def index(self, name=None):
if name is None:
return (
"<!DOCTYPE html><html><body>Images will be here</body></html>")
else:
try:
#(img_name,img_ext)=name.rsplit('.',1)
finfo = self.qc_files[int(name)]
path = os.path.abspath(finfo[0])
if finfo[3] == 'png':
return serve_file(path, 'image/png', None, None)
elif finfo[3] == 'jpg':
return serve_file(path, 'image/jpeg', None, None)
elif (finfo[3] == 'mnc'
or finfo[3] == 'minc') and minc_supported:
# dynamically render minc here
img_file = self.tempdir + name + '.png'
if not os.path.exists(img_file):
qc(finfo[0], img_file, format='png')
return serve_file(img_file, 'image/png', None, None)
else:
cherrypy.response.status = 503
return f"Unsupported image file format:{finfo[0]}"
except:
print(f"Exception in index:{sys.exc_info()[0]}")
traceback.print_exc(file=sys.stdout)
cherrypy.response.status = 503
return ("<!DOCTYPE html>"
"<html>"
f"<body>Image {name} not found!</body>"
"</html>")
def create_qc(source, target, xfm, qc_file):
with mincTools() as m:
m.resample_smooth(source,
m.tmp('source.mnc'),
order=1,
like=target,
transform=xfm)
qc(m.tmp('source.mnc'),
qc_file,
mask=target,
image_cmap='red',
mask_cmap='green',
use_max=True) # ,ialpha=0.5,oalpha=0.5
def draw_qc_nl(in_scan, in_outline, nl_xfm, qc_nl, options={}):
with mincTools() as m:
m.resample_labels(in_outline.scan,
m.tmp('outline.mnc'),
transform=nl_xfm.xfm,
invert_transform=True)
qc(in_scan.scan,
qc_nl.fname,
mask=m.tmp('outline.mnc'),
mask_range=[0.0, 1.0],
samples=20 if options.get('big', False) else 6,
mask_bg=0.5,
use_max=True)
def draw_qc_lobes(in_scan, in_lobes, out_qc, options={}):
if options.get('big'):
with mincTools() as m:
m.qc(in_scan.scan,
out_qc.fname,
big=True,
mask=in_lobes.scan,
spectral_mask=True)
else:
qc(in_scan.scan,
out_qc.fname,
mask=in_lobes.scan,
mask_cmap='spectral',
mask_bg=0.5,
use_max=True)
def draw_qc_mask(in_scan, out_qc, options={}):
if options.get('big'):
with mincTools() as m:
m.qc(in_scan.scan,
out_qc.fname,
big=True,
mask=in_scan.mask,
mask_range=[0.0, 1.0])
else:
qc(in_scan.scan,
out_qc.fname,
mask=in_scan.mask,
mask_range=[0.0, 1.0],
mask_bg=0.5,
use_max=True)
def draw_qc_lobes(in_scan, in_lobes, out_qc, options={}):
if options.get('big', False):
qc(in_scan.scan,
out_qc.fname,
mask=in_lobes.scan,
mask_cmap='spectral',
mask_bg=0.5,
use_max=True,
samples=20)
else:
qc(in_scan.scan,
out_qc.fname,
mask=in_lobes.scan,
mask_cmap='spectral',
mask_bg=0.5,
use_max=True)
def draw_qc_mask(in_scan, out_qc, options={}):
if options.get('big', False):
qc(in_scan.scan,
out_qc.fname,
mask=in_scan.mask,
mask_range=[0.0, 1.0],
mask_bg=0.5,
use_max=True,
samples=20)
else:
qc(in_scan.scan,
out_qc.fname,
mask=in_scan.mask,
mask_range=[0.0, 1.0],
mask_bg=0.5,
use_max=True)
def draw_qc_stx(in_scan, in_outline, out_qc, options={}):
if options.get('big', False):
qc(in_scan.scan,
out_qc.fname,
mask=in_outline.scan,
mask_range=[0.0, 1.0],
samples=20,
mask_bg=0.5,
use_max=True)
else:
qc(in_scan.scan,
out_qc.fname,
mask=in_outline.scan,
mask_range=[0.0, 1.0],
mask_bg=0.5,
use_max=True)
def draw_qc_add(in_scan1, in_scan2, out_qc, options={}):
if options.get('big'):
with mincTools() as m:
m.qc(in_scan1.scan,
out_qc.fname,
big=True,
red=True,
mask=in_scan2.scan,
green_mask=True)
else:
qc(in_scan1.scan,
out_qc.fname,
mask=in_scan2.scan,
image_cmap='red',
mask_cmap='green',
mask_bg=0.5,
use_max=True)
def draw_qc_add(in_scan1, in_scan2, out_qc, options={}):
if options.get('big', False):
qc(in_scan1.scan,
out_qc.fname,
mask=in_scan2.scan,
image_cmap='red',
mask_cmap='green',
mask_bg=0.5,
use_max=True,
samples=20)
else:
qc(in_scan1.scan,
out_qc.fname,
mask=in_scan2.scan,
image_cmap='red',
mask_cmap='green',
mask_bg=0.5,
use_max=True)
