{ "cells": [ { "cell_type": "code", "execution_count": 27, "id": "e07ab359", "metadata": {}, "outputs": [], "source": [ "import os\n", "import tifffile\n", "import skimage\n", "import numpy as np\n", "import shutil" ] }, { "cell_type": "code", "execution_count": 28, "id": "c32a4dd3", "metadata": {}, "outputs": [], "source": [ "forder_name=\"20240909_754606_slide19\"\n", "cycle_name='bcseq03'\n", "linux_server='imagestorage@10.128.30.152'\n", "if \"hyb\" in cycle_name:\n", " channel_list=[\"C\", \"G\", \"TxRed\",\"Cy5\", \"DAPI\", \"DIC\"]\n", "elif \"bcseq01\" in cycle_name:\n", " channel_list = [\"G\", \"T\", \"A\", \"C\", \"DAPI\"]\n", "else:\n", " channel_list = [\"G\", \"T\", \"A\", \"C\"]" ] }, { "cell_type": "code", "execution_count": 29, "id": "2c0610d9", "metadata": {}, "outputs": [], "source": [ "work_path=os.getcwd()\n", "work_path\n", "pos_list=os.listdir(os.path.join(cycle_name))" ] }, { "cell_type": "code", "execution_count": 30, "id": "c0dacaa7", "metadata": {}, 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"Pos4_009_002_1\n", "Pos4_009_003_1\n", "Pos4_009_004_1\n", "Pos4_009_005_1\n", "Pos4_009_006_1\n", "Pos4_009_007_1\n", "Pos4_010_000_1\n", "Pos4_010_001_1\n", "Pos4_010_002_1\n", "Pos4_010_003_1\n", "Pos4_010_004_1\n", "Pos4_010_005_1\n", "Pos4_010_006_1\n", "Pos4_010_007_1\n" ] } ], "source": [ "for pos in pos_list:\n", " print(pos)\n", " pos_name=pos[0:-2]\n", " tif_name=pos_name+\"_NDTiffStack.tif\"\n", " img=skimage.io.imread(os.path.join(cycle_name,pos,tif_name))\n", " img=np.reshape(img,(len(channel_list),20,3200,3200))\n", " img_max = []\n", " for i in range(len(channel_list)):\n", " if channel_list[i]!='DIC':\n", " img_max.append(np.max(img[i, :], axis=(0)))\n", " else:\n", " img_max.append(img[i, 9,:,:])\n", " tifffile.imwrite(os.path.join(cycle_name,pos,cycle_name+\".tif\"),np.array(img_max), photometric='minisblack')\n", "# max_name = 'MAX_' + pos_name\n", "# server_name=cycle_name+'.tif'\n", "# image_local_path=os.path.join(work_path,cycle_name,pos,server_name)\n", "# server_path='/mnt/imagestorage/'+forder_name+\"/\"+\"MAX_\" +pos\n", "# cmd2=\"scp \"+image_local_path+\" \"+linux_server+\":\"+server_path+\"/\"+server_name\n", "# os.system(cmd2)\n", "# shutil.rmtree(cycle_name)\n" ] }, { "cell_type": "code", "execution_count": null, "id": "2277b794", "metadata": {}, "outputs": [], "source": [] } ], "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": "3.8.18" } }, "nbformat": 4, "nbformat_minor": 5 }