Source code for sunpy.io._jp2

"""
This module provides a JPEG 2000 file reader for internal use.

.. warning::

    ``sunpy.io.jp2`` is deprecated, and will be removed in sunpy 4.1. This is
    because it was designed for internal use only.
"""
import os
from xml.etree import ElementTree as ET

import numpy as np

from sunpy.io.header import FileHeader
from sunpy.util.io import HDPair, string_is_float
from sunpy.util.xml import xml_to_dict

__all__ = ['read', 'get_header', 'write']


[docs] def read(filepath, **kwargs): """ Reads a JPEG2000 file. Parameters ---------- filepath : `str` The file to be read. **kwargs : `dict` Unused. Returns ------- `list` A list of (data, header) tuples. """ # Put import here to speed up sunpy.io import time from glymur import Jp2k header = get_header(filepath) data = Jp2k(filepath)[...][::-1] return [HDPair(data, header[0])]
[docs] def get_header(filepath): """ Reads the header from the file. Parameters ---------- filepath : `str` The file to be read. Returns ------- `list` A list of one header read from the file. """ # Put import here to speed up sunpy.io import time from glymur import Jp2k jp2 = Jp2k(filepath) xml_box = [box for box in jp2.box if box.box_id == 'xml '] xmlstring = ET.tostring(xml_box[0].xml.find('fits')) pydict = xml_to_dict(xmlstring)["fits"] # Fix types for k, v in pydict.items(): if v.isdigit(): pydict[k] = int(v) elif string_is_float(v): pydict[k] = float(v) # Remove newlines from comment if 'comment' in pydict: pydict['comment'] = pydict['comment'].replace("\n", "") # Is this file a Helioviewer Project JPEG2000 file? pydict['helioviewer'] = xml_box[0].xml.find('helioviewer') is not None return [FileHeader(pydict)]
def header_to_xml(header): """ Converts image header metadata into an XML Tree that can be inserted into a JP2 file header. Parameters ---------- header : `MetaDict` A header dictionary to convert to xml. Returns ---------- `lxml.etree._Element` A fits element where each child is an xml element in the form <key>value</key> derived from the key/value pairs in the given header dictionary """ # glymur uses lxml and will crash if trying to use # python's builtin xml.etree import lxml.etree as ET fits = ET.Element("fits") already_added = set() for key in header: # Some headers span multiple lines and get duplicated as keys # header.get will appropriately return all data, so if we see # a key again, we can assume it was already added to the xml tree. if (key in already_added): continue # Add to the set so we don't duplicate entries already_added.add(key) el = ET.SubElement(fits, key) data = header.get(key) if isinstance(data, bool): data = "1" if data else "0" else: data = str(data) el.text = data return fits def generate_jp2_xmlbox(header): """ Generates the JP2 XML box to be inserted into the jp2 file. Parameters ---------- header : `MetaDict` A header dictionary. Returns ---------- `XMLBox` XML box containing FITS metadata to be used in jp2 headers """ # glymur uses lxml and will crash if trying to use # python's builtin xml.etree import lxml.etree as ET from glymur import jp2box header_xml = header_to_xml(header) meta = ET.Element("meta") meta.append(header_xml) tree = ET.ElementTree(meta) return jp2box.XMLBox(xml=tree)
[docs] def write(fname, data, header, **kwargs): """ Take a data header pair and write a JP2 file. Parameters ---------- fname : `str` File name, with extension. data : `numpy.ndarray` n-dimensional data array. header : `dict` A header dictionary. kwargs : Additional keyword args are passed to the glymur.Jp2k constructor Notes ----- Saving as a JPEG2000 will cast the data array to uint8 values to support the JPEG2000 format. """ from glymur import Jp2k tmpname = fname + "tmp.jp2" jp2_data = np.uint8(data) jp2 = Jp2k(tmpname, jp2_data, **kwargs) # Append the XML data to the header information stored in jp2.box meta_boxes = jp2.box target_index = len(meta_boxes) - 1 fits_box = generate_jp2_xmlbox(header) meta_boxes.insert(target_index, fits_box) # Rewrites the jp2 file on disk with the xml data in the header jp2.wrap(fname, boxes=meta_boxes) os.remove(tmpname)