Release070

CHANGELOG.rst

@@ -28,10 +28,15 @@ and the release date, in year-month-day format (see examples below).
 Unreleased
 ----------
 
+0.7.0 (2023-02-05)
+------------------
+
 Changed
 ^^^^^^^
 - The light_records.py table now just records state changes (from 'on' to 'off' or
   vice-versa).
+- create_image.py's create() method now has an imgtype argument that default to TIFF
+  (but can be PNG).
 - junc_image_req_ldst.py got some additional columns to manage the Science Team
   evaluation of images acquired from Image Requests.
 - create_pano.py's make_pano_product() function renamed to make_pano_record().
@@ -73,6 +78,7 @@ Removed
 - ldst_verification.py because the evaluation activity reflected here was on a per-image
   basis, but it has been revised to be on a per-Image-Request basis.
 
+
 0.6.1 (2023-09-25)
 ------------------
 

CONTRIBUTING.rst

@@ -60,8 +60,7 @@ Get Started!
 Ready to contribute? Here's how to set up `vipersci` for local development.
 
 At this time, the target version of Python for this library is 3.8 in order to
-align with current anticipated mission systems.  The intent is to allow this library
-to work successfully against Python as early as version 3.6.
+align with current anticipated mission systems.
 
 1. Fork the `vipersci` repo on GitHub.
 2. Clone your fork locally::
@@ -89,7 +88,7 @@ to work successfully against Python as early as version 3.6.
    <https://www.conventionalcommits.org/>`_ in styling your commit messages.
 
 5. When you're done making changes, check that your changes pass flake8 and the
-   tests, including testing other Python versions with tox::
+   tests, including testing other Python versions (optionally with tox)::
 
     $ flake8 src/vipersci tests
     $ python setup.py test or pytest
@@ -116,7 +115,7 @@ Before you submit a pull request, check that it meets these guidelines:
 2. If the pull request adds functionality, the docs should be updated. Put
    your new functionality into a function with a docstring, and add the
    feature to the list in CHANGELOG.rst.
-3. The pull request should work for Python 3.7, 3.8 and 3.9, and optionally for PyPy.
+3. The pull request should work for Python 3.8, 3.9, 3.10 and 3.11, and optionally for PyPy.
    And make sure that the tests pass for all supported Python versions.
 
 

setup.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.7.0-dev
+current_version = 0.7.0
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+))?
@@ -68,29 +68,29 @@ console_scripts =
 	accrual = vipersci.carto.accrual:main
 	anaglyph = vipersci.vis.anaglyph:main
 	anom_pixel = vipersci.vis.anom_pixel:main
-    bundle_install = vipersci.pds.bundle_install:main
+	bundle_install = vipersci.pds.bundle_install:main
 	colorforge = vipersci.carto.colorforge:main
 	dice_buffer = vipersci.carto.dice_buffer:main
 	dissolve_dice = vipersci.carto.dissolve_dice:main
 	get_position = vipersci.carto.get_position:main
 	image_stats = vipersci.vis.image_statistics:main
-    labelmaker = vipersci.pds.labelmaker.cli:main
+	labelmaker = vipersci.pds.labelmaker.cli:main
 	msolo_simulator = vipersci.carto.msolo_simulator:main
 	nirvss_simulator = vipersci.carto.nirvss_simulator:main
 	nss_modeler = vipersci.carto.nss_modeler:main
 	nss_simulator = vipersci.carto.nss_simulator:main
 	traverse_interpolator = vipersci.carto.traverse_interpolator:main
 	tri2gpkg = vipersci.carto.tri2gpkg:main
 	template_test = vipersci.vis.pds.template_test:main
-    vis_create_browse = vipersci.vis.pds.create_browse:main
+	vis_create_browse = vipersci.vis.pds.create_browse:main
 	vis_create_image = vipersci.vis.create_image:main
-    vis_create_mmgis_pano = vipersci.vis.create_mmgis_pano:main
+	vis_create_mmgis_pano = vipersci.vis.create_mmgis_pano:main
 	vis_create_pano = vipersci.vis.create_pano:main
-    vis_create_pano_product = vipersci.vis.pds.create_pano_product:main
+	vis_create_pano_product = vipersci.vis.pds.create_pano_product:main
 	vis_create_tif = vipersci.vis.create_tif:main
 	vis_create_raw = vipersci.vis.pds.create_raw:main
 	vis_create_dbs = vipersci.vis.db.create_vis_dbs:main
-    vis_pano_check = vipersci.vis.pano_check:main
+	vis_pano_check = vipersci.vis.pano_check:main
 	viseer = vipersci.vis.viseer:main
 
 [bdist_wheel]

src/vipersci/__init__.py

@@ -2,4 +2,4 @@
 
 __author__ = """vipersci Developers"""
 __email__ = "[email protected]"
-__version__ = "0.7.0-dev"
+__version__ = "0.7.0"

src/vipersci/carto/colorforge.py

@@ -295,8 +295,7 @@ def example_plot(palette: Palette, output=None):
     x = np.arange(-3.0, 3.0, dx)
     x_grid, y_grid = np.meshgrid(x, x)
     z = rescale(
-        (1 - x_grid / 2 + x_grid**5 + y_grid**3)
-        * np.exp(-(x_grid**2 + y_grid**2)),
+        (1 - x_grid / 2 + x_grid**5 + y_grid**3) * np.exp(-(x_grid**2 + y_grid**2)),
         palette.vmin,
         palette.vmax,
     )

src/vipersci/carto/traverse_interpolator.py

@@ -49,7 +49,7 @@ def arg_parser():
     parser.add_argument(
         "json",
         type=Path,
-        help="The JSON file that contains a traverse."
+        help="The JSON file that contains a traverse.",
         # Assumed to be GeoJSON from the Map Server.
     )
 

src/vipersci/pds/labelmaker/__init__.py

@@ -83,41 +83,58 @@ def get_common_label_info(element: ET.Element, area="pds:Observation_Area"):
     d = {
         "lid": lid,
         "vid": find_text(element, "./pds:Identification_Area/pds:version_id"),
-        "start_date_time": None
-        if area is None
-        else fromisozformat(
-            find_text(element, f"./{area}/pds:Time_Coordinates/pds:start_date_time")
+        "start_date_time": (
+            None
+            if area is None
+            else fromisozformat(
+                find_text(element, f"./{area}/pds:Time_Coordinates/pds:start_date_time")
+            )
+        ),
+        "stop_date_time": (
+            None
+            if area is None
+            else fromisozformat(
+                find_text(element, f"./{area}/pds:Time_Coordinates/pds:stop_date_time")
+            )
+        ),
+        "investigation_name": (
+            None
+            if area is None
+            else find_text(element, f"./{area}/pds:Investigation_Area/pds:name")
         ),
-        "stop_date_time": None
-        if area is None
-        else fromisozformat(
-            find_text(element, f"./{area}/pds:Time_Coordinates/pds:stop_date_time")
+        "investigation_type": (
+            None
+            if area is None
+            else find_text(element, f"./{area}/pds:Investigation_Area/pds:type")
         ),
-        "investigation_name": None
-        if area is None
-        else find_text(element, f"./{area}/pds:Investigation_Area/pds:name"),
-        "investigation_type": None
-        if area is None
-        else find_text(element, f"./{area}/pds:Investigation_Area/pds:type"),
-        "investigation_lid": None
-        if area is None
-        else find_text(
-            element,
-            f"./{area}/pds:Investigation_Area/pds:Internal_Reference/pds:lid_reference",
+        "investigation_lid": (
+            None
+            if area is None
+            else find_text(
+                element,
+                f"./{area}/pds:Investigation_Area/pds:Internal_Reference/"
+                "pds:lid_reference",
+            )
         ),
         "host_name": host_name,
         "host_lid": host_lid,
-        "target_name": None
-        if area is None
-        else find_text(element, ".//pds:Target_Identification/pds:name"),
-        "target_type": None
-        if area is None
-        else find_text(element, ".//pds:Target_Identification/pds:type"),
-        "target_lid": None
-        if area is None
-        else find_text(
-            element,
-            ".//pds:Target_Identification/pds:Internal_Reference/pds:lid_reference",
+        "target_name": (
+            None
+            if area is None
+            else find_text(element, ".//pds:Target_Identification/pds:name")
+        ),
+        "target_type": (
+            None
+            if area is None
+            else find_text(element, ".//pds:Target_Identification/pds:type")
+        ),
+        "target_lid": (
+            None
+            if area is None
+            else find_text(
+                element,
+                ".//pds:Target_Identification/pds:Internal_Reference/pds:lid_reference",
+            )
         ),
         "instruments": instruments,
         "purposes": purposes,

src/vipersci/vis/create_image.py

@@ -41,6 +41,7 @@
 
 import numpy as np
 import numpy.typing as npt
+from PIL import Image
 from PIL.PngImagePlugin import PngInfo
 from skimage.io import imread, imsave  # maybe just imageio here?
 from skimage.util import img_as_ubyte, img_as_uint
@@ -143,7 +144,7 @@
     outdir: Path = Path.cwd(),
     session: Optional[Session] = None,
     json: bool = True,
-    png: bool = False,
+    imgtype="tif",
 ):
     """
     Creates a TIFF file / JSON file pair in *outdir* based on the provided
@@ -171,7 +172,7 @@
     # db insert (otherwise the outfile-writing would need to happen in the
     # context of the session).  However, if the db insert fails, the files
     # already exist on disk.  Is that a problem?  Maybe that's fine?
-    rp = make_image_record(metadata, image, outdir, png)
+    rp = make_image_record(metadata, image, outdir, imgtype)
 
     if json:
         write_json(rp.asdict(), outdir)
@@ -227,35 +228,46 @@
     metadata: dict,
     image: Union[ImageType, Path, None] = None,
     outdir: Path = Path.cwd(),
-    make_png=False,
+    imgtype="tif",
 ) -> ImageRecord:
     """
     Returns an ImageRecord created from the provided meta-data, and
-    if *image* is a numpy array, it will also use write_tiff() to
-    create a TIFF file in *outdir* (defaults to current
-    working directory).
+    if *image* is a numpy array, it will write out an image file
+    in TIFF format (default or if *imgtype* is "tif") or PNG format
+    (if *imgtype* is "png") in *outdir* (defaults to current
+    working directory).  The *imgtype* is ignored if *image* is
+    a Path to an existing image file.
     """
     ir = ImageRecord(**metadata)
     pid = pds.VISID(ir.product_id)
 
     if image is not None:
         if isinstance(image, Path):
-            tif_d = tif_info(image)
+            if image.suffix.casefold() in (".tif", ".tiff"):
+                img_d = tif_info(image)
+            elif image.suffix.casefold() == ".png":
+                img_d = png_info(image)
+            else:
+                raise ValueError(f"Don't know how to evaluate {image}")
         else:
-            tif_d = tif_info(write_tiff(pid, image, outdir))
-            if make_png:
-                write_png(pid, image, outdir)
+            if imgtype.casefold() == "tif":
+                img_d = tif_info(write_tiff(pid, image, outdir))
+            elif imgtype.casefold() == "png":
+                img_d = png_info(write_png(pid, image, outdir))
+            else:
+                raise ValueError(f"The value {imgtype} is not a recognized imgtype.")
 
         for k in ("lines", "samples"):
-            if getattr(ir, k) != tif_d[k]:
+            if getattr(ir, k) != img_d[k]:
                 raise ValueError(
-                    f"The value of {k} from the TIFF ({tif_d[k]}) does not "
+                    f"The value of {k} from the image ({img_d[k]}) does not "
                     f"match the value from the metadata ({getattr(ir, k)})"
                 )
 
-        check_bit_depth(pid, tif_d["file_data_type"])
+        if "file_data_type" in img_d:
+            check_bit_depth(pid, img_d["file_data_type"])
 
-        ir.update(tif_d)
+        ir.update(img_d)
     else:
         ir.update(
             {
@@ -278,13 +290,41 @@
     return ir
 
 
+def file_info(p: Path) -> dict:
+    """
+    Returns a dict containing meta-data from a file at the provided path, *p*.
+    """
+    dt = datetime.fromtimestamp(p.stat().st_mtime, timezone.utc)
+
+    d = {
+        "file_creation_datetime": dt,
+        "file_md5_checksum": util.md5(p),
+        "file_path": p.name,
+    }
+    return d
+
+
+def png_info(p: Path) -> dict:
+    """
+    Returns a dict containing meta-data from the PNG file at the
+    provided path, *p*.
+    """
+    im = Image.open(p)
+
+    d = {
+        # "file_data_type": f"Unsigned{dt_end}",
+        "lines": im.size[1],
+        "samples": im.size[0],
+    }
+    d.update(file_info(p))
+    return d
+
+
 def tif_info(p: Path) -> dict:
     """
     Returns a dict containing meta-data from the TIFF file at the
     provided path, *p*.
     """
-    dt = datetime.fromtimestamp(p.stat().st_mtime, timezone.utc)
-
     info = read_tiff(str(p))
     tags = info["ifds"][0]["tags"]
 
@@ -300,13 +340,11 @@
 
     d = {
         "file_byte_offset": tags[273]["data"][0],  # Tag 273 is StripOffsets
-        "file_creation_datetime": dt,
         "file_data_type": f"Unsigned{dt_end}",
-        "file_md5_checksum": util.md5(p),
-        "file_path": p.name,
         "lines": tags[257]["data"][0],  # Tag 257 is ImageWidth,
         "samples": tags[256]["data"][0],  # Tag 256 is ImageWidth,
     }
+    d.update(file_info(p))
     return d
 
 
@@ -361,5 +399,5 @@
     logger.debug(desc)
     outpath = (outdir / str(pid)).with_suffix(".png")
 
-    imsave(str(outpath), image, check_contrast=False, pnginfo=info, compress_level=0)
+    imsave(str(outpath), image, check_contrast=False, pnginfo=info)
     return outpath

src/vipersci/vis/db/image_records.py

@@ -127,7 +127,7 @@ class ImageRecord(Base):
     capture_id = mapped_column(
         Integer,
         nullable=False,
-        doc="The captureId from the command sequence."
+        doc="The captureId from the command sequence.",
         # TODO: learn more about captureIds to provide better doc here.
     )
     captureId = synonym("capture_id")
@@ -284,7 +284,7 @@ class ImageRecord(Base):
     stereo = mapped_column(
         Boolean,
         nullable=False,
-        doc="The stereo parameter from the Yamcs imageHeader."
+        doc="The stereo parameter from the Yamcs imageHeader.",
         # TODO: learn more about stereo to provide better doc here.
     )
     stop_time = mapped_column(DateTime(timezone=True), nullable=False)

src/vipersci/vis/pds/create_browse.py

@@ -96,9 +96,9 @@
         parser.error(str(err))
 
     metadata["source_lidvid"] = metadata["lid"] + "::" + metadata["vid"]
-    metadata[
-        "source_product_type"
-    ] = f"data_to_{metadata['type'].lower()}_source_product"
+    metadata["source_product_type"] = (
+        f"data_to_{metadata['type'].lower()}_source_product"
+    )
 
     # Adjust LID
     lid_tokens = metadata["lid"].split(":")