tomwer 1.3.0.dev2__py3-none-any.whl → 1.3.0rc10__py3-none-any.whl

tomwer/core/test/test_utils.py

@@ -279,8 +279,8 @@ class TestMockNXtomo(unittest.TestCase):
             n_ini_proj=20,
             n_alignement_proj=2,
             create_ini_dark=True,
-            create_ini_ref=True,
-            create_final_ref=True,
+            create_ini_flat=True,
+            create_final_flat=True,
             n_refs=10,
         )
         self.assertTrue(0 in mock.scan.darks.keys())

tomwer/core/volume/edfvolume.py

@@ -86,11 +86,11 @@ class EDFVolume(_EDFVolume, TomwerVolumeBase, Dataset):
             file_prefix=self._volume_basename,
             metadata={
                 "name": self.url.file_path(),
-                "creation_time": datetime.fromtimestamp(stat.st_ctime)
-                if stat
-                else None,
-                "modification_time": datetime.fromtimestamp(stat.st_ctime)
-                if stat
-                else None,
+                "creation_time": (
+                    datetime.fromtimestamp(stat.st_ctime) if stat else None
+                ),
+                "modification_time": (
+                    datetime.fromtimestamp(stat.st_ctime) if stat else None
+                ),
             },
         )

tomwer/core/volume/hdf5volume.py

@@ -103,11 +103,11 @@ class HDF5Volume(_HDF5Volume, TomwerVolumeBase, Dataset):
             entry=self.url.data_path(),
             metadata={
                 "name": self.url.file_path(),
-                "creation_time": datetime.fromtimestamp(stat.st_ctime)
-                if stat
-                else None,
-                "modification_time": datetime.fromtimestamp(stat.st_ctime)
-                if stat
-                else None,
+                "creation_time": (
+                    datetime.fromtimestamp(stat.st_ctime) if stat else None
+                ),
+                "modification_time": (
+                    datetime.fromtimestamp(stat.st_ctime) if stat else None
+                ),
             },
         )

tomwer/core/volume/jp2kvolume.py

@@ -87,11 +87,11 @@ class JP2KVolume(_JP2KVolume, TomwerVolumeBase, Dataset):
             file_prefix=self._volume_basename,
             metadata={
                 "name": self.url.file_path(),
-                "creation_time": datetime.fromtimestamp(stat.st_ctime)
-                if stat
-                else None,
-                "modification_time": datetime.fromtimestamp(stat.st_ctime)
-                if stat
-                else None,
+                "creation_time": (
+                    datetime.fromtimestamp(stat.st_ctime) if stat else None
+                ),
+                "modification_time": (
+                    datetime.fromtimestamp(stat.st_ctime) if stat else None
+                ),
             },
         )

tomwer/core/volume/rawvolume.py

@@ -97,11 +97,11 @@ class RawVolume(_RawVolume, TomwerVolumeBase, Dataset):
             file_path=self.url.file_path(),
             metadata={
                 "name": self.url.file_path(),
-                "creation_time": datetime.fromtimestamp(stat.st_ctime)
-                if stat
-                else None,
-                "modification_time": datetime.fromtimestamp(stat.st_ctime)
-                if stat
-                else None,
+                "creation_time": (
+                    datetime.fromtimestamp(stat.st_ctime) if stat else None
+                ),
+                "modification_time": (
+                    datetime.fromtimestamp(stat.st_ctime) if stat else None
+                ),
             },
         )

tomwer/core/volume/tiffvolume.py

@@ -103,12 +103,12 @@ class TIFFVolume(_TIFFVolume, TomwerVolumeBase, Dataset):
             file_prefix=self._volume_basename,
             metadata={
                 "name": self.url.file_path(),
-                "creation_time": datetime.fromtimestamp(stat.st_ctime)
-                if stat
-                else None,
-                "modification_time": datetime.fromtimestamp(stat.st_ctime)
-                if stat
-                else None,
+                "creation_time": (
+                    datetime.fromtimestamp(stat.st_ctime) if stat else None
+                ),
+                "modification_time": (
+                    datetime.fromtimestamp(stat.st_ctime) if stat else None
+                ),
             },
         )
 
@@ -145,12 +145,12 @@ class MultiTIFFVolume(_MultiTIFFVolume, TomwerVolumeBase, Dataset):
             tiff_file=self.url.file_path(),
             metadata={
                 "name": self.url.file_path(),
-                "creation_time": datetime.fromtimestamp(stat.st_ctime)
-                if stat
-                else None,
-                "modification_time": datetime.fromtimestamp(stat.st_ctime)
-                if stat
-                else None,
+                "creation_time": (
+                    datetime.fromtimestamp(stat.st_ctime) if stat else None
+                ),
+                "modification_time": (
+                    datetime.fromtimestamp(stat.st_ctime) if stat else None
+                ),
             },
         )
 

tomwer/gui/cluster/slurm.py

@@ -168,6 +168,7 @@ class SlurmSettingsWindow(qt.QMainWindow):
                         "job_name": settingsClass.PROJECT_NAME,
                         "walltime": settingsClass.DEFAULT_WALLTIME,
                         "python_venv": settingsClass.PYTHON_VENV,
+                        "modules": settingsClass.MODULES_TO_LOAD,
                     }
                 )
 
@@ -270,7 +271,7 @@ class SlurmSettingsWidget(qt.QWidget):
         self.layout().addRow(self._preProcessingGroup)
 
         # python venv
-        self._pythonVenv = qt.QLineEdit("", self)
+        self._pythonVenv = qt.QLineEdit("/scisoft/tomotools/activate stable", self)
         self._sourceScriptCB = qt.QRadioButton("source script (python venv)", self)
         self._preProcessingButtonGroup.addButton(self._sourceScriptCB)
         self._preProcessingGroup.layout().addRow(self._sourceScriptCB, self._pythonVenv)
@@ -280,13 +281,13 @@ class SlurmSettingsWidget(qt.QWidget):
             """
         )
 
-        self._modulesQLE = qt.QLineEdit("tomotools,", self)
-        self._modulesCB = qt.QRadioButton("module to load", self)
+        self._modulesQLE = qt.QLineEdit(", ".join(SlurmSettings.MODULES_TO_LOAD), self)
+        self._modulesCB = qt.QRadioButton("module(s) to load", self)
         self._preProcessingButtonGroup.addButton(self._modulesCB)
         self._preProcessingGroup.layout().addRow(self._modulesCB, self._modulesQLE)
         self._preProcessingGroup.setToolTip(
             """
-            Optional list of modules to load before executing the script.
+            Optional list of modules to load before executing the script. each module must be separated by a coma
             """
         )
 
@@ -372,8 +373,7 @@ class SlurmSettingsWidget(qt.QWidget):
         self._nGpu.setValue(n_gpu)
         self._jobName.setText(SlurmSettings.PROJECT_NAME)
         self._wallTimeQLE.setText(SlurmSettings.DEFAULT_WALLTIME)
-        self._pythonVenv.setText(SlurmSettings.PYTHON_VENV)
-        self._sourceScriptCB.setChecked(True)
+        self._modulesCB.setChecked(True)  # by default we go for modules
         self._preProcessingModeChanged()
         self._partitionChanged()
         self._nGpuChanged()
@@ -569,7 +569,7 @@ class SlurmSettingsWidget(qt.QWidget):
         self.sigConfigChanged.emit()
 
     def getConfiguration(self) -> dict:
-        return {
+        config = {
             "cpu-per-task": self.getNCores(),
             "n_tasks": self.getNWorkers(),
             "n_jobs": self.getNJobs(),
@@ -578,10 +578,15 @@ class SlurmSettingsWidget(qt.QWidget):
             "n_gpus": self.getNGPU(),
             "job_name": self.getProjectName(),
             "walltime": self.getWallTime(),
-            "python_venv": self.getPythonExe(),
-            "modules": self.getModulesToLoad(),
             "sbatch_extra_params": self.getSBatchExtraParams(),
         }
+        if self._modulesCB.isChecked():
+            config["modules"] = self.getModulesToLoad()
+        elif self._sourceScriptCB.isChecked():
+            config["python_venv"] = self.getPythonExe()
+        else:
+            raise ValueError("'modules' or python environement should be enable")
+        return config
 
     def getSlurmClusterConfiguration(self):
         from tomwer.core.cluster import SlurmClusterConfiguration

tomwer/gui/cluster/supervisor.py

@@ -102,6 +102,7 @@ class FutureTomwerScanObserverWidget(qt.QWidget):
             )
             if future_tomo_obj is not None:
                 self.sigConversionRequested.emit(future_tomo_obj)
+        self.observationTable.model().updateIndices()
         self.observationTable.model().layoutChanged.emit()
 
     def _cancelSelected(self, *args, **kwargs):
@@ -123,6 +124,7 @@ class FutureTomwerScanObserverWidget(qt.QWidget):
         self.observationTable.model().filtered_status = (
             self.filterWidget.getFilteredStatus()
         )
+        self.observationTable.model().endResetModel()
 
     def updateView(self):
         """
@@ -265,6 +267,16 @@ class _DatasetProcessModel(qt.QAbstractTableModel):
             del self._tomoObjStatus[future_tomo_obj]
         self.layoutChanged.emit()
 
+    def updateIndices(self):
+        """
+        Update tomo object indices when a tomo object has been removed (during a convertion for example)
+        """
+        tomo_objs = list(self.futureTomoObjs.values())
+        self.futureTomoObjs.clear()
+        for i_tomo_obj, tomo_obj in enumerate(tomo_objs):
+            self.futureTomoObjs[i_tomo_obj] = tomo_obj
+        self._computeUnfilteredFutureTomoObjs()
+
     def getUnfilteredFutureTomoObjs(self):
         return self._filteredFutureTomoObjs
 

tomwer/gui/cluster/test/test_cluster.py

@@ -61,9 +61,8 @@ class TestSlurmWidget(TestCaseQt):
             "partition": SlurmSettings.PARTITION,
             "n_gpus": SlurmSettings.N_GPUS_PER_WORKER,
             "job_name": "tomwer_{scan}_-_{process}_-_{info}",
-            "modules": tuple(),
             "n_jobs": 1,
-            "python_venv": "/scisoft/tomotools/activate stable",
+            "modules": ("tomotools/stable",),
             "walltime": "01:00:00",
             "sbatch_extra_params": {
                 "export": "NONE",

tomwer/gui/cluster/test/test_supervisor.py

@@ -57,7 +57,7 @@ class TestSupervisor(TestCaseQt):
                 n_proj=10,
                 n_ini_proj=10,
                 create_ini_dark=False,
-                create_ini_ref=False,
+                create_ini_flat=False,
                 dim=10,
             ).scan
             self._scans.append(scan)

tomwer/gui/control/datalist.py

@@ -242,6 +242,11 @@ class BlissHDF5DataListDialog(_DataListDialog):
             os.environ["TOMWER_DEFAULT_INPUT_DIR"]
         ):
             dialog.setDirectory(os.environ["TOMWER_DEFAULT_INPUT_DIR"])
+        elif dialog.directory() != os.getcwd() or str(dialog.directory()).startswith(
+            "/data"
+        ):
+            # if the directory as already been set by the user. Avoid redefining it
+            pass
         elif os.path.isdir("/data"):
             dialog.setDirectory("/data")
 

tomwer/gui/control/datawatcher/controlwidget.py

@@ -99,10 +99,8 @@ class ControlWidget(qt.QWidget):
         """
         Ask the user the path to the folder to observe
         """
-        defaultDirectory = self.getFolderObserved()
+        defaultDirectory = self._qteFolderSelected.text()
         if defaultDirectory is None or not os.path.isdir(defaultDirectory):
-            if os.path.isdir(self.DEFAULT_DIRECTORY):
-                defaultDirectory = self.DEFAULT_DIRECTORY
             if defaultDirectory is None:
                 defaultDirectory = get_default_directory()
 
@@ -113,4 +111,4 @@ class ControlWidget(qt.QWidget):
             dialog.close()
             return
 
-        self.setFolderObserved(dialog.selectedFiles()[0])
+        self._qteFolderSelected.setText(dialog.selectedFiles()[0])

tomwer/gui/control/reducedarkflatselector.py

@@ -12,7 +12,7 @@ from silx.gui.dialog.DataFileDialog import DataFileDialog
 
 from tomoscan.esrf.scan.utils import cwd_context
 from tomoscan.framereducer.target import REDUCER_TARGET
-from tomoscan.io import HDF5File
+from tomoscan.io import HDF5File, get_swmr_mode
 
 from tomwer.io.utils import get_default_directory
 
@@ -249,7 +249,7 @@ class ReduceDarkFlatSelectorTableWidget(qt.QWidget):
         if not os.path.exists(file_path):
             _logger.error(f"file doesn't exists ({file_path})")
 
-        with HDF5File(file_path, mode="r") as h5f:
+        with HDF5File(file_path, mode="r", swmr=get_swmr_mode()) as h5f:
             entries = tuple(h5f.keys())
 
         res = []
@@ -289,16 +289,16 @@ class ReduceDarkFlatSelectorTableWidget(qt.QWidget):
             for target in REDUCER_TARGET.values():
                 if target in reduced_info_dict:
                     reduced_frames = reduced_info_dict[target]
-                    reduced_frames[
-                        "reduce_frames_name"
-                    ] = f"{target} from {url.data_path()}@{os.path.basename(url.file_path())}"
+                    reduced_frames["reduce_frames_name"] = (
+                        f"{target} from {url.data_path()}@{os.path.basename(url.file_path())}"
+                    )
                     result.append(reduced_frames)
 
             if len(reduced_frames) == 0:
                 # else we consider the data_path is the valid one
-                reduced_frames[
-                    "reduce_frames_name"
-                ] = f"{url.data_path()}@{os.path.basename(url.file_path())}"
+                reduced_frames["reduce_frames_name"] = (
+                    f"{url.data_path()}@{os.path.basename(url.file_path())}"
+                )
                 result.append(reduced_frames)
 
         return tuple(result)

tomwer/gui/control/test/test_single_tomo_obj.py

@@ -34,7 +34,7 @@ class TestSingletomoObj(TestCaseQt):
             n_proj=10,
             n_ini_proj=10,
             create_ini_dark=False,
-            create_ini_ref=False,
+            create_ini_flat=False,
             dim=10,
         ).scan
 

tomwer/gui/edit/dkrfpatch.py

@@ -37,7 +37,7 @@ from silx.gui.dialog.DataFileDialog import DataFileDialog
 from silx.io.url import DataUrl
 from silx.io.utils import h5py_read_dataset
 from nxtomo.nxobject.nxdetector import ImageKey
-from tomoscan.io import HDF5File
+from tomoscan.io import HDF5File, get_swmr_mode
 
 import tomwer.core.utils.nxtomoutils as nxtomo_utils
 from tomwer.core.scan.nxtomoscan import NXtomoScan
@@ -83,7 +83,7 @@ class _DarkOrFlatUrl(qt.QWidget):
         url = self._redirectDataPath(url, logger=_logger)
 
         def dataset_invalid(url):
-            with HDF5File(url.file_path(), mode="r") as h5s:
+            with HDF5File(url.file_path(), mode="r", swmr=get_swmr_mode()) as h5s:
                 if not isinstance(h5s[url.data_path()], h5py.Dataset):
                     return True
             return False
@@ -113,7 +113,7 @@ class _DarkOrFlatUrl(qt.QWidget):
 
     def _redirectDataPath(self, url, logger=None):
         try:
-            with HDF5File(url.file_path(), mode="r") as h5s:
+            with HDF5File(url.file_path(), mode="r", swmr=get_swmr_mode()) as h5s:
                 node = h5s[url.data_path()]
 
                 if NXtomoScan.entry_is_nx_tomo(node):
@@ -188,7 +188,7 @@ class _DarkOrFlatUrl(qt.QWidget):
     def _getImageKey(self, url):
         # if we are on a 'detector / data dataset' then we can try to reach
         # image_key information
-        with HDF5File(url.file_path(), mode="r") as h5s:
+        with HDF5File(url.file_path(), mode="r", swmr=get_swmr_mode()) as h5s:
             dataset = h5s[url.data_path()]
             grp_parent = dataset.parent
             if grp_parent is not None and NXtomoScan.is_nxdetector(grp_parent):

tomwer/gui/edit/nxtomowarmer.py

@@ -3,7 +3,7 @@ import h5py
 from silx.gui import qt
 from tomwer.core.scan.nxtomoscan import NXtomoScan
 from tomwer.gui import icons
-from tomoscan.io import HDF5File
+from tomoscan.io import HDF5File, get_swmr_mode
 
 
 class NXtomoProxyWarmer(qt.QWidget):
@@ -44,7 +44,7 @@ class NXtomoProxyWarmer(qt.QWidget):
         if scan is None:
             self._activateWarning(False)
         elif isinstance(scan, NXtomoScan):
-            with HDF5File(scan.master_file, mode="r") as h5f:
+            with HDF5File(scan.master_file, mode="r", swmr=get_swmr_mode()) as h5f:
                 entry = h5f.get(
                     name=scan.entry, getclass=True, getlink=True, default=None
                 )

tomwer/gui/edit/test/test_dkrf_patch.py

@@ -67,8 +67,8 @@ class TestDarkOrFlatUrl(TestCaseQt):
             n_ini_proj=20,
             n_proj=20,
             create_ini_dark=True,
-            create_ini_ref=True,
-            create_final_ref=True,
+            create_ini_flat=True,
+            create_final_flat=True,
         )
         self._scan = hdf5_mock.scan
         self.scan_url = DataUrl(
@@ -135,8 +135,8 @@ class TestDarkRefPatchWidget(TestCaseQt):
             n_ini_proj=20,
             n_proj=20,
             create_ini_dark=True,
-            create_ini_ref=True,
-            create_final_ref=True,
+            create_ini_flat=True,
+            create_final_flat=True,
         )
         self._scanWithDarkAndRef = hdf5_mock.scan
 
@@ -145,8 +145,8 @@ class TestDarkRefPatchWidget(TestCaseQt):
             n_ini_proj=20,
             n_proj=20,
             create_ini_dark=False,
-            create_ini_ref=False,
-            create_final_ref=False,
+            create_ini_flat=False,
+            create_final_flat=False,
         )
         self._scan = hdf5_mock.scan
         assert len(self._scan.darks) == 0

tomwer/gui/imagefromfile.py

@@ -34,7 +34,7 @@ import logging
 
 from silx.gui import qt
 from silx.io.url import DataUrl
-from tomoscan.io import HDF5File
+from tomoscan.io import HDF5File, get_swmr_mode
 
 from tomwer.core.scan.scanbase import TomwerScanBase
 from tomwer.synctools.imageloaderthread import ImageLoaderThread
@@ -71,7 +71,7 @@ class ImageFromFile(_Image):
 
                 def get_nabu_entry():
                     try:
-                        with HDF5File(_file, mode="r", swmr=True) as h5s:
+                        with HDF5File(_file, mode="r", swmr=get_swmr_mode()) as h5s:
                             for node in h5s:
                                 if "reconstruction" in h5s[node]:
                                     return "/".join(

tomwer/gui/qfolderdialog.py

@@ -78,6 +78,11 @@ class QDataDialog(qt.QFileDialog):
             os.environ["TOMWER_DEFAULT_INPUT_DIR"]
         ):
             self.setDirectory(os.environ["TOMWER_DEFAULT_INPUT_DIR"])
+        elif self.directory() != os.getcwd() or str(self.directory()).startswith(
+            "/data"
+        ):
+            # if the directory as already been set by the user. Avoid redefining it
+            pass
         elif os.path.isdir("/data"):
             self.setDirectory("/data")