Error when specifying pad in TimeSeries.fetch
Created by: SeanDS
When running this script:
from gwpy.timeseries import TimeSeries
from matplotlib import pyplot as plt
data = TimeSeries.fetch(start="2018-10-24 00:00", end="2018-10-24 14:00", channel="G2:PEM-BASE_PART_300", host="pt-firefly", port=8088, pad=0.0)
plt.plot(data)
plt.show()I get this error:
(ligo) sean@totoro ~/Workspace $ python plot_particles.py
/home/sean/Workspace/anaconda/envs/ligo/lib/python3.6/importlib/_bootstrap.py:219: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 88 from C header, got 96 from PyObject
return f(*args, **kwds)
Traceback (most recent call last):
File "plot_particles.py", line 5, in <module>
data = TimeSeries.fetch(start="2018-10-24 00:00", end="2018-10-24 14:00", channel="G2:PEM-BASE_PART_300", host="pt-firefly", port=8088, pad=0.0)
File "/home/sean/Workspace/anaconda/envs/ligo/lib/python3.6/site-packages/gwpy/timeseries/core.py", line 335, in fetch
allow_tape=allow_tape, type=type, dtype=dtype)[str(channel)]
File "/home/sean/Workspace/anaconda/envs/ligo/lib/python3.6/site-packages/gwpy/timeseries/core.py", line 1073, in fetch
series_class=cls.EntryClass).crop(start, end)
File "/home/sean/Workspace/anaconda/envs/ligo/lib/python3.6/site-packages/gwpy/io/nds2.py", line 347, in wrapped_func
return func(*args, **kwargs)
File "/home/sean/Workspace/anaconda/envs/ligo/lib/python3.6/site-packages/gwpy/timeseries/io/nds2.py", line 135, in fetch
qsegs = _get_data_segments(ndschannels, start, end, connection) & span
File "/home/sean/Workspace/anaconda/envs/ligo/lib/python3.6/site-packages/gwpy/timeseries/io/nds2.py", line 170, in _get_data_segments
connection=connection)
File "/home/sean/Workspace/anaconda/envs/ligo/lib/python3.6/site-packages/gwpy/io/nds2.py", line 347, in wrapped_func
return func(*args, **kwargs)
File "/home/sean/Workspace/anaconda/envs/ligo/lib/python3.6/site-packages/gwpy/io/nds2.py", line 545, in get_availability
result = connection.get_availability(names)
File "/home/sean/Workspace/anaconda/envs/ligo/lib/python3.6/site-packages/nds2.py", line 3684, in get_availability
channel_names = _hack_for_python2_strings(channel_names)
File "/home/sean/Workspace/anaconda/envs/ligo/lib/python3.6/site-packages/nds2.py", line 3858, in _hack_for_python2_strings
elif len(args) > 0:
TypeError: object of type 'map' has no len()The error goes away if I remove pad=0.0 from the call to TimeSeries.fetch.
I am running the script within a fresh conda environment. I found that python-nds2-client was not installed by gwpy by default so I had to install that too. The install sequence is provided below.
There are two other potential causes for concern: the RuntimeWarning about Numpy at the top of the output above, and the SafetyError from installing sip below. Neither prevent the script working when I remove pad.
My client is Ubuntu 18.04.1, and I'm accessing an NDS1 server, if that makes any difference.
sean@totoro ~/Workspace $ conda create -n ligo
Solving environment: done
## Package Plan ##
environment location: /home/sean/Workspace/anaconda/envs/ligo
Proceed ([y]/n)? y
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
# $ conda activate ligo
#
# To deactivate an active environment, use
#
# $ conda deactivate
sean@totoro ~/Workspace $ conda config --add channels conda-forge
sean@totoro ~/Workspace $ conda install -n ligo gwpy
Solving environment: done
## Package Plan ##
environment location: /home/sean/Workspace/anaconda/envs/ligo
added / updated specs:
- gwpy
The following packages will be downloaded:
package | build
---------------------------|-----------------
tornado-5.1.1 | py36h470a237_0 669 KB conda-forge
hdf5-1.10.3 | hc401514_2 4.8 MB conda-forge
astropy-3.0.5 | py36h470a237_0 9.6 MB conda-forge
gwpy-0.12.2 | py36_1000 1.4 MB conda-forge
pytz-2018.6 | py_0 228 KB conda-forge
glib-2.56.2 | h464dc38_0 4.9 MB conda-forge
atomicwrites-1.2.1 | py_0 9 KB conda-forge
pytest-3.9.2 | py36_1000 334 KB conda-forge
py-1.7.0 | py_0 65 KB conda-forge
h5py-2.8.0 | py36h097b052_4 3.7 MB conda-forge
pluggy-0.8.0 | py_0 17 KB conda-forge
gstreamer-1.12.5 | h5856ed1_0 2.1 MB conda-forge
wheel-0.32.2 | py36_0 34 KB conda-forge
tqdm-4.28.1 | py_0 38 KB conda-forge
pyparsing-2.2.2 | py_0 51 KB conda-forge
more-itertools-4.3.0 | py36_1000 83 KB conda-forge
------------------------------------------------------------
Total: 28.0 MB
The following NEW packages will be INSTALLED:
astropy: 3.0.5-py36h470a237_0 conda-forge
atomicwrites: 1.2.1-py_0 conda-forge
attrs: 18.2.0-py_0 conda-forge
blas: 1.0-mkl
ca-certificates: 2018.10.15-ha4d7672_0 conda-forge
certifi: 2018.10.15-py36_1000 conda-forge
cycler: 0.10.0-py_1 conda-forge
dbus: 1.13.0-h3a4f0e9_0 conda-forge
expat: 2.2.5-hfc679d8_2 conda-forge
fontconfig: 2.13.1-h65d0f4c_0 conda-forge
freetype: 2.9.1-h6debe1e_4 conda-forge
gettext: 0.19.8.1-h5e8e0c9_1 conda-forge
glib: 2.56.2-h464dc38_0 conda-forge
gst-plugins-base: 1.12.5-hde13a9d_0 conda-forge
gstreamer: 1.12.5-h5856ed1_0 conda-forge
gwpy: 0.12.2-py36_1000 conda-forge
h5py: 2.8.0-py36h097b052_4 conda-forge
hdf5: 1.10.3-hc401514_2 conda-forge
icu: 58.2-hfc679d8_0 conda-forge
intel-openmp: 2019.0-118
jpeg: 9c-h470a237_1 conda-forge
kiwisolver: 1.0.1-py36h2d50403_2 conda-forge
libffi: 3.2.1-hfc679d8_5 conda-forge
libgcc-ng: 7.2.0-hdf63c60_3 conda-forge
libgfortran: 3.0.0-1 conda-forge
libgfortran-ng: 7.2.0-hdf63c60_3 conda-forge
libiconv: 1.15-h470a237_3 conda-forge
libpng: 1.6.35-ha92aebf_2 conda-forge
libstdcxx-ng: 7.2.0-hdf63c60_3 conda-forge
libuuid: 2.32.1-h470a237_2 conda-forge
libxcb: 1.13-h470a237_2 conda-forge
libxml2: 2.9.8-h422b904_5 conda-forge
ligo-common: 1.0.3-py_0 conda-forge
ligo-segments: 1.0.1-py36h470a237_0 conda-forge
ligotimegps: 1.2.3-py_0 conda-forge
matplotlib: 2.2.3-py36h8e2386c_0 conda-forge
mkl: 2019.0-118
mkl_fft: 1.0.6-py36_0 conda-forge
mkl_random: 1.0.1-py36_0 conda-forge
more-itertools: 4.3.0-py36_1000 conda-forge
ncurses: 6.1-hfc679d8_1 conda-forge
numpy: 1.15.0-py36h1b885b7_0
numpy-base: 1.15.0-py36h3dfced4_0
openssl: 1.0.2p-h470a237_1 conda-forge
pcre: 8.41-hfc679d8_3 conda-forge
pip: 18.1-py36_1000 conda-forge
pluggy: 0.8.0-py_0 conda-forge
psutil: 5.4.7-py36h470a237_1 conda-forge
pthread-stubs: 0.4-h470a237_1 conda-forge
py: 1.7.0-py_0 conda-forge
pyparsing: 2.2.2-py_0 conda-forge
pyqt: 5.6.0-py36h8210e8a_7 conda-forge
pytest: 3.9.2-py36_1000 conda-forge
pytest-arraydiff: 0.2-py_0 conda-forge
pytest-astropy: 0.4.0-py_0 conda-forge
pytest-doctestplus: 0.1.3-py_0 conda-forge
pytest-openfiles: 0.3.0-py_0 conda-forge
pytest-remotedata: 0.3.0-py_0 conda-forge
python: 3.6.6-h5001a0f_3 conda-forge
python-dateutil: 2.7.3-py_0 conda-forge
pytz: 2018.6-py_0 conda-forge
qt: 5.6.2-hf70d934_9 conda-forge
readline: 7.0-haf1bffa_1 conda-forge
scipy: 1.1.0-py36hc49cb51_0
setuptools: 40.4.3-py36_0 conda-forge
sip: 4.18.1-py36hfc679d8_0 conda-forge
six: 1.11.0-py36_1001 conda-forge
sqlite: 3.25.2-hb1c47c0_0 conda-forge
tk: 8.6.8-ha92aebf_0 conda-forge
tornado: 5.1.1-py36h470a237_0 conda-forge
tqdm: 4.28.1-py_0 conda-forge
wheel: 0.32.2-py36_0 conda-forge
xorg-libxau: 1.0.8-h470a237_6 conda-forge
xorg-libxdmcp: 1.1.2-h470a237_7 conda-forge
xz: 5.2.4-h470a237_1 conda-forge
zlib: 1.2.11-h470a237_3 conda-forge
Proceed ([y]/n)? y
Downloading and Extracting Packages
tornado-5.1.1 | 669 KB | ######################################################################################################################### | 100%
hdf5-1.10.3 | 4.8 MB | ######################################################################################################################### | 100%
astropy-3.0.5 | 9.6 MB | ######################################################################################################################### | 100%
gwpy-0.12.2 | 1.4 MB | ######################################################################################################################### | 100%
pytz-2018.6 | 228 KB | ######################################################################################################################### | 100%
glib-2.56.2 | 4.9 MB | ######################################################################################################################### | 100%
atomicwrites-1.2.1 | 9 KB | ######################################################################################################################### | 100%
pytest-3.9.2 | 334 KB | ######################################################################################################################### | 100%
py-1.7.0 | 65 KB | ######################################################################################################################### | 100%
h5py-2.8.0 | 3.7 MB | ######################################################################################################################### | 100%
pluggy-0.8.0 | 17 KB | ######################################################################################################################### | 100%
gstreamer-1.12.5 | 2.1 MB | ######################################################################################################################### | 100%
wheel-0.32.2 | 34 KB | ######################################################################################################################### | 100%
tqdm-4.28.1 | 38 KB | ######################################################################################################################### | 100%
pyparsing-2.2.2 | 51 KB | ######################################################################################################################### | 100%
more-itertools-4.3.0 | 83 KB | ######################################################################################################################### | 100%
Preparing transaction: done
Verifying transaction: /
SafetyError: The package for sip located at /home/sean/Workspace/anaconda/pkgs/sip-4.18.1-py36hfc679d8_0
appears to be corrupted. The path 'bin/sip'
has a sha256 mismatch.
reported sha256: 660de583bfb72b513b209f94fa2eeddd77e37b446c436d2a9f894cdb7d860a75
actual sha256: 28c774abd99feec762bb1d589d226171d6029d3d2624c26731fd9d4ef94e35ac
SafetyError: The package for sip located at /home/sean/Workspace/anaconda/pkgs/sip-4.18.1-py36hfc679d8_0
appears to be corrupted. The path 'include/python3.6m/sip.h'
has a sha256 mismatch.
reported sha256: 4bb5b5668ccb46db3285977936a0cce3c35971308a0cc771eec423077a2bb617
actual sha256: a1993a4e3de79cc5ab948cba7b4197a24600f361a6b69e63e89e9c25933f1cec
done
Executing transaction: done
sean@totoro ~/Workspace $ source activate ligo
(ligo) sean@totoro ~/Workspace $ python plot_particles.py
/home/sean/Workspace/anaconda/envs/ligo/lib/python3.6/importlib/_bootstrap.py:219: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 88 from C header, got 96 from PyObject
return f(*args, **kwds)
Traceback (most recent call last):
File "plot_particles.py", line 5, in <module>
data = TimeSeries.fetch(start="2018-10-24 00:00", end="2018-10-24 14:00", channel="G2:PEM-BASE_PART_300", host="pt-firefly", port=8088, pad=0.0)
File "/home/sean/Workspace/anaconda/envs/ligo/lib/python3.6/site-packages/gwpy/timeseries/core.py", line 335, in fetch
allow_tape=allow_tape, type=type, dtype=dtype)[str(channel)]
File "/home/sean/Workspace/anaconda/envs/ligo/lib/python3.6/site-packages/gwpy/timeseries/core.py", line 1018, in fetch
connection = io_nds2.auth_connect(host, port)
File "/home/sean/Workspace/anaconda/envs/ligo/lib/python3.6/site-packages/gwpy/io/nds2.py", line 317, in auth_connect
raise ImportError("No module named nds2")
ImportError: No module named nds2
(ligo) sean@totoro ~/Workspace $ conda install -n ligo python-nds2-client
Solving environment: done
## Package Plan ##
environment location: /home/sean/Workspace/anaconda/envs/ligo
added / updated specs:
- python-nds2-client
The following NEW packages will be INSTALLED:
cyrus-sasl: 2.1.26-h20670df_3
krb5: 1.16.1-hbb41f41_0 conda-forge
libcurl: 7.61.1-hbdb9355_2 conda-forge
libedit: 3.1.20170329-haf1bffa_1 conda-forge
libntlm: 1.4-h470a237_1 conda-forge
libssh2: 1.8.0-h5b517e9_2 conda-forge
nds2-client: 0.16.0-hfc679d8_2 conda-forge
python-nds2-client: 0.16.1-py36h24bf2e0_1001 conda-forge
Proceed ([y]/n)? y
Preparing transaction: done
Verifying transaction: done
Executing transaction: done