Converting a bunch of .dat files(images) to an avi file?-CodePudding

I am working on project to analyze the rotation of cells. The information is stored in a .dat file that contains an image of a cell. I have to convert it to a tiff file then concatenate all the images to have an avi video. The problem is that I didn't find documentation about dat and tiff files. and when I try to open a .dat file using Python I get this error message :

UnicodeDecodeError: 'utf-8' codec can't decode byte 0x9f in position 1: invalid start byte

The camera is Andor Neo5.5 scmos(https://andor.oxinst.com/assets/uploads/products/andor/documents/andor-neo-scmos-specifications.pdf)

and this is an example of a .dat file :

https://drive.google.com/file/d/180VuU7XO9suUK0v8G1mlQu_ZGRdUHD0z/view?usp=sharing

Color mode is GrayScale

Characteristics of the camera

CodePudding user response：

According to the AndorSDK and some reverse engineering, the 38.dat file contains a 4 byte integer, specifying the length of the data to follow, followed by the Mono12Packed encoded frame data and some additional metadata, all in little-endian byte order.

The frame data from a sequence of .DAT files can be decoded and written to a multi-page TIFF file without precision loss. Some metadata from the DAT files is lost:

import glob
import numpy
import tifffile

width = 2560
height = 2160

datfiles = glob.glob('*.dat')

with tifffile.TiffWriter('datfiles.tif', bigtiff=False) as tif:
    for datfile in datfiles:
        data = numpy.fromfile(
            datfile,
            count=width * height * 3 // 2,  # 12 bit packed
            offset=4,  # 4 byte integer header
            dtype=numpy.uint8,
        ).astype(numpy.uint16)
        image = numpy.zeros(width * height, numpy.uint16)
        image[0::2] = (data[1::3] & 15) | (data[0::3] << 4)
        image[1::2] = (data[1::3] >> 4) | (data[2::3] << 4)
        image.shape = height, width
        tif.write(
            image, photometric='minisblack', compression=None, metadata=None
        )

Depending on the total size of the frame data, use compression and/or the BigTIFF format. When saving the frame data as AVI, some data will be lost.