The heart is a moving tissue and often one image set is produced for each phase of the cardiac cycle. To visualise the motion of the heart in the 2D slices you can use the Cineloop tool of Mimics. You can access it via View menu → Cineloop.
This script will help you to create the cineloop for the Parts that correspond to the segmentated anatomy of the different phases of the cardiac cycle.
Before you start the script you need to segment the phases of the cardiac cycle and create parts out of the masks. Make sure that you name the parts that represent the same anatomy with the same name. For example the part that represents the Aorta in all the phases should have the same name everywhere in order to be taken into account from the script. In case you want to run the script immediately after the segmentation (only the masks are present) set the CALCULATE_PARTS_FROM_MASKS variable to True. This action will create automatically the Parts from the Masks and will link them in the respective image sets. Additionally, correct names and colors will be set. After you get the Parts calculated, save the project and set the CALCULATE_PARTS_FROM_MASKS to False. Afterwards you can create the video again from different viewing angles of your choice without calculating again the Parts from the Masks.
The output of this script is a video that shows the motion of the heart accross the cardiac cycle in a specific angle of your choice.
Before you run the script:
- Segment the image sets that you want to be visualised the 4D Parts Cineloop.
- Make sure that you have installed the required packages to run this script. To create the video a special Python package, Open CV, is required. You can find more information about the package in the following link: https://pypi.org/project/opencv-python/
For instructions on how to install a Python package, please refer to Section 2.3 of the Introduction of this guide.
# import modules
import mimics
import logging
import os
import time
import datetime
try:
import cv2 # First need to install Open CV package for Python. Type pip install opencv-python in your cmd
except ImportError as ie:
print("================================================================")
print("=== The 3rd party Python package OpenCV is not installed! ===")
print("=== To install it, use pip install opencv-python in your cmd! ===")
print("================================================================")
raise
##########################################################################################
##########################################################################################
# config
# Here is the configuration area of the script.
# List the names of the anatomy of the Left Heart that you want to visualise in the video.
# In the provided script it is assumed that Left Atrium is LA, Left Ventricle is LV and Aorta is Aorta
LEFT_HEART = ["LA", "LV", "Aorta"]
# List the names of the anatomy of the Right Heart that you want to visualise in the video.
# In the provided script it is assumed that Right Atrium is RA, Right Ventricle is RV and Pulmonary Artery is PA
RIGHT_HEART = ["RA", "RV", "PA"]
# Here you select with part of the heart to visualise in the video.
HEART = LEFT_HEART + RIGHT_HEART
# The name (prefix) of the folder where the screenshots and the video will be saved. The suffix of the folder is the
# name of the Mimics file from where you run the script.
TARGET_FOLDER_NAME = "Output"
# Name of the file of the output video
VIDEO_NAME = "Cineloop_in_parts"
# Frames per second of the video. You can change this value to make the heart beating faster or slower.
FRAMES = 12
# If you want to visualise a logo in your video, the logo should be placed in the same folder as the script.
# If you do not want a logo to be visualised, just leave the script empty. Example: LOGO = ""
LOGO = "mat_logo.jpg"
# To calculate first the 3D Parts from the segmentation masks, set the value of the variable below to True.
# In case you have the Parts already calculated, you can leave it to False
CALCULATE_PARTS_FROM_MASKS = False
##########################################################################################
##########################################################################################
# settings
# Please do NOT modify this value
VIEW_OF_INTEREST = "3D"
IMAGE_FILE_SUFFIX = "jpg"
FONT = cv2.FONT_HERSHEY_DUPLEX
# Here you can change the size of the text that appears in the bottom right side of the video.
# It indicates the name of the cardiac phase that is visualised.
FONT_SIZE = 0.7
# Here you can change the colour (in RGB [0,255]) of the text that appears in the bottom right side of the video.
# It indicates the name of the cardiac phase that is visualised.
FONT_COLOR = (0, 0, 0)
LINE_TYPE = 1
##########################################################################################
class Phase:
def __init__(self, image_obj):
self.mimics_obj = image_obj
self.patient_name = self.get_patient_name()
self.image_name = self.mimics_obj.name
self.guid = self.mimics_obj.guid
self.linked_objs = self.mimics_obj.linked_objects
def get_patient_name(self) -> str:
info = self.mimics_obj.get_image_information()
return info.patient_name
##########################################################################################
def get_correct_phases() -> dict:
phases = {}
for im in mimics.data.images:
size = im.physical_dimensions
phases[im.guid] = size
return mimics.data.images
def get_initial_status() -> tuple:
overlay = mimics.view.is_overlay_enabled()
active_is = mimics.data.images.get_active()
visible_objs = []
for obj in mimics.data.objects:
if not isinstance(obj, mimics.ImageData) and obj.visible is True:
visible_objs.append(obj.guid)
return overlay, active_is, visible_objs
def set_initial_status(overlay, active_is, visible_objs) -> None:
if not overlay:
mimics.view.disable_overlay()
mimics.data.images.set_active(active_is)
for obj in mimics.data.objects:
if not isinstance(obj, mimics.ImageData):
obj.visible = False
if obj.guid in visible_objs:
obj.visible = True
return
def reset_views() -> None:
# enable Overlay that will make our life easier
if not mimics.view.is_overlay_enabled():
mimics.view.enable_overlay()
# Get current active IS
currently_active_is = mimics.data.images.get_active()
# switch to the Standard single IS layout
mimics.view.set_layout(layout_name=mimics.Layouts.Standard, images=currently_active_is)
# switch off 3D mask preview if ON
mimics.view.disable_mask_3d_preview()
# reset the objects that are visualised
for obj in mimics.data.objects:
if not isinstance(obj, mimics.ImageData):
obj.visible = False
return None
def calculate_parts() -> None:
# show the correct objects
for im in mimics.data.images:
if im.linked_objects is not None:
mimics.data.images.set_active(im)
for objs in im.linked_objects:
if isinstance(objs, mimics.segment.Mask) and objs.name in HEART:
prt = mimics.segment.calculate_part(objs)
prt.name = objs.name
prt.image = objs.image
prt.color = objs.color
prt.visible = False
return None
def prepare_objects(image) -> None:
# show the correct objects
phase_visible_objs = []
for objs in image.linked_objs:
if isinstance(objs, mimics.Part) and objs.name in HEART:
objs.visible = True
phase_visible_objs.append(objs.name)
logging.info("Phase name:")
logging.info(image.image_name)
logging.info("Objects that will be included in the video:")
logging.info(phase_visible_objs)
return None
def get_camera() -> tuple:
view = None
for v in mimics.data.views:
if v.type == VIEW_OF_INTEREST:
cam = v.get_camera()
settings = cam.get_settings()
view = v
return settings, view
def set_camera(settings) -> None:
for v in mimics.data.views:
if v.type == VIEW_OF_INTEREST:
cam = v.get_camera()
cam.set_settings(settings)
return None
def capture_frame(view, counter, directory, phase_name) -> bool:
filename = os.path.join(directory, str(counter) + "." + IMAGE_FILE_SUFFIX)
try:
mimics.file.export_view(filename, view)
except RuntimeError:
print("It was not possible to export the frame.")
return False
img = cv2.imread(filename, 1)
height, width, _ = img.shape
txt_size = cv2.getTextSize(phase_name, FONT, FONT_SIZE, LINE_TYPE)
text_location = (width - txt_size[0][0] - 10, height - txt_size[0][1] - 10)
cv2.putText(img, phase_name, text_location, FONT, FONT_SIZE, FONT_COLOR, LINE_TYPE)
if get_logo(LOGO):
logo = cv2.imread(get_logo(LOGO), 1)
rows, cols, channels = logo.shape
# logo_location = img[rows:-1, cols:-1]
# print(len(logo_location))
img[50:rows + 50, width - cols - 50:-50] = logo
cv2.imwrite(filename, img)
return True
def create_dir() -> tuple:
p = mimics.file.get_project_information()
path = p.project_path
name_of_file_with_extension = os.path.basename(path)
name_of_file = os.path.splitext(name_of_file_with_extension)[0]
target_folder = TARGET_FOLDER_NAME + "_" + name_of_file
root = os.path.dirname(__file__)
new_dir = False
if not os.path.isdir(os.path.join(root, target_folder)):
try:
os.makedirs(os.path.join(root, target_folder))
new_dir = True
logging.info("A new folder Output is created")
except PermissionError:
logging.info("=== The script does not have the permissions to create a folder here! ===")
raise
else:
logging.info("The Output folder already exists.")
return os.path.join(root, target_folder), new_dir
def clean_dir(directory) -> None:
filelist = os.listdir(directory)
for file in filelist:
os.remove(os.path.join(directory, file))
logging.info("The Output folder is cleaned.")
return None
def get_logo(logo_name) -> str:
root = os.path.dirname(__file__)
logo_full_path = os.path.join(root, logo_name)
if os.path.isfile(logo_full_path):
return logo_full_path
def create_the_video(directory) -> None:
image_folder = directory
video_name = VIDEO_NAME
images = [img for img in os.listdir(image_folder) if img.endswith("." + IMAGE_FILE_SUFFIX)]
frame = cv2.imread(os.path.join(image_folder, images[0]))
height, width, _ = frame.shape
fourcc = cv2.VideoWriter_fourcc(*'WMV1')
video = cv2.VideoWriter(os.path.join(image_folder, video_name + ".avi"), fourcc, FRAMES, (width, height))
for image in images:
video.write(cv2.imread(os.path.join(image_folder, image)))
cv2.destroyAllWindows()
video.release()
return None
if __name__ == "__main__":
log_file = os.path.join(os.path.dirname(__file__), 'report.log')
logging.basicConfig(filename=log_file, filemode='w', level=logging.INFO)
with open(log_file, "w")as f:
f.truncate()
logging.info('Cineloop in Parts is started. Mimics UI will be frozen for a few seconds...')
start = time.time()
now = datetime.datetime.now()
logging.info("Date and Time:{}".format(now.now()))
mimics.disable_update_gui()
phases = get_correct_phases()
logging.info("The following image sets will be included in the script: ")
t = []
for p in phases:
t.append(p.name)
logging.info(t)
output_dir, is_dir_new = create_dir()
if not is_dir_new:
clean_dir(output_dir)
if CALCULATE_PARTS_FROM_MASKS:
calculate_parts()
mimics.dialogs.question_box(
message='Set the desired camera view in the 3D viewport. Then click OK to continue..', buttons='OK',
title='Set the camera', ui_blocking=False)
cl_phases = []
overlay, active_is, visible_objs = get_initial_status()
settings, view = get_camera()
# print(settings, view)
for c, p in enumerate(phases):
ph = Phase(p)
cl_phases.append(ph)
reset_views()
prepare_objects(ph)
set_camera(settings)
export = True
if view:
if not capture_frame(view, c, output_dir, ph.image_name):
export = False
else:
logging.info('The 3D view is not visible in Mimics. Please select a layout where the 3D view is visible.')
export = False
set_initial_status(overlay, active_is, visible_objs)
if export:
create_the_video(output_dir)
logging.info('The video is exported.')
mimics.enable_update_gui()
logging.info("The script is terminated.")