normalization: one more round of bug fix

orangecontrib/tomwer/widgets/reconstruction/NormIOW.py

@@ -51,6 +51,8 @@ from tomwer.core.process.reconstruction.normalization import (
 )
 from tomwer.core import settings
 from tomwer.core import utils
+from tomoscan.normalization import Method as NormMethod
+from tomwer.core.process.reconstruction.normalization.params import _ValueSource
 import functools
 
 _logger = logging.getLogger(__name__)
@@ -217,7 +219,9 @@ class NormIOW(WidgetLongProcessing, SuperviseOW):
         # save processing result for the one with interaction. Otherwise
         # this will be saved in the processing thread
         extra_infos = scan.intensity_normalization.get_extra_infos()
-        tomwer_processing_res_code = extra_infos.get("tomwer_processing_res_code")
+        tomwer_processing_res_code = extra_infos.pop(
+            "tomwer_processing_res_code", "unprocessed"
+        )
         IntensityNormalizationTask._register_process(
             process_file=scan.process_file,
             process=IntensityNormalizationTask,
@@ -234,8 +238,28 @@ class NormIOW(WidgetLongProcessing, SuperviseOW):
             self.notify_succeed(scan=scan)
         elif tomwer_processing_res_code is False:
             self.notify_failed(scan=scan)
-        else:
+        elif tomwer_processing_res_code is None:
             self.notify_skip(scan=scan)
+        elif tomwer_processing_res_code == "unprocessed":
+            # if validate manually we must set current method + value
+            scan.intensity_normalization = self.getCurrentMethod()
+
+            if self.getCurrentMethod() in (
+                NormMethod.NONE,
+                NormMethod.CHEBYSHEV,
+                NormMethod.LSQR_SPLINE,
+            ):
+                extra_infos = {}
+            elif self.getCurrentSource() is _ValueSource.DATASET:
+                extra_infos = {
+                    "dataset_url": self._window._optsWidget._datasetWidget.getDatasetUrl().path(),
+                }
+            else:
+                extra_infos = {"value": self.getCurrentlyDefinedValues()}
+            self.notify_succeed(scan=scan)
+
+        # clear flag
+        scan.intensity_normalization.set_extra_infos(extra_infos)
 
         self.Outputs.data_out.send(scan)
 
@@ -255,6 +279,9 @@ class NormIOW(WidgetLongProcessing, SuperviseOW):
             self.notify_skip(scan=scan, details=details)
             self.Outputs.data_out.send(scan)
 
+    def getCurrentlyDefinedValues(self):
+        return self._window._crtWidget.getResult()
+
     def validateCurrentScan(self):
         scan = self._window.getScan()
         self._validate(scan)

orangecontrib/tomwer/widgets/reconstruction/test/test_i_norm.py

@@ -169,13 +169,6 @@ class TestProcessing(TestCaseQt):
             ),
             DatasetState.SUCCEED,
         )
-        # insure a normalization has been registered
-        self.assertTrue(
-            self.scan_3.intensity_normalization.get_extra_infos().get(
-                "tomwer_processing_res_code"
-            ),
-            True,
-        )
 
     def testTestLbsram(self):
         """Test scan are all validated if 'low memory on lbsram' scenario is

tomwer/core/process/reconstruction/nabu/nabucommon.py

@@ -488,7 +488,7 @@ class _NabuBaseReconstructor:
         )
         os.makedirs(nabu_cfg_folders, exist_ok=True)
         serving_hatch_file = os.path.join(
-            nabu_cfg_folders, "nabu_tomwer_serving_hatch.h5"
+            nabu_cfg_folders, settings.NABU_TOMWER_SERVING_HATCH
         )
 
         source = extra_infos.get("source", INormSource.NONE)
@@ -520,9 +520,11 @@ class _NabuBaseReconstructor:
                             [entry_path, str(uuid.uuid1())]
                         )
                     h5f[serving_hatch_data_path] = extra_infos["value"]
-
+                file_path = os.path.join(
+                    settings.NABU_CFG_FILE_FOLDER, settings.NABU_TOMWER_SERVING_HATCH
+                )
                 serving_hatch_url = DataUrl(
-                    file_path="nabu_tomwer_serving_hatch.h5",  # configuration file and nabu_tomwer_serving_hatch are in the same folder
+                    file_path=file_path,  # configuration file and nabu_tomwer_serving_hatch are in the same folder
                     data_path=serving_hatch_data_path,
                     scheme="silx",
                 )

tomwer/core/process/reconstruction/nabu/settings.py

@@ -38,6 +38,10 @@ NABU_FILE_PER_GROUP = 100
 NABU_CONFIG_FILE_EXTENSION = ".cfg"
 
 NABU_CFG_FILE_FOLDER = "nabu_cfg_files"
+# foler where nabu configuraiton will be saved
+
+NABU_TOMWER_SERVING_HATCH = "nabu_tomwer_serving_hatch.h5"
+# file used to insure some passing from tomwer to nabu like providing normalization values
 
 try:
     import nabu.app.reconstruct  # noqa: F401

tomwer/core/process/reconstruction/normalization/normalization.py

@@ -112,7 +112,7 @@ class IntensityNormalizationTask(
         scan.intensity_normalization.method = params.method
         # after this processing the source
         try:
-            if params.method is NormMethod.NONE:
+            if params.method in (NormMethod.NONE, NormMethod.CHEBYSHEV):
                 final_norm_info = {}
             elif params.source is _ValueSource.MANUAL_ROI:
                 value = self._compute_from_manual_roi(scan)

tomwer/gui/reconstruction/normalization/intensity.py

@@ -642,9 +642,6 @@ class _NormIntensityOptions(qt.QWidget):
                 }
             elif source is _ValueSource.DATASET:
                 return {
-                    "calc_fct": self._intensityCalcOpts.getCalculationFct().value,
-                    "calc_area": self._intensityCalcOpts.getCalculationArea().value,
-                    "calc_method": self._intensityCalcOpts.getCalculationMethod().value,
                     "dataset_url": self._datasetWidget.getDatasetUrl().path(),
                 }
             else:
@@ -740,6 +737,7 @@ class _NormIntensityControl(ControlWidget):
         ControlWidget.__init__(self, parent)
         self._resultWidget = qt.QWidget(self)
         self._resultWidget.setLayout(qt.QFormLayout())
+        self._result = None
 
         self._resultQLE = qt.QLineEdit("", self)
         self._resultWidget.layout().addRow("value:", self._resultQLE)
@@ -749,10 +747,14 @@ class _NormIntensityControl(ControlWidget):
         self._computeBut.hide()
 
     def setResult(self, result):
+        self._result = result
         if isinstance(result, tuple):
             result = ",".join([str(element) for element in result])
         self._resultQLE.setText(str(result))
 
+    def getResult(self):
+        return self._result
+
     def clear(self):
         self._resultQLE.clear()
 

tomwer/gui/reconstruction/normalization/test/test_intensity.py

@@ -105,9 +105,6 @@ class TestNormIntensityWindow(TestCaseQt):
         output_configuration = self._widget.getConfiguration()
         assert output_configuration["method"] == "division"
         assert output_configuration["source"] == "from dataset"
-        assert "calc_area" in output_configuration
-        assert "calc_fct" in output_configuration
-        assert "calc_method" in output_configuration
         assert "dataset_url" in output_configuration
 
         self._widget.setCurrentMethod(NormalizationMethod.DIVISION)