Python PDS4 Tools

From The SBN Wiki
Revision as of 18:39, 7 October 2015 by Lnagdi1 (talk | contribs) (Clarified that PDS3 is not supported)
Jump to navigation Jump to search


This document describes the current status and usage of Python tools developed at PDS-SBN to read and visualize PDS4 data in Python. Please note that a PDS4 reader and visualizer for IDL is also available.

Reading and Displaying PDS4 Data


This section describes a Python package that can read and display PDS4 data and meta data. In the future this tool is expected to support all PDS4 objects, currently support is limited to objects given in the Supported Objects section. The package expects labels that pass PDS4 Schema and Schematron validation.

Contact Lev Nagdimunov with questions or comments regarding this code or its description.


Python 2.6 or 2.7

pds4_read: None
pds4_viewer: NumPy, matplotlib

You may use pds4_read to read-in data without any extra packages; pds4_viewer requires recent versions of the additional packages.

Optional Features

pds4_read: NumPy
Recommended for Arrays and Tables containing GROUP fields to allow for multi-dimensional indexing. Can result in significant improvements in memory usage and read-in speed for some data objects.

pds4_viewer: None

Supported Data Structures

PDS4 Data Standards < v1.3 are not officially supported but may work.
PDS4 Data Standards >= v1.3 are supported.
PDS3 Data Standards are not supported.

The table below lists the main PDS4 data objects and the current status.

Read-in column indicates support by pds4_read()
Display columns indicate support by pds4_viewer().

Structure Read-in Display as Table Display as Image Display Columns as Plot
Array Yes Yes 2D and 3D only Under Development
Array_2D Yes Yes Yes Under Development
Array_2D_* Yes Yes Yes Under Development
Array_3D Yes Yes Yes Under Development
Array_3D_* Yes Yes Yes Under Development
Table_Character Yes Yes No Under Development
Table_Binary Yes, except BitFields Yes No Under Development
Table_Delimited Future development Future development Future Development Future Development


Download the ZIP file File:PDS4


Option 1

Use "pip install" or "easy_install". You can also extract the ZIP file and use "python /path/to/extracted/ install". Note that there is no uninstall script provided (although "pip uninstall pds4_tools" should work), and that this tool will be updated in the future.

Option 2

Extract the downloaded file to a directory Python can find. To use it follow the instructions in Example Usage except with the following lines first,

import sys

# On a windows machine use backslashes (/) instead of windows' normal forward slashes to specify paths

Example Usage


You may call pds4_read from command line or from your own script. The following is the docstring for pds4_read:

    Reads PDS4 compliant data into a `StructureList`

    Given a PDS4 label, reads the PDS4 data described in the label and
    associated label meta data into an `StructureList`, with each PDS4 data
    structure (e.g. Array_2D, Table_Binary, etc) as its own `Structure`. By
    default all data structures described in the label are read-in.


        Currently supports Array structures, Table_Character and Table_Binary.
        Packed bit fields in Table_Binary are not yet supported, all other
        features of previously mentioned structures are fully supported.


        filename: str
            The filename, including full or relative path if necessary, of
            the PDS4 label describing the data.
        quiet: bool, optional
            Suppresses all info/warnings from being output.
        use_numpy: bool, optional
            Returned data will be an ndarray and use NumPy data types. On
            by default if NumPy is installed.
        structure_num: integer, optional
            Instead of reading all data structures, only read the n^th
            structure, where n = structure_num.
        structure_name: str, optional
            Instead of reading all data structures, only read the structure
            with a name equal to structure_name.
        structure_lid: str, optional
            Instead of reading all data structures, only read the structure
            with a local identifier equal to structure_lid.


            Contains PDS4 structures and label data. Can be treated/accessed/used
            like a `dict` or `list`.

    Example usage:

        Below we document how to read data described by an example label
        which has two data structures, an Array_2D_Image and a Table_Binary.
        An outline of the label, including the array and a table with 3
        fields, is given.

        >>> struct_list = pds4_read('/path/to/Example_Label.xml')

        Example Label Outline:

            Array_2D_Image: unnamed
            Table_Binary: Observations
                Field: order
                Field: wavelength
                Group: unnamed
                    Field: pos_vector

        All below documentation assumes that the above outlined label,
        containing an array that does not have a name indicated in the label,
        and a table has the name 'Observations' with 3 fields as shown
        has been read-in.

        Accessing Example Structures:

            To access the data structures in `StructureList`, which is returned by
            pds4_read(), you may use any combination of `dict` or `list`.

            >>> unnamed_array = struct_list[0]
            >>>              or struct_list['ARRAY_0']

            >>> obs_table = struct_list[1]
            >>>          or struct_list['Observations']

        Label or Structure Overview:

            To see a summary of the data structures, which for Arrays shows the
            type and dimensions of the array, and for Tables shows the type
            and number of fields, you may use the info() method. Calling
            info() on the `Structure` instead of `StructureList` will provide
            a more detailed summary, including all Fields for a table.


        Accessing Example Label data:

            To access the read-in data, as an array-like (either list,
            array.array or ndarray), you can use the data attribute for a
            PDS4 Array data structure, or the field() method to access a field
            for a table.

            >>> obs_table.field('wavelength')
            >>> obs_table.field('pos_vector')

        Accessing Example Label meta data:

            You can access all meta data in the label for a given PDS4 data
            structure or field via the `OrderedDict` meta_data attribute. The
            below examples use the 'description' element.

            >>> unnamed_array.meta_data['description']

            >>> obs_table.field('wavelength').meta_data['description']
            >>> obs_table.field('pos_vector').meta_data['description']

        Accessing Example Label:

            The XML for a label is also accessible via the label attribute,
            either the entire label or for each PDS4 data structure.

            Entire label:
                >>> struct_list.label

            Part of label describing Observations table:
                >>> struct_list['Observations'].label
                >>> struct_list[1].label

            The returned object is similar to an ElementTree instance. It is
            searchable via find() and findall() methods and XPATH. Consult
            ElementTree manual for more details. For example,

            >>> struct_list.label.findall('.//disp:Display_Settings')

            Will find all elements in the entire label named 'Display_Settings'
            which are in the 'disp' namespace. You can additionally use the
            to_dict() and to_string() methods.


To display the objects in a label you may call pds4_viewer from the command line, or import it in the Python interpreter:

usage: [-h] [--quiet] [--structure_num STRUCTURE_NUM]
                      [--structure_name STRUCTURE_NAME]
                      [--structure_lid STRUCTURE_LID]

positional arguments:
  filename              Filename, including full path, of the label

optional arguments:
  -h, --help            show this help message and exit
  --quiet               Suppresses all info/warnings
  --structure_num STRUCTURE_NUM
                        Only reads the data structure specified by zero-based
                        order (integer)
  --structure_name STRUCTURE_NAME
                        Only reads the data structure specified by name
  --structure_lid STRUCTURE_LID
                        Only reads the data structure specified by local identifier

It is not necessary to include the filename parameter for pds4_viewer, you may simplify call it without any options or arguments and a GUI will open from which you can open labels.

You may also call pds4_viewer from another module or script. All the above arguments are available as optional named parameters. A basic example usage is as follows:

""" Basic pds4_viewer example """

from pds4_tools import pds4_read, pds4_viewer


# or


# or 

struct_list = pds4_read('label.xml')
pds4_viewer('label.xml', from_existing_structures=struct_list) # Won't re-read the data