coordfile = OUTPUTDIR + options.coords
else:
coordfile = OUTPUTDIR + '/'.join(filepattern.split('/')[:-1]) +\
dirstring + fnameroot +\
"_goodcoords.npy"
if not os.path.isfile(coordfile):
print("need coordinate file ", coordfile)
sys.exit()
coords = np.load(coordfile)
# load one image to get size
if os.path.isfile(OUTPUTDIR + options.stack):
img = np.load(OUTPUTDIR + options.stack)
print("there is a stack", OUTPUTDIR + options.stack)
else: img = flist[0]
imsize = findsize(img, filepattern = filepattern)
img = flist[0]
img = np.fromfile(img, dtype=np.uint8).reshape(imsize['nrows'],
imsize['ncols'],
imsize['nbands'])
print("Image size: ", imsize)
# imshow(np.repeat((windows == l),3).reshape(stack.shape)*stack)
mask = np.zeros((img.shape[0], img.shape[1]))*False
# load windows families
if not os.path.isfile(OUTPUTDIR + options.families):
print("need coordinate file ", OUTPUTDIR + options.families)
sys.exit()
if len(args) < 1:
sys.argv.append('--help')
options, args = parser.parse_args()
sys.exit(0)
xmax = 0
phaseflist = []
ref = [np.nan, np.nan]
if options.ref:
ref = (int(float(options.ref.split(',')[0])),
int(float(options.ref.split(',')[1]))) #if 2117.12,502.52
if options.coordfile:
stack = np.load(options.coordfile.replace("_coords.npy", ".npy"))
imsize = findsize(stack,
filepattern=options.coordfile.replace(
'.npy', '.txt'))
if PLOTSTACK:
stackfig = pl.figure()
axstack2 = stackfig.add_subplot(111)
axstack2.imshow(stack, interpolation='nearest')
axstack2.set_xlim(0, axstack2.get_xlim()[1])
axstack2.set_ylim(axstack2.get_ylim()[0], 0)
axstack2.axis('off')
circle1 = pl.Circle(ref, 30, color='r', fill=False, lw=2)
axstack2.add_artist(circle1)
stackfig.savefig("reflight_stack.pdf")
fig = pl.figure(figsize=(20, 10))
axstack = fig.add_subplot(224)
options, args = parser.parse_args()
if len(args) < 1:
sys.argv.append('--help')
options, args = parser.parse_args()
sys.exit(0)
xmax = 0
phaseflist = []
ref = [np.nan,np.nan]
if options.ref:
ref = (int(float(options.ref.split(',')[0])), int(float(options.ref.split(',')[1]))) #if 2117.12,502.52
if options.coordfile:
stack = np.load(options.coordfile.replace("_coords.npy",".npy"))
imsize = findsize(stack,
filepattern=options.coordfile.replace('.npy','.txt'))
if PLOTSTACK:
stackfig = pl.figure()
axstack2 = stackfig.add_subplot(111)
axstack2.imshow(stack, interpolation='nearest')
axstack2.set_xlim(0, axstack2.get_xlim()[1])
axstack2.set_ylim(axstack2.get_ylim()[0], 0)
axstack2.axis('off')
circle1 = pl.Circle(ref, 30, color='r', fill=False, lw=2)
axstack2.add_artist(circle1)
stackfig.savefig("reflight_stack.pdf")
fig = pl.figure(figsize=(20,10))
axstack = fig.add_subplot(224)
axstack.imshow(stack, interpolation='nearest')
flist = glob.glob(impath)
img = flist[0]
# extract the filename from the path
fnameroot = filepattern.split('/')[-1]
# creates the directory to store the stacks
os.system('mkdir -p ../outputs/stacks/' + '/'.\
join(filepattern.split('/')[:-1]))
# creates the directory to store the other produts
os.system('mkdir -p ../outputs/'+'/'.join(filepattern.split('/')[:-1]))
# find image size
if not options.imsize == '':
imsize = findsize(img, imsizefile=options.imsize)
else:
imsize = findsize(img, filepattern=filepattern)
rgb = np.zeros((len(flist[:options.nstack]), imsize['nrows'],
imsize['ncols'], imsize['nbands']), np.uint8)
for i, f in enumerate(flist[:options.nstack]):
try:
# reads in raw images
rgb[i] = np.fromfile(f, dtype=np.uint8).clip(0, 255).\
reshape(imsize['nrows'],
imsize['ncols'],
imsize['nbands']).astype(float)
except: pass
def runit((arg, options)):
filepattern = arg
fnameroot = filepattern.split('/')[-1]
impath = os.getenv("UIdata") + filepattern
print("\n\nUsing image path: %s\n\n" % impath)
flist = sorted(glob.glob(impath + "*.raw"))
##print (flist)
if options.stack:
print("(There is a stack", options.stack, ")")
stack = np.load(options.stack)
imsize = findsize(stack,
filepattern=options.stack.replace('.npy', '.txt'))
else:
print("Please pass a stack with option --stack")
print("Image size: ", imsize)
nmax = min(options.nmax, len(flist) - options.skipfiles)
print("Number of timestamps (files): %d" % (nmax))
if nmax < 30: return 0
flist = flist[options.skipfiles:nmax + options.skipfiles]
imgmask = np.load(options.stack.replace(".npy", "_mask.npy"))
if not options.lmax:
lmax = (imgmask.sum(axis=2).sum(axis=1) > 0).sum()
else:
lmax = options.lmax
print(lmax)
outdir = '/'.join(filepattern.split(
'/')[:-1]) + '/N%04dW%04dS%04d' % (nmax, lmax, options.skipfiles)
if not os.path.isdir(outdir):
subprocess.Popen('mkdir -p %s ' % outdir, shell=True)
#os.system('mkdir -p %s '%outdir)
print("Output directory: ", '/'.join(filepattern.split('/')[:-1]), outdir)
if options.fft:
#bsoutfile = outdir + "/" + fnameroot + "_bs_fft.npy"
#coordsoutfile = outdir + "/" + fnameroot + "_coords_fft.npy"
goodcoordsoutfile = outdir + "/" + fnameroot + "_goodcoords_fft.npy"
#kmresultfile = outdir + "/" + fnameroot + "_kmresult_fft.pkl"
else:
#bsoutfile = outdir + "/" + fnameroot + "_bs.npy"
#coordsoutfile = outdir + "/" + fnameroot + "_coords.npy"
goodcoordsoutfile = outdir + "/" + fnameroot + "_goodcoords.npy"
#kmresultfile = outdir + "/" + fnameroot + "_kmresult.pkl"
print("")
print("must read: ", goodcoordsoutfile)
pl.figure()
img = np.load(options.stack)
imgm = imgmask.sum(axis=0)
pl.imshow(img)
pl.savefig(filepattern + "_mask.stack.png")
imgma = np.zeros((img.shape[0], imgm.shape[1], 4))
imgma[imgm == 1] = [1, 1, 1, 1]
pl.imshow(imgma)
pl.savefig(filepattern + "_mask.img.png")
print("saved figure mask", filepattern + "_mask.img.png")
gw = np.load(outdir + "/" + filepattern.split('/')[-1] + "_goodcoords.npy")
imgmagood = np.zeros((img.shape[0], imgm.shape[1], 4))
for g in gw.T:
if not np.isnan(g[2]) and not np.isnan(g[3]):
imgmagood[:, :, 0] = imgmagood[:, :, 0] + (
imgmask[imgmask[:, int(g[3]), int(g[2])] > 0]).squeeze()
imgmagood[:, :, 3] = imgmagood[:, :, 3] + (
imgmask[imgmask[:, int(g[3]), int(g[2])] > 0]).squeeze()
pl.imshow(img)
pl.imshow(imgma)
pl.imshow(imgmagood)
pl.savefig(filepattern + "_goodmask.img.png")
def runit((arg, options)):
filepattern = arg
fnameroot = filepattern.split('/')[-1]
impath = os.getenv("UIdata") + filepattern
print ("\n\nUsing image path: %s\n\n"%impath)
flist = sorted(glob.glob(impath+"*.raw"))
##print (flist)
if options.stack:
print ("(There is a stack", options.stack,")")
stack = np.load(options.stack)
imsize = findsize(stack,
filepattern=options.stack.replace('.npy','.txt'))
else:
print ("Please pass a stack with option --stack")
print ("Image size: ", imsize)
nmax = min(options.nmax, len(flist)-options.skipfiles)
print ("Number of timestamps (files): %d"%(nmax))
if nmax<30: return 0
flist = flist[options.skipfiles:nmax+options.skipfiles]
imgmask = np.load(options.stack.replace(".npy","_mask.npy"))
if not options.lmax:
lmax = (imgmask.sum(axis=2).sum(axis=1)>0).sum()
else: lmax = options.lmax
print (lmax)
outdir = '/'.join(filepattern.split('/')[:-1])+'/N%04dW%04dS%04d'%(nmax,lmax,options.skipfiles)
if not os.path.isdir(outdir):
subprocess.Popen('mkdir -p %s '%outdir, shell=True)
#os.system('mkdir -p %s '%outdir)
print ("Output directory: ",
'/'.join(filepattern.split('/')[:-1]), outdir)
if options.fft:
#bsoutfile = outdir + "/" + fnameroot + "_bs_fft.npy"
#coordsoutfile = outdir + "/" + fnameroot + "_coords_fft.npy"
goodcoordsoutfile = outdir + "/" + fnameroot + "_goodcoords_fft.npy"
#kmresultfile = outdir + "/" + fnameroot + "_kmresult_fft.pkl"
else:
#bsoutfile = outdir + "/" + fnameroot + "_bs.npy"
#coordsoutfile = outdir + "/" + fnameroot + "_coords.npy"
goodcoordsoutfile = outdir + "/" + fnameroot + "_goodcoords.npy"
#kmresultfile = outdir + "/" + fnameroot + "_kmresult.pkl"
print ("")
print ("must read: ", goodcoordsoutfile)
pl.figure()
img = np.load(options.stack)
imgm = imgmask.sum(axis=0)
pl.imshow(img)
pl.savefig(filepattern+"_mask.stack.png")
imgma = np.zeros((img.shape[0],imgm.shape[1],4))
imgma[imgm==1]=[1,1,1,1]
pl.imshow(imgma)
pl.savefig(filepattern+"_mask.img.png")
print ("saved figure mask", filepattern+"_mask.img.png")
gw = np.load(outdir+"/"+filepattern.split('/')[-1]+"_goodcoords.npy")
imgmagood = np.zeros((img.shape[0],imgm.shape[1],4))
for g in gw.T:
if not np.isnan(g[2]) and not np.isnan(g[3]):
imgmagood[:,:,0] = imgmagood[:,:,0]+(imgmask[imgmask[:,int(g[3]),int(g[2])]>0]).squeeze()
imgmagood[:,:,3] = imgmagood[:,:,3]+(imgmask[imgmask[:,int(g[3]),int(g[2])]>0]).squeeze()
pl.imshow(img)
pl.imshow(imgma)
pl.imshow(imgmagood)
pl.savefig(filepattern+"_goodmask.img.png")
