running LineRatioFit with measurements as a dict gives error

[Aaron Bryant]

Hi Marc,

using version 2.3.0

if I put measurements into LineRatioFit as a dictionary, with keys as line identifiers, when doing lrf.run() I get an Attribute Error. See below for comparison with measurements as a list, which works fine:

type(meas_list), type(meas_dict)
Out[35]: (list, dict)

lrf_list = LineRatioFit(ms, measurements = meas_list)

lrf_dict = LineRatioFit(ms, measurements = meas_dict)

lrf_list.run()
0%| | 0/8118 [00:00<?, ?it/s]
fitted 6949 of 8118 pixels
got 0 exceptions

lrf_dict.run()
Traceback (most recent call last):

Input In [39] in <cell line: 1>
lrf_dict.run()

File C:\ProgramData\Anaconda3\lib\site-packages\pdrtpy\tool\lineratiofit.py:387 in run
self._reset_masks()

File C:\ProgramData\Anaconda3\lib\site-packages\pdrtpy\tool\lineratiofit.py:417 in _reset_masks
self._measurements[m].mask = deepcopy(self._masks[m])

AttributeError: 'LineRatioFit' object has no attribute '_masks'

lrf_list._masks
Out[40]:
{'OI_63': array([[ True, True, True, ..., True, True, True],
[ True, True, True, ..., True, True, True],
[ True, True, True, ..., True, True, True],
...,
[False, False, False, ..., True, True, True],
[False, False, False, ..., True, True, True],
[False, False, False, ..., True, True, True]]),
'OI_145': array([[ True, True, True, ..., True, True, True],
[ True, True, True, ..., True, True, True],
[ True, True, True, ..., True, True, True],
...,
[False, False, False, ..., True, True, True],
[False, False, False, ..., True, True, True],
[False, False, False, ..., True, True, True]]),
'CII_158': array([[ True, True, True, ..., True, True, True],
[ True, True, True, ..., True, True, True],
[ True, True, True, ..., True, True, True],
...,
[False, False, False, ..., True, True, True],
[False, False, False, ..., True, True, True],
[False, False, False, ..., True, True, True]])}

lrf_dict._masks
Traceback (most recent call last):

Input In [41] in <cell line: 1>
lrf_dict._masks

AttributeError: 'LineRatioFit' object has no attribute '_masks'

I see in line 50 of lineratiofit.py, dict measurements get turned straight into self._measurements, whereas list measurements go to _init_measurements where self gets the _masks attribute. So I think this may be the source of the problem.

thanks,

Aaron

[Marc W. Pound]

Dear Aaron,

Thanks for finding a bug and the hint for where to look!   Can you provide a minimal running/failing example python script?  I am working on a new release for ~next week so can possibly get this bug fix in if it is simple.

Marc

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Dr. Marc Pound
Research Scientist
Astronomy Department
University of Maryland, College Park

https://www.astro.umd.edu/~mpound

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[Aaron Bryant]

Hi Marc,

using the example data:

from pdrtpy.modelset import ModelSet
from pdrtpy.tool.lineratiofit import LineRatioFit
from pdrtpy.measurement import Measurement
import pdrtpy.pdrutils as utils

cii_flux = utils.get_testdata("n22_cii_flux.fits")
cii_err = utils.get_testdata("n22_cii_error.fits")
oi_flux = utils.get_testdata("n22_oi_flux.fits")
oi_err = utils.get_testdata("n22_oi_error.fits")
FIR_flux = utils.get_testdata("n22_FIR.fits")

cii_combined = "n22_cii_flux_error.fits"
oi_combined = "n22_oi_flux_error.fits"
FIR_combined = "n22_FIR_flux_error.fits"

Measurement.make_measurement(cii_flux, cii_err, cii_combined,overwrite=True)
Measurement.make_measurement(oi_flux, oi_err, oi_combined,overwrite=True)
Measurement.make_measurement(FIR_flux, error='10%', outfile=FIR_combined,overwrite=True)

cii_meas = Measurement.read(cii_combined, identifier="CII_158")
FIR_meas = Measurement.read(FIR_combined, identifier="FIR")
oi_meas = Measurement.read(oi_combined, identifier="OI_63")

ms = ModelSet("wk2020", z=1)

meas_list = (cii_meas, oi_meas, FIR_meas)
lrf_list = LineRatioFit(ms, meas_list)
lrf_list.run()

meas_dict = {cii_meas.id: cii_meas, oi_meas.id: oi_meas, FIR_meas.id: FIR_meas}
lrf_dict = LineRatioFit(ms, meas_dict)
lrf_dict.run()

lrf_dict.run() will raise an AttributeError

at least from my side I could fix it by editing lineratiofit.py like this, starting at line 49, the parts I added being in bold:

        if type(measurements) == dict or measurements is None:
            self._measurements = measurements
            self._masks = dict()
            for key in measurements:
                self._masks[key] = deepcopy(measurements[key].mask)
        else:
            self._init_measurements(measurements)

regards,

Aaron

[Marc W. Pound]

Aaron 

This is now fixed in version 2.3.1 just released

Marc