noao.twodspec.apextract.apall TYPEERROR

[yunyi302]

I am utilizing IRAF version 2.16.1 and PyRAF version 2.1.15, with Python version 3.8.5.
Upon executing the apall function to extract 1D spectra in Python, such as iraf.apall(input='cbfztLS20221027_000256.fits'),
I encountered an error message stating 'TypeError: 'float' object is not callable'.
What steps can I take to resolve this issue?

[olebole]

The versions you use are long out of date: you should update PyRAF to 2.2.2 and possibly IRAF to 2.18. Most probably it is PyRAF that has a problem here. If the error persists after upgrading PyRAF, please post the full stacktrace, not just the message itself.

Keep in mind that also Python 3.8.x will reach its end of life in October 2024.

[yunyi302]

Ok thanks! I'll check it right now.

[yunyi302]

Even after updating IRAF to version 2.18 and PyRAF to version 2.2.2 (Python version 3.12.3),
I continue to encounter the same error message.
The full stack trace is provided below for reference.

TypeError                                 Traceback (most recent call last)
Cell In[12], line 1
----> 1 apall(imlist_name='cbfzt*.fits', dispaxis=2, linee='1000', backgro='none', interactive='yes')
      2 #parameters at second row are used in background extraction (backgro='none')
      3 #parameters at fourth row are tracing parameters
      4 #parameters at fifth row are DEFAULT APERTURE PARAMETERS
      5 #parameters at sixth row are PROCESSING PARAMETERS

Cell In[11], line 59, in apall(imlist_name, dispaxis, linee, backgro, interactive)
     57     inim = imlist[i]
     58     print('1d extraction for '+inim+'...')
---> 59     iraf.apall(input=inim, apertures='', interactive=interactive, find='yes', \
     60                b_funct='legendre', b_order=15, b_sample="-20:-16,16:20", b_niter=3, \
     61                backgro=backgro, weight="variance", clean='yes', gain=2.3, extras='yes', extract='yes', readnoi=9.3, \
     62                t_function="legendre", t_order=5, t_niterate=3, t_low_reject = 3, t_high_reject = 3., \
     63                lower=-3, upper=3,\
     64                nsum=5, line=linee )   
     65 print('Done.')

File ~/anaconda3/envs/py312/lib/python3.12/site-packages/pyraf/iraftask.py:834, in IrafTask.__call__(self, *args, **kw)
    833 def __call__(self, *args, **kw):
--> 834     return self.run(*args, **kw)

File ~/anaconda3/envs/py312/lib/python3.12/site-packages/pyraf/iraftask.py:373, in IrafTask.run(self, *args, **kw)
    371 if executionMonitor:
    372     executionMonitor(self)
--> 373 self._run(redirKW, specialKW)
    374 self._updateParList(save)
    375 if Verbose > 1:

File ~/anaconda3/envs/py312/lib/python3.12/site-packages/pyraf/iraftask.py:878, in IrafTask._run(self, redirKW, specialKW)
    873 """Execute task after parameters, I/O redirection are prepared.
    874 
    875 The implementation of this can differ for each type of task.
    876 """
    877 try:
--> 878     irafexecute.IrafExecute(self, iraf.getVarDict(), **redirKW)
    879 except irafexecute.IrafProcessError as value:
    880     raise IrafError("Error running IRAF task " + self._name + "\n" +
    881                     str(value))

File ~/anaconda3/envs/py312/lib/python3.12/site-packages/pyraf/irafexecute.py:338, in IrafExecute(task, envdict, stdin, stdout, stderr, stdgraph)
    336     gki.kernel.pushStdio(None, None, None)
    337 try:
--> 338     irafprocess.run(task, pstdin=stdin, pstdout=stdout, pstderr=stderr)
    339 finally:
    340     if stdgraph:
    341         # undo graphics redirection

File ~/anaconda3/envs/py312/lib/python3.12/site-packages/pyraf/irafexecute.py:496, in IrafProcess.run(self, task, pstdin, pstdout, pstderr)
    493 self.running = 1
    494 try:
    495     # begin slave mode
--> 496     self.slave()
    497 finally:
    498     self.running = 0

File ~/anaconda3/envs/py312/lib/python3.12/site-packages/pyraf/irafexecute.py:677, in IrafProcess.slave(self)
    673     par_get(mcmd)
    674 elif mcmd is None:
    675     #                   L.log('NO match!:\n'+('='*60+'\n')+msg+'\n'+('='*60))
    676     # Could be any legal CL command.
--> 677     executeClCommand()
    678 else:
    679     # should never get here
    680     #                   L.log("Program bug: uninterpreted message: " + msg)
    681     raise RuntimeError(
    682         f"Program bug: uninterpreted message `{msg}'")

File ~/anaconda3/envs/py312/lib/python3.12/site-packages/pyraf/irafexecute.py:960, in IrafProcess.executeClCommand(self)
    956     self.msg = ""
    957 if not (cmd.find(IPCOUT) >= 0):
    958     # normal case -- execute the CL script code
    959     # redirect I/O (but don't use graphics status line)
--> 960     iraf.clExecute(cmd,
    961                    Stdout=self.default_stdout,
    962                    Stdin=self.default_stdin,
    963                    Stderr=self.default_stderr)
    964 else:
    965     #
    966     # Bizzaro protocol -- redirection to file with special
   (...)
    972     # Just raise an exception if it does not fit my preconceptions.
    973     #
    974     ll = -(len(IPCOUT) + 3)

File ~/anaconda3/envs/py312/lib/python3.12/site-packages/pyraf/iraffunctions.py:3352, in clExecute(s, locals, mode, local_vars_dict, local_vars_list, verbose, **kw)
   3350     exec(codeObject, locals)
   3351     if pycode.vars.proc_name:
-> 3352         exec(pycode.vars.proc_name + "(taskObj=iraf.cl)", locals)
   3353     return code
   3354 finally:

File <string>:1

File <CL script CL1>:12, in string_proc(mode, DOLLARnargs, taskObj)

TypeError: 'clFloat' object is not callable

[olebole]

I can't reproduce this; running the APALL call in a small self-contained script

from pyraf import iraf
from iraf import noao, twodspec, apextract, apall

inim = "pix.fits"  # that is just a copy of dev$pix
interactive = "yes"
backgro = "none"
linee = "1000"

apall(
    input=inim,
    apertures="",
    interactive=interactive,
    find="yes",
    b_funct="legendre",
    b_order=15,
    b_sample="-20:-16,16:20",
    b_niter=3,
    backgro=backgro,
    weight="variance",
    clean="yes",
    gain=2.3,
    extras="yes",
    extract="yes",
    readnoi=9.3,
    t_function="legendre",
    t_order=5,
    t_niterate=3,
    t_low_reject=3,
    t_high_reject=3.0,
    lower=-3,
    upper=3,
    nsum=5,
    line=linee,
)

works for me. I suspect that you have a problem with the parameter file of APALL. Could you remove that (both in your local directory and in ~/.iraf) and re-run?
What could also help is to remove the PyRAF cache which is usually in ~/.iraf/pyraf/clcache.sqlite3.
Otherwise, can you provide a small, self-containing Python script that shows the problem?

[yunyi302]

It seems that removing the aptapall.par files, which appear to have been generated by running IRAF with the command line (cl) rather than through PyRAF, did not resolve the issue.
Additionally, clearing all caches did not provide a solution.
Below is the code.
Even when executing the code you provided, the same error persists.

    imlist_name='cbfztL*.fits'
    dispaxis=2, linee=1111
    backgro='none'
    nteractive='yes'
    iraf.noao()
    iraf.twodspec()
    iraf.apextract(dispaxis=dispaxis)
    imlist = glob.glob(imlist_name); imlist.sort()
    for i in range(len(imlist)):
        inim = imlist[i]
        print('1d extraction for '+inim+'...')
        iraf.apall(input=inim, apertures='', interactive=interactive, find='yes', \
                   b_funct='legendre', b_order=15, b_sample="-20:-16,16:20", b_niter=3, \
                   backgro=backgro, weight="variance", clean='yes', gain=2.3, extras='yes', extract='yes', readnoi=9.3, \
                   t_function="legendre", t_order=5, t_niterate=3, t_low_reject = 3, t_high_reject = 3., \
                   lower=-3, upper=3,\
                   nsum=5, line=linee )   
    print('Done.')

[olebole]

I must say that I then don't have an idea; specifically because it works for me.

If you want to further debug, you could edit the file pyraf/iraffunctions.py (in conda, where the error appears) and replace the line 3352

            exec(pycode.vars.proc_name + "(taskObj=iraf.cl)", locals)

with

            try:
                exec(pycode.vars.proc_name + "(taskObj=iraf.cl)", locals)
            except TypeError as e:
                e.add_note(f"While executing\n\n{code}")
                raise

resp., as a diff

--- a/pyraf/iraffunctions.py
+++ b/pyraf/iraffunctions.py
@@ -3349,7 +3349,11 @@ def clExecute(s,
             locals = {}
         exec(codeObject, locals)
         if pycode.vars.proc_name:
-            exec(pycode.vars.proc_name + "(taskObj=iraf.cl)", locals)
+            try:
+                exec(pycode.vars.proc_name + "(taskObj=iraf.cl)", locals)
+            except TypeError as e:
+                e.add_note(f"While executing\n\n{code}")
+                raise
         return code
     finally:
         _clExecuteCount = _clExecuteCount - 1

This should output the code in question together with the error so that we can see what goes wrong here.