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)
class HistUpload():
"""
finame : category name
"""
def __init__(self, webparent=u'LYMPH_NODE_METASTASES_V2 / '):
self.mysite = Piwigo(url='http://qmul.piwigo.com/')
self.mysite.login(username="******", password="******")
self.webfdlist = self.mysite.plan
self.webparent = webparent # u'LYMPH_NODE_METASTASES_V2 / ' ## " " space is necessary
def __del__(self):
self.mysite.logout()
def Upload(self, image_path, subfolder=None, name=None, comment=None):
"""
if multi-layer subfolder : 'Test / Test_v1 / Test_v2'
"""
if subfolder is not None:
if self.webfdlist.has_key(self.webparent + subfolder) == False:
self.mysite.mkdir(self.webparent + subfolder)
fdpath = self.webparent + subfolder
try:
if name is not None:
self.mysite.upload(image_path,
fdpath,
name=name,
comment=comment)
else:
self.mysite.upload(image_path, fdpath, comment=comment)
except Exception as e:
print e
if name is not None:
self.mysite.upload(image_path,
fdpath,
name=name,
comment=comment)
else:
self.mysite.upload(image_path, fdpath, comment=comment)
os.remove(image_path)
def Check_exist(self, image_path, subfolder=None, name=None, comment=None):
fdpath = self.webparent + subfolder
tname = image_path.split('/')[-1].split(
'.')[0] if name is None else name
if self.webfdlist.has_key(fdpath):
#int(webimlist['paging']['count'])/500
#--todo
webimlist = self.mysite.pwg.categories.getImages(
cat_id=self.mysite.plan[fdpath], per_page=1000)
for webim in webimlist['images']:
#existID.append([int(webim['name'].split('-')[1]),webim['id']])
if webim['name'] == tname:
return webim['id']
return False
def Delete(self, image_path, subfolder=None, name=None, comment=None):
tid = Check_exist(image_path, subfolder, name, comment)
self.mysite.pwg.images.delete(image_id=tid,
pwg_token=test_histo.mysite.token)
def Logout(self):
self.mysite.logout()
class BasicTestCase(unittest.TestCase):
"""
Class for Basic Test for piwigotools
"""
def setUp(self):
self.url = "http://mygallery.piwigo.com/"
self.usertest = 'USERTEST'
self.passwordtest = 'xxxxxx'
self.piwigo = Piwigo(self.url)
def test_basic(self):
self.assertTrue(self.piwigo.pwg.getVersion())
def test_checkLogin(self):
self.assertTrue(self.piwigo.login(self.usertest, self.passwordtest))
self.assertTrue(self.piwigo.logout())
self.assertRaises(LoginException, self.piwigo.mkdir)
self.assertRaises(LoginException, self.piwigo.makedirs)
self.assertRaises(LoginException, self.piwigo.upload)
def test_createCategory(self):
self.piwigo.login(self.usertest, self.passwordtest)
self.assertTrue(self.piwigo.mkdir('level'))
self.assertTrue(self.piwigo.mkdir('level / sublevel'))
self.assertTrue(self.piwigo.makedirs('level2 / sublevel2'))
self.piwigo.removedirs('level2')
self.piwigo.removedirs('level')
self.piwigo.logout()
def test_checkpath(self):
self.piwigo.login(self.usertest, self.passwordtest)
self.piwigo.mkdir('level')
self.assertTrue(self.piwigo.iscategory('level'))
self.assertTrue(self.piwigo.iscategory('level /'))
self.piwigo.removedirs('level')
self.piwigo.logout()
def test_removeCategory(self):
self.piwigo.login(self.usertest, self.passwordtest)
self.piwigo.makedirs('level2 / sublevel2')
self.assertTrue(self.piwigo.removedirs('level2'))
self.assertFalse(self.piwigo.iscategory('level2'))
self.piwigo.logout()
def test_uploadImage(self):
self.piwigo.login(self.usertest, self.passwordtest)
self.piwigo.mkdir('level')
img = os.path.join(os.path.dirname(os.path.abspath(__file__)),
'samplepiwigotools.jpg')
id = self.piwigo.upload(image=img, path="level")
self.assertTrue(id)
self.assertTrue(self.piwigo.isimage('level / samplepiwigotools.jpg'))
self.piwigo.pwg.images.delete(image_id=id, pwg_token=self.piwigo.token)
self.piwigo.removedirs('level')
self.piwigo.logout()
def test_removeImage(self):
self.piwigo.login(self.usertest, self.passwordtest)
self.piwigo.mkdir('level')
img = os.path.join(os.path.dirname(os.path.abspath(__file__)),
'samplepiwigotools.jpg')
id = self.piwigo.upload(image=img, path="level")
self.assertTrue(self.piwigo.remove('level / samplepiwigotools.jpg'))
self.assertFalse(self.piwigo.isimage('level / samplepiwigotools.jpg'))
self.piwigo.removedirs('level')
self.piwigo.logout()
def test_sublevel(self):
self.piwigo.login(self.usertest, self.passwordtest)
self.piwigo.makedirs('level2 / sublevel2')
self.assertTrue(len(self.piwigo.sublevels('level2')))
self.piwigo.removedirs('level2')
self.piwigo.logout()
def test_downloadImage(self):
self.piwigo.login(self.usertest, self.passwordtest)
self.piwigo.mkdir('level')
img = os.path.join(os.path.dirname(os.path.abspath(__file__)),
'samplepiwigotools.jpg')
id = self.piwigo.upload(image=img, path="level")
imgdst = os.path.join(os.path.dirname(os.path.abspath(__file__)),
'download.jpg')
self.assertTrue(
self.piwigo.download("level / samplepiwigotools.jpg", imgdst))
os.remove(imgdst)
self.piwigo.remove('level / samplepiwigotools.jpg')
self.piwigo.removedirs('level')
self.piwigo.logout()
class BasicTestCase(unittest.TestCase):
"""
Class for Basic Test for piwigotools
"""
def setUp(self):
self.url = "http://mygallery.piwigo.com/"
self.usertest = 'USERTEST'
self.passwordtest = 'xxxxxx'
self.piwigo = Piwigo(self.url)
def test_basic(self):
self.assertTrue(self.piwigo.pwg.getVersion())
def test_checkLogin(self):
self.assertTrue(self.piwigo.login(self.usertest, self.passwordtest))
self.assertTrue(self.piwigo.logout())
self.assertRaises(LoginException, self.piwigo.mkdir)
self.assertRaises(LoginException, self.piwigo.makedirs)
self.assertRaises(LoginException, self.piwigo.upload)
def test_createCategory(self):
self.piwigo.login(self.usertest, self.passwordtest)
self.assertTrue(self.piwigo.mkdir('level'))
self.assertTrue(self.piwigo.mkdir('level / sublevel'))
self.assertTrue(self.piwigo.makedirs('level2 / sublevel2'))
self.piwigo.removedirs('level2')
self.piwigo.removedirs('level')
self.piwigo.logout()
def test_checkpath(self):
self.piwigo.login(self.usertest, self.passwordtest)
self.piwigo.mkdir('level')
self.assertTrue(self.piwigo.iscategory('level'))
self.assertTrue(self.piwigo.iscategory('level /'))
self.piwigo.removedirs('level')
self.piwigo.logout()
def test_removeCategory(self):
self.piwigo.login(self.usertest, self.passwordtest)
self.piwigo.makedirs('level2 / sublevel2')
self.assertTrue(self.piwigo.removedirs('level2'))
self.assertFalse(self.piwigo.iscategory('level2'))
self.piwigo.logout()
def test_uploadImage(self):
self.piwigo.login(self.usertest, self.passwordtest)
self.piwigo.mkdir('level')
img = os.path.join(os.path.dirname(os.path.abspath(__file__)),'samplepiwigotools.jpg')
id = self.piwigo.upload(image=img, path="level")
self.assertTrue(id)
self.assertTrue(self.piwigo.isimage('level / samplepiwigotools.jpg'))
self.piwigo.pwg.images.delete(image_id=id, pwg_token=self.piwigo.token)
self.piwigo.removedirs('level')
self.piwigo.logout()
def test_removeImage(self):
self.piwigo.login(self.usertest, self.passwordtest)
self.piwigo.mkdir('level')
img = os.path.join(os.path.dirname(os.path.abspath(__file__)),'samplepiwigotools.jpg')
id = self.piwigo.upload(image=img, path="level")
self.assertTrue(self.piwigo.remove('level / samplepiwigotools.jpg'))
self.assertFalse(self.piwigo.isimage('level / samplepiwigotools.jpg'))
self.piwigo.removedirs('level')
self.piwigo.logout()
def test_sublevel(self):
self.piwigo.login(self.usertest, self.passwordtest)
self.piwigo.makedirs('level2 / sublevel2')
self.assertTrue(len(self.piwigo.sublevels('level2')))
self.piwigo.removedirs('level2')
self.piwigo.logout()
def test_downloadImage(self):
self.piwigo.login(self.usertest, self.passwordtest)
self.piwigo.mkdir('level')
img = os.path.join(os.path.dirname(os.path.abspath(__file__)),'samplepiwigotools.jpg')
id = self.piwigo.upload(image=img, path="level")
imgdst = os.path.join(os.path.dirname(os.path.abspath(__file__)),'download.jpg')
self.assertTrue(self.piwigo.download("level / samplepiwigotools.jpg",imgdst))
os.remove(imgdst)
self.piwigo.remove('level / samplepiwigotools.jpg')
self.piwigo.removedirs('level')
self.piwigo.logout()
class HistUpload():
def __init__(self,hist):
self.mysite = Piwigo(url='http://qmul.piwigo.com/')
self.mysite.login(username="******", password="******")
self.webfdlist = self.mysite.plan
self.webparent = u'CRLM_V2 / ' ## " " space is necessary
self.hist = hist
self.finame = hist.finame
if self.webfdlist.has_key(self.webparent+self.finame) == False:
self.mysite.mkdir(self.webparent+self.finame)
def __del__(self):
self.mysite.logout()
def Upload(self,imgname):
if imgname == None:
pass
else:
fdpath = self.webparent+self.finame+u' / '+imgname[-1].upper()
self.webfdlist = self.mysite.plan
if self.webfdlist.has_key(fdpath) == False:
self.mysite.mkdir(fdpath)
try:
self.mysite.upload(tfprefix+imgname+'.png',fdpath)
except Exception as e:
print imgname
print e
self.mysite.upload(tfprefix+imgname+'.png',fdpath)
os.remove(tfprefix+imgname+'.png')
def ExistID(self):
existID = []
for cat in Abr_list:
fdpath = self.webparent+self.finame+u' / '+cat
if self.webfdlist.has_key(fdpath):
webimlist = self.mysite.pwg.categories.getImages(cat_id=self.mysite.plan[fdpath],per_page = 1000)
for webim in webimlist['images']:
existID.append([int(webim['name'].split('-')[1]),webim['id']])
existID.sort()
return existID
def Update(self):
existID = self.ExistID()
webindex = 0
localindex =0
while(localindex<self.hist.root.__len__()):
#for index in range(hist.root.__len__()):
tmpid = int(self.hist.root[localindex].attrib['id'])
if existID==[]:
self.Upload(self.hist.ExtractImage(localindex))
localindex +=1
print localindex,' Uploaded'
elif tmpid>existID[-1][0] or webindex>existID.__len__():
self.Upload(self.hist.ExtractImage(localindex))
localindex +=1
print localindex,' Uploaded'
elif tmpid>existID[webindex][0]:
self.mysite.pwg.images.delete(image_id=existID[webindex][1],pwg_token = self.mysite.token)
webindex +=1
print 'ID-',webindex,'Deleted'
elif tmpid == existID[webindex][0]:
webindex +=1
localindex+=1
else:
self.Upload(self.hist.ExtractImage(localindex))
localindex +=1
print localindex,' Uploaded'
def Logout(self):
self.mysite.logout()
