def get_histogram(seq, nbins, bin_min, bin_max):
"""Generate two lists with central values and histogram counts."""
print('%s, %s, %s' % (nbins, bin_min, bin_max))
hist = Histogram.compute(seq, nbins, bin_min, bin_max)
print("hist.getBinWidth(): %s" % hist.getBinWidth())
hist_list = [[], []]
for i in xrange(nbins):
bin = hist.getBin(i)
val = bin.getCentralValue()
count = bin.getCount()
hist_list[0].append(val)
hist_list[1].append(count)
return hist_list
from icy.main import Icy
from plugins.ylemontag.histogram import Histogram
seq = Icy.getMainInterface().getFocusedSequence()
#print dir(seq)
hist = Histogram.compute(seq, 16, 0, 15);
print dir(hist)
for ibin in xrange(hist.getNbBins()):
bin = hist.getBin(ibin)
# print dir(bin)
val = bin.getCentralValue()
count = bin.getCount()
print("%i: %i" % (val, count))
print "--------------------------------"
# print seq.name
# rois = seq.getROIs()
# for roi in rois:
# print dir(roi)
from icy.main import Icy
from icy.util import XLSUtil
from plugins.ylemontag.histogram import Histogram
seq = Icy.getMainInterface().getFocusedSequence()
xls_out = '/tmp/icy_py_excel_test.xls'
wb = XLSUtil.createWorkbook(xls_out) # create excel document
ws = XLSUtil.createNewPage(wb, "result") # create new page
XLSUtil.setCellString(ws, 0, 0, "filename") # set headers
XLSUtil.setCellString(ws, 1, 0, seq.name)
# hist = Histogram.compute(seq, 16, 0, 15)
hist = Histogram.compute(seq, 16, 7, 248)
overall = 0
for i in xrange(hist.getNbBins()):
bin = hist.getBin(i)
val = bin.getCentralValue()
count = bin.getCount()
print("%i: %i" % (val, count))
XLSUtil.setCellNumber(ws, 0, i+3, val)
XLSUtil.setCellNumber(ws, 1, i+3, count)
overall += count
XLSUtil.saveAndClose(wb) # close and save the excel file
numpixels = seq.getSizeX() * seq.getSizeY() * seq.getSizeZ()
diff = overall - numpixels
print('Number of pixels: %s x %s x %s = %s' %
(seq.getSizeX(), seq.getSizeY(), seq.getSizeZ(), numpixels))
print('Overall count from bins: %s' % overall)