Merge pull request #268 from creatermaker/main

This is the improved version of image-tiling.

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: []

component-library/input/image-tiling.ipynb

@@ -0,0 +1,182 @@
+{
+ "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
+}

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

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}