def center_camera(self):
'''Center the camera at whatever interesting thing this class displays
'''
transforms = _get_transforms(self.ImageTransformViewList)
bbox = utils.FixedBoundingBox(transforms)
bbox_rect = nornir_imageregistration.spatial.Rectangle.CreateFromBounds(
bbox)
self.camera.lookat(bbox_rect.Center)
self.camera.scale = bbox_rect.Width
def VolumeBounds(self):
# Boundaries of the volume based on locations where sections will map points into the volume
return tutils.FixedBoundingBox(self.SectionToVolumeTransforms.values())
def TilesToImage(transforms,
imagepaths,
TargetRegion=None,
target_space_scale=None,
source_space_scale=None):
'''
Generate an image of the TargetRegion.
:param tuple TargetRegion: (MinX, MinY, Width, Height) or Rectangle class. Specifies the SourceSpace to render from
:param float target_space_scale: Scalar for the target space coordinates. Used to downsample or upsample the output image. Changes the coordinates of the target space control points of the transform.
:param float target_space_scale: Scalar for the source space coordinates. Must match the change in scale of input images relative to the transform source space coordinates. So if downsampled by
4 images are used, this value should be 0.25. Calculated to be correct if None. Specifying is an optimization to reduce I/O of reading image files to calculate.
'''
assert (len(transforms) == len(imagepaths))
# logger = logging.getLogger(__name__ + '.TilesToImage')
if source_space_scale is None:
source_space_scale = tiles.MostCommonScalar(transforms, imagepaths)
if target_space_scale is None:
target_space_scale = source_space_scale
distanceImage = None
original_fixed_rect_floats = None
if not TargetRegion is None:
if isinstance(TargetRegion, spatial.Rectangle):
original_fixed_rect_floats = TargetRegion
else:
original_fixed_rect_floats = spatial.Rectangle.CreateFromPointAndArea(
(TargetRegion[0], TargetRegion[1]),
(TargetRegion[2] - TargetRegion[0],
TargetRegion[3] - TargetRegion[1]))
else:
original_fixed_rect_floats = tutils.FixedBoundingBox(transforms)
scaled_targetRect = nornir_imageregistration.Rectangle.scale_on_origin(
original_fixed_rect_floats, target_space_scale)
scaled_targetRect = nornir_imageregistration.Rectangle.SafeRound(
scaled_targetRect)
targetRect = nornir_imageregistration.Rectangle.scale_on_origin(
scaled_targetRect, 1.0 / target_space_scale)
(fullImage,
fullImageZbuffer) = __CreateOutputBufferForArea(scaled_targetRect.Height,
scaled_targetRect.Width,
target_space_scale)
for i, transform in enumerate(transforms):
regionToRender = None
original_transform_fixed_rect = spatial.Rectangle(
transform.FixedBoundingBox)
transform_target_rect = nornir_imageregistration.Rectangle.SafeRound(
original_transform_fixed_rect)
regionToRender = nornir_imageregistration.Rectangle.Intersect(
targetRect, transform_target_rect)
if regionToRender is None:
continue
if regionToRender.Area == 0:
continue
scaled_region_rendered = nornir_imageregistration.Rectangle.scale_on_origin(
regionToRender, target_space_scale)
scaled_region_rendered = nornir_imageregistration.Rectangle.SafeRound(
scaled_region_rendered)
imagefullpath = imagepaths[i]
distanceImage = __GetOrCreateDistanceImage(
distanceImage,
nornir_imageregistration.GetImageSize(imagefullpath))
transformedImageData = TransformTile(
transform,
imagefullpath,
distanceImage,
target_space_scale=target_space_scale,
TargetRegion=regionToRender,
SingleThreadedInvoke=True)
if transformedImageData.image is None:
logger = logging.getLogger('TilesToImageParallel')
logger.error('Convert task failed: ' + str(transformedImageData))
if not transformedImageData.errormsg is None:
logger.error(transformedImageData.errormsg)
continue
CompositeOffset = scaled_region_rendered.BottomLeft - scaled_targetRect.BottomLeft
CompositeOffset = CompositeOffset.astype(np.int64)
CompositeImageWithZBuffer(fullImage, fullImageZbuffer,
transformedImageData.image,
transformedImageData.centerDistanceImage,
CompositeOffset)
del transformedImageData
mask = fullImageZbuffer < __MaxZBufferValue(fullImageZbuffer.dtype)
del fullImageZbuffer
fullImage[fullImage < 0] = 0
# Checking for > 1.0 makes sense for floating point images. During the DM4 migration
# I was getting images which used 0-255 values, and the 1.0 check set them to entirely black
# fullImage[fullImage > 1.0] = 1.0
if isinstance(fullImage, np.memmap):
fullImage.flush()
return (fullImage, mask)
def TilesToImageParallel(transforms,
imagepaths,
TargetRegion=None,
target_space_scale=None,
source_space_scale=None,
pool=None):
'''Assembles a set of transforms and imagepaths to a single image using parallel techniques.
:param tuple TargetRegion: (MinX, MinY, Width, Height) or Rectangle class. Specifies the SourceSpace to render from
:param float target_space_scale: Scalar for the target space coordinates. Used to downsample or upsample the output image. Changes the coordinates of the target space control points of the transform.
:param float target_space_scale: Scalar for the source space coordinates. Must match the change in scale of input images relative to the transform source space coordinates. So if downsampled by
4 images are used, this value should be 0.25. Calculated to be correct if None. Specifying is an optimization to reduce I/O of reading image files to calculate.
'''
assert (len(transforms) == len(imagepaths))
logger = logging.getLogger('TilesToImageParallel')
if pool is None:
pool = nornir_pools.GetGlobalMultithreadingPool()
# pool = nornir_pools.GetGlobalSerialPool()
tasks = []
if source_space_scale is None:
source_space_scale = tiles.MostCommonScalar(transforms, imagepaths)
if target_space_scale is None:
target_space_scale = source_space_scale
original_fixed_rect_floats = None
if not TargetRegion is None:
if isinstance(TargetRegion, spatial.Rectangle):
original_fixed_rect_floats = TargetRegion
else:
original_fixed_rect_floats = spatial.Rectangle.CreateFromPointAndArea(
(TargetRegion[0], TargetRegion[1]),
(TargetRegion[2] - TargetRegion[0],
TargetRegion[3] - TargetRegion[1]))
else:
original_fixed_rect_floats = tutils.FixedBoundingBox(transforms)
scaled_targetRect = nornir_imageregistration.Rectangle.scale_on_origin(
original_fixed_rect_floats, target_space_scale)
scaled_targetRect = nornir_imageregistration.Rectangle.SafeRound(
scaled_targetRect)
targetRect = nornir_imageregistration.Rectangle.scale_on_origin(
scaled_targetRect, 1.0 / target_space_scale)
(fullImage,
fullImageZbuffer) = __CreateOutputBufferForArea(scaled_targetRect.Height,
scaled_targetRect.Width,
target_space_scale)
CheckTaskInterval = 16
for i, transform in enumerate(transforms):
regionToRender = None
original_transform_target_rect = spatial.Rectangle(
transform.FixedBoundingBox)
transform_target_rect = nornir_imageregistration.Rectangle.SafeRound(
original_transform_target_rect)
regionToRender = nornir_imageregistration.Rectangle.Intersect(
targetRect, transform_target_rect)
if regionToRender is None:
continue
if regionToRender.Area == 0:
continue
scaled_region_rendered = nornir_imageregistration.Rectangle.scale_on_origin(
regionToRender, target_space_scale)
scaled_region_rendered = nornir_imageregistration.Rectangle.SafeRound(
scaled_region_rendered)
imagefullpath = imagepaths[i]
task = pool.add_task("TransformTile" + imagefullpath,
TransformTile,
transform=transform,
imagefullpath=imagefullpath,
distanceImage=None,
target_space_scale=target_space_scale,
TargetRegion=regionToRender,
SingleThreadedInvoke=False)
task.transform = transform
task.regionToRender = regionToRender
task.scaled_region_rendered = scaled_region_rendered
task.transform_fixed_rect = transform_target_rect
tasks.append(task)
if not i % CheckTaskInterval == 0:
continue
if len(tasks) > multiprocessing.cpu_count():
iTask = len(tasks) - 1
while iTask >= 0:
t = tasks[iTask]
if t.iscompleted:
transformedImageData = t.wait_return()
__AddTransformedTileTaskToComposite(
t, transformedImageData, fullImage, fullImageZbuffer,
scaled_targetRect)
del transformedImageData
del tasks[iTask]
iTask -= 1
logger.info('All warps queued, integrating results into final image')
while len(tasks) > 0:
t = tasks.pop(0)
transformedImageData = t.wait_return()
__AddTransformedTileTaskToComposite(t, transformedImageData, fullImage,
fullImageZbuffer,
scaled_targetRect)
del transformedImageData
del t
# Pass through the entire loop and eliminate completed tasks in case any finished out of order
iTask = len(tasks) - 1
while iTask >= 0:
t = tasks[iTask]
if t.iscompleted:
transformedImageData = t.wait_return()
__AddTransformedTileTaskToComposite(t, transformedImageData,
fullImage,
fullImageZbuffer,
scaled_targetRect)
del transformedImageData
del tasks[iTask]
iTask -= 1
logger.info('Final image complete, building mask')
mask = fullImageZbuffer < __MaxZBufferValue(fullImageZbuffer.dtype)
del fullImageZbuffer
fullImage[fullImage < 0] = 0
# Checking for > 1.0 makes sense for floating point images. During the DM4 migration
# I was getting images which used 0-255 values, and the 1.0 check set them to entirely black
# fullImage[fullImage > 1.0] = 1.0
logger.info('Assemble complete')
if isinstance(fullImage, np.memmap):
fullImage.flush()
return (fullImage, mask)
def FixedBoundingBox(self):
'''Calculate the bounding box of the warped position for a set of transforms
(minX, minY, maxX, maxY)'''
return tutils.FixedBoundingBox(list(self.ImageToTransform.values()))