reading *.his (image) file in Python

Question

I am trying to read an image file which is in *.his format. Honestly, I do not know much about this format, on spending some time on google I figured out that its a binary format and it can be read in ImageJ software as a raw format import. On further inquiry, I found the following details of the *.his file:

Image type = 16-bit unsigned
Matrix dimensions in pixels = w1024 x h1024
Skip header info = 100 Bytes (The number of bytes in the file before the first byte of image data).
Little-Endian Byte Order

With this information in hand, I started out …

Just wanted to print the values in one by one, just to see the output:

f = open("file.his", 'rb')
f.seek(100) 
try:
   byte = f.read(2)
   while byte != "":
      byte = f.read(2)
      print unpack('<H', byte) 
finally:
f.close()

It prints some numbers out and then the error message :
…..
(64846,)
(64846,)
(64830,)

Traceback (most recent call last):
print unpack(‘

Plz can someone suggest me how to read this kind of file. I still think ‘unpack’ is the right function however if someone has similar experience, any response greatly appreciated.

Rky.

Asked By: Rocky

||

Source

Answer 1

I’ve done a very similar task with *.inr image file maybe the logic could help you, here its what you could apply:

1-Reading the file

First you need to read the file.

file = open(hisfile, 'r')
inp = file.readlines()

2-Get header

In my case i done a for loop until the number of characters was 256, in your case you need to count the bits so you could “print” line by line to find out when you need to stop or try to use this to count the bits:

import sys
sys.getsizeof(line) #returns the size of the object

3-Data

When you already know that the following lines are the raw data you need to put them in one variable with a for loop:

for line in inp:
    raw_data += line

4-Convert the data

To convert the string to a numpy array you could do:

data = fromstring(raw_data, dtype='uint16')

And then aplying the shape data:

data = data.reshape((1024,1024)).transpose() #You need to see if the transpose part its relevant,because in my case was fundamental.

Maybe if you have an example of the file i could try to read it and help you more. Of course you could do all the process in 1 for loop using if’s.

Answered By: CCP

Answer 2

Recently we need to work on HIS files. I got help from what posted here. This is our code to read a HIS file:

f = open(myfile, 'rb')
f.seek(100)
data=[]
try:
    byte=f.read(2)
    while byte!='':
        a=unpack('<H', byte)
        b=list(a)
        data.append(list(a)[0])
        byte=f.read(2)
        if len(byte)!=2:
            break
finally:
    f.close()

nF=20 # 20 frames stored in our HIS file. Sum the 20 frames to get an image.
dataArray=np.array(data)
dataRe=np.array_split(dataArray,nF)
dataReArray=np.array(dataRe)
dataSum=dataReArray.sum(axis=0)

Answered By: Qianxia Wang

reading *.his (image) file in Python

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