'updates'

jgrss · Feb 5, 2017 · a43f7c1 · a43f7c1
1 parent 83eef78
commit a43f7c1
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diff --git a/setup.py b/setup.py
@@ -1,3 +1,5 @@
+# -*- coding: utf-8 -*-
+
 """
 To build .tar.gz:
     1. Setup directory structure
@@ -43,15 +45,23 @@
 with open('AUTHORS.txt') as f:
     author_file = f.read()
 
-required_packages = ['numpy>=1.12.0', 'scipy>=0.18.1', 'scikit-learn>=0.18.1', 'scikit-image>=0.12.3',
-                     'numexpr>=2.6.2', 'tables>=3.3', 'pandas>=0.19.2', 'matplotlib>=1.5.1', 'psutil>=4.3.1',
-                     'joblib>=0.10.3', 'BeautifulSoup4>=4.5.1', 'PyYAML>=3.12', 'colorama>=0.3.7',
-                     'cython>=0.25.2', 'bottleneck>=1.2.0', 'xmltodict', 'retrying',
-                     'opencv-python>=3.1.0', 'PySAL>=1.11.2', 'six>=1.10.0', 'pyFFTW>=0.10.4']
+required_packages = ['matplotlib>=1.5.1', 'psutil>=4.3.1',
+                     'joblib>=0.10.3', 'BeautifulSoup4>=4.5.1',
+                     'PyYAML>=3.12', 'colorama>=0.3.7',
+                     'xmltodict', 'retrying',
+                     'PySAL>=1.11.2', 'six>=1.10.0']
 
 if platform.system() == 'Darwin':
 
-    for pkg in ['Rtree>=0.8.2', 'gdal>=2.1']:
+    for pkg in ['numpy>=1.12.0', 'scipy>=0.18.1',
+                'scikit-image>=0.12.3',
+                'Rtree>=0.8.2', 'gdal>=2.1',
+                'numexpr>=2.6.2', 'tables>=3.3',
+                'bottleneck>=1.2.0', 'statsmodels>=0.8.0',
+                'opencv-python>=3.1.0', 'cython>=0.25.2',
+                'scikit-learn>=0.18.1', 'pandas>=0.19.2',
+                'pyFFTW>=0.10.4']:
+
         required_packages.append(pkg)
 
 
@@ -98,6 +108,7 @@ def setup_package():
                     zip_safe=False,
                     download_url=git_url,
                     install_requires=required_packages,
+                    include_package_data=True,
                     entry_points=get_console_dict())
 
     setup(**metadata)

diff --git a/spfeas/notebooks/INSTALLATION.ipynb b/spfeas/notebooks/INSTALLATION.ipynb
@@ -2,7 +2,10 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "metadata": {},
+   "metadata": {
+    "deletable": true,
+    "editable": true
+   },
    "source": [
     "## <span style=\"color:#0B3B2E;float:right;font-family:Calibri\">Jordan Graesser</span>\n",
     "\n",
@@ -12,7 +15,10 @@
   },
   {
    "cell_type": "markdown",
-   "metadata": {},
+   "metadata": {
+    "deletable": true,
+    "editable": true
+   },
    "source": [
     "## <span style=\"color:blue\">Python</span>\n",
     "---\n",
@@ -34,7 +40,10 @@
   },
   {
    "cell_type": "markdown",
-   "metadata": {},
+   "metadata": {
+    "deletable": true,
+    "editable": true
+   },
    "source": [
     "## <span style=\"color:blue\">Installing SpFeas on OSX</span>\n",
     "---\n",
@@ -60,7 +69,10 @@
   },
   {
    "cell_type": "markdown",
-   "metadata": {},
+   "metadata": {
+    "deletable": true,
+    "editable": true
+   },
    "source": [
     "## <span style=\"color:blue\">Installing SpFeas on Windows</span>\n",
     "---\n",
@@ -75,44 +87,24 @@
     "### <span style=\"color:green\">Installing SpFeas from the Windows Command Prompt</span>\n",
     "> The command prompt can be found under the Start menu. Open it by typing 'cmd' in the **search box**. \n",
     "\n",
-    "1. Download the following wheel files from [Gohlke's site](http://www.lfd.uci.edu/~gohlke/pythonlibs/) and save them to C:\\Downloads.\n",
+    "1. Download **SpFeas-0.1.0-MpGlue-0.1.0-cp27-cp27m-win_amd64.zip** from the [SpFeas Releases](https://github.com/jgrss/spfeas/releases) page and save in **\\Downloads**.\n",
     "\n",
-    "    > numpy‑1.12.0rc2+mkl‑cp27‑cp27m‑win32.whl or numpy‑1.12.0rc2+mkl‑cp27‑cp27m‑win_amd64.whl \n",
-    "    \n",
-    "    > Bottleneck-1.2.0-cp27-cp27m-win32.whl or Bottleneck‑1.2.0‑cp27‑cp27m‑win_amd64.whl\n",
-    "    \n",
-    "    > numexpr-2.6.1-cp27-cp27m-win32.whl or numexpr‑2.6.1‑cp27‑cp27m‑win_amd64.whl\n",
-    "    \n",
-    "    > scikit_image-0.12.3-cp27-cp27m-win32.whl or scikit_image‑0.12.3‑cp27‑cp27m‑win_amd64.whl\n",
-    "    \n",
-    "    > scipy-0.18.1-cp27-cp27m-win32.whl or scipy‑0.18.1‑cp27‑cp27m‑win_amd64.whl\n",
-    "    \n",
-    "    > tables-3.3.0-cp27-cp27m-win32.whl or tables‑3.3.0‑cp27‑cp27m‑win_amd64.whl  \n",
-    "    \n",
-    "    > statsmodels-0.8.0rc1-cp27-cp27m-win32.whl or statsmodels‑0.8.0rc1‑cp27‑cp27m‑win_amd64.whl\n",
-    "    \n",
-    "    > GDAL‑2.1.2‑cp27‑cp27m‑win32.whl or GDAL‑2.1.2‑cp27‑cp27m‑win_amd64.whl\n",
-    "        \n",
-    "2. Either download [git for Windows](https://www.atlassian.com/git/tutorials/install-git/mac-os-x) **OR** download the [MpGlue](https://github.com/jgrss/mpglue/releases) and [SpFeas](https://github.com/jgrss/spfeas/releases) tarballs. \n",
-    "    * If you choose to download and configure **git**, then you DO NOT need to download the MpGlue and SpFeas tarballs.\n",
-    "    * Without **git**, you need to have the MpGlue and SpFeas tarballs downloaded for the installer to find them.\n",
-    "    * Save the SpFeas and MpGlue tarballs to C:\\Downloads.\n",
+    "2. Unzip **\\Downloads\\SpFeas-0.1.0-MpGlue-0.1.0-cp27-cp27m-win_amd64.zip**\n",
+    "\n",
+    "3. Open a command prompt window and move to the **C:\\Downloads\\SpFeas-0.1.0-MpGlue-0.1.0-cp27-cp27m-win_amd64** directory by typing or copying the command below into the window (hit **return** to execute).\n",
+    "    > `cd \\Downloads\\SpFeas-0.1.0-MpGlue-0.1.0-cp27-cp27m-win_amd64`\n",
     "    \n",
-    "3. Download [the INSTALL_Windows.sh](https://github.com/jgrss/spfeas/blob/master/spfeas/files/INSTALL_Windows.cmd). \n",
-    "    * To save, click **Raw**, then **File>Save Page As** and choose _All Files_.\n",
-    "    * Save to the **C:\\Downloads** folder on your local machine.\n",
-    "4. Open a command prompt window and move to the **C:\\Downloads** directory by typing or copying the command below into the window (hit **return** to execute).\n",
-    "    > `cd C:\\Downloads`\n",
-    "5. Run the INSTALL_Windows.cmd installer by typing or copying the command below into the terminal window (hit **return** to execute).\n",
-    "    > `INSTALL_Windows.cmd`\n",
-    "6. Command line prompts\n",
-    "    * When prompted, hit **enter**, type **y**, or type your **computer password** or **GitHub username and password** to continue the installation process.\n",
-    "    * Note that your password will not be shown on the screen when you type."
+    "4. Run the INSTALL_Windows.cmd installer by typing or copying the command below into the terminal window (hit **return** to execute).\n",
+    "    > `INSTALL_Windows_x64.cmd`\n",
+    "    "
    ]
   },
   {
    "cell_type": "markdown",
-   "metadata": {},
+   "metadata": {
+    "deletable": true,
+    "editable": true
+   },
    "source": [
     "---\n",
     "### <span style=\"color:blue\">The installation is complete when the screen has stopped printing and it says 'The installation has finished!'</span>\n",
@@ -129,7 +121,7 @@
   "language_info": {
    "codemirror_mode": {
     "name": "ipython",
-    "version": 2.0
+    "version": 2
    },
    "file_extension": ".py",
    "mimetype": "text/x-python",
@@ -141,4 +133,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 0
-}
+}
diff --git a/spfeas/spfeas.py b/spfeas/spfeas.py
@@ -33,7 +33,7 @@ def set_defaults(self, **kwargs):
 
         # Set the features dictionary.
         self.features_dict = dict(mean=2, pantex=1, ctr=1,
-                                  lsr=3, hough=4, hog=7,
+                                  lsr=3, grad=2, hough=4, hog=7,
                                   lbp=62, lbpm=7, gabor=2*8,
                                   surf=4, seg=1, fourier=2,
                                   sfs=6, evi2=2, ndvi=2,
@@ -42,27 +42,28 @@ def set_defaults(self, **kwargs):
                                   sfsorf=6)
 
         # Set the output bands based on the trigger.
-        self.out_bands_dict = dict(ctr=len(self.scales) * self.features_dict['ctr'],
-                                   dmp=len(self.scales) * self.features_dict['dmp'],
-                                   evi2=len(self.scales) * self.features_dict['evi2'],
-                                   fourier=len(self.scales) * self.features_dict['fourier'],
-                                   gabor=len(self.scales) * self.features_dict['gabor'],
-                                   hog=len(self.scales) * self.features_dict['hog'],
-                                   hough=len(self.scales) * self.features_dict['hough'],
-                                   lac=len(self.scales) * self.features_dict['lac'],
-                                   lbp=len(self.scales) * self.features_dict['lbp'],
-                                   lbpm=len(self.scales) * self.features_dict['lbpm'],
-                                   lsr=len(self.scales) * self.features_dict['lsr'],
-                                   mean=len(self.scales) * self.features_dict['mean'],
-                                   ndvi=len(self.scales) * self.features_dict['ndvi'],
-                                   orb=len(self.scales) * self.features_dict['orb'],
-                                   pantex=len(self.scales) * self.features_dict['pantex'],
-                                   saliency=len(self.scales) * self.features_dict['saliency'],
-                                   seg=len(self.scales) * self.features_dict['seg'],
-                                   sfs=len(self.scales) * self.features_dict['sfs'],
-                                   sfsorf=len(self.scales) * self.features_dict['sfsorf'],
-                                   surf=len(self.scales) * self.features_dict['surf'],
-                                   xy=len(self.scales) * self.features_dict['xy'])
+        self.out_bands_dict = dict(ctr=len(self.scales)*self.features_dict['ctr'],
+                                   dmp=len(self.scales)*self.features_dict['dmp'],
+                                   evi2=len(self.scales)*self.features_dict['evi2'],
+                                   fourier=len(self.scales)*self.features_dict['fourier'],
+                                   gabor=len(self.scales)*self.features_dict['gabor'],
+                                   grad=len(self.scales)*self.features_dict['grad'],
+                                   hog=len(self.scales)*self.features_dict['hog'],
+                                   hough=len(self.scales)*self.features_dict['hough'],
+                                   lac=len(self.scales)*self.features_dict['lac'],
+                                   lbp=len(self.scales)*self.features_dict['lbp'],
+                                   lbpm=len(self.scales)*self.features_dict['lbpm'],
+                                   lsr=len(self.scales)*self.features_dict['lsr'],
+                                   mean=len(self.scales)*self.features_dict['mean'],
+                                   ndvi=len(self.scales)*self.features_dict['ndvi'],
+                                   orb=len(self.scales)*self.features_dict['orb'],
+                                   pantex=len(self.scales)*self.features_dict['pantex'],
+                                   saliency=len(self.scales)*self.features_dict['saliency'],
+                                   seg=len(self.scales)*self.features_dict['seg'],
+                                   sfs=len(self.scales)*self.features_dict['sfs'],
+                                   sfsorf=len(self.scales)*self.features_dict['sfsorf'],
+                                   surf=len(self.scales)*self.features_dict['surf'],
+                                   xy=len(self.scales)*self.features_dict['xy'])
 
         # Update the feature dictionary for feature neighbors.
         if self.neighbors:
@@ -148,6 +149,7 @@ def _options():
                   Fore.GREEN + Style.BRIGHT + 'evi2' + Style.RESET_ALL + '    -- EVI2 mean (2 x n scales)',
                   Fore.GREEN + Style.BRIGHT + 'fourier' + Style.RESET_ALL + ' -- Fourier transform (2 x n scales)',
                   Fore.GREEN + Style.BRIGHT + 'gabor' + Style.RESET_ALL + '   -- Gabor filter bank (n scales x 2 x kernels(Default=24))',
+                  Fore.GREEN + Style.BRIGHT + 'grad' + Style.RESET_ALL + '    -- Edge gradient magnitude (2 x n scales)',
                   Fore.GREEN + Style.BRIGHT + 'hog' + Style.RESET_ALL + '     -- Histogram of Oriented Gradients (7 (max,m1,m2,m3,m4,skew,kurtosis) x n scales)',
                   Fore.RED + Style.BRIGHT + 'hough' + Style.RESET_ALL + '   -- Local line statistics from Probabilistic Hough Transform (4 x n scales)' + Fore.RED + ' **Currently out of order**',
                   Fore.GREEN + Style.BRIGHT + 'lac' + Style.RESET_ALL + '     -- Lacunarity (n scales)',
@@ -189,7 +191,7 @@ def main():
     parser.add_argument('--block', dest='block', help='The block size', default=2, type=int)
     parser.add_argument('--scales', dest='scales', help='The scales', default=[8], type=int, nargs='+')
     parser.add_argument('-tr', '--triggers', dest='triggers', help='The feature triggers', default=['mean'],
-                        nargs='+', choices=['dmp', 'evi2', 'fourier', 'gabor', 'hog', 'lac',
+                        nargs='+', choices=['dmp', 'evi2', 'fourier', 'gabor', 'grad', 'hog', 'lac',
                                             'lbp', 'lbpm', 'lsr', 'mean', 'ndvi',
                                             'pantex', 'saliency', 'sfs'])
     parser.add_argument('-lth', '--hline-threshold', dest='hline_threshold', help='The Hough line threshold',

diff --git a/spfeas/spfunctions.py b/spfeas/spfunctions.py
@@ -1,5 +1,7 @@
 from .sphelpers import lsr
 
+from skimage.exposure import rescale_intensity
+
 try:
     from skimage.feature import hog as HOG
     from skimage.feature import local_binary_pattern as LBP
@@ -55,6 +57,26 @@ def get_kernels():
             [roberts_filter_y_3, roberts_filter_x_3], [roberts_filter_y_4, roberts_filter_x_4]]
 
 
+def get_mag_avg(img):
+
+    img = np.sqrt(img)
+
+    kernels = get_kernels()
+
+    mag = np.zeros(img.shape, dtype='float32')
+
+    for kernel_filter in kernels:
+
+        gx = cv2.filter2D(np.float32(img), cv2.CV_32F, kernel_filter[1], borderType=cv2.BORDER_CONSTANT)
+        gy = cv2.filter2D(np.float32(img), cv2.CV_32F, kernel_filter[0], borderType=cv2.BORDER_CONSTANT)
+
+        mag += cv2.magnitude(gx, gy)
+
+    mag /= len(kernels)
+
+    return np.uint8(rescale_intensity(mag, out_range=(0, 255)))
+
+
 def get_mag_ang(img):
 
     """
@@ -69,27 +91,11 @@ def get_mag_ang(img):
 
     img = np.sqrt(img)
 
-    # kernels = get_kernels()
-    #
-    # mag = np.zeros(img.shape, dtype='float32')
-    # ang = np.zeros(img.shape, dtype='float32')
-    #
-    # for kernel_filter in kernels:
-    #
-    #     gx = cv2.filter2D(np.float32(img), cv2.CV_32F, kernel_filter[1], borderType=cv2.BORDER_CONSTANT)
-    #     gy = cv2.filter2D(np.float32(img), cv2.CV_32F, kernel_filter[0], borderType=cv2.BORDER_CONSTANT)
-
     gx = cv2.Sobel(np.float32(img), cv2.CV_32F, 1, 0)
     gy = cv2.Sobel(np.float32(img), cv2.CV_32F, 0, 1)
 
     mag, ang = cv2.cartToPolar(gx, gy)
 
-    # mag += mag_
-    # ang += ang_
-
-    # mag /= len(kernels)
-    # ang /= len(kernels)
-
     return mag, ang, gx, gy