updated notebooks to import functions from qd_rdf

analyze-107.ipynb

@@ -6,44 +6,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import matplotlib.pyplot as plt\n",
-    "from skimage.exposure import rescale_intensity\n",
-    "from skimage import io, filters, color, measure\n",
-    "from skimage.feature import peak_local_max\n",
-    "from scipy import ndimage \n",
-    "import numpy as np\n",
-    "import xlrd\n",
-    "import freud.box\n",
-    "from freud import box, density\n",
-    "from scipy import stats\n",
-    "import os\n",
-    "%matplotlib inline\n",
-    "    \n",
-    "def get_dots2(file,microns=2,compare=False,spacing=5,size=4):\n",
-    "    image = color.rgb2gray(io.imread(file))\n",
-    "    i1 = filters.gaussian(image,sigma=.7)\n",
-    "    i1 = ndimage.maximum_filter(i1,size=size,mode='constant')\n",
-    "    coordinates = peak_local_max(i1, min_distance=spacing,indices=False)\n",
-    "    if compare:\n",
-    "        io.imshow(image -coordinates)\n",
-    "    label_img = measure.label(coordinates)\n",
-    "    centroids = []\n",
-    "    for region in measure.regionprops(label_img):\n",
-    "        centroids.append(region.centroid)\n",
-    "    scaled = microns*np.asarray(centroids)/image.shape - [microns/2,microns/2]\n",
-    "    return np.append(scaled,np.zeros((len(scaled),1)),axis=1)\n",
-    "\n",
-    "def plot_rdf(dots,L,plot=True):\n",
-    "    box = freud.box.Box(L,L,is2D=True)\n",
-    "    box.periodic=[True,True,False]\n",
-    "    rdf = freud.density.RDF(20,.49,normalize=True)\n",
-    "    rdf.compute(system=(box,dots),reset=True)\n",
-    "    if plot:\n",
-    "        plt.scatter(rdf.bin_centers, rdf.rdf)\n",
-    "        plt.xlabel(\"r (μm)\")\n",
-    "        plt.ylabel(\"<g(r)>\")\n",
-    "        plt.show()\n",
-    "    return rdf.bin_centers, rdf.rdf"
+    "from qd_rdf import get_dots, data_path, plot_rdf\n",
+    "import numpy as np"
    ]
   },
   {

analyze-156.ipynb

@@ -22,11 +22,9 @@
     "def get_dots2(file,microns=2,compare=False,spacing=5,size=4):\n",
     "    image = color.rgb2gray(io.imread(file))\n",
     "    i1 = filters.gaussian(image,sigma=2)\n",
-    "    #i1 = filters.gaussian(i1,sigma=1.5)\n",
     "    i1 = ndimage.maximum_filter(i1,size=size,mode='constant')\n",
     "    coordinates = peak_local_max(i1, min_distance=spacing,indices=False)\n",
     "    if compare:\n",
-    "        #io.imshow(coordinates)\n",
     "        io.imshow(image -coordinates)\n",
     "    label_img = measure.label(coordinates)\n",
     "    centroids = []\n",

qd_rdf.py

@@ -56,4 +56,5 @@ def plot_rdf(dots,L,plot=True):
         plt.ylabel("<g(r)>")
         plt.show()
     return rdf.bin_centers, rdf.rdf
-data_path = './'
+
+data_path = "raw_samples/"

update-notebooks.sh

@@ -0,0 +1 @@
+for f in analyze*; do G=87.ipynb; head -n 11 analyze-106.ipynb >87.ipynb; echo -e },n{>>87.ipynb;tail -n +50 analyze-87.ipynb >>87.ipynb; done