issue loading pretrained model for unet segmentation

[Boehmin]

I have been slowly working through the example notebooks - thank you so much for providing them first of all - they are immensely helpful!

I am trying to do the segmentation notebook, however, I am stuck on the UNET segmentation. (I also wanted to ask whether there is an example notebook for cellpose segmentation within big-fish, since I believe this might be more appropriate for my case?)

My issue is the following:

1. All the deeplearning packages are installed, versions are:

2.6.2
0.14.0

2. When I run:

# load pretrained model
model_nuc = segmentation.unet_3_classes_nuc()
model_nuc.summary()

I get the following error which seems to me as if the models require loading and internet connection? I run the jupyter notebooks on our computing cluster which has no access to internet - the no route to host error is now quite familiar to me. I haven`t been able to figure out how to circumvent this, or how to download the models potentially in the terminal where I do have access to the internet and load them locally within the jupyter notebook.

downloading model weights...
---------------------------------------------------------------------------
OSError                                   Traceback (most recent call last)
~/miniconda3/envs/bigfish_env/lib/python3.6/urllib/request.py in do_open(self, http_class, req, **http_conn_args)
   1348                 h.request(req.get_method(), req.selector, req.data, headers,
-> 1349                           encode_chunked=req.has_header('Transfer-encoding'))
   1350             except OSError as err: # timeout error

~/miniconda3/envs/bigfish_env/lib/python3.6/http/client.py in request(self, method, url, body, headers, encode_chunked)
   1286         """Send a complete request to the server."""
-> 1287         self._send_request(method, url, body, headers, encode_chunked)
   1288 

~/miniconda3/envs/bigfish_env/lib/python3.6/http/client.py in _send_request(self, method, url, body, headers, encode_chunked)
   1332             body = _encode(body, 'body')
-> 1333         self.endheaders(body, encode_chunked=encode_chunked)
   1334 

~/miniconda3/envs/bigfish_env/lib/python3.6/http/client.py in endheaders(self, message_body, encode_chunked)
   1281             raise CannotSendHeader()
-> 1282         self._send_output(message_body, encode_chunked=encode_chunked)
   1283 

~/miniconda3/envs/bigfish_env/lib/python3.6/http/client.py in _send_output(self, message_body, encode_chunked)
   1041         del self._buffer[:]
-> 1042         self.send(msg)
   1043 

~/miniconda3/envs/bigfish_env/lib/python3.6/http/client.py in send(self, data)
    979             if self.auto_open:
--> 980                 self.connect()
    981             else:

~/miniconda3/envs/bigfish_env/lib/python3.6/http/client.py in connect(self)
   1439 
-> 1440             super().connect()
   1441 

~/miniconda3/envs/bigfish_env/lib/python3.6/http/client.py in connect(self)
    951         self.sock = self._create_connection(
--> 952             (self.host,self.port), self.timeout, self.source_address)
    953         self.sock.setsockopt(socket.IPPROTO_TCP, socket.TCP_NODELAY, 1)

~/miniconda3/envs/bigfish_env/lib/python3.6/socket.py in create_connection(address, timeout, source_address)
    723     if err is not None:
--> 724         raise err
    725     else:

~/miniconda3/envs/bigfish_env/lib/python3.6/socket.py in create_connection(address, timeout, source_address)
    712                 sock.bind(source_address)
--> 713             sock.connect(sa)
    714             # Break explicitly a reference cycle

OSError: [Errno 113] No route to host

During handling of the above exception, another exception occurred:

URLError                                  Traceback (most recent call last)
<ipython-input-3-b4ffa3482168> in <module>
      1 # load pretrained model
----> 2 model_nuc = segmentation.unet_3_classes_nuc()
      3 model_nuc.summary()

~/miniconda3/envs/bigfish_env/lib/python3.6/site-packages/bigfish/segmentation/nuc_segmentation.py in unet_3_classes_nuc()
     34 
     35     # load model
---> 36     model = dl.load_pretrained_model("nuc", "3_classes")
     37 
     38     return model

~/miniconda3/envs/bigfish_env/lib/python3.6/site-packages/bigfish/deep_learning/models_segmentation.py in load_pretrained_model(channel, model_name)
     63 
     64     # load weights
---> 65     path_pretrained_directory = check_pretrained_weights(channel, model_name)
     66     path_checkpoint = os.path.join(
     67         path_pretrained_directory, "checkpoint")

~/miniconda3/envs/bigfish_env/lib/python3.6/site-packages/bigfish/deep_learning/models_segmentation.py in check_pretrained_weights(channel, model_name)
    181         stack.load_and_save_url(
    182             remote_url=url_zip_file,
--> 183             directory=path_weights_directory)
    184 
    185         # unzip

~/miniconda3/envs/bigfish_env/lib/python3.6/site-packages/bigfish/stack/utils.py in load_and_save_url(remote_url, directory, filename)
    338 
    339     # download and save data
--> 340     urlretrieve(remote_url, path)
    341 
    342     return path

~/miniconda3/envs/bigfish_env/lib/python3.6/urllib/request.py in urlretrieve(url, filename, reporthook, data)
    246     url_type, path = splittype(url)
    247 
--> 248     with contextlib.closing(urlopen(url, data)) as fp:
    249         headers = fp.info()
    250 

~/miniconda3/envs/bigfish_env/lib/python3.6/urllib/request.py in urlopen(url, data, timeout, cafile, capath, cadefault, context)
    221     else:
    222         opener = _opener
--> 223     return opener.open(url, data, timeout)
    224 
    225 def install_opener(opener):

~/miniconda3/envs/bigfish_env/lib/python3.6/urllib/request.py in open(self, fullurl, data, timeout)
    524             req = meth(req)
    525 
--> 526         response = self._open(req, data)
    527 
    528         # post-process response

~/miniconda3/envs/bigfish_env/lib/python3.6/urllib/request.py in _open(self, req, data)
    542         protocol = req.type
    543         result = self._call_chain(self.handle_open, protocol, protocol +
--> 544                                   '_open', req)
    545         if result:
    546             return result

~/miniconda3/envs/bigfish_env/lib/python3.6/urllib/request.py in _call_chain(self, chain, kind, meth_name, *args)
    502         for handler in handlers:
    503             func = getattr(handler, meth_name)
--> 504             result = func(*args)
    505             if result is not None:
    506                 return result

~/miniconda3/envs/bigfish_env/lib/python3.6/urllib/request.py in https_open(self, req)
   1390         def https_open(self, req):
   1391             return self.do_open(http.client.HTTPSConnection, req,
-> 1392                 context=self._context, check_hostname=self._check_hostname)
   1393 
   1394         https_request = AbstractHTTPHandler.do_request_

~/miniconda3/envs/bigfish_env/lib/python3.6/urllib/request.py in do_open(self, http_class, req, **http_conn_args)
   1349                           encode_chunked=req.has_header('Transfer-encoding'))
   1350             except OSError as err: # timeout error
-> 1351                 raise URLError(err)
   1352             r = h.getresponse()
   1353         except:

URLError: <urlopen error [Errno 113] No route to host>