clipping claimed component for the xView dataset

component-library/input/input-xView-clipping.cwl

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+cwlVersion: v1.2
+class: CommandLineTool
+
+baseCommand: "claimed"
+
+inputs:
+  component:
+    type: string
+    default: docker.io/mdorzweiler/claimed-input-xview-clipping: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
+  window_size:
+    type: string
+    default: None
+    inputBinding:
+      position: 4
+      prefix: --window_size
+  step_size:
+    type: string
+    default: None
+    inputBinding:
+      position: 5
+      prefix: --step_size
+
+
+outputs: []

component-library/input/input-xView-clipping.ipynb

@@ -0,0 +1,178 @@
+{
+ "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": 98,
+   "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": 96,
+   "id": "0b7ad533-dabc-488e-bf65-59a54a85f3f9",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "\n",
+    "import os\n",
+    "from PIL import Image\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 90,
+   "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",
+    "#Each image is cropped using a square window with edge_length window_size which has to be given in number of pixels \n",
+    "window_size = os.environ.get(\"window_size\")\n",
+    "\n",
+    "#step_size is the length in pixels the sliding window is moved after each step\n",
+    "#For tumbling window step_size must equal window_size\n",
+    "step_size = os.environ.get(\"step_size\")\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 91,
+   "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": 92,
+   "id": "d6e89f94-490a-4c1a-80cd-f2ab30adb374",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "\n",
+    "def sliding_window(directory_path, window_size, step_size):\n",
+    "    \n",
+    "    parent_dir = os.path.dirname(directory_path)\n",
+    "\n",
+    "    clipped = os.path.join(parent_dir, \"clipped\")\n",
+    "    if os.path.isdir(clipped):\n",
+    "        clear_directory(clipped)\n",
+    "    else: \n",
+    "        os.makedirs(clipped)\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(clipped, 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] + step_size + window_size < width):\n",
+    "            x_range += [x_range[-1] + step_size]\n",
+    "        \n",
+    "        y_range = [0]\n",
+    "        while(y_range[-1] + step_size + window_size < height):\n",
+    "            y_range += [y_range[-1] + step_size]\n",
+    "        \n",
+    "        counter = 0\n",
+    "        for x in x_range:\n",
+    "            for y in y_range:\n",
+    "                cropped = image.crop((x,y, x+window_size, y+window_size))\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"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 93,
+   "id": "ce60bf47-7235-43a1-a4f7-5b81080d617d",
+   "metadata": {},
+   "outputs": [
+    {
+     "ename": "TypeError",
+     "evalue": "expected str, bytes or os.PathLike object, 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[93], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m sliding_window(directory_path, window_size, step_size)\n",
+      "Cell \u001b[0;32mIn[92], line 3\u001b[0m, in \u001b[0;36msliding_window\u001b[0;34m(directory_path, window_size, step_size)\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, window_size, step_size):\n\u001b[0;32m----> 3\u001b[0m     parent_dir \u001b[38;5;241m=\u001b[39m os\u001b[38;5;241m.\u001b[39mpath\u001b[38;5;241m.\u001b[39mdirname(directory_path)\n\u001b[1;32m      5\u001b[0m     clipped \u001b[38;5;241m=\u001b[39m os\u001b[38;5;241m.\u001b[39mpath\u001b[38;5;241m.\u001b[39mjoin(parent_dir, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mclipped\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m      6\u001b[0m     \u001b[38;5;28;01mif\u001b[39;00m os\u001b[38;5;241m.\u001b[39mpath\u001b[38;5;241m.\u001b[39misdir(clipped):\n",
+      "File \u001b[0;32m<frozen posixpath>:152\u001b[0m, in \u001b[0;36mdirname\u001b[0;34m(p)\u001b[0m\n",
+      "\u001b[0;31mTypeError\u001b[0m: expected str, bytes or os.PathLike object, not NoneType"
+     ]
+    }
+   ],
+   "source": [
+    "sliding_window(directory_path, window_size, step_size)"
+   ]
+  }
+ ],
+ "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/input-xView-clipping.job.yaml

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+apiVersion: batch/v1
+kind: Job
+metadata:
+  name: input-xview-clipping
+spec:
+  template:
+    spec:
+      containers:
+      - name: input-xview-clipping
+        image: docker.io/mdorzweiler/claimed-input-xview-clipping:0.1
+        workingDir: /opt/app-root/src/
+        command: ["/opt/app-root/bin/ipython","claimed_input-xView-clipping.ipynb"]
+        env:
+        - name: log_level
+          value: value_of_log_level
+        - name: directory_path
+          value: value_of_directory_path
+        - name: window_size
+          value: value_of_window_size
+        - name: step_size
+          value: value_of_step_size
+      restartPolicy: OnFailure
+      imagePullSecrets:
+        - name: image_pull_secret

component-library/input/input-xView-clipping.yaml

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+name: input-xview-clipping
+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: window_size, type: String, description: "Each image is cropped using a square window with edge_length window_size which has to be given in number of pixels"}
+- {name: step_size, type: String, description: "For tumbling window step_size must equal window_size"}
+
+
+outputs:
+
+
+implementation:
+    container:
+        image: docker.io/mdorzweiler/claimed-input-xview-clipping:0.1
+        command:
+        - sh
+        - -ec
+        - |
+          ipython ./claimed_input-xView-clipping.ipynb log_level="${0}" directory_path="${1}" window_size="${2}" step_size="${3}" 
+        - {inputValue: log_level}
+        - {inputValue: directory_path}
+        - {inputValue: window_size}
+        - {inputValue: step_size}