tomwer 1.3.13__py3-none-any.whl → 1.3.14__py3-none-any.whl

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/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/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/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 +665,12 @@ 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 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 +682,18 @@ 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 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/synctools/stacks/reconstruction/dkrefcopy.py

@@ -26,11 +26,11 @@ __authors__ = ["H.Payno"]
 __license__ = "MIT"
 __date__ = "13/08/2021"
 
-import os
 import functools
 import logging
 import shutil
 import tempfile
+import os
 
 from processview.core.manager import DatasetState, ProcessManager
 from processview.core.superviseprocess import SuperviseProcess

tomwer/version.py

@@ -77,7 +77,7 @@ RELEASE_LEVEL_VALUE = {
 
 MAJOR = 1
 MINOR = 3
-MICRO = 13
+MICRO = 14
 RELEV = "final"  # <16
 SERIAL = 0  # <16
 

{tomwer-1.3.13.dist-info → tomwer-1.3.14.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: tomwer
-Version: 1.3.13
+Version: 1.3.14
 Summary: "tomography workflow tools"
 Home-page: https://gitlab.esrf.fr/tomotools/tomwer
 Author: data analysis unit
@@ -18,7 +18,7 @@ Classifier: Operating System :: POSIX
 Classifier: Natural Language :: English
 Classifier: Topic :: Scientific/Engineering :: Physics
 Classifier: Topic :: Software Development :: Libraries :: Python Modules
-Requires-Python: >=3.6
+Requires-Python: >=3.8
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: numpy

{tomwer-1.3.13.dist-info → tomwer-1.3.14.dist-info}/RECORD

@@ -1,4 +1,4 @@
-tomwer-1.3.13-py3.11-nspkg.pth,sha256=UYCZtLWueceGiAlmXKRJUZ0TWQEubpPoQ1pVnAAsME0,502
+tomwer-1.3.14-py3.11-nspkg.pth,sha256=UYCZtLWueceGiAlmXKRJUZ0TWQEubpPoQ1pVnAAsME0,502
 orangecontrib/tomwer/__init__.py,sha256=B4DXy1gY_wXmNYa2aOfapmJb2mEuCAjoaNEGnpBs70g,148
 orangecontrib/tomwer/state_summary.py,sha256=5_dPzweL3r0ye4ZfJo6IV2ThJI8fQhWoO2ySdJJajj8,1711
 orangecontrib/tomwer/orange/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -220,7 +220,7 @@ orangecontrib/tomwer/widgets/visualization/icons/volumeviewer.svg,sha256=2uT9_px
 tomwer/__init__.py,sha256=82Jp1abyG4UWdGuT4nNU7LxaUV6xxkOte5pIz3w69Do,1745
 tomwer/__main__.py,sha256=jsDfWA2yl5am0dHQVkYwlKLxxqKNont6VDF-LusuawE,8575
 tomwer/utils.py,sha256=EgVwJ5CQVjoBvcKNwyVoXv_P4ciI11oxb8fNyy82Lck,8465
-tomwer/version.py,sha256=NB9NVW9JDgrzz_rw-aJi5JYGnpnQP-hHA1sASP_uZ14,4387
+tomwer/version.py,sha256=x8jsewPb2ljshg5rFK4miHGjNsGSt3FPoRBsXH_cfI4,4387
 tomwer/app/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 tomwer/app/axis.py,sha256=Ax0wlTp9u0Ll_3ax23QP5Ck16_M9Kop7wx0hAbXrXyM,6004
 tomwer/app/canvas.py,sha256=RbQqgE7DuNjv4nGG6BNfnSevQO5_lCl7N71hGcLoxwE,1561
@@ -318,7 +318,7 @@ tomwer/core/process/reconstruction/axis/params.py,sha256=y1RgFAk1wiJMeueSNJH5enU
 tomwer/core/process/reconstruction/axis/projectiontype.py,sha256=0w_NZ0N95iInHuEQCIxJIxt7K-YpCUo2fZ-_vhZ6D7Q,1543
 tomwer/core/process/reconstruction/darkref/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 tomwer/core/process/reconstruction/darkref/darkrefs.py,sha256=gbRq1IJ-9fxD71684wajQj3D_M9G6chm7ahZsjxTmpM,20862
-tomwer/core/process/reconstruction/darkref/darkrefscopy.py,sha256=cWT2bM_ReVJ18cJKqQXp3IcKk0Z6W5NeJ03wpqTzjNk,13754
+tomwer/core/process/reconstruction/darkref/darkrefscopy.py,sha256=Oe65TZUS0XZ-5IuuuFMFGuu4aGxKChREPvVa_Ti85EU,14451
 tomwer/core/process/reconstruction/darkref/params.py,sha256=Pnl8XJ4et-u169wzUdhB8_woBEXPXtrGPLZEbXSwZDQ,10080
 tomwer/core/process/reconstruction/darkref/settings.py,sha256=35jliuOIjMKTOJjgn4uiotcDEr6RskpLHfRWWLm76dc,188
 tomwer/core/process/reconstruction/nabu/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -494,12 +494,12 @@ tomwer/gui/debugtools/objectinspector.py,sha256=Mva9iK4bIxHvs3CcuHboWa4kiUEMoBeu
 tomwer/gui/edit/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 tomwer/gui/edit/dkrfpatch.py,sha256=UCXfEq3wV1x3OzEdzIzi6YxRN6SaEIZb-Yudt2YwnUs,17533
 tomwer/gui/edit/imagekeyeditor.py,sha256=NjnPdKJif9bhfPXejJuRrj2TqTTMlOxlk4mb6mSBoHw,29728
-tomwer/gui/edit/nxtomoeditor.py,sha256=1mV5EIHTclg1YxDLMncbErNwC58jEOGxjxO7I1dRzyQ,28095
+tomwer/gui/edit/nxtomoeditor.py,sha256=Bf2dVU73pV8oJXdS9Zms-L2e7KJTzfLdlwZeeKerPTk,28586
 tomwer/gui/edit/nxtomowarmer.py,sha256=Vmsg8oUSzHpIvJVqF6xZd0aYKzPi_DDoNrGOIQbqBwU,2349
 tomwer/gui/edit/test/__init__.py,sha256=OLK9ip_LryBfM_L40MReqjvJS3wdbWP_CpnBeD1NQTA,1368
 tomwer/gui/edit/test/test_dkrf_patch.py,sha256=578ZPdVGOHls236XQqId7QqRrpdN5h3Hh8BePTlV03g,8001
 tomwer/gui/edit/test/test_image_key_editor.py,sha256=hkeiB5plRR17YD499j6_yQatuIgKLa4F4NfjWVMzhY4,5965
-tomwer/gui/edit/test/test_nx_editor.py,sha256=iz6dcebE-IBOjdlzYIkDreRzpVJbkElEzTKvWqIJrkA,11285
+tomwer/gui/edit/test/test_nx_editor.py,sha256=KMpptfEURWAKGwuPxRtrOpNYlbxSxu0Tulla2uLXVmw,13201
 tomwer/gui/icat/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 tomwer/gui/icat/createscreenshots.py,sha256=IeKBF-urVsEsjDH2gXpt3oG5Sx_OstC1mNJB7zFeWkk,3123
 tomwer/gui/icat/gallery.py,sha256=puBAkqlwgV1Orki_g2IVXjssCn_PCPjNGJtC0RIPpxI,8700
@@ -507,7 +507,7 @@ tomwer/gui/icat/publish.py,sha256=E1DwyABMZeIHDcy88YFtLpg2GpvN_AFHn4aAJbcK13c,62
 tomwer/gui/reconstruction/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 tomwer/gui/reconstruction/axis/CompareImages.py,sha256=mrlXPCgq71lzmA_XACqrjdzRTK1iYJQBMrJMaeKZAq8,12870
 tomwer/gui/reconstruction/axis/__init__.py,sha256=fUKWiRiG2o4Y-9RN-41VZMMM8L9Srl6QCn942VL5szY,94
-tomwer/gui/reconstruction/axis/axis.py,sha256=QLyrJzJrShjlnO3tLkcnv2oexzVkxw-SGgn3cYfmmEY,27260
+tomwer/gui/reconstruction/axis/axis.py,sha256=AasGGK9wjnn9l6ryo9biptcDKxRTQG7KFHIHnMZd70o,27489
 tomwer/gui/reconstruction/axis/radioaxis.py,sha256=hTweuwS-X32ZlpkHvP5X910zJ8p4fiJMsn_oUVtfvXM,92755
 tomwer/gui/reconstruction/darkref/__init__.py,sha256=g9LASP8OJjxCPEHXO14hN0OLjLkeUve6etaPm1LIz4c,1373
 tomwer/gui/reconstruction/darkref/darkrefcopywidget.py,sha256=cfU2EJv_9LfCrKTHwnYwt2Kj4G6lMPbw0lbD-yjyT-Y,12053
@@ -758,7 +758,7 @@ tomwer/synctools/stacks/edit/imagekeyeditor.py,sha256=NNDQWMJEuE50zBk_2zJAWbf6hC
 tomwer/synctools/stacks/reconstruction/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 tomwer/synctools/stacks/reconstruction/axis.py,sha256=9Gqh0isvLYupypOq3P7XM_lU4Hcni4l3V2aUZsAVLrc,8876
 tomwer/synctools/stacks/reconstruction/castvolume.py,sha256=PaoMuTxcj4Ms6N2MFnrCzmaCCC3wEZItYAwQ8NApe_o,8282
-tomwer/synctools/stacks/reconstruction/dkrefcopy.py,sha256=01YdLs9xfmKFl7Wz3Qf9jawY6ePGp7fxcTus9BHNBeM,7402
+tomwer/synctools/stacks/reconstruction/dkrefcopy.py,sha256=cHkvyOtbaqtaftnCyIhDF3oXRM-lXMWqBf-CVTqF198,7402
 tomwer/synctools/stacks/reconstruction/nabu.py,sha256=dDqw74kobhkawquJIwLDQH--PN6LbbthlqZ9MQUBJi4,7816
 tomwer/synctools/stacks/reconstruction/normalization.py,sha256=wcw-tHjKUQMcija0bCExDl0InYsKHZNTeTk4w_hnaDI,5362
 tomwer/synctools/stacks/reconstruction/saaxis.py,sha256=N5LM4QPE1H06WXjEH-PGIMfWgCHkwR02QR3PENZ_JzE,7126
@@ -776,10 +776,10 @@ tomwer/tests/test_utils.py,sha256=D0rNDSK6csEOYBY_7gD-4A3jp8rYAm8L1_Xg34A9I2s,30
 tomwer/tests/utils.py,sha256=RAXx5A99WD4Vyuv_wjHBdr-Xu7UiThHRKw2eiB5GX10,107
 tomwer/third_part/WaitingOverlay.py,sha256=GnqiytcJDp_24Cmz_2nZAP5HfpL3Yh7AzR2ATIusGsg,3906
 tomwer/third_part/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-tomwer-1.3.13.dist-info/LICENSE,sha256=yR_hIZ1MfDh9x2_s23uFqBH7m5DgrBl9nJKkE37YChM,1877
-tomwer-1.3.13.dist-info/METADATA,sha256=wWs75qkhJSr9ujUassUsmSCC5PGtRboBkMv07SI5Fu0,11460
-tomwer-1.3.13.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-tomwer-1.3.13.dist-info/entry_points.txt,sha256=fIcDnCxjgwzfIylLYhUsFyiNZjZMxsfRQBxi4f-cJg8,440
-tomwer-1.3.13.dist-info/namespace_packages.txt,sha256=Iut-JTfT11SZHHm77_ZeszD7pZDWXcTweCbvrJpqDyQ,14
-tomwer-1.3.13.dist-info/top_level.txt,sha256=Yz5zKh0FPiImtzHYcPuztG1AO8-6KEpUWgoChGbA0Ys,21
-tomwer-1.3.13.dist-info/RECORD,,
+tomwer-1.3.14.dist-info/LICENSE,sha256=yR_hIZ1MfDh9x2_s23uFqBH7m5DgrBl9nJKkE37YChM,1877
+tomwer-1.3.14.dist-info/METADATA,sha256=yc29gleRofOwWWwjUVeO8n0RbmTjEblhC5rSondwT2o,11460
+tomwer-1.3.14.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
+tomwer-1.3.14.dist-info/entry_points.txt,sha256=fIcDnCxjgwzfIylLYhUsFyiNZjZMxsfRQBxi4f-cJg8,440
+tomwer-1.3.14.dist-info/namespace_packages.txt,sha256=Iut-JTfT11SZHHm77_ZeszD7pZDWXcTweCbvrJpqDyQ,14
+tomwer-1.3.14.dist-info/top_level.txt,sha256=Yz5zKh0FPiImtzHYcPuztG1AO8-6KEpUWgoChGbA0Ys,21
+tomwer-1.3.14.dist-info/RECORD,,