From 4d8830d349f83bad35240eb4dca769cc69f584a7 Mon Sep 17 00:00:00 2001 From: Sean Orzolek <44307229+smo216@users.noreply.github.com> Date: Mon, 21 Oct 2019 12:29:33 -0400 Subject: [PATCH] Slices up 16 bit images into a 24x24 grid of 256x170 pixels --- Image_Slicing_Script.ipynb | 1100 ++++++++++++++++++++++++++++++++++++ 1 file changed, 1100 insertions(+) create mode 100644 Image_Slicing_Script.ipynb diff --git a/Image_Slicing_Script.ipynb b/Image_Slicing_Script.ipynb new file mode 100644 index 0000000..29d48d2 --- /dev/null +++ b/Image_Slicing_Script.ipynb @@ -0,0 +1,1100 @@ +{ + "nbformat": 4, + "nbformat_minor": 0, + "metadata": { + "colab": { + "name": "Image Slicing Script.ipynb", + "provenance": [], + "collapsed_sections": [], + "machine_shape": "hm", + "include_colab_link": true + }, + "kernelspec": { + "name": "python3", + "display_name": "Python 3" + } + }, + "cells": [ + { + "cell_type": "markdown", + "metadata": { + "id": "view-in-github", + "colab_type": "text" + }, + "source": [ + "\"Open" + ] + }, + { + "cell_type": "code", + "metadata": { + "id": "VTFUhEmITcxd", + "colab_type": "code", + "outputId": "3a6dd7fa-b44c-4528-82c4-54ce2eeb4d25", + "colab": { + "base_uri": "https://localhost:8080/", + "height": 70 + } + }, + "source": [ + "#load multiple data\n", + "\"\"\"Utilize histogram matching to normalize images? https://scikit-image.org/docs/stable/auto_examples/transform/plot_histogram_matching.html#sphx-glr-auto-examples-transform-plot-histogram-matching-py\"\"\"\n", + "## For Image portion\n", + "\n", + "from google.colab import drive\n", + "drive.mount('/content/gdrive')\n", + "from PIL import Image\n", + "from pylab import *\n", + "# importing os module \n", + "import os \n", + "from skimage import io\n", + "import matplotlib.pyplot as plt\n", + "import numpy as np\n", + "import glob\n", + "import cv2\n", + "from skimage.io import imread_collection\n", + "from skimage.util import img_as_ubyte\n", + "from skimage import data\n", + "from skimage.exposure import histogram\n", + "import skimage\n", + "import pandas as pd\n", + "from pandas import read_csv\n", + "from skimage.transform import rescale, resize, downscale_local_mean\n", + "\n", + "slicepath=\"//content//gdrive//My Drive//PhD Image Processing//Python HP//HP-16-Test\"\n", + "os.chdir(slicepath)\n", + "slicecol=imread_collection('*.tif') #grab all files with .tif format\n", + "print(slicecol)\n", + "Ls=len(slicecol)\n", + "sliceim=array(slicecol[:])\n", + "cropslice=sliceim[:,0:4095,:] #crop array to remove scalebar\n", + "#print(scaleim17)\n" + ], + "execution_count": 0, + "outputs": [ + { + "output_type": "stream", + "text": [ + "Drive already mounted at /content/gdrive; to attempt to forcibly remount, call drive.mount(\"/content/gdrive\", force_remount=True).\n", + "['Copy of HP-16_16.tif', 'Copy of HP-16_17.tif', 'Copy of HP-16_18.tif', 'Copy of HP-16_19.tif', 'Copy of HP-16_20.tif', 'Copy of HP-16_21.tif', 'Copy of HP-16_22.tif', 'Copy of HP-16_23.tif', 'Copy of HP-16_24.tif', 'Copy of HP-16_25.tif']\n" + ], + "name": "stdout" + } + ] + }, + { + "cell_type": "code", + "metadata": { + "id": "ACSlOrPGCVnK", + "colab_type": "code", + "outputId": "be0182cc-b166-4821-9fc3-64c4a3630128", + "colab": { + "base_uri": "https://localhost:8080/", + "height": 1000 + } + }, + "source": [ + "\"\"\"THIS WORKS!!!!!!!!!!!!\"\"\"\n", + "from PIL import Image\n", + "img = sliceim[3]#.astype(np.uint16)#Image.open('HP-17_0.tif').convert('LA')\n", + "img=img[0:4080,:]\n", + "gridx=256\n", + "gridy=170\n", + "rangex=int(6144/gridx)\n", + "print(rangex)\n", + "rangey=int(4080/gridy)\n", + "print(rangey)\n", + "print (rangex*rangey)\n", + "for x in range(rangex):\n", + " for y in range(rangey):\n", + " slice_bit=img[y*gridy:y*gridy+gridy,x*gridx:x*gridx+gridx]\n", + " io.imsave(('Slice/HP-16_3_'+str(x)+'_'+str(y)+'.png'),slice_bit)\n", + " print('HP-16_3_'+str(x)+'_'+str(y)+'.png')\n", + "print(gridx)" + ], + "execution_count": 0, + "outputs": [ + { + "output_type": "stream", + "text": [ + "24\n", + "24\n", + "576\n", + "HP-16_3_0_0.png\n", + "HP-16_3_0_1.png\n", + "HP-16_3_0_2.png\n", + "HP-16_3_0_3.png\n", + "HP-16_3_0_4.png\n", + "HP-16_3_0_5.png\n", + "HP-16_3_0_6.png\n", + "HP-16_3_0_7.png\n", + "HP-16_3_0_8.png\n", + "HP-16_3_0_9.png\n", + "HP-16_3_0_10.png\n", + "HP-16_3_0_11.png\n", + "HP-16_3_0_12.png\n", + "HP-16_3_0_13.png\n", + "HP-16_3_0_14.png\n", + "HP-16_3_0_15.png\n", + "HP-16_3_0_16.png\n", + "HP-16_3_0_17.png\n", + "HP-16_3_0_18.png\n", + "HP-16_3_0_19.png\n", + "HP-16_3_0_20.png\n", + "HP-16_3_0_21.png\n", + "HP-16_3_0_22.png\n", + "HP-16_3_0_23.png\n", + "HP-16_3_1_0.png\n", + "HP-16_3_1_1.png\n", + "HP-16_3_1_2.png\n", + "HP-16_3_1_3.png\n", + "HP-16_3_1_4.png\n", + "HP-16_3_1_5.png\n", + "HP-16_3_1_6.png\n", + "HP-16_3_1_7.png\n", + "HP-16_3_1_8.png\n", + "HP-16_3_1_9.png\n", + "HP-16_3_1_10.png\n", + "HP-16_3_1_11.png\n", + "HP-16_3_1_12.png\n", + "HP-16_3_1_13.png\n", + "HP-16_3_1_14.png\n", + "HP-16_3_1_15.png\n", + "HP-16_3_1_16.png\n", + "HP-16_3_1_17.png\n", + "HP-16_3_1_18.png\n", + "HP-16_3_1_19.png\n", + "HP-16_3_1_20.png\n", + "HP-16_3_1_21.png\n", + "HP-16_3_1_22.png\n", + "HP-16_3_1_23.png\n", + "HP-16_3_2_0.png\n", + "HP-16_3_2_1.png\n", + "HP-16_3_2_2.png\n", + "HP-16_3_2_3.png\n", + "HP-16_3_2_4.png\n", + "HP-16_3_2_5.png\n", + "HP-16_3_2_6.png\n", + "HP-16_3_2_7.png\n", + "HP-16_3_2_8.png\n", + "HP-16_3_2_9.png\n", + "HP-16_3_2_10.png\n", + "HP-16_3_2_11.png\n", + "HP-16_3_2_12.png\n", + "HP-16_3_2_13.png\n", + "HP-16_3_2_14.png\n", + "HP-16_3_2_15.png\n", + "HP-16_3_2_16.png\n", + "HP-16_3_2_17.png\n", + "HP-16_3_2_18.png\n", + "HP-16_3_2_19.png\n", + "HP-16_3_2_20.png\n", + "HP-16_3_2_21.png\n", + "HP-16_3_2_22.png\n", + "HP-16_3_2_23.png\n", + "HP-16_3_3_0.png\n" + ], + "name": "stdout" + }, + { + "output_type": "stream", + "text": [ + "/usr/local/lib/python3.6/dist-packages/skimage/io/_io.py:141: UserWarning: Slice/HP-16_3_3_1.png is a low contrast image\n", + " warn('%s is a low contrast image' % fname)\n" + ], + "name": "stderr" + }, + { + "output_type": "stream", + "text": [ + "HP-16_3_3_1.png\n", + "HP-16_3_3_2.png\n", + "HP-16_3_3_3.png\n", + "HP-16_3_3_4.png\n", + "HP-16_3_3_5.png\n", + "HP-16_3_3_6.png\n", + "HP-16_3_3_7.png\n", + "HP-16_3_3_8.png\n" + ], + "name": "stdout" + }, + { + "output_type": "stream", + "text": [ + "/usr/local/lib/python3.6/dist-packages/skimage/io/_io.py:141: UserWarning: Slice/HP-16_3_3_4.png is a low contrast image\n", + " warn('%s is a low contrast image' % fname)\n", + "/usr/local/lib/python3.6/dist-packages/skimage/io/_io.py:141: UserWarning: Slice/HP-16_3_3_5.png is a low contrast image\n", + " warn('%s is a low contrast image' % fname)\n" + ], + "name": "stderr" + }, + { + "output_type": "stream", + "text": [ + "HP-16_3_3_9.png\n", + "HP-16_3_3_10.png\n", + "HP-16_3_3_11.png\n", + "HP-16_3_3_12.png\n", + "HP-16_3_3_13.png\n", + "HP-16_3_3_14.png\n", + "HP-16_3_3_15.png\n", + 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