def output_filename(file_name):
dirname = os.path.dirname(file_name)
if len(dirname) > 0:
dirname += "/"
product_id = info.get_product_id(file_name)
target = info.get_target(file_name)
filter1, filter2 = info.get_filters(file_name)
image_time = info.get_image_time(file_name)
out_file = "{dirname}{product_id}_{target}_{filter1}_{filter2}_{image_date}".format(
dirname=dirname,
product_id=product_id[2:-4],
target=target,
filter1=filter1,
filter2=filter2,
image_date=image_time.strftime('%Y-%m-%d_%H.%M.%S'))
return out_file
def process_pds_data_file(from_file_name, is_verbose=False, skip_if_cub_exists=False, init_spice=True, nocleanup=False, additional_options={}):
product_id = info.get_product_id(from_file_name)
out_file_tiff = "%s.tif" % output_filename(from_file_name)
out_file_cub = "%s.cub" % output_filename(from_file_name)
if skip_if_cub_exists and os.path.exists(out_file_cub):
print "File %s exists, skipping processing" % out_file_cub
return
if "ringplane" in additional_options:
is_ringplane = additional_options["ringplane"].upper() in ("TRUE", "YES")
else:
is_ringplane = False
source_dirname = os.path.dirname(from_file_name)
if source_dirname == "":
source_dirname = "."
work_dir = "%s/work" % source_dirname
if not os.path.exists(work_dir):
os.mkdir(work_dir)
if is_verbose:
print "Importing to cube..."
else:
printProgress(0, 11, prefix="%s: "%from_file_name)
s = voyager.voy2isis(from_file_name, "%s/__%s_raw.cub"%(work_dir, product_id))
if is_verbose:
print s
if is_verbose:
print "Finding Reseaus..."
else:
printProgress(1, 11, prefix="%s: "%from_file_name)
s = geometry.findrx("%s/__%s_raw.cub"%(work_dir, product_id))
if is_verbose:
print s
if is_verbose:
print "Removing Reseaus..."
else:
printProgress(2, 11, prefix="%s: "%from_file_name)
s = geometry.remrx("%s/__%s_raw.cub"%(work_dir, product_id),
"%s/__%s_remrx.cub" % (work_dir, product_id),
action="BILINEAR")
if is_verbose:
print s
try:
if init_spice is True:
if is_verbose:
print "Initializing Spice..."
else:
printProgress(3, 11, prefix="%s: "%from_file_name)
s = cameras.spiceinit("%s/__%s_remrx.cub" % (work_dir, product_id), is_ringplane)
if is_verbose:
print s
if is_verbose:
print "Calibrating cube..."
else:
printProgress(4, 11, prefix="%s: "%from_file_name)
s = voyager.voycal("%s/__%s_raw.cub"%(work_dir, product_id),
"%s/__%s_cal.cub"%(work_dir, product_id))
if is_verbose:
print s
# TODO: Determine when to run this (on Io approach) and do so
#if is_verbose:
# print "Plasma torus irradiation correction..."
#else:
# printProgress(4, 11, prefix="%s: "%from_file_name)
#s = voyager.voycal("%s/__%s_cal.cub"%(work_dir, product_id),
# "%s/__%s_ramp.cub"%(work_dir, product_id))
#if is_verbose:
# print s
last_cube = "%s/__%s_cal.cub"%(work_dir, product_id)
except:
if is_verbose:
traceback.print_exc(file=sys.stdout)
last_cube = "%s/__%s_remrx.cub" % (work_dir, product_id)
if is_verbose:
print "Filling in Gaps..."
else:
printProgress(5, 11, prefix="%s: "%from_file_name)
s = mathandstats.fillgap(last_cube,
"%s/__%s_fill.cub" % (work_dir, product_id))
if is_verbose:
print s
if is_verbose:
print "Stretch Fix..."
else:
printProgress(5, 11, prefix="%s: "%from_file_name)
s = utility.stretch("%s/__%s_fill.cub" % (work_dir, product_id),
"%s/__%s_stretch.cub" % (work_dir, product_id))
if is_verbose:
print s
if is_verbose:
print "Running Noise Filter..."
else:
printProgress(6, 11, prefix="%s: "%from_file_name)
s = filters.noisefilter("%s/__%s_stretch.cub"%(work_dir, product_id),
"%s/__%s_stdz.cub"%(work_dir, product_id))
if is_verbose:
print s
if is_verbose:
print "Filling in Nulls..."
else:
printProgress(7, 11, prefix="%s: "%from_file_name)
s = filters.lowpass("%s/__%s_stdz.cub"%(work_dir, product_id),
"%s/__%s_fill0.cub"%(work_dir, product_id))
if is_verbose:
print s
if is_verbose:
print "Removing Frame-Edge Noise..."
else:
printProgress(8, 11, prefix="%s: "%from_file_name)
s = trimandmask.trim("%s/__%s_fill0.cub"%(work_dir, product_id),
out_file_cub,
top=2,
right=2,
bottom=2,
left=2)
if is_verbose:
print s
"""
if is_verbose:
print "Trimming Corners..."
else:
printProgress(9, 11, prefix="%s: "%from_file_name)
s = trimandmask.circle("%s/__%s_noise.cub" % (work_dir, product_id),
out_file_cub,
rad=500)
if is_verbose:
print s
"""
if is_verbose:
print "Exporting TIFF..."
else:
printProgress(9, 11, prefix="%s: "%from_file_name)
s = importexport.isis2std_grayscale("%s"%(out_file_cub),
"%s"%(out_file_tiff))
if is_verbose:
print s
if nocleanup is False:
if is_verbose:
print "Cleaning up..."
else:
printProgress(10, 11, prefix="%s: "%from_file_name)
map(os.unlink, glob.glob('%s/__%s*.cub'%(work_dir, product_id)))
else:
if is_verbose:
print "Skipping clean up..."
else:
printProgress(10, 11, prefix="%s: "%from_file_name)
dirname = os.path.dirname(out_file_tiff)
if len(dirname) > 0:
dirname += "/"
if os.path.exists("%sprint.prt"%dirname):
os.unlink("%sprint.prt"%dirname)
if not is_verbose:
printProgress(11, 11, prefix="%s: "%from_file_name)
def test_get_product_id_cub(self):
assert info.get_product_id(TestIsis3Galileo.CUB_FILE) == "25I0045"
def test_get_product_id_lbl(self):
assert info.get_product_id(TestIsis3Galileo.LBL_FILE) == "25I0045"
is_verbose = args.verbose
match_stretch = args.match
red_cub_file, r_min, r_max = process_file(args.red)
green_cub_file, g_min, g_max = process_file(args.green)
blue_cub_file, b_min, b_max = process_file(args.blue)
a = np.array([r_min, r_max, g_min, g_max, b_min, b_max])
min = np.min(a)
max = np.max(a)
print "Max:", max
print "Min:", min
red_product_id = info.get_product_id(red_cub_file)
green_product_id = info.get_product_id(green_cub_file)
blue_product_id = info.get_product_id(blue_cub_file)
targets = get_target_filename_portion(red_cub_file, green_cub_file,
blue_cub_file)
output_tiff = "%s_%s_%s_%s_RGB-composed.tif" % (
red_product_id, green_product_id, blue_product_id, targets)
s = importexport.isis2std_rgb(red_cub_file,
green_cub_file,
blue_cub_file,
output_tiff,
minimum=min,
maximum=max,
match_stretch=match_stretch)
def test_get_product_id_cub(self):
assert info.get_product_id(TestIsis3Voyager.CUB_FILE) == "1739S2-001"
def process_data_file(lbl_file_name, require_target, require_filters,
require_width, require_height, metadata_only, is_verbose,
skip_existing, init_spice, nocleanup,
additional_options):
source = utils.guess_from_filename_prefix(lbl_file_name)
source_dirname = os.path.dirname(source)
if source_dirname == "":
source_dirname = "."
if not os.path.exists(source):
print "File %s does not exist" % source
else:
print_if_verbose("Processing %s" % source, is_verbose)
target = info.get_target(source)
print_if_verbose("Target: %s" % target, is_verbose)
product_id = info.get_product_id(source)
print_if_verbose("Product ID: %s" % product_id, is_verbose)
try:
filter1, filter2 = info.get_filters(source)
except:
filter1, filter2 = (None, None)
print_if_verbose("Filter #1: %s" % filter1, is_verbose)
print_if_verbose("Filter #2: %s" % filter2, is_verbose)
width = info.get_num_line_samples(source)
height = info.get_num_lines(source)
lines = info.get_num_lines(source)
print_if_verbose("Lines: %s" % lines, is_verbose)
line_samples = info.get_num_line_samples(source)
print_if_verbose("Samples per line: %s" % line_samples, is_verbose)
image_date = info.get_image_time(source)
print_if_verbose("Image Date: %s" % image_date, is_verbose)
out_file_base = utils.output_filename(source)
out_file_tiff = "%s.tif" % out_file_base
print_if_verbose("Output Tiff: %s" % out_file_tiff, is_verbose)
out_file_cub = "%s.cub" % out_file_base
print_if_verbose("Output Cube: %s" % out_file_cub, is_verbose)
if metadata_only:
return
if skip_existing and os.path.exists(out_file_cub) and os.path.exists(
out_file_tiff):
print "Output exists, skipping."
return
if require_target is not None and not require_target.upper(
) == target.upper():
print "Target mismatch, exiting."
return
if require_filters is not None and not (filter1 in require_filters
or filter2 in require_filters):
print "Filter mismatch, exiting."
return
if require_height is not None and not (str(height) in require_height):
print "Height filter mismatch, exiting"
if require_width is not None and not (str(width) in require_width):
print "Width filter mismatch, exiting"
utils.process_pds_data_file(source,
is_verbose=is_verbose,
init_spice=init_spice,
nocleanup=nocleanup,
additional_options=additional_options)
def process_pds_data_file(lbl_file_name,
is_verbose=False,
skip_if_cub_exists=False,
init_spice=True,
nocleanup=False,
additional_options={}):
product_id = info.get_product_id(lbl_file_name)
out_file_tiff = "%s.tif" % output_filename(lbl_file_name)
out_file_cub = "%s.cub" % output_filename(lbl_file_name)
if skip_if_cub_exists and os.path.exists(out_file_cub):
print "File %s exists, skipping processing" % out_file_cub
return
if "ringplane" in additional_options:
is_ringplane = additional_options["ringplane"].upper() in ("TRUE",
"YES")
else:
is_ringplane = False
source_dirname = os.path.dirname(lbl_file_name)
if source_dirname == "":
source_dirname = "."
work_dir = "%s/work" % source_dirname
if not os.path.exists(work_dir):
os.mkdir(work_dir)
if is_verbose:
print "Importing to cube..."
else:
printProgress(0, 9, prefix="%s: " % lbl_file_name)
s = cassini.ciss2isis(lbl_file_name,
"%s/__%s_raw.cub" % (work_dir, product_id))
if is_verbose:
print s
if is_verbose:
print "Filling in Gaps..."
else:
printProgress(1, 9, prefix="%s: " % lbl_file_name)
s = mathandstats.fillgap("%s/__%s_raw.cub" % (work_dir, product_id),
"%s/__%s_fill0.cub" % (work_dir, product_id))
if is_verbose:
print s
if init_spice is True:
if is_verbose:
print "Initializing Spice..."
else:
printProgress(2, 9, prefix="%s: " % lbl_file_name)
s = cameras.spiceinit("%s/__%s_fill0.cub" % (work_dir, product_id),
is_ringplane)
if is_verbose:
print s
if is_verbose:
print "Calibrating cube..."
else:
printProgress(3, 9, prefix="%s: " % lbl_file_name)
s = cassini.cisscal("%s/__%s_fill0.cub" % (work_dir, product_id),
"%s/__%s_cal.cub" % (work_dir, product_id))
if is_verbose:
print s
if is_verbose:
print "Running Noise Filter..."
else:
printProgress(4, 9, prefix="%s: " % lbl_file_name)
s = filters.noisefilter("%s/__%s_cal.cub" % (work_dir, product_id),
"%s/__%s_stdz.cub" % (work_dir, product_id))
if is_verbose:
print s
if is_verbose:
print "Filling in Nulls..."
else:
printProgress(5, 9, prefix="%s: " % lbl_file_name)
s = filters.lowpass("%s/__%s_stdz.cub" % (work_dir, product_id),
"%s/__%s_fill.cub" % (work_dir, product_id))
if is_verbose:
print s
if is_verbose:
print "Removing Frame-Edge Noise..."
else:
printProgress(6, 9, prefix="%s: " % lbl_file_name)
s = trimandmask.trim("%s/__%s_fill.cub" % (work_dir, product_id),
"%s" % (out_file_cub))
if is_verbose:
print s
if is_verbose:
print "Exporting TIFF..."
else:
printProgress(7, 9, prefix="%s: " % lbl_file_name)
s = importexport.isis2std_grayscale("%s" % (out_file_cub),
"%s" % (out_file_tiff))
if is_verbose:
print s
if nocleanup is False:
if is_verbose:
print "Cleaning up..."
else:
printProgress(8, 9, prefix="%s: " % lbl_file_name)
map(os.unlink, glob.glob('%s/__%s*.cub' % (work_dir, product_id)))
else:
if is_verbose:
print "Skipping clean up..."
else:
printProgress(8, 9, prefix="%s: " % lbl_file_name)
if not is_verbose:
printProgress(9, 9, prefix="%s: " % lbl_file_name)
def test_get_product_id_cub(self):
assert info.get_product_id(
TestIsis3Info.CUB_FILE) == "1_N1489034146.123"
def test_get_product_id_lbl(self):
assert info.get_product_id(
TestIsis3Info.LBL_FILE) == "1_N1489034146.123"
def process_pds_data_file(from_file_name,
is_verbose=False,
skip_if_cub_exists=False,
init_spice=True,
nocleanup=False,
additional_options={}):
#out_file = output_filename(from_file_name)
#out_file_tiff = "%s.tif" % out_file
#out_file_cub = "%s.cub" % out_file
num_steps = 14
if "projection" in additional_options:
projection = additional_options["projection"]
else:
projection = "equirectangular"
source_dirname = os.path.dirname(from_file_name)
if source_dirname == "":
source_dirname = "."
work_dir = "%s/work" % source_dirname
if not os.path.exists(work_dir):
os.mkdir(work_dir)
product_id = info.get_product_id(from_file_name)
mapped_dir = "%s/work/mapped" % source_dirname
if not os.path.exists(mapped_dir):
os.mkdir(mapped_dir)
if is_verbose:
print "Importing to cube..."
else:
printProgress(0, num_steps, prefix="%s: " % from_file_name)
s = juno.junocam2isis(from_file_name,
"%s/__%s_raw.cub" % (work_dir, product_id))
if is_verbose:
print s
if "vt" in additional_options:
trim_pixels = int(additional_options["vt"])
if is_verbose:
print "Trimming Framelets..."
print "Vertical trimming: %d pixels" % trim_pixels
else:
printProgress(0, num_steps, prefix="%s: " % from_file_name)
trim_cubes(work_dir, product_id, trim_pixels=trim_pixels)
if init_spice is True:
if is_verbose:
print "Initializing Spice..."
else:
printProgress(1, num_steps, prefix="%s: " % from_file_name)
cub_files = glob.glob('%s/__%s_raw_*.cub' % (work_dir, product_id))
for cub_file in cub_files:
s = cameras.spiceinit(cub_file,
is_ringplane=False,
spkpredict=True,
ckpredicted=True,
cknadir=True)
if is_verbose:
print s
mid_num = int(
round(
len(glob.glob('%s/__%s_raw_*.cub' % (work_dir, product_id))) /
3.0 / 2.0))
mid_file = "%s/__%s_raw_GREEN_00%d.cub" % (work_dir, product_id, mid_num)
map_file = "%s/__%s_map.cub" % (work_dir, product_id)
if is_verbose:
print "Starting Map..."
else:
printProgress(2, num_steps, prefix="%s: " % from_file_name)
s = cameras.cam2map(mid_file, map_file, projection=projection)
if is_verbose:
print s
if is_verbose:
print "Map Projecting Stripes..."
else:
printProgress(3, num_steps, prefix="%s: " % from_file_name)
cub_files = glob.glob('%s/__%s_raw_*.cub' % (work_dir, product_id))
for cub_file in cub_files:
try: # Not all of them will work.
bn = os.path.basename(cub_file)
out_file = "%s/%s" % (mapped_dir, bn)
s = cameras.cam2map(cub_file,
out_file,
map=map_file,
resolution="MAP")
if is_verbose:
print s
except:
pass # Probably shouldn't eat the exception here.
if is_verbose:
print "Assembling Red Mosaic..."
else:
printProgress(4, num_steps, prefix="%s: " % from_file_name)
out_file_red = assemble_mosaic("RED", source_dirname, product_id,
is_verbose)
if is_verbose:
print "Assembling Green Mosaic..."
else:
printProgress(5, num_steps, prefix="%s: " % from_file_name)
out_file_green = assemble_mosaic("GREEN", source_dirname, product_id,
is_verbose)
if is_verbose:
print "Assembling Blue Mosaic..."
else:
printProgress(6, num_steps, prefix="%s: " % from_file_name)
out_file_blue = assemble_mosaic("BLUE", source_dirname, product_id,
is_verbose)
if "histeq" in additional_options and additional_options["histeq"].upper(
) in ("TRUE", "YES"):
if is_verbose:
print "Running histogram equalization on map projected cubes..."
else:
printProgress(7, num_steps, prefix="%s: " % from_file_name)
histeq_cube(out_file_red, work_dir, product_id)
histeq_cube(out_file_green, work_dir, product_id)
histeq_cube(out_file_blue, work_dir, product_id)
if is_verbose:
print "Exporting Map Projected Tiffs..."
else:
printProgress(8, num_steps, prefix="%s: " % from_file_name)
export(out_file_red, is_verbose)
export(out_file_green, is_verbose)
export(out_file_blue, is_verbose)
if is_verbose:
print "Camera Projecting Mosaics..."
else:
printProgress(9, num_steps, prefix="%s: " % from_file_name)
pad_file = "%s/__%s_raw_GREEN_00%d_padded.cub" % (work_dir, product_id,
mid_num)
utility.pad(mid_file, pad_file, top=2300, right=0, bottom=2300, left=0)
out_file_red_cam = "%s/%s_%s_Recammed.cub" % (source_dirname, product_id,
"RED")
cameras.map2cam(out_file_red, out_file_red_cam, pad_file)
out_file_green_cam = "%s/%s_%s_Recammed.cub" % (source_dirname, product_id,
"GREEN")
cameras.map2cam(out_file_green, out_file_green_cam, pad_file)
out_file_blue_cam = "%s/%s_%s_Recammed.cub" % (source_dirname, product_id,
"BLUE")
cameras.map2cam(out_file_blue, out_file_blue_cam, pad_file)
if "histeq" in additional_options and additional_options["histeq"].upper(
) in ("TRUE", "YES"):
if is_verbose:
print "Running histogram equalization on camera projected cubes..."
else:
printProgress(10, num_steps, prefix="%s: " % from_file_name)
histeq_cube(out_file_red_cam, work_dir, product_id)
histeq_cube(out_file_green_cam, work_dir, product_id)
histeq_cube(out_file_blue_cam, work_dir, product_id)
if is_verbose:
print "Exporting Camera Projected Tiffs..."
else:
printProgress(11, num_steps, prefix="%s: " % from_file_name)
export(out_file_red_cam, is_verbose)
export(out_file_green_cam, is_verbose)
export(out_file_blue_cam, is_verbose)
if is_verbose:
print "Exporting Color Camera Projected Tiff..."
else:
printProgress(12, num_steps, prefix="%s: " % from_file_name)
out_file_cam_rgb_tiff = "%s/%s_RGB.tif" % (source_dirname, product_id)
s = importexport.isis2std_rgb(from_cube_red=out_file_red_cam,
from_cube_green=out_file_green_cam,
from_cube_blue=out_file_blue_cam,
to_tiff=out_file_cam_rgb_tiff)
if is_verbose:
print s
if nocleanup is False:
if is_verbose:
print "Cleaning up..."
else:
printProgress(13, num_steps, prefix="%s: " % from_file_name)
clean_dir(work_dir, product_id)
clean_dir(mapped_dir, product_id)
dirname = os.path.dirname(out_file_red)
if len(dirname) > 0:
dirname += "/"
if os.path.exists("%sprint.prt" % dirname):
os.unlink("%sprint.prt" % dirname)
else:
if is_verbose:
print "Skipping clean up..."
else:
printProgress(13, num_steps, prefix="%s: " % from_file_name)
if not is_verbose:
printProgress(14, num_steps, prefix="%s: " % from_file_name)