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Fixed numpy chained indexing bug #21

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Fixed numpy chained indexing bug #21

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4ddcd9a
Fixed numpy chained indexing bug
dpieterse Jun 1, 2026
43f73f8
Change path header table MeerLICHT
dpieterse Jul 15, 2026
0a82940
Permission errors prevent copying metadata over when updated files
dpieterse Jul 17, 2026
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2 changes: 1 addition & 1 deletion force_phot.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2808,7 +2808,7 @@ def str2None (value):
# able to infer the table description used futher down below
if tel == 'ML1':

fits_hdrtable_list = ['/idia/projects/meerlicht/Headers/'
fits_hdrtable_list = ['/idia/projects/meerlicht/data/hdrtables/'
'ML1_headers_cat.fits']
else:

Expand Down
56 changes: 45 additions & 11 deletions zogy.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1641,8 +1641,12 @@ def prep_fits (fits_in, header, gain, satlevel, str2add):
elif str2add is not None:

# name was updated; copy (unzipped) fits_in to fits_out
shutil.copy2 (fits_in, fits_out)

try:
shutil.copy2 (fits_in, fits_out)
except PermissionError as e:
log.warning('could not copy timestamps/metadata/permissions for '
'{} -> {} ({}). file data was copied successfully though'
.format(fits_in, fits_out, e))


return fits_out, header
Expand Down Expand Up @@ -3625,7 +3629,12 @@ def format_cat (cat_in, cat_out, cat_type=None, header2add=None,
if get_par(set_zogy.keep_tmp,tel):
# save catalog before formatting
cat_preformat = cat_in.replace('.fits', '_preformat.fits')
shutil.copy2 (cat_in, cat_preformat)
try:
shutil.copy2 (cat_in, cat_preformat)
except PermissionError as e:
log.warning('could not copy timestamps/metadata/permissions for'
' {} -> {} ({}). file data was copied successfully though'
.format(cat_in, cat_preformat, e))


# read data and header of [cat_in]
Expand Down Expand Up @@ -4322,8 +4331,12 @@ def get_trans (fits_new, fits_ref_remap, fits_D, fits_Scorr, fits_Fpsf,
# keep a copy of the original Scorr image if keep_tmp is True
if get_par(set_zogy.keep_tmp,tel):
fits_Scorr_orig = '{}_Scorr_orig.fits'.format(base)
shutil.copy2 (fits_Scorr, fits_Scorr_orig)

try:
shutil.copy2 (fits_Scorr, fits_Scorr_orig)
except PermissionError as e:
log.warning('could not copy timestamps/metadata/permissions for '
'{} -> {} ({}). file data was copied successfully though'
.format(fits_Scorr, fits_Scorr_orig, e))

if trim_image:
# trim_image: write smaller relevant section of Scorr and the
Expand All @@ -4337,7 +4350,12 @@ def get_trans (fits_new, fits_ref_remap, fits_D, fits_Scorr, fits_Fpsf,

# same for mask, but save original
fits_newref_mask_orig = '{}_mask_newref_orig.fits'.format(base)
shutil.copy2 (fits_newref_mask, fits_newref_mask_orig)
try:
shutil.copy2 (fits_newref_mask, fits_newref_mask_orig)
except PermissionError as e:
log.warning('could not copy timestamps/metadata/permissions for '
'{} -> {} ({}). file data was copied successfully though'
.format(fits_newref_mask, fits_newref_mask_orig, e))
data_newref_mask = read_hdulist (fits_newref_mask, dtype='uint8')
fits.writeto (fits_newref_mask, data_newref_mask[y1:y2+1,x1:x2+1],
overwrite=True)
Expand Down Expand Up @@ -8705,7 +8723,9 @@ def flux_optimal_iter (P, D, bkg_var, mask_use, nsigma_inn, nsigma_out,
idx_limfrac = idx_sort[mask_use_inn][:npix_limfrac]

# update inner mask_rej
mask_rej[mask_inn][idx_limfrac] = True
inner_indices = np.where(mask_inn)[0]
mask_rej[mask_inn] = False # reset mask
mask_rej[inner_indices[idx_limfrac]] = True

if False:
log.warning (
Expand Down Expand Up @@ -9472,7 +9492,12 @@ def help_swarp (fits2remap, data2remap, header2remap=header,
# overwriting it with the Gaia forced-photometry catalog
sexcat = '{}_sexcat.fits'.format(base)
if os.path.exists(fits_cat):
shutil.copy2 (fits_cat, sexcat)
try:
shutil.copy2 (fits_cat, sexcat)
except PermissionError as e:
log.warning('could not copy timestamps/metadata/permissions'
' for {} -> {} ({}). file data was copied successfully '
'though'.format(fits_cat, sexcat, e))


# write fits table to file
Expand Down Expand Up @@ -18141,8 +18166,12 @@ def run_sextractor (image, cat_out, file_config, file_params, pixscale,
if get_par(set_zogy.keep_tmp,tel):
image_orig = '{}_orig.fits'.format(base)
if not isfile(image_orig):
shutil.copy2 (image, image_orig)

try:
shutil.copy2 (image, image_orig)
except PermissionError as e:
log.warning('could not copy timestamps/metadata/permissions for '
'{} -> {} ({}). file data was copied successfully though'
.format(image, image_orig, e))

# if fraction less than one, run SExtractor on specified fraction of
# the image
Expand Down Expand Up @@ -18189,7 +18218,12 @@ def run_sextractor (image, cat_out, file_config, file_params, pixscale,

# create updated parameters file starting from original file
file_params_edited = '{}_params.txt'.format(base)
shutil.copy2(file_params, file_params_edited)
try:
shutil.copy2 (file_params, file_params_edited)
except PermissionError as e:
log.warning('could not copy timestamps/metadata/permissions for '
'{} -> {} ({}). file data was copied successfully though'
.format(file_params, file_params_edited, e))

# update size of VIGNET
if psfex_mode:
Expand Down