Pynovisao - Adicionando segmentadores Felzenszwalb e Quickshift

README.md

@@ -96,9 +96,9 @@ Pacote de Visão Computacional do Inovisão.
 
 ### Ubuntu 
 
-    ```
-    $ sudo apt-get install tk tk-dev
-    ```
+```
+$ sudo apt-get install tk tk-dev
+```
     
     Na ocorrência do erro 'cannot import name _tkagg', tentar os seguintes comandos:
     

src/extraction/__init__.py

-from extractor import Extractor
-from feature_extraction import FeatureExtractor
-from color_summarizer import ColorStats
-from glcm import GLCM
-from hog import HOG
-from image_moments import ImageMoments
-from lbp import LBP
+from .extractor import Extractor
+from .feature_extraction import FeatureExtractor
+from .color_summarizer import ColorStats
+from .glcm import GLCM
+from .hog import HOG
+from .image_moments import RawCentralMoments, HuMoments
+from .lbp import LBP
 
 __all__ = ["extractor",
             "color_summarizer",
@@ -18,13 +18,14 @@ from collections import OrderedDict
 from util.config import Config
 
 
-_extractor_list = OrderedDict( { 
-                            "color_summarizer" : Config("Color Statistics", True, bool, meta=ColorStats),
-                            "hog" : Config("Histogram of Oriented Gradients", True, bool, meta=HOG),
-                            "glcm" : Config("Gray-Level Co-Occurrence Matrix", True, bool, meta=GLCM),
-                            "image_moments" : Config("Image Moments (Hu)", True, bool, meta=ImageMoments),
-                            "lbp" : Config("Local Binary Patterns", True, bool, meta=LBP)
-                        } )
+_extractor_list = OrderedDict( [ 
+                            ["color_summarizer", Config("Color Statistics", True, bool, meta=ColorStats)],
+                            ["glcm", Config("Gray-Level Co-Occurrence Matrix", True, bool, meta=GLCM)],
+                            ["hog", Config("Histogram of Oriented Gradients", True, bool, meta=HOG)],
+                            ["hu_moments", Config("Hu Image Moments", True, bool, meta=HuMoments)],
+                            ["rc_moments", Config("Image Moments (Raw/Central)", False, bool, meta=RawCentralMoments)],
+                            ["lbp", Config("Local Binary Patterns", True, bool, meta=LBP)]
+                        ] )
 
 def get_extractor_config():
     return _extractor_list
@@ -33,5 +34,6 @@ def set_extractor_config(configs):
         _extractor_list["color_summarizer"] = Config.nvl_config(configs["color_summarizer"], _extractor_list["color_summarizer"])
         _extractor_list["glcm"] = Config.nvl_config(configs["glcm"], _extractor_list["glcm"])
         _extractor_list["hog"] = Config.nvl_config(configs["hog"], _extractor_list["hog"])
-        _extractor_list["image_moments"] = Config.nvl_config(configs["image_moments"], _extractor_list["image_moments"])
+        _extractor_list["hu_moments"] = Config.nvl_config(configs["hu_moments"], _extractor_list["hu_moments"])
+        _extractor_list["rc_moments"] = Config.nvl_config(configs["rc_moments"], _extractor_list["rc_moments"])
         _extractor_list["lbp"] = Config.nvl_config(configs["lbp"], _extractor_list["lbp"])

src/extraction/feature_extraction.py

@@ -80,7 +80,7 @@ class FeatureExtractor(object):
 
         arff.write("%s %s\n\n" % ('@relation ', relation))
 
-        for label, t in zip(labels,types):
+        for label, t in zip(labels, types):
             arff.write("%s %s %s\n" % ('@attribute', label, t))
 
         arff.write("%s %s {%s}\n\n" % ('@attribute','classe',', '.join(classes)))

src/extraction/image_moments.py

@@ -13,7 +13,7 @@ from util.utils import ImageUtils
 
 from extractor import Extractor
 
-class ImageMoments(Extractor):
+class RawCentralMoments(Extractor):
 
     
     def __init__(self):
@@ -37,15 +37,40 @@ class ImageMoments(Extractor):
         values_mu = [mu[p, q] for (p, q) in self._moments_order]
         labels_mu = [M+str(p)+str(q) for M,(p,q) in zip(['Mu_'] * len(self._moments_order), self._moments_order)]
         
+        labels = labels_m + labels_mu
+        types = [Extractor.NUMERIC] * len(labels)
+        values = values_m + values_mu
+        
+        return labels, types, values
+
+
+class HuMoments(Extractor):
+
+    
+    def __init__(self):
+        pass
+        
+    
+    def run(self, image):
+        
+        image_grayscale = ImageUtils.image_grayscale(image, bgr = True)
+        
+        m = measure.moments(image_grayscale)
+        
+        row = m[0, 1] / m[0, 0]
+        col = m[1, 0] / m[0, 0]
+
+        mu = measure.moments_central(image_grayscale, row, col)
+        
         nu = measure.moments_normalized(mu)
         hu = measure.moments_hu(nu)
 
         values_hu = list(hu)
         labels_hu = [m+n for m,n in zip(['Hu_'] * len(values_hu),map(str,range(0,len(values_hu))))]
         
-        labels = labels_m + labels_mu + labels_hu
+        labels = labels_hu
         types = [Extractor.NUMERIC] * len(labels)
-        values = values_m + values_mu + values_hu
+        values = values_hu
         
         return labels, types, values
 

src/interface/__init__.py

-from interface import Interface, InterfaceException
-from tk_interface import TkInterface
+from .interface import Interface, InterfaceException
+from .tk_interface import TkInterface
 
 __all__ = ["interface", 
             "tk_interface"]
\ No newline at end of file

src/interface/tk/__init__.py

-from tk_canvas import Image
-from tk_config import TkConfig
-from tk_customdialog import SimpleDialog, ConfigDialog, ChooseOneDialog, SelectDialog
-from tk_customframe import CustomGrid
-from tk_logger import Log
-from tk_menu import Menu
-from tk_itemmenu import ItemMenu, Command, Separator, CheckButton
-from tk_utils import Utils
+from .tk_canvas import Image
+from .tk_config import TkConfig
+from .tk_customdialog import SimpleDialog, ConfigDialog, ChooseOneDialog, SelectDialog
+from .tk_customframe import CustomGrid
+from .tk_logger import Log
+from .tk_menu import Menu
+from .tk_itemmenu import ItemMenu, Command, Separator, CheckButton
+from .tk_utils import Utils
 
 __all__ = ["tk_canvas", 
             "tk_config", 

src/pynovisao.py

@@ -186,7 +186,7 @@ class Act(object):
             self.segmenter = [new_config[segmenter].meta for segmenter in new_config
                                 if new_config[segmenter].value == True ][0]()
 
-            self.tk.append_log("\nConfig updated:\nSegmenter: %s", str(self.segmenter.get_name()))
+            self.tk.append_log("\nSegmenter: %s\n%s", str(self.segmenter.get_name()), str(self.segmenter.get_summary_config()))
             segmentation.set_segmenter_config(new_config)
 
         self.tk.dialogue_choose_one(title, current_config, process_config)

src/segmentation/__init__.py

-from segmenter import Segmenter
-from slic import Slic
+from .segmenter import Segmenter
+from .felzenszwalb import Felzenszwalb
+from .quickshift import Quickshift
+from .slic import Slic
 
 __all__ = ["segmenter",
+           "felzenszwalb"
+           "quickshift"
             "slic"]
 
 
@@ -9,13 +13,17 @@ from collections import OrderedDict
 from util.config import Config
 
 
-_segmenter_list = OrderedDict( { 
-                            "slic" : Config(Slic().get_name(), True, bool, meta=Slic),
-                            "invalid" : Config("Invalid", False, bool, meta=None, hidden=True)
-                        } )
+_segmenter_list = OrderedDict( [ 
+                            ["felzenszwalb", Config(Felzenszwalb().get_name(), False, bool, meta=Felzenszwalb)],
+                            ["quickshift", Config(Quickshift().get_name(), False, bool, meta=Quickshift)],
+                            ["slic", Config(Slic().get_name(), True, bool, meta=Slic)],
+                            ["invalid", Config("Invalid", False, bool, meta=None, hidden=True)]
+                        ] )
 
 def get_segmenter_config():
     return _segmenter_list
 
 def set_segmenter_config(configs):
+    _segmenter_list["felzenszwalb"] = Config.nvl_config(configs["felzenszwalb"], _segmenter_list["felzenszwalb"])
+    _segmenter_list["quickshift"] = Config.nvl_config(configs["quickshift"], _segmenter_list["quickshift"])
     _segmenter_list["slic"] = Config.nvl_config(configs["slic"], _segmenter_list["slic"])

src/segmentation/felzenszwalb.py

+#!/usr/bin/python
+# -*- coding: utf-8 -*-
+#
+"""
+    Runs Segmenter Felzenszwalb's method implemented in skimage.segmentation.
+    
+    Efficient graph-based image segmentation, Felzenszwalb, P.F. and Huttenlocher, D.P. International Journal of Computer Vision, 2004
+    
+    Name: felzenszwalb.py
+    Author: Alessandro dos Santos Ferreira ( santosferreira.alessandro@gmail.com )
+"""
+
+from skimage.segmentation import felzenszwalb
+from collections import OrderedDict
+
+from util.config import Config
+
+from segmenter import Segmenter
+from skimage_segmenter import SkimageSegmenter
+
+class Felzenszwalb(Segmenter, SkimageSegmenter):
+    
+    def __init__(self, scale = 100.0, sigma = 1.0, min_size = 20, border_color = 'Yellow', border_outline = 'No'):
+        super(self.__class__, self).__init__(border_color, border_outline)
+        
+        self.scale = Config("Scale", scale, float)
+        self.sigma = Config("Sigma", sigma, float)
+        self.min_size = Config("Min Size", min_size, int)
+        
+    
+    def get_config(self):
+        felzenszwalb_config = OrderedDict()
+        
+        felzenszwalb_config["scale"] = self.scale
+        felzenszwalb_config["sigma"] = self.sigma
+        felzenszwalb_config["min_size"] = self.min_size
+        felzenszwalb_config["border_color"] = self.border_color
+        felzenszwalb_config["border_outline"] = self.border_outline
+        
+        return felzenszwalb_config
+        
+    def set_config(self, configs):
+        self.scale = Config.nvl_config(configs["scale"], self.scale)
+        self.sigma = Config.nvl_config(configs["sigma"], self.sigma)
+        self.min_size = Config.nvl_config(configs["min_size"], self.min_size)
+        self.border_color = Config.nvl_config(configs["border_color"], self.border_color)
+        self.border_outline = Config.nvl_config(configs["border_outline"], self.border_outline)
+        
+        self.border_outline.value = self.border_outline.value if self.border_outline.value == 'Yes' else 'No'
+
+    def get_summary_config(self):
+        felzenszwalb_config = OrderedDict()
+        
+        felzenszwalb_config[self.scale.label] = self.scale.value
+        felzenszwalb_config[self.sigma.label] = self.sigma.value
+        felzenszwalb_config[self.min_size.label] = self.min_size.value
+        felzenszwalb_config[self.border_color.label] = self.border_color.value
+        felzenszwalb_config[self.border_outline.label] = self.border_outline.value
+        
+        summary = ''
+        for config in felzenszwalb_config:
+            summary += "%s: %s\n" % (config, str(felzenszwalb_config[config]))
+        
+        return summary
+
+
+    def get_segment(self, px = 0, py = 0, idx_segment = None):
+        return self.get_segment_skimage(px, py, idx_segment)
+    
+    def paint_segment(self, image, color, px = 0, py = 0, idx_segment = None, border = True, clear = False):
+        return self.paint_segment_skimage(image, color, px, py, idx_segment, border, clear)
+
+
+    def run(self, image):
+        
+        args = { "scale": self.scale.get_cast_val(), 
+                   "sigma": self.sigma.get_cast_val(), 
+                   "min_size": self.min_size.get_cast_val()
+                }
+
+        return self.run_skimage(image, felzenszwalb, **args)

src/segmentation/quickshift.py

+#!/usr/bin/python
+# -*- coding: utf-8 -*-
+#
+"""
+    Runs Segmenter Quickshift implemented in skimage.segmentation.
+    
+    Quick shift and kernel methods for mode seeking, Vedaldi, A. and Soatto, S. European Conference on Computer Vision, 2008
+    
+    Name: quickshift.py
+    Author: Alessandro dos Santos Ferreira ( santosferreira.alessandro@gmail.com )
+"""
+
+from skimage.segmentation import quickshift
+from collections import OrderedDict
+
+from util.config import Config
+
+from segmenter import Segmenter
+from skimage_segmenter import SkimageSegmenter
+
+class Quickshift(Segmenter, SkimageSegmenter):
+
+    def __init__(self, ratio = 0.5, kernel_size = 2.0, max_dist = 10.0, border_color = 'Yellow', border_outline = 'No'):
+        super(self.__class__, self).__init__(border_color, border_outline)
+        
+        self.ratio = Config("Ratio [0-1]", ratio, float)
+        self.kernel_size = Config("Kernel Size", kernel_size, float)
+        #self.sigma = Config("Sigma", sigma, float)
+        self.max_dist = Config("Max Dist", max_dist, float)
+        
+    
+    def get_config(self):
+        quickshift_config = OrderedDict()
+        
+        quickshift_config["ratio"] = self.ratio
+        quickshift_config["kernel_size"] = self.kernel_size
+        #quickshift_config["sigma"] = self.sigma
+        quickshift_config["max_dist"] = self.max_dist
+        quickshift_config["border_color"] = self.border_color
+        quickshift_config["border_outline"] = self.border_outline
+        
+        return quickshift_config
+        
+    def set_config(self, configs):
+        self.ratio = Config.nvl_config(configs["ratio"], self.ratio)
+        self.kernel_size = Config.nvl_config(configs["kernel_size"], self.kernel_size)
+        #self.sigma = Config.nvl_config(configs["sigma"], self.sigma)
+        self.max_dist = Config.nvl_config(configs["max_dist"], self.max_dist)
+        self.border_color = Config.nvl_config(configs["border_color"], self.border_color)
+        self.border_outline = Config.nvl_config(configs["border_outline"], self.border_outline)
+        
+        self.ratio.value = self.ratio.value if self.ratio.value <= 1 else 1
+        self.border_outline.value = self.border_outline.value if self.border_outline.value == 'Yes' else 'No'
+
+    def get_summary_config(self):
+        quickshift_config = OrderedDict()
+        
+        quickshift_config[self.ratio.label] = self.ratio.value
+        quickshift_config[self.kernel_size.label] = self.kernel_size.value
+        #quickshift_config[self.sigma.label] = self.sigma.value
+        quickshift_config[self.max_dist.label] = self.max_dist.value
+        quickshift_config[self.border_color.label] = self.border_color.value
+        quickshift_config[self.border_outline.label] = self.border_outline.value
+        
+        summary = ''
+        for config in quickshift_config:
+            summary += "%s: %s\n" % (config, str(quickshift_config[config]))
+        
+        return summary
+
+
+    def get_segment(self, px = 0, py = 0, idx_segment = None):
+        return self.get_segment_skimage(px, py, idx_segment)
+    
+    def paint_segment(self, image, color, px = 0, py = 0, idx_segment = None, border = True, clear = False):
+        return self.paint_segment_skimage(image, color, px, py, idx_segment, border, clear)
+
+
+    def run(self, image):
+        
+        args = { "ratio": self.ratio.get_cast_val(), 
+                   "kernel_size": self.kernel_size.get_cast_val(), 
+                   #"sigma": self.sigma.get_cast_val(), 
+                   "max_dist": self.max_dist.get_cast_val()
+                }
+
+        return self.run_skimage(image, quickshift, **args)

src/segmentation/skimage_segmenter.py

+#!/usr/bin/python
+# -*- coding: utf-8 -*-
+#
+"""
+    Abstract class for segmenters implemented in skimage.segmentation.
+    
+    Name: skimage_segmenter.py
+    Author: Alessandro dos Santos Ferreira ( santosferreira.alessandro@gmail.com )
+"""
+
+import cv2
+import numpy as np
+from skimage.segmentation import mark_boundaries
+from skimage.util import img_as_float, img_as_ubyte
+
+from util.config import Config
+from util.utils import TimeUtils
+from util.x11_colors import X11Colors
+
+from abc import ABCMeta, abstractmethod
+
+class SkimageSegmenter(object):
+    
+    __metaclass__ = ABCMeta
+    
+    def __init__(self, border_color = 'Yellow', border_outline = 'No'):
+        self.border_color = Config("Border Color", border_color, 'color')
+        self.border_outline = Config("Border Outline", border_outline, str)
+        
+        self._segments = None
+        self._original_image = None
+        
+    
+    def get_segment_skimage(self, px = 0, py = 0, idx_segment = None):
+        if self._segments is None:
+            return None, 0, -1, 0
+        
+        start_time = TimeUtils.get_time()
+        
+        if idx_segment is None:
+            idx_segment = self._segments[py, px]
+        
+        mask_segment = np.zeros(self._original_image.shape[:2], dtype="uint8")
+        mask_segment[self._segments == idx_segment] = 255
+        size_segment = mask_segment[self._segments == idx_segment].size
+
+        segment = self._original_image.copy()
+        segment = cv2.bitwise_and(segment, segment, mask=mask_segment)
+
+        contours, _  = cv2.findContours(mask_segment,cv2.RETR_LIST,cv2.CHAIN_APPROX_SIMPLE)[-2:]
+
+        m = -1
+        max_contour = None
+        for cnt in contours:
+            if (len(cnt) > m):
+                m = len(cnt)
+                max_contour = cnt
+
+        x,y,w,h = cv2.boundingRect(max_contour)
+        segment = segment[y:y+h, x:x+w]
+        
+        end_time = TimeUtils.get_time()
+        
+        return segment, size_segment, idx_segment, (end_time - start_time)
+        
+        
+    def paint_segment_skimage(self, image, color, px = 0, py = 0, idx_segment = None, border = True, clear = False):
+        if self._segments is None:
+            return image, 0
+            
+        start_time = TimeUtils.get_time()
+        
+        if idx_segment is None:
+            idx_segment = self._segments[py, px]
+        height, width, channels = self._original_image.shape
+        
+        mask_segment = np.zeros(self._original_image.shape[:2], dtype="uint8")
+        mask_segment[self._segments == idx_segment] = 255
+        mask_inv = cv2.bitwise_not(mask_segment)
+            
+        class_color = np.zeros((height,width,3), np.uint8)
+        class_color[:, :] = X11Colors.get_color(color)
+        if clear == False:
+            colored_image = cv2.addWeighted(self._original_image, 0.7, class_color, 0.3, 0)
+        else:
+            colored_image = self._original_image
+        colored_image = cv2.bitwise_and(colored_image, colored_image, mask=mask_segment)
+        
+        new_image = cv2.bitwise_and(image, image, mask=mask_inv)
+        mask_segment[:] = 255
+        new_image = cv2.bitwise_or(new_image, colored_image, mask=mask_segment)
+
+        if border == True:
+            color = X11Colors.get_color_zero_one(self.border_color.get_cast_val())
+            outline_color = color if self.border_outline.value == 'Yes' else None
+            
+            new_image = img_as_ubyte( mark_boundaries(img_as_float(new_image), self._segments.astype(np.int8), color=color, outline_color=outline_color) ) 
+            
+        end_time = TimeUtils.get_time()
+        
+        return new_image, (end_time - start_time)
+
+
+    def run_skimage(self, image, method, **kwargs):
+        self._original_image = image
+        
+        start_time = TimeUtils.get_time()
+        self._segments = method(img_as_float(image), **kwargs)
+        end_time = TimeUtils.get_time()
+        
+        color = X11Colors.get_color_zero_one(self.border_color.get_cast_val())
+        outline_color = color if self.border_outline.value == 'Yes' else None
+
+        #  Ignore UserWarning: Possible precision loss when converting from float64 to uint8
+        #  because the returned image is used just for visualization
+        #  The original image, without loss, is stored in self._original_image
+        return img_as_ubyte( mark_boundaries(image, self._segments.astype(np.int8), color=color, outline_color=outline_color) ), (end_time - start_time)
+        

src/segmentation/slic.py

@@ -4,15 +4,13 @@
 """
     Runs Segmenter SLIC (Simple Linear Iterative Clustering) implemented in skimage.segmentation.
     
+    Radhakrishna Achanta, Appu Shaji, Kevin Smith, Aurelien Lucchi, Pascal Fua, and Sabine Suesstrunk, SLIC Superpixels Compared to State-of-the-art Superpixel Methods, TPAMI, May 2012.
+    
     Name: slic.py
     Author: Alessandro dos Santos Ferreira ( santosferreira.alessandro@gmail.com )
 """
 
-import cv2
-import numpy as np
 from skimage.segmentation import slic
-from skimage.segmentation import mark_boundaries
-from skimage.util import img_as_float, img_as_ubyte
 from collections import OrderedDict
 
 from util.config import Config
@@ -20,20 +18,16 @@ from util.utils import TimeUtils
 from util.x11_colors import X11Colors
 
 from segmenter import Segmenter
+from skimage_segmenter import SkimageSegmenter
 
-class Slic(Segmenter):
+class Slic(Segmenter, SkimageSegmenter):
 
+    def __init__(self, n_segments = 250, sigma = 5.0, compactness = 10.0, border_color = 'Yellow', border_outline = 'No'):
+        super(self.__class__, self).__init__(border_color, border_outline)
         
-    def __init__(self, n_segments = 100, sigma = 5.0, compactness = 10.0, border_color = 'Yellow', border_outline = 'No'):
         self.n_segments = Config("Segments", n_segments, int)
         self.sigma = Config("Sigma", sigma, float)
         self.compactness = Config("Compactness", compactness, float)
-        self.border_color = Config("Border Color", border_color, 'color')
-        self.border_outline = Config("Border Outline", border_outline, str)
-        
-        self._segments = None
-    
-        self._original_image = None
         
     
     def get_config(self):
@@ -73,92 +67,18 @@ class Slic(Segmenter):