[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]
Reply to: [list | sender only]
[Imgcif-l] Adding references to external files to imgCIF
- To: The Crystallographic Binary File and its imgCIF application to image data<imgcif-l@iucr.org>
- Subject: [Imgcif-l] Adding references to external files to imgCIF
- From: James Hester <jamesrhester@gmail.com>
- Date: Wed, 13 Feb 2019 16:15:45 +1100
- DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025;h=mime-version:reply-to:from:date:message-id:subject:to;bh=bYcMWY1wNzZjNh8AOGqpC/hXOtYkcF3DJX0ZUhWxSFM=;b=fkym7ishsQl0b17uGLm5LASrc6cpVgVq5/S1Rb3VT+h/3xkKsz+rr2OxIQjrjYKumrVTym1Y0SPDugTdexqdPfjmIylAbFjPZtaJjhs/R+63hQhQnkGPXZEWggeAJKLNHXdC7GYy2IjkXsfsIzu+a5ZYuup6JW4g4hnCOIugbN47vDSHZqtL6d9N7eeZW/GRqYIrrALp6FwVLY9bp5xoq7jiHyJ4V+IM0mhwbbBGQmRgeu04ss4DP1XIOf7GPALuVrXGTjV8g1WsVys4niAOWSsolPjKJL6ATn1ssEXatzzjPqEb6UWzW7dgXKKWj4UzK41jGqz9iiUVcTKXrVPQkw==
Dear All, Recent Commdat discussion revealed a desire to reference external images from within an imgCIF file. This would allow the metadata for a dataset to be held within a single imgCIF file, while the frames themselves remain separate. This avoids the impracticality of navigating through an enormous mulit-frame imgCIF file in order to extract a relatively compact amount of information. As a starting proposal, I suggest we extend the _array_data category with the following three datanames: (1) _array_data.external_format A value drawn from an enumerated list of formats (e.g. "SMV","HDF5","Bruker"). The definition for each enumerated value would explain how to interpret _array_data.internal_path (2) _array_data.location_url A URI for the file containing the image. A relative URL is relative to the location of the imgCIF file (3) _array_data.internal_path A format-specific string describing the location of the frame within the file identified by _array_data.location_uri, interpreted according to the value given in _array_data.external_format So for a multi-frame HDF5 file buried in a subdirectory of the location referenced with a DOI, with appropriate definitions of the path notation: loop_ _array_data.array_id _array_data.binary_id _array_data.external_format _array_data.location_uri _array_data.internal_path 1 1 NXMX doi:x.y.z directory/run/masterfilename:/entry1/detector/data[0] 1 2 NXMX doi:x.y.z directory/run/masterfilename:/entry1/detector/data[1] ... Or for a bunch of single-frame files generated by an ADSC detector in the same directory as the imgCIF file _array_data.array_id _array_data.binary_id _array_data.external_format _array_data.location_uri 1 1 ADSC ./tartaric.001 1 2 ADSC ./tartaric.002 1 3 ADSC ./tartaric.003 ... The imgCIF data items describing the structure of the data array would refer to the data after it has been provided by the format. The form in which it is provided should be specified in the definition of each value of "_array_data.external_format". So, for example, the various compression methods in HDF5 would be invisible if the data as returned are specified to be an array of Reals. From the point of view of initial data validation, it would be sufficient to check that all referenced files are accessible, and that the provided locations exist. Thoughts? James. -- T +61 (02) 9717 9907 F +61 (02) 9717 3145 M +61 (04) 0249 4148 _______________________________________________ imgcif-l mailing list imgcif-l@iucr.org http://mailman.iucr.org/cgi-bin/mailman/listinfo/imgcif-l
Reply to: [list | sender only]
- Next by Date: Re: [Imgcif-l] Adding references to external files to imgCIF
- Prev by thread: Re: [Imgcif-l] Where are _diffrn_detector_element.center[1],[2]?
- Next by thread: Re: [Imgcif-l] Adding references to external files to imgCIF
- Index(es):