NithyaSathyan
commented
9 months ago Hii.. I have installed fermipy using conda. When running the script for FERMI LAT analysis i get the error message as follows :
2023-12-27 18:16:09 INFO GTAnalysis.init():
fermipy version 1.2.0 ScienceTools version 2.2.0 2023-12-27 18:16:10 INFO GTAnalysis.setup(): Running setup. 2023-12-27 18:16:10 INFO GTBinnedAnalysis.setup(): Running setup for component 00 2023-12-27 18:16:10 INFO GTBinnedAnalysis._select_data(): Skipping data selection. 2023-12-27 18:16:10 INFO GTBinnedAnalysis._create_ltcube(): Skipping LT Cube. 2023-12-27 18:16:12 INFO GTBinnedAnalysis._create_expcube(): Skipping gtexpcube. WARNING: FITSFixedWarning: RADECSYS= 'FK5 ' the RADECSYS keyword is deprecated, use RADESYSa. [astropy.wcs.wcs] WARNING: FITSFixedWarning: 'datfix' made the change 'Set DATEREF to '2001-01-01T00:01:04.184' from MJDREF. Set MJD-OBS to 54682.655283 from DATE-OBS. Set MJD-END to 59852.000000 from DATE-END'. [astropy.wcs.wcs] Traceback (most recent call last): File "/home/dell/anaconda3/envs/fermipy/lib/python3.9/site-packages/fermipy/gtanalysis.py", line 5196, in setup self._bexp = Map.read(self.files['bexpmap'], hdu=hpxhduname) File "/home/dell/anaconda3/envs/fermipy/lib/python3.9/site-packages/gammapy/maps/core.py", line 240, in read return Map.from_hdulist( File "/home/dell/anaconda3/envs/fermipy/lib/python3.9/site-packages/gammapy/maps/core.py", line 308, in from_hdulist map_type = Map._get_map_type(hdulist, hdu) File "/home/dell/anaconda3/envs/fermipy/lib/python3.9/site-packages/gammapy/maps/core.py", line 339, in _get_map_type header = hdu_list[hdu_name].header File "/home/dell/anaconda3/envs/fermipy/lib/python3.9/site-packages/astropy/io/fits/hdu/hdulist.py", line 390, in getitem super().getitem, self._positive_index_of(key) File "/home/dell/anaconda3/envs/fermipy/lib/python3.9/site-packages/astropy/io/fits/hdu/hdulist.py", line 857, in _positive_index_of index = self.index_of(key) File "/home/dell/anaconda3/envs/fermipy/lib/python3.9/site-packages/astropy/io/fits/hdu/hdulist.py", line 839, in index_of raise KeyError(f"Extension {key!r} not found.") KeyError: "Extension 'HPXEXPOSURES' not found."
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/dell/data backup ubuntu dell mint/Documents/low_z_BLLACs/1ES0647+250/xx.py", line 3, in
How to fix this error?
astroSyvertHE
clodoN1109
Hi, I installed fermipy with mamba. When running gta.setup() an error occurs: 2023-12-23 11:16:42 INFO GTBinnedAnalysis.run_gtapp(): Finished gtexpcube2. Execution time: 1.41 s WARNING: FITSFixedWarning: RADECSYS= 'FK5 ' the RADECSYS keyword is deprecated, use RADESYSa. [astropy.wcs.wcs] WARNING: FITSFixedWarning: 'datfix' made the change 'Set DATEREF to '2001-01-01T00:01:04.184' from MJDREF. Set MJD-OBS to 54769.000000 from DATE-OBS. Set MJD-END to 60278.000000 from DATE-END'. [astropy.wcs.wcs]
The error is:
KeyError Traceback (most recent call last) File ~/miniforge3/envs/fermipy/lib/python3.9/site-packages/fermipy/gtanalysis.py:5196, in GTBinnedAnalysis.setup(self, overwrite, **kwargs) 5195 try: -> 5196 self._bexp = Map.read(self.files['bexpmap'], hdu=hpxhduname) 5197 except KeyError:
File ~/miniforge3/envs/fermipy/lib/python3.9/site-packages/gammapy/maps/core.py:240, in Map.read(filename, hdu, hdu_bands, map_type, format, colname) 239 with fits.open(str(make_path(filename)), memmap=False) as hdulist: --> 240 return Map.from_hdulist( 241 hdulist, hdu, hdu_bands, map_type, format=format, colname=colname 242 )
File ~/miniforge3/envs/fermipy/lib/python3.9/site-packages/gammapy/maps/core.py:308, in Map.from_hdulist(hdulist, hdu, hdu_bands, map_type, format, colname) 307 if map_type == "auto": --> 308 map_type = Map._get_map_type(hdulist, hdu) 309 cls_out = Map._get_map_cls(map_type)
File ~/miniforge3/envs/fermipy/lib/python3.9/site-packages/gammapy/maps/core.py:339, in Map._get_map_type(hdu_list, hdu_name) 338 else: --> 339 header = hdu_list[hdu_name].header 341 if ("PIXTYPE" in header) and (header["PIXTYPE"] == "HEALPIX"):
File ~/miniforge3/envs/fermipy/lib/python3.9/site-packages/astropy/io/fits/hdu/hdulist.py:390, in HDUList.getitem(self, key) 388 try: 389 return self._try_while_unread_hdus( --> 390 super().getitem, self._positive_index_of(key) 391 ) 392 except IndexError as e: 393 # Raise a more helpful IndexError if the file was not fully read.
File ~/miniforge3/envs/fermipy/lib/python3.9/site-packages/astropy/io/fits/hdu/hdulist.py:857, in HDUList._positive_index_of(self, key) 844 """ 845 Same as index_of, but ensures always returning a positive index 846 or zero. (...) 855 inefficient. 856 """ --> 857 index = self.index_of(key) 859 if index >= 0:
File ~/miniforge3/envs/fermipy/lib/python3.9/site-packages/astropy/io/fits/hdu/hdulist.py:839, in HDUList.index_of(self, key) 838 if found is None: --> 839 raise KeyError(f"Extension {key!r} not found.") 840 else:
KeyError: "Extension 'HPXEXPOSURES' not found."
During handling of the above exception, another exception occurred:
ModuleNotFoundError Traceback (most recent call last) Cell In[8], line 1 ----> 1 gta.setup()
File ~/miniforge3/envs/fermipy/lib/python3.9/site-packages/fermipy/gtanalysis.py:1087, in GTAnalysis.setup(self, init_sources, overwrite, **kwargs) 1085 # Run setup for each component 1086 for i, c in enumerate(self.components): -> 1087 c.setup(overwrite=overwrite) 1089 # Create likelihood 1090 self._create_likelihood()
File ~/miniforge3/envs/fermipy/lib/python3.9/site-packages/fermipy/gtanalysis.py:5198, in GTBinnedAnalysis.setup(self, overwrite, **kwargs) 5196 self._bexp = Map.read(self.files['bexpmap'], hdu=hpxhduname) 5197 except KeyError: -> 5198 self._bexp = Map.read(self.files['bexpmap']) 5200 # Write ROI XML 5201 self.roi.write_xml(self.files['srcmdl'], self.config['model'])
File ~/miniforge3/envs/fermipy/lib/python3.9/site-packages/gammapy/maps/core.py:240, in Map.read(filename, hdu, hdu_bands, map_type, format, colname) 213 """Read a map from a FITS file. 214 215 Parameters (...) 237 Map object 238 """ 239 with fits.open(str(make_path(filename)), memmap=False) as hdulist: --> 240 return Map.from_hdulist( 241 hdulist, hdu, hdu_bands, map_type, format=format, colname=colname 242 )
File ~/miniforge3/envs/fermipy/lib/python3.9/site-packages/gammapy/maps/core.py:315, in Map.from_hdulist(hdulist, hdu, hdu_bands, map_type, format, colname) 311 return cls_out.from_hdulist( 312 hdulist, hdu=hdu, hdu_bands=hdu_bands, format=format, colname=colname 313 ) 314 else: --> 315 return cls_out.from_hdulist( 316 hdulist, hdu=hdu, hdu_bands=hdu_bands, format=format 317 )
File ~/miniforge3/envs/fermipy/lib/python3.9/site-packages/gammapy/maps/wcs/core.py:142, in WcsMap.from_hdulist(cls, hdu_list, hdu, hdu_bands, format) 138 hdu_bands = hdu_list[hdu_bands] 140 format = identify_wcs_format(hdu_bands) --> 142 wcs_map = cls.from_hdu(hdu, hdu_bands, format=format) 144 if wcs_map.unit.is_equivalent(""): 145 if format == "fgst-template":
File ~/miniforge3/envs/fermipy/lib/python3.9/site-packages/gammapy/maps/wcs/ndmap.py:88, in WcsNDMap.from_hdu(cls, hdu, hdu_bands, format) 70 @classmethod 71 def from_hdu(cls, hdu, hdu_bands=None, format=None): 72 """Make a WcsNDMap object from a FITS HDU. 73 74 Parameters (...) 86 Wcs map 87 """ ---> 88 geom = WcsGeom.from_header(hdu.header, hdu_bands, format=format) 89 shape = geom.axes.shape 90 shape_wcs = tuple([np.max(geom.npix[0]), np.max(geom.npix[1])])
File ~/miniforge3/envs/fermipy/lib/python3.9/site-packages/gammapy/maps/wcs/geom.py:485, in WcsGeom.from_header(cls, header, hdu_bands, format) 482 # TODO: see https://github.com/astropy/astropy/issues/9259 483 wcs._naxis = wcs._naxis[:2] --> 485 axes = MapAxes.from_table_hdu(hdu_bands, format=format) 486 shape = axes.shape 488 if hdu_bands is not None and "NPIX" in hdu_bands.columns.names:
File ~/miniforge3/envs/fermipy/lib/python3.9/site-packages/gammapy/maps/axes.py:1962, in MapAxes.from_table_hdu(cls, hdu, format) 1959 return cls([]) 1961 table = Table.read(hdu) -> 1962 return cls.from_table(table, format=format)
File ~/miniforge3/envs/fermipy/lib/python3.9/site-packages/gammapy/maps/axes.py:1980, in MapAxes.from_table(cls, table, format) 1964 @classmethod 1965 def from_table(cls, table, format="gadf"): 1966 """Create MapAxes from table 1967 1968 Parameters (...) 1978 Map axes object 1979 """ -> 1980 from gammapy.irf.io import IRF_DL3_AXES_SPECIFICATION 1982 axes = [] 1984 # Formats that support only one energy axis
File ~/miniforge3/envs/fermipy/lib/python3.9/site-packages/gammapy/irf/init.py:6 2 """ 3 Instrument response functions (IRFs). 4 """ 5 from gammapy.utils.registry import Registry ----> 6 from .background import Background2D, Background3D 7 from .core import FoVAlignment, IRFMap 8 from .edisp import EDispKernel, EDispKernelMap, EDispMap, EnergyDispersion2D
File ~/miniforge3/envs/fermipy/lib/python3.9/site-packages/gammapy/irf/background.py:10 8 from gammapy.maps import MapAxes, MapAxis 9 from gammapy.maps.axes import UNIT_STRING_FORMAT ---> 10 from .core import IRF 11 from .io import gadf_is_pointlike 13 all = ["Background3D", "Background2D"]
File ~/miniforge3/envs/fermipy/lib/python3.9/site-packages/gammapy/irf/core.py:17 12 from gammapy.utils.interpolation import ( 13 ScaledRegularGridInterpolator, 14 interpolation_scale, 15 ) 16 from gammapy.utils.scripts import make_path ---> 17 from .io import IRF_DL3_HDU_SPECIFICATION, IRF_MAP_HDU_SPECIFICATION, gadf_is_pointlike 19 log = logging.getLogger(name) 22 class FoVAlignment(str, Enum):
File ~/miniforge3/envs/fermipy/lib/python3.9/site-packages/gammapy/irf/io.py:4 2 import logging 3 from astropy.io import fits ----> 4 from gammapy.data.hdu_index_table import HDUIndexTable 5 from gammapy.utils.deprecation import deprecated 6 from gammapy.utils.fits import HDULocation
File ~/miniforge3/envs/fermipy/lib/python3.9/site-packages/gammapy/data/init.py:3 1 # Licensed under a 3-clause BSD style license - see LICENSE.rst 2 """Data and observation handling.""" ----> 3 from .data_store import DataStore 4 from .event_list import EventList 5 from .filters import ObservationFilter
File ~/miniforge3/envs/fermipy/lib/python3.9/site-packages/gammapy/data/data_store.py:15 13 from .hdu_index_table import HDUIndexTable 14 from .obs_table import ObservationTable, ObservationTableChecker ---> 15 from .observations import Observation, ObservationChecker, Observations 17 all = ["DataStore"] 19 ALL_IRFS = ["aeff", "edisp", "psf", "bkg", "rad_max"]
File ~/miniforge3/envs/fermipy/lib/python3.9/site-packages/gammapy/data/observations.py:22 20 from gammapy.utils.testing import Checker 21 from gammapy.utils.time import time_ref_to_dict, time_relative_to_ref ---> 22 from .event_list import EventList, EventListChecker 23 from .filters import ObservationFilter 24 from .gti import GTI
File ~/miniforge3/envs/fermipy/lib/python3.9/site-packages/gammapy/data/event_list.py:8 6 from astropy import units as u 7 from astropy.coordinates import AltAz, Angle, SkyCoord ----> 8 from astropy.coordinates.angle_utilities import angular_separation 9 from astropy.io import fits 10 from astropy.table import Table
ModuleNotFoundError: No module named 'astropy.coordinates.angle_utilities'
I noted that this module is in python2. I'm running the code in jupyterlab with python2, but with the command !which python the output is python3.9.
How can I solve that? Thank you very much for your help!
Best,
sofiav