def runCellDetection(parameter):
"""Detect cells in data"""
timer = Timer()
pp = parameter.StackProcessing
ps = parameter.DataSource
# run segmentation
if parameter.ImageProcessing.Method == "SpotDetection":
detectCells = iDISCO.ImageProcessing.SpotDetection.detectCells
centers, intensities = parallelProcessStack(
ps.ImageFile,
x=ps.XRange,
y=ps.YRange,
z=ps.ZRange,
processes=pp.Processes,
chunksizemax=pp.ChunkSizeMax,
chunksizemin=pp.ChunkSizeMin,
chunkoverlap=pp.ChunkOverlap,
optimizechunks=pp.OptimizeChunks,
optimizechunksizeincrease=pp.OptimizeChunkSizeIncrease,
segmentation=detectCells,
parameter=parameter.ImageProcessing)
else:
if haveIlastik:
#ilastik does parallel processing so do sequential processing here
detectCells = iDISCO.ImageProcessing.IlastikClassification.detectCells
centers, intensities = sequentiallyProcessStack(
ps.ImageFile,
x=ps.XRange,
y=ps.YRange,
z=ps.ZRange,
chunksizemax=pp.ChunkSizeMax,
chunksizemin=pp.ChunkSizeMin,
chunkoverlap=pp.ChunkOverlap,
segmentation=detectCells,
parameter=parameter.ImageProcessing)
else:
raise RuntimeError(
"No Ilastik installed use SpotDectection instead!")
timer.printElapsedTime("Main")
if not parameter.ImageProcessing.Parameter.ThresholdSave is None:
iid = intensities > parameter.ImageProcessing.Parameter.ThresholdSave
centers = centers[iid, :]
if not parameter.ImageProcessing.PointFile is None:
io.writePoints(parameter.ImageProcessing.PointFile, centers)
if not parameter.ImageProcessing.IntensityFile is None:
io.writePoints(parameter.ImageProcessing.IntensityFile, intensities)
return centers, intensities
def runCellDetection(parameter):
"""Detect cells in data"""
timer = Timer();
pp = parameter.StackProcessing;
ps = parameter.DataSource;
# run segmentation
if parameter.ImageProcessing.Method == "SpotDetection":
detectCells = iDISCO.ImageProcessing.SpotDetection.detectCells;
centers, intensities = parallelProcessStack(ps.ImageFile, x = ps.XRange, y = ps.YRange, z = ps.ZRange,
processes = pp.Processes, chunksizemax = pp.ChunkSizeMax, chunksizemin = pp.ChunkSizeMin, chunkoverlap = pp.ChunkOverlap,
optimizechunks = pp.OptimizeChunks, optimizechunksizeincrease = pp.OptimizeChunkSizeIncrease,
segmentation = detectCells, parameter = parameter.ImageProcessing);
else:
if haveIlastik:
#ilastik does parallel processing so do sequential processing here
detectCells = iDISCO.ImageProcessing.IlastikClassification.detectCells;
centers, intensities = sequentiallyProcessStack(ps.ImageFile, x = ps.XRange, y = ps.YRange, z = ps.ZRange,
chunksizemax = pp.ChunkSizeMax, chunksizemin = pp.ChunkSizeMin, chunkoverlap = pp.ChunkOverlap,
segmentation = detectCells, parameter = parameter.ImageProcessing);
else:
raise RuntimeError("No Ilastik installed use SpotDectection instead!");
timer.printElapsedTime("Main");
if not parameter.ImageProcessing.Parameter.ThresholdSave is None:
iid = intensities > parameter.ImageProcessing.Parameter.ThresholdSave;
centers = centers[iid,:];
if not parameter.ImageProcessing.PointFile is None:
io.writePoints(parameter.ImageProcessing.PointFile, centers);
if not parameter.ImageProcessing.IntensityFile is None:
io.writePoints(parameter.ImageProcessing.IntensityFile, intensities);
return centers, intensities;
from iDISCO.ImageProcessing.Filter.StructureElement import structureElement
from iDISCO.Visualization.Plot import plotTiling, plotOverlayLabel
from iDISCO.Utils.Timer import Timer;
img = numpy.random.rand(2000,2000) * 65535;
img = img.astype('int')
dataraw = dataset[:,:,1160];
img = dataraw[:,:];
img.shape
t = Timer();
res = grey_opening(img,#DoG filter
t.printElapsedTime('scipy');
#t.reset();
#res2 = open(img, structureElement('Disk', (30,30)).astype('bool'));
#t.printElapsedTime('mahotas');
#t.reset();
#res2 = open(img, structureElement('Disk', (30,30)).astype('bool'));
#t.printElapsedTime('mahotas');
t.reset();
se = structureElement('Disk', (15,15)).astype('uint8');
res2 = cv2.morphologyEx(img, cv2.MORPH_OPEN, se)
