def write_np_colormask(img, path, num_labels=8):
create_directories_for_file_name(path)
im_out = sitk.GetArrayFromImage(img)
im_out = np.asarray(im_out, dtype=np.float32)
im_out -= np.amin(im_out)
im_out /= (num_labels - 1)
#im_out /= np.amax(im_out)
plt.imsave(path, im_out, cmap='tab20')
def save_string_txt(string, file_name):
"""
Saves a string as a text file.
:param string: The string to write.
:param file_name: The file name.
"""
create_directories_for_file_name(file_name)
with open(file_name, 'w') as file:
file.write(string)
def save(self, image_canvas_merged, filename):
"""
Save the merged image canvas to the filename.
:param image_canvas_merged: A merged image canvas (returned by merge_image_canvas).
:param filename: The filename to save the image canvas to.
"""
create_directories_for_file_name(filename)
image_canvas_merged_sitk = np_to_sitk(np.transpose(image_canvas_merged, [1, 2, 0]), is_vector=True)
write(image_canvas_merged_sitk, filename, compress=True)
def save(self, image_canvas_merged, filename):
"""
Save the merged image canvas to the filename.
:param image_canvas_merged: A merged image canvas (returned by merge_image_canvas).
:param filename: The filename to save the image canvas to.
"""
create_directories_for_file_name(filename)
plt.tight_layout()
plt.savefig(filename, dpi=self.dpi)
plt.close()
def save_list_txt(string_list, file_name):
"""
Saves string list as a text file. Each list entry is a new line.
:param string_list: The string list to write.
:param file_name: The file name.
"""
create_directories_for_file_name(file_name)
with open(file_name, 'w') as file:
string_list_with_endl = [string + '\n' for string in string_list]
file.writelines(string_list_with_endl)
def write(img, path, compress=True):
"""
Write a volume to a file path.
:param img: the volume
:param path: the target path
:return:
"""
create_directories_for_file_name(path)
writer = sitk.ImageFileWriter()
writer.Execute(img, path, compress)
def save_json(obj, file_name, *args, **kwargs):
"""
Saves an object as a json file.
:param obj: The object to save.
:param file_name: The filename.
:param args: args to pass to json.dump()
:param kwargs: kwargs to pass to json.dump()
:return:
"""
create_directories_for_file_name(file_name)
with open(file_name, 'w') as f:
json.dump(obj, f, *args, **kwargs)
def write(img, path, compress=True):
"""
Write an sitk image to a file path.
:param img: The sitk image.
:param path: The target path.
:param compress: If true, compress the file.
"""
create_directories_for_file_name(path)
writer = sitk.ImageFileWriter()
writer.SetFileName(path)
writer.SetUseCompression(compress)
writer.Execute(img)
def save_points_csv(landmarks_dict, filename, id_preprocessing=None):
create_directories_for_file_name(filename)
with open(filename, 'w') as csv_file:
writer = csv.writer(csv_file)
for key, values in sorted(landmarks_dict.items()):
current_id = key
if id_preprocessing is not None:
current_id = id_preprocessing(current_id)
row = [current_id]
for landmark in values:
row += list(landmark.coords)
writer.writerow(row)
def save_list_csv(l, file_name, header=None, **kwargs):
create_directories_for_file_name(file_name)
with open(file_name, 'w') as file:
writer = csv.writer(file, **kwargs)
if header is not None:
writer.writerow(header)
for value in l:
if isinstance(value, list):
writer.writerow(value)
elif isinstance(value, tuple):
writer.writerow(list(value))
else:
writer.writerow([value])
def save_dict_csv(d, file_name, header=None, **kwargs):
create_directories_for_file_name(file_name)
with open(file_name, 'w') as file:
writer = csv.writer(file, **kwargs)
if header is not None:
writer.writerow(header)
for key, value in sorted(d.items()):
if isinstance(value, list):
writer.writerow([key] + value)
elif isinstance(value, tuple):
writer.writerow([key] + list(value))
else:
writer.writerow([key, value])
def save_points_idl(landmarks_dict, filename, id_preprocessing=None):
create_directories_for_file_name(filename)
with open(filename, 'w') as file:
for key, values in sorted(landmarks_dict.items()):
current_id = key
if id_preprocessing is not None:
current_id = id_preprocessing(current_id)
string = '"' + current_id + '": '
for landmark in values:
point = landmark.coords
if len(point) == 2:
string += '(' + '{:.3f}'.format(point[0]) + ',' + '{:.3f}'.format(point[1]) + ',0),'
else:
string += '(' + '{:.3f}'.format(point[0]) + ',' + '{:.3f}'.format(point[1]) + ',' + '{:.3f}'.format(point[2]) + '),'
string = string[:-1] + '\n'
file.write(string)
def save_dict_csv(d, file_name, header=None):
"""
Saves a dictionary as a .csv file. The key is written as the first column. If the value is a list or a tuple,
each entry is written as a consecutive column. Otherwise, the value is written as the second column
:param d: The dictionary to write
:param file_name: The file name.
:param header: If given, this list will be written as a header.
"""
create_directories_for_file_name(file_name)
with open(file_name, 'w') as file:
writer = csv.writer(file)
if header is not None:
writer.writerow(header)
for key, value in sorted(d.items()):
if isinstance(value, list):
writer.writerow([key] + value)
elif isinstance(value, tuple):
writer.writerow([key] + list(value))
else:
writer.writerow([key, value])
def save_list_csv(l, file_name, header=None, **kwargs):
"""
Saves a list as a .csv file. If the list entries are a list or a tuple,
each entry is written as a consecutive column. Otherwise, the value is written as the second column
:param l: The (possibly nested) list to write
:param file_name: The file name.
:param header: If given, this list will be written as a header.
"""
create_directories_for_file_name(file_name)
with open(file_name, 'w') as file:
writer = csv.writer(file, **kwargs)
if header is not None:
writer.writerow(header)
for value in l:
if isinstance(value, list):
writer.writerow(value)
elif isinstance(value, tuple):
writer.writerow(list(value))
else:
writer.writerow([value])
