added SwAK rotate 180 degrees

pylattice · Aug 11, 2019 · 468b109 · 468b109
1 parent 50339ff
commit 468b109
Showing 1 changed file with 109 additions and 0 deletions.
diff --git a/src/SwAK_tools/rotate180/SwAK_rotate180.ipynb b/src/SwAK_tools/rotate180/SwAK_rotate180.ipynb
@@ -0,0 +1,109 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 37,
+   "metadata": {
+    "collapsed": true
+   },
+   "outputs": [],
+   "source": [
+    "%matplotlib inline\n",
+    "import numpy as np\n",
+    "import skimage\n",
+    "import os"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# input"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 38,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def rotate180(inputFolder,outputFolder,file):\n",
+    "    latticeMovieFrame = skimage.external.tifffile.imread(inputFolder+file)\n",
+    " \n",
+    "    latticeMovieFrame_rotated = np.rot90(latticeMovieFrame,k=2, axes=(1, 2))\n",
+    "    \n",
+    "# slower option\n",
+    "#    latticeMovieFrame_rotated = skimage.transform.rotate(latticeMovieFrame, 180, resize=False, center=None, order=1, mode='constant', cval=0, clip=True, preserve_range=False)    \n",
+    "\n",
+    "# not working option    \n",
+    "#    latticeMovieFrame_rotated = scipy.ndimage.rotate(latticeMovieFrame, 180, axes=(0, 1), reshape=True, output=None, order=3, mode='constant', cval=0.0, prefilter=True)\n",
+    "    \n",
+    "    skimage.external.tifffile.imsave(outputFolder+file,latticeMovieFrame_rotated.astype('uint16'))\n",
+    "    print(outputFolder+file)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 39,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "/Users/johannesschoeneberg/git/JohSchoeneberg/pyLattice2/SwAK_toolkit/outputFolder/cropped_560_pm50px_maxAmpl_0003.tif\n",
+      "/Users/johannesschoeneberg/git/JohSchoeneberg/pyLattice2/SwAK_toolkit/outputFolder/cropped_560_pm50px_maxAmpl_0002.tif\n",
+      "/Users/johannesschoeneberg/git/JohSchoeneberg/pyLattice2/SwAK_toolkit/outputFolder/cropped_560_pm50px_maxAmpl_0000.tif\n",
+      "/Users/johannesschoeneberg/git/JohSchoeneberg/pyLattice2/SwAK_toolkit/outputFolder/cropped_560_pm50px_maxAmpl_0001.tif\n",
+      "/Users/johannesschoeneberg/git/JohSchoeneberg/pyLattice2/SwAK_toolkit/outputFolder/cropped_560_pm50px_maxAmpl_0005.tif\n",
+      "/Users/johannesschoeneberg/git/JohSchoeneberg/pyLattice2/SwAK_toolkit/outputFolder/cropped_560_pm50px_maxAmpl_0004.tif\n",
+      "/Users/johannesschoeneberg/git/JohSchoeneberg/pyLattice2/SwAK_toolkit/outputFolder/cropped_560_pm50px_maxAmpl_0006.tif\n",
+      "/Users/johannesschoeneberg/git/JohSchoeneberg/pyLattice2/SwAK_toolkit/outputFolder/cropped_560_pm50px_maxAmpl_0007.tif\n",
+      "/Users/johannesschoeneberg/git/JohSchoeneberg/pyLattice2/SwAK_toolkit/outputFolder/cropped_488_pm50px_maxAmpl_0004.tif\n",
+      "/Users/johannesschoeneberg/git/JohSchoeneberg/pyLattice2/SwAK_toolkit/outputFolder/cropped_488_pm50px_maxAmpl_0005.tif\n",
+      "/Users/johannesschoeneberg/git/JohSchoeneberg/pyLattice2/SwAK_toolkit/outputFolder/cropped_488_pm50px_maxAmpl_0007.tif\n",
+      "/Users/johannesschoeneberg/git/JohSchoeneberg/pyLattice2/SwAK_toolkit/outputFolder/cropped_488_pm50px_maxAmpl_0006.tif\n",
+      "/Users/johannesschoeneberg/git/JohSchoeneberg/pyLattice2/SwAK_toolkit/outputFolder/cropped_488_pm50px_maxAmpl_0002.tif\n",
+      "/Users/johannesschoeneberg/git/JohSchoeneberg/pyLattice2/SwAK_toolkit/outputFolder/cropped_488_pm50px_maxAmpl_0003.tif\n",
+      "/Users/johannesschoeneberg/git/JohSchoeneberg/pyLattice2/SwAK_toolkit/outputFolder/cropped_488_pm50px_maxAmpl_0001.tif\n",
+      "/Users/johannesschoeneberg/git/JohSchoeneberg/pyLattice2/SwAK_toolkit/outputFolder/cropped_488_pm50px_maxAmpl_0000.tif\n",
+      "/Users/johannesschoeneberg/git/JohSchoeneberg/pyLattice2/SwAK_toolkit/outputFolder/cropped_488_pm50px_maxAmpl_0008.tif\n",
+      "/Users/johannesschoeneberg/git/JohSchoeneberg/pyLattice2/SwAK_toolkit/outputFolder/cropped_488_pm50px_maxAmpl_0009.tif\n",
+      "/Users/johannesschoeneberg/git/JohSchoeneberg/pyLattice2/SwAK_toolkit/outputFolder/cropped_560_pm50px_maxAmpl_0009.tif\n",
+      "/Users/johannesschoeneberg/git/JohSchoeneberg/pyLattice2/SwAK_toolkit/outputFolder/cropped_560_pm50px_maxAmpl_0008.tif\n"
+     ]
+    }
+   ],
+   "source": [
+    "inputFolder = '/Users/johannesschoeneberg/Dropbox/pyLattice_public_test_data/'\n",
+    "outputFolder = '/Users/johannesschoeneberg/git/JohSchoeneberg/pyLattice2/SwAK_toolkit/outputFolder/' \n",
+    "\n",
+    "import os\n",
+    "for file in os.listdir(inputFolder):\n",
+    "    if file.endswith(\".tif\"):\n",
+    "        rotate180(inputFolder,outputFolder,file)\n"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "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": "3.6.3"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}