write_videofile jumps

[SalvatoreScaramuzzino]

Hi to all

i'm trying to create a pipeline for frame-by-frame analysis of medical images (cineangiographies)

i wrote a little script that reads a DICOM file that contains an angiograpy and generates the corresponding .avi file

from moviepy.editor import *
import numpy as np
import matplotlib.pyplot as plt
import SimpleITK as stk
import dicom
import os
import shutil

dicomfilePath = "/home/salvatore/Didattica/data/IMG00001"
outputVideoPath = "/home/salvatore/Videos/"

fileDicom = stk.ReadImage(dicomfilePath)
infoDicom = dicom.read_file(dicomfilePath)

matrice = stk.GetArrayFromImage(fileDicom)

nframes = matrice.shape[0]
cine_fps = infoDicom.CineRate
patient_id = infoDicom.PatientID
study_id = infoDicom.StudyID
altro = infoDicom.InstanceNumber

# i create a temporary directory
directory = "/home/salvatore/Documents/appoggio"
if not os.path.exists(directory):
    os.makedirs(directory)

# then i save all frames
for i in range(0,nframes):
    plt.imsave(directory + "/frame" + str(i) + ".tiff", matrice[i,:,:], cmap=plt.cm.gray)

# using such frames to create a Sequence Clip
newVideo = ImageSequenceClip(directory,fps=cine_fps)

# write to video file
newVideo.write_videofile(outputVideoPath + patient_id + ".avi", fps=cine_fps , codec='png' ) 

# delete dir
shutil.rmtree(directory)

i have this "jumps" in my final video

https://www.youtube.com/watch?v=VfinQD6buZA&feature=youtu.be

ideas?

[Zulko]

I am not sure but I think the issue is that the frames are taken in aphanumerical order by ImageSequenceClip, and the way you wrote it "frame2.tiff" will be between "frame19.tiff" and "frame20.tiff", which explains the jumps. If you rename it to "frame02.tiff" it will work.

So you should use plt.imsave(directory+"/frame%02d.tiff"%i, matrice[i,:,:], etc.)

[Zulko]

On a side note, maybe you could avoid writing everything as image files, because ImageSequenceClip can be fed directly by numpy arrays. Theoretically you could pass "matrice" as as arguments directly, but I am not sure what their format is. So what is matrice made of ? Numbers between 0 and 1, or numbers between 0 and 255 ?

[SalvatoreScaramuzzino]

I previously tried to pass "matrice" to ImageSequenceClip but it doesn't work

matrice is a numpy matrix from 0 to 255

thanks very much for early reply... i will give u a feedback as soon as possible

[Zulko]

Yeah ImageSequenceClip only accepts RGB pictures. You should try to convert the levels in matrice into RGB, like that (works on my computer):

matrice2 = [ np.dstack(3*[im]).astype("uint8") for im in matrice]
clip = mpy.ImageSequenceClip(matrice2, fps=cine_fps)

[SalvatoreScaramuzzino]

it works perfectly!

it now write from directory of frames and also from numpy shaped as you wrote

thank you very much for this wonderful library :)

[Zulko]

Cool ! Maybe you can remove the video you put on youtube now, it makes a bad publicity for the library ;)

[SalvatoreScaramuzzino]

sure :)