admin/prepare-bioformats_reader-to-work-with-new-bioformats_jar-based-on-scyjava

README.md

@@ -55,8 +55,10 @@ optionally installed using `[...]` syntax.
 -   For multiple additional supported formats: `pip install aicsimageio[base-imageio,nd2]`
 -   For all additional supported (and openly licensed) formats: `pip install aicsimageio[all]`
 -   Due to the GPL license, LIF support is not included with the `[all]` extra, and must be installed manually with `pip install aicsimageio readlif>=0.6.4`
--   Due to the GPL license, Bio-Formats support is not included with the `[all]` extra, and must be installed manually with `pip install aicsimageio bioformats_jar`
 -   Due to the GPL license, CZI support is not included with the `[all]` extra, and must be installed manually with `pip install aicsimageio aicspylibczi>=3.0.5`
+-   Due to the GPL license, Bio-Formats support is not included with the `[all]` extra, and must be installed manually with `pip install aicsimageio bioformats_jar`.
+
+    **Important!!** Bio-Formats support also requires a `java` executable in the environment. The simplest method is to install `bioformats_jar` from conda: `conda install -c conda-forge bioformats_jar` (which will additionally bring `openjdk`).
 
 ## Documentation
 

aicsimageio/readers/bioformats_reader.py

@@ -24,6 +24,7 @@
 from .reader import Reader
 
 if TYPE_CHECKING:
+    from bioformats_jar import _loci
     from fsspec.spec import AbstractFileSystem
 
     from .. import types
@@ -32,21 +33,27 @@
 try:
     import jpype
     from bioformats_jar import get_loci
-except ImportError:
+except ImportError as e:
     raise ImportError(
         "bioformats_jar is required for this reader. "
-        "Install with `pip install bioformats_jar`"
-    )
+        "Install with `pip install bioformats_jar` or `conda install bioformats_jar`"
+    ) from e
+try:
+    from jgo.jgo import ExecutableNotFound
+except ImportError:
+
+    class ExecutableNotFound(Exception):  # type: ignore
+        ...
 
 
 class BioformatsReader(Reader):
     """Read files using bioformats.
 
     This reader requires `bioformats_jar` to be installed in the environment, and
-    requires the java executable to be available on the path, or via the JAVA_HOME
-    environment variable.
+    requires the java executable to be available on the path (or via the JAVA_HOME
+    environment variable), along with the `mvn` executable.
 
-    To install java with conda, run `conda install -c conda-forge openjdk`.
+    To install java and maven with conda, run `conda install -c conda-forge scyjava`.
     You may need to deactivate/reactivate your environment after installing.  If you
     are *still* getting a `JVMNotFoundException`, try setting JAVA_HOME as follows:
 
@@ -84,6 +91,7 @@ class BioformatsReader(Reader):
     tile_size: Optional[Tuple[int, int]]
         Tuple that sets the tile size of y and x axis, respectively
         By default, it will use optimal values computed by bioformats itself
+
     Raises
     ------
     exceptions.UnsupportedFileFormatError
@@ -133,12 +141,12 @@ def __init__(
                 self._scenes: Tuple[str, ...] = tuple(
                     str(md.getImageName(i)) for i in range(md.getImageCount())
                 )
-        except jpype.JVMNotFoundException:
+        except RuntimeError:
             raise
-        except Exception:
+        except Exception as e:
             raise exceptions.UnsupportedFileFormatError(
                 self.__class__.__name__, self._path
-            )
+            ) from e
 
     @property
     def scenes(self) -> Tuple[str, ...]:
@@ -198,9 +206,7 @@ def _to_xarray(self, delayed: bool = True) -> xr.DataArray:
     @staticmethod
     def bioformats_version() -> str:
         """The version of the bioformats_package.jar being used."""
-        from bioformats_jar import get_loci
-
-        return get_loci().__version__
+        return _try_get_loci().__version__
 
 
 class CoreMeta(NamedTuple):
@@ -280,20 +286,7 @@ def __init__(
         dask_tiles: bool = False,
         tile_size: Optional[Tuple[int, int]] = None,
     ):
-        try:
-            loci = get_loci()
-        except jpype.JVMNotFoundException as e:
-            raise type(e)(
-                str(e) + "\n\nBioformatsReader requires a java executable to be "
-                "available in your environment. If you are using conda, you can "
-                "install with `conda install -c conda-forge openjdk`.\n\n"
-                "Note: you may need to reactivate your conda environment after "
-                "installing opendjk. If you still have this error, try:\n\n"
-                "# mac and linux:\n"
-                "export JAVA_HOME=$CONDA_PREFIX\n\n"
-                "# windows:\n"
-                "set JAVA_HOME=%CONDA_PREFIX%\\Library"
-            )
+        loci = _try_get_loci()  # may raise RuntimeError
 
         self._path = str(path)
         self._r = loci.formats.ImageReader()
@@ -533,9 +526,7 @@ def _dask_chunk(self, block_id: Tuple[int, ...]) -> np.ndarray:
     @classmethod
     def _create_ome_meta(cls) -> Any:
         """create an OMEXMLMetadata object to populate"""
-        from bioformats_jar import get_loci
-
-        loci = get_loci()
+        loci = _try_get_loci()
         if not cls._service:
             factory = loci.common.services.ServiceFactory()
             cls._service = factory.getInstance(loci.formats.services.OMEXMLService)
@@ -544,9 +535,7 @@ def _create_ome_meta(cls) -> Any:
 
 def _pixtype2dtype(pixeltype: int, little_endian: bool) -> np.dtype:
     """Convert a loci.formats PixelType integer into a numpy dtype."""
-    from bioformats_jar import get_loci
-
-    FT = get_loci().formats.FormatTools
+    FT = _try_get_loci().formats.FormatTools
     fmt2type: Dict[int, str] = {
         FT.INT8: "i1",
         FT.UINT8: "u1",
@@ -617,3 +606,36 @@ def _hide_memoization_warning() -> None:
 
     System = jpype.JPackage("java").lang.System
     System.err.close()
+
+
+MAVEN_ERROR_MSG = """
+BioformatsReader requires the maven ('mvn') executable to be
+available in your environment. If you are using conda, you can 
+install with `conda install -c conda-forge scyjava`.
+
+Alternatively, install from https://maven.apache.org/download.cgi
+"""
+
+JAVA_ERROR_MSG = """
+BioformatsReader requires a java executable to be available
+in your environment. If you are using conda, you can install
+with `conda install -c conda-forge scyjava`.
+
+Note: you may need to reactivate your conda environment after 
+installing opendjk. If you still have this error, try:
+
+# mac and linux:
+export JAVA_HOME=$CONDA_PREFIX
+
+# windows:
+set JAVA_HOME=%CONDA_PREFIX%\\Library
+"""
+
+
+def _try_get_loci() -> _loci.__module_protocol__:
+    try:
+        return get_loci()
+    except ExecutableNotFound as e:
+        raise RuntimeError(MAVEN_ERROR_MSG) from e
+    except jpype.JVMNotFoundException as e:
+        raise RuntimeError(JAVA_ERROR_MSG) from e

aicsimageio/tests/readers/extra_readers/test_bioformats_reader.py

@@ -16,6 +16,15 @@
 
 from ...conftest import LOCAL, get_resource_full_path, host
 
+try:
+    bfj = pytest.importorskip("bioformats_jar")
+    bf_version = tuple(int(x) for x in str(bfj.__version__).split(".")[:2])
+except Exception:
+    bf_version = (6, 7)
+
+# bioformats changed their DICOM scene labeling scheme at some point
+SERIES_0 = "PRIMARY" if bf_version > (6, 7) else "Series 0"
+
 
 @host
 @pytest.mark.parametrize(
@@ -209,8 +218,8 @@
         ),
         (
             "DICOM_samples_MR-MONO2-8-16x-heart.dcm",
-            "Series 0",
-            ("Series 0",),
+            SERIES_0,
+            (SERIES_0,),
             (1, 1, 16, 256, 256),
             np.uint8,
             dimensions.DEFAULT_DIMENSION_ORDER,

setup.cfg

@@ -29,6 +29,7 @@ xfail_strict = true
 filterwarnings = 
 	ignore::UserWarning
 	ignore::FutureWarning
+	ignore:distutils Version classes are deprecated:
 addopts = -p no:faulthandler
 
 [flake8]

setup.py

@@ -85,7 +85,7 @@ def run(self):
     "wheel>=0.34.2",
     # reader deps
     *all_formats,
-    "bioformats_jar",  # to test bioformats
+    "bioformats_jar @ git+ssh://[email protected]/tlambert03/bioformats_jar.git#egg=bioformats_jar",  # to test bioformats
     "bfio>=2.3.0",
     "readlif>=0.6.4",  # to test lif
     "aicspylibczi>=3.0.5",  # to test czi