insituTEM 0.1.6__py3-none-any.whl → 0.1.8__py3-none-any.whl

insituTEM/insitu_IO.py

@@ -15,30 +15,28 @@ Update 20200303:
         Add stroke to scalebar and text
 """
 
-import moviepy.editor as mp
-#from moviepy.editor import concatenate_videoclips,ImageClip,VideoFileClip,vfx
+
 import cv2
 import tifffile
 import tqdm #not necessary just provides a progress bar and timer
 import numpy as np
 
 
-def tiff2mp4(path):
+def tiff2mp4(path,fps):
     """
     function to convert any input file to H264 High quality mp4 using openCV
     Inputs: filepath
     Output: file in the same folder named '..._fps.mp4'
     """
     video = tifffile.imread(path)
-    nFrames, h,w = video.shape
-    fps = int(input('Input desired output fps:'))
+    nFrames, h,w = video.shape[:3]
     # dur=1/fps    
     pathout =path[:-4]+'_'+str(fps)+'.mp4'    
     # pathout2 =path[:-4]+'_St.tif'
     codec  = cv2.VideoWriter_fourcc(*'H264')
     out = cv2.VideoWriter(pathout, codec , fps, (w,  h))
     print("---------------------------------------------")
-    print('Converting Tiff stack to the movie')    
+    print('Converting Tiff stack to mp4')    
     for i in tqdm.tqdm(range(nFrames)):        
         img=video[i]  
         out.write(img)
@@ -47,89 +45,133 @@ def tiff2mp4(path):
     print("==============================================")
     print("MP4 convertion Done!")
 
+def tiff2avi(path,fps,is_color=False):
+    #convert tiff stack to movie
+    import tifffile
+    import cv2
+    
+    # path = 
+    stack = tifffile.imread(path)
+    nFrames,h,w = stack.shape[:3]
+    
+    # # fps = int(input('Input desired output fps:'))
+    # # dur=1/fps    
+    # pathout =path[:-4]+'_'+str(fps)+'.avi'    
+       
+    
+    # codec  = cv2.VideoWriter_fourcc(*'MJPG')
+    
+    # video_out = cv2.VideoWriter(pathout, codec , fps, (w,  h))
+    # print("---------------------------------------------")
+    # print('Converting Tiff stack to avi')    
+    # for i in tqdm.tqdm(range(nFrames)):        
+    #     img=stack[i] 
+    #     video_out.write(img)
+        
+    # video_out.release()
+    # cv2.destroyAllWindows()
+    # print("==============================================")
+    # print("AVI convertion Done!")
+    size=(int(w),int(h))
 
 
-# print("---------------------------------------------")
-# print('Done! Enjoy~')
-# def f2mp4(path,fps,is_gray=1):
-#     """
-#     function to convert any input file to H264 High quality mp4
-#     Inputs: filepath, output fps,is_gray: 1 for grayscale, 0 for rgb
-#     Output: file in the same folder named '..._cv.mp4'
-#     """
-
-#     print("==============================================")
-#     print("Convert file to MP4!")
-#     pathout = path[:-4]+'_'+str(fps)+'.mp4'
-#     if path.endswith('.tif'):            
-# #        import tifffile
-#         im = tifffile.imread(path)
-#         if is_gray == 1:
-#             nFrames, h,w = im.shape
-#         else:
-#             nFrames, h,w,c = im.shape
-#         fps=int(input("Enter desired fps: "))
-#         dur=1/fps
-#         clip = []
-#         print("---------------------")
-#         print("Read TIF file!")
-#         for i in tqdm.tqdm(range(nFrames)):
-#             if is_gray ==1: 
-#                 fr = cv2.cvtColor(im[i],cv2.COLOR_GRAY2RGB)
-#             else:
-#                 fr=im[i]
-#             clip.append(mp.ImageClip(fr).set_duration(dur))
-#         video = mp.concatenate_videoclips(clip, method="compose",ismask=False)#ismask=True to make grayscale
-
-#     else:
-#         video = mp.VideoFileClip(path)
-#         fpsIn = int(video.fps)
-#         if fps != fpsIn:
-#             print("Conflict in fps! \n",              "[0] Use fps of input file;\n",              "[1] Use desired fps w/o speedup;\n",
-#               "[2] Use desired fps w/ speedup:")
-#             k = input('Input your selection: ')
-#             if k == 2:
-#                 sf = fps/fpsIn
-#                 video =video.fx(mp.vfx.speedx, sf)
-#             elif k == 0:
-#                 fps = fpsIn
-#         video.reader.close()# To fix handel error problem
-#     print("---------------------")
-
-#     print("Save to mp4!")
-#     video.write_videofile(pathout, fps=fps,codec='libx264', bitrate='32 M',preset='ultrafast') 
-   
-#     print("==============================================")
-#     print("MP4 convertion Done!")
-    
-
-def f2tif(path,is_gray=1):
-    """
-    function to convert any input file to tif stack
-    Inputs: filepath, is_gray: 1 for grayscale, 0 for rgb
+    pathout =path[:-4]+'_'+str(fps)+'.avi'    
+
+    # # Check if the image stack is grayscale or color
+    is_color = len(stack.shape) == 4 and stack.shape[3] == 3
+
+    codec  = cv2.VideoWriter_fourcc(*'MJPG')
+    video_out = cv2.VideoWriter(pathout, codec , fps, size,isColor=is_color)
+    print("---------------------------------------------")
+    print('Converting Tiff stack to avi')    
+    for i in tqdm.tqdm(range(nFrames)):        
+        img=stack[i]
+
+        # Ensure the image is in 8-bit format
+        
+        if img.dtype != np.uint8:
+            img = cv2.normalize(img, None, 0, 255, cv2.NORM_MINMAX)
+            img = np.uint8(img)
+        # Convert RGB to BGR if the image is in color
+        if is_color ==True:
+            img = cv2.cvtColor(img, cv2.COLOR_RGB2BGR)
+        # else:
+        #     img = cv2.normalize(img, None, 0, 255, cv2.NORM_MINMAX)
+        #     img = np.uint8(img)
+        # Convert RGB to BGR if the image is in color
+        
+            
+        video_out.write(img)
+        
+    video_out.release()
+    cv2.destroyAllWindows()
+    print("==============================================")
+    print("AVI convertion Done!")
+
+def movie2tif(path,is_gray=1,exp_time=0.2):
+    """
+    function to convert any input movie file to tif stack
+    Inputs: filepath of movie, is_gray: 1 for grayscale, 0 for rgb
+            exp_time= exposure time of real movie, remove dup frame if fps > exp_time
     
     Output: file in the same folder named '..._cv.tif'
     """   
-#    import tifffile
+    import moviepy.editor as mp
+    import tifffile
     import tqdm
     print("==============================================")
     print("Convert file to tif stack!")
     pathout = path[:-4]+'_'+str(is_gray)+'.tif'    
     video = mp.VideoFileClip(path)
-    i=0
-    for fr in tqdm.tqdm(video.iter_frames()):
-        if is_gray == 1:
-            fr= cv2.cvtColor(fr, cv2.COLOR_BGR2GRAY) 
-        if i == 0:
-            tifffile.imwrite(pathout,fr, append=False)
-        else:
-            tifffile.imwrite(pathout,fr, append=True)
-        i += 1
+    fps = int(video.fps)
+    w = int(video.w)
+    h = int(video.h)
+    nFrames = int(fps*video.duration)
+    dup= fps*exp_time
+    nFramesOut=int(nFrames/dup)
+    with tifffile.TiffWriter(pathout,bigtiff=True) as tif:
+        for j in tqdm.tqdm(range(nFramesOut)):
+            i=int(j*dup)
+            fr = video.get_frame(mp.cvsecs(i/fps))
+            if is_gray==1:
+                fr = cv2.cvtColor(fr, cv2.COLOR_BGR2GRAY)
+            tif.write(fr, contiguous=True)
+
+
+    video.reader.close()
+        # for fr in tqdm.tqdm(video.iter_frames()):
+        #     if is_gray==1:
+        #         fr = cv2.cvtColor(fr, cv2.COLOR_BGR2GRAY) 
+        #     tif.write(fr,continuous=True)
+
     print("==============================================")
     print("TIF convertion Done!")
-    print("nFrames="+str(i))
     video.reader.close()# To fix handel error problem
 
+def folder2tif(path,isGray=True):
+    """
+    Function to convert folder of single images into tif stack
+    Input: path: folder path
+    Output: tif stack with the same name as the folder in the parent folder.
+    """
+    import tifffile
+    img_name=os.listdir(path) 
+    nFrames= len(img_name)
+    pathout=path+'.tif'
+    if movieout == True:
+        video_out.write(img)
+
+    with tifffile.TiffWriter(pathout,bigtiff=True) as tif:
+        for i in tqdm.tqdm(range(nFrames)):
+            # img_name = f'{i:03d}.tif'
+            compare_path=os.path.join(path,f'{i:03d}.tif')
+            overlay =cv2.imread(compare_path)
+            if isGray==True:
+                overlay = cv2.cvtColor(overlay,cv2.COLOR_BGR2GRAY)
+            else:
+                overlay = cv2.cvtColor(overlay, cv2.COLOR_BGR2RGB) #tifffile usedRGB, cv2 used BGR
+        
+            tif.write(overlay, contiguous=True)
 
 def f2gif(path,fps):
     """
@@ -165,8 +207,8 @@ def f2gif(path,fps):
             elif k == 0:
                 fps = fpsIn
 
-    video.write_gif(pathout,fps=fps)
-    video.reader.close()# To fix handel error problem
+        video.write_gif(pathout,fps=fps)
+        video.reader.close()# To fix handel error problem
 #    if path.endswith('.gif'):
 #        clip.write_videofile(pathout,fps=fps,codec='libx264', bitrate='32 M',preset='ultrafast')
     print("==============================================")
@@ -295,22 +337,96 @@ def ExtractFrame(path,framelist,is_gray=1):
     if path.endswith('.tif')==0:
         video.reader.close()
         
-        
 def writeCSV(pathout,data,fmt='%1.1d'):
 #    import csv
     import numpy as np
 #    (length,width)=np.shape(data)
     np.savetxt(pathout, data, fmt=fmt, delimiter=",")
-
-#
-#def Time2List()       
+     
 def showFr(im):
     from PIL import Image
     img = Image. fromarray(im)
     img.show() 
+
+#functions for scalebar
+def readscale(path,dy=5):
+    """
+    Function to measure scale from movie first frame
+    Input: path - movie path; dy: shift from the bottom in px
+    scalebarcolr- 0 for black, 255 for white
+    """
+    import os
+    os.environ["IMAGEIO_FFMPEG_EXE"] = "/opt/homebrew/bin/ffmpeg"
+    import moviepy.editor as mp
+    import cv2
     
+    video = mp.VideoFileClip(path)
+    fr = video.get_frame(mp.cvsecs(0))
+    fr = cv2.cvtColor(fr, cv2.COLOR_BGR2GRAY)
+
+    # Select ROI using cv2.selectROI()
+    roi = cv2.selectROI('Select scalebar ROI, quit with SPACE', fr)
+    cv2.waitKey(10)
+    cv2.destroyWindow('Select scalebar ROI, quit with SPACE')
+
+    # Crop the image based on the selected ROI
+    cropped_image = fr[int(roi[1]):int(roi[1] + roi[3]), int(roi[0]):int(roi[0] + roi[2])]
+
+    # # # Display the cropped image
+    showFr(cropped_image)
+
+    import numpy as np
 
-def AddScale(img,barLen =2, scale = 34.5, px=0.02,py=0.96, color = 255,thick=5,lw=1,stroke=1):
+    scalebar_color = int(input("Input the scalebar color,  0-black, 255-white: "))
+    dy2=dy
+    while dy2 != 0: 
+        print(cropped_image[-dy,:])
+        dy2=int(input("input 0 if the crop is correct, otherwise input the estimated distance from bottom to the scalebar: "))
+        if dy2 !=0:
+            dy=dy2
+            
+    scalebar_px =  np.count_nonzero(cropped_image[-dy,:]==scalebar_color)
+    print("scalebar_px=", scalebar_px)
+    scale_nm = int(input("Input the scalebar in nm: "))
+    scale =scalebar_px/scale_nm
+    print("==============")
+    print("scale=",scale,"px/nm")
+    return scale
+
+def getScalePix(scale,barLenPix=250):
+    """
+    Function to convert truescale into str with correct format
+    Input: 
+        barLenPix : pixel length of the scalebar region
+        scale: scale: px/nm
+    Output: 
+        text: string of the scalebar text, in the format such as 100, 200, 500 nm .
+        scalepix: pixel distance of the realoutput scalebar
+    """
+    truescale= barLenPix/scale
+    
+    # Find the nearest power of 10 to the truescale
+    nearest_power = 10 ** np.floor(np.log10(truescale))
+
+    # Determine the most appropriate scale bar value
+    if truescale >= 5 * nearest_power:
+        scalebar = 5 * nearest_power
+    elif truescale >= 2 * nearest_power:
+        scalebar = 2 * nearest_power
+    else:
+        scalebar = nearest_power
+
+    # Calculate the scale in pixels
+    scalepix = int(scalebar * scale)
+
+    # Determine the appropriate unit for the scale bar text
+    if scalebar >= 1000:
+        text = f"{int(scalebar/1000)} um"
+    else:
+        text = f"{int(scalebar)} nm"
+    return scalepix, text
+
+def AddScalePix(img,barLenPix =250, scale = 34.5, px=0.02,py=0.96, barthick=5,lw=1,stroke=True,tscale=1,textThick=4):
     """
     Function to add scale to image
     Input:
@@ -322,54 +438,214 @@ def AddScale(img,barLen =2, scale = 34.5, px=0.02,py=0.96, color = 255,thick=5,l
         stroke=1: add stroke; stroke=0 No stroke
  
     """
+    import cv2
     h,w=img.shape
-    w_scale=int(scale*barLen)
+
+    scalepix, text = getScalePix(barLenPix, scale)
+
+    # w_scale=int(scale*barLen)
     x1=int(w*px)
     y1=int(h*py)
-    x2=x1+w_scale
-    y2=y1+thick
+    x2=x1+scalepix
+    y2=y1+barthick
+
+
+    #find bcakground color and make the reverse as scalebar color
+    img_bg=img[y1:y2,x1:x2]
+    mean_intensity=np.mean(img_bg)
+
+    if mean_intensity<128:
+        color = 255
+    else:
+        color = 0
+
     
     bcolor=255-color
-    
-    
- 
- 
-    text = str(barLen)+' nm'
+
     font = cv2.FONT_HERSHEY_SIMPLEX#CV_FONT_HERSHEY_SIMPLEX normal size sans-serif font
-    if stroke == 1:
-        cv2.putText(img,text,(x1,y1-8), font, 1, bcolor, 3, cv2.LINE_AA) #Stroke  
+    if stroke == True:
+        cv2.putText(img,text,(x1,y1-8), font, tscale, bcolor,int(textThick+lw), cv2.LINE_AA) #Stroke  
         cv2.rectangle(img,(x1,y1),(x2,y2),bcolor,2)#boarder color
 
         
     cv2.rectangle(img,(x1,y1),(x2,y2),color,-1)
     
-    cv2.putText(img,text,(x1,y1-8), font, 1, color, 2, cv2.LINE_AA)
+    cv2.putText(img,text,(x1,y1-8), font,tscale, color, textThick, cv2.LINE_AA)
+
+def AddScale(img,barLen =2, scale = 34.5, px=0.02,py=0.96, color = 255,fontScale=1.5, barthick=5,textthick=2,stroke=1):
+    """
+    Function to add scale to image
+    Input:
+        img: greyscale image
+        barLen: desired scale length
+        scale: scale of the image: px/nm: 1000kX- 49.5; 700kX - 34.5
+        (px,py): position of the scale bar: r(0-1)
+        color: color of the scalebar
+        stroke=1: add stroke with thickness,  stroke=0 No stroke
+  
+        fontScale: scale of the text, default is 1.
+        barthick: scalebar thickness
+        textthick: thickness of the text without stroke
  
-def AddText(img,text, px=0.98,py=0.96, color = 255,s=0.9,lw=1,stroke=1):
+    """
+    h,w=img.shape
+    w_scale=int(scale*barLen)
+    x1=int(w*px)
+    y1=int(h*py)
+    x2=x1+w_scale
+    y2=y1+barthick
+
+    bcolor=255-color
+    
+    text = str(barLen)+' nm'
+    font = cv2.FONT_HERSHEY_SIMPLEX#CV_FONT_HERSHEY_SIMPLEX normal size sans-serif font
+    shifty=int(8*fontScale)
+    if stroke != 0:
+        strokethick = int(stroke + textthick)
+        rectangle_thickness = max(1, strokethick // 2)  # halve it for visual match
+        cv2.putText(img, text, (x1, y1 - shifty), font, fontScale, bcolor, strokethick, lineType=cv2.LINE_AA)  # Stroke  
+        cv2.rectangle(img, (x1, y1), (x2, y2), bcolor, rectangle_thickness)  # Border color
+
+    cv2.rectangle(img, (x1, y1), (x2, y2), color, -1)
+    cv2.putText(img, text, (x1, y1 - shifty), font, fontScale, color, textthick, cv2.LINE_AA)
+
+def AddText(img,text, px=0.98,py=0.96, color = 255,fontScale=0.9,thickness=2,stroke=1):
     """
     Function to add text str to image
     Input:
         img: greyscale image
         text: textstr to display
         (px,py): position of the text: right,middle corner
-        lw: boarder of the text
-        stroke=1: add stroke; stroke=0 No stroke
+        fontScale: scale of the text
+        thickness: line thickness of the text
+  
+        stroke=1: add stroke width of 1; stroke=0 No stroke
  
     """
     h,w=img.shape
  
     font = cv2.FONT_HERSHEY_SIMPLEX#CV_FONT_HERSHEY_SIMPLEX normal size sans-serif font
-    D,sd=cv2.getTextSize(text, font, s, lw)
+    D,sd=cv2.getTextSize(text, font, fontScale,thickness)
     wt=int(D[0])
     bcolor=255-color #color of stroke
-    bw =lw+1 #stroke thickness
+    # bw =lw+1 #stroke thickness
+    strokethick=thickness+stroke
  
     x=int(w*px-wt)
     y=int(h*py)
-    if stroke == 1:
-        cv2.putText(img,text,(x,y), font, s, bcolor, bw, cv2.LINE_AA) #Stroke      
-    cv2.putText(img,text,(x,y), font, s, color, lw, cv2.LINE_AA)   
+    if stroke !=0:
+        cv2.putText(img,text,(x,y), font, fontScale, bcolor, strokethick, cv2.LINE_AA) #Stroke      
+    cv2.putText(img,text,(x,y), font, fontScale, color, thickness, cv2.LINE_AA)   
+
+def AddScaleTime2Stack(path,bar,Scale,dt=0.2,fps=15,color=255, time_txt_scale=1.2,textthick=2,stroke=1):
+    """
+    Function to add scalebar and timestamp to stack
+    Input:
+        path: path to tiff stack
+        bar: scale bar to show in nm
+        Scale: scale for the image stack: px/nm
+        dt: time interval of each frame
+        others: parameters for adjusting scalebar text size
+    Output:
+        Tiff stack and avi movie of the added scale&time
+
+    Example: 
+    AddScaleTime2Stack(path,bar=20,Scale=22.2,dt=0.5,fps=15,color=255, time_txt_scale=1.2)
+
+    """
+    stack=tifffile.imread(path)
+    nFrames, h,w = stack.shape
+    
+    pathout =path[:-4]+'_St.tif'    
+
+    print("---------------------------------------------")
+    print('Testing positions! ')
+    fr=stack[0]
+    px=0.96
+    py=0.96
+
+    text='0.0 s'
+    AddScale(fr,barLen=bar,fontScale=time_txt_scale,scale=Scale,color=color,textthick=textthick,stroke=stroke)
+    AddText(fr,text,px=px,py=py,fontScale=time_txt_scale,color=color,thickness=textthick,stroke=stroke)
+    showFr(fr)
 
+    prompt = input("Check the position, press 0 if you are satisfied, any other key to exit: ")
+    print("---------------------------------------------")
+
+    if prompt == "0":
+        print("Adding scalebar and timestamp to full stack")
+        with tifffile.TiffWriter(pathout,bigtiff=True) as tif:
+        
+            for i in tqdm.tqdm(range(nFrames)):        
+                img=stack[i]        
+                time = i * dt    
+                text=str('%02.1f' %time)+' s'  
+                AddScale(img,barLen=bar,fontScale=time_txt_scale,scale=Scale,color=color,textthick=textthick,stroke=stroke)
+                AddText(img,text,px=px,py=py,fontScale=time_txt_scale,color=color,thickness=textthick,stroke=stroke)        
+                
+                tif.write(img, contiguous=True)
+        
+        
+        tiff2avi(pathout,fps=fps)
+        print("Done adding scalebar and timestamp to tiff stack! ")
+    else:
+        print("Exit to change settings")
+
+def apply_colormap(image,cmap='viridis'):
+    """
+    Function to apply false color to grayscale image
+    input: 
+    Image: grayscale image
+    camp: colormap string. such as 'viridis'
+    """
+    import matplotlib.pyplot as plt
+    colormap = plt.get_cmap(cmap)
+    colored_image = colormap(image / 255.0)  # Normalize the image and apply colormap
+    colored_image = (colored_image[:, :, :3] * 255).astype(np.uint8)  # Convert to 8-bit RGB
+    return colored_image
+
+def tiff2avi_falsecolor(path,cmap='viridis',fps=15):
+    """
+    Function to convert tiff to false color avi movie
+    input: path : path of tiff stack
+    cmap: colormap of the falsecolor
+    """
+
+    import tifffile
+    import numpy as np
+    import cv2
+    import matplotlib.pyplot as plt
+    import tqdm
+
+    print("------------------------------------------")
+    print("Convert stack to faulse color avi")
+    stack = tifffile.imread(path)
+    nFrames,h,w = stack.shape #make sure the order of h and w!
+    
+ 
+    pathout =path[:-4]+'_c_'+str(fps)+'.avi'    
+    
+    
+    #Check the colormap effect
+    fr = stack[0]
+    fr_color=apply_colormap(fr,cmap)
+    plt.imshow(fr_color)
+    
+    
+    fourcc = cv2.VideoWriter_fourcc(*'MJPG')
+    
+    video_writer = cv2.VideoWriter(pathout, fourcc, fps, (w, h),isColor=True)
+    
+    # Process each frame and write to the video
+    for i in tqdm.tqdm(range(nFrames)):
+        grayscale_image = stack[i]
+        colored_image = apply_colormap(grayscale_image,cmap)
+        colored_image = cv2.cvtColor(colored_image, cv2.COLOR_RGB2BGR)  # Convert RGB to BGR
+    
+        video_writer.write(colored_image)
+    
+    # Release the video writer
+    video_writer.release()
 
 def AverageFrame(path,AveN):
     #Average frames by AveN to increase SNR
@@ -379,14 +655,139 @@ def AverageFrame(path,AveN):
     pathout = path[:-4]+'_'+str(AveN)+'ave.tif'
     nFramesOut=math.floor(nFrames/AveN)
     
-    for i in tqdm.tqdm(range(nFramesOut)):
-        AveFr= im[i*AveN]-im[i*AveN]
-        for m in range(AveN):
-            fr=im[i*AveN+m]
-            AveFr=AveFr+fr/AveN
-        img = AveFr.astype(np.uint8)
-        if i == 0:
-            tifffile.imwrite(pathout,img, append=False)
-        else:
-            tifffile.imwrite(pathout,img, append=True)
+    with tifffile.TiffWriter(pathout,bigtiff=True) as tif:
+        for i in tqdm.tqdm(range(nFramesOut)):
+            AveFr= im[i*AveN]-im[i*AveN]
+            for m in range(AveN):
+                fr=im[i*AveN+m]
+                AveFr=AveFr+fr/AveN
+            img = AveFr.astype(np.uint8)
+            tif.write(fr,continuous=True)
+
+def apply_colormap(image,cmap='viridis'):
+    """
+    Function to apply false color to grayscale image
+    input: 
+    Image: grayscale image
+    camp: colormap string. such as 'viridis'
+    """
+    import matplotlib.pyplot as plt
+    colormap = plt.get_cmap(cmap)
+    colored_image = colormap(image / 255.0)  # Normalize the image and apply colormap
+    colored_image = (colored_image[:, :, :3] * 255).astype(np.uint8)  # Convert to 8-bit RGB
+    return colored_image
+
+def falsecolorstack(path,cmap='viridis',fps=15):
+    import tifffile
+    import numpy as np
+    import cv2
+    import tqdm
+    print('Convert tiff stack to false color movie')
+     
+
+    stack = tifffile.imread(path)
+    nFrames,h,w = stack.shape #make sure the order of h and w!
+  
+    pathout =path[:-4]+'_c_'+str(fps)+'.avi'    
+    
+
+    fourcc = cv2.VideoWriter_fourcc(*'MJPG')
+    
+    video_writer = cv2.VideoWriter(pathout, fourcc, fps, (w, h),isColor=True)
+    
+    # Process each frame and write to the video
+    for i in tqdm.tqdm(range(nFrames)):
+        grayscale_image = stack[i]
+        colored_image = apply_colormap(grayscale_image,cmap)
+        colored_image = cv2.cvtColor(colored_image, cv2.COLOR_RGB2BGR)  # Convert RGB to BGR
+    
+        video_writer.write(colored_image)
+    
+    # Release the video writer
+    video_writer.release()
+    print('Convertion done!')
+
+def convertAVIcodec(path,fpsout=0,exp_t=0.2,nFrames=None,isColor=False):
+    """
+    Function to Directly convert screen recording avi to avi that mac can read
+    If fpsout=0, the framerate will not be changed (same as original)
+    exp_t: actual exposure time, to remove dupulicate frames
+    else fpsout will be changed to set value
+    """
+
+    import moviepy.editor as mp
+    print("======================")
+    print("Convert AVI codec!")
+    video = mp.VideoFileClip(path)
+    fps = int(video.fps)
+    w = int(video.w)
+    h = int(video.h)
+    if nFrames==None:
+        nFrames = int(fps*video.duration)
+        duration =video.duration
+    print("fps=", fps, "   w =",w, "   h=", h)
+    print("Total number of Frames=", nFrames)
+    #Remove duplic frames
+    if fpsout==0:
+        fpsout=fps
+        nFramesOut=nFrames
+        dup=1
+    else:
+        dup=fps*exp_t
+        nFramesOut=int(nFrames/dup)
+  
+    # Export avi
+    if nFrames==None:
+        pathout2 =path[:-4]+'_'+str(fpsout)+'.avi'      
+        pathout= path[:-4]+'_DB.tif'    
+    else:
+        pathout2 =path[:-4]+'_Trim_'+str(fpsout)+'.avi'      
+        pathout= path[:-4]+'_Trim_DB.tif'   
+    codec  = cv2.VideoWriter_fourcc(*'MJPG')
+    video_out = cv2.VideoWriter(pathout2, codec , fpsout, (w,  h),isColor=isColor)
+    
+    with tifffile.TiffWriter(pathout,bigtiff=True) as tif:
+        for j in tqdm.tqdm(range(nFramesOut)):
+            i=j*dup
+            fr = video.get_frame(mp.cvsecs(i/fps))
+            if isColor==False:
+                fr = cv2.cvtColor(fr, cv2.COLOR_BGR2GRAY)
+
+            tif.write(fr, contiguous=True)
+            if isColor== True:
+                fr = cv2.cvtColor(fr,cv2.COLOR_BGR2RGB)#since open cv uses different color sequence
+            video_out.write(fr)
+        
+    
+    video.reader.close()
+    video_out.release()
+    print("Conversion done!")
+
+
+def invertLUT(path):
+    import tifffile
+    import tqdm
+
+    video = tifffile.imread(path)
+    nFrames, h,w = video.shape[:3]
+    pathout =path[:-4]+'_Inv.tiff'    
+
+    with tifffile.TiffWriter(pathout,bigtiff=True) as tif:
+        
+        print("---------------------------------------------")
+        print('Inverting Tiff stack LUT')    
+        for i in tqdm.tqdm(range(nFrames)):        
+            img=video[i]  
+            img_IV=255-img
+            tif.write(img_IV, contiguous=True)
+        print("Invert LUT done!")
+
+
+
+
+
+
+
+
+