def readDataFiles(filename, x=all, y=all, z=all, **args):
"""Read data from individual images assuming they are the z slices
Arguments:
filename (str): file name as regular expression
x,y,z (tuple): data range specifications
Returns:
array: image data
"""
fpath, fl = readFileList(filename)
nz = len(fl)
#read first image to get data size and type
rz = io.toDataRange(nz, r=z)
sz = io.toDataSize(nz, r=z)
fn = os.path.join(fpath, fl[rz[0]])
img = io.readData(fn, x=x, y=y)
nxy = img.shape
data = numpy.zeros(nxy + (sz, ), dtype=img.dtype)
data[:, :, 0] = img
for i in range(rz[0] + 1, rz[1]):
fn = os.path.join(fpath, fl[i])
data[:, :, i - rz[0]] = io.readData(fn, x=x, y=y)
return data
def readDataFiles(filename, x=all, y=all, z=all, **args):
"""Read data from individual images assuming they are the z slices
Arguments:
filename (str): file name as regular expression
x,y,z (tuple): data range specifications
Returns:
array: image data
"""
fpath, fl = readFileList(filename)
nz = len(fl)
# read first image to get data size and type
rz = io.toDataRange(nz, r=z)
sz = io.toDataSize(nz, r=z)
fn = os.path.join(fpath, fl[rz[0]])
img = io.readData(fn, x=x, y=y)
nxy = img.shape
data = numpy.zeros(nxy + (sz,), dtype=img.dtype)
data[:, :, 0] = img
for i in range(rz[0] + 1, rz[1]):
fn = os.path.join(fpath, fl[i])
data[:, :, i - rz[0]] = io.readData(fn, x=x, y=y)
return data
def dataZSize(filename, z = all, **args):
"""Returns z size of data in tif file
Arguments:
filename (str): file name as regular expression
z (tuple): z data range specification
Returns:
int: z data size
"""
t = tiff.TiffFile(filename);
d2 = t.pages[0].shape;
if len(d2) == 3:
return io.toDataSize(d2[0], r = z);
d3 = len(t.pages);
if d3 > 1:
return io.toDataSize(d3, r = z);
else:
return None;
def dataZSize(filename, z = all, **args):
"""Returns z size of data in tif file
Arguments:
filename (str): file name as regular expression
z (tuple): z data range specification
Returns:
int: z data size
"""
t = tiff.TiffFile(filename);
d2 = t.pages[0].shape;
if len(d2) == 3:
return io.toDataSize(d2[0], r = z);
d3 = len(t.pages);
if d3 > 1:
return io.toDataSize(d3, r = z);
else:
return None;
def dataZSize(filename, z=all, **args):
"""Returns size of data stored as a file list
Arguments:
filename (str): file name as regular expression
z (tuple): z data range specification
Returns:
int: z data size
"""
fp, fl = readFileList(filename)
nz = len(fl)
return io.toDataSize(nz, r=z)
def dataZSize(filename, z=all, **args):
"""Returns size of data stored as a file list
Arguments:
filename (str): file name as regular expression
z (tuple): z data range specification
Returns:
int: z data size
"""
fp, fl = readFileList(filename)
nz = len(fl)
return io.toDataSize(nz, r=z)
def dataZSize(filename, z = all, **args):
"""Read data z size from nrrd image
Arguments:
filename (str): file name as regular expression
z (tuple): z data range specification
Returns:
int: z data size
"""
header = readHeader(filename);
dims = header['sizes'];
if len(dims) > 2:
return io.toDataSize(dims[2], r = z);
else:
return None;
def dataZSize(filename, z=all, **args):
"""Read data z size from nrrd image
Arguments:
filename (str): file name as regular expression
z (tuple): z data range specification
Returns:
int: z data size
"""
header = readHeader(filename)
dims = header['sizes']
if len(dims) > 2:
return io.toDataSize(dims[2], r=z)
else:
return None
def dataZSize(filename, z = all, **args):
"""Read z data size from raw/mhd image
Arguments:
filename (str): imaris file name
z (tuple or all): range specification
Returns:
int: raw image z data size
"""
imr = vtk.vtkMetaImageReader()
imr.SetFileName(filename);
imr.Update()
im = imr.GetOutput()
dims = im.GetDimensions()
if len(dims) > 2:
return io.toDataSize(dims[2], r = z);
else:
return None;
def dataZSize(filename, z=all, **args):
"""Read z data size from raw/mhd image
Arguments:
filename (str): imaris file name
z (tuple or all): range specification
Returns:
int: raw image z data size
"""
imr = vtk.vtkMetaImageReader()
imr.SetFileName(filename)
imr.Update()
im = imr.GetOutput()
dims = im.GetDimensions()
if len(dims) > 2:
return io.toDataSize(dims[2], r=z)
else:
return None
