class MeasurementPoint(object):
"""
This class holds all data associated with a single measurement point.
This includes an XML file, the image from the spectrometer and a
background reference image.
"""
PD_SCOPE_CHANNEL = 0
ION_SCOPE_CHANNEL = 1
collection = None
def __init__(self, date, avgnum, xmlfile, imgfile, bgfile=None):
#print("Reading XML file %s" % xmlfile)
self.date = date
self.avgnum = avgnum
self.read_xml(xmlfile)
self.read_image(imgfile,bgfile)
def read_xml(self, xmlfile):
""" xmlfile should be ('/path/to/folder','filename.xml') """
self.xmlfile = xmlfile
f = open(xmlfile, "r")
tree = parse(f)
self.xml = tree.getroot()
f.close()
def read_image(self, imgfile, bgfile=None):
""" imgfile and bgfile should be ('/path/to/folder','filename.tif') """
self.imgfile, self.bgfile = imgfile, bgfile
self.img = TIFF(os.path.join(imgfile))
if bgfile:
self.img.data -= TIFF(os.path.join(bgfile)).data
self.minmax = self.img.minmax
self.percentiles = self.img.percentiles([1,5,99,99.995])
self.blobs = find_blobs(self.img.data)
def display_image(self, rescale=False, rescale_to_global_minmax=False, rescale_to_percentile_and_max=False):
""" Displayes the spectrometer image using OpenCV's function :py:func:`cv2.imshow` """
if rescale:
i = self.img
if rescale_to_global_minmax:
print("Rescaling to global min and max values (%d,%d)" % self.collection.minmax)
img_data = i.rescale(self.collection.minmax)
elif rescale_to_percentile_and_max:
print("Rescaling image using 5 percent percentile to local maximum value: (%d,%d)." % (self.percentiles[5], i.minmax[1]))
img_data = i.rescale((self.percentiles[5], i.minmax[1]))
else:
img_data = i.rescale(i.minmax)
else:
img_data = self.img.data
cv2.imshow('test',img_data)
return cv2.waitKey()
def __str__(self):
return "MeasurementPoint: (date: %s, xml: %s, image: %s, bgimage: %s)" % (self.date, self.xmlfile, self.imgfile, self.bgfile)
def dump_xml_structure(self, level=0):
""" Returns a human readable dump of the xml structure.
Implemented as a recursive function.
Therefore call without providing the `level` argument."""
output = ''
for element in self.xml:
output += ''.join(['--' for i in range(level)])
output += "> " + element.tag
if element.text != None:
content = element.text.replace("\n"," ")
output += " : "
if len(content) < 20:
output += content
else:
output += content[:20] + " ..."
output += "\n"
output += self.dump_xml_structure(element, level+1)
return output
def get_stage_positions(self):
raise NotImplementedError
def get_photodiode_scope_channel(self):
return self.get_scope_channel(self.PD_SCOPE_CHANNEL)
def get_ion_scope_channel(run):
return self.get_scope_channel(self.ION_SCOPE_CHANNEL)
def get_scope_channel(run, channel_no):
for scope in run:
if scope.tag == 'NI_TCP_Scope':
for channel in scope:
if channel.tag == 'CH' + str(channel_no):
data = channel.text
data = [float(value) for value in data.split()]
return data
def calculate_ion_signal(self):
ion_signal_point = 0.0
for ion_signal_point in self.get_ion_scope_channel():
ion_signal += ion_signal_point
return ion_signal
