def testRigidTransformAssemblyFactory(self):
angle = -132.0
X = -4
Y = 22
__transform_tolerance = 1e-5
angle = (angle / 180) * np.pi
WarpedImagePath = os.path.join(
self.ImportedDataPath,
"0017_TEM_Leveled_image__feabinary_Cel64_Mes8_sp4_Mes8.png")
FixedImagePath = os.path.join(
self.ImportedDataPath,
"mini_TEM_Leveled_image__feabinary_Cel64_Mes8_sp4_Mes8.png")
warped_size = nornir_imageregistration.GetImageSize(WarpedImagePath)
half_warped_size = np.asarray(warped_size) / 2.0
fixed_size = nornir_imageregistration.GetImageSize(FixedImagePath)
half_fixed_size = np.asarray(fixed_size) / 2.0
reference_transform = nornir_imageregistration.transforms.Rigid(
[Y, X], half_fixed_size, angle)
reference_ImageData = nornir_imageregistration.assemble.WarpedImageToFixedSpace(
reference_transform, None, WarpedImagePath)
r_transform = nornir_imageregistration.transforms.factory.CreateRigidTransform(
target_image_shape=fixed_size,
source_image_shape=warped_size,
rangle=angle,
warped_offset=[Y, X],
flip_ud=False)
m_transform = nornir_imageregistration.transforms.factory.CreateRigidMeshTransform(
target_image_shape=fixed_size,
source_image_shape=warped_size,
rangle=angle,
warped_offset=[Y, X],
flip_ud=False)
np.testing.assert_allclose(r_transform.MappedBoundingBox.Corners,
m_transform.MappedBoundingBox.Corners,
atol=__transform_tolerance)
np.testing.assert_allclose(r_transform.FixedBoundingBox.Corners,
m_transform.FixedBoundingBox.Corners,
atol=__transform_tolerance)
r_transformedImageData = nornir_imageregistration.assemble.WarpedImageToFixedSpace(
r_transform, None, WarpedImagePath)
m_transformedImageData = nornir_imageregistration.assemble.WarpedImageToFixedSpace(
m_transform, None, WarpedImagePath)
self.assertTrue(
nornir_imageregistration.ShowGrayscale(
[[FixedImagePath, WarpedImagePath], [reference_ImageData],
[r_transformedImageData, m_transformedImageData]],
title=
"Middle row image should be perfectly aligned with the top left\nBottom row should match middle row",
PassFail=True))
def testRigidTransformAssemblyDirect(self):
angle = -132.0
X = -4
Y = 22
angle = (angle / 180) * np.pi
WarpedImagePath = os.path.join(
self.ImportedDataPath,
"0017_TEM_Leveled_image__feabinary_Cel64_Mes8_sp4_Mes8.png")
FixedImagePath = os.path.join(
self.ImportedDataPath,
"mini_TEM_Leveled_image__feabinary_Cel64_Mes8_sp4_Mes8.png")
warped_size = nornir_imageregistration.GetImageSize(WarpedImagePath)
half_warped_size = np.asarray(warped_size) / 2.0
fixed_size = nornir_imageregistration.GetImageSize(FixedImagePath)
half_fixed_size = np.asarray(fixed_size) / 2.0
transform = nornir_imageregistration.transforms.Rigid([Y, X],
half_fixed_size,
angle)
transformedImageData = nornir_imageregistration.assemble.WarpedImageToFixedSpace(
transform, None, WarpedImagePath)
self.assertTrue(
nornir_imageregistration.ShowGrayscale(
[FixedImagePath, transformedImageData, WarpedImagePath],
title="Second image should be perfectly aligned with the first",
PassFail=True))
def TestReadWriteTransform(self):
'''A simple test of a transform which maps points from a 10,10 image to a 100,100 without translation or rotation'''
WarpedImagePath = os.path.join(self.ImportedDataPath, "10x10.png")
self.assertTrue(os.path.exists(WarpedImagePath), "Missing test input")
FixedImagePath = os.path.join(self.ImportedDataPath, "1000x100.png")
self.assertTrue(os.path.exists(FixedImagePath), "Missing test input")
FixedSize = (100, 1000)
WarpedSize = (10, 10)
arecord = nornir_imageregistration.AlignmentRecord(peak=(0, 0),
weight=100,
angle=0)
alignmentTransform = arecord.ToTransform(FixedSize, WarpedSize)
self.assertEqual(
FixedSize[0],
nornir_imageregistration.GetImageSize(FixedImagePath)[0])
self.assertEqual(
FixedSize[1],
nornir_imageregistration.GetImageSize(FixedImagePath)[1])
self.assertEqual(
WarpedSize[0],
nornir_imageregistration.GetImageSize(WarpedImagePath)[0])
self.assertEqual(
WarpedSize[1],
nornir_imageregistration.GetImageSize(WarpedImagePath)[1])
TransformCheck(self, alignmentTransform, [[0, 0]], [[45, 495]])
TransformCheck(self, alignmentTransform, [[9, 9]], [[54, 504]])
# OK, try to save the stos file and reload it. Make sure the transforms match
savedstosObj = arecord.ToStos(FixedImagePath,
WarpedImagePath,
PixelSpacing=1)
self.assertIsNotNone(savedstosObj)
stosfilepath = os.path.join(self.VolumeDir, 'TestRWScaleOnly.stos')
savedstosObj.Save(stosfilepath)
loadedStosObj = StosFile.Load(stosfilepath)
self.assertIsNotNone(loadedStosObj)
loadedTransform = nornir_imageregistration.transforms.LoadTransform(
loadedStosObj.Transform)
self.assertIsNotNone(loadedTransform)
self.assertTrue(
(alignmentTransform.points == loadedTransform.points).all(),
"Transform different after save/load")
TransformCheck(self, loadedTransform, [[0, 0]], [[45, 495]])
TransformCheck(self, alignmentTransform, [[9, 9]], [[54, 504]])
def AddOrUpdateFilterImageSet(self, channel_obj, filter_obj, imageset_obj,
ZLevel):
transform_name = imageset_obj.InputTransform
db_coord_space = GetCoordSpace(channel_obj, transform_name)
(db_channel,
created) = models.Channel.objects.get_or_create(name=channel_obj.Name)
if created:
db_channel.save()
(db_filter,
created) = models.Filter.objects.get_or_create(name=filter_obj.Name,
channel=db_channel)
if created:
db_filter.save()
for (level_number, image) in imageset_obj.GetImages():
img_name = os.path.basename(image.fullpath)
(height,
width) = nornir_imageregistration.GetImageSize(image.fullpath)
db_data = models.Data2D(name=img_name,
image=os.path.abspath(image.fullpath),
filter=db_filter,
level=level_number,
relative_path=image.fullpath,
coord_space=db_coord_space,
width=width,
height=height)
def EnsureTransformsHaveMappedBoundingBoxes(self,
image_scale,
image_path,
all_same_dims=True):
'''
If a transform does not have a mapped bounding box, define it using the image dimensions
:param float image_scale: Downsample factor of image files
:parma str image_path: Directory containing image files
:param bool all_same_dims: If true, cache image dimensions and re-use for all transforms.
'''
cached_tile_shape = None
for (file, transform) in self.ImageToTransform.items():
if transform.MappedBoundingBox is None:
if all_same_dims == True:
mapped_bbox_shape = cached_tile_shape
if mapped_bbox_shape is None:
image_full_path = os.path.join(image_path, file)
mapped_bbox_shape = nornir_imageregistration.GetImageSize(
image_full_path)
mapped_bbox_shape = np.array(
mapped_bbox_shape,
dtype=np.int32) * (1.0 / image_scale)
cached_tile_shape = mapped_bbox_shape
transform.MappedBoundingBox = nornir_imageregistration.Rectangle.CreateFromPointAndArea(
(0, 0), mapped_bbox_shape)
def RunStosAssemble(self, stosFullPath):
OutputPath = os.path.join(self.VolumeDir, "test_StosAssemble.png")
warpedImage = assemble.TransformStos(stosFullPath, OutputPath,
self.FixedImagePath,
self.WarpedImagePath)
self.assertIsNotNone(warpedImage)
self.assertTrue(os.path.exists(OutputPath),
"RegisteredImage does not exist")
self.assertEquals(
nornir_imageregistration.GetImageSize(self.FixedImagePath)[0],
nornir_imageregistration.GetImageSize(OutputPath)[0])
self.assertEquals(
nornir_imageregistration.GetImageSize(self.FixedImagePath)[1],
nornir_imageregistration.GetImageSize(OutputPath)[1])
def TestTranslateReadWriteAlignment(self):
WarpedImagePath = os.path.join(
self.ImportedDataPath,
"0017_TEM_Leveled_image__feabinary_Cel64_Mes8_sp4_Mes8.png")
self.assertTrue(os.path.exists(WarpedImagePath), "Missing test input")
FixedImagePath = os.path.join(
self.ImportedDataPath,
"mini_TEM_Leveled_image__feabinary_Cel64_Mes8_sp4_Mes8.png")
self.assertTrue(os.path.exists(FixedImagePath), "Missing test input")
peak = (20, 5)
arecord = nornir_imageregistration.AlignmentRecord(peak,
weight=100,
angle=0)
FixedSize = nornir_imageregistration.GetImageSize(FixedImagePath)
WarpedSize = nornir_imageregistration.GetImageSize(WarpedImagePath)
alignmentTransform = arecord.ToTransform(FixedSize, WarpedSize)
TransformCheck(self, alignmentTransform, [[(WarpedSize[0] / 2.0),
(WarpedSize[1] / 2.0)]],
[[(FixedSize[0] / 2.0) + peak[0],
(FixedSize[1] / 2.0) + peak[1]]])
# OK, try to save the stos file and reload it. Make sure the transforms match
savedstosObj = arecord.ToStos(FixedImagePath,
WarpedImagePath,
PixelSpacing=1)
self.assertIsNotNone(savedstosObj)
stosfilepath = os.path.join(self.VolumeDir, '17-18_brute.stos')
savedstosObj.Save(stosfilepath)
loadedStosObj = StosFile.Load(stosfilepath)
self.assertIsNotNone(loadedStosObj)
loadedTransform = nornir_imageregistration.transforms.LoadTransform(
loadedStosObj.Transform)
self.assertIsNotNone(loadedTransform)
self.assertTrue(
(alignmentTransform.points == loadedTransform.points).all(),
"Transform different after save/load")
def TransformStos(transformData,
OutputFilename=None,
fixedImage=None,
warpedImage=None,
scalar=1.0,
CropUndefined=False):
'''Assembles an image based on the passed transform.
:param str fixedImage: Image describing the size we want the warped image to fill, either a string or ndarray
:param str warpedImage: Image we will warp into fixed space, either a string or ndarray
:param float scalar: Amount to scale the transform before passing the image through
:param bool CropUndefined: If true exclude areas outside the convex hull of the transform, if it exists
:param bool Dicreet: True causes points outside the defined transform region to be clipped instead of interpolated
:return: transformed image
'''
stos = None
stostransform = ParameterToStosTransform(transformData)
if fixedImage is None:
if stos is None:
return None
fixedImage = stos.ControlImageFullPath
if warpedImage is None:
if stos is None:
return None
warpedImage = stos.MappedImageFullPath
fixedImageSize = nornir_imageregistration.GetImageSize(fixedImage)
fixedImageShape = np.array(fixedImageSize) * scalar
warpedImage = nornir_imageregistration.ImageParamToImageArray(warpedImage)
stostransform.points = stostransform.points * scalar
warpedImage = TransformImage(stostransform, fixedImageShape, warpedImage,
CropUndefined)
if not OutputFilename is None:
imsave(OutputFilename, warpedImage, cmap='gray')
return warpedImage
def DimensionsMatch(imageFullPath, area):
'''Return true if the area matches the area of the image.
:param str imageFullPath: Path to image file on disk
:param tuple area: (Width, Height)
'''
if area is None:
raise TypeError(
"RemoveOnDimensionMismatch area parameter should be a (Width,Height) tuple instead of None"
)
try:
size = nornir_imageregistration.GetImageSize(imageFullPath)
except IOError as e:
# Unable to read the size, assume the dimensions do not Match
logging.error("IOError reading dimensions of file: %s\n%s" %
(imageFullPath, str(e)))
return False
if size is None:
return False
else:
return size[1] == area[1] and size[0] == area[0]
def EnsureTileHasMappedBoundingBox(self,
image_scale,
cached_tile_shape=None):
'''
If our tile does not have a mapped bounding box, define it using the tile's image dimensions
:param float image_scale: Downsample factor of image files
:param tuple cached_tile_shape: If not None, use these dimensions for the mapped bounding box instead of loading the image to obtain the shape
'''
if self._transform.MappedBoundingBox is None:
if cached_tile_shape is not None:
mapped_bbox_shape = cached_tile_shape
else:
mapped_bbox_shape = nornir_imageregistration.GetImageSize(
self._imagepath)
mapped_bbox_shape = np.array(
mapped_bbox_shape, dtype=np.int32) * (1.0 / image_scale)
self._transform.MappedBoundingBox = nornir_imageregistration.Rectangle.CreateFromPointAndArea(
(0, 0), mapped_bbox_shape)
return mapped_bbox_shape
return None
def ParsePMG(filename, TileOverlapPercent=None):
if TileOverlapPercent is None:
TileOverlapPercent = 0.1
# Create a dictionary to store tile position
Tiles = dict()
# OutFilepath = os.path.join(SectionPath, OutFilename)
PMGDir = os.path.dirname(filename)
if (DEBUG):
prettyoutput.Log("Filename: " + filename)
# prettyoutput.Log("PMG to: " + OutFilepath)
Data = ''
with open(filename, 'r') as SourceFile:
Data = SourceFile.read()
SourceFile.close()
Data = Data.replace('\r\n', '\n')
Tuple = Data.partition('VISPIECES')
Tuple = Tuple[2].partition('\n')
NumPieces = int(Tuple[0])
Tuple = Data.partition('VISSCALE')
Tuple = Tuple[2].partition('\n')
ScaleFactor = 1 / float(Tuple[0])
Tuple = Data.partition('IMAGEREDUCTION')
Tuple = Tuple[2].partition('\n')
ReductionFactor = 1 / float(Tuple[0])
Data = Tuple[2]
if (DEBUG):
prettyoutput.Log(("Num Tiles: " + str(NumPieces)))
prettyoutput.Log(("Scale : " + str(ScaleFactor)))
prettyoutput.Log(("Reduction: " + str(ReductionFactor)))
Tuple = Data.partition('PIECE')
Data = Tuple[2]
# What type of files did Syncroscan write? We have to assume BMP and then switch to tif
# if the BMP's do not exist.
FileTypeExt = "BMP"
TileWidth = 0
TileHeight = 0
while Data:
Tuple = Data.partition('ENDPIECE')
# Remaining unprocessed file goes into data
Data = Tuple[2]
Entry = Tuple[0]
# Find filename
Tuple = Entry.partition('PATH')
# Probably means we skipped the last tile in a PMG
if (Tuple[1] != "PATH"):
continue
Tuple = Tuple[2].partition('<')
Tuple = Tuple[2].partition('>')
TileFilename = Tuple[0]
TileFullPath = os.path.join(PMGDir, TileFilename)
# PMG files for some reason always claim the tile is a .bmp. So we trust them first and if it doesn't
# exist we try to find a .tif
if not os.path.exists(TileFullPath):
[base, ext] = os.path.splitext(TileFilename)
TileFilename = base + '.tif'
TileFullPath = os.path.join(PMGDir, TileFilename)
FileTypeExt = 'tif'
if not os.path.exists(TileFullPath):
prettyoutput.Log('Skipping missing tile in PMG: ' + TileFilename)
continue
if (TileWidth == 0):
try:
[TileHeight, TileWidth
] = nornir_imageregistration.GetImageSize(TileFullPath)
if (DEBUG):
prettyoutput.Log(
str(TileWidth) + ',' + str(TileHeight) + " " +
TileFilename)
except:
prettyoutput.Log('Could not determine size of tile: ' +
TileFilename)
continue
# prettyoutput.Log("Adding tile: " + TileFilename)
# Prevent rounding errors later when we divide these numbers
TileWidth = float(TileWidth)
TileHeight = float(TileHeight)
TileWidthMinusOverlap = TileWidth - (TileWidth * TileOverlapPercent)
TileHeightMinusOverlap = TileHeight - (TileHeight * TileOverlapPercent)
# Find Position
Tuple = Entry.partition('CORNER')
Tuple = Tuple[2].partition('\n')
Position = Tuple[0].split()
# prettyoutput.Log( Position
X = float(Position[0])
Y = float(Position[1])
# Convert Position into pixel units using Reduction and Scale factors
X = X * ScaleFactor * ReductionFactor
Y = Y * ScaleFactor * ReductionFactor
# Syncroscan lays out tiles in grids, so find the nearest grid coordinates of this tile
# This lets us use the last captured tile per grid cell, so users can manually correct
# focus
iX = round(X / TileWidthMinusOverlap)
iY = round(Y / TileHeightMinusOverlap)
if (DEBUG):
prettyoutput.Log(("Name,iX,iY: " + TileFilename + " " + str(
(iX, iY))))
# Add tile to dictionary
# Using the indicies will replace any existing tiles in that location.
# Syncroscan adds the tiles to the file in order of capture, so the older, blurry
# tiles will be replaced.
Tiles[TileFilename] = X, Y
# Prime for next iteration
Tuple = Data.partition('PIECE')
Data = Tuple[2]
return Tiles
def ToMosaic(cls,
VolumeObj,
PMGFullPath,
scaleValueInNm,
OutputPath=None,
Extension=None,
OutputImageExt=None,
TileOverlap=None,
TargetBpp=None,
debug=None,
*args,
**kwargs):
'''#Converts a PMG
#PMG files are created by Objective Imaging's Surveyor.
#This function expects a directory to contain a single PMG file with the tile images in the same directory
#Returns the SectionNumber and ChannelName of PMG processed. Otherwise [None,None]'''
ParentDir = os.path.dirname(PMGFullPath)
sectionDir = os.path.basename(PMGFullPath)
# Default to the directory above ours if an output path is not specified
if OutputPath is None:
OutputPath = os.path.join(PMGFullPath, "..")
# If the user did not supply a value, use a default
if (TileOverlap is None):
TileOverlap = 0.10
if (TargetBpp is None):
TargetBpp = 8
# Report the current stage to the user
# prettyoutput.CurseString('Stage', "PMGToMosaic " + InputPath)
BlockName = 'TEM'
BlockObj = BlockNode.Create('TEM')
[addedBlock, BlockObj] = VolumeObj.UpdateOrAddChild(BlockObj)
ChannelName = None
# TODO wrap in try except and print nice error on badly named files?
PMG = ParseFilename(PMGFullPath, pmgMappings)
PMGDir = os.path.dirname(PMGFullPath)
if (PMG is None):
raise Exception("Could not parse section from PMG filename: %s" +
PMGFullPath)
if PMG.Section is None:
PMG.Section = PMG.Spot
sectionObj = SectionNode.Create(PMG.Section)
[addedSection,
sectionObj] = BlockObj.UpdateOrAddChildByAttrib(sectionObj, 'Number')
# Calculate our output directory. The scripts expect directories to have section numbers, so use that.
ChannelName = PMG.Probe
ChannelName = ChannelName.replace(' ', '_')
channelObj = ChannelNode.Create(ChannelName)
channelObj.SetScale(scaleValueInNm)
[channelAdded,
channelObj] = sectionObj.UpdateOrAddChildByAttrib(channelObj, 'Name')
channelObj.Initials = PMG.Initials
channelObj.Mag = PMG.Mag
channelObj.Spot = PMG.Spot
channelObj.Slide = PMG.Slide
channelObj.Block = PMG.Block
FlipList = GetFlipList(ParentDir)
Flip = PMG.Section in FlipList
if (Flip):
prettyoutput.Log("Flipping")
# TODO: Add scale element
# OutFilename = ChannelName + "_supertile.mosaic"
# OutFilepath = os.path.join(SectionPath, OutFilename)
# Preserve the PMG file
# PMGBasename = os.path.basename(filename)
# PMGOutputFile = os.path.join(OutputPath, PMGBasename)
# ir.RemoveOutdatedFile(filename, PMGOutputFile)
# if not os.path.exists(PMGOutputFile):
# shutil.copy(filename, PMGOutputFile)
#
# #See if we need to remove the old supertile mosaic
# ir.RemoveOutdatedFile(filename, OutFilepath)
# if(os.path.exists(OutFilepath)):
# continue
#
Tiles = ParsePMG(PMGFullPath)
if len(Tiles) == 0:
raise Exception("No tiles found within PMG file")
NumImages = len(Tiles)
# Create a filter and mosaic
FilterName = 'Raw' + str(TargetBpp)
if (TargetBpp is None):
FilterName = 'Raw'
[added_filter, filterObj] = channelObj.GetOrCreateFilter(FilterName)
filterObj.BitsPerPixel = TargetBpp
SupertileName = 'Stage'
SupertileTransform = SupertileName + '.mosaic'
[addedTransform, transformObj] = channelObj.UpdateOrAddChildByAttrib(
TransformNode.Create(Name=SupertileName,
Path=SupertileTransform,
Type='Stage'), 'Path')
[added, PyramidNodeObj] = filterObj.UpdateOrAddChildByAttrib(
TilePyramidNode.Create(Type='stage', NumberOfTiles=NumImages),
'Path')
[added, LevelObj
] = PyramidNodeObj.UpdateOrAddChildByAttrib(LevelNode.Create(Level=1),
'Downsample')
# Make sure the target LevelObj is verified
VerifyTiles(LevelNode=LevelObj)
OutputImagePath = os.path.join(channelObj.FullPath, filterObj.Path,
PyramidNodeObj.Path, LevelObj.Path)
os.makedirs(OutputImagePath, exist_ok=True)
InputTileToOutputTile = {}
PngTiles = {}
TileKeys = list(Tiles.keys())
imageSize = []
for inputTile in TileKeys:
[base, ext] = os.path.splitext(inputTile)
pngMosaicTile = base + '.png'
OutputTileFullPath = os.path.join(LevelObj.FullPath, pngMosaicTile)
InputTileFullPath = os.path.join(PMGDir, inputTile)
if not os.path.exists(OutputTileFullPath):
InputTileToOutputTile[InputTileFullPath] = OutputTileFullPath
PngTiles[pngMosaicTile] = Tiles[inputTile]
(Height,
Width) = nornir_imageregistration.GetImageSize(InputTileFullPath)
imageSize.append((Width, Height))
nornir_imageregistration.ConvertImagesInDict(InputTileToOutputTile,
Flip=False,
OutputBpp=TargetBpp)
if not os.path.exists(transformObj.FullPath):
mosaicfile.MosaicFile.Write(transformObj.FullPath,
PngTiles,
Flip=Flip,
ImageSize=imageSize)
return [PMG.Section, ChannelName]
def BulkAddData2D(self, channel, full_path, rel_path, extension,
db_channel, db_filter, ZLevel, level_number):
image_paths = glob.glob(os.path.join(full_path, '*' + extension))
if len(image_paths) == 0:
return
(height, width) = nornir_imageregistration.GetImageSize(image_paths[0])
db_bounds = CreateBoundingBox((ZLevel, 0, 0, ZLevel, height, width))
db_data_list = []
img_rel_path_table = {}
for image_path in image_paths:
# if os.path.exists(image_path):
img_name = os.path.basename(image_path)
(img_number, ext) = os.path.splitext(img_name)
# (height, width) = nornir_imageregistration.GetImageSize(image_path)
# db_bounds = CreateBoundingRect(Rectangle.CreateFromPointAndArea((0, 0), (height, width)), minZ=ZLevel)
(db_tile_coordspace,
created_tile_coordspace) = self.GetOrCreateTileCoordSpace(
channel, 'Tile%d' % int(img_number), bounds=db_bounds)
# db_tile_mapping = GetTileMapping(tile_number=img_number, Z=ZLevel, )
img_rel_path = os.path.join(rel_path, img_name)
if img_rel_path in img_rel_path_table:
print("Trying to create this tile twice: %s" % (img_rel_path))
continue
img_rel_path_table[img_rel_path] = True
existing_db_data = models.Data2D.objects.filter(
relative_path=img_rel_path)
if existing_db_data.exists():
#Update path
db_data = existing_db_data.first()
db_data.image = os.path.abspath(image_path)
db_data.filter = db_filter
db_data.level = level_number
db_data.coord_space = db_tile_coordspace
db_data.width = width
db_data.height = height
db_data.save()
else:
#Create new, bulk update path
db_data = models.Data2D(name=img_name,
image=os.path.abspath(image_path),
filter=db_filter,
level=level_number,
relative_path=img_rel_path,
coord_space=db_tile_coordspace,
width=width,
height=height)
db_data_list.append(db_data)
if len(db_data_list) > 0:
models.Data2D.objects.bulk_create(db_data_list)
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)
