def ShowSourceSlide(self):
if os.path.exists(self.filename):
arr = HamaWrapper.getSlideImage(self.filename)
im = Image.frombuffer("RGB", (arr.shape[2], arr.shape[1]), arr.data)
im.show()
else:
print "Error: File not found!"
def GetMap(self, desired_frame_width, desired_frame_height):
"""Arguments:
frame_width: long with the width in pixel.
frame_height: long with the height in pixel.
"""
if os.path.exists(self.filename):
return HamaWrapper.getMap(self.filename, desired_frame_width, desired_frame_height)
else:
print "Error: File not found!"
def ShowMap(self, desired_frame_width, desired_frame_height):
"""Arguments:
frame_width: long with the width in pixel.
frame_height: long with the height in pixel.
"""
if os.path.exists(self.filename):
arr = HamaWrapper.getMap(self.filename, desired_frame_width, desired_frame_height)
im = Image.frombuffer("RGB", (arr.shape[2], arr.shape[1]), arr.data)
im.show()
else:
print "Error: File not found!"
def GetImageData(self, frame_width, frame_height, x_center, y_center, z_plan, magnification):
"""Arguments:
frame_width: long with the width in pixel.
frame_height: long with the height in pixel.
x_center: long with the physical X pos of the desired image in nm.
y_center: long with the physical Y pos of the desired image in nm.
z_plan: long with the physical Z (focal) pos of the desired image in nm.
magnification: long with the objective magnification.
"""
if os.path.exists(self.filename):
return HamaWrapper.getImageData(
self.filename, frame_width, frame_height, x_center, y_center, z_plan, magnification
)
else:
print "Error: File not found!"
def GetImageDataNm(self, physical_width, physical_height, x_center, y_center, z_plan, magnification):
"""Arguments:
physical_width: long with the width in nm.
physical_height: long with the height in nm.
x_center: long with the physical X pos of the desired image in nm.
y_center: long with the physical Y pos of the desired image in nm.
z_plan: long with the physical Z (focal) pos of the desired image in nm.
magnification: long with the objective magnification.
"""
width = round(magnification * physical_width / self.CONV_FACT) + 1
height = round(magnification * physical_height / self.CONV_FACT) + 1
if os.path.exists(self.filename):
return HamaWrapper.getImageData(self.filename, width, height, x_center, y_center, z_plan, magnification)
else:
print "Error: File not found!"
def GetImageNm(self, physical_width, physical_height, x_coord, y_coord, z_depth, magnification):
"""Arguments:
physical_width: long with the width in nm.
physical_height: long with the height in nm.
x_center: long with the physical X pos of the desired image in nm.
y_center: long with the physical Y pos of the desired image in nm.
z_plan: long with the physical Z (focal) pos of the desired image in nm.
magnification: long with the objective magnification.
"""
width = round(1.0 * magnification * physical_width / self.CONV_FACT) + 1
height = round(1.0 * magnification * physical_height / self.CONV_FACT) + 1
if os.path.exists(self.filename):
arr = HamaWrapper.getImageData(self.filename, width, height, x_coord, y_coord, z_depth, magnification)
im = Image.frombuffer("RGB", (arr.shape[2], arr.shape[1]), arr.data)
return im
else:
print "Error: File not found!"
def GetImage(self, desired_frame_width, desired_frame_height, x_coord, y_coord, z_depth, magnification):
"""Arguments:
frame_width: long with the width in pixel.
frame_height: long with the height in pixel.
x_center: long with the physical X pos of the desired image in nm.
y_center: long with the physical Y pos of the desired image in nm.
z_plan: long with the physical Z (focal) pos of the desired image in nm.
magnification: long with the objective magnification.
"""
if os.path.exists(self.filename):
arr = HamaWrapper.getImageData(
self.filename, desired_frame_width, desired_frame_height, x_coord, y_coord, z_depth, magnification
)
im = Image.frombuffer("RGB", (arr.shape[2], arr.shape[1]), arr.data)
return im
else:
print "Error: File not found!"
def GetSlideImage(self):
if os.path.exists(self.filename):
return HamaWrapper.getSlideImage(self.filename)
else:
print "Error: File not found!"
def GetSourcePixelSize(self):
if os.path.exists(self.filename):
return HamaWrapper.getSourcePixelSize(self.filename)
else:
print "Error: File not found!"
def ColorConvolution(self, width, height, x, y, z, mag, stain_matrix):
if os.path.exists(self.filename):
arr = HamaWrapper.convolution(self.filename, width, height, x, y, z, mag, stain_matrix)
return arr
else:
print "Error: File not found!"
def GetLastErrorMessage(self):
print HamaWrapper.getLastErrorMessage()
def CleanUp(self):
return HamaWrapper.cleanUp()
