Merge pull request #1487 from DavidT3/refine/moveXSPECNumChanCheck

Moved the XSPEC template script's check for a minimum number of noticed channels to before model declaration

Author: DavidT3

xga/__init__.py

@@ -1,10 +1,10 @@
 #  This code is a part of X-ray: Generate and Analyse (XGA), a module designed for the XMM Cluster Survey (XCS).
-#  Last modified by David J Turner (turne540@msu.edu) 16/07/2025, 12:25. Copyright (c) The Contributors
+#  Last modified by David J Turner (turne540@msu.edu) 09/12/2025, 15:20. Copyright (c) The Contributors
 from . import _version
 __version__ = _version.get_versions()['version']
 
 from .utils import (xga_conf, CENSUS, OUTPUT, NUM_CORES, XGA_EXTRACT, BASE_XSPEC_SCRIPT, MODEL_PARS,
-    MODEL_UNITS, ABUND_TABLES, XSPEC_FIT_METHOD, COUNTRATE_CONV_SCRIPT, NHC, BLACKLIST, HY_MASS, MEAN_MOL_WEIGHT,
-    SAS_VERSION, XSPEC_VERSION, SAS_AVAIL, DEFAULT_COSMO, TELESCOPES, USABLE, DEFAULT_TELE_SEARCH_DIST, COMBINED_INSTS,
-    eSASS_AVAIL, SRC_REGION_COLOURS, check_telescope_choices, PRETTY_TELESCOPE_NAMES, CIAO_AVAIL, CIAO_VERSION, CALDB_AVAIL,
-    CALDB_VERSION, ESASS_VERSION, RAD_MATCH_PRECISION)
+                    MODEL_UNITS, ABUND_TABLES, XSPEC_FIT_METHOD, COUNTRATE_CONV_SCRIPT, NHC, BLACKLIST, HY_MASS, MEAN_MOL_WEIGHT,
+                    SAS_VERSION, XSPEC_VERSION, SAS_AVAIL, DEFAULT_COSMO, TELESCOPES, USABLE, DEFAULT_TELE_SEARCH_DIST, COMBINED_INSTS,
+                    ESASS_AVAIL, SRC_REGION_COLOURS, check_telescope_choices, PRETTY_TELESCOPE_NAMES, CIAO_AVAIL, CIAO_VERSION, CALDB_AVAIL,
+                    CALDB_VERSION, ESASS_VERSION, RAD_MATCH_PRECISION)

xga/generate/ciao/spec.py

@@ -1,5 +1,5 @@
 #  This code is a part of X-ray: Generate and Analyse (XGA), a module designed for the XMM Cluster Survey (XCS).
-#  Last modified by David J Turner (turne540@msu.edu) 26/03/2025, 10:57. Copyright (c) The Contributors
+#  Last modified by David J Turner (turne540@msu.edu) 09/12/2025, 10:36. Copyright (c) The Contributors
 
 import os
 from copy import copy
@@ -46,6 +46,15 @@ def _chandra_spec_cmds(sources: Union[BaseSource, BaseSample], outer_radius: Uni
     :param bool force_gen: This boolean flag will force the regeneration of spectra, even if they already exist.
     """
 
+    # Early XGA could generate spectra within the detection regions of the source, but
+    #  that has been deprecated for quite a while, as it was a bad idea. The generation
+    #  of spectra within user-specified regions will be possible, but it will be
+    #  implemented differently. The original way was bad because the detection region
+    #  could/almost certainly would be different for each observation
+    if outer_radius == 'region':
+        raise ValueError("The string 'region' is no longer a valid option for "
+                         "the 'outer_radius' argument.")
+
     stack = False  # This tells the ciao_call routine that this command won't be part of a stack.
     execute = True  # This should be executed immediately.
     # This function supports passing both individual sources and samples - but if it is a source we like to be able

xga/generate/common.py

@@ -1,5 +1,5 @@
 #  This code is a part of X-ray: Generate and Analyse (XGA), a module designed for the XMM Cluster Survey (XCS).
-#  Last modified by David J Turner (turne540@msu.edu) 08/07/2025, 17:26. Copyright (c) The Contributors
+#  Last modified by David J Turner (turne540@msu.edu) 09/12/2025, 10:39. Copyright (c) The Contributors
 
 import os
 import sys
@@ -45,10 +45,27 @@ def execute_cmd(cmd: str, p_type: Union[str, List[str]], p_path: list, extra_inf
         if "DYLD_LIBRARY_PATH" in sys_env:
             cmd = f"export DYLD_LIBRARY_PATH={sys_env['DYLD_LIBRARY_PATH']} && {cmd}"
 
+    # This runs the passed command - it captures the stdout and stderr as well
     out, err = Popen(cmd, shell=True, stdout=PIPE, stderr=PIPE).communicate()
+    # Captured out/err are byte type, will decode that into str for easier use
     out = out.decode("UTF-8", errors='ignore')
     err = err.decode("UTF-8", errors='ignore')
 
+    # We will assume that the first entry in the product path argument is the
+    #  primary output file, and will name the log files after it
+    log_stem = p_path[0][:p_path[0].rfind('.')]
+    # One file for out and one for error
+    std_out_file = log_stem + "_stdout.log"
+    std_err_file = log_stem + "_stderr.log"
+
+    # Write the standard out to a log file
+    with open(std_out_file, "w") as std_outo:
+        std_outo.write(cmd + "\n\n" + out)
+    # If there are standard error entries, write them to a file as well
+    if len(err) > 0:
+        with open(std_err_file, "w") as std_erro:
+            std_erro.write(cmd + "\n\n" + err)
+
     # Trying to make sure that any passed arrays get smoothed out into the list type we want
     if type(p_path) == np.ndarray:
         p_path = list(p_path)

xga/generate/esass/_common.py

@@ -0,0 +1,7 @@
+#  This code is a part of X-ray: Generate and Analyse (XGA), a module designed for the XMM Cluster Survey (XCS).
+#  Last modified by David J Turner (turne540@msu.edu) 09/12/2025, 11:57. Copyright (c) The Contributors
+
+from astropy.units import Quantity
+
+EROSITA_EXTMAP_LO_EN = Quantity(0.2, 'keV')
+EROSITA_EXTMAP_HI_EN = Quantity(10.0, 'keV')

xga/generate/esass/lightcurve.py

@@ -1,5 +1,5 @@
 #  This code is a part of X-ray: Generate and Analyse (XGA), a module designed for the XMM Cluster Survey (XCS).
-#  Last modified by David J Turner (turne540@msu.edu) 03/07/2025, 10:55. Copyright (c) The Contributors
+#  Last modified by David J Turner (turne540@msu.edu) 09/12/2025, 10:36. Copyright (c) The Contributors
 
 import os
 from copy import deepcopy
@@ -191,6 +191,15 @@ def _append_lc_info(evt_list):
                             "hi_en": hi_en,
                             "telescope": 'erosita'})
 
+    # Early XGA could generate spectra within the detection regions of the source, but
+    #  that has been deprecated for quite a while, as it was a bad idea. The generation
+    #  of spectra within user-specified regions will be possible, but it will be
+    #  implemented differently. The original way was bad because the detection region
+    #  could/almost certainly would be different for each observation
+    if outer_radius == 'region':
+        raise ValueError("The string 'region' is no longer a valid option for "
+                         "the 'outer_radius' argument.")
+
     # We check to see whether there is an eROSITA entry in the 'telescopes' property. If sources is a Source
     #  object, then that property contains the telescopes associated with that source, and if it is a Sample object
     #  then 'telescopes' contains the list of unique telescopes that are associated with at least one member source.

xga/generate/esass/run.py

@@ -1,5 +1,5 @@
 #  This code is a part of X-ray: Generate and Analyse (XGA), a module designed for the XMM Cluster Survey (XCS).
-#  Last modified by David J Turner (turne540@msu.edu) 08/07/2025, 10:05. Copyright (c) The Contributors
+#  Last modified by David J Turner (turne540@msu.edu) 09/12/2025, 15:20. Copyright (c) The Contributors
 
 from functools import wraps
 from multiprocessing.dummy import Pool
@@ -9,7 +9,7 @@
 from tqdm import tqdm
 
 from ..common import execute_cmd
-from ... import eSASS_AVAIL
+from ... import ESASS_AVAIL
 from ...exceptions import eSASSNotFoundError, ProductGenerationError
 from ...products import BaseProduct, AnnularSpectra
 from ...samples.base import BaseSample
@@ -27,7 +27,7 @@ def esass_call(esass_func):
     @wraps(esass_func)
     def wrapper(*args, **kwargs):
         # Checking eSASS is installed and available on the system
-        if not eSASS_AVAIL:
+        if not ESASS_AVAIL:
             raise eSASSNotFoundError("No eSASS installation has been found on this machine.")
 
         # The first argument of all of these eSASS functions will be the source object (or a list of),