tomwer 1.4.0rc6__py3-none-any.whl → 1.4.1__py3-none-any.whl

orangecontrib/tomwer/tutorials/simple_volume_to_slurm_reconstruction.ows

@@ -21,8 +21,8 @@
 		<link id="5" source_node_id="8" sink_node_id="6" source_channel="data" sink_channel="data" enabled="true" source_channel_id="data" sink_channel_id="data" />
 		<link id="6" source_node_id="7" sink_node_id="3" source_channel="cluster_config" sink_channel="cluster_config" enabled="true" source_channel_id="config_out" sink_channel_id="cluster_in" />
 		<link id="7" source_node_id="3" sink_node_id="9" source_channel="future_tomo_obj" sink_channel="future_tomo_obj" enabled="true" source_channel_id="future_out" sink_channel_id="future_tomo_obj" />
-		<link id="8" source_node_id="9" sink_node_id="5" source_channel="volume" sink_channel="data" enabled="true" source_channel_id="volume" sink_channel_id="data" />
-		<link id="9" source_node_id="9" sink_node_id="4" source_channel="data" sink_channel="data" enabled="true" source_channel_id="data" sink_channel_id="data" />
+		<link id="8" source_node_id="9" sink_node_id="4" source_channel="data" sink_channel="data" enabled="true" source_channel_id="data" sink_channel_id="data" />
+		<link id="9" source_node_id="9" sink_node_id="5" source_channel="data" sink_channel="data" enabled="true" source_channel_id="data" sink_channel_id="data" />
 	</links>
 	<annotations>
 		<arrow id="0" start="(267.0, 56.0)" end="(194.0, 105.0)" fill="#C1272D" />

orangecontrib/tomwer/widgets/reconstruction/AxisOW.py

@@ -22,7 +22,9 @@ from tomwer.core import settings
 from tomwer.core.utils.lbsram import is_low_on_memory
 from tomwer.core.process.reconstruction.axis import AxisTask
 from tomwer.core.process.reconstruction.axis.mode import AxisMode
-from tomwer.core.scan.nxtomoscan import NXtomoScan
+from tomwer.core.process.reconstruction.params_cache import (
+    save_reconstruction_parameters_to_cache,
+)
 from tomwer.core.scan.scanbase import TomwerScanBase, _TomwerBaseDock
 from tomwer.gui.reconstruction.axis import AxisMainWindow
 from tomwer.synctools.axis import QAxisRP
@@ -296,11 +298,12 @@ class AxisOW(SuperviseOW, WidgetLongProcessing):
                 self.__scan._axis_params.set_relative_value(
                     self._axis_params.relative_cor_value
                 )
-                _cor_value = self.__scan.axis_params.relative_cor_value
+                relative_cor_value = self.__scan.axis_params.relative_cor_value
+                save_reconstruction_parameters_to_cache(scan=self.__scan)
                 pv_helpers.notify_succeed(
                     process=self,
                     dataset=self.__scan,
-                    details=f"axis calculation defined for {self.__scan.path}: {_cor_value} (using manual)",
+                    details=f"axis calculation defined for {self.__scan.path}: {relative_cor_value} (using manual)",
                 )
             # validate the center of rotation
             pm = ProcessManager()
@@ -415,36 +418,18 @@ class AxisOW(SuperviseOW, WidgetLongProcessing):
                     self._axis_params.relative_cor_value
                 )
                 cor = scan._axis_params.relative_cor_value
-                if isinstance(scan, NXtomoScan):
-                    entry = scan.entry
-                else:
-                    entry = "entry"
-                with scan.acquire_process_file_lock():
-                    ap = AxisTask(
-                        process_id=self.process_id,
-                        inputs={
-                            "data": None,
-                        },
-                    )
-                    try:
-                        AxisTask._register_process(
-                            process_file=scan.process_file,
-                            entry=entry,
-                            process=ap,
-                            results={
-                                "center_of_rotation": cor if cor is not None else "-"
-                            },
-                            configuration=self._axis_params.to_dict(),
-                            process_index=scan.pop_process_index(),
-                            overwrite=True,
-                        )
-                    except Exception as e:
-                        logger.warning(f"Fail to register Axis process. Error is {e}")
-                    ProcessManager().notify_dataset_state(
-                        dataset=scan,
-                        process=ap,
-                        state=DatasetState.SUCCEED,
-                    )
+                save_reconstruction_parameters_to_cache(scan=scan)
+                ap = AxisTask(
+                    process_id=self.process_id,
+                    inputs={
+                        "data": None,
+                    },
+                )
+                ProcessManager().notify_dataset_state(
+                    dataset=scan,
+                    process=ap,
+                    state=DatasetState.SUCCEED,
+                )
             else:
                 processing_class = AxisTask(
                     inputs={
@@ -459,23 +444,10 @@ class AxisOW(SuperviseOW, WidgetLongProcessing):
                 self.scan_ready(scan=scan)
 
         elif self.isValueLock():
-            entry = scan.entry if isinstance(scan, NXtomoScan) else "entry"
             cor = self._axis_params.relative_cor_value
             scan.axis_params.set_relative_value(cor)
+            save_reconstruction_parameters_to_cache(scan=scan)
             scan._axis_params.mode = "manual"
-            with scan.acquire_process_file_lock():
-                try:
-                    AxisTask._register_process(
-                        process_file=scan.process_file,
-                        entry=entry,
-                        process=AxisTask,
-                        results={"center_of_rotation": cor if cor is not None else "-"},
-                        configuration=self._axis_params.to_dict(),
-                        process_index=scan.pop_process_index(),
-                        overwrite=True,
-                    )
-                except Exception as e:
-                    logger.warning(f"Fail to register Axis process. Error is {e}")
             ProcessManager().notify_dataset_state(
                 dataset=scan,
                 process=AxisTask(

orangecontrib/tomwer/widgets/reconstruction/NabuOW.py

@@ -11,10 +11,13 @@ from orangewidget.settings import Setting
 from orangewidget.widget import Input, Output
 from silx.gui import qt
 
+from tomwer.core.process.reconstruction.params_cache import (
+    load_reconstruction_parameters_from_cache,
+    save_reconstruction_parameters_to_cache,
+)
 import tomwer.core.process.reconstruction.nabu.nabuslices
 from tomwer.core.cluster import SlurmClusterConfiguration
 from tomwer.core.futureobject import FutureTomwerObject
-from tomwer.core.process.reconstruction.nabu.nabuslices import NabuSlicesTask
 from tomwer.core.scan.scanbase import TomwerScanBase, _TomwerBaseDock
 from tomwer.core.volume.volumefactory import VolumeFactory
 
@@ -165,14 +168,15 @@ class NabuOW(WidgetLongProcessing, SuperviseOW):
         if scan is None:
             return
 
+        self._nabuWidget.setScan(scan)
+
         if scan.axis_params is None or scan.axis_params.relative_cor_value is None:
             # try to retrieve last computed cor value from nabu process
-            r_cor = NabuSlicesTask.retrieve_last_relative_cor(scan)
             if scan.axis_params is None:
                 from tomwer.synctools.axis import QAxisRP
 
                 scan.axis_params = QAxisRP()
-            scan.axis_params.set_relative_value(float(r_cor))
+            load_reconstruction_parameters_from_cache(scan=scan)
 
         self.show()
         with NabuOW.DialogCM(self._buttons):
@@ -211,6 +215,7 @@ class NabuOW(WidgetLongProcessing, SuperviseOW):
     def _endProcessing(self, scan, future_tomo_obj):
         WidgetLongProcessing._endProcessing(self, scan)
         if scan is not None:
+            save_reconstruction_parameters_to_cache(scan=scan)
             # send scan
             self.Outputs.data.send(scan)
             # send slice urls

orangecontrib/tomwer/widgets/reconstruction/NabuVolumeOW.py

@@ -15,6 +15,9 @@ from tomoscan.identifier import VolumeIdentifier
 
 import tomwer.core.process.reconstruction.nabu.nabuvolume
 from orangecontrib.tomwer.widgets.utils import WidgetLongProcessing
+from tomwer.core.process.reconstruction.params_cache import (
+    load_reconstruction_parameters_from_cache,
+)
 from tomwer.core import settings
 from tomwer.core.cluster import SlurmClusterConfiguration
 from tomwer.core.futureobject import FutureTomwerObject
@@ -22,7 +25,6 @@ from tomwer.core.process.drac.processeddataset import (
     DracReconstructedVolumeDataset,
 )
 from tomwer.core.process.reconstruction.nabu import utils as nabu_utils
-from tomwer.core.process.reconstruction.nabu.nabuvolume import NabuVolumeTask
 from tomwer.core.scan.scanbase import TomwerScanBase
 from tomwer.core.utils.char import BETA_CHAR, DELTA_CHAR
 from tomwer.core.utils.scanutils import format_output_location
@@ -231,15 +233,11 @@ class NabuVolumeOW(WidgetLongProcessing, SuperviseOW):
             or dataset.axis_params.relative_cor_value is None
         ):
             # try to retrieve last computed cor value from nabu process
-            r_cor = NabuVolumeTask.retrieve_last_relative_cor(dataset)
             if dataset.axis_params is None:
                 from tomwer.synctools.axis import QAxisRP
 
                 dataset.axis_params = QAxisRP()
-            try:
-                dataset.axis_params.set_relative_value(float(r_cor))
-            except Exception:
-                pass
+            load_reconstruction_parameters_from_cache(scan=dataset)
 
         self.process(dataset)
 

orangecontrib/tomwer/widgets/reconstruction/SAAxisOW.py

@@ -18,7 +18,9 @@ from tomwer.core import settings
 from tomwer.core.utils.lbsram import is_low_on_memory
 from tomwer.core.cluster import SlurmClusterConfiguration
 from tomwer.core.process.reconstruction.axis import AxisTask
-from tomwer.core.process.reconstruction.saaxis.saaxis import SAAxisTask
+from tomwer.core.process.reconstruction.params_cache import (
+    save_reconstruction_parameters_to_cache,
+)
 from tomwer.core.scan.scanbase import TomwerScanBase, _TomwerBaseDock
 from tomwer.gui.reconstruction.saaxis.saaxis import SAAxisWindow as _SAAxisWindow
 from tomwer.synctools.axis import QAxisRP
@@ -41,6 +43,8 @@ class SAAxisWindow(_SAAxisWindow):
         self._processing_stack = SAAxisProcessStack(
             saaxis_params=self._saaxis_params, process_id=process_id
         )
+        if process_id is not None:
+            assert self._processing_stack.process_id == process_id
 
         # connect signal / slot
         self.sigValidated.connect(self.validateCurrentScan)
@@ -187,6 +191,8 @@ class SAAxisWindow(_SAAxisWindow):
             )
         else:
             scan.axis_params.set_relative_value(selected_cor_value)
+            save_reconstruction_parameters_to_cache(scan=scan)
+
             if scan.nabu_recons_params is not None:
                 if "reconstruction" not in scan.nabu_recons_params:
                     scan.nabu_recons_params["reconstruction"] = {}
@@ -200,9 +206,7 @@ class SAAxisWindow(_SAAxisWindow):
             pv_helpers.notify_succeed(
                 process=self._processing_stack, dataset=scan, details=infos
             )
-        SAAxisTask.process_to_tomwer_processes(
-            scan=scan,
-        )
+
         self.Outputs.data.send(scan)
 
     def getConfiguration(self) -> dict:

orangecontrib/tomwer/widgets/reconstruction/SADeltaBetaOW.py

@@ -18,7 +18,6 @@ from orangecontrib.tomwer.orange.settings import CallbackSettingsHandler
 from tomwer.core import settings
 from tomwer.core.utils.lbsram import is_low_on_memory
 from tomwer.core.cluster import SlurmClusterConfiguration
-from tomwer.core.process.reconstruction.sadeltabeta import SADeltaBetaTask
 from tomwer.core.scan.scanbase import TomwerScanBase, _TomwerBaseDock
 from tomwer.gui.reconstruction.sadeltabeta import (
     SADeltaBetaWindow as _SADeltaBetaWindow,
@@ -136,9 +135,6 @@ class SADeltaBetaWindow(_SADeltaBetaWindow):
             pv_helpers.notify_succeed(
                 process=self._processing_stack, dataset=scan, details=infos
             )
-        SADeltaBetaTask.process_to_tomwer_processes(
-            scan=scan,
-        )
         self.Outputs.data.send(scan)
 
     def getConfiguration(self) -> dict:

orangecontrib/tomwer/widgets/reconstruction/SinoNormOW.py

@@ -15,7 +15,6 @@ from orangecontrib.tomwer.widgets.utils import WidgetLongProcessing
 
 from tomwer.core import settings
 from tomwer.core.utils.lbsram import is_low_on_memory
-from tomwer.core.process.reconstruction.normalization import SinoNormalizationTask
 from tomwer.core.process.reconstruction.normalization.params import _ValueSource
 from tomwer.core.scan.scanbase import TomwerScanBase
 from tomwer.gui.reconstruction.normalization.intensity import (
@@ -189,18 +188,7 @@ class SinoNormOW(WidgetLongProcessing, SuperviseOW):
         tomwer_processing_res_code = extra_infos.pop(
             "tomwer_processing_res_code", "unprocessed"
         )
-        with scan.acquire_process_file_lock():
-            SinoNormalizationTask._register_process(
-                process_file=scan.process_file,
-                process=SinoNormalizationTask,
-                entry=scan.entry,
-                configuration=self.getConfiguration(),
-                results={
-                    "method": scan.intensity_normalization.method.value,
-                    "extra_infos": extra_infos,
-                },
-                process_index=scan.pop_process_index(),
-            )
+
         if tomwer_processing_res_code is True:
             # if defined by manual scalar we need to set the value
             if extra_infos.get("source", None) == _ValueSource.MANUAL_SCALAR.value:

tomwer/app/axis.py

@@ -161,7 +161,6 @@ def main(argv):
 
     requires_reduced_dark_and_flat(scan=scan, logger_=_logger)
     # define the process_index is any tomwer_processes_existing
-    scan.set_process_index_frm_tomwer_process_file()
     if scan.axis_params is None:
         scan.axis_params = QAxisRP()
 

tomwer/app/intensitynormalization.py

@@ -70,20 +70,6 @@ class NormIntensityWindow(_SinoNormWindow):
         self._processingThread.finished.connect(self._threadedProcessEnded)
 
     def _validated(self):
-        scan = self.getScan()
-        if scan is not None:
-            with scan.acquire_process_file_lock():
-                SinoNormalizationTask._register_process(
-                    process_file=scan.process_file,
-                    process=SinoNormalizationTask,
-                    entry=scan.entry,
-                    configuration=self.getConfiguration(),
-                    results={
-                        "method": scan.intensity_normalization.method.value,
-                        "extra_infos": scan.intensity_normalization.get_extra_infos(),
-                    },
-                    process_index=scan.pop_process_index(),
-                )
         self.close()
 
     def _launchProcessing(self):

tomwer/app/multicor.py

@@ -13,21 +13,17 @@ import time
 
 import silx
 from silx.gui import qt
-from silx.io.utils import h5py_read_dataset
 
-from tomwer.core.process import utils as core_utils
 from tomwer.core.process.reconstruction.axis.axis import AxisTask, NoAxisUrl
 from tomwer.core.process.reconstruction.darkref.darkrefs import (
     requires_reduced_dark_and_flat,
 )
 from tomwer.core.process.reconstruction.saaxis.saaxis import SAAxisTask
-from tomwer.core.process.task import Task
 from tomwer.core.scan.scanfactory import ScanFactory
 from tomwer.core.utils.resource import increase_max_number_file
 from tomwer.gui import icons
 from tomwer.gui.reconstruction.saaxis.saaxis import SAAxisWindow as _SAAxisWindow
 from tomwer.gui.utils.splashscreen import getMainSplashScreen
-from tomwer.io.utils.h5pyutils import EntryReader
 from tomwer.synctools.axis import QAxisRP
 from tomwer.synctools.saaxis import QSAAxisParams
 
@@ -254,7 +250,7 @@ def main(argv):
     window.setScan(scan)
     window.setDumpScoreROI(options.dump_roi)
     if options.read_existing is True:
-        scores, selected = _load_latest_scores(scan)
+        scores, selected = SAAxisTask.load_results_from_disk(scan)
         if scores is not None:
             window.setCorScores(scores, score_method="standard deviation")
             if selected not in (None, "-"):
@@ -267,34 +263,6 @@ def main(argv):
     exit(app.exec_())
 
 
-def _load_latest_scores(scan) -> tuple:
-    """
-
-    :param scan:
-    :return: loaded score as (scores, selected). Scores is None or a dict.
-             selected is None or a float
-    """
-    scores = None
-    selected = None
-    if scan.process_file is None:
-        _logger.warning(
-            "Unable to find process file. Unable to read " "existing processing"
-        )
-        return scores, selected
-
-    with EntryReader(scan.process_file_url) as h5f:
-        latest_saaxis_node = Task.get_most_recent_process(h5f, SAAxisTask)
-        if latest_saaxis_node and "results" in latest_saaxis_node:
-            scores = core_utils.get_scores(latest_saaxis_node)
-            if "center_of_rotation" in latest_saaxis_node["results"]:
-                selected = h5py_read_dataset(
-                    latest_saaxis_node["results"]["center_of_rotation"]
-                )
-        else:
-            _logger.warning(f"no results found for {scan}")
-    return scores, selected
-
-
 def getinputinfo():
     return "tomwer saaxis [scanDir]"
 

tomwer/app/multipag.py

@@ -13,9 +13,7 @@ import time
 
 import silx
 from silx.gui import qt
-from silx.io.utils import h5py_read_dataset
 
-from tomwer.core.process import utils as core_utils
 from tomwer.core.process.reconstruction.axis.axis import AxisTask, NoAxisUrl
 from tomwer.core.process.reconstruction.darkref.darkrefs import (
     requires_reduced_dark_and_flat,
@@ -27,7 +25,6 @@ from tomwer.core.process.reconstruction.utils.cor import (
     relative_pos_to_absolute,
     absolute_pos_to_relative,
 )
-from tomwer.core.process.task import Task
 from tomwer.core.scan.scanfactory import ScanFactory
 from tomwer.core.utils.resource import increase_max_number_file
 from tomwer.gui import icons
@@ -36,7 +33,6 @@ from tomwer.gui.reconstruction.sadeltabeta.saadeltabeta import (
     SADeltaBetaWindow as _SADeltaBetaWindow,
 )
 from tomwer.gui.utils.splashscreen import getMainSplashScreen
-from tomwer.io.utils.h5pyutils import EntryReader
 from tomwer.synctools.axis import QAxisRP
 from tomwer.synctools.sadeltabeta import QSADeltaBetaParams
 
@@ -328,7 +324,7 @@ def main(argv):
         scan.sa_delta_beta_params = QSADeltaBetaParams()
     window.setScan(scan)
     if options.read_existing is True:
-        scores, selected = _load_latest_scores(scan)
+        scores, selected = SADeltaBetaTask.load_results_from_disk(scan)
         if scores is not None:
             window.setDBScores(scores, score_method="standard deviation")
             if selected not in (None, "-"):
@@ -350,31 +346,5 @@ def sigintHandler(*args):
     qt.QApplication.quit()
 
 
-def _load_latest_scores(scan) -> tuple:
-    """
-
-    :param scan:
-    :return: loaded scores and selected score as (scores, selected).
-             "scores" can be None or a dict. "selected" can be None or a float
-    """
-    scores = None
-    selected = None
-    if scan.process_file is None:
-        _logger.warning(
-            "Unable to find process file. Unable to read " "existing processing"
-        )
-        return scores, selected
-
-    with EntryReader(scan.process_file_url) as h5f:
-        latest_sa_db_node = Task.get_most_recent_process(h5f, SADeltaBetaTask)
-        if latest_sa_db_node and "results" in latest_sa_db_node:
-            scores = core_utils.get_scores(latest_sa_db_node)
-            if "delta_beta" in latest_sa_db_node["results"]:
-                selected = h5py_read_dataset(latest_sa_db_node["results"]["delta_beta"])
-        else:
-            _logger.warning(f"no results found for {scan}")
-    return scores, selected
-
-
 if __name__ == "__main__":
     main(sys.argv)

tomwer/app/nabuapp.py

@@ -229,7 +229,6 @@ def main(argv):
     scan = ScanFactory.create_scan_object(options.scan_path, entry=options.entry)
     widget = NabuWindow(parent=None)
     widget.setScan(scan)
-    scan.set_process_index_frm_tomwer_process_file()
     if options.output_dir is not None:
         widget.setOutputDir(options.output_dir)
     # for the application we run for the reconstruction to be finished

tomwer/app/patchrawdarkflat.py

@@ -103,9 +103,6 @@ def main(argv):
         scan_path=options.scan_path, entry=options.entry
     )
 
-    # define the process_index is any tomwer_processes_existing
-    scan.set_process_index_frm_tomwer_process_file()
-
     if options.debug:
         _logger.setLevel(logging.DEBUG)
 

tomwer/app/reducedarkflat.py

@@ -179,7 +179,6 @@ def main(argv):
     increase_max_number_file()
 
     scan = ScanFactory.create_scan_object(options.scan_path, entry=options.entry)
-    scan.set_process_index_frm_tomwer_process_file()
 
     dark_method = ReduceMethod.from_value(options.dark_method)
     flat_method = ReduceMethod.from_value(options.flat_method)