Glymur 0.13.8__py3-none-any.whl → 0.14.0.post1__py3-none-any.whl

glymur/__init__.py

@@ -5,7 +5,7 @@ __all__ = [
     'get_option', 'set_option', 'reset_option',
     'get_printoptions', 'set_printoptions',
     'get_parseoptions', 'set_parseoptions',
-    'Jp2k', 'Jp2kr', 'Tiff2Jp2k',
+    'Jp2k', 'Jp2kr', 'JPEG2JP2', 'Tiff2Jp2k',
 ]
 
 # Local imports
@@ -13,6 +13,7 @@ from glymur import version
 from .options import (get_option, set_option, reset_option,
                       get_printoptions, set_printoptions,
                       get_parseoptions, set_parseoptions)
+from .jpeg import JPEG2JP2
 from .jp2k import Jp2k, Jp2kr
 from .tiff import Tiff2Jp2k
 from . import data

glymur/_core_converter.py

@@ -0,0 +1,390 @@
+"""Core definitions to be shared amongst the modules."""
+# standard library imports
+import io
+import logging
+import shutil
+import struct
+from typing import Tuple
+from uuid import UUID
+
+# local imports
+from . import jp2box
+from .lib.tiff import DATATYPE2FMT
+from .jp2k import Jp2k
+from glymur.core import RESTRICTED_ICC_PROFILE
+
+# Mnemonics for the two TIFF format version numbers.
+TIFF = 42
+BIGTIFF = 43
+
+
+class _2JP2Converter(object):
+    """
+    This private class is used by both the TIFF2JP2 and the JPEG2JP2
+    converters.
+
+    Attributes
+    ----------
+    create_exif_uuid : bool
+        Create a UUIDBox for the TIFF IFD metadata.
+    tilesize : tuple
+        The dimensions of a tile in the JP2K file.
+    verbosity : int
+        Set the level of logging, i.e. WARNING, INFO, etc.
+    """
+
+    def __init__(
+        self,
+        create_exif_uuid: bool,
+        create_xmp_uuid: bool,
+        include_icc_profile: bool,
+        tilesize: Tuple[int, int] | None,
+        verbosity: int
+    ):
+
+        self.create_exif_uuid = create_exif_uuid
+        self.create_xmp_uuid = create_xmp_uuid
+        self.include_icc_profile = include_icc_profile
+        self.tilesize = tilesize
+
+        # Assume that there is no ICC profile tag until we know otherwise.
+        self.icc_profile = None
+
+        self.setup_logging(verbosity)
+
+    def read_ifd(self, tfp):
+        """Process either the main IFD or an Exif IFD
+
+        Parameters
+        ----------
+        tfp : file-like
+            FILE pointer for TIFF
+
+        Returns
+        -------
+        dictionary of the TIFF IFD
+        """
+
+        self.found_geotiff_tags = False
+
+        tag_length = 20 if self.version == BIGTIFF else 12
+
+        # how many tags?
+        if self.version == BIGTIFF:
+            buffer = tfp.read(8)
+            (num_tags,) = struct.unpack(self.endian + "Q", buffer)
+        else:
+            buffer = tfp.read(2)
+            (num_tags,) = struct.unpack(self.endian + "H", buffer)
+
+        # Ok, so now we have the IFD main body, but following that we have
+        # the tag payloads that cannot fit into 4 bytes.
+
+        # the IFD main body in the TIFF.  As it might be big endian, we
+        # cannot just process it as one big chunk.
+        buffer = tfp.read(num_tags * tag_length)
+
+        if self.version == BIGTIFF:
+            tag_format_str = self.endian + "HHQQ"
+            tag_payload_offset = 12
+            max_tag_payload_length = 8
+        else:
+            tag_format_str = self.endian + "HHII"
+            tag_payload_offset = 8
+            max_tag_payload_length = 4
+
+        tags = {}
+
+        for idx in range(num_tags):
+
+            self.logger.debug(f"tag #: {idx}")
+
+            tag_data = buffer[idx * tag_length:(idx + 1) * tag_length]
+
+            tag, dtype, nvalues, offset = struct.unpack(
+                tag_format_str, tag_data
+            )  # noqa : E501
+
+            if tag == 34735:
+                self.found_geotiff_tags = True
+
+            payload_length = DATATYPE2FMT[dtype]["nbytes"] * nvalues
+
+            if tag in (34665, 34853):
+
+                # found exif or gps ifd
+                # save our location, go get that IFD, and come on back
+                orig_pos = tfp.tell()
+                tfp.seek(offset)
+                payload = self.read_ifd(tfp)
+                tfp.seek(orig_pos)
+
+            elif payload_length > max_tag_payload_length:
+                # the payload does not fit into the tag entry, so use the
+                # offset to seek to that position
+                current_position = tfp.tell()
+                tfp.seek(offset)
+                payload_buffer = tfp.read(payload_length)
+                tfp.seek(current_position)
+
+                # read the payload from the TIFF
+                payload_format = DATATYPE2FMT[dtype]["format"] * nvalues
+                payload = struct.unpack(
+                    self.endian + payload_format,
+                    payload_buffer
+                )
+
+            else:
+                # the payload DOES fit into the TIFF tag entry
+                payload_buffer = tag_data[tag_payload_offset:]
+
+                # read ALL of the payload buffer
+                fmt = DATATYPE2FMT[dtype]["format"]
+                nelts = max_tag_payload_length / DATATYPE2FMT[dtype]["nbytes"]
+                num_items = int(nelts)
+                payload_format = self.endian + fmt * num_items
+                payload = struct.unpack(payload_format, payload_buffer)
+
+                # Extract the actual payload.  Two things going
+                # on here.  First of all, not all of the items may
+                # be used.  For example, if the payload length is
+                # 4 bytes but the format string was HHH, the that
+                # last 16 bit value is not wanted, so we should
+                # discard it.  Second thing is that the signed and
+                # unsigned rational datatypes effectively have twice
+                # the number of values so we need to account for that.
+                if dtype in [5, 10]:
+                    payload = payload[: 2 * nvalues]
+                else:
+                    payload = payload[:nvalues]
+
+            tags[tag] = {"dtype": dtype, "nvalues": nvalues, "payload": payload}
+
+        return tags
+
+    def setup_logging(self, verbosity):
+
+        self.logger = logging.getLogger("tiff2jp2")
+        self.logger.setLevel(verbosity)
+        ch = logging.StreamHandler()
+        ch.setLevel(verbosity)
+        self.logger.addHandler(ch)
+
+    def read_tiff_header(self, tfp):
+        """Get the endian-ness of the TIFF, seek to the main IFD"""
+
+        buffer = tfp.read(4)
+        data = struct.unpack("BB", buffer[:2])
+
+        # big endian or little endian?
+        if data[0] == 73 and data[1] == 73:
+            # little endian
+            self.endian = "<"
+        elif data[0] == 77 and data[1] == 77:
+            # big endian
+            self.endian = ">"
+        # no other option is possible, libtiff.open would have errored out
+        # else:
+        #     msg = (
+        #         f"The byte order indication in the TIFF header "
+        #         f"({data}) is invalid.  It should be either "
+        #         f"{bytes([73, 73])} or {bytes([77, 77])}."
+        #     )
+        #     raise RuntimeError(msg)
+
+        # version number and offset to the first IFD
+        (version,) = struct.unpack(self.endian + "H", buffer[2:4])
+        self.version = TIFF if version == 42 else BIGTIFF
+
+        if self.version == BIGTIFF:
+            buffer = tfp.read(12)
+            _, _, offset = struct.unpack(self.endian + "HHQ", buffer)
+        else:
+            buffer = tfp.read(4)
+            (offset,) = struct.unpack(self.endian + "I", buffer)
+        tfp.seek(offset)
+
+    def append_exif_uuid_box(self):
+        """Append an EXIF UUID box onto the end of the JPEG 2000 file.  It will
+        contain metadata from the TIFF IFD.
+        """
+        if not self.create_exif_uuid:
+            return
+
+        # create a bytesio object for the IFD
+        b = io.BytesIO()
+
+        # write this 32-bit header into the UUID, no matter if we had bigtiff
+        # or regular tiff or big endian
+        data = struct.pack("<BBHI", 73, 73, 42, 8)
+        b.write(data)
+
+        self.write_ifd(b, self.tags)
+
+        # create the Exif UUID
+        if self.found_geotiff_tags:
+            # geotiff UUID
+            the_uuid = UUID("b14bf8bd-083d-4b43-a5ae-8cd7d5a6ce03")
+            payload = b.getvalue()
+        else:
+            # Make it an exif UUID.
+            the_uuid = UUID(bytes=b"JpgTiffExif->JP2")
+            payload = b"EXIF\0\0" + b.getvalue()
+
+        # the length of the box is the length of the payload plus 8 bytes
+        # to store the length of the box and the box ID
+        box_length = len(payload) + 8
+
+        uuid_box = jp2box.UUIDBox(the_uuid, payload, box_length)
+        with self.jp2_path.open(mode="ab") as f:
+            uuid_box.write(f)
+
+        self.jp2.finalize(force_parse=True)
+
+    def write_ifd(self, b, tags):
+        """Write the IFD out to the UUIDBox.  We will always write IFDs
+        for 32-bit TIFFs, i.e. 12 byte tags, meaning just 4 bytes within
+        the tag for the tag data
+        """
+
+        little_tiff_tag_length = 12
+        max_tag_payload_length = 4
+
+        # exclude any unwanted tags
+        if self.exclude_tags is not None:
+            for tag in self.exclude_tags:
+                if tag in tags:
+                    tags.pop(tag)
+
+        num_tags = len(tags)
+        write_buffer = struct.pack("<H", num_tags)
+        b.write(write_buffer)
+
+        # Ok, so now we have the IFD main body, but following that we have
+        # the tag payloads that cannot fit into 4 bytes.
+
+        ifd_start_loc = b.tell()
+        after_ifd_position = ifd_start_loc + num_tags * little_tiff_tag_length
+
+        for idx, tag in enumerate(tags):
+
+            tag_offset = ifd_start_loc + idx * little_tiff_tag_length
+            self.logger.debug(f"tag #: {tag}, writing to {tag_offset}")
+            self.logger.debug(f"tag #: {tag}, after IFD {after_ifd_position}")
+
+            b.seek(tag_offset)
+
+            try:
+                dtype = tags[tag]["dtype"]
+            except IndexError:
+                breakpoint()
+                pass
+
+            nvalues = tags[tag]["nvalues"]
+            payload = tags[tag]["payload"]
+
+            payload_length = DATATYPE2FMT[dtype]["nbytes"] * nvalues
+
+            if payload_length > max_tag_payload_length:
+
+                # the payload does not fit into the tag entry
+
+                # read the payload from the TIFF
+                payload_format = DATATYPE2FMT[dtype]["format"] * nvalues
+
+                # write the tag entry to the UUID
+                new_offset = after_ifd_position
+                buffer = struct.pack("<HHII", tag, dtype, nvalues, new_offset)
+                b.write(buffer)
+
+                # now write the payload at the outlying position and then come
+                # back to the same position in the file stream
+                cpos = b.tell()
+                b.seek(new_offset)
+
+                format = "<" + DATATYPE2FMT[dtype]["format"] * nvalues
+                buffer = struct.pack(format, *payload)
+                b.write(buffer)
+
+                # keep track of the next position to write out-of-IFD data
+                after_ifd_position = b.tell()
+                b.seek(cpos)
+
+            else:
+
+                # the payload DOES fit into the TIFF tag entry
+                # write the tag metadata
+                buffer = struct.pack("<HHI", tag, dtype, nvalues)
+                b.write(buffer)
+
+                payload_format = DATATYPE2FMT[dtype]["format"] * nvalues
+
+                # we may need to alter the output format
+                if payload_format in ["H", "B", "I"]:
+                    # just write it as an integer
+                    payload_format = "I"
+
+                if tag in (34665, 34853):
+
+                    # special case for an EXIF or GPS IFD
+                    buffer = struct.pack("<I", after_ifd_position)
+                    b.write(buffer)
+                    b.seek(after_ifd_position)
+                    after_ifd_position = self.write_ifd(b, payload)
+
+                else:
+
+                    buffer = struct.pack("<" + payload_format, *payload)
+                    b.write(buffer)
+
+        return after_ifd_position
+
+    def append_xmp_uuid_box(self):
+        """Append an XMP UUID box onto the end of the JPEG 2000 file if there
+        was an XMP tag in the TIFF IFD.
+        """
+
+        if self.xmp_data is None:
+            return
+
+        if not self.create_xmp_uuid:
+            return
+
+        # create the XMP UUID
+        the_uuid = jp2box.UUID("be7acfcb-97a9-42e8-9c71-999491e3afac")
+        box_length = len(self.xmp_data) + 8
+        uuid_box = jp2box.UUIDBox(the_uuid, self.xmp_data, box_length)
+        with self.jp2_path.open(mode="ab") as f:
+            uuid_box.write(f)
+
+    def rewrap_for_icc_profile(self):
+        """Consume an ICC profile, if one is there."""
+        if self.icc_profile is None and self.include_icc_profile:
+            self.logger.warning("No ICC profile was found.")
+
+        if self.icc_profile is None or not self.include_icc_profile:
+            return
+
+        self.logger.info(
+            "Consuming an ICC profile into JP2 color specification box."
+        )
+
+        colr = jp2box.ColourSpecificationBox(
+            method=RESTRICTED_ICC_PROFILE,
+            precedence=0,
+            icc_profile=self.icc_profile
+        )
+
+        # construct the new set of JP2 boxes, insert the color specification
+        # box with the ICC profile
+        jp2 = Jp2k(self.jp2_path)
+        boxes = jp2.box
+        boxes[2].box = [boxes[2].box[0], colr]
+
+        # re-wrap the codestream, involves a file copy
+        tmp_filename = str(self.jp2_path) + ".tmp"
+
+        with open(tmp_filename, mode="wb") as tfile:
+            jp2.wrap(tfile.name, boxes=boxes)
+
+        shutil.move(tmp_filename, self.jp2_path)

glymur/command_line.py

@@ -7,7 +7,7 @@ import warnings
 
 # Local imports ...
 from . import Jp2k, set_option, lib
-from . import tiff
+from . import tiff, jpeg
 
 
 def main():
@@ -78,6 +78,134 @@ def main():
             )
 
 
+def jpeg2jp2():
+    """Entry point for console script jpeg2jp2."""
+
+    kwargs = {
+        'description': 'Convert JPEG to JPEG 2000.',
+        'formatter_class': argparse.ArgumentDefaultsHelpFormatter,
+        'add_help': False
+    }
+    parser = argparse.ArgumentParser(**kwargs)
+
+    group1 = parser.add_argument_group(
+        'JP2K', 'Pass-through arguments to Jp2k.'
+    )
+
+    help = 'Capture resolution parameters'
+    group1.add_argument(
+        '--capture-resolution', nargs=2, type=float, help=help,
+        metavar=('VRESC', 'HRESC')
+    )
+
+    help = 'Display resolution parameters'
+    group1.add_argument(
+        '--display-resolution', nargs=2, type=float, help=help,
+        metavar=('VRESD', 'HRESD')
+    )
+
+    help = 'Compression ratios for successive layers.'
+    group1.add_argument('--cratio', nargs='+', type=int, help=help)
+
+    help = 'PSNR for successive layers.'
+    group1.add_argument('--psnr', nargs='+', type=int, help=help)
+
+    help = 'Codeblock size.'
+    group1.add_argument(
+        '--codeblocksize', nargs=2, type=int, help=help,
+        metavar=('cblkh', 'cblkw')
+    )
+
+    help = 'Number of decomposition levels.'
+    group1.add_argument('--numres', type=int, help=help, default=6)
+
+    help = 'Progression order.'
+    choices = ['lrcp', 'rlcp', 'rpcl', 'prcl', 'cprl']
+    group1.add_argument('--prog', choices=choices, help=help, default='lrcp')
+
+    help = 'Use irreversible 9x7 transform.'
+    group1.add_argument('--irreversible', help=help, action='store_true')
+
+    help = 'Generate EPH markers.'
+    group1.add_argument('--eph', help=help, action='store_true')
+
+    help = 'Generate PLT markers.'
+    group1.add_argument('--plt', help=help, action='store_true')
+
+    help = 'Generate SOP markers.'
+    group1.add_argument('--sop', help=help, action='store_true')
+
+    help = 'Use this many threads/cores.'
+    group1.add_argument(
+        '--num-threads', type=int, default=1, help=help,
+    )
+
+    help = (
+        'Dimensions of JP2K tile.  If not provided, the JPEG2000 image will '
+        'be written as a single tile.'
+    )
+    group1.add_argument(
+        '--tilesize', nargs=2, type=int, help=help, metavar=('NROWS', 'NCOLS')
+    )
+
+    group2 = parser.add_argument_group(
+        'JPEG', 'Arguments specific to conversion of JPEG imagery.'
+    )
+
+    help = (
+        'If specified, subsume any ICC profile found in an APP2 segment(s) '
+        'into the colour specification box.  This will involve a file copy '
+        'and is therefore a potentially costly operation.'
+    )
+    group2.add_argument(
+        '--include-icc-profile', help=help, action='store_true'
+    )
+
+    group2.add_argument('jpeg', help='Input JPEG file.')
+    group2.add_argument('jp2k', help='Output JPEG 2000 file.')
+
+    # These arguments are not specific to either group.
+    help = 'Show this help message and exit'
+    parser.add_argument('--help', '-h', action='help', help=help)
+
+    help = (
+        'Logging level, one of "critical", "error", "warning", "info", '
+        'or "debug".'
+    )
+    parser.add_argument(
+        '--verbosity', help=help, default='warning',
+        choices=['critical', 'error', 'warning', 'info', 'debug']
+    )
+
+    args = parser.parse_args()
+
+    logging_level = getattr(logging, args.verbosity.upper())
+
+    jpegp = pathlib.Path(args.jpeg)
+    jp2kp = pathlib.Path(args.jp2k)
+
+    kwargs = {
+        'cbsize': args.codeblocksize,
+        'cratios': args.cratio,
+        'capture_resolution': args.capture_resolution,
+        'display_resolution': args.display_resolution,
+        'eph': args.eph,
+        'include_icc_profile': args.include_icc_profile,
+        'irreversible': args.irreversible,
+        'numres': args.numres,
+        'num_threads': args.num_threads,
+        'plt': args.plt,
+        'prog': args.prog,
+        'psnr': args.psnr,
+        'sop': args.sop,
+        'tilesize': args.tilesize,
+        'verbosity': logging_level,
+    }
+
+    with jpeg.JPEG2JP2(jpegp, jp2kp, **kwargs) as j:
+        j.run()
+
+
 def tiff2jp2():
     """Entry point for console script tiff2jp2."""
 

glymur/jp2box.py

@@ -33,6 +33,7 @@ except (ImportError, ModuleNotFoundError):  # pragma: no cover
     _HAVE_GDAL = False
 else:
     gdal.UseExceptions()
+import lxml.objectify
 import lxml.etree as ET
 import numpy as np
 
@@ -3647,36 +3648,58 @@ class UUIDBox(Jp2kBox):
         lst = [text]
 
         if not get_option("print.xml") and self.uuid == _XMP_UUID:
+
             # If it's an XMP UUID, don't print the XML contents.
             pass
 
         elif self.uuid == _XMP_UUID:
-            b = ET.tostring(self.data, encoding="utf-8", pretty_print=True)
-            s = b.decode("utf-8").strip()
-            text = f"UUID Data:\n{s}"
+
+            s = self.raw_data.decode('utf-8').rstrip('\0')
+            e = lxml.objectify.fromstring(s)
+            xml = ET.tostring(e, pretty_print=True).decode('utf-8').strip()
+            text = f"UUID Data:\n{xml}"
             lst.append(text)
+
         elif self.uuid == _EXIF_UUID:
+
             s = io.StringIO()
 
             if self.data is None:
                 # If the UUID was malformed, just say so and go on.  This
                 # should not be a showstopper.
                 text = "UUID Data:  Invalid Exif UUID"
-                lst.append(text)
             else:
                 with np.printoptions(threshold=4):
                     pprint.pprint(self.data, stream=s, indent=4)
                 text = f"UUID Data:  {s.getvalue().rstrip()}"
-                lst.append(text)
+
+            lst.append(text)
+
         elif self.uuid == _GEOTIFF_UUID:
 
             options = gdal.InfoOptions(showColorTable=False)
-            txt = gdal.Info(self._fptr.name, options=options)
-            txt = textwrap.indent(txt, " " * 4).rstrip()
+            gdal_txt = gdal.Info(self._fptr.name, options=options)
+            gdal_txt = textwrap.indent(gdal_txt, " " * 4).rstrip()
+
+            # now append the raw IFD
+            s = io.StringIO()
+            with np.printoptions(threshold=4):
+                pprint.pprint(self.data, stream=s, indent=4)
+
+                ifd_txt = s.getvalue().rstrip()
+
+            txt = (
+                    f'UUID Data:'
+                    f'\n\n'
+                    f'Geo Metadata:\n{gdal_txt}'
+                    f'\n\n'
+                    f'Raw IFD Metadata:\n{ifd_txt}'
+            )
 
-            txt = f"UUID Data:\n{txt}"
             lst.append(txt)
+
         else:
+
             text = f"UUID Data:  {len(self.raw_data)} bytes"
             lst.append(text)