def __call__(self, context, *args):
LOG.info(self.mess)
tsi = args[0]
self.image = tsi.pixels
meanIntensity = np.mean(self.image)
if meanIntensity < self.minIntensity:
# FIXME: this should be handled with an error.
LOG.warn('Image is too dark, skiping colorcard detection!')
return([self.image, [None, None, None]])
if not self.useWhiteBackground:
self.imagePyramid = cd.createImagePyramid(self.image)
ccdImg = cv2.imread(self.ccf)[:, :, ::-1]
if ccdImg is None:
raise ValueError("Failed to read %s" % self.ccf)
self.colorcardPyramid = cd.createImagePyramid(ccdImg)
# create image pyramid for multiscale matching
SearchRange = [self.colorcardPyramid[0].shape[1],
self.colorcardPyramid[0].shape[0]]
score, loc, angle = cd.matchTemplatePyramid(
self.imagePyramid,
self.colorcardPyramid,
0,
EstimatedLocation=self.colorcardPosition,
SearchRange=SearchRange
)
if score > 0.3:
# extract color information
self.foundCard = self.image[
loc[1] - ccdImg.shape[0] // 2:loc[1] + ccdImg.shape[0] // 2,
loc[0] - ccdImg.shape[1] // 2:loc[0] + ccdImg.shape[1] // 2]
self.ccdColors, _ = cd.getColorcardColors(self.foundCard,
GridSize=[6, 4])
self.colorcardParams = cd.estimateColorParameters(
self.colorcardTrueColors,
self.colorcardColors
)
# Save colourcard image to instance
self.colorcardImage = ccdImg
# for displaying
self.loc = loc
else:
# FIXME: this should be handled with an error.
LOG.warn('Cannot find color card')
self.colorcardParams = [None, None, None]
else:
self.colorcardParams = cd.estimateColorParametersFromWhiteBackground(
self.image, self.backgroundWindow, self.maxIntensity)
return([tsi, self.colorcardParams])
def correctColor(self):
if self.colorcardParams == None:
if len(self.colorcardList) > 0:
medianSize = cd.getMedianRectSize(self.colorcardList)
capturedColorcards = cd.rectifyRectImages(self.image, self.colorcardList, medianSize)
self.colorcardColors, _ = cd.getColorcardColors(capturedColorcards[0], GridSize = [6, 4])
self.colorcardParams = cd.estimateColorParameters(cd.CameraTrax_24ColorCard, self.colorcardColors)
else:
self.status.append('Need to select a color card first.')
return
colorMatrix, colorConstant, colorGamma = self.colorcardParams
self.imageCorrected = cd.correctColorVectorised(self.image.astype(np.float), colorMatrix, colorConstant, colorGamma)
self.imageCorrected[np.where(self.imageCorrected < 0)] = 0
self.imageCorrected[np.where(self.imageCorrected > 255)] = 255
self.imageCorrected = self.imageCorrected.astype(np.uint8)
self.updateFigure(self.imageCorrected)
def __exec__(self, context, *args):
tsi = args[0]
self.image = tsi.pixels
meanIntensity = np.mean(self.image)
if meanIntensity < self.minIntensity:
raise PCExImageTooDark(tsi.path)
if not self.useWhiteBackground:
self.imagePyramid = cd.createImagePyramid(self.image)
ccdImg = read_image(self.ccf)[:, :, 0:3]
if ccdImg is None:
raise PCExBadImage(self.ccf)
self.ccdPyramid = cd.createImagePyramid(ccdImg)
# create image pyramid for multiscale matching
SearchRange = [self.ccdPyramid[0].shape[1] * 1.5,
self.ccdPyramid[0].shape[0] * 1.5]
score, loc, angle = cd.matchTemplatePyramid(
self.imagePyramid, self.ccdPyramid,
0, EstimatedLocation=self.colorcardPosition,
SearchRange=SearchRange)
if score > 0.3:
# extract color information
self.foundCard = self.image[
loc[1] - ccdImg.shape[0] // 2:loc[1] + ccdImg.shape[0] // 2,
loc[0] - ccdImg.shape[1] // 2:loc[0] + ccdImg.shape[1] // 2]
self.ccdColors, _ = cd.getColorcardColors(self.foundCard,
GridSize=[6, 4])
self.ccdParams = cd.estimateColorParameters(
self.colorcardTrueColors,
self.ccdColors)
# Save colourcard image to instance
self.colorcardImage = ccdImg
# for displaying
self.loc = loc
else:
raise PCExCannotFindColorCard(tsi.path)
else:
self.ccdParams = cd.estimateColorParametersFromWhiteBackground(
self.image, self.backgroundWindow, self.maxIntensity)
return([tsi, self.ccdParams])
def savePipelineSettings(self):
''' save to pipeline setting file'''
self.settingFileName = str(QtGui.QFileDialog.getSaveFileName(self, \
'Save selection (default in ./_data)', self.timestreamRootPath))
if len(self.settingFileName) == 0:
return
self.settingPath = os.path.relpath(os.path.dirname(self.settingFileName), self.timestreamRootPath)
self.settings = {}
if self.ImageSize != None and self.CameraMatrix != None and self.DistCoefs != None:
undistortDic = {'cameraMatrix': self.CameraMatrix.tolist(), \
'distortCoefs': self.DistCoefs.tolist(), \
'imageSize': list(self.ImageSize),
'rotationAngle': self.rotationAngle + self.smaleRotationAngle
}
else:
undistortDic = {}
self.settings['undistort'] = undistortDic
if len(self.colorcardList) > 0:
medianSize = cd.getMedianRectSize(self.colorcardList)
capturedColorcards = cd.rectifyRectImages(self.image, self.colorcardList, medianSize)
colorCardFile = 'CapturedColorcard.png'
cv2.imwrite(os.path.join(self.timestreamRootPath, self.settingPath, colorCardFile), capturedColorcards[0][:,:,::-1].astype(np.uint8))
colorcardColors, colorStd = cd.getColorcardColors(capturedColorcards[0], GridSize = [6,4])
colorcardPosition, Width, Height, Angle = cd.getRectangleParamters(self.colorcardList[0])
colorcardDic = {'colorcardFile': colorCardFile,\
'colorcardPosition': colorcardPosition.tolist(),\
'colorcardTrueColors': cd.CameraTrax_24ColorCard,\
'settingPath': '_data'
}
else:
colorcardDic = {}
self.settings['colorcarddetect'] = colorcardDic
self.settings['colorcorrect'] = {'minIntensity': 15}
if len(self.trayList) > 0:
trayMedianSize = cd.getMedianRectSize(self.trayList)
trayImages = cd.rectifyRectImages(self.image, self.trayList, trayMedianSize)
trayDict = {}
trayDict['settingPath'] = '_data'
trayDict['trayNumber'] = len(self.trayList)
trayDict['trayFiles'] = 'Tray_%02d.png'
trayPositions = []
for i,tray in enumerate(trayImages):
cv2.imwrite(os.path.join(self.timestreamRootPath, self.settingPath, trayDict['trayFiles'] %i), tray[:,:,::-1].astype(np.uint8))
trayPosition, Width, Height, Angle = cd.getRectangleParamters(self.trayList[i])
trayPositions.append(trayPosition.tolist())
trayDict['trayPositions'] = trayPositions
else:
trayDict = {}
self.settings['traydetect'] = trayDict
if len(self.potList) > 0:
trayMedianSize = cd.getMedianRectSize(self.trayList)
potPosition, Width, Height, Angle = cd.getRectangleParamters(self.potList[0])
Width, Height = int(Width), int(Height)
topLeft = [int(self.potList[0][0][0]), int(self.potList[0][0][1])]
self.potImage = self.image[topLeft[1]:topLeft[1]+Height, topLeft[0]:topLeft[0]+Width, :]
potFile = 'Pot.png'
cv2.imwrite(os.path.join(self.timestreamRootPath, self.settingPath, potFile), self.potImage[:,:,::-1].astype(np.uint8))
potDict = {}
potDict['potPositions'] = potPosition.tolist()
potDict['potSize'] = [int(Width), int(Height)]
potDict['traySize'] = [int(trayMedianSize[0]), int(trayMedianSize[1])]
potDict['potFile'] = potFile
potDict['potTemplateFile'] = 'PotTemplate.png'
potDict['settingPath'] = '_data'
potTemplatePathIn = os.path.join(self.scriptPath, './data/PotTemplate.png')
potTemplatePathOut = os.path.join(self.timestreamRootPath, self.settingPath, potDict['potTemplateFile'])
shutil.copyfile(potTemplatePathIn, potTemplatePathOut)
if self.potTemplate != None:
potTemplateFile = 'potTemplate.png'
cv2.imwrite(os.path.join(self.timestreamRootPath, self.settingPath, potTemplateFile), self.potTemplate[:,:,::-1])
potDict['potTemplateFile'] = potTemplateFile
else:
potDict = {}
self.settings['potdetect'] = potDict
self.settings['plantextract'] = {'meth': 'method1',
'methargs': {'threshold' : 0.6,
'kSize' : 5, 'blobMinSize' : 50} }
with open(self.settingFileName, 'w') as outfile:
outfile.write( yaml.dump(self.settings, default_flow_style=None) )
self.status.append('Saved initial data to ' + self.settingFileName)
