add the new class from the ScanAnnotation.py

GetAnnFromXml.py

@@ -1,10 +1,9 @@
+"""
+This program is used for read an annotation xml File and store in class Annotation
+"""
 import xml.etree.cElementTree as ET
 import os.path
 import math
-"""
-This program is used for read an annotation part and store in class Annotation
-border = [0,0,0,0] #A 4 - index list [leftmost, rightmost, upmost, downmost]
-"""
 class Annotation(object):
   def __init__(self):
     self.name = " "
@@ -18,7 +17,12 @@ def __init__(self):
     self.yMin = 0
     self.yMax = 0
 
-class getAnnFromXml(object):
+    # Use for record which patch is in the annotation
+    self.patchInAnn = {}
+    # patch size
+    self.patchSize = 50
+
+class GetAnnFromXml(object):
   def __init__(self, fileName):
       self.tree = ET.ElementTree(file = fileName)
       self.annList = []

GetPatchInAnn.py

@@ -0,0 +1,52 @@
+"""
+This program is used to store patches which have all their 4 angles' coordinates are in the annotation Anngon
+"""
+import sys
+sys.path.append("../IsPointInAnn")
+from IsPointInAnn import point, isPointInAnn
+import openslide
+from openslide import open_slide # http://openslide.org/api/python/
+from PIL import Image
+
+class GetPatchInAnn(object):
+  def __init__(self, currentAnn) :
+    self.ann = currentAnn
+    self.annPointGroup = []
+    self.pointInAnn = {}
+
+  def getPatch(self):
+    self.groupXY()
+    self.checkPointsInAnn()
+    self.checkPatchInAnn()
+
+  def groupXY(self):
+    for i in range(0, len(self.ann.coordinateX)):
+        self.annPointGroup.append(point(float(self.ann.coordinateX[i]), float(self.ann.coordinateY[i])))
+    self.annPointGroup.append(self.annPointGroup[0])
+
+  # Find out if each point is in the Annotation, and tag True if it is, tag False if it is not
+  def checkPointsInAnn(self):
+    for i in range(self.ann.xMin, self.ann.xMax, self.ann.patchSize):
+      for j in range(self.ann.yMin, self.ann.yMax, self.ann.patchSize):
+        if isPointInAnn().isInAnn(point(i, j), self.annPointGroup):
+          self.pointInAnn.update({(i, j) : True})
+        else:
+          self.pointInAnn.update({(i, j) : False})
+
+  #Find out if a patch is in annotation, and tag True if it is, tag False if it is not
+  def checkPatchInAnn(self):
+    for i in range(self.ann.xMin, self.ann.xMax, self.ann.patchSize):
+      for j in range(self.ann.yMin, self.ann.yMax, self.ann.patchSize):
+        if self.isFourAnglesInAnn(i, j):
+          self.ann.patchInAnn.update({(i, j) : True})
+        else:
+          self.ann.patchInAnn.update({(i, j) : False})
+
+  def isFourAnglesInAnn(self, i, j):
+    inAnn = False
+    if self.pointInAnn.get((i, j))\
+       and self.pointInAnn.get((i + self.ann.patchSize, j))\
+       and self.pointInAnn.get((i , j + self.ann.patchSize))\
+       and self.pointInAnn.get((i + self.ann.patchSize, j + self.ann.patchSize)):
+       inAnn = True
+    return inAnn

IsPointInAnn.py

@@ -16,10 +16,13 @@ def __init__(self):
   def isInAnn(self, testPoint, annPointGroup):
     inAnn = False
     for i in range(0, len(annPointGroup) - 1):
+        # If there are odd number of lines line in the left of the points,
+        # then the point is in in the annotation
         if (self.pointLieRight(testPoint, annPointGroup[i], annPointGroup[i+1])):
           inAnn = not inAnn
     return inAnn
 
+  # Check if the point is lying right of the line(annPoint1 - annPoint2)
   def pointLieRight(self, testPoint, annPoint1, annPoint2):
     lieRight = False
     if min(annPoint1.y, annPoint2.y) < testPoint.y <= max(annPoint1.y, annPoint2.y)\

PlotPatchInAnn.py

@@ -0,0 +1,34 @@
+"""
+Draw the graph that include the annotation part and patches part
+"""
+import matplotlib.pyplot as plt
+
+class PlotPatchInAnn(object):
+  def __init__(self, currentAnn):
+    self.annImg = plt.subplot(111)
+    self.ann = currentAnn
+
+  def plotPatch(self):
+    self.addAnnGraph()
+    for i in range(self.ann.xMin, self.ann.xMax, self.ann.patchSize):
+      for j in range(self.ann.yMin, self.ann.yMax, self.ann.patchSize):
+        if self.ann.patchInAnn.get((i, j)):
+          self.addPatchGraph(i, j)
+    self.showAnnGraph()
+
+  def addAnnGraph(self):
+    AnnPoints = []
+    for i in range(0, len(self.ann.coordinateX)):
+       AnnPoints.append((self.ann.coordinateX[i], self.ann.coordinateY[i]))
+    AnnGraph = plt.Polygon(AnnPoints, fill = None, edgecolor = 'r')
+    self.annImg.add_patch(AnnGraph)
+
+  def addPatchGraph(self, i, j):
+    print (i, j)
+    patchPoints = [(i,j), (i + self.ann.patchSize, j), (i + self.ann.patchSize, j + self.ann.patchSize), (i, j + self.ann.patchSize)]
+    patch = plt.Polygon(patchPoints, fill = None, edgecolor = 'b')
+    self.annImg.add_patch(patch)
+
+  def showAnnGraph (self):
+    self.annImg.plot()
+    plt.show()

SavePatchInAnn.py

@@ -0,0 +1,22 @@
+
+dirFolder = r'C:\Users\nctu\Desktop\ScanAnnotation\inAnn'
+
+class SavePatchInAnn(object):
+  def __init__(self, scan, currentAnn, currentSaveIndex):
+    self.scan = scan
+    self.ann = currentAnn
+    self.saveIndex = currentSaveIndex
+
+  def savePatch(self):
+    for i in range(self.ann.xMin, self.ann.xMax, self.ann.patchSize):
+      for j in range(self.ann.yMin, self.ann.yMax, self.ann.patchSize):
+        if self.ann.patchInAnn.get((i, j)):
+          self.savePatchFromSlide(i, j)
+
+  def savePatchFromSlide(self, i, j):
+    img  = self.scan.read_region((i,j), 0 , (self.ann.patchSize, self.ann.patchSize))
+    img.save(str(dirFolder)+ '\\' + str(self.saveIndex) + ".png")
+    self.saveIndex += 1
+
+  def updateSaveIndex(self):
+      return self.saveIndex

ScanAnnotations.py

@@ -1,24 +1,43 @@
 import sys
-sys.path.append("../CutAnnToPatches")
 sys.path.append("../GetAnnFromXml")
-from CutAnnToPatches import cutAnnToPatches
-from GetAnnFromXml import getAnnFromXml
+sys.path.append("../GetPatchInAnn")
+sys.path.append("../SavePatchInAnn")
+sys.path.append("../PlotPatchInAnn")
+from GetAnnFromXml import GetAnnFromXml
+from GetPatchInAnn import GetPatchInAnn
+from SavePatchInAnn import SavePatchInAnn
+from PlotPatchInAnn import PlotPatchInAnn
 import openslide
 from openslide import open_slide # http://openslide.org/api/python/
 
 sysFilePath = r'C:\Users\nctu\Desktop\svs_scanner\svs_image\patient_004_node_4.tif'
 xmlFilePath = "patient_004_node_4.xml"
 
-class scanAnnotations(object):
+class ScanAnnotations(object):
   def __init__(self, sysFilePath, xmlFilePath):
-      getAnn = getAnnFromXml(xmlFilePath)
+      getAnn = GetAnnFromXml(xmlFilePath)
       self.annList = getAnn.readXml()
       self.scan = openslide.OpenSlide(sysFilePath)
+      self.currentSaveIndex = 0
 
   def scanAnnotations(self):
     for  currentAnn in self.annList:
-        ann = cutAnnToPatches( self.scan, currentAnn)
-        ann.cutAnn()
+      self.getPatchInAnnotation(currentAnn)
+      self.savePatchInAnnotation(self.scan, currentAnn, self.currentSaveIndex)
+      self.plotPatchInAnnotation(currentAnn)
 
-test = scanAnnotations(sysFilePath, xmlFilePath)
+  def getPatchInAnnotation(self, ann):
+    annGet = GetPatchInAnn(ann)
+    annGet.getPatch()
+
+  def savePatchInAnnotation(self, scan, ann, saveIndex):
+    annSave = SavePatchInAnn(scan, ann, saveIndex)
+    annSave.savePatch()
+    self.currentSaveIndex = annSave.updateSaveIndex()
+
+  def plotPatchInAnnotation(self, ann):
+    annShow = PlotPatchInAnn(ann)
+    annShow.plotPatch()
+
+test = ScanAnnotations(sysFilePath, xmlFilePath)
 test.scanAnnotations()