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Make set_image_count() efficient with large values. #115

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Make set_image_count() efficient with large values. #115

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50 changes: 29 additions & 21 deletions bioformats/omexml.py
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Original file line number Diff line number Diff line change
Expand Up @@ -327,6 +327,9 @@ def __init__(self, xml=None):
if self.ns['ome'] is None:
raise Exception("Error: String not in OME-XML format")

# make sure this exists or `get_image_count()` dies
self._image_count = None

def __str__(self):
#
# need to register the ome namespace because BioFormats expects
Expand Down Expand Up @@ -354,7 +357,9 @@ def root_node(self):

def get_image_count(self):
'''The number of images (= series) specified by the XML'''
return len(self.root_node.findall(qn(self.ns['ome'], "Image")))
if self._image_count is None:
self._image_count = len(self.root_node.findall(qn(self.ns['ome'], "Image")))
return self._image_count

def set_image_count(self, value):
'''Add or remove image nodes as needed'''
Expand All @@ -364,26 +369,29 @@ def set_image_count(self, value):
image_nodes = root.find(qn(self.ns['ome'], "Image"))
for image_node in image_nodes[value:]:
root.remove(image_node)
while(self.image_count < value):
new_image = self.Image(ElementTree.SubElement(root, qn(self.ns['ome'], "Image")))
new_image.ID = str(uuid.uuid4())
new_image.Name = "default.png"
new_image.AcquisitionDate = xsd_now()
new_pixels = self.Pixels(
ElementTree.SubElement(new_image.node, qn(self.ns['ome'], "Pixels")))
new_pixels.ID = str(uuid.uuid4())
new_pixels.DimensionOrder = DO_XYCTZ
new_pixels.PixelType = PT_UINT8
new_pixels.SizeC = 1
new_pixels.SizeT = 1
new_pixels.SizeX = 512
new_pixels.SizeY = 512
new_pixels.SizeZ = 1
new_channel = self.Channel(
ElementTree.SubElement(new_pixels.node, qn(self.ns['ome'], "Channel")))
new_channel.ID = "Channel%d:0" % self.image_count
new_channel.Name = new_channel.ID
new_channel.SamplesPerPixel = 1
if self.image_count < value:
for i in range(value - self.image_count):
new_image = self.Image(ElementTree.SubElement(root, qn(self.ns['ome'], "Image")))
new_image.ID = str(uuid.uuid4())
new_image.Name = "default.png"
new_image.AcquisitionDate = xsd_now()
new_pixels = self.Pixels(
ElementTree.SubElement(new_image.node, qn(self.ns['ome'], "Pixels")))
new_pixels.ID = str(uuid.uuid4())
new_pixels.DimensionOrder = DO_XYCTZ
new_pixels.PixelType = PT_UINT8
new_pixels.SizeC = 1
new_pixels.SizeT = 1
new_pixels.SizeX = 512
new_pixels.SizeY = 512
new_pixels.SizeZ = 1
new_channel = self.Channel(
ElementTree.SubElement(new_pixels.node, qn(self.ns['ome'], "Channel")))
new_channel.ID = "Channel%d:0" % (self.image_count + i)
new_channel.Name = new_channel.ID
new_channel.SamplesPerPixel = 1
# force recomputation next time `self.image_count` is accessed
self._image_count = None

image_count = property(get_image_count, set_image_count)

Expand Down