def test_store_image_as_short_nifti(test_output_dirs: TestOutputDirectories,
norm_method: PhotometricNormalizationMethod,
image_range: Any,
window_level: Any) -> None:
window, level = window_level if window_level else (400, 0)
image = np.random.random_sample((1, 2, 3))
image_shape = image.shape
args = SegmentationModelBase(norm_method=norm_method, window=window, level=level, should_validate=False)
# Get integer values that are in the image range
image1 = LinearTransform.transform(data=image, input_range=(0, 1), output_range=args.output_range)
image = image1.astype(np.short) # type: ignore
header = ImageHeader(origin=(1, 1, 1), direction=(1, 0, 0, 0, 1, 0, 0, 0, 1), spacing=(1, 1, 1))
nifti_name = test_output_dirs.create_file_or_folder_path(default_image_name)
io_util.store_image_as_short_nifti(image, header, nifti_name, args)
if norm_method == PhotometricNormalizationMethod.CtWindow:
output_range = get_range_for_window_level(args.level, args.window)
image = LinearTransform.transform(data=image, input_range=args.output_range, output_range=output_range)
image = image.astype(np.short)
else:
image = image * 1000
t = np.unique(image)
assert_nifti_content(nifti_name, image_shape, header, list(t), np.short)
def to_unique_bytes(a: np.ndarray, input_range: Tuple[float, float]) -> Any:
"""Returns an array of unique ubytes after applying LinearTransform on the input array."""
ubyte_range = (np.iinfo(np.ubyte).min, np.iinfo(np.ubyte).max)
a = LinearTransform.transform(data=a,
input_range=input_range,
output_range=ubyte_range)
return np.unique(a.astype(np.ubyte))
def _load_and_scale_image(name: str) -> ImageWithHeader:
image_with_header = load_nifti_image(full_ml_test_data_path(name))
return ImageWithHeader(image=LinearTransform.transform(
data=image_with_header.image,
input_range=(0, 255),
output_range=(0, 1)),
header=image_with_header.header)
def store_as_nifti(
image: np.ndarray,
header: ImageHeader,
file_name: PathOrString,
image_type: Union[str, type, np.dtype],
scale: bool = False,
input_range: Optional[Iterable[Union[int, float]]] = None,
output_range: Optional[Iterable[Union[int, float]]] = None) -> Path:
"""
Saves an image in nifti format (uploading to Azure also if an online Run), and performs the following operations:
1) transpose the image back into X,Y,Z from Z,Y,X
2) if scale is true, then performs a linear scaling to either the input/output range or
byte range (0,255) as default.
3) cast the image values to the given type before saving
:param image: 3D image in shape: Z x Y x X.
:param header: The image header
:param file_name: The name of the file for this image.
:param scale: Should perform linear scaling of the image, to desired output range or byte range by default.
:param input_range: The input range the image belongs to.
:param output_range: The output range to scale the image to.
:param image_type: The type to save the image in.
:return: the path to the saved image
"""
if image.ndim != 3:
raise Exception("Image must have 3 dimensions, found: {}".format(
len(image.shape)))
if image_type is None:
raise Exception("You must specify a valid image type.")
if scale and ((input_range is not None and output_range is None) or
(input_range is None and output_range is not None)):
raise Exception(
"You must provide both input and output ranges to apply custom linear scaling."
)
# rescale image for visualization in the app
if scale:
if input_range is not None and output_range is not None:
# noinspection PyTypeChecker
image = LinearTransform.transform(
data=image,
input_range=input_range, # type: ignore
output_range=tuple(output_range) # type: ignore
)
else:
image = (image + 1) * 255
image = sitk.GetImageFromArray(image.astype(image_type))
image.SetSpacing(sitk.VectorDouble(reverse_tuple_float3(
header.spacing))) # Spacing needs to be X Y Z
image.SetOrigin(header.origin)
image.SetDirection(header.direction)
sitk.WriteImage(image, str(file_name))
return Path(file_name)
def test_store_as_scaled_ubyte_nifti(test_output_dirs: TestOutputDirectories, input_range: Any) -> None:
image = np.random.random_sample((dim_z, dim_y, dim_x))
header = ImageHeader(origin=(1, 1, 1), direction=(1, 0, 0, 0, 1, 0, 0, 0, 1), spacing=(1, 2, 4))
io_util.store_as_scaled_ubyte_nifti(image, header,
test_output_dirs.create_file_or_folder_path(default_image_name),
input_range)
image = LinearTransform.transform(data=image, input_range=input_range, output_range=(0, 255))
t = np.unique(image.astype(np.ubyte))
assert_nifti_content(test_output_dirs.create_file_or_folder_path(default_image_name), image.shape, header, list(t),
np.ubyte)
def test_scale_and_unscale_image(
test_output_dirs: TestOutputDirectories) -> None:
"""
Test if an image in the CT value range can be recovered when we save dataset examples
(undoing the effects of CT Windowing)
"""
image_size = (5, 5, 5)
spacing = (1, 2, 3)
header = ImageHeader(origin=(0, 1, 0),
direction=(-1, 0, 0, 0, -1, 0, 0, 0, -1),
spacing=spacing)
np.random.seed(0)
# Random image values with mean -100, std 100. This will cover a range
# from -400 to +200 HU
image = np.random.normal(-100, 100, size=image_size)
window = 200
level = -100
# Lower and upper bounds of the interval of raw CT values that will be retained.
lower = level - window / 2
upper = level + window / 2
# Create a copy of the image with all values outside of the (Window, Level) range set to the boundaries.
# When saving and loading back in, we will not be able to recover any values that fell outside those boundaries.
image_restricted = image.copy()
image_restricted[image < lower] = lower
image_restricted[image > upper] = upper
# The image will be saved with voxel type short
image_restricted = image_restricted.astype(int)
# Apply window and level, mapping to the usual CNN input value range
cnn_input_range = (-1, +1)
image_windowed = LinearTransform.transform(data=image,
input_range=(lower, upper),
output_range=cnn_input_range)
args = SegmentationModelBase(
norm_method=PhotometricNormalizationMethod.CtWindow,
output_range=cnn_input_range,
window=window,
level=level,
should_validate=False)
file_name = test_output_dirs.create_file_or_folder_path(
"scale_and_unscale_image.nii.gz")
io_util.store_image_as_short_nifti(image_windowed, header, file_name, args)
image_from_disk = io_util.load_nifti_image(file_name)
# noinspection PyTypeChecker
assert_nifti_content(file_name, image_size, header,
np.unique(image_restricted).tolist(), np.short)
assert np.array_equal(image_from_disk.image, image_restricted)
def test_store_as_nifti(test_output_dirs: TestOutputDirectories, image_type: Any, scale: Any, input_range: Any,
output_range: Any) \
-> None:
image = np.random.random_sample((dim_z, dim_y, dim_x))
spacingzyx = (1, 2, 3)
path_image = test_output_dirs.create_file_or_folder_path(default_image_name)
header = ImageHeader(origin=(1, 1, 1), direction=(1, 0, 0, 0, 1, 0, 0, 0, 1), spacing=spacingzyx)
io_util.store_as_nifti(image, header, path_image,
image_type, scale, input_range, output_range)
if scale:
linear_transform = LinearTransform.transform(data=image, input_range=input_range, output_range=output_range)
image = linear_transform.astype(image_type) # type: ignore
assert_nifti_content(test_output_dirs.create_file_or_folder_path(default_image_name),
image.shape, header, list(np.unique(image.astype(image_type))), image_type)
loaded_image = io_util.load_nifti_image(path_image, image_type)
assert loaded_image.header.spacing == spacingzyx
def mri_window(image_in: np.ndarray,
mask: Optional[np.ndarray],
output_range: Tuple[float, float] = (-1.0, 1.0),
sharpen: float = 1.9,
tail: Union[List[float], float] = 1.0,
debug_mode: bool = False) -> Tuple[np.array, str]:
"""
This function takes an MRI Image, removes to first peak of values (air). Then a window range is found centered
around the mean of the remaining values and with a range controlled by the standard deviation and the sharpen
input parameter. The larger sharpen is, the wider the range. The resulting values are the normalised to the given
output_range, with values below and above the range being set the the boundary values.
:param image_in: The image to normalize.
:param mask: Consider only pixel values of the input image for which the mask is non-zero. If None the whole
image is considered.
:param output_range: The desired value range of the result image.
:param sharpen: number of standard deviation either side of mean to include in the window
:param tail: Default 1, allow window range to include more of tail of distribution.
:param debug_mode: If true, create diagnostic plots.
:return: normalized image
"""
nchannel = image_in.shape[0]
imout = np.zeros_like(image_in)
if isinstance(tail, int):
tail = float(tail)
if isinstance(tail, float):
tail = [tail] * nchannel
status = ""
for ichannel in range(nchannel):
if ichannel > 0:
status += "Channel {}: ".format(ichannel)
# Flatten to apply Otsu_thresholding
imflat = image_in[ichannel, ...].flatten()
if mask is None:
maflat = None
in_mask = False
else:
maflat = mask.flatten()
in_mask = mask > 0
# Find Otsu's threshold for the values of the input image
threshold = threshold_otsu(imflat)
# Find window level
level, std_i, _, max_foreground = robust_mean_std(
imflat[imflat > threshold])
# If lower value of window is below threshold replace lower value with threshold
input_range = (max(level - std_i * sharpen, threshold),
min(max_foreground,
level + tail[ichannel] * std_i * sharpen))
im_thresh = image_in[ichannel, ...]
im_thresh[image_in[ichannel, ...] < threshold] = 0
# Use Polynomial transform function to convert data to output range
imout[ichannel,
...] = LinearTransform.transform(im_thresh, input_range,
output_range)
status += f"Otsu {threshold:0.0f}, level {level:0.0f}, range ({input_range[0]:0.0f}, {input_range[1]:0.0f}) "
logging.debug(status)
if debug_mode:
print('Otsu {}, range {}'.format(threshold, input_range))
if mask is None:
no_thresh = np.sum(imflat < threshold)
no_high = np.sum(imout == output_range[1])
pc_thresh = no_thresh / np.numel(imflat) * 100
pc_high = no_high / np.numel(imflat) * 100
else:
no_thresh = np.sum(imflat[maflat == 1] < threshold)
no_high = np.sum(imout == output_range[1])
pc_thresh = no_thresh / np.sum(in_mask) * 100
pc_high = no_high / np.sum(in_mask) * 100
print('Percent of values outside window range: low,high',
pc_thresh, pc_high, no_high)
with open("channels_trim.txt", 'a') as fileout:
fileout.write(
"Thresholded: {ich:d}, {pl:4.2f}, {ph:4.2f} \n".format(
ich=ichannel, pl=pc_thresh, ph=pc_high))
# Plot input distribution
fig, axs = plt.subplots(2, 2, figsize=(9, 9))
axs[0, 0].set_title("Original Image")
axs[0, 0].imshow(image_in[ichannel, :, :, 70], cmap='gray')
# axs[1,0].hist(image.flatten(), 100)
axs[1, 0].set_title("Original Image - Histogram with Mask")
if mask is None:
axs[1, 0].hist(image_in[ichannel, ...].flatten(), 200)
else:
axs[1, 0].hist(image_in[ichannel, ...][in_mask].flatten(), 200)
axs[0, 1].set_title(
"Normalised Image, Level= {level:4.1f},\n "
"Window range {in1:4.1f} to {in2:4.1f}, \n"
"{pt:4.1f} % below threshold, {ph:4.1f} % above window \n"
"Threshold= {th:4.1f}".format(level=level,
in1=input_range[0],
in2=input_range[1],
pt=pc_thresh,
ph=pc_high,
th=threshold))
axs[0, 1].imshow(imout[ichannel, :, :, 70], cmap='gray')
axs[1, 1].set_title("Normalised Image - Histogram with Mask")
if mask is None:
axs[1, 1].hist(imout[ichannel, ...].flatten(), 200)
else:
axs[1, 1].hist(imout[ichannel, ...][in_mask].flatten(), 200)
plt.show()
return imout, status
def normalize_trim(image: np.ndarray,
mask: np.ndarray,
output_range: Tuple[float, float] = (-1.0, 1.0),
sharpen: float = 1.9,
trim_percentiles: Tuple[float, float] = (2.0, 98.0),
debug_mode: bool = False) -> np.array:
"""
Normalizes a single image to have mean 0 and standard deviation 1
Normalising occurs after percentile thresholds have been applied to strip out extreme values
:param image: The image to normalize, size Channels x Z x Y x X
:param mask: Consider only pixel values of the input image for which the mask is non-zero. Size Z x Y x X
:param output_range: The desired value range of the result image.
:param sharpen: number of standard deviation either side of mean to include in the window.
:param trim_percentiles: Only consider voxel values between those two percentiles when computing mean and std.
:param debug_mode: If true, create a diagnostic plot (interactive)
:return: trimmed-normalized image
"""
image_shape = image.shape
imout = np.zeros_like(image)
in_mask = mask > 0.5
status = ""
for ichannel in range(image_shape[0]):
if ichannel > 0:
status += "Channel {}: ".format(ichannel)
channel_image = image[ichannel, ...]
pixels_inside_mask = channel_image[in_mask].flatten().astype(float)
# First remove all values that fall outside the trim_percentiles
thresholds = np.percentile(pixels_inside_mask,
trim_percentiles,
interpolation='midpoint')
lower_threshold = thresholds[0]
upper_threshold = thresholds[1]
above_lower = pixels_inside_mask > lower_threshold
below_upper = pixels_inside_mask < upper_threshold
inside_thresholds = np.logical_and(above_lower, below_upper)
# Compute robust statistics off the pixel values that are inside the trim values
median, estimated_std, min_value, max_value = robust_mean_std(
pixels_inside_mask[inside_thresholds])
# Compute an input value range from median and robust std, going as many standard deviations
# as specified by the sharpen parameter
input_range = (max(median - estimated_std * sharpen, min_value),
min(median + estimated_std * sharpen, max_value))
# Use Polynomial transform function to convert data to output range. This also sets values outside
# the input_range to the boundary values.
channel_output = LinearTransform.transform(data=channel_image,
input_range=input_range,
output_range=output_range)
channel_output[np.logical_not(in_mask)] = output_range[0]
imout[ichannel, ...] = channel_output
status += "Range ({0:0.0f}, {1:0.0f}) ".format(input_range[0],
input_range[1])
logging.info(status)
if debug_mode:
print('median, estimated_std', median, estimated_std)
#
# Normalise values to zero mean and unit variance
#
fig, axs = plt.subplots(2, 2, figsize=(9, 9))
axs[0, 0].set_title("Original Image")
axs[0, 0].imshow(image[0, :, :, 70], cmap='gray')
# axs[1,0].hist(image.flatten(), 100)
axs[1, 0].set_title("Original Image - Histogram with Mask")
axs[1, 0].set_xlim(lower_threshold, upper_threshold)
axs[1, 0].hist(channel_image[in_mask].flatten(), 20)
axs[0, 1].set_title("Normalised Image, Level= {level:4.1f},\n "
"Window range {in1} to {in2}".format(
level=median,
in1=lower_threshold,
in2=upper_threshold))
axs[0, 1].imshow(imout[0, :, :, 70], cmap='gray')
axs[1, 1].set_title("Normalised Image - Histogram with Mask")
axs[1, 1].hist(channel_image[in_mask], 20)
plt.show()
return imout, status