I am trying to load a .mrc file in python. But, I am getting error.
Code(ReadMrcTest.py)::
import numpy as np
import h5py
imgPath = 'usr/Task1/emd-62.mrc' #Even for 'usr/task1/emd-62.mrc', same error
image = h5py.File(imgPath)
print image
Error:
Traceback (most recent call last):
File "ReadMrcTest.py", line 8, in <module>
image = h5py.File(imgPath)
File "/usr/s029/.local/lib/python2.7/site-packages/h5py/_hl/files.py", line 271, in __init__
fid = make_fid(name, mode, userblock_size, fapl, swmr=swmr)
File "/usr/s029/.local/lib/python2.7/site-packages/h5py/_hl/files.py", line 126, in make_fid
fid = h5f.create(name, h5f.ACC_EXCL, fapl=fapl, fcpl=fcpl)
File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper (/tmp/pip-nCYoKW-build/h5py/_objects.c:2840)
File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper (/tmp/pip-nCYoKW-build/h5py/_objects.c:2798)
File "h5py/h5f.pyx", line 98, in h5py.h5f.create (/tmp/pip-nCYoKW-build/h5py/h5f.c:2284)
**IOError: Unable to create file (Unable to open file: name = '/usr/task1/emd-62.mrc', errno = 17, error message = 'file exists', flags = 15, o_flags = c2)**
Thanks in advance
Related
HI~ I want to query xml data from Oracle db with cx_Oracle, but it doesn't work with Ora-19011 error message. I think size of query data is larger than string buffer, but i don't know how to solve this problem
Oracle DB is an external DB and it's not my own DB, So i can't access directly. Therefore, I want to fix my problem on my code and print query data on python terminal.
(my software version)
windows 10 64bit
python 2.7 64bit
oracle-instant client 19.3 64bit
cx_oracle 7.2.2
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import cx_Oracle
import sys
import csv
import codecs
printHeader = True
conn = cx_Oracle.connect('id/passwd#ip:port/orcl')
print(conn.version)
curs = conn.cursor()
curs.execute('SELECT * FROM tablename')
for record in curs:
print(record)
Error occured at line 18(for record in curs) and here are error messages.
11.2.0.4.0
We've got an error while stopping in unhandled exception: <class 'cx_Oracle.DatabaseError'>.
Traceback (most recent call last):
File "c:\Users\goo41\.vscode\extensions\ms-python.python-2019.8.30787\pythonFiles\lib\python\ptvsd\_vendored\pydevd\pydevd.py", line 1740, in do_stop_on_unhandled_exception
self.do_wait_suspend(thread, frame, 'exception', arg, is_unhandled_exception=True)
File "c:\Users\goo41\.vscode\extensions\ms-python.python-2019.8.30787\pythonFiles\lib\python\ptvsd\_vendored\pydevd\pydevd.py", line 1615, in do_wait_suspend
with self._threads_suspended_single_notification.notify_thread_suspended(thread_id, stop_reason):
File "C:\Python27\lib\contextlib.py", line 17, in __enter__
return self.gen.next()
File "c:\Users\goo41\.vscode\extensions\ms-python.python-2019.8.30787\pythonFiles\lib\python\ptvsd\_vendored\pydevd\pydevd.py", line 360, in notify_thread_suspended
with AbstractSingleNotificationBehavior.notify_thread_suspended(self, thread_id, stop_reason):
File "C:\Python27\lib\contextlib.py", line 17, in __enter__
return self.gen.next()
File "c:\Users\goo41\.vscode\extensions\ms-python.python-2019.8.30787\pythonFiles\lib\python\ptvsd\_vendored\pydevd\pydevd.py", line 308, in notify_thread_suspended
self.send_suspend_notification(thread_id, stop_reason)
File "c:\Users\goo41\.vscode\extensions\ms-python.python-2019.8.30787\pythonFiles\lib\python\ptvsd\_vendored\pydevd\pydevd.py", line 354, in send_suspend_notification
py_db.writer.add_command(py_db.cmd_factory.make_thread_suspend_single_notification(py_db, thread_id, stop_reason))
File "c:\Users\goo41\.vscode\extensions\ms-python.python-2019.8.30787\pythonFiles\lib\python\ptvsd\_vendored\pydevd\_pydevd_bundle\pydevd_net_command_factory_json.py", line 309, in make_thread_suspend_single_notification
return NetCommand(CMD_THREAD_SUSPEND_SINGLE_NOTIFICATION, 0, event, is_json=True)
File "c:\Users\goo41\.vscode\extensions\ms-python.python-2019.8.30787\pythonFiles\lib\python\ptvsd\_vendored\pydevd\_pydevd_bundle\pydevd_net_command.py", line 57, in __init__
text = json.dumps(as_dict)
File "C:\Python27\lib\json\__init__.py", line 244, in dumps
return _default_encoder.encode(obj)
File "C:\Python27\lib\json\encoder.py", line 207, in encode
chunks = self.iterencode(o, _one_shot=True)
File "C:\Python27\lib\json\encoder.py", line 270, in iterencode
return _iterencode(o, 0)
UnicodeDecodeError: 'utf8' codec can't decode byte 0xb9 in position 11: invalid start byte
Traceback (most recent call last):
File "c:\Users\goo41\.vscode\extensions\ms-python.python-2019.8.30787\pythonFiles\ptvsd_launcher.py", line 43, in <module>
main(ptvsdArgs)
File "c:\Users\goo41\.vscode\extensions\ms-python.python-2019.8.30787\pythonFiles\lib\python\ptvsd\__main__.py", line 432, in main
run()
File "c:\Users\goo41\.vscode\extensions\ms-python.python-2019.8.30787\pythonFiles\lib\python\ptvsd\__main__.py", line 316, in run_file
runpy.run_path(target, run_name='__main__')
File "C:\Python27\lib\runpy.py", line 252, in run_path
return _run_module_code(code, init_globals, run_name, path_name)
File "C:\Python27\lib\runpy.py", line 82, in _run_module_code
mod_name, mod_fname, mod_loader, pkg_name)
File "C:\Python27\lib\runpy.py", line 72, in _run_code
exec code in run_globals
File "c:\PythonWorkspace\oraclePrc\test1.py", line 18, in <module>
for record in curs:
cx_Oracle.DatabaseError: ORA-19011: Character string buffer too small
When you connect to the database, try using this code instead:
conn = cx_Oracle.connect('id/passwd#ip:port/orcl', encoding="UTF-8", nencoding="UTF-8")
This will ensure that you are using a universal encoding -- which may eliminate the first error, and possibly the second as well. If not, adjust the code sample and error messages noted above.
I am trying to connect to hbase-1.2.6 from python code, is as:
import happybase
connection = happybase.Connection(host='localhost',port=16010)
table = connection.table('blogpost')
table.put('1', {'post:title': 'hello world1'})
I manually created the table-"blogpost" in hbase. I am using python-2.7 and happybase-1.1.0.
error log are as:
/usr/bin/python2.7 /home/spark/PycharmProjects/PySpark/hbase.py
Traceback (most recent call last):
File "/home/spark/PycharmProjects/PySpark/hbase.py", line 5, in <module>
table.put('1', {'post:title': 'hello world1'})
File "/usr/local/lib/python2.7/dist-packages/happybase/table.py", line 464, in put
batch.put(row, data)
File "/usr/local/lib/python2.7/dist-packages/happybase/batch.py", line 137, in __exit__
self.send()
File "/usr/local/lib/python2.7/dist-packages/happybase/batch.py", line 60, in send
self._table.connection.client.mutateRows(self._table.name, bms, {})
File "/usr/local/lib/python2.7/dist-packages/thriftpy/thrift.py", line 198, in _req
return self._recv(_api)
File "/usr/local/lib/python2.7/dist-packages/thriftpy/thrift.py", line 210, in _recv
fname, mtype, rseqid = self._iprot.read_message_begin()
File "thriftpy/protocol/cybin/cybin.pyx", line 439, in cybin.TCyBinaryProtocol.read_message_begin (thriftpy/protocol/cybin/cybin.c:6470)
cybin.ProtocolError: No protocol version header
thanks.
Process finished with exit code 1
I am using pandas v0.14.1 with python 2.7
I have a groupby object and I am trying to pull out a group identified by particular key. The key is in fact in the group:
>>> key in key_groups.groups.keys()
True
but when I try to make the get_group call it fails with a memory error:
>>>> key_groups.get_group(key)
*** MemoryError:
The full stacktrace is:
Traceback (most recent call last):
File "main.py", line 141, in <module>
main(num_days=arguments.days, num_variants=arguments.variants)
File "main.py", line 76, in main
problem, solution = Solver.Solve(request, num_variants)
File "/srv/compunctuator/src/Solver.py", line 49, in Solve
solution = attempt_minimization(t)
File "/srv/compunctuator/src/Solver.py", line 41, in attempt_minimization
t.scruple()
File "/srv/compunctuator/src/Compunctuator.py", line 136, in scruple
self.__iterate__()
File "/srv/compunctuator/src/Compunctuator.py", line 95, in __iterate__
self.__maximize_impressions__()
File "/srv/compunctuator/src/Compunctuator.py", line 583, in __maximize_impressions__
df = key_groups.get_group(key)
File "/srv/compunctuator/.virtualenvs/compunctuator/local/lib/python2.7/site-packages/pandas/core/groupby.py", line 573, in get_group
inds = self._get_index(name)
File "/srv/compunctuator/.virtualenvs/compunctuator/local/lib/python2.7/site-packages/pandas/core/groupby.py", line 429, in _get_index
sample = next(iter(self.indices))
File "/srv/compunctuator/.virtualenvs/compunctuator/local/lib/python2.7/site-packages/pandas/core/groupby.py", line 414, in indices
return self.grouper.indices
File "properties.pyx", line 34, in pandas.lib.cache_readonly.__get__ (pandas/lib.c:36380)
File "/srv/compunctuator/.virtualenvs/compunctuator/local/lib/python2.7/site-packages/pandas/core/groupby.py", line 1253, in indices
return _get_indices_dict(label_list, keys)
File "/srv/compunctuator/.virtualenvs/compunctuator/local/lib/python2.7/site-packages/pandas/core/groupby.py", line 3474, in _get_indices_dict
np.prod(shape))
File "algos.pyx", line 1997, in pandas.algos.groupsort_indexer (pandas/algos.c:37521) MemoryError
If I actually use the dictionary lookup I can get the indices out:
>>>> key_groups.groups[key]
[0, 2]
It seems like everything should work here.
I realize a similar question was asked here pandas get_group causes memory error
but it was never resolved and I thought I could give more details if necessary.
I am trying to render an SVG map using Kartograph.py. It throws me the TypeError. Here is the python code:
import kartograph
from kartograph import Kartograph
import sys
from kartograph.options import read_map_config
css = open("stylesheet.css").read()
K = Kartograph()
cfg = read_map_config(open("config.json"))
K.generate(cfg, outfile='dd.svg', format='svg', stylesheet=css)
Here is the error it throws
Traceback (most recent call last):
File "<pyshell#33>", line 1, in <module>
K.generate(cfg, outfile='dd.svg', format='svg', stylesheet=css)
File "C:\Python27\lib\site-packages\kartograph.py-0.6.8-py2.7.egg\kartograph\kartograph.py", line 46, in generate
_map = Map(opts, self.layerCache, format=format)
File "C:\Python27\lib\site-packages\kartograph.py-0.6.8-py2.7.egg\kartograph\map.py", line 61, in __init__
layer.get_features()
File "C:\Python27\lib\site-packages\kartograph.py-0.6.8-py2.7.egg\kartograph\maplayer.py", line 81, in get_features
charset=layer.options['charset']
File "C:\Python27\lib\site-packages\kartograph.py-0.6.8-py2.7.egg\kartograph\layersource\shplayer.py", line 121, in get_features
geom = shape2geometry(shp, ignore_holes=ignore_holes, min_area=min_area, bbox=bbox, proj=self.proj)
File "C:\Python27\lib\site-packages\kartograph.py-0.6.8-py2.7.egg\kartograph\layersource\shplayer.py", line 153, in shape2geometry
geom = shape2polygon(shp, ignore_holes=ignore_holes, min_area=min_area, proj=proj)
File "C:\Python27\lib\site-packages\kartograph.py-0.6.8-py2.7.egg\kartograph\layersource\shplayer.py", line 217, in shape2polygon
poly = MultiPolygon(polygons)
File "C:\Python27\lib\site-packages\shapely\geometry\multipolygon.py", line 74, in __init__
self._geom, self._ndim = geos_multipolygon_from_polygons(polygons)
File "C:\Python27\lib\site-packages\shapely\geometry\multipolygon.py", line 30, in geos_multipolygon_from_polygons
N = len(ob[0][0][0])
TypeError: 'Polygon' object does not support indexing
I had a look at shapely and it seems like you are using an outdated version.
Update your current install:
pip install -U shapely
The whole error is:
Traceback (most recent call last):
File "C:/Documents and Settings/aaa/trysphinx/views.py", line 30, in <module>
print list(results)
File "C:\Python27\lib\site-packages\django_sphinx-2.2.4-py2.7.egg\djangosphinx\models.py", line 243, in __iter__
return iter(self._get_data())
File "C:\Python27\lib\site-packages\django_sphinx-2.2.4-py2.7.egg\djangosphinx\models.py", line 422, in _get_data
self._result_cache = list(self._get_results())
File "C:\Python27\lib\site-packages\django_sphinx-2.2.4-py2.7.egg\djangosphinx\models.py", line 557, in _get_results
results = self._get_sphinx_results()
File "C:\Python27\lib\site-packages\django_sphinx-2.2.4-py2.7.egg\djangosphinx\models.py", line 529, in _get_sphinx_results
results = client.Query(self._query, self._index)
File "C:\Python27\lib\site-packages\django_sphinx-2.2.4-py2.7.egg\djangosphinx\apis\api263\__init__.py", line 388, in Query
response = self._GetResponse(sock, VER_COMMAND_SEARCH)
File "C:\Python27\lib\site-packages\django_sphinx-2.2.4-py2.7.egg\djangosphinx\apis\api263\__init__.py", line 144, in _GetResponse
chunk = sock.recv(left)
MemoryError
Please help me.
You're loading more data into memory than your computer can handle. Perhaps rather than:
print list(results)
…do:
for r in results:
print r