Added support for multiple tags on a single model

.flatpak-builder/cache/objects/bc/a7254a3e0d33bc46b3d2521f9d9b8b2f46542f706d7d443b5dae002c69922a.file

@@ -0,0 +1,4 @@
+# This file is protected via CODEOWNERS
+from __future__ import annotations
+
+__version__ = "2.2.1"

.flatpak-builder/cache/objects/bc/b02f0c5d1848ac2ab4e1081c8f1a79e83ba21d762976bb76bedd14bac46b6a.file

@@ -0,0 +1,318 @@
+#
+# The Python Imaging Library.
+#
+# SPIDER image file handling
+#
+# History:
+# 2004-08-02    Created BB
+# 2006-03-02    added save method
+# 2006-03-13    added support for stack images
+#
+# Copyright (c) 2004 by Health Research Inc. (HRI) RENSSELAER, NY 12144.
+# Copyright (c) 2004 by William Baxter.
+# Copyright (c) 2004 by Secret Labs AB.
+# Copyright (c) 2004 by Fredrik Lundh.
+#
+
+##
+# Image plugin for the Spider image format. This format is used
+# by the SPIDER software, in processing image data from electron
+# microscopy and tomography.
+##
+
+#
+# SpiderImagePlugin.py
+#
+# The Spider image format is used by SPIDER software, in processing
+# image data from electron microscopy and tomography.
+#
+# Spider home page:
+# https://spider.wadsworth.org/spider_doc/spider/docs/spider.html
+#
+# Details about the Spider image format:
+# https://spider.wadsworth.org/spider_doc/spider/docs/image_doc.html
+#
+from __future__ import annotations
+
+import os
+import struct
+import sys
+
+from . import Image, ImageFile
+
+
+def isInt(f):
+    try:
+        i = int(f)
+        if f - i == 0:
+            return 1
+        else:
+            return 0
+    except (ValueError, OverflowError):
+        return 0
+
+
+iforms = [1, 3, -11, -12, -21, -22]
+
+
+# There is no magic number to identify Spider files, so just check a
+# series of header locations to see if they have reasonable values.
+# Returns no. of bytes in the header, if it is a valid Spider header,
+# otherwise returns 0
+
+
+def isSpiderHeader(t):
+    h = (99,) + t  # add 1 value so can use spider header index start=1
+    # header values 1,2,5,12,13,22,23 should be integers
+    for i in [1, 2, 5, 12, 13, 22, 23]:
+        if not isInt(h[i]):
+            return 0
+    # check iform
+    iform = int(h[5])
+    if iform not in iforms:
+        return 0
+    # check other header values
+    labrec = int(h[13])  # no. records in file header
+    labbyt = int(h[22])  # total no. of bytes in header
+    lenbyt = int(h[23])  # record length in bytes
+    if labbyt != (labrec * lenbyt):
+        return 0
+    # looks like a valid header
+    return labbyt
+
+
+def isSpiderImage(filename):
+    with open(filename, "rb") as fp:
+        f = fp.read(92)  # read 23 * 4 bytes
+    t = struct.unpack(">23f", f)  # try big-endian first
+    hdrlen = isSpiderHeader(t)
+    if hdrlen == 0:
+        t = struct.unpack("<23f", f)  # little-endian
+        hdrlen = isSpiderHeader(t)
+    return hdrlen
+
+
+class SpiderImageFile(ImageFile.ImageFile):
+    format = "SPIDER"
+    format_description = "Spider 2D image"
+    _close_exclusive_fp_after_loading = False
+
+    def _open(self):
+        # check header
+        n = 27 * 4  # read 27 float values
+        f = self.fp.read(n)
+
+        try:
+            self.bigendian = 1
+            t = struct.unpack(">27f", f)  # try big-endian first
+            hdrlen = isSpiderHeader(t)
+            if hdrlen == 0:
+                self.bigendian = 0
+                t = struct.unpack("<27f", f)  # little-endian
+                hdrlen = isSpiderHeader(t)
+            if hdrlen == 0:
+                msg = "not a valid Spider file"
+                raise SyntaxError(msg)
+        except struct.error as e:
+            msg = "not a valid Spider file"
+            raise SyntaxError(msg) from e
+
+        h = (99,) + t  # add 1 value : spider header index starts at 1
+        iform = int(h[5])
+        if iform != 1:
+            msg = "not a Spider 2D image"
+            raise SyntaxError(msg)
+
+        self._size = int(h[12]), int(h[2])  # size in pixels (width, height)
+        self.istack = int(h[24])
+        self.imgnumber = int(h[27])
+
+        if self.istack == 0 and self.imgnumber == 0:
+            # stk=0, img=0: a regular 2D image
+            offset = hdrlen
+            self._nimages = 1
+        elif self.istack > 0 and self.imgnumber == 0:
+            # stk>0, img=0: Opening the stack for the first time
+            self.imgbytes = int(h[12]) * int(h[2]) * 4
+            self.hdrlen = hdrlen
+            self._nimages = int(h[26])
+            # Point to the first image in the stack
+            offset = hdrlen * 2
+            self.imgnumber = 1
+        elif self.istack == 0 and self.imgnumber > 0:
+            # stk=0, img>0: an image within the stack
+            offset = hdrlen + self.stkoffset
+            self.istack = 2  # So Image knows it's still a stack
+        else:
+            msg = "inconsistent stack header values"
+            raise SyntaxError(msg)
+
+        if self.bigendian:
+            self.rawmode = "F;32BF"
+        else:
+            self.rawmode = "F;32F"
+        self._mode = "F"
+
+        self.tile = [("raw", (0, 0) + self.size, offset, (self.rawmode, 0, 1))]
+        self._fp = self.fp  # FIXME: hack
+
+    @property
+    def n_frames(self):
+        return self._nimages
+
+    @property
+    def is_animated(self):
+        return self._nimages > 1
+
+    # 1st image index is zero (although SPIDER imgnumber starts at 1)
+    def tell(self):
+        if self.imgnumber < 1:
+            return 0
+        else:
+            return self.imgnumber - 1
+
+    def seek(self, frame):
+        if self.istack == 0:
+            msg = "attempt to seek in a non-stack file"
+            raise EOFError(msg)
+        if not self._seek_check(frame):
+            return
+        self.stkoffset = self.hdrlen + frame * (self.hdrlen + self.imgbytes)
+        self.fp = self._fp
+        self.fp.seek(self.stkoffset)
+        self._open()
+
+    # returns a byte image after rescaling to 0..255
+    def convert2byte(self, depth=255):
+        (minimum, maximum) = self.getextrema()
+        m = 1
+        if maximum != minimum:
+            m = depth / (maximum - minimum)
+        b = -m * minimum
+        return self.point(lambda i, m=m, b=b: i * m + b).convert("L")
+
+    # returns a ImageTk.PhotoImage object, after rescaling to 0..255
+    def tkPhotoImage(self):
+        from . import ImageTk
+
+        return ImageTk.PhotoImage(self.convert2byte(), palette=256)
+
+
+# --------------------------------------------------------------------
+# Image series
+
+
+# given a list of filenames, return a list of images
+def loadImageSeries(filelist=None):
+    """create a list of :py:class:`~PIL.Image.Image` objects for use in a montage"""
+    if filelist is None or len(filelist) < 1:
+        return
+
+    imglist = []
+    for img in filelist:
+        if not os.path.exists(img):
+            print(f"unable to find {img}")
+            continue
+        try:
+            with Image.open(img) as im:
+                im = im.convert2byte()
+        except Exception:
+            if not isSpiderImage(img):
+                print(img + " is not a Spider image file")
+            continue
+        im.info["filename"] = img
+        imglist.append(im)
+    return imglist
+
+
+# --------------------------------------------------------------------
+# For saving images in Spider format
+
+
+def makeSpiderHeader(im):
+    nsam, nrow = im.size
+    lenbyt = nsam * 4  # There are labrec records in the header
+    labrec = int(1024 / lenbyt)
+    if 1024 % lenbyt != 0:
+        labrec += 1
+    labbyt = labrec * lenbyt
+    nvalues = int(labbyt / 4)
+    if nvalues < 23:
+        return []
+
+    hdr = [0.0] * nvalues
+
+    # NB these are Fortran indices
+    hdr[1] = 1.0  # nslice (=1 for an image)
+    hdr[2] = float(nrow)  # number of rows per slice
+    hdr[3] = float(nrow)  # number of records in the image
+    hdr[5] = 1.0  # iform for 2D image
+    hdr[12] = float(nsam)  # number of pixels per line
+    hdr[13] = float(labrec)  # number of records in file header
+    hdr[22] = float(labbyt)  # total number of bytes in header
+    hdr[23] = float(lenbyt)  # record length in bytes
+
+    # adjust for Fortran indexing
+    hdr = hdr[1:]
+    hdr.append(0.0)
+    # pack binary data into a string
+    return [struct.pack("f", v) for v in hdr]
+
+
+def _save(im, fp, filename):
+    if im.mode[0] != "F":
+        im = im.convert("F")
+
+    hdr = makeSpiderHeader(im)
+    if len(hdr) < 256:
+        msg = "Error creating Spider header"
+        raise OSError(msg)
+
+    # write the SPIDER header
+    fp.writelines(hdr)
+
+    rawmode = "F;32NF"  # 32-bit native floating point
+    ImageFile._save(im, fp, [("raw", (0, 0) + im.size, 0, (rawmode, 0, 1))])
+
+
+def _save_spider(im, fp, filename):
+    # get the filename extension and register it with Image
+    ext = os.path.splitext(filename)[1]
+    Image.register_extension(SpiderImageFile.format, ext)
+    _save(im, fp, filename)
+
+
+# --------------------------------------------------------------------
+
+
+Image.register_open(SpiderImageFile.format, SpiderImageFile)
+Image.register_save(SpiderImageFile.format, _save_spider)
+
+if __name__ == "__main__":
+    if len(sys.argv) < 2:
+        print("Syntax: python3 SpiderImagePlugin.py [infile] [outfile]")
+        sys.exit()
+
+    filename = sys.argv[1]
+    if not isSpiderImage(filename):
+        print("input image must be in Spider format")
+        sys.exit()
+
+    with Image.open(filename) as im:
+        print("image: " + str(im))
+        print("format: " + str(im.format))
+        print("size: " + str(im.size))
+        print("mode: " + str(im.mode))
+        print("max, min: ", end=" ")
+        print(im.getextrema())
+
+        if len(sys.argv) > 2:
+            outfile = sys.argv[2]
+
+            # perform some image operation
+            im = im.transpose(Image.Transpose.FLIP_LEFT_RIGHT)
+            print(
+                f"saving a flipped version of {os.path.basename(filename)} "
+                f"as {outfile} "
+            )
+            im.save(outfile, SpiderImageFile.format)

.flatpak-builder/cache/objects/bc/b9456a5b06f11c8583fa702c087a35b1b015c3fe70260a5c2d6f4dd1a091f3.file

@@ -0,0 +1,347 @@
+#
+# The Python Imaging Library.
+# $Id$
+#
+# im.show() drivers
+#
+# History:
+# 2008-04-06 fl   Created
+#
+# Copyright (c) Secret Labs AB 2008.
+#
+# See the README file for information on usage and redistribution.
+#
+from __future__ import annotations
+
+import abc
+import os
+import shutil
+import subprocess
+import sys
+from shlex import quote
+from typing import Any
+
+from . import Image
+
+_viewers = []
+
+
+def register(viewer, order: int = 1) -> None:
+    """
+    The :py:func:`register` function is used to register additional viewers::
+
+        from PIL import ImageShow
+        ImageShow.register(MyViewer())  # MyViewer will be used as a last resort
+        ImageShow.register(MySecondViewer(), 0)  # MySecondViewer will be prioritised
+        ImageShow.register(ImageShow.XVViewer(), 0)  # XVViewer will be prioritised
+
+    :param viewer: The viewer to be registered.
+    :param order:
+        Zero or a negative integer to prepend this viewer to the list,
+        a positive integer to append it.
+    """
+    try:
+        if issubclass(viewer, Viewer):
+            viewer = viewer()
+    except TypeError:
+        pass  # raised if viewer wasn't a class
+    if order > 0:
+        _viewers.append(viewer)
+    else:
+        _viewers.insert(0, viewer)
+
+
+def show(image: Image.Image, title: str | None = None, **options: Any) -> bool:
+    r"""
+    Display a given image.
+
+    :param image: An image object.
+    :param title: Optional title. Not all viewers can display the title.
+    :param \**options: Additional viewer options.
+    :returns: ``True`` if a suitable viewer was found, ``False`` otherwise.
+    """
+    for viewer in _viewers:
+        if viewer.show(image, title=title, **options):
+            return True
+    return False
+
+
+class Viewer:
+    """Base class for viewers."""
+
+    # main api
+
+    def show(self, image: Image.Image, **options: Any) -> int:
+        """
+        The main function for displaying an image.
+        Converts the given image to the target format and displays it.
+        """
+
+        if not (
+            image.mode in ("1", "RGBA")
+            or (self.format == "PNG" and image.mode in ("I;16", "LA"))
+        ):
+            base = Image.getmodebase(image.mode)
+            if image.mode != base:
+                image = image.convert(base)
+
+        return self.show_image(image, **options)
+
+    # hook methods
+
+    format: str | None = None
+    """The format to convert the image into."""
+    options: dict[str, Any] = {}
+    """Additional options used to convert the image."""
+
+    def get_format(self, image: Image.Image) -> str | None:
+        """Return format name, or ``None`` to save as PGM/PPM."""
+        return self.format
+
+    def get_command(self, file: str, **options: Any) -> str:
+        """
+        Returns the command used to display the file.
+        Not implemented in the base class.
+        """
+        msg = "unavailable in base viewer"
+        raise NotImplementedError(msg)
+
+    def save_image(self, image: Image.Image) -> str:
+        """Save to temporary file and return filename."""
+        return image._dump(format=self.get_format(image), **self.options)
+
+    def show_image(self, image: Image.Image, **options: Any) -> int:
+        """Display the given image."""
+        return self.show_file(self.save_image(image), **options)
+
+    def show_file(self, path: str, **options: Any) -> int:
+        """
+        Display given file.
+        """
+        os.system(self.get_command(path, **options))  # nosec
+        return 1
+
+
+# --------------------------------------------------------------------
+
+
+class WindowsViewer(Viewer):
+    """The default viewer on Windows is the default system application for PNG files."""
+
+    format = "PNG"
+    options = {"compress_level": 1, "save_all": True}
+
+    def get_command(self, file: str, **options: Any) -> str:
+        return (
+            f'start "Pillow" /WAIT "{file}" '
+            "&& ping -n 4 127.0.0.1 >NUL "
+            f'&& del /f "{file}"'
+        )
+
+    def show_file(self, path: str, **options: Any) -> int:
+        """
+        Display given file.
+        """
+        subprocess.Popen(
+            self.get_command(path, **options),
+            shell=True,
+            creationflags=getattr(subprocess, "CREATE_NO_WINDOW"),
+        )  # nosec
+        return 1
+
+
+if sys.platform == "win32":
+    register(WindowsViewer)
+
+
+class MacViewer(Viewer):
+    """The default viewer on macOS using ``Preview.app``."""
+
+    format = "PNG"
+    options = {"compress_level": 1, "save_all": True}
+
+    def get_command(self, file: str, **options: Any) -> str:
+        # on darwin open returns immediately resulting in the temp
+        # file removal while app is opening
+        command = "open -a Preview.app"
+        command = f"({command} {quote(file)}; sleep 20; rm -f {quote(file)})&"
+        return command
+
+    def show_file(self, path: str, **options: Any) -> int:
+        """
+        Display given file.
+        """
+        subprocess.call(["open", "-a", "Preview.app", path])
+        executable = sys.executable or shutil.which("python3")
+        if executable:
+            subprocess.Popen(
+                [
+                    executable,
+                    "-c",
+                    "import os, sys, time; time.sleep(20); os.remove(sys.argv[1])",
+                    path,
+                ]
+            )
+        return 1
+
+
+if sys.platform == "darwin":
+    register(MacViewer)
+
+
+class UnixViewer(Viewer):
+    format = "PNG"
+    options = {"compress_level": 1, "save_all": True}
+
+    @abc.abstractmethod
+    def get_command_ex(self, file: str, **options: Any) -> tuple[str, str]:
+        pass
+
+    def get_command(self, file: str, **options: Any) -> str:
+        command = self.get_command_ex(file, **options)[0]
+        return f"({command} {quote(file)}"
+
+
+class XDGViewer(UnixViewer):
+    """
+    The freedesktop.org ``xdg-open`` command.
+    """
+
+    def get_command_ex(self, file: str, **options: Any) -> tuple[str, str]:
+        command = executable = "xdg-open"
+        return command, executable
+
+    def show_file(self, path: str, **options: Any) -> int:
+        """
+        Display given file.
+        """
+        subprocess.Popen(["xdg-open", path])
+        return 1
+
+
+class DisplayViewer(UnixViewer):
+    """
+    The ImageMagick ``display`` command.
+    This viewer supports the ``title`` parameter.
+    """
+
+    def get_command_ex(
+        self, file: str, title: str | None = None, **options: Any
+    ) -> tuple[str, str]:
+        command = executable = "display"
+        if title:
+            command += f" -title {quote(title)}"
+        return command, executable
+
+    def show_file(self, path: str, **options: Any) -> int:
+        """
+        Display given file.
+        """
+        args = ["display"]
+        title = options.get("title")
+        if title:
+            args += ["-title", title]
+        args.append(path)
+
+        subprocess.Popen(args)
+        return 1
+
+
+class GmDisplayViewer(UnixViewer):
+    """The GraphicsMagick ``gm display`` command."""
+
+    def get_command_ex(self, file: str, **options: Any) -> tuple[str, str]:
+        executable = "gm"
+        command = "gm display"
+        return command, executable
+
+    def show_file(self, path: str, **options: Any) -> int:
+        """
+        Display given file.
+        """
+        subprocess.Popen(["gm", "display", path])
+        return 1
+
+
+class EogViewer(UnixViewer):
+    """The GNOME Image Viewer ``eog`` command."""
+
+    def get_command_ex(self, file: str, **options: Any) -> tuple[str, str]:
+        executable = "eog"
+        command = "eog -n"
+        return command, executable
+
+    def show_file(self, path: str, **options: Any) -> int:
+        """
+        Display given file.
+        """
+        subprocess.Popen(["eog", "-n", path])
+        return 1
+
+
+class XVViewer(UnixViewer):
+    """
+    The X Viewer ``xv`` command.
+    This viewer supports the ``title`` parameter.
+    """
+
+    def get_command_ex(
+        self, file: str, title: str | None = None, **options: Any
+    ) -> tuple[str, str]:
+        # note: xv is pretty outdated.  most modern systems have
+        # imagemagick's display command instead.
+        command = executable = "xv"
+        if title:
+            command += f" -name {quote(title)}"
+        return command, executable
+
+    def show_file(self, path: str, **options: Any) -> int:
+        """
+        Display given file.
+        """
+        args = ["xv"]
+        title = options.get("title")
+        if title:
+            args += ["-name", title]
+        args.append(path)
+
+        subprocess.Popen(args)
+        return 1
+
+
+if sys.platform not in ("win32", "darwin"):  # unixoids
+    if shutil.which("xdg-open"):
+        register(XDGViewer)
+    if shutil.which("display"):
+        register(DisplayViewer)
+    if shutil.which("gm"):
+        register(GmDisplayViewer)
+    if shutil.which("eog"):
+        register(EogViewer)
+    if shutil.which("xv"):
+        register(XVViewer)
+
+
+class IPythonViewer(Viewer):
+    """The viewer for IPython frontends."""
+
+    def show_image(self, image: Image.Image, **options: Any) -> int:
+        ipython_display(image)
+        return 1
+
+
+try:
+    from IPython.display import display as ipython_display
+except ImportError:
+    pass
+else:
+    register(IPythonViewer)
+
+
+if __name__ == "__main__":
+    if len(sys.argv) < 2:
+        print("Syntax: python3 ImageShow.py imagefile [title]")
+        sys.exit()
+
+    with Image.open(sys.argv[1]) as im:
+        print(show(im, *sys.argv[2:]))