def batchseeds(args):
"""
%prog batchseeds folder
Extract seed metrics for each image in a directory.
"""
from jcvi.formats.pdf import cat
xargs = args[1:]
p = OptionParser(batchseeds.__doc__)
opts, args, iopts = add_seeds_options(p, args)
if len(args) != 1:
sys.exit(not p.print_help())
folder, = args
folder = folder.rstrip('/')
outdir = folder + "-debug"
outfile = folder + "-output.tsv"
assert op.isdir(folder)
images = []
jsonfile = opts.calibrate or op.join(folder, "calibrate.json")
if not op.exists(jsonfile):
jsonfile = None
for im in iglob(folder, "*.jpg", "*.JPG", "*.png"):
if im.endswith(".resize.jpg") or \
im.endswith(".main.jpg") or \
im.endswith(".label.jpg"):
continue
if op.basename(im).startswith("calibrate"):
continue
images.append(im)
fw = must_open(outfile, 'w')
print >> fw, Seed.header(calibrate=jsonfile)
nseeds = 0
for im in images:
imargs = [im, "--noheader", "--outdir={0}".format(outdir)] + xargs
if jsonfile:
imargs += ["--calibrate={0}".format(jsonfile)]
objects = seeds(imargs)
for o in objects:
print >> fw, o
nseeds += len(objects)
fw.close()
logging.debug("Processed {0} images.".format(len(images)))
logging.debug("A total of {0} objects written to `{1}`.".\
format(nseeds, outfile))
pdfs = iglob(outdir, "*.pdf")
outpdf = folder + "-output.pdf"
cat(pdfs + ["--outfile={0}".format(outpdf)])
logging.debug("Debugging information written to `{0}`.".format(outpdf))
return outfile
def batchseeds(args):
"""
%prog batchseeds folder
Extract seed metrics for each image in a directory.
"""
from jcvi.formats.pdf import cat
xargs = args[1:]
p = OptionParser(batchseeds.__doc__)
opts, args, iopts = add_seeds_options(p, args)
if len(args) != 1:
sys.exit(not p.print_help())
folder, = args
folder = folder.rstrip('/')
outdir = folder + "-debug"
outfile = folder + "-output.tsv"
assert op.isdir(folder)
images = []
jsonfile = opts.calibrate or op.join(folder, "calibrate.json")
if not op.exists(jsonfile):
jsonfile = None
for im in iglob(folder, "*.jpg,*.JPG,*.png"):
if im.endswith(".resize.jpg") or \
im.endswith(".main.jpg") or \
im.endswith(".label.jpg"):
continue
if op.basename(im).startswith("calibrate"):
continue
images.append(im)
fw = must_open(outfile, 'w')
print >> fw, Seed.header(calibrate=jsonfile)
nseeds = 0
for im in images:
imargs = [im, "--noheader", "--outdir={0}".format(outdir)] + xargs
if jsonfile:
imargs += ["--calibrate={0}".format(jsonfile)]
objects = seeds(imargs)
for o in objects:
print >> fw, o
nseeds += len(objects)
fw.close()
logging.debug("Processed {0} images.".format(len(images)))
logging.debug("A total of {0} objects written to `{1}`.".\
format(nseeds, outfile))
pdfs = iglob(outdir, "*.pdf")
outpdf = folder + "-output.pdf"
cat(pdfs + ["--outfile={0}".format(outpdf)])
logging.debug("Debugging information written to `{0}`.".format(outpdf))
return outfile