def register(view_index,
filepaths,
modelclass,
csv_dir,
params,
n_threads=0,
workaround2487=True):
# Work around jython bug https://bugs.jython.org/issue2487 , a race condition on type initialization
if 0 == view_index and workaround2487:
# bogus call for first two filepaths: single-threaded execution to initalize types
register(view_index, {view_index: filepaths[view_index][0:2]},
modelclass,
"/tmp/",
params,
n_threads=1,
workaround2487=False)
exe = newFixedThreadPool(n_threads)
paths = filepaths[view_index]
try:
name = "matrices-view-%i" % view_index
matrices = loadMatrices(name, csv_dir)
if not matrices:
matrices = computeForwardTransforms(paths, klb_loader,
getCalibration, csv_dir, exe,
modelclass, params)
# Debug: print identity transforms
identity_indices = [
i for i, m in enumerate(matrices) if 1.0 == m[0]
and 0.0 == m[1] and 0.0 == m[2] and 0.0 == m[3] and 0.0 == m[4]
and 1.0 == m[5] and 0.0 == m[6] and 0.0 == m[7] and 0.0 == m[8]
and 0.0 == m[9] and 1.0 == m[10] and 0.0 == m[11]
]
syncPrint("View %i: identity matrices at [%s]" %
(view_index, ", ".join(
str(index) for index in identity_indices)))
saveMatrices(name, matrices, csv_dir)
finally:
exe.shutdown()
transforms = asBackwardConcatTransforms(matrices,
transformclass=Translation3D)
path_transforms = dict(izip(paths, transforms))
registered_loader = RegisteredLoader(klb_loader, path_transforms)
return Load.lazyStack(paths, registered_loader)
def align(filepaths, csvDir, params, paramsTileConfiguration):
name = "matrices"
matrices = loadMatrices(name, csvDir)
if matrices:
return matrices
# Optimize
tiles = makeLinkedTiles(filepaths, csvDir, params,
paramsTileConfiguration["n_adjacent"])
tc = TileConfiguration()
tc.addTiles(tiles)
tc.fixTile(tiles[len(tiles) / 2]) # middle tile
maxAllowedError = paramsTileConfiguration["maxAllowedError"]
maxPlateauwidth = paramsTileConfiguration["maxPlateauwidth"]
maxIterations = paramsTileConfiguration["maxIterations"]
damp = paramsTileConfiguration["damp"]
tc.optimizeSilentlyConcurrent(ErrorStatistic(maxPlateauwidth + 1),
maxAllowedError, maxIterations,
maxPlateauwidth, damp)
# TODO problem: can fail when there are 0 inliers
# Return model matrices as double[] arrays with 6 values
matrices = []
for tile in tiles:
# BUG in TransformationModel2D.toMatrix # TODO can be updated now, it's been fixed
#a = nativeArray('d', [2, 3])
#tile.getModel().toMatrix(a)
#matrices.append(a[0] + a[1])
# Instead:
a = zeros(6, 'd')
tile.getModel().toArray(a)
matrices.append(array([a[0], a[2], a[4], a[1], a[3], a[5]], 'd'))
saveMatrices(name, matrices,
csvDir) # TODO check: saving correctly, now that it's 2D?
return matrices
import sys
sys.path.append("/home/albert/lab/scripts/python/imagej/IsoView-GCaMP/")
from lib.registration import saveMatrices, loadMatrices
from jarray import array
matrices = [array((j + i for i in xrange(12)), 'd') for j in xrange(3)]
print matrices
saveMatrices("matrices", matrices, "/tmp/")
m = loadMatrices("matrices", "/tmp/")
print m
# Triggers the whole alignment and ends by showing a virtual stack of the aligned sections.
# Crashware: can be restarted anytime, will resume from where it left off.
viewAligned(filepaths, csvDir, params, paramsSIFT, paramsTileConfiguration,
dimensions, FinalInterval([x0, y0], [x1, y1]))
# When the alignment is good enough, then export as N5 by swapping "False" for "True" below:
if False:
# Write the whole volume in N5 format
name = srcDir.split('/')[-2]
exportDir = os.path.join(tgtDir, "n5")
# Export ROI:
# x=864 y=264 width=15312 h=17424
interval = FinalInterval([0, 0], [dimensions[0] - 1, dimensions[1] - 1])
export8bitN5(
filepaths,
loadFn,
dimensions,
loadMatrices("matrices",
csvDir), # expects matrices.csv file to exist already
name,
exportDir,
interval,
gzip_compression=
0, # Don't use compression: less than 5% gain, at considerable processing cost
invert=True,
CLAHE_params=[200, 256, 3.0],
n5_threads=0,
block_size=[256, 256, 64]) # ~4 MB per block