from __future__ import with_statement
import sys, os, csv
sys.path.append(os.path.dirname(os.path.dirname(sys.argv[0]))
from lib.io import readN5
from lib.synthetic import virtualPointsRAI
from lib.ui import showStack, wrap, showAsComposite
from lib.deltaFoverF import computeDeltaFOverF
from net.imglib2.view import Views
baseDir = "/home/albert/shares/cardonalab/Albert/2017-05-10_1018/"
srcDir = baseDir + "deconvolved/"
n5dir = os.path.join(srcDir, "n5")
dataset_name = "2017-5-10_1018_0-399_X203_Y155_Z65"
# Load entire 4D IsoView deconvolved and registered data set
img4D = readN5(n5dir, dataset_name)
# A mask: only nuclei whose x,y,z coordinate has a non-zero value in the mask will be considered
mask = None
# Split CM00+CM01 (odd) from CM02+CM03 (even) into two series
series = ["CM00-CM01", "CM02-CM03"]
img4Da = Views.subsample(img4D,
[1, 1, 1, 2]) # step
img4Db = Views.subsample(Views.interval(img4D, [0, 0, 0, 1], Intervals.maxAsLongArray(img4D)),
[1, 1, 1, 2]) # step
showStack(img4Da, title="%s registered+deconvolved" % series[0])
showStack(img4Db, title="%s registered+deconvolved" % series[1])
calibration = [1.0, 1.0, 1.0]
import sys
sys.path.append("/home/albert/lab/scripts/python/imagej/IsoView-GCaMP/")
from lib.io import readN5
n5dir = "/home/albert/shares/cardonalab/Albert/2017-05-10_1018/deconvolved/n5"
#dataset_name = "2017-5-10_1018_0-399_fullXY_25sections"
dataset_name = "2017-5-10_1018_0-399_X203_Y155_Z65"
img = readN5(n5dir, dataset_name, show="IJ")
#img = readN5(n5dir, dataset_name, show="BDV")
"/groups/cardona/home/cardonaa/lab/scripts/python/imagej/IsoView-GCaMP/")
from lib.io import readN5
from lib.dogpeaks import createDoG
from lib.synthetic import virtualPointsRAI
from lib.ui import showStack, wrap, showAsComposite
from lib.nuclei import findPeaks, mergePeaks, filterNuclei, findNucleiByMaxProjection
from net.imglib2.util import Intervals, ConstantUtils
from net.imglib2.view import Views
from net.imglib2 import RealPoint
from ij import IJ
from net.imglib2.img.display.imagej import ImageJFunctions as IL
from net.imglib2.roi.geom.real import ClosedWritableSphere
from net.imglib2.roi import Masks, Regions
from itertools import imap, islice, izip
from jarray import zeros, array
baseDir = "/groups/cardona/cardonalab/Albert/2017-05-10_2_1019/"
dataset_name = "2017-05-10_2_1019_0-399_409x509x305x800"
# Load entire 4D IsoView deconvolved and registered data set
img4D = readN5(baseDir, dataset_name)
# Split CM00+CM01 (odd) from CM02+CM03 (even) into two series
series = ["CM00-CM01", "CM02-CM03"]
img4Da = Views.subsample(img4D, [1, 1, 1, 2]) # step
img4Db = Views.subsample(
Views.interval(img4D, [0, 0, 0, 1], Intervals.maxAsLongArray(img4D)),
[1, 1, 1, 2]) # step
showStack(img4Da, title="%s registered+deconvolved" % series[0])
showStack(img4Db, title="%s registered+deconvolved" % series[1])
import sys
#sys.path.append("/lmb/home/acardona/lab/scripts/python/imagej/IsoView-GCaMP/")
sys.path.append("/home/albert/lab/scripts/python/imagej/IsoView-GCaMP/")
from net.imglib2.view import Views
from net.imglib2 import FinalInterval
from lib.io import readN5
from lib.ui import showStack, wrap, navigate2DROI
from java.awt import Rectangle
name = "s0"
img3D = readN5("/home/albert/ark/raw/fibsem/amphioxus/groucho/n5", name, show=None)
#fov = Views.interval(img3D, FinalInterval([4096, 4096, 0], [8192 -1, 8192 -1, 13770 -1]))
fov = img3D # whole
# UNCOMMENT to open the whole stack
#imp = showStack(fov, title=name)
#imp.show()
# Directly open section 8031 and only for an ROI over a bit of the brain
x = 11227
y = 7897
width = 3240
height = 3320
"""
fov = Views.interval(img3D, FinalInterval([x, y, 0], # min coords
[x + width - 1, # max coords
y + height -1,
img3D.dimension(2) -1]))
imp = wrap(fov, title="Small ROI in the Groucho brain", n_channels=1)
import sys
sys.path.append(
"/groups/cardona/home/cardonaa/lab/scripts/python/imagej/IsoView-GCaMP/")
from net.imglib2.view import Views
from net.imglib2 import FinalInterval
from lib.io import readN5
from lib.ui import showStack
name = "FIBSEM_L1116"
img3D = readN5("/groups/cardona/cardonalab/FIBSEM_L1116_exports/n5/",
name,
show=None)
#fov = Views.interval(img3D, FinalInterval([4096, 4096, 0], [8192 -1, 8192 -1, 13770 -1]))
fov = img3D # whole
imp = showStack(fov, title=name)
#imp.setPosition(imp.getStack().size()) # last slice