Merge pull request #87 from bayer-science-for-a-better-life/fix-m1-jv…

…m-issue

Fix m1 jvm issue

paquo/.paquo.defaults.toml

@@ -31,6 +31,8 @@ java_opts = [
 # paquo options
 safe_truncate = true
 
+# allows to use a different jvm_path for running qupath
+jvm_path_override = ""
 
 # internal settings
 # -----------------

paquo/images.py

@@ -136,7 +136,7 @@ def uri(self, image_id: SimpleFileImageId) -> Optional['URIString']:
         """accepts a path and returns a URIString"""
         if not isinstance(image_id, (Path, str, ImageProvider.FilenamePathId)):
             raise TypeError("image_id not of correct format")  # pragma: no cover
-        if isinstance(image_id, str) and "://" in image_id:
+        if isinstance(image_id, str) and image_id.startswith("file:/"):
             # image_id is uri
             image_id = _normalize_pathlib_uris(image_id)
             return ImageProvider.URIString(image_id)

paquo/jpype_backend.py

@@ -3,6 +3,7 @@
 import re
 import shlex
 import sys
+import textwrap
 from contextlib import contextmanager
 from contextlib import nullcontext
 from itertools import chain
@@ -14,8 +15,8 @@
 from typing import Dict
 from typing import Iterable
 from typing import List
+from typing import NamedTuple
 from typing import Optional
-from typing import Tuple
 from typing import Union
 from warnings import warn
 
@@ -25,20 +26,27 @@
 
 # types
 PathOrStr = Union[Path, str]
-QuPathJVMInfo = Tuple[Path, Path, Path, List[str]]
 
 __all__ = ["JClass", "start_jvm", "find_qupath"]
 
 JClass = jpype.JClass
 
 
+class QuPathJVMInfo(NamedTuple):
+    app_dir: Path
+    runtime_dir: Path
+    jvm_path: Path
+    jvm_options: List[str]
+
+
 def find_qupath(*,
                 qupath_dir: Optional[PathOrStr] = None,
                 qupath_search_dirs: Optional[Union[PathOrStr, List[PathOrStr]]] = None,
                 qupath_search_dir_regex: Optional[str] = None,
                 qupath_search_conda: Optional[bool] = None,
                 qupath_prefer_conda: Optional[bool] = None,
                 java_opts: Optional[Union[List[str], str]] = None,
+                jvm_path_override: Optional[PathOrStr] = None,
                 **_kwargs) -> QuPathJVMInfo:
     """find current qupath installation and jvm paths/options
 
@@ -55,12 +63,24 @@ def find_qupath(*,
     elif isinstance(java_opts, str):
         java_opts = shlex.split(java_opts)
 
+    if jvm_path_override:
+        jvm_path_override = Path(jvm_path_override)
+        if not jvm_path_override.exists():
+            raise FileNotFoundError(jvm_path_override)
+        if jvm_path_override.is_dir():
+            raise IsADirectoryError(jvm_path_override)
+    else:
+        jvm_path_override = None
+
     if qupath_dir:
         # short circuit in case we provide a qupath_dir
         # --> when qupath_dir is provided, search is disabled
         if isinstance(qupath_dir, str):
             qupath_dir = Path(qupath_dir)
-        return qupath_jvm_info_from_qupath_dir(qupath_dir, java_opts)
+        info = qupath_jvm_info_from_qupath_dir(qupath_dir, java_opts)
+        if jvm_path_override:
+            return info._replace(jvm_path=jvm_path_override)
+        return info
 
     if qupath_search_dirs is None:
         qupath_search_dirs = []
@@ -80,9 +100,13 @@ def find_qupath(*,
 
     for qupath_dir in search_dirs:
         try:
-            return qupath_jvm_info_from_qupath_dir(qupath_dir, java_opts)
+            info = qupath_jvm_info_from_qupath_dir(qupath_dir, java_opts)
         except FileNotFoundError:
             continue
+        else:
+            if jvm_path_override:
+                return info._replace(jvm_path=jvm_path_override)
+            return info
     else:
         raise ValueError("no valid qupath installation found")
 
@@ -121,30 +145,30 @@ def qupath_jvm_info_from_qupath_dir(qupath_dir: Path, jvm_options: List[str]) ->
     if system == "Linux":
         app_dir = qupath_dir / "lib" / "app"
         runtime_dir = qupath_dir / "lib" / "runtime"
-        jvm_dir = runtime_dir / "lib" / "server" / "libjvm.so"
+        jvm_path = runtime_dir / "lib" / "server" / "libjvm.so"
 
     elif system == "Darwin":
         app_dir = qupath_dir / "Contents" / "app"
         runtime_dir = qupath_dir / "Contents" / "runtime" / "Contents" / "Home"
-        jvm_dir = runtime_dir / "lib" / "libjli.dylib"  # not server/libjvm.dylib
+        jvm_path = runtime_dir / "lib" / "libjli.dylib"  # not server/libjvm.dylib
 
     elif system == "Windows":
         app_dir = qupath_dir / "app"
         runtime_dir = qupath_dir / "runtime"
-        jvm_dir = runtime_dir / "bin" / "server" / "jvm.dll"
+        jvm_path = runtime_dir / "bin" / "server" / "jvm.dll"
 
     else:  # pragma: no cover
         raise ValueError(f'Unknown platform {system}')
 
     # verify that paths are sane
-    if not (app_dir.is_dir() and runtime_dir.is_dir() and jvm_dir.is_file()):
+    if not (app_dir.is_dir() and runtime_dir.is_dir() and jvm_path.is_file()):
         raise FileNotFoundError('qupath installation is incompatible')
 
     # Add java.library.path so that the qupath provided openslide works
     jvm_options.append(f"-Djava.library.path={app_dir}")
     jvm_options = list(dict.fromkeys(jvm_options))  # keep options unique and in order
 
-    return app_dir, runtime_dir, jvm_dir, jvm_options
+    return QuPathJVMInfo(app_dir, runtime_dir, jvm_path, jvm_options)
 
 
 # stores qupath version to handle consecutive calls to start_jvm
@@ -226,6 +250,30 @@ def is_windows_store_python() -> bool:
                 ignoreUnrecognized=False,
                 convertStrings=False
             )
+        except OSError as err:
+            if (
+                err.errno == 0
+                and "JVM DLL not found:" in str(err)
+                and jvm_path.is_file()
+                and platform.uname().machine == "arm64"
+            ):
+                msg = textwrap.dedent("""\
+                Probably a JVM and Python architecture issue on M1:
+                You can fix this by running a JVM with the same architecture as your
+                Python interpreter. Usually paquo uses the JVM that ships with QuPath,
+                but you can override this by setting 'jvm_path_override' in `.paquo.toml`
+
+                In case you are running an arm64 Python interpreter on your mac try
+                installing an arm jvm from
+                https://www.azul.com/downloads/?version=java-17-lts&os=macos&architecture=arm-64-bit&package=jdk
+                ```
+                $ cat .paquo.toml
+                # use the path to libjli.dylib valid on your machine:
+                jvm_path_override = "/Library/Java/JavaVirtualMachines/zulu-17.jdk/Contents/Home/lib/libjli.dylib"
+                ```
+                If this doesn't work, please open an issue on github.
+                """)
+                raise RuntimeError(msg) from err
         except RuntimeError as jvm_error:  # pragma: no cover
             # there's a chance that this RuntimeError occurred because a user provided
             # jvm_option is incorrect. let's try if that is the case and crash with a

paquo/tests/test_images.py

@@ -74,6 +74,10 @@ def test_image_properties_from_image_server(image_entry):
     assert image_entry.num_z_slices == 1
 
 
+@pytest.mark.xfail(
+    platform.uname().machine == "arm64",
+    reason="QuPath-vendored openslide not working on arm64"
+)
 def test_image_downsample_levels(image_entry):
     levels = [
         {'downsample': 1.0,