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Merge pull request #268 from creatermaker/main
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This is the improved version of image-tiling.
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@romeokienzler
romeokienzler authored May 31, 2024
2 parents 8a05abd + 3a1008f commit 2dcb166
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57 changes: 57 additions & 0 deletions component-library/input/image-tiling.cwl
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cwlVersion: v1.2
class: CommandLineTool

baseCommand: "claimed"

inputs:
component:
type: string
default: docker.io/mdorzweiler/claimed-image-tiling:0.1
inputBinding:
position: 1
prefix: --component
log_level:
type: string
default: "INFO"
inputBinding:
position: 2
prefix: --log_level
directory_path:
type: string
default: None
inputBinding:
position: 3
prefix: --directory_path
destination:
type: string
default: None
inputBinding:
position: 4
prefix: --destination
tile_size_x:
type: string
default: None
inputBinding:
position: 5
prefix: --tile_size_x
tile_size_y:
type: string
default: None
inputBinding:
position: 6
prefix: --tile_size_y
stride_x:
type: string
default: None
inputBinding:
position: 7
prefix: --stride_x
stride_y:
type: string
default: None
inputBinding:
position: 8
prefix: --stride_y


outputs: []
182 changes: 182 additions & 0 deletions component-library/input/image-tiling.ipynb
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{
"cells": [
{
"cell_type": "markdown",
"id": "2e8a0fac-adbd-4428-90ea-869aee2b95bf",
"metadata": {},
"source": [
"## Xview Dataset clipping\n",
"This is a component designed to clip the dataset provided by xview. "
]
},
{
"cell_type": "code",
"execution_count": 3,
"id": "c0421aaf-4da4-4a66-b626-e8962315afe8",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Requirement already satisfied: Pillow in /Users/maxdorzweiler/anaconda3/lib/python3.11/site-packages (9.4.0)\n"
]
}
],
"source": [
"!pip install Pillow"
]
},
{
"cell_type": "code",
"execution_count": 2,
"id": "0b7ad533-dabc-488e-bf65-59a54a85f3f9",
"metadata": {},
"outputs": [],
"source": [
"\n",
"import os\n",
"from PIL import Image\n"
]
},
{
"cell_type": "code",
"execution_count": 4,
"id": "c8df047b-6167-43f1-9a31-d836580180ac",
"metadata": {},
"outputs": [],
"source": [
"\n",
"#directory_path is the path to the folder with the unzipped .tif images from xview dataset \n",
"directory_path = os.environ.get(\"directory_path\")\n",
"\n",
"#destination is the path to the folder which saves all the extracted tiles. \n",
"destination = os.environ.get(\"destination\")\n",
"\n",
"#Each image is cropped using a rectangular window with edge_length tile_size_x and tile_size_y which has to be given in number of pixels \n",
"tile_size_x = os.environ.get(\"tile_size_x\")\n",
"tile_size_y = os.environ.get(\"tile_size_y\")\n",
"\n",
"#stride_x is the length in pixels the sliding window is moved to the right after each step\n",
"#stride_y is the length in pixels the sliding window is moved down after completing a row\n",
"#For tumbling window stride_x must equal tile_size_x and stride_y must equal tile_size_y\n",
"stride_x = os.environ.get(\"stride_x\")\n",
"stride_y = os.environ.get(\"stride_y\")\n"
]
},
{
"cell_type": "code",
"execution_count": 5,
"id": "8ed74228-937d-4d5d-b6d9-97026af3eb50",
"metadata": {},
"outputs": [],
"source": [
"\n",
"def clear_directory(directory):\n",
" for item in os.listdir(directory):\n",
" item_path = os.path.join(directory, item)\n",
" # Check if the item is a file\n",
" if os.path.isfile(item_path):\n",
" # If it's a file, remove it\n",
" os.remove(item_path)\n",
" # If it's a directory, recursively clear it\n",
" elif os.path.isdir(item_path):\n",
" clear_directory(item_path)\n",
" os.rmdir(item_path)\n",
" "
]
},
{
"cell_type": "code",
"execution_count": 9,
"id": "d6e89f94-490a-4c1a-80cd-f2ab30adb374",
"metadata": {},
"outputs": [],
"source": [
"\n",
"def sliding_window(directory_path, destination, tile_size_x, tile_size_y, stride_x, stride_y):\n",
" \n",
" if os.path.isdir(destination):\n",
" clear_directory(destination)\n",
" else: \n",
" os.makedirs(destination)\n",
" \n",
" \n",
" for item in os.listdir(directory_path):\n",
" if item == \".DS_Store\":\n",
" continue\n",
" item_path = os.path.join(directory_path, item)\n",
" clipped_item = os.path.join(destination, item)\n",
" os.makedirs(clipped_item)\n",
" \n",
" image = Image.open(item_path)\n",
" width, height = image.size\n",
" \n",
" x_range = [0]\n",
" while(x_range[-1] + stride_x + tile_size_x < width):\n",
" x_range += [x_range[-1] + stride_x]\n",
" \n",
" y_range = [0]\n",
" while(y_range[-1] + stride_y + tile_size_y < height):\n",
" y_range += [y_range[-1] + stride_y]\n",
" \n",
" counter = 0\n",
" for x in x_range:\n",
" for y in y_range:\n",
" cropped = image.crop((x,y, x+tile_size_x, y+tile_size_y))\n",
"\n",
" file_name = \"{}\".format(y)\n",
" file_name += \"_{}\".format(x) + \".tif\"\n",
" path = os.path.join(clipped_item, file_name)\n",
" \n",
" cropped.save(path)\n",
" \n"
]
},
{
"cell_type": "code",
"execution_count": 10,
"id": "ce60bf47-7235-43a1-a4f7-5b81080d617d",
"metadata": {},
"outputs": [
{
"ename": "TypeError",
"evalue": "stat: path should be string, bytes, os.PathLike or integer, not NoneType",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mTypeError\u001b[0m Traceback (most recent call last)",
"Cell \u001b[0;32mIn[10], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m sliding_window(directory_path, destination, tile_size_x, tile_size_y, stride_x, stride_y)\n",
"Cell \u001b[0;32mIn[9], line 3\u001b[0m, in \u001b[0;36msliding_window\u001b[0;34m(directory_path, destination, tile_size_x, tile_size_y, stride_x, stride_y)\u001b[0m\n\u001b[1;32m 1\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21msliding_window\u001b[39m(directory_path, destination, tile_size_x, tile_size_y, stride_x, stride_y):\n\u001b[0;32m----> 3\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m os\u001b[38;5;241m.\u001b[39mpath\u001b[38;5;241m.\u001b[39misdir(destination):\n\u001b[1;32m 4\u001b[0m clear_directory(destination)\n\u001b[1;32m 5\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m: \n",
"File \u001b[0;32m<frozen genericpath>:42\u001b[0m, in \u001b[0;36misdir\u001b[0;34m(s)\u001b[0m\n",
"\u001b[0;31mTypeError\u001b[0m: stat: path should be string, bytes, os.PathLike or integer, not NoneType"
]
}
],
"source": [
"sliding_window(directory_path, destination, tile_size_x, tile_size_y, stride_x, stride_y)"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3 (ipykernel)",
"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": "3.11.9"
}
},
"nbformat": 4,
"nbformat_minor": 5
}
30 changes: 30 additions & 0 deletions component-library/input/image-tiling.job.yaml
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apiVersion: batch/v1
kind: Job
metadata:
name: image-tiling
spec:
template:
spec:
containers:
- name: image-tiling
image: docker.io/mdorzweiler/claimed-image-tiling:0.1
workingDir: /opt/app-root/src/
command: ["/opt/app-root/bin/ipython","claimed_image-tiling.ipynb"]
env:
- name: log_level
value: value_of_log_level
- name: directory_path
value: value_of_directory_path
- name: destination
value: value_of_destination
- name: tile_size_x
value: value_of_tile_size_x
- name: tile_size_y
value: value_of_tile_size_y
- name: stride_x
value: value_of_stride_x
- name: stride_y
value: value_of_stride_y
restartPolicy: OnFailure
imagePullSecrets:
- name: image_pull_secret
31 changes: 31 additions & 0 deletions component-library/input/image-tiling.yaml
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name: image-tiling
description: "## Xview Dataset clipping – CLAIMED V0.1"

inputs:
- {name: log_level, type: String, description: "update log level", default: "INFO"}
- {name: directory_path, type: String, description: "directory_path is the path to the folder with the unzipped .tif images from xview dataset"}
- {name: destination, type: String, description: "destination is the path to the folder which saves all the extracted tiles."}
- {name: tile_size_x, type: String, description: "Each image is cropped using a rectangular window with edge_length tile_size_x and tile_size_y which has to be given in number of pixels"}
- {name: tile_size_y, type: String, description: ""}
- {name: stride_x, type: String, description: "For tumbling window stride_x must equal tile_size_x and stride_y must equal tile_size_y"}
- {name: stride_y, type: String, description: ""}


outputs:


implementation:
container:
image: docker.io/mdorzweiler/claimed-image-tiling:0.1
command:
- sh
- -ec
- |
ipython ./claimed_image-tiling.ipynb log_level="${0}" directory_path="${1}" destination="${2}" tile_size_x="${3}" tile_size_y="${4}" stride_x="${5}" stride_y="${6}"
- {inputValue: log_level}
- {inputValue: directory_path}
- {inputValue: destination}
- {inputValue: tile_size_x}
- {inputValue: tile_size_y}
- {inputValue: stride_x}
- {inputValue: stride_y}

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