def main(image_path, psf_path):
image = imageio.volread(image_path) # z 0.6u
psf = imageio.volread(psf_path) # z 0.2u
image, psf = image.astype(np.float32), psf.astype(np.float32)
# crop image (too large)
image = image[:, 768:768 + 512, 768:768 + 512]
imageio.volwrite("input.tif", image)
raise RuntimeError("DEBUG")
# rescale psf
psf = rescale(psf, (1 / 3, 1, 1), anti_aliasing=False)
# normalize
psf = (psf - psf.max()) / (psf.max() - psf.min())
psf /= psf.sum()
print(f"psf range [{psf.min(), psf.max()}]")
print(f"image shape {image.shape}, psf shape {psf.shape}")
try:
deconv = deconvlucy(image, psf, 10)
except Exception:
raise
else:
print("saving...")
imageio.volwrite("result.tif", deconv)
def _check_inputs(self):
print("checking training data dims ... ")
hr_im_list = sorted(
tl.files.load_file_list(path=self.train_hr_path,
regx='.*.tif',
printable=False))
lr_im_list = sorted(
tl.files.load_file_list(path=self.train_lr_path,
regx='.*.tif',
printable=False))
len(hr_im_list) == len(lr_im_list) or _raise(
ValueError("Num of HR and LR not equal"))
for hr_file, lr_file in zip(hr_im_list, lr_im_list):
hr = imageio.volread(os.path.join(self.train_hr_path, hr_file))
lr = imageio.volread(os.path.join(self.train_lr_path, lr_file))
# print('checking dims: \n%s %s\n%s %s' % (hr_file, str(hr.shape), lr_file, str(lr.shape)))
if 'factor' not in dir(self):
self.factor = hr.shape[0] // lr.shape[0]
valid_dim = [
self.factor == hs / ls for hs, ls in zip(hr.shape, lr.shape)
]
if not all(valid_dim):
raise (ValueError(
'dims mismatch: \n%s %s\n%s %s' %
(hr_file, str(hr.shape), lr_file, str(lr.shape))))
def processFile(filepath, zfile=None):
"""
Get datatypes based on file extension
"""
datatypes = []
if endsWith(filepath, ['.nii', '.nii.gz', '.xrw', '.dcm']):
datatypes = ['volume']
elif endsWith(filepath, ['.obj', '.mtl']):
datatypes = ['mesh']
elif endsWith(filepath, ['.las', '.laz', '.ptx', '.ply', '.xyz', '.txt']):
datatypes = ['point']
elif endsWith(filepath, ['.jpg', '.jpeg', '.png', '.gif']):
datatypes = ['image', 'photogrammetry']
elif endsWith(filepath, ['.tif', '.tiff']):
if (zfile != None):
ofile = zfile.extract(filepath, path='/tmp/')
img = imageio.volread(ofile)
os.remove('/tmp/' + filepath)
else:
img = imageio.volread(filepath)
shape = img.shape[::-1]
dim = len(shape)
if dim <= 2 or (dim == 3 and shape[2] <= 3):
datatypes = ['image']
else:
datatypes = ['volume']
return datatypes
def test_different_read_modes():
dname1, dname2, fname1, fname2 = _prepare()
for fname, dname, n in [(fname1, dname1, 1), (fname2, dname2, 2)]:
# Test imread()
im = imageio.imread(fname)
assert isinstance(im, np.ndarray)
assert im.shape == (512, 512)
# Test mimread()
ims = imageio.mimread(fname)
assert isinstance(ims, list)
assert ims[0].shape == im.shape
assert len(ims) > 1
#
ims2 = imageio.mimread(dname)
assert len(ims) == len(ims2)
# Test volread()
vol = imageio.volread(dname)
assert vol.ndim == 3
assert vol.shape[0] > 10
assert vol.shape[1:] == (512, 512)
#
vol2 = imageio.volread(fname) # fname works as well
assert (vol == vol2).all()
# Test mvolread()
vols = imageio.mvolread(dname)
assert isinstance(vols, list)
assert len(vols) == n
assert vols[0].shape == vol.shape
assert sum([v.shape[0] for v in vols]) == len(ims)
def load_training_data(root, image_folder, labels_folder, ext):
# get the image and label mask paths and validate them
image_pattern = os.path.join(root, image_folder, f'*{ext}')
print("Looking for images with the pattern", image_pattern)
train_images = glob(image_pattern)
assert len(train_images) > 0, "Did not find any images"
train_images.sort()
label_pattern = os.path.join(root, labels_folder, f'*{ext}')
print("Looking for labels with the pattern", image_pattern)
train_labels = glob(label_pattern)
assert len(train_labels) > 0, "Did not find any labels"
train_labels.sort()
check_training_data(train_images, train_labels)
# normalization parameters: lower and upper percentile used for image normalization
# maybe these should be exposed
lower_percentile = 1
upper_percentile = 99.8
ax_norm = (0, 1, 2)
train_images = [imageio.volread(im) for im in train_images]
train_labels = [imageio.volread(im) for im in train_labels]
check_training_images(train_images, train_labels)
train_images = [
normalize(im, lower_percentile, upper_percentile, axis=ax_norm)
for im in train_images
]
train_labels = [fill_label_holes(im) for im in train_labels]
return train_images, train_labels
def test_different_read_modes():
dname1, dname2, fname1, fname2 = _prepare()
for fname, dname, n in [(fname1, dname1, 1), (fname2, dname2, 2)]:
# Test imread()
im = imageio.imread(fname)
assert isinstance(im, np.ndarray)
assert im.shape == (512, 512)
# Test mimread()
ims = imageio.mimread(fname)
assert isinstance(ims, list)
assert ims[0].shape == im.shape
assert len(ims) > 1
#
ims2 = imageio.mimread(dname)
assert len(ims) == len(ims2)
# Test volread()
vol = imageio.volread(dname)
assert vol.ndim == 3
assert vol.shape[0] > 10
assert vol.shape[1:] == (512, 512)
#
vol2 = imageio.volread(fname) # fname works as well
assert (vol == vol2).all()
# Test mvolread()
vols = imageio.mvolread(dname)
assert isinstance(vols, list)
assert len(vols) == n
assert vols[0].shape == vol.shape
assert sum([v.shape[0] for v in vols]) == len(ims)
def getmaskarray(self):
if self.mfn is None:
return None
try:
im = imageio.volread(self.mfn, flatten=True)
except TypeError:
try:
im = imageio.volread(self.mfn)
except Exception:
# require tifffile only if imageio fails
from skimage.external.tifffile import tifffile
im = tifffile.imread(self.mfn)
return im
def check_result(self, in_path, res_path, check_range=False):
res = imageio.volread(res_path)
exp = imageio.volread(in_path).astype(res.dtype)
if check_range:
min_res = res.min()
min_exp = exp.min()
self.assertEqual(min_res, min_exp)
max_res = res.max()
max_exp = exp.max()
self.assertEqual(max_res, max_exp)
else:
un_res = np.unique(res)
un_exp = np.unique(exp)
self.assertTrue(np.array_equal(un_exp, un_res))
def __set_image_volume(self):
pathname = url2pathname(self.get_url())
# Volume loading is currently limited to tiffs/numpy files only
if is_numpy_file(self.__filename):
data = numpy.load(pathname)
else:
data = imageio.volread(pathname)
# https://github.com/CellProfiler/python-bioformats/blob/855f2fb7807f00ef41e6d169178b7f3d22530b79/bioformats/formatreader.py#L768-L791
if data.dtype in [numpy.int8, numpy.uint8]:
self.scale = 255
elif data.dtype in [numpy.int16, numpy.uint16]:
self.scale = 65535
elif data.dtype == numpy.int32:
self.scale = 2**32 - 1
elif data.dtype == numpy.uint32:
self.scale = 2**32
else:
self.scale = 1
self.__image = Image(
image=data,
path_name=self.get_pathname(),
file_name=self.get_filename(),
dimensions=3,
scale=self.scale,
spacing=self.__spacing,
)
def pack_itk_snap(dst_path: str, raw, label, overwrite: bool = True):
"""
Pack raw-label product from an ITK-SNAP project.
Args:
dst_path (str): destination file
raw (array-like): the source NRRD file
label (array-like): the NIFTI label file
overwrite (bool, optional): overwrite destination file
"""
try:
import imageio
except ImportError:
logger.error('requires "imageio" to load the source')
raise
logger.debug('loading raw data')
raw = imageio.volread(raw) # volread can actually handle 2-D as well
logger.debug('loading label')
label = _read_nifti(label)
assert raw.shape == label.shape, "shape mis-matched between raw data and the label"
mode = "w" if overwrite else "x"
with h5py.File(dst, mode) as h:
h["raw"] = raw
h["label"] = label.astype(np.uint8)
def processTiffStack(infile, outdir, channel, timestep, verbose):
"""
Process multi-dimensional tiff
:param infile:
:param outdir:
:param verbose:
:return:
"""
if verbose: print('processTiffStack')
#img = Image.open(infile)
img = imageio.volread(infile)
volinfo = parseVolInfo(img.shape)
volinfo["shape"] = img.shape
#volinfo["dtype"] = getNumpyType(img.dtype.name)
volinfo["dtype"] = getFrameData(img, volinfo, 0, 0, 0).dtype
if verbose:
print(volinfo)
if volinfo["numslices"] < 5:
raise NameError("Tiff has less than 5 frames")
fullW = volinfo["size"][0]
fullH = volinfo["size"][1]
voldata = np.zeros((fullH, fullW, volinfo["numslices"]), volinfo["dtype"])
for i in range(volinfo["numslices"]):
voldata[:, :, i] = getFrameData(img, volinfo, i, channel, timestep)
# normalize 16 bit data
if volinfo["dtype"] == np.dtype(np.uint16) or volinfo["dtype"] == np.dtype(
np.int16):
voldata = normalize16bitData(voldata, verbose)
saveVolume(voldata, volinfo, outdir, verbose)
def _LoadKer(file, fold=FOLD_TMP, *, fmt=FMT.TIF):
"""
Reads the 4D array `ker` [T,Z,Y,X] from a multilayer .tif image
"""
## Read from File ##
return np.moveaxis(np.array(imageio.volread(fold + file + str(fmt))),
(3, 2), (0, 1))
def read_logpack(fn):
data = -1.0 + np.array(imageio.volread(fn), dtype='float') / 2**15
scale = float(".".join(fn.split('.')[:-1]).split('_lp')[-1])
return np.exp2(data * scale)
# write_logpack(main_imgfile[:-4]+'_fdata' , flepith.fdata3d)
def getGlom_im(file_name):
#print(imageio.volread(file_name).astype(float).dtype)
im = torch.tensor(imageio.volread(file_name).astype(float),
dtype=torch.float32)
im /= torch.max(im) - 0.5
im = im.unsqueeze(0)
return im
def main(image, colormap, scan_type, lateral, axial, angle, suffix):
# load image
logger.info("loading \"{}\"".format(image))
I = imageio.volread(image)
logger.info("image shape {}".format(I.shape))
# load colormap
cm = imageio.imread(colormap)
cm = cm[0, :, :]
logger.info("colormap contains {} steps".format(cm.shape[0]))
nz, ny, nx = I.shape
rad = radians(angle)
if scan_type == 'spl':
scale = (np.float32(0.), np.float32(nx * sin(rad)))
convert = lambda x, y: colored_by_depth_spl(x, y, lateral, axial, rad)
elif scan_type == 'obj':
raise NotImplementedError
elif scan_type == 'ortho':
raise NotImplementedError
lookup = create_lookup_function(cm, scale)
J = convert(I, lookup)
# apply suffix
fn, ext = os.path.splitext(image)
for iz in tqdm(range(nz), total=nz, file=tqdm_log):
imageio.imwrite('{}_{:03d}_{}{}'.format(fn, iz, suffix, ext), J[iz,
...])
def main(src_dir, binning=(4, 4, 1), host=None, n_workers=1):
desc_bin = "-".join(str(b) for b in binning)
parent, dname = os.path.split(src_dir)
dst_dir = os.path.join(parent, f"{dname}_bin{desc_bin}")
logger.info(f'destination: "{dst_dir}"')
try:
os.makedirs(dst_dir)
except FileExistsError:
logger.warning(f"destination folder already exists")
file_list = glob.glob(os.path.join(src_dir, "*.tif"))
logger.info(f"found {len(file_list)} file(s) to process")
# test read
array = imageio.volread(file_list[0])
shape, dtype = array.shape, array.dtype
del array
logger.info(f"array info {shape}, {dtype}")
# build sampler
sampler = tuple(slice(None, None, b) for b in reversed(binning))
@delayed
def volread_np(uri):
return np.array(imageio.volread(uri))
def volread_da(uri):
return da.from_delayed(volread_np(uri), shape, dtype)
tasks = []
for src_path in file_list:
array = volread_da(src_path)
array = array[sampler]
fname = os.path.basename(src_path)
dst_path = os.path.join(dst_dir, fname)
task = delayed(imageio.volwrite)(dst_path, array)
tasks.append(task)
def downsample(src_path, dst_path=None):
if dst_path is None:
fname = os.path.basename(src_path)
dst_path = os.path.join(dst_dir, fname)
# extract
array = volread_da(src_path)
# transform
array = array[sampler]
# load
imageio.volwrite(dst_path, array)
return dst_path
with get_client(address=host, n_workers=n_workers, threads_per_worker=8):
dst_path = batch_submit(downsample, file_list, return_results=True)
for i, path in enumerate(dst_path):
print(f"{i+1}/{len(file_list)}, {os.path.basename(path)}")
"""
def volread(filename):
""" volread(filename)
Read volume from a file. If filename is 'stent', read a dedicated
test dataset. For reading any other kind of volume, the imageio
package is required.
"""
if filename == 'stent':
# Get full filename
path = vv.misc.getResourceDir()
filename2 = os.path.join(path, 'stent_vol.ssdf')
if os.path.isfile(filename2):
filename = filename2
else:
raise IOError("File '%s' does not exist." % filename)
# Load
s = vv.ssdf.load(filename)
return s.vol.astype('int16') * s.colorscale
elif imageio is not None:
return imageio.volread(filename)
else:
raise RuntimeError("visvis.volread needs the imageio package to read arbitrary files.")
def load_segmentation_from_tif(segmentation_fpath):
volume = volread(segmentation_fpath)
transposed = np.transpose(volume, axes=(1, 2, 0))
segmentation = transposed.view(Segmentation3D)
return segmentation
def get_normalized_im(path, normalize='fixed'):
"""read 3-D tiff and normalize
Params:
normalize: str, in ['fixed', 'percentile']
Return:
np.adarray in shape of [depth, height, width, channels=1]
"""
assert normalize in ['fixed', 'percentile']
im = imageio.volread(path) # [depth, height, width]
max_val = 255.
if im.dtype in [np.uint8, 'uint8']:
pass
elif im.dtype in [np.uint16, 'uint16']:
max_val = 65535.
elif im.dtype in [np.float32, 'float32']:
pass
else:
raise Exception('\nunsupported image bitdepth %s\n' % str(im.dtype))
if (im.dtype == np.float32) and normalize == 'percentile':
raise ValueError(
'normalization mode "fixed" cannot be applied to image with dtype float32'
)
im = normalize_max(
im, max_val) if normalize == 'fixed' else normalize_percentile(im)
im = im[..., np.newaxis] # [depth, height, width, channels=1]
return im
def readvol(filename, dataset=None, drop_channel=True):
r"""Load a image volume in HDF5, TIFF or PNG formats.
"""
img_suf = filename[filename.rfind('.') + 1:]
if img_suf in ['h5', 'hdf5']:
data = readh5(filename, dataset)
elif 'tif' in img_suf:
data = imageio.volread(filename).squeeze()
if data.ndim == 4:
# convert (z,c,y,x) to (c,z,y,x) shape
data = data.transpose(1, 0, 2, 3)
elif 'png' in img_suf:
data = readimgs(filename)
if data.ndim == 4:
# convert (z,y,x,c) to (c,z,y,x) shape
data = data.transpose(3, 0, 1, 2)
else:
raise ValueError('unrecognizable file format for %s' % (filename))
if drop_channel and data.ndim == 4:
# convert multiple channels to grayscale by average
data = np.mean(data, axis=0).astype(np.uint8)
assert data.ndim in [3,
4], "Volume data should be 3D or 4D, got {}D".format(
data.ndim)
return data
def _load_test_images(self):
images = []
for im_path in self.test_names:
im = imageio.volread(im_path).astype('float32')
for i in range(im.shape[0]):
images.append(im[i, :, :])
images = np.stack(images)
print('%d images' % len(images))
# Put images in correct format
norm = lambda im: (im / 255.0).reshape((512, 512, 1))
np_test_imgs = np.array([norm(im) for im in images])
# Take a crop size, crop size chunk from the center of the image
np_test_imgs = np_test_imgs[:, (512 // 2) -
self.params.crop // 2:(512 // 2) +
self.params.crop // 2, (512 // 2) -
self.params.crop // 2:(512 // 2) +
self.params.crop // 2, :]
if self.params.network_dimension == 3:
np_test_imgs = np.expand_dims(np_test_imgs, axis=0)
# Split images into chunks of length self.params.depth
np_test_imgs = np.array_split(np_test_imgs,
np_test_imgs.shape[1] //
self.params.depth,
axis=1)
elif self.params.network_dimension == 2:
# Split images into chunks of length 1
np_test_imgs = np.array_split(np_test_imgs,
np_test_imgs.shape[0],
axis=0)
self.test_imgs = np_test_imgs
def find_spots_in_round(sample_name, round_index, imaging_round,
input_directory, output_directory):
"""
"""
round_directory = ("round%d" % round_index)
sample_input_subdirectory = input_directory / sample_name / round_directory
sample_output_subdirectory = output_directory / sample_name / round_directory
sample_output_subdirectory.mkdir(parents=True, exist_ok=True)
channels = imaging_round["channels"]
filename = imaging_round["filename"]
reference_channel = imaging_round["reference_channel"]
for channel_index, channel in enumerate(channels):
input_filename = filename + ("_fused_tp_0_ch_%d.tif" % channel_index)
output_filename = channel + ".tif"
input_path = sample_input_subdirectory / input_filename
output_path = sample_output_subdirectory / output_filename
if channel_index == reference_channel:
image_stack = imageio.volread(input_path)
max_filtered_image_stack = image_stack.max(0)
imageio.imsave(output_path, max_filtered_image_stack)
else:
find_spots(input_path, output_path)
def volread_HWD(filename, path, make_mask=False):
im = imageio.volread(os.path.join(path,
filename)) # [depth, height, width]
if make_mask:
im = otsu_thresholding(im)
return rearrange3d(im)
def __getitem__(self, idx: int) -> Dict[str, Union[numpy.ndarray, list]]:
sample = super().__getitem__(idx)
path_idx = idx // self.info.datasets_per_file
idx %= self.info.datasets_per_file
img_path = self.paths[path_idx]
try:
img: numpy.ndarray = imageio.volread(img_path)
except Exception as e:
logger.error("Cannot load %s due to %s", img_path, e)
raise e
img = numpy.asarray(img)
if self.info.datasets_per_file > 1:
img = img[idx:idx + 1]
for axis in self.remove_singleton_axes_at:
if img.shape[axis] == 1:
img = numpy.squeeze(img, axis=axis)
for axis in self.insert_singleton_axes_at:
img = numpy.expand_dims(img, axis=axis)
while len(img.shape) > 5 and img.shape[0] == 1:
logger.warning("squeeze(0) %s", img.shape)
img = img.squeeze(0)
assert len(img.shape) == 5, (self.info.name, idx, img.shape)
sample[self.tensor_name] = img
sample["batch_len"] = img.shape[0]
return self.transform(sample)
def main(settings):
# Initiate the analysis pipline by parameters in SETTINGS.
with open(settings, 'r') as fd:
settings = yaml.safe_load(fd)
# Set logger.
handler = logging.StreamHandler()
formatter = logging.Formatter(
'%(levelname).1s %(asctime)s [%(name)s] %(message)s', '%H:%M:%S'
)
handler.setFormatter(formatter)
log_level = logging.WARNING if settings['VERBOSE'] == 0 else logging.DEBUG
logging.basicConfig(level=log_level, handlers=[handler])
logger = logging.getLogger(__name__)
# Start the image analysis.
frames = imageio.volread(settings['INPF_RAW_IMAGE'])
analyzer = Analyzer(settings)
analyzer.process(frames)
#DEBUG
#from pprint import pprint
#pprint(settings)
print(frames.shape)
def __getitem__(
self,
idx: int) -> typing.OrderedDict[str, Union[numpy.ndarray, list]]:
path_idx = idx // self.info.datasets_per_file
idx %= self.info.datasets_per_file
try:
img_path = self.paths[path_idx]
except IndexError as e:
logger.error(
f"idx: {idx}, path_idx: {path_idx}, paths: {self.paths}")
raise e
try:
img: numpy.ndarray = numpy.asarray(imageio.volread(img_path))
except Exception as e:
logger.error("Cannot load %s", img_path)
raise e
if self.info.datasets_per_file > 1:
img = img[idx:idx + 1]
for axis in self.remove_singleton_axes_at:
img = numpy.squeeze(img, axis=axis)
for axis in self.insert_singleton_axes_at:
img = numpy.expand_dims(img, axis=axis)
return self.transform(OrderedDict(**{self.tensor_name: img}))
def analyze_psf(ctx, path, ratio, lateral, axial, preview, save_roi,
no_fix_negative):
path = os.path.abspath(path)
data = imageio.volread(path)
if not no_fix_negative:
vmin = np.min(data)
if vmin < 0:
data -= vmin
analyzer = PSFAverage((axial, lateral, lateral), ratio)
rois, table = analyzer(data)
out_dir, _ = os.path.splitext(path)
out_dir = f'{out_dir}_psf'
try:
os.mkdir(out_dir)
except FileExistsError:
logger.warning(f'output directory "{out_dir}" exists')
if save_roi:
logger.info("saving ROIs...")
for i, roi in enumerate(rois):
out_path = os.path.join(out_dir, f'psf_{i:03d}.tif')
imageio.volwrite(out_path, roi)
if preview:
fig, ax = plt.subplots()
plt.ion()
plt.show()
def __init__(self, parent=None):
# initialization of the superclass
super(VideoMainWindow, self).__init__(parent)
# setup the GUI
self.setupUi(self)
# Use a file dialog to choose tiff stack
file, mask = QFileDialog.getOpenFileName(self, 'Open a .tif/.tiff stack')
# Read image data
self.img = volread(file)
# Transpose second and third axes (y, x) to correct orientation (x, y)
self.img = np.transpose(self.img, (0, 2, 1))
# for i in range(0, len(self.img)):
# self.img[i] = self.img[i].T
# connect the signals with the slots
# self.actionLoad.triggered.connect(self.open_tiff)
# self.actionClose.triggered.connect(self.close)
# self.actionTIFF.triggered.connect(self.open_tiff)
# self.actionFolder.triggered.connect(self.open_folder)
# self.actionStart_ImageProcess.triggered.connect(self.image_process)
self.ptr = 0
self.lastTime = ptime.time()
self.fps = None
# self.start()
self.timer = QtCore.QTimer()
self.timer.timeout.connect(self.update)
self.timer.start(0)
def volread(filename):
""" volread(filename)
Read volume from a file. If filename is 'stent', read a dedicated
test dataset. For reading any other kind of volume, the imageio
package is required.
"""
if filename == 'stent':
# Get full filename
path = vv.misc.getResourceDir()
filename2 = os.path.join(path, 'stent_vol.ssdf')
if os.path.isfile(filename2):
filename = filename2
else:
raise IOError("File '%s' does not exist." % filename)
# Load
s = vv.ssdf.load(filename)
return s.vol.astype('int16') * s.colorscale
elif imageio is not None:
return imageio.volread(filename)
else:
raise RuntimeError(
"visvis.volread needs the imageio package to read arbitrary files."
)
def fetch_test_data():
try:
from urllib.request import urlopen
except ImportError:
from urllib2 import urlopen
try:
from io import BytesIO as Buffer
except ImportError:
from StringIO import StringIO as Buffer
import zipfile
from imageio import volread
im_url = "https://imagej.nih.gov/ij/images/t1-head-raw.zip"
with closing(urlopen(im_url)) as response:
if response.status != 200:
raise RuntimeError(
"Test data could not be found at {}, status code {}".format(
im_url, response.status))
zip_buffer = Buffer(response.read())
with zipfile.ZipFile(zip_buffer) as zf:
tif_buffer = Buffer(zf.read('JeffT1_le.tif'))
return np.asarray(volread(tif_buffer, format='tif'), dtype=np.uint8)
def run(file_list, train_on, name="untitled", dst_dir="."):
try:
os.makedirs(dst_dir)
except FileExistsError:
pass
model_dir = os.path.join(dst_dir, "model")
try:
os.makedirs(model_dir)
except FileExistsError:
pass
logger.info("preloading image for training")
image = imageio.volread(train_on)
train(image, name=name, model_dir=model_dir)
def load_image():
for file_path in file_list:
yield imageio.volread(file_path)
for file_name, result in zip(
file_list, infer(load_image(), name=name, model_dir=model_dir)):
fname = os.path.basename(file_name)
file_path = os.path.join(dst_dir, fname)
imageio.imwrite(file_path, result)
def __readimage(self, fn):
try:
im = imageio.volread(fn)
except Exception:
# require tifffile only if imageio fails
from skimage.external.tifffile import tifffile
im = tifffile.imread(fn)
return self.__fix_image_dimensions(im)
def test_volume():
vol1 = imageio.imread("imageio:stent.npz")
assert vol1.shape == (256, 128, 128)
fname = os.path.join(test_dir, "stent.bsdf")
imageio.volsave(fname, vol1)
vol2 = imageio.volread(fname)
assert vol1.shape == vol2.shape
assert np.all(vol1 == vol2)
def test_npz_reading_writing():
""" Test reading and saveing npz """
if IS_PYPY:
return # no support for npz format :(
im2 = np.ones((10, 10), np.uint8) * 2
im3 = np.ones((10, 10, 10), np.uint8) * 3
im4 = np.ones((10, 10, 10, 10), np.uint8) * 4
filename1 = os.path.join(test_dir, 'test_npz.npz')
# One image
imageio.imsave(filename1, im2)
im = imageio.imread(filename1)
ims = imageio.mimread(filename1)
assert (im == im2).all()
assert len(ims) == 1
# Multiple images
imageio.mimsave(filename1, [im2, im2, im2])
im = imageio.imread(filename1)
ims = imageio.mimread(filename1)
assert (im == im2).all()
assert len(ims) == 3
# Volumes
imageio.mvolsave(filename1, [im3, im3])
im = imageio.volread(filename1)
ims = imageio.mvolread(filename1)
assert (im == im3).all()
assert len(ims) == 2
# Mixed
W = imageio.save(filename1)
assert W.format.name == 'NPZ'
W.append_data(im2)
W.append_data(im3)
W.append_data(im4)
raises(RuntimeError, W.set_meta_data, {}) # no meta data support
W.close()
#
R = imageio.read(filename1)
assert R.format.name == 'NPZ'
ims = list(R) # == [im for im in R]
assert (ims[0] == im2).all()
assert (ims[1] == im3).all()
assert (ims[2] == im4).all()
# Fail
raises(IndexError, R.get_data, -1)
raises(IndexError, R.get_data, 3)
raises(RuntimeError, R.get_meta_data, None) # no meta data support
raises(RuntimeError, R.get_meta_data, 0) # no meta data support
def test_spe_reading():
need_internet()
fname = get_remote_file("images/test_000_.SPE")
fr1 = np.zeros((32, 32), np.uint16)
fr2 = np.ones_like(fr1)
# Test imread
im = imageio.imread(fname)
ims = imageio.mimread(fname)
np.testing.assert_equal(im, fr1)
np.testing.assert_equal(ims, [fr1, fr2])
# Test volread
vol = imageio.volread(fname)
vols = imageio.mvolread(fname)
np.testing.assert_equal(vol, [fr1, fr2])
np.testing.assert_equal(vols, [[fr1, fr2]])
# Test get_reader
r = imageio.get_reader(fname)
np.testing.assert_equal(r.get_data(1), fr2)
np.testing.assert_equal(list(r), [fr1, fr2])
pytest.raises(IndexError, r.get_data, -1)
pytest.raises(IndexError, r.get_data, 2)
# check metadata
md = r.get_meta_data()
assert md["ROIs"] == [
{"top_left": [238, 187], "bottom_right": [269, 218], "bin": [1, 1]}
]
cmt = [
"OD 1.0 in r, g "
" ",
"000200000000000004800000000000000000000000000000000000000000000000"
"0002000001000X",
" "
" ",
" "
" ",
"ACCI2xSEQU-1---10000010001600300EA SW"
"0218COMVER0500",
]
assert md["comments"] == cmt
np.testing.assert_equal(md["frame_shape"], fr1.shape)
def test_dicom():
# Test volread()
fname1 = get_remote_file('images/dicom_sample.zip', test_dir)
dname1 = fname1[:-4]
z = ZipFile(fname1)
z.extractall(dname1)
#
vol = imageio.volread(dname1, 'DICOM')
assert vol.ndim == 3
assert vol.shape[0] > 20
assert vol.shape[1] == 512
assert vol.shape[2] == 512
# Test volsave()
raises(ValueError, imageio.volsave, dname1, vol)
raises(ValueError, imageio.volsave, dname1, np.zeros((100, 100, 100, 3)))
# todo: we have no format to save volumes yet!
# Test mvolread()
vols = imageio.mvolread(dname1, 'DICOM')
assert isinstance(vols, list)
assert len(vols) == 1
assert vols[0].shape == vol.shape
def test_functions():
""" Test the user-facing API functions """
# Test help(), it prints stuff, so we just check whether that goes ok
imageio.help() # should print overview
imageio.help("PNG") # should print about PNG
fname1 = get_remote_file("images/chelsea.png", test_dir)
fname2 = fname1[:-3] + "jpg"
fname3 = fname1[:-3] + "notavalidext"
open(fname3, "wb")
# Test read()
R1 = imageio.read(fname1)
R2 = imageio.read(fname1, "png")
assert R1.format is R2.format
# Fail
raises(ValueError, imageio.read, fname3) # existing but not readable
raises(FileNotFoundError, imageio.read, "notexisting.barf")
raises(IndexError, imageio.read, fname1, "notexistingformat")
# Test save()
W1 = imageio.save(fname2)
W2 = imageio.save(fname2, "JPG")
W1.close()
W2.close()
assert W1.format is W2.format
# Fail
raises(FileNotFoundError, imageio.save, "~/dirdoesnotexist/wtf.notexistingfile")
# Test imread()
im1 = imageio.imread(fname1)
im2 = imageio.imread(fname1, "png")
assert im1.shape[2] == 3
assert np.all(im1 == im2)
# Test imsave()
if os.path.isfile(fname2):
os.remove(fname2)
assert not os.path.isfile(fname2)
imageio.imsave(fname2, im1[:, :, 0])
imageio.imsave(fname2, im1)
assert os.path.isfile(fname2)
# Test mimread()
fname3 = get_remote_file("images/newtonscradle.gif", test_dir)
ims = imageio.mimread(fname3)
assert isinstance(ims, list)
assert len(ims) > 1
assert ims[0].ndim == 3
assert ims[0].shape[2] in (1, 3, 4)
# Test protection
with raises(RuntimeError):
imageio.mimread("imageio:chelsea.png", "dummy", length=np.inf)
if IS_PYPY:
return # no support for npz format :(
# Test mimsave()
fname5 = fname3[:-4] + "2.npz"
if os.path.isfile(fname5):
os.remove(fname5)
assert not os.path.isfile(fname5)
imageio.mimsave(fname5, [im[:, :, 0] for im in ims])
imageio.mimsave(fname5, ims)
assert os.path.isfile(fname5)
# Test volread()
fname4 = get_remote_file("images/stent.npz", test_dir)
vol = imageio.volread(fname4)
assert vol.ndim == 3
assert vol.shape[0] == 256
assert vol.shape[1] == 128
assert vol.shape[2] == 128
# Test volsave()
volc = np.zeros((10, 10, 10, 3), np.uint8) # color volume
fname6 = os.path.join(test_dir, "images", "stent2.npz")
if os.path.isfile(fname6):
os.remove(fname6)
assert not os.path.isfile(fname6)
imageio.volsave(fname6, volc)
imageio.volsave(fname6, vol)
assert os.path.isfile(fname6)
# Test mvolread()
vols = imageio.mvolread(fname4)
assert isinstance(vols, list)
assert len(vols) == 1
assert vols[0].shape == vol.shape
# Test mvolsave()
if os.path.isfile(fname6):
os.remove(fname6)
assert not os.path.isfile(fname6)
imageio.mvolsave(fname6, [volc, volc])
imageio.mvolsave(fname6, vols)
assert os.path.isfile(fname6)
# Fail for save functions
raises(ValueError, imageio.imsave, fname2, np.zeros((100, 100, 5)))
raises(ValueError, imageio.imsave, fname2, 42)
raises(ValueError, imageio.mimsave, fname5, [np.zeros((100, 100, 5))])
raises(ValueError, imageio.mimsave, fname5, [42])
raises(ValueError, imageio.volsave, fname6, np.zeros((100, 100, 100, 40)))
raises(ValueError, imageio.volsave, fname6, 42)
raises(ValueError, imageio.mvolsave, fname6, [np.zeros((90, 90, 90, 40))])
raises(ValueError, imageio.mvolsave, fname6, [42])
def test_tifffile_reading_writing():
""" Test reading and saving tiff """
need_internet() # We keep a test image in the imageio-binary repo
im2 = np.ones((10, 10, 3), np.uint8) * 2
filename1 = os.path.join(test_dir, 'test_tiff.tiff')
# One image
imageio.imsave(filename1, im2)
im = imageio.imread(filename1)
ims = imageio.mimread(filename1)
assert im.shape == im2.shape
assert (im == im2).all()
assert len(ims) == 1
# Multiple images
imageio.mimsave(filename1, [im2, im2, im2])
im = imageio.imread(filename1)
ims = imageio.mimread(filename1)
assert im.shape == im2.shape
assert (im == im2).all() # note: this does not imply that the shape match!
assert len(ims) == 3
for i in range(3):
assert ims[i].shape == im2.shape
assert (ims[i] == im2).all()
# Read all planes as one array - we call it a volume for clarity
vol = imageio.volread(filename1)
vols = imageio.mvolread(filename1)
assert vol.shape == (3, ) + im2.shape
assert len(vols) == 1 and vol.shape == vols[0].shape
for i in range(3):
assert (vol[i] == im2).all()
# remote multipage rgb file
filename2 = get_remote_file('images/multipage_rgb.tif')
img = imageio.mimread(filename2)
assert len(img) == 2
assert img[0].shape == (3, 10, 10)
# Mixed
W = imageio.save(filename1)
W.set_meta_data({'planarconfig': 'SEPARATE'}) # was "planar"
assert W.format.name == 'TIFF'
W.append_data(im2)
W.append_data(im2)
W.close()
#
R = imageio.read(filename1)
assert R.format.name == 'TIFF'
ims = list(R) # == [im for im in R]
assert (ims[0] == im2).all()
# meta = R.get_meta_data()
# assert meta['orientation'] == 'top_left' # not there in later version
# Fail
raises(IndexError, R.get_data, -1)
raises(IndexError, R.get_data, 3)
# Ensure imread + imwrite works round trip
filename3 = os.path.join(test_dir, 'test_tiff2.tiff')
im1 = imageio.imread(filename1)
imageio.imwrite(filename3, im1)
im3 = imageio.imread(filename3)
assert im1.ndim == 3
assert im1.shape == im3.shape
assert (im1 == im3).all()
# Ensure imread + imwrite works round trip - volume like
filename3 = os.path.join(test_dir, 'test_tiff2.tiff')
im1 = imageio.volread(filename1)
imageio.volwrite(filename3, im1)
im3 = imageio.volread(filename3)
assert im1.ndim == 4
assert im1.shape == im3.shape
assert (im1 == im3).all()
# Read metadata
md = imageio.get_reader(filename2).get_meta_data()
assert md['is_imagej'] is None
assert md['description'] == 'shape=(2,3,10,10)'
assert md['description1'] == ''
assert md['datetime'] == datetime.datetime(2015, 5, 9, 9, 8, 29)
assert md['software'] == 'tifffile.py'
# Write metadata
dt = datetime.datetime(2018, 8, 6, 15, 35, 5)
w = imageio.get_writer(filename1, software='testsoftware')
w.append_data(np.zeros((10, 10)), meta={'description': 'test desc',
'datetime': dt})
w.close()
r = imageio.get_reader(filename1)
md = r.get_meta_data()
assert 'datetime' in md
assert md['datetime'] == dt
assert 'software' in md
assert md['software'] == 'testsoftware'
assert 'description' in md
assert md['description'] == 'test desc'
def test_functions():
""" Test the user-facing API functions """
# Test help(), it prints stuff, so we just check whether that goes ok
imageio.help() # should print overview
imageio.help('PNG') # should print about PNG
fname1 = get_remote_file('images/chelsea.png', test_dir)
fname2 = fname1[:-3] + 'jpg'
fname3 = fname1[:-3] + 'notavalidext'
open(fname3, 'wb')
# Test read()
R1 = imageio.read(fname1)
R2 = imageio.read(fname1, 'png')
assert R1.format is R2.format
# Fail
raises(ValueError, imageio.read, fname3) # existing but not readable
raises(IOError, imageio.read, 'notexisting.barf')
raises(IndexError, imageio.read, fname1, 'notexistingformat')
# Test save()
W1 = imageio.save(fname2)
W2 = imageio.save(fname2, 'JPG')
assert W1.format is W2.format
# Fail
raises(ValueError, imageio.save, 'wtf.notexistingfile')
# Test imread()
im1 = imageio.imread(fname1)
im2 = imageio.imread(fname1, 'png')
assert im1.shape[2] == 3
assert np.all(im1 == im2)
# Test imsave()
if os.path.isfile(fname2):
os.remove(fname2)
assert not os.path.isfile(fname2)
imageio.imsave(fname2, im1[:, :, 0])
imageio.imsave(fname2, im1)
assert os.path.isfile(fname2)
# Test mimread()
fname3 = get_remote_file('images/newtonscradle.gif', test_dir)
ims = imageio.mimread(fname3)
assert isinstance(ims, list)
assert len(ims) > 1
assert ims[0].ndim == 3
assert ims[0].shape[2] in (1, 3, 4)
if IS_PYPY:
return # no support for npz format :(
# Test mimsave()
fname5 = fname3[:-4] + '2.npz'
if os.path.isfile(fname5):
os.remove(fname5)
assert not os.path.isfile(fname5)
imageio.mimsave(fname5, [im[:, :, 0] for im in ims])
imageio.mimsave(fname5, ims)
assert os.path.isfile(fname5)
# Test volread()
fname4 = get_remote_file('images/stent.npz', test_dir)
vol = imageio.volread(fname4)
assert vol.ndim == 3
assert vol.shape[0] == 256
assert vol.shape[1] == 128
assert vol.shape[2] == 128
# Test volsave()
volc = np.zeros((10, 10, 10, 3), np.uint8) # color volume
fname6 = fname4[:-4] + '2.npz'
if os.path.isfile(fname6):
os.remove(fname6)
assert not os.path.isfile(fname6)
imageio.volsave(fname6, volc)
imageio.volsave(fname6, vol)
assert os.path.isfile(fname6)
# Test mvolread()
vols = imageio.mvolread(fname4)
assert isinstance(vols, list)
assert len(vols) == 1
assert vols[0].shape == vol.shape
# Test mvolsave()
if os.path.isfile(fname6):
os.remove(fname6)
assert not os.path.isfile(fname6)
imageio.mvolsave(fname6, [volc, volc])
imageio.mvolsave(fname6, vols)
assert os.path.isfile(fname6)
# Fail for save functions
raises(ValueError, imageio.imsave, fname2, np.zeros((100, 100, 5)))
raises(ValueError, imageio.imsave, fname2, 42)
raises(ValueError, imageio.mimsave, fname5, [np.zeros((100, 100, 5))])
raises(ValueError, imageio.mimsave, fname5, [42])
raises(ValueError, imageio.volsave, fname4, np.zeros((100, 100, 100, 40)))
raises(ValueError, imageio.volsave, fname4, 42)
raises(ValueError, imageio.mvolsave, fname4, [np.zeros((90, 90, 90, 40))])
raises(ValueError, imageio.mvolsave, fname4, [42])