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 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