def stack_to_tif(stack_path, compress=1, wipe=False):
"""
:param stack_path: string, full path of .stack file to be converted to .tif
:param compress: int, compression level to use for tif file
:param wipe: bool, if True stack file will be deleted after saving as tif
:return:
"""
from numpy import array_equal
from os import remove
from os.path import split, sep
from numpy import fromfile
import volTools as volt
from skimage.external import tifffile as tif
dims = volt.getStackDims(split(stack_path)[0] + sep)
im = fromfile(stack_path, dtype='int16')
im = im.reshape(dims[-1::-1])
tif_path = stack_path.split('.')[0] + '.tif'
tif.imsave(tif_path, im, compress=compress)
if wipe:
check_file = tif.imread(tif_path)
if array_equal(check_file, im):
print('Deleting {0}...'.format(stack_path))
remove(stack_path)
else:
print('{0} and {1} differ... something went wrong!'.format(stack_path, tif_path))
def save_TiffStack(dataset,filename="image",outputPath="./"):
filename = filename.rstrip(".tiff")
filename = filename.rstrip(".tif")
outputFile = outputPath + filename + ".tiff"
print("saving ... : " + outputFile)
skTiff.imsave(outputFile,dataset)
print("save complete: " + outputFile)
def save_tiff(img_stack, pwd):
if pwd.endswith('.tif'):
tiff.imsave(pwd, img_stack)
else:
for z,frame in enumerate(img_stack):
fname = pwd + '_%03d' % (z+1) + '.tif'
dir, file = os.path.split(fname)
if not os.path.exists(dir):
os.makedirs(dir)
tiff.imsave(fname, frame)
def save_frame_to_tif(timestep, label_image, options):
if options.is_groundtruth:
filename = options.output_dir + '/man_track' + format(timestep, "0{}".format(options.filename_zero_padding)) + '.tif'
else:
filename = options.output_dir + '/mask' + format(timestep, "0{}".format(options.filename_zero_padding)) + '.tif'
# label_image = np.swapaxes(label_image, 0, 1)
if len(label_image.shape) == 2: # 2d
vigra.impex.writeImage(label_image.astype('uint16'), filename)
else: # 3D
label_image = np.transpose(label_image, axes=[2, 0, 1])
tifffile.imsave(filename, label_image.astype('uint16'))
def save_log(self):
if self.display_length is None:
self.clear()
raise LookupError("Please display sequence first!")
if self.file_name is None:
self._get_file_name()
if self.keep_display == True:
self.file_name += '-complete'
elif self.keep_display == False:
self.file_name += '-incomplete'
# set up log object
directory = os.path.join(self.log_dir, 'visual_display_log')
if not (os.path.isdir(directory)):
os.makedirs(directory)
logFile = dict(self.seq_log)
displayLog = dict(self.__dict__)
displayLog.pop('seq_log')
displayLog.pop('sequence')
logFile.update({'presentation': displayLog})
file_name = self.file_name + ".pkl"
# generate full log dictionary
path = os.path.join(directory, file_name)
ft.saveFile(path, logFile)
print("\nLog file generated successfully. Log file path: ")
print('{}'.format(path))
if self.is_save_sequence:
tf.imsave(os.path.join(directory, self.file_name + '.tif'),
self.sequence.astype(np.float32))
print('\nSequence file generated successfully. File path: ')
print('{}'.format(os.path.join(directory, self.file_name + '.tif')))
backupFileFolder = self._get_backup_folder()
if backupFileFolder is not None:
if not (os.path.isdir(backupFileFolder)):
os.makedirs(backupFileFolder)
backupFilePath = os.path.join(backupFileFolder, file_name)
ft.saveFile(backupFilePath, logFile)
if self.is_save_sequence:
tf.imsave(os.path.join(backupFileFolder, self.file_name + '.tif'),
self.sequence.astype(np.float32))
print("\nBackup log file generated successfully. Backup log file path: ")
print('{}'.format(backupFilePath))
else:
print("\nDid not find backup path, no backup was saved.")
def transform(f):
path = f
city_dir_name = f.split("/")[-3]
image = tifffile.imread(path)
bands = []
for band in range(8):
bands.append(equalize_adapthist(image[..., band]) * 2047)
img = np.array(np.stack(bands, axis=-1), dtype="uint16")
clahe_city_dir = os.path.join(wdata_dir, city_dir_name)
os.makedirs(clahe_city_dir, exist_ok=True)
mul_dir = os.path.join(clahe_city_dir, 'CLAHE-MUL-PanSharpen')
os.makedirs(mul_dir, exist_ok=True)
tifffile.imsave(os.path.join(mul_dir, f.split("/")[-1]), img, planarconfig='contig')
def SaveTopographImage(self, FileName=None):
if FileName is None or FileName == False:
# Set the default filename to the type of image (SumImage, etc...)
FileName = os.path.join(self.Defaults['DefaultFileDialogDir'],
str(self.comboTopograph.itemData(self.comboTopograph.currentIndex())) + '.tif')
Opts = QtWidgets.QFileDialog.Option(0x40) # QtWidgets.QFileDialog.HideNameFilterDetails
FileName, _ = QtWidgets.QFileDialog.getSaveFileName(self, caption='Save Topograph Image.', directory=FileName,
filter='TIF image (*.tif);;All files(*.*)', options=Opts)
if FileName != '':
# Store the default path now that the user has selected a file.
self.Defaults['DefaultFileDialogDir'], _ = os.path.split(str(FileName))
# Write the image file to disk.
imsave(FileName, self.canvasTopograph.ImageData[:].astype('float32'))
def _save_frame_to_tif(self, timestep, label_image, output_dir, filename_zero_padding=3):
"""
Save a single frame to a 2D or 3D tif
"""
filename = os.path.join(output_dir, f"mask{timestep:0{filename_zero_padding}}.tif")
# import ipdb; ipdb.set_trace()
label_image = np.swapaxes(label_image.squeeze(), 0, 1)
if len(label_image.shape) == 2: # 2d
vigra.impex.writeImage(label_image.astype('uint16'), filename)
elif len(label_image.shape) == 3: # 3D
label_image = np.transpose(label_image, axes=[2, 0, 1])
tifffile.imsave(filename, label_image.astype('uint16'))
else:
raise ValueError("Image had the wrong dimensions, can only save 2 or 3D images with a single channel")
def stack_writer(out_dir="",file_name="",stack=[],metadata=""):
stack_data=np.array(stack)
md_name=file_name+".html"
file_name+=".tif"
full_save_path=os.path.join(out_dir,file_name)
full_md_save_path=os.path.join(out_dir,md_name)
imsave(full_save_path,stack_data)
if metadata:
if isinstance(metadata,str):
with open(full_md_save_path,"w") as md_file:
md_file.write(metadata)
elif isinstance(metadata, list):
metadata_str="<html>%s</html>" % "<br>".join(metadata)
with open(full_md_save_path,"w") as md_file:
md_file.write(metadata_str)
def stack_to_tif(stack_path):
"""
:param stack_path: string, full path of .stack file to be converted to .tif
:return:
"""
from os.path import split, sep
from numpy import fromfile
import volTools as volt
from skimage.external import tifffile as tif
dims = volt.getStackDims(split(stack_path)[0] + sep)
im = fromfile(stack_path, dtype='int16')
im = im.reshape(dims[-1::-1])
tif_path = stack_path.split('.')[0] + '.tif'
tif.imsave(tif_path, im, compress=1)
def imsave_al(image, im, path):
dic = oib.image_info(im)
if dic['time_interval'] == None:
t = 0
else:
t = float(dic['time_interval'])
sx = (1/float(dic['xsize']))
filename = [os.path.splitext(filename)[0] for filename in os.listdir(path) if filename.endswith(('.nd2'))]
filename
i = 0
for img in image:
i+=1
filename_save = (path+ '/' + ('%s%i' %(filename[0], i)) + '.tif')
filename_save
if os.path.isfile(filename_save) == True:
print 'the file already exist'
else:
tifffile.imsave(filename_save, img.transpose(0,1,4,2,3), imagej=True, resolution = (sx,sx), metadata = {'mode' : 'color', 'finterval' : t, 'unit' : 'micron'})
def file_writer(filename, signal, **kwds):
"""Writes data to tif using Christoph Gohlke's tifffile library
Parameters
----------
filename: str
signal: a Signal instance
"""
data = signal.data
if signal.is_rgbx is True:
data = rgb_tools.rgbx2regular_array(data)
photometric = "rgb"
else:
photometric = "minisblack"
if description not in kwds:
if signal.metadata.General.title:
kwds['description'] = signal.metadata.General.title
imsave(filename, data,
software="hyperspy",
photometric=photometric,
**kwds)
def importRawJCamF(path,
saveFolder=None,
dtype=np.dtype('<u2'),
headerLength=116,
tailerLength=218,
column=2048,
row=2048,
frame=None, # how many frame to read
crop=None):
if frame:
data = np.fromfile(path, dtype=dtype, count=frame * column * row + headerLength)
header = data[0:headerLength]
tailer = []
mov = data[headerLength:].reshape((frame, column, row))
else:
data = np.fromfile(path, dtype=dtype)
header = data[0:headerLength]
tailer = data[len(data) - tailerLength:len(data)]
frame = (len(data) - headerLength - tailerLength) / (column * row)
mov = data[headerLength:len(data) - tailerLength].reshape((frame, column, row))
if saveFolder:
if crop:
try:
mov = mov[:, crop[0]:crop[1], crop[2]:crop[3]]
fileName = path.split('\\')[-1] + '_cropped.tif'
except Exception as e:
print 'importRawJCamF: Can not understant the paramenter "crop":' + str(
crop) + '\ncorp should be: [rowStart,rowEnd,colStart,colEnd]'
print '\nTrace back: \n' + e
else:
fileName = path.split('\\')[-1] + '.tif'
tf.imsave(os.path.join(saveFolder, fileName), mov)
return mov, header, tailer
else:
ims = axs2[1].imshow(
(np.abs(pupil)),
extent=[-Kextent * n, Kextent * n, -Kextent * n,
Kextent * n]) #plot the phase of the pupil
axs2[1].set_title('|Pupil|')
# finally, render the figures
plt.show()
############################
##### Save Psf to .tif file
if SaveData:
wavelength = 0.520 #um #you may want to specify a wavelength to save a calibrated PSF
from skimage.external import tifffile as tif
psf16 = np.transpose(np.abs(PSF), (2, 0, 1))
psf16 = (psf16 * (2**16 - 1) / np.amax(psf16)).astype(
'uint16') #normalize and convert to 16 bit
psf16.shape = 1, N, 1, N, N, 1 # dimensions in TZCYXS order
sampling = pixel_size / n * wavelength
tif.imsave('psf.tif',
psf16,
imagej=True,
resolution=(1.0 / sampling, 1.0 / sampling),
metadata={
'spacing': sampling,
'unit': 'um'
})
def write_ometiff(output_path, array, omexml_string):
tifffile.imsave(output_path,
array,
photometric='minisblack',
description=omexml_string,
metadata={'axes': 'TZCXY'})
def tif_writer(numpy_array="",path="",md_string=""):
imsave("%s.tif" % path,numpy_array)
if md_string:
with open("%s.html" % path,"w") as md_file:
md_file.write(md_string)
zyx = load_np(converted_points)
zyx = np.asarray([
str((int(xx[0]), int(xx[1]), int(xx[2])))
for xx in load_np(converted_points)
])
from collections import Counter
zyx_cnt = Counter(zyx)
#manually call transformix..
c_rfe = '/home/wanglab/wang/pisano/tracing_output/antero_4x/20170115_tp_bl6_lob6a_1000r_02/20170115_tp_bl6_lob6a_1000r_647_010na_z7d5um_125msec_10povlp_resized_ch00_resampledforelastix.tif'
transformed_dst = '/home/wanglab/wang/pisano/tracing_output/antero_4x/20170115_tp_bl6_lob6a_1000r_02/3dunet_output/transformed_points'
transformfile = '/home/wanglab/wang/pisano/tracing_output/antero_4x/20170115_tp_bl6_lob6a_1000r_02/elastix/TransformParameters.1.txt'
transformix_command_line_call(c_rfe, transformed_dst, transformfile)
#cell_registered channel
cell_reg = tifffile.imread(
'/home/wanglab/wang/pisano/tracing_output/antero_4x/20170115_tp_bl6_lob6a_1000r_02/3dunet_output/transformed_points/result.tif'
)
cell_cnn = np.zeros_like(cell_reg)
for zyx, v in zyx_cnt.iteritems():
z, y, x = [
int(xx) for xx in zyx.replace(
'(',
'',
).replace(')', '').split(',')
]
cell_cnn[z, y, x] = v * 100
merged = np.stack([cell_cnn, cell_reg, np.zeros_like(cell_reg)], -1)
tifffile.imsave('/home/wanglab/Downloads/merged.tif', merged)
#out = np.concatenate([cell_cnn, cell_reg, ], 0)
'(',
'',
).replace(')', '').split(',')
]
try:
cnn_cellvolloaded[z, y, x] = v * 100
except Exception as e:
print(e)
merged = np.stack([
cnn_cellvolloaded, cellvolloaded,
np.zeros_like(cellvolloaded)
], -1)
merged = np.swapaxes(merged, 0, 2) #reorient to horizontal
tifffile.imsave(
os.path.join(
dst,
'generate_downsized_overlay_{}_points_merged_resampled_for_elastix.tif'
.format(os.path.basename(fld))), merged)
#EXAMPLE USING LIGHTSHEET - assumes marking centers in the 'raw' full sized cell channel. This will transform those centers into "atlas" space (in this case the moving image)
#in this case the "inverse transform has the atlas as the moving image in the first step, and the autofluorescence channel as the moving image in the second step
r2s0 = [
xx for xx in listall(cellvol.inverse_elastixfld,
'reg2sig_TransformParameters.0.txt')
if 'cellch' in xx
][0]
r2s1 = [
xx for xx in listall(cellvol.inverse_elastixfld,
'reg2sig_TransformParameters.1.txt')
if 'cellch' in xx
][0]
self.stack = self.stack.astype(np.uint8)
# test
s = AlignStack('C:/Users/ad245339/Desktop/images/Dissolution Mesbah-Tocino 2011/AM39-FDA-suivi disso X5000')
s.run4()
s.cropage()
imsave('test.tif', s.stackAligne)
"""
"""
def build_iscat_training(bf_filepaths, iscat_filepaths, sampling=4):
"""Creates iscat training data and target in data/iscat_seg/[REF_FRAMES / MASKS] for the iSCAT cell segmentation task
ARGS:
bf_filepaths (list(str)): filepaths of all the bright field images to input as returned by utilitiues.load_data_paths()
iscat_filepaths (list(str)): filepaths of all the iscat images to input as returned by utilitiues.load_data_paths()
sampling (int): sampling interval of the saved images (lower storage footprint)
"""
OUT_PATH = DATA_PATH + 'iscat_seg/'
os.makedirs(os.path.join(OUT_PATH, 'REF_FRAMES/'), exist_ok=True)
os.makedirs(os.path.join(OUT_PATH, 'MASKS/'), exist_ok=True)
# Range of non filtered elements [px]
min_size, max_size = 1, 13
iscat_stacks = (utilities.load_imgs(path) for path in iscat_filepaths)
bf_stacks = (utilities.load_imgs(path) for path in bf_filepaths)
# Returns the metadata of the exwperiments such as frame rate
metadatas = get_experiments_metadata(iscat_filepaths)
if torch.cuda.is_available():
device = torch.cuda.current_device()
torch.cuda.set_device(device)
print("Running on: {:s}".format(torch.cuda.get_device_name(device)))
cuda = torch.device('cuda')
else:
# Doesn't run on CPU only machines comment if no GPU
print("No CUDA device found")
sys.exit(1)
unet = UNetCell(1, 1, device=cuda, bilinear_upsampling=False)
unet.load_state_dict(torch.load('outputs/saved_models/bf_unet.pth'))
for i, (bf_stack, iscat_stack,
metadata) in enumerate(zip(bf_stacks, iscat_stacks, metadatas)):
if i < 45: continue
bf_stack = bf_stack.astype('float32')
print(bf_stack.shape)
if bf_stack.shape[1:] != iscat_stack.shape[1:]:
bf_stack = processing.coregister(bf_stack, 1.38)
print(bf_stack.shape)
normalize(bf_stack)
# Samples iscat image to correct for the difference in framefate
iscat_stack = iscat_stack[::sampling * int(metadata['iscat_fps'] /
metadata['tirf_fps'])]
torch_stack = torch.from_numpy(bf_stack).unsqueeze(1).cuda()
mask = unet.predict_stack(
torch_stack).detach().squeeze().cpu().numpy() > 0.05
mask = morphology.grey_erosion(mask * 255,
structure=processing.structural_element(
'circle', (3, 5, 5)))
mask = morphology.grey_closing(mask,
structure=processing.structural_element(
'circle', (3, 7, 7)))
mask = (mask > 50).astype('uint8')
# Median filtering and normalization
iscat_stack = processing.image_correction(iscat_stack)
# Contrast enhancement
iscat_stack = processing.enhance_contrast(iscat_stack,
'stretching',
percentile=(1, 99))
# Fourier filtering of image
iscat_stack = processing.fft_filtering(iscat_stack, min_size, max_size,
True)
iscat_stack = processing.enhance_contrast(iscat_stack,
'stretching',
percentile=(3, 97))
for j in range(0, min(iscat_stack.shape[0], mask.shape[0]), sampling):
if iscat_stack[j].shape == mask[j].shape:
# Doesn't save images without detected cells
if mask[j].max() == 0: continue
print("\rSaving to stack_{}_{}.png".format(i + 1, j + 1),
end=' ' * 5)
tifffile.imsave(
os.path.join(OUT_PATH, 'REF_FRAMES/',
"stack_{}_{}.png".format(i + 1, j + 1)),
rescale(iscat_stack[j]))
tifffile.imsave(
os.path.join(OUT_PATH, 'MASKS/',
"mask_{}_{}.png".format(i + 1, j + 1)),
mask[j] * 255)
else:
print("Error, shape: {}, {}".format(iscat_stack[j].shape,
mask[j].shape))
break
print('')
def test(self):
del self.WGANVGG
# load
self.WGANVGG_G = WGAN_VGG_generator().to(self.device)
self.load_model()
# compute PSNR, SSIM, RMSE
ori_psnr_avg, ori_ssim_avg = 0, 0
pred_psnr_avg, pred_ssim_avg = 0, 0
with torch.no_grad():
num_total_img = len(self.test_list)
for img_idx, img_path in enumerate(self.test_list):
img_name = os.path.basename(img_path)
img_path = os.path.abspath(img_path)
print("[{}/{}] processing {}".format(
img_idx, num_total_img, os.path.abspath(img_path)))
gt_img_path = self.test_gt_list[img_idx]
gt_img = imread(gt_img_path)
input_img = imread(img_path)
img_patch_dataset = ImageDataset(self.opt, input_img)
img_patch_dataloader = DataLoader(
dataset=img_patch_dataset,
batch_size=self.opt.batch_size,
shuffle=False)
img_shape = img_patch_dataset.get_img_shape()
pad_img_shape = img_patch_dataset.get_padded_img_shape()
out_list = []
for i, x in enumerate(img_patch_dataloader):
x = x.float().to(self.device)
pred = self.WGANVGG_G(x)
pred = pred.to('cpu').detach().numpy()
out_list.append(pred)
out = np.concatenate(out_list, axis=0)
out = out.squeeze()
img_name = 'out-' + img_name
base_name = os.path.basename(self.opt.checkpoint_dir)
test_result_dir = os.path.join(self.opt.test_result_dir,
base_name)
if not os.path.exists(test_result_dir):
os.makedirs(test_result_dir)
dst_img_path = os.path.join(test_result_dir, img_name)
out_img = mp.recon_patches(out, pad_img_shape[1],
pad_img_shape[0],
self.opt.patch_size,
self.opt.patch_offset)
out_img = mp.unpad_img(out_img, self.opt.patch_offset,
img_shape)
input_img = torch.Tensor(input_img)
out_img = torch.Tensor(out_img)
gt_img = torch.Tensor(gt_img)
input_img = self.trunc(
self.denormalize_(input_img).cpu().detach())
out_img = self.trunc(self.denormalize_(out_img).cpu().detach())
gt_img = self.trunc(self.denormalize_(gt_img).cpu().detach())
# x = self.trunc(self.denormalize_(x))
# out_img = self.trunc(self.denormalize_(out_img))
# gt_img = self.trunc(self.denormalize_(gt_img))
data_range = self.trunc_max - self.trunc_min
original_result, pred_result = compute_measure(
input_img, gt_img, out_img, data_range)
op, oos, _ = original_result
pp, ps, _ = pred_result
ori_psnr_avg += op
ori_ssim_avg += oos
pred_psnr_avg += pp
pred_ssim_avg += ps
out_img = self.normalize_(out_img)
out_img = out_img.cpu().numpy()
imsave(dst_img_path, out_img)
aop = ori_psnr_avg / (img_idx + 1)
aos = ori_ssim_avg / (img_idx + 1)
app = pred_psnr_avg / (img_idx + 1)
aps = pred_ssim_avg / (img_idx + 1)
print(
"((ORIGIN)) PSNR : {:.5f}, SSIM : {:.5f}, ((PREP)) PSNR : {:.5f}, SSIM : {:.5f}"
.format(aop, aos, app, aps))
b = []
x_range = np.arange(0, 100, 1)
y_range = np.arange(0, 100, 1)
z_range = np.arange(40, 43, 3)
try:
a, b = fastScan(piStage,
ps,
n_captures=3000,
x_range=x_range,
y_range=y_range,
z_range=z_range)
print('TotalTime:', time.time() - start0)
print(piStage.CloseConnection())
ps.close()
imsave('dataA.tif', a)
imsave('dataB.tif', a)
from pylab import *
matshow(a[0])
show(0)
except:
traceback.print_exc()
print(piStage.CloseConnection())
ps.close()
#plot(dataA)
#plot(dataB)
#show(0)
as of march 2019 numpy and scikit-image need updating to newer versions using conda
conda install -c anaconda numpy=1.16.0
conda install -c anaconda scikit-image=0.14.2
as does tensor flow gpu - the version installed by flowdec have a dll load error.
watch out for cuda / tensorflow versions compatabiliries.
conda install -c anaconda tensorflow-gpu
I got a load dll error before this install, but tensor flow updated to v1.13 tested ok
"""
from skimage.external.tifffile import imsave, imread
from flowdec import data as fd_data
from flowdec import restoration as fd_restoration
# Load test image from same dir as we execute in
raw = imread('C1-YeastTNA1_1516_conv_RG_26oC_003.tif')
# Load psf kernel image from same dir
kernel = imread('gpsf_3D_1514_a3_001_WF-sub105.tif')
# Run the deconvolution process and note that deconvolution initialization is best kept separate from
# execution since the "initialize" operation corresponds to creating a TensorFlow graph, which is a
# relatively expensive operation and should not be repeated across multiple executions
n_iter = 500
algo = fd_restoration.RichardsonLucyDeconvolver(raw.ndim).initialize()
res = algo.run(fd_data.Acquisition(data=raw, kernel=kernel), niter=n_iter).data
# save the result,
print('Saving result image TIFF file')
# using skimage.external.tifffile.imsave
imsave(('result' + str(n_iter) + 'iterations.tif'), res)
from skimage.external import tifffile
print(sys.argv)
print(os.environ["SLURM_ARRAY_TASK_ID"])
jobid = int(os.environ["SLURM_ARRAY_TASK_ID"])
src = "/jukebox/scratch/kellyms"
pths = [
os.path.join(src, xx) for xx in os.listdir(src) if "m6" in xx or "f6" in xx
]
if jobid > len(pths) + 1:
print("array jobs greater than number of brains")
else:
print("processing brain: {}".format(pths[jobid]))
arrpth = os.path.join(
pths[jobid], "transformed_annotations/transformed_annotations.npy")
dst = os.path.join(pths[jobid], "annotations_as_single_tifs")
if not os.path.exists(dst): os.mkdir(dst)
arr = np.lib.format.open_memmap(arrpth, dtype="uint16", mode="r")
print("\nfile with shape: {}".format(arr.shape))
for z in range(arr.shape[0]):
tifffile.imsave(os.path.join(
dst, "annotation_Z{}.tif".format(str(z).zfill(4))),
arr[z],
compress=6)
print("\nmade z plane # {}".format(z))
mm = stat.readDataGroup(mm_du_heatmaps)
fm = stat.readDataGroup(fm_du_heatmaps)
mf = stat.readDataGroup(mf_du_heatmaps)
#find mean and standard deviation of heatmap in each group
mm_mean = np.mean(mm, axis=0)
mm_std = np.std(mm, axis=0)
fm_mean = np.mean(fm, axis=0)
fm_std = np.std(fm, axis=0)
mf_mean = np.mean(mf, axis=0)
mf_std = np.std(mf, axis=0)
#write mean and standard dev maps to destination
tifffile.imsave(os.path.join(pvaldst, "mm_mean.tif"),
np.transpose(mm_mean, [1, 0, 2]).astype("float32"))
tifffile.imsave(os.path.join(pvaldst, "mm_std.tif"),
np.transpose(mm_std, [1, 0, 2]).astype("float32"))
tifffile.imsave(os.path.join(pvaldst, "fm_mean.tif"),
np.transpose(fm_mean, [1, 0, 2]).astype("float32"))
tifffile.imsave(os.path.join(pvaldst, "fm_std.tif"),
np.transpose(fm_std, [1, 0, 2]).astype("float32"))
tifffile.imsave(os.path.join(pvaldst, "mf_mean.tif"),
np.transpose(mf_mean, [1, 0, 2]).astype("float32"))
tifffile.imsave(os.path.join(pvaldst, "mf_std.tif"),
np.transpose(mf_std, [1, 0, 2]).astype("float32"))
#Generate the p-values map
##########################
def generate_patch(**params):
"""
Function to patch up data and make into memory mapped array
Inputs
-----------
src = folder containing tiffs
patch_dst = location to save memmap array
patchlist = list of patches generated from make_indices function
stridesize = (90,90,30) - stride size in 3d ZYX
patchsize = (180,180,60) - size of window ZYX
mode = "folder" #"folder" = list of files where each patch is a file, "memmap" = 4D array of patches by Z by Y by X
Returns
------------
location of patched memory mapped array of shape (patches, patchsize_z, patchsize_y, patchsize_x)
"""
#load array
input_arr = load_memmap_arr(
os.path.join(params["data_dir"], "input_memmap_array.npy"))
#set patch destination
patch_dst = os.path.join(params["data_dir"], "input_chnks")
#set variables
if patch_dst[-4:] == ".npy": patch_dst = patch_dst[:-4]
if not os.path.exists(patch_dst): os.mkdir(patch_dst)
window = params["window"]
patchsize = params["patchsz"]
jobid = int(params["jobid"]) #set patch no. to run through cnn
#select the file to process for this array job
if jobid > len(params["patchlist"]) - 1:
sys.stdout.write("\njobid {} > number of files".format(jobid))
sys.stdout.flush()
else:
#patch
for i, p in enumerate(params["patchlist"]):
if i == jobid:
v = input_arr[p[0]:p[0] + patchsize[0],
p[1]:p[1] + patchsize[1],
p[2]:p[2] + patchsize[2]]
#padding to prevent cnn erros
if v.shape[0] < window[0]:
pad = np.zeros(
(window[0] - v.shape[0], v.shape[1], v.shape[2]))
v = np.append(v, pad, axis=0)
if v.shape[1] < window[1]:
pad = np.zeros(
(v.shape[0], window[1] - v.shape[1], v.shape[2]))
v = np.append(v, pad, axis=1)
if v.shape[2] < window[2]:
pad = np.zeros(
(v.shape[0], v.shape[1], window[2] - v.shape[2]))
v = np.append(v, pad, axis=2)
#saving out
tifffile.imsave(os.path.join(
patch_dst, "patch_{}.tif".format(str(i).zfill(10))),
v.astype("float32"),
compress=1)
if params["verbose"]:
print("{} of {}".format(i, len(params["patchlist"])))
#return
return patch_dst
#run_list = ['scenes_run1','scenes_run2','scenes_run3','scenes_run3','scenes_run4','scenes_run5','scenes_run6','scenes_run7','scenes_run8','scenes_run9','scenes_run10']
#figure out directories to search
dst_dir = os.path.join(rootdir, animalid, session, acquisition, 'all_combined',
'block_reduced')
if not os.path.isdir(dst_dir):
os.makedirs(dst_dir)
for run in run_list:
#run = run_list[0]
data_dir = os.path.join(rootdir, animalid, session, acquisition, run)
raw_dir = glob.glob(os.path.join(data_dir, 'raw*'))[0]
print(raw_dir)
src_dir = os.path.join(raw_dir, '*.tif')
for fn in glob.glob(src_dir):
i0 = findOccurrences(fn, '/')[-1]
i1 = findOccurrences(fn, '_')[-1]
new_fn = '%s_%s_%s' % (acquisition, run, fn[i1 + 1:])
print(new_fn)
stack0 = imread(fn)
stack1 = block_mean_stack(stack0, (2, 2))
print(stack1.shape)
imsave(os.path.join(dst_dir, new_fn), stack1)
requires installation of python and other python packlages,
which are included in the anaconda python release.
pyCUDAdecon and instructions to install and use are at
https://github.com/tlambert03/pycudadecon
"""
#import required packages
from pycudadecon import decon, make_otf
from skimage.external.tifffile import imsave
# set input a and output file paths
image_path = 'C1-YeastTNA1_1516_conv_RG_26oC_003.tif'
psf_path = 'gpsf_3D_1514_a3_001_WF-sub105.tif'
otfOutPath = 'otf.tif'
# do the deconvolution on GPU
numIters = 30
result = decon(image_path, psf_path, n_iters=numIters)
print("result data type is " + str(result.dtype))
print('results numpy array shape is ')
print(result.shape)
# save the result,
print('Saving result image TIFF file')
# using skimage.external.tifffile.imsave
imsave(('result' + str(numIters) + 'iterations.tif'), result) #, imagej)
# save otf tiff file from PSF image tiff.
print('making otf')
make_otf(psf_path, otfOutPath, dzpsf=0.15, dxpsf=0.05, wavelength=510, na=1.3, nimm=1.333, otf_bgrd=None, krmax=0, fixorigin=10, cleanup_otf=True, max_otf_size=60000)
labels = np.unique(fov_ins_array[fov_ins_array > 0])
i = 0
for label in labels:
i += 1
if i > 5: break
fov_seg_array = closing(fov_ins_array == label, ball(1))
fov_label_array = skimage.measure.label(fov_seg_array)
fov_labels = np.unique(fov_label_array[fov_label_array > 0])
label_sel = fov_labels[np.argmax(
[np.sum(fov_label_array == x) for x in fov_labels])]
fov_seg_array = fov_label_array == label_sel
if np.sum(fov_seg_array) < 50:
continue
fov_skel_array, skel = skel_cal(fov_seg_array)
skels_array[fov_skel_array > 0] = 1
ends, vecs = ends_cal(skel)
ends_array[ends[:, 0], ends[:, 1], ends[:, 2]] = 1
fname = osp.splitext(osp.basename(fov_ins_path))[0]
fpath_ends = osp.join(osp.dirname(fov_ins_path),
"{}_ends.tif".format(fname))
fpath_skels = osp.join(osp.dirname(fov_ins_path),
"{}_skels.tif".format(fname))
tifffile.imsave(fpath_ends, ends_array)
tifffile.imsave(fpath_skels, skels_array)
def main():
# Initialize common configurations
common_config = Config("../../config/common.config")
# Get image sequence path and filename
path = common_config["Image Sequence"]["Path"]
filename = common_config["Image Sequence"]["Filename"]
try:
input_folder = sys.argv[1]
make_legend = True
except:
# Get output folder
output_folder = os.path.join("..", "..", "output", "tracking/", common_config["Output"]["Folder"])
# Get latest folder
latest_results = get_latest_folder(output_folder)
# Make input folder
input_folder = os.path.join(output_folder, latest_results)
# Do not make legend
make_legend = False
print "Input folder:", input_folder
# Read trajectories
filenames = filter(lambda fn: fn.lower().endswith(".zip"), os.listdir(input_folder))
labels = map(lambda fn: os.path.splitext(fn)[0], filenames)
# Upload trajectories
contours = {label : unzip_csv(os.path.join(input_folder, filename)) for filename, label in zip(filenames, labels)}
contours_n = len(contours)
# Read image sequence
input_sequence = np.squeeze(imread(os.path.join(path, filename))).astype(np.float32)
input_sequence /= input_sequence.max()
frame_n = len(input_sequence)
try:
fns, colors = colors_from_csv(os.path.join(input_folder, "colors.csv"))
color_map = {fn: clr for fn, clr in zip(fns, colors)}
except:
colors = get_random_colors(contours_n, "hsv")
color_map = {fn: clr for fn, clr in zip(labels, colors)}
rgb_stack = []
filaments_mask = np.zeros_like(input_sequence[0], dtype=np.uint16)
for frame_i in xrange(frame_n):
sys.stdout.write("\r Frame: " + str(frame_i))
image_rgb = np.dstack([input_sequence[frame_i]] * 3)
for filament_i, filament_data in enumerate(contours.items()):
tname, tcoords = filament_data
try:
fiber_color = color_map[tname]
except:
fiber_color = colors[fiber_color]
cv2.polylines(image_rgb, [tcoords[frame_i].astype(np.int32)], False, fiber_color, 1, 8)
cv2.polylines(filaments_mask[frame_i], [tcoords[frame_i].astype(np.int32)], False, filament_i + 1)
rgb_stack.append((image_rgb * 255).astype(np.uint8))
sys.stdout.write("\r Finished.\n")
imsave(os.path.join(input_folder, "overlay.tif"), np.asarray(rgb_stack))
imsave(os.path.join(input_folder, "index.tif"), filaments_mask)
# Make legend
if make_legend:
labels = contours.keys()
filament = [contour[0] for contour in contours.values()]
legend = gen_legend(filament, labels, colors, input_sequence[0])
# Save legend
imsave(os.path.join(input_folder, "legend.tif"), (legend * 255).astype(np.uint8))
p2=swc_array[i + 1, 2:5][::-1],
size=shape)
else:
print("The line {} have error. s: {}".format(i, s))
break
mask[line > 0] = label
mask = dilation(mask, ball(1))
return mask
if __name__ == "__main__":
# test()
# m = Connect_2_points(p1=[173, 140, 10], p2=[173, 139, 9])
# m = Connect_2_points(p1=[172, 136, 3], p2=[173, 138, 4])
# m = Connect_2_points(p1=[0, 0, 3], p2=[0, 0, 8])
# print(m.sum())
# connect_2_points_()
swc_path = r"C:\Users\Administrator\Desktop\Syn_chaos_300_5_2_4_6_000\swcs\Syn_chaos_300_5_2_4_6_000_4.swc"
path, name = os.path.split(swc_path)
label = str_to_float(name.split('.')[0].split('_')[-1])
swc_num = np.array(psc(path, name.split('.')[0]))
c_e = find_cross_end(swc_num)
mask = sparse2dense_Loop(swc_num, shape=[300, 300, 300], label=label)
tifffile.imsave(os.path.join(path,
name.split('.')[0] + '.tif'),
(mask > 0).astype(np.float32))
print('')
array = labelled [0]
# array = array.astype(np.uint8)
# calculating frequency of label numbers
unique, counts = np.unique(array, return_counts=True)
#threshold frequency(volume)
volume_thres = 400
# list of objects smaller than threshold
rmv = []
for i in range(len(counts)):
if counts[i] < volume_thres:
rmv.append(i)
#%%
for i in range(50):
image = array[i]
image = vol_filter(image)
imsave('00000' + str(i) + '.tif', image)
## single image of stack
#filtered = np.zeros(stack.shape,dtype = np.uint8)
#for idx, frame in tqdm(enumerate(array)):
# filtered[idx] = vol_filter(frame)
#save_path = r'\Users\aishw\Desktop\ImgProc\zstack\PythonVer\Ver2\Filtered.tif'
#imsave(save_path, filtered)
def toarray(f):
with open(f) as fid:
return frombuffer(fid.read(), dtype).reshape(dims, order='F')
os.system('mkdir neurofinder.%s/images-tif' % name)
if downsample:
for i in range(len(files) / 4):
if i * 4 + 4 <= len(files):
tmp = zeros(dims)
for j in range(4):
im = toarray(files[i * 4 + j])
im = im.clip(0, im.max()).astype('uint16')
tmp += im
tmp = (tmp / 4.0).astype('uint16')
tifffile.imsave(
'neurofinder.%s/images-tif/image%05g.tiff' % (name, i), im)
else:
for i, f in enumerate(files):
im = toarray(f)
im = im.clip(0, im.max()).astype('uint16')
tifffile.imsave(
'neurofinder.%s/images-tif/image%05g.tiff' % (name, i), im)
os.system('rm -rf neurofinder.%s/images' % name)
os.system('mv neurofinder.%s/images-tif neurofinder.%s/images' %
(name, name))
else:
print('skipping tiff conversion\n\n')
print('creating zip\n\n')
os.system('zip -r neurofinder.%s.zip neurofinder.%s' % (name, name))
def identify_structures_w_contours(jobid,
cores=5,
make_color_images=False,
overlay_on_original_data=False,
consider_only_multipln_contours=False,
**kwargs):
'''function to take 3d detected contours and apply elastix transform
'''
#######################inputs and setup#################################################
###inputs
kwargs = load_kwargs(**kwargs)
outdr = kwargs['outputdirectory']
vols = kwargs['volumes']
reg_vol = [xx for xx in vols if xx.ch_type == 'regch'][0]
###get rid of extra jobs
if jobid >= len([xx for xx in vols if xx.ch_type != 'regch'
]): ###used to end jobs if too many are called
print('jobid({}) >= volumes {}'.format(
jobid, len([xx for xx in vols if xx.ch_type != 'regch'])))
return
###volumes to process: each job represents a different contour volume
vol_to_process = [xx for xx in vols if xx.ch_type != 'regch'][jobid]
ch = vol_to_process.channel
print(vol_to_process.ch_type)
#find appropriate folders for contours
if vol_to_process.ch_type == 'cellch':
detect3dfld = reg_vol.celldetect3dfld
coordinatesfld = reg_vol.cellcoordinatesfld
elif vol_to_process.ch_type == 'injch':
detect3dfld = reg_vol.injdetect3dfld
coordinatesfld = reg_vol.injcoordinatesfld
#set scale and atlas
xscl, yscl, zscl = reg_vol.xyz_scale ###micron/pixel
zmx, ymx, xmx = reg_vol.fullsizedimensions
AtlasFile = reg_vol.atlasfile
print('Using {} CORES'.format(cores))
try:
p
except NameError:
p = mp.Pool(cores)
resizefactor = kwargs['resizefactor']
brainname = reg_vol.brainname
############################################################################################################
#######################use regex to sort np files by ch and then by zpln####################################
############################################################################################################
fl = [f for f in os.listdir(detect3dfld)
if '.p' in f and 'ch' in f] #sorted for raw files
reg = re.compile(r'(.*h+)(?P<ch>\d{2})(.*)(.p)')
matches = map(reg.match, fl)
##load .np files
sys.stdout.write(
'\njobid({}), loading ch{} .p files to extract contour_class objects....'
.format(jobid, ch))
contour_class_lst = []
for fl in [
os.path.join(detect3dfld, ''.join(xx.groups())) for xx in matches
if xx.group('ch')[-2:] in ch
]:
tmpkwargs = {}
pckl = open(fl, 'rb')
tmpkwargs.update(pickle.load(pckl))
pckl.close()
if consider_only_multipln_contours == False:
tmplst = tmpkwargs['single']
[tmplst.append(xx) for xx in tmpkwargs['multi']]
elif consider_only_multipln_contours == True:
tmplst = tmpkwargs['multi']
[contour_class_lst.append(xx) for xx in tmplst]
sys.stdout.write('\ndone loading contour_class objects.\n')
#check for successful loading
if len(contour_class_lst) == 0:
print('Length of contours in ch{} was {}, ending process...'.format(
jobid, len(contour_class_lst)))
try:
p.terminate()
except:
1
return
############################################################################################################
##############################make color files##############################################################
############################################################################################################
if make_color_images == True:
sys.stdout.write('\nmaking 3d planes...')
sys.stdout.flush()
valid_plns = range(0, zmx + 1)
svlc = os.path.join(outdr, 'ch{}_3dcontours'.format(ch))
removedir(svlc)
if overlay_on_original_data == False:
ovly = False
elif overlay_on_original_data == True:
ovly = True
iterlst = []
[
iterlst.append(
(ch, svlc, contour_class_lst, valid_plns, outdr,
vol_to_process, resizefactor, contour_class_lst,
consider_only_multipln_contours, ovly, core, cores))
for core in range(cores)
]
p.starmap(ovly_3d, iterlst)
lst = os.listdir(svlc)
lst1 = [os.path.join(svlc, xx) for xx in lst]
lst1.sort()
del lst
del iterlst
###load ims and return dct of keys=str(zpln), values=np.array
sys.stdout.write(
'\n3d planes made, saved in {},\nnow compressing into single tifffile'
.format(svlc))
imstack = tifffile.imread(lst1)
del lst1
if len(imstack.shape) > 3:
imstack = np.squeeze(imstack)
try: ###check for orientation differences, i.e. from horiztonal scan to sagittal for atlas registration
imstack = np.swapaxes(imstack, *kwargs['swapaxes'])
except:
pass
tiffstackpth = os.path.join(
outdr, '3D_contours_ch{}_{}'.format(ch, brainname))
tifffile.imsave(tiffstackpth, imstack.astype('uint16'))
del imstack
gc.collect()
shutil.rmtree(svlc)
sys.stdout.write('\ncolor image stack made for ch{}'.format(ch))
else:
sys.stdout.write('\nmake_color_images=False, not creating images')
############################################################################################################
######################apply point transform and make transformix input file#################################
############################################################################################################
###find centers and add 1's to make nx4 array for affine matrix multiplication to account for downsizing
###everything is in PIXELS
contourarr = np.empty((len(contour_class_lst), 3))
for i in range(len(contour_class_lst)):
contourarr[i, ...] = contour_class_lst[
i].center ###full sized dimensions: if 3x3 tiles z(~2000),y(7680),x(6480) before any rotation
try:
contourarr = swap_cols(
contourarr, *kwargs['swapaxes']
) ###change columns to account for orientation changes between brain and atlas: if horizontal to sagittal==>x,y,z relative to horizontal; zyx relative to sagittal
z, y, x = swap_cols(np.array([
vol_to_process.fullsizedimensions
]), *kwargs['swapaxes'])[
0] ##convert full size cooridnates into sagittal atlas coordinates
sys.stdout.write('\nSwapping Axes')
except: ###if no swapaxes then just take normal z,y,x dimensions in original scan orientation
z, y, x = vol_to_process.fullsizedimensions
sys.stdout.write('\nNo Swapping of Axes')
d1, d2 = contourarr.shape
nx4centers = np.ones((d1, d2 + 1))
nx4centers[:, :-1] = contourarr
###find resampled elastix file dim
print(os.listdir(outdr))
print([xx.channel for xx in vols if xx.ch_type == 'regch'])
with tifffile.TiffFile([
os.path.join(outdr, f) for f in os.listdir(outdr)
if 'resampledforelastix' in f and 'ch{}'.format(
[xx.channel for xx in vols if xx.ch_type == 'regch'][0]) in f
][0]) as tif:
zr = len(tif.pages)
yr, xr = tif.pages[0].shape
tif.close()
####create transformmatrix
trnsfrmmatrix = np.identity(4) * (
zr / z, yr / y, xr / x, 1) ###downscale to "resampledforelastix size"
sys.stdout.write('trnsfrmmatrix:\n{}\n'.format(trnsfrmmatrix))
#nx4 * 4x4 to give transform
trnsfmdpnts = nx4centers.dot(trnsfrmmatrix) ##z,y,x
sys.stdout.write('first three transformed pnts:\n{}\n'.format(
trnsfmdpnts[0:3]))
#create txt file, with elastix header, then populate points
txtflnm = '{}_zyx_transformedpnts_ch{}.txt'.format(brainname, ch)
pnts_fld = os.path.join(outdr, 'transformedpoints_pretransformix')
makedir(pnts_fld)
transforminput = os.path.join(pnts_fld, txtflnm)
removedir(transforminput) ###prevent adding to an already made file
writer(pnts_fld, 'index\n{}\n'.format(len(trnsfmdpnts)), flnm=txtflnm)
sys.stdout.write(
'\nwriting centers to transfomix input points text file: {}....'.
format(transforminput))
stringtowrite = '\n'.join([
'\n'.join(['{} {} {}'.format(i[2], i[1], i[0])]) for i in trnsfmdpnts
]) ####this step converts from zyx to xyz*****
writer(pnts_fld, stringtowrite, flnm=txtflnm)
#[writer(pnts_fld, '{} {} {}\n'.format(i[2],i[1],i[0]), flnm=txtflnm, verbose=False) for i in trnsfmdpnts] ####this step converts from zyx to xyz*****
sys.stdout.write('...done writing centers.')
sys.stdout.flush()
del trnsfmdpnts, trnsfrmmatrix, nx4centers, contourarr
gc.collect()
############################################################################################################
####################################elastix for inverse transform###########################################
############################################################################################################
transformfile = make_inverse_transform(vol_to_process, cores, **kwargs)
assert os.path.exists(transformfile)
sys.stdout.write(
'\n***Elastix Inverse Transform File: {}***'.format(transformfile))
############################################################################################################
####################################transformix#############################################################
############################################################################################################
if make_color_images != False:
#apply transform to 3d_tiffstack:
transformimageinput = tiffstackpth
elastixpth = os.path.join(outdr, 'elastix')
trnsfrm_outpath = os.path.join(
elastixpth, '3D_contours_ch{}_{}'.format(ch, brainname))
makedir(trnsfrm_outpath)
writer(trnsfrm_outpath, '\nProcessing ch{} 3D...'.format(ch))
#transformfiles=[os.path.join(elastixpth, xx) for xx in os.listdir(os.path.join(outdr, 'elastix')) if "TransformParameters" in xx]; mxx=max([xx[-5] for xx in transformfiles])
#transformfile=os.path.join(elastixpth, 'TransformParameters.{}.txt'.format(mxx))
trnsfrm_out_file = os.path.join(trnsfrm_outpath,
'result.tif') #output of transformix
transformimageinput_resized = transformimageinput[:-4] + '_resampledforelastix.tif'
print('Resizing {}'.format(transformimageinput_resized))
resample_par(cores,
transformimageinput,
AtlasFile,
svlocname=transformimageinput_resized,
singletifffile=True,
resamplefactor=1.7)
sp.call([
'transformix', '-in', transformimageinput_resized, '-out',
trnsfrm_outpath, '-tp', transformfile
])
writer(trnsfrm_outpath,
'\n Transformix File Generated: {}'.format(trnsfrm_out_file))
writer(
trnsfrm_outpath, '\n Passing colorcode: {} file as {}'.format(
ch, os.path.join(trnsfrm_outpath, 'depthcoded.png')))
###depth coded image of transformix result; not functional yet
#depth.colorcode(trnsfrm_out_file, trnsfrm_outpath)
#getvoxels(trnsfrm_out_file, os.path.join(trnsfrm_outpath, 'zyx_voxels_{}.npy'.format(ch)))
#allen_compare(AtlasFile, svlc, trnsfrm_outpath)
##if successful delete contour cooridnates and maybe contourdetect3d flds
############################################################
##############apply transform to points#####################
elastixpth = os.path.join(outdr, 'elastix_inverse_transform')
trnsfrm_outpath = os.path.join(elastixpth, 'ch{}_3dpoints'.format(ch))
makedir(trnsfrm_outpath)
writer(trnsfrm_outpath,
'\n***********Starting Transformix for: {}***********'.format(ch))
sys.stdout.flush()
#transformfiles=[os.path.join(elastixpth, xx) for xx in os.listdir(os.path.join(outdr, 'elastix')) if "TransformParameters" in xx]; mxx=max([xx[-5] for xx in transformfiles])
#transformfile=os.path.join(elastixpth, 'TransformParameters.{}.txt'.format(mxx))
trnsfrm_out_file = os.path.join(
trnsfrm_outpath, 'outputpoints.txt') #MIGHT NEED TO CHANGE THIS
sp.call([
'transformix', '-def', transforminput, '-out', trnsfrm_outpath, '-tp',
transformfile
])
#sp.call(['transformix', '-def', 'all', '-out', trnsfrm_outpath, '-tp', transformfile]) ##displacement field
writer(trnsfrm_outpath,
'\n Transformix File Generated: {}'.format(trnsfrm_out_file))
####################################################################################
##############generate list and image overlaid onto allen atlas#####################
####################################################################################
name = 'job{}_{}'.format(jobid, vol_to_process.ch_type)
transformed_pnts_to_allen(trnsfrm_out_file, ch, cores, name=name, **kwargs)
writer(outdr, '*************STEP 5*************\n Finished')
print('end of script')
try:
p.terminate()
except:
1
return
def save_tiff(img, filename):
tifffile.imsave(filename, img)
def transformed_pnts_to_allen(trnsfrm_out_file,
ch,
cores,
point_or_index=None,
name=False,
**kwargs):
'''function to take elastix point transform file and return anatomical locations of those points
point_or_index=None/point/index: determines which transformix output to use: point is more accurate, index is pixel value(?)
Elastix uses the xyz convention rather than the zyx numpy convention
###ASSUMES INPUT OF XYZ
'''
#####inputs
assert type(trnsfrm_out_file) == str
if point_or_index == None:
point_or_index = 'OutputPoint'
elif point_or_index == 'point':
point_or_index = 'OutputPoint'
elif point_or_index == 'index':
point_or_index = 'OutputIndexFixed'
try: #check to see if pool processes have already been spawned
p
except NameError:
p = mp.Pool(cores)
kwargs = load_kwargs(**kwargs)
vols = kwargs['volumes']
reg_vol = [xx for xx in vols if xx.ch_type == 'regch'][0]
####load files
id_table = pd.read_excel(
os.path.join(kwargs['packagedirectory'], 'supp_files/id_table.xlsx')
) ##use for determining neuroanatomical locations according to allen
ann = sitk.GetArrayFromImage(sitk.ReadImage(
kwargs['annotationfile'])) ###zyx
with open(trnsfrm_out_file, "rb") as f:
lines = f.readlines()
f.close()
#####populate post-transformed array of contour centers
sys.stdout.write('\n{} points detected'.format(len(lines)))
arr = np.empty((len(lines), 3))
for i in range(len(lines)):
arr[i,
...] = lines[i].split()[lines[i].split().index(point_or_index) +
3:lines[i].split().index(point_or_index) +
6] #x,y,z
#optional save out of points
np.save(kwargs['outputdirectory'] + '/injection/zyx_voxels.npy',
np.asarray([(z, y, x) for x, y, z in arr]))
pnts = transformed_pnts_to_allen_helper_func(arr, ann)
pnt_lst = [xx for xx in pnts if xx != 0]
if len(pnt_lst) == 0:
raise ValueError('pnt_lst is empty')
else:
sys.stdout.write('\nlen of pnt_lst({})'.format(len(pnt_lst)))
imstack = brain_structure_keeper(
ann, True,
*pnt_lst) ###annotation file, true=to depict density, list of pnts
df = count_structure_lister(id_table, *pnt_lst)
#########save out imstack and df
nametosave = '{}{}_{}'.format(name, ch, reg_vol.brainname)
tifffile.imsave(
os.path.join(kwargs['outputdirectory'],
nametosave + '_structure_density_map.tif'), imstack)
excelfl = os.path.join(kwargs['outputdirectory'],
nametosave + '_stuctures_table.xlsx')
df.to_excel(excelfl)
print('file saved as: {}'.format(excelfl))
try:
p.terminate()
except:
1
return
def pool_injections_for_analysis(**kwargs):
inputlist = kwargs['inputlist']
dst = kwargs['dst']; makedir(dst)
injscale = kwargs['injectionscale'] if 'injectionscale' in kwargs else 1
imagescale = kwargs['imagescale'] if 'imagescale' in kwargs else 1
axes = kwargs['reorientation'] if 'reorientation' in kwargs else ('0','1','2')
cmap = kwargs['colormap'] if 'colormap' in kwargs else 'plasma'
id_table = kwargs['id_table'] if 'id_table' in kwargs else '/jukebox/temp_wang/pisano/Python/lightsheet/supp_files/allen_id_table.xlsx'
save_tif = kwargs['save_tif'] if 'save_tif' in kwargs else False
num_sites_to_keep = kwargs['num_sites_to_keep'] if 'num_sites_to_keep' in kwargs else 1
nonzeros = []
ann = sitk.GetArrayFromImage(sitk.ReadImage(kwargs['annotation']))
if kwargs['crop']: ann = eval('ann{}'.format(kwargs['crop']))
allen_id_table=pd.read_excel(id_table)
for i in range(len(inputlist)):
impth = inputlist[i]
animal = os.path.basename(os.path.dirname(os.path.dirname(os.path.dirname(impth))))
print('\n\n_______\n{}'.format(animal))
print(' loading:\n {}'.format(animal))
im = tifffile.imread(impth)
if kwargs['crop']: im = eval('im{}'.format(kwargs['crop']))#; print im.shape
#reorient to coronal?
#segment
arr = find_site(im, thresh=kwargs['threshold'], filter_kernel=kwargs['filter_kernel'], num_sites_to_keep=num_sites_to_keep)*injscale
if save_tif: tifffile.imsave(os.path.join(dst,'{}'.format(os.path.dirname(impth))+'_inj.tif'), arr.astype('float32'))
#optional 'save_individual'
if kwargs['save_individual']:
im = im*imagescale
a=np.concatenate((np.max(im, axis=0), np.max(arr.astype('uint16'), axis=0)), axis=1)
b=np.concatenate((np.fliplr(np.rot90(np.max(fix_orientation(im, axes=axes), axis=0),k=3)), np.fliplr(np.rot90(np.max(fix_orientation(arr.astype('uint16'), axes=axes), axis=0),k=3))), axis=1)
plt.figure()
plt.imshow(np.concatenate((b,a), axis=0), cmap=cmap, alpha=1); plt.axis('off')
plt.savefig(os.path.join(dst,'{}'.format(animal)+'.pdf'), dpi=300, transparent=True)
plt.close()
#cell counts to csv
print(' finding nonzero pixels for voxel counts...')
nz = np.nonzero(arr)
nonzeros.append(zip(*nz)) #<-for pooled image
pos = transformed_pnts_to_allen_helper_func(np.asarray(zip(*[nz[2], nz[1], nz[0]])), ann)
tdf = count_structure_lister(allen_id_table, *pos)
if i == 0:
df = tdf.copy()
countcol = 'count' if 'count' in df.columns else 'cell_count'
df.drop([countcol], axis=1, inplace=True)
df[animal] = tdf[countcol]
df.to_csv(os.path.join(dst,'voxel_counts.csv'))
print('\n\nCSV file of cell counts, saved as {}\n\n\n'.format(os.path.join(dst,'voxel_counts.csv')))
#condense nonzero pixels
nzs = [str(x) for xx in nonzeros for x in xx] #this list has duplicates if two brains had the same voxel w label
c = Counter(nzs)
array = np.zeros(im.shape)
print('Collecting nonzero pixels for pooled image...')
tick = 0
#generating pooled array where voxel value = total number of brains with that voxel as positive
for k,v in c.iteritems():
k = [int(xx) for xx in k.replace('(','').replace(')','').split(',')]
array[k[0], k[1], k[2]] = int(v)
tick+=1
if tick % 50000 == 0: print(' {}'.format(tick))
#load atlas and generate final figure
print('Generating final figure...')
atlas = tifffile.imread(kwargs['atlas'])
arr = fix_orientation(array, axes=axes)
#cropping
#if 'crop_atlas' not in kwargs:
if kwargs['crop']: atlas = eval('atlas{}'.format(kwargs['crop']))
atlas = fix_orientation(atlas, axes=axes)
my_cmap = eval('plt.cm.{}(np.arange(plt.cm.RdBu.N))'.format(cmap))
my_cmap[:1,:4] = 0.0
my_cmap = mpl.colors.ListedColormap(my_cmap)
my_cmap.set_under('w')
plt.figure()
plt.imshow(np.max(atlas, axis=0), cmap='gray')
plt.imshow(np.max(arr, axis=0), alpha=0.99, cmap=my_cmap); plt.colorbar(); plt.axis('off')
dpi = int(kwargs['dpi']) if 'dpi' in kwargs else 300
plt.savefig(os.path.join(dst,'heatmap.pdf'), dpi=dpi, transparent=True);
plt.close()
print('Saved as {}'.format(os.path.join(dst,'heatmap.pdf')))
return df
def savetiff(name, data):
fdir = os.path.dirname(name)
if not os.path.isdir(fdir):
os.makedirs(fdir, exist_ok=True)
skitiff.imsave(name, data)
def writeOmeTiff(outputPath, array, omexmlString):
tifffile.imsave(outputPath,
array,
description=omexmlString,
metadata={'axes': 'TZCXY'})
# -*- coding: utf-8 -*-
import os, sys
from pydaily import filesystem
from skimage.external.tifffile import imsave
sys.path.insert(0, '.')
from kfb_io.io_image import patch_read_slide
if __name__ == "__main__":
input_root = str(sys.argv[1]) # kfb folder
save_root = str(sys.argv[2]) # tif folder
if not os.path.exists(save_root):
os.makedirs(save_root)
kfb_files = filesystem.find_ext_files(input_root, "kfb")
for ind, this_kfb_path in enumerate(kfb_files):
print("Processing {}/{}".format(ind+1, len(kfb_files)))
img_name = os.path.basename(this_kfb_path)
img_name_noext = os.path.splitext(img_name)[0]
this_raw_data = patch_read_slide(this_kfb_path, level=1)
save_path = os.path.join(save_root, img_name_noext+'.tif')
imsave(save_path, this_raw_data, compress=9, bigtiff=True)
def build_hand_segmentation_iscat_testval():
"""Creates dataset of manually segmented iSCAT images for validation and testing"""
OUT_PATH_CELL = DATA_PATH + 'hand_seg_iscat_cell/'
os.makedirs(os.path.join(OUT_PATH_CELL, 'REF_FRAMES/'), exist_ok=True)
os.makedirs(os.path.join(OUT_PATH_CELL, 'MASKS/'), exist_ok=True)
OUT_PATH_PILI = DATA_PATH + 'hand_seg_iscat_pili/'
os.makedirs(os.path.join(OUT_PATH_PILI, 'REF_FRAMES/'), exist_ok=True)
os.makedirs(os.path.join(OUT_PATH_PILI, 'MASKS/'), exist_ok=True)
ROOT_TEST_PATH = "data/hand-segmentation/"
iscat_files = glob.glob(os.path.join(ROOT_TEST_PATH, 'iSCAT/*.tif'))
cell_seg_files = glob.glob(os.path.join(ROOT_TEST_PATH, 'cell_seg/*.txt'))
pili_seg_files = glob.glob(os.path.join(ROOT_TEST_PATH, 'pili_seg/*.txt'))
iscat_files.sort()
cell_seg_files.sort()
pili_seg_files.sort()
for i, (iscat, cell_seg, pili_seg) in enumerate(
zip(iscat_files, cell_seg_files, pili_seg_files)):
# Loading tirf and iSCAT images
iscat_stack = tifffile.imread(iscat)
# iSCAT preprocessing
iscat_stack = processing.image_correction(iscat_stack)
iscat_stack = processing.enhance_contrast(iscat_stack,
'stretching',
percentile=(1, 99))
iscat_stack = processing.fft_filtering(iscat_stack, 1, 13, True)
iscat_stack = processing.enhance_contrast(iscat_stack,
'stretching',
percentile=(3, 97))
# Loading ground truth masks
mask_cell = utilities.cell_mask_from_segmentation(cell_seg)
mask_pili = utilities.pili_mask_from_segmentation(pili_seg)
for j in range(0, iscat_stack.shape[0], 8):
print("\rSaving to stack_{}_{}.png".format(i + 1, j + 1),
end=' ' * 5)
tifffile.imsave(
os.path.join(OUT_PATH_CELL, 'REF_FRAMES/',
"stack_{}_{}.png".format(i + 1, j + 1)),
rescale(iscat_stack[j]))
tifffile.imsave(
os.path.join(OUT_PATH_CELL, 'MASKS/',
"mask_{}_{}.png".format(i + 1, j + 1)),
mask_cell[j // 2].astype('uint8'))
print('')
for j in range(iscat_stack.shape[0]):
if not (mask_pili != 0).any(): continue
print("\rSaving to stack_{}_{}.png".format(i + 1, j + 1),
end=' ' * 5)
tifffile.imsave(
os.path.join(OUT_PATH_PILI, 'REF_FRAMES/',
"stack_{}_{}.png".format(i + 1, j + 1)),
rescale(iscat_stack[j]))
tifffile.imsave(
os.path.join(OUT_PATH_PILI, 'MASKS/',
"mask_{}_{}.png".format(i + 1, j + 1)),
mask_pili[j].astype('uint8'))
print('')
"a") as txt:
txt.write("Allen Atlas CCF coordinates (in zyx):\n%s" % zyx_rois)
#atlas (horizontal)
atl = tifffile.imread(
"/jukebox/LightSheetData/witten-mouse/atlas/average_template_25_sagittal_forDVscans.tif"
)
atl = np.transpose(atl, [2, 1, 0])
atl_cnn = np.zeros_like(atl)
for i in range(zyx_rois.shape[0]):
atl_cnn[zyx_rois[i][0], zyx_rois[i][1], zyx_rois[i][2]] = 1
merged = np.stack([atl, atl_cnn, np.zeros_like(atl)], -1)
tifffile.imsave(
os.path.join(
dst, "{}_ROI_merged_to_Allen_horizontal.tif".format(brain)),
merged)
coronal = np.transpose(merged, [1, 0, 2, 3]) #make coronal sections
#save out coronal sections - based on the fact that you click 5 points in each site in HORIZONTAL sectionss
tifffile.imsave(
os.path.join(dst,
"{}_ROI_merged_to_Allen_coronal.tif".format(brain)),
coronal)
#doing a max projection, in case you just want to look at that
maxip = np.max(coronal, 0)
alpha = 0.6 #determines transparency, don"t need to alter
cmap = matplotlib.colors.LinearSegmentedColormap.from_list(
from skimage.external.tifffile import imsave, imread
import os
result_dir = "../../../data/CycleGAN-data/result_mayo_blur_gaussian/128_longskip_mstd_r9/128_longskip_mstd_r9/test_latest/FakeClean/"
result_list = sorted(os.listdir(result_dir))
for i in range(len(result_list)):
im = imread(result_dir + result_list[i])
im[im < 0] = 0
im[im > 1] = 1
print(result_dir + result_list[i])
imsave(result_dir + result_list[i], im)
def overlay_qc(args):
#unpacking this way for multiprocessing
fld, folder_suffix, output_folder, verbose, doubletransform, make_volumes = args
try:
#get 3dunet cell dataframe csv file
input_csv = listdirfull(os.path.join(fld, folder_suffix), ".csv")
assert len(input_csv) == 1, "multiple csv files"
dataframe = pd.read_csv(input_csv[0])
#location to save out
dst = os.path.join(output_folder, os.path.basename(fld)); makedir(dst)
#EXAMPLE USING LIGHTSHEET - assumes marking centers in the "raw" full sized cell channel. This will transform those
#centers into "atlas" space (in this case the moving image)
#in this case the "inverse transform has the atlas as the moving image in the first step,
#and the autofluorescence channel as the moving image in the second step
#NOTE - it seems that the registration of cell to auto is failing on occasion....thus get new files...
################################
cell_inverse_folder = listdirfull(os.path.join(fld, "elastix_inverse_transform"), "cellch")[0]
a2r = listall(cell_inverse_folder, "atlas2reg_TransformParameters"); a2r.sort()
r2s = listall(cell_inverse_folder, "reg2sig_TransformParameters"); r2s.sort() #possibly remove
#IMPORTANT. the idea is to apply cfos->auto->atlas
transformfiles = r2s + a2r if doubletransform else a2r #might get rid of r2s
lightsheet_parameter_dictionary = os.path.join(fld, "param_dict.p")
converted_points = generate_transformed_cellcount(dataframe, dst, transformfiles,
lightsheet_parameter_dictionary, verbose=verbose)
#load and convert to single voxel loc
zyx = np.asarray([str((int(xx[0]), int(xx[1]), int(xx[2]))) for xx in np.nan_to_num(np.load(converted_points))])
from collections import Counter
zyx_cnt = Counter(zyx)
#check...
if make_volumes:
#manually call transformix
kwargs = load_dictionary(lightsheet_parameter_dictionary)
vol = [xx for xx in kwargs["volumes"] if xx.ch_type == "cellch"][0].resampled_for_elastix_vol
transformed_vol = os.path.join(dst, "transformed_volume"); makedir(transformed_vol)
if not doubletransform:
transformfiles = [os.path.join(fld, "elastix/TransformParameters.0.txt"), os.path.join(fld,
"elastix/TransformParameters.1.txt")]
transformfiles = modify_transform_files(transformfiles, transformed_vol) #copy over elastix files
transformix_command_line_call(vol, transformed_vol, transformfiles[-1])
else:
v=[xx for xx in kwargs["volumes"] if xx.ch_type == "cellch"][0]
#sig to reg
tps = [listall(os.path.dirname(v.ch_to_reg_to_atlas), "/TransformParameters.0")[0],
listall(os.path.dirname(v.ch_to_reg_to_atlas), "/TransformParameters.1")[0]]
#reg to atlas
transformfiles = tps+[os.path.join(fld, "elastix/TransformParameters.0.txt"),
os.path.join(fld, "elastix/TransformParameters.1.txt")]
transformfiles = modify_transform_files(transformfiles, transformed_vol) #copy over elastix files
transformix_command_line_call(vol, transformed_vol, transformfiles[-1])
#cell_registered channel
cell_reg = tifffile.imread(os.path.join(transformed_vol, "result.tif"))
tifffile.imsave(os.path.join(transformed_vol, "result.tif"), cell_reg, compress=1)
cell_cnn = np.zeros_like(cell_reg)
tarr = []; badlist=[]
for zyx,v in zyx_cnt.items():
z,y,x = [int(xx) for xx in zyx.replace("(","",).replace(")","").split(",")]
tarr.append([z,y,x])
try:
cell_cnn[z,y,x] = v*100
except:
badlist.append([z,y,x])
#apply x y dilation
r = 2
selem = ball(r)[int(r/2)]
cell_cnn = cell_cnn.astype("uint8")
cell_cnn = np.asarray([cv2.dilate(cell_cnn[i], selem, iterations = 1) for i in range(cell_cnn.shape[0])])
tarr=np.asarray(tarr)
if len(badlist)>0:
print("{} errors in mapping with cell_cnn shape {}, each max dim {}, \npossibly due to a registration overshoot \
or not using double transform\n\n{}".format(len(badlist), cell_cnn.shape, np.max(tarr,0), badlist))
merged = np.stack([cell_cnn, cell_reg, np.zeros_like(cell_reg)], -1)
tifffile.imsave(os.path.join(transformed_vol, "merged.tif"), merged)#, compress=1)
#out = np.concatenate([cell_cnn, cell_reg, ], 0)
#####check at the resampled for elastix phase before transform...this mapping looks good...
if make_volumes:
#make zyx numpy arry
zyx = dataframe[["z","y","x"]].values
kwargs = load_dictionary(lightsheet_parameter_dictionary)
vol = [xx for xx in kwargs["volumes"] if xx.ch_type =="cellch"][0]
fullsizedimensions = get_fullsizedims_from_kwargs(kwargs) #don"t get from kwargs["volumes"][0].fullsizedimensions it"s bad! use this instead
zyx = fix_contour_orientation(zyx, verbose=verbose, **kwargs) #now in orientation of resample
zyx = points_resample(zyx, original_dims = fix_dimension_orientation(fullsizedimensions, **kwargs),
resample_dims = tifffile.imread(vol.resampled_for_elastix_vol).shape, verbose = verbose)[:, :3]
#cell channel
cell_ch = tifffile.imread(vol.resampled_for_elastix_vol)
cell_cnn = np.zeros_like(cell_ch)
tarr = []; badlist=[]
for _zyx in zyx:
z,y,x = [int(xx) for xx in _zyx]
tarr.append([z,y,x])
try:
cell_cnn[z,y,x] = 100
except:
badlist.append([z,y,x])
tarr=np.asarray(tarr)
merged = np.stack([cell_cnn, cell_ch, np.zeros_like(cell_ch)], -1)
tifffile.imsave(os.path.join(transformed_vol, "resampled_merged.tif"), merged)#, compress=1)
except Exception as e:
print(e)
with open(error_file, "a") as err_fl:
err_fl.write("\n\n{} {}\n\n".format(fld, e))
def save_tiff(path, np_image):
imsave(path, np_image)
print("{} save".format(path))
def sim_images(mphi=None, ephi=None, pscope=None, isl_shape=None, del_px=1,
def_val=0, add_random=False, save_path=None, save_name=None,
isl_thk=20, isl_xip0=50, mem_thk=50, mem_xip0=1000, v=1, Filter=True):
"""Simulate LTEM images for a given electron phase shift through a sample.
This function returns LTEM images simulated for in-focus and at +/- def_val
for comparison to experimental data and reconstruction.
It was primarily written for simulating images of magnetic island
structures, and as such the sample is defined in two parts: a uniform
support membrane across the region and islands of magnetic material defined
by an array isl_shape. The magnetization is defined with 2D arrays
corresponding to the x- and y-components of the magnetization vector.
There are many required parameters here that must be set to account for the
support membrane. The default values apply to 20nm permalloy islands on a
50nm SiN membrane window.
There is a known bug where sharp edges in the ephi creates problems with the
image simulations. As a workaround, this function applies a light gaussian
filter (sigma = 1 pixel) to the ephi and isl_shape arrays. This can be
controlled with the ``filter`` argument.
Args:
mphi (2D array): Numpy array of size (M, N), magnetic phase shift
ephi (2D array): Numpy array of size (M, N), Electrostatic phase shift
pscope (``Microscope`` object): Contains all microscope parameters
as well as methods for propagating electron wave functions.
isl_shape (2D/3D array): Array of size (z,y,x) or (y,x). If 2D the
thickness will be taken as the isl_shape values multiplied by
isl_thickness. If 3D, the isl_shape array will be summed along
the z-axis becoming and multiplied by isl_thickness.
(Default) None -> uniform flat material with thickness = isl_thk.
del_px (Float): Scale factor (nm/pixel). Default = 1.
def_val (Float): The defocus values at which to calculate the images.
add_random (Float): Whether or not to add amorphous background to
the simulation. True or 1 will add a default background, any
other value will be multiplied to scale the additional phase term.
save_path: String. Will save a stack [underfocus, infocus, overfocus]
as well as (mphi+ephi) as tiffs along with a params.text file.
(Default) None -> Does not save.
save_name (str): Name prepended to saved files.
v (int): Verbosity. Set v=0 to suppress print statements.
isl_thk (float): Island thickness (nm). Default 20 (nm).
isl_xip0 (float): Island extinction distance (nm). Default 50 (nm).
mem_thk (float): Support membrane thickness (nm). Default 50 (nm).
mem_xip0 (float): Support membrane extinction distance (nm). Default
1000 (nm).
Filter (Bool): Apply a light gaussian filter to ephi and isl_shape.
Returns:
tuple: (Tphi, im_un, im_in, im_ov)
- Tphi (`2D array`) -- Numpy array of size (M,N). Total electron phase shift (ephi+mphi).
- im_un (`2D array`) -- Numpy array of size (M,N). Simulated image at delta z = -def_val.
- im_in (`2D array`) -- Numpy array of size (M,N). Simulated image at zero defocus.
- im_ov (`2D array`) -- Numpy array of size (M,N). Simulated image at delta z = +def_val.
"""
vprint = print if v>=1 else lambda *a, **k: None
if Filter:
ephi = gaussian_filter(ephi, sigma=1)
Tphi = mphi + ephi
vprint(f'Total fov is ({np.shape(Tphi)[1]*del_px:.3g},{np.shape(Tphi)[0]*del_px:.3g}) nm')
dy, dx = Tphi.shape
if add_random:
if type(add_random) == bool:
add_random = 1.0
ran_phi = np.random.uniform(low = -np.pi/128*add_random,
high = np.pi/128*add_random,
size=[dy,dx])
if np.max(ephi) > 1: # scale by ephi only if it's given and relevant
ran_phi *= np.max(ephi)
Tphi += ran_phi
#amplitude
if isl_shape is None:
thk_map = np.ones(Tphi.shape)*isl_thk
else:
if type(isl_shape) != np.ndarray:
isl_shape = np.array(isl_shape)
if isl_shape.ndim == 3:
thk_map = np.sum(isl_shape, axis=0)*isl_thk
elif isl_shape.ndim == 2:
thk_map = isl_shape*isl_thk
else:
vprint(textwrap.dedent(f"""
Mask given must be 2D (y,x) or 3D (z,y,x) array.
It was given as a {isl_shape.ndim} dimension array."""))
sys.exit(1)
if Filter:
thk_map = gaussian_filter(thk_map, sigma=1)
Amp = np.exp((-np.ones([dy,dx]) * mem_thk / mem_xip0) - (thk_map / isl_xip0))
ObjWave = Amp * (np.cos(Tphi) + 1j * np.sin(Tphi))
# compute unflipped images
qq = dist(dy, dx, shift=True)
pscope.defocus = 0.0
im_in = pscope.getImage(ObjWave,qq,del_px)
pscope.defocus = -def_val
im_un = pscope.getImage(ObjWave,qq,del_px)
pscope.defocus = def_val
im_ov = pscope.getImage(ObjWave,qq,del_px)
if save_path is not None:
vprint(f'saving to {save_path}')
im_stack = np.array([im_un, im_in, im_ov])
if not os.path.exists(save_path):
os.makedirs(save_path)
res = 1/del_px
tifffile.imsave(os.path.join(save_path, f'{save_name}_align.tiff'), im_stack.astype('float32'),
imagej = True,
resolution = (res, res),
metadata={'unit': 'nm'})
tifffile.imsave(os.path.join(save_path, f'{save_name}_phase.tiff'), Tphi.astype('float32'),
imagej = True,
resolution = (res, res),
metadata={'unit': 'nm'})
with io.open(os.path.join(save_path, f'{save_name}_params.txt'), 'w') as text:
text.write(f"def_val (nm) \t{def_val:g}\n")
text.write(f"del_px (nm/pix) \t{del_px:g}\n")
text.write(f"scope En. (V) \t{pscope.E:g}\n")
text.write(f"im_size (pix) \t({dy:g},{dx:g})\n")
text.write(f"sample_thk (nm) \t{isl_thk:g}\n")
text.write(f"sample_xip0 (nm) \t{isl_xip0:g}\n")
text.write(f"mem_thk (nm) \t{mem_thk:g}\n")
text.write(f"mem_xip0 (nm) \t{mem_xip0:g}\n")
text.write(f"add_random \t{add_random:g}\n")
return (Tphi, im_un, im_in, im_ov)
def record(model, class_indices):
#valdir = os.path.join(args.data, 'val')
#val_data = MSdata(image_dir=valdir, resize_height=max(input_size), resize_width=max(input_size))
#val_loader = DataLoader(dataset=val_data, batch_size=args.batch_size, shuffle=False)
#for i, (input, target) in enumerate(val_loader):
class_name = list(class_indices.keys())
data_name = os.path.basename(args.data)
ads_path = os.path.join(os.path.dirname(args.data), 'AEs', data_name,
args.arch, args.tasks, args.attack_type)
ads_record = open(
os.path.join(
ads_path, '{}_{}_{}_{}.txt'.format(data_name, args.arch,
args.tasks, args.attack_type)),
'w')
file_path = os.path.join(args.data, args.tasks)
files = get_fils(file_path)
mean = np.array([
1353.036, 1116.468, 1041.475, 945.344, 1198.498, 2004.878, 2376.699,
2303.738, 732.957, 12.092, 1818.820, 1116.271, 2602.579
])
mean = mean / mean.max()
std = np.array([
65.479, 154.008, 187.997, 278.508, 228.122, 356.598, 456.035, 531.570,
98.947, 1.188, 378.993, 303.851, 503.181
])
std = std / std.max()
preprocessing = dict(mean=mean, std=std, axis=-3)
fmodel = foolbox.models.PyTorchModel(model,
bounds=(0, 1),
num_classes=len(class_name),
preprocessing=preprocessing)
attack = ad_type(fmodel, args.attack_type)
for batch_files in yield_mb(files, args.batch_size, shuffle=False):
categorical_label_from_full_file_name(batch_files, class_indices)
images, labels = data_generator(batch_files, model.input_size[1:],
class_indices)
labels = np.argmax(labels, axis=1)
#print(images.shape, labels.shape)
cfds = fmodel.forward(images)
cfds = softmax(cfds, axis=1)
adversarials = attack(images, labels)
ads_cfds = fmodel.forward(adversarials)
ads_cfds = softmax(ads_cfds, axis=1)
for i in range(args.batch_size):
_class = batch_files[i].split('/')[-2]
file_name = os.path.basename(batch_files[i]).split('.')[-2]
model_idx = cfds[i].argmax(-1)
model_cla = class_name[model_idx]
model_cfs = cfds[i].max() * 100
model_flg = (model_idx == labels[i])
ads_idx = ads_cfds[i].argmax(-1)
ads_cla = class_name[ads_idx]
ads_cfs = ads_cfds[i].max() * 100
ads_flg = bool(1 - (ads_idx == labels[i]))
ads_record.write(
"{_class}+{file_name}+{model_cfs:.2f}+{ads_cla}+{ads_cfs:.2f}.tif,{_class},{model_cla},{model_idx},{model_cfs:.2f},{model_flg},{ads_cla},{ads_idx},{ads_cfs:.2f},{ads_flg}\n"
.format(_class=_class,
file_name=file_name,
model_idx=model_idx,
model_cla=model_cla,
model_cfs=model_cfs,
model_flg=model_flg,
ads_idx=ads_idx,
ads_cla=ads_cla,
ads_cfs=ads_cfs,
ads_flg=ads_flg))
if model_flg and ads_flg:
image_path = os.path.join(ads_path, _class)
imsave(
"{image_path}/{_class}+{file_name}+{model_cfs:.2f}+{ads_cla}+{ads_cfs:.2f}.tif"
.format(image_path=image_path,
_class=_class,
file_name=file_name,
model_cfs=model_cfs,
ads_cla=ads_cla,
ads_cfs=ads_cfs),
img_as_ubyte(np.transpose(adversarials[i], (1, 2, 0))))
binary_global = img > global_thresh
block_size = 40
# True False binary matrix represent color value of the img using adaptive thresholding
binary_adaptive = threshold_adaptive(img, block_size, offset=0)
# 0 1 binary matrix
img_bin_global = clear_border(img_as_uint(binary_global))
# 0 1 binary matrix
img_bin_adaptive = clear_border(img_as_uint(binary_adaptive))
savedImg = img_as_float(binary_adaptive)
imsave('../pics/result.tif', img_as_uint(binary_adaptive))
bin_pos_mat = ocr.binary_matrix_to_position(binary_adaptive)
fig, axes = plt.subplots(nrows=3, figsize=(7, 8))
ax0, ax1, ax2 = axes
figure(1)
subplot(311)
imshow(image)
subplot(312)
scatter(bin_pos_mat[:,1], bin_pos_mat[:,0])
# imshow(np.flipud(clustered))
subplot(313)
imshow(binary_adaptive)