From 1bb2e60ad19271c7dca57f87989735b2acfbd2ed Mon Sep 17 00:00:00 2001
From: Marc Pound <22331890+mpound@users.noreply.github.com>
Date: Wed, 17 Jun 2026 12:44:38 -0700
Subject: [PATCH 01/25] add TS copy section
---
scripts/distribute.py | 45 ++++++++++++++++++++++++++++---------------
1 file changed, 29 insertions(+), 16 deletions(-)
diff --git a/scripts/distribute.py b/scripts/distribute.py
index 48d3b4e7..e023a747 100755
--- a/scripts/distribute.py
+++ b/scripts/distribute.py
@@ -11,6 +11,9 @@
parser.add_argument("--file", "-f", action="store", help="input filename")
parser.add_argument("--verbose", "-v", action="store_true", help="verbose output")
parser.add_argument("--no-untar", "-n", action="store_true", help="don't untar the file (it's already untarred)")
+parser.add_argument(
+ "--copyts", "-t", action="store_true", help="copy the surface temperature (T_s) maps to all leaf directories"
+)
parser.add_argument(
"--dry-run",
"-d",
@@ -28,24 +31,34 @@
f.extractall(path="./00NEWMODELS")
os.chdir("00NEWMODELS")
dirs = glob.glob("LINEFITS/*")
+tsfile = None
for d in dirs:
angmods = glob.glob(d + "/*")
for a in angmods:
- # avperp = f'avperp={a[-1]}'
- b = a.replace("Av0", "") # remove extraneous Av on some filenames
- losangle = f"losangle={b[-2:]}"
- outdir = losangle # + "/" + avperp
- if args.verbose or args.dry_run:
- print(f"{a=} {outdir=}")
- if not args.dry_run:
- os.makedirs(outdir, exist_ok=True)
- fits = glob.glob(a + "/*.fits")
- for file in fits:
- base = os.path.basename(file)
- outfile = f"{outdir}/{base}"
+ # for surface temperature, grab the location of the FITS file
+ # if it is being copied
+ if "TSAV0P01" in a:
+ if args.copyts and "sm.fits" in a:
+ tsfile = a
+ else:
+ # avperp = f'avperp={a[-1]}'
+ b = a.replace("Av0", "") # remove extraneous Av on some filenames
+ losangle = f"losangle={b[-2:]}"
+ outdir = losangle # + "/" + avperp
if args.verbose or args.dry_run:
- print(f"cp {file} {outfile}")
+ print(f"{a=} {outdir=}")
if not args.dry_run:
- shutil.copy(file, outfile)
-
-# @TODO add copying of TsAV0p01sm.fits from losangle=00 to losangle=*
+ os.makedirs(outdir, exist_ok=True)
+ fits = glob.glob(a + "/*.fits")
+ for file in fits:
+ base = os.path.basename(file)
+ outfile = f"{outdir}/{base}"
+ if args.verbose or args.dry_run:
+ print(f"cp {file} {outfile}")
+ if not args.dry_run:
+ shutil.copy(file, outfile)
+ if args.copyts and tsfile is not None:
+ tsout = f"{outdir}/TSAV0p01sm.fits"
+ if args.verbose:
+ print(f"cp {tsfile} {tsout}")
+ shutil.copy(tsfile, tsout)
From 6e6a064053b4717961e82bd75b0c0788abca31c6 Mon Sep 17 00:00:00 2001
From: Marc Pound <22331890+mpound@users.noreply.github.com>
Date: Wed, 17 Jun 2026 12:45:32 -0700
Subject: [PATCH 02/25] simple FITS file spotcheck script for new models
---
scripts/spotcheck | 7 +++++++
1 file changed, 7 insertions(+)
create mode 100755 scripts/spotcheck
diff --git a/scripts/spotcheck b/scripts/spotcheck
new file mode 100755
index 00000000..1cb26a55
--- /dev/null
+++ b/scripts/spotcheck
@@ -0,0 +1,7 @@
+#!/bin/tcsh
+# simple FITS file spotcheck script for new models
+
+foreach file ( $* )
+ echo $file
+ ds9 -geometry 1500x1500 -cmap Heat -zscale -zoom 16 -log $file
+end
From 1b6b480a17af1d6fe30339eadaeb490d9e901b51 Mon Sep 17 00:00:00 2001
From: Marc Pound <22331890+mpound@users.noreply.github.com>
Date: Thu, 18 Jun 2026 10:58:37 -0700
Subject: [PATCH 03/25] add arguments
---
scripts/findmissing.csh | 23 ++++++++++++++---------
1 file changed, 14 insertions(+), 9 deletions(-)
diff --git a/scripts/findmissing.csh b/scripts/findmissing.csh
index 88c4293c..710be468 100755
--- a/scripts/findmissing.csh
+++ b/scripts/findmissing.csh
@@ -1,21 +1,26 @@
#!/bin/csh -f
# Identify if any model files are not listed in models.tab
#
-foreach z ( 1 )
- cd ../pdrtpy/models/wolfirekaufman/version2020/constant_density/z=${z}
- foreach dir ( losangle=* )
- cd $dir
+set dir=../pdrtpy/models/wolfirekaufman/version2020/constant_density/
+set tab=models.tab
+foreach arg (${argv})
+ set ${arg}
+ #echo "set ${arg}"
+end
+#foreach zed ( 1 )
+ cd ${dir}/${z}
+ foreach angle ( losangle=* )
+ cd $angle
+ #echo doing $dir/$z/$angle
foreach file ( *sm.fits )
set basefile = `basename $file`
set search = ${basefile:r}
- #echo "grep -L $search models.tab"
- set x=`grep -L $search models.tab`
- #if ( "$x" == "models.tab" ) then
+ set x=`grep -L $search ${tab}`
if ( $? == 1 ) then
- echo $dir/models.tab missing $file
+ echo ${dir}/${angle}/${tab} missing $file
endif
#echo $search
end
cd ..
end
-end
+#end
From 1af2b2be4d931ae1e0671c34d9e0fe0b99e35be4 Mon Sep 17 00:00:00 2001
From: Marc Pound <22331890+mpound@users.noreply.github.com>
Date: Thu, 18 Jun 2026 16:18:53 -0700
Subject: [PATCH 04/25] update stuff
---
CHANGES.md | 38 ++++++++++++++++++++++++++++++++++++++
1 file changed, 38 insertions(+)
diff --git a/CHANGES.md b/CHANGES.md
index a5b3e2bd..65dc2048 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -1,5 +1,43 @@
## Change Log
+### Release 3.0
+
+#### _Models_
+
+- New models for the Small Magellanic Cloud (z=0.2) including alternate view angles.
+
+- Previous 2006 SMC models deprecated.
+
+#### _Measurement_
+
+- *Measurement.to()* method added to convert units
+
+#### _LineRatioFit_
+
+- significant performance improvement for map data, ~10x via addition of `joint_fit` keyword and parallel workers
+
+#### _Excitation Tool_
+
+- add C18O, 13C18O, CH+ to provided molecules
+- Robust piecewise initialization for first fit guess instead of quick and dirty which could sometimes fail.
+- parallel workers for ~2x performance improvement
+
+#### _Code cleanup, refactoring, etc._
+
+- `pdrutils.py` split into individual modules *utils.fits*, *utils.helpers*, *utils.paths*, *utils.units*, *utils.wcs*. Done in a backwards compatiable way so *import pdrutils as utils* still works.
+- `pdrtpy.plot` module refactored and new tests added
+- `excitation.py` - refactored to remove dead code, dedupe, vectorize
+- all documentation changed to `numpydoc` format
+- benchmark code for performance improvements
+
+#### _Issues_
+
+- Issues closed
+
+#### _Notebooks_
+
+- blah
+
### Release 2.6.4
#### _Models_
From ef4de7c2ce1d87914c5f9c5b4583d6fe703d278d Mon Sep 17 00:00:00 2001
From: Marc Pound <22331890+mpound@users.noreply.github.com>
Date: Thu, 18 Jun 2026 16:19:15 -0700
Subject: [PATCH 05/25] add smc
---
pdrtpy/tables/all_models.tab | 16 ++++++++++------
1 file changed, 10 insertions(+), 6 deletions(-)
diff --git a/pdrtpy/tables/all_models.tab b/pdrtpy/tables/all_models.tab
index 7388d96f..eda96933 100644
--- a/pdrtpy/tables/all_models.tab
+++ b/pdrtpy/tables/all_models.tab
@@ -4,12 +4,16 @@
| null| null| null| null| null| null| null| null| null| null|
Wolfire/Kaufman wk2006 2006 wolfirekaufman/version2006/constant_density/z=1/ models.tab constant density 1.0 0 null Wolfire/Kaufman 2006 constant density models
Wolfire/Kaufman wk2006 2006 wolfirekaufman/version2006/constant_density/z=3/ models.tab constant density 3.0 0 null Wolfire/Kaufman 2006 constant density models
- Wolfire/Kaufman wk2020 2020 wolfirekaufman/version2020/constant_density/z=1/losangle=00/ models.tab constant density 1.0 0 null Wolfire/Kaufman 2020 constant density models, $A_V$=7, no freeze-out
- Wolfire/Kaufman wk2020 2020 wolfirekaufman/version2020/constant_density/z=1/losangle=75/ models.tab constant density 1.0 75 null Wolfire/Kaufman 2020 constant density models, $A_V$=7, no freeze-out
- Wolfire/Kaufman wk2020 2020 wolfirekaufman/version2020/constant_density/z=1/losangle=60/ models.tab constant density 1.0 60 null Wolfire/Kaufman 2020 constant density models, $A_V$=7, no freeze-out
- Wolfire/Kaufman wk2020 2020 wolfirekaufman/version2020/constant_density/z=1/losangle=60/ models.tab constant density 1.0 45 null Wolfire/Kaufman 2020 constant density models, $A_V$=7, no freeze-out
- Wolfire/Kaufman wk2020 2020 wolfirekaufman/version2020/constant_density/z=1/losangle=30/ models.tab constant density 1.0 30 null Wolfire/Kaufman 2020 constant density models, $A_V$=7, no freeze-out
- Wolfire/Kaufman smc 2006 wolfirekaufman/version2006/constant_density/smc/ models.tab constant density 0.1 0 null Wolfire/Kaufman 2006 limited set of constant density models for Small Magellanic Cloud
+ Wolfire/Kaufman wk2020 2020 wolfirekaufman/version2020/constant_density/z=1/losangle=00/ models.tab constant density 1.0 0 null Wolfire/Kaufman 2020 constant density models, $A_V$=7, Dust abundance=0.1, no freeze-out
+ Wolfire/Kaufman wk2020 2020 wolfirekaufman/version2020/constant_density/z=1/losangle=75/ models.tab constant density 1.0 75 null Wolfire/Kaufman 2020 constant density models, $A_V$=7, Dust abundance=0.1, no freeze-out
+ Wolfire/Kaufman wk2020 2020 wolfirekaufman/version2020/constant_density/z=1/losangle=60/ models.tab constant density 1.0 60 null Wolfire/Kaufman 2020 constant density models, $A_V$=7, Dust abundance=0.1, no freeze-out
+ Wolfire/Kaufman wk2020 2020 wolfirekaufman/version2020/constant_density/z=1/losangle=45/ models.tab constant density 1.0 45 null Wolfire/Kaufman 2020 constant density models, $A_V$=7, Dust abundance=0.1, no freeze-out
+ Wolfire/Kaufman wk2020 2020 wolfirekaufman/version2020/constant_density/z=1/losangle=30/ models.tab constant density 1.0 30 null Wolfire/Kaufman 2020 constant density models, $A_V$=7, Dust abundance=0.1, no freeze-out
+ Wolfire/Kaufman smc 2020 wolfirekaufman/version2020/constant_density/smc/losangle=00/ models.tab constant density 0.2 0 null Wolfire/Kaufman 2020+ Small Magellanic Cloud, $A_V$=7, Dust abundance=0.1, no freeze-out
+ Wolfire/Kaufman smc 2020 wolfirekaufman/version2020/constant_density/smc/losangle=75/ models.tab constant density 0.2 75 null Wolfire/Kaufman 2020+ Small Magellanic Cloud, $A_V$=7, Dust abundance=0.1, no freeze-out
+ Wolfire/Kaufman smc 2020 wolfirekaufman/version2020/constant_density/smc/losangle=60/ models.tab constant density 0.2 60 null Wolfire/Kaufman 2020+ Small Magellanic Cloud, $A_V$=7, Dust abundance=0.1, no freeze-out
+ Wolfire/Kaufman smc 2020 wolfirekaufman/version2020/constant_density/smc/losangle=45/ models.tab constant density 0.2 45 null Wolfire/Kaufman 2020+ Small Magellanic Cloud, $A_V$=7, Dust abundance=0.1, no freeze-out
+ Wolfire/Kaufman smc 2020 wolfirekaufman/version2020/constant_density/smc/losangle=30/ models.tab constant density 0.2 30 null Wolfire/Kaufman 2020+ Small Magellanic Cloud, $A_V$=7, Dust abundance=0.1, no freeze-out
Wolfire/Kaufman lmc 2020 wolfirekaufman/version2020/constant_density/lmc/ models.tab constant density 0.5 0 null Wolfire/Kaufman 2020 limited set of constant density models for Large Magellanic Cloud, surface chemistry turned off
KOSMA-tau kt2013wd01-7 WD01-7 kosmatau/2013/WD01-7/clumpy/Z=1/M=100/ models.tab clumpy 1.0 0 100.0 KOSMA-tau 2013 models, Weingarter & Draine 2001 $R_V$=3.1, clumpy, maximum clump mass = 100 M$_\odot$
KOSMA-tau kt2013wd01-7 WD01-7 kosmatau/2013/WD01-7/non-clumpy/Z=1/M=100/ models.tab non-clumpy 1.0 0 100.0 KOSMA-tau 2013 models, Weingarter & Draine 2001 $R_V$=3.1, non-clumpy, single clump 100 M$_\odot$
From 1f06a3d04ffd9883dca3df518565c136243164fa Mon Sep 17 00:00:00 2001
From: Marc Pound <22331890+mpound@users.noreply.github.com>
Date: Wed, 1 Jul 2026 15:33:11 -0700
Subject: [PATCH 06/25] update
---
scripts/spotcheck | 2 ++
1 file changed, 2 insertions(+)
diff --git a/scripts/spotcheck b/scripts/spotcheck
index 1cb26a55..f3cce4ac 100755
--- a/scripts/spotcheck
+++ b/scripts/spotcheck
@@ -1,6 +1,8 @@
#!/bin/tcsh
# simple FITS file spotcheck script for new models
+
+#ds9 --cmap Heat -zscale -zoom 16 -log -tile $file
foreach file ( $* )
echo $file
ds9 -geometry 1500x1500 -cmap Heat -zscale -zoom 16 -log $file
From d405183e802f79825373e6431e32e09d26eec302 Mon Sep 17 00:00:00 2001
From: Marc Pound <22331890+mpound@users.noreply.github.com>
Date: Wed, 8 Jul 2026 08:45:51 -0700
Subject: [PATCH 07/25] update issues resolved
---
CHANGES.md | 8 +++++++-
1 file changed, 7 insertions(+), 1 deletion(-)
diff --git a/CHANGES.md b/CHANGES.md
index 65dc2048..e5615fca 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -32,7 +32,13 @@
#### _Issues_
-- Issues closed
+- Reorganized `pdrutils.py` into `utils` submodules while preserving backward compatibility ([#204](https://github.com/mpound/pdrtpy/issues/204))
+- Added option to use wavelength on the X-axis of H2 excitation diagrams ([#176](https://github.com/mpound/pdrtpy/issues/176))
+- Converted all code documentation to numpydoc format ([#103](https://github.com/mpound/pdrtpy/issues/103))
+- Verified test suite parallelization across platforms ([#70](https://github.com/mpound/pdrtpy/issues/70))
+- Added `Measurement.to()` method for unit conversion ([#62](https://github.com/mpound/pdrtpy/issues/62))
+- Fixed weird colorbar spacing in `LineRatioPlot.ratios_on_models` ([#35](https://github.com/mpound/pdrtpy/issues/35))
+- Fixed missing centerlines in `overlay_all_ratios` plot when exported to PDF ([#23](https://github.com/mpound/pdrtpy/issues/23))
#### _Notebooks_
From b9bb3d7d01de271bbb61e937accfb0dc03596c78 Mon Sep 17 00:00:00 2001
From: Marc Pound <22331890+mpound@users.noreply.github.com>
Date: Wed, 8 Jul 2026 08:56:40 -0700
Subject: [PATCH 08/25] update description
---
CHANGES.md | 1 +
README.rst | 8 +++++---
2 files changed, 6 insertions(+), 3 deletions(-)
diff --git a/CHANGES.md b/CHANGES.md
index e5615fca..9e436173 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -29,6 +29,7 @@
- `excitation.py` - refactored to remove dead code, dedupe, vectorize
- all documentation changed to `numpydoc` format
- benchmark code for performance improvements
+- update scripts for verifying and adding new models
#### _Issues_
diff --git a/README.rst b/README.rst
index 8591f7ed..dfb5a48b 100644
--- a/README.rst
+++ b/README.rst
@@ -49,7 +49,7 @@ Spitzer, STO, and Herschel. Given a set of observations of spectral line or
continuum intensities, PDR Toolbox can compute best-fit FUV incident
intensity and cloud density based on our models of PDR emission.
-The PDR Toolbox will cover a wide range of spectral lines and metallicities
+The PDR Toolbox covers a wide range of spectral lines and metallicities
and allows map-based analysis so users can quickly compute spatial
images of density and radiation field from map data. We provide Jupyter
`Example Notebooks`_ for data analysis. It also can support models from
@@ -67,7 +67,7 @@ excitation rates for |OI| from
communication) and have included |13C| chemistry along with the
emitted line intensities for |13CII| and |13CO|.
-We also support fitting of temperatures and column densities of excitation diagrams of |H2|, CO, and |13CO| excitation diagrams. Users can fit other molecules by providing appropriate transition data.
+We also support fitting of temperatures and column densities of excitation diagrams of |H2|, CO, |13CO|. |C18O|, and |CH+|, in both single pixels and maps. Users can fit other molecules by providing appropriate transition data.
Up to date documentation can be found at `pdrtpy.readthedocs.io `_.
@@ -95,7 +95,7 @@ Requirements
``pdrtpy`` requires Python 3 and recent versions of `astropy `_, `numpy `_, `scipy `_, `lmfit `_, and `matplotlib `_. If you want to run the `Example Notebooks`_, you also need `jupyter `_.
-First make sure you are using Python 3.10 or higher:
+First make sure you are using Python 3.11 or higher:
.. code-block:: sh
@@ -197,6 +197,8 @@ You may want to use a virtual environment to protect from polluting your daily w
.. |reg| unicode:: U+000AE .. REGISTERED SIGN
.. |13C| replace:: :sup:`13`\ C
.. |13CO| replace:: :sup:`13`\ CO
+.. |C18O| replace:: C\ :sup:`18`\ O
+.. |CH+| replace:: CH\ :sup:`+`
.. |13CII| replace:: [\ :sup:`13`\ C II]
.. |OI| replace:: [O I]
.. |CII| replace:: [C II]
From a8141056ab1b37ca0f709d9b4a2d61a4b76b4d9f Mon Sep 17 00:00:00 2001
From: Marc Pound <22331890+mpound@users.noreply.github.com>
Date: Wed, 8 Jul 2026 12:06:06 -0700
Subject: [PATCH 09/25] Remove OBSGEO header variables that cause fits/wcs to
warn. They are not needed for the H2 map notebook
---
pdrtpy/testdata/H200S1_CenA.fits | Bin 60480 -> 60480 bytes
pdrtpy/testdata/H200S2_CenA.fits | Bin 60480 -> 60480 bytes
pdrtpy/testdata/H200S3_CenA.fits | Bin 60480 -> 60480 bytes
pdrtpy/testdata/H200S4_CenA.fits | Bin 60480 -> 60480 bytes
pdrtpy/testdata/H200S5_CenA.fits | Bin 60480 -> 60480 bytes
pdrtpy/testdata/H200S6_CenA.fits | Bin 60480 -> 60480 bytes
pdrtpy/testdata/H200S7_CenA.fits | Bin 60480 -> 60480 bytes
pdrtpy/testdata/H200S8_CenA.fits | Bin 60480 -> 60480 bytes
8 files changed, 0 insertions(+), 0 deletions(-)
diff --git a/pdrtpy/testdata/H200S1_CenA.fits b/pdrtpy/testdata/H200S1_CenA.fits
index 0e41d878d9cc0974125ff4c46824cf4f88fb832e..e10535282845b4bc2466ad87f0220a2e153c3623 100644
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zxv_zzxq*d=A;=^M&{qH&kf>0amstWfRe_MPoBs|WRO^hA%S
z^dQ%?^a$6e^azUGYhhw$VrFS!U`&yFixfFFAE*}KLw0InYGP_qa!7JwaugU->{Me*
UBXdi0b4ydooO+RcvBRV&08HSOlK=n!
delta 395
zcmX?bgZaP><_!*PTK-PK?ymkW5w;3IplfQZXJ%k*VQg$>X=-X_X{?~H5S^=E9IKF?
znm@UQRYgZZ0jePqs=?4w&(y-y$jsEh*wWn05=FxqWDQXe4TgpWdgdl(7Um`<21aHk
zW+)nD*i<&#v3=sQg;=5sag~Cup`p1sP`QPffu4!6p&?jLtU`WLacWUnVo82cr9y;m
za(;eMN@iYSN$SK#VVD6BS1KqN8JZZFnVVRc>zSGvnHga*AQHO)5LYWG7+YEznHyOe
zn(CRD0%s21RZ@;<_!*Pn+@1Ma7`8v{!s7i;p*%i9O`SUpq}fP<(qGw?w#uh#HQ)q>Iw=9
z`U)N{p$f?vsma;JrMU{F1u2OosVNFZ21aJO2Ijg379oZPR>nqFMutGeAmHK{;s`WO
z0cf7Fg@LJwxw)~KF~}qc&{qH&kf>0amstWfRe_MPoBs|Upo
zv_#jav>>OXv<_!*PTK-PK?ymkW5w;3IplfQZXJ%k*VQg$>X=-X_X{?~H5S^=E9IKF?
znm@UQRYgZZ0jePqs=?4w&(y-y$jsEh*wWn05=FxqWDQXe4TgpWdgdl(7Um`<21aHk
zW+)nD*i<&#v3=sQg;=5sag~Cup`p1sP`QPffu4!6p&?jLtU`WLacWUnVo82cr9y;m
za(;eMN@iYSN$SK#VVD6BS1KqN8JZZFnVVRc>zSGvnHga*AQHO)5LYWG7+YEznHyOe
zn(CRD0%s21RZ@;<_!*Pn+@1Ma7`8v{!s7i;p*%i9O`SUpdRAsof+=wksboY>Iw=9`U)N{
zp$f?vsma;JrMU{F1u2OosVNFZ21aJO2Ijg379oZPR>nqFMutGeAmHK{;s`WO0cf7F
zfr+7sk)?%+1;``_&{qH&kf>0amstWfRe_MPoBs|W=jv_#j$
zlwjw?lt>V!)V)R)mga^=md2I_6uGxZkz@0LY5_iErve@5ks9ITo&v>`I@Q?F$k5Qz
R#MHu)GN)c-U+gd`3IGHRl{NqX
delta 395
zcmX?bgZaP><_!*PTK-PK?ymkW5w;3IplfQZXJ%k*VQg$>X=-X_X{?~H5S^=E9IKF?
znm@UQRYgZZ0jePqs=?4w&(y-y$jsEh*wWn05=FxqWDQXe4TgpWdgdl(7Um`<21aHk
zW+)nD*i<&#v3=sQg;=5sag~Cup`p1sP`QPffu4!6p&?jLtU`WLacWUnVo82cr9y;m
za(;eMN@iYSN$SK#VVD6BS1KqN8JZZFnVVRc>zSGvnHga*AQHO)5LYWG7+YEznHyOe
zn(CRD0%s21RZ@;<^>}4&K|DL-oc^1whHQ@j)~!6mLcJxj*;P^mXYD=3JMDP3LY+@3dtF%
z$=SuFxeBEPDTyViDGEjgMrOJO=DG$JA%+H4#zs~~hCsz2;NlqK2sBOsXr8f!iIJI+
ziJ5@`$Rr5RR{$E2s8E`hSpqgyfsnDA{|i54+}t465QFSg%ZS7P$M8^pZ50
delta 52
zcmX?bgZaP><^>{~7l=GyoP3~o!R7|BhM36@L>DYRP|Pt|fl*=efocIhkig~x#TVEY
IJ4}iK0G7)bSO5S3
From 256f6723a9af0dda5f5f77e0f33c3aca41ee9a08 Mon Sep 17 00:00:00 2001
From: Marc Pound <22331890+mpound@users.noreply.github.com>
Date: Wed, 8 Jul 2026 12:08:08 -0700
Subject: [PATCH 10/25] pass kwargs to CCData.read. Rename kwd to kwargs
---
pdrtpy/measurement.py | 20 ++++++++++----------
1 file changed, 10 insertions(+), 10 deletions(-)
diff --git a/pdrtpy/measurement.py b/pdrtpy/measurement.py
index cd7d7e3f..40550e82 100755
--- a/pdrtpy/measurement.py
+++ b/pdrtpy/measurement.py
@@ -357,7 +357,7 @@ def to(self, unit: str | u.Unit, equivalencies: list | None = None):
equivalencies = []
return self.convert_unit_to(unit, equivalencies)
- def write(self, filename, **kwd):
+ def write(self, filename, **kwargs):
"""Write this Measurement to a FITS file with value in 1st HDU and error in 2nd HDU.
See :meth:`astropy.nddata.CCDData.write`.
@@ -366,11 +366,11 @@ def write(self, filename, **kwd):
----------
filename : str
Name of file.
- **kwd
+ **kwargs
All additional keywords are passed to :py:mod:`astropy.io.fits`.
"""
hdu = self.to_hdu()
- hdu.writeto(filename, **kwd)
+ hdu.writeto(filename, **kwargs)
def _set_up_for_interp(self, kind="linear"):
# @TODO this will always return nan if there are nan in the data.
@@ -700,7 +700,7 @@ def from_table(filename, format="ipac", array=False):
def fits_measurement_reader(
- filename, hdu=0, unit=None, hdu_mask="MASK", hdu_flags=None, key_uncertainty_type="UTYPE", **kwd
+ filename, hdu=0, unit=None, hdu_mask="MASK", hdu_flags=None, key_uncertainty_type="UTYPE", **kwargs
):
"""FITS file reader for Measurement class, called by :meth:`Measurement.read`.
@@ -729,7 +729,7 @@ def fits_measurement_reader(
Currently not implemented. Default: None.
key_uncertainty_type : str, optional
Header key name where the uncertainty class name is stored. Default: ``'UTYPE'``.
- **kwd
+ **kwargs
Additional keyword parameters passed to the FITS reader in :mod:`astropy.io.fits`.
Raises
@@ -738,14 +738,14 @@ def fits_measurement_reader(
If the conversion from CCDData to Measurement fails.
"""
- _id = kwd.pop("identifier", "unknown")
- _title = kwd.pop("title", None)
- _squeeze = kwd.pop("squeeze", True)
- _restfreq = kwd.pop("restfreq", None)
+ _id = kwargs.pop("identifier", "unknown")
+ _title = kwargs.pop("title", None)
+ _squeeze = kwargs.pop("squeeze", True)
+ _restfreq = kwargs.pop("restfreq", None)
# suppress INFO messages about units in FITS file. e.g. useless ones like:
# "INFO: using the unit erg / (cm2 s sr) passed to the FITS reader instead of the unit erg s-1 cm-2 sr-1 in the FITS file."
log.setLevel("WARNING")
- z = CCDData.read(filename, unit=unit)
+ z = CCDData.read(filename, unit=unit, **kwargs)
if _squeeze:
z = utils.squeeze(z)
From 77c3f2a542df99c03882f8325119e5078e317290 Mon Sep 17 00:00:00 2001
From: Marc Pound <22331890+mpound@users.noreply.github.com>
Date: Wed, 8 Jul 2026 12:09:21 -0700
Subject: [PATCH 11/25] version
---
pdrtpy/__init__.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/pdrtpy/__init__.py b/pdrtpy/__init__.py
index cb27bab3..c6e6031d 100644
--- a/pdrtpy/__init__.py
+++ b/pdrtpy/__init__.py
@@ -1,6 +1,6 @@
"""Top level package for pdrtpy"""
-__version__ = "2.7.4"
+__version__ = "3.0.1"
VERSION = __version__
AUTHORS = "Marc W. Pound, Mark G. Wolfire"
From 52cfa85f024bb74f3482feb8213f6bfb83e32e2b Mon Sep 17 00:00:00 2001
From: Marc Pound <22331890+mpound@users.noreply.github.com>
Date: Wed, 8 Jul 2026 12:09:47 -0700
Subject: [PATCH 12/25] smc notes
---
CHANGES.md | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/CHANGES.md b/CHANGES.md
index 9e436173..ef8c53ec 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -4,9 +4,9 @@
#### _Models_
-- New models for the Small Magellanic Cloud (z=0.2) including alternate view angles.
+- New models for the Small Magellanic Cloud (z=0.2) including alternate view angles i=0 (face-on) to i=75.
-- Previous 2006 SMC models deprecated.
+- Previous 2006 SMC models are now deprecated.
#### _Measurement_
From 20eb9c08ca1c027439f6af6922cc0d6cae98fc2a Mon Sep 17 00:00:00 2001
From: Marc Pound <22331890+mpound@users.noreply.github.com>
Date: Wed, 8 Jul 2026 13:06:49 -0700
Subject: [PATCH 13/25] remove OBSGEO header keywords
---
pdrtpy/testdata/H200S8_CenA.fits | Bin 60480 -> 60480 bytes
1 file changed, 0 insertions(+), 0 deletions(-)
diff --git a/pdrtpy/testdata/H200S8_CenA.fits b/pdrtpy/testdata/H200S8_CenA.fits
index a5d34c7b9e555f1824cafe36bfa8101ab6867cda..50db258a84f62689cc9ab63703a92f544b972ca2 100644
GIT binary patch
delta 29
lcmX?bgZaP><_!*Pn+@1MaBUV4E@0k#p!fmf<_56?R{_9X4F3QC
delta 364
zcmX?bgZaP><_!*PTK-PK?ymkW5w;3IplfQZXJ%k*VQg$>X=-X_X{?~H5S^=E9IKF?
znm@UQRYgZZ0jePqs=?4w&(y-y$jsEh*wWn05=FxqWDQXe4TgpWdgdl(7Um`<21aHk
zW+)nD*i<&#v3=sQg;=5sag~Cup`p1sP`QPffu4!6p&?jLtU`WLacWUnVo82cr9y;m
za(;eMN@iYSN$SK#VVD6BS1KqN8JZZFnVVRc>zSGvnHga*AQHO)5LYWG7+YEznHyOe
an(CRD0%d2@r
Date: Tue, 21 Jul 2026 14:01:46 -0700
Subject: [PATCH 14/25] better view
---
scripts/spotcheck | 12 ++++++++----
1 file changed, 8 insertions(+), 4 deletions(-)
diff --git a/scripts/spotcheck b/scripts/spotcheck
index f3cce4ac..c8508977 100755
--- a/scripts/spotcheck
+++ b/scripts/spotcheck
@@ -1,9 +1,13 @@
#!/bin/tcsh
# simple FITS file spotcheck script for new models
+# ds9 -geometry 1500x1500 -cmap Heat -zscale -zoom 16 -log $file
-#ds9 --cmap Heat -zscale -zoom 16 -log -tile $file
-foreach file ( $* )
- echo $file
- ds9 -geometry 1500x1500 -cmap Heat -zscale -zoom 16 -log $file
+foreach dir ( losangle* )
+ echo $dir
+ cd $dir
+ ds9 -cmap Heat -zscale -zoom 4 -log -tile *sm.fits
+ echo -n Hit Return for next angle
+ set CR =$<
+ cd ..
end
From 29c019dfe9771ea06ad2207c2b972bf3aa536937 Mon Sep 17 00:00:00 2001
From: Marc Pound <22331890+mpound@users.noreply.github.com>
Date: Tue, 21 Jul 2026 15:54:36 -0700
Subject: [PATCH 15/25] SMC models added!
---
.../smc/losangle=00/13CO10.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/13CO10_CO10.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/13CO10_CO10sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/13CO10sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/13CO21.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/13CO21_CO21.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/13CO21_CO21sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/13CO21sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/13CO32.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/13CO32_13CO10.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/13CO32_13CO10sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/13CO32_CO21.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/13CO32_CO21sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/13CO32sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/13CO43_CO21.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/13CO43_CO21sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/13CO54_CO21.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/13CO54_CO21sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/13CO65_CO21.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/13CO65_CO21sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/13CO76_CO21.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/13CO76_CO21sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CI370.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CI370_CI609.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CI370_CI609sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CI370sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CI609.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CI609_13CO10.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CI609_13CO10sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CI609_13CO21.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CI609_13CO21sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CI609_13CO32.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CI609_13CO32sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CI609_CO10.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CI609_CO10sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CI609_CO21.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CI609_CO21sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CI609_CO43.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CI609_CO43sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CI609sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CII158.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CII158_13CO10.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CII158_13CO10sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CII158_13CO65.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CII158_13CO65sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CII158_CI609.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CII158_CI609sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CII158_CO10.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CII158_CO10sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CII158_CO21.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CII158_CO21sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CII158_CO32.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CII158_CO32sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CII158_CO65.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CII158_CO65sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CII158_FIR.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CII158_FIRsm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CII158_OI145.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CII158_OI145sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CII158sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO10.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO109_CO54.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO109_CO54sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO109_CO65.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO109_CO65sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO109_CO76.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO109_CO76sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO10sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO1110.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO1110_CO54.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO1110_CO54sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO1110_CO65.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO1110_CO65sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO1110_CO87.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO1110_CO87sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO1110sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO1211_CO54.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO1211_CO54sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO1211_CO65.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO1211_CO65sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO1312_CO54.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO1312_CO54sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO1312_CO65.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO1312_CO65sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO1413_CO54.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO1413_CO54sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO1413_CO65.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO1413_CO65sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO1514_CO54.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO1514_CO54sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO1514_CO65.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO1514_CO65sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO1615_CO54.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO1615_CO54sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO1615_CO65.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO1615_CO65sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO1716_CO54.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO1716_CO54sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO1716_CO65.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO1716_CO65sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO1817_CO54.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO1817_CO54sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO1817_CO65.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO1817_CO65sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO21.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO21_CO10.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO21_CO10sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO21sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO32.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO32_CO10.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO32_CO10sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO32_CO21.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO32_CO21sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO32sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO43.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO43_CO21.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO43_CO21sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO43sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO54.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO54sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO65.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO65_CO10.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO65_CO10sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO65sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO76.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO76_CO10.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO76_CO10sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO76_CO21.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO76_CO21sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO76_CO43.fits | Bin 0 -> 17280 bytes
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.../smc/losangle=00/CO76_CO54.fits | Bin 0 -> 17280 bytes
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.../smc/losangle=00/CO76_CO65.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO76_CO65sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO76sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO87.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO87_CO54.fits | Bin 0 -> 17280 bytes
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.../smc/losangle=00/CO87_CO65.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO87_CO65sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO87sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO98_CO54.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO98_CO54sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO98_CO65.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/CO98_CO65sm.fits | Bin 0 -> 17280 bytes
.../constant_density/smc/losangle=00/FIR.fits | 1 +
.../smc/losangle=00/FIRsm.fits | 50 ++++++
.../smc/losangle=00/H200S0.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/H200S0sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/H200S1.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/H200S1sm.fits | Bin 0 -> 17280 bytes
.../smc/losangle=00/H200S2.fits | Bin 0 -> 17280 bytes
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create mode 100644 pdrtpy/models/wolfirekaufman/version2020/constant_density/smc/losangle=00/13CO32.fits
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create mode 100644 pdrtpy/models/wolfirekaufman/version2020/constant_density/smc/losangle=00/CI609_13CO32.fits
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create mode 100644 pdrtpy/models/wolfirekaufman/version2020/constant_density/smc/losangle=00/CII158.fits
create mode 100644 pdrtpy/models/wolfirekaufman/version2020/constant_density/smc/losangle=00/CII158_13CO10.fits
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create mode 100644 pdrtpy/models/wolfirekaufman/version2020/constant_density/smc/losangle=00/CII158_CO10.fits
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create mode 100644 pdrtpy/models/wolfirekaufman/version2020/constant_density/smc/losangle=00/CO1110sm.fits
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