.gitattributes

+trollimage/version.py export-subst

.stickler.yml

 linters:
   flake8:
-    fixer: true
-fixers:
-  enable: true
+    python: 3
+    config: setup.cfg

CHANGELOG.md

+## Version 1.6.3 (2018/12/20)
+
+
+### Pull Requests Merged
+
+#### Bugs fixed
+
+* [PR 38](https://github.com/pytroll/trollimage/pull/38) - Fix casting and scaling float arrays in finalize
+
+In this release 1 pull request was closed.
+
+
+## Version 1.6.2 (2018/12/20)
+
+
+### Pull Requests Merged
+
+#### Bugs fixed
+
+* [PR 37](https://github.com/pytroll/trollimage/pull/37) - Fix and cleanup alpha and fill value handling in XRImage finalize
+* [PR 35](https://github.com/pytroll/trollimage/pull/35) - Fix xrimage alpha creation in finalize
+
+In this release 2 pull requests were closed.
+
+
+## Version 1.6.1 (2018/12/19)
+
+
+### Pull Requests Merged
+
+#### Bugs fixed
+
+* [PR 34](https://github.com/pytroll/trollimage/pull/34) - Fix XRImage's finalize method when input data are integers
+
+In this release 1 pull request was closed.
+
+
+## Version 1.6.0 (2018/12/18)
+
+### Issues Closed
+
+* [Issue 30](https://github.com/pytroll/trollimage/issues/30) - ReadTheDoc page builds not up to date ([PR 32](https://github.com/pytroll/trollimage/pull/32))
+* [Issue 21](https://github.com/pytroll/trollimage/issues/21) - Add 'convert' method to XRImage
+
+In this release 2 issues were closed.
+
+### Pull Requests Merged
+
+#### Bugs fixed
+
+* [PR 33](https://github.com/pytroll/trollimage/pull/33) - Fix crude stretch not calculating min/max per-band
+
+#### Features added
+
+* [PR 28](https://github.com/pytroll/trollimage/pull/28) - Add convert method of XRImage
+
+In this release 2 pull requests were closed.
+
+## Previous Versions
+
+See changelog.rst for previous release notes.

MANIFEST.in

 include LICENSE.txt
 include README.rst
+include versioneer.py
+include trollimage/version.py

RELEASING.md

+# Releasing trollimage
+
+1. checkout master
+2. pull from repo
+3. run the unittests
+4. run `loghub` and update the `CHANGELOG.md` file:
+
+```
+loghub pytroll/trollimage -u <username> -st v0.8.0 -plg bug "Bugs fixed" -plg enhancement "Features added" -plg documentation "Documentation changes" -plg backwards-incompatibility "Backwards incompatible changes"
+```
+
+Don't forget to commit!
+
+5. Create a tag with the new version number, starting with a 'v', eg:
+
+```
+git tag -a v0.22.45 -m "Version 0.22.45"
+```
+
+See [semver.org](http://semver.org/) on how to write a version number.
+
+6. push changes to github `git push --follow-tags`
+7. Verify travis tests passed and deployed sdist and wheel to PyPI

debian/changelog

-trollimage (1.5.7-1) unstable; urgency=medium
+trollimage (1.6.3-1) unstable; urgency=medium
 
   * Initial version (Closes: #916550)
 
- -- Antonio Valentino <antonio.valentino@tiscali.it>  Sat, 15 Dec 2018 21:02:06 +0000
+ -- Antonio Valentino <antonio.valentino@tiscali.it>  Tue, 25 Dec 2018 11:57:08 +0000

debian/control

@@ -8,7 +8,7 @@ Build-Depends: debhelper (>= 11),
                dh-python,
                python3-all,
                python3-dask,
-               python3-numpy,
+               python3-numpy (>= 1:1.13),
                python3-pil,
                python3-rasterio,
                python3-setuptools,
@@ -21,7 +21,7 @@ Homepage: https://github.com/pytroll/trollimage
 
 Package: python3-trollimage
 Architecture: all
-Depends: python3-numpy,
+Depends: python3-numpy (>= 1:1.13),
          python3-pil,
          python3-six,
          ${python3:Depends},

debian/copyright

@@ -7,6 +7,10 @@ Files: *
 Copyright: 2009-2018 Martin Raspaud
 License: GPL-3+
 
+Files: versioneer.py
+Copyright: 2018, Brian Warner
+License: CC0-1.0
+
 Files: debian/*
 Copyright: 2018 Antonio Valentino <antonio.valentino@tiscali.it>
 License: GPL-3+
@@ -27,3 +31,14 @@ License: GPL-3+
  .
  On Debian systems, the complete text of the GNU General
  Public License version 3 can be found in "/usr/share/common-licenses/GPL-3".
+
+License: CC0-1.0
+ To the extent possible under law, the author(s) have dedicated all copyright
+ and related and neighboring rights to this software to the public domain
+ worldwide. This software is distributed without any warranty.
+ .
+ You should have received a copy of the CC0 Public Domain Dedication along with
+ this software. If not, see <http://creativecommons.org/publicdomain/zero/1.0/>.
+ .
+ On Debian systems, the complete text of the CC0 1.0 Universal license can be
+ found in ‘/usr/share/common-licenses/CC0-1.0’.

doc/colorspaces.rst

+===========
 Colorspaces
------------
+===========
 
 .. automodule:: trollimage.colorspaces
    :members:

doc/image.rst

+=============
 Simple images
--------------
+=============
 
 .. automodule:: trollimage.image
    :members:

doc/index.rst

@@ -23,7 +23,6 @@ Contents:
    colormap
 
 
-
 Indices and tables
 ==================
 

doc/xrimage.rst

-Simple images
--------------
+=============
+XArray images
+=============
 
-.. automodule:: trollimage.xrimage
+.. autoclass:: trollimage.xrimage.XRImage
   :members:
-   :undoc-members:
+  :special-members:
+  :exclude-members: __dict__,__weakref__

rtd_requirements.txt

+pillow
+six
+rasterio
+xarray
+dask[array]
\ No newline at end of file

setup.cfg

@@ -2,4 +2,20 @@
 requires=numpy python-pillow
 release=1
 
+[bdist_wheel]
+universal=1
 
+[flake8]
+max-line-length = 120
+
+[versioneer]
+VCS = git
+style = pep440
+versionfile_source = trollimage/version.py
+versionfile_build =
+tag_prefix = v
+
+[coverage:run]
+omit =
+    trollimage/version.py
+    versioneer.py

setup.py

@@ -26,12 +26,11 @@
 """
 
 from setuptools import setup
-import imp
-
-version = imp.load_source('trollimage.version', 'trollimage/version.py')
+import versioneer
 
 setup(name="trollimage",
-      version=version.__version__,
+      version=versioneer.get_version(),
+      cmdclass=versioneer.get_cmdclass(),
       description='Pytroll imaging library',
       author='Martin Raspaud',
       author_email='martin.raspaud@smhi.se',
@@ -45,7 +44,7 @@ setup(name="trollimage",
       url="https://github.com/pytroll/trollimage",
       packages=['trollimage'],
       zip_safe=False,
-      install_requires=['numpy >=1.6', 'pillow', 'six'],
+      install_requires=['numpy >=1.13', 'pillow', 'six'],
       extras_require={
           'geotiff': ['rasterio'],
           'xarray': ['xarray', 'dask[array]'],

trollimage/__init__.py

@@ -23,4 +23,6 @@
 """The trollimage package
 """
 
-from trollimage.version import __version__  # noqa
+from .version import get_versions
+__version__ = get_versions()['version']
+del get_versions

trollimage/version.py

-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
 
-# Copyright (c) 2013, 2014 Martin Raspaud
+# This file helps to compute a version number in source trees obtained from
+# git-archive tarball (such as those provided by githubs download-from-tag
+# feature). Distribution tarballs (built by setup.py sdist) and build
+# directories (produced by setup.py build) will contain a much shorter file
+# that just contains the computed version number.
 
-# Author(s):
+# This file is released into the public domain. Generated by
+# versioneer-0.18 (https://github.com/warner/python-versioneer)
 
-#   Martin Raspaud <martin.raspaud@smhi.se>
+"""Git implementation of _version.py."""
 
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
+import errno
+import os
+import re
+import subprocess
+import sys
 
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
 
-# You should have received a copy of the GNU General Public License
-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+def get_keywords():
+    """Get the keywords needed to look up the version information."""
+    # these strings will be replaced by git during git-archive.
+    # setup.py/versioneer.py will grep for the variable names, so they must
+    # each be defined on a line of their own. _version.py will just call
+    # get_keywords().
+    git_refnames = " (HEAD -> master, tag: v1.6.3)"
+    git_full = "69942415f7bfbd9160189534ca60782eaa2e4b59"
+    git_date = "2018-12-20 15:10:36 -0600"
+    keywords = {"refnames": git_refnames, "full": git_full, "date": git_date}
+    return keywords
 
-"""Version file.
+
+class VersioneerConfig:
+    """Container for Versioneer configuration parameters."""
+
+
+def get_config():
+    """Create, populate and return the VersioneerConfig() object."""
+    # these strings are filled in when 'setup.py versioneer' creates
+    # _version.py
+    cfg = VersioneerConfig()
+    cfg.VCS = "git"
+    cfg.style = "pep440"
+    cfg.tag_prefix = "v"
+    cfg.parentdir_prefix = "None"
+    cfg.versionfile_source = "trollimage/version.py"
+    cfg.verbose = False
+    return cfg
+
+
+class NotThisMethod(Exception):
+    """Exception raised if a method is not valid for the current scenario."""
+
+
+LONG_VERSION_PY = {}
+HANDLERS = {}
+
+
+def register_vcs_handler(vcs, method):  # decorator
+    """Decorator to mark a method as the handler for a particular VCS."""
+    def decorate(f):
+        """Store f in HANDLERS[vcs][method]."""
+        if vcs not in HANDLERS:
+            HANDLERS[vcs] = {}
+        HANDLERS[vcs][method] = f
+        return f
+    return decorate
+
+
+def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False,
+                env=None):
+    """Call the given command(s)."""
+    assert isinstance(commands, list)
+    p = None
+    for c in commands:
+        try:
+            dispcmd = str([c] + args)
+            # remember shell=False, so use git.cmd on windows, not just git
+            p = subprocess.Popen([c] + args, cwd=cwd, env=env,
+                                 stdout=subprocess.PIPE,
+                                 stderr=(subprocess.PIPE if hide_stderr
+                                         else None))
+            break
+        except EnvironmentError:
+            e = sys.exc_info()[1]
+            if e.errno == errno.ENOENT:
+                continue
+            if verbose:
+                print("unable to run %s" % dispcmd)
+                print(e)
+            return None, None
+    else:
+        if verbose:
+            print("unable to find command, tried %s" % (commands,))
+        return None, None
+    stdout = p.communicate()[0].strip()
+    if sys.version_info[0] >= 3:
+        stdout = stdout.decode()
+    if p.returncode != 0:
+        if verbose:
+            print("unable to run %s (error)" % dispcmd)
+            print("stdout was %s" % stdout)
+        return None, p.returncode
+    return stdout, p.returncode
+
+
+def versions_from_parentdir(parentdir_prefix, root, verbose):
+    """Try to determine the version from the parent directory name.
+
+    Source tarballs conventionally unpack into a directory that includes both
+    the project name and a version string. We will also support searching up
+    two directory levels for an appropriately named parent directory
+    """
+    rootdirs = []
+
+    for i in range(3):
+        dirname = os.path.basename(root)
+        if dirname.startswith(parentdir_prefix):
+            return {"version": dirname[len(parentdir_prefix):],
+                    "full-revisionid": None,
+                    "dirty": False, "error": None, "date": None}
+        else:
+            rootdirs.append(root)
+            root = os.path.dirname(root)  # up a level
+
+    if verbose:
+        print("Tried directories %s but none started with prefix %s" %
+              (str(rootdirs), parentdir_prefix))
+    raise NotThisMethod("rootdir doesn't start with parentdir_prefix")
+
+
+@register_vcs_handler("git", "get_keywords")
+def git_get_keywords(versionfile_abs):
+    """Extract version information from the given file."""
+    # the code embedded in _version.py can just fetch the value of these
+    # keywords. When used from setup.py, we don't want to import _version.py,
+    # so we do it with a regexp instead. This function is not used from
+    # _version.py.
+    keywords = {}
+    try:
+        f = open(versionfile_abs, "r")
+        for line in f.readlines():
+            if line.strip().startswith("git_refnames ="):
+                mo = re.search(r'=\s*"(.*)"', line)
+                if mo:
+                    keywords["refnames"] = mo.group(1)
+            if line.strip().startswith("git_full ="):
+                mo = re.search(r'=\s*"(.*)"', line)
+                if mo:
+                    keywords["full"] = mo.group(1)
+            if line.strip().startswith("git_date ="):
+                mo = re.search(r'=\s*"(.*)"', line)
+                if mo:
+                    keywords["date"] = mo.group(1)
+        f.close()
+    except EnvironmentError:
+        pass
+    return keywords
+
+
+@register_vcs_handler("git", "keywords")
+def git_versions_from_keywords(keywords, tag_prefix, verbose):
+    """Get version information from git keywords."""
+    if not keywords:
+        raise NotThisMethod("no keywords at all, weird")
+    date = keywords.get("date")
+    if date is not None:
+        # git-2.2.0 added "%cI", which expands to an ISO-8601 -compliant
+        # datestamp. However we prefer "%ci" (which expands to an "ISO-8601
+        # -like" string, which we must then edit to make compliant), because
+        # it's been around since git-1.5.3, and it's too difficult to
+        # discover which version we're using, or to work around using an
+        # older one.
+        date = date.strip().replace(" ", "T", 1).replace(" ", "", 1)
+    refnames = keywords["refnames"].strip()
+    if refnames.startswith("$Format"):
+        if verbose:
+            print("keywords are unexpanded, not using")
+        raise NotThisMethod("unexpanded keywords, not a git-archive tarball")
+    refs = set([r.strip() for r in refnames.strip("()").split(",")])
+    # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of
+    # just "foo-1.0". If we see a "tag: " prefix, prefer those.
+    TAG = "tag: "
+    tags = set([r[len(TAG):] for r in refs if r.startswith(TAG)])
+    if not tags:
+        # Either we're using git < 1.8.3, or there really are no tags. We use
+        # a heuristic: assume all version tags have a digit. The old git %d
+        # expansion behaves like git log --decorate=short and strips out the
+        # refs/heads/ and refs/tags/ prefixes that would let us distinguish
+        # between branches and tags. By ignoring refnames without digits, we
+        # filter out many common branch names like "release" and
+        # "stabilization", as well as "HEAD" and "master".
+        tags = set([r for r in refs if re.search(r'\d', r)])
+        if verbose:
+            print("discarding '%s', no digits" % ",".join(refs - tags))
+    if verbose:
+        print("likely tags: %s" % ",".join(sorted(tags)))
+    for ref in sorted(tags):
+        # sorting will prefer e.g. "2.0" over "2.0rc1"
+        if ref.startswith(tag_prefix):
+            r = ref[len(tag_prefix):]
+            if verbose:
+                print("picking %s" % r)
+            return {"version": r,
+                    "full-revisionid": keywords["full"].strip(),
+                    "dirty": False, "error": None,
+                    "date": date}
+    # no suitable tags, so version is "0+unknown", but full hex is still there
+    if verbose:
+        print("no suitable tags, using unknown + full revision id")
+    return {"version": "0+unknown",
+            "full-revisionid": keywords["full"].strip(),
+            "dirty": False, "error": "no suitable tags", "date": None}
+
+
+@register_vcs_handler("git", "pieces_from_vcs")
+def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
+    """Get version from 'git describe' in the root of the source tree.
+
+    This only gets called if the git-archive 'subst' keywords were *not*
+    expanded, and _version.py hasn't already been rewritten with a short
+    version string, meaning we're inside a checked out source tree.
+    """
+    GITS = ["git"]
+    if sys.platform == "win32":
+        GITS = ["git.cmd", "git.exe"]
+
+    out, rc = run_command(GITS, ["rev-parse", "--git-dir"], cwd=root,
+                          hide_stderr=True)
+    if rc != 0:
+        if verbose:
+            print("Directory %s not under git control" % root)
+        raise NotThisMethod("'git rev-parse --git-dir' returned error")
+
+    # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty]
+    # if there isn't one, this yields HEX[-dirty] (no NUM)
+    describe_out, rc = run_command(GITS, ["describe", "--tags", "--dirty",
+                                          "--always", "--long",
+                                          "--match", "%s*" % tag_prefix],
+                                   cwd=root)
+    # --long was added in git-1.5.5
+    if describe_out is None:
+        raise NotThisMethod("'git describe' failed")
+    describe_out = describe_out.strip()
+    full_out, rc = run_command(GITS, ["rev-parse", "HEAD"], cwd=root)
+    if full_out is None:
+        raise NotThisMethod("'git rev-parse' failed")
+    full_out = full_out.strip()
+
+    pieces = {}
+    pieces["long"] = full_out
+    pieces["short"] = full_out[:7]  # maybe improved later
+    pieces["error"] = None
+
+    # parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty]
+    # TAG might have hyphens.
+    git_describe = describe_out
+
+    # look for -dirty suffix
+    dirty = git_describe.endswith("-dirty")
+    pieces["dirty"] = dirty
+    if dirty:
+        git_describe = git_describe[:git_describe.rindex("-dirty")]
+
+    # now we have TAG-NUM-gHEX or HEX
+
+    if "-" in git_describe:
+        # TAG-NUM-gHEX
+        mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe)
+        if not mo:
+            # unparseable. Maybe git-describe is misbehaving?
+            pieces["error"] = ("unable to parse git-describe output: '%s'"
+                               % describe_out)
+            return pieces
+
+        # tag
+        full_tag = mo.group(1)
+        if not full_tag.startswith(tag_prefix):
+            if verbose:
+                fmt = "tag '%s' doesn't start with prefix '%s'"
+                print(fmt % (full_tag, tag_prefix))
+            pieces["error"] = ("tag '%s' doesn't start with prefix '%s'"
+                               % (full_tag, tag_prefix))
+            return pieces
+        pieces["closest-tag"] = full_tag[len(tag_prefix):]
+
+        # distance: number of commits since tag
+        pieces["distance"] = int(mo.group(2))
+
+        # commit: short hex revision ID
+        pieces["short"] = mo.group(3)
+
+    else:
+        # HEX: no tags
+        pieces["closest-tag"] = None
+        count_out, rc = run_command(GITS, ["rev-list", "HEAD", "--count"],
+                                    cwd=root)
+        pieces["distance"] = int(count_out)  # total number of commits
+
+    # commit date: see ISO-8601 comment in git_versions_from_keywords()
+    date = run_command(GITS, ["show", "-s", "--format=%ci", "HEAD"],
+                       cwd=root)[0].strip()
+    pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1)
+
+    return pieces
+
+
+def plus_or_dot(pieces):
+    """Return a + if we don't already have one, else return a ."""
+    if "+" in pieces.get("closest-tag", ""):
+        return "."
+    return "+"
+
+
+def render_pep440(pieces):
+    """Build up version string, with post-release "local version identifier".
+
+    Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you
+    get a tagged build and then dirty it, you'll get TAG+0.gHEX.dirty
+
+    Exceptions:
+    1: no tags. git_describe was just HEX. 0+untagged.DISTANCE.gHEX[.dirty]
+    """
+    if pieces["closest-tag"]:
+        rendered = pieces["closest-tag"]
+        if pieces["distance"] or pieces["dirty"]:
+            rendered += plus_or_dot(pieces)
+            rendered += "%d.g%s" % (pieces["distance"], pieces["short"])
+            if pieces["dirty"]:
+                rendered += ".dirty"
+    else:
+        # exception #1
+        rendered = "0+untagged.%d.g%s" % (pieces["distance"],
+                                          pieces["short"])
+        if pieces["dirty"]:
+            rendered += ".dirty"
+    return rendered
+
+
+def render_pep440_pre(pieces):
+    """TAG[.post.devDISTANCE] -- No -dirty.
+
+    Exceptions:
+    1: no tags. 0.post.devDISTANCE
+    """
+    if pieces["closest-tag"]:
+        rendered = pieces["closest-tag"]
+        if pieces["distance"]:
+            rendered += ".post.dev%d" % pieces["distance"]
+    else:
+        # exception #1
+        rendered = "0.post.dev%d" % pieces["distance"]
+    return rendered
+
+
+def render_pep440_post(pieces):
+    """TAG[.postDISTANCE[.dev0]+gHEX] .
+
+    The ".dev0" means dirty. Note that .dev0 sorts backwards
+    (a dirty tree will appear "older" than the corresponding clean one),
+    but you shouldn't be releasing software with -dirty anyways.
+
+    Exceptions:
+    1: no tags. 0.postDISTANCE[.dev0]
+    """
+    if pieces["closest-tag"]:
+        rendered = pieces["closest-tag"]
+        if pieces["distance"] or pieces["dirty"]:
+            rendered += ".post%d" % pieces["distance"]
+            if pieces["dirty"]:
+                rendered += ".dev0"
+            rendered += plus_or_dot(pieces)
+            rendered += "g%s" % pieces["short"]
+    else:
+        # exception #1
+        rendered = "0.post%d" % pieces["distance"]
+        if pieces["dirty"]:
+            rendered += ".dev0"
+        rendered += "+g%s" % pieces["short"]
+    return rendered
+
+
+def render_pep440_old(pieces):
+    """TAG[.postDISTANCE[.dev0]] .
+
+    The ".dev0" means dirty.
+
+    Eexceptions:
+    1: no tags. 0.postDISTANCE[.dev0]
+    """
+    if pieces["closest-tag"]:
+        rendered = pieces["closest-tag"]
+        if pieces["distance"] or pieces["dirty"]:
+            rendered += ".post%d" % pieces["distance"]
+            if pieces["dirty"]:
+                rendered += ".dev0"
+    else:
+        # exception #1
+        rendered = "0.post%d" % pieces["distance"]
+        if pieces["dirty"]:
+            rendered += ".dev0"
+    return rendered
+
+
+def render_git_describe(pieces):
+    """TAG[-DISTANCE-gHEX][-dirty].
+
+    Like 'git describe --tags --dirty --always'.
+
+    Exceptions:
+    1: no tags. HEX[-dirty]  (note: no 'g' prefix)
+    """
+    if pieces["closest-tag"]:
+        rendered = pieces["closest-tag"]
+        if pieces["distance"]:
+            rendered += "-%d-g%s" % (pieces["distance"], pieces["short"])
+    else:
+        # exception #1
+        rendered = pieces["short"]
+    if pieces["dirty"]:
+        rendered += "-dirty"
+    return rendered
+
+
+def render_git_describe_long(pieces):
+    """TAG-DISTANCE-gHEX[-dirty].
+
+    Like 'git describe --tags --dirty --always -long'.
+    The distance/hash is unconditional.
+
+    Exceptions:
+    1: no tags. HEX[-dirty]  (note: no 'g' prefix)
     """
+    if pieces["closest-tag"]:
+        rendered = pieces["closest-tag"]
+        rendered += "-%d-g%s" % (pieces["distance"], pieces["short"])
+    else:
+        # exception #1
+        rendered = pieces["short"]
+    if pieces["dirty"]:
+        rendered += "-dirty"
+    return rendered
+
+
+def render(pieces, style):
+    """Render the given version pieces into the requested style."""
+    if pieces["error"]:
+        return {"version": "unknown",
+                "full-revisionid": pieces.get("long"),
+                "dirty": None,
+                "error": pieces["error"],
+                "date": None}
+
+    if not style or style == "default":
+        style = "pep440"  # the default
+
+    if style == "pep440":
+        rendered = render_pep440(pieces)
+    elif style == "pep440-pre":
+        rendered = render_pep440_pre(pieces)
+    elif style == "pep440-post":
+        rendered = render_pep440_post(pieces)
+    elif style == "pep440-old":
+        rendered = render_pep440_old(pieces)
+    elif style == "git-describe":
+        rendered = render_git_describe(pieces)
+    elif style == "git-describe-long":
+        rendered = render_git_describe_long(pieces)
+    else:
+        raise ValueError("unknown style '%s'" % style)
+
+    return {"version": rendered, "full-revisionid": pieces["long"],
+            "dirty": pieces["dirty"], "error": None,
+            "date": pieces.get("date")}
+
+
+def get_versions():
+    """Get version information or return default if unable to do so."""
+    # I am in _version.py, which lives at ROOT/VERSIONFILE_SOURCE. If we have
+    # __file__, we can work backwards from there to the root. Some
+    # py2exe/bbfreeze/non-CPython implementations don't do __file__, in which
+    # case we can only use expanded keywords.
+
+    cfg = get_config()
+    verbose = cfg.verbose
+
+    try:
+        return git_versions_from_keywords(get_keywords(), cfg.tag_prefix,
+                                          verbose)
+    except NotThisMethod:
+        pass
+
+    try:
+        root = os.path.realpath(__file__)
+        # versionfile_source is the relative path from the top of the source
+        # tree (where the .git directory might live) to this file. Invert
+        # this to find the root from __file__.
+        for i in cfg.versionfile_source.split('/'):
+            root = os.path.dirname(root)
+    except NameError:
+        return {"version": "0+unknown", "full-revisionid": None,
+                "dirty": None,
+                "error": "unable to find root of source tree",
+                "date": None}
+
+    try:
+        pieces = git_pieces_from_vcs(cfg.tag_prefix, root, verbose)
+        return render(pieces, cfg.style)
+    except NotThisMethod:
+        pass
+
+    try:
+        if cfg.parentdir_prefix:
+            return versions_from_parentdir(cfg.parentdir_prefix, root, verbose)
+    except NotThisMethod:
+        pass
 
-__version__ = "v1.5.7"
+    return {"version": "0+unknown", "full-revisionid": None,
+            "dirty": None,
+            "error": "unable to compute version", "date": None}

trollimage/xrimage.py

@@ -164,17 +164,16 @@ def color_interp(data):
 
 
 class XRImage(object):
-    """Image class using xarray as internal storage."""
+    """Image class using an :class:`xarray.DataArray` as internal storage."""
 
     def __init__(self, data):
-        """Initialize the image."""
+        """Initialize the image with a :class:`~xarray.DataArray`."""
         data = self._correct_dims(data)
 
         # 'data' is an XArray, get the data from it as a dask array
         if not isinstance(data.data, da.Array):
             logger.debug("Convert image data to dask array")
-            data.data = da.from_array(data.data, chunks=(data.sizes['bands'],
-                                                         4096, 4096))
+            data.data = da.from_array(data.data, chunks=(data.sizes['bands'], 4096, 4096))
 
         self.data = data
         self.height, self.width = self.data.sizes['y'], self.data.sizes['x']
@@ -378,21 +377,160 @@ class XRImage(object):
 
         return meta
 
-    def fill_or_alpha(self, data, fill_value=None):
-        """Fill the data with fill_value, or create an alpha channels."""
-        if fill_value is None and not self.mode.endswith("A"):
+    def _create_alpha(self, data, fill_value=None):
+        """Create an alpha band DataArray object.
+
+        If `fill_value` is provided and input data is an integer type
+        then it is used to determine invalid "null" pixels instead of
+        xarray's `isnull` and `notnull` methods.
+
+        The returned array is 1 where data is valid, 0 where invalid.
+
+        """
         not_alpha = [b for b in data.coords['bands'].values if b != 'A']
+        null_mask = data.sel(bands=not_alpha)
+        if np.issubdtype(data.dtype, np.integer) and fill_value is not None:
+            null_mask = null_mask != fill_value
+        else:
+            null_mask = null_mask.notnull()
         # if any of the bands are valid, we don't want transparency
-            null_mask = data.sel(bands=not_alpha).notnull().any(dim='bands')
+        null_mask = null_mask.any(dim='bands')
         null_mask = null_mask.expand_dims('bands')
         null_mask['bands'] = ['A']
+        # match data dtype
+        return null_mask
 
-            data = xr.concat([data, null_mask.astype(data.dtype)],
-                             dim="bands")
-        elif fill_value is not None:
-            data = data.fillna(fill_value)
+    def _add_alpha(self, data, alpha=None):
+        """Create an alpha channel and concatenate it to the provided data.
+
+        If ``data`` is an integer type then the alpha band will be scaled
+        to use the smallest (min) value as fully transparent and the largest
+        (max) value as fully opaque. For float types the alpha band spans
+        0 to 1.
+
+        """
+        null_mask = alpha if alpha is not None else self._create_alpha(data)
+        # if we are using integer data, then alpha needs to be min-int to max-int
+        # otherwise for floats we want 0 to 1
+        if np.issubdtype(data.dtype, np.integer):
+            # xarray sometimes upcasts this calculation, so cast again
+            null_mask = self._scale_to_dtype(null_mask, data.dtype).astype(data.dtype)
+        data = xr.concat([data, null_mask], dim="bands")
+        return data
+
+    def _scale_to_dtype(self, data, dtype):
+        """Scale provided data to dtype range assuming a 0-1 range.
+
+        Float input data is assumed to be normalized to a 0 to 1 range.
+        Integer input data is not scaled, only clipped. A float output
+        type is not scaled since both outputs and inputs are assumed to
+        be in the 0-1 range already.
+
+        """
+        if np.issubdtype(dtype, np.integer):
+            if np.issubdtype(data, np.integer):
+                # preserve integer data type
+                data = data.clip(np.iinfo(dtype).min, np.iinfo(dtype).max)
+            else:
+                # scale float data (assumed to be 0 to 1) to full integer space
+                dinfo = np.iinfo(dtype)
+                data = data.clip(0, 1) * (dinfo.max - dinfo.min) + dinfo.min
+            data = data.round()
         return data
 
+    def _check_modes(self, modes):
+        """Check that the image is in one of the given *modes*, raise an exception otherwise."""
+        if not isinstance(modes, (tuple, list, set)):
+            modes = [modes]
+        if self.mode not in modes:
+            raise ValueError("Image not in suitable mode, expected: %s, got: %s" % (modes, self.mode))
+
+    def _from_p(self, mode):
+        """Convert the image from P or PA to RGB or RGBA."""
+        self._check_modes(("P", "PA"))
+
+        if self.mode.endswith("A"):
+            alpha = self.data.sel(bands=["A"]).data
+            mode = mode + "A" if not mode.endswith("A") else mode
+        else:
+            alpha = None
+
+        if not self.palette:
+            raise RuntimeError("Can't convert palettized image, missing palette.")
+
+        pal = np.array(self.palette)
+        pal = da.from_array(pal, chunks=pal.shape)
+        flat_indexes = self.data.data[0].ravel().astype('int64')
+        new_shape = (3,) + self.data.shape[1:3]
+        new_data = pal[flat_indexes].reshape(new_shape)
+        coords = dict(self.data.coords)
+        coords["bands"] = list(mode)
+
+        if alpha is not None:
+            new_arr = da.concatenate((new_data, alpha), axis=0)
+            data = xr.DataArray(new_arr, coords=coords, attrs=self.data.attrs, dims=self.data.dims)
+        else:
+            data = xr.DataArray(new_data, coords=coords, attrs=self.data.attrs, dims=self.data.dims)
+
+        return data
+
+    def _l2rgb(self, mode):
+        """Convert from L (black and white) to RGB.
+        """
+        self._check_modes(("L", "LA"))
+
+        bands = ["L"] * 3
+        if mode[-1] == "A":
+            bands.append("A")
+        data = self.data.sel(bands=bands)
+        data["bands"] = list(mode)
+        return data
+
+    def convert(self, mode):
+        if mode == self.mode:
+            return self.__class__(self.data)
+
+        if mode not in ["P", "PA", "L", "LA", "RGB", "RGBA"]:
+            raise ValueError("Mode %s not recognized." % (mode))
+
+        if mode == self.mode + "A":
+            data = self._add_alpha(self.data).data
+            coords = dict(self.data.coords)
+            coords["bands"] = list(mode)
+            data = xr.DataArray(data, coords=coords, attrs=self.data.attrs, dims=self.data.dims)
+            new_img = XRImage(data)
+        elif mode + "A" == self.mode:
+            # Remove the alpha band from our current image
+            no_alpha = self.data.sel(bands=[b for b in self.data.coords["bands"].data if b != "A"]).data
+            coords = dict(self.data.coords)
+            coords["bands"] = list(mode)
+            data = xr.DataArray(no_alpha, coords=coords, attrs=self.data.attrs, dims=self.data.dims)
+            new_img = XRImage(data)
+        elif mode.endswith("A") and not self.mode.endswith("A"):
+            img = self.convert(self.mode + "A")
+            new_img = img.convert(mode)
+        elif self.mode.endswith("A") and not mode.endswith("A"):
+            img = self.convert(self.mode[:-1])
+            new_img = img.convert(mode)
+        else:
+            cases = {
+                "P": {"RGB": self._from_p},
+                "PA": {"RGBA": self._from_p},
+                "L": {"RGB": self._l2rgb},
+                "LA": {"RGBA": self._l2rgb}
+            }
+            try:
+                data = cases[self.mode][mode](mode)
+                new_img = XRImage(data)
+            except KeyError:
+                raise ValueError("Conversion from %s to %s not implemented !"
+                                 % (self.mode, mode))
+
+        if self.mode.startswith('P') and new_img.mode.startswith('P'):
+            # need to copy the palette
+            new_img.palette = self.palette
+        return new_img
+
     def _finalize(self, fill_value=None, dtype=np.uint8):
         """Wrapper around 'finalize' method for backwards compatibility."""
         import warnings
@@ -401,32 +539,51 @@ class XRImage(object):
         return self.finalize(fill_value, dtype)
 
     def finalize(self, fill_value=None, dtype=np.uint8):
-        """Finalize the image.
+        """Finalize the image to be written to an output file.
+
+        This adds an alpha band or fills data with a fill_value (if specified).
+        It also scales float data to the output range of the data type (0-255
+        for uint8, default). For integer input data this method assumes the
+        data is already scaled to the proper desired range. It will still fill
+        in invalid values and add an alpha band if needed. Integer input
+        data's fill value is determined by a special ``_FillValue`` attribute
+        in the ``DataArray`` ``.attrs`` dictionary.
 
-        This sets the channels in unsigned 8bit format ([0,255] range)
-        (if the *dtype* doesn't say otherwise).
         """
-        # if self.mode == "P":
-        #     self.convert("RGB")
-        # if self.mode == "PA":
-        #     self.convert("RGBA")
-        #
+        if self.mode == "P":
+            return self.convert("RGB").finalize(fill_value=fill_value, dtype=dtype)
+        if self.mode == "PA":
+            return self.convert("RGBA").finalize(fill_value=fill_value, dtype=dtype)
 
         if np.issubdtype(dtype, np.floating) and fill_value is None:
             logger.warning("Image with floats cannot be transparent, so "
                            "setting fill_value to 0")
             fill_value = 0
 
-        final_data = self.fill_or_alpha(self.data, fill_value)
-
-        if np.issubdtype(dtype, np.integer):
-            final_data = final_data.clip(0, 1) * np.iinfo(dtype).max
-            final_data = final_data.round().astype(dtype)
+        final_data = self.data
+        # if the data are integers then this fill value will be used to check for invalid values
+        ifill = final_data.attrs.get('_FillValue') if np.issubdtype(final_data, np.integer) else None
+        if fill_value is None and not self.mode.endswith('A'):
+            # We don't have a fill value or an alpha, let's add an alpha
+            alpha = self._create_alpha(final_data, fill_value=ifill)
+            final_data = self._scale_to_dtype(final_data, dtype).astype(dtype)
+            final_data = self._add_alpha(final_data, alpha=alpha)
         else:
-            final_data = final_data.astype(dtype)
+            # scale float data to the proper dtype
+            # this method doesn't cast yet so that we can keep track of NULL values
+            final_data = self._scale_to_dtype(final_data, dtype)
+            # Add fill_value after all other calculations have been done to
+            # make sure it is not scaled for the data type
+            if ifill is not None and fill_value is not None:
+                # cast fill value to output type so we don't change data type
+                fill_value = dtype(fill_value)
+                # integer fields have special fill values
+                final_data = final_data.where(final_data != ifill, dtype(fill_value))
+            elif fill_value is not None:
+                final_data = final_data.fillna(dtype(fill_value))
 
+        final_data = final_data.astype(dtype)
         final_data.attrs = self.data.attrs
-
         return final_data, ''.join(final_data['bands'].values)
 
     def pil_image(self, fill_value=None):
@@ -546,9 +703,11 @@ class XRImage(object):
         the [0,1] range.
         """
         if min_stretch is None:
-            min_stretch = self.data.min()
+            non_band_dims = tuple(x for x in self.data.dims if x != 'bands')
+            min_stretch = self.data.min(dim=non_band_dims)
         if max_stretch is None:
-            max_stretch = self.data.max()
+            non_band_dims = tuple(x for x in self.data.dims if x != 'bands')
+            max_stretch = self.data.max(dim=non_band_dims)
 
         if isinstance(min_stretch, (list, tuple)):
             min_stretch = self.xrify_tuples(min_stretch)
@@ -696,8 +855,12 @@ class XRImage(object):
                                                    img.channels[i].mask)
 
     def colorize(self, colormap):
-        """Colorize the current image using
-        *colormap*. Works only on"L" or "LA" images.
+        """Colorize the current image using `colormap`.
+
+        .. note::
+
+            Works only on "L" or "LA" images.
+
         """
 
         if self.mode not in ("L", "LA"):
@@ -710,16 +873,14 @@ class XRImage(object):
 
         l_data = self.data.sel(bands=['L'])
 
-        # TODO: dask-ify colorize
-        def _colorize(colormap, l_data):
-            channels = colormap.colorize(l_data.data)
+        def _colorize(l_data, colormap):
+            # 'l_data' is (1, rows, cols)
+            # 'channels' will be a list of 3 (RGB) or 4 (RGBA) arrays
+            channels = colormap.colorize(l_data)
             return np.concatenate(channels, axis=0)
 
-        # TODO: xarray-ify colorize
-        # delayed = dask.delayed(colormap.colorize)(l_data.data)
-        delayed = dask.delayed(_colorize)(colormap, l_data)
-        shape = (3, l_data.sizes['y'], l_data.sizes['x'])
-        new_data = da.from_delayed(delayed, shape=shape, dtype=np.float64)
+        new_data = l_data.data.map_blocks(_colorize, colormap,
+                                          chunks=(3,) + l_data.data.chunks[1:], dtype=np.float64)
 
         if alpha is not None:
             new_data = da.concatenate([new_data, alpha.data], axis=0)
@@ -732,12 +893,15 @@ class XRImage(object):
         coords['bands'] = list(mode)
         attrs = self.data.attrs
         dims = self.data.dims
-        self.data = xr.DataArray(new_data, coords=coords, attrs=attrs,
-                                 dims=dims)
+        self.data = xr.DataArray(new_data, coords=coords, attrs=attrs, dims=dims)
 
     def palettize(self, colormap):
-        """Palettize the current image using
-        *colormap*. Works only on"L" or "LA" images.
+        """Palettize the current image using `colormap`.
+
+        .. note::
+
+            Works only on "L" or "LA" images.
+
         """
 
         if self.mode not in ("L", "LA"):
@@ -746,31 +910,23 @@ class XRImage(object):
         l_data = self.data.sel(bands=['L'])
 
         def _palettize(data):
-            arr, palette = colormap.palettize(data.reshape(data.shape[1:]))
-            new_shape = (1, arr.shape[0], arr.shape[1])
-            arr = arr.reshape(new_shape)
-            return arr, palette
-
-        delayed = dask.delayed(_palettize)(l_data.data)
-        new_data, palette = delayed[0], delayed[1]
-        new_data = da.from_delayed(new_data, shape=l_data.shape,
-                                   dtype=l_data.dtype)
-        # XXX: Can we complete this method without computing the data?
-        new_data, self.palette = da.compute(new_data, palette)
-        new_data = da.from_array(new_data,
-                                 chunks=self.data.data.chunks)
+            # returns data and palette, only need data
+            return colormap.palettize(data)[0]
+
+        new_data = l_data.data.map_blocks(_palettize, dtype=l_data.dtype)
+        self.palette = tuple(colormap.colors)
 
         if self.mode == "L":
             mode = "P"
         else:
             mode = "PA"
+            new_data = da.concatenate([new_data, self.data.sel(bands=['A'])], axis=0)
 
         self.data.data = new_data
         self.data.coords['bands'] = list(mode)
 
     def blend(self, other):
-        """Alpha blend *other* on top of the current image.
-        """
+        """Alpha blend *other* on top of the current image."""
         raise NotImplementedError("This method has not be implemented for "
                                   "xarray support.")