# #im_l_out.append(imout_lrud) + + # same as _lrud + #im180 = image_folder + root + '_rot180.jpg' + #cv2.imwrite(image_folder + root + '_rot180.jpg', image_rot180) + #rot_out180.to_csv(label_folder + root + '_rot180.txt', sep=' ', header=False) + # im_l_out.append(im180) + + # rotate 90 degrees or 270 randomly + if bool(random.getrandbits(1)): + im90_path = os.path.join(image_folder_out, root + '_rot90' + ext) + #lab90 = label_folder + root + '_rot90.txt' + cv2.imwrite(im90_path, image_rot90) + rot_out90.to_csv(os.path.join(label_folder_out, + root + '_rot90.txt'), sep=' ', header=False) + im_l_out.append(im90_path) + + else: + # rotate 270 degrees () + im270_path = os.path.join(image_folder_out, root + '_rot270' + ext) + cv2.imwrite(im270_path, image_rot270) + rot_out270.to_csv(os.path.join(label_folder_out, + root + '_rot270.txt'), sep=' ', header=False) + im_l_out.append(im270_path) + + return im_l_out + + +############################################################################### +def rm_augment_training_data(label_folder, image_folder, tmp_dir): + '''Remove previusly created augmented data since it's done in yolt.c and + need not be doubly augmented''' + + # mv augmented labels + for label_file in os.listdir(label_folder): + + if (label_file.endswith(('_lr.txt', '_ud.txt', '_lrud.txt', '_rot90.txt', '_rot180.txt', '_rot270.txt'))): + + try: + os.mkdir(tmp_dir) + except: + print("") + + # mv files to tmp_dir + print("label_file", label_file) + #shutil.move(label_file, tmp_dir) + # overwrite: + shutil.move(os.path.join(label_folder, label_file), + os.path.join(tmp_dir, label_file)) + + # just run images separately below to make sure we get errthing + # get image + # print "image loc:", label_file + #root = label_file.split('.')[0] + #im_loc = image_folder + root + '.jpg' + # mv files to tmp_dir + #shutil.move(im_loc, tmp_dir) + + # mv augmented images + for image_file in os.listdir(image_folder): + + if (image_file.endswith(('_lr.jpg', '_ud.jpg', '_lrud.jpg', '_rot90.jpg', '_rot180.jpg', '_rot270.jpg'))): + + try: + os.mkdir(tmp_dir) + except: + print("") + + # mv files to tmp_dir + #shutil.move(image_file, tmp_dir) + # overwrite + shutil.move(os.path.join(image_folder, image_file), + os.path.join(tmp_dir, image_file)) + + return + + +############################################################################### +def yolt_from_df(im_path, df_polys, + window_size=512, + jitter_frac=0.1, + min_obj_frac=0.7, + max_obj_count=1000, + geometry_col='geometry', + category_col='make_id', + image_fname_col='image_fname', + outdir_ims=None, + outdir_labels=None, + outdir_yolt_plots=None, + outdir_ims_aug=None, + outdir_labels_aug=None, + outdir_yolt_plots_aug=None, + aug_count_dict=None, + yolt_image_ext='.jpg', + max_plots=10, + flip_vert_prob=0, + verbose=True, super_verbose=False): + ''' + Extract yolt cutouts and labels from a singe image. + df_polys is created from: DA_Dataset/gj_to_px_bboxes.ipynb, which converts geojsons to csvs with columns: + image_fname, cat_id, loc_id, location, original_make, make, da_make_id, pnp_id, geometry + aug_count_dict is a dictionary detailing the number of augmentations to make, + set to none to not augment + flip_vert_prob is the probabilty of randomly flipping each extracted chip vertically (set to 0 to skip) + ''' + + # ensure image exists + if not os.path.exists(im_path): + print (" Image file {} DNE...".format(im_path) ) + return + else: + im = skimage.io.imread(im_path) + im_name = os.path.basename(im_path) + im_root = im_name.split('.')[0] + image_h, image_w = im.shape[:2] + # filter dataframe + df_im_tmp = df_polys[df_polys[image_fname_col] == im_name] + + if verbose: + print("image", im_name) + print(" im.shape:", im.shape) + print(" object count:", df_im_tmp[category_col].value_counts().to_dict()) + # print(" len df_im:", len(df_im_tmp)) + + # get window cutouts centered at each object + window_geoms, window_geoms_aug = get_window_geoms(df_im_tmp, + window_size=window_size, + image_w=image_w, image_h=image_h, + jitter_frac=jitter_frac, + geometry_col=geometry_col, + category_col=category_col, + aug_count_dict=aug_count_dict, + verbose=super_verbose) + + # set up dicts for counting objects + idx_count_dic = {} + for idx_tmp in df_im_tmp.index: + idx_count_dic[idx_tmp] = 0 + idx_count_tot_dic = {} + for idx_tmp in df_im_tmp.index: + idx_count_tot_dic[idx_tmp] = 0 + + # get objects in each window + win_iter = 0 + for i, window_geom in enumerate(window_geoms): + + (minx_win, miny_win, maxx_win, maxy_win) = window_geom.bounds + + # get window + window = get_image_window(im, window_geom) + h, w = window.shape[:2] + if (h==0) or (w==0): + continue + + # get objects in window + obj_list = get_objs_in_window(df_im_tmp, window_geom, + min_obj_frac=min_obj_frac, + geometry_col=geometry_col, + category_col=category_col, + use_box_geom=True, + verbose=super_verbose) + if super_verbose: + print ("\nWindow geom:", window_geom ) + print (" window shape:", window.shape ) + print (" obj_list:", obj_list ) + + if len(obj_list) > 0 : + + # update idx_count_tot_dic + idxs_list = [z[0] for z in obj_list] + for idx_tmp in idxs_list: + idx_count_tot_dic[idx_tmp] += 1 + + # Check idx count dic. If an object has appeared too frequently, + # skip the window + excess = False + for idx_tmp in idxs_list: + if idx_count_dic[idx_tmp] >= max_obj_count: + print ("Index", idx_tmp, "seen too frequently, skipping..." ) + excess = True + break + if excess: + continue + + # create and save yolt images and labels + outroot = im_root + '__' + 'x0_' + str(int(minx_win)) + '_y0_' \ + + str(int(miny_win)) + '_dxdy_' \ + + str(int(window_size)) + + if not (outdir_ims and outdir_labels): + return + + # get yolt labels + #if verbose: + # print (" Creating yolt labels..." + yolt_coords = [] + for row in obj_list: + [index_nest, cat_nest, x0, y0, x1, y1] = row + yolt_row = [cat_nest] + list(convert((w,h), [x0,x1,y0,y1])) + # cat_idx = cat_idx_dic[cat_nest] + # yolt_row = [cat_idx, cat_nest] + list(convert.convert((w,h), [x0,x1,y0,y1])) + yolt_coords.append(yolt_row) + if super_verbose: + print (" yolt_coords:", yolt_coords ) + + # if desired, and randomly selected, flip vertically + use_flip = False + flip_rand_val = random.uniform(0, 1) + if (flip_vert_prob > 0) and (flip_rand_val < flip_vert_prob): + use_flip = True + # flip yolt coords ((cat, x, y, w, h)) + yolt_coords_flip = [] + for yc in yolt_coords: + yolt_coords_flip.append([yc[0], yc[1], 1.0 - yc[2], yc[3], yc[4]]) + yolt_coords = yolt_coords_flip + # flip image + window = np.flipud(window) + flip_suff = '_ud' + else: + flip_suff = '' + + # set outfiles + image_outfile = os.path.join(outdir_ims, outroot + flip_suff + yolt_image_ext) + label_outfile = os.path.join(outdir_labels, outroot +flip_suff + '.txt') + + # save image + skimage.io.imsave(image_outfile, window) + # cv2.imwrite(image_outfile, window) + + # save labels + txt_outfile = open(label_outfile, "w") + for j, yolt_row in enumerate(yolt_coords): + cls_id = yolt_row[0] + bb = yolt_row[1:] + # bb = yolt_row[2:] + outstring = str(cls_id) + " " + " ".join([str(a) for a in bb]) + '\n' + # print("outstring:", outstring + txt_outfile.write(outstring) + txt_outfile.close() + + # update idx_count_dic + for idx_tmp in idxs_list: + idx_count_dic[idx_tmp] += 1 + # update win_iter + win_iter += 1 + + # make sure labels and images are created correctly + print ("\nPlotting yolt training bounding boxes..." ) + print (" outdir_labels:", outdir_labels ) + print (" outdir_ims:", outdir_ims ) + plot_training_bboxes(outdir_labels, outdir_ims, + ignore_augment=True, + figsize=(10,10), color=(0,0,255), thickness=2, + max_plots=max_plots, sample_label_vis_dir=outdir_yolt_plots, + ext=yolt_image_ext, show_plot=False, + specific_labels=[], label_dic=[], output_width=500, + shuffle=True, verbose=super_verbose) + + + # now handle augmented windows + # rotate the windows. yolo already does lr flips, so we can skip any of that type of aug + if len(window_geoms_aug) > 0: + + # get objects in each window + win_iter = 0 + for i, window_geom in enumerate(window_geoms_aug): + (minx_win, miny_win, maxx_win, maxy_win) = window_geom.bounds + # get window + window = get_image_window(im, window_geom) + h, w = window.shape[:2] + if (h==0) or (w==0): + continue + # get objects in window + obj_list = get_objs_in_window(df_im_tmp, window_geom, + min_obj_frac=min_obj_frac, + geometry_col=geometry_col, + category_col=category_col, + use_box_geom=True, + verbose=super_verbose) + if super_verbose: + print ("\nWindow geom:", window_geom ) + print (" window shape:", window.shape ) + print (" obj_list:", obj_list ) + + # skip if empty, obviously + if len(obj_list) == 0: + continue + + # elif not empty, rotate, see augment_training_data() for code + # just apply a rotation to every third ( + # (l-r flipping is standard within yolo, so we can skip that augmentation) + else: + # get yolt labels + yolt_coords = [] + for row in obj_list: + [index_nest, cat_nest, x0, y0, x1, y1] = row + yolt_row = [cat_nest] + list(convert((w,h), [x0,x1,y0,y1])) + # cat_idx = cat_idx_dic[cat_nest] + # yolt_row = [cat_idx, cat_nest] + list(convert.convert((w,h), [x0,x1,y0,y1])) + yolt_coords.append(yolt_row) + df_yc = pd.DataFrame(yolt_coords, columns=['cat', 'x', 'y', 'w', 'h']) + + # first, flip vertically + n_options = 3 + if (i % n_options) == 0: + suff = '_ud' + win_out = np.flipud(window) + df_out = df_yc.copy() + df_out['y'] = 1. - df_yc['y'] + # second, rotate 90 + elif ((i-1) % n_options) == 0: + suff = '_rot90' + win_out = np.rot90(window) + # 90 degrees + origin = [0.5, 0.5] + point = [df_yc['x'], df_yc['y']] + angle = -1*np.pi/2 + xn, yn = rotate(origin, point, angle) + df_out = df_yc.copy() + df_out['x'] = xn + df_out['y'] = yn + df_out['h'] = df_yc['w'] + df_out['w'] = df_yc['h'] + # third, rotate 270 + elif ((i-2) % n_options) == 0: + suff = '_rot270' + win_out = np.rot90(window, 3) + # 90 degrees + origin = [0.5, 0.5] + point = [df_yc['x'], df_yc['y']] + angle = -3*np.pi/2 + xn, yn = rotate(origin, point, angle) + df_out = df_yc.copy() + df_out['x'] = xn + df_out['y'] = yn + df_out['h'] = df_yc['w'] + df_out['w'] = df_yc['h'] + # # fourth, rotate 180 + # elif ((i-3) % n_options) == 0: + # suff = '_rot180' + # win_out = np.rot180(window, 3) + # # 90 degrees + # origin = [0.5, 0.5] + # point = [df_yc['x'], df_yc['y']] + # angle = np.pi + # xn, yn = rotate(origin, point, angle) + # df_out = df_yc.copy() + # df_out['x'] = xn + # df_out['y'] = yn + # df_out['h'] = df_yc['h'] + # df_out['w'] = df_yc['w'] + # # fifth, flip rotate 180? + + # create and save yolt images and labels + outroot = im_root + '__' + 'x0_' + str(int(minx_win)) + '_y0_' \ + + str(int(miny_win)) + '_dxdy_' \ + + str(int(window_size)) + suff + # paths + image_outfile = os.path.join(outdir_ims_aug, outroot + yolt_image_ext) + label_outfile = os.path.join(outdir_labels_aug, outroot + '.txt') + # save + skimage.io.imsave(image_outfile, win_out) + df_out.to_csv(label_outfile, sep=' ', header=False, index=False) + + # make sure labels and images are created correctly + print ("\nPlotting yolt training bounding boxes..." ) + print (" outdir_labels:", outdir_labels ) + print (" outdir_ims:", outdir_ims ) + plot_training_bboxes(outdir_labels_aug, outdir_ims_aug, + ignore_augment=False, + figsize=(10,10), color=(0,0,255), thickness=2, + max_plots=max_plots, sample_label_vis_dir=outdir_yolt_plots_aug, + ext=yolt_image_ext, show_plot=False, + specific_labels=[], label_dic=[], output_width=500, + shuffle=True, verbose=super_verbose) + + return + + +############################################################################### +def yolt_from_visdrone(im_path, label_path, + geometry_col='geometry', + category_col='object_category', + window_size=416, + overlap_frac=0.1, + min_obj_frac=0.7, + max_obj_count=10000, + outdir_ims=None, + outdir_labels=None, + outdir_yolt_plots=None, + yolt_image_ext='.jpg', + # min_bbox_extent=24, + min_bbox_area_pix=256, + max_plots=10, + label_sep=',', + label_col_names=['bbox_left','bbox_top','bbox_width','bbox_height','score','object_category','truncation','occlusion'], + input_label_name_dict={0:'ignored', 1:'pedestrian', 2:'people', 3:'bicycle', 4:'car', + 5:'van', 6:'truck', 7:'tricycle', 8:'awning-tricycle', 9:'bus', 10:'motor', 11:'others'}, + label_int_conv_dict={1:0, 2:1, 3:2, 4:3, 5:4, 6:5, 7:6, 8:7, 9:8, 10:9, 11:10}, + max_occlusion_int=1, + category_prime_col='category_int', + category_prime_col_str='category_str', + overwrite=False, verbose=True, super_verbose=False): + ''' + Extract yolt cutouts and labels from a singe image/label pair in + the VisDrone dataset (https://github.com/VisDrone/VisDrone2018-DET-toolkit). + The object category indicates the type of annotated object, (i.e., ignored regions(0), pedestrian(1), + people(2), bicycle(3), car(4), van(5), truck(6), tricycle(7), awning-tricycle(8), bus(9), motor(10), + others(11)) + The score in the DETECTION file should be set to the constant -1. + The score in the GROUNDTRUTH file indicates the fraction of objects being occluded (i.e., no occlusion = 0 + (occlusion ratio 0%), partial occlusion = 1 (occlusion ratio 1% ~ 50%), and heavy occlusion = 2 + (occlusion ratio 50% ~ 100%)).data + + label_int_conv_dict is a dict to convert the raw labels (from input_label_name_dict) to the desired output integers labels. + skip category 0 because these are ignored regions + min_bbox_area_pix is the minimum area (in pixels) of a bounding box - any smaller and we drop it + (unused): min_bbox_extent is the minimum size of a bounding box - any smaller and we drop it. + ''' + + # define label_str_dict + label_str_dict={} + for k,v in label_int_conv_dict.items(): + label_str_dict[v] = input_label_name_dict[k] + + # ensure image exists + if not os.path.exists(im_path): + print (" Image file {} DNE...".format(im_path) ) + return + else: + # read in image + im = skimage.io.imread(im_path) + im_name = os.path.basename(im_path) + im_root = im_name.split('.')[0] + image_h, image_w = im.shape[:2] + + # read in labels, get coords + df_label = pd.read_csv(label_path, sep=label_sep, names=label_col_names, header=None) + df_label['xmin'] = df_label['bbox_left'] + df_label['xmax'] = df_label['bbox_left'] + df_label['bbox_width'] + df_label['ymin'] = df_label['bbox_top'] + df_label['ymax'] = df_label['bbox_top'] + df_label['bbox_height'] + # xext = df_label['xmax'] - df_label['xmin'] + # yext = df_label['ymax'] - df_label['ymin'] + # df_label['extent'] = [min(a,b) for (a,b) in zip(xext, yext)] + + # ceate geometry, area column + geom_list_tmp = [] + area_list_tmp = [] + for idx_tmp, row_tmp in df_label.iterrows(): + geom_tmp = shapely.geometry.box(row_tmp['xmin'], row_tmp['ymin'], row_tmp['xmax'], row_tmp['ymax'], ccw=True) + geom_list_tmp.append(geom_tmp) + area_list_tmp.append(geom_tmp.area) + df_label[geometry_col] = geom_list_tmp + df_label['area'] = area_list_tmp + # get label names? + # df_label[category_str_col] = [input_label_name_dict[z] for z in df_label[category_col].values] + + ######################### + # now address category 0 = 'ignored' + # let's black out the portion of the image that's supposed to be ignored, also remove label + df_ig = df_label[df_label[category_col] == 0] + for idx_tmp, row_ig in df_ig.iterrows(): + # set image to 0 in these regions + im[row_ig['ymin']:row_ig['ymax'], row_ig['xmin']:row_ig['xmax']] = 0 + # remove all cats where category == 0! + df_label_filt = df_label[df_label[category_col] > 0] + + # now let's shift labels (actually, do this later now) + # df_label[category_prime_col] = df_label[category_col] - 1 + # make new dict with subtracted keys? + # actually, we import label_dict_prime now... + # label_name_dict_prime = {} + # for k,v in input_label_name_dict.items(): + # if k == 0: + # continue + # else: + # label_name_dict_prime[k-1] = v + ######################### + + # remove rows with labels not in label_name_dict_prime + good_cats_list = list(label_int_conv_dict.keys()) + df_label_filt = df_label_filt[df_label_filt[category_col].isin(good_cats_list)] + + # filter out bboxes that are too small + df_label_filt = df_label_filt[df_label_filt['area'] >= min_bbox_area_pix] + # df_label_filt = df_label_filt[df_label_filt['extent'] >= min_bbox_extent] + + # filter out bboxes that are too occluded + df_label_filt = df_label_filt[df_label_filt['occlusion'] <= max_occlusion_int] + + # now let's create output labels + df_label_filt[category_prime_col] = [label_int_conv_dict[z] for z in df_label_filt[category_col].values] + df_label_filt[category_prime_col_str] = [label_str_dict[z] for z in df_label_filt[category_prime_col].values] + + # get window geoms + window_geoms = tile_window_geoms(image_w, image_h, window_size=window_size, + overlap_frac=overlap_frac, verbose=super_verbose) + + # set up dicts for counting objects + idx_count_dic = {} + for idx_tmp in df_label_filt.index: + idx_count_dic[idx_tmp] = 0 + idx_count_tot_dic = {} + for idx_tmp in df_label_filt.index: + idx_count_tot_dic[idx_tmp] = 0 + + # get objects in each window + win_iter = 0 + for i, window_geom in enumerate(window_geoms): + + (minx_win, miny_win, maxx_win, maxy_win) = window_geom.bounds + + # name root + outroot = im_root + '__' + 'x0_' + str(int(minx_win)) + '_y0_' \ + + str(int(miny_win)) + '_dxdy_' \ + + str(int(window_size)) + flip_suff = '' + # set outfiles + image_outfile = os.path.join(outdir_ims, outroot + flip_suff + yolt_image_ext) + label_outfile = os.path.join(outdir_labels, outroot +flip_suff + '.txt') + # skip if we don't want to overwrite + if not overwrite and os.path.exists(image_outfile): + continue + + # get window + window = get_image_window(im, window_geom) + h, w = window.shape[:2] + if (h==0) or (w==0): + continue + + # get objects in window + obj_list = get_objs_in_window(df_label_filt, window_geom, + min_obj_frac=min_obj_frac, + geometry_col=geometry_col, + category_col=category_prime_col, + use_box_geom=True, + verbose=super_verbose) + if super_verbose: + print ("\nWindow geom:", window_geom ) + print (" window shape:", window.shape ) + print (" obj_list:", obj_list ) + + if len(obj_list) > 0 : + + # update idx_count_tot_dic + idxs_list = [z[0] for z in obj_list] + for idx_tmp in idxs_list: + idx_count_tot_dic[idx_tmp] += 1 + + # Check idx count dic. If an object has appeared too frequently, + # skip the window + excess = False + for idx_tmp in idxs_list: + if idx_count_dic[idx_tmp] >= max_obj_count: + print ("Index", idx_tmp, "seen too frequently, skipping..." ) + excess = True + break + if excess: + continue + + # create and save yolt images and labels + if not (outdir_ims and outdir_labels): + return + + # get yolt labels + #if verbose: + # print (" Creating yolt labels..." + yolt_coords = [] + for row in obj_list: + [index_nest, cat_nest, x0, y0, x1, y1] = row + yolt_row = [cat_nest] + list(convert((w,h), [x0,x1,y0,y1])) + # cat_idx = cat_idx_dic[cat_nest] + # yolt_row = [cat_idx, cat_nest] + list(convert.convert((w,h), [x0,x1,y0,y1])) + yolt_coords.append(yolt_row) + if super_verbose: + print (" yolt_coords:", yolt_coords ) + + # # if desired, and randomly selected, flip vertically + # use_flip = False + # flip_rand_val = random.uniform(0, 1) + # if (flip_vert_prob > 0) and (flip_rand_val < flip_vert_prob): + # use_flip = True + # # flip yolt coords ((cat, x, y, w, h)) + # yolt_coords_flip = [] + # for yc in yolt_coords: + # yolt_coords_flip.append([yc[0], yc[1], 1.0 - yc[2], yc[3], yc[4]]) + # yolt_coords = yolt_coords_flip + # # flip image + # window = np.flipud(window) + # flip_suff = '_ud' + # else: + # flip_suff ='' + + # save image + skimage.io.imsave(image_outfile, window) + # cv2.imwrite(image_outfile, window) + + # save labels + txt_outfile = open(label_outfile, "w") + for j, yolt_row in enumerate(yolt_coords): + cls_id = yolt_row[0] + bb = yolt_row[1:] + # bb = yolt_row[2:] + outstring = str(cls_id) + " " + " ".join([str(a) for a in bb]) + '\n' + # print("outstring:", outstring + txt_outfile.write(outstring) + txt_outfile.close() + + # update idx_count_dic + for idx_tmp in idxs_list: + idx_count_dic[idx_tmp] += 1 + # update win_iter + win_iter += 1 + + # plot to make sure labels and images are created correctly + if super_verbose: + print ("\nPlotting yolt training bounding boxes..." ) + print (" outdir_labels:", outdir_labels ) + print (" outdir_ims:", outdir_ims ) + if not overwrite: + plot_training_bboxes(outdir_labels, outdir_ims, + ignore_augment=True, + figsize=(10,10), color=(0,0,255), thickness=2, + max_plots=max_plots, sample_label_vis_dir=outdir_yolt_plots, + ext=yolt_image_ext, show_plot=False, + specific_labels=[], label_dic=label_str_dict, output_width=500, + shuffle=True, verbose=super_verbose) + + return + + +############################################################################### +def yolt_from_df_v0(im_path, df_polys, + window_size=512, + jitter_frac=0.1, + min_obj_frac=0.7, + max_obj_count=1000, + geometry_col='geometry', + category_col='da_make_id', + image_fname_col='image_fname', + outdir_ims=None, + outdir_labels=None, + outdir_plots=None, + outdir_yolt_plots=None, + aug_count_dict=None, + yolt_image_ext='.jpg', + max_plots=10, + verbose=True, super_verbose=False): + ''' + Extract yolt cutouts and labels from a singe image. + df_polys is created from: DA_Dataset/gj_to_px_bboxes.ipynb, which converts geojsons to csvs with columns: + image_fname, cat_id, loc_id, location, original_make, make, da_make_id, pnp_id, geometry + ''' + + # ensure image exists + if not os.path.exists(im_path): + print (" Image file {} DNE...".format(im_path) ) + return + else: + im = skimage.io.imread(im_path) + im_name = os.path.basename(im_path) + im_root = im_name.split('.')[0] + image_h, image_w = im.shape[:2] + # filter dataframe + df_im_tmp = df_polys[df_polys[image_fname_col] == im_name] + + if verbose: + print("image", im_name) + print(" im.shape:", im.shape) + print(" object count:", df_im_tmp[category_col].value_counts().to_dict()) + # print(" len df_im:", len(df_im_tmp)) + + # get window cutouts centered at each object + window_geoms, window_geoms_aug = get_window_geoms(df_im_tmp, + window_size=window_size, + image_w=image_w, image_h=image_h, + jitter_frac=jitter_frac, + geometry_col=geometry_col, + category_col=category_col, + aug_count_dict=aug_count_dict, + verbose=super_verbose) + + # set up dicts for counting objects + idx_count_dic = {} + for idx_tmp in df_im_tmp.index: + idx_count_dic[idx_tmp] = 0 + idx_count_tot_dic = {} + for idx_tmp in df_im_tmp.index: + idx_count_tot_dic[idx_tmp] = 0 + + # get objects in each window + win_iter = 0 + for i, window_geom in enumerate(window_geoms): + + (minx_win, miny_win, maxx_win, maxy_win) = window_geom.bounds + + # get window + window = get_image_window(im, window_geom) + h, w = window.shape[:2] + if (h==0) or (w==0): + continue + + # get objects in window + obj_list = get_objs_in_window(df_im_tmp, window_geom, + min_obj_frac=min_obj_frac, + geometry_col=geometry_col, + category_col=category_col, + use_box_geom=True, + verbose=super_verbose) + if super_verbose: + print ("\nWindow geom:", window_geom ) + print (" window shape:", window.shape ) + print (" obj_list:", obj_list ) + + if len(obj_list) > 0 : + + # update idx_count_tot_dic + idxs_list = [z[0] for z in obj_list] + for idx_tmp in idxs_list: + idx_count_tot_dic[idx_tmp] += 1 + + # Check idx count dic. If an object has appeared too frequently, + # skip the window + excess = False + for idx_tmp in idxs_list: + if idx_count_dic[idx_tmp] >= max_obj_count: + print ("Index", idx_tmp, "seen too frequently, skipping..." ) + excess = True + break + if excess: + continue + + # create and save yolt images and labels + outroot = im_root + '__' + 'x0_' + str(int(minx_win)) + '_y0_' \ + + str(int(miny_win)) + '_dxdy_' \ + + str(int(window_size)) + + if not (outdir_ims and outdir_labels): + return + + image_outfile = os.path.join(outdir_ims, outroot + yolt_image_ext) + label_outfile = os.path.join(outdir_labels, outroot + '.txt') + + # get yolt labels + #if verbose: + # print (" Creating yolt labels..." + yolt_coords = [] + for row in obj_list: + [index_nest, cat_nest, x0, y0, x1, y1] = row + yolt_row = [cat_nest] + list(convert((w,h), [x0,x1,y0,y1])) + # cat_idx = cat_idx_dic[cat_nest] + # yolt_row = [cat_idx, cat_nest] + list(convert.utils.convert((w,h), [x0,x1,y0,y1])) + yolt_coords.append(yolt_row) + if super_verbose: + print (" yolt_coords:", yolt_coords ) + + # try flipping, rotating if desired, see augment func above... + # ... + + # save image + # if verbose: + # print (" Saving window to file..." ) + # print (" window.dtype:", window.dtype ) + # print (" window.shape:", window.shape ) + skimage.io.imsave(image_outfile, window) + # cv2.imwrite(image_outfile, window) + + # save labels + txt_outfile = open(label_outfile, "w") + for j, yolt_row in enumerate(yolt_coords): + cls_id = yolt_row[0] + bb = yolt_row[1:] + # bb = yolt_row[2:] + outstring = str(cls_id) + " " + " ".join([str(a) for a in bb]) + '\n' + # print("outstring:", outstring + txt_outfile.write(outstring) + txt_outfile.close() + + # # make plots + # plot_outfile = os.path.join(outdir_plots, outroot + yolt_image_ext) + # if i <= args.max_plots: + # if verbose: + # print ("obj_list:",obj_list ) + # print ("plot outfile:", plot_outfile ) + # #im_copy = im.copy() + # #plot_obj_list(im_copy, window_geom, obj_list, color_dic, + # plot_obj_list(window.copy(), obj_list, color_dic, + # thickness=plot_thickness, show_plot=False, + # outfile=plot_outfile) + + # update idx_count_dic + for idx_tmp in idxs_list: + idx_count_dic[idx_tmp] += 1 + # update win_iter + win_iter += 1 + + + # # augment, if desired + # if args.augment.upper() == 'TRUE': + # yolt_data_prep_funcs.augment_training_data(outdir_labels, outdir_ims, + # hsv_range=[0.5,1.5], + # ext=ext, + # skip_hsv_transform=False) + + # make sure labels and images are created correctly + print ("\nPlotting yolt training bounding boxes..." ) + print (" outdir_labels:", outdir_labels ) + print (" outdir_ims:", outdir_ims ) + plot_training_bboxes(outdir_labels, outdir_ims, + ignore_augment=True, + figsize=(10,10), color=(0,0,255), thickness=2, + max_plots=max_plots, sample_label_vis_dir=outdir_yolt_plots, + ext=yolt_image_ext, show_plot=False, + specific_labels=[], label_dic=[], output_width=500, + shuffle=True, verbose=super_verbose) + + return + + +############################################################################### +def get_labels(csv_path, xmin, ymin, width, height, label_col, min_overlap=0, classes=True): + """Credit: Nick Weir + The function below will retrieve labels from AOI csvs given: + `csv_path`, `xmin`, `ymin`, `width`, `height`, and `min_overlap`. + `label_col` specifies which column contains integral label IDs. + + Read in labels from a pixel coordinate csv input. + + Notes + ----- + WARNING: This function will not raise any kind of error if the x, y, width, + or height values selected don't fall within the bounds of the image. Make + sure that the values you select fall within the pixel extent of the image + before using. + + Arguments + --------- + csv_path : str + The path to the CSV file containing geometries for an AOI of interest. + xmin : int + The starting X pixel index for the tile to be extracted. + ymin : int + The starting Y pixel index for the tile to be extracted. + width : int + The width of the tile to be extracted, in pixel units. + height : int + The height of the tile to be extracted, in pixel units. + label_col : str + The name of the column in the CSV containing integral label IDs. + min_overlap : float, optional + The fraction of a geometry area that must overlap with the extracted + tile for the label to be included in the output. Defaults to 0 (any + portion of an overlapping geometry, however small, will be labeled in + the output). + + Returns + ------- + geom_bounds : :class:`numpy.ndarray` + A NumPy array of shape ``(n_labels, 4)``. Each row corresponds to a single + label's ``[xmin, ymin, xmax, ymax]`` coordinates. The units are the fraction + of the image's extent in the given direction (width for ``xmin`` and ``xmax``, + height for ``ymin`` and ``ymax``.) + """ + # needs to be read as a gdf for spatial operations + gdf = gpd.GeoDataFrame(pd.read_csv(csv_path)) + gdf.geometry = gdf.geometry.apply(loads) + tile_bbox = box(xmin, ymin, xmin+width, ymin+height) + + to_keep = gdf.geometry.apply(lambda x: tile_bbox.intersects(x)) + kept_inds = gdf.index[to_keep].values + tile_gdf = gdf.loc[to_keep, :] + frac_overlap = tile_gdf.geometry.apply(lambda x: tile_bbox.intersection(x).area/x.area) + if len(frac_overlap) == 0: + return [], [], [] + tile_gdf = tile_gdf.loc[frac_overlap > min_overlap, :] + if len(tile_gdf) == 0: + return [], [], [] + tile_gdf.geometry = tile_gdf.geometry.apply(lambda x: tile_bbox.intersection(x)) + tile_gdf.geometry = tile_gdf.geometry.apply( + translate, xoff=-xmin, yoff=-ymin) + + geom_bounds = tile_gdf.bounds + geom_bounds['minx'] = geom_bounds['minx'].apply( + lambda x: x/width) + geom_bounds['maxx'] = geom_bounds['maxx'].apply( + lambda x: x/width) + geom_bounds['miny'] = geom_bounds['miny'].apply( + lambda y: y/height) + geom_bounds['maxy'] = geom_bounds['maxy'].apply( + lambda y: y/height) + geom_bounds['width'] = geom_bounds['maxx'] - geom_bounds['minx'] + geom_bounds['midx'] = geom_bounds['minx'] + geom_bounds['width']/2 + geom_bounds['height'] = geom_bounds['maxy'] - geom_bounds['miny'] + geom_bounds['midy'] = geom_bounds['miny'] + geom_bounds['height']/2 + + geom_bounds = np.around(geom_bounds[['midx', 'midy', 'width', 'height']].to_numpy(), 6).tolist() + if classes: + labels = tile_gdf[label_col].tolist() + else: + labels = len(tile_gdf) + + return geom_bounds, labels, kept_inds + + +############################################################################### +def map_wrapper(x): + '''For multi-threading''' + return x[0](*(x[1:])) + + +############################################################################### +def weighted_avg_and_std(values, weights): + """ + Return the weighted average and standard deviation. + values, weights -- Numpy ndarrays with the same shape. + """ + + weighted_stats = DescrStatsW(values, weights=weights, ddof=0) + + # weighted mean of data (equivalent to np.average(array, weights=weights)) + mean = weighted_stats.mean + # standard deviation with default degrees of freedom correction + std = weighted_stats.std + # variance with default degrees of freedom correction + var = weighted_stats.var + + return (mean, std, var) + +def slice_im_plus_boxes(image_path, out_name, out_dir_images, + boxes=[], yolo_classes=[], out_dir_labels=None, + mask_path=None, out_dir_masks=None, + sliceHeight=416, sliceWidth=416, + overlap=0.1, slice_sep='|', pad=0, + skip_highly_overlapped_tiles=False, + overwrite=False, + out_ext='.png', verbose=False): + + """ + Slice a large image into smaller windows, and also bin boxes + Adapted from: + https://github.com/avanetten/simrdwn/blob/master/simrdwn/core/slice_im.py + + Arguments + --------- + image_path : str + Location of image to slice + out_name : str + Root name of output files (coordinates will be appended to this) + out_dir_images : str + Output directory for images + boxes : arr + List of bounding boxes in image, in pixel coords + [ [xb0, yb0, xb1, yb1], ...] + Defaults to [] + yolo_classes : list + list of class of objects for each box [0, 1, 0, ...] + Defaults to [] + out_dir_labels : str + Output directory for labels + Defaults to None + sliceHeight : int + Height of each slice. Defaults to ``416``. + sliceWidth : int + Width of each slice. Defaults to ``416``. + overlap : float + Fractional overlap of each window (e.g. an overlap of 0.2 for a window + of size 256 yields an overlap of 51 pixels). + Default to ``0.1``. + slice_sep : str + Character used to separate outname from coordinates in the saved + windows. Defaults to ``|`` + out_ext : str + Extension of saved images. Defaults to ``.png``. + verbose : boolean + Switch to print relevant values to screen. Defaults to ``False`` + + Returns + ------- + None + """ + + if len(out_ext) == 0: + im_ext = '.' + image_path.split('.')[-1] + else: + im_ext = out_ext + + t0 = time.time() + image = skimage.io.imread(image_path) #, as_grey=False).astype(np.uint8) # [::-1] + print("image.shape:", image.shape) + if mask_path: + mask = skimage.io.imread(mask_path) + win_h, win_w = image.shape[:2] + win_size = sliceHeight*sliceWidth + dx = int((1. - overlap) * sliceWidth) + dy = int((1. - overlap) * sliceHeight) + + n_ims = 0 + for y0 in range(0, image.shape[0], dy): + for x0 in range(0, image.shape[1], dx): + out_boxes_yolo = [] + out_classes_yolo = [] + n_ims += 1 + + if (n_ims % 100) == 0: + print(n_ims) + + # make sure we don't have a tiny image on the edge + if y0+sliceHeight > image.shape[0]: + # skip if too much overlap (> 0.6) + if skip_highly_overlapped_tiles: + if (y0+sliceHeight - image.shape[0]) > (0.6*sliceHeight): + continue + else: + y = image.shape[0] - sliceHeight + else: + y = image.shape[0] - sliceHeight + else: + y = y0 + if x0+sliceWidth > image.shape[1]: + # skip if too much overlap (> 0.6) + if skip_highly_overlapped_tiles: + if (x0+sliceWidth - image.shape[1]) > (0.6*sliceWidth): + continue + else: + x = image.shape[1] - sliceWidth + else: + x = image.shape[1] - sliceWidth + else: + x = x0 + + xmin, xmax, ymin, ymax = x, x+sliceWidth, y, y+sliceHeight + + # find boxes that lie entirely within the window + if len(boxes) > 0: + out_path_label = os.path.join( + out_dir_labels, + out_name + slice_sep + str(y) + '_' + str(x) + '_' + + str(sliceHeight) + '_' + str(sliceWidth) + + '_' + str(pad) + '_' + str(win_w) + '_' + str(win_h) + + '.txt') + for j,b in enumerate(boxes): + yolo_class = yolo_classes[j] + xb0, yb0, xb1, yb1 = b + if (xb0 >= xmin) and (yb0 >= ymin) \ + and (xb1 <= xmax) and (yb1 <= ymax): + # get box coordinates within window + out_box_tmp = [xb0 - xmin, xb1 - xmin, + yb0 - ymin, yb1 - ymin] + print(" out_box_tmp:", out_box_tmp) + # out_boxes.append(out_box_tmp) + # convert to yolo coords (x,y,w,h) + yolo_coords = convert((sliceWidth, sliceHeight), + out_box_tmp) + print(" yolo_coords:", yolo_coords) + out_boxes_yolo.append(yolo_coords) + out_classes_yolo.append(yolo_class) + + # skip if no labels? + if len(out_boxes_yolo) == 0: + continue + + # save yolo labels + txt_outfile = open(out_path_label, "w") + for yolo_class, yolo_coord in zip(out_classes_yolo, out_boxes_yolo): + outstring = str(yolo_class) + " " + " ".join([str(a) for a in yolo_coord]) + '\n' + if verbose: + print(" outstring:", outstring.strip()) + txt_outfile.write(outstring) + txt_outfile.close() + + # save mask, if desired + if mask_path: + mask_c = mask[y:y + sliceHeight, x:x + sliceWidth] + outpath_mask = os.path.join( + out_dir_masks, + out_name + slice_sep + str(y) + '_' + str(x) + '_' + + str(sliceHeight) + '_' + str(sliceWidth) + + '_' + str(pad) + '_' + str(win_w) + '_' + str(win_h) + + im_ext) + skimage.io.imsave(outpath_mask, mask_c, check_contrast=False) + + # extract image + window_c = image[y:y + sliceHeight, x:x + sliceWidth] + outpath = os.path.join( + out_dir_images, + out_name + slice_sep + str(y) + '_' + str(x) + '_' + + str(sliceHeight) + '_' + str(sliceWidth) + + '_' + str(pad) + '_' + str(win_w) + '_' + str(win_h) + + im_ext) + if not os.path.exists(outpath): + skimage.io.imsave(outpath, window_c, check_contrast=False) + elif overwrite: + skimage.io.imsave(outpath, window_c, check_contrast=False) + else: + print("outpath {} exists, skipping".format(outpath)) + + print("Num slices:", n_ims, + "sliceHeight", sliceHeight, "sliceWidth", sliceWidth) + print("Time to slice", image_path, time.time()-t0, "seconds") + + return +############################################################################### +def twinx_function(x, raw=False): + V = 3./x + if raw: + return V + else: + return ["%.1f" % z for z in V] + # return [z for z in V] + + +############################################################################### +def piecewise_linear(x, x0, y0, k1, k2): + return np.piecewise(x, + [x < x0], + [lambda x:k1*x + y0-k1*x0, lambda x:k2*x + y0-k2*x0]) + + +############################################################################### +def _file_len(fname): + '''Return length of file''' + try: + with open(fname) as f: + for i, l in enumerate(f): + pass + return i + 1 + except: + return 0 + + +############################################################################### +def _run_cmd(cmd): + '''Write to stdout, etc,(incompatible with nohup)''' + p = Popen(cmd, stdout=PIPE, stderr=STDOUT, shell=True) + while True: + line = p.stdout.readline() + if not line: + break + print(line.replace('\n', '')) + return + + + +# https://github.com/CosmiQ/simrdwn/blob/master/simrdwn/data_prep/yolt_data_prep_funcs.py +############################################################################### +def convert(size, box): + '''Input = image size: (w,h), box: [x0, x1, y0, y1] + Return yolo coords: normalized (x, y, w, h)''' + dw = 1./size[0] + dh = 1./size[1] + xmid = (box[0] + box[1])/2.0 + ymid = (box[2] + box[3])/2.0 + w0 = box[1] - box[0] + h0 = box[3] - box[2] + x = xmid*dw + y = ymid*dh + w = w0*dw + h = h0*dh + return (x,y,w,h) + + +# https://github.com/CosmiQ/simrdwn/blob/master/simrdwn/data_prep/yolt_data_prep_funcs.py +############################################################################### +def convert_reverse(size, box): + '''Back out pixel coords from yolo format + input = image_size (w,h), + box = [x,y,w,h]''' + x, y, w, h = box + dw = 1./size[0] + dh = 1./size[1] + + w0 = w/dw + h0 = h/dh + xmid = x/dw + ymid = y/dh + + x0, x1 = xmid - w0/2., xmid + w0/2. + y0, y1 = ymid - h0/2., ymid + h0/2. + + return [x0, x1, y0, y1] + +############################################################################### + + + +############################################################################### +def slice_im_plus_df(image_path, out_name, out_dir_images, + label_df=None, + min_obj_frac=0.7, + geometry_col='geometry_poly_pixel', + category_col='Category', + out_dir_geojson=None, + sliceHeight=416, sliceWidth=416, + overlap=0.1, slice_sep='|', pad=0, + skip_highly_overlapped_tiles=False, + overwrite=False, + keep_empty_geojsons=False, + out_ext='.png', verbose=False): + + """ + Slice a large image into smaller windows, and also return boxes labels + withing the window (label_df is a geojson of labels) + Adapted from: + https://github.com/avanetten/simrdwn/blob/master/simrdwn/core/slice_im.py + + Arguments + --------- + image_path : str + Location of image to slice + out_name : str + Root name of output files (coordinates will be appended to this) + out_dir_images : str + Output directory for images + label_df : dataframe + dataframe of labels + sliceHeight : int + Height of each slice. Defaults to ``416``. + sliceWidth : int + Width of each slice. Defaults to ``416``. + overlap : float + Fractional overlap of each window (e.g. an overlap of 0.2 for a window + of size 256 yields an overlap of 51 pixels). + Default to ``0.1``. + slice_sep : str + Character used to separate outname from coordinates in the saved + windows. Defaults to ``|`` + out_ext : str + Extension of saved images. Defaults to ``.png``. + verbose : boolean + Switch to print relevant values to screen. Defaults to ``False`` + + Returns + ------- + None + """ + + if len(out_ext) == 0: + im_ext = '.' + image_path.split('.')[-1] + else: + im_ext = out_ext + + t0 = time.time() + image = skimage.io.imread(image_path) #, as_grey=False).astype(np.uint8) # [::-1] + if verbose: + print("image.shape:", image.shape) + win_h, win_w = image.shape[:2] + win_size = sliceHeight*sliceWidth + dx = int((1. - overlap) * sliceWidth) + dy = int((1. - overlap) * sliceHeight) + + n_ims = 0 + for y0 in range(0, image.shape[0], dy): + for x0 in range(0, image.shape[1], dx): + out_boxes_yolo = [] + out_classes_yolo = [] + n_ims += 1 + + if (n_ims % 100) == 0: + print(n_ims) + + # make sure we don't have a tiny image on the edge + if y0+sliceHeight > image.shape[0]: + # skip if too much overlap (> 0.6) + if skip_highly_overlapped_tiles: + if (y0+sliceHeight - image.shape[0]) > (0.6*sliceHeight): + continue + else: + y = image.shape[0] - sliceHeight + else: + y = image.shape[0] - sliceHeight + else: + y = y0 + if x0+sliceWidth > image.shape[1]: + # skip if too much overlap (> 0.6) + if skip_highly_overlapped_tiles: + if (x0+sliceWidth - image.shape[1]) > (0.6*sliceWidth): + continue + else: + x = image.shape[1] - sliceWidth + else: + x = image.shape[1] - sliceWidth + else: + x = x0 + + xmin, xmax, ymin, ymax = x, x+sliceWidth, y, y+sliceHeight + + # extract labels from window + if label_df is not None: + # get geom of window (see prep_train.get_window_geoms()) + win_p1 = shapely.geometry.Point(xmin, ymin) + win_p2 = shapely.geometry.Point(xmax, ymin) + win_p3 = shapely.geometry.Point(xmax, ymax) + win_p4 = shapely.geometry.Point(xmin, ymax) + pointList = [win_p1, win_p2, win_p3, win_p4, win_p1] + geom_window = shapely.geometry.Polygon([[p.x, p.y] for p in pointList]) + + # get objects within the window + # obj_list has form: [[index_nest, cat_nest, x0_obj, y0_obj, x1_obj, y1_obj], ...] + obj_list = get_objs_in_window(label_df, geom_window, + min_obj_frac=min_obj_frac, + geometry_col=geometry_col, category_col=category_col, + use_box_geom=True, verbose=False) + + # create output gdf, geojson + outpath_geojson = os.path.join( + out_dir_geojson, + out_name + slice_sep + str(y) + '_' + str(x) + '_' + + str(sliceHeight) + '_' + str(sliceWidth) + + '_' + str(pad) + '_' + str(win_w) + '_' + str(win_h) + + '.geojson') + if len(obj_list) == 0: + if keep_empty_geojsons: + if out_dir_geojson: + # print("Empty dataframe, writing empty gdf", output_path) + open(outpath_geojson, 'a').close() + else: + index_l, cat_l, geom_l = [], [], [] + for row in obj_list: + index_nest, cat_nest, xmin_tmp, ymin_tmp, xmax_tmp, ymax_tmp = row + tmp_p1 = shapely.geometry.Point(xmin_tmp, ymin_tmp) + tmp_p2 = shapely.geometry.Point(xmax_tmp, ymin_tmp) + tmp_p3 = shapely.geometry.Point(xmax_tmp, ymax_tmp) + tmp_p4 = shapely.geometry.Point(xmin_tmp, ymax_tmp) + pointList = [tmp_p1, tmp_p2, tmp_p3, tmp_p4, tmp_p1] + geom_tmp = shapely.geometry.Polygon([[p.x, p.y] for p in pointList]) + index_l.append(index_nest) + cat_l.append(cat_nest) + geom_l.append(geom_tmp) + # construct dataframe + dict_tmp = {'index_nest': index_l, category_col: cat_l, geometry_col: geom_l} + gdf_tmp = gpd.GeoDataFrame(dict_tmp) + # print("gdf_tmp:", gdf_tmp) + # save to geojson, if desired + if out_dir_geojson: + gdf_tmp.to_file(outpath_geojson, driver='GeoJSON') + + # extract image + window_c = image[y:y + sliceHeight, x:x + sliceWidth] + outpath = os.path.join( + out_dir_images, + out_name + slice_sep + str(y) + '_' + str(x) + '_' + + str(sliceHeight) + '_' + str(sliceWidth) + + '_' + str(pad) + '_' + str(win_w) + '_' + str(win_h) + + im_ext) + if not os.path.exists(outpath): + skimage.io.imsave(outpath, window_c, check_contrast=False) + elif overwrite: + skimage.io.imsave(outpath, window_c, check_contrast=False) + else: + if verbose: + print("outpath {} exists, skipping".format(outpath)) + + print("Num slices:", n_ims, + "sliceHeight", sliceHeight, "sliceWidth", sliceWidth) + print("Time to slice", image_path, time.time()-t0, "seconds") + return +