v2.5.8

Author: fbordignon

src/ltrace/ltrace/remote/handlers/InstanceSegmenterHandler.py

@@ -3,7 +3,7 @@
 import re
 import shutil
 from datetime import datetime
-from pathlib import Path, PurePosixPath, WindowsPath
+from pathlib import Path, PurePosixPath
 from typing import Any, Callable
 
 import numpy as np
@@ -21,7 +21,7 @@
     generateName,
     separateLabelmapVolumeIntoSlices,
     maskInputWithROI,
-    LazyLoad2
+    LazyLoad2,
 )
 
 ThinSectionInstanceSegmenter = LazyLoad2("ThinSectionInstanceSegmenter.ThinSectionInstanceSegmenter")
@@ -30,7 +30,7 @@
 
 class ThinSectionInstanceSegmenterExecutionHandler:
     REMOTE_DIR = PurePosixPath("/nethome/drp")
-    NFS_DIR = WindowsPath("\\\\dfs.petrobras.biz\\cientifico\\cenpes\\res\\drp")
+    NFS_DIR = Path(r"\\dfs.petrobras.biz\cientifico\cenpes\res\drp")
 
     job_id_pattern = re.compile("job_id = ([a-zA-Z0-9]+)")
 
@@ -386,7 +386,9 @@ def __call__(self, results):
                         helpers.updateSegmentationFromLabelMap(outNode, labelmapVolumeNode=node)
                         Segmenter.revertColorTable(invmap, outNode)
 
-                        Segmenter.setupResultInScene(outNode, referenceNode, None, croppedReferenceNode=tmpReferenceNode)
+                        Segmenter.setupResultInScene(
+                            outNode, referenceNode, None, croppedReferenceNode=tmpReferenceNode
+                        )
                         outNode.GetDisplayNode().SetVisibility(True)
 
                         slicer.mrmlScene.RemoveNode(node)
@@ -441,4 +443,4 @@ def __call__(self, results):
         except Exception as e:
             tmpPrefix = outputPrefix.replace("LabelMap.nrrd", "TMP_*")
             clearPattern(tmpPrefix)
-            raise
+            raise

src/ltrace/ltrace/remote/handlers/PUCModelExecutionHandler.py

@@ -2,7 +2,7 @@
 import shutil
 from typing import Any, Callable
 import re
-from pathlib import Path, PurePosixPath, WindowsPath
+from pathlib import Path, PurePosixPath
 
 import slicer
 
@@ -14,7 +14,7 @@
 class PUCModelExecutionHandler:
     REMOTE_DIR = PurePosixPath("/nethome/drp")
     # TODO handle linux cases
-    NFS_DIR = WindowsPath("\\\\dfs.petrobras.biz\\cientifico\\cenpes\\res\\drp")
+    NFS_DIR = Path(r"\\dfs.petrobras.biz\cientifico\cenpes\res\drp")
 
     job_id_pattern = re.compile("job_id = ([a-zA-Z0-9]+)")
 

src/ltrace/ltrace/remote/handlers/__init__.py

@@ -1,2 +1,2 @@
 from .OneResultSlurm import OneResultSlurmHandler
-from .MonaiLabelServerHandler import MonaiLabelServerHandler
+from .MonaiLabelServerHandler import MonaiLabelServerHandler

src/ltrace/ltrace/remote/jobs.py

@@ -21,6 +21,7 @@ class JobManager:
     worker: Thread = None
     endstates = set(("FAILED", "CANCELLED", "IDLE", "DONE"))
     compilers = {}
+    keep_working: bool = True
 
     read_lock = Lock()
 
@@ -38,7 +39,9 @@ def mount(cls, job: JobExecutor):
         except Exception as e:
             logging.error(f"Failed to mount job {job.uid}. Cause: {repr(e)}")
 
-        return job
+    @staticmethod
+    def keepWorking():
+        return JobManager.keep_working
 
     @classmethod
     def register(cls, key: str, compiler: Callable):
@@ -281,7 +284,7 @@ def loadjson(path: Path):
 
 def start_monitor():
     def jobspy():
-        while True:
+        while JobManager.keepWorking():
             try:
                 uid, event = JobManager.agenda.get()
                 JobManager.communicate(uid, event)

src/ltrace/ltrace/slicer/helpers.py

@@ -2350,6 +2350,7 @@ def __getattr__(self, name):
 
         return getattr(self.module, name)
 
+
 def checkUniqueNames(nodes):
     nodeNames = set()
     for node in nodes:

src/ltrace/ltrace/slicer/project_manager.py

@@ -359,23 +359,22 @@ def __hasWriteAccess(self, path: Path) -> bool:
         except (PermissionError, IOError):
             return False
 
-    def getWritableStorageInfo(self, userHome: Path) -> int:
+    def getWritableStorageInfo(self, storageDestination: Path) -> int:
         """Get writable storage information for the user home directory."""
 
-        if self.__hasWriteAccess(userHome):
-            usage = psutil.disk_usage(userHome.as_posix())
+        if self.__hasWriteAccess(storageDestination):
+            usage = psutil.disk_usage(storageDestination.as_posix())
             return usage.free
         else:
-            logging.error(f"Warning: No write access to {userHome}!")
+            logging.error(f"Warning: No write access to {storageDestination}!")
             return 0
 
     def __validateProjectIsWritable(self, scenePath: str) -> bool:
         """Checks if project can be written and if has enough space for expected files sizes"""
         try:
-            userHomeDirectory = Path.home()
-            hdSize = self.getWritableStorageInfo(userHomeDirectory)
+            hdSize = self.getWritableStorageInfo(Path(scenePath).parent)
             sceneSize = self.__listAllStorableNodes(scenePath)
-
+            print(f"hdSize: {hdSize}, sceneSize: {sceneSize}", scenePath)
             if hdSize <= sceneSize:
                 logging.error(
                     f"Not enough space in drive ({naturalsize(hdSize)}) for scene ({naturalsize(sceneSize)})."

src/ltrace/ltrace/slicer/widget/help_button.py

@@ -7,17 +7,26 @@
 from ltrace.slicer_utils import getResourcePath
 import re
 
+
 def is_url(url: str) -> bool:
     if url is None:
         return False
 
     return re.match(r"^(?:https|file)s?://", url) is not None
 
+
 class HelpButton(qt.QToolButton):
 
     DEFAULT_URL = (getResourcePath("manual") / "index.html").as_posix()
 
-    def __init__(self, message: str = None, url: str = None, replacer: typing.Union[None, typing.Callable] = None, *args, **kwargs) -> None:
+    def __init__(
+        self,
+        message: str = None,
+        url: str = None,
+        replacer: typing.Union[None, typing.Callable] = None,
+        *args,
+        **kwargs,
+    ) -> None:
         super().__init__(*args, **kwargs)
 
         if not is_url(url):

src/modules/AppContext/AppContext.py

@@ -205,7 +205,6 @@ def __init__(self, projectManager):
         self.nodeAddedObserverHandler = None
 
     def __del__(self):
-        super().__del__()
         slicer.mrmlScene.RemoveObserver(self.startCloseSceneObserverHandler)
         slicer.mrmlScene.RemoveObserver(self.endCloseSceneObserverHandler)
         slicer.mrmlScene.RemoveObserver(self.nodeAddedObserverHandler)

src/modules/ImageLogCustomSegmenter/ImageLogCustomSegmenter.py

@@ -342,6 +342,3 @@ def dispatch(self, image, coi: str, depthInterval: typing.Iterable[np.uint32], o
         job_name = f"segmentation: {outputPrefix} ({coi}, {depthInterval})"
 
         slicer.modules.RemoteServiceInstance.cli.run(cmd_handler, name=job_name, job_type="pucnet")
-
-
-

src/modules/ImageLogCustomSegmenter/ImageLogCustomSegmenterRemoteTask/PUCModelExecutionHandler.py

@@ -2,7 +2,7 @@
 import shutil
 from typing import Any, Callable
 import re
-from pathlib import Path, PurePosixPath, WindowsPath
+from pathlib import Path, PurePosixPath
 
 import slicer
 
@@ -14,7 +14,7 @@
 class PUCModelExecutionHandler:
     REMOTE_DIR = PurePosixPath("/nethome/drp")
     # TODO handle linux cases
-    NFS_DIR = WindowsPath("\\\\dfs.petrobras.biz\\cientifico\\cenpes\\res\\drp")
+    NFS_DIR = Path(r"\\dfs.petrobras.biz\cientifico\cenpes\res\drp")
 
     job_id_pattern = re.compile("job_id = ([a-zA-Z0-9]+)")