def main():
parser = argparse.ArgumentParser()
parser.add_argument('in_path',help='input tiff file or directory')
parser.add_argument('min_size',help='minimum w*h*d',nargs='?',default=0,type=int)
args = parser.parse_args()
files = []
if os.path.isdir(args.in_path):
for r,_,fnames in os.walk(args.in_path):
for fname in fnames:
files.append((r+'/'+fname))
elif os.path.isfile(args.in_path):
files.append(args.in_path)
resol,stepsize,C = 256,64,0
print('Found {} file{}'.format(len(files),'' if len(files)==1 else 's'))
for f in files:
img = tf.imread(f)
d,h,w = img.shape
print(f,w,h,d,args.min_size,img.nbytes//1e6)
img = tf.transpose_axes(img, 'YXZ', 'XYZ')
d,h,w = img.shape
aux = 1
cmap = matplotlib.cm.get_cmap('inferno',stepsize)
bounds = list(range(0,resol, resol//stepsize))
bounds.append(resol)
norm = matplotlib.colors.BoundaryNorm(bounds, cmap.N)
if C:
npz = np.arange(resol).astype('uint8')
z11 = np.array([3.17108944e-04, 9.92360110e-01, 1.61116136e+00])
for i in range(len(npz)):
aux = round(z11[0]*npz[i]*npz[i]+z11[1]*npz[i]+z11[2])
if aux < 256 and aux > 0:
npz[i] = int(aux)
elif aux > 255:
npz[i] = 255
else:
npz[i] = 0
with np.nditer(img, flags=['external_loop'], op_flags=['readwrite']) as it:
for x in it:
x[...] = npz[x]
print(f,w,h,d,args.min_size)
if d*h*w>=args.min_size:
tf.imshow(img,cmap = cmap, norm = norm, title=f,origin='lower')
# tf.imshow(img,title=f,cmap=plt.cm.magma)
plt.show()
C = 1
def __init__(self, filename):
with TiffFile(filename) as tif:
images = tif.asarray()
images = transpose_axes(images, "XYZCT")
images = images.squeeze(4)
if tif.series[0].axes == "TZCYX":
images = images.swapaxes(2, 3)
self._image = images
self._shape = self._image.shape
def array2cmap(data: numpy.ndarray, axes: str, cmapfile: PathLike,
**kwargs) -> None:
"""Save numpy ndarray to Chimera MAP files, one per channel.
Parameters
----------
data : ndarray
Three to 5 dimensional array.
axes : str
Specifies type and order of axes in data array.
May contain only 'CTZYX'.
cmapfile : str
Name of the output CMAP file.
**kwargs
Optional extra arguments passed to the CmapFile.addmap function,
e.g. verbose, step, origin, cell_angles, rotation_axis,
rotation_angle, subsample, chunks, and compression.
"""
if len(data.shape) != len(axes):
raise ValueError('Number of axes do not match data shape')
data = transpose_axes(data, axes, 'CTZYX')
try:
# create one CMAP file per channel
cmaps = []
cmapfile = os.fspath(cmapfile)
if cmapfile.lower().endswith('.cmap'):
cmapfile = cmapfile[:-5]
if data.shape[0] > 1:
cmaps = [
CmapFile(f'{cmapfile}.ch{i:04d}.cmap')
for i in range(data.shape[0])
]
else:
cmaps = [CmapFile(f'{cmapfile}.cmap')]
# iterate over data and write cmaps
for c in range(data.shape[0]): # channels
for t in range(data.shape[1]): # times
cmaps[c].addmap(data=data[c, t], **kwargs)
finally:
for f in cmaps:
f.close()
def transpose_axes(self, axes, dtype='float'):
"""Loads the stack in the order specified by axes"""
stack = self.asarray().astype(dtype)
actual_axes = self.get_axes()
return tif.transpose_axes(stack, actual_axes, asaxes=axes)