pydicom函数中的缺陷

Question

我想和pydicom一起处理dicom图像。不幸的是，我得到了错误

File "/usr/local/lib/python2.7/dist-packages/dicom/dataset.py", line 372, in _pixel_data_numpy
    raise TypeError(msg % (numpy_format, self.PixelRepresentation,
UnboundLocalError: local variable 'numpy_format' referenced before assignment

在函数中

def _pixel_data_numpy(self):
"""Return a NumPy array of the pixel data.

NumPy is a numerical package for python. It is used if available.

:raises TypeError: if no pixel data in this dataset.
:raises ImportError: if cannot import numpy.

"""
if 'PixelData' not in self:
    raise TypeError("No pixel data found in this dataset.")

if not have_numpy:
    msg = "The Numpy package is required to use pixel_array, and numpy could not be imported.\n"
    raise ImportError(msg)

# determine the type used for the array
need_byteswap = (self.is_little_endian != sys_is_little_endian)

# Make NumPy format code, e.g. "uint16", "int32" etc
# from two pieces of info:
#    self.PixelRepresentation -- 0 for unsigned, 1 for signed;
#    self.BitsAllocated -- 8, 16, or 32
format_str = '%sint%d' % (('u', '')[self.PixelRepresentation],
                          self.BitsAllocated)
try:
    numpy_format = numpy.dtype(format_str)
print numpy_format
except TypeError:
print "Data type not understood by NumPy!"
print format_str
    msg = ("Data type not understood by NumPy: "
           "format='%s', PixelRepresentation=%d, BitsAllocated=%d")
    raise TypeError(msg % (numpy_format, self.PixelRepresentation,
                    self.BitsAllocated))

# Have correct Numpy format, so create the NumPy array
arr = numpy.fromstring(self.PixelData, numpy_format)

# XXX byte swap - may later handle this in read_file!!?
if need_byteswap:
    arr.byteswap(True)  # True means swap in-place, don't make a new copy
# Note the following reshape operations return a new *view* onto arr, but don't copy the data
if 'NumberOfFrames' in self and self.NumberOfFrames > 1:
    if self.SamplesPerPixel > 1:
        arr = arr.reshape(self.SamplesPerPixel, self.NumberOfFrames, self.Rows, self.Columns)
    else:
        arr = arr.reshape(self.NumberOfFrames, self.Rows, self.Columns)
else:
    if self.SamplesPerPixel > 1:
        if self.BitsAllocated == 8:
            arr = arr.reshape(self.SamplesPerPixel, self.Rows, self.Columns)
        else:
            raise NotImplementedError("This code only handles SamplesPerPixel > 1 if Bits Allocated = 8")
    else:
        arr = arr.reshape(self.Rows, self.Columns)
return arr

当我打印变量format_str时，我得到了uint12。不幸的是，我无法解决这个错误。我能做些什么来解决这个问题吗？

即使我删除了所有的print命令(我为调试添加了它们)，我也会得到相同的错误。

Answer 1

这里有两个问题。首先，pydicom中的一个bug :在引发错误时，它错误地使用了未定义的numpy_format。它应该使用format_str。我将添加一个问题来纠正这个问题。

第二个问题是，该文件声称BitsAllocated为12，这是非常不寻常的。DICOM文件通常有12位像素值，但在文件中每像素使用16位。

您可以通过比较Rows和Columns与像素数据的大小来检查它实际分配的内容。对于单个帧映像(下面的示例使用pydicom的CT_small.dcm示例文件)：

>>> len(ds.PixelData)
32768
>>> ds.Rows * ds.Columns * 2  # 2 bytes for 16-bit allocation
32768

如果图像有多个帧，那么您也必须将帧数乘以。同样适用于SamplesPerPixel。

如果像素数据的大小与上面使用的每个像素的2个字节相匹配，那么在请求ds.BitsAllocated之前，您可以通过将pixel_array设置为16来纠正问题。

Answer 2

我假设代码的格式如下：

try:
    numpy_format = numpy.dtype(format_str)
    print numpy_format
except TypeError:
    print "Data type not understood by NumPy!"
    print format_str
    msg = ("Data type not understood by NumPy: "
           "format='%s', PixelRepresentation=%d, BitsAllocated=%d")
    raise TypeError(msg % (numpy_format, self.PixelRepresentation,
                    self.BitsAllocated))

在try块中，为numpy_format分配了一个值。如果numpy.dtype(format_str)抛出一个TypeError，它直接进入except块，而不将值绑定到numpy_format。这意味着当numpy_format在引发TypeError时再次被引用时，它会抛出一个UnboundLocalError，因为它从一开始就没有绑定过。