Re: [Psidev-ms-dev] mzML base64binary conversion

[Joshua K. <mob...@gm...>]

Hello,

I'm the author of the psims, and unfortunately it doesn't actually do any
reading itself, just writing. Internally, it uses Pyteomics (
https://pypi.org/project/pyteomics/) to read mzML files, which does decode
the array data for you. Pyteomics is great in that it gets you the data
into memory in a structure you can see through and then gets out of the
way. There's also pymzML (https://pypi.org/project/pymzML/), which provides
several additional tools to then manipulate the spectrum. And of course,
pyOpenMS.

While we're assuming Python is the target language, Hannes provided great
self-contained examples, but here's a function that lets you indicate your
data were compressed, and unpacks the data into a numpy array:
```python
import base64
import zlib

import numpy as np

def decode_array(bytestring, compressed=False, dtype=np.float32):
    # make sure we're dealing with bytes
    try:
        decoded_string = bytestring.encode("ascii")
    except AttributeError:
        decoded_string = bytestring
    decoded_string = base64.decodestring(decoded_string)
    if compressed:
        decoded_string = zlib.decompress(decoded_string)
    array = np.fromstring(decoded_string, dtype=dtype)
    return array
```

On Tue, Jan 8, 2019 at 8:10 PM Eric Deutsch <ede...@sy...>
wrote:

> Hi Da Qi, there are many libraries out there for many languages that read
> mzML, so you may not need to re-implement it yourself. If Python is a
> language of choice, you might look at this recent paper:
>
>
>
> http://www.mcponline.org/content/early/2018/12/18/mcp.RP118.001070?papetoc
> =
>
>
>
>
>
>
>
> *From:* Shofstahl, Jim <jim...@th...>
> *Sent:* Tuesday, January 8, 2019 6:50 AM
> *To:* Mass spectrometry standard development <
> psi...@li...>
> *Subject:* Re: [Psidev-ms-dev] mzML base64binary conversion
>
>
>
> The spectral data (and chromatogram data) is stored as a Base64 encoded
> string.  Most of the programming languages will contain methods/functions
> to convert to and from the
>
> Base64 format.  In C# those methods are part of the Convert class.
>
>
>
>
> https://docs.microsoft.com/en-us/dotnet/api/system.convert?view=netframework-4.7.2
>
>
>
> The FromBase64String method takes a string value and converts it to a
> byte[] array which can then be converted to another data type.  We tend to
> convert it using
>
> as a MemoryStream object but there are other ways to do the conversion:
>
>
>
>         protected static float[] ConvertToFloat(byte[] array, int points)
>
>         {
>
>             var arrayValues = new float[points];
>
>
>
>             using (var memStream = new MemoryStream(array))
>
>             {
>
>                 using (var binReader = new BinaryReader(memStream))
>
>                 {
>
>                     for (var i = 0; i < points; i++)
>
>                     {
>
>                         arrayValues[i] = binReader.ReadSingle();
>
>                     }
>
>                 }
>
>             }
>
>
>
>             // Return the value(s)
>
>             return arrayValues;
>
>         }
>
>
>
> *From:* 戚达(Da Qi) <qi...@ge...>
> *Sent:* Monday, January 7, 2019 5:43 PM
> *To:* psi...@li...
> *Subject:* [Psidev-ms-dev] mzML base64binary conversion
>
>
>
> *CAUTION:* This email originated from outside of the organization. Do not
> click links or open attachments unless you recognize the sender and know
> the content is safe.
>
>
>
> Hi,
>
>
>
> Does anyone know how to decode the binary string to real data in mzML?
>
>
>
> <binaryDataArrayList count="2">
>
>
> <binaryDataArray encodedLength="268">
>
>
> <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" unitCvRef="MS"
> unitAccession="MS:1000040" unitName="m/z"/>
>
>
> <cvParam cvRef="MS" accession="MS:1000576" name="no compression"/>
>
>
> <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float"/>
>
>
> <binary>O6+NQ43Hp0N978lDce3XQ6Zr5kORjf9DdUMLRCfJDEThihJEqO4SRGiZGERKzBpEKwcbRKjOKURoIS1EFJ4wRI1XMUQpvDdEIeA5RJjmQkQr70NERGNGRMeDR0RMh0hE2Y5JRG/KTEQncU5EHXJPRMupUETZ9lNEQiBURLS4VETjxVVEbTdYRMk2WkQ34VpEBhFbRN10W0Q5/FtExxteRAqvX0QSY2BEJZ5gRJ5HYUQ/jWFEEutkRGCNZURcx2VErg9vROF6fEQ=</binary>
>
>
> </binaryDataArray>
>
>
> <binaryDataArray encodedLength="268">
>
>
> <cvParam cvRef="MS" accession="MS:1000515" name="intensity array"
> unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts"/>
>
>
> <cvParam cvRef="MS" accession="MS:1000576" name="no compression"/>
>
>
> <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float"/>
>
>
> <binary>AEB6RADQakUAwOxEAGwGRgDgE0UAcDxFAMDIRABASEQA4N5EAMBWRAAAJ0UAIAZFADA+RQBgu0QAAB5EAMB+RQDAhUUAwLREANCpRQBwA0UAABFEAEAsRADgJkUAMAlFAOAbRQDAlEQAAKZEALBBRQAgpEQA4F1FAMDBRADAi0QAIDZFAIBFRQAAEEUAoHRFAKCMRACAL0QAINtEAGAKRQDAO0QAQONFAHAIRQD4gUUAgONDAGDaRADQLkUAAGJEAABNRAAA0EQ=</binary>
>
>
> </binaryDataArray>
>
>                                                 </binaryDataArrayList>
>
>
>
> Best,
>
> Da Qi
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