From 3990adec04e2d5ff5adda7d917d4c13989ab320d Mon Sep 17 00:00:00 2001
From: leminen <slm@eng.au.dk>
Date: Mon, 10 Feb 2020 22:43:44 +0100
Subject: [PATCH] Added first files
---
.gitattributes | 1 +
.../T01_Box007_2017-05-19T07-04-11-349.jpg | 3 +
.../T01_Box007_2017-05-19T07-04-11-349.json | 1 +
.../T01_Box007_2017-06-03T09-02-22-390.jpg | 3 +
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SCRIPTS/OPPD_utils.py | 182 ++++++++++++++++++
79 files changed, 364 insertions(+)
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diff --git a/DATA/images_fullbox/CENCY/T01_Box051_2017-05-19T10-33-58-890.json b/DATA/images_fullbox/CENCY/T01_Box051_2017-05-19T10-33-58-890.json
new file mode 100644
index 0000000000..62253a51d7
--- /dev/null
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+[{"filename": "edb986e5-ec23-9ab9-3436-f2a100dd52c5.jpg", "plant_id": "EROCI_edb986e5-ec23-9ab9-3436-f2a100dd52c5", "eppo": "EROCI", "date": "2017-09-04T13:10:59.983000", "trial_id": "T02", "box_id": "Box050", "growth_condition": "G3", "source_img_filename": "T02_Box050_2017-09-04T13-10-59-983.jpg", "source_image_id": 278467, "source_bndbox_id": "edb986e5-ec23-9ab9-3436-f2a100dd52c5"}, {"filename": "0f37652f-bd29-45cd-b060-e5a012c81cb2.jpg", "plant_id": "EROCI_8b5b9445-f5cb-4fd5-815a-6f9cb43eccbc", "eppo": "EROCI", "date": "2017-09-13T06:44:49.843000", "trial_id": "T02", "box_id": "Box006", "growth_condition": "G1", "source_img_filename": "T02_Box006_2017-09-13T06-44-49-843.jpg", "source_image_id": 278915, "source_bndbox_id": "0f37652f-bd29-45cd-b060-e5a012c81cb2"}, {"filename": "0488fb3f-880e-f96e-1baa-384ab9ccf8e2.jpg", "plant_id": "EROCI_f4596441-959f-3255-8855-359d1d14d11c", "eppo": "EROCI", "date": "2017-09-04T13:10:59.983000", "trial_id": "T02", "box_id": "Box050", "growth_condition": "G3", "source_img_filename": "T02_Box050_2017-09-04T13-10-59-983.jpg", "source_image_id": 278467, "source_bndbox_id": "0488fb3f-880e-f96e-1baa-384ab9ccf8e2"}, {"filename": "84358abe-e9bd-ca8b-3d7a-bc6e904f7a41.jpg", "plant_id": "EROCI_99cb994e-e8c8-4169-acf7-b98750c5df42", "eppo": "EROCI", "date": "2017-09-10T05:55:33.299000", "trial_id": "T02", "box_id": "Box006", "growth_condition": "G1", "source_img_filename": "T02_Box006_2017-09-10T05-55-33-299.jpg", "source_image_id": 278745, "source_bndbox_id": "84358abe-e9bd-ca8b-3d7a-bc6e904f7a41"}, {"filename": "42805a38-e926-4645-adcf-dd6b21b5a08a.jpg", "plant_id": "EROCI_d6c540f7-503a-1ca2-4fd1-593c2d7ed739", "eppo": "EROCI", "date": "2017-09-04T13:12:46.847000", "trial_id": "T02", "box_id": "Box006", "growth_condition": "G1", "source_img_filename": "T02_Box006_2017-09-04T13-12-46-847.jpg", "source_image_id": 278483, "source_bndbox_id": "42805a38-e926-4645-adcf-dd6b21b5a08a"}, {"filename": "9eb386f9-82b4-4278-9a46-e7bb4922577d.jpg", "plant_id": "EROCI_9eb386f9-82b4-4278-9a46-e7bb4922577d", "eppo": "EROCI", "date": "2017-09-04T07:12:50.005000", "trial_id": "T02", "box_id": "Box006", "growth_condition": "G1", "source_img_filename": "T02_Box006_2017-09-04T07-12-50-005.jpg", "source_image_id": 278387, "source_bndbox_id": "9eb386f9-82b4-4278-9a46-e7bb4922577d"}, {"filename": "be05445c-d8ff-4e39-b2e8-89e9dc667a0b.jpg", "plant_id": "EROCI_42581edd-93b3-d696-febe-7fe1d71e2089", "eppo": "EROCI", "date": "2017-09-12T09:17:28.007000", "trial_id": "T02", "box_id": "Box050", "growth_condition": "G3", "source_img_filename": "T02_Box050_2017-09-12T09-17-28-007.jpg", "source_image_id": 278874, "source_bndbox_id": "be05445c-d8ff-4e39-b2e8-89e9dc667a0b"}, {"filename": "4abbea57-b1bc-fe60-fc5e-d0d71beba7dd.jpg", "plant_id": "EROCI_16a07947-c388-473a-9172-860a877207f8", "eppo": "EROCI", "date": "2017-09-06T11:15:08.371000", "trial_id": "T02", "box_id": "Box028", "growth_condition": "G2", "source_img_filename": "T02_Box028_2017-09-06T11-15-08-371.jpg", "source_image_id": 278604, "source_bndbox_id": "4abbea57-b1bc-fe60-fc5e-d0d71beba7dd"}, {"filename": "268f7ff1-7c0f-1a1e-2d03-78882befaf1e.jpg", "plant_id": "EROCI_0dc9bdf2-0a63-8398-3057-82834eeecf3c", "eppo": "EROCI", "date": "2017-09-18T08:55:12.543000", "trial_id": "T02", "box_id": "Box050", "growth_condition": "G3", "source_img_filename": "T02_Box050_2017-09-18T08-55-12-543.jpg", "source_image_id": 279129, "source_bndbox_id": "268f7ff1-7c0f-1a1e-2d03-78882befaf1e"}, {"filename": "0ff1c30b-5dfc-402a-bbc1-3d7824e863dc.jpg", "plant_id": "EROCI_737d64c1-1478-4b38-bf24-54326e0b7000", "eppo": "EROCI", "date": "2017-09-05T09:21:18.676000", "trial_id": "T02", "box_id": "Box006", "growth_condition": "G1", "source_img_filename": "T02_Box006_2017-09-05T09-21-18-676.jpg", "source_image_id": 278533, "source_bndbox_id": "0ff1c30b-5dfc-402a-bbc1-3d7824e863dc"}]
\ No newline at end of file
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diff --git a/DATA/images_plants/GALAP/annotations.json b/DATA/images_plants/GALAP/annotations.json
new file mode 100644
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+[{"filename": "8853bfdf-0acb-4059-9cd2-108212df987d.jpg", "plant_id": "GALAP_fe137bbe-3b53-4b9d-a1c6-852e8ec7c981", "eppo": "GALAP", "date": "2017-09-24T10:27:20.351000", "trial_id": "T02", "box_id": "Box001", "growth_condition": "G1", "source_img_filename": "T02_Box001_2017-09-24T10-27-20-351.jpg", "source_image_id": 279411, "source_bndbox_id": "8853bfdf-0acb-4059-9cd2-108212df987d"}, {"filename": "caa35dc8-72ab-49eb-8b26-ef7b12d5b6a1.jpg", "plant_id": "GALAP_a022f2c6-06ab-499a-9f8c-7c342276f64e", "eppo": "GALAP", "date": "2017-09-20T10:34:38.173000", "trial_id": "T02", "box_id": "Box023", "growth_condition": "G2", "source_img_filename": "T02_Box023_2017-09-20T10-34-38-173.jpg", "source_image_id": 279262, "source_bndbox_id": "caa35dc8-72ab-49eb-8b26-ef7b12d5b6a1"}, {"filename": "253bf46c-d929-4024-b81a-73c6bb361548.jpg", "plant_id": "GALAP_1b245f19-0271-4459-a0ca-76f3de8fe6fc", "eppo": "GALAP", "date": "2017-09-21T10:55:42.093000", "trial_id": "T02", "box_id": "Box045", "growth_condition": "G3", "source_img_filename": "T02_Box045_2017-09-21T10-55-42-093.jpg", "source_image_id": 279305, "source_bndbox_id": "253bf46c-d929-4024-b81a-73c6bb361548"}, {"filename": "f09ad88a-0e56-65ae-2ce8-b0c41ffd87e6.jpg", "plant_id": "GALAP_e218aa95-0c05-0ef0-cbe3-3c34852ae966", "eppo": "GALAP", "date": "2017-10-23T10:26:19.806000", "trial_id": "T02", "box_id": "Box045", "growth_condition": "G3", "source_img_filename": "T02_Box045_2017-10-23T10-26-19-806.jpg", "source_image_id": 280732, "source_bndbox_id": "f09ad88a-0e56-65ae-2ce8-b0c41ffd87e6"}, {"filename": "bd8c8bb0-73d4-6300-16df-a91b9988030f.jpg", "plant_id": "GALAP_048ab68c-782d-49fe-a0e4-9ba24dba976e", "eppo": "GALAP", "date": "2017-10-13T08:10:36.555000", "trial_id": "T02", "box_id": "Box001", "growth_condition": "G1", "source_img_filename": "T02_Box001_2017-10-13T08-10-36-555.jpg", "source_image_id": 280332, "source_bndbox_id": "bd8c8bb0-73d4-6300-16df-a91b9988030f"}, {"filename": "6a231827-d9ea-5349-756d-2649d607d354.jpg", "plant_id": "GALAP_4dd3c4f5-3627-c97c-48cb-e13fae7b8522", "eppo": "GALAP", "date": "2017-09-11T10:36:24.936000", "trial_id": "T02", "box_id": "Box045", "growth_condition": "G3", "source_img_filename": "T02_Box045_2017-09-11T10-36-24-936.jpg", "source_image_id": 278768, "source_bndbox_id": "6a231827-d9ea-5349-756d-2649d607d354"}, {"filename": "f390d137-6af3-46de-9e40-191d3505fa66.jpg", "plant_id": "GALAP_f390d137-6af3-46de-9e40-191d3505fa66", "eppo": "GALAP", "date": "2017-09-13T06:19:59.034000", "trial_id": "T02", "box_id": "Box023", "growth_condition": "G2", "source_img_filename": "T02_Box023_2017-09-13T06-19-59-034.jpg", "source_image_id": 278912, "source_bndbox_id": "f390d137-6af3-46de-9e40-191d3505fa66"}, {"filename": "e591f251-2249-4129-85d7-24b9609b178c.jpg", "plant_id": "GALAP_023f2cbf-c65e-49f2-ada7-6537f15e5622", "eppo": "GALAP", "date": "2017-09-13T06:46:40.472000", "trial_id": "T02", "box_id": "Box045", "growth_condition": "G3", "source_img_filename": "T02_Box045_2017-09-13T06-46-40-472.jpg", "source_image_id": 278929, "source_bndbox_id": "e591f251-2249-4129-85d7-24b9609b178c"}, {"filename": "8265d984-99b1-49b5-8d7e-44f5b326d64a.jpg", "plant_id": "GALAP_a63a124f-58f9-4776-b325-e1d38e53133c", "eppo": "GALAP", "date": "2017-09-20T10:34:38.173000", "trial_id": "T02", "box_id": "Box023", "growth_condition": "G2", "source_img_filename": "T02_Box023_2017-09-20T10-34-38-173.jpg", "source_image_id": 279262, "source_bndbox_id": "8265d984-99b1-49b5-8d7e-44f5b326d64a"}, {"filename": "8522a1ab-4333-48d7-a7b5-de638fdf1632.jpg", "plant_id": "GALAP_bb579e69-89c5-416a-87bd-0b4a347a51a7", "eppo": "GALAP", "date": "2017-10-05T12:22:22.022000", "trial_id": "T02", "box_id": "Box023", "growth_condition": "G2", "source_img_filename": "T02_Box023_2017-10-05T12-22-22-022.jpg", "source_image_id": 279990, "source_bndbox_id": "8522a1ab-4333-48d7-a7b5-de638fdf1632"}]
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diff --git a/SCRIPTS/OPPD_utils.py b/SCRIPTS/OPPD_utils.py
new file mode 100644
index 0000000000..2bdebaa4ef
--- /dev/null
+++ b/SCRIPTS/OPPD_utils.py
@@ -0,0 +1,182 @@
+import os
+import json
+import platform
+import pandas as pd
+import numpy as np
+import cv2
+
+
+def createIfNotExist(directory):
+ """ Create directory if it does not exist
+
+ params:
+ directory (string): directort to be created
+ """
+ if not os.path.exists(directory):
+ os.makedirs(directory)
+
+def getImagesInFolder(path, extensions = ('.jpg','.png')):
+ """ Get a list of all images in a folder, including subfolders
+
+ params:
+ path: path to be searched
+ extensions: extensions to be searched for
+
+ returns:
+ lstImages: list of tuples containing folder and filename for each image
+ """
+ lstImages = []
+ for root, dirs, files in os.walk(path):
+ for name in files:
+ if name.endswith(extensions):
+ lstImages.append((root,name))
+ return lstImages
+
+
+def readJSONAnnotation(pathAnno):
+ """ Load JSON annotation file
+
+ params:
+ pathAnno: Where the JSON annotation file is located
+
+ returns:
+ anno: Dictionary containing the annotation data
+ """
+
+ with open(pathAnno) as data_file:
+ anno = json.load(data_file)
+
+ return anno
+
+def writeJSONAnnotation(pathAnno, anno):
+ """ Write annotation to JSON file
+
+ params:
+ pathAnno: Where to save the JSON annotation file
+ anno: Dictionary containing the annotation data
+ """
+ with open(pathAnno, 'w') as data_file:
+ json.dump(anno, data_file)
+
+
+def printWithStyle(msg, colour=None, formating=None):
+ """ Print to terminal with colour and formating style,
+
+ params:
+ msg: Message to print
+ colour: string with color for msg. Supported values {'GRAY','RED','GREEN','YELLOW','BLUE','MAGENTA','CYAN'}
+ formating: list of strings with formating options. Supported values: {'BOLD','ITALIC','UNDERLINE'}
+ """
+
+ class pcolors:
+ ENDC = '\033[0m'
+ GRAY = '\033[90m'
+ RED = '\033[91m'
+ GREEN = '\033[92m'
+ YELLOW = '\033[93m'
+ BLUE = '\033[94m'
+ MAGENTA = '\033[95m'
+ CYAN = '\33[96m'
+
+ class pformats:
+ ENDC = '\033[0m'
+ BOLD = '\033[1m'
+ ITALIC = '\033[3m'
+ UNDERLINE = '\033[4m'
+
+ # ADD colour
+ if colour == 'GRAY':
+ msg = pcolors.GRAY + msg + pcolors.ENDC
+ elif colour == 'RED':
+ msg = pcolors.RED + msg + pcolors.ENDC
+ elif colour == 'GREEN':
+ msg = pcolors.GREEN + msg + pcolors.ENDC
+ elif colour == 'YELLOW':
+ msg = pcolors.YELLOW + msg + pcolors.ENDC
+ elif colour == 'BLUE':
+ msg = pcolors.BLUE + msg + pcolors.ENDC
+ elif colour == 'MAGENTA':
+ msg = pcolors.MAGENTA + msg + pcolors.ENDC
+ elif colour == 'CYAN':
+ msg = pcolors.CYAN + msg + pcolors.ENDC
+ else:
+ msg = msg
+
+ # ADD formating
+ if formating:
+ if "BOLD" in formating:
+ msg = pformats.BOLD + msg + pformats.ENDC
+ if "ITALIC" in formating:
+ msg = pformats.ITALIC + msg + pformats.ENDC
+ if "UNDERLINE" in formating:
+ msg = pformats.UNDERLINE + msg + pformats.ENDC
+
+ print(msg)
+
+
+def unique_lst(lst):
+ # intilize a null list
+ lst_unique = []
+
+ # traverse for all elements
+ for element in lst:
+ if element not in lst_unique:
+ lst_unique.append(element)
+
+ return lst_unique
+
+def addPolygon2Image(img, polygon, color=(255,0,0), alpha=0.2, thickness=5):
+ """ Add polygon to an image
+
+ params:
+ img: cv2 image
+ polygon: array of corner coordinates
+ color: color for polygon
+ alpha: transparency of polygon fill
+ thickness: thickness of polygon lines
+
+ returns:
+ output: image with added polygon
+ """
+ overlay = img.copy()
+ output = img.copy()
+ polygon = [np.int32(polygon)]
+
+ # cv2.polylines(overlay, [corners], 1, color)
+ cv2.fillPoly(overlay, polygon, color)
+ cv2.addWeighted(overlay, alpha, output, 1 - alpha, 0, output)
+ cv2.polylines(output, polygon, 1, color, thickness)
+
+ return output
+
+def bndbox2polygon(bndbox):
+ polygon = np.array([[bndbox['xmin'],bndbox['ymin']],
+ [bndbox['xmin'],bndbox['ymax']],
+ [bndbox['xmax'],bndbox['ymax']],
+ [bndbox['xmax'],bndbox['ymin']]],dtype=np.int32)
+ return polygon
+
+def addBndBoxes2Image(path_img, color=(255,0,0), alpha=0.2, thickness=5):
+ """ Add a polygon for each bounding box annotation associated with the image
+
+ params:
+ path_img: path to image
+ color: color of the polygons
+ alpha: transparency of polygons fill
+ thickness: thickness of polygons lines
+
+ returns:
+ output: image with added polygons for each bounding box
+ """
+ path_anno = path_img.replace('.jpg','.json')
+ image = cv2.imread(path_img)
+ anno = readJSONAnnotation(path_anno)
+
+ output = image.copy()
+ for plant in anno['plants']:
+ bndbox = plant['bndbox']
+ coor_bndbox = bndbox2polygon(bndbox)
+
+ output = addPolygon2Image(output,coor_bndbox, color,alpha, thickness)
+
+ return output
--
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