hpparvi/opents

Open exoplanet transit search pipeline

Open exoplanet transit search pipeline

Open exoplanet transit search pipeline (OpenTS) is a Python package for searching exoplanet transit signals from photometric light curves. OpenTS currently supports K2SC and SPOC TESS light curves, but more input sources will be supported soon.

The pipeline is a successor to the "Oxford K2 planet search pipeline" that was used in Pope et al. (2016).

Installation

python setup.py install

Usage

At its simplest, the transit search can be run as

opents data_directory

or as

mpirun -n X opents data_directory

where X is the number of nodes to use.

By default, the search is carried our for all the targets in data_directory, combining all the TESS sectors or K2 Campaigns for each target.

Example output

Authors

• Hannu Parviainen
• Benjamin Pope
• Suzanne Aigrain

opents's Issues

Can't install on MacOS x86

Hi Hannu,

Digging up k2ps again, it's not installing right on my Mac: seems that the fortran isn't finding x86 links for Python:

Undefined symbols for architecture x86_64:
"_PyArg_ParseTupleAndKeywords", referenced from:
_f2py_rout_blsf_bls_bin in blsfmodule.o
_f2py_rout_blsf_bls_eebls in blsfmodule.o
"_PyBytes_FromString", referenced from:
_PyInit_blsf in blsfmodule.o
"_PyCapsule_GetPointer", referenced from:
_PyInit_blsf in blsfmodule.o
_F2PyCapsule_AsVoidPtr in fortranobject.o
"_PyCapsule_New", referenced from:
_fortran_getattr in fortranobject.o
_F2PyCapsule_FromVoidPtr in fortranobject.o
"_PyCapsule_Type", referenced from:
_PyInit_blsf in blsfmodule.o
_F2PyCapsule_Check in fortranobject.o
"_PyComplex_Type", referenced from:
_int_from_pyobj in blsfmodule.o
_double_from_pyobj in blsfmodule.o
"_PyDict_DelItemString", referenced from:
_fortran_setattr in fortranobject.o
"_PyDict_GetItemString", referenced from:
_fortran_getattr in fortranobject.o
"_PyDict_New", referenced from:
_PyFortranObject_New in fortranobject.o
_PyFortranObject_NewAsAttr in fortranobject.o
_fortran_setattr in fortranobject.o
"_PyDict_SetItemString", referenced from:
_PyInit_blsf in blsfmodule.o
_F2PyDict_SetItemString in fortranobject.o
_PyFortranObject_New in fortranobject.o
_fortran_getattr in fortranobject.o
_fortran_setattr in fortranobject.o
"_PyErr_Clear", referenced from:
_int_from_pyobj in blsfmodule.o
_double_from_pyobj in blsfmodule.o
_F2PyDict_SetItemString in fortranobject.o
_fortran_getattr in fortranobject.o
_fortran_repr in fortranobject.o
_F2PyCapsule_FromVoidPtr in fortranobject.o
_F2PyCapsule_AsVoidPtr in fortranobject.o
...
"_PyErr_Format", referenced from:
_PyInit_blsf in blsfmodule.o
_fortran_call in fortranobject.o
_check_and_fix_dimensions in fortranobject.o
"_PyErr_NewException", referenced from:
_PyInit_blsf in blsfmodule.o
"_PyErr_NoMemory", referenced from:
_fortran_getattr in fortranobject.o
"_PyErr_Occurred", referenced from:
_PyInit_blsf in blsfmodule.o
_f2py_rout_blsf_bls_bin in blsfmodule.o
_f2py_rout_blsf_bls_eebls in blsfmodule.o
_int_from_pyobj in blsfmodule.o
_double_from_pyobj in blsfmodule.o
_F2PyDict_SetItemString in fortranobject.o
"_PyErr_Print", referenced from:
_PyInit_blsf in blsfmodule.o
_F2PyDict_SetItemString in fortranobject.o
"_PyErr_SetString", referenced from:
_PyInit_blsf in blsfmodule.o
_f2py_rout_blsf_bls_bin in blsfmodule.o
_f2py_rout_blsf_bls_eebls in blsfmodule.o
_int_from_pyobj in blsfmodule.o
_double_from_pyobj in blsfmodule.o
_fortran_setattr in fortranobject.o
_array_from_pyobj in fortranobject.o
...
"_PyExc_AttributeError", referenced from:
_PyInit_blsf in blsfmodule.o
_fortran_setattr in fortranobject.o
"_PyExc_ImportError", referenced from:
_PyInit_blsf in blsfmodule.o
"_PyExc_RuntimeError", referenced from:
_PyInit_blsf in blsfmodule.o
_fortran_call in fortranobject.o
"_PyExc_TypeError", referenced from:
_fortran_call in fortranobject.o
_array_from_pyobj in fortranobject.o
"_PyExc_ValueError", referenced from:
_array_from_pyobj in fortranobject.o
_check_and_fix_dimensions in fortranobject.o
"_PyFloat_Type", referenced from:
_double_from_pyobj in blsfmodule.o
"_PyImport_ImportModule", referenced from:
_PyInit_blsf in blsfmodule.o
"_PyLong_AsLong", referenced from:
_int_from_pyobj in blsfmodule.o
"_PyMem_Free", referenced from:
_fortran_dealloc in fortranobject.o
_fortran_getattr in fortranobject.o
"_PyMem_Malloc", referenced from:
_fortran_getattr in fortranobject.o
"_PyModule_Create2", referenced from:
_PyInit_blsf in blsfmodule.o
"_PyModule_GetDict", referenced from:
_PyInit_blsf in blsfmodule.o
"_PyNumber_Float", referenced from:
_double_from_pyobj in blsfmodule.o
"_PyNumber_Long", referenced from:
_int_from_pyobj in blsfmodule.o
"_PyOS_snprintf", referenced from:
_fortran_getattr in fortranobject.o
"_PyObject_GenericGetAttr", referenced from:
_fortran_getattr in fortranobject.o
"_PyObject_GetAttrString", referenced from:
_PyInit_blsf in blsfmodule.o
_int_from_pyobj in blsfmodule.o
_double_from_pyobj in blsfmodule.o
_fortran_repr in fortranobject.o
"_PySequence_Check", referenced from:
_int_from_pyobj in blsfmodule.o
_double_from_pyobj in blsfmodule.o
"_PySequence_GetItem", referenced from:
_int_from_pyobj in blsfmodule.o
_double_from_pyobj in blsfmodule.o
"_PyType_IsSubtype", referenced from:
_int_from_pyobj in blsfmodule.o
_double_from_pyobj in blsfmodule.o
_array_from_pyobj in fortranobject.o
"_PyType_Type", referenced from:
_PyInit_blsf in blsfmodule.o
"_PyUnicode_Concat", referenced from:
_fortran_getattr in fortranobject.o
"_PyUnicode_FromFormat", referenced from:
_fortran_repr in fortranobject.o
"_PyUnicode_FromString", referenced from:
_PyInit_blsf in blsfmodule.o
_fortran_getattr in fortranobject.o
_fortran_repr in fortranobject.o
"_PyUnicode_FromStringAndSize", referenced from:
_fortran_getattr in fortranobject.o
"_Py_BuildValue", referenced from:
_f2py_rout_blsf_bls_bin in blsfmodule.o
_f2py_rout_blsf_bls_eebls in blsfmodule.o
"__PyObject_New", referenced from:
_PyFortranObject_New in fortranobject.o
_PyFortranObject_NewAsAttr in fortranobject.o
"__Py_NoneStruct", referenced from:
_f2py_rout_blsf_bls_bin in blsfmodule.o
_f2py_rout_blsf_bls_eebls in blsfmodule.o
_fortran_getattr in fortranobject.o
_fortran_setattr in fortranobject.o
_array_from_pyobj in fortranobject.o
"_main", referenced from:
implicit entry/start for main executable
ld: symbol(s) not found for architecture x86_64
collect2: error: ld returned 1 exit status
Undefined symbols for architecture x86_64:
"_PyArg_ParseTupleAndKeywords", referenced from:
_f2py_rout_blsf_bls_bin in blsfmodule.o
_f2py_rout_blsf_bls_eebls in blsfmodule.o
"_PyBytes_FromString", referenced from:
_PyInit_blsf in blsfmodule.o
"_PyCapsule_GetPointer", referenced from:
_PyInit_blsf in blsfmodule.o
_F2PyCapsule_AsVoidPtr in fortranobject.o
"_PyCapsule_New", referenced from:
_fortran_getattr in fortranobject.o
_F2PyCapsule_FromVoidPtr in fortranobject.o
"_PyCapsule_Type", referenced from:
_PyInit_blsf in blsfmodule.o
_F2PyCapsule_Check in fortranobject.o
"_PyComplex_Type", referenced from:
_int_from_pyobj in blsfmodule.o
_double_from_pyobj in blsfmodule.o
"_PyDict_DelItemString", referenced from:
_fortran_setattr in fortranobject.o
"_PyDict_GetItemString", referenced from:
_fortran_getattr in fortranobject.o
"_PyDict_New", referenced from:
_PyFortranObject_New in fortranobject.o
_PyFortranObject_NewAsAttr in fortranobject.o
_fortran_setattr in fortranobject.o
"_PyDict_SetItemString", referenced from:
_PyInit_blsf in blsfmodule.o
_F2PyDict_SetItemString in fortranobject.o
_PyFortranObject_New in fortranobject.o
_fortran_getattr in fortranobject.o
_fortran_setattr in fortranobject.o
"_PyErr_Clear", referenced from:
_int_from_pyobj in blsfmodule.o
_double_from_pyobj in blsfmodule.o
_F2PyDict_SetItemString in fortranobject.o
_fortran_getattr in fortranobject.o
_fortran_repr in fortranobject.o
_F2PyCapsule_FromVoidPtr in fortranobject.o
_F2PyCapsule_AsVoidPtr in fortranobject.o
...
"_PyErr_Format", referenced from:
_PyInit_blsf in blsfmodule.o
_fortran_call in fortranobject.o
_check_and_fix_dimensions in fortranobject.o
"_PyErr_NewException", referenced from:
_PyInit_blsf in blsfmodule.o
"_PyErr_NoMemory", referenced from:
_fortran_getattr in fortranobject.o
"_PyErr_Occurred", referenced from:
_PyInit_blsf in blsfmodule.o
_f2py_rout_blsf_bls_bin in blsfmodule.o
_f2py_rout_blsf_bls_eebls in blsfmodule.o
_int_from_pyobj in blsfmodule.o
_double_from_pyobj in blsfmodule.o
_F2PyDict_SetItemString in fortranobject.o
"_PyErr_Print", referenced from:
_PyInit_blsf in blsfmodule.o
_F2PyDict_SetItemString in fortranobject.o
"_PyErr_SetString", referenced from:
_PyInit_blsf in blsfmodule.o
_f2py_rout_blsf_bls_bin in blsfmodule.o
_f2py_rout_blsf_bls_eebls in blsfmodule.o
_int_from_pyobj in blsfmodule.o
_double_from_pyobj in blsfmodule.o
_fortran_setattr in fortranobject.o
_array_from_pyobj in fortranobject.o
...
"_PyExc_AttributeError", referenced from:
_PyInit_blsf in blsfmodule.o
_fortran_setattr in fortranobject.o
"_PyExc_ImportError", referenced from:
_PyInit_blsf in blsfmodule.o
"_PyExc_RuntimeError", referenced from:
_PyInit_blsf in blsfmodule.o
_fortran_call in fortranobject.o
"_PyExc_TypeError", referenced from:
_fortran_call in fortranobject.o
_array_from_pyobj in fortranobject.o
"_PyExc_ValueError", referenced from:
_array_from_pyobj in fortranobject.o
_check_and_fix_dimensions in fortranobject.o
"_PyFloat_Type", referenced from:
_double_from_pyobj in blsfmodule.o
"_PyImport_ImportModule", referenced from:
_PyInit_blsf in blsfmodule.o
"_PyLong_AsLong", referenced from:
_int_from_pyobj in blsfmodule.o
"_PyMem_Free", referenced from:
_fortran_dealloc in fortranobject.o
_fortran_getattr in fortranobject.o
"_PyMem_Malloc", referenced from:
_fortran_getattr in fortranobject.o
"_PyModule_Create2", referenced from:
_PyInit_blsf in blsfmodule.o
"_PyModule_GetDict", referenced from:
_PyInit_blsf in blsfmodule.o
"_PyNumber_Float", referenced from:
_double_from_pyobj in blsfmodule.o
"_PyNumber_Long", referenced from:
_int_from_pyobj in blsfmodule.o
"_PyOS_snprintf", referenced from:
_fortran_getattr in fortranobject.o
"_PyObject_GenericGetAttr", referenced from:
_fortran_getattr in fortranobject.o
"_PyObject_GetAttrString", referenced from:
_PyInit_blsf in blsfmodule.o
_int_from_pyobj in blsfmodule.o
_double_from_pyobj in blsfmodule.o
_fortran_repr in fortranobject.o
"_PySequence_Check", referenced from:
_int_from_pyobj in blsfmodule.o
_double_from_pyobj in blsfmodule.o
"_PySequence_GetItem", referenced from:
_int_from_pyobj in blsfmodule.o
_double_from_pyobj in blsfmodule.o
"_PyType_IsSubtype", referenced from:
_int_from_pyobj in blsfmodule.o
_double_from_pyobj in blsfmodule.o
_array_from_pyobj in fortranobject.o
"_PyType_Type", referenced from:
_PyInit_blsf in blsfmodule.o
"_PyUnicode_Concat", referenced from:
_fortran_getattr in fortranobject.o
"_PyUnicode_FromFormat", referenced from:
_fortran_repr in fortranobject.o
"_PyUnicode_FromString", referenced from:
_PyInit_blsf in blsfmodule.o
_fortran_getattr in fortranobject.o
_fortran_repr in fortranobject.o
"_PyUnicode_FromStringAndSize", referenced from:
_fortran_getattr in fortranobject.o
"_Py_BuildValue", referenced from:
_f2py_rout_blsf_bls_bin in blsfmodule.o
_f2py_rout_blsf_bls_eebls in blsfmodule.o
"__PyObject_New", referenced from:
_PyFortranObject_New in fortranobject.o
_PyFortranObject_NewAsAttr in fortranobject.o
"__Py_NoneStruct", referenced from:
_f2py_rout_blsf_bls_bin in blsfmodule.o
_f2py_rout_blsf_bls_eebls in blsfmodule.o
_fortran_getattr in fortranobject.o
_fortran_setattr in fortranobject.o
_array_from_pyobj in fortranobject.o
"_main", referenced from:
implicit entry/start for main executable
ld: symbol(s) not found for architecture x86_64
collect2: error: ld returned 1 exit status
error: Command "/usr/local/bin/gfortran -Wall -g -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs build/temp.macosx-10.9-x86_64-3.7/build/src.macosx-10.9-x86_64-3.7/k2ps/blsfmodule.o build/temp.macosx-10.9-x86_64-3.7/build/src.macosx-10.9-x86_64-3.7/build/src.macosx-10.9-x86_64-3.7/k2ps/fortranobject.o build/temp.macosx-10.9-x86_64-3.7/src/bls.o build/temp.macosx-10.9-x86_64-3.7/build/src.macosx-10.9-x86_64-3.7/k2ps/blsf-f2pywrappers2.o -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. -lgomp -lm -lgfortran -o build/lib.macosx-10.9-x86_64-3.7/k2ps/blsf.cpython-37m-darwin.so" failed with exit status 1

No module named 'pytransit.orbits_f'

Hi,
When I run k2search command after install, I got the following error. It seems like pytransit.orbits_f is removed from your PyTransit repository. Can you help update the code?

Traceback (most recent call last):
  File "/usr/local/bin/k2search", line 28, in <module>
    from k2ps.psearch import *
  File "/home/zcw607/.local/lib/python3.6/site-packages/k2ps/psearch.py", line 23, in <module>
    from pytransit.orbits_f import orbits as of
ModuleNotFoundError: No module named 'pytransit.orbits_f'

TESS fast cadence

Fits files of TESS fast cadence (20s) are not automatically detected by opents. I.e. it shows "0 targets". The name of these files are similar to standard 120s cadence - only except for "s-" at the end of the filename is "a_fast-". So, its format is tess*-s*-{}-*a_fast-lc.fits.

TESS QLP data

Hi,
how to use QLP data from TESS (https://archive.stsci.edu/hlsp/qlp) with opents? Is it possible? When I tried it, I got this error:

OpenTS - Open exoplanet transit search pipeline
===============================================
- Running the search for data files in '/home/pavolg/fits-qlp'
- Saving results to '/home/pavolg/fits-qlp'
- Saving plots to '/home/pavolg/fits-qlp'
- Running in serial mode
Traceback (most recent call last):
File "/usr/local/bin/opents", line 4, in <module>
__import__('pkg_resources').run_script('OpenTS==1.0.0b0', 'opents')
File "/usr/local/lib/python3.8/dist-packages/pkg_resources/__init__.py", line 651, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/usr/local/lib/python3.8/dist-packages/pkg_resources/__init__.py", line 1448, in run_script
exec(code, namespace, namespace)
File "/usr/local/lib/python3.8/dist-packages/OpenTS-1.0.0b0-py3.8.egg/EGG-INFO/scripts/opents", line 197, in <module>
logger.info(f"Chose {TSC.__name__} transit search class")
AttributeError: 'NoneType' object has no attribute '__name__'

Other sources of data (TESS 2-minute cadence data, data from Eleanor) work fine.