COSMOS LePhare example
The default data for testing LePHARE is the COSMOS dataset.
In this example we use RAIL to run the standard LePHARE COSMOS example.
In this example we use fluxes not magnitudes. In order to use magnitudes you must both update the config and the values.
Note: If you’re interested in running this in pipeline mode, see
15_LePhare_COSMOS.ipynb
in the pipeline_examples/estimation_examples/ folder.
import os
from collections import OrderedDict
import lephare as lp
import matplotlib.pyplot as plt
import numpy as np
from astropy.table import Table
from rail import interactive as ri
LEPHAREDIR is being set to the default cache directory:
/home/runner/.cache/lephare/data
More than 1Gb may be written there.
LEPHAREWORK is being set to the default cache directory:
/home/runner/.cache/lephare/work
Default work cache is already linked.
This is linked to the run directory:
/home/runner/.cache/lephare/runs/20260504T123336
Install FSPS with the following commands:
pip uninstall fsps
git clone --recursive https://github.com/dfm/python-fsps.git
cd python-fsps
python -m pip install .
export SPS_HOME=$(pwd)/src/fsps/libfsps
A module that was compiled using NumPy 1.x cannot be run in
NumPy 2.2.6 as it may crash. To support both 1.x and 2.x
versions of NumPy, modules must be compiled with NumPy 2.0.
Some module may need to rebuild instead e.g. with 'pybind11>=2.12'.
If you are a user of the module, the easiest solution will be to
downgrade to 'numpy<2' or try to upgrade the affected module.
We expect that some modules will need time to support NumPy 2.
Traceback (most recent call last): File "/opt/hostedtoolcache/Python/3.10.20/x64/lib/python3.10/runpy.py", line 196, in _run_module_as_main
return _run_code(code, main_globals, None,
File "/opt/hostedtoolcache/Python/3.10.20/x64/lib/python3.10/runpy.py", line 86, in _run_code
exec(code, run_globals)
File "/opt/hostedtoolcache/Python/3.10.20/x64/lib/python3.10/site-packages/ipykernel_launcher.py", line 18, in <module>
app.launch_new_instance()
File "/opt/hostedtoolcache/Python/3.10.20/x64/lib/python3.10/site-packages/traitlets/config/application.py", line 1075, in launch_instance
app.start()
File "/opt/hostedtoolcache/Python/3.10.20/x64/lib/python3.10/site-packages/ipykernel/kernelapp.py", line 758, in start
self.io_loop.start()
File "/opt/hostedtoolcache/Python/3.10.20/x64/lib/python3.10/site-packages/tornado/platform/asyncio.py", line 211, in start
self.asyncio_loop.run_forever()
File "/opt/hostedtoolcache/Python/3.10.20/x64/lib/python3.10/asyncio/base_events.py", line 603, in run_forever
self._run_once()
File "/opt/hostedtoolcache/Python/3.10.20/x64/lib/python3.10/asyncio/base_events.py", line 1909, in _run_once
handle._run()
File "/opt/hostedtoolcache/Python/3.10.20/x64/lib/python3.10/asyncio/events.py", line 80, in _run
self._context.run(self._callback, *self._args)
File "/opt/hostedtoolcache/Python/3.10.20/x64/lib/python3.10/site-packages/ipykernel/utils.py", line 71, in preserve_context
return await f(*args, **kwargs)
File "/opt/hostedtoolcache/Python/3.10.20/x64/lib/python3.10/site-packages/ipykernel/kernelbase.py", line 621, in shell_main
await self.dispatch_shell(msg, subshell_id=subshell_id)
File "/opt/hostedtoolcache/Python/3.10.20/x64/lib/python3.10/site-packages/ipykernel/kernelbase.py", line 478, in dispatch_shell
await result
File "/opt/hostedtoolcache/Python/3.10.20/x64/lib/python3.10/site-packages/ipykernel/ipkernel.py", line 372, in execute_request
await super().execute_request(stream, ident, parent)
File "/opt/hostedtoolcache/Python/3.10.20/x64/lib/python3.10/site-packages/ipykernel/kernelbase.py", line 834, in execute_request
reply_content = await reply_content
File "/opt/hostedtoolcache/Python/3.10.20/x64/lib/python3.10/site-packages/ipykernel/ipkernel.py", line 464, in do_execute
res = shell.run_cell(
File "/opt/hostedtoolcache/Python/3.10.20/x64/lib/python3.10/site-packages/ipykernel/zmqshell.py", line 663, in run_cell
return super().run_cell(*args, **kwargs)
File "/opt/hostedtoolcache/Python/3.10.20/x64/lib/python3.10/site-packages/IPython/core/interactiveshell.py", line 3077, in run_cell
result = self._run_cell(
File "/opt/hostedtoolcache/Python/3.10.20/x64/lib/python3.10/site-packages/IPython/core/interactiveshell.py", line 3132, in _run_cell
result = runner(coro)
File "/opt/hostedtoolcache/Python/3.10.20/x64/lib/python3.10/site-packages/IPython/core/async_helpers.py", line 128, in _pseudo_sync_runner
coro.send(None)
File "/opt/hostedtoolcache/Python/3.10.20/x64/lib/python3.10/site-packages/IPython/core/interactiveshell.py", line 3336, in run_cell_async
has_raised = await self.run_ast_nodes(code_ast.body, cell_name,
File "/opt/hostedtoolcache/Python/3.10.20/x64/lib/python3.10/site-packages/IPython/core/interactiveshell.py", line 3519, in run_ast_nodes
if await self.run_code(code, result, async_=asy):
File "/opt/hostedtoolcache/Python/3.10.20/x64/lib/python3.10/site-packages/IPython/core/interactiveshell.py", line 3579, in run_code
exec(code_obj, self.user_global_ns, self.user_ns)
File "/tmp/ipykernel_4685/2887657405.py", line 9, in <module>
from rail import interactive as ri
File "/opt/hostedtoolcache/Python/3.10.20/x64/lib/python3.10/site-packages/rail/interactive/__init__.py", line 3, in <module>
from . import calib, creation, estimation, evaluation, tools
File "/opt/hostedtoolcache/Python/3.10.20/x64/lib/python3.10/site-packages/rail/interactive/calib/__init__.py", line 3, in <module>
from rail.utils.interactive.initialize_utils import _initialize_interactive_module
File "/opt/hostedtoolcache/Python/3.10.20/x64/lib/python3.10/site-packages/rail/utils/interactive/initialize_utils.py", line 17, in <module>
from rail.utils.interactive.base_utils import (
File "/opt/hostedtoolcache/Python/3.10.20/x64/lib/python3.10/site-packages/rail/utils/interactive/base_utils.py", line 10, in <module>
rail.stages.import_and_attach_all(silent=True)
File "/opt/hostedtoolcache/Python/3.10.20/x64/lib/python3.10/site-packages/rail/stages/__init__.py", line 74, in import_and_attach_all
RailEnv.import_all_packages(silent=silent)
File "/opt/hostedtoolcache/Python/3.10.20/x64/lib/python3.10/site-packages/rail/core/introspection.py", line 541, in import_all_packages
_imported_module = importlib.import_module(pkg)
File "/opt/hostedtoolcache/Python/3.10.20/x64/lib/python3.10/importlib/__init__.py", line 126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "/opt/hostedtoolcache/Python/3.10.20/x64/lib/python3.10/site-packages/rail/som/__init__.py", line 1, in <module>
from rail.creation.degraders.specz_som import *
File "/opt/hostedtoolcache/Python/3.10.20/x64/lib/python3.10/site-packages/rail/creation/degraders/specz_som.py", line 15, in <module>
from somoclu import Somoclu
File "/opt/hostedtoolcache/Python/3.10.20/x64/lib/python3.10/site-packages/somoclu/__init__.py", line 11, in <module>
from .train import Somoclu
File "/opt/hostedtoolcache/Python/3.10.20/x64/lib/python3.10/site-packages/somoclu/train.py", line 25, in <module>
from .somoclu_wrap import train as wrap_train
File "/opt/hostedtoolcache/Python/3.10.20/x64/lib/python3.10/site-packages/somoclu/somoclu_wrap.py", line 11, in <module>
import _somoclu_wrap
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
File /opt/hostedtoolcache/Python/3.10.20/x64/lib/python3.10/site-packages/numpy/core/_multiarray_umath.py:44, in __getattr__(attr_name)
39 # Also print the message (with traceback). This is because old versions
40 # of NumPy unfortunately set up the import to replace (and hide) the
41 # error. The traceback shouldn't be needed, but e.g. pytest plugins
42 # seem to swallow it and we should be failing anyway...
43 sys.stderr.write(msg + tb_msg)
---> 44 raise ImportError(msg)
46 ret = getattr(_multiarray_umath, attr_name, None)
47 if ret is None:
ImportError:
A module that was compiled using NumPy 1.x cannot be run in
NumPy 2.2.6 as it may crash. To support both 1.x and 2.x
versions of NumPy, modules must be compiled with NumPy 2.0.
Some module may need to rebuild instead e.g. with 'pybind11>=2.12'.
If you are a user of the module, the easiest solution will be to
downgrade to 'numpy<2' or try to upgrade the affected module.
We expect that some modules will need time to support NumPy 2.
Warning: the binary library cannot be imported. You cannot train maps, but you can load and analyze ones that you have already saved.
The problem occurs because either compilation failed when you installed Somoclu or a path is missing from the dependencies when you are trying to import it. Please refer to the documentation to see your options.
Here we load previously created synthetic data
Retrieve all the required filter and template files
lephare_config = lp.default_cosmos_config
# For useable science results you must use a denser redshift grid by commenting out the following line which will revert to the config dz of 0.01.
lephare_config["Z_STEP"] = ".1,0.,7."
nobj = 100 # Increase to run on more objects. Set to -1 to run on all.
lp.data_retrieval.get_auxiliary_data(
keymap=lephare_config,
additional_files=["examples/COSMOS.in", "examples/output.para"],
)
Registry file downloaded and saved as data_registry.txt.
Downloading file 'filt/hsc/gHSC.pb' from 'https://raw.githubusercontent.com/lephare-photoz/lephare-data/main/filt/hsc/gHSC.pb' to '/home/runner/.cache/lephare/data'.
Downloading file 'filt/hsc/iHSC.pb' from 'https://raw.githubusercontent.com/lephare-photoz/lephare-data/main/filt/hsc/iHSC.pb' to '/home/runner/.cache/lephare/data'.
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Created directory: /home/runner/.cache/lephare/data/filt/hsc
Created directory: /home/runner/.cache/lephare/data/filt/cosmos
Created directory: /home/runner/.cache/lephare/data/filt/vista
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bands = lephare_config["FILTER_LIST"].split(",")
len(bands)
30
# For a test lets just look at the first 100 objects
cosmos = Table.read(os.path.join(lp.LEPHAREDIR, "examples/COSMOS.in"), format="ascii")[
:nobj
]
print(f"We will run on {len(cosmos)} objects.")
We will run on 100 objects.
# The example file is in the historical lephare format.
data = OrderedDict()
flux_cols = []
flux_err_cols = []
for n, b in enumerate(bands):
# print(1+2*n,2+2*n)
flux = cosmos[cosmos.colnames[1 + 2 * n]]
flux_err = cosmos[cosmos.colnames[2 + 2 * n]]
data[f"flux_{b}"] = flux
flux_cols.append(f"flux_{b}")
data[f"flux_err_{b}"] = flux_err
flux_err_cols.append(f"flux_err_{b}")
data["redshift"] = np.array(cosmos[cosmos.colnames[-2]])
We use the inform stage to create the library of SEDs with various redshifts, extinction parameters, and reddening values.
lephare_model = ri.estimation.algos.lephare.lephare_informer(
training_data=data,
name="inform_COSMOS",
nondetect_val=np.nan,
hdf5_groupname="",
lephare_config=lephare_config,
bands=flux_cols,
err_bands=flux_err_cols,
ref_band=flux_cols[0],
)["model"]
Inserting handle into data store. input: None, inform_COSMOS
rail_lephare is setting the Z_STEP config to 0.01,0.0,3.0 based on the informer params.
User defined LEPHAREDIR is set. Code runs depend on all required
auxiliary data being present at /home/runner/.cache/lephare/data.
User defined LEPHAREWORK is set. All intermediate files will be written to:
/home/runner/.cache/lephare/runs/inform_COSMOS
# NAME IDENT Lbda_mean Lbeff(Vega) FWHM AB-cor TG-cor VEGA M_sun(AB) CALIB Lb_eff Fac_corr
u_cfht.lowres 1 0.3844 0.3908 0.0538 0.3150 -0.3891 -20.6345 6.0327 0 0.3815 1.0000
u_new.pb 2 0.3690 0.3750 0.0456 0.6195 -0.2745 -20.8527 6.3135 0 0.3668 1.0000
gHSC.pb 3 0.4851 0.4760 0.1194 -0.0860 -0.2458 -20.7272 5.0764 0 0.4780 1.0000
rHSC.pb 4 0.6241 0.6142 0.1539 0.1466 0.2580 -21.5143 4.6523 0 0.6178 1.0000
iHSC.pb 5 0.7716 0.7637 0.1476 0.3942 0.6138 -22.2286 4.5323 0 0.7666 1.0000
zHSC.pb 6 0.8915 0.8907 0.0768 0.5169 0.7625 -22.6733 4.5147 0 0.8903 1.0000
yHSC.pb 7 0.9801 0.9771 0.0797 0.5534 0.7763 -22.9145 4.5081 0 0.9782 1.0000
Y.lowres 8 1.0222 1.0196 0.0919 0.6043 0.8180 -23.0574 4.5130 0 1.0206 1.0000
J.lowres 9 1.2555 1.2481 0.1712 0.9228 -99.0000 -23.8194 4.5638 0 1.2514 1.0000
H.lowres 10 1.6497 1.6352 0.2893 1.3701 -99.0000 -24.8565 4.7045 0 1.6409 1.0000
K.lowres 11 2.1577 2.1435 0.2926 1.8335 -99.0000 -25.9057 5.1316 0 2.1502 1.0000
IB427.lowres 12 0.4264 0.4256 0.0207 -0.1446 -0.4942 -20.4117 5.5152 0 0.4262 1.0000
IB464.lowres 13 0.4636 0.4633 0.0218 -0.1520 -0.3463 -20.5860 5.0658 0 0.4634 1.0000
IB484.lowres 14 0.4851 0.4846 0.0228 -0.0241 -0.1770 -20.8122 4.9880 0 0.4849 1.0000
IB505.lowres 15 0.5064 0.5061 0.0231 -0.0656 -0.1366 -20.8639 4.9423 0 0.5061 1.0000
IB527.lowres 16 0.5262 0.5259 0.0242 -0.0260 -0.0464 -20.9871 4.8937 0 0.5260 1.0000
IB574.lowres 17 0.5766 0.5762 0.0272 0.0657 0.1377 -21.2773 4.7042 0 0.5763 1.0000
IB624.lowres 18 0.6234 0.6230 0.0301 0.1527 0.2768 -21.5339 4.6386 0 0.6232 1.0000
IB679.lowres 19 0.6783 0.6779 0.0336 0.2542 0.4288 -21.8183 4.5709 0 0.6779 1.0000
IB709.lowres 20 0.7075 0.7071 0.0316 0.2982 0.4968 -21.9541 4.5558 0 0.7072 1.0000
IB738.lowres 21 0.7363 0.7358 0.0323 0.3460 0.5577 -22.0886 4.5449 0 0.7360 1.0000
IB767.lowres 22 0.7687 0.7681 0.0364 0.3992 0.6164 -22.2351 4.5243 0 0.7683 1.0000
IB827.lowres 23 0.8246 0.8241 0.0344 0.4891 0.7300 -22.4777 4.5161 0 0.8243 1.0000
NB711.lowres 24 0.7120 0.7119 0.0073 0.3072 0.5084 -21.9774 4.5542 0 0.7120 1.0000
NB816.lowres 25 0.8150 0.8149 0.0120 0.4713 0.7098 -22.4349 4.5154 0 0.8149 1.0000
NB118.lowres 26 1.1909 1.1909 0.0112 0.8376 -99.0000 -23.6250 4.5554 0 1.1909 1.0000
irac_ch1.lowres 27 3.5763 3.5264 0.7411 2.7951 -99.0000 -27.9585 6.0679 1 3.5634 1.0036
irac_ch2.lowres 28 4.5290 4.4609 1.0105 3.2634 -99.0000 -28.9384 6.5680 1 4.5111 1.0040
irac_ch3.lowres 29 5.7873 5.6765 1.3509 3.7537 -99.0000 -29.9581 7.0472 1 5.7592 1.0050
irac_ch4.lowres 30 8.0442 7.7033 2.8394 4.3959 -99.0000 -31.2962 7.6701 1 7.9590 1.0110
#######################################
# It s translating SEDs to binary library #
# with the following options :
# Config file :
# Library type : STAR
# STAR_SED :/home/runner/.cache/lephare/data/sed/STAR/STAR_MOD_ALL.list
# STAR_LIB :LIB_STAR
# STAR_LIB doc:/home/runner/.cache/lephare/runs/inform_COSMOS/lib_bin/LIB_STAR.doc
# STAR_FSCALE :0.0000
#######################################
Number of SED in the list 254
WRONG NUMBER OF ARGUMENTS FOR OPTION MOD_EXTINC
We have 2 instead of 8
Use default value 0,0 for all filters
#######################################
# It s computing the SYNTHETIC MAGNITUDES #
# For Gal/QSO libraries with these OPTIONS #
# with the following options :
# Config file :
# Filter file : filter_cosmos
# Magnitude type : AB
# COSMOLOGY :70.0000,0.3000,0.7000
# STAR_LIB_IN :/home/runner/.cache/lephare/runs/inform_COSMOS/lib_bin/LIB_STAR(.doc & .bin)
# STAR_LIB_OUT :/home/runner/.cache/lephare/runs/inform_COSMOS/lib_mag/STAR_COSMOS(.doc & .bin)
# LIB_ASCII YES
# CREATION_DATE Mon May 4 12:40:22 2026
#############################################
#######################################
# It s translating SEDs to binary library #
# with the following options :
# Config file :
# Library type : GAL
# GAL_SED :/home/runner/.cache/lephare/data/sed/GAL/COSMOS_SED/COSMOS_MOD.list
# GAL_LIB :LIB_CE
# GAL_LIB doc:/home/runner/.cache/lephare/runs/inform_COSMOS/lib_bin/LIB_CE.doc
# GAL_LIB phys:/home/runner/.cache/lephare/runs/inform_COSMOS/lib_bin/LIB_CE.phys
# SEL_AGE :none
# GAL_FSCALE :1.0000
# AGE_RANGE 0.0000 15000000000.0000
#######################################
Number of SED in the list 31
#######################################
# It s computing the SYNTHETIC MAGNITUDES #
# For Gal/QSO libraries with these OPTIONS #
# with the following options :
# Config file :
# Filter file : filter_cosmos
# Magnitude type : AB
# GAL_LIB_IN :/home/runner/.cache/lephare/runs/inform_COSMOS/lib_bin/LIB_CE(.doc & .bin)
# GAL_LIB_OUT :/home/runner/.cache/lephare/runs/inform_COSMOS/lib_mag/CE_COSMOS(.doc & .bin)
# Z_STEP :0.0100 0.0000 3.0000
# COSMOLOGY :70.0000,0.3000,0.7000
# EXTINC_LAW :SMC_prevot.dat SB_calzetti.dat SB_calzetti_bump1.dat SB_calzetti_bump2.dat
# MOD_EXTINC :18 26 26 33 26 33 26 33
# EB_V :0.0000 0.0500 0.1000 0.1500 0.2000 0.2500 0.3000 0.3500 0.4000 0.5000
# EM_LINES EMP_UV
# EM_DISPERSION 0.5000,0.7500,1.0000,1.5000,2.0000,
# LIB_ASCII YES
# CREATION_DATE Mon May 4 12:40:23 2026
#############################################
#######################################
# It s translating SEDs to binary library #
# with the following options :
# Config file :
# Library type : QSO
# QSO_SED :/home/runner/.cache/lephare/data/sed/QSO/SALVATO09/AGN_MOD.list
# QSO_LIB :LIB_QSO
# QSO_LIB doc:/home/runner/.cache/lephare/runs/inform_COSMOS/lib_bin/LIB_QSO.doc
# QSO_FSCALE :1.0000
#######################################
Number of SED in the list 30
#######################################
# It s computing the SYNTHETIC MAGNITUDES #
# For Gal/QSO libraries with these OPTIONS #
# with the following options :
# Config file :
# Filter file : filter_cosmos
# Magnitude type : AB
# QSO_LIB_IN :/home/runner/.cache/lephare/runs/inform_COSMOS/lib_bin/LIB_QSO(.doc & .bin)
# QSO_LIB_OUT :/home/runner/.cache/lephare/runs/inform_COSMOS/lib_mag/QSO_COSMOS(.doc & .bin)
# Z_STEP :0.0100 0.0000 3.0000
# COSMOLOGY :70.0000,0.3000,0.7000
# EXTINC_LAW :SB_calzetti.dat
# MOD_EXTINC :0 1000
# EB_V :0.0000 0.1000 0.2000 0.3000 # LIB_ASCII YES
# CREATION_DATE Mon May 4 12:44:03 2026
#############################################
Using user columns from input table assuming they are in the standard order.
Processing 100 objects with 30 bands
#######################################
# PHOTOMETRIC REDSHIFT with OPTIONS #
# Config file :
# CAT_IN : change_me_to_output_filename_required.ascii
# CAT_OUT : zphot.out
# CAT_LINES : 0 1000000000
# PARA_OUT : /home/runner/.cache/lephare/data/examples/output.para
# INP_TYPE : F
# CAT_FMT[0:MEME 1:MMEE] : 0
# CAT_MAG : AB
# ZPHOTLIB : CE_COSMOS STAR_COSMOS QSO_COSMOS
# FIR_LIB :
# FIR_LMIN : 7.000000
# FIR_CONT : -1.000000
# FIR_SCALE : -1.000000
# FIR_FREESCALE : YES
# FIR_SUBSTELLAR : NO
# ERR_SCALE : 0.020000 0.020000 0.020000 0.020000 0.020000 0.020000 0.020000 0.050000 0.050000 0.050000 0.050000 0.020000 0.020000 0.020000 0.020000 0.020000 0.020000 0.020000 0.020000 0.020000 0.020000 0.020000 0.020000 0.050000 0.050000 0.050000 0.050000 0.100000 0.200000 0.300000
# ERR_FACTOR
: 1.500000
# GLB_CONTEXT : 0
# FORB_CONTEXT : -1
# DZ_WIN : 1.000000
# MIN_THRES : 0.020000
# MAG_ABS : -24.000000 -5.000000
# MAG_ABS_AGN : -30.000000 -10.000000
# MAG_REF : 3
# NZ_PRIOR : -1 -1
# Z_INTERP : YES
# Z_METHOD : BEST
# MABS_METHOD : 1
# MABS_CONTEXT : 33556478
# MABS_REF : 11
# AUTO_ADAPT : NO
# ADAPT_BAND : 5
# ADAPT_LIM : 1.500000 23.000000
# ADAPT_ZBIN : 0.010000 6.000000
# ZFIX : NO
# SPEC_OUT : NO
# CHI_OUT : NO
# PDZ_OUT : test
#######################################
Reading input librairies ...
Read lib
Number of keywords to be read in the doc: 13
Number of keywords read at the command line (excluding -c config): 0
Reading keywords from /home/runner/.cache/lephare/runs/inform_Offsets from auto-adapt: 0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
COSMOS/lib_mag/QSO_COSMOS.doc
Number of keywords read in the config file: 16
Keyword NUMBER_ROWS not provided
Keyword NUMBER_SED not provided
Keyword Z_FORM not provided
Reading library: /home/runner/.cache/lephare/runs/inform_COSMOS/lib_mag/QSO_COSMOS.bin
Done with the library reading with 36120 SED read.
Number of keywords to be read in the doc: 13
Number of keywords read at the command line (excluding -c config): 0
Reading keywords from /home/runner/.cache/lephare/runs/inform_COSMOS/lib_mag/STAR_COSMOS.doc
Number of keywords read in the config file: 16
Keyword NUMBER_ROWS not provided
Keyword NUMBER_SED not provided
Keyword Z_FORM not provided
Reading library: /home/runner/.cache/lephare/runs/inform_COSMOS/lib_mag/STAR_COSMOS.bin
Done with the library reading with 36374 SED read.
Number of keywords to be read in the doc: 13
Number of keywords read at the command line (excluding -c config): 0
Reading keywords from /home/runner/.cache/lephare/runs/inform_COSMOS/lib_mag/CE_COSMOS.doc
Number of keywords read in the config file: 16
Keyword NUMBER_ROWS not provided
Keyword NUMBER_SED not provided
Keyword Z_FORM not provided
Reading library: /home/runner/.cache/lephare/runs/inform_COSMOS/lib_mag/CE_COSMOS.bin
Done with the library reading with 448744 SED read.
Read lib out
Read filt
# NAME IDENT Lbda_mean Lbeff(Vega) FWHM AB-cor VEGA CALIB Fac_corr
u_cfht.lowres 1 0.3844 0.3908 0.0538 0.3150 -20.6300 0 1.0000
u_new.pb 2 0.3690 0.3750 0.0456 0.6195 -20.8500 0 1.0000
gHSC.pb 3 0.4851 0.4760 0.1194 -0.0860 -20.7300 0 1.0000
rHSC.pb 4 0.6241 0.6142 0.1539 0.1466 -21.5100 0 1.0000
iHSC.pb 5 0.7716 0.7637 0.1476 0.3942 -22.2300 0 1.0000
zHSC.pb 6 0.8915 0.8907 0.0768 0.5169 -22.6700 0 1.0000
yHSC.pb 7 0.9801 0.9771 0.0797 0.5534 -22.9100 0 1.0000
Y.lowres 8 1.0220 1.0200 0.0919 0.6043 -23.0600 0 1.0000
J.lowres 9 1.2550 1.2480 0.1712 0.9228 -23.8200 0 1.0000
H.lowres 10 1.6500 1.6350 0.2893 1.3700 -24.8600 0 1.0000
K.lowres 11 2.1580 2.1430 0.2926 1.8330 -25.9100 0 1.0000
IB427.lowres 12 0.4264 0.4256 0.0207 -0.1446 -20.4100 0 1.0000
IB464.lowres 13 0.4636 0.4633 0.0218 -0.1520 -20.5900 0 1.0000
IB484.lowres 14 0.4851 0.4846 0.0228 -0.0241 -20.8100 0 1.0000
IB505.lowres 15 0.5064 0.5061 0.0231 -0.0656 -20.8600 0 1.0000
IB527.lowres 16 0.5262 0.5259 0.0242 -0.0260 -20.9900 0 1.0000
IB574.lowres 17 0.5766 0.5762 0.0272 0.0657 -21.2800 0 1.0000
IB624.lowres 18 0.6234 0.6230 0.0301 0.1527 -21.5300 0 1.0000
IB679.lowres 19 0.6783 0.6779 0.0336 0.2542 -21.8200 0 1.0000
IB709.lowres 20 0.7075 0.7071 0.0316 0.2982 -21.9500 0 1.0000
IB738.lowres 21 0.7363 0.7358 0.0323 0.3460 -22.0900 0 1.0000
IB767.lowres 22 0.7687 0.7681 0.0364 0.3992 -22.2400 0 1.0000
IB827.lowres 23 0.8246 0.8241 0.0344 0.4891 -22.4800 0 1.0000
NB711.lowres 24 0.7120 0.7119 0.0073 0.3072 -21.9800 0 1.0000
NB816.lowres 25 0.8150 0.8149 0.0120 0.4713 -22.4300 0 1.0000
NB118.lowres 26 1.1910 1.1910 0.0112 0.8376 -23.6200 0 1.0000
irac_ch1.lowres 27 3.5760 3.5260 0.7411 2.7950 -27.9600 1 1.0040
irac_ch2.lowres 28 4.5290 4.4610 1.0100 3.2630 -28.9400 1 1.0040
irac_ch3.lowres 29 5.7870 5.6760 1.3510 3.7540 -29.9600 1 1.0050
irac_ch4.lowres 30 8.0440 7.7030 2.8390 4.3960 -31.3000 1 1.0110
Inserting handle into data store. model_inform_COSMOS: inprogress_model_inform_COSMOS.pkl, inform_COSMOS
Now we take the sythetic test data, and find the best fits from the library. This results in a PDF, zmode, and zmean for each input test data.
lephare_estimated = ri.estimation.algos.lephare.lephare_estimator(
input_data=data,
name="test_Lephare_COSMOS",
nondetect_val=np.nan,
model=lephare_model,
hdf5_groupname="",
aliases=dict(input="test_data", output="lephare_estim"),
bands=flux_cols,
err_bands=flux_err_cols,
ref_band=flux_cols[0],
)["output"]
Inserting handle into data store. test_data: None, test_Lephare_COSMOS
Inserting handle into data store. model: {'lephare_version': '0.3.1', 'lephare_config': {'ADAPT_BAND': '5', 'ADAPT_CONTEXT': '-1', 'ADAPT_LIM': '1.5,23.0', 'ADAPT_MODBIN': '1,1000', 'ADAPT_ZBIN': '0.01,6', 'ADDITIONAL_MAG': 'none', 'ADD_DUSTEM': 'NO', 'ADD_EMLINES': '0,10000', 'AGE_RANGE': '0.,15.e9', 'AUTO_ADAPT': 'NO', 'CAT_FMT': 'MEME', 'CAT_IN': 'change_me_to_output_filename_required.ascii', 'CAT_LINES': '0,1000000000', 'CAT_MAG': 'AB', 'CAT_OUT': 'zphot.out', 'CAT_TYPE': 'LONG', 'CHI2_OUT': 'NO', 'COSMOLOGY': '70,0.3,0.7', 'DZ_WIN': '1.0', 'EBV_RANGE': '0,9', 'EB_V': '0.,0.05,0.1,0.15,0.2,0.25,0.3,0.35,0.4,0.5', 'EM_DISPERSION': '0.5,0.75,1.,1.5,2.', 'EM_LINES': 'EMP_UV', 'ERR_FACTOR': '1.5', 'ERR_SCALE': '0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.05,0.05,0.05,0.05,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.05,0.05,0.05,0.05,0.1,0.2,0.3', 'EXTERNALZ_FILE': 'NONE', 'EXTINC_LAW': 'SMC_prevot.dat,SB_calzetti.dat,SB_calzetti_bump1.dat,SB_calzetti_bump2.dat', 'FILTER_CALIB': '0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,1,1', 'FILTER_FILE': 'filter_cosmos', 'FILTER_LIST': 'cosmos/u_cfht.lowres,cosmos/u_new.pb,hsc/gHSC.pb,hsc/rHSC.pb,hsc/iHSC.pb,hsc/zHSC.pb,hsc/yHSC.pb,vista/Y.lowres,vista/J.lowres,vista/H.lowres,vista/K.lowres,cosmos/IB427.lowres,cosmos/IB464.lowres,cosmos/IB484.lowres,cosmos/IB505.lowres,cosmos/IB527.lowres,cosmos/IB574.lowres,cosmos/IB624.lowres,cosmos/IB679.lowres,cosmos/IB709.lowres,cosmos/IB738.lowres,cosmos/IB767.lowres,cosmos/IB827.lowres,cosmos/NB711.lowres,cosmos/NB816.lowres,vista/NB118.lowres,cosmos/irac_ch1.lowres,cosmos/irac_ch2.lowres,cosmos/irac_ch3.lowres,cosmos/irac_ch4.lowres', 'FILTER_REP': '/home/runner/.cache/lephare/data/filt', 'FIR_CONT': '-1', 'FIR_FREESCALE': 'YES', 'FIR_LIB': 'NONE', 'FIR_LMIN': '7.0', 'FIR_SCALE': '-1', 'FIR_SUBSTELLAR': 'NO', 'FORB_CONTEXT': '-1', 'GAL_FSCALE': '1.', 'GAL_LIB': 'LIB_CE', 'GAL_LIB_IN': 'LIB_CE', 'GAL_LIB_OUT': 'CE_COSMOS', 'GAL_SED': '/home/runner/.cache/lephare/data/sed/GAL/COSMOS_SED/COSMOS_MOD.list', 'GLB_CONTEXT': '0', 'INP_TYPE': 'F', 'LIB_ASCII': 'NO', 'LIMITS_MAPP_CUT': '90', 'LIMITS_MAPP_REF': '1', 'LIMITS_MAPP_SEL': '1', 'LIMITS_ZBIN': '0,99', 'MABS_CONTEXT': '33556478', 'MABS_FILT': '1,2,3,4', 'MABS_METHOD': '1', 'MABS_REF': '11', 'MABS_ZBIN': '0,0.5,2,4,6', 'MAGTYPE': 'AB', 'MAG_ABS': '-24,-5', 'MAG_ABS_QSO': '-30,-10', 'MAG_REF': '3', 'MIN_THRES': '0.02', 'MOD_EXTINC': '0,0', 'PARA_OUT': '/home/runner/.cache/lephare/data/examples/output.para', 'PDZ_OUT': 'test', 'PDZ_TYPE': 'BAY_ZG', 'QSO_FSCALE': '1.', 'QSO_LIB': 'LIB_QSO', 'QSO_LIB_IN': 'LIB_QSO', 'QSO_LIB_OUT': 'QSO_COSMOS', 'QSO_SED': '/home/runner/.cache/lephare/data/sed/QSO/SALVATO09/AGN_MOD.list', 'RF_COLORS': '32,4,4,13', 'RM_DISCREPANT_BD': '500', 'SPEC_OUT': 'NO', 'STAR_FSCALE': '3.432E-09', 'STAR_LIB': 'LIB_STAR', 'STAR_LIB_IN': 'LIB_STAR', 'STAR_LIB_OUT': 'STAR_COSMOS', 'STAR_SED': '/home/runner/.cache/lephare/data/sed/STAR/STAR_MOD_ALL.list', 'TRANS_TYPE': '1', 'VERBOSE': 'NO', 'ZFIX': 'NO', 'ZGRID_TYPE': '0', 'ZPHOTLIB': 'CE_COSMOS,STAR_COSMOS,QSO_COSMOS', 'Z_INTERP': 'YES', 'Z_METHOD': 'BEST', 'Z_RANGE': '0.,99.99', 'Z_STEP': '0.01,0.0,3.0'}, 'offsets': [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], 'run_dir': '/home/runner/.cache/lephare/runs/inform_COSMOS', 'star_config': {'LIB_ASCII': 'YES'}, 'gal_config': {'LIB_ASCII': 'YES', 'MOD_EXTINC': '18,26,26,33,26,33,26,33', 'EXTINC_LAW': 'SMC_prevot.dat,SB_calzetti.dat,SB_calzetti_bump1.dat,SB_calzetti_bump2.dat', 'EM_LINES': 'EMP_UV', 'EM_DISPERSION': '0.5,0.75,1.,1.5,2.'}, 'qso_config': {'LIB_ASCII': 'YES', 'MOD_EXTINC': '0,1000', 'EB_V': '0.,0.1,0.2,0.3', 'EXTINC_LAW': 'SB_calzetti.dat'}}, test_Lephare_COSMOS
User defined LEPHAREDIR is set. Code runs depend on all required
auxiliary data being present at /home/runner/.cache/lephare/data.
User defined LEPHAREWORK is set. All intermediate files will be written to:
/home/runner/.cache/lephare/runs/inform_COSMOS
Process 0 running estimator on chunk 0 - 100
Using user columns from input table assuming they are in the standard order.
Processing 100 objects with 30 bands
#######################################
# PHOTOMETRIC REDSHIFT with OPTIONS #
# Config file :
# CAT_IN : change_me_to_output_filename_required.ascii
# CAT_OUT : zphot.out
# CAT_LINES : 0 1000000000
# PARA_OUT : /home/runner/.cache/lephare/data/examples/output.para
# INP_TYPE : F
# CAT_FMT[0:MEME 1:MMEE] : 0
# CAT_MAG : AB
# ZPHOTLIB : CE_COSMOS STAR_COSMOS QSO_COSMOS
# FIR_LIB :
# FIR_LMIN : 7.000000
# FIR_CONT : -1.000000
# FIR_SCALE : -1.000000
# FIR_FREESCALE : YES
# FIR_SUBSTELLAR : NO
# ERR_SCALE : 0.020000 0.020000 0.020000 0.020000 0.020000 0.020000 0.020000 0.050000 0.050000 0.050000 0.050000 0.020000 0.020000 0.020000 0.020000 0.020000 0.020000 0.020000 0.020000 0.020000 0.020000 0.020000 0.020000 0.050000 0.050000 0.050000 0.050000 0.100000 0.200000 0.300000
# ERR_FACTOR
AUTO_ADAPT is set to YES. Computing offsets. : 1.500000
# GLB_CONTEXT : 0
# FORB_CONTEXT : -1
# DZ_WIN : 1.000000
# MIN_THRES : 0.020000
# MAG_ABS : -24.000000 -5.000000
# MAG_ABS_AGN : -30.000000 -10.000000
# MAG_REF : 3
# NZ_PRIOR : -1 -1
# Z_INTERP : YES
# Z_METHOD : BEST
# MABS_METHOD : 1
# MABS_CONTEXT : 33556478
# MABS_REF : 11
# AUTO_ADAPT : NO
# ADAPT_BAND : 5
# ADAPT_LIM : 1.500000 23.000000
# ADAPT_ZBIN : 0.010000 6.000000
# ZFIX : NO
# SPEC_OUT : NO
# CHI_OUT : NO
# PDZ_OUT : test
#######################################
Reading input librairies ...
Read lib
Number of keywords to be read in the doc: 13
Number of keywords read at the command line (excluding -c config): 0
Reading keywords from /home/runner/.cache/lephare/runs/inform_
# Offsets added to the modeled magnitudes (or substracted to the observed): 0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
COSMOS/lib_mag/QSO_COSMOS.doc
Number of keywords read in the config file: 16
Keyword NUMBER_ROWS not provided
Keyword NUMBER_SED not provided
Keyword Z_FORM not provided
Reading library: /home/runner/.cache/lephare/runs/inform_COSMOS/lib_mag/QSO_COSMOS.bin
Done with the library reading with 36120 SED read.
Number of keywords to be read in the doc: 13
Number of keywords read at the command line (excluding -c config): 0
Reading keywords from /home/runner/.cache/lephare/runs/inform_COSMOS/lib_mag/STAR_COSMOS.doc
Number of keywords read in the config file: 16
Keyword NUMBER_ROWS not provided
Keyword NUMBER_SED not provided
Keyword Z_FORM not provided
Reading library: /home/runner/.cache/lephare/runs/inform_COSMOS/lib_mag/STAR_COSMOS.bin
Done with the library reading with 36374 SED read.
Number of keywords to be read in the doc: 13
Number of keywords read at the command line (excluding -c config): 0
Reading keywords from /home/runner/.cache/lephare/runs/inform_COSMOS/lib_mag/CE_COSMOS.doc
Number of keywords read in the config file: 16
Keyword NUMBER_ROWS not provided
Keyword NUMBER_SED not provided
Keyword Z_FORM not provided
Reading library: /home/runner/.cache/lephare/runs/inform_COSMOS/lib_mag/CE_COSMOS.bin
Done with the library reading with 448744 SED read.
Read lib out
Read filt
# NAME IDENT Lbda_mean Lbeff(Vega) FWHM AB-cor VEGA CALIB Fac_corr
u_cfht.lowres 1 0.3844 0.3908 0.0538 0.3150 -20.6300 0 1.0000
u_new.pb 2 0.3690 0.3750 0.0456 0.6195 -20.8500 0 1.0000
gHSC.pb 3 0.4851 0.4760 0.1194 -0.0860 -20.7300 0 1.0000
rHSC.pb 4 0.6241 0.6142 0.1539 0.1466 -21.5100 0 1.0000
iHSC.pb 5 0.7716 0.7637 0.1476 0.3942 -22.2300 0
1.0000
zHSC.pb 6 0.8915 0.8907 0.0768 0.5169 -22.6700 0 1.0000
yHSC.pb 7 0.9801 0.9771 0.0797 0.5534 -22.9100 0 1.0000
Y.lowres 8 1.0220 1.0200 0.0919 0.6043 -23.0600 0 1.0000
J.lowres 9 1.2550 1.2480 0.1712 0.9228 -23.8200 0 1.0000
H.lowres 10 1.6500 1.6350 0.2893 1.3700 -24.8600 0 1.0000
K.lowres 11 2.1580 2.1430 0.2926 1.8330 -25.9100 0 1.0000
IB427.lowres 12 0.4264 0.4256 0.0207 -0.1446 -20.4100 0 1.0000
IB464.lowres 13 0.4636 0.4633 0.0218 -0.1520 -20.5900 0 1.0000
IB484.lowres 14 0.4851 0.4846 0.0228 -0.0241 -20.8100 0 1.0000
IB505.lowres 15 0.5064 0.5061 0.0231 -0.0656 -20.8600 0 1.0000
IB527.lowres 16 0.5262 0.5259 0.0242 -0.0260 -20.9900 0 1.0000
IB574.lowres 17 0.5766 0.5762 0.0272 0.0657 -21.2800 0 1.0000
IB624.lowres 18 0.6234 0.6230 0.0301 0.1527 -21.5300 0 1.0000
IB679.lowres 19 0.6783 0.6779 0.0336 0.2542 -21.8200 0 1.0000
IB709.lowres 20 0.7075 0.7071 0.0316 0.2982 -21.9500 0 1.0000
IB738.lowres 21 0.7363 0.7358 0.0323 0.3460 -22.0900 0 1.0000
IB767.lowres 22 0.7687 0.7681 0.0364 0.3992 -22.2400 0 1.0000
IB827.lowres 23 0.8246 0.8241 0.0344 0.4891 -22.4800 0 1.0000
NB711.lowres 24 0.7120 0.7119 0.0073 0.3072 -21.9800 0 1.0000
NB816.lowres 25 0.8150 0.8149 0.0120 0.4713 -22.4300 0 1.0000
NB118.lowres 26 1.1910 1.1910 0.0112 0.8376 -23.6200 0 1.0000
irac_ch1.lowres 27 3.5760 3.5260 0.7411 2.7950 -27.9600 1 1.0040
irac_ch2.lowres 28 4.5290 4.4610 1.0100 3.2630 -28.9400 1 1.0040
irac_ch3.lowres 29 5.7870 5.6760 1.3510 3.7540 -29.9600 1 1.0050
irac_ch4.lowres 30 8.0440 7.7030 2.8390 4.3960 -31.3000 1 1.0110
Inserting handle into data store. output_test_Lephare_COSMOS: inprogress_output_test_Lephare_COSMOS.hdf5, test_Lephare_COSMOS
lephare_config["AUTO_ADAPT"]
'NO'
An example lephare PDF and comparison to the true value
indx = 1
zgrid = np.linspace(0, 7, 1000)
plt.plot(zgrid, np.squeeze(lephare_estimated[indx].pdf(zgrid)), label="Estimated PDF")
plt.axvline(x=data["redshift"][indx], color="r", label="True redshift")
plt.legend()
plt.xlabel("z")
plt.show()
More example fits
indxs = [8, 16, 32, 64, 65, 66, 68, 69] # , 128, 256, 512, 1024]
zgrid = np.linspace(0, 7, 1000)
fig, axs = plt.subplots(2, 4, figsize=(20, 6))
for i, indx in enumerate(indxs):
ax = axs[i // 4, i % 4]
ax.plot(
zgrid,
np.squeeze(lephare_estimated[indx].pdf(zgrid)),
label="Estimated PDF",
)
ax.axvline(x=data["redshift"][indx], color="r", label="True redshift")
ax.set_xlabel("z")
Histogram of the absolute difference between lephare estimate and true redshift
estimate_diff_from_truth = np.abs(lephare_estimated.ancil["zmode"] - data["redshift"])
plt.figure()
plt.hist(estimate_diff_from_truth, 100)
plt.xlabel("abs(z_estimated - z_true)")
plt.show()
plt.scatter(data["redshift"], lephare_estimated.ancil["Z_BEST"])
plt.xlabel("$z_{spec}$")
plt.ylabel("$z_{LePHARE}$")
Text(0, 0.5, '$z_{LePHARE}$')
plt.scatter(data["redshift"], lephare_estimated.ancil["zmean"])
plt.xlabel("$z_{spec}$")
plt.ylabel("$z_{LePHARE}$")
Text(0, 0.5, '$z_{LePHARE}$')
