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Bug #1526

open

redux does not read some spider files

Added by Anchi Cheng over 12 years ago. Updated over 12 years ago.

Status:
Assigned
Priority:
Low
Assignee:
Jim Pulokas
Category:
Image Processing
Target version:
Appion/Leginon Future Version
Start date:
01/18/2012
Due date:
% Done:

0%

Estimated time:
Affected Version:
Appion/Leginon 2.1.0
Show in known bugs:
No
Workaround:

Description

Here is an example spider stack file from 2D alignment. The file can be read by eman's v2. There are 566 frames in it. 112 x 112 pixels each.

Files

alignstack_hed.spi (27.8 MB) alignstack_hed.spi Anchi Cheng, 01/18/2012 01:34 PM
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 #1

Updated by Anchi Cheng over 12 years ago

  • Tracker changed from Task to Bug
  • Subject changed from make redux reading spider files to redux does not read some spider files
  • Affected Version set to Appion/Leginon 2.1.0
  • Show in known bugs set to No

----------------------------------------
REQUEST: filename=/myamiImages/appion/sample/align/noref1/alignstack_hed.spi&info=1&oformat=JSON
Running Read(139976206558032,filename=/myamiImages/appion/sample/align/noref1/alignstack_hed.spi,info=True)
Running Format(139976206560656,oformat=JSON,rgb=False)
----------------------------------------
Exception happened during processing of request from ('127.0.0.1', 40362)
Traceback (most recent call last):
File "/usr/lib64/python2.6/SocketServer.py", line 560, in process_request_thread
self.finish_request(request, client_address)
File "/usr/lib64/python2.6/SocketServer.py", line 322, in finish_request
self.RequestHandlerClass(request, client_address, self)
File "/usr/lib64/python2.6/SocketServer.py", line 617, in init
self.handle()
File "/usr/lib/python2.6/site-packages/redux/server.py", line 23, in handle
self.run_process(request)
File "/usr/lib/python2.6/site-packages/redux/server.py", line 34, in run_process
result = pipeline.process(**kwargs)
File "/usr/lib/python2.6/site-packages/redux/pipeline.py", line 102, in process
result = pipe(result)
File "/usr/lib/python2.6/site-packages/redux/pipe.py", line 162, in call
return self.run(input, **self.kwargs)
File "/usr/lib/python2.6/site-packages/redux/pipes/format.py", line 34, in run
s = self.run_json(input)
File "/usr/lib/python2.6/site-packages/redux/pipes/format.py", line 48, in run_json
outstring = redux.utility.json_encode(input)
File "/usr/lib/python2.6/site-packages/redux/utility.py", line 76, in json_encode
outstring = json.dumps(input, cls=ReduxJSONEncoder)
File "/usr/lib64/python2.6/json/__init__.py", line 237, in dumps
**kw).encode(obj)
File "/usr/lib64/python2.6/json/encoder.py", line 367, in encode
chunks = list(self.iterencode(o))
File "/usr/lib64/python2.6/json/encoder.py", line 309, in _iterencode
for chunk in self._iterencode_dict(o, markers):
File "/usr/lib64/python2.6/json/encoder.py", line 275, in _iterencode_dict
for chunk in self._iterencode(value, markers):
File "/usr/lib64/python2.6/json/encoder.py", line 317, in _iterencode
for chunk in self._iterencode_default(o, markers):
File "/usr/lib64/python2.6/json/encoder.py", line 294, in _iterencode
yield encoder(o)
UnicodeDecodeError: 'utf8' codec can't decode byte 0x81 in position 840: invalid start byte
----------------------------------------

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