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[Imgcif-l] [Fwd: RE: Reading CBF files from Python]

Hi Herbert, Graeme,

I had a quick look with the pycbf bindings and ran into a problem with 
the example image (http://www.ccp4.ac.uk/xia/image.cbf). I get a slew of 
warnings and finally an error coming from CBFlib:

coral24:~/cbflib_jun2010/CBFlib_0.7.9/pycbf % python tst.py image.cbf 
2>&1 | more
CBFlib: warning input line 26 (1) -- invalid character
CBFlib: warning input line 26 (2) -- invalid character
CBFlib: warning input line 26 (3) -- invalid character
...
CBFlib: warning input line 26 (1978) -- invalid character
CBFlib: warning input line 26 (1979) -- invalid character
CBFlib: error input line 26 (1) -- value without tag


The code in python is essentially:

    import pycbf
    o = pycbf.cbf_handle_struct()
    o.read_file("image.cbf", pycbf.MSG_DIGEST)

In c this translates into something like the following, and gives the 
same output:

#include "cbf_simple.h"
#include <stdlib.h>
#include <stdio.h>
int main (int argc, char *argv [])
{
   FILE *in;
   cbf_handle cbf;
   if (!(in = fopen (argv[1], "rb"))) {
      fprintf (stderr,"Couldn't open the input cbf file %s\n", argv[1]);
      exit (1);
    }
   cbf_failnez (cbf_make_handle (&cbf));
   cbf_failnez (cbf_read_widefile (cbf, in, MSG_DIGEST));
}


A workaround is to copy the binary section into a valid file and then 
read that file, but I don't think it is what Graeme is after. Code to do 
that is attached in case it is useful in the meantime.

Sorry I can't be more useful,

Jon






-------- Original Message --------
Subject: RE: [Imgcif-l] Reading CBF files from Python
Date: Mon, 21 Jun 2010 14:20:38 +0100
From: <Graeme.Winter@Diamond.ac.uk>
To: <wright@esrf.fr>
CC: <Graeme.Winter@Diamond.ac.uk>
References: 
<4854F2500EA8C4478A508D2D92973E5206D6B5F9@EXCHANGE25.fed.cclrc.ac.uk> 
<4C1F2B5C.30400@esrf.fr><4854F2500EA8C4478A508D2D92973E5206D6B5FA@EXCHANGE25.fed.cclrc.ac.uk> 
<4C1F3784.6060107@esrf.fr>

Hi Jon,

Thanks - I think that the problem is more than this image does not
behave like a real cbf, though having some similarities. However I tried
building pycbf as you suggest and the build failed - I think the
configuration is not right in the way the cctbx folks use cbflib.

I have attached the image (picture would be a better word) - when I try
to load it in to cctbx using the MiniCBFImage loader it fails indicating
I think that it is poorly structured.

I am sure that there is code in cbflib which will do exactly what I
need, the only problem is gaining access to it!

Best wishes,

Graeme



-----Original Message-----
From: imgcif-l-bounces@iucr.org [mailto:imgcif-l-bounces@iucr.org] On
Behalf Of Jon Wright
Sent: 21 June 2010 10:57
To: The Crystallographic Binary File and its imgCIF application to image
data
Subject: Re: [Imgcif-l] Reading CBF files from Python

Hi Graeme,

To use the binding the wrapper needs to be compiled, which should just
mean typing "python setup.py build" in the pycbf subfolder. Then you
just need to drop pycbf.py and _pycbf.so somewhere on your python path
(import sys; print sys.path). The binding runs entirely via calls to
CBFlib, so if there is something useful in there, it should be possible
to include it. Herbert can probably help more for knowing where to look.

If you can send an example image off-list I'll try to take a look

Best

Jon

Graeme.Winter@Diamond.ac.uk wrote:
> Hi Jon,
> 
> Thanks - I see that this is bundled with cctbx and Labelit, which was 
> awesome. However it seems that the modules from pycbf aren't available

> as standard :o(  - I am slightly hamstrung by the fact that I use the 
> cctbx python, so having access to other python extensions presents a 
> problem. However I *really need* cctbx :o) - xia2 won't work without 
> it now.
> 
> My rate limiting step right now is the reading and writing of the byte

> offset compression. I am going to guess that if I messed with the 
> python paths and such I should be able to find your implementation. Do

> you have a method in there which will allow me to just pack and unpack

> the byte_offset compressed regions?
> 
> This is the data in question:
> 
> ###CBF: Version July 2008 generated by XDS
> 
> data_FRAME.cbf
> 
> _array_data.header_convention "XDS special"
> _array_data.header_contents
> ;
> ;
> 
> _array_data.data
> ;
> --CIF-BINARY-FORMAT-SECTION--
> Content-Type: application/octet-stream;
>      conversions="x-CBF_BYTE_OFFSET"
> Content-Transfer-Encoding: BINARY
> X-Binary-Size:   9450352
> X-Binary-ID: 1
> X-Binary-Element-Type: "signed 32-bit integer"
> X-Binary-Element-Byte-Order: LITTLE_ENDIAN
> X-Binary-Number-of-Elements:   9437184
> X-Binary-Size-Fastest-Dimension:    3072
> X-Binary-Size-Second-Dimension:    3072
> (massive binary blob)
> 
> The bit which is causing me problems is that the cbflib adaptor raises

> an exception as most of the "proper" cbf stuff (i.e. the CIF) is not 
> present. Erk.
> 
> Any suggestions will be pounced apon!
> 
> Many thanks,
> 
> Graeme
> 
> -----Original Message-----
> From: imgcif-l-bounces@iucr.org [mailto:imgcif-l-bounces@iucr.org] On 
> Behalf Of Jon Wright
> Sent: 21 June 2010 10:06
> To: The Crystallographic Binary File and its imgCIF application to 
> image data
> Subject: Re: [Imgcif-l] Reading CBF files from Python
> 
> Hi Graeme,
> 
> There is a swig based python binding included with CBFlib in the pycbf

> subfolder. It should work for reading files (see pycbf_test1.py).
> Further work was needed for writing. Let me know if you run into 
> problems. Improvements are most welcome.
> 
> Best
> 
> Jon
> 
> Graeme.Winter@Diamond.ac.uk wrote:
>> Hi Folks,
>>  
>> Does anyone know if CBF images can be read from Python? I coded up 
>> something in Python to do this but it's a spot slow to say the least.
>> My interest is partly in reading the cbf "image" files calculated by 
>> XDS to explain what it has been up to. I could code something up in 
>> 'c' or a bridge to CBFlib but that would be hardish to maintain, so a

>> solution using existing Python libraries would suit me better.
>>  
>> I looked quickly at PyCIFrw but this appears to be mostly about the 
>> CIF side of things rather than the MIME encoded chunks. Please 
>> correct
> 
>> me if I am wrong. I also tried iotbx.detectors.cbf.CBFImage but hit 
>> an
> 
>> exception which probably relates to this being more of a picture than

>> a diffraction image.
>>  
>> Thanks,
>>  
>> Graeme
>>  
>> Dr. Graeme Winter
>> Software and MX Support Scientist
>> Diamond Light Source
>>  
>> +44 1235 778091 (work)
>> +44 7786 662784 (work mobile)
>>  
>>  
>>
>>
>>
> 
> _______________________________________________
> imgcif-l mailing list
> imgcif-l@iucr.org
> http://scripts.iucr.org/mailman/listinfo/imgcif-l
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import pycbf, sys, tempfile, time, numpy as np

def fix_im( barecbf, template, tempname ):
    temp = open(tempname, "wb")
    tag = "--CIF-BINARY-FORMAT-SECTION--"
    good = open(template,"rb").read()
    s = good.find(tag) + len(tag)
    temp.write( good[:s] )
    eg = s + good[s:].find("--CIF")
    bin = open(barecbf, "rb").read()
    s = bin.find(tag)+len(tag)
    e = s + bin[s:].find("--CIF")
    temp.write( bin[s:e] )
    temp.write( good[ eg: ] )
    temp.flush()
    temp.close()




def read_binary(name ):
    object = pycbf.cbf_handle_struct()
    object.read_file(name,pycbf.MSG_DIGEST)
    object.rewind_datablock()
    object.select_datablock(0)
    object.rewind_category()
    categories = object.count_categories()
    for i in range(categories):
        object.select_category(i)
        category_name = object.category_name()
        rows=object.count_rows()
        cols = object.count_columns()
        loop=1
        object.rewind_column()
        while loop is not 0:
            column_name = object.column_name()
            try:
                object.next_column()
            except:
                break
        for j in range(rows):
            object.select_row(j)
            object.rewind_column()
            for k in range(cols):
                name=object.column_name()
                object.select_column(k)
                typeofvalue=object.get_typeofvalue()
                if typeofvalue.find("bnry") > -1:
                    s=object.get_integerarray_as_string()
                    ar = np.fromstring(s,np.int32)
                else:
                    value=object.get_value()
                    # print "Val:",value,i
    del(object)
    return ar

start = time.time()
fix_im(sys.argv[1], sys.argv[2], sys.argv[3] )
print "fixing",time.time()-start
start = time.time()
image = read_binary(sys.argv[3])
print "reading",time.time()-start
print image.max(), image.min(), image.mean()

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