def input_select(self, **kwargs):
"""
use the selected available input images
"""
print("ENTERING input_select")
self.new_key()
self.init_cfg()
print("key = " + self.key)
# kwargs contains input_id.x and input_id.y
input_id = kwargs.keys()[0].split('.')[0]
assert input_id == kwargs.keys()[1].split('.')[0]
# get the images
input_dict = config.file_dict(self.input_dir)
idir = self.input_dir + input_dict[input_id]['subdir'] + '/'
print("idir = " + idir)
fnames = [os.path.basename(f) for f in glob.glob(idir + 'i????.png')]
for f in fnames:
shutil.copy(idir + f, self.work_dir + f)
hastruth = os.path.isfile(idir + "a.png")
self.cfg['meta']['hastruth'] = hastruth
self.cfg['meta']['maxframes'] = len(fnames)
if (hastruth):
shutil.copy(idir + "a.png", self.work_dir + "a.png")
self.log("input selected : %s" % input_id)
self.cfg['meta']['original'] = False
self.cfg['meta']['height'] = image(self.work_dir + '/i0000.png').size[1]
self.cfg.save()
# jump to the params page
return self.params(msg="(no message)", key=self.key)
def input_select(self, **kwargs):
"""
use the selected available input images
"""
#print("ENTERING input_select")
self.new_key()
self.init_cfg()
#print("key = " + self.key)
# kwargs contains input_id.x and input_id.y
input_id = kwargs.keys()[0].split('.')[0]
assert input_id == kwargs.keys()[1].split('.')[0]
# get the images
input_dict = config.file_dict(self.input_dir)
idir = self.input_dir + input_dict[input_id]['subdir'] + '/'
#print("idir = " + idir)
fnames = [os.path.basename(f) for f in glob.glob(idir + 'i????.png')]
for f in fnames:
shutil.copy(idir + f, self.work_dir + f)
hastruth = os.path.isfile(idir + "a.png")
self.cfg['meta']['hastruth'] = hastruth
self.cfg['meta']['maxframes'] = len(fnames)
if (hastruth):
shutil.copy(idir + "a.png", self.work_dir + "a.png")
self.log("input selected : %s" % input_id)
self.cfg['meta']['original'] = False
self.cfg['meta']['height'] = image(self.work_dir +
'/i0000.png').size[1]
self.cfg.save()
# jump to the params page
return self.params(msg="(no message)", key=self.key)
def index(self):
"""
demo presentation and input menu
"""
print("ENTERING index")
tn_size = 192
# read the input index as a dict
inputd = config.file_dict(self.input_dir)
print(inputd)
for (input_id, input_info) in inputd.items():
fname = ["a.png", "b.png", "t.png"]
tn_fname = [thumbnail(self.input_dir + \
input_info['subdir'] \
+ '/a.png',(tn_size,tn_size))]
inputd[input_id]['hastruth'] = os.path.isfile(
self.input_dir + input_info['subdir']+'/t.tiff')
inputd[input_id]['height'] = image(self.input_dir
+ input_info['subdir'] + '/a.png').size[1]
inputd[input_id]['baseinput'] = \
self.input_url + input_info['subdir'] + '/'
inputd[input_id]['url'] = [self.input_url
+ input_info['subdir']
+ '/' + os.path.basename(f)
for f in fname]
inputd[input_id]['tn_url'] = [self.input_url
+ input_info['subdir']
+ '/'
+ os.path.basename(f)
for f in tn_fname]
return self.tmpl_out("input.html", inputd=inputd)
def input_select(self, **kwargs):
"""
use the selected available input images
"""
self.init_cfg()
#kwargs contains input_id.x and input_id.y
input_id = kwargs.keys()[0].split('.')[0]
assert input_id == kwargs.keys()[1].split('.')[0]
# get the images
input_dict = config.file_dict(self.input_dir)
fnames = input_dict[input_id]['files'].split()
for i in range(len(fnames)):
shutil.copy(self.input_dir + fnames[i],
self.work_dir + 'input_%i' % i)
if input_dict[input_id]['type'] == "3d":
fnames = input_dict[input_id]['volume'].split()
for i in range(len(fnames)):
shutil.copy(self.input_dir + fnames[i],
self.work_dir + 'inputVol_%i' % i + '.vol')
msg = self.process_input()
self.log("input selected : %s" % input_id)
self.cfg['meta']['original'] = False
self.cfg['meta']['is3d'] = input_dict[input_id]['type'] == "3d"
self.cfg.save()
# jump to the params page
return self.params(msg=msg, key=self.key)
def index(self):
"""
demo presentation and input menu
"""
# read the input index as a dict
inputd = config.file_dict(self.input_dir)
tn_size = int(cherrypy.config.get('input.thumbnail.size', '192'))
# TODO: build via list-comprehension
for (input_id, input_info) in inputd.items():
# convert the files to a list of file names
# by splitting at blank characters
# and generate thumbnails and thumbnail urls
fname = input_info['files'].split()
# GENERATE THUMBNAIL EVEN FOR FILES IN SUBDIRECTORIES OF INPUT
inputd[input_id]['tn_url'] = [self.input_url +'/'+ os.path.dirname(f) + '/' +
os.path.basename(thumbnail(self.input_dir + f, (tn_size, tn_size)))
for f in fname]
inputd[input_id]['url'] = [self.input_url + os.path.basename(f)
for f in fname]
# tn_fname = [thumbnail(self.input_dir + f, (tn_size, tn_size))
# for f in fname]
# inputd[input_id]['url'] = [self.input_url + os.path.basename(f)
# for f in fname]
# inputd[input_id]['tn_url'] = [self.input_url + os.path.basename(f)
# for f in tn_fname]
return self.tmpl_out("input.html",
inputd=inputd)
def input_select(self, **kwargs):
"""
use the selected available input images
"""
print("ENTERING input_select")
self.new_key()
self.init_cfg()
print("key = " + self.key)
# kwargs contains input_id.x and input_id.y
input_id = kwargs.keys()[0].split('.')[0]
assert input_id == kwargs.keys()[1].split('.')[0]
# get the images
input_dict = config.file_dict(self.input_dir)
idir = self.input_dir + input_dict[input_id]['subdir'] + '/'
fnames = "a.png b.png".split()
for f in fnames:
shutil.copy(idir + f, self.work_dir + f)
hastruth = os.path.isfile(idir + "t.tiff")
self.cfg['meta']['hastruth'] = hastruth
if (hastruth):
shutil.copy(idir + "t.tiff", self.work_dir + "t.tiff")
shutil.copy(idir + "t.png", self.work_dir + "t.png")
#fnames = input_dict[input_id]['files'].split()
#for i in range(len(fnames)):
# shutil.copy(self.input_dir + fnames[i],
# self.work_dir + 'input_%i' % i)
#msg = self.process_input()
self.log("input selected : %s" % input_id)
self.cfg['meta']['original'] = False
self.cfg['meta']['height'] = image(self.work_dir + '/a.png').size[1]
self.cfg.save()
# jump to the params page
return self.params(msg="(no message)", key=self.key)
def index(self):
"""
demo presentation and input menu
"""
# read the input index as a dict
inputd = config.file_dict(self.input_dir)
tn_size = int(cherrypy.config.get('input.thumbnail.size', '192'))
# TODO: build via list-comprehension
for (input_id, input_info) in inputd.items():
# convert the files to a list of file names
# by splitting at blank characters
# and generate thumbnails and thumbnail urls
fname = input_info['files'].split()
# GENERATE THUMBNAIL EVEN FOR FILES IN SUBDIRECTORIES OF INPUT
inputd[input_id]['tn_url'] = [
self.input_url + '/' + os.path.dirname(f) + '/' +
os.path.basename(
thumbnail(self.input_dir + f, (tn_size, tn_size)))
for f in fname
]
inputd[input_id]['url'] = [
self.input_url + os.path.basename(f) for f in fname
]
return self.tmpl_out("input.html", inputd=inputd)
def input_select(self, **kwargs):
"""
use the selected available input images
"""
self.init_cfg()
#kwargs contains input_id.x and input_id.y
input_id = kwargs.keys()[0].split('.')[0]
assert input_id == kwargs.keys()[1].split('.')[0]
# get the images
input_dict = config.file_dict(self.input_dir)
fnames = input_dict[input_id]['files'].split()
for i in range(len(fnames)):
shutil.copy(self.input_dir + fnames[i],
self.work_dir + 'input_%i' % i)
if input_dict[input_id]['type'] == "3d":
fnames = input_dict[input_id]['volume'].split()
for i in range(len(fnames)):
shutil.copy(self.input_dir + fnames[i],
self.work_dir + 'inputVol_%i' % i +'.vol')
msg = self.process_input()
self.log("input selected : %s" % input_id)
self.cfg['meta']['original'] = False
self.cfg['meta']['is3d'] = input_dict[input_id]['type'] == "3d"
self.cfg.save()
# jump to the params page
return self.params(msg=msg, key=self.key)
def input_select(self, **kwargs):
"""
use the selected available input images
"""
print("ENTERING input_select")
self.new_key()
self.init_cfg()
print("key = " + self.key)
# kwargs contains input_id.x and input_id.y
input_id = kwargs.keys()[0].split('.')[0]
assert input_id == kwargs.keys()[1].split('.')[0]
# get the images
input_dict = config.file_dict(self.input_dir)
idir = self.input_dir + input_dict[input_id]['subdir'] + '/'
fnames = "a.png b.png".split()
for f in fnames:
shutil.copy(idir + f, self.work_dir + f)
hastruth = os.path.isfile(idir + "t.tiff")
self.cfg['meta']['hastruth'] = hastruth
if (hastruth):
shutil.copy(idir + "t.tiff", self.work_dir + "t.tiff")
shutil.copy(idir + "t.png", self.work_dir + "t.png")
#fnames = input_dict[input_id]['files'].split()
#for i in range(len(fnames)):
# shutil.copy(self.input_dir + fnames[i],
# self.work_dir + 'input_%i' % i)
#msg = self.process_input()
self.log("input selected : %s" % input_id)
self.cfg['meta']['original'] = False
self.cfg['meta']['height'] = image(self.work_dir + '/a.png').size[1]
self.cfg.save()
# jump to the params page
return self.params(msg="(no message)", key=self.key)
def index(self):
"""
demo presentation and input menu
"""
#print("ENTERING index")
tn_size = 192
# read the input index as a dict
inputd = config.file_dict(self.input_dir)
#print(inputd)
for (input_id, input_info) in inputd.items():
tn_fname = [thumbnail(self.input_dir + \
input_info['subdir'] \
+ '/i0000.png',(tn_size,tn_size))]
inputd[input_id]['hastruth'] = os.path.isfile(
self.input_dir + input_info['subdir'] + '/a.png')
inputd[input_id]['height'] = image(self.input_dir +
input_info['subdir'] +
'/i0000.png').size[1]
inputd[input_id]['baseinput'] = \
self.input_url + input_info['subdir'] + '/'
inputd[input_id]['url'] = [
self.input_url + input_info['subdir'] + '/' +
os.path.basename(f) for f in ["i0000.png"]
]
inputd[input_id]['tn_url'] = [
self.input_url + input_info['subdir'] + '/' +
os.path.basename(f) for f in tn_fname
]
return self.tmpl_out("input.html", inputd=inputd)
def input_select(self, **kwargs):
"""
use the selected available input images
"""
# When we arrive here, self.key should be empty.
# If not, it means that the execution belongs to another thread
# and therefore we need to reuse the app object
key_is_empty = (self.key == "")
if key_is_empty:
# New execution: create new app object
self2 = base_app(self.base_dir)
self2.__class__ = self.__class__
self2.__dict__.update(self.__dict__)
else:
# Already known execution
self2 = self
self2.new_key()
self2.init_cfg()
# Add app to object pool
if key_is_empty:
pool = AppPool.get_instance() # Singleton pattern
pool.add_app(self2.key, self2)
# custom roi_max, passed by the user directly in the URL
roi_max = 1000
if 'roi_max' in kwargs:
roi_max = int(kwargs['roi_max'])
kwargs.pop('roi_max')
# get the dataset id
# kwargs contains input_id.x and input_id.y
input_id = kwargs.keys()[0].split('.')[0]
assert input_id == kwargs.keys()[1].split('.')[0]
# save paths to the tiff images
# either one of the two keys dzi8 or dzi16 must exist
input_dict = config.file_dict(self2.input_dir)
self2.cfg['param']['tif_paths'] = input_dict[input_id]['tif'].split()
self2.cfg['param']['nb_images'] = len(input_dict[input_id]['tif'].split())
if input_dict[input_id].has_key('dzi8'):
self2.cfg['param']['dzi_paths'] = input_dict[input_id]['dzi8'].split()
else:
self2.cfg['param']['dzi_paths'] = input_dict[input_id]['dzi16'].split()
self2.cfg.save()
# jump to the display page
return self2.params(key=self2.key, roi_max=roi_max)
def input_select(self, **kwargs):
"""
After this method has run, the images have been:
downloaded, converted and renamed to standard names
IF the ground truth is provided, then the mask images
are also generated
The format for the images is PNG, except for the ground truth, which is encoded as TIFF
A PNG thumbnail of the ground truth is also generated
"""
from lib import config
import urlparse
self.new_key()
self.init_cfg()
# get parameters for the preconfigured experiments
# kwargs contains input_id.x and input_id.y
# The html form uses the input identifiers as names of the field
input_id = kwargs.keys()[0].split('.')[0]
assert input_id == kwargs.keys()[1].split('.')[0]
# load the input.cfg either from a local path or from an url
input_cfg_path = config.file_dict(self.input_dir)[input_id]['path']
if urlparse.urlparse(input_cfg_path).netloc == '':
# it should be a relative path
cfg_path_or_url = os.path.join(self.base_dir,'input',input_cfg_path , 'param.cfg')
self.copy_cfg_from_path(cfg_path_or_url, self.work_dir)
else:
# it is an url
cfg_path_or_url = urlparse.urljoin(input_cfg_path , 'param.cfg')
self.download_cfg_from_url(cfg_path_or_url, self.work_dir)
# download the files_url, that may be left from both cases
self.download_remaining_url_files(self.work_dir)
# process the input files
msg = self.process_input_files()
self.log("input selected : %s" % input_id)
self.cfg['meta']['input_id'] = input_id
self.cfg['meta']['original'] = False
self.cfg.save()
# jump to the params page
return self.params(msg=msg, key=self.key)
def input_select(self, **kwargs):
"""
After this method has run, the images have been:
downloaded, converted and renamed to standard names
IF the ground truth is provided, then the mask images
are also generated
The format for the images is PNG, except for the ground truth, which is encoded as TIFF
A PNG thumbnail of the ground truth is also generated
"""
from lib import config
import urlparse
self.new_key()
self.init_cfg()
# get parameters for the preconfigured experiments
# kwargs contains input_id.x and input_id.y
# The html form uses the input identifiers as names of the field
input_id = kwargs.keys()[0].split('.')[0]
assert input_id == kwargs.keys()[1].split('.')[0]
# load the input.cfg either from a local path or from an url
input_cfg_path = config.file_dict(self.input_dir)[input_id]['path']
if urlparse.urlparse(input_cfg_path).netloc == '':
# it should be a relative path
cfg_path_or_url = os.path.join(self.base_dir, 'input',
input_cfg_path, 'param.cfg')
self.copy_cfg_from_path(cfg_path_or_url, self.work_dir)
else:
# it is an url
cfg_path_or_url = urlparse.urljoin(input_cfg_path, 'param.cfg')
self.download_cfg_from_url(cfg_path_or_url, self.work_dir)
# download the files_url, that may be left from both cases
self.download_remaining_url_files(self.work_dir)
# process the input files
msg = self.process_input_files()
self.log("input selected : %s" % input_id)
self.cfg['meta']['input_id'] = input_id
self.cfg['meta']['original'] = False
self.cfg.save()
# jump to the params page
return self.params(msg=msg, key=self.key)
def index(self):
"""
demo presentation and input menu
"""
print("ENTERING index")
# read the input index as a dict
inputd = config.file_dict(self.input_dir)
print(inputd)
for (input_id, input_info) in inputd.items():
fname = ["a.png", "b.png", "t.png"]
inputd[input_id]['baseinput'] = self.input_url + input_info['subdir']+'/'
inputd[input_id]['url'] = [self.input_url
+ input_info['subdir']
+ '/' + os.path.basename(f)
for f in fname]
inputd[input_id]['tn_url'] = [self.input_url
+ input_info['subdir']
+ '/'
+ os.path.basename(f)
for f in fname]
return self.tmpl_out("input.html", inputd=inputd)
def get_params_from_url(self, input_id=None, x=None, y=None, r=None, n_bins= None, sigma=None):
"""
redirects to the wait method with the provided parameters
This method was made only to be able to launch one precise experiment from one url
"""
self.new_key()
self.init_cfg()
# get the images
input_dict = config.file_dict(self.input_dir)
fnames = input_dict[input_id]['files'].split()
for i in range(len(fnames)):
shutil.copy(self.input_dir + fnames[i],
self.work_dir + 'input_%i' % i)
msg = self.process_input()
self.log("input selected : %s" % input_id)
self.cfg['meta']['original'] = False
self.cfg['meta']['input_id'] = input_id
self.cfg.save()
# jump to the wait page
return self.wait(key=self.key, newrun=False, xold="0", yold="0",
x=x, y=y, r=r, sigma=sigma, n_bins=n_bins)
def input_select(self, **kwargs):
"""
use the selected available input images
"""
# When we arrive here, self.key should be empty.
# If not, it means that the execution belongs to another thread
# and therefore we need to reuse the app object
key_is_empty = (self.key == "")
if key_is_empty:
# New execution: create new app object
self2 = base_app(self.base_dir)
self2.__class__ = self.__class__
self2.__dict__.update(self.__dict__)
else:
# Already known execution
self2 = self
self2.new_key()
self2.init_cfg()
# Add app to object pool
if key_is_empty:
pool = AppPool.get_instance() # Singleton pattern
pool.add_app(self2.key, self2)
# custom roi_max, passed by the user directly in the URL
roi_max = 1000
if 'roi_max' in kwargs:
roi_max = int(kwargs['roi_max'])
kwargs.pop('roi_max')
# get the dataset id
# kwargs contains input_id.x and input_id.y
input_id = kwargs.keys()[0].split('.')[0]
assert input_id == kwargs.keys()[1].split('.')[0]
# read the dictionary of inputs
input_dict = config.file_dict(self.input_dir)
# create symlinks to the full images and rpc files. There must be the
# same number of image files and rpc files. The number of previews
# doesn't matter.
img_files = input_dict[input_id]['tif'].split()
rpc_files = input_dict[input_id]['rpc'].split()
assert len(img_files) == len(rpc_files)
img_files_abs = [os.path.join(self.input_dir, f) for f in img_files]
rpc_files_abs = [os.path.join(self.input_dir, f) for f in rpc_files]
for i in range(len(img_files)):
os.symlink(img_files_abs[i],
os.path.join(self.work_dir, 'img_%02d.tif' % (i + 1)))
os.symlink(rpc_files_abs[i],
os.path.join(self.work_dir, 'rpc_%02d.xml' % (i + 1)))
# if it's an xs dataset, create a link to the clr reference image
if 'clr' in input_dict[input_id]:
clr_files = input_dict[input_id]['clr'].split()
clr_files_abs = [
os.path.join(self.input_dir, f) for f in clr_files
]
os.symlink(clr_files_abs[0],
os.path.join(self.work_dir, 'img_01_clr.tif'))
# link to the preview files, needed by the archive
prv_files = input_dict[input_id]['files'].split()
prv_files_abs = [os.path.join(self.input_dir, f) for f in prv_files]
for i, f in enumerate(prv_files_abs):
os.symlink(f, os.path.join(self.work_dir,
'prv_%02d.png' % (i + 1)))
# save params of the dataset
self.log("input selected : %s" % input_id)
self.cfg['meta']['original'] = False
self.cfg['meta']['input_id'] = input_id
self.cfg['meta']['nb_img'] = len(img_files)
self.cfg['meta']['color'] = input_dict[input_id]['color']
# either one of the two keys dzi8 or dzi16 must exist
self.cfg['param']['tif_paths'] = input_dict[input_id]['tif'].split()
if input_dict[input_id].has_key('dzi8'):
self.cfg['param']['dzi_paths'] = input_dict[input_id][
'dzi8'].split()
else:
self.cfg['param']['dzi_paths'] = input_dict[input_id][
'dzi16'].split()
self.cfg.save()
# jump to the display page
return self.params(key=self.key, roi_max=roi_max)
def input_select(self, **kwargs):
"""
use the selected available input images
"""
# When we arrive here, self.key should be empty.
# If not, it means that the execution belongs to another thread
# and therefore we need to reuse the app object
key_is_empty = (self.key == "")
if key_is_empty:
# New execution: create new app object
self2 = base_app(self.base_dir)
self2.__class__ = self.__class__
self2.__dict__.update(self.__dict__)
else:
# Already known execution
self2 = self
self2.new_key()
self2.init_cfg()
# Add app to object pool
if key_is_empty:
pool = AppPool.get_instance() # Singleton pattern
pool.add_app(self2.key, self2)
# custom roi_max, passed by the user directly in the URL
roi_max = 1000
if 'roi_max' in kwargs:
roi_max = int(kwargs['roi_max'])
kwargs.pop('roi_max')
# get the dataset id
# kwargs contains input_id.x and input_id.y
input_id = kwargs.keys()[0].split('.')[0]
assert input_id == kwargs.keys()[1].split('.')[0]
# read the dictionary of inputs
input_dict = config.file_dict(self.input_dir)
# create symlinks to the full images and rpc files. There must be the
# same number of image files and rpc files. The number of previews
# doesn't matter.
img_files = input_dict[input_id]['tif'].split()
rpc_files = input_dict[input_id]['rpc'].split()
assert len(img_files) == len(rpc_files)
img_files_abs = [os.path.join(self.input_dir, f) for f in img_files]
rpc_files_abs = [os.path.join(self.input_dir, f) for f in rpc_files]
for i in range(len(img_files)):
os.symlink(img_files_abs[i], os.path.join(self.work_dir,
'img_%02d.tif' % (i+1)))
os.symlink(rpc_files_abs[i], os.path.join(self.work_dir,
'rpc_%02d.xml' % (i+1)))
# if it's an xs dataset, create a link to the clr reference image
if 'clr' in input_dict[input_id]:
clr_files = input_dict[input_id]['clr'].split()
clr_files_abs = [os.path.join(self.input_dir, f) for f in clr_files]
os.symlink(clr_files_abs[0], os.path.join(self.work_dir, 'img_01_clr.tif'))
# link to the preview files, needed by the archive
prv_files = input_dict[input_id]['files'].split()
prv_files_abs = [os.path.join(self.input_dir, f) for f in prv_files]
for i, f in enumerate(prv_files_abs):
os.symlink(f, os.path.join(self.work_dir, 'prv_%02d.png' % (i+1)))
# save params of the dataset
self.log("input selected : %s" % input_id)
self.cfg['meta']['original'] = False
self.cfg['meta']['input_id'] = input_id
self.cfg['meta']['nb_img'] = len(img_files)
self.cfg['meta']['color'] = input_dict[input_id]['color']
# either one of the two keys dzi8 or dzi16 must exist
self.cfg['param']['tif_paths'] = input_dict[input_id]['tif'].split()
if input_dict[input_id].has_key('dzi8'):
self.cfg['param']['dzi_paths'] = input_dict[input_id]['dzi8'].split()
else:
self.cfg['param']['dzi_paths'] = input_dict[input_id]['dzi16'].split()
self.cfg.save()
# jump to the display page
return self.params(key=self.key, roi_max=roi_max)
