mrc_filename = realpath(args[0])
try:
mrc = MRC(mrc_filename, readonly=True)
except BaseException as e:
help_msg(2, "Failed to open MRC file: " + str(e))
out_dir = realpath(args[1])
if not make_dir(out_dir):
help_msg(
2,
"Output directory already exists as regular file, choose another directory"
)
# Check other arguments, getting values for optional args, etc.
ext = "png" if ext == None else ext.lstrip('.')
if basename == None: basename = "%04d"
if x == None: x = (0, mrc.nx - 1)
elif x[0] < 0 or x[1] < x[0] or x[1] >= mrc.nx:
help_msg(2, "Invalid x argument supplied")
if y == None: y = (0, mrc.ny - 1)
elif y[0] < 0 or y[1] < y[0] or y[1] >= mrc.ny:
help_msg(2, "Invalid x argument supplied")
if z:
min_z, max_z = min(z), max(z)
if min_z < 0 or max_z >= mrc.nz:
help_msg(2, "Invalid z argument supplied")
imf = imfilter_util.list2imfilter(imfilters)
# Do the actual work!
mrc2stack(mrc.view(x, y, (0, mrc.nz - 1)), out_dir, z,
basename + "." + ext, imf)
x = (int(x[0]), int(x[1]))
elif o == "-y":
if y != None: help_msg(2, "May be only one y argument")
y = y.split("-")
if len(y) != 2 or not y[0].isdigit() or not y[1].isdigit(): help_msg(2, "Invalid y argument supplied")
y = (int(y[0]), int(y[1]))
else: imfilters += [imfilter_util.parse_opt(o,a,help_msg)]
# Make sure paths are good
if len(args) != 2: help_msg(2, "You need to provide an MRC and image output directory as arguments")
mrc_filename = realpath(args[0])
try: mrc = MRC(mrc_filename, readonly=True)
except BaseException as e: help_msg(2, "Failed to open MRC file: " + str(e))
out_dir = realpath(args[1])
if not make_dir(out_dir): help_msg(2, "Output directory already exists as regular file, choose another directory")
# Check other arguments, getting values for optional args, etc.
ext = "png" if ext == None else ext.lstrip('.')
if basename == None: basename = "%04d"
if x == None: x = (0, mrc.nx - 1)
elif x[0] < 0 or x[1] < x[0] or x[1] >= mrc.nx: help_msg(2, "Invalid x argument supplied")
if y == None: y = (0, mrc.ny - 1)
elif y[0] < 0 or y[1] < y[0] or y[1] >= mrc.ny: help_msg(2, "Invalid x argument supplied")
if z:
min_z, max_z = min(z), max(z)
if min_z < 0 or max_z >= mrc.nz: help_msg(2, "Invalid z argument supplied")
imf = imfilter_util.list2imfilter(imfilters)
# Do the actual work!
mrc2stack(mrc.view(x, y, (0, mrc.nz - 1)), out_dir, z, basename+"."+ext, imf)
