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change usage of deprecated np.int to int #148

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change usage of deprecated np.int to int #148

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36 changes: 18 additions & 18 deletions jwst_reffiles/bad_pixel_mask/badpix_from_flats.py
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Original file line number Diff line number Diff line change
Expand Up @@ -373,8 +373,8 @@ def combine_individual_maps(bad_maps, do_not_use_flags):

# Convert each type of bad pixel input to have the proper value,
# and add to the final map
do_not_use_map = np.zeros((bad_maps['DEAD'].shape)).astype(np.int)
use_map = np.zeros((bad_maps['DEAD'].shape)).astype(np.int)
do_not_use_map = np.zeros((bad_maps['DEAD'].shape)).astype(int)
use_map = np.zeros((bad_maps['DEAD'].shape)).astype(int)
for pix_type in do_not_use_flags:
if pix_type in dq_defs.keys():
if pix_type in bad_maps.keys():
Expand Down Expand Up @@ -564,8 +564,8 @@ def dead_pixels_sigma_rate(rate_image, mean_rate, stdev_rate, sigma=5.):
dead_pix_map : numpy.ndarray
2D map showing DEAD pixels. Good pixels have a value of 0.
"""
dead_pix_map = (rate_image < (mean_rate - sigma * stdev_rate)).astype(np.int)
return dead_pix_map.astype(np.int)
dead_pix_map = (rate_image < (mean_rate - sigma * stdev_rate)).astype(int)
return dead_pix_map.astype(int)


def dead_pixels_absolute_rate(rate_image, max_dead_signal=0.05):
Expand All @@ -586,8 +586,8 @@ def dead_pixels_absolute_rate(rate_image, max_dead_signal=0.05):
dead_pix_map : numpy.ndarray
2D map showing DEAD pixels. Good pixels have a value of 0.
"""
dead_pix_map = (rate_image < max_dead_signal).astype(np.int)
return dead_pix_map.astype(np.int)
dead_pix_map = (rate_image < max_dead_signal).astype(int)
return dead_pix_map.astype(int)


def dead_pixels_flux_check(dead_pix_map, ave_group, flux_check):
Expand Down Expand Up @@ -620,12 +620,12 @@ def dead_pixels_flux_check(dead_pix_map, ave_group, flux_check):

ibad = len(index[0])

updated_pix_map = np.logical_and(dead_pix_map == 1, final_ave_group < flux_check).astype(np.int)
updated_pix_map = np.logical_and(dead_pix_map == 1, final_ave_group < flux_check).astype(int)
index = np.where(updated_pix_map == 1)

iupdated = len(index[0])
print('Number of pixels removed from dead pixel mask after flux check', ibad - iupdated)
return updated_pix_map.astype(np.int)
return updated_pix_map.astype(int)


def extract_10th_group(hdu_list):
Expand Down Expand Up @@ -738,9 +738,9 @@ def find_open_and_low_qe_pixels(rate_image, max_dead_signal=0.05, max_low_qe=0.5
"""
ydim, xdim = rate_image.shape

low_qe_map = np.zeros((ydim, xdim)).astype(np.int)
open_pix_map = np.zeros((ydim, xdim)).astype(np.int)
adj_pix_map = np.zeros((ydim, xdim)).astype(np.int)
low_qe_map = np.zeros((ydim, xdim)).astype(int)
open_pix_map = np.zeros((ydim, xdim)).astype(int)
adj_pix_map = np.zeros((ydim, xdim)).astype(int)
low_sig_y, low_sig_x = np.where((rate_image >= max_dead_signal) & (rate_image < max_low_qe))

for x, y in zip(low_sig_x, low_sig_y):
Expand Down Expand Up @@ -931,7 +931,7 @@ def manual_flags(filename, map_shape, no_use):
tab = ascii.read(filename)

# Create empty mask
mask = np.zeros(map_shape).astype(np.int)
mask = np.zeros(map_shape).astype(int)

# Pixel index columns can have string or integer data.
# If we have strings, convert to integer, watching for
Expand Down Expand Up @@ -1001,7 +1001,7 @@ def miri_bad_columns(dimensions):

print('*************',dimensions)

shorted_map = np.zeros(dimensions).astype(np.int)
shorted_map = np.zeros(dimensions).astype(int)
shorted_map[:, 384:386] = 1
return shorted_map

Expand Down Expand Up @@ -1217,7 +1217,7 @@ def reference_pixel_map(dimensions, instrument_name):

"""
yd, xd = dimensions
ref_map = np.zeros(dimensions).astype(np.int)
ref_map = np.zeros(dimensions).astype(int)

ref_map[:, 0:4] = 1
ref_map[:, xd-4:xd] = 1
Expand Down Expand Up @@ -1249,15 +1249,15 @@ def range_format(table_cell, total_dimension):
The maximum index number to be returned
"""
try:
value = np.int(table_cell)
value = int(table_cell)
vals = [value, value+1]
except ValueError:
vals = table_cell.split(':')
if vals[0] == '':
vals[0] = 0
if vals[1] == '':
vals[1] = total_dimension - 1
vals = [np.int(val) for val in vals]
vals = [int(val) for val in vals]
vals[1] += 1
return vals

Expand Down Expand Up @@ -1468,8 +1468,8 @@ def split_row(line, colname):
a range is given (e.g. 200:210), then values will be [200, 210].
"""
try:
val = np.int(line[colname])
val = int(line[colname])
values = [val]
except ValueError:
values = [np.int(e) for e in line[colname].split(':')]
values = [int(e) for e in line[colname].split(':')]
return values
6 changes: 3 additions & 3 deletions jwst_reffiles/dark_current/dark_reffile.py
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Original file line number Diff line number Diff line change
Expand Up @@ -132,15 +132,15 @@ def __init__(self, file_list=[], max_equivalent_groups=60, sigma_threshold=3, pe
pix_per_fullframe_group = x_fullframe_dim * y_fullframe_dim

pix_per_group = self.metadata['SUBSIZE1'] * self.metadata['SUBSIZE2']
pix_ratio = np.int(pix_per_fullframe_group / pix_per_group)
pix_ratio = int(pix_per_fullframe_group / pix_per_group)

# The number of groups that can be read in from each file is the
# user-entered max number of groups, divided by the ratio of the
# number of pixels in a full frame exposure to the number of pixels
# in the input aperture, divided by the number of files, and
# finally divided by 2, since we will also need to read in the
# cosmic ray flags associated with each file
delta_groups = np.int(max_equivalent_groups / pix_ratio / len(self.file_list)) # / 2.)
delta_groups = int(max_equivalent_groups / pix_ratio / len(self.file_list)) # / 2.)
if delta_groups == 0:
raise ValueError(('ERROR: max_equivalent_groups incompatible with the number/size '
'of input files. Even reading just a single group at a time from '
Expand Down Expand Up @@ -373,7 +373,7 @@ def prepare_cr_maps(self):
first_hits = dq_flags.collapse_cr_map(file_cr_map)

print('Temporarily save CR maps for development, into CR_maps.fits')
hh0 = fits.PrimaryHDU(file_cr_map.astype(np.int))
hh0 = fits.PrimaryHDU(file_cr_map.astype(int))
hh1 = fits.ImageHDU(first_hits)
hlist = fits.HDUList([hh0, hh1])
hlist.writeto('CR_maps.fits', overwrite=True)
Expand Down
6 changes: 3 additions & 3 deletions jwst_reffiles/utils/dq_flags.py
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Original file line number Diff line number Diff line change
Expand Up @@ -38,7 +38,7 @@ def collapse_cr_map(dq_map):
nints, ngroups, ny, nx = dq_map.shape

# Create an array containing all group indexes
all_groups = np.zeros((1, ngroups, 1, 1), dtype=np.int)
all_groups = np.zeros((1, ngroups, 1, 1), dtype=int)
all_groups[0, :, 0, 0] = np.arange(ngroups)
intermediate1 = np.repeat(all_groups, nints, axis=0)
intermediate2 = np.repeat(intermediate1, ny, axis=2)
Expand Down Expand Up @@ -165,8 +165,8 @@ def signals_per_group(number_of_good, ngroup):
within each group
"""
nint, ny, nx = number_of_good.shape
good_per_group = np.zeros((ngroup, ny, nx)).astype(np.int)
bad_per_group = np.zeros((ngroup, ny, nx)).astype(np.int)
good_per_group = np.zeros((ngroup, ny, nx)).astype(int)
bad_per_group = np.zeros((ngroup, ny, nx)).astype(int)

for group in range(ngroup):
grp_map = np.sum(group < number_of_good, axis=0)
Expand Down
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