class HisImage():
def __init__(self, fdname, finame):
self.fdname = fdname
self.finame = finame
self.webparent = r'/Test2/'
self.im = ops.OpenSlide(self.fdname + self.finame + '.ndpi')
self.root = self.ExtractRoot()
self.an_num = self.root.__len__()
self.mysite = Piwigo(url='http://qmul.piwigo.com/')
self.login = self.Login()
self.webimlist = self.mysite.images(self.mysite.plan.keys()[0])
self.webfdlist = self.mysite.plan
self.update = self.CheckMysite() #Update or
def __del__(self):
self.Logout()
def Logout(self):
self.mysite.logout()
def Login(self):
return self.mysite.login(username="******", password="******")
def CheckMysite(self):
if self.webfdlist.has_key(self.webparent + self.finame):
return True
else:
self.mysite.mkdir(self.webparent + self.finame)
return False
def ExtractRoot(self):
with open(self.fdname + self.finame + '.ndpi.ndpa') as f:
tree = ElementTree.parse(f)
return tree.getroot()
def ConvertXY(self, ax, by):
xmpp = float(self.im.properties['openslide.mpp-x'])
xoff = float(self.im.properties['hamamatsu.XOffsetFromSlideCentre'])
ympp = float(self.im.properties['openslide.mpp-y'])
yoff = float(self.im.properties['hamamatsu.YOffsetFromSlideCentre'])
ld = self.im.dimensions
nax = int((ax - xoff) / (xmpp * 1000.0) + ld[0] / 2.0)
nby = int((by - yoff) / (ympp * 1000.0) + ld[1] / 2.0)
return nax, nby
def Upload(self, imgname):
fdpath = self.webparent + self.finame + r'/' + imgname[-1].upper()
if self.webfdlist.has_key(fdpath) == False:
self.mysite.mkdir(fdpath)
try:
self.mysite.upload(imgname + '.png', fdpath)
except Exception as e:
print imgname
print e
self.mysite.upload(imgname + '.png', fdpath)
os.remove(imgname + '.png')
def NameAnnotation(self, index):
if self.root[index][0].text != None and self.root[index][
0].text != 'roi':
name = 'ID-' + self.root[index].attrib['id'] + '-' + self.root[
index][0].text
elif self.root[index][0].text == 'roi' or self.root[index][
0].text == 'ROI':
name = 'ID-' + self.root[index].attrib['id'] + '-' + 'R'
else:
name = 'ID-' + self.root[index].attrib['id'] + '-' + 'O'
return name
def AnnotationDots(self, index):
if self.root[index][-1][-1].tag == 'pointlist':
tplist = self.root[index][-1][-1]
elif self.root[index][-1][-1].tag == 'specialtype' and self.root[
index][-1][-3].tag == 'pointlist':
tplist = self.root[index][-1][-3]
else:
return np.array([])
Plist1 = []
for i in range(tplist.__len__()):
Plist1.append(
self.ConvertXY(int(tplist[i][0].text), int(tplist[i][1].text)))
return np.array(Plist1)
def LocateROI(self):
ROIlist = []
for index in range(self.root.__len__()):
if self.root[index][0].text == 'roi' or self.root[index][
0].text == 'ROI':
ROIlist.append([index, self.AnnotationDots(index)])
return ROIlist
def ExtractImage(self, index):
name = self.NameAnnotation(index)
pl_arr = self.AnnotationDots(index)
pl_arr = np.vstack((pl_arr, pl_arr[0]))
xi = pl_arr[:, 0].min()
xa = pl_arr[:, 0].max()
yi = pl_arr[:, 1].min()
ya = pl_arr[:, 1].max()
if (xa - xi) * (ya - yi) > 1000 * 1000:
level = 2
else:
level = 0
tmpim = self.im.read_region(
(xi - 100, yi - 100), level,
((xa - xi + 200) / 2**level, (ya - yi + 200) / 2**level))
fig, ax = plt.subplots()
ax.imshow(tmpim)
ax.axis('image')
ax.axis('off')
ax.plot((pl_arr[:, 0] - xi + 100.0) / 2**level,
(pl_arr[:, 1] - yi + 100.0) / 2**level,
'y-',
linewidth=3)
#plt.savefig(name,dpi=fig.dpi )
self.SaveFigureAsImage(name,
fig=fig,
orig_size=(np.array(tmpim).shape[0],
np.array(tmpim).shape[1]))
plt.close(fig)
return name
def ExtractandUpload(self, index):
#ROIlist = LocateROI()
#if self.root[index][0].text == 'roi' or self.root[index][0].text == 'ROI' :
name = self.ExtractImage(index)
self.Upload(name)
def ExtractandUploadAll(self):
#ROIlist = LocateROI()
print 'uploading started'
for index in range(self.root.__len__()):
#if self.root[index][0].text == 'roi' or self.root[index][0].text == 'ROI' :
#continue
name = self.ExtractImage(index)
self.Upload(name)
print index + 'Uploaded'
def ExtractandUpload_bak(self):
for index in range(self.root.__len__()):
#for index in range(2):
name = self.NameAnnotation(index)
pl_arr = self.AnnotationDots(index)
xi = pl_arr[:, 0].min()
xa = pl_arr[:, 0].max()
yi = pl_arr[:, 1].min()
ya = pl_arr[:, 1].max()
tmpim = self.im.read_region((xi - 100, yi - 100), 0,
(xa - xi + 200, ya - yi + 200))
fig, ax = plt.subplots()
ax.imshow(tmpim)
ax.axis('image')
ax.axis('off')
ax.plot(pl_arr[:, 0] - xi + 100,
pl_arr[:, 1] - yi + 100,
'y-',
linewidth=3)
#plt.savefig(name,dpi=fig.dpi )
self.SaveFigureAsImage(name,
fig=fig,
orig_size=(np.array(tmpim).shape[0],
np.array(tmpim).shape[1]))
plt.close(fig)
del (pl_arr)
del (tmpim)
self.Upload(name)
self.Logout()
def SaveFigureAsImage(self, fileName, fig=None, **kwargs):
''' Save a Matplotlib figure as an image without borders or frames.
Args:
fileName (str): String that ends in .png etc.
fig (Matplotlib figure instance): figure you want to save as the image
Keyword Args:
orig_size (tuple): width, height of the original image used to maintain
aspect ratio.
'''
fig_size = fig.get_size_inches()
w, h = fig_size[0], fig_size[1]
fig.patch.set_alpha(0)
if kwargs.has_key('orig_size'): # Aspect ratio scaling if required
w, h = kwargs['orig_size']
w2, h2 = fig_size[0], fig_size[1]
fig.set_size_inches([(w2 / w) * w, (w2 / w) * h])
fig.set_dpi((w2 / w) * fig.get_dpi())
a = fig.gca()
a.set_frame_on(False)
a.set_xticks([])
a.set_yticks([])
plt.axis('off')
plt.xlim(0, h)
plt.ylim(w, 0)
fig.savefig(fileName,
transparent=True,
bbox_inches='tight',
pad_inches=0)
def main():
usage = USAGE
parser = OptionParser(version="%s %s" % (PROG,VERSION), usage=usage)
parser.description= DESCRIPTION
parser.epilog = AUTHOR
try:
add_dynamic_option(parser)
(options, args) = parser.parse_args()
verb = args[0]
if verb == 'ws':
piwigo = Piwigo(url=options.url)
if 'user' and 'password' in options.__dict__:
piwigo.login(options.user, options.password)
kw = purge_kw(options.__dict__,('user','password','url'))
pp = pprint.PrettyPrinter(indent=4)
pp.pprint(Ws(piwigo, options.method)(**kw))
if piwigo.islogged:
piwigo.logout()
if verb == "download":
ana = Analyse('Analyze')
ana.start()
try:
piwigo = Piwigo(url=options.url)
piwigo.login(options.user, options.password)
# check
if not os.path.isdir(options.dest):
os.makedirs(options.dest)
options.dest = os.path.abspath(options.dest)
piwigo.iscategory(options.category)
if options.category[-2:] == ' /' : options.category = options.category[:-2]
# treatment
run = Run(verb, options.thread)
kw = purge_kw(options.__dict__,('user','password','url','dest','category','thread'))
for img in piwigo.images(options.category, **kw):
run.add(piwigo.download,
["%s / %s" % (options.category, str(img)), "%s%s%s" % (options.dest, os.path.sep, str(img))],
kw)
except Exception as e:
ana.stop()
raise e
ana.stop()
run.start()
piwigo.logout()
if run.error:
parser.error(run.strerror)
if verb == "upload":
ana = Analyse('Analyze')
ana.start()
try:
piwigo = Piwigo(url=options.url)
piwigo.login(options.user, options.password)
# check
piwigo.makedirs(options.category)
# treatment
run = Run(verb, options.thread)
kw = purge_kw(options.__dict__,('user','password','url','source','category','thread'))
for img in glob.glob(options.source):
run.add(piwigo.upload,
[os.path.abspath(img), options.category],
kw)
ana.stop()
except Exception as e:
ana.stop()
raise e
run.start()
piwigo.logout()
if run.error:
parser.error(run.strerror)
if verb == "sync-up":
ana = Analyse('Analyze')
ana.start()
try:
piwigo = Piwigo(url=options.url)
piwigo.login(options.user, options.password)
# check
options.source = os.path.abspath(options.source)
if not os.path.isdir(options.source):
raise Exception("%s is not directory" % options.source)
piwigo.iscategory(options.category)
if len(options.category) and options.category[-1] != '/' and options.category[:-3] != ' / ':
options.category = options.category+ ' / '
# treatment
run = Run(verb, options.thread)
kw = purge_kw(options.__dict__,('user','password','url','source','category','thread'))
# local -> piwigo
for root, dirnames, filenames in os.walk(options.source):
filtering = fnmatch.filter(filenames, options.extension.split(',')[0])
for ext in options.extension.split(',')[1:]:
filtering = filtering + fnmatch.filter(filenames, ext)
for filename in filtering:
pathrel = os.path.abspath(os.path.join(root, filename))[len(options.source)+1:]
pathabs = os.path.abspath(os.path.join(root, filename))
category = options.category + ' / '.join(pathrel.split(os.sep)[:-1])
if not piwigo.isimage(category + ' / ' + filename):
run.add(piwigo.makedirs,[category,], kw)
run.add(piwigo.upload,[pathabs, category], kw)
ana.stop()
except Exception as e:
ana.stop()
raise e
run.start()
piwigo.logout()
if run.error:
parser.error(run.strerror)
if verb == "sync-down":
ana = Analyse('Analyze')
ana.start()
try:
piwigo = Piwigo(url=options.url)
piwigo.login(options.user, options.password)
# check
options.source = os.path.abspath(options.source)
if not os.path.isdir(options.source):
raise Exception("%s is not directory" % options.source)
piwigo.iscategory(options.category)
if len(options.category) and options.category[-1] != '/' and options.category[:-3] != ' / ':
options.category = options.category+ ' / '
# treatment
run = Run(verb, options.thread)
kw = purge_kw(options.__dict__,('user','password','url','source','category','thread'))
# piwigo -> local
for category, item in piwigo.plan.iteritems():
if options.category == category[0:len(options.category)]:
path = os.path.join(options.source, *category[len(options.category):].split(' / '))
if not os.path.exists(path):
os.makedirs(path)
for img in piwigo.images(category):
pathimg = os.path.join(path, img)
if not os.path.exists(pathimg):
run.add(piwigo.download,
["%s / %s" % (category, str(img)), pathimg],
kw)
ana.stop()
except Exception as e:
ana.stop()
raise e
run.start()
piwigo.logout()
if run.error:
parser.error(run.strerror)
except Exception as e:
parser.error(e)
sys.exit(1)
#print mysite.plan
#print mysite.idcategory(mysite.plan.keys()[0])
#print mysite.images(mysite.plan.keys()[-1])
#mysite.removedirs('/Test3')
flist = os.listdir('../Samples')
'''
for tmp in flist:
if tmp[-3:] != 'png':
flist.remove(tmp)
for im in flist:
mysite.upload(im,mysite.plan.keys()[0])
'''
imlist = mysite.images(mysite.plan.keys()[0])
def UploadFolders(fp):
mysite.mkdir('/Test2/' + fp)
for category in ['T', 'M', 'F', 'H']:
pathid = mysite.mkdir('/Test2/' + fp + r'/' + category)
fdpath = '../Samples/' + fp + r'/' + category + r'/'
flist = os.listdir(fdpath)
for im in flist:
# Return the image ID
mysite.upload(
fdpath + im,
mysite.plan.keys()[mysite.plan.values().index(pathid)])
def main():
usage = USAGE
parser = OptionParser(version="%s %s" % (PROG, VERSION), usage=usage)
parser.description = DESCRIPTION
parser.epilog = AUTHOR
try:
add_dynamic_option(parser)
(options, args) = parser.parse_args()
verb = args[0]
if verb == 'ws':
piwigo = Piwigo(url=options.url)
if 'user' and 'password' in options.__dict__:
piwigo.login(options.user, options.password)
kw = purge_kw(options.__dict__, ('user', 'password', 'url'))
pp = pprint.PrettyPrinter(indent=4)
pp.pprint(Ws(piwigo, options.method)(**kw))
if piwigo.islogged:
piwigo.logout()
if verb == "download":
ana = Analyse('Analyze')
ana.start()
try:
piwigo = Piwigo(url=options.url)
piwigo.login(options.user, options.password)
# check
if not os.path.isdir(options.dest):
os.makedirs(options.dest)
options.dest = os.path.abspath(options.dest)
piwigo.iscategory(options.category)
if options.category[-2:] == ' /':
options.category = options.category[:-2]
# treatment
run = Run(verb, options.thread)
kw = purge_kw(
options.__dict__,
('user', 'password', 'url', 'dest', 'category', 'thread'))
for img in piwigo.images(options.category, **kw):
run.add(piwigo.download, [
"%s / %s" % (options.category, str(img)),
"%s%s%s" % (options.dest, os.path.sep, str(img))
], kw)
except Exception as e:
ana.stop()
raise e
ana.stop()
run.start()
piwigo.logout()
if run.error:
parser.error(run.strerror)
if verb == "upload":
ana = Analyse('Analyze')
ana.start()
try:
piwigo = Piwigo(url=options.url)
piwigo.login(options.user, options.password)
# check
piwigo.makedirs(options.category)
# treatment
run = Run(verb, options.thread)
kw = purge_kw(options.__dict__,
('user', 'password', 'url', 'source', 'category',
'thread'))
for img in glob.glob(options.source):
run.add(piwigo.upload,
[os.path.abspath(img), options.category], kw)
ana.stop()
except Exception as e:
ana.stop()
raise e
run.start()
piwigo.logout()
if run.error:
parser.error(run.strerror)
if verb == "sync-up":
ana = Analyse('Analyze')
ana.start()
try:
piwigo = Piwigo(url=options.url)
piwigo.login(options.user, options.password)
# check
options.source = os.path.abspath(options.source)
if not os.path.isdir(options.source):
raise Exception("%s is not directory" % options.source)
piwigo.iscategory(options.category)
if len(options.category) and options.category[
-1] != '/' and options.category[:-3] != ' / ':
options.category = options.category + ' / '
# treatment
run = Run(verb, options.thread)
kw = purge_kw(options.__dict__,
('user', 'password', 'url', 'source', 'category',
'thread'))
# local -> piwigo
for root, dirnames, filenames in os.walk(options.source):
filtering = fnmatch.filter(filenames,
options.extension.split(',')[0])
for ext in options.extension.split(',')[1:]:
filtering = filtering + fnmatch.filter(filenames, ext)
for filename in filtering:
pathrel = os.path.abspath(os.path.join(
root, filename))[len(options.source) + 1:]
pathabs = os.path.abspath(os.path.join(root, filename))
category = options.category + ' / '.join(
pathrel.split(os.sep)[:-1])
if not piwigo.isimage(category + ' / ' + filename):
run.add(piwigo.makedirs, [
category,
], kw)
run.add(piwigo.upload, [pathabs, category], kw)
ana.stop()
except Exception as e:
ana.stop()
raise e
run.start()
piwigo.logout()
if run.error:
parser.error(run.strerror)
if verb == "sync-down":
ana = Analyse('Analyze')
ana.start()
try:
piwigo = Piwigo(url=options.url)
piwigo.login(options.user, options.password)
# check
options.source = os.path.abspath(options.source)
if not os.path.isdir(options.source):
raise Exception("%s is not directory" % options.source)
piwigo.iscategory(options.category)
if len(options.category) and options.category[
-1] != '/' and options.category[:-3] != ' / ':
options.category = options.category + ' / '
# treatment
run = Run(verb, options.thread)
kw = purge_kw(options.__dict__,
('user', 'password', 'url', 'source', 'category',
'thread'))
# piwigo -> local
for category, item in piwigo.plan.iteritems():
if options.category == category[0:len(options.category)]:
path = os.path.join(
options.source,
*category[len(options.category):].split(' / '))
if not os.path.exists(path):
os.makedirs(path)
for img in piwigo.images(category):
pathimg = os.path.join(path, img)
if not os.path.exists(pathimg):
run.add(piwigo.download, [
"%s / %s" % (category, str(img)), pathimg
], kw)
ana.stop()
except Exception as e:
ana.stop()
raise e
run.start()
piwigo.logout()
if run.error:
parser.error(run.strerror)
except Exception as e:
parser.error(e)
sys.exit(1)
