tomwer 1.3.13__tar.gz → 1.3.15__tar.gz

{tomwer-1.3.13/tomwer.egg-info → tomwer-1.3.15}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: tomwer
-Version: 1.3.13
+Version: 1.3.15
 Summary: "tomography workflow tools"
 Home-page: https://gitlab.esrf.fr/tomotools/tomwer
 Author: data analysis unit
@@ -18,8 +18,8 @@ Classifier: Operating System :: POSIX
 Classifier: Natural Language :: English
 Classifier: Topic :: Scientific/Engineering :: Physics
 Classifier: Topic :: Software Development :: Libraries :: Python Modules
-Requires-Python: >=3.6
-Description-Content-Type: text/markdown
+Requires-Python: >=3.8
+Description-Content-Type: text/x-rst
 License-File: LICENSE
 Requires-Dist: numpy
 Requires-Dist: setuptools

{tomwer-1.3.13 → tomwer-1.3.15}/setup.cfg

@@ -5,7 +5,7 @@ author = data analysis unit
 author_email = henri.payno@esrf.fr
 description = "tomography workflow tools"
 long_description = file: README.rst
-long_description_content_type = text/markdown
+long_description_content_type = text/x-rst
 license = MIT
 url = https://gitlab.esrf.fr/tomotools/tomwer
 project_urls = 
@@ -26,7 +26,7 @@ keywords =
 
 [options]
 packages = find:
-python_requires = >=3.6
+python_requires = >=3.8
 install_requires = 
 	numpy
 	setuptools

{tomwer-1.3.13 → tomwer-1.3.15}/tomwer/core/process/reconstruction/darkref/darkrefscopy.py

@@ -199,6 +199,15 @@ class DarkRefsCopy(DarkRefsTask):
             update_mode="replace",
         )
 
+    def clear_cache(self):
+        """
+        remove the file used to cache the reduced darks / flats.
+        This can be used in the case it contain unrelevant data. Like frame with another shape...
+        """
+        cache_file = DarkRefsCopy.get_save_file(self._savedir)
+        if os.path.exists(cache_file):
+            os.remove(cache_file)
+
     def _clear_cache_data_path(self, file_path: str, data_path: str):
         if not os.path.exists(file_path):
             return
@@ -207,7 +216,14 @@ class DarkRefsCopy(DarkRefsTask):
                 del h5f[data_path]
 
     def set_darks_and_flats_from_scan(self, scan: TomwerScanBase) -> bool:
-        if scan.reduced_flats in (None, {}):
+        has_flats = scan.reduced_flats not in (None, {})
+        has_darks = scan.reduced_darks not in (None, {})
+        if has_flats and has_darks:
+            # if the scan has darks and flats remove directly the cache file
+            # else in append mode HDF5 is not removing the dataset and
+            # the cache size will continue to increase
+            self.clear_cache()
+        if not has_flats:
             logger.warning(f"No flat found for {scan}. Unable to copy them")
         else:
             self._clear_cache_data_path(
@@ -221,7 +237,7 @@ class DarkRefsCopy(DarkRefsTask):
                 mode="a",
                 update_mode="replace",
             )
-        if scan.reduced_darks in (None, {}):
+        if not has_darks:
             logger.warning(f"No dark found for {scan}. Unable to copy them")
         else:
             self._clear_cache_data_path(

{tomwer-1.3.13 → tomwer-1.3.15}/tomwer/gui/edit/nxtomoeditor.py

@@ -574,28 +574,36 @@ class NXtomoEditor(qt.QWidget):
                 ),
                 solve_empty_dependency=True,
             )
-            detector_transformation_path = "/".join(
-                (
-                    nexus_paths.INSTRUMENT_PATH,
-                    nexus_paths.nx_instrument_paths.DETECTOR_PATH,
-                    nexus_paths.nx_detector_paths.NX_TRANSFORMATIONS,
-                ),
-            )
-            if detector_transformation_path in entry:
-                del entry[detector_transformation_path]
-
-            detector_transformation_path = "/".join(
-                (scan.entry, detector_transformation_path)
+            if nexus_paths.nx_detector_paths.NX_TRANSFORMATIONS is not None:
+                # old NXtomo are not handling NX_TRANSFORMATIONS
+                detector_transformation_path = "/".join(
+                    (
+                        nexus_paths.INSTRUMENT_PATH,
+                        nexus_paths.nx_instrument_paths.DETECTOR_PATH,
+                        nexus_paths.nx_detector_paths.NX_TRANSFORMATIONS,
+                    ),
+                )
+                if detector_transformation_path in entry:
+                    del entry[detector_transformation_path]
+
+                detector_transformation_path = "/".join(
+                    (scan.entry, detector_transformation_path)
+                )
+            else:
+                _logger.debug(
+                    "Old version of NXtomo found. No information about transformation will be saved"
+                )
+                detector_transformation_path = None
+
+        if detector_transformation_path is not None:
+            dicttonx(
+                nx_dict,
+                h5file=scan.master_file,
+                h5path=detector_transformation_path,
+                update_mode="replace",
+                mode="a",
             )
 
-        dicttonx(
-            nx_dict,
-            h5file=scan.master_file,
-            h5path=detector_transformation_path,
-            update_mode="replace",
-            mode="a",
-        )
-
         # clear caches to make sure all modifications will be considered
         scan.clear_caches()
         scan.clear_frames_caches()

{tomwer-1.3.13 → tomwer-1.3.15}/tomwer/gui/edit/test/test_nx_editor.py

@@ -1,4 +1,5 @@
 import os
+import h5py
 
 import numpy
 import pytest
@@ -252,7 +253,7 @@ def test_nx_editor_lock(
     # 3.0 save the nxtomo
     widget.overwriteNXtomo()
 
-    # 4.0 check save went twell
+    # 4.0 check save went well
     overwrite_nx_tomo = NXtomo().load(
         file_path=file_path,
         data_path=entry,
@@ -305,3 +306,59 @@ def test_nx_editor_lock(
         "instrument.detector.x_flipped": (False, False),
         "instrument.detector.y_flipped": (True, False),
     }
+
+
+def test_nxtomo_editor_with_missing_paths(
+    tmp_path,
+    qtapp,  # noqa F811
+):
+    """
+    test widget behavior in the case some nxtomo path don't exist
+    """
+
+    # create nx tomo with raw data
+    nx_tomo = NXtomo()
+    nx_tomo.instrument.detector.image_key_control = [ImageKey.PROJECTION.value] * 12
+    nx_tomo.instrument.detector.data = numpy.empty(shape=(12, 10, 10))
+    nx_tomo.sample.rotation_angle = numpy.linspace(0, 20, num=12)
+
+    file_path = os.path.join(tmp_path, "nxtomo.nx")
+    entry = "entry0000"
+    nx_tomo.save(
+        file_path=file_path,
+        data_path=entry,
+    )
+    # delete some path that can be missing in some case
+    with h5py.File(file_path, mode="a") as h5f:
+        assert "entry0000" in h5f
+        assert "entry0000/beam" not in h5f
+        assert "entry0000/instrument/beam" not in h5f
+        assert "entry0000/instrument/detector/distance" not in h5f
+        assert "entry0000/instrument/detector/x_pixel_size" not in h5f
+        assert "entry0000/instrument/detector/y_pixel_size" not in h5f
+        assert "entry0000/instrument/detector/transformations" not in h5f
+
+    scan = NXtomoScan(file_path, entry)
+
+    # create the widget and do the edition
+    widget = NXtomoEditor()
+
+    widget.setScan(scan=scan)
+
+    widget._distanceMetricEntry.setValue(0.05)
+    widget._energyEntry.setValue(50)
+    widget._xPixelSizeMetricEntry.setValue(0.02)
+    widget._yPixelSizeMetricEntry.setValue(0.03)
+
+    # overwrite the NXtomo
+    widget.overwriteNXtomo()
+
+    # check save went well
+    overwrite_nx_tomo = NXtomo().load(
+        file_path=file_path,
+        data_path=entry,
+    )
+    assert overwrite_nx_tomo.instrument.detector.x_pixel_size.value == 0.02
+    assert overwrite_nx_tomo.instrument.detector.y_pixel_size.value == 0.03
+    assert overwrite_nx_tomo.energy.value == 50
+    assert overwrite_nx_tomo.instrument.detector.distance.value == 0.05

{tomwer-1.3.13 → tomwer-1.3.15}/tomwer/gui/reconstruction/axis/axis.py

@@ -31,6 +31,7 @@ __license__ = "MIT"
 __date__ = "14/10/2019"
 
 
+import numpy
 import logging
 from typing import Optional
 
@@ -272,6 +273,7 @@ class _AxisWidget(qt.QMainWindow):
                 self._axis_params.relative_cor_value,
                 self._axis_params.absolute_cor_value,
             )
+        self._controlWidget._positionInfo.setAxis(self._axis_params)
 
         # connect signal / slots
         self._controlWidget.sigComputationRequest.connect(self.sigComputationRequested)
@@ -663,7 +665,13 @@ class _PositionInfoWidget(qt.QWidget):
         if self._relativePositionQLE.text().startswith((".", "?")):
             return
         else:
-            self.sigRelativeValueSet.emit(float(self._relativePositionQLE.text()))
+            value = float(self._relativePositionQLE.text())
+            # make sure we only emit the signal if the value changed (and when the Qline has been edited).
+            if self._axis.relative_cor_value is None or (
+                self._axis is not None
+                and not numpy.isclose(value, self._axis.relative_cor_value, atol=1e-3)
+            ):
+                self.sigRelativeValueSet.emit(value)
 
     def _userUpdatedAbsolutePosition(self, *args, **kwargs):
         palette = self.palette()
@@ -675,24 +683,19 @@ class _PositionInfoWidget(qt.QWidget):
         if self._absolutePositionQLE.text().startswith((".", "?")):
             return
         else:
-            self.sigAbsolueValueSet.emit(float(self._absolutePositionQLE.text()))
+            value = float(self._absolutePositionQLE.text())
+            # make sure we only emit the signal if the value changed (and when the Qline has been edited).
+            if self._axis.absolute_cor_value is None or (
+                self._axis is not None
+                and not numpy.isclose(value, self._axis.absolute_cor_value, atol=1e-3)
+            ):
+                self.sigAbsolueValueSet.emit(value)
 
     def setAxis(self, axis):
         assert isinstance(axis, QAxisRP)
         if axis == self._axis:
             return
-        if self._axis is not None:
-            self._axis.sigChanged.disconnect(self._updatePosition)
         self._axis = axis
-        self._axis.sigChanged.connect(self._updatePosition)
-        self._updatePosition()
-
-    def _updatePosition(self):
-        if self._axis:
-            self.setPosition(
-                relative_cor=self._axis.relative_cor_value,
-                abs_cor=self._axis.absolute_cor_value,
-            )
 
     def getPosition(self):
         return float(self._relativePositionQLE.text())

{tomwer-1.3.13 → tomwer-1.3.15}/tomwer/gui/reconstruction/nabu/nabuconfig/preprocessing.py

@@ -188,13 +188,14 @@ class _NabuPreProcessingConfig(_NabuStageConfigBase, qt.QWidget):
 
         # option dedicated to Helical
         ## process file
-        self._processFileQLE = qt.QLabel("file containing weights maps", self)
+        self._processFileLabel = qt.QLabel("file containing weights maps", self)
+        self.registerWidget(self._processFileLabel, "advanced")
+        self.layout().addWidget(self._processFileLabel, 20, 0, 1, 1)
+        self._processFileQLE = qt.QLineEdit("", self)
+        self.registerWidget(self._processFileQLE, "advanced")
         self._processFileQLE.setToolTip(
             "also know as 'process_file'. If you don't have this file it can be created from the 'helical-prepare-weights' widget"
         )
-        self.layout().addWidget(self._processFileQLE, 20, 0, 1, 1)
-        self._processFileQLE = qt.QLineEdit("", self)
-        self.registerWidget(self._processFileQLE, "advanced")
         self.layout().addWidget(self._processFileQLE, 20, 1, 1, 3)
 
         # style

{tomwer-1.3.13 → tomwer-1.3.15}/tomwer/version.py

@@ -77,7 +77,7 @@ RELEASE_LEVEL_VALUE = {
 
 MAJOR = 1
 MINOR = 3
-MICRO = 13
+MICRO = 15
 RELEV = "final"  # <16
 SERIAL = 0  # <16
 

{tomwer-1.3.13 → tomwer-1.3.15/tomwer.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: tomwer
-Version: 1.3.13
+Version: 1.3.15
 Summary: "tomography workflow tools"
 Home-page: https://gitlab.esrf.fr/tomotools/tomwer
 Author: data analysis unit
@@ -18,8 +18,8 @@ Classifier: Operating System :: POSIX
 Classifier: Natural Language :: English
 Classifier: Topic :: Scientific/Engineering :: Physics
 Classifier: Topic :: Software Development :: Libraries :: Python Modules
-Requires-Python: >=3.6
-Description-Content-Type: text/markdown
+Requires-Python: >=3.8
+Description-Content-Type: text/x-rst
 License-File: LICENSE
 Requires-Dist: numpy
 Requires-Dist: setuptools