def crop_along_cline(filename):
print(filename)
# logpath = os.path.join(logdir, filename + ".txt")
# file = open(logpath, 'w')
# file.write(repr(filename) + '\n')
srcpath = os.path.join(srcdir, filename)
dstpath = os.path.join(dstdir, filename)
field_path = os.path.join(field_dir, filename)
clinepath = os.path.join(preclinedir, filename)
if srcmskdir:
srcmskpath = os.path.join(srcmskdir, filename)
dstmskpath = os.path.join(dstmskdir, filename)
# print(clinepath)
srcdata, header = nrrd.read(srcpath)
clinedata, header = nrrd.read(clinepath)
if srcmskdir:
srcmskdata, header = nrrd.read(srcmskpath)
# print("srcmsk", np.unique(srcmskdata))
# file.write("srcmsk: " + repr(np.unique(srcmskdata)) + '\n')
# print(srcdata.shape)
# print(srcmskdata.shape)
# print(clinedata.shape)
# clines = get_center_lines(clinedata, point_cnt=500)
clines = get_centerlines_by_points(clinedata, point_cnt=500)
# print(type(clines))
# print(len(clines))
src_results = expand_along_curves(srcdata, clines, 50)
if srcmskdir:
srcmsk_results = expand_along_curves(srcmskdata, clines, 50)
# print(len(src_results))
# print(len(srcmsk_results))
src_rst = src_results[0][0]
src_dp_field = src_results[0][1]
src_rst = src_rst.astype(np.int32)
src_rst = np.transpose(src_rst, (1, 2, 0))
nrrd.write(dstpath, src_rst)
nrrd.write(field_path, src_dp_field)
if srcmskdir: # src with mask
msk_rst = srcmsk_results[0][0]
# print(type(msk_rst))
msk_rst = msk_rst.astype(np.int16)
# print(type(msk_rst))
msk_rst = np.transpose(msk_rst, (1, 2, 0))
# print("dstmsk", np.unique(msk_rst))
nrrd.write(dstmskpath, msk_rst)
# print("finished", filename)
# file.close()
return
def crop_along_cline(sfilename, cl_idx):
print("data:", sfilename)
basename = os.path.splitext(sfilename)[0]
srcpath = os.path.join(srcdir, sfilename)
srcmask_path = os.path.join(srcmask_dir, sfilename)
srcdata, _ = nrrd.read(srcpath)
srcmsk_data, _ = nrrd.read(srcmask_path)
# print("srcmask: ", np.unique(srcmsk_data))
clines = get_center_lines(clinedata, point_cnt=500)
src_results = expand_along_curves(srcdata, clines, win)
srcmsk_results = expand_along_curves(srcmsk_data, clines, win)
src_rst = src_results[0][0].astype(np.int32)
# print("src: ", np.unique(src_rst))
src_rst = scale_range(src_rst, -1000, 1000, 1, 254)
src_rst = src_rst.astype(np.uint8)
src_warp = np.transpose(src_rst, (1, 2, 0))
# print("src: ", np.unique(src_warp))
srcmsk_rst = srcmsk_results[0][0]
# print("srcmask: ", np.unique(srcmsk_rst))
srcmsk_rst = (srcmsk_rst >= 0.5)
srcmsk_rst = srcmsk_rst.astype(np.uint8)
srcmsk_warp = np.transpose(srcmsk_rst, (1, 2, 0))
# print("srcmask: ", np.unique(srcmsk_warp))
(h, w, c) = src_rst.shape
for img_idx in range(c):
if not 1 in srcmsk_warp[:, :, img_idx]:
continue
imgname = basename + '_cl_' + str(cl_idx) + '_slice_' + str(
img_idx) + '.png'
imgpath = os.path.join(pngdir, imgname)
imgmaskpath = os.path.join(pngmask_dir, imgname)
imgmaskvispath = os.path.join(pngmaskvis_dir, imgname)
im = Image.fromarray(src_warp[:, :, img_idx], mode="L")
im.save(imgpath)
im = Image.fromarray(srcmsk_warp[:, :, img_idx], mode="L")
im.save(imgmaskpath)
im = Image.fromarray(255 * srcmsk_warp[:, :, img_idx], mode="L")
im.save(imgmaskvispath)
def crop_along_cline(sfilename, cl_idx):
print("data:", sfilename)
basename = os.path.splitext(sfilename)[0]
srcpath = os.path.join(srcdir, sfilename)
srcmask_path = os.path.join(srcmask_dir, sfilename)
srcdata, _ = nrrd.read(srcpath)
srcmsk_data, _ = nrrd.read(srcmask_path)
# print("srcmask: ", np.unique(srcmsk_data))
clines = get_center_lines(clinedata, point_cnt=500)
src_results = expand_along_curves(srcdata, clines, win)
srcmsk_results = expand_along_curves(srcmsk_data, clines, win)
src_rst = src_results[0][0].astype(np.int32)
# print("src: ", np.unique(src_rst))
src_rst = scale_range(src_rst, -1000, 1000, 1, 254)
src_rst = src_rst.astype(np.uint8)
src_warp = np.transpose(src_rst, (1, 2, 0))
# print("src: ", np.unique(src_warp))
srcmsk_rst = srcmsk_results[0][0]
# print("srcmask: ", np.unique(srcmsk_rst))
srcmsk_rst = (srcmsk_rst >= 0.5)
srcmsk_rst = srcmsk_rst.astype(np.uint8)
srcmsk_warp = np.transpose(srcmsk_rst, (1, 2, 0))
# print("srcmask: ", np.unique(srcmsk_warp))
(h, w, c) = src_rst.shape
for img_idx in range(20, c - 20): # skip 20 layers both ends
if not 1 in srcmsk_warp[:, :, img_idx]:
continue
slice_name = basename + '_cl_' + str(cl_idx) + '_slice_' + str(img_idx) + '.npz'
slice_path = os.path.join(npzdir, slice_name)
slice_mask_path = os.path.join(npzmaskdir, slice_name)
slice_maskvis_path = os.path.join(npzmaskvisdir, slice_name)
npz_slice = src_warp[:, :, img_idx - 20:img_idx + 20:5] # TODO: modify second 20 to 21
np.savez(slice_path, npz_slice)
# print(np.unique(npz_slice))
npzmask_slice = srcmsk_warp[:, :, img_idx]
np.savez(slice_mask_path, npzmask_slice)
npzmaskvis_slice = srcmsk_warp[:, :, img_idx] * 255
np.savez(slice_maskvis_path, npzmaskvis_slice)
def crop_along_cline(sfilename, cidx):
if verbose:
print("data", sfilename)
basename, ext = os.path.splitext(sfilename)
sfilename_cidx = basename + '_cline' + str(cidx) + ext
srcpath = os.path.join(srcdir, sfilename)
dstpath = os.path.join(dstdir, sfilename_cidx)
if field_dir:
field_path = os.path.join(field_dir, sfilename)
if not os.path.isfile(srcpath):
print("cannot find", srcpath)
return
srcdata, header = nrrd.read(srcpath)
if verbose:
print("original mask: ", np.unique(srcdata))
srcdata = srcdata.astype(np.int32)
clinedata = cline_list[cidx]
clines = get_center_lines(clinedata, point_cnt=500)
src_results = expand_along_curves(srcdata, clines, 50)
if if_mask:
src_rst = src_results[0][0]
# print("src_rst dtype: ", src_rst.dtype)
# print("transformed mask0: ", np.unique(src_rst))
src_rst = src_rst.astype(np.uint8)
else:
src_rst = src_results[0][0].astype(np.int32)
src_rst = np.transpose(src_rst, (1, 2, 0))
if field_dir:
src_field = src_results[0][1]
if verbose:
print("transformed mask: ", np.unique(src_rst))
nrrd.write(dstpath, src_rst)
if field_dir:
nrrd.write(field_path, src_field)